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. 2005 Dec;187(23):8088–8103. doi: 10.1128/JB.187.23.8088-8103.2005

TABLE 2.

Selected list of Erwinia amylovora genes induced during infection of immature pear tissuea

Function pfi no. Geneb Organism Blastx_BestHitc GenBank accession no. Previously reportedd
TTSS and effectors 1 dspE* Erwinia amylovora DspE/pathogenicity factor AAC04850 Ech, 77
2 hrpGF E. amylovora Type III secretion HrpG/F AAB49178 Pst, 12
3 hrpL* E. amylovora Type III sensor kinase HrpL AAD24682
4 hrpX* E. amylovora Type III secretion HrpX AAD24681
5 hopPtoC Pseudomonas syringae pv. tomato Type III effector HopPtoC NP_790436 Pst, 12
GSP 6 secA* Salmonella enterica serovar Typhimurium Preprotein translocase SecA NP_459141
7 secDF* Yersinia pestis Protein export membrane protein SecDF NP_406663 Apl, 47
8 secB* Escherichia coli Protein export protein SecB NP_756294 Ppu, 60
T2SS and proteins secreted by T2SS 9 yts11J Yersinia enterocolitica Type II secretion Yts1IJ protein CAC83035 Rso, Ech; 16, 77
10 lsc* E. amylovora Levansucrase CAA52972
11 peh Pectobacterium carotovorum Peh (polygalacturonase) BAA74431 Pst, 12
Proteins known to be secreted by other secretion systems 12 fhaB* Escherichia coli Putative adhesin/hemagglutinin/hemolysin AAQ19127 Rso, 16
13 hecA Erwinia chrysanthemi Hemolysin/hemagglutinin-like protein HecA AAN38708 Rso, 16
14 mltE Yersinia pestis Membrane-bound lytic murein transglycosylase NP_405972 Pst, 12
15 prtA* Erwinia amylovora Zinc-binding metalloprotease CAB42873
General, ion, sugar, amino acid, and nucleotide transport 16 abc Yersinia pestis ABC transporter ATP-binding protein (inorganic ion transport) NP_404687 Ech, 77
17 pstA Yersinia pestis Putative phosphate transport system permease NP_406342
18 ppx Pantoea agglomerans Exopolyphosphatase AAQ14878 Sty, 55
19 ftn Yersinia pestis Cytoplasmic ferritin (an iron storage protein) NP_669829
20 kefB Salmonella enterica serovar Typhimurium K+/H+ antiporter NP_462361 Rso, 16
21 c3774* Escherichia coli Ferric enterobactin transport ATP-binding protein NP_755645
22 btuB Serratia marcescens Outer membrane receptor for iron transport AAL50647
23 Gmet1925 Geobacter metallireducens ABC-type nitrate/sulfonate/bicarbonate transport system ZP_00081179
24 exbB Salmonella enterica Biopolymer transport ExbB protein NP_457552
25 kgtP* Salmonella enterica serovar Typhimurium Alpha-ketoglutarate permease NP_461589 Rso, 16
26 ECs2608 Escherichia coli ATP-binding component of high-affinity l-arabinose transport system NP_310635
27 citA Pseudomonas aeruginosa Citrate transporter NP_254163
28 rbsD Yersinia pestis High-affinity d-ribose permease NP_403673
29 gntU Salmonella enterica serovar Typhimurium Low-affinity gluconate permease NP_462442
30 mglA* Salmonella enterica serovar Typhimurium Methylgalactoside transport protein NP_461134
31 emrB Escherichia coli Multidrug resistance protein B NP_755121 Rso/Eco; 16, 68
32 mdl Klebsiella pneumoniae Multidrug resistance-like ATP-binding protein CAA07091
33 putP* Salmonella sp. Proline permease AAA99282
34 Avin4550* Azotobacter vinelandii Permeases of the major facilitator superfamily ZP_00092807 Pfl, 67
35 rbsB Streptococcus agalactiae Ribose ABC transporter, periplasmic d-ribose-binding protein NP_687150
36 livK Yersinia pestis High-affinity leucine-specific-binding periplasmic protein; branched-chain amino acid ABC transport system NP_667760
37 ECs3191 Escherichia coli Histidine transport system membrane protein M NP_311218
38 lysP Shigella flexneri Lysine-specific permease NP_708053
39 YPO3257* Yersinia pestis Amino acid ABC transporter, periplasmic protein NP_406727 Rso, 16
40 metC* E. coli Beta-cystathionase AAA69175
41 lysC Yersinia pestis Lysine-sensitive aspartokinase III NP_407170
42 avtA* Escherichia coli Valine-pyruvate aminotransferase NP_756255
43 oppA Yersinia pestis Oligopeptide ABC transporter; periplasmic binding protein NP_669341
44 oppC Yersinia pestis Oligopeptide transport system permease protein NP_405727
45 tsx Salmonella Nucleoside-specific channel-forming protein NP_455008
46 hemH Yersinia enterocolitica Ferrochelatase AAC60760
47 uup Salmonella enterica serovar Typhimurium Putative ABC transporter ATPase component NP_460036 Rso, 16
48 sbmA Salmonella enterica serovar Typhimurium Putative ABC transporter membrane protein NP_459371 Rso, 16
49 y0619* Yersinia pestis Putative periplasmic binding transport protein AAM84207
50 hemT Yersinia enterocolitica Hemin binding protein (periplasm binding protein-hemin transport) CAA54866
51 yadH* Salmonella enterica serovar Typhimurium Putative transport protein NP_459178
Bacterial cell surface and transmembrane 52 nlpA* Escherichia coli Lipoprotein 28 NP_418117 Rso, 16
53 dacB Yersinia pestis d-Alanyl-d-alanine carboxypeptidase/penicillin-binding protein 4 NP_668015 Rso, 16
54 kpsC Escherichia coli Capsule polysaccharide export protein P42217 Eco, 68
55 dinF Salmonella enterica DNA damage-inducible membrane protein NP_458536 Rso, 16
56 corB* Salmonella enterica Putative membrane protein NP_457149 Ech, 77
57 ytfK* Salmonella enterica serovar Typhimurium Putative cytoplasmic protein NP_463267 Ech, 77
58 YPO2305 Yersinia pestis Putative exported protein NP_405842
59 tolA Salmonella enterica serovar Typhimurium Tol import system inner membrane protein NP_459732
60 tolR Erwinia chrysanthemi TolR protein inner membrane protein interacting with TolA and TolQ CAC82707
61 matE* Salmonella enterica Putative inner membrane protein NP_456567 Rso, 16
62 STM0278* Salmonella enterica serovar Typhimurium Putative periplasmic protein NP_459276 Rso, 16
63 ydiY Salmonella enterica serovar Typhimurium Putative outer membrane protein (salt inducible) NP_460293
64 ompC Escherichia coli Outer membrane protein C (porin OmpC) Q54471
65 ompA* Salmonella enterica Putative outer membrane protein (OmpA) NP_458280
66 Z1931* Escherichia coli Outer membrane protein 3b (a), protease VII NP_287408
67 ptrA* Yersinia pestis Protease III precursor NP_404633
68 mrdB Escherichia coli Rod shape-determining protein RodA NP_752655
69 flgN Shigella flexneri Flagellum synthesis protein FlgN NP_836779
70 fliG Shigella flexneri Flagellar motor switch protein FliG NP_707824
71 fliM Escherichia coli Flagellar motor switch protein FliM NP_754254
72 ycgB Escherichia coli Putative sporulation protein NP_287427
Mobile elements-phage 73 STY4666* Salmonella enterica Probable phage integrase NP_458745
74 intD Escherichia coli Prophage DLP12 integrase NP_415069
Stress response 75 mutS Yersinia pestis DNA mismatch repair protein MutS NP_406817 Sen, 33
76 recA Yersinia pestis RecA protein NP_406773 Sau, 47
77 sulA Enterobacter aerogenes Cell division inhibitor, SOS regulon gene C29016
78 dps Serratia marcescens DNA protection during starvation protein (Dsp) AAO47741
79 cstA Salmonella enterica Carbon starvation protein NP_458955
80 ycbP* Escherichia coli Sulfate starvation-induced protein 4/FMNe reductase NP_753005
81 ahpC* Photorhabdus luminescens Alkyl hydroperoxide reductase, small subunit (antioxidant) NP_931108
82 cyoB* Escherichia coli Cytochrome o ubiquinol oxidase subunit I NP_286173
83 ydiJ Salmonella enterica serovar Typhimurium Putative oxidase NP_460330
84 bacA Salmonella enterica serovar Typhimurium Bacitracin resistance protein NP_462120 Ech, 77
85 pqiB Yersinia pestis Paraquat-inducible protein B NP_670048
86 grpE Photorhabdus luminescens GrpE protein (HSP-70 cofactor) (heat shock protein B25.3) NP_930590 Rso, 16
87 y1165 Yersinia pestis Putative cold shock protein NP_668491
88 pspB* Yersinia enterocolitica Phage shock protein B AAG22114
89 pspC Yersinia enterocolitica Phage shock protein C AAG22115
90 tsr* Salmonella enterica serovar Typhimurium Methyl-accepting chemotaxis protein I NP_463392 Ech, 77
Regulation 91 rlsA Erwinia amylovora RlsA protein/LysR homolog CAA10420
92 rcsA* Erwinia amylovora Colanic acid capsular biosynthesis activation protein A A45828
93 grrS* Serratia plymuthica Putative global response regulation sensor kinase AAL11449
94 envZ* Yersinia pestis Histidine kinase/EnvZ/osmolarity sensor protein NP_403793 Sty, 33
95 fliZ Yersinia pestis Putative alternative sigma factor regulatory protein NP_405408
96 gntR Salmonella enterica Gluconate utilization operon repressor NP_458376
97 deoR Salmonella enterica DeoR/deoxyribose operon repressor NP_455391
98 metJ Photorhabdus luminescens Met repressor (Met regulon regulatory protein MetJ)/repressor of the methionine regulon NP_931917
99 hlfK Shigella flexneri Protease specific for phage lambda cII repressor NP_710039
100 yqhC* Escherichia coli Putative AraC-type regulatory protein NP_289587
101 ybiQ Shigella flexneri Transcriptional regulator MntR NP_706694
102 budR Raoultella terrigena HTH-type transcriptional regulator P52666
103 c5058* Escherichia coli Putative transcriptional regulator LysR NP_756910 Ech, 77
104 PSPTO3576 Pseudomonas syringae pv. tomato TetR family transcriptional regulator NP_793355
105 YPO3913* Yersinia pestis TetR family transcriptional regulatory protein NP_407358
106 YPO0736 Yersinia pestis Putative regulatory protein NP_404367
107 YPO0315* Yersinia pestis Regulatory protein (multiple antibiotic resistance) NP_403966
108 fnr Escherichia coli Fumarate and nitrate reduction regulatory protein NP_753709
109 glnK Yersinia pestis Nitrogen regulatory protein P-II NP_406618
110 modE Escherichia coli Molybdate uptake regulatory protein NP_286482
111 pspF Salmonella enterica Psp operon transcriptional activator NP_455812
112 hlyB Yersinia pestis Putative hemolysin activator protein NP_406025
113 rbsR* Shigella flexneri Regulator for rbs operon NP_839112
114 Psyr0512 Pseudomonas syringae Rhs family protein ZP_00124230
115 STY4601* Salmonella enterica Putative regulator of late gene expression NP_458684
116 kdpE Salmonella enterica serovar Typhimurium Response regulator in two-component regulatory system with KdpD AAL19646
117 PA2177 Pseudomonas aeruginosa Probable sensor/response regulator hybrid NP_250867
118 y3531* Yersinia pestis Putative kinase NP_670828
119 YPO0014 Yersinia pestis Putative type II homoserine kinase/YihE NP_403681
120 Avin4532 Azotobacter vinelandii Serine/threonine protein kinase ZP_00092789
121 Bcep3208 Burkholderia fungorum Sugar kinases, ribokinase family ZP_00030390
122 NE2503 Nitrosomonas europaea TonB-dependent receptor protein NP_842492
123 hrpA Escherichia coli ATP-dependent helicase HrpA P43329 Rso, 16
124 dbpA* Yersinia pestis ATP-dependent RNA helicase NP_405343
125 rpoN Klebsiella pneumoniae RNA polymerase sigma-54 factor P06223 Rso, 16
126 rpoD Pantoea agglomerans RNA polymerase sigma-70 subunit AAL11450
Metabolism and nutrient scavenging 127 ilvI* Yersinia pestis Acetolactate synthase III NP_670937 Pst, 12
128 purF Escherichia coli Amidophosphoribosyltransferase NP_288886 Rso, 16
129 argG* Photorhabdus luminescens Argininosuccinate synthase NP_931904 Rso, 16
130 pheA Erwinia herbicola Chorismate mutase/prephenate dehydratase S26053 Ech, 77
131 hemB Salmonella enterica Delta-aminolevulinic acid dehydratase NP_454967 Rso, 16
132 glgX Escherichia coli Glucose-1-phosphate adenylyltransferase NP_756082 Rso, 16
133 murB* Escherichia coli Oxidoreductase/UDP-N-acetylpyruvoylglucosamine reductase AAA24185 Rso/Pst; 16,12
134 pksC* Mycobacterium leprae Polyketide synthase PksC S73013 Rso, 16
135 YPO2195 Yersinia pestis Putative acyl coenzyme A thioester hydrolase NP_405738 Pst, 12
136 ygfZ Salmonella enterica serovar Typhimurium Putative aminomethyltransferase NP_461964 Pst, 12
137 YPO2310 Yersinia pestis Putative carboxypeptidase NP_405847 Pst, 12
138 truD Yersinia pestis Putative hydrogenase subunit AAM84415 Pst, 12
139 aceE Salmonella enterica Pyruvate dehydrogenase E1 component NP_454766 Pst, 12
140 rhsD Yersinia pestis RhsD protein NP_667608
141 hemD Salmonella enterica serovar Typhimurium Uroporphyrinogen III synthase NP_462823
142 pyrG* Salmonella enterica CTP synthase (UTP-ammonia ligase) NP_457342 Rso, 16
143 dnaQ* Escherichia coli DNA polymerase III, epsilon chain NP_752198 Rso, 16
144 argA Yersinia pestis Amino acid acetyltransferase NP_404636 Vch, 50
145 pepN* Salmonella enterica serovar Typhimurium Aminopeptidase N NP_460031 Rso, 16
146 glnA* Yersinia pestis Glutamine synthetase NP_671098 Rso/Eco, 16,68
147 cheR Yersinia pestis Glutamate methyltransferase NP_669155
148 moaC* Salmonella enterica Molybdenum cofactor biosynthesis protein C NP_455345 Pfl, 67
149 moeC Yersinia pestis Molybdopterin biosynthesis protein NP_669976
150 YPO2420* Yersinia pestis Probable formyl transferase NP_405953
151 YPO2174* Yersinia pestis Putative nucleotide sugar dehydrogenase NP_405718
152 YPO1009 Yersinia pestis Probable peptidase (PepT) NP_286807
153 fbp Escherichia coli Fructose-1,6-bisphosphatase NP_757176
154 gnd Yersinia pestis Gluconate-6-phosphate dehydrogenase NP_669932
155 zwf Yersinia pestis Glucose-6-phosphate dehydrogenase NP_405618
156 pckA Salmonella enterica serovar Typhimurium Phosphoenolpyruvate carboxykinase NP_462403
157 ECs0188 Escherichia coli Lysine decarboxylase 2 NP_308215
a

Hypothetical and unknown genes are not listed.

b

Gene name designations were based on originally reported gene products that shared high similarity to pfi clone sequences. Asterisks after the gene name indicate that two or more clones were identified for the same gene in the experiment.

c

Predicted proteins or functions based on similar proteins identified using BlastX searches.

d

Genes identified to be induced in other bacterium plant or animal systems using a similar IVET screen or other in vivo expression systems. Rso, Ralstonia solanacearum; Ech, Erwinia chrysanthemi; Pst, Pseudomonas syringae pv. tomato; Pfl, Pseudomonas fluorescens; Ppu, Pseudomonas putida; Sen, Salmonella enterica; Sty, Salmonella enterica serovar Typhimurium; Sau, Staphylococcus aureus; Apl, Actinobacillus pleuropneumoniae; Vch, Vibrio cholerae; Eco, Escherichia coli. Numbers indicate the references.

e

FMN, flavin mononucleotide.