International Journal of Proteomics

Research Article

Top-Down Characterization of the Post-Translationally Modified Intact Periplasmic Proteome from the Bacterium Novosphingobium aromaticivorans

Table 1

Modifications of identified proteins using top-down approach.
Locus_TagGenbank Protein DescExport signalDetected signal peptideaN-terminalOther modifications
Saro_2004Alkyl hydroperoxide reductase/Thiol specific antioxidant/Mal allergenSecPNoneRemoval of met 
Saro_2586Cold-shock DNA-binding protein familySecPNoneRemoval of met 
Saro_0565Glutathione peroxidaseSecPNoneRemoval of met 
Saro_0483Superoxide dismutaseSecPNoneRemoval of met 
Saro_3290Thiamine biosynthesis protein ThiSSecPNoneRemoval of met 
Saro_1996ThioredoxinSecPNoneRemoval of metDisulfide bond
Saro_1332CsbD-like proteinSecP/TatPNoneRemoval of met 
Saro_1919Hypothetical proteinSecP/TatPUnknownProteolytic fragment 
Saro_1314Conserved hypothetical proteinSecP/TatPYesAXADisulfide bond, pyro glu
Saro_2385Hypothetical proteinSecP/TatPYesAXAPyro glu
Saro_3257Conserved hypothetical proteinSignalPNoneProteolytic fragment 
Saro_3518Cupin 2, conserved barrel domain proteinSignalPNoneRemoval of met (wrong starting site) 
Saro_3173OmpA/MotBSignalPNoneProteolytic fragment 
Saro_1303Hypothetical proteinSignalPUnknownProteolytic fragment 
Saro_1685Amine dehydrogenaseSignalPYesAXA 
Saro_2852AnkyrinSignalPYesAXAPyro glu
Saro_3053Beta-Ig-H3/fasciclinSignalPYesAXA 
Saro_0830Cell wall surface anchor family proteinSignalPYesVAA, not AXA 
Saro_2955Conserved hypothetical proteinSignalPYesAXA 
Saro_1378Conserved hypothetical proteinSignalPYesAXA 
Saro_0103Conserved hypothetical proteinSignalPYesAXADisulfide bond
Saro_2067Conserved hypothetical proteinSignalPYesSHA, not AXAPyro glu
Saro_1721Conserved hypothetical proteinSignalPYesTHA, not AXA
Saro_2522Hypothetical proteinSignalPYesASN, not AXADisulfide bond
Saro_3326Hypothetical proteinSignalPYesAXADisulfide bond
Saro_2384Hypothetical proteinSignalPYesAXAPyro glu
Saro_1978Hypothetical proteinSignalPYesAXAPyro glu
Saro_1502Hypothetical proteinSignalPYesAXA 
Saro_1412Hypothetical proteinSignalPYesAXADisulfide bond
Saro_2350Peptidase M28SignalPYesAXA 
Saro_0837Peptidyl-prolyl cis-trans isomerase, cyclophilin typeSignalPYesLVA, not AXA 
Saro_2251Peptidylprolyl isomeraseSignalPYesVAA, not AXAPyro glu
Saro_0989Peptidylprolyl isomerase, FKBP-typeSignalPYesAIS, not AXADisulfide bond
Saro_0823Protein of unknown function DUF192SignalPYesAXA 
Saro_3075TonB-dependent receptorSignalPYesAXAProteolytic fragment
Saro_2265YceISignalPYesMVA, not AXAPyro glu
Saro_1171Hypothetical proteinSignalP/SecPNoneRemoval of metDisulfide bond
Saro_1420Antibiotic biosynthesis monooxygenaseTatPNoneRemoval of metDisulfide bond
Saro_3279Arsenate reductaseTatPNoneN/AS-glutathiolation on cysteine
Saro_1703(2Fe-2S)-binding protein NoneRemoval of metDisulfide bond
Saro_1346(2Fe-2S)-binding protein NoneRemoval of metDisulfide bond
Saro_1339Acyl carrier protein NoneRemoval of metModification (382 Da)
Saro_2520BolA-like protein NoneRemoval of met 
Saro_0034Chaperonin Cpn10 NoneRemoval of met 
Saro_2299Conserved hypothetical protein NoneRemoval of met 
Saro_2229GreA/GreB family elongation factor NoneRemoval of metBoth acetylation and n/a
Saro_2403H+-transporting two-sector ATPase, delta/epsilon subunit NoneRemoval of met 
Saro_1768Hypothetical protein NoneRemoval of met 
Saro_1177Hypothetical protein NoneRemoval of met 
Saro_1778Molybdopterin binding domain NoneRemoval of metS-glutathiolation on cysteine
Saro_0894Nucleoside diphosphate kinase NoneRemoval of met 
Saro_1830PhnA protein NoneRemoval of met 
Saro_1033Phosphoribosylformylglycinamidine synthetase PurS NoneN/A 
Saro_0209Tetratricopeptide TPR_4 NoneRemoval of met (wrong starting site)Pyro glu
Saro_1194Hypothetical protein YesAXA, unusualbDisulfide bond
peptide cleavage was annotated as described in the Experimental section.
bThe unusual cleavage site was further validated. See discussion in text and Figure 3.