Table 1.
Transcripts down-regulated in a Δlpp mutant of Y. pestis CO92 cultured at 26°C, compared to wild-type bacteria, based on microarray analyses.
| Yer ID | Gene Name | Gene Symbol | Function | Δlpp/WT |
|---|---|---|---|---|
| FC | ||||
|
| ||||
| Cell envelope | ||||
|
| ||||
| YPO2394 | major outer membrane lipoprotein | mlpA | lpp gene—cell envelope | −361.9 |
| YPO1125 | peptidoglycan-associated lipoprotein Pal | excC | Maintenance of cell envelope integrity | −22.3 |
| YPO0448 | putative lipoprotein | — | Cell envelope | −26 |
|
| ||||
| Genomic functions | ||||
|
| ||||
| y2424 | putative transposase | — | Mobile and extrachromosomal element functions | −76.8 |
| Y1119.1n | replication protein A | repA | DNA replication, recombination, and repair | −31.9 |
| YPO1968 | transposase for insertion sequence IS100 | ypmt1/y1093 | Mobile and extrachromosomal element functions | −22.3 |
|
| ||||
| Metabolism | ||||
|
| ||||
| YPO2705 | conserved hypothetical protein | — | Fermentation | −93.1 |
| YPO2805 | putative aldo/keto reductase | — | Central intermediary metabolism | −20.3 |
| YPO3387 | conserved hypothetical protein | — | Nitrogen fixation | −16.7 |
| y1601 | acetyl CoA carboxylase, carboxytransferase component, beta subunit | accD | Fatty acid and phospholipid metabolism | −48.3 |
| YPO1161 | molybdopterin [mpt] converting factor, subunit 1 | chlM/chlA4 | Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides | −15.7 |
| YPO1177 | D-lactate dehydrogenase | dld | Fermentation | −6.4 |
| YPO3376 | enolase | eno | Glycolysis/gluconeogenesis | −127.7 |
| y1362 | IMP dehydrogenase | guaB | Purine salvage pathway | −22 |
| YPO2993 | PTS system, phosphocarrier protein | hpr | Degradation of proteins, peptides, and glycopeptides | −29.3 |
| YPO2329 | D-lactate dehydrogenase | htpH/hslI | Fermentation | −7 |
| YPO2300 | fumarate and nitrate reduction regulatory protein | nirR | Regulation of metabolic functions | −15.7 |
| YPO1413 | putative nicotinate phosphoribosyltransferase | pncB | Biosynthesis of cofactors, prosthetic groups, and carriers | −51.7 |
| YPO3521 | inorganic pyrophosphatase | ppa | Central intermediary metabolism | −44.1 |
| YPO0915 | ribose 5-phosphate isomerase A | rpiA | Pentose phosphate pathway | −124.7 |
|
| ||||
| Protein synthesis and repair | ||||
|
| ||||
| YPO0242 | polypeptide deformylase | fms | Protein modification and repair | −4.1 |
| y0688 | protein chain initiation factor IF-2 | infB | Translation | −30.2 |
| YPO3074 | peptidyl-prolyl cis-trans isomerase B | ppiB | Protein folding and stabilization | −405.1 |
| YPO0233 | 30S ribosomal protein S4 | ramA | Protein synthesis | −3.2 |
| YPO3748 | 50S ribosomal protein L7/L12 | rplL | Protein synthesis | −6.7 |
| YPO0228 | 50S ribosomal protein L15 | rplO | Protein synthesis | −11.4 |
| YPO0225 | 50S ribosomal protein L18 | rplR | Protein synthesis | −8.7 |
| YPO0218 | 50S ribosomal protein L29 | rpmC | Protein synthesis | −11.6 |
| y0299 | 50S ribosomal subunit protein L31 | rpmE | Protein synthesis | −15.1 |
|
| ||||
| Transport | ||||
|
| ||||
| YPO2672 | putative urea transporter | — | Transport and binding proteins | −33.3 |
| YPO3156 | ATP-dependent Clp protease ATP-binding subunit ClpX | lopC | Carbohydrate transport | −29.3 |
| YPO1783 | ferritin | rsgA/ftn | Iron transport | −12.4 |
|
| ||||
| Type III Secretion System | ||||
|
| ||||
| YPO2905 | attachment invasion locus protein | ail | Invasion of eukaryotic cells; Type III Secretion System |
−3.3 |
| YPCD1.67c | putative protein-tyrosine phosphatase Yop effector | yopH | Type III secretion effector protein | −100.7 |
| YPCD1.71c | putative targeted effector protein | yopJ/yopP | Type III secretion effector protein | −68.2 |
| FC | ||||
|
| ||||
| YPCD1.72c | putative targeted effector protein kinase | ypkA | Type III secretion effector protein | −21.2 |
| YPCD1.40 | putative Yops secretion ATP synthase | yscN | Type III secretion system component | −30.7 |
| YPCD1.42 | putative type III secretion protein | yscP | Type III secretion system component | −66.9 |
|
| ||||
| Other functions | ||||
|
| ||||
| y0223 | cold shock-like protein | cspI | Response to cold shock | −68.7 |
| YPO1363 | putative virulence factor | — | Pathogenesis | −34.8 |
| y0815 | superoxide dismutase precursor (Cu-Zn) | sodC | Resistance to reactive oxygen species | −18.2 |
|
| ||||
| Unknown functions | ||||
|
| ||||
| various genes (y3398, YPO0130, 0198, 1087, 1560, 1996, 2153, 2854, and 3699) | * | |||
Functions were obtained from the CMR online database (http://cmr.jcvi.org) and from the literature. FC = fold-change, which was calculated as the ratio between the hybridization signals for that gene in the Y. pestis Δlpp mutant and WT bacteria (Δlpp/WT). Expression differences were deemed as statistically significant if the fold-change was ≥1.5 and P value ≤.05. A negative sign (“−”) before the FC indicates down-regulation of the gene in the Y. pestis Δlpp mutant, relative to the WT strain. *FCs for genes with unknown functions (grouped together in the last line) ranged from −9.3 to −903.2.