TABLE 2.

Lactobacillus reuteri genes induced or repressed during acid shock at pH 2.7

Gene and function	Accession no.a	Description of encoded proteinb	Expression ratioc		Mean M pHd
			5 min	15 min
Genes up-regulated at pH 2.7
Stress response
lr1864	DQ219976	ClpL ATPase with chaperone activity	N	++	1.1
lr1797	DQ219975	Phosphatidylglycerophosphatase A and related proteins	N	++	1.0
Regulation and signal transduction
lr1474	DQ219969	Rrf2 transcriptional regulator	++	+++	1.3
lr1468	DQ219968	Transcriptional regulator	N	+++	0.83
lr1933	DQ219977	Transcriptional regulator	N	++	0.91
lr1993	DQ219980	Transcriptional regulator	N	+++	Te
lr2076	DQ219989	Transcriptional regulator	N	++++	T
rr7 (lr1804)	DQ219942	Two-component signal transduction response regulator	N	++	0.78
Transport and metabolism
lr1028	DQ219961	6-Phosphogluconolactonase/glucosamine-6-phosphate isomerase/deaminase	N	++	1.3
lr0811	DQ219956	Deoxyxylulose-5-phosphate synthase	N	++	0.87
Translation and posttranslational modifications
lr0807	DQ219955	Cysteinyl-tRNA synthetase	N	++	0.90
lr0597	DQ219952	Thioredoxin domain-containing protein	N	++	T
Cell envelope biogenesis
lr2064	DQ219988	Endopeptidases/phage-associated protein	N	++	0.83
lr1516	DQ219970	Putative esterase	++	++++	3.2
Phage-associated genes
lr1463	DQ074903	Phage terminase-like protein, large subunit	++	+++	1.4
lr2045	DQ219981	Phage-associated protein	N	++	1.1
lr2047	DQ219982	Phage-associated protein	N	++	1.1
lr2051	DQ219983	Phage terminase	N	++	0.82
lr2054	DQ219984	Phage head maturation protease	++	++	1.4
lr2055	DQ219985	Phage φC31 gp36 major capsid-like protein	N	++	1.1
lr2057	DQ219986	Phage protein	+	++	1.1
lr2058	DQ219987	Phage protein	N	++	0.93
Unknown function
lr0922	DQ074860	Extracellular hydrolase	N	++	1.1
lr1158	DQ074883	Extracellular hydrolase	N	++	0.77
lr1794	DQ219974	Flavoprotein	N	++	1.1
lr1937	DQ219979	Conserved intracellular protein of unknown function	N	++	1.1
lr1139	AY970988	Conserved intracellular protein of unknown function	N	++	1.5
lr2103	DQ219991	Conserved intracellular protein of unknown function	+	+++	1.2
lr0997	DQ219958	Conserved membrane protein of unknown function	+	++++	2.1
lr1191	DQ219999	Conserved membrane protein of unknown function	N	++	1.3
lr1515	DQ074905	Unconserved extracellular protein of unknown function	++	++++	2.5
lr2117	DQ220006	Unconserved intracellular protein of unknown function	++	+++	1.8
lr2090	DQ219990	Conserved membrane protein of unknown function	++	++	1.6
lr1934	DQ219978	Conserved intracellular protein of unknown function	N	++	T
Genes down-regulated at pH 2.7
Stress response
lr0722	DQ219953	Cold shock protein	−	−−	−1.6
Regulation and signal transduction
lr0021	DQ220000	Guanosine polyphosphate pyrophosphohydrolases/ synthetases	−−−	−−−	−2.4
lr0190	DQ219995	Transcriptional regulator	N	−−−	T
lr1578	DQ219971	Transcriptional regulator	−	−−	−0.82
Transport and metabolism
lr0382	AY971000	Branched-chain amino acid transport protein	−−	−−	−1.6
lr0153	DQ219993	Arabinose efflux permease	N	−−	T
lr0115	DQ219946	Deoxynucleoside kinase	−	−−	−2.5
lr1001	DQ219959	ADP-ribose pyrophosphatase	−	−−	−0.89
lr1297	DQ219963	Thymidine kinase	−	−−	−1.3
lr1401	DQ219964	Xanthine/uracil permeases	−−	−−−	−1.7
lr1433	DQ219965	Cytidylate kinase	−−	−−	−1.6
lr0320	DQ219998	Transport protein	−−	−−−	−2.0
lr0562	DQ220002	MntH, Mn2+ and Fe2+ transporter of the NRAMPf family	−−	−−	−1.3
Energy production and conversion
lr0229	DQ219949	Flavodoxin	−−	−−	−1.4
DNA replication, recombination, and repair
lr0119	DQ219948	DNA polymerase III, delta subunit	N	−−−	−1.6
lr1014	DQ220003	Site-specific recombinase XerD	N	−−	−1.3
lr1240	DQ219962	Recombinational DNA repair ATPase	N	−−	−1.6
Translation and posttranslational modification
lr0118	DQ219947	Ribosomal protein S20	N	−−−	−1.3
lr0277	DQ219997	Ribosomal protein L10	−−	−−−	−1.8
lr0862	DQ219957	Asp-tRNAAsn/Glu-tRNAGln amidotransferase C subunit	−−	−−	−1.3
lr1432	DQ220005	Ribosomal protein S1	−−	−−−−	−1.8
lr1690	DQ219973	Ribosomal protein L31	N	−−	−1.4
lr0251	DQ219950	RNase P-protein component	N	−−	T
lr1002	DQ219960	Peroxiredoxin	−−	−−	−0.95
lr1465	DQ219967	Protease subunit of ATP-dependent Clp proteases	−−	−−−	−1.5
Cell division
lr1411	DQ220004	Actin-like ATPase involved in cell morphogenesis	−−	N	−1.1
lr0145	DQ219992	Cell division protein	N	−−	−0.89
Cell envelope biogenesis
lr0537	DQ074830	Apf-like protein	−−−−	−−−	−4.3
lr0858	DQ074851	Apf-like protein	−−	−−	−2.2
Intracellular trafficking and secretion
lr1103	AY970986	Protein translocase subunit YajC	N	−−	−0.87
Unknown function
lr0546	DQ220001	Recombination protein	−−	N	−1.1
lr1422	DQ074901	Conserved extracellular protein of unknown function	−	−−	−1.4
lr0318	DQ219951	Conserved intracellular protein of unknown function	−−	−−−	−2.0
lr0733	DQ219954	Conserved intracellular protein of unknown function	N	−−	−1.5
lr1628	DQ219972	Conserved intracellular protein, MarZ, of unknown function	−−	−	−1.0
lr1434	DQ074902	Unconserved extracellular protein of unknown function	−−	−−−	−1.7
lr2118	DQ220007	Unconserved intracellular protein of unknown function	−−	−−	−1.3
lr0195	DQ219996	5-Formyltetrahydrofolate cycloligase or methenyl-tetrahydrofolate synthetase	−−	−−	−1.4

^aThe GenBank accession numbers are given.

^bBased on COG classes or high similarity to characterized proteins.

^cRatio of expression for cells after 5 or 15 min at pH 2.7 and cells at time zero. Comparisons between pH 5.1 and time zero or between pH 2.7 and pH 5.1 are not displayed. The symbols show the degree of up-regulation (+) or down-regulation (−) of the genes as follows: +, 1.75 to 2-fold up-regulation; ++, 2-fold to 3-fold up-regulation; +++, 3-fold to 5-fold up-regulation; ++++, more than 5-fold up-regulation of the gene; −, 1.75 to 2-fold down-regulation; −−, 2-fold to 3-fold down-regulation; −−−, 3-fold to 5-fold down-regulation; −−−−, more than 5-fold down-regulation. N, the expression is up- or down-regulated but the changes were less than 1.75-fold.

^dMean M (log₂) for parameter pH.

^eThe gene is selected because it is likely to be changed by time (parameter T).

^fNRAMP, natural resistance-associated macrophage protein.