Identification of the First Gene Transfer Agent (GTA) Small Terminase in
            <i>Rhodobacter capsulatus</i>
            and Its Role in GTA Production and Packaging of DNA

Sherlock, David; Leong, Jia Xuan; Fogg, Paul C. M.

doi:10.1128/jvi.01328-19

“…When particular functional genome modules in their respective order were focused on, the following differences were observed. A comparison of the amino acid sequences of the terminase small subunit (TerS), which tends to be one of the least conserved phage proteins (42), divides known S. epidermidis phietaviruses into two subgroups, where phages 27, 48, and E72 represent one and phages 456 and 459 represent the other (Fig. 5A).…”

Section: Resultsmentioning

confidence: 99%

Staphylococcus epidermidis Phages Transduce Antimicrobial Resistance Plasmids and Mobilize Chromosomal Islands

Fišarová

¹

,

Botka

²

,

Du

³

et al. 2021

mSphere

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Staphylococcus epidermidis is a leading opportunistic pathogen causing nosocomial infections that is notable for its ability to form a biofilm and for its high rates of antibiotic resistance. It serves as a reservoir of multiple antimicrobial resistance genes that spread among the staphylococcal population by horizontal gene transfer such as transduction. While phage-mediated transduction is well studied in Staphylococcus aureus, S. epidermidis transducing phages have not been described in detail yet. Here, we report the characteristics of four phages, 27, 48, 456, and 459, previously used for S. epidermidis phage typing, and the newly isolated phage E72, from a clinical S. epidermidis strain. The phages, classified in the family Siphoviridae and genus Phietavirus, exhibited an S. epidermidis-specific host range, and together they infected 49% of the 35 strains tested. A whole-genome comparison revealed evolutionary relatedness to transducing S. aureus phietaviruses. In accordance with this, all the tested phages were capable of transduction with high frequencies up to 10−4 among S. epidermidis strains from different clonal complexes. Plasmids with sizes from 4 to 19 kb encoding resistance to streptomycin, tetracycline, and chloramphenicol were transferred. We provide here the first evidence of a phage-inducible chromosomal island transfer in S. epidermidis. Similarly to S. aureus pathogenicity islands, the transfer was accompanied by phage capsid remodeling; however, the interfering protein encoded by the island was distinct. Our findings underline the role of S. epidermidis temperate phages in the evolution of S. epidermidis strains by horizontal gene transfer, which can also be utilized for S. epidermidis genetic studies. IMPORTANCE Multidrug-resistant strains of S. epidermidis emerge in both nosocomial and livestock environments as the most important pathogens among coagulase-negative staphylococcal species. The study of transduction by phages is essential to understanding how virulence and antimicrobial resistance genes spread in originally commensal bacterial populations. In this work, we provide a detailed description of transducing S. epidermidis phages. The high transduction frequencies of antimicrobial resistance plasmids and the first evidence of chromosomal island transfer emphasize the decisive role of S. epidermidis phages in attaining a higher pathogenic potential of host strains. To date, such importance has been attributed only to S. aureus phages, not to those of coagulase-negative staphylococci. This study also proved that the described transducing bacteriophages represent valuable genetic modification tools in S. epidermidis strains where other methods for gene transfer fail.

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“…The RcGTA gene g1 , which is adjacent to the terL gene (g2) in the RcGTA genome, has been recently shown to encode TerS ( Sherlock, Leong, and Fogg 2019 ). Sherlock, Leong, and Fogg (2019) demonstrated that the RcGTA TerS binds non-specifically to DNA with low affinity due to the absence of a specific DNA-binding domain and the retention of non-specific DNA binding activity. A TerS protein with altered DNA-binding characteristics and a modified headful TerL might together underlie the random packaging that is characteristic of RcGTA.…”

Section: Discussionmentioning

confidence: 99%

Evolution of DNA packaging in gene transfer agents

Esterman

¹

,

Wolf

²

,

Kogay

³

et al. 2021

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Gene transfer agents (GTAs) are virus-like particles encoded and produced by many bacteria and archaea. Unlike viruses, GTAs package fragments of the host genome instead of the genes that encode the components of the GTA itself. As a result of this non-specific DNA packaging, GTAs can transfer genes within bacterial and archaeal communities. GTAs clearly evolved from viruses and are thought to have been maintained in prokaryotic genomes due to the advantages associated with their DNA transfer capacity. The most-studied GTA is produced by the alphaproteobacterium Rhodobacter capsulatus (RcGTA), which packages random portions of the host genome at a lower DNA density than usually observed in tailed bacterial viruses. How the DNA packaging properties of RcGTA evolved from those of the ancestral virus remains unknown. To address this question, we reconstructed the evolutionary history of the large subunit of the terminase (TerL), a highly conserved enzyme used by viruses and GTAs to package DNA. We found that RcGTA-like TerLs grouped within viruses that employ the headful packaging strategy. Because distinct mechanisms of viral DNA packaging correspond to differences in the TerL amino acid sequence, our finding suggests that RcGTA evolved from a headful packaging virus. Headful packaging is the least sequence-specific mode of DNA packaging, which would facilitate the switch from packaging of the viral genome to packaging random pieces of the host genome during GTA evolution.

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“…In addition to TerL, other GTA proteins that are involved in DNA packaging, including TerS and portal, might contribute to the unique DNA packaging features of RcGTA. In particular, the RcGTA gene g1, which is adjacent to the terL gene (g2) in the RcGTA genome, has been recently shown to encode TerS (Sherlock et al, 2019). Sherlock et al (2019) demonstrated that the RcGTA TerS binds non-specifically to DNA with low affinity due to the absence of a specific DNA-binding domain and the retention of non-specific DNA binding activity.…”

Section: Discussionmentioning

confidence: 99%

“…In particular, the RcGTA gene g1, which is adjacent to the terL gene (g2) in the RcGTA genome, has been recently shown to encode TerS (Sherlock et al, 2019). Sherlock et al (2019) demonstrated that the RcGTA TerS binds non-specifically to DNA with low affinity due to the absence of a specific DNA-binding domain and the retention of non-specific DNA binding activity. A TerS protein with altered DNA-binding characteristics and a modified headful TerL might together underlie the random packaging that is characteristic of RcGTA.…”

Section: Discussionmentioning

confidence: 99%

Phylogenetic evidence of headful packaging strategy in gene transfer agents

Esterman

¹

,

Wolf²,

Kogay³

et al. 2020

Preprint

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Gene transfer agents (GTAs) are virus-like particles encoded and produced by many bacteria and archaea. Unlike viruses, GTAs package fragments of the host genome instead of the genes that encode the components of the GTA itself. As a result of this non-specific DNA packaging, GTAs can transfer genes within bacterial and archaeal communities. GTAs clearly evolved from viruses and are thought to have been maintained in prokaryotic genomes due to the advantages associated with their DNA transfer capacity. The most-studied GTA is produced by the alphaproteobacterium Rhodobacter capsulatus (RcGTA), which packages random portions of the host genome at a lower DNA density than usually observed in tailed bacterial viruses. How the DNA packaging properties of RcGTA evolved from those of the ancestral virus remains unknown. To address this question, we reconstructed the evolutionary history of the large subunit of the terminase (TerL), a highly conserved enzyme used by viruses and GTAs to package DNA. We found that RcGTA-like TerLs grouped within viruses that employ the headful packaging strategy. Because distinct mechanisms of viral DNA packaging correspond to differences in the TerL amino acid sequence, our finding suggests that RcGTA evolved from a headful packaging virus. Headful packaging is the least sequence-specific mode of DNA packaging, which would facilitate the switch from packaging of the viral genome to packaging random pieces of the host genome during GTA evolution.

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Identification of the First Gene Transfer Agent (GTA) Small Terminase in Rhodobacter capsulatus and Its Role in GTA Production and Packaging of DNA

Cited by 18 publications

References 63 publications

Staphylococcus epidermidis Phages Transduce Antimicrobial Resistance Plasmids and Mobilize Chromosomal Islands

Staphylococcus epidermidis Phages Transduce Antimicrobial Resistance Plasmids and Mobilize Chromosomal Islands

Evolution of DNA packaging in gene transfer agents

Phylogenetic evidence of headful packaging strategy in gene transfer agents

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