Home Proteomes Families Hamap-Scan Documents Downloads Links
HAMAP: Paracoccus denitrificans (strain Pd 1222) complete proteome
General information

Species:  Paracoccus denitrificans (strain Pd 1222)
Species code: PARDP
Taxonomy: Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales; Rhodobacteraceae; Paracoccus (TaxID: 318586) [NEWT/ NCBI]
Description: Paracoccus denitrificans is a Gram-negative, non-motile coccoid soil bacterium from the alpha subdivision of the proteobacteria. Formerly known as Micrococcus denitrificans, it was first isolated in 1910 by M. Beijerinck, and renamed in 1969 to Paracoccus denitrificans by Davis. P. denitrificans is a model organism for the study of denitrification. Besides its intrinsic interest, denitrification also represents a source of atmosphere damaging compounds (nitric oxide and nitrous oxide), is a route for the loss of nitrogen fertilizer from agricultural soil, and has potential applications in the water treatment industry. P. denitrificans is a popular model for investigators with interests in a variety of aspects of microbial physiology. The organism grows well under aerobic conditions, expressing a respiratory chain very similar to that of the eukaryotic mitochondrion. P. denitrificans has been, and continues to be, the subject of many studies of the fundamental biochemical and bioenergetic properties of the aerobic electron transport chain. The evidence from 16S rRNA analysis indicates that the evolutionary precursor of the mitochondrion was a close relative of P. denitrificans (both fall in the alpha sub-group of the proteobacteria), justifying the use of P. denitrificans as a model for the mitochondrial respiratory chain. P. denitrificans has also been extensively studied for its ability to grow on C1 compounds such as methanol and methylamine, what it does by oxidation to carbon dioxide, then assimilation via the Calvin cycle. The organism can also grow as a chemolithoautotroph, using inorganic energy sources with carbon dioxide as the carbon source. P. denitrificans is now being exploited as a model organism for the study of poorly characterized sulfur compound transformations, because of its ability to use hydrogen and sulfur compounds, such as thiosulfate. Metabolic flexibility in this organism is reflected in an underlying flexibility of regulatory networks, which are currently only partially understood. Paracoccus is a biochemically versatile Genus, with a wide range of diverse degradative capabilities and potential applications in bioremediation. Strains have been isolated that utilize thiocyanate as an energy source, for the possible bioremediation of thiocyanate-contaminated wastewater from coke-oven factories. Strains that degrade halobenzoates under anaerobic denitrifying conditions, and that degrade sulfonates under anaerobic growth conditions have been described. Several strains of P. denitrificans have been isolated that grow chemolithoautotrophically using carbon disulfide or carbonyl sulfide as energy sources, and strains have been isolated from activated sludge that are capable of degrading quaternary carbon compounds such as dimethylmalonate under denitrifying conditions. Another strain isolated from activated sludge degrades a variety of methylated amines under both aerobic and anaerobic conditions. Some strains are capable of 'aerobic denitrification', the complete dissimilation of nitrate to dinitrogen (or nitrous oxide) under aerobic growth conditions. P. denitrificans also has the very unusual ability to oxidize ammonia to nitrite during growth on organic energy sources ('heterotrophic nitrification'). Coupled to denitrification, heterotrophic nitrification allows for the complete transformation of ammonia to dinitrogen by a single organism.
Properties: Presence of flagella: Yes
Human pathogen: No
Interaction: No
Number of membranes: 2
Number of inteins:0
Statistics: Number of PARDP entries in the UniProt Knowledgebase: 5019 (317 in UniProtKB/Swiss-Prot + 4702 in UniProtKB/TrEMBL)


Genome(s) sequenced

Strain:    Pd 1222
Genome structure:
• Chromosome 1 EMBL accession number CP000489 (circular; 2,852,282 bp) (download entry)
• Chromosome 2 EMBL accession number CP000490 (circular; 1,730,097 bp) (download entry)
• Plasmid pPD1222 EMBL accession number CP000491 (circular; 653,815 bp) (download entry)
Reference(s):
[1] Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S., Munk A.C., Brettin T., Bruce D., Han C., Tapia R., Gilna P., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N., Lykidis A., Spiro S., Richardson D.J., Moir J.W.B., Ferguson S.J., van Spanning R.J.M., Richardson P. ;
"Complete sequence of chromosome 1 of Paracoccus denitrificans PD1222.";
Submitted (DEC-2006) to the EMBL/GenBank/DDBJ databases.
[2] Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S., Munk A.C., Brettin T., Bruce D., Han C., Tapia R., Gilna P., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N., Lykidis A., Spiro S., Richardson D.J., Moir J.W.B., Ferguson S.J., van Spanning R.J.M., Richardson P. ;
"Complete sequence of chromosome 2 of Paracoccus denitrificans PD1222.";
Submitted (DEC-2006) to the EMBL/GenBank/DDBJ databases.
[3] Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S., Munk A.C., Brettin T., Bruce D., Han C., Tapia R., Gilna P., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N., Lykidis A., Spiro S., Richardson D.J., Moir J.W.B., Ferguson S.J., van Spanning R.J.M., Richardson P. ;
"Complete sequence of plasmid 1 of Paracoccus denitrificans PD1222.";
Submitted (DEC-2006) to the EMBL/GenBank/DDBJ databases.
Web links:
Official genome site(s):
http://genome.jgi-psf.org/finished_microbes/parde/parde.home.html
Other web sites:
Entrez Genome Project: http://www.ncbi.nlm.nih.gov/sites/entrez?Db=genomeprj&Cmd=DetailsSearch&Term=txid318586%5Borgn%5D
Genome Atlas: http://www.cbs.dtu.dk/services/gwBrowser/project.php?pid=13020
GIB (DDBJ): http://gib.genes.nig.ac.jp/single/index.php?spid=Pden_PD1222
PEDANT: http://pedant.gsf.de/pedant3htmlview/pedant3view?Method=analysis&Db=p3_p13020_Par_denit
 EBI Proteome Analysis page



Tools