Table 1.

Isolated and characterized Paracoccus loci

StrainGene clusterAccession no.Known functionsReference(s)
P. denitrificans71.11adkU64203ATP regeneration: adenylate kinase (adk)66
P. denitrificansPd1222ahemAU12508Cytochromec biosynthesis: 5-ALA synthase (hemA)214
P. denitrificansPd1222secF-hisH-ccmABCDG-ORF36-ORF117Z71971Cytochromec biosynthesis: secretory apparatus protein (secF), histidinol phosphate transaminase (hisH)215
P. denitrificansPd1222ccmF-ccmHAF023247Cytochrome cbiosynthesis216
P. denitrificans LMD 92.63bnarGHJIZ26255Z37158Denitrification: membrane-bound nitrate reductase α subunit (narG), β subunit (narH), γ subunit (narI)23
P. denitrificansPd1222nirISECFDU05002Denitrification: nitrite reductase transcriptional regulator (nirI), structural gene (nirS), S-adenosyl-l-methionine uroporphyrinogen methyltransferase (nirE), smallc-type cytochrome (nirC)59
P. denitrificans LMD 92.63bnirSEU75413Denitrification: nitrite reductase structural gene (nirS)5, 6
P. denitrificansPd1222nirIXAJ001308Denitrification: regulation ofnir gene expression307
P. denitrificans Pd1222norCBQDEFU28078Denitrification: nitric oxide reductase large subunit (norB), small subunit (norC)60
P. denitrificansNCIMB 8944nosRZDX74792Denitrification: nitrous oxide reductase transcriptional regulator (nosR), structural gene (nosZ)125
P. denitrificanscnosZAF016058Denitrification: nitrous oxide reductase structural gene (nosZ)255
P. denitrificansPd1222nnrU17435Denitrification: FNR-like transcriptional activator (nnr)309
P. denitrificans LMD 92.63bpazSZ73141Denitrification: pseudoazurin structural protein (pazS)168
P. denitrificansPd1222cycA-ctaDIIY07533Electron transport: cytochromec550 (cycA), iso-cytochromec oxidase subunit II (ctaDII)235
P. denitrificansPd1222cycA-ctaDIIM27304Electron transport: cytochromec550 (cycA), iso-cytochromec oxidase subunit II (ctaDII)315
P. versutus ATCC 25364ORF1-cycA-ctaDIIX62808S37058Electron transport: cytochrome c550 (cycA), iso-cytochrome c oxidase subunit II (ctaDII)296, 297
P. denitrificans Pd1235cycMX70367Electron transport: cytochrome c552(cycM)294
P. denitrificansPd1235qoxABCDX78196Electron transport: cytochromeba3 quinol oxidase subunit II (qoxA), subunit I (qoxB), subunit III (qoxC), subunit IV (qoxD)244
P. denitrificansATCC 13543fbcFBCM17522Electron transport: cytochromebc1 complex iron sulfur subunit (fbcF), cytochrome b subunit (fbcB), cytochrome c subunit (fbcC)162
P. denitrificansPd1222ctaDIX05829Electron transport: cytochrome oxidase subunit I (ctaDI)235
P. denitrificans PD 1235ctaCX05934Electron transport: cytochrome oxidase subunits II (ctaC)277
P. denitrificansPd1222ctaC-ctaB-ORF1-ctaG-ctaEX05828Electron transport: cytochrome oxidase subunits II (ctaC) and III (ctaE)234
P. denitrificansS1657cctaEX04406Electron transport: cytochrome oxidase subunit III (ctaE)251
P. denitrificansPd1222ctaHY08372Electron transport: cytochrome coxidase subunit IV (ctaH)325
P. denitrificanscphaABD49362Energy storage: acetoacetyl-CoA reductase (phaA), β-ketothiolase (phaB)336
P. denitrificanscphaCD43764Energy storage: poly (3-hydroxyalkanoate) synthase (phaC)298
P. denitrificansPd1222pta-ORF3-ORF4-ORF1-ORF2-ORF5U08864Insertion sequence IS1248: phosphate acetyltransferase (pta)311
P. denitrificansPd1222ORF3-ORF4-ORF1-ORF2-ORF5U08856Insertion sequence IS1248b312
P. denitrificansPd1222ORF1-ORF2-flhA-clpP-ORF3-fghA-xoxF-cycB-xoxJI-ORF4U34346C1metabolism: NAD-GSH-dependent formaldehyde dehydrogenase (flhA), S-formylglutathione hydrolase (fghA), PQQ-dependent dehydrogenase large subunit (xoxF), cytochrome c553i(cycB)116, 117, 237, 239, 240
P. denitrificansPd1222ORF1-flhS-ORF2-flhR-abcABC-pqqEAJ223460C1metabolism: transcriptional activator proteins (flhS,flhR), ABC transporter-type proteins (abcA,abcB, abcC), coenzyme PQQ synthesis protein E (pqqE)241
P. denitrificansPd1222mxaFM17339Methanol oxidation: methanol dehydrogenase large subunit (mxaF)114
P. denitrificans Pd1222mxaGIJM57684Methanol oxidation: cytochrome c551i (mxaG), methanol dehydrogenase β subunit (mxaI)314
P. denitrificansPd1222ORF1-cycB-ORF2M75583Methanol oxidation: cytochromec553i(cycB)239
P. denitrificansPd1222mxaZYXM92421Methanol oxidation: two-component regulatory proteins (mxaX,mxaY)118
P. denitrificansPd1222ORF1-mxaACKLD-ORF2-ORF3AJ000884Methanol oxidation242
P. versutus ATCC 25364mauB-ORF1L08575Methylamine oxidation: methylamine dehydrogenase α subunit (mauB)130
P. denitrificans Pd1222mauB-amiX55665Methylamine oxidation: methylamine dehydrogenase α subunit (mauB), amicyanin (ami)317
P. versutus ATCC 25364ORF1-mauB-amiM58001Methylamine oxidation: methylamine dehydrogenase α subunit (mauB), amicyanin (ami)172, 297
P. denitrificanscmauDAM90098Methylamine oxidation: methylamine dehydrogenase small subunits (mauA,mauD)49
P. denitrificanscmauFBEM90099Methylamine oxidation: methylamine dehydrogenase small subunits (mauF,mauB, mauE)48
P. denitrificans Pd1222ORF1-mauRFBU12464Methylamine oxidation: LysR-type transcriptional activator (mauR), methylamine dehydrogenase large subunit (mauB)313
P. denitrificansPd1222mauEDX98581Methylamine oxidation303, 304
P. versutus ATCC 25364mauEDL36951Methylamine oxidation130, 297
P. versutus ATCC 25364ORF5-mauFL36952Methylamine oxidation129
P. versutus ATCC 25364mauGL36953Methylamine oxidation130, 297
P. denitrificansPd1222mauJGMNU15028Methylamine oxidation: ferredoxin-like proteins (mauM, mauN), cytochrome cperoxidase-like protein (mauG)304
P. denitrificans NDH-1cnqo1M64432 ,J05331NADH dehydrogenase: 50-kDa subunit (nqo1)332
P. denitrificansNDH-1cnqo2M74171 , J05337NADH dehydrogenase: 25-kDa subunit (nqo2)331
P. denitrificansNDH-1cURF3-nqo3M84572NADH dehydrogenase: 66-kDa subunit (nqo3)334
P. denitrificansNDH-1cuvrA-nqo7-nqo6-nqo5-nqo4M93015NADH dehydrogenase: nd3 subunit (nqo7), ndhK subunit (nqo6), 25-kDa subunit (nqo5), 48-kDa subunit (nqo4); DNA repair protein (uvrA)333
P. denitrificansNDH-1cURF4-nqo8nqo9-URF5-URF6-nqo10-nqo11-nqo12-nqo14-birAL02354 ,L01096NADH dehydrogenase: subunit VIII (nqo8), subunit IX (nqo9), subunit X (nqo10), subunit XI (nqo11), subunit XII (nqo12), subunit XIV (nqo14); biotin (acetyl-CoA carboxylase) ligase (birA)335
P. denitrificansLMD 92.63bdctM-napEDABCZ36773Nitrate reduction: periplasmic nitrate reductase molybdenum-iron-sulfur-heme subunit (napA), diheme subunit (napB); Membrane transport: integral membrane subunit of a dicarboxylate transporter (dctM)24, 25, 35
P. versutusORF1-ORF2U42228Plasmid pTAV2039
P. versutusrepABCU60522Plasmid pTAV203: replication proteins8
Paracoccus sp. strain 164oriAF020624Plasmid pTM164: origin of replication266
P. denitrificans71.11csecYU64202Protein translocation: preprotein translocase (secY)228
P. denitrificansPd1222ORF1-fnrN-ORF278-ccoNOQPGHU34353Regulation of anaerobic growth: transcriptional regulator (fnrP)63
Electron transport: alternative oxidase cytochrome cbb3monoheme subunit (ccoN), diheme subunit (ccoQ)
P. denitrificanscrrfAX01501Ribosome assembly: 5S rRNA (rrfA)181
Paracoccus sp. strain Y4rrnAAB012914Ribosome assembly: 16S rRNA (rrnA)111
P. alcaliphilus JCM 7364rrnAD32238Ribosome assembly: 16S rRNA (rrnA)145
P. alkeniferrrnAY13827Ribosome assembly: 16S rRNA (rrnA)170
P. aminophilus JCM 7686rrnAD32239Ribosome assembly: 16S rRNA (rrnA)145
P. aminovorans JCM 7685rrnAD32240Ribosome assembly: 16S rRNA (rrnA)145
P. denitrificansIAM 12479rrnAD13480Ribosome assembly: 16S rRNA (rrnA)146, 147
P. denitrificans LMG 4218brrnAX69159Ribosome assembly: 16S rRNA (rrnA)178
P. kocurii JCM 7684rrnAD32241Ribosome assembly: 16S rRNA (rrnA)145
P. marcusiirrnAY12703Ribosome assembly: 16S rRNA (rrnA)112
P. solventivoransDSM 6637rrnAY07705Ribosome assembly: 16S rRNA (rrnA)264
P. solventivoransrrnAY13826Ribosome assembly: 16S rRNA (rrnA)170
P. thiocyanatusTHIO11rrnAD32242Ribosome assembly: 16S rRNA (rrnA)145
P. versutus IAM 12814rrnAD32243Ribosome assembly: 16S rRNA (rrnA)145
P. versutus IAM 12815rrnAD32244Ribosome assembly: 16S rRNA (rrnA)145
P. denitrificansKS1brrnAU58015Ribosome assembly: 16S rRNA (rrnA)139
P. denitrificansKS2brrnAU58016Ribosome assembly: 16S rRNA (rrnA)139
P. denitrificansKL1brrnAU58017Ribosome assembly: 16S rRNA (rrnA)139
P. denitrificans LMG 4218brrlAX87287Ribosome assembly: 23S rRNA (rrlA)179
P. denitrificans71.11crpsMU64204Ribosome assembly: ribosomal protein S13 (rpsM)228
P. denitrificans ATCC 13543csdhCDABU31902Succinate oxidation: succinate dehydrogenase b-type cytochrome subunit (sdhC), hydrophobic membrane anchor (sdhD), flavoprotein subunit (sdhA), iron-sulfur protein subunit (sdhB)69
P. denitrificansLMD 82.5bsoxABCDEFX79242Sulfur oxidation: protein B (soxB), sulfite oxidase (soxC), cytochrome (soxD), cytochrome (soxE)326, 327
P. denitrificans Pd1222porGY09451Membrane proteins: porin structural protein (porG)254
P. denitrificans Pd1222recAU59631DNA recombination75
P. denitrificans IFO 12442ctyrBY08272Amino acid biosynthesis: aromatic amino acid transferase (tyrB)207
  • a P. denitrificans Pd1222 is a derivative of DSM 413.

  • b Now proposed to be P. pantotrophus(233).

  • c Classification as P. denitrificansor P. pantotrophus not yet determined.