Skip to main content
NIHPA Author Manuscripts logoLink to NIHPA Author Manuscripts
. Author manuscript; available in PMC: 2011 Apr 13.
Published in final edited form as: Adv Exp Med Biol. 2010;675:179–209. doi: 10.1007/978-1-4419-1528-3_11

A Glimpse into the Proteome of Photorophic Bacterium Rhodobacter capsulatus

Ozlem Onder 1, Semra Aygun-Sunar 1, Nur Selamoglu 1, Fevzi Daldal 1
PMCID: PMC3075558  NIHMSID: NIHMS255082  PMID: 20532742

Abstract

A first glimpse into the proteome of Rhodobacter capsulatus revealed more than 450 [with over 210 cytoplasmic and 185 extracytoplasmic known as well as 55 unknown] proteins that are identified with high degree of confidence using nLC-MS/MS analyses. The accumulated data provide a solid platform for ongoing efforts to establish the proteome of this species and the cellular locations of its constituents. They also indicate that, at least 40 of the identified proteins, which were annotated in genome databases as unknown hypothetical proteins, correspond to predicted translation products that are indeed present in cells under the growth conditions used in this work. In addition, matching the identification labels of the proteins reported between the two available R. capsulatus genome databases (ERGO-light with RRCxxxxx and NT05 with NT05RCxxxx numbers) indicated that eleven such proteins are listed only in the latter database.

Introduction

The Gram negative, purple non-sulfur facultative phototrophic bacterium Rhodobacter capsulatus is a model organism that is intensely studied for various aspects of major metabolic pathways such as photosynthesis and respiration (Zannoni 1995; Hunter, Daldal et al. 2009). Using this species, which exhibits highly versatile growth modes including anoxygenic light (i. e., photosynthesis), anoxygenic dark (i. e. anaerobic respiration) and oxygenic (i. e., light independent aerobic respiration) metabolisms, physiologically relevant cellular responses to the availability of light or oxygen can be examined at the molecular level (Hunter, Daldal et al. 2009). Indeed, a complete definition of the presence, regulation and biogenesis of various cellular components in response to the changing environmental conditions greatly benefits from global analyses approaches, including transcriptomic and proteomic studies (Park et al. 2005; Wasinger 2006). Thus, along with the transcriptional studies, availability of qualitative and quantitative description of R. capsulatus proteomes under defined growth conditions is extremely invaluable. Towards this end, we have initiated an effort to define the complete proteome of this species (Onder et al. 2008), and we present here a first glimpse to this developing protein identification dataset.

Materials and Methods

Wild type R. capsulatus strain MT1131 was grown under respiratory growth condition in enriched MPYE (mineral-peptone-yeast extracts) medium (Daldal, Chen et al. 1986), under standard culture conditions (1 L medium in 2 L flask, shaken at approximately 150 rpm at 35°C in dark for approximately 36 hrs) (Myllykallio, Jenney et al. 1997). Cells were harvested by centrifugation at 4°C (5000 × g, 20 min), washed with ice cold 20 mM Tris-HCl, pH 8.0, and gently resuspended in cold extraction buffer consisting of 1 mg/ml of polymyxin B sulfate, 20 mM Tris-HCl, 250 mM NaCl, [pH 8.0] (5 ml/g of wet cells) (Ren and Thony-Meyer 2001; Onder, Turkarslan et al. 2008). The suspension was gently stirred for 1 hour at 4 °C and centrifuged at 10,000 × g for 20 min at 4 °C. The supernatant was carefully transferred into a clean tube, re-centrifuged at 150,000 × g for 2 hours at 4 °C and saved as the periplasmic fractions at −20 °C. Polymyxin treated cells pellets were then resuspended in 50 mM MOPS, 100 mM KCl (pH 8.0) buffer and processed using a French pressure cell, as described earlier (Onder, Turkarslan et al. 2008). After centrifugation for 2 hrs at 45,000 rpm, supernatants (i. e., cytoplasmic fractions) and pellets (i. e., membrane fractions) were processed separately for analyses of their protein contents.

Soluble or periplasmic proteins were precipitated with trichloroacetic (TCA)/acetone (20% w/v), washed twice with ice-cold acetone to remove residual TCA, and dried under vacuum. Pellets were resuspended in two dimensional-gel electrophoresis (2D-GE) sample solubilization buffer (SSB: 8 M urea, 4% CHAPS, 40 mM Tris, 0.2% Bio-Lyte-pH 3–10, 65 mM DTT) at room temperature until complete solubilization. For 2D-GE, samples containing 300 μg of solubilized proteins were applied to an 18 cm, pH 4–7 immobilized pH gradient (IPG) strips (Bio-Rad), and following a 12 hours passive rehydration, isoelectrofocusing (IEF) was carried out by using PROTEAN IEF Cell (Bio-Rad) at 20 °C at a maximum of 7000 V for 15–18 hours, and the strips thus prepared were kept frozen at −20 °C until use. For the second dimension sodium dodecylsulfate-polyacrylamide gel electrophoresis (SDS-PAGE), IPG strips were reduced with 1% w/v dithiothreitol (DTT) and alkylated with 2.5% w/v iodoacetamide at room temperature, both prepared in equilibration buffer consisting of 50 mM Tris-HCl, pH 8.8, 6 M urea, 30% v/v glycerol, 2% SDS and 0.02% bromophenol blue. After equilibration, the IPG strips were layered on top of the second dimension resolving gel slabs and overlaid with a solution of molten 0.5% agarose in SDS electrophoresis buffer. The second dimension Laemmli-type SDS-PAGE was carried out using 11% gels without any stacking at 40 mA per gel in a Protean II XL cell (Bio-Rad), and gels were stained with colloidal coomassie brillant blue (Neuhoff, Stamm et al. 1990). Spots or bands were manually excised from gels and subjected to in-gel trypsin digestions (Onder, Yoon et al. 2006). Tryptic peptide extracts were analyzed using a nanoLC-MS/MS set up (LCQ Deca XP Plus mass spectrometer from Thermo Scientific, coupled to an Ultimate Nano liquid chromatography system from DIONEX). Tryptic peptide mixtures were first loaded onto a μ-precolumn (C18, 5 μm, 100 Å, 300 μm i.d. × 5 mm) (DIONEX), and washed for 4 min at a flow rate of 0.25 μl/min with the LC buffer A, then transferred onto an analytical C18-nanocapillary HPLC column (DIONEX, Acclaim PepMap100, C18 column (75 μm i.d. by 150 mm) with a 3 μm particle size and a 100 Å pore diameter for fractionation. A fused silica tip with 8-μm aperture (New Objective, Woburn, MA) was used for nanospray ionization of peptides eluting from the column. Mass spectra were analyzed using the DTA generation and SEQUEST search algorithms within Bioworks 3.3 software (Thermo Scientific) and R. capsulatus protein databases (ERGO Light from http://www.ergo-light.com or in-house available NT05 data bases). The following parameters were used for SEQUEST analyses: as appropriate trypsin or GluC were selected as the proteolytic enzymes, with trypsin cleavage only after arginine and lysine was allowed, and the number of maximal internal (missed) cleavage sites was set to 2–4. Mass tolerance for precursor and fragment ions was 2.0–2.5 and 1.0, respectively. Methionine oxidation and cysteine carbamidomethylation were set as variable modification with maximum modification set to 2, and default setting was used for all other variables. Matching peptides were filtered according to correlation scores (XCorr at least 1.5, 2.0 and 2.5 for +1, +2 and +3 charged peptides, respectively, and ΔCN > 0.1) to give high confidence of protein identification, and proteins were considered as significant only when at least two peptides were identified with the SEQUEST filter settings mentioned above. The R. capsulatus proteins thus identified were examined with bioinformatic tools. Prediction softwares SignalP (version 3.0) (Bendtsen, Nielsen et al. 2004) (http://www.cbs.dtu.dk/services/SignalP/) and PSORTb (version 2.0) (Gardy, Laird et al. 2005) (http://www.psort.org/psortb/) were used to predict the likely sub-cellular localization of identified proteins.

Results and Discussion

A long-term objective of this study is the establishment of a comprehensive proteomic reference database for R. capsulatus under different growth conditions. This physiological proteomics will then establish an important step to enable detailed analyses of major metabolic pathways of this organism extending from photosynthesis to respiration. To this end, we use modern proteomic approaches involving 1D- and 2D-GE combined with liquid chromatography and tandem mass spectrometry techniques. In addition, as comprehensive proteome analyses are often limited by physiological constraints and technical issues, to maximize the number of proteins identified, to reduce the sample complexity and also to detect low abundance proteins, we prepare overlapping subproteomes of periplasmic, cytoplasmic and membrane fractions of R. capsulatus cells grown under different conditions, and analyze these samples as described in Materials and Methods. These analyzes identified so far more than over 450 R. capsulatus proteins that are grouped into different cellular function categories listed in Table 1. Tentative sub-cellular localizations of these proteins are also indicated using the PSORTb v 2.0 prediction software trained on bacterial protein sub-cellular localization prediction (Gardy, Laird et al. 2005). Of these proteins, 218 are predicted to be cytoplasmic and 187 are assigned to be exported proteins. Among the latter extracytoplasmic proteins, 52 and 94 of them are considered to be periplasmic and integral membrane proteins, respectively. Clearly, the predictive analysis is highly successful as for only 53 out of the 450 identified proteins a cellular localization could not be attributed reliably using PSORTb program. Moreover, global distributions of the identified proteins into different cellular function categories are also analyzed, and the results are presented as a pie chart. Even though the available data set is not yet exhaustive, it appears that “Energy Metabolism” and “Transport and Binding Proteins” categories are among the most populated groups of proteins with 82 and 79 members, respectively. Remarkably, while a large fraction of the identified proteins correspond to proteins of known functions, yet 49 of them have undefined roles, and among the latter group 41 of them were initially annotated as hypothetical proteins in either or both (ERGO-light with RRCxxxxx and NT05 with NT05RCxxxx numbers) of R. capsulatus genome databases (Table 1). Our data establish that these translation products are indeed real, and searches for defining their functions can now be initiated on firm grounds. We believe that data set that is under construction is of great value for rapid progress of current and future studies focused on Rhodobacter species (Du et al. 2008). This ever-growing data set is providing a platform onto which we can build future qualitative and quantitative comparisons for various cellular components under defined physiological conditions. A current example to the point is illustrated by one of our recent studies where a portion of our accumulated proteomics data of R. capsulatus, once combined with standard in-depth biochemical and molecular genetic approaches, yielded exquisite understanding in detailed molecular terms of an unusual physiological situation simply detected by a growth phenotype (Onder, Turkarslan et al. 2008). We believe that establishment of a comprehensive proteomic data for R. capsulatus species, like in many other cases, will be invaluable to provide much needed impetus for understanding the global biology of this organism with a “systems” level organization.

Table I.

Complete list of R. capsulatus proteins identified by nLC-MS/MS analyses. Identified proteins are categorized according to their predominant function as reported in the current literature (ref). Protein names, enzyme commission (EC) numbers, gene acronyms, ERGO-light (RRCxxxxx) and NT05 (NT05RCxxxx) identification numbers are indicated. Sub-cellular localization of each protein was predicted by PSORTb and SignalP analyses, and C, EC, P, IM, OM and M were used to designate cytoplasmic, extracytoplasmic, periplasmic, inner membrane, outer membrane and membrane proteins, respectively.

Protein Name EC Number Gene Name ERGO* NT05* Location
AMINO ACID BIOSYNTHESIS
Aromatic amino acid family
Ornithine cyclodeaminase, Ocd 4.3.1.12 arcB RRC00632 NT05RC2206 C
Tryptophan synthase beta subunit, TrpB 4.2.1.20 trpB RRC01000 NT05RC2658 C
Tryptophan synthase alpha subunit, TrpA 4.2.1.20 trpA RRC00192 NT05RC3179 C
Aromatic-aminoacid aminotransferase, Arat (aroat) 2.6.1.57 tyrB RRC01763 NT05RC3527 C

Aspartate family
Dihydrodipicolinate synthase 4.2.1.52 dapA RRC02939 NT05RC0396 C
Aspartokinase (Aspartate kinase) 2.7.2.4 lysC RRC02984 NT05RC0439 C
5,10-Methylenetetrahydrofolate reductase 1.5.1.20 metF RRC03981 NT05RC0510 C
5-Methyltetrahydrofolate homocysteine methyltransferase/Methionine synthase I 2.1.1.13 metH RRC01233 NT05RC2273 C
Threonine synthase, ThrC 4.2.99.2 thrC RRC00242 NT05RC3231 C

Glutamate family
Glutamate synthase NADPH large chain, NADPH-Gogat 1.4.1.13 gltA RRC04596 NT05RC0170 C
Glutamate synthase NADPH small chain, NADPH-Gogat 1.4.1.13 gltD RRC03219 NT05RC0172 C
Argininosuccinate synthase 6.3.4.5 argG RRC03172 NT05RC0219 C
Glutamate N-acetyl transferase/Arginine biosynthesis bifunctional protein, ArgJ 2.3.1.35/2.3.1.1 argJ RRC04654 NT05RC0229 C
N-acetyl-gamma-glutamyl-phosphate reductase, ArgC 1.2.1.38 argC RRC03917 NT05RC0575 C
Pyrroline-5-carboxylate reductase 1.5.1.2 proC RRC04153 NT05RC1196 C
Glutamine synthetase, GlnA 6.3.1.2 glnA RRC03526 NT05RC1748 C
Acetyltransferase/gnat family 2.3.1.- RRC01355 NT05RC2400

Histidine family
Imidazole glycerol phosphate synthase, cyclase subunit, HisF 4.1.3.- hisF RRC04158 NT05RC1201 C
Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase 5.3.1.16 hisA RRC04159 NT05RC1202 C
Imidazole glycerol phosphate synthase, glutamine amidotransferase subunit, HisH 2.4.2.- hisH RRC04493 NT05RC1232 C
Histidinol dehydrogenase, HisD 1.1.1.23 hisD RRC01022 NT05RC2681 C

Pyruvate family
3-Isopropylmalate dehydrogenase 1.1.1.85 leuB RRC03293 NT05RC0087 C
Ketol-acid reductoisomerase/2-Dehydropantoate 2-reductase 1.1.1.86 ilvC RRC02733 NT05RC1266 C

Serine family
Cysteine synthase A, CysK 2.5.1.47 cysK RRC00998 NT05RC2657
O-acetylhomoserine thiol-lyase (O-acetylhomoserinesulfhydrylase)/Homocysteine synthase 2.5.1.49/4.2.99.8 metY RRC00762 NT05RC2915 C
Cysteine synthase (O-acetylserine sulfhydrylase)/O-acetylserine thiol-lyase, CSase 2.5.1.47/4.2.99.8 RRC00087 NT05RC3089
Phosphoserine aminotransferase 2.6.1.52 serC RRC05753 NT05RC3593 CM

BIOSYNTHESIS OF COFACTORS, PROSTHETIC GROUPS, AND CARRIERS
Chlorophyll and bacteriochlorphyll
Light-independent protochlorophyllide reductase, iron-sulfur ATP-binding protein 1.18.-.- bchL RRC02850 NT05RC0691 C
Bacteriochlorophyll synthase 33 kDa chain/Geranylgeranylbacteriochlorophyllide synthase 2.5.1.- bchG RRC02841 NT05RC0700 CM
Bacteriochlorophyll-geranylgeranyl reductase 1.3.1.- bchP RRC02839 NT05RC0702 CM
Magnesium chelatase ATPase subunit I 6.6.1.1 bchI RRC02835 NT05RC0706 C
2-Desacetyl-2-hydroxyethyl bacteriochlorophyllide A dehydrogenase, BchC 1.-.-.- bchC RRC02826 NT05RC0715 CM
Chlorophyllide reductase 35 kDa protein, BchA(XYZ) 1.18.-.- bchA RRC02825 NT05RC0716 C

Folic acid
MoxR-like ATPase/AAA_3 ATPase RRC04552 NT05RC0619 C
5-methyltetrahydrofolate corrinoid iron sulfur protein methyltransferase/Dihydropteroate synthase, Dhps 1.2.99.2 acsE RRC03586 NT05RC1686 C
Para-aminobenzoate synthetase component I, PabB 4.1.3.-/6.3.5.8 pabB RRC01115 NT05RC2770 C
Methylenetetrahydrofolate dehydrogenase (NADP+)/Methenyltetrahydrofolate cyclohydrolase/Bifunctional protein, FolD 1.5.1.5/3.5.4.9 folD RRC00338 NT05RC3327 C

Glutathione and analogs
Glutathione synthetase 6.3.2.3 gshB RRC04009 NT05RC0483 C

Heme, porphyrin, and cobalamin
Ferrochelatase 4.99.1.1 hemH RRC04666 NT05RC0206 C
Cobaltochelatase subunit, CobS 6.6.1.2 cobS RRC01954 NT05RC0874 C
Uroporphyrinogen decarboxylase 4.1.1.37 hemE RRC04134 NT05RC1222 CM
Porphobilinogen deaminase 2.5.1.61 hemC RRC04136 NT05RC1223 C
5-aminolevulinic acid synthase 2.3.1.37 hemA RRC04400 NT05RC1506 CM
Delta-aminolevulinic acid dehydratase 4.2.1.24 hemB RRC06033 NT05RC1890
Precorrin-8X methylmutase/Precorrin isomerase, HBAsynthase 5.4.1.2 cobH RRC00650 NT05RC2138 C
Cobalamin biosynthesis protein, CobD cobD RRC00706 NT05RC2147 CM
Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase, CobT 2.4.2.21 cobT RRC00590 NT05RC2151 C

Menaquinone and ubiquinone
3-Demethylubiquinone 3-methyltransferase 2.1.1.64 ubiG RRC03170 NT05RC0221 C
Ubiquinone biosynthesis protein AARF/2-Polyprenylphenol 6-hydroxylase ubiB RRC03386 NT05RC3680 CM

Pantothenate and coenzyme A
Pantoate-beta-alanine Ligase 6.3.2.1 panC RRC02990 NT05RC0445 C

Pyridine nucleotides
UDP-sugar diphosphatase/5′-Nucleotidase 3.6.1.45/3.1.3.5 ushA RRC01089 NT05RC2743 P

Riboflavin, FMN, and FAD
Riboflavin biosynthesis protein, RibF 2.7.1.26/2.7.7.2 ribF RRC00565 NT05RC2178 C
Riboflavin biosynthesis protein, RibAB/GTP cyclohydrolase II/3,4-dihydroxy-2-butanone-4-phosphate synthase 3.5.4.25/4.1.2.- ribAB RRC00220 NT05RC3210 C

Thiamine
Thiamin-phosphate pyrophosphorylase 2.5.1.3 thiE RRC06023 NT05RC1674 C

Other
Iron-sulfur cluster assembly ATP-dependent transporter, SufC sufC RRC01541 NT05RC1963 C, CM

CELL ENVELOPE
Biosynthesis and degradation of murein sacculus and peptidoglycan
Glucose-1-phosphate thymidylyltransferase 2.7.7.24 rfbA RRC03209 NT05RC0184 C
dTDP-4-dehydrorhamnose reductase 1.1.1.133 rfbD RRC03208 NT05RC0185 EC
dTDP-glucose-4,6-dehydratase 4.2.1.46 rfbB RRC03206 NT05RC0187 EC
dTDP-4-dehydrorhamnose 3,5-epimerase (reductase) 5.1.3.13 rfbC RRC03205 NT05RC0188 EC
Glucans biosynthesis protein, MdoG mdoG RRC04027 NT05RC0391 P
Soluble lytic murein transglycosylase 3.2.1.- slt RRC02941 NT05RC0397 P
Cell elongation specific D,D-transpeptidase/Peptidoglycan glycosyltransferase 2.4.1.129 ftsl RRC04232 NT05RC0836 C, CM
UDP-N-acetylglucosamine-N-acetylmuramyl-pentapeptide-pyrophosphoryl-undecaprenol N-acetylglucosamine transferase 2.4.1.227 murG RRC04656 NT05RC0856 CM
Peptidoglycan-binding domain 1 protein RRC02722 NT05RC1256 EC
D-alanyl-D-alanine serine-type carboxypeptidase 3.4.16.4 RRC02699 NT05RC1306 CM
UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase, GlmU 2.7.7.23/2.3.1.157 glmU RRC04347 NT05RC1565 C
Alanine racemase, Alr 5.1.1.1 alr RRC03627 NT05RC1640 C
Succinoglycan biosynthesis transport protein, ExoP 2.7.1.112 exoP RRC01472 NT05RC2037 CM
D-alanyl-D-alanine carboxypeptidase (D-alanyl-D-alanine-endopeptidase)/Penicillin-binding protein 4, PBP-4 dacB RRC01098 NT05RC2752 C
Peptidoglycan-associated lipoprotein/OmpA-MotB family protein RRC04613 NT05RC3334 OM
Membrane-bound lytic murein transglycosylase B 3.2.1.- mltB RRC05698 NT05RC3538 CM, P

Other
Competence lipoprotein/Tetratricopeptide TPR_2 repeat protein comL RRC01947 NT05RC0865 M

CELLULAR PROCESSES
Adaptations to atypical conditions
Transcriptional regulator/Methionine-R-sulfoxide reductase 1.8.4.- msrB RRC00410 NT05RC3399 EC

Cell division
Cell division ATP-binding protein, FtsE 3.6.3.- ftsE RRC00317 NT05RC3307 CM

Chemotaxis and motility
Flagellar hook protein, FlgE flgE RRC00713 NT05RC0007 OM
Flagellar hook-associated protein 1, FlgK flgK RRC00714 NT05RC0008 OM
Flagellar hook-associated protein 3, FlgL flgL RRC00715 NT05RC0009 OM
Flagellar biosynthetic protein, FlhA flhA RRC03323 NT05RC0057 CM
Methyl-accepting chemotaxis sensory transducer RRC04109 NT05RC1237 CM
Methyl-accepting chemotaxis protein, McpA mcpA RRC01082 NT05RC2737 CM
Flagellin protein fliC RRC03417 NT05RC3674 P

Detoxification
Dihaem cytochrome c551 peroxidase 1.11.1.5 ccpA RRC00728 NT05RC0020 P
Glutathione peroxidase 1.11.1.9 gpx RRC02811 NT05RC0730 P
Phosphinothricin N-acetyltransferase/gnat family 2.3.1.- pat RRC04226 NT05RC0842
NAD-dependent aldehyde dehydrogenase 1.1.1.1 adh RRC04460 NT05RC1433 C
Catalase/peroxidase, HPI 1.11.1.6/1.11.1.7 katG RRC03460 NT05RC1815
Beta-lactamase/hypothetical protein 3.5.2.6 RRC00641 NT05RC2200 CM
Beta-lactamase family protein/putative beta-lactamase 3.5.2.6 bla RRC00550 NT05RC2365 P
Superoxide dismutase (Fe) 1.15.1.1 sodB RRC01365 NT05RC2413
Toluene tolerance protein, Ttg2D ttg2D RRC01770 NT05RC3534
Peroxiredoxin, AhpC/Glutaredoxin domain protein 1.11.1.15 ahpC RRC05718 NT05RC3559

Pathogenesis
Virulence-associated protein E RRC00816 NT05RC2862
Iron-regulated protein frpC/Rhizobiocin, RzcA frpC/rzcA RRC00341 NT05RC3330 EC

Toxin production and resistance
Bicyclomycin resistance protein/Drug resistance transporter, Bcr RRC02414 NT05RC1893 M
Iron-regulated protein, FrpC/Bifunctional hemolysin-adenylate cyclase (cyclolysin), AC-HLY frpC RRC01135 NT05RC2792 EC

CENTRAL INTERMEDIARY METABOLISM
Amino sugars
N-acetylglucosamine-6-phosphate deacetylase 3.5.1.25 nagA RRC05751 NT05RC3592

Nitrogen fixation
Nitrogenase Iron Protein 1.18.6.1 nifH RRC03785 NT05RC0610 C
Iron-sulfur cluster assembly NifU domain protein 1.18.6.1 nifU RRC00380 NT05RC3369 C
Nitrogenase cofactor biosynthesis protein, NifB 1.18.6.1 nifB RRC03905 NT05RC3406 C
Nitrogenase MoFe cofactor biosynthesis protein, NifE 1.18.6.1 nifE RRC00431 NT05RC3420 C

Nitrogen metabolism
Nitrogen regulatory protein P-II glnB RRC03527 NT05RC1747 C

Polyamine biosynthesis
Agmatinase 3.5.3.11 speB RRC03474 NT05RC1799 C
Arginase, RocF 3.5.3.1 rocF RRC00631 NT05RC2207 C

One-carbon metabolism
Trimethylamine methyltransferase family protein, MttB mttB RRC02448 NT05RC1856 CM
2-Hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase or acyltransferase 3.7.1.- bphD RRC01136 NT05RC2793 C

Phosphorus compounds
Bacterial phosphonate metabolism protein, PhnI phnI RRC04121 NT05RC1247 C

Sulfur metabolism
Nitrilotriacetate monooxygenase component B 1.14.13.- ntaB RRC00711 NT05RC0005 C
3′(2′),5′-bisphosphate nucleotidase 3.1.3.7 cysQ RRC05208 NT05RC0131 C, CM

Other
Succinate-semialdehyde dehydrogenase [NADP+], Ssdh 1.2.1.16 gabD RRC02976 NT05RC0431 C
Methylmalonyl-CoA mutase alpha subunit 5.4.99.2 mutB RRC02025 NT05RC0954
S-adenosylmethionine synthetase 2.5.1.6 metK RRC01795 NT05RC1167 C
Gamma-aminobutyrate aminotransferase/Aminotransferase class-III 2.6.1.19/2.6.1.18 RRC01241 NT05RC2282 C
Exopolyphosphatase/Pyrophosphate phosphohydrolase family II 3.6.1.11 ppx RRC00932 NT05RC2590 C
Acetate-CoA ligase, AcsA 6.2.1.1 acsA RRC01093 NT05RC2746 CM

DNA METABOLISM
DNA replication, recombination, and repair
DNA Polymerase III beta chain 2.7.7.7 dnaN RRC00708 NT05RC0002 C
ATP-dependent DNA helicase II, PcrA 3.6.1.- pcrA RRC04357 NT05RC1555
Replicative DNA helicase 3.6.1.- dnaB RRC03626 NT05RC1641 C
NAD-dependent DNA ligase, LigA 6.5.1.2 ligA RRC03535 NT05RC1737 C
Single-stranded DNA-binding protein, Ssb/Helix-destabilizing protein ssb RRC02420 NT05RC1887 C
DNA polymerase I, Pol I 2.7.7.7 pol1 RRC00937 NT05RC2594 C
DNA primase 2.7.7.- dnaG RRC00201 NT05RC3187 C
Primosomal protein N′ priA RRC00361 NT05RC3351 C
Exodeoxyribonuclease III 3.1.11.2 exoDNase_III RRC00493 NT05RC3477
DNA mismatch repair protein, MutS mutS RRC05797 NT05RC3643 CM

ENERGY METABOLISM
Amino acids and amines
Adenosylhomocysteinase 3.3.1.1 ahcY RRC03330 NT05RC0050 C
Serine hydroxymethyl transferase 2.1.2.1 glyA RRC03001 NT05RC0457 C
Alanine dehydrogenase 1.4.1.1 ald RRC03987 NT05RC0504 C
Tyrosine phenol-lyase/Beta-tyrosinase 4.1.99.2 tlp RRC03952 NT05RC0536 CM
Sarcosine oxidase beta subunit/FAD dependent oxidoreductase 1.5.3.1 soxB RRC03939 NT05RC0550 CM
Aminomethyltransferase/Glycine cleavage system T protein 2.1.2.10 gcvT RRC03644 NT05RC1190 C
Methylmalonate-semialdehyde dehydrogenase (acylating) 1.2.1.27 mmsA RRC03635 NT05RC1631 C
Propanediol utilization protein, PduB pduB RRC01267 NT05RC2309
Tyrosine phenol-lyase/Beta-tyrosinase 4.1.99.2 tpl RRC01364 NT05RC2411 C
Sarcosine oxidase gamma subunit 1.5.3.1 soxG RRC01367 NT05RC2415
Sarcosine oxidase alpha subunit 1.5.3.1 soxA RRC01368 NT05RC2416 C
Sarcosine oxidase beta subunit 1.5.3.1 soxB RRC01370 NT05RC2418 C
Aminotransferase, DegT/DnrJ/EryC1/StrS family RRC00767 NT05RC2910
LMW-protein-tyrosine-phosphatase, PTPase/Small, acidic phosphotyrosine protein phosphatase (PYprotein phosphatase) 3.1.3.48 ptpA RRC00274 NT05RC3261
D-alanine aminotransferase (D-aspartateaminotransferase)/D-amino acid aminotransferase/D-amino acidtransaminase, Daat 2.6.1.21 daat RRC01700 NT05RC3299 C
Ornithine cyclodeaminase 4.3.1.12 arcB RRC05768 NT05RC3610 C

Anaerobic
Trimethylamine-N-oxide reductase 1, TMAO reductase 1 1.7.2.3 RRC05612 NT05RC2976 P

ATP-proton motive force interconversion
ATP synthase subunit I b chain 3.6.3.14 ATP_synt_b RRC04287 NT05RC0776 EC
ATP synthase F1 beta subunit, AtpD 3.6.1.34 atpD RRC00103 NT05RC3105 C
ATP synthase F1 alpha subunit, AtpA 3.6.1.34 atpA RRC00106 NT05RC3107 C
ATP synthase F1 delta subunit, AtpH 3.6.1.34 atpH RRC00107 NT05RC3108 C

Biosynthesis and degradation of polysaccharides
Anhydromuramoyl-peptide exo-beta-N-acetylglucosaminidase 3.2.1.- nagZ RRC01974 NT05RC0895 C
Periplasmic beta-glucosidase (Gentiobiase) (Cellobiase)/Beta-D-glucoside glucohydrolase 3.2.1.21 bglX RRC01186 NT05RC2528 P

Electron transport
Glutaryl-CoA dehydrogenase, Gcd 1.3.99.7 gcd RRC04664 NT05RC0023 C
Electron transfer flavoprotein alpha or large subunit (alpha-Etf or Etfls) alpha-etf RRC03239 NT05RC0149
Electron transfer flavoprotein beta or small subunit (beta-Etf or Etfss) beta-etf RRC03238 NT05RC0150
Oxidoreductase, FAD-binding/Homologous to D-amino acid dehydrogenase/Glycine oxidase family RRC02945 NT05RC0400
Electron transfer flavoprotein-ubiquinone oxidoreductase. EFT-Qo (Electron-transferring-flavoprotein dehydrogenase) 1.5.5.1 EFT-Qo RRC03955 NT05RC0533
Sulfide-quinone reductase, Sqr 1.8.5.- sqr RRC04245 NT05RC0820 CM, P
Cytochrome c oxidase, cbb3-type, subunit I 1.9.3.1 ccoN RRC04162 NT05RC1206 CM
Cytochrome c oxidase, cbb3-type, subunit II monoheme subunit 1.9.3.1 ccoO RRC04163 NT05RC1207 CM
Cytochrome c oxidase, cbb3-type, subunit III, diheme subunit 1.9.3.1 ccoP RRC04165 NT05RC1209 CM
Cytochrome c2 cycA RRC02712 NT05RC1293 P
NADH-quinone oxidoreductase chain D 1.6.5.3 nuoD RRC02454 NT05RC1585 C
NADH-quinone oxidoreductase chain E 1.6.5.3 nuoE RRC02455 NT05RC1586 CM
Acyl-CoA dehydrogenase family member 8, Acad-8/Isobutyryl-coa dehydrogenase/activator-recruited cofactor 42 kDa component, Arc42 1.3.99.2 RRC02499 NT05RC1630 C
Ferredoxin-NADP reductase 1.18.1.2 fpr RRC03609 NT05RC1659 C
N-ethylmaleimide reductase/Xenobiotic reductase, XenB 1.7.1.- xenB RRC03600 NT05RC1668
Cytochrome c551 peroxidase/cytochrome c peroxidase, Ccp 1.11.1.5 ccpA RRC03475 NT05RC1798 P
Thiol-disulfide Isomerase/Thioredoxin, redoxin domain protein RRC02397 NT05RC1909
Cytochrome P450 like protein RRC01166 NT05RC2544 C
Cytochrome c-type cyt cy cycY RRC00961 NT05RC2616 CM, P
Ubiquinol-cytochrome c reductase iron-sulfur subunit, PetA 1.10.2.2 petA RRC00780 NT05RC2896 CM
Ubiquinol-cytochrome c reductase cytochrome b subunit, PetB 1.10.2.2 petB RRC00781 NT05RC2897 CM
Ubiquinol-cytochrome c reductase Cytochrome c1 subunit, PetC 1.10.2.2 petC RRC00779 NT05RC2898 CM
Ferredoxin I, FdI fd1 RRC00758 NT05RC2920 C
Cytochrome c-type biogenesis protein CcmH (Ccl2) ccl2/ccmH RRC00287 NT05RC3273 CM, P
Cytochrome P450 family protein 1.14.15.3 RRC00405 NT05RC3394 C
Sulfide dehydrogenase (flavocytochrome c)/FAD-dependent pyridine nucleotide-disulphide oxidoreductase 1.8.2.- fccB RRC00443 NT05RC3435 EC

Fermentation
Phosphate acetyltransferase/Phosphate butyryltransferase 2.3.1.8/2.3.1.19 pta RC01951 NT05RC0870 C

Glycolysis/gluconeogenesis
Phosphoenolpyruvate-protein phosphotransferase, PtsP 2.7.3.9 ptsP RRC02985 NT05RC0440 C
Triosephosphate isomerase 5.3.1.1 tpiA RRC03602 NT05RC1666 C
Fructose-bisphosphate aldolase type I 4.1.2.13 fba RRC03492 NT05RC1781 C
Phosphoglycerate kinase 2.7.2.3 pgk RRC03491 NT05RC1782 C
Enolase/Phosphopyruvate hydratase 4.2.1.11 eno RRC03484 NT05RC1789 C
Fructose-bisphosphate aldolase, class II, Calvin cycle subtype 4.1.2.13 fba RRC02394 NT05RC1912 C
Glyceraldehyde 3-phosphate dehydrogenase B 1.2.1.12 gap RRC02393 NT05RC1913 C
Glyceraldehyde-3-phosphate dehydrogenase, type I Gap 1.2.1.12 gap RRC04329 NT05RC2258 C
Fructose-bisphosphate aldolase, putative aldolase, YneB 4.1.2.13 yneB RRC00008 NT05RC3011 CM
L-lactate dehydrogenase (FMN-linked) [cytochrome]/(S)-2-hydroxy-acid oxidase 1.1.2.3/1.1.3.15 lldD RRC00194 NT05RC3180

Pentose phosphate pathway
Ribose 5-phosphate isomerase A 5.3.1.6 rpiA RRC01215 NT05RC2502 C
Ribulose-phosphate 3-epimerase/Pentose-5-phosphate 3-epimerase 5.1.3.1 rpe RRC00013 NT05RC3016 CM
Fructose-1,6-bisphosphatase, class II GlpX 3.1.3.11 glpX RRC00208 NT05RC3195 CM
Transaldolase, putative 2.2.1.2 RRC00360 NT05RC3349 C

Photosynthesis
Light-harvesting protein B-870, alpha chain pufA RRC02820 NT05RC0721 P
Light-harvesting protein B-800/850, alpha chain pucA RRC02342 NT05RC2651 P
Light-harvesting protein B-800/850, gamma chain pucE RRC00994 NT05RC2653 CM
Photosynthetic reaction center H subunit puhA RRC02853 NT05RC0688 CM
Photosynthetic reaction center L subunit pufL RRC02819 NT05RC0722 CM
Photosynthetic reaction center M subunit pufM RRC02818 NT05RC0723 CM

Sugars
Xylose Isomerase 5.3.1.5 xylA RRC00720 NT05RC0014 C
Xylulose kinase 2.7.1.17 xylB RRC00721 NT05RC0015 C
Nucleoside-diphosphate-sugar epimerase RRC03125 NT05RC0264 CM
Phosphoglycolate phosphatase, Gph 3.1.3.18 gph RRC02398 NT05RC1908
Phosphoribulokinase 1 2.7.1.19 cbbP RRC02391 NT05RC1915 C
Ribulose bisphosphate carboxylase large chain 2 4.1.1.39 rbcL RRC02395 NT05RC1911 C
Phosphoglucomutase/Glucose phosphomutase, Pgm 5.4.2.2 pgm RRC02387 NT05RC1919 C

TCA cycle
Malate dehydrogenase, NAD-dependent 1.1.1.37 mdh RRC02795 NT05RC0747 C
Succinyl-CoA synthetase beta chain 6.2.1.5 sucC RRC02793 NT05RC0750 C
Succinyl-CoA synthetase alpha chain 6.2.1.5 sucD RRC02792 NT05RC0751 C
Isocitrate dehydrogenase, NADP-dependent 1.1.1.42 idh2 RRC01533 NT05RC1971 C
Aconitate hydratase 4.2.1.3 acnA RRC04337 NT05RC2248 C

FATTY ACID AND PHOSPHOLIPID METABOLISM
Biosynthesis
CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase 2.7.8.5 pgsA RRC02959 NT05RC0413 CM
MaoC domain protein dehydratase maoC RRC02782 NT05RC0761 C
Dehydrogenase with MaoC-like domain RRC02783 NT05RC0761 C
Putative phosphatidylserine decarboxylase homolog 4.1.1.65 psd RRC04174 NT05RC0957 CM
Acyl-CoA thioesterase I precurser/Lipolytic enzyme, G-D-S-L family 3.1.2- acot1 RRC04139 NT05RC1226 P
Malonyl-CoA-[acyl-carrier-protein] transacylase, FabD 2.3.1.39 fabD RRC03525 NT05RC1749
3-Oxoacyl-[acyl-carrier protein] synthase, FabF 2.3.1.179 fabF RRC03521 NT05RC1754 C
Enoyl-[acyl-carrier protein] reductase (NADH) 1.3.1.9 fab1 RRC01406 NT05RC2453 C
3-Oxoacyl-(acyl-carrier protein) reductase/Short-chain dehydrogenase/reductase, SDR 1.1.1.100 fabG RRC01189 NT05RC2525 C
Enoyl-[acyl-carrier-protein] reductase [NADH] (NADH-dependent enoyl-ACP reductase) 1.3.1.9 RRC05546 NT05RC2794 C
3-oxoacyl-[acyl-carrier-protein] synthase II, FabF fabF RRC01138 NT05RC2795 C
Beta-hydroxyacyl-(acyl-carrier-protein) dehydratase, FabA 4.2.1.60 fabA RRC01139 NT05RC2796 C
3-Hydroxyacyl-Coa dehydrogenase type-2, type II HADH/3-Hydroxy-2-methylbutyryl-Coa Dehydrogenase 1.1.1.35 hadh RRC00129 NT05RC3126 C

Degradation
Succinyl-CoA:3-ketoacid-coenzyme A transferase subunit b, Oxct b 2.8.3.5 scoB RRC00248 NT05RC3237 C

Other
Acetyl-CoA acetyltransferase/Acetoacetyl-CoA thiolase 2.3.1.9 Acat RRC00329 NT05RC3317 C

PROTEIN FATE
Degradation of proteins, peptides, and glycopeptides
Secreted protease C precursor 3.4.24.- RRC03223 NT05RC0167 EC
Peptidase T, PepT 3.4.11.- pepT -- NT05RC0370 C
Peptidase, M20/M25/M40 family 3.5.1.14 RRC04401 NT05RC1505 C
N-acyl-L-amino acid amidohydrolase/Hippuricase 3.5.1.14 RRC02444 NT05RC1861 C
ATP-dependent protease La/ATP-dependent endopeptidase, Lon 3.4.21.53 RRC01049 NT05RC2706 C
Leucyl/phenylalanyl-tRNA-protein transferase 2.3.2.- aat RRC01073 NT05RC2731 CM
ATP-dependent endopeptidase clp proteolytic subunit, ClpP 3.4.21.92 clpP RRC01078 NT05RC2735 CM
Oligoendopeptidase F, putative 3.4.24.- pepF RRC00748 NT05RC2930 C

Protein and peptide secretion and trafficking
Protein-export chaperone, SecB secB RRC00736 NT05RC0029 C
Protein secretion ABC efflux permease and ATP-binding protein/Type I secretion processing peptidase RRC03199 NT05RC0194 CM
Preprotein translocase, SecA subunit secA RRC03160 NT05RC0231 C
Peptidase M16 domain protein/Zinc protease 3.4.99.- RRC03108 NT05RC0280 CM
Peptidase M16 domain protein/Insulinase family Zinc protease 3.4.99.- RRC03107 NT05RC0281 EC
60 kDa inner membrane insertion protein, YidC yidC RRC03045 NT05RC0360 CM
General secretion pathway protein D/Type II and III secretion system protein gspD RRC03968 NT05RC0522 OM
SecY stabilizing Integral membrane protein secY RRC01986 NT05RC0911 CM
Hemin import ATP-binding protein, HmuV/Transporter hmuV RRC04502 NT05RC1071 C, CM
Preprotein translocase, YajC subunit yajC RRC02443 NT05RC1862 CM
Survival protein, SurA/PpiC-type peptidyl-prolyl cis-trans isomerase 5.2.1.8 surA -- NT05RC2819 EC
Microcin-processing peptidase 2 protein, TldD tldD RRC00243 NT05RC3232 M
Tol system periplasmic component, YbgF/tetratricopeptide TPR_2 ybgF RRC05669 NT05RC3333 EC
Outer membrane lipoprotein carrier protein, LolA lolA RRC00485 NT05RC3469 EC
Type I secretion adaptor protein (HlyD family)/RTX secretion protein D type_I_hlyD RRC05697 NT05RC3537 C, CM

Protein folding and stabilization
PpiC-type peptidyl-prolyl cis-trans isomerase 5.2.1.8 -- NT05RC0230 OM
Chaperone protein, DnaK dnaK RRC03154 NT05RC0235 C
Thiol:disulfide interchange protein DsbA (DsbA oxidoreductase) dsbA RRC03149 NT05RC0240 EC
Peptidyl-prolyl cis-trans isomerase, cyclophilin type RRC03490 NT05RC1783 P
Peptidyl-prolyl cis-trans isomerase, PPIase/Rotamase/Cyclophilin/Cyclosporin A-bindingprotein, CYP B 5.2.1.8 cypB RRC03489 NT05RC1784 CM
Outer membrane protein thiol:disulfide interchange protein DsbA-like dsbA RRC03455 NT05RC1820 EC
Trigger Factor, PPIase, Tig 5.2.1.8 tig RRC00692 NT05RC2098 C
Putative peptidyl-prolyl cis-trans isomerase 5.2.1.8 RRC01410 NT05RC2457
Endopeptidase, DegP/Periplasmic serine protease 3.4.21.- degP RRC01208 NT05RC2508 P
10 kDa chaperonin, GroES groS RRC00934 NT05RC2591 C
60 kDa chaperonin, GroEL groL RRC00935 NT05RC2592 C
ATP-dependent chaperone, ClpB clpB RRC05711 NT05RC3551 C
Co-chaperone, GrpE grpE RRC05796 NT05RC3642 C

Protein modification and repair
Carboxyl-processing protease (Tail specific protease) 3.4.21.102 RRC03302 NT05RC0077 CM
Universal stress family protein uspA RRC02802 NT05RC0740 C
Universal stress protein UspA and related nucleotide-binding domain protein uspA RRC04161 NT05RC1205 C
Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase RRC01014 NT05RC2673
Leucyl aminopeptidase 3.4.11.1 pepA RRC04532 NT05RC2823 C
Protein-L-isoaspartate o-methyltransferase 2.1.1.77 Pcmt1 RRC00264 NT05RC3250 C

Other
Von Willebrand factor type A domain protein/CBBO RRC03776 NT05RC0600 C

PROTEIN SYNTHESIS
Ribosomal proteins: synthesis and modification
LSU ribosomal protein, L12 (L7/L12) rplL RRC03083 NT05RC0305 C
SSU ribosomal protein, S3 rpsC RRC03069 NT05RC0320 C
LSU ribosomal protein, L14 rplN RRC03064 NT05RC0325 C
LSU ribosomal protein, L6 rpl6P RRC03059 NT05RC0330 C
SSU ribosomal protein, S5 rpsE RRC03057 NT05RC0332 C
SSU ribosomal protein, S13 rpsM RRC03051 NT05RC0339 C
SSU ribosomal protein, S11 rpsK RRC03050 NT05RC0340 C
LSU ribosomal protein, L19 (or L31) rpmE RRC03026 NT05RC0377 C
SSU ribosomal protein, S1 rpsA RRC01790 NT05RC1173 C
SSU ribosomal protein, S2 rpsB RRC02403 NT05RC1903 C
LSU ribosomal protein, L9 rplI RRC00691 NT05RC2101 C

Translation factors
Translation elongation factor Tu tuf RRC03808 NT05RC0153 C
Protein translation elongation factor G (EF-G) fusA RRC02509 NT05RC0311 C
Protein translation elongation factor Tu (EF-TU) tuf RRC03235 NT05RC0312 C
Protein translation elongation factor Tu (EF-TU) tuf RRC03808 NT05RC0312 C
Translation Elongation and release factor G (GTPase) GTPase RRC04353 NT05RC1559 C
Peptide chain release factor 2, RF-2 prfB RRC02481 NT05RC1613 C
Protein translation elongation factor Ts (EF-Ts) tsf RRC02402 NT05RC1904 C
Bacterial peptide chain release factor 3 (RF-3), PrfC prfC RRC06068 NT05RC2425 C

tRNA and rRNA base modification
Aspartyl/glutamyl-tRNA amidotransferase subunit A 6.3.5.- gatA RRC00798 NT05RC2879 CM
Aspartyl/glutamyl-tRNA amidotransferase subunit B (Asp/Glu-ADT subunit B) 6.3.5.- gatB RRC01959 NT05RC0880 C
D-Tyrosyl-tRNA deacylase, Dtd 3.1.-.- dtd RRC00975 NT05RC2630 C

tRNA aminoacylation
Tryptophanyl-tRNA synthetase 6.1.1.2 trpS RRC04002 NT05RC0490 C
Aspartyl-tRNA synthetase 6.1.1.12 aspS RRC03937 NT05RC0553 C
Seryl-tRNA synthetase 6.1.1.11 serS RRC04397 NT05RC1510 C, CM
Prolyl-tRNA synthetase proRS -- NT05RC2575 C
Phenylalanyl-tRNA synthetase, beta subunit 6.1.1.20 pheT RRC06104 NT05RC3289 C

PURINES, PYRIMIDINES, NUCLEOSIDES, AND NUCLEOTIDES
Nucleotide and nucleoside interconversions
Adenylate kinase (ATP-AMP transphosphorylase)/Nucleoside-diphosphate kinase 2.7.4.3/2.7.4.6 adk RRC03052 NT05RC0338 C
Nucleoside diphosphate kinase, Ndk/NDP kinase/Nucleoside-2-P kinase 2.7.4.6 ndk RRC03479 NT05RC1794 C

Purine ribonucleotide biosynthesis
GMP synthase [glutamine-hydrolyzing] 6.3.5.2 guaA RRC00895 NT05RC1941 C
Formyltetrahydrofolate deformylase 3.5.1.10 purU RRC01205 NT05RC2511

Pyrimidine ribonucleotide biosynthesis
Carbamoyl-phosphate synthase, large subunit 6.3.5.5 carB RRC03938 NT05RC0552 CM, P
Orotate phosphoribosyltransferase 2.4.2.10 pyrE RRC03625 NT05RC1642 C
Dihydropyrimidine dehydrogenase [NADP+] beta subunit/dihydroorotate dehydrogenase family protein 1.3.1.2 DPYD RRC00991 NT05RC2646 C

Salvage of nucleosides and nucleotides
Adenine phosphoribosyltransferase, Apt 2.4.2.7 apt RRC01698 NT05RC3227 C
Purine nucleotide phosphorylase 2.4.2.1 RRC00387 NT05RC3376 C

2′-Deoxyribonucleotide metabolism
Pyrimidine-specific ribonucleoside hydrolase, RihA/Cytidine/uridine-specific hydrolase 3.2.-.- rihA RRC03481 NT05RC1792 C

Other
Nucleoside-binding protein/Bmp family protein RRC04244 NT05RC0821 EC
Xanthine dehydrogenase, small subunit 1.17.1.4 xdhA RRC04239 NT05RC0827 C

REGULATORY FUNCTIONS
DNA interactions
Transcriptional regulator, LuxR family luxR RRC03806 NT05RC0343 C
Cell cycle transcriptional regulator, CtrA/Response regulator SokA ctrA RRC03536 NT05RC1736 C
Transcriptional regulatory protein BaeR, Alkaline phosphatase synthesis baeR RRC00026 NT05RC3031 C

Protein interactions
Regulatory protein, SenC(PrrC) senC/prrC/sco1 RRC03336 NT05RC0044 CM
Phosphohistidine phosphatase, SixA/Phosphoglycerate mutase family protein 3.1.3.- sixA RRC04024 NT05RC0354
Protease activity modulator hflK RRC01212 NT05RC2505

Small molecule interactions
Diguanylate cyclase/phosphodiesterase with PAS/PAC and GAF sensor 2.7.7.65 RRC00149 NT05RC3141 C

Two-component systems
Two component response regulator (winged helix family) -- NT05RC0276 C

Other
Response regulator/ggdef domain protein RRC06082 NT05RC2762
Phosphate transport system regulatory protein, PhoU phoU RRC05801 NT05RC3647 C

SIGNAL TRANSDUCTION
Two-component systems
Methyl-accepting chemotaxis sensory transducer, McpA mcpA RRC04620 NT05RC1409 CM
Sensory transduction histidine protein kinase 2.7.3.- RRC05028 NT05RC1570 CM
Methyl-accepting chemotaxis protein, McpC mcpC RRC03579 NT05RC1694 CM
Sensory transduction protein kinase 2.7.3.- RRC01105 NT05RC2760
Two-component response sensory transduction histidine kinase, potential phosphate regulatory protein RRC06094 NT05RC2997 C
Two component system integral membrane signal transduction histidine kinase 2.7.3.- RRC00027 NT05RC3032 CM

TRANSCRIPTION
Degradation of RNA
Polyribonucleotide nucleotidyltransferase/Polynucleotidephosphorylase, PNPase 2.7.7.8 RRC03090 NT05RC0297 C
Ribonuclease E, RNase E 3.1.4.- RNaseEG RRC05484 NT05RC2263 C
Translation initiation inhibitor/Endoribonuclease L-PSP RRC05722 NT05RC3562 CM

DNA-dependent RNA polymerase
DNA-directed RNA polymerase beta subunit 2.7.7.6 rpoB RRC03082 NT05RC0306 C
DNA-directed RNA polymerase beta’ subunit 2.7.7.6 rpoC RRC03080 NT05RC0307 C
DNA-directed RNA polymerase, alpha subunit 2.7.7.6 rpoA RRC03049 NT05RC0341 C

Transcription factors
Sigma 54 modulation protein/ribosomal protein S30EA or factor Y rpoX RRC03265 NT05RC0121 C
Transcription elongation factor, GreA greA RRC03954 NT05RC0534 C
Transcriptional regulator, LysR family lysR RRC03919 NT05RC0572 C
Transcription elongation factor, NusA/N utilization substance protein A nusA RRC03167 NT05RC224 C

Other
Putative AraC family transcriptional regulator RRC04375 NT05RC1537 CM

TRANSPORT AND BINDING PROTEINS
Amino acids, peptides and amines
Transporter/import inner membrane translocase, subunit Tim44 homolog Sec? RRC00738 NT05RC0031 CM
Oligopeptide-binding protein, OppA/Extracellular solute-binding protein, family 5 oppA RRC03230 NT05RC0161 P
Glutamate/glutamine/aspartate/asparagine-binding protein, BztA bztA RRC03799 NT05RC0350 P
Glutamine-binding protein/Extracellular solute-binding protein, family 3 RRC04018 NT05RC0474 P
Type II secretion system protein E RRC03965 NT05RC0525 CM, P
Putative lysine-arginine-ornithine or histidine binding periplasmic protein RRC02872 NT05RC0650 P
Oligopeptide-binding Protein OppA/Extracellular solute-binding protein family oppA RRC02807 NT05RC0735 CM, P
Dipeptide-binding protein/Extracellular solute-binding protein, family RRC01964 NT05RC0885 P
Dipeptide transport ATP-binding protein, DppD/Oligopeptide transport ATP-binding protein, OppD oppD RRC01967 NT05RC0888 C, CM
Glycine betaine/L-proline transport system binding protein, ProX proX RRC02010 NT05RC0936
Spermidine/putrescine ABC transporter ATP-binding subunit RRC02709 NT05RC1297 C, CM
Putative polyamine ABC transporter, periplasmic polyamine-binding protein RRC02708 NT05RC1298 EC
Polyamine ABC transporter, permease protein RRC02707 NT05RC1299 CM
Probable phosphatidylinositol-4-phosphate-5-kinase RRC04081 NT05RC1419 EC
ABC Polyamine/Opine/Phosphonate transporter, periplasmic ligand binding protein RRC04469 NT05RC1423 EC
ABC transporter ATP-binding protein/Methionine import ATP-binding protein, MetN metN RRC03629 NT05RC1638 CM
Leucine-, Isoleucine-, Valine-, Threonine and Alanine-binding Protein/Extracellular ligand-binding receptor braC RRC00901 NT05RC1935 P
Putrescine transport ATP-binding protein, PotG potG RRC01528 NT05RC1977 C
Putrescine transport system permease protein, PotI potI RRC01527 NT05RC1978 CM
Spermidine/putrescine transport system permease protein, PotB/Binding-protein-dependent inner membrane transport component potB RRC01526 NT05RC1979 CM
Spermidine/putrescine-binding protein/Extracellular solute-binding protein, family 1 RRC01245 NT05RC2286 P
Taurine ABC transporter, periplasmic taurine-binding protein RRC01299 NT05RC2343 EC
Spermidine/Putrescine-binding periplasmic protein RRC01326 NT05RC2370 P
Oligopeptide-binding protein, OppA oppA RRC01333 NT05RC2377 P
Branched-chain amino acid ABC transporter, ATP-binding protein, LivF livF RRC01157 NT05RC2553 C, CM
His/Glu/Gln/Arg/opine family ABC transporter/Periplasmic His/Glu/Gln/Arg/opine family-binding protein RRC00775 NT05RC2902 P
Spermidine/putrescine-binding protein, ABC polyamine transporter, periplasmic substrate-binding protein RRC00091 NT05RC3093 P
Branched-chain amino acid aminotransferase 2.6.1.42 RRC00377 NT05RC3367 C
ABC transporter, Cyd cysteine exporter family permease/ATP-binding protein, CydC cydC RRC00404 NT05RC3393 CM
ABC branched amino acid transporter family, periplasmic substrate-binding subunit RRC05738 NT05RC3577 EC
ABC branched amino acid transporter family, ATPase subunit RRC05739 NT05RC3578 C, CM

Anions
Molybdate ABC transporter, periplasmic molybdate-binding protein modA RRC03762 NT05RC0585 P
Molybdate ABC transporter, ATP-binding protein, ModC modC RRC03907 NT05RC0587 C, CM
Thiosulfate-binding protein -- NT05RC2870 P
Membrane protein MosC, major facilitator superfamily MFS_1 mosC RRC00195 NT05RC3181 CM
Phosphate transport ATP-binding protein, PstB pstB RRC05802 NT05RC3648 C, CM
Phosphate ABC transporter, permease protein, PstA pstA RRC05803 NT05RC3649 CM
ABC phosphate transporter, inner membrane subunit, PstC pstC RRC03394 NT05RC3650 CM
Phosphate-Binding Periplasmic Protein RRC03395 NT05RC3651 P

Carbohydrates, organic alcohols, and acids
D-xylose ABC transporter, D-xylose-binding protein xylF RRC00724 NT05RC0018 P
Mannitol-binding protein/Trap dicarboxylate transporter, Dctp subunit RRC04462 NT05RC1431 EC
Alpha-glucoside-binding protein/ABC alpha-glucoside transporter, periplasmic substrate-binding protein algE RRC03427 NT05RC1851 EC
Alpha-glucoside transport ATP-binding protein, AglK algK RRC03422 NT05RC1855 C, CM
Fructose binding periplasmic protein, FrcB frcB -- NT05RC2111 P
Sorbitol-binding protein/Potential maltose-binding protein RRC00677 NT05RC2114 EC
ABC sugar transporter, periplasmic binding protein/D-Galactose-binding/Ribitol-binding protein RRC02337 NT05RC2476 P
Mannitol-binding protein RRC01191 NT05RC2524 EC
Ribose ABC transporter, D-ribose-binding protein RRC01127 NT05RC2784 P
Ribose transport ATP-binding protein RbsA/ABC transporter, carbohydrate uptake transporter-2 (CUT2) family rbsA RRC01129 NT05RC2786 C, CM
C4-dicarboxylate-binding periplasmic protein RRC00169 NT05RC3156 P

Cations and iron carrying compounds
Manganese transport protein, MntH mntH RRC03871 NT05RC0626 CM
Iron (III) Dicitrate-binding periplasmic protein fecB RRC04484 NT05RC1088 EC
Outer membrane siderophore receptor/TonB-dependent siderophore receptorR fiu RRC04402 NT05RC1504 OM
Sensor protein, KdpD 2.7.3.- kdpD RRC01313 NT05RC2357 CM
Transporter/TrkA-C domain protein -- NT05RC2388 CM
TonB-system energizer ExbB/TolQ protein exbB RRC01434 NT05RC2479 CM
2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase/short-chain dehydrogenase/reductase, SDR 1.3.1.28 entA RRC01183 NT05RC2531 C
25 kD Outer-membrane immunogenic protein/Rhizobiocin, RzcA rzcA RRC01603 NT05RC2572 OM
Iron-regulated protein, FrpC frpC RRC01604 NT05RC2573 EC
Iron-regulated protein FrpC/poly(beta-D-mannuronate) C5 epimerase 3 (Mannuronanepimerase 3) frpC RRC00309 NT05RC3297 EC

Porins
Porin RRC03116 NT05RC0272 OM

Other
Putative membrane protein RRC03140 NT05RC0250 CM
Acetyltransferase/MobC protein 2.3.1.- mobC RRC02973 NT05RC0428
Acriflavin resistance plasma membrane protein B acrB RRC02995 NT05RC0450 CM
Acriflavin resistance periplasmic protein RRC02881 NT05RC0641 P
Periplasmic component of efflux system/HlyD family protein RRC02879 NT05RC0643 CM, P
ABC transporter, substrate-binding protein, aliphatic sulphonates/Taurine-Binding Periplasmic Protein RRC06012 NT05RC1459 EC
ABC transporter ATP-binding protein RRC04420 NT05RC1484 CM
Transporter RRC04392 NT05RC1517
ABC transporter, fused ATPase and inner membrane subunit RRC01360 NT05RC2407 CM
Putative transport protein, YidE/Integral membrane protein with TrkA domains yidE RRC01177 NT05RC2535 CM
Oligopeptide-binding protein/extracellular solute-binding protein, family 5 RRC00960 NT05RC2615 EC
ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic component, TauA tauA RRC00984 NT05RC2639 EC
Iron(III)-binding periplasmic protein RRC01044 NT05RC2700 P
Thiamin/thiamin pyrophosphate ABC transporter, thiamin/thiamin pyrophospate-binding protein, ThiB thiB RRC01667 NT05RC2825 P
Acriflavin resistance protein E/Efflux transporter, RND family, MFP subunit RRC00805 NT05RC2872 CM, P
Acriflavin resistance plasma membrane protein RRC00803 NT05RC2873 CM
TolB protein tolB RRC00346 NT05RC3335 P
ABC transporter, periplasmic substrate-binding protein RRC00383 NT05RC3372 P

UNCLASSIFIED
Role category not yet assigned
Myo-inositol-1(or 4)-monophosphatase (I-1-Pase) 3.1.3.25 RRC03984 NT05RC0507 C
Myo-inositol-1(or 4)-monophosphatase family protein 3.1.3.25 RRC01989 NT05RC0915
Lipoprotein, putative RRC01112 NT05RC2767 EC
Inositol monophosphatase/ADP-ribosylglycohydrolase, CysQ Protein 3.1.3.25 RRC00266 NT05RC3253

UNKNOWN FUNCTION
General
Filament-A precursor (Peptidase M23B) filA RRC03301 NT05RC0078 C, CM
Putative iojap protein family homolog RRC03298 NT05RC0081 C
Pentapeptide repeat family protein RRC04445 NT05RC1451 EC
Outer membrane protein E/Membrane protein involved in aromatic hydrocarbon degradation RRC01502 NT05RC2007 OM

HYPOTHETICAL PROTEINS
Conserved Domain proteins
ErfK/YbiS/YcfS/YnhG family protein RRC02993 NT05RC0448
Conserved hypothetical protein RRC03927 NT05RC0563
Conserved hypothetical protein RRC03926 NT05RC0564
Conserved hypothetical membrane spanning protein RRC02854 NT05RC0687 CM
Conserved hypothetical protein RRC02456 NT05RC1587
Hypothetical cytosolic protein of unknown function RRC02483 NT05RC1615 C
Hypothetical protein/GfdT protein RRC03541 NT05RC1732 C
Conserved hypothetical membrane associated protein RRC03520 NT05RC1755 C, CM
Hypothetical Membrane Associated Protein/Invasion associated family protein RRC00884 NT05RC1952 EC
Hypothetical protein RRC01494 NT05RC2016
Conserved hypothetical cytosolic protein RRC00597 NT05RC2240 C
Hypothetical Exported Protein RRC01358 NT05RC2405 EC
Hypothetical membrane associated protein/pyrrolo-quinoline quinone RRC01359 NT05RC2406 CM
Hypothetical protein -- NT05RC2634
Hypothetical protein/lipoprotein, putative RRC01128 NT05RC2785
Hypothetical membrane spanning protein of unknown function RRC06091 NT05RC2994 CM
Conserved hypothetical protein RRC06095 NT05RC3026
Conserved hypothetical protein, Phage Minor Tail Protein RRC02354 NT05RC3046 CM
Hypothetical protein RRC05643 NT05RC3064 C
Hypothetical cytosolic protein, prophage Lp2 protein RRC00072 NT05RC3071 CM
Conserved hypothetical protein -- NT05RC3075
Conserved hypothetical Protein RRC00313 NT05RC3301 C
Conserved hypothetical protein/Permease RRC00389 NT05RC3378 EC
Conserved hypothetical protein RRC00393 NT05RC3382 EC
Conserved hypothetical cytosolic protein RRC00413 NT05RC3402 C
Conserved hypothetical Exported Protein RRC01759 NT05RC3524 CM, P
Conserved hypothetical protein RRC03402 NT05RC3658 P

Conserved Hypothetical proteins
Conserved hypothetical (transglutaminase-like) protein RRC03327 NT05RC0053
Conserved hypothetical cytosolic protein RRC03249 NT05RC0139 C
Conserved hypothetical protein/Glucose-1-phosphate adenyltransferase 2.7.7.27 -- NT05RC0925
OmpA family hypothetical protein RRC03674 NT05RC0952 EC
Conserved hypothetical protein/Aminomethyltransferase 2.1.2.10 RRC03662 NT05RC0993 C
Conserved hypothetical protein RRC01788 NT05RC1175
Hypothetical Cytosolic Protein RRC03645 NT05RC1186
Hypothetical protein RRC02694 NT05RC1315
Conserved hypothetical protein RRC02685 NT05RC1327
Conserved hypothetical protein RRC06004 NT05RC1351 EC
Outer membrane protein/Inner membrane lipoprotein YiaD yiaD RRC00951 NT05RC2605 OM
Hypothetical Membrane Spanning Protein RRC01102 NT05RC2757 CM
Conserved hypothetical Exported Protein (Mucoidy inhibitor A) RRC01654 NT05RC2839 EC
Conserved hypothetical Exported Protein RRC03610 NT05RC2917 CM, P
GTP-binding protein/conserved hypothetical protein RRC00370 NT05RC3360 C

graphic file with name nihms255082u1.jpg

Figure 1.

Figure 1

Representative 1D- and 2D-gel analyses of R. capsulatus protein samples. A. Periplasmic fraction proteins of R. capsulatus were separated by 2D-GE, with pH 4–7 IPG and SDS–PAGE, as first and second dimensions. B. Chromatophore membranes of R. capsulatus were separated on 1D-GE using SDS PAGE. In both cases, protein samples were prepared as described in Materials and Methods, gels were stained with colloidal coomassie blue and protein spots or bands were excised and trypsin digested for identification by nano-LC-MS/MS.

Acknowledgments

This work is supported by grants from DOE ER9120053 and NIH GM38237 to F.D.

References

  1. Myllykallio H, Jenney FE Jr, Jr, Moomaw CR, et al. Cytochrome c(y) of Rhodobacter capsulatus is attached to the cytoplasmic membrane by an uncleaved signal sequence-like anchor. J Bacteriol. 1997;179:2623–2631. doi: 10.1128/jb.179.8.2623-2631.1997. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Ren Q, Thony-Meyer L. Physical interaction of CcmC with heme and the heme chaperone CcmE during cytochrome c maturation. J Biol Chem. 2001;276:32591–32596. doi: 10.1074/jbc.M103058200. [DOI] [PubMed] [Google Scholar]
  3. Onder O, Yoon H, Naumann B, et al. Modifications of the lipoamide-containing mitochondrial subproteome in a yeast mutant defective in cysteine desulfurase. Mol Cell Proteomics. 2006;5:1426–1436. doi: 10.1074/mcp.M600099-MCP200. [DOI] [PubMed] [Google Scholar]
  4. Onder O, Turkarslan S, Sun D, et al. Overproduction or absence of the periplasmic protease DegP severly compromises bacterial growth in the absence of the dithiol:disulfide oxidoreductase DsbA. Mol Cell Proteomics. 2008;7:875–890. doi: 10.1074/mcp.M700433-MCP200. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Neuhoff V, Stamm R, Pardowitz I, et al. Essential problems in quantification of proteins following colloidal staining with coomassie brilliant blue dyes in polyacrylamide gels, and their solution. Electrophoresis. 1990;11:101–117. doi: 10.1002/elps.1150110202. [DOI] [PubMed] [Google Scholar]
  6. Bendtsen JD, Nielsen H, von Heijne G, et al. Improved prediction of signal peptides: SignalP 3.0. J Mol Biol. 2004;340:783–795. doi: 10.1016/j.jmb.2004.05.028. [DOI] [PubMed] [Google Scholar]
  7. Gardy JL, Laird MR, Chen F, et al. PSORTb v.2.0: expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis. Bioinformatics. 2005;21:617–623. doi: 10.1093/bioinformatics/bti057. [DOI] [PubMed] [Google Scholar]
  8. Zannoni D. Aerobic and anaerobic electron transport chains in anoxygenic phototrophic bacteria. In: Blankenship RE, Madigan MT, Bauer CE, editors. Anoxygenic photosynthetic bacteria. Kluwer Academic Publishers; Dordrecht, The Netherlands: 1995. pp. 949–971. [Google Scholar]
  9. Park SJ, Lee SY, Cho J, et al. Global physiological understanding and metabolic engineering of microorganisms based on omics studies. Appl Microb Biotechnol. 2005;68:567–79. doi: 10.1007/s00253-005-0081-z. [DOI] [PubMed] [Google Scholar]
  10. Wasinger V. Holistic biology of microorganisms: genomics, transcriptomics, andproteomics. Methods Biochem Anal. 2006;49:3–14. [PubMed] [Google Scholar]
  11. Daldal F, Cheng S, Applebaum J, et al. Cytochrome c(2) is not essential for photosynthetic growth of Rhodopseudomonas capsulata. Proc Natl Acad Sci U S A. 1986;83:2012–2016. doi: 10.1073/pnas.83.7.2012. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Hunter NC, Daldal F, Thurnauer MC, Beatty JT, editors. The Purple Phototrophic Bacteria. Springer; Dordrecht, The Netherlands: 2009. [Google Scholar]
  13. Du X, Callister SJ, Manes NP, et al. A computational strategy to analyze label-free temporal bottom-up proteomics data. J Proteome Res. 2008;7:2595–604. doi: 10.1021/pr0704837. [DOI] [PMC free article] [PubMed] [Google Scholar]

RESOURCES