Summary of Prochlorococcus marinus marinus CCMP1375, version 28.5

Tier 2 Curated Database

Database Authors: Ron Caspi¹, Lisa Moore², Ian Paulsen², Peter D Karp¹

¹SRI International, ²Macquarie University

Summary:
Prochlorococcus marinus
NCBI Taxonomy ID: 1219
Rank: species
Lineage:
cellular organisms
Bacteria <bacteria>
Terrabacteria group
Cyanobacteriota/Melainabacteria group
Cyanobacteriota
Cyanophyceae
Synechococcales
Prochlorococcaceae
Prochlorococcus'>Prochlorococcus marinus is the dominant photosynthetic organism in most of the tropical and temperate open ocean ecosystems. It is also the smallest photosynthetic organism known to date, with a cell size of less than 1 μm. Prochlorococcus marinus marinus CCMP1375
NCBI Taxonomy ID: 167539
Rank: strain
Lineage:
cellular organisms
Bacteria <bacteria>
Terrabacteria group
Cyanobacteriota/Melainabacteria group
Cyanobacteriota
Cyanophyceae
Synechococcales
Prochlorococcaceae
Prochlorococcus
Prochlorococcus marinus
Prochlorococcus marinus marinus'>Prochlorococcus marinus marinus CCMP1375 (also known as P. marinus SS120) is a low-light-adapted strain falling within the LLII/III clade with one of the smallest genomes of a photosynthetic organism known. The genome is composed of a single circular chromosome of only 1,751,080 bp containing 1,881 predicted protein-coding genes. Despite their small sizes, the genomes of Prochlorococcus
NCBI Taxonomy ID: 1218
Rank: genus
Lineage:
cellular organisms
Bacteria <bacteria>
Terrabacteria group
Cyanobacteriota/Melainabacteria group
Cyanobacteriota
Cyanophyceae
Synechococcales
Prochlorococcaceae'>Prochlorococcus strains are highly diverse, and the pangenome contains more than 80,000 genes ["Photophysiology of the marine cyanobacterium Prochlorococcus: Ecotypic differences among cultured isolates." Limnology and Oceanography 44(3);628-638.'>Moore99, "Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome." Proc Natl Acad Sci U S A 100(17);10020-5. PMID: 12917486'>Dufresne03, "Prochlorococcus: the structure and function of collective diversity." Nat Rev Microbiol 13(1);13-27. PMID: 25435307'>Biller15].

The major pigments of Prochlorococcus
NCBI Taxonomy ID: 1218
Rank: genus
Lineage:
cellular organisms
Bacteria <bacteria>
Terrabacteria group
Cyanobacteriota/Melainabacteria group
Cyanobacteriota
Cyanophyceae
Synechococcales
Prochlorococcaceae'>Prochlorococcus are divinyl derivatives of chlorophyll a and b (Chl a₂ and b₂), which are unique to this genus. They lack phycobilisomes, the large extrinsic multisubunit light-harvesting complexes found in typical cyanobacteria. Some Prochlorococcus, such as strain SS120 (CCMP1375), do contain phycoerythrin ["Photophysical properties of Prochlorococcus marinus SS120 divinyl chlorophylls and phycoerythrin in vitro and in vivo." FEBS Lett 553(1-2);79-84. PMID: 14550550'>Steglich03].

Prochlorococcus marinus marinus CCMP1375
NCBI Taxonomy ID: 167539
Rank: strain
Lineage:
cellular organisms
Bacteria <bacteria>
Terrabacteria group
Cyanobacteriota/Melainabacteria group
Cyanobacteriota
Cyanophyceae
Synechococcales
Prochlorococcaceae
Prochlorococcus
Prochlorococcus marinus
Prochlorococcus marinus marinus'>Prochlorococcus marinus marinus CCMP1375 is derived from the SARG strain, the first Prochlorococcus
NCBI Taxonomy ID: 1218
Rank: genus
Lineage:
cellular organisms
Bacteria <bacteria>
Terrabacteria group
Cyanobacteriota/Melainabacteria group
Cyanobacteriota
Cyanophyceae
Synechococcales
Prochlorococcaceae'>Prochlorococcus strain to be isolated. It was collected in May 1988 from the bottom of the euphotic zone in the Sargasso Sea at a depth of 120m ["Multiple evolutionary origins of prochlorophytes, the chlorophyll b-containing prokaryotes." Nature 355(6357);265-7. PMID: 1731224'>Palenik92]. Its genome was sequenced in 2003 ["Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome." Proc Natl Acad Sci U S A 100(17);10020-5. PMID: 12917486'>Dufresne03].

This Pathway/Genome Database (PGDB) was generated by the PathoLogic ["The pathway tools pathway prediction algorithm." Stand Genomic Sci 5(3);424-9. PMID: 22675592'>Karp11, "Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biology." Brief Bioinform. PMID: 31813964'>Karp19] component of the Pathway Tools software version 24.0 and MetaCyc ["The MetaCyc database of metabolic pathways and enzymes - a 2019 update." Nucleic Acids Res 48(D1);D445-D453. PMID: 31586394'>Caspi20] version 24.0 on 19-Feb-2020.

Development of this PGDB was supported by BioCyc subscription revenues and by grant GM080746 from the National Institute of Health.

Synonyms: Prochlorococcus marinus subsp. marinus str. CCMP1375, Prochlorococcus marinus SS120, Prochlorococcus marinus CCMP1375

Unification Links: NCBI BioProject:PRJNA57995, NCBI-Taxonomy:167539

Organism or Sample Properties
Environment:	marine
Geographic Location:	North Atlantic
Latitude/Longitude:	30.0 N 60.0 W
Altitude (m):	120.0
Collection Date:	1988-05
Relationship to Oxygen:	aerobe
Trophic Level:	photoautotroph
Temperature Range:	mesophile
Biotic Relationship:	free-living
Pathogenicity:	plant

Replicon	Total Genes	Protein Genes	RNA Genes	Pseudogenes	Size (bp)	NCBI Link

chromosome	1,931	1,885	46	0	1,751,080	RefSeq:NC_005042.1

Ortholog data available?	Yes

Genes:	1,931
Pathways:	191
Enzymatic Reactions:	870
Transport Reactions:	40
Polypeptides:	1,886
Protein Complexes:	68
Enzymes:	505
Transporters:	84
Compounds:	716
Transcription Units:	1,317
tRNAs:	40
Protein Features:	6,585
GO Terms:	16,426

Genetic Code Number:
11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)

PGDB Unique ID: 1ZN3

References

Biller15: Biller SJ, Berube PM, Lindell D, Chisholm SW (2015). "Prochlorococcus: the structure and function of collective diversity." Nat Rev Microbiol 13(1);13-27. PMID: 25435307

Caspi20: Caspi R, Billington R, Keseler IM, Kothari A, Krummenacker M, Midford PE, Ong WK, Paley S, Subhraveti P, Karp PD (2020). "The MetaCyc database of metabolic pathways and enzymes - a 2019 update." Nucleic Acids Res 48(D1);D445-D453. PMID: 31586394

Dufresne03: Dufresne A, Salanoubat M, Partensky F, Artiguenave F, Axmann IM, Barbe V, Duprat S, Galperin MY, Koonin EV, Le Gall F, Makarova KS, Ostrowski M, Oztas S, Robert C, Rogozin IB, Scanlan DJ, Tandeau de Marsac N, Weissenbach J, Wincker P, Wolf YI, Hess WR (2003). "Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome." Proc Natl Acad Sci U S A 100(17);10020-5. PMID: 12917486

Karp11: Karp PD, Latendresse M, Caspi R (2011). "The pathway tools pathway prediction algorithm." Stand Genomic Sci 5(3);424-9. PMID: 22675592

Karp19: Karp PD, Midford PE, Billington R, Kothari A, Krummenacker M, Latendresse M, Ong WK, Subhraveti P, Caspi R, Fulcher C, Keseler IM, Paley SM (2019). "Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biology." Brief Bioinform. PMID: 31813964

ID: PUB-MOORE1999'> Moore99: Moore LR, Chisholm SW (1999). "Photophysiology of the marine cyanobacterium Prochlorococcus: Ecotypic differences among cultured isolates." Limnology and Oceanography 44(3);628-638.

Palenik92: Palenik B, Haselkorn R (1992). "Multiple evolutionary origins of prochlorophytes, the chlorophyll b-containing prokaryotes." Nature 355(6357);265-7. PMID: 1731224

Steglich03: Steglich C, Mullineaux CW, Teuchner K, Hess WR, Lokstein H (2003). "Photophysical properties of Prochlorococcus marinus SS120 divinyl chlorophylls and phycoerythrin in vitro and in vivo." FEBS Lett 553(1-2);79-84. PMID: 14550550

Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of Ss120Cyc: Copyright SRI International 2022
Page generated by Pathway Tools version 28.5 (software by SRI International) on Wed Dec 25, 2024, BIOCYC16B.

References

General Information

Data and Services

Credits

Follow Us

Select One or More Databases:

Current Selection

Search

Genome

Metabolism

Analysis

References