Database Authors
Ron Caspi1, Lisa Moore2, Ian T 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 pastoris CCMP1986 (also known as P. marinus MED4) is a high-light-adapted strain [Moore95] from the HLI clade that has one of the smallest known genome of a photosynthetic organism. The genome is composed of a single circular chromosome of only 1,657,990 bp containing 1,796 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 [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 [Chisholm92].

Prochlorococcus marinus pastoris CCMP1986 is derived from the MED strain, which was collected from surface waters (5m depth) of the north-west Mediterranean Sea in January 1989 [Vaulot90, Partensky99] and is considered characteristic of the open ocean surface layer. It's genome was sequenced in 2003 [Rocap03].

This Pathway/Genome Database (PGDB) was generated by the PathoLogic [Karp11, Karp19] component of 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
chromosome1,8491,7964491,657,990RefSeq:NC_005072
Ortholog data available?Yes
Database Contents
Genes1,849
Pathways234
Enzymatic Reactions1,365
Transport Reactions56
Polypeptides1,797
Protein Complexes68
Enzymes574
Transporters93
Compounds1,051
Transcription Units1,197
tRNAs37
Protein Features3,326
GO Terms16,111
Database Version29.0
Synonyms Prochlorococcus marinus subsp. pastoris str. CCMP1986
Prochlorococcus marinus MED4
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Cyanobacteriota/Melainabacteria group
Cyanobacteriota
Cyanophyceae
Synechococcales
Prochlorococcaceae
Prochlorococcus
Prochlorococcus marinus
Prochlorococcus marinus pastoris
Prochlorococcus marinus pastoris CCMP1986
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMEA3138209
NCBI BioProjectPRJNA224116
NCBI-Taxonomy59919
Environmentmarine
Geographic LocationNorth Atlantic
Latitude/Longitude35.0 N 20.0 E
Altitude (m)5.0
Collection Date1989-01
Relationship to Oxygenaerobe
Trophic Levelphotoautotroph
Temperature Rangemesophile
Biotic Relationshipfree-living
Annotation ProviderNCBI RefSeq
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.10
Annotation CommentBest-placed reference protein set; GeneMarkS-2+
Copyright SRI International 2022

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

Chisholm92: Chisholm SW, Frankel SL, Goericke R, Olson RJ, Palenik B, Waterbury JB, West-Johnsrud L, Zettler ER (1992). "Prochlorococcus marinus nov. gen. nov. sp.: an oxyphototrophic marine prokaryote containing divinyl chlorophyll a and b." Archives of Microbiology 157(3);297-300.

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

Moore95: Moore L, Goericke R, Chisholm S (1995). "Comparative physiology of Synechococcus and Prochlorococcus: influence of light and temperature on growth, pigments, fluorescence and absorptive properties." Marine Ecology Progress Series 116;259-275.

Partensky99: Partensky F, Hess WR, Vaulot D (1999). "Prochlorococcus, a marine photosynthetic prokaryote of global significance." Microbiol Mol Biol Rev 63(1);106-27. PMID: 10066832

Rocap03: Rocap G, Larimer FW, Lamerdin J, Malfatti S, Chain P, Ahlgren NA, Arellano A, Coleman M, Hauser L, Hess WR, Johnson ZI, Land M, Lindell D, Post AF, Regala W, Shah M, Shaw SL, Steglich C, Sullivan MB, Ting CS, Tolonen A, Webb EA, Zinser ER, Chisholm SW (2003). "Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation." Nature 424(6952);1042-7. PMID: 12917642

Vaulot90: Vaulot D, Partensky F, Neveux J, Mantoura R FC, Llewellyn CA (1990). "Winter presence of prochlorophytes in surface waters of the northwestern Mediterranean Sea." Limnology and Oceanography 35(5);1156-1164.

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