Database Authors
Ron Caspi1, Lisa Moore2, Ian T Paulsen2, Peter D Karp1
1SRI International, 2Macquarie University
Summary Parasynechococcus marenigrum, more commonly known as Synechococcus sp. WH8102, is a motile marine cyanobacterium that was isolated from the Atlantic Ocean in 1986. The organism has a high ratio of phycourobilin to phycoerythrobilin (PUB:PEB) in the rods of its phycobilisomes, a chromophore composition known as type3c, which dominates in the oligotrophic, i.e. nutrient deplete, oceanic waters [Waterbury86, Six05, Six07, Scanlan09].

Phylogenetically, strain WH8102 falls within the Marine α-cyanobacteria subcluster 5.1, clade III [Rocap02, Mazard12, Ahlgren12]. Note that NCBI Taxonomy Browser refers to Synechococcus sp. WH8102 as Parasynechococcus marenigrum based on the proposed taxonomical revision by [Komarek20], but this has not been widely accepted by the research community.

The marine picocyanobacteria, consisting of Synechococcus and Prochlorococcus species, are major contributors to primary production in open ocean waters of the subtropical and tropical regions. Along with a third of the open ocean Synechococcus isolates, strain WH8102 possesses a unique type of swimming motility not seen in other microorganisms. They can move at speeds of up to 25 mm/sec in response to gradients of nitrogenous compounds in the absence of any demonstrable external organelle [Waterbury85].

Strain WH8102 is amenable to biochemical and genetic manipulation [Brahamsha96] and was among the first marine cyanobacteria to have their genome sequenced, back in 2003 [Palenik03].

Reviews: [Scanlan09, Scanlan12]

This Pathway/Genome Database (PGDB) was generated by the PathoLogic [Karp11, Karp16] component of Pathway Tools software version 23.5 and MetaCyc [Caspi20] version 23.5 on 13-Dec-2019, and was upgraded to a tier 2 status by manual curation.

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
chromosome2,6302,52454522,434,428RefSeq:NC_005070.1
Ortholog data available?Yes
Database Contents
Genes2,630
Pathways219
Enzymatic Reactions1,173
Transport Reactions54
Polypeptides2,528
Protein Complexes91
Enzymes670
Transporters143
Compounds889
Transcription Units1,600
tRNAs44
Transcriptional Regulation63
Protein Features4,195
GO Terms19,732
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Cyanobacteriota/Melainabacteria group
Cyanobacteriota
Cyanophyceae
Synechococcales
Prochlorococcaceae
Parasynechococcus
Parasynechococcus marenigrum
Parasynechococcus marenigrum
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMEA3138327
NCBI BioProjectPRJNA224116
NCBI-Taxonomy84588
Environmentmarine
Geographic LocationNorth Atlantic Ocean
Latitude/Longitude22.0 N 65.0 W
Collection Date1981-03-14
Relationship to Oxygenaerobe
Trophic Levelphotoautotroph
Temperature Rangemesophile
Biotic Relationshipfree-living
Annotation ProviderNCBI RefSeq
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.9
Annotation CommentBest-placed reference protein set; GeneMarkS-2+
Copyright SRI International 2022

References

Ahlgren12: Ahlgren NA, Rocap G (2012). "Diversity and Distribution of Marine Synechococcus: Multiple Gene Phylogenies for Consensus Classification and Development of qPCR Assays for Sensitive Measurement of Clades in the Ocean." Front Microbiol 3;213. PMID: 22723796

Brahamsha96: Brahamsha B (1996). "A genetic manipulation system for oceanic cyanobacteria of the genus Synechococcus." Appl Environ Microbiol 62(5);1747-51. PMID: 8633873

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

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

Karp16: Karp PD, Latendresse M, Paley SM, Krummenacker M, Ong QD, Billington R, Kothari A, Weaver D, Lee T, Subhraveti P, Spaulding A, Fulcher C, Keseler IM, Caspi R (2016). "Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology." Brief Bioinform 17(5);877-90. PMID: 26454094

Komarek20: Komarek J, Johansen JR, Smarda J, Strunecky O (2020). "Phylogeny and taxonomy of Synechococcus-like cyanobacteria." Fottea 20(2);171-191.

Mazard12: Mazard S, Ostrowski M, Partensky F, Scanlan DJ (2012). "Multi-locus sequence analysis, taxonomic resolution and biogeography of marine Synechococcus." Environ Microbiol 14(2);372-86. PMID: 21651684

Palenik03: Palenik B, Brahamsha B, Larimer FW, Land M, Hauser L, Chain P, Lamerdin J, Regala W, Allen EE, McCarren J, Paulsen I, Dufresne A, Partensky F, Webb EA, Waterbury J (2003). "The genome of a motile marine Synechococcus." Nature 424(6952);1037-42. PMID: 12917641

Rocap02: Rocap G, Distel DL, Waterbury JB, Chisholm SW (2002). "Resolution of Prochlorococcus and Synechococcus ecotypes by using 16S-23S ribosomal DNA internal transcribed spacer sequences." Appl Environ Microbiol 68(3);1180-91. PMID: 11872466

Scanlan09: Scanlan DJ, Ostrowski M, Mazard S, Dufresne A, Garczarek L, Hess WR, Post AF, Hagemann M, Paulsen I, Partensky F (2009). "Ecological genomics of marine picocyanobacteria." Microbiol Mol Biol Rev 73(2);249-99. PMID: 19487728

Scanlan12: Scanlan, David J (2012). "Marine Cyanobacteria in B.A. Whitton (ed.), Ecology of Cyanobacteria II: Their Diversity in Space and Time, Springer." NIL.

Six05: Six C, Thomas JC, Thion L, Lemoine Y, Zal F, Partensky F (2005). "Two novel phycoerythrin-associated linker proteins in the marine cyanobacterium Synechococcus sp. strain WH8102." J Bacteriol 187(5);1685-94. PMID: 15716439

Six07: Six C, Thomas JC, Garczarek L, Ostrowski M, Dufresne A, Blot N, Scanlan DJ, Partensky F (2007). "Diversity and evolution of phycobilisomes in marine Synechococcus spp.: a comparative genomics study." Genome Biol 8(12);R259. PMID: 18062815

Waterbury85: Waterbury JB, Willey JM, Franks DG, Valois FW, Watson SW (1985). "A cyanobacterium capable of swimming motility." Science 230(4721);74-6. PMID: 17817167

Waterbury86: Waterbury J B., Watson F W., Valois F W., Franks D G. (1986). "Biological and ecological characterization of the marine unicellular cyanobacterium Synechococcus." In: Platt T, Li W K W, editors. Photosynthetic picoplankton. Ottawa, Ontario, Canada: Canadian Department of Fisheries and Oceans; pp. 71-120.

References

Blot09: Blot N, Wu XJ, Thomas JC, Zhang J, Garczarek L, Bohm S, Tu JM, Zhou M, Ploscher M, Eichacker L, Partensky F, Scheer H, Zhao KH (2009). "Phycourobilin in trichromatic phycocyanin from oceanic cyanobacteria is formed post-translationally by a phycoerythrobilin lyase-isomerase." J Biol Chem 284(14);9290-8. PMID: 19182270


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