Diversity, taxonomy, and evolution of archaeal viruses of the class Caudoviricetes

Liu, Ying; Demina, Tatiana A.; Roux, Simon; Aiewsakun, Pakorn; Kazlauskas, Darius; Simmonds, Peter; Prangishvili, David; Oksanen, Hanna M.; Krupovìč, Mart

doi:10.1371/journal.pbio.3001442

Cited by 68 publications

(97 citation statements)

References 101 publications

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“…The diversification of Nucleocytoviricota before LECA is indeed supported by the RNA polymerase phylogenetic tree including both viral and cellular enzymes (Guglielmini et al 2019). Moreover it has been suggested that Caudoviricetes , which also infect archaeal hosts (Liu et al 2021), have diverged even prior to the emergence of LUCA (Krupovic et al 2020).…”

Section: Discussionmentioning

confidence: 99%

Viral origin of eukaryotic type IIA DNA topoisomerases

Guglielmini

Gaïa

Cunha³

et al. 2022

Preprint

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Type II DNA topoisomerases of the family A (Topo IIA) are present in all bacteria (DNA gyrase) and eukaryotes. In eukaryotes, they play a major role in transcription, DNA replication, chromosome segregation and modulation of chromosome architecture. The origin of eukaryotic Topo IIA remains mysterious since they are very divergent from their bacterial homologues and have no orthologues in Archaea. Interestingly, eukaryotic Topo IIA have close homologues in viruses of the phylum Nucleocytoviricota, an expansive assemblage of large and giant viruses formerly known as the nucleocytoplasmic large DNA viruses (NCLDV). Topo IIA are also encoded by some bacterioviruses of the class Caudoviricetes (tailed bacteriophages). To elucidate the origin of the eukaryotic Topo IIA, we performed in-depth phylogenetic analyses combining viral and cellular Topo IIA homologs. Topo IIA encoded by bacteria and eukaryotes form two monophyletic groups nested within Topo IIA encoded by Caudoviricetes and Nucleocytoviricota, respectively. Importantly, Nucleocytoviricota remained well separated from eukaryotes after removing both bacteria and Caudoviricetes from the dataset, indicating that the separation of Nucleocytoviricota and eukaryotes is probably not due to long branch attraction artefact. The topology of our tree suggests that the eukaryotic Topo IIA was probably acquired from an ancestral member of the Nucleocytoviricota of the class Megaviricetes, before the emergence of the last eukaryotic common ancestor (LECA). This result further highlights a key role of these viruses in eukaryogenesis and suggests that early proto-eukaryotes used a Topo IIB instead of a Topo IIA for solving their DNA topological problems.

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Section: Discussionmentioning

confidence: 99%

Viral origin of eukaryotic type IIA DNA topoisomerases

Guglielmini

Gaïa

Cunha³

et al. 2022

Preprint

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“…Biologists describe them as natural parasites (or predators) of bacteria and associate them with maintaining the balance of microorganisms on Earth (Wittebole et al, 2014). Tailed phages of the class Caudoviricetes including podovirus, myovirus, and siphovirus (Liu et al, 2021), and the polyhedral Microviridae family are usually associated with phage therapy applications (Supplementary Figure 1; Harper and Enright, 2011;Lin et al, 2017). Scientists attribute the phages' antibacterial activity to their well-established life cycle (lytic or lysogenic; Supplementary Figure 2).…”

Section: Phages In Seamentioning

confidence: 99%

Phage Revolution Against Multidrug-Resistant Clinical Pathogens in Southeast Asia

Carascal

Cruz-Papa

Remenyi³

et al. 2022

Front. Microbiol.

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Southeast Asia (SEA) can be considered a hotspot of antimicrobial resistance (AMR) worldwide. As recent surveillance efforts in the region reported the emergence of multidrug-resistant (MDR) pathogens, the pursuit of therapeutic alternatives against AMR becomes a matter of utmost importance. Phage therapy, or the use of bacterial viruses called bacteriophages to kill bacterial pathogens, is among the standout therapeutic prospects. This narrative review highlights the current understanding of phages and strategies for a phage revolution in SEA. We define phage revolution as the radical use of phage therapy in infectious disease treatment against MDR infections, considering the scientific and regulatory standpoints of the region. We present a three-phase strategy to encourage a phage revolution in the SEA clinical setting, which involves: (1) enhancing phage discovery and characterization efforts, (2) creating and implementing laboratory protocols and clinical guidelines for the evaluation of phage activity, and (3) adapting regulatory standards for therapeutic phage formulations. We hope that this review will open avenues for scientific and policy-based discussions on phage therapy in SEA and eventually lead the way to its fullest potential in countering the threat of MDR pathogens in the region and worldwide.

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“…HF2 is a myovirus belonging to the species Haloferacalesvirus HF1, within the genus Haloferacalesvirus (family: Hafunaviridae, previously Myoviridae) [1]. It is lytic and can infect two species of extremely halophilic archaea, Halorubrum saccharovorum and Halorubrum coriense [2].…”

Section: Introductionmentioning

confidence: 99%

“…The modular gene organization in haloferacalesviruses is well conserved [1,6]. Genes are organized as modular units in two genomic arms so that most genes are directed towards the centre.…”

Section: Introductionmentioning

confidence: 99%

“…Although many new isolates and genome sequences of haloviruses have recently become available [1], little is known regarding the regulation of gene expression during lytic infection or in the provirus state. Within both classes of IRs are AT-rich sequences that could represent promoter motifs, but experimental evidence supporting this hypothesis has so far been lacking.…”

Section: Introductionmentioning

confidence: 99%

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Halovirus HF2 Intergenic Repeat Sequences Carry Promoters

Russ

Pfeiffer

Dyall‐Smith

2021

Viruses

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Halovirus HF2 was the first member of the Haloferacalesvirus genus to have its genome fully sequenced, which revealed two classes of intergenic repeat (IR) sequences: class I repeats of 58 bp in length, and class II repeats of 29 bp in length. Both classes of repeat contain AT-rich motifs that were conjectured to represent promoters. In the present study, nine IRs were cloned upstream of the bgaH reporter gene, and all displayed promoter activity, providing experimental evidence for the previous conjecture. Comparative genomics showed that IR sequences and their relative genomic positions were strongly conserved among other members of the same virus genus. The transcription of HF2 was also examined by the reverse-transcriptase-PCR (RT-PCR) method, which demonstrated very long transcripts were produced that together covered most of the genome, and from both strands. The presence of long counter transcripts suggests a regulatory role or possibly unrecognized coding potential.

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Diversity, taxonomy, and evolution of archaeal viruses of the class Caudoviricetes

Cited by 68 publications

References 101 publications

Viral origin of eukaryotic type IIA DNA topoisomerases

Viral origin of eukaryotic type IIA DNA topoisomerases

Phage Revolution Against Multidrug-Resistant Clinical Pathogens in Southeast Asia

Halovirus HF2 Intergenic Repeat Sequences Carry Promoters

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