The Complete Genome Sequence of the Lactic Acid Bacterium Lactococcus lactis ssp. lactis IL1403

Alexander Bolotin; Patrick Wincker; Stéphane Mauger; Olivier Jaillon; Karine Malarme; Jean Weissenbach; S Dusko Ehrlich; Alexei Sorokin

doi:10.1101/gr.169701

. 2001 May;11(5):731–753. doi: 10.1101/gr.169701

The Complete Genome Sequence of the Lactic Acid Bacterium Lactococcus lactis ssp. lactis IL1403

Alexander Bolotin ¹, Patrick Wincker ², Stéphane Mauger ^1,³, Olivier Jaillon ², Karine Malarme ¹, Jean Weissenbach ², S Dusko Ehrlich ¹, Alexei Sorokin ^1,⁴

PMCID: PMC311110 PMID: 11337471

Abstract

Lactococcus lactis is a nonpathogenic AT-rich gram-positive bacterium closely related to the genus Streptococcus and is the most commonly used cheese starter. It is also the best-characterized lactic acid bacterium. We sequenced the genome of the laboratory strain IL1403, using a novel two-step strategy that comprises diagnostic sequencing of the entire genome and a shotgun polishing step. The genome contains 2,365,589 base pairs and encodes 2310 proteins, including 293 protein-coding genes belonging to six prophages and 43 insertion sequence (IS) elements. Nonrandom distribution of IS elements indicates that the chromosome of the sequenced strain may be a product of recent recombination between two closely related genomes. A complete set of late competence genes is present, indicating the ability of L. lactis to undergo DNA transformation. Genomic sequence revealed new possibilities for fermentation pathways and for aerobic respiration. It also indicated a horizontal transfer of genetic information from Lactococcus to gram-negative enteric bacteria of Salmonella-Escherichia group.

[The sequence data described in this paper has been submitted to the GenBank data library under accession no. AE005176.]

Lactic acid bacteria (LAB) are a heterogeneous group of microorganisms that convert carbohydrates into lactic acid. They comprise both pathogens (such as Streptococcus pneumoniae or Streptococcus pyogenes) and useful bacteria (such as Streptococcus thermophilus and Lactococcus lactis, which were used for millennia in milk fermentation). Determination and analysis of the genome sequence of a representative LAB is therefore of great interest, as it would provide information allowing us to combat the former and use the latter more efficiently. Until now, no complete and annotated genome sequence of either LAB class has been reported.

In nature, L. lactis occupies a niche related to plant or animal surfaces and the animal gastrointestinal tract. It is believed to be dormant on the plant surfaces and to multiply in the gastrointestinal tract after being swallowed by a ruminant. In contrast, “domesticated” species of L. lactis, used by dairy industry as starters in cheese fermentation, live in a different niche, which is defined by technological considerations, such as fast growth and rapid production of lactic acid in milk. The importance of L. lactis for humankind can be appreciated from the estimate that close to 10⁷ tons of cheese are made annually (Fox 1989), leading to human consumption of close to 10¹⁸ lactococci.

There are two subspecies of L. lactis, designated initially as Streptococcus lactis and Streptococcus cremoris and reclassified more recently as L. lactis ssp. lactis and L. lactis ssp. cremoris, respectively (Schleifer et al. 1985). The former is preferred for making of soft cheeses and the latter for the hard ones. The two subspecies have been intensely studied, mainly because of their industrial interest, and have became excellent models for research on metabolism, physiology, genetics, and molecular biology of LAB.

The questions addressed in research on useful bacteria are often antithetical to those involving pathogens, because one of the basic objectives is to improve rather than to limit bacterial growth. Efficient use of lactococci by dairy industry requires understanding of many aspects of bacterial physiology, such as use of sugars and proteins from milk for growth, conversion of sugars to lactate, and synthesis of substances involved in cheese flavor, and thus of the relationship between different types of fermentation. The potential for new applications of LAB, such as oral vaccines (Steidler et al. 2000) or production of foreign proteins and metabolites, leads to questions concerning the protein secretion system, biosynthesis of cofactors, and regulation of central metabolism. In addition to questions related to the industrial use of lactococci, fundamental biological questions, such as retrohoming of introns (Cousineau et al. 1998), are also being addressed in L. lactis.

A genetic map of a “laboratory workhorse” L. lactis ssp. lactis strain IL1403, based on a low-fidelity diagnostic genome sequencing, has been reported (Bolotin et al. 1999). Here we present the analysis of the accurate sequence of the IL1403 genome, which is the first such report for any lactic acid bacterium. We focus mainly on features related to the importance of L. lactis for humankind, which is its use in dairy fermentation. Also, several unexpected findings are reported, such as a putative chimerical structure of the genome, the possibility that L. lactis can respire, the existence of genes required for DNA transformation, and a discovery of a transfer of genetic information from lactococci to gram-negative enteric bacteria.

RESULTS AND DISCUSSION

Two-Step Sequencing Strategy

The first step of our strategy, designated diagnostic genome sequencing, was described before (Bolotin et al. 1999). Briefly, it implies cloning of relatively short (1–20 kb) genome fragments in Escherichia coli plasmid and phage vectors, and sequencing of a limited number of randomly chosen clones, to a redundancy of about one. A novel procedure, designated multiplex long accurate PCR (MLA PCR), developed and tested in the course of the Bacillus subtilis genome sequencing project (Sorokin et al. 1996; Kunst et al. 1997), is then applied for connecting the resulting contigs and synthesizing the missing genome regions, sequenced subsequently by standard methods. This approach allowed us to establish the entire L. lactis genome sequence and assemble it in a unique contig, with a sequencing redundancy of less than two (Bolotin et al. 1999). Three- to fourfold fewer sequencing reactions were required to reach this goal than if the fully random approach were used. For comparison, only 10,235 reactions were needed to assemble L. lactis genome sequence, whereas 40,020 were required for the genome of Neisseria meningitidis (Tettelin et al. 2000), which is of a similar size. Diagnostic sequence allowed us to identify all L. lactis genes that encode proteins sufficiently similar to those present in the databases. However, the elevated error rate, estimated to be ∼1%, did not allow us to predict the genes unique for L. lactis or the borders of coding region. To obtain a more complete and reliable description of the L. lactis genome, we carried out a second step of our strategy. It involved random sequencing of additional clones until the overall redundancy of ∼6.4 was reached and then primer walking on PCR-generated templates to ensure that each base was sequenced at least four times and at least once on each strand. We designated this step “shotgun polishing” and concluded that the strategy presented here can be a good alternative to the fully random strategy used in most cases (Fraser and Fleischmann 1997). Its advantages should increase even more when a greater number of completely sequenced and thoroughly annotated bacterial genomes becomes available. Carrying out the diagnostic step and polishing only a very little will then be sufficient to determine a reliable genome sequence of bacteria relatively close to the ones that were already sequenced and annotated.

Gene Content

The circular chromosome of L. lactis IL1403 has 2,365,589 bp and an average G+C content of 35.4%. We detected 2310 open reading frames (ORFs) in the sequence, with an average length of 879 bp. Protein-coding genes represent 86% of the genome, stable RNA 1.4%, and noncoding regions 12.6%. These values are similar to those observed for genomes of other bacteria. We have assigned a biochemical or biological role to 64.2% (1482 ORFs) of the genes and classified them into functional categories (Table 1). There are 20.1% of genes (465 ORFs) that match hypothetical coding sequences of unknown function, and the remaining 15.7% (363 ORFs) represent genes with no similarity to known proteins, which can be considered specific for lactococci.

Table 1.

Functional Classification of the Lactococcus lactis Protein-Coding Genes^#

AMINO-ACID BIOSYNTHESIS
Aromatic amino-acid family
*aroA*	1802	3-phosphoshikimate 1-carboxyvinyltransferase
aroB	1814	3-dehydroquinate synthase
aroC	1811	chorismate synthase
aroD	1690	3-dehydroquinate dehydratase
aroE	1815	shikimate 5-dehydrogenase
aroF	120	Tyr-sensitive phospho-2-dehydro-deoxyheptonate aldolase
aroH	1281	Trp-sensitive phospho-2-dehydro-deoxyheptonate aldolase
*aroK*	1801	shikimate kinase
*pheA*	1801	prephenate dehydratase
*trpA*	1494	tryptophan synthase alpha chain
*trpB*	1495	tryptophan synthase beta chain
*trpC*	1498	indole-3-glycerol phosphate synthase
*trpD*	1499	anthranilate phosphoribosyltransferase
*trpE*	1501	anthranilate synthase component I
*trpF*	1497	phosphorybosyl-anthranilate isomerase
*trpG*	1500	anthranilate synthase component II
*tyrA*	1803	prephenate dehydrogenase
Aspartate family
asnB	357	asparagine synthetase B
asnH	2312	asparagine synthetase
aspB	1897	aspartate aminotransferase
aspC	163	aspartate aminotransferase
*ceo*	1265	N5-carboxyethyl-ornithine synthase
dapA	1665	dihydrodipicolinate synthase
dapB	1605	dihydrodipicolinate reductase
*hom*	1172	homoserine dehydrogenase
lysA	1314	diaminopimelate decarboxylase
metA	1997	homoserine O-succinyltransferase
metB1	1996	cystathionine gamma-synthase
metB2	791	cystathionine gamma-synthase
metE	1284	5-methionine synthase
metF	1282	5,10-methylenetetrahydrofolate reductase
thrA	748	aspartokinase
*thrB*	1173	homoserine kinase
thrC	2173	threonine synthase
Branched chain family
*ilvA*	1251	threonine deaminase
*ilvB*	1248	acetolactate synthase large subunit
*ilvC*	1250	ketol-acid reductoisomerase
*ilvD*	1247	dihydroxy-acid dehydratase
*ilvN*	1249	acetolactate synthase small subunit
*leuA*	1240	2-isopropylmalate synthase
*leuB*	1242	3-isopropylmalate dehydrogenase
*leuC*	1244	3-isopropylmalate dehydratase large subunit
*leuD*	1245	3-isopropylmalate dehydratase small subunit
Glutamate family
argB	808	acetylglutamate kinase
argC	805	N-acetyl-gamma-glutamyl-phosphate reductase
argD	807	acetylornithine aminotransferase
argE	560	acetylornithine deacetylase
argG	127	argininosuccinate synthase
argH	129	argininosuccinate lyase
argJ	806	ornithine acetyltransferase
glnA	2283	glutamine synthetase
gltA	668	citrate synthase
gltB	1319	glutamate synthase large subunit
gltD	1316	glutamate synthase small subunit
proA	1651	gamma-glutamyl phosphate reductase
proB	1652	glutamate 5-kinase
proC	1953	pyrroline-5-carboxylate reductase
Histidine family
*hisA*	1236	phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase
*hisB*	1234	imidazoleglycerol-phosphate dehydratase
*hisC*	1229	histidinol-phosphate aminotransferase
*hisD*	1232	histidinol dehydrogenase
*hisF*	1237	cyclase HisF
*hisG*	1231	ATP phosphoribosyltransferase
*hisH*	1235	amidotransferase
*hisI*	1237	phosphoribosyl-AMP cyclohydrolase
hisK	1238	histidinol phosphatase
*hisZ*	1230	ATP phosphoribosyltransferase regulatory subunit
Serine family
cysD	77	O-acetylhomoserine sulfhydrylase
cysE	1921	serine acetyltransferase
cysK	792	cysteine synthase
cysM	527	cysteine synthase
glyA	592	serine hydroxymethyltransferase
serA	595	D-3-phosphoglycerate dehydrogenase
serB	596	phosphoserine phosphatase
serC	594	phosphoserine aminotransferase
BIOSYNTHESIS OF COFACTORS, PROSTHETIC GROUPS, AND CARRIERS
Folic acid
dfrA	1163	dihydropholate reductase
fhs	961	formyltetrahydrofolate synthetase
folB	1166	dihydroneopterin aldolase
folC	1169	folylpolyglutamate synthase
folD	877	tetrahydrofolate dehydrogenase/cyclohydrolase
folE	1167	GTP cyclohydrolase I
folP	1168	dihydropteroate synthase
pabA	1349	para-aminobenzoate synthase component II
pabB	1348	para-aminobenzoate synthase component I
Heme and porphyrin
hemH	1609	ferrohelatase
hemK	589	protoporphyrinogen oxidase
hemN	1154	oxygen-independent coproporphyrogen III oxidase
Menaquinone and ubiquinone
ispA	881	farnesyl diphosphate synthase
ispB	1380	heptaprenyl diphosphate synthase component II
menB	735	dihydroxynaphthonic acid synthase
menD	737	2-oxoglutarate decarboxylase
menE	734	O-succinylbenzoic acid-CoA ligase
menF	739	menaquinone-specific isochorismate synthase
menX	736	protein in menaquinone biosynthesis pathway
preA	187	prenyl transferase
ubiE	1718	menaquinone biosynthesis methylase
yhdB	732	racemase
Pantothenate
coaA	1467	pantothenate kinase
dfpA	567	pantothenate metabolism flavoprotein
dfpB	568	flavoprotein
panE	1358	ketopantoate reductase
Riboflavin and cobalamin
cobC	1889	alpha-ribazole-5'-phosphate phosphatase
cobQ	1115	cobyric acid synthase
ribA	1024	GTP cyclohydrolase II / 3,4-dihydroxy-2-butanone 4-phosphate synthase
ribB	1023	ribiflavin synthase alpha chain
ribC	1142	riboflavin kinase
ribG	1023	riboflavin-specific deaminase
ribH	1025	ribiflavin synthase beta chain
Thioredoxin, glutaredoxin, and glutathione
gpo	1402	glutathione peroxidase
gshR	864	glutathione reductase
trxA	1692	thioredoxin
trxB1	966	thioredoxin reductase
trxB2	1695	thioredoxin reductase
trxH	396	thioredoxin H-type
Thiamin
apbE	1125	thiamine biosynthesis lipoprotein
thiD1	1295	phosphomethylpyrimidine kinase
thiD2	485	phosphomethylpyrimidine kinase
thiE	1294	thiamin-phosphate pyrophosphorylase
thiM	1295	hydroxyethylthiazole kinase
Pyridine nucleotides
nadE	1110	NAD-synthetase
yvdG	2139	pyridine nucleotide-disulfide oxidoreductase
CELL ENVELOPE
Membranes, lipoproteins, and porins
bmpA	1462	basic membrane protein A
cdsA	2200	phosphatidate cytidylyltransferase
clsA	988	cardiolipin synthase
clsB	1188	cardiolipin synthase
dgkA	1095	diacylglycerol kinase
lgt	606	prolipoprotein diacylglycerol transferase
pgsA	2047	CDP-diacylglycerol-phosphate phosphatidyltransferase
plpA	318	outer membrane lipoprotein precursor
plpB	319	outer membrane lipoprotein precursor
plpC	320	outer membrane lipoprotein precursor
plpD	321	outer membrane lipoprotein precursor
yfjC	596	acylphosphate phosphohydrolase
Murein sacculus and peptidoglycan
*acmA*	269	N-acetylmuramidase
acmB	1977	N-acetylmuramidase
acmC	1403	N-acetylmuramidase
acmD	528	N-acetylmuramidase
asd	1667	aspartate-semialdehyde dehydrogenase
dacA	2356	D-alanyl-D-alanine carboxypeptidase
dacB	976	D-alanyl-D-alanine carboxypeptidase
dal	862	alanine racemase
ddl	341	D-alanine-D-alanine ligase
glmU	1952	UDP-N-acetylglucosamine pyrophosphorylase
mraY	892	phospho-N-acetylmuramoyl-pentapeptide transferase
mreC	2316	cell shape determining protein
mreD	2315	cell shape determining protein
murA1	1314	UDP-N-acetylglucosamine 1-carboxyvinyltransferase
murA2	535	UDP-N-acetylglucosamine 1-carboxyvinyltransferase
murB	1175	UDP-N-acetylenolpyruvoylglucosamine reductase
murC	2119	UDP-N-acetylmuramate-alanine ligase
murD	1634	UDP-N-acetylmuramoylalanine D-glutamate ligase
murE	1871	UDP-MurNac-tripeptide synthetase
murF	342	D-Ala-D-Ala adding enzyme
murG	1633	peptidoglycan synthesis protein MurG
murI	1313	glutamate racemase
pbp1B	393	penicillin-binding protein 1B
pbp2A	2178	penicillin-binding protein 2a
pbp2B	339	penicillin-binding protein 2B
pbpX	890	penicillin-binding protein
ponA	530	penicillin-binding protein 1A
racD	2310	aspartate racemase
uppS	2201	undecaprenyl pyrophosphate synthetase
Surface polysaccharides, lipopolysaccharides and antigens
dltA	1293	D-alanine activating enzyme
dltB	1291	peptidoglycan biosynthesis protein
dltC	1290	D-alanyl carrier protein
dltD	1290	D-alanine transfer protein DltD
dltE	145	oxidoreductase
floL	746	flotillin-like protein
hasC	1378	UTP-glucose-1-phosphate uridylyltransferase
icaA	681	glycosyl transferase
icaB	683	intercellular adhesion protein IcaB
icaC	684	collagen adhesin
kdtB	2239	lipopolysaccharide core biosynthesis protein
mvaA	1611	hydroxymethylglutaryl-CoA reductase
mycA	981	myosin-crossreactive antigen
pspA	2304	glucosyltransferase-S
pspB	2306	glucosyltransferase-S
rgpA	202	rhamnosyltransferase
rgpB	203	rhamnosyltransferase
rgpE	207	glycosyltransferase
rgpF	209	polysaccharide biosynthesis protein
tagB	953	teichoic acid biosynthesis protein B
tagD1	220	glycerol-3-phosphate cytidiltransferase
tagD2	951	glycerol-3-phosphate cytidyltransferase
tagF	952	teichoic acid biosynthesis protein F
tagL	936	exopolysaccharide biosynthesis protein
tagX	948	teichoic acid biosynthesis protein
tagY	945	teichoic acid biosynthesis protein
tagZ	943	teichoic acid biosynthesis protein
ycbB	212	glycosyltransferase
ycbD	213	UDP-glucose 4-epimerase
ycbF	215	LPS biosynthesis protein
ycbG	216	LPS biosynthesis protein
ycbH	217	sugar transferase
ycbI	218	sugar transferase
ycbJ	219	LPS biosynthesis protein
ycbK	214	polysaccharide biosynthesis export protein
yijG	899	glycosyl transferase
yjeF	949	lipopolysaccharide biosynthesis protein
ymjE	1297	glycosyl transferase
ymjF	1299	UDP-N-acetylglucosamine 2-epimerase
yohH	1478	lipopolysaccharide biosynthesis protein
yohJ	1479	lipopolysaccharide biosynthesis protein
ysfC	1853	polysacharide biosynthesis protein
ywaF	2206	glycosyltransferase
ywaG	2207	lipopolysaccharide biosynthesis protein
CELLULAR PROCESSES
Cell division
ezrA	2225	cell division regulator
ftsA	1940	cell division protein FtsA
ftsE	1000	cell-division ATP-binding protein FtsE
*ftsH*	27	cell division protein FtsH
ftsK	1705	cell division protein FtsK
ftsQ	1632	cell division protein FtsQ
ftsW1	663	cell division protein FtsW
ftsW2	908	cell division protein FtsW
ftsX	1001	cell division protein
ftsY	825	cell division protein FtsY
ftsZ	1938	cell division protein FtsZ
gidA	1915	glucose inhibited division protein GidA
gidB	1381	glucose-inhibited division protein GidB
gidC	1257	glucose inhibited division protein GidC
mesJ	24	cell cycle protein MesJ
parA	99	chromosome partitioning protein
rodA	917	rod-shape determining protein
smc	812	chromosome segregation SMC protein
Cell killing
hly	498	hemolysin like protein
Chaperones
*dnaK*	979	DnaK protein
*groEL*	400	60 KD chaperonin
*groES*	399	10 KD chaperonin
sugE	25	SugE protein
Detoxification
ahpC	336	alkyl hydroperoxide reductase
ahpF	337	alkyl hydroperoxide reductase
*sodA*	413	superoxide dismutase
Protein and peptide secretion
ffh	1658	signal recognition particle protein Ffh
lspA	1026	lipoprotein signal peptidase
secA	118	preprotein translocase SecA subunit
secE	2175	preprotein translocase SecE subunit
secG	967	protein-export protein SecG
secY	2159	preprotein translocase SecY subunit
sipL	2351	signal peptidase I
tig	536	trigger factor
Transformation
coiA	1785	competence protein CoiA
comC	2104	type 4 prepilin-like protein specific leader peptidase
comEA	1833	competence protein ComEA
comEC	1832	competence protein ComEC
comFA	1098	competence protein ComFA
comFC	1097	competence protein ComFC
comGA	2189	competence protein ComGA
comGB	2188	competence protein ComGB
comGC	2187	competence protein ComGC
comGD	2187	competence protein ComGD
comX	2224	competence regulator ComX
dprA	1254	DNA processing SMF protein
radA	2150	DNA repair protein RadA
recQ	1874	ATP-dependent DNA helicase RecQ
CENTRAL INTERMEDIARY METABOLISM
General
metK	1971	S-adenosylmethionine synthetase
pcaC	2052	gamma-carboxymuconolactone decarboxylase
Amino sugars
femD	436	phosphoglucosamine mutase
glmS	1035	glucosamine-fructose-6-phosphate aminotransferase
nagA	1374	N-acetylglucosamine-6-phosphate deacetylase
nagB	1615	glucosamine-6-P isomerase
ylfH	1157	N-acetylglucosamine catabolic protein
ypcD	1524	endo-beta-N-acetylglucosaminidase
Degradation of polysaccharides
agl	1732	alpha-glucosidase
amyL	1278	alpha-amylase
amyY	1734	alpha-amylase
apu	703	amylopullulanase
chiA	2027	chitinase
dexA	1736	oligo-1,6-glucosidase
dexB	1526	alpha 1-6-glucosidase
dexC	1738	neopullulanase
lnbA	1527	lacto-N-biosidase
xynD	282	endo-1,4-beta-xylanase D
yucG	2028	chitin binding protein
Phosphorus compounds
apl	719	alkaline phosphatase
Polyamine biosynthesis
yqfF	1657	spermidine acetyltransferase
Other
glgA	699	glycogen synthase
glgB	147	1,4-alpha-glucan branching enzyme
glgC	697	glucose-1-phosphate adenylyltransferase
glgD	698	glucose-1-phosphate adenylyltransferase
glgP	701	glycogen phosphorylase
mapA	1730	maltosephosphorylase
xylH	568	4-oxalocrotonate tautomerase
ENERGY METABOLISM
Aerobic
cbr	144	carbonyl reductase
noxA	841	NADH dehydrogenase
noxB	842	NADH dehydrogenase
noxC	795	NADH oxidase
noxD	2195	NADH oxidase
noxE	397	NADH oxidase
poxL	2130	pyruvate oxidase
yahI	78	short-chain type dehydrogenase
ybdE	134	oxidoreductase
ybiE	186	oxidoreductase
ycdG	234	oxidoreductase
ycgD	264	oxidoreductase
ycgG	267	oxidoreductase
yddB	333	oxidoreductase
ygcA	620	oxidoreductase
yhgA	760	oxidoreductase
yiaB	802	oxidoreductase
ymgK	1268	oxidoreductase
yneD	1343	oxidoreductase
ypaI	1509	oxidoreductase
ypgB	1562	oxidoreductase
yphA	1571	NADH dehydrogenase
yphC	1574	oxidoreductase
ypiA	1580	oxidoreductase
ypjA	1591	dehydrogenase
ypjF	1595	oxidoreductase
ypjH	1599	oxidoreductase
yrbA	1711	oxidoreductase
yrfB	1751	NADH-dependent oxidoreductase
yrjB	1791	oxidoreductase
yrjC	1792	iron-binding oxidase subunit
ysjB	1892	oxidoreductase
yteC	1944	oxidoreductase
yudI	2036	oxidoreductase
yugB	2066	oxidoreductase
yugC	2068	dehydrogenase
yxdE	2338	oxidoreductase
Amino acids and amines
ansB	743	L-asparaginase
*araT*	57	aromatic amino acid specific aminotransferase
arcA	2115	arginine deiminase
arcB	2114	ornithine carbamoyltransferase
arcC1	2111	carbamate kinase
arcC2	2110	carbamate kinase
arcC3	1752	carbamate kinase
arcT	2109	aminotransferase
argF	809	ornithine carbamoyltransferase
bcaT	1322	branched-chain amino acid aminotransferase
*gadB*	1325	glutamate decarboxylase
hicD	490	L-2-hydroxyisocaproate dehydrogenase
ipd	1340	indole-3-pyruvate decarboxylase
otcA	1757	ornithine carbamoyltransferase
pdc	2011	phenolic acid decarboxylase
pfs	1950	5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
sdaA	845	alpha-subuni L-serine dehydratase
sdaB	844	beta-subunit of L-serine dehydratase
yciA	281	amino acid amidohydrolase
yjiB	983	amino acid aminohydrolase
ytjE	1995	aminotransferase
ywjF	2299	3-hydroxyisobutyrate dehydrogenase
Anaerobic
dhaK	245	dihydroxyacetone kinase
dhaL	246	dihydroxyacetone kinase
dhaM	247	dihydroxyacetone kinase
glpD	1271	glycerol-3-phosphate dehydrogenase
glpK	1273	glycerol kinase
gpdA	1377	glycerol-3-phosphate dehydrogenase
lctO	1280	L-lactate oxidase
ylbE	1120	oxidoreductase
ATP-proton motive force interconversion
atpA	1826	ATP synthase alpha subunit
atpB	1829	ATP synthase subunit a
atpD	1824	ATP synthase alpha subunit
atpE	1823	ATP synthase epsilon subunit
atpF	1828	ATP synthase subunit b
atpG	1825	ATP synthase gamma subunit
atpH	1828	ATP synthase delta subunit
Electron transport
cydA	708	cytochrome D ubiquinol oxidase subunit I
cydB	710	cytochrome D ubiquinol oxidase subunit II
fer	1762	ferredoxin
ndrH	1006	glutaredoxin-like protein NrdH
ndrI	1005	ribonucleotide reductase
nifJ	431	pyruvate-flavodoxin oxidoreductase
nifS	1928	pyridoxal-phosphate dependent aminotransferase NifS
nifU	1848	NifU protein
nifZ	523	pyridoxal-phosphate dependent aminotransferase
qor	724	quinone oxidoreductase
yfiJ	588	NADPH-flavin oxidoreductase
yfjE	598	flavodoxin
yviC	2181	FMN-binding protein
Entner-Doudoroff
kdgA	1672	2-dehydro-3-deoxyphosphogluconate aldolase
kdgK	1673	2-dehydro-3-deoxygluconokinase
Fermentation
ackA1	2091	acetate kinase
ackA2	2089	acetate kinase
adhA	1873	alcohol dehydrogenase
*adhE*	2231	alcohol-acetaldehyde dehydrogenase
*aldB*	1253	alpha-acetolactate decarboxylase
aldC	1117	alpha-acetolactate decarboxylase
als	1201	alpha-acetolactate synthase
butA	919	acetoin reductase
butB	918	2,3-butanediol dehydrogenase
frdC	1139	fumarate reductase flavoprotein subunit
mae	1204	malate oxidoreductase
*mleS*	923	malolactic enzyme
*pfl*	659	pyruvate-formate lyase
pflA	1881	pyruvate-formate lyase activating enzyme
pta	1709	phosphate acetyltransferase
yseE	1846	2-nitropropane deoxygenase
Gluconeogenesis
fbp	255	fructose-1,6-bisphosphatase
Glycolysis
enoA	634	enolase
enoB	275	2-phosphoglycerate dehydratase
fbaA	1980	fructose-bisphosphate aldolase
*gapA*	554	glyceraldehyde 3-phosphate dehydrogenase
gapB	2333	glyceraldehyde 3-phosphate dehydrogenase
*ldh*	1370	L-lactate dehydrogenase
ldhB	380	L-lactate dehydrogenase
ldhX	1143	L-lactate dehydrogenase
*pfk*	1372	6-phosphofructokinase
pgiA	2245	glucose-6-phosphate isomerase A
pgk	243	phosphoglycerate kinase
*pgmB*	442	beta-phosphoglucomutase
pmg	335	phosphoglycerate mutase
pycA	665	pyruvate carboxylase
*pyk*	1371	pyruvate kinase
*tpiA*	1149	triosephosphate isomerase
yjhF	975	phosphoglycerate mutase
yrjI	1800	phosphoglycerate mutase
Pentose phosphate pathway
dxsA	1510	1-deoxyxylulose-5-phosphate synthase
dxsB	1725	1-deoxyxylulose-5-phosphate synthase
gnd	609	decarboxylating 6-phosphogluconate dehydrogenase
ptk	1540	phosphoketolase
rpe	2004	ribulose-phosphate 3-epimerase
rpiA	2317	ribose 5-phosphate isomerase A
tkt	1670	transketolase
zwf	2302	glucose-6-phosphate 1-dehydrogenase
Pyruvate dehydrogenase
pdhA	64	PDH E1 component alpha subunit
pdhB	63	PDH E1 component beta subunit
pdhC	61	dihydrolipoamide acetyltransferase component of PDH complex
pdhD	60	lipoamide dehydrogenase component of PDH complex
Sugars
bglA	423	phospho-beta-glucosidase
bglH	1490	beta-glucosidase
bglS	180	beta-glucosidase A
galE	2055	UDP-glucose 4-epimerase
galK	2061	galactokinase
galM	2062	aldose 1-epimerase
galT	2060	galactose-1-phosphate uridylyltransferase
glk	2101	glucose kinase
gntK	2269	gluconate kinase
gntZ	2271	6-phosphogluconate dehydrogenase
lacC	985	tagatose-6-phosphate kinase
lacZ	2057	beta-galactosidase
maa	1735	maltose O-acetyltransferase
malQ	695	4-alpha-glucanotransferase
mtlD	34	mannitol 1-phosphate 5-dehydrogenase
pmi	780	mannose-6-phosphate isomerase
rbsK	1687	ribokinase
scrK	1518	fructokinase
thgA	2058	thiogalactoside acetyltransferase
uxaC	1674	glucuronate isomerase
uxuA	1678	D-mannonate dehydratase
uxuB	1679	fructuronate reductase
xylA	1550	xylose isomerase
xylB	1548	xylulose kinase
xylM	1547	aldose 1-epimerase
xylX	1543	acetyltransferase hypothetical protein
xynB	1544	beta-1,4-xylosidase
yeeB	443	sugar hydrolase
ygjD	694	4-alpha-glucanotransferase
yidC	834	beta-glucosidase
yncA	1321	acetyltransferase
ypbG	1519	sugar kinase
ypcA	1521	beta-glucosidase
ypdB	1532	sugar hydrolase
ypdD	1537	sugar hydrolase
yrcA	1722	phospho-beta-glucosidase
TCA cycle
citB	670	aconitate hydratase
citC	1207	acetate-SH-citrate lyase ligase
citD	1208	citrate lyase acyl-carrier protein
citE	1209	citrate lyase beta chain
citF	1210	citrate lyase alpha chain
citG	1211	CitG protein
icd	672	isocitrate dehydrogenase
FATTY ACID AND PHOSPHOLIPID METABOLISM
General
accA	790	acetyl-CoA carboxylase carboxyl transferase subunit alpha
accB	786	biotin carboxyl carrier protein of acetyl-CoA carboxylase
accC	788	biotin carboxylase
accD	789	acetyl-CoA carboxylase carboxyl transferase subunit betta
acpA	782	acyl carrier protein
acpD	116	acyl carrier protein phosphodiesterase
acpS	862	acyl carrier protein synthase
cfa	1972	cyclopropane fatty acid synthase
fabD	783	malonyl CoA-acyl carrier protein transacylase
fabF	785	3-oxoacyl-acyl carrier protein synthase II
fabG1	784	3-oxoacyl-acyl carrier protein reductase
fabG2	1845	3-oxoacyl-acyl carrier protein reductase
fabH	782	3-oxoacyl-acyl-carrier-protein synthase III
fabI	562	NADH-dependent enoyl-ACP reductase
fabZ1	561	hydroxymyristoyl-acyl carrier protein dehydratase
fabZ2	787	3R-hydroxymyristoyl-acyl carrier protein dehydratase
fadA	1843	acetyl coenzyme A acetyltransferase
fadD	655	long-chain acyl-CoA synthetase
hmcM	1614	hydroxymethylglutaryl-CoA synthase
lplL	65	lipoate-protein ligase
plsX	72	fatty acid/phospholipid synthesis protein
thiL	1613	acetyl coenzyme A acetyltransferase
ydiD	386	acyl carrier protein phosphodiesterase
yeaG	408	mevalonate kinase
yeaH	410	diphosphomevalonate decarboxylase
yebA	411	mevalonate kinase
yscE	1830	lipase
PURINES, PYRIMIDINES, NUCLEOSIDES AND NUCLEOTIDES
2'-deoxyribonucleotide metabolism
dcdA	1156	dCMP deaminase
nrdE	1004	ribonucleoside-diphosphate reductase alpha chain
nrdF	1002	ribonucleoside-diphosphate reductase beta chain
Nucleotide and nucleoside interconversions
cmk	1761	cytidine monophosphate kinase
dukA	494	deoxynucleoside kinase
dukB	1171	deoxynucleoside kinase
nucA	1101	nucleotidase
pyrH	2088	UMP-kinase
ycjM	301	phosphatase
Purine ribonucleotide biosynthesis
guaA	1517	GMP synthase
guaB	222	IMP dehydrogenase
guaC	1159	GMP reductase
hprT	1561	hypoxanthine-guanine phosphoribosyltransferase
purA	2029	adenylosuccinate synthase
purB	1689	adenylosuccinate lyase
purC	1578	phosphoribosylaminoimidazole-succinocarboxamide synthetase
*purD*	1554	phosphoribosylamine-glycine ligase
*purE*	1553	phosphoribosylaminoimidazole carboxylase
purF	1572	phosphoribosylpyrophosphate amidotransferase
purH	1560	bifunctional purine biosynthesis protein PurH
*purK*	1552	phosphoribosylaminoimidazole carboxylase
purL	1575	phosphoribosyl formylglycinamidine synthase II
purM	1566	phosphoribosyl-aminoimidazole synthetase
purN	1565	phosphoribosylglycinamide formyltransferase
purQ	1577	phosphoribosyl formylglycinamidine synttase I
Pyrimidine ribonucleotide biosynthesis
carA	1645	glutaminase of carbamoyl-phosphate synthase
*carB*	1400	carbamoylphosphate synthetase
dut	181	deoxyuridine 5'-triphosphate nucleotidhydrolase
*pydA*	1593	dihydroorotate dehydrogenase A
*pydB*	1383	dihydroorotate dehydrogenase B
pyrB	1646	aspartate carbamoyltransferase
pyrC	1082	dihydroorotase
pyrE	1081	orotate phosphoribosyltransferase
*pyrF*	1382	orotidine-phosphate decarboxylase
pyrZ	1384	dihydroorotate dehydrogenase electron transfer subunit
*thyA*	1583	thymidylate synthase
yeaB	404	thymidylate kinase
Salvage of nucleosides and nucleotides
add	288	adenosine deaminase
adk	2158	adenylate kinase
apt	623	adenine phosphoribosyltransferase
cdd	1463	cytidine deaminase
*deoB*	956	phosphopentomutase
deoC	1464	deoxyribose-phosphate aldolase
*deoD*	957	purine nucleoside phosphorylase
gmk	1967	guanylate kinase
*hpt*	25	hypoxantine-guanine phosphorybosyltransferase
nrdD	272	anaerobic ribonucleoside-triphosphate reductase
nrdG	273	anaerobic ribonucleoside-triphosphate reductase activating protein
pdp	1465	pyrimidine-nucleoside phosphorylase
prsA	826	ribose-phosphate pyrophosphokinase
prsB	1926	ribose-phosphate pyrophosphokinase
udk	1710	uridine kinase
udp	855	uridine phosphorylase
*upp*	1992	uracil phosphoribosyltransferase
xpt	1160	xanthine phosphoribosyltransferase
yfiG	585	thymidine kinase
Sugar-nucleotide biosynthesis and interconversions
cpsM	199	dTDP-4-keto-6-deoxyglucose-3,5-epimerase
rmlA	197	glucose-1-phosphate thymidylyltransferase
rmlB	200	dTDP-glucose 4,6-dehydratase
rmlC	201	dTDP-L-rhamnose synthase
REGULATORY FUNCTIONS
General
ahrC	883	transcriptional regulator
aldR	1253	regulatory protein AldR
argR	2118	arginine catabolic regulator
birA1	1840	bifunctional protein BirA
birA2	1973	bifunctional protein BirA
codY	164	transcriptional regulator
codZ	1865	transcriptional regulator
copR	845	transcriptional regulator
fur	1506	ferric uptake regulator
*gadR*	1327	positive regulator
glnB	1636	nitrogen regulatory protein P-II
glnR	2284	glutamine synthetase repressor
gntR	2272	transcription regulator
nadR	2067	transcriptional regulator
phoU	1771	phosphate transport system regulator
purR	2351	regulator of purine biosynthetic genes
pyrR	1648	pyrimidine operon regulator
rarA	1649	transcriptional regulator
rcfA	2083	transcriptional regulator
rcfB	2318	transcriptional regulator
relA	108	ppGpp synthetase I
rmeA	1947	transcriptional regulator
rmeB	1508	transcriptional regulator
rmeC	237	transcriptional regulator
rmeD	2053	transcriptional regulator
tagR	936	transcriptional regulator
tenA	1839	transcriptional regulator TenA
yabA	11	transcriptional regulator
yabB	13	transcriptional regulator
ybdA	131	transcription regulator
ybdG	135	transcriptional regulator
ybeD	146	transcriptional regulator
ycdF	235	transcriptional regulator
ycfA	250	transcriptional regulator
ydbF	316	transcriptional regulator
ydcG	327	transcriptional regulator
yebF	418	transcriptional regulator
yecA	420	transcriptional regulator
yecE	427	transcriptional regulator
yeeG	446	transcriptional regulator
yfbM	518	transcriptional regulator
yfeA	548	transcription regulator
yfjG	600	transcriptional regulator
ygfC	654	transcriptional regulator
yhgC	763	transcriptional regulator
yidA	831	transcription regulator
yjaD	904	transcriptional regulator
yjaJ	910	transcriptional regulator
yjfE	955	transcription regulator
yjjB	992	transcriptional regulator
ykhI	1078	transcriptional regulator
yleF	1148	transcription regulator
yliA	1180	positive transcriptional regulator
yljC	1193	transcriptional regulator
ymcE	1223	transcriptional regulator
ymiA	1285	metalloregulator
ynaB	1303	transcriptional regulator
yogL	1469	transcriptional regulator
yohC	1472	transcriptional regulator
ypfD	1555	transcriptional regulator
ypgC	1563	transcription regulator
yqbH	1618	transcriptional regulator
yrbI	1717	transcriptional regulator
yrfA	1750	transcription regulator
yrfE	1760	transcription regulator
ysfD	1854	regulatory protein
ysfG	1857	transcriptional regulator
ysgA	1866	transcriptional regulator
yugA	2065	transcription regulator
ywdE	2237	transcription regulator
ywiI	228	transcriptional regulator
ywjD	2297	transcription regulator
yxcB	2326	transcriptional regulator
yxdD	2337	transcriptional regulator
Two-component systems
*kinA*	1638	sensor protein kinase
*kinB*	1460	sensor protein kinase
*kinC*	402	sensor protein kinase
*kinD*	912	sensor protein kinase
*kinE*	1032	sensor protein kinase
kinF	1726	sensor protein kinase
kinG	1804	sensor protein kinase
llrA	1639	two-component system regulator
llrB	1458	two-component system regulator
llrC	403	two-component system regulator
llrD	913	two-component system regulator
llrE	1031	two-component system regulator
llrF	1727	two-component system regulator
llrG	1805	two-component system regulator
llrH	1758	two-component system regulator
LacI-family regulators
*ccpA*	1696	catabolite control protein A
rbsR	1688	ribose operon repressor
rliA	1728	transcriptional regulator
rliB	1536	transcriptional regulator
rliC	731	transcriptional regulator
rliDA	2215	transcriptional regulator
rliDB	2218	transcriptional regulator
LysR-family regulators
fhuR	331	fhu operon transcriptional regulator
*mleR*	896	malolactic fermentation system transcriptional activator
mtlR	32	transcriptional regulator
rlrA	1264	transcriptional regulator
rlrB	1946	transcriptional regulator
rlrC	1341	transcriptional regulator
rlrD	381	transcriptional regulator
rlrE	1598	transcriptional regulator
rlrG	378	transcriptional regulator
AraC-family regulators
adaA	519	methylphosphotriester-DNA alkyltransferase
xylR	1551	xylose operon regulator
yneE	1344	transcriptional regulator
GntR-family regulators
busR	1476	transcriptional regulator
kdgR	1680	transcriptional regulator
rgrA	437	transcriptional regulator
rgrB	1461	transcriptional regulator
DeoR-family regulators
citR	1206	citrate lyase regulator
*lacR*	984	lactose transport regulator
rdrA	797	transcriptional regulator
rdrB	1332	transcriptional regulator
MarR-family regulators
rmaA	750	transcriptional regulator
rmaB	715	transcriptional regulator
rmaC	1503	transcriptional regulator
rmaD	115	transcriptional regulator
rmaE	1511	transcriptional regulator
rmaF	1341	transcriptional regulator
rmaG	781	transcriptional regulator
rmaH	932	transcriptional regulator
rmaI	1583	transcriptional regulator
rmaJ	584	transcriptional regulator
zitR	2185	zinc transport transcriptional regulator
BglG-family regulators
*bglR*	1493	beta-glucoside operon antiterminator
GTP-binding proteins
eraL	355	GTP-binding protein Era
hflX	225	GTP-binding protein HflX
obgL	1630	GTP-binding protein Obg
thdF	2328	GTP-binding protein ThdF
typA	2094	GTP-binding protein TypA/BipA
ylqL	1330	GTP-binding protein
yphL	762	GTP-binding protein
yqeL	224	GTP-binding protein
ysxL	1165	GTP-binding protein
yyaL	12	GTP-binding protein
REPLICATION
Degradation of DNA
exoA	799	exodeoxyribonuclease A
nth	1084	endonuclease III
recJ	622	single-stranded DNA specific exonuclease
*rexA*	8	subunit A of ATP-dependent exonuclease
*rexB*	5	subunit B of ATP-dependent exonuclease
sbcC	1354	ATP-dependent dsDNA exonuclease
sbcD	1357	exonuclease SbcD
uvrA	1887	excinuclease ABC subunit A
uvrB	557	excinuclease ABC subunit B
uvrC	857	excinuclease ABC subunit C
xseA	878	exonuclease VII large subunit
xseB	879	exonuclease VII small subunit
DNA replication, restriction, modification, recombination, and repair
cshA	100	chromosome segregation helicase
dinG	1900	ATP-dependent helicase DinG
dnaA	1	replication initiation protein DnaA
dnaB	758	replication protein DnaB
dnaC	754	replicative DNA helicase
dnaD	1083	DNA replication protein DnaD
dnaE	496	DNA polymerase III, alpha chain 2
dnaG	545	DNA primase
dnaH	2279	DNA polymerase III, subunits beta and tau
dnaI	759	primosomal protein DnaI
*dnaJ*	2308	DnaJ protein
dnaN	2	DNA polymerase III, beta chain
dnaQ	1010	DNA polymerase III, epsilon chain
gyrA	1123	DNA gyrase subunit A
gyrB	929	DNA gyrase subunit B
hexA	2294	mismatch repair protein MutS
hexB	2291	DNA mismatch repair protein MutL
holB	405	DNA polymerase III, delta' subunit
*hsdM*	645	type I restriction enzyme M protein
*hsdR*	642	type I restriction enzyme R protein
*hsdS*	646	type I restriction enzyme specificity protein
hslA	502	HU like DNA-binding protein
hslB	903	HU-like DNA-binding protein
ligA	425	DNA ligase
*mutM*	358	formamidopyrimidine-DNA glycosylase
mutS	1693	DNA mismatch repair protein MutS
mutX	1136	mutator protein MutT
mutY	859	A/G-specific adenine glycosylase
ogt	519	6-O-methylguanine-DNA methyltransferase
parC	1012	topoisomerase IV subunit B
parE	1008	topoisomerase IV subunit B
pcrA	1135	ATP-dependent helicase PcrA
polA	2212	DNA polymerase I
polC	2192	DNA polymerase III, alpha chain
priA	1965	primosomal protein N'
radC	1036	DNA repair protein RadC
*recA*	359	RecA protein
recD	1798	exodeoxyribonuclease V alpha chain
recF	2052	RecF protein
recG	2331	ATP-dependent DNA helicase RecG
recM	340	RecM protein
recN	884	DNA repair protein RecN
ruvA	2290	DNA helicase RuvA
ruvB	2289	DNA helicase RuvB
snf	2122	SWI/SNF family helicase
ssbA	398	single-strand binding protein
ssbB	2274	single-strand binding protein
tag	1137	DNA-3-methyladenine glycosidase I
topA	1256	DNA topoisomerase I
*umuC*	581	SOS responce UmuC protein
ung	233	uracil-DNA glycosilase
xerD	635	integrase-recombinase
ybaH	101	acetyl transferase
yffD	556	diadenosine 5',5”'-P1,P4-tetraphosphate hydrolase
ymgA	1260	integrase-recombinase
TRANSCRIPTION
Degradation of RNA
pnpA	1923	polyribonucleotide nucleotidyltransferase
rnc	810	ribonuclease III
rnhA	2350	ribonuclease HII
rnhB	1329	ribonuclease HII
vacB1	968	ribonuclease
vacB2	1227	ribonuclease
RNA synthesis, modification, and DNA transcription
greA	626	transcription elongation factor GreA
mfd	19	transcription-repair coupling factor
nusA	774	transcription termination protein NusA
nusB	693	transcription termination protein NusB
nusG	2174	transcription antitermination protein
papL	1603	poly(A) polymerase
queA	1617	S-adenosylmethionine tRNA ribosyltransferase
rluA	2182	pseudouridine synthase
rluB	1308	pseudouridine synthase
rluC	1390	pseudouridine synthase
rluD	1027	pseudouridine synthase
rluE	368	pseudouridine synthase
rpoA	2153	DNA-directed RNA polymerase alpha chain
rpoB	1863	DNA-directed RNA polymerase beta chain
rpoC	1859	DNA-directed RNA polymerase beta' chain
*rpoD*	547	major RNA polymerase sigma factor
rpoE	624	DNA-directed RNA polymerase delta chain
rrmA	1365	rRNA methyltransferase
rsuA	2327	ribosomal small subunit pseudouridine synthase A
sigX	2243	RNA polymerase ECF sigma factor
smpB	1777	tmRNA-binding protein SmpB
sunL	1958	rRNA methylase
trmD	1607	tRNA methyltransferase
yfjD	597	tRNA/rRNA methyltransferase
RNA processing
rheA	354	ATP-dependent RNA helicase
rheB	416	ATP-dependent RNA helicase
rimM	1607	16S rRNA processing protein
TRANSLATION
Amino acyl tRNA synthetases
alaS	1780	alanyl-tRNA synthetase
argS	2117	arginyl-tRNA synthetase
asnS	1896	asparaginyl-tRNA synthetase
aspS	2041	aspartyl-tRNA synthetase
cysS	1919	cysteinyl-tRNA synthetase
gltX	2141	glutamyl-tRNA synthetase
glyS	1102	glycyl-tRNA synthetase alpha chain
glyT	1104	glycyl-tRNA synthetase beta chain
hisS	2043	histidyl-tRNA synthetase
ileS	1933	isoleucyl-tRNA synthetase
leuS	829	leucyl-tRNA synthetase
lysS	377	lysyl-tRNA synthetase
metS	800	methyonyl-tRNA synthetase
pheS	2010	phenylalanil-tRNA synthetase alpha chain
pheT	2008	phenylalanyl-tRNA synthetase beta chain
proS	2197	prolyl-tRNA synthetase
serS	1768	seryl-tRNA synthetase
thrS	1988	theronyl-tRNA synthetase
trpS	68	tryptophanyl-tRNA synthetase
tyrS	391	tyrosyl-tRNA synthetase 1
valS	2250	valyl-tRNA synthetase
Degradation of proteins, peptides, and glycopeptides
gcp	294	O-sialoglycoprotein endopeptidase
htrA	2205	exported serine protease
*pepA*	394	glutamyl aminopeptidase
*pepC*	1948	aminopeptidase C
pepDA	249	dipeptidase
pepDB	1601	dipeptidase
*pepF*	1784	oligoendopeptidase F
pepM	601	mathionine aminopeptidase
*pepN*	304	aminopeptidase N
*pepO*	1867	neutral endopeptidase
*pepP*	691	aminopeptidase P
pepQ	1698	proline dipeptidase
*pepT*	1878	tripeptidase
*pepV*	861	dipeptidase
*pepXP*	2136	X-prolyl dipeptidyl aminopeptidase
yueE	2049	protease
yueF	2050	protease
yugD	2069	protease
yuhB	2071	protease
Protein modification
def	555	polypeptide deformylase
pknB	1956	serine/threonine protein kinase
pmpA	1782	protein maturation protein
pmsR	2085	peptide methionine sulfoxide reductase
pmsX	1594	peptide methionine sulfoxide reductase
ppiA	369	peptidyl-prolyl cis-trans isomerase
ppiB	914	peptidyl-prolyl cis-trans isomerase
pppL	1957	protein serine/threonine phosphatase
ptpL	2284	protein-tyrosine phosphatase
ytaD	1905	protein-tyrosine phosphatase
Ribosomal proteins: synthesis and modification
prmA	105	methyltransferase
rplA	2079	50S ribosomal protein L1
rplB	2168	50S ribosomal protein L2
rplC	2170	50S ribosomal protein L3
rplD	2169	50S ribosomal protein L4
rplE	2164	50S ribosomal protein L5
rplF	2162	50S ribosomal protein L6
rplI	753	50S ribosomal protein L9
rplJ	1302	50S ribosomal protein L10
rplK	2080	50S ribosomal protein L11
rplL	1301	50S ribosomal protein L7/L12
rplM	2347	50S ribosomal protein L13
rplN	2165	50S ribosomal protein L14
rplO	2160	50S ribosomal protein L15
rplP	2166	50S ribosomal protein L16
rplQ	2152	50S ribosomal protein L17
rplR	2161	50S ribosomal protein L18
rplS	898	50S ribosomal protein L19
rplT	1911	50S ribosomal protein L20
rplU	1091	50S ribosomal protein L21
rplV	2167	50S ribosomal protein L22
rplW	2169	50S ribosomal protein L23
rplX	2165	50S ribosomal protein L24
rpmA	1091	50S ribosomal protein L27
rpmB	196	50S ribosomal protein L28
rpmC	2166	50S ribosomal protein L29
rpmD	2160	50S ribosomal protein L30
rpmE	1640	50S ribosomal protein L31
rpmF	96	50S ribosomal protein L32
rpmGA	662	50S ribosomal protein L33
rpmGB	96	50S ribosomal protein L33
rpmGC	2175	50S ribosomal protein L33
rpmH	134	50S ribosomal protein L34
rpmI	1912	50S ribosomal protein L35
rpmJ	2154	50S ribosomal protein L36
rpsA	854	30S ribosomal protein S1
rpsB	2228	30S ribosomal protein S2
rpsC	2166	30S ribosomal protein S3
rpsD	284	30S ribosomal protein S4
rpsE	2161	30S ribosomal protein S5
rpsF	2275	30S ribosomal protein S6
rpsG	2355	30S ribosomal protein S7
rpsH	2162	30S ribosomal protein S8
rpsI	2347	30S ribosomal protein S9
rpsJ	2170	30S ribosomal protein S10
rpsK	2153	30S ribosomal protein S11
rpsL	2355	30S ribosomal protein S12
rpsM	2154	30S ribosomal protein S13
rpsN	2164	30S ribosomal protein S14
rpsN2	911	30S ribosomal protein S14
rpsO	1955	30S ribosomal protein S15
rpsP	1611	30S ribosomal protein S16
rpsQ	2165	30S ribosomal protein S17
rpsR	2274	30S ribosomal protein S18
rpsS	2167	30S ribosomal protein S19
rpsT	1797	30S ribosomal protein S20
rpsU	237	30S ribosomal protein S21
ycjC	293	acetyltransferase
ycjD	293	acetyltransferase
yhdC	740	acetyl transferase
yhjG	798	acetyl transferase
ylxQ	776	probable ribosomal protein
fmt	1962	methyonyl-tRNA formyltransferase
gatA	166	Glu-tRNA amidotransferase subunit A
gatB	168	Glu-tRNA amidotransferase subunit B
gatC	165	Glu-tRNA amidotransferase subunit C
ksgA	690	kasugamycin dimethyltransferase
miaA	615	tRNA isopentenyltransferase
pth	17	peptidyl-tRNA hydrolase
rnpA	132	ribonuclease P protein component
tgt	156	queuine tRNA-ribosyltransferase
trmH	1942	tRNA-guanosine methyltransferase
trmU	853	tRNA-methyltransferase
truA	485	tRNA pseudouridine synthase A
truB	1141	tRNA pseudouridine synthase B
Translation factors
efp	692	elongation factor P
frr	2087	ribosome recycling factor
fusA	2353	elongation factor G
infA	2154	translation initiation factor IF-1
infB	777	translation initiation factor IF-2
infC	1912	translation initiation factor IF-3
lepA	1118	GTP-binding protein LepA
prfA	586	peptide chain release factor 1
prfB	999	peptide chain release factor 2
prfC	352	peptide chain release factor 3
rbfA	779	ribosome-binding factor A
tsf	2227	elongation factor Ts
tuf	1930	elongation factor Tu
TRANSPORT AND BINDING PROTEINS
General
ecsA	2075	ABC transporter ATP binding protein
ecsB	2074	ABC transporter permease protein
mscL	2171	large conductance mechanosensitive channel protein
yabE	16	ABC transporter ATP-binding protein
yahG	74	ABC transporter ATP binding protein
yaiE	87	transporter
yajA	90	transporter
ybaB	102	ABC transporter ATP binding protein
ycfB	251	ABC transporter ATP binding protein
ycfC	252	ABC transporter permease protein
ycfI	260	ABC transporter ATP binding protein
ycgA	261	ABC transporter ATP binding protein
ycgB	262	ABC transporter ATP binding protein
ychD	276	ABC transporter ATP-binding protein
ychE	277	ABC transporter ATP-binding protein
ychF	278	ABC transporter permease protein
ydaG	310	ABC transporter ATP binding and permease protein
ydbA	312	ABC transporter ATP binding and permease protein
ydcE	325	ABC transporter ATP binding protein
ydcF	326	ABC transporter permease protein
ydiA	382	permease
yfcA	520	ABC transporter ATP binding protein
yfcB	521	ABC transporter permease protein
yfgE	563	ABC transporter ATP binding protein
yfgF	564	ABC transporter permease protein
ygfA	652	ABC transporter ATP-binding protein
ygfB	653	ABC transporter permease protein
yhcA	721	ABC transporter ATP-binding and permease protein
yiiF	886	transporter
yijC	894	ABC transporter permease protein
yijD	895	ABC transporter ATP binding protein
yjcA	921	ABC transporter ATP binding protein
yjjC	993	ABC transporter ATP-binding protein
yjjD	994	ABC transporter permease protein
yjjF	996	transporter
ykhF	1074	ABC transporter ATP binding protein
ylbA	1111	ABC transporter ATP-binding protein
ylbB	1113	ABC transporter permease protein
yljI	1199	permease
ymeB	1245	ABC transporter ATP binding protein
ynaC	1304	ABC transporter ABC binding and permease protein
ynaD	1306	ABC transporter ABC binding and permease protein
yngB	1364	fibronectin-binding protein
ypgD	1564	ABC transporter ATP binding and permease protein
ypjG	1597	ABC transporter ATP binding protein
yrjE	1794	transport permease
ysaB	1808	ABC transporter permease and substrate binding protein
ysaC	1809	ABC transporter ATP-binding protein
ysdA	1834	ABC transporter permease protein
ysdB	1835	ABC transporter ATP binding protein
ysfB	1852	ABC transporter ATP-binding protein
ysiA	1882	transport protein
ysiB	1883	permease
ytaB	1902	transport protein
yteD	1945	transmembrane efflux protein
yudA	2031	transport protein
yujD	2097	ABC transporter ATP binding protein
ywiG	2285	ABC transporter ATP binding protein
ywiH	2286	ABC transporter permease protein
yxaA	2300	permease
yxdG	2340	transporter
yxeB	2349	ABC transporter ATP-binding protein
yxfA	2358	transporter
Amino acids, peptides and amines
arcD1	2112	arginine/ornitine antiporter
arcD2	2107	arginine/ornitine antiporter
brnQ	685	branched chain amino acid permease
*busAA*	1475	betaine ABC transporter ATP binding protein
*busAB*	1474	betaine ABC transporter permease and substrate binding protein
choQ	865	choline ABC transporter ATP binding protein
choS	867	choline ABC transporter permease and substrate binding protein
ctrA	113	cationic amino acid transporter
*dtpT*	705	di-/tripeptide transporter
*gadC*	1326	glutamate-gamma-aminobutyrate antiporter
glnP	1818	glutamine ABC transporter permease and substrate binding protein
glnQ	1819	glutamine ABC transporter ATP-binding protein
gltP	1856	glutamate ABC transporter permease protein
gltQ	1855	glutamate ABC transporter ATP-binding protein
gltS	559	glutamate or arginine ABC transporter substrate binding protein
lysP	2277	lysine specific permease
lysQ	370	lysine specific permease
*oppA*	1906	oligopeptide ABC trasporter substrate binding protein
*oppB*	1908	oligopeptide ABC trasporter permease protein
*oppC*	1907	oligopeptide ABC trasporter permease protein
*oppD*	1910	oligopeptide ABC trasporter ATP binding protein
*oppF*	1909	oligopeptide ABC trasporter ATP binding protein
optA	346	oligopeptide ABC transporter substrate binding protein
optB	347	oligopeptide ABC trasporter permease protein
optC	348	oligopeptide ABC trasporter permease protein
optD	349	oligopeptide ABC trasporter ATP binding protein
optF	350	oligopeptide ABC trasporter ATP binding protein
optS	344	oligopeptide ABC transporter substrate binding protein
potA	1176	spermidine/putrescine ABC transporter ATP-binding protein
potB	1177	spermidine/putrescine ABC transporter permease protein
potC	1178	spermidine/putrescine ABC transporter permease protein
potD	1179	spermidine/putrescine ABC transporter substrate binding protein
yagE	70	amino acid permease
ydcB	322	amino acid ABC transporter ATP binding protein
ydcC	323	amino acid ABC trasporter permease protein
ydgB	361	amino acid permease
ydgC	362	amino acid permease
yfcG	525	peptide-binding protein
yibG	819	amino acid permease
yjgC	963	amino acid ABC transporter substrate binding protein
yjgD	964	amino acid ABC transporter permease protein
yjgE	965	amino acid ABC transporter ATP binding protein
ylcA	1121	amino acid permease
yqfD	1655	amino acid permease
yrfD	1756	amino acid antiporter
yshA	1876	amino acid permease
ysjA	1891	amino acid permease
yvdF	2138	amino acid ABC transporter substrate binding protein
Anions
phnA	2332	alkylphosphonate uptake protein
phnB	299	phosphonate ABC transporter permease protein
phnC	298	phosphonate ABC transporter ATP-binding protein
phnE	299	phosphonate ABC transporter permease protein
pstA	1772	phosphate ABC transporter ATP binding protein
pstB	1772	phosphate ABC transporter ATP binding protein
pstC	1773	phosphate ABC transporter permease protein
pstD	1774	phosphate ABC transporter permease protein
pstE	1775	phosphate ABC transporter substrate binding protein
pstF	1776	phosphate ABC transporter substrate binding protein
yafB	52	sulfate transporter
Carbohydrates, organic alcohols and acids
glpF1	248	glycerol uptake facilitator
glpF2	1270	glycerol uptake facilitator
glpT	549	glycerol-3-phosphatase transporter
gntP	2266	gluconate permease
lacS	2063	lactose permease
maeP	1205	malate permease
malE	1740	maltose ABC transporter substrate binding protein
malF	1741	maltose ABC transporter permease protein
malG	1742	maltose ABC transporter permease protein
*mleP*	924	malate transporter
msmK	428	multiple sugar ABC transporter ATP-binding protein
rbsA	1685	ribose ABC transporter ATP binding protein
rbsB	1683	ribose ABC transporter substrate binding protein
rbsC	1684	ribose ABC transporter permease protein
rbsD	1686	ribose ABC transporter permease protein
rgpC	204	polysaccharide ABC transporter permease protein
rgpD	205	polysaccharide ABC transporter ATP-binding protein
tagG	939	teichoic acid ABC transporter permease protein
tagH	938	teichoic acid ABC transporter ATP binding protein
uxuT	1676	Na-galactoside symporter
xylT	1542	D-xylose proton-symporter
xynT	1546	xyloside transporter
yngE	1366	sugar ABC transporter ATP binding protein
yngF	1368	sugar ABC transporter permease protein
yngG	1369	sugar ABC transporter permease protein
ypbD	1515	sugar transport symporter
ypcG	1528	sugar ABC transporter substrate binding protein
ypcH	1529	sugar ABC transporter permease protein
ypdA	1530	sugar ABC transporter substrate binding protein
yqgE	1668	transporter
yvdD	2134	transporter
Cations
amtB	1636	ammonium transporter
cadA	97	cadmium efflux ATPase
copA	847	copper/potassium-transporting ATPase
copB	872	copper-potassium transporting ATPase B
feoA	192	ferrous ion transport protein A
feoB	191	ferrous ion transport protein B
fhuB	328	ferrichrome ABC transporter permease protein
fhuC	327	ferrichrome ABC transporter ATB binding protein
fhuD	330	ferrichrome ABC transporter substrate binding protein
fhuG	329	ferrichrome ABC transporter permease protein
kupA	610	potassium uptake protein
kupB	613	potassium uptake protein
mgtA	1287	cation-transporting P-ATPase
mtsA	1350	manganese ABC transporter substrate binding protein
mtsB	1351	manganese ABC transporter ATP binding protein
mtsC	1351	manganese ABC transporter permease protein
nah	1994	Na+/H+ antiporter
pacL	677	cation-transporting ATPase
ydaE	308	cation transporter
yddA	332	transporter
ydiF	388	Na+/H+ antiporter
yfgQ	570	cation-transporting ATPase
ygfE	657	divalent cation transport-related protein
yieF	846	mercuric reductase
yjdJ	937	potassium channel protein
yliI	1190	cation-transporting ATPase
yndG	1337	metal ABC transporter substrate binding protein
yoaB	1404	cation-transporting ATPase
yogJ	1468	cation transporter
ypbB	1512	cationic transporter
yqeI	1650	cation transport protein
yqgG	1664	cation transport ATPase
ysdE	1838	cation transporter
ytjB	1990	manganese transporter
yuiA	2081	metal transporting ATPase
yxdC	2336	cation-transporting ATPase
zitP	2183	zinc ABC transporter permease protein
zitQ	2183	zinc ABC transporter ATP binding protein
zitS	2184	zinc ABC transporter substrate binding protein
Nucleosides, purines and pyrimidines
pbuX	1161	xanthine permease
pnuC1	856	nicotinamide mononucleotide transporter
pnuC2	901	nicotinamide mononucleotide transporter
pyrP	1647	uracil permease
PTS system
celB	178	cellobiose-specific PTS system IIC component
fruA	986	fructose-specific PTS system enzyme IIBC component
mtlA	29	mannitol-specific PTS system IIBC component
mtlF	33	mannitol-specific PTS system IIA component
ptbA	1492	beta-glucoside-specific PTS system IIABC component
ptcA	419	cellobiose-specific PTS system IIA component
ptcB	419	cellobiose-specific PTS system IIB component
ptcC	421	cellobiose-specific PTS system IIC component
ptnAB	1763	mannose-specific PTS system component IIAB
ptnC	1764	mannose-specific PTS system component IIC
ptnD	1765	mannose-specific PTS system component IID
ptsH	120	phosphocarrier protein Hpr
ptsI	122	phosphoenolpyruvate-protein phosphotransferase
ptsK	605	Hpr(Ser) kinase
yedF	439	beta-glucoside-specific PTS system IIABC component
yidB	832	cellobiose-specific PTS system IIC component
yleD	1146	sucrose-specific PTS system IIBC component
yleE	1147	beta-glucoside-specific PTS system IIABC component
Multidrug resistance
blt	126	multidrug efflux transporter
cydC	711	cytochrome D ABC transporter ATP binding and permease protein
cydD	713	cytochrome D ABC transporter ATP binding and permease protein
*lcnC*	84	lactococcin A ABC transporter ATP binding and permease protein
*lcnD*	85	lactococcin A ABC transporter permease protein
*lmrA*	717	multidrug resistance ABC transporter ATP binding and permease protein
lmrP	2242	integral membrane protein LmrP
napC	306	multidrug-efflux transporter
pmrA	661	multidrug resistance efflux pump
pmrB	130	multidrug resistance efflux pump
ybfD	158	transporter
ycdH	236	transporter
ydiC	385	efflux pump antibiotic resistance protein
yfjF	599	membrane-bound transport protein
yjdE	933	multidrug resistance protein
yniG	1386	drug-export protein
ypfE	1557	transport protein
ypiB	1582	transporter
yqiA	1682	multidrug transporter
yweA	2240	membrane protein
yxbD	2319	transporter
OTHER CATEGORIES
Adaptations and atypical conditions
arsC	1412	arsenate reductase
clpB	1568	ClpB protein
clpC	631	ATP-dependent protease ATP-binding subunit
clpE	552	ATP-dependent protease ATP-binding subunit
clpP	673	ATP-dependent Clp protease proteolytic subunit
clpX	1164	ATP dependent Clp protease
cpo	835	non-heme chloride peroxidase
cspD	517	cold shock protein D
cspE	173	cold shock protein E
cstA	414	carbon starvation protein
ctsR	630	transctiptional regulator CtsR
dinF	172	damage-inducible protein DinF
dinP	2105	DNA-damage-inducible protein P
dpsA	2102	non-heme iron-binding ferritin
grpE	978	stress responce protein GrpE
hrcA	977	heat-inducible transcription repressor HrcA
osmC	69	osmotically inducible protein
phoL	1094	phosphate starvation inducible protein
tpx	302	thiol peroxidase
ybjA	193	reductase
yjbE	915	general stress protein GSP13
Drug and analog sensitivity
bacA	2276	undecaprenol kinase
bar	1837	acyltransferase
pacA	1150	penicillin acylase
pacB	1904	penicillin acylase
ymdC	1234	kanamycin kinase
Phage related functions and prophages
pi101	448	prophage pi1 protein 01, integrase
pi102	449	prophage pi1 protein 02
*pi103*	450	prophage pi1 protein 03, transcriptional regulator
pi104	450	prophage pi1 protein 04, transcriptional regulator
pi105	451	prophage pi1 protein 05
pi106	451	prophage pi1 protein 06
pi107	451	prophage pi1 protein 07
pi108	452	prophage pi1 protein 08
pi109	452	prophage pi1 protein 09
pi110	453	prophage pi1 protein 10, transcriptional regulator
pi111	453	prophage pi1 protein 11, recombinase
pi112	454	prophage pi1 protein 12
pi113	455	prophage pi1 protein 13, replisome organiser
pi114	456	prophage pi1 protein 14, DNA replication protein
pi115	457	prophage pi1 protein 15
pi116	457	prophage pi1 protein 16
pi117	458	prophage pi1 protein 17
pi118	458	prophage pi1 protein 18
pi119	459	prophage pi1 protein 19
pi120	459	prophage pi1 protein 16, deoxyuridine 5'-triphosphate nucleotidohydrolase
pi121	459	prophage pi1 protein 21
pi122	460	prophage pi1 protein 22
pi123	460	prophage pi1 protein 23
pi124	460	prophage pi1 protein 24
pi125	461	prophage pi1 protein 25
pi126	461	prophage pi1 protein 26
pi127	461	prophage pi1 protein 27
pi128	462	prophage pi1 protein 28
pi129	462	prophage pi1 protein 29
pi130	462	prophage pi1 protein 30
pi131	463	prophage pi1 protein 31
pi132	464	prophage pi1 protein 32
pi133	464	prophage pi1 protein 33, terminase small subunit
pi134	465	prophage pi1 protein 34, terminase large subunit
pi135	467	prophage pi1 protein 35
pi136	468	prophage pi1 protein 36, prohead protease
pi137	469	prophage pi1 protein 37, capsid protein
pi138	470	prophage pi1 protein 38
pi139	470	prophage pi1 protein 39
pi140	470	prophage pi1 protein 40, tail component
pi141	471	prophage pi1 protein 41, tail component
pi142	471	prophage pi1 protein 42, small major structural protein
pi143	472	prophage pi1 protein 43
pi144	474	prophage pi1 protein 44, tail component
pi145	477	prophage pi1 protein 45, tail component
pi146	480	prophage pi1 protein 46, tail component
pi147	482	prophage pi1 protein 47
pi148	482	prophage pi1 protein 48, holin
pi149	483	prophage pi1 protein 49, muramidase
pi201	1037	prophage pi2 protein 01, integrase
pi202	1038	prophage pi2 protein 02
pi203	1039	prophage pi2 protein 03
pi204	1039	prophage pi2 protein 04 hypothetical protein
pi205	1040	prophage pi2 protein 05
pi206	1040	prophage pi2 protein 06
pi207	1041	prophage pi2 protein 07
pi208	1041	prophage pi2 protein 08
pi209	1042	prophage pi2 protein 09
pi210	1042	prophage pi2 protein 10
pi211	1043	prophage pi2 protein 11, topoisomerase
pi212	1043	prophage pi2 protein 12, single strand binding protein
pi213	1044	prophage pi2 protein 13, replisome organiser
pi214	1045	prophage pi2 protein 14
pi215	1045	prophage pi2 protein 15
pi216	1046	prophage pi2 protein 16
pi217	1046	prophage pi2 protein 17
pi218	1047	prophage pi2 protein 18
pi219	1048	prophage pi2 protein 19
pi220	1048	prophage pi2 protein 20 hypothetical protein
pi221	1049	prophage pi2 protein 21, deoxyuridine 5'-triphosphate nucleotidohydrolase
pi222	1049	prophage pi2 protein 22
pi223	1049	prophage pi2 protein 23
pi224	1050	prophage pi2 protein 24
pi225	1051	prophage pi2 protein 25
pi226	1051	prophage pi2 protein 26
pi227	1052	prophage pi2 protein 27
pi228	1052	prophage pi2 protein 28
pi229	1053	prophage pi2 protein 29
pi230	1054	prophage pi2 protein 30, terminase
pi231	1055	prophage pi2 protein 31
pi232	1056	prophage pi2 protein 32
pi233	1057	prophage pi2 protein 33, capsid protein
pi234	1058	prophage pi2 protein 34
pi235	1059	prophage pi2 protein 35
pi236	1059	prophage pi2 protein 36
pi237	1059	prophage pi2 protein 37
pi238	1060	prophage pi2 protein 38
pi239	1060	prophage pi2 protein 39
pi240	1061	prophage pi2 protein 40
pi241	1061	prophage pi2 protein 41
pi242	1062	prophage pi2 protein 42
pi243	1064	prophage pi2 protein 43
pi244	1065	prophage pi2 protein 44
pi245	1068	prophage pi2 protein 45
pi246	1069	prophage pi2 protein 46
pi247	1069	prophage pi2 protein 47
pi248	1070	prophage pi2 protein 48
pi249	1070	prophage pi2 protein 49
pi250	1070	prophage pi2 protein 50
pi251	1071	prophage pi2 protein 51, holin
pi252	1071	prophage pi2 protein 52, muramidase
pi301	1414	prophage pi3 protein 01
pi302	1415	prophage pi3 protein 02
pi303	1415	prophage pi3 protein 03
pi304	1416	prophage pi3 protein 04
pi305	1416	prophage pi3 protein 05, muramidase
pi306	1417	prophage pi3 protein 06, holin
pi307	1418	prophage pi3 protein 07
pi308	1419	prophage pi3 protein 08
pi309	1420	prophage pi3 protein 09
pi310	1421	prophage pi3 protein 10
pi311	1422	prophage pi3 protein 11
pi312	1424	prophage pi3 protein 12
pi313	1425	prophage pi3 protein 13, tail component
pi314	1428	prophage pi3 protein 14
pi315	1431	prophage pi3 protein 15
pi316	1431	prophage pi3 protein 16, tail component
pi317	1432	prophage pi3 protein 17, major tail protein
pi318	1433	prophage pi3 protein 18, tail component
pi319	1433	prophage pi3 protein 19, tail component
pi320	1433	prophage pi3 protein 20, head-tail joining protein
pi321	1434	prophage pi3 protein 21
pi322	1435	prophage pi3 protein 22, major head protein precursor
pi323	1436	prophage pi3 protein 23, ATP dependent Clp protease
pi324	1436	prophage pi3 protein 24
pi325	1437	prophage pi3 protein 25, head-tail joining protein
pi326	1438	prophage pi3 protein 26, terminase large subunit
pi327	1439	prophage pi3 protein 27, terminase small subunit
pi328	1440	prophage pi3 protein 28
pi329	1440	prophage pi3 protein 29
pi330	1441	prophage pi3 protein 30
pi331	1441	prophage pi3 protein 31
pi332	1442	prophage pi3 protein 32
pi333	1443	prophage pi3 protein 33
pi334	1443	prophage pi3 protein 34
pi335	1443	prophage pi3 protein 35, deoxyuridine 5'-triphosphate nucleotidohydrolase
pi336	1444	prophage pi3 protein 36
pi337	1444	prophage pi3 protein 37
pi338	1445	prophage pi3 protein 38
pi339	1445	prophage pi3 protein 39
pi340	1446	prophage pi3 protein 40
pi341	1446	prophage pi3 protein 41
pi342	1446	prophage pi3 protein 42
pi343	1447	prophage pi3 protein 43
pi344	1447	prophage pi3 protein 44
pi345	1447	prophage pi3 protein 45
pi346	1448	prophage pi3 protein 46, DNA replication protein
pi347	1449	prophage pi3 protein 47, replisome organiser
pi348	1450	prophage pi3 protein 48, single strand binding helix destabilising protein
pi349	1450	prophage pi3 protein 49
pi350	1451	prophage pi3 protein 50
pi351	1451	prophage pi3 protein 51
pi352	1452	prophage pi3 protein 52
pi353	1452	prophage pi3 protein 53
pi354	1452	prophage pi3 protein 54
pi355	1453	prophage pi3 protein 55, antirepressor
pi356	1453	prophage pi3 protein 56, cro-like repressor
pi357	1454	prophage pi3 protein 57, cI-like repressor
pi358	1455	prophage pi3 protein 58
pi359	1455	prophage pi3 protein 59
pi360	1456	prophage pi3 protein 60, integrase
*pip*	1720	phage infection protein
ps101	36	prophage ps1 protein 01, hypothetical regulator
ps102	36	prophage ps1 protein 02
ps103	37	prophage ps1 protein 03, terminase subunit
ps104	37	prophage ps1 protein 04
ps105	38	prophage ps1 protein 05, DNA primase
ps106	40	prophage ps1 protein 06
ps107	40	prophage ps1 protein 07
ps108	41	prophage ps1 protein 08
ps109	41	prophage ps1 protein 09
ps110	41	prophage ps1 protein 10
ps111	42	prophage ps1 protein 11, transcriptional regulator
ps112	42	prophage ps1 protein 12
ps113	42	prophage ps1 protein 13
ps114	43	prophage ps1 protein 14
ps115	44	prophage ps1 protein 15, transcriptional regulator
ps116	44	prophage ps1 protein 16
ps117	45	prophage ps1 protein 17
ps118	45	prophage ps1 protein 18
ps119	45	prophage ps1 protein 19
ps120	46	prophage ps1 protein 20
ps121	47	prophage ps1 protein 21
ps122	48	prophage ps1 protein 22
ps123	49	prophage ps1 protein 23, integrase
ps201	503	prophage ps2 protein 01, integrase
ps202	504	prophage ps2 protein 02
ps203	505	prophage ps2 protein 03
ps204	505	prophage ps2 protein 04
ps205	506	prophage ps2 protein 05, transcriptional repressor
ps206	506	prophage ps2 protein 06
ps207	506	prophage ps2 protein 07, excisionase
ps208	507	prophage ps2 protein 08
ps209	507	prophage ps2 protein 09
ps210	507	prophage ps2 protein 10
ps211	508	prophage ps2 protein 11
ps212	508	prophage ps2 protein 12
ps213	508	prophage ps2 protein 13
ps214	509	prophage ps2 protein 14
ps215	510	prophage ps2 protein 15
ps216	511	prophage ps2 protein 16
ps218	512	prophage ps2 protein 18
ps219	512	prophage ps2 protein 19
ps220	513	prophage ps2 protein 20
ps221	514	prophage ps2 protein 21
ps301	2014	prophage ps3 protein 01
ps302	2015	prophage ps3 protein 02
ps303	2015	prophage ps3 protein 03
ps304	2016	prophage ps3 protein 04
ps305	2016	prophage ps3 protein 05
ps306	2018	prophage ps3 protein 06
ps307	2019	prophage ps3 protein 07
ps308	2019	prophage ps3 protein 08
ps309	2019	prophage ps3 protein 09
ps310	2020	prophage ps3 protein 10
ps311	2021	prophage ps3 protein 11
ps312	2022	prophage ps3 protein 12
ps313	2023	prophage ps3 protein 13
ps314	2023	prophage ps3 protein 14, transcriptional regulator
ps315	2024	prophage ps3 protein 15
ps316	2025	prophage ps3 protein 16, integrase
Transposon related functions
*tra1077A*	53	transposase of IS1077A
*tra1077B*	140	transposase of IS1077B
*tra1077C*	375	transposase of IS1077C
*tra1077D*	628	transposase of IS1077D
*tra1077E*	838	transposase of IS1077E
*tra1077F*	2156	transposase of IS1077F
*tra1077G*	2217	transposase of IS1077G
*tra904A*	54	transposase of IS904A
*tra904B*	138	transposase of IS904B
*tra904C*	40	transposase of IS904C
*tra904D*	374	transposase of IS904D
*tra904E*	627	transposase of IS904E
*tra904F*	836	transposase of IS904F
*tra904G*	839	transposase of IS904G
*tra904H*	2155	transposase of IS904H
*tra904I*	2215	transposase of IS904I
*tra905*	1225	transposase of IS905
*tra981A*	92	transposase of IS981A
*tra981B*	93	transposase of IS981B
*tra981C*	651	transposase of IS981C
*tra981D*	729	transposase of IS981D
*tra981E*	1217	transposase of IS981E
*tra981F*	1222	transposase of IS981F
*tra981G*	1276	transposase of IS981G
*tra981H*	1586	transposase of IS981H
*tra981I*	1748	transposase of IS981I
*tra981J*	2103	transposase of IS981J
*tra982*	640	transposase of IS982
tra983A	682	transposase of IS983A
tra983B	707	transposase of IS983B
tra983C	958	transposase of IS983C
tra983D	1338	transposase of IS983D
tra983E	1396	transposase of IS983E
tra983F	1556	transposase of IS983F
tra983G	1755	transposase of IS983G
tra983H	1954	transposase of IS983H
tra983I	1978	transposase of IS983I
tra983J	2012	transposase of IS983J
tra983K	2017	transposase of IS983K
tra983L	2084	transposase of IS983L
tra983M	2148	transposase of IS983M
tra983N	2203	transposase of IS983N
tra983O	2268	transposase of IS983O
yafG	53	hypothetical protein
yafI	55	hypothetical protein
yajE	92	transposase
yajG	94	transposase
ybdK	138	hypothetical protein
ybdL	139	hypothetical protein
ybeG	141	hypothetical protein
ydhD	373	hypothetical protein
ydhE	375	hypothetical protein
yfjB	593	transposon-related protein
ygcD	628	hypothetical protein
ygcE	629	hypothetical protein
ygfF	651	transposase
yhcJ	729	transposase
yidF	837	hypothetical protein
yidG	838	hypothetical protein
yidH	839	hypothetical protein
ymbA	1212	integrase
ymbI	1217	transposase
ymcD	1222	transposase
ymfD	1259	integrase-recombinase
ymhB	1276	transposase
ypiI	1587	transposase
yrdA	1748	transposase
yuiI	2104	transposase
yvfC	2157	hypothetical protein
yvfD	2156	hypothetical protein
yvjF	2216	hypothetical protein
ywbC	2217	hypothetical protein
Other
crtK	574	carotenoid biosynthetic protein CrtK
yebB	412	carotenoid biosynthetic protein

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^#Gene symbols, coordinates in kb, and definitions are shown. Bold italic symbols correspond to gene functions experimentally confirmed in L. lactis.

Origin and Terminus of Replication

Approximate position of the replication origin and terminus of the L. lactis chromosome was determined previously, using the GC and AT skews (Fig. 1; Bolotin et al. 1999). It should be noted that the precision of the origin mapping is greater than that of the terminus, as there are conserved elements (dnaA and dnaN genes, DnaA boxes) in the vicinity of the former but not of the latter (rtp gene was not found). We choose as the coordinate 1 of the genome the middle of a HindIII site localized near the replication origin (Fig 1).

Distribution of IS elements and prophages in the IL1403 chromosome. Outer circle shows the scale in basepairs. IS981, IS983, and IS1077 are shown by yellow, red, and blue squares, respectively (enlarged for clarity). Red and blue arcs show the areas of IS983 and IS1077 insertions. pi prophages are shown in violet, and ps in black. Green circle shows GC skews (C−G/C+G) distribution (window 20 kb, step 5 kb), which indicates the origin (near bp 1) and terminus (near bp 1,260,000) of replication.

RNA, IS Elements, and Prophages

Location of six rRNA operons, 62 tRNA genes, the RNA component of RNAse P gene (rnpB), and the 10S RNA (ssrA) were determined earlier from the diagnostic sequence (Bolotin et al. 1999). There are six different IS elements in the IL1403 chromosome: IS981, IS982, IS983, IS904, IS905, and IS1077, present in 10, 1, 15, 9, 1, and 7 copies, respectively (Fig. 1) and totaling 42 kb. It is remarkable that one or two copies of IS904 always accompany IS1077 and that the relative orientation of the two is generally not the same. The former element might be a satellite of the latter. Another remarkable feature is that three of the IS elements are not randomly distributed over the chromosome (Fig. 1). Seven copies of IS1077 (and the associated IS904) occupy the region between 2150 and 840 kb, encompassing the replication origin, whereas 15 copies of IS983 occupy a different region, between 680 and 2270 kb. The two regions overlap by only ∼150 kb. As the 10 copies of IS981 are distributed over the whole genome, the uneven distribution of three other IS elements is not caused by a particular property of the L. lactis cell. We suggest that this distribution indicates a lateral transfer of a large portion of the genome from a lactococcus donor, carrying one type of IS, to a recipient, carrying the other type. Two lines of evidence lend support to this hypothesis. First, IS1076, which corresponds to the association of IS1077 and IS904 described above, is distributed over the whole genome of the strain L. lactis ssp. cremoris MG1363 (Le Bourgeois et al. 1995) rather than being restricted to one region of the genome, as is the case in IL1403. This transposon has, therefore, no particular hot region for insertion in the lactococcal genome. Second, the restriction map of another strain, L. lactis ssp. lactis DL11, coincides with that of IL1403 in the area between rrnF (550 kb) and rrnE (1980 kb), while it is divergent elsewhere (Le Bourgeois et al. 1992). We suggest that DL11 may be close to one of the putative parental strains of IL1403. Investigations of the distribution of IS1077 and IS983 among different lactococci might allow identification of both putative parents of the IL1403 strain.

Three potential prophages, designated pi1, pi2, and pi3, were detected at positions near 460, 1050, and 1460 kb (Fig. 1). They are large (35–44 kb), encode 49–60 proteins, and are related to known temperate phages of L. lactis. Another three prophages, designated ps1, ps2, and ps3, are localized near 42, 509, and 2020 kb (Fig. 1). They are small (11–15 kb), encode only 16–23 proteins and might be satellites of the other phages, as they lack most of the genes that code for phage structural elements. A copy of IS983 is present in ps3, which might, thus, be defective. The six prophages comprise a total of 175 kb of DNA and 221 protein coding genes. Recently, Chopin et al. (2001) characterized five phages, which can be found in the supernatant of IL1403 after mitomycin C treatment, and demonstrated the correspondence between the phage DNA extracted from the supernatant and the chromosome sequence. Phage bIL285 from the supernatant corresponds to pi2, bIL286 to pi3, bIL309 to pi1, bIL310 to ps1, and bIL312 to ps2. ps3, designated also as bIL311 (Chopin et al. 2001), cannot be induced, probably because of the IS983 element present in its genome. Detecting the circular forms of DNA of these phages allowed precise determination of the integration sites. About 9.2% of the L. lactis genome is thus formed by IS elements and prophages, suggesting that they may be important for horizontal gene transfer in these bacteria.

Paralogous Gene Families

We define here as a paralogous protein family a group of proteins within which each protein shares at least one homologous domain with another protein of the group. By this criterion, there are 370 paralogous families, comprising 1189 gene products, in the L. lactis genome. Among the smaller families (<10 members) there are 208 of two members, 80 of three, 36 of four, 13 of five, 13 of six, 8 of seven, 4 of eight, and 2 of nine. The larger families contain 10, 11, 15, 18, 26, and 60 members, the last corresponding to ATP-binding proteins of ABC transporters, as is the case in many bacteria. In the four smallest families, distribution of the number of proteins resembles that of B. subtilis (Kunst et al. 1997). It decreases, very approximately, twofold when the family member count increases by one (568:273:168:100 in B. subtilis and 416:240:144:65 in L. lactis for doublets, triplets, quadruplets, and quintuplets, respectively).

Information Processing and Gene Regulation

Information processing refers to the genes constituting replication, transcription, and translation machinery. In L. lactis, it is overall very similar to that of B. subtilis, the best characterized AT-rich gram-positive bacterium (Kunst et al. 1997). There are 67 genes involved in DNA metabolism in L. lactis. All the genes involved in DNA replication in B. subtilis are present in L. lactis, including counterparts of dnaB, dnaD, and dnaI, genes essential for initiation of replication in B. subtilis and absent in gram-negative bacteria. Two DNA-polymerase III α-chain genes, one corresponding to polC and another to dnaE of B. subtilis, were also detected in L. lactis. In contrast, E. coli has only the dnaE gene.

Transcription machinery in both L. lactis and B. subtilis comprises some 30 genes other than the ς-factors. However, the number of ς-factors differs greatly, as there are only three in L. lactis, while there are 18 in B. subtilis, pointing to a considerable difference in the mode of gene-expression regulation in the two organisms. Translation machinery comprises 119 genes in L. lactis and 131 genes in B. subtilis. There are no duplicated aminoacyl-tRNA synthetase genes in L. lactis, while there are three (for threonine, tyrosine, and histidine) in B. subtilis. Posttranslational protein modification genes mostly differ, as there are 27 such genes in B. subtilis and only 10 in L. lactis. A particular regulation of translation might also operate in L. lactis. As discussed more fully below, all the late competence genes of L. lactis seem to be controlled by a mechanism relaying on leaderless mRNAs and, thus, on a particular mode of translation. Recent evidence shows that the involvement of translation initiation factor 3, present in all bacteria, in start codon recognition is important for restriction of translation in such systems (Tedin et al. 1999). This provides a link between regulation of translation and competence in L. lactis. Such interaction has not been detected previously.

Analysis of homology allowed us to assign regulatory functions to 138 genes, half of which were classified further by their similarity to regulatory proteins of known families. The overall number of regulatory systems is about twofold lower in L. lactis than in B. subtilis, but the proportion of these genes is similar in the two organisms. Among the interesting differences is a much lower number of the two-component signal transducers in L. lactis than in B. subtilis (eight instead of 34) and of ς-factors (three instead of 18), both of which regulate complex responses to changing environmental conditions.

Energy Metabolism and Transporters

The most important industrial applications of L. lactis are based on its energy metabolism, which leads mainly to the production of high amounts of lactic acid (homolactic fermentation). Anaerobic glycolysis is the principal energy-generating process in L. lactis, and very little of the fermented sugar (∼5%) is used for synthetic reactions (Poolman 1993). All the genes required for the conversion of the glucose to pyruvate are present in the genome. The pyruvate is converted into lactic acid, thus allowing the oxidation of reduced NAD, and the lactate dehydrogenase gene ldh, essential for this process, was studied intensely (Griffin et al. 1992). Three other genes, highly similar to ldh, (ldhB, ldhX and hicD) are present in the genome, but their role is not known. The product of the last gene has a high similarity (42% identity) to hydroxyisocaproate dehydrogenase and may, therefore, be involved in the catabolism of branched-chain amino acids. Lactate is transported into the growth medium, causing the efflux of protons and, thus, providing transmembrane potential indispensable for growth and energy recycling (Ten Brink et al. 1985).

Genome analysis indicates that the full citric acid cycle, gluconeogenesis enzymes, and many anaplerotic reactions do not exist in L. lactis. Unexpectedly, the functions necessary for aerobic respiration are encoded in the genome. L. lactis has men and cytABCD operons, encoding proteins required for menaquinone synthesis and cytochrome d biogenesis. It also has three genes involved in the late steps of heme synthesis (hemH, hemK, and hemN, required for oxidation of porphyrinogen and attachment of iron to heme) but not the genes required for the early steps. L. lactis may thus be able to carry out oxidative phosphorylation if the protoporphyrinogen is provided. Indeed, improved growth properties in media containing hemin were observed for certain Streptococci (Sijpesteijn 1970; Mickelson 1972). The genome analysis thus suggests the existence of aerobic respiration in this bacterium, generally considered an exclusively fermentative microorganism.

Use of L. lactis in the food industry also exploits its ability to form fermentation products other than lactate (mixed acid fermentation). The balance of products depends on activities of enzymes that act on the key metabolite generated by glycolysis, the pyruvate. A number of genes encoding such enzymes (pyruvate dehydrogenase, pdhABCD; α-acetolactate synthase, als; pyruvate-formate lyase, pfl; and lactate dehydrogenase, ldh) have been identified previously in L. lactis and confirmed by genome analysis. We detected a novel gene, poxL, encoding pyruvate oxidase, which also acts on pyruvate and might, therefore, play a role in switching between different fermentation modes.

Besides gene activity, the availability of cofactors, such as NADH and FAD, also affects the balance of different fermentation products. Artificial changing of NADH/NAD ratio in L. lactis can redirect carbon flow from lactic acid to acetoin and diacetyl (Lopez de Felipe et al. 1998). There are more than five NADH dehydrogenase genes in the L. lactis genome, which may affect the type of fermentation products. Some NADH dehydrogenases generate hydrogen peroxide, which is toxic for the cells. L. lactis has no gene encoding catalase, which can remove the toxic H₂O₂. However, there is a gene encoding thiol peroxidase (tpx) and two genes (ahpC and ahpF) encoding alkyl hyperoxide reductases. These proteins could possibly act on H₂O₂. Active sodA, encoding superoxid dismutase, which converts oxygen radicals to H₂O₂, was shown to be important for the oxidative stress response (Sanders et al. 1995). Also, the gshR gene encoding glutathion reductase may be involved in response of L. lactis to the aerobic growth conditions.

The heterofermentative metabolism takes place in L. lactis when pentoso-phosphate pathway is active, as in this case, glycolysis generates not only a three-carbon compound that can be converted to lactate but also a two-carbon compound. We detected glucose-6P dehydrogenase (zwf), phosphogluconate dehydrogenase (gnd), and ribuloso-5P epimerase (rpe), which can lead to the formation of xyluloso-5P. Phosphoketolase, encoded by ptk gene, can catalyze formation of glyceraldehyde-3P and acetyl-P, which enter the fermentation pathways that yield lactate and ethanol, respectively.

Understanding the molecular basis of the switch between different fermentation types is of interest not only for standard uses of L. lactis but also for the metabolic engineering in this organism, aiming to enhance synthesis of certain metabolites to industrially useful levels. We detected a correlation between the presence of the phosphoenolpyruvate dependent transport system (PTS) and the fermentation profile for a given carbon source. PTS systems for fructose, mannose, sucrose or trehalose, mannitol, and cellobiose are present in the genome, and the homolactic fermentation profiles were reported for growth on fructose, mannose, glucose (which uses mannose or mannitol PTS) and sucrose (Cocaign-Bousquet et al. 1996). In contrast, mixed acid or heterofermentation profiles were observed for growth on galactose, xylose, maltose, gluconate, ribose, and lactose, which are not imported by a PTS system. When L. lactis cells harbor a plasmid encoding lactose-specific PTS system, lactose fermentation becomes homolactic (Gasson 1983). Our genome analysis thus strengthens the proposal that sugar consumption rate, which is the highest when PTS system is available, determines the ability for efficient homolactic fermentation (Cocaign-Bousquet et al. 1996). The correlation of information derived from genome analysis with experimental data on fermentation product distribution indicates that critical parameters regulating the final product balance may be found by a thorough analysis of the carbon source use and transport systems.

Proteases and Amino Acid Catabolism Genes

Proteases and peptidases provide a selective advantage for bacteria growing in milk, as this medium is rich in caseins and relatively poor in free amino acids. Amino acid catabolism has an impact on fermentation regulation and on the flavor of dairy products.

Genome sequence revealed 19 protease-encoding genes (Table 1). These include the membrane protease HtrA, which is responsible for degradation of the precursors of foreign exported proteins (Pouquet et al. 2000). Some 16 peptidases from LAB were characterized previously, including the products of 13 genes detected in L. lactis (Christensen et al. 1999).

Catabolism of amino acids usually starts by deamination. Arginine catabolic genes, organized in an operon near 2110 kb, encode the enzymes for the deaminase pathway as well as the arginine tRNA synthetase, suggesting complex regulation. Another operon for arginine catabolism, near 1755 kb, contains genes arcC3 and otcA. It could have a regulatory function, as it also contains the genes llrH and yrfE, representing a signal transduction system of a new type. Aspartate aminotransferase (aspC) and asparaginase (ansB) are involved in aspartate and asparagine catabolism. No genes for aspartate decarboxylase or aspartase were detected, although such enzymatic activities were identified in Lactobacillus, another prominent group of LAB (Rollan et al. 1985). Recent studies on catabolism and biosynthesis of glutamate in L. lactis identified the existence of a pathway leading to the production of γ-aminobutyrate (GABA; Sanders et al. 1998). We identified gadRCB operon for GABA production, gltBD genes for glutamate synthase, and an operon involved in citric acid metabolism: pycA, gltA, citB, and icd. Under appropriate physiological conditions, products of some of these genes might carry out glutamate catabolism, rather than biosynthesis. Serine can be directly converted to pyruvate by serine dehydratase encoded by the sdaAB operon.

Genome sequence provides inventory of 12 aminotransferases, of which some can initiate degradation of aromatic, branched-chain, and sulfur-containing amino acids, important for cheese flavor. The specificity of seven aminotransferases (aspC, serC, argD, glmS, hisC, aspB, and arcT) can be predicted from sequence comparisons, whereas those of other five (araT, nifZ, yeiG, bcaT, and ytjE) are less obvious. It was recently shown that araT and bcaT are involved in the degradation of aromatic and branched-chain amino acids, respectively (Yvon et al. 2000). The product of ytjE might be specific for methionine, as the gene is cotranscribed with the relevant biosynthesis genes. Degradation of tryptophane seems to proceed via indole aldehyde because of indole pyruvate decarboxylase gene ipd. It is not clear which pathways L. lactis uses to catabolize phenylalanine and tyrosine. It is possible that phenyl pyruvate and p-OH-phenyl pyruvate are degraded further by decarboxylation. This would depend on the specificity of the phenolic acid decarboxylase encoded by pdc.

Amino Acid, Vitamin, and Nucleotide Biosynthesis

L. lactis requires certain metabolites in the growth medium, although it has a genetic potential to synthesize some of them. Synthetic medium for L. lactis should contain at least six amino acids (isoleucine, valine, leucine, histidine, methionine, and glutamic acid) and seven vitamins (biotin, pyridoxal, folic acid, riboflavin, nicotinamide, thiamine, and pantothenic acid; Jensen and Hammer 1993). L. lactis has the genes to synthesize the 20 standard amino acids and at least four cofactors (folic acid, menaquinone, riboflavin, and thioredoxin). One reason for the requirement of the compounds that can potentially be synthesized is that some of the existing genes are not functional, as was reported previously for amino acid biosynthesis genes (Godon et al. 1993). We carefully checked sequencing tracks for the genes that could contain a frameshift mutation and could not rule out the presence of a mutation in 30 of them. This relatively high level of pseudogenes in IL1403 could possibly be, at least in part, caused by the treatments used to cure the parental strain of its plasmids (Chopin et al. 1984).

Milk does not contain sufficient levels of purine compounds to support growth of L. lactis and, therefore, de novo biosynthesis is necessary (Dickely et al. 1995). We detected 57 genes involved in this metabolism. Therefore, physiological and genomic evidence shows that L. lactis has sufficient and fairly active capacities for biosynthesis and also for salvage of nucleic acid compounds.

Cell Wall Metabolism

Many L. lactis properties that are important for applications, such as phage sensitivity, stress resistance, autolysis, and mucosal immunostimulation, depend on the structure of the cell wall. There are 29 genes encoding enzymes required for the synthesis of the main cell wall component, peptidoglycan. Among these, three encode amino acid racemases: dal for alanine, murI for glutamate, and racD for aspartate. D-alanine and D-glutamate are the components of linear peptide moiety of peptidoglycan, whereas D-aspartate forms cross-bridges. There are no genes for synthesis of modified peptidoglycan, containing D-lactate or D-serine instead of D-alanine, reported for several other LAB.

Cheese ripening can be accelerated by induction of enzymes that process peptidoglycan. There are six genes related to such processing in L. lactis: dacA and dacB, encoding alanine–alanine carboxypeptidase; and acmA, B, C, and D, encoding four lysozymes. Carboxypeptidases alone cannot cause the cell lysis, as their activity does not destabilize the wall. Modulation of the level of their production can, however, influence the action of lysozymes. acmA, responsible for separation of daughter cells, was used for artificial induction of autolysis (Buist et al. 1997).

Lipoteichoic acid is another main component of the L. lactis cell wall. Neither teichoic nor teichuronic acids were detected in this microorganism (Valyasevi et al. 1990). However, there is a cluster of seven tag genes near 950 kb. Only three genes from teichuronic acid biosynthesis pathway were found: ycbK, ycbF, and ycbH, corresponding to tuaB, tuaC, and tuaG of B. subtilis. dlt operon, encoding D-alanylation of lipoteichoic acid, is of crucial importance for properties of the cell wall and whole-cell physiology. A knockout mutation in dltD causes filamentous growth and UV sensitivity and facilitates penetrability of the cells (Duwat et al. 1997).

Synthesis of extracellular polysaccharides is important for the industrial use of many LAB, as these polymers affect the texture of the fermented products. There are >20 genes involved in the biosynthesis of such molecules in the region near 200 kb. They encode functions providing activated sugars and other components involved in production of surface or extracellular polysacharide. A plasmid that carries an operon involved in the formation of the repeating unit, linking activated sugar to the lipid carrier, export, and polymerization, was recently identified (Van Kranenburg et al. 1997). Conjunction of plasmid-carried and chromosomal functions presumably determine the amounts and the structure of extracellular polysaccharides.

Protein Secretion

L. lactis has only eight genes identified as implicated in protein secretion. Contrary to B. subtilis and E. coli, this bacterium does not have secDF genes, known to improve the secretion efficiency (Pogliano and Beckwith 1994; Bolhuis et al. 1998). There is only one membrane protease, HtrA, involved in degradation of hybrid exported proteins (Pouquet et al. 2000). Gene pmpA (protein maturation protein) encodes a homolog of PrsA from B. subtilis and might be involved in stabilization of secreted proteins by facilitating their folding. L. lactis was shown to secrete up to 20 mg/L of foreign protein with optimized gene constructs (Le Loir et al. 1998). This value could possibly be improved by manipulating the gene expression levels and supplying the missing components of the secretion machinery.

Competence to Genetic Transformation

Natural competence to DNA transformation was not demonstrated in L. lactis. We detected four operons (comE, comF, comC, and comG) containing genes similar to the late competence genes from B. subtilis and S. pneumoniae. In addition, we found a gene for ComX, which is similar to the S. pneumoniae ECF-type ς-factor required for transcription of the competence genes (Lee and Morrison 1999). The regions preceding the first ORF of the four operons resemble competence promoters from S. pneumoniae and might be transcribed by ComX. There are three common sequences in front of all competence operons, two of which, GTTACATT and TTTTCGTATA, are in the −35 and −10 domains of the promoter, while the third, AGTATG, includes the ATG start codon of the first gene in each operon. The relative position of the three conserved elements indicates that all mRNAs start at the ATG codon of the first gene and are, therefore, leaderless, lacking the canonical ribosome-binding site. Search for the consensus sequence over the whole genome, using PatScan (Dsouza et al. 1997), revealed six such promoters other than those of the late competence operons. The genes downstream of these promoters are radA, coiA, dprA, recQ, ssbA, and yqfG. Only the radA gene, encoding a DNA repair protein, has leaderless mRNA. Three of the genes, coiA, dprA, and recQ, affect DNA transformation in S. pneumoniae, H. influenzae, and B. subtilis, respectively (Karudapuram et al. 1995; Fernandes et al. 1998; Pestova and Morrison 1998). ssbA encodes single-strand DNA-binding protein and could be involved in the processing of transforming DNA, which enter gram-positive bacteria in the single-stranded form. yqfG encodes a protein of unknown function. The existence of the competence-related genes in L. lactis indicates that this bacterium might be naturally transformable by DNA. There are no genes homologous to those involved in early steps of competence development in S. pneumoniae, which indicates that, in L. lactis, the regulation cascade upstream of ComX ς-factor is very different from that in Streptococcae.

Another difference between L. lactis and S. pneumoniae competence systems is that the leaderless mRNAs are present in the former organism only. The translation of such mRNAs requires that they start precisely at the initiation codon of the gene (Kravchenko et al. 1988; Van Etten and Janssen 1998). Synthesis of competence-related proteins would, therefore, not take place on spurious transcription of the cognate genes by leakage from upstream operons. This might tighten the control of the competence development and does limit it to very strict environmental conditions.

Horizontal Gene Transfer between Lactococci and Gram-Negative Enteric Bacteria

We detected a gene of unknown function, designated ycdB, which appears to be present in all bacteria and some eukaryotes. The level of identity between the YcdB protein and a homolog from S. pyogenes or S. pneumococcus, phylogenetically close to L. lactis, is ∼80%, while the identity with the homologous genes from gram-negative bacteria is ∼40%. Very surprisingly, the E. coli and S. typhimurium genomes encode not only a protein that is 40% identical with YcdB but also a protein that is 94% identical to YcdB. We conclude that this second ycdB gene has been transferred from lactococci to enteric bacteria. The divergence of the synonymous nucleotide sites in L. lactis IL1403, compared with Salmonella and E. coli, is ∼10%. If the rate of nucleotide changes at such sites is ∼1% per million years (Ochman et al. 1999), the genes in Salmonella/E. coli and L. lactis IL1403 started to diverge 10 million years ago. However, comparison of the ycdB genes in different strains of lactococci and in gram-negative enteric bacteria may reveal even more closely related genes and allow us to better assess the time of the gene transfer, the species that may have been involved in the transfer, and the mechanism of the transfer. Nevertheless, anticipating that closer homologs will be found, it is tempting to speculate that the transfer may have taken place in the digestive tract of ruminants, if it involved wild-type lactococci, or of humans, if it involved the domesticated lactococci, massively introduced there by cheese consumption.

Analysis of completely sequenced genomes, available from the NCBI server, revealed that most bacteria have only one homolog to YcdB. Some (E. coli, S. typhimurium, B. subtilis, E. faecalis, and Shewanella putrefaciens), however, have two, indicating that the family might be undergoing an expansion where, at least for enteric bacteria, a lateral gene transfer from lactococci might be a driving force. As the function of this gene is unknown, the advantage that the second copy confers is not known. Elucidation of the gene function would help to answer this question.

METHODS

Genome Cloning, Sequencing, and Data Verification

The strain IL1403 is a plasmid-free derivative of the strain IL594, isolated from a cheese starter culture (Chopin et al. 1984). Diagnostic sequencing, involving 10,235 sequencing reactions and yielding a total of 4,687,630 bases, has been described previously (Bolotin et al. 1999). Further sequencing was carried out to assure us that each nucleotide in the genome was read at least four times and at least once on each strand. For this purpose, a collection of short insert clones was constructed. A total of 9,888,620 bases, covering 93% of the total genome, were produced by 15,578 more sequencing reactions. To reduce the error rate level to <0.01%, 978 more reactions, with average read length of 632 bases, were carried out using genome-specific primers. The redundancy of the final assembling is 6.44.

Informatics and Gene Nomenclature

Assembling manual corrections of sequencing errors and consensus generation were carried out concurrently with data accumulation, using the XBAP program (Dear and Staden 1991; version 14.0). To predict protein-coding regions, we used a conceptual translation of the whole genome in six possible coding frames. The predicted proteins >60 amino acids were checked for the statistical consistency with the output of the GENMARK program (Borodovsky and McIninch 1993) using parameters for Streptococcal genes. EBI server (http://www2.ebi.ac.uk/genemark) and pyogenes_3.xdr matrix dated November 14, 1996, were used for this analysis. The presence of a putative ribosome-binding site upstream of the 5′ end of the candidate was searched next. As a ribosome binding site, we considered the presence of initiator codon ATG, TTG, or GTG and a short sequence homologous to the 3′ end of 16S rRNA of L. lactis (5′…GGAUCACCUCCUUUCUAA 3′) upstream of it (Chiaruttini and Milet 1993). Genome annotation was done by using several homemade shell or Perl scripts, generating convenient html format tables linked to BLAST (Altschul et al. 1990) output files. NCBI server (http://www.ncbi.nlm.nih.gov/Entrez) was used to generate updated bacterial protein databases. Homology analysis of YcdB with the unpublished genome sequences was carried out by using the relevant NCBI server (http://www.ncbi.nlm.nih.gov/Microb_blast/unfinishedgenome.html). The functional classification of genes was done according to the list of categories presented earlier (Bolotin et al. 1999). Fully automatic computer-generated classification was used as the starting material. Each protein was then analyzed by an expert to improve the category assignment, which is presented in Table 1 and Figure 2. The expert usually used three means to confirm or to alter the automated function assignment and classification: first, phylogenetic or COGnitor (Tatusov et al. 1997) assisted scrutiny of BLAST or FASTA reslts (performed with different parameters); second, complete knowledge of particular biochemical pathways or biological systems, existing in other than L. lactis IL1403 organisms (such as protein secretion or the competence system). Phage-specific proteins were classified to those because of their clustering in the areas identified as prophages. Also, specialized databases (Quentin et al. 1999) were used by the expert to classify the ABC transporters; third, results of numerous experiments in L. Lactis, published previously (148 functional assignments). Although it is never absolutely explicit, the provided classification of gene functions in L. lactis IL1403 is biological, rather than biochemical.

Linear map of the *Lactococcus lactis* ssp. *lactis* IL1403 chromosome. Coding regions are shown as arrows color-coded to the assigned functional categories. IS-elements and rRNA genes are shown as black arrows with white designation numbers inside. Symbols shown in pink identify genes in which frameshifts were detected.

L. lactis paralogous gene families were constructed by searching each predicted protein against all predicted proteins, using BLASTP with different parameters. Alignments of proteins in the identified families were then scrutinized to make a decision of how many proteins belong to a family. This decision was based either on the size of homologous domains or on the similarity levels. A protein was always assigned to only one family of paralogs.

We tried to keep the same gene symbols as proposed by the previous authors for ORFs with functions experimentally confirmed in L. lactis (148 genes). A y prefix with the gene symbol consistent with its position on the chromosome (Fig. 2) was kept for unascertained functions (1149 genes). Other gene symbols, consistent with those for homologs found in other bacteria, are proposed here (1017 genes).

Accessibility of Data

The nucleotide sequence of the L. lactis IL1403 genome is available from NCBI with accession no. AE005176. Updated annotations are supported at the Génétique Microbienne (INRA) server at http://spock.jouy.inra.fr. A PatScan of Ross Overbeek (Dsouza et al. 1997) for pattern searches in DNA sequence and proteins, implemented for IL1403, and peptide spectrum identification tool PeptOko for L. lactis proteome research are also available from this server.

Acknowledgments

We thank Jacek Bordovski and Saulius Kulakauskas for giving samples of the L. lactis IL1403 strain and Marie-Christine and Alain Chopin, Patrick Duwat, Emmanuel Jamet, Alexandra Gruss, Emmanuelle Maguin, Isabelle Poquet, Pierre Renault, and Catherine Robert for helpful discussions. We thank also the Genome Centers that contributed to the Unfinished Microbial Genome Database available for BLAST search through the NCBI server (http://www.ncbi.nlm.nih.gov/Microb_blast/unfinishedgenome.html).

The publication costs of this article were defrayed in part by payment of page charges. This article must therefore be hereby marked “advertisement” in accordance with 18 USC section 1734 solely to indicate this fact.

Footnotes

E-MAIL sorokine@biotec.jouy.inra.fr; FAX 33-1-34-65-25-21.

Article published on-line before print: Genome Res., 10.1101/gr.169701.

Article and publication are at www.genome.org/cgi/doi/10.1101/gr.169701.

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Bolotin A, Mauger S, Malarme K, Ehrlich SD, Sorokin A. Low-redundancy sequencing of the entire Lactococcus lactis IL1403 genome. Antonie Leeuwenhoek. 1999;76:27–76. [PubMed] [Google Scholar]
Borodovsky M, McIninch J. GENMARK: A parallel gene recognition for both DNA strands. Comput Chem. 1993;17:123–133. [Google Scholar]
Buist G, Karsens H, Nauta A, van Sinderen D, Venema G, Kok J. Autolysis of Lactococcus lactis caused by induced overproduction of its major autolysin, AcmA. Appl Environ Microbiol. 1997;63:2722–2728. doi: 10.1128/aem.63.7.2722-2728.1997. [DOI] [PMC free article] [PubMed] [Google Scholar]
Chiaruttini C, Milet M. Gene organization, primary structure and RNA processing analysis of a ribosomal RNA operon in Lactococcus lactis. J Mol Biol. 1993;230:57–76. doi: 10.1006/jmbi.1993.1126. [DOI] [PubMed] [Google Scholar]
Chopin A, Chopin MC, Moillo-Batt A, Langella P. Two plasmid-determined restriction and modification systems in Streptococcus lactis. Plasmid. 1984;11:260–263. doi: 10.1016/0147-619x(84)90033-7. [DOI] [PubMed] [Google Scholar]
Chopin A, Bolotin A, Sorokin A, Ehrlich SD, Chopin MC. Analysis of six prophages in Lactococcus lactis IL1403: Different genetic structure of temperate and virulent phage populations. Nucleic Acids Res. 2001;29:644–651. doi: 10.1093/nar/29.3.644. [DOI] [PMC free article] [PubMed] [Google Scholar]
Christensen J, Dudley E, Pederson J, Steele J. Peptidases and amino acid catabolism in lactic acid bacteria. Antonie Leeuwenhoek. 1999;76:217–246. [PubMed] [Google Scholar]
Cocaign-Bousquet M, Garrigues C, Loubiere P, Lindley ND. Physiology of pyruvate metabolism in Lactococcus lactis. Antonie Leeuwenhoek. 1996;70:253–267. doi: 10.1007/BF00395936. [DOI] [PubMed] [Google Scholar]
Cousineau B, Smith D, Lawrence-Cavanagh S, Mueller JE, Yang J, Mills D, Manias D, Dunny G, Lambowitz AM, Belfort M. Retrohoming of a bacterial group II intron: Mobility via complete reverse splicing, independent of homologous DNA recombination. Cell. 1998;94:451–462. doi: 10.1016/s0092-8674(00)81586-x. [DOI] [PubMed] [Google Scholar]
Dear S, Staden R. A sequence assembly and editing program for efficient management of large projects. Nucl Acids Res. 1991;19:3907–3911. doi: 10.1093/nar/19.14.3907. [DOI] [PMC free article] [PubMed] [Google Scholar]
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Dsouza M, Larsen N, Overbeek R. Searching for patterns in genomic data. Trends Genet. 1997;13:497–498. doi: 10.1016/s0168-9525(97)01347-4. [DOI] [PubMed] [Google Scholar]
Duwat P, Cochu A, Ehrlich SD, Gruss A. Characterization of Lactococcus lactis UV-sensitive mutants obtained by ISS1 transposition. J Bacteriol. 1997;179:4473–4479. doi: 10.1128/jb.179.14.4473-4479.1997. [DOI] [PMC free article] [PubMed] [Google Scholar]
Fernandez S, Sorokin A, Alonso JC. Genetic recombination in Bacillus subtilis 168: Effects of recU and recS mutations on DNA repair and homologous recombination. J Bacteriol. 1998;180:3405–3409. doi: 10.1128/jb.180.13.3405-3409.1998. [DOI] [PMC free article] [PubMed] [Google Scholar]
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Fraser CM, Fleischmann RD. Strategies for whole microbial genome sequencing and analysis. Electrophoresis. 1997;18:1207–1216. doi: 10.1002/elps.1150180803. [DOI] [PubMed] [Google Scholar]
Gasson MJ. Plasmid complements of Streptococcus lactis NCDO 712 and other lactic streptococci after protoplast-induced curing. J Bacteriol. 1983;154:1–9. doi: 10.1128/jb.154.1.1-9.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
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Griffin HG, Swindell SR, Gasson MJ. Cloning and sequence analysis of the gene encoding L-lactate dehydrogenase from Lactococcus lactis: Evolutionary relationships between 21 different LDH enzymes. Gene. 1992;122:193–197. doi: 10.1016/0378-1119(92)90049-u. [DOI] [PubMed] [Google Scholar]
Jensen PR, Hammer K. Minimal requirements for exponential growth of Lactococcus lactis. Appl Environ Microbiol. 1993;59:4363–4366. doi: 10.1128/aem.59.12.4363-4366.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
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Le Bourgeois P, Lautier M, Mata M, Ritzenthaler P. Physical and genetic map of the chromosome of Lactococcus lactis subsp. lactis IL1403. J Bacteriol. 1992;174:6752–6762. doi: 10.1128/jb.174.21.6752-6762.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
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Sanders JW, Leenhouts KJ, Haandrikman AJ, Venema G, Kok J. Stress response in Lactococcus lactis: Cloning, expression analysis, and mutation of the lactococcal superoxide dismutase gene. J Bacteriol. 1995;177:5254–5260. doi: 10.1128/jb.177.18.5254-5260.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
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[B1] Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]

[B2] Bolhuis A, Broekhuizen CP, Sorokin A, van Roosmalen ML, Venema G, Bron S, Quax WJ, van Dijl JM. SecDF of Bacillus subtilis, a molecular Siamese twin required for the efficient secretion of proteins. J Biol Chem. 1998;273:21217–21224. doi: 10.1074/jbc.273.33.21217. [DOI] [PubMed] [Google Scholar]

[B3] Bolotin A, Mauger S, Malarme K, Ehrlich SD, Sorokin A. Low-redundancy sequencing of the entire Lactococcus lactis IL1403 genome. Antonie Leeuwenhoek. 1999;76:27–76. [PubMed] [Google Scholar]

[B4] Borodovsky M, McIninch J. GENMARK: A parallel gene recognition for both DNA strands. Comput Chem. 1993;17:123–133. [Google Scholar]

[B5] Buist G, Karsens H, Nauta A, van Sinderen D, Venema G, Kok J. Autolysis of Lactococcus lactis caused by induced overproduction of its major autolysin, AcmA. Appl Environ Microbiol. 1997;63:2722–2728. doi: 10.1128/aem.63.7.2722-2728.1997. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B6] Chiaruttini C, Milet M. Gene organization, primary structure and RNA processing analysis of a ribosomal RNA operon in Lactococcus lactis. J Mol Biol. 1993;230:57–76. doi: 10.1006/jmbi.1993.1126. [DOI] [PubMed] [Google Scholar]

[B7] Chopin A, Chopin MC, Moillo-Batt A, Langella P. Two plasmid-determined restriction and modification systems in Streptococcus lactis. Plasmid. 1984;11:260–263. doi: 10.1016/0147-619x(84)90033-7. [DOI] [PubMed] [Google Scholar]

[B8] Chopin A, Bolotin A, Sorokin A, Ehrlich SD, Chopin MC. Analysis of six prophages in Lactococcus lactis IL1403: Different genetic structure of temperate and virulent phage populations. Nucleic Acids Res. 2001;29:644–651. doi: 10.1093/nar/29.3.644. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B9] Christensen J, Dudley E, Pederson J, Steele J. Peptidases and amino acid catabolism in lactic acid bacteria. Antonie Leeuwenhoek. 1999;76:217–246. [PubMed] [Google Scholar]

[B10] Cocaign-Bousquet M, Garrigues C, Loubiere P, Lindley ND. Physiology of pyruvate metabolism in Lactococcus lactis. Antonie Leeuwenhoek. 1996;70:253–267. doi: 10.1007/BF00395936. [DOI] [PubMed] [Google Scholar]

[B11] Cousineau B, Smith D, Lawrence-Cavanagh S, Mueller JE, Yang J, Mills D, Manias D, Dunny G, Lambowitz AM, Belfort M. Retrohoming of a bacterial group II intron: Mobility via complete reverse splicing, independent of homologous DNA recombination. Cell. 1998;94:451–462. doi: 10.1016/s0092-8674(00)81586-x. [DOI] [PubMed] [Google Scholar]

[B12] Dear S, Staden R. A sequence assembly and editing program for efficient management of large projects. Nucl Acids Res. 1991;19:3907–3911. doi: 10.1093/nar/19.14.3907. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B13] Dickely F, Nilsson D, Hansen EB, Johansen E. Isolation of Lactococcus lactis nonsense suppressors and construction of a food-grade cloning vector. Mol Microbiol. 1995;15:839–847. doi: 10.1111/j.1365-2958.1995.tb02354.x. [DOI] [PubMed] [Google Scholar]

[B14] Dsouza M, Larsen N, Overbeek R. Searching for patterns in genomic data. Trends Genet. 1997;13:497–498. doi: 10.1016/s0168-9525(97)01347-4. [DOI] [PubMed] [Google Scholar]

[B15] Duwat P, Cochu A, Ehrlich SD, Gruss A. Characterization of Lactococcus lactis UV-sensitive mutants obtained by ISS1 transposition. J Bacteriol. 1997;179:4473–4479. doi: 10.1128/jb.179.14.4473-4479.1997. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B16] Fernandez S, Sorokin A, Alonso JC. Genetic recombination in Bacillus subtilis 168: Effects of recU and recS mutations on DNA repair and homologous recombination. J Bacteriol. 1998;180:3405–3409. doi: 10.1128/jb.180.13.3405-3409.1998. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B17] Fox PF. Cheese: An overview. In: Fox PF, editor. Cheese: Chemistry, Physics and Microbiology. London: Chapman & Hall; 1989. pp. 1–36. [Google Scholar]

[B18] Fraser CM, Fleischmann RD. Strategies for whole microbial genome sequencing and analysis. Electrophoresis. 1997;18:1207–1216. doi: 10.1002/elps.1150180803. [DOI] [PubMed] [Google Scholar]

[B19] Gasson MJ. Plasmid complements of Streptococcus lactis NCDO 712 and other lactic streptococci after protoplast-induced curing. J Bacteriol. 1983;154:1–9. doi: 10.1128/jb.154.1.1-9.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B20] Godon JJ, Delorme C, Bardowski J, Chopin MC, Ehrlich SD, Renault P. Gene inactivation in Lactococcus lactis: Branched-chain amino acid biosynthesis. J Bacteriol. 1993;175:4383–4390. doi: 10.1128/jb.175.14.4383-4390.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B21] Griffin HG, Swindell SR, Gasson MJ. Cloning and sequence analysis of the gene encoding L-lactate dehydrogenase from Lactococcus lactis: Evolutionary relationships between 21 different LDH enzymes. Gene. 1992;122:193–197. doi: 10.1016/0378-1119(92)90049-u. [DOI] [PubMed] [Google Scholar]

[B22] Jensen PR, Hammer K. Minimal requirements for exponential growth of Lactococcus lactis. Appl Environ Microbiol. 1993;59:4363–4366. doi: 10.1128/aem.59.12.4363-4366.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B23] Karudapuram S, Zhao X, Barcak GJ. DNA sequence and characterization of Haemophilus influenzae dprA+, a gene required for chromosomal but not plasmid DNA transformation. J Bacteriol. 1995;177:3235–3240. doi: 10.1128/jb.177.11.3235-3240.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B24] Kravchenko VV, Gileva IP, Dobrynin VN, Filipov SA, Korobko VG. Location of the initiation codon AUG in relation to the 5′-end of mRNA mediates the effectiveness of translation in E. coli cells. Bioorg Khim. 1988;14:1387–1392. [PubMed] [Google Scholar]

[B25] Kunst F, Ogasawara N, Moszer I, Albertini AM, Alloni G, Azevedo V, Bertero MG, Bessieres P, Bolotin A, Borchert S, et al. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature. 1997;390:249–256. doi: 10.1038/36786. [DOI] [PubMed] [Google Scholar]

[B26] Le Bourgeois P, Lautier M, Mata M, Ritzenthaler P. Physical and genetic map of the chromosome of Lactococcus lactis subsp. lactis IL1403. J Bacteriol. 1992;174:6752–6762. doi: 10.1128/jb.174.21.6752-6762.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B27] Le Bourgeois P, Lautier M, van den Berghe L, Gasson M, Ritzenthaler P. Physical and genetic map of the chromosome of Lactococcus lactis subsp. cremoris MG1363 chromosome: Comparison with that of Lactococcus lactis subsp. lactis IL1403 reveals a large genome inversion. J Bacteriol. 1995;177:2840–2850. doi: 10.1128/jb.177.10.2840-2850.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B28] Lee MS, Morrison DA. Identification of a new regulator in Streptococcus pneumoniae linking quorum sensing to competence for genetic transformation. J Bacteriol. 1999;181:5004–5016. doi: 10.1128/jb.181.16.5004-5016.1999. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B29] Le Loir Y, Gruss A, Ehrlich SD, Langella P. A nine-residue synthetic propeptide enhances secretion efficiency of heterologous proteins in Lactococcus lactis. J Bacteriol. 1998;180:1895–1903. doi: 10.1128/jb.180.7.1895-1903.1998. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B30] Lopez de Felipe FL, Kleerebezem M, de Vos WM, Hugenholtz J. Cofactor engineering: A novel approach to metabolic engineering in Lactococcus lactis by controlled expression of NADH oxidase. J Bacteriol. 1998;180:3804–3808. doi: 10.1128/jb.180.15.3804-3808.1998. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B31] Mickelson MN. Glucose degradation, molar growth yields, and evidence for oxidative phosphorylation in Streptococcus agalactiae. J Bacteriol. 1972;109:96–105. doi: 10.1128/jb.109.1.96-105.1972. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B32] Ochman H, Elwyn S, Moran NA. Calibrating bacterial evolution. Proc Natl Acad Sci. 1999;96:12638–12643. doi: 10.1073/pnas.96.22.12638. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B33] Pestova EV, Morrison DA. Isolation and characterization of three Streptococcus pneumoniae transformation-specific loci by use of a lacZ reporter insertion vector. J Bacteriol. 1998;180:2701–2710. doi: 10.1128/jb.180.10.2701-2710.1998. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B34] Pogliano JA, Beckwith J. SecD and SecF facilitate protein export in Escherichia coli. EMBO J. 1994;13:554–561. doi: 10.1002/j.1460-2075.1994.tb06293.x. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B35] Poolman B. Energy transduction in lactic acid bacteria. FEMS Microbiol Rev. 1993;12:125–147. doi: 10.1111/j.1574-6976.1993.tb00015.x. [DOI] [PubMed] [Google Scholar]

[B36] Pouquet I, Saint V, Seznec E, Simoes N, Bolotin A, Gruss A. HtrA in the unique surface housekeeping protease in Lactococcus lactis and is required for natural protein processing. Mol Microbiol. 2000;35:1042–1051. doi: 10.1046/j.1365-2958.2000.01757.x. [DOI] [PubMed] [Google Scholar]

[B37] Quentin Y, Fichant G, Denizot F. Inventory, assembly and analysis of Bacillus subtilus ABC transport systems. J Mol Biol. 1999;287:467–484. doi: 10.1006/jmbi.1999.2624. [DOI] [PubMed] [Google Scholar]

[B38] Rollan G, de Nadra MCM, Holgado PR, Oliver G. Aspartate metabolism in Lactobacillus murinus CNRS 313. I. Aspartase. J Gen Appl Microbiol. 1985;31:403–409. [Google Scholar]

[B39] Sanders JW, Leenhouts KJ, Haandrikman AJ, Venema G, Kok J. Stress response in Lactococcus lactis: Cloning, expression analysis, and mutation of the lactococcal superoxide dismutase gene. J Bacteriol. 1995;177:5254–5260. doi: 10.1128/jb.177.18.5254-5260.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B40] Sanders JW, Leenhouts K, Burghoorn J, Brands JR, Venema G, Kok J. A chloride-inducible acid resistance mechanism in Lactococcus lactis and its regulation. Mol Microbiol. 1998;27:299–310. doi: 10.1046/j.1365-2958.1998.00676.x. [DOI] [PubMed] [Google Scholar]

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PERMALINK

The Complete Genome Sequence of the Lactic Acid Bacterium Lactococcus lactis ssp. lactis IL1403

Alexander Bolotin

Patrick Wincker

Stéphane Mauger

Olivier Jaillon

Karine Malarme

Jean Weissenbach

S Dusko Ehrlich

Alexei Sorokin

Abstract

RESULTS AND DISCUSSION

Two-Step Sequencing Strategy

Gene Content

Table 1.

Origin and Terminus of Replication

Figure 1.

RNA, IS Elements, and Prophages

Paralogous Gene Families

Information Processing and Gene Regulation

Energy Metabolism and Transporters

Proteases and Amino Acid Catabolism Genes

Amino Acid, Vitamin, and Nucleotide Biosynthesis

Cell Wall Metabolism

Protein Secretion

Competence to Genetic Transformation

Horizontal Gene Transfer between Lactococci and Gram-Negative Enteric Bacteria

METHODS

Genome Cloning, Sequencing, and Data Verification

Informatics and Gene Nomenclature

Figure 2.

Accessibility of Data

Acknowledgments

Footnotes

REFERENCES

ACTIONS

PERMALINK

RESOURCES

Cite

Add to Collections

PERMALINK

The Complete Genome Sequence of the Lactic Acid Bacterium Lactococcus lactis ssp. lactis IL1403

Alexander Bolotin

Patrick Wincker

Stéphane Mauger

Olivier Jaillon

Karine Malarme

Jean Weissenbach

S Dusko Ehrlich

Alexei Sorokin

Abstract

RESULTS AND DISCUSSION

Two-Step Sequencing Strategy

Gene Content

Table 1.

Origin and Terminus of Replication

Figure 1.

RNA, IS Elements, and Prophages

Paralogous Gene Families

Information Processing and Gene Regulation

Energy Metabolism and Transporters

Proteases and Amino Acid Catabolism Genes

Amino Acid, Vitamin, and Nucleotide Biosynthesis

Cell Wall Metabolism

Protein Secretion

Competence to Genetic Transformation

Horizontal Gene Transfer between Lactococci and Gram-Negative Enteric Bacteria

METHODS

Genome Cloning, Sequencing, and Data Verification

Informatics and Gene Nomenclature

Figure 2.

Accessibility of Data

Acknowledgments

Footnotes

REFERENCES

ACTIONS

PERMALINK

RESOURCES

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