The smallest ssDNA phage infecting a marine bacterium

Zhan, Yuanchao; Chen, Feng

doi:10.1111/1462-2920.14394

Cited by 26 publications

(23 citation statements)

References 78 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The lysis gene shares homologues with prophage/prophage‐like regions in several bacterial genomes, such as Campylobacter , Bacteroides and Firmicutes (Roux et al ., ; Zhan and Chen, ). Acquisition of the lysis gene, which originated from the prophage region of alpha‐proteobacteria, suggests that in addition to point mutation, horizontal gene transfer may be another important driving force for the evolution of ssDNA phages (Zhan and Chen, ). The limited number of ORFs and the presence of peptidases have also been observed in many ssDNA phages, which were assembled from diverse marine viromes, suggesting that the vB_RpoMi‐Mini‐like ssDNA phages are widely distributed in the ocean.…”

Section: Genomic Diversity Of Roseophagesmentioning

confidence: 99%

“…Phage vB_RpoMi‐Mini is a ssDNA bacteriophage isolated from R. pomeroyi DSS‐3 from Baltimore Inner Harbor. It represents the first ssDNA phage that infects marine roseobacters (Zhan and Chen, ). More recently, another ssDNA bacteriophage, vB_RpoMi‐V15, which infects the same host, was isolated from a water sample also collected from Baltimore Inner Harbor but at a different time, and this bacteriophage shares 100% nucleotide identity with vB_RpoMi‐Mini.…”

Section: Genomic Diversity Of Roseophagesmentioning

confidence: 99%

“…Among the known marine bacteriophages, vB_RpoMi‐Mini and vB_RpoMi‐V15 have the smallest genome size (4.3 kb) and contain the fewest number of ORFs (four ORFs) (Table and Fig. ) (Zhan and Chen, ). In contrast to other Microviridae phages that utilize overlapping reading frames to minimize the genome size (Cherwa and Fane, ), the genomes of vB_RpoMi‐Mini and vB_RpoMi‐V15 only contain four genes, three of which are essential for the viral lifecycle.…”

Section: Genomic Diversity Of Roseophagesmentioning

confidence: 99%

See 2 more Smart Citations

Bacteriophages that infect marine roseobacters: genomics and ecology

Zhan

Chen

2019

Environmental Microbiology

Self Cite

View full text Add to dashboard Cite

Summary Viruses are the most abundant biological entities in seawater. They influence microbial population dynamics, genetic heterogeneity and biogeochemical cycles in marine ecosystems. The isolation and characterization of viruses that infect specific hosts have greatly advanced our knowledge of the biological and ecological interactions between viruses and their hosts. Marine Roseobacter are abundant, ubiquitous and diverse in the ocean and play active roles in global biogeochemical cycling, especially the sulfur cycle. Currently, 32 bacteriophages that infect multiple lineages of roseobacters have been isolated and sequenced. These roseophages exhibit diverse morphologies, nucleic acid types and genomic features. Here, we provide the most up‐to‐date overview of roseophages. Most roseophages are host specific and have a wide range of genome sizes and open reading frames. Based on a genome‐wide comparison, at least eight distinctly different types of roseophages were identified, indicating their diversity. Lysogenic‐related and gene transfer agent‐related genes are commonly found in roseophage genomes, implying the importance of genetic transfer within roseobacters. This feature could provide the versatility for roseobacters to quickly adapt to the changing environments. A wide distribution range of roseophages in the global ocean, especially in coastal environments, has been observed, reflecting the cosmopolitan nature of the Roseobacter lineage.

show abstract

Section: Genomic Diversity Of Roseophagesmentioning

confidence: 99%

Section: Genomic Diversity Of Roseophagesmentioning

confidence: 99%

Section: Genomic Diversity Of Roseophagesmentioning

confidence: 99%

See 1 more Smart Citation

Bacteriophages that infect marine roseobacters: genomics and ecology

Zhan

Chen

2019

Environmental Microbiology

Self Cite

View full text Add to dashboard Cite

show abstract

“…Bacterial viruses (bacteriophages or phages) are ubiquitous across environments. Their genomes vary considerably in size, from less than ten genes, up to hundreds (Hatfull and Hendrix 2011;Zhan and Chen 2019;Callanan et al 2020). Double-stranded DNA phages have by far the largest genomes and are usually regarded as the most abundant (Dion et al 2020).…”

Section: Introductionmentioning

confidence: 99%

Causes and consequences of bacteriophage diversification via genetic exchanges across lifestyles and bacterial taxa

Sousa

Pfeifer

Touchon

et al. 2020

Preprint

View full text Add to dashboard Cite

11 12Bacteriophages (henceforth phages) evolve by mutation and recombination. Temperate 13 phages are known to evolve rapidly by genetic exchanges. In contrast, recombination events 14 between virulent and between temperate and virulent phages have rarely been reported. A 15 gene flow barrier between these two large distinct groups of phages could affect the ability of 16 phages to acquire novel functions. Here, we show that genomes of temperate and virulent 17 phages are very distinct but often have a few almost identical genes. These cases are due to 18 recent genetic exchanges of both phage-like and bacterial-like genes. These exchanges were 19 probably mediated by phage recombinases with low homology requirements and mechanisms 20 of non-homologous end joining, since both were over-represented in recombinant phages and 21 their hosts. When assessing the impact of gene flow across the two populations of phages we 22 realized that temperate phages have narrower host ranges than virulent phages. This 23 suggests, and we find some evidence, that gene flow between temperate phages infecting 24 distant bacterial hosts might be mediated by recombination with the broader host virulent 25 phages. Hence, gene flow across phages with distinct lifestyles could drastically increase the 26 gene repertoire available for phage evolution, including the transfer of functional innovations 27 across taxa. These results also have implications for bacterial evolution because of the impact 28 of phage predation in bacterial population dynamics and the contribution of temperate phages 29 to the evolution of bacterial gene repertoires. 31 SIGNIFICANCE STATEMENT 33Many microbial communities are intensely predated by temperate and virulent 34 bacteriophages. The former also contribute to bacterial gene repertoires. Gene transfers 35 between bacteriophages favor their rapid adaptation, but are thought to occur rarely between 36 virulent and temperate bacteriophages because their genomes are very different in terms of 37 gene repertoires and genetic organization. We found that genetic exchanges occur frequently 38 3 between these types of bacteriophages, involve different phage and bacterial functions, and 39 are likely due to multiple DNA repair processes. Since we show that virulent bacteriophages 40 have broader host ranges, they can shuttle genes between temperate bacteriophages present 41 in taxa that are beyond the typical range of the latter. This enhances phages diversification 42 and has multiple impacts on bacterial evolution. 43 65 accretion in virulent phages, even if some families of virulent phages have remarkable 66 diversity in their genomes' size, suggesting the existence of mechanisms of gene exchange 67 (12). The genomic plasticity of temperate lambdoid phages has been much more extensively 68 studied (9, 13, 14). Their analyses reveal that pairs of phages tend to have patches of regions 69 of very similar sequences within genomes that are often very dissimilar. This genome 70 mosaicism is facilitated by the modular or...

show abstract

“…However, the presence of prophages belonging to several undescribed groups of 72 microviruses within the genomes of some Bacteroidetes and Alphaproteobacteria 73 (Krupovic and Forterre, 2011;Zhan and Chen, 2018;Zheng et al, 2018) raises the 74 possibility that some can be integrated through the use of host-proteins, in a similar 75 manner to the XerC/XerD dependent integration of ssDNA Inoviridae (Krupovic and 76 Forterre, 2015). 77…”

Section: Introduction 43mentioning

confidence: 99%