TABLE 2

Selected differentially expressed proteins in cocultures of E. coli and R. palustris compared to monoculturese

SpeciesGeneGene description or general roleNormalized relative protein intensity
R. palustris Nx + WT E. colicR. palustris NxΔAmtB + WT E. colidR. palustris ΔAmtB + WT E. colid
E. coliargTa,bLysine/arginine/ornithine binding protein10.911.110.3
ddpAa,bd-Ala dipeptide permease5.87.26.8
gssBifunctional glutathionylspermidine synthetase/amidase4.54.74.0
tktBTransketolase4.15.53.8
potFa,bPutrescine binding periplasmic protein3.84.24.1
modAMolybdate binding periplasmic protein3.84.04.9
gabDa,bSuccinate-semialdehyde dehydrogenase3.74.83.5
dapB4-Hydroxy-tetrahydrodipicolinate reductase3.62.82.7
talATransaldolase A3.64.24.4
amtBa,bAmmonium transporter3.53.53.5
asnSAsparagine biosynthesis−2.1−1.9−1.9
serASerine biosynthesis−2.1−2.5−2.3
secEProtein translocase subunit−2.1−1.8−2.3
glfLipopolysaccharide biosynthesis−2.1−1.9−1.9
yjiMPutative dehydratase−2.2−1.9−1.8
sstTSerine/threonine transporter−2.2−2.4−2.4
rmlA1Carbohydrate biosynthesis−2.3−2.1−2.4
ompFOuter membrane porin−2.3−2.3−2.6
ribERiboflavin biosynthesis−2.3−1.7−1.9
secYProtein translocase subunit−2.6−2.0−2.0
glyAGlycine biosynthesis−3.2−3.0−3.4
purEaPurine biosynthesis−3.3−3.6−3.5
yqjITranscriptional regulator−3.6−3.0−3.4
asnAAspartate-ammonia ligase−6.4−3.8−3.7
R. palustrisRPA1206aAldehyde dehydrogenase10.03.3
RPA1205aPutative alcohol dehydrogenase7.81.23.9
RPA3101aUnknown7.11.52.6
RPA3093ABC transporter urea/short-chain binding protein4.81.63.4
RPA3297ABC transporter urea/short-chain binding protein4.71.53.2
RPA4019Putative amino acid ABC transport3.91.42.5
RPA4045aPutative amino acid ABC transport3.31.42.1
RPA1009aPossible cytochrome P4503.21.32.1
RPA1748Putative branched-chain-amino-acid transport−2.1−1.4−2.5
RPA2378aPutative TonB-dependent receptor protein−2.1−1.2−1.1
RPA2124TonB-dependent iron siderophore receptor−2.3−1.5−1.7
RPA1260aUniversal stress protein−2.5−1.5−1.8
RPA2050Unknown−2.7−1.6−2.6
RPA3669Putative urea short-chain amide or branched-chain amino acid ABC transport−2.8−1.1−1.3
RPA2120Periplasmic binding protein−6.0−1.6−1.7
  • a Genes were also identified as differentially expressed transcripts in coculture (Table 1 and supplemental material).

  • b The gene is transcriptionally activated by E. coli NtrC.

  • c Values represent mean normalized relative protein intensities for two biological replicates. Positive values indicate that the gene was upregulated in coculture. Negative values indicate that the gene was downregulated in coculture.

  • d Values represent mean normalized relative protein intensity for one biological replicate. Positive values indicate that the gene was upregulated in coculture. Negative values indicate that the gene was downregulated in coculture.

  • e Proteins shown here are directly or indirectly mentioned in the text. For a full list of differentially expressed proteins, see the supplemental material.