Two Inducible Prophages of an Antarctic Pseudomonas sp. ANT_H14 Use the Same Capsid for Packaging Their Genomes – Characterization of a Novel Phage Helper-Satellite System

Dziewit, Łukasz; Radlińska, Monika

doi:10.1371/journal.pone.0158889

Cited by 12 publications

(8 citation statements)

References 84 publications

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“…The high coverage of some of these genomes together with the recovery of the same contig length from several individual samples (which were circularly permuted relative to each other; 37851 bp contig ex 9 S detected as circular) suggests that these genomes are complete, or nearly so. It may be that the terminase, in this case, is radically different from those found in current databases or this role may be fulfilled by other terminases present in the host analogous to the ΦAH14a and ΦAH14b satellite phage helper system 60 .…”

Section: Resultsmentioning

confidence: 84%

Novel phages of healthy skin metaviromes from South Africa

Zyl

Abrahams

Stander

et al. 2018

Sci Rep

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Recent skin metagenomic studies have investigated the harbored viral diversity and its possible influence on healthy skin microbial populations, and tried to establish global patterns of skin-phage evolution. However, the detail associated with the phages that potentially play a role in skin health has not been investigated. While skin metagenome and -metavirome studies have indicated that the skin virome is highly site specific and shows marked interpersonal variation, they have not assessed the presence/absence of individual phages. Here, we took a semi-culture independent approach (metaviromic) to better understand the composition of phage communities on skin from South African study participants. Our data set adds over 130 new phage species of the skin to existing databases. We demonstrated that identical phages were present on different individuals and in different body sites, and we conducted a detailed analysis of the structural organization of these phages. We further found that a bacteriophage related to the Staphylococcus capitis phage Stb20 may be a common skin commensal virus potentially regulating its host and its activities on the skin.

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Section: Resultsmentioning

confidence: 84%

Novel phages of healthy skin metaviromes from South Africa

Zyl

Abrahams

Stander

et al. 2018

Sci Rep

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“…To identify a suitable insertion site for the efflux pump genes, we considered the replacement of proviral segments. Prophages often contain superfluous or burdensome DNA components that can eventually become harmful under certain circumstances such as stress-triggering conditions, since complete prophages can re-enter the lytic cycle and kill the cell . However, in some cases the prophage might also encode beneficial features .…”

Section: Results and Discussionmentioning

confidence: 99%

Streamlined Pseudomonas taiwanensis VLB120 Chassis Strains with Improved Bioprocess Features

et al. 2019

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Microbes harbor many traits that are dispensable or even unfavorable under industrial and laboratory settings. The elimination of such traits could improve the host's efficiency, genetic stability, and robustness, thereby increasing the predictability and boosting its performance as a microbial cell factory. We engineered solvent-tolerant Pseudomonas taiwanensis VLB120 to yield streamlined chassis strains with higher growth rates and biomass yields, enhanced solvent tolerance, and improved process performance. In total, the genome was reduced by up to 10%. This was achieved by the elimination of genes that enable the cell to swim and form biofilms and by the deletion of the megaplasmid pSTY and large proviral segments. The resulting strain GRC1 had a 15% higher growth rate and biomass yield than the wildtype. However, this strain lacks the pSTY-encoded efflux pump TtgGHI, rendering it solventsensitive. Through reintegration of ttgGHI by chromosomal insertion without (GRC2) and with (GRC3) the corresponding regulator genes, the solvent-tolerant phenotype was enhanced. The generated P. taiwanensis GRC strains enlarge the repertoire of streamlined chassis with enhanced key performance indicators, making them attractive hosts for biotechnological applications. The different solvent tolerance levels of GRC1, GRC2, and GRC3 enable the selection of a fitting host platform in relation to the desired process requirements in a chassis àla carte principle. This was demonstrated in a metabolic engineering approach for the production of phenol from glycerol. The streamlined producer GRC1Δ5-TPL38 outperformed the equivalent nonstreamlined producer VLB120Δ5-TPL38 concerning phenol titer, rate, and yield, thereby highlighting the added value of the streamlined chassis.

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“…HTS has been used to a large extent in Antarctic environmental virology to study soil (Adriaenssens et al, 2017;Zablocki et al, 2014), lake (Aguirre de Cárcer et al, 2016;Lopez-Bueno et al, 2015, 2009Yau et al, 2011) and marine (Brum et al, 2017;Miranda et al, 2016) viral ecology. Novel viral genomes from various soils and lake samples (Dziewit and Radlinska, 2016;Kerepesi and Grolmusz, 2017;Meiring et al, 2012;Swanson et al, 2012;Zawar-Reza et al, 2014) have been determined using HTS approaches. In contrast, relatively little is known about viruses associated with Antarctic animals and the associated virus ecology despite the advent of HTS.…”

Section: Concluding Remarks and Future Directionsmentioning

confidence: 99%

Viruses associated with Antarctic wildlife: From serology based detection to identification of genomes using high throughput sequencing

2018

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The Antarctic, sub-Antarctic islands and surrounding sea-ice provide a unique environment for the existence of organisms. Nonetheless, birds and seals of a variety of species inhabit them, particularly during their breeding seasons. Early research on Antarctic wildlife health, using serology-based assays, showed exposure to viruses in the families Birnaviridae, Flaviviridae, Herpesviridae, Orthomyxoviridae and Paramyxoviridae circulating in seals (Phocidae), penguins (Spheniscidae), petrels (Procellariidae) and skuas (Stercorariidae). It is only during the last decade or so that polymerase chain reaction-based assays have been used to characterize viruses associated with Antarctic animals. Furthermore, it is only during the last five years that full/whole genomes of viruses (adenoviruses, anelloviruses, orthomyxoviruses, a papillomavirus, paramyoviruses, polyomaviruses and a togavirus) have been sequenced using Sanger sequencing or high throughput sequencing (HTS) approaches. This review summaries the knowledge of animal Antarctic virology and discusses potential future directions with the advent of HTS in virus discovery and ecology.

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Two Inducible Prophages of an Antarctic Pseudomonas sp. ANT_H14 Use the Same Capsid for Packaging Their Genomes – Characterization of a Novel Phage Helper-Satellite System

Cited by 12 publications

References 84 publications

Novel phages of healthy skin metaviromes from South Africa

Novel phages of healthy skin metaviromes from South Africa

Streamlined Pseudomonas taiwanensis VLB120 Chassis Strains with Improved Bioprocess Features

Viruses associated with Antarctic wildlife: From serology based detection to identification of genomes using high throughput sequencing

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