Single cell genomes of Prochlorococcus, Synechococcus, and sympatric microbes from diverse marine environments

Berube, Paul M.; Biller, Steven J.; Hackl, Thomas; Satinsky, Brandon M.; Becker, Jamie W.; Braakman, Rogier; Collins, Sara B.; Kelly, Libusha; Berta-Thompson, Jessie W; Coe, Allison; Bergauer, Kristin; Bouman, Heather A.; Browning, Thomas J.; Corte, Daniele De; Hassler, Christel; Hulata, Yotam; Jacquot, Jeremy E.; Maas, Elizabeth W.; Reinthaler, Thomas; Sintes, Eva; Yokokawa, Taichi; Lindell, Debbie; Stepanauskas, Ramunas; Chisholm, Sallie W.

doi:10.1038/sdata.2018.154

Cited by 78 publications

(87 citation statements)

References 45 publications

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“…Overall, we demonstrated that the methods used (AAI, core protein sequences and MLSA) correlated and provided significant taxonomic resolution for differentiation of genera and species in PC (Figure 2 and 3). The proposed genera are in complete agreement with previous literature and support previous theories on the evolution of Prochlorococcus [11,13,14,19,45,47,50]. The PC genomic signatures were more similar between closely related species than distantly related species.…”

Section: In Silico Phenotype Predictionsupporting

confidence: 90%

“…If natural selection plays such a strong role in determining % GC content, it suggests that there are no truly neutrally evolving sites. 14 The species and genus delimitations were based on clusters with three or more genomes that shared ≥95% or ≥70% amino acid average identity (AAI), respectively. Here, we revisit the current taxonomy of the PC and propose the creation of a new genus Riococcus and 113 novel species (N=122 species) (Table 1 and S1).…”

Section: Gc Content Reveals Great Genomic Diversity In the Pcmentioning

confidence: 99%

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Unlocking the genomic taxonomy of the Prochlorococcus collective

Tschoeke

Vidal

Campeão

et al. 2020

Preprint

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1Prochlorococcus is the most abundant photosynthetic prokaryote on our planet. The extensive ecological literature on the Prochlorococcus collective (PC) is based on the assumption that it comprises one single genus comprising the species Prochlorococcus marinus, containing itself a collective of ecotypes. Ecologists adopt the distributed genome hypothesis of an open pan-genome to explain the observed genomic diversity and evolution patterns of the ecotypes within PC. Novel genomic data for the PC prompted us to revisit this group, applying the current methods used in genomic taxonomy. As a result, we were able to distinguish the five genera: Prochlorococcus, Eurycolium, Prolificoccus, Thaumococcus and Riococcus. The novel genera have distinct genomic and ecological attributes.

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Section: In Silico Phenotype Predictionsupporting

confidence: 90%

Section: Gc Content Reveals Great Genomic Diversity In the Pcmentioning

confidence: 99%

Unlocking the genomic taxonomy of the Prochlorococcus collective

Tschoeke

Vidal

Campeão

et al. 2020

Preprint

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“…Matches with sequences not identical to the query were retrieved and aligned in ClustalX v. 2.1 (40). Additionally, the same query sequence was used in a BLASTP search of the 703 genomes of Prochlorococcus and marine Synechococcus available via IMG/ProPortal (41). This database includes both isolates and single cell genomes, the latter ones with an average completion of 60% (41).…”

Section: Survey Of Pshcp Taxonomic Distribution and Amino Acid Consermentioning

confidence: 99%

The structure of a highly conserved picocyanobacterial protein reveals a Tudor domain with a novel tRNA binding function

Bauer

Dicovitsky

Pellegrini

et al. 2019

Preprint

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Cyanobacteria of the Prochlorococcus and marine Synechococcus genera are the most abundant photosynthetic microbes in the ocean. Intriguingly, the genomes of these bacteria are very divergent even within each genus, both in gene content and at amino acid level of the encoded proteins. One striking exception to this is a 62 amino acid protein, termed Prochlorococcus/Synechococcus Hyper Conserved Protein (PSHCP). PSHCP is not only found in all sequenced Prochlorococcus and marine Synechococcus genomes but it is also nearly 100% identical in its amino acid sequence across all sampled genomes. Such universal distribution and sequence conservation suggests an essential cellular role of the encoded protein in these bacteria. However, the function of PSHCP is unknown. We used Nuclear Magnetic Resonance (NMR) spectroscopy to determine its structure. We found that 52 of the 62 amino acids in PSHCP form a Tudor domain, while the remainder of the protein is disordered. NMR titration experiments revealed that PSHCP has only a weak affinity for DNA, but an 18.5 fold higher affinity for tRNA, hinting at an involvement of PSHCP in translation. Computational docking and mutagenesis studies identified a positively charged patch surrounding residue K30 that serves as the primary docking site for tRNA on PSHCP. These results provide the first insight into the structure and function of PSHCP and suggest a new function for Tudor domains in recognizing tRNA.

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“…Specialized (reviewed in [22], [23] ) and lateral [24] transduction in bacteria are strictly mediated by lysogenic phages, as they enter and leave their host chromosome. Prophages, the hallmarks of lysogeny, however, have not been observed in the hundreds of Prochlorococcus isolates and single-cell genomes from the wild [25] , suggesting that the vast majority of phages infecting Prochlorococcus are strictly lytic. This leaves generalized transduction -the random mispackaging of host DNA into capsids and its subsequent injection and recombination in a recipient cell -as the dominant route of phage-mediated HGT in these bacteria.…”

Section: Introductionmentioning

confidence: 99%

Frequency of mispackaging ofProchlorococcusDNA by cyanophage

Raho

Laurenceau

Forget

et al. 2020

Preprint

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Prochlorococcus cells are the numerically dominant phototrophs in the open ocean. Cyanophages that infect them are thus a notable fraction of the total viral population in the euphotic zone, and, as vehicles of horizontal gene transfer, appear to drive their evolution. Here we examine the propensity of three cyanophages -a podovirus, a siphovirus, and a myovirus -to mispackage host DNA in their capsids while infecting Prochlorococcus , the first step in phage-mediated horizontal gene transfer. We find the mispackaging frequencies are distinctly different among the three phages. Myoviruses mispackage host DNA at low and stable frequencies, while podo-and siphoviruses vary in their mispackaging frequencies by orders of magnitude depending on growth light intensity. We attribute this difference to the concentration of intracellular reactive oxygen species and protein synthesis rates. Based on our findings, we propose a model of mispackaging frequency determined by the imbalance between the production of capsids and the number of phage genome copies during infection. RESULTS AND DISCUSSIONHost DNA mispackaging frequency in cyanophage capsids. Using six different loci on the Prochlorococcus MED4 chromosome (representative of the entire chromosome, see Table 3), we quantified the level of mispackaging of MED4 DNA in the capsids of the three different cyanophages (Fig. 1A, Table 2) during infection (Fig. 1B, C). The packaging strategy of the podovirus is T7-like [26] , the myovirus' is likely T4-like headful packaging [27] while the siphovirus' is unknown, but 490 bp direct terminal repeats suggest a T7-like packaging mechanism [28] . Host DNA was detected in the capsids of all 3 cyanophages (Fig. 1C). The levels of mispackaging are low compared to those reported for high transducing phages in S. aureus [29] for example, but comparable to levels (~10 PPM) reported for the marine Synechococcus cyanophage S-PM2 [30] . Corresponding gene Putative functionPrimer sequences (forward and reverse, 5'-3')

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Single cell genomes of Prochlorococcus, Synechococcus, and sympatric microbes from diverse marine environments

Cited by 78 publications

References 45 publications

Unlocking the genomic taxonomy of the Prochlorococcus collective

Unlocking the genomic taxonomy of the Prochlorococcus collective

The structure of a highly conserved picocyanobacterial protein reveals a Tudor domain with a novel tRNA binding function

Frequency of mispackaging ofProchlorococcusDNA by cyanophage

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