Database Authors
Ron Caspi1, Lisa Moore2, Ian Paulsen2, Peter D Karp1
1SRI International, 2Macquarie University
Summary 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 (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 strains are highly diverse, and the pangenome contains more than 80,000 genes [Moore99, Dufresne03, Biller15].

The major pigments of 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 [Steglich03].

Prochlorococcus marinus marinus CCMP1375 is derived from the SARG strain, the first 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 [Palenik92]. Its genome was sequenced in 2003 [Dufresne03].

This Pathway/Genome Database (PGDB) was generated by the PathoLogic [Karp11, Karp19] component of the Pathway Tools software version 24.0 and MetaCyc [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.

Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
chromosome1,9311,8854601,751,080RefSeq:NC_005042.1
Ortholog data available?Yes
Database Contents
Genes1,931
Pathways191
Enzymatic Reactions870
Transport Reactions40
Polypeptides1,886
Protein Complexes70
Enzymes505
Transporters84
Compounds718
Transcription Units1,317
tRNAs40
Protein Features6,585
GO Terms16,426
Database Version29.0
Synonyms Prochlorococcus marinus subsp. marinus str. CCMP1375
Prochlorococcus marinus SS120
Prochlorococcus marinus CCMP1375
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Cyanobacteriota/Melainabacteria group
Cyanobacteriota
Cyanophyceae
Synechococcales
Prochlorococcaceae
Prochlorococcus
Prochlorococcus marinus
Prochlorococcus marinus marinus
Prochlorococcus marinus marinus CCMP1375
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
NCBI BioProjectPRJNA57995
NCBI-Taxonomy167539
Environmentmarine
Geographic LocationNorth Atlantic
Latitude/Longitude30.0 N 60.0 W
Altitude (m)120.0
Collection Date1988-05
Relationship to Oxygenaerobe
Trophic Levelphotoautotroph
Temperature Rangemesophile
Biotic Relationshipfree-living
Pathogenicityplant

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

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

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