Table 1

Selected proteins present in the secretome of 630Δerm, 630Δerm fliC::erm, 630Δerm CD0240::erm, and 630Δerm fliM::erma

Mutant and accession no.bRatio of protein abundance of mutant/wild typecMass (kDa)pILocus tagbGeneProductLocateP pathwaydCOGePSORTb locationd
630Δerm fliC::erm
    126697780Not observed in 630Δerm fliC::erm47.84.9CD0209Putative sugar-phosphate kinaseNo pathwayGCytoplasmic
    1266977977.8 ± 2.124.56.6CD0226Putative transglycosylaseNo pathwayMUnknown
    12669780216.1 ± 3.148.04.9CD0231flgKPutative flagellar hook-associated proteinNo pathwayNUnknown
    12669780813.2 ± 2.156.05.4CD0237fliDFlagellar cap proteinNo pathwayNExtracellular
    126697810Not observed in 630Δerm fliC::erm30.77.9CD0239fliCFlagellin subunitNo pathwayRCytoplasmic
    12669824018.6 ± 1.43085.5CD0663tcdAToxin ANo pathwayRExtracellular
    126698301Not observed in 630Δerm fliC::erm24.25.6CD0721Hypothetical proteinNo pathwayUnknown
    126699039Not observed in 630Δerm fliC::erm545.3CD1435Hypothetical proteinSec (SPI)Cytoplasmic membrane
    126699235Not observed in 630Δerm fliC::erm27.26.5CD1631sodASuperoxide dismutase (Mn)Sec (SPI)PExtracellular
    126700229Not observed in 630Δerm fliC::erm21.65.8CD2615TetR family transcriptional regulatorNo pathwayKUnknown
    126701136Not observed in 630Δerm fliC::erm63.25.8CD3512Type IV pilus assembly proteinNo pathwayUCytoplasmic
630Δerm CD0240::erm
    1266977960.33 ± 0.1140.65.1CD0225purLFormylglycinamidine ribonucleotide synthetaseNo pathwayFCytoplasmic
    1266978080.32 ± 0.06565.4CD0237fliDFlagellar cap proteinNo pathwayNExtracellular
    1266978100.19 ± 0.0630.87.9CD0239fliCFlagellin subunitNo pathwayNUnknown
    126697822Not observed in 630Δerm CD0240::erm48.15.6CD0251fliIFlagellum-specific ATP synthaseNo pathwayUCytoplasmic
    126697824Not observed in 630Δerm CD0240::erm46.15.2CD0253fliKPutative flagellar hook-length control proteinNo pathwayNUnknown
    126697836Not observed in 630Δerm CD0240::erm38.25.4CD0264flhFFlagellar biosynthesis regulator FlhFNo pathwayNCytoplasmic membrane
    1266982405.1 ± 0.203085.5CD0663tcdAToxin ANo pathwayRExtracellular
    126698424Not observed in 630Δerm CD0240::erm33.75.2CD0844Cell surface proteinSec (SPI)MCell wall
    1266990730.33 ± 0.10111.16.4CD1469Cell surface protein (putative penicillin-binding protein)Sec (SPI)VUnknown
    126699412Not observed in 630Δerm CD0240::erm63.78.8CD1803Cell surface proteinSec (SPI)MCell wall
    1267001640.33 ± 0.10685CD2547Hypothetical proteinNo pathwayCytoplasmic
    1267002860.11 ± 0.00358.15.4CD2672appAOligopeptide ABC transporter, substrate-binding proteinSec (SPII)ECell wall
    126700383Not observed in 630Δerm CD0240::erm77.78.6CD2767Cell surface proteinSec (SPI)SCell wall
    126700402Not observed in 630Δerm CD0240::erm57.16.7CD2786Cell surface proteinSec-(SPI)MCell wall
    1267004030.16 ± 0.0387.27.0CD2787cwp84Cell surface protein (putative cell surface-associated cysteine protease)Sec (SPI)OCell wall
    1267004050.46 ± 0.1066.75.3CD2789cwp66Cell surface proteinSec (SPI)MCell wall
    1267004070.15 ± 0.0166.46.2CD2791Cell surface protein (putative S-layer protein precursor)Sec (SPI)MCell wall
630Δerm fliM::erm
    1266982400.40 ± 0.063085.5CD0663tcdAToxin ANo pathwayRExtracellular
    1267004070.41 ± 0.0366.46.2CD2791Cell surface protein (putative S-layer protein precursor)Sec (SPI)MCell wall
    126697802Not observed in 630Δerm fliM::erm48.04.9CD0231flgKPutative flagellar hook-associated proteinNo pathwayNUnknown
    1266978080.026 ± 0.01565.4CD0237fliDFlagellar cap proteinNo pathwayNExtracellular
    126697810Not observed in 630Δerm fliM::erm30.77.9CD0239fliCFlagellin subunitNo pathwayNUnknown
    126697824Not observed in 630Δerm fliM::erm46.15.2CD0253fliKPutative flagellar hook-length control proteinNo pathwayNUnknown
    126697844Not observed in 630Δerm fliM::erm54.25.4CD0272Hypothetical proteinPossibly Sec (SPI)Unknown
    126700402Not observed in 630Δerm fliM::erm57.26.7CD2786Cell surface proteinSec (SPI)MCell wall
    126700403Not observed in 630Δerm fliM::erm87.26.9CD2787cwp84Cell surface protein (putative cell surface-associated cysteine protease)Sec (SPI)OCell wall
    126700405Not observed in 630Δerm fliM::erm66.75.3CD2789cwp66Cell surface proteinSec (SPI)MCell wall
  • a The table includes selected protein identifications of cell surface or virulence-related proteins observed at a greater than 2-fold difference in abundance compared to the levels in wild type (P < 0.05). A full listing of proteins altered in abundance at 4-fold or greater levels is shown in Table S1 in the supplemental material.

  • b Accession number according to the C. difficile 630 genome sequence (NCBI reference sequence NC_009089).

  • c The relative peptide abundance value was assigned by the Mascot software using the exponentially modified protein abundance index (emPAI) (22). The estimated false-positive rate for peptide identification was less than 1%.

  • d The protein subcellular localization for all proteins in the genome was predicted using both LocateP-DB and PSORTb (version 3.0) (http://www.cmbi.ru.nl/locatep-db).

  • e COG, clusters of orthologous groups, which was used to assign the protein functional category.