Closing the gaps on the viral photosystem‐I psaDCAB gene organization

Abstract

SummaryMarine photosynthesis is largely driven by cyanobacteria, namely Synechococcus and Prochlorococcus. Genes encoding for photosystem (PS) I and II reaction centre proteins are found in cyanophages and are believed to increase their fitness. Two viral PSI gene arrangements are known, psaJF→C→A→B→K→E→D and psaD→C→A→B. The shared genes between these gene cassettes and their encoded proteins are distinguished by %G + C and protein sequence respectively. The data on the psaD→C→A→B gene organization were reported from only two partial gene cassettes coming from Global Ocean Sampling stations in the Pacific and Indian oceans. Now we have extended our search to 370 marine stations from six metagenomic projects. Genes corresponding to both PSI gene arrangements were detected in the Pacific, Indian and Atlantic oceans, confined to a strip along the equator (30°N and 30°S). In addition, we found that the predicted structure of the viral PsaA protein from the psaD→C→A→B organization contains a lumenal loop conserved in PsaA proteins from Synechococcus, but is completely absent in viral PsaA proteins from the psaJF→C→A→B→K→E→D gene organization and most Prochlorococcus strains. This may indicate a co‐evolutionary scenario where cyanophages containing either of these gene organizations infect cyanobacterial ecotypes biogeographically restricted to the 30°N and 30°S equatorial strip.

Novel chaperonins are prevalent in the virioplankton and demonstrate links to viral biology and ecology

“…The observed links between GroEL phylogeny, chaperonin gene order and associations with nearby genes demonstrated that large subunit chaperonins are a defining feature of certain virioplankton populations. Similar to findings for DNA polymerase A ( Schmidt et al , 2014 ), ribonucleotide reductase ( Dwivedi et al , 2013 ; Sakowski et al , 2014 ) and photosystem genes ( Mann et al , 2003 ; Sullivan et al , 2006 ; Roitman et al , 2015 ), important biological and ecological characteristics may be linked with the type and organization of chaperonin genes a virus carries. Given the common observation of chaperonin genes within viromes, it is surprising that so few known viruses carry chaperonin genes.…”

Cyanophage-encoded lipid desaturases: oceanic distribution, diversity and function

“…In contrast, vFAD-IIs are present only in the Southern Pacific and Southern Atlantic Oceans, as well as in the Indian Ocean ( Figure 3a , purple dots). Interestingly, the geographical distribution and abundance of vFAD-II resembles the data found for uncultured phages carrying the vPSI-4 gene cassette ( Roitman et al , 2015 ), which is also found in the 94 kbp contig ( Figure 1 ). To estimate the vFAD relative abundance, we mapped the raw reads from the Tara Ocean metagenomes corresponding to bacterial, giant viruses and viral fractions to the viral desC genes.…”

“…Errors in the assembly were corrected using two read-mapping-based in-house tools as described elsewhere ( Philosof et al , 2017 ). Viral psaD sequences obtained in a previous study of vPSI-4 genes ( Roitman et al , 2015 ) were used as query to recruit scaffolds in the reassembled Tara Ocean data set using TBLASTX ( Altschul et al , 1990 ; Camacho et al , 2009 ) with the default parameters. One of the identified scaffolds, SAMEA2621085 (station 70, depth 5 m, 0–0.22 filter), contains the four genes of vPSI-4 ( psaD , C , A and B ).…”

“…Cyanophages, phages infecting marine cyanobacteria, display a broad array of AMGs, including photosynthetic light reaction components ( Mann et al , 2003 ; Lindell et al , 2004 ; Millard et al , 2004 , 2009 ; Zeidner et al , 2005 ; Sullivan et al , 2006 , 2010 ; Sharon et al , 2009 , 2011 ; Zheng et al , 2013 ). Photosystem-I (PSI) genes in cyanophages (viral PSI (vPSI)) are found in two main genotypes, arranged in cassettes of seven ( psaJF , C , A , B , K , E and D ) and four ( psaD , C , A and B ) genes, dubbed vPSI-7 and vPSI-4, respectively ( Sharon et al , 2009 ; Beja et al , 2012 ; Roitman et al , 2015 ; Fridman et al , 2017 ). Since there are no cultured representatives of vPSI-4 phages, little is known regarding their potential influence on the infected host metabolic capacities.…”

XXes Journées francophones de virologie

“…Les bactériophages sans gaine contractile sont les plus abondants [2]. 1600 nouveaux génomes viraux ont été rassemblés [3] à partir de diverses populations [4], et des connaissances plus spécifiques sur divers processus biologiques ont été acquises [3,[5][6][7]. Les grands virus à ADN des eucaryotes sont abondants et diversifiés [8][9][10], et notre laboratoire a récemment montré que la résistance aux prasinovirus peut être acquise et provoque des changements importants dans le génome de l'algue phytoplanctonique Ostreococcus tari [11].…”