Table 3.
Selected differentially expressed proteins with carbon and energy metabolism functions
| Protein name | Protein descriptiona | Avg relative abundanceb |
Transcriptional regulator(s)c | Functional role(s) | ||
|---|---|---|---|---|---|---|
| In vitro | Ext | Int | ||||
| PfkI | 6-Phosphofructokinase 1 | 590 | 3,497 | 1,913 | Cra− | Glycolysis |
| PfkII | 6-Phosphofructokinase 2 | 851 | 552 | 1,334 | Glycolysis | |
| GpmA | Phosphoglyceromutase | 14,384 | 11,311 | 23,438 | Fur− | Glycolysis |
| CsrA | Carbon storage regulator | 31,178 | 33,401 | 6,548 | Regulator of glycolysis, glycogen synthesis and storage, biofilm formation, motility | |
| AdhE | Bifunctional acetaldehyde CoA/alcohol dehydrogenase | 914 | 10,113 | 11,712 | Fnr+, Fis+, NarL−, FruR− | Mixed-acid fermentation: acetate |
| LldD | l-Lactate dehydrogenase | 460 | 909 | 3,497 | ArcA− | Mixed-acid fermentation: l-lactate |
| PflB | Formate acetyltransferase 1 | 9,921 | 15,006 | 15,500 | DksA+, ArgR− | Mixed-acid fermentation: pyruvate |
| FucO | l-1,2-Propanediol oxidoreductase | 1,464 | 1,608 | 2,969 | FruR− | Mixed-acid fermentation: fucose |
| YfiD | Autonomous glycyl radical cofactor | 14,343 | 17,557 | 26,553 | ArcA+, Fis+, Fur− | Mixed-acid fermentation: pyruvate |
| FrdA | Fumarate reductase flavoprotein subunit | 2,912 | 2,582 | 1687 | Fnr+, NarL− | Mixed-acid fermentation: fumarate |
| FocA | Formate transporter | 236 | 1,197 | 0 | ArcA+, Fnr+, Crp+ | Mixed-acid fermentation: formate export; acid stress response |
| SucC | Succinyl CoA synthetase β subunitd | 10,429 | 7,795 | 3,616 | Crp+, Fur+, Fnr− | TCA cycle |
| SucA | α-Ketoglutarate decarboxylase | 5,503 | 3,617 | 1,472 | Crp+, Fur+, Fnr− | TCA cycle |
| IcdA | Isocitrate dehydrogenase | 21,212 | 13,872 | 9,595 | FruR+, ArcA− | TCA cycle |
| SdhA | Succinate dehydrogenase flavoprotein | 8,711 | 4,567 | 1,580 | Crp+, Fur+, Fnr− | TCA cycle |
| SdhB | Succinate dehydrogenase Fe-S subunitd | 5,069 | 2,455 | 637 | Crp+, Fur+, Fnr− | TCA cycle |
| AcnB | Bifunctional aconitate hydratase 2/2-methylisocitrate dehydratased | 15,645 | 11,454 | 3,584 | Crp+, ArcA−, Fis− | TCA cycle |
| GlgB | Glycogen branching enzyme | 1,409 | 457 | 2,131 | PhoP+ | Glycogen biosynthesis and storage |
| GlgC | Glucose-1-phosphate adenylyltransferase | 2,157 | 2,187 | 3,301 | PhoP+ | Glycogen biosynthesis and storage |
| FruK | 1-Phosphofructokinase | 0 | 3,582 | 680 | Cra− | Carbohydrate import and utilization |
| FruA | Fructose-specific PTS IIBC component | 73 | 3,674 | 2,342 | Cra− | Carbohydrate import and utilization |
| FruB | Bifunctional fructose-specific PTS IIA protein | 497 | 8,386 | 4,883 | Cra− | Carbohydrate import and utilization |
| ManZ | Mannose-specific PTS protein IID | 1,718 | 3,277 | 5,693 | Crp+, FruR−, NagC− | Carbohydrate import and utilization |
| ManX | Mannose-specific PTS enzyme IIAB | 7,466 | 10,121 | 18,857 | Crp+, FruR− | Carbohydrate import and utilization |
| GlpD | Glycerol-3-phosphate dehydrogenase | 2,539 | 1,120 | 249 | TrpR− | Phospholipid and glycerol metabolism |
| GlpQ | Periplasmic glycerophosphodiester phosphodiesterase | 5,858 | 3,487 | 2,328 | Fis+, Fnr+, IhfB− | Phospholipid and glycerol metabolism |
| DppA | Dipeptide transport protein | 421 | 385 | 9,775 | IhfB+, Fnr− | Peptide and heme import |
| YdgR | Tripeptide/dipeptide:H+ symporter | 0 | 83 | 1,407 | OmpR+ | Peptide import |
| MglB | Galactose-binding transport protein | 12,567 | 6,840 | 2,926 | Crp+, GalR− | Carbohydrate import and utilization |
| NuoE | NADH dehydrogenase subunit Ed | 2,074 | 2,288 | 117 | Fis+, NarL+, ArcA+ | Major aerobic electron transport chain |
| NuoC | Bifunctional NADH:ubiquinone oxidoreductase subunit C/D | 2,235 | 1,522 | 380 | Fis+, NarL+, ArcA+ | Major aerobic electron transport chain |
| NuoB | NADH dehydrogenase subunit Bd | 994 | 2,033 | 247 | Fis+, NarL+, ArcA+ | Major aerobic electron transport chain |
| VhcB | Predicted cytochrome d ubiquinol oxidase, subunit III | 7,501 | 3,515 | 9,440 | Electron transport in microaerobic milieu | |
| CydB | Cytochrome d terminal oxidase, subunit II | 2,083 | 2,643 | 4,167 | ArcA+, Cra+ | Electron transport, iron limitation |
| FdoG | Formate dehydrogenase O, major subunitd | 2,045 | 1,489 | 232 | Crp+ | Electron transport, oxygen limitation |
| FdoH | Formate dehydrogenase O, Fe-S subunitd | 1,734 | 1,046 | 97 | Crp+ | Electron transport, oxygen limitation |
| NarH | Nitrate reductase A, β subunitd | 2,906 | 2,345 | 139 | Fnr+, NarL+, Fis− | Electron transport, oxygen limitation |
| NarG | Nitrate reductase A, α subunitd | 3,210 | 1,953 | 205 | Fnr+, NarL+, Fis− | Electron transport, oxygen limitation |
| PntA | NAD(P) transhydrogenase α subunit | 902 | 1,133 | 3,055 | Reversible NADP reduction by NADH | |
| PntB | NAD(P) transhydrogenase β subunit | 3,290 | 2,195 | 4,122 | Reversible NADP reduction by NADH | |
| SthA | Pyridine nucleotide transhydrogenase | 778 | 725 | 192 | NADPH reoxidation with NAD+ | |
a
CoA, coenzyme A; PTS, phosphotransferase system.
b
Average relative APEXi protein abundance levels for in vitro-grown S. flexneri and for extracellular (Ext) and intracellular (Int) bacteria during coculture with Henle cells. More-detailed analyses are provided in Data Set S2 in the supplemental material.
c
Known or predicted transcriptional regulator(s) of the indicated gene, based on data for the closely related bacterium E. coli (www.ecocyc.org). +, positive regulation; −, negative regulation.
d
Fe-S cluster or iron-heme or iron cofactor.