Jumbo Phages: A Comparative Genomic Overview of Core Functions and Adaptions for Biological Conflicts
Jumbo phages have attracted much attention by virtue of their extraordinary genome size and unusual aspects of biology. By performing a comparative genomics analysis of 224 jumbo phages, we suggest an objective inclusion criterion based on genome size distributions and present a synthetic overview o...
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doaj-4334188b47ed4d62bde09055c30c37222021-01-06T00:04:19ZengMDPI AGViruses1999-49152021-01-0113636310.3390/v13010063Jumbo Phages: A Comparative Genomic Overview of Core Functions and Adaptions for Biological ConflictsLakshminarayan M. Iyer0Vivek Anantharaman1Arunkumar Krishnan2A. Maxwell Burroughs3L. Aravind4National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USANational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USADepartment of Biological Sciences, Indian Institute of Science Education and Research (IISER) Berhampur, Odisha 760010, IndiaNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USANational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USAJumbo phages have attracted much attention by virtue of their extraordinary genome size and unusual aspects of biology. By performing a comparative genomics analysis of 224 jumbo phages, we suggest an objective inclusion criterion based on genome size distributions and present a synthetic overview of their manifold adaptations across major biological systems. By means of clustering and principal component analysis of the phyletic patterns of conserved genes, all known jumbo phages can be classified into three higher-order groups, which include both myoviral and siphoviral morphologies indicating multiple independent origins from smaller predecessors. Our study uncovers several under-appreciated or unreported aspects of the DNA replication, recombination, transcription and virion maturation systems. Leveraging sensitive sequence analysis methods, we identify novel protein-modifying enzymes that might help hijack the host-machinery. Focusing on host–virus conflicts, we detect strategies used to counter different wings of the bacterial immune system, such as cyclic nucleotide- and NAD<sup>+</sup>-dependent effector-activation, and prevention of superinfection during pseudolysogeny. We reconstruct the RNA-repair systems of jumbo phages that counter the consequences of RNA-targeting host effectors. These findings also suggest that several jumbo phage proteins provide a snapshot of the systems found in ancient replicons preceding the last universal ancestor of cellular life.https://www.mdpi.com/1999-4915/13/1/63DNA virusesanti-phage systemsnicotinamide dinucleotideDNA polymerasesDNA polymerase IIIRNA polymerase |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Lakshminarayan M. Iyer Vivek Anantharaman Arunkumar Krishnan A. Maxwell Burroughs L. Aravind |
spellingShingle |
Lakshminarayan M. Iyer Vivek Anantharaman Arunkumar Krishnan A. Maxwell Burroughs L. Aravind Jumbo Phages: A Comparative Genomic Overview of Core Functions and Adaptions for Biological Conflicts Viruses DNA viruses anti-phage systems nicotinamide dinucleotide DNA polymerases DNA polymerase III RNA polymerase |
author_facet |
Lakshminarayan M. Iyer Vivek Anantharaman Arunkumar Krishnan A. Maxwell Burroughs L. Aravind |
author_sort |
Lakshminarayan M. Iyer |
title |
Jumbo Phages: A Comparative Genomic Overview of Core Functions and Adaptions for Biological Conflicts |
title_short |
Jumbo Phages: A Comparative Genomic Overview of Core Functions and Adaptions for Biological Conflicts |
title_full |
Jumbo Phages: A Comparative Genomic Overview of Core Functions and Adaptions for Biological Conflicts |
title_fullStr |
Jumbo Phages: A Comparative Genomic Overview of Core Functions and Adaptions for Biological Conflicts |
title_full_unstemmed |
Jumbo Phages: A Comparative Genomic Overview of Core Functions and Adaptions for Biological Conflicts |
title_sort |
jumbo phages: a comparative genomic overview of core functions and adaptions for biological conflicts |
publisher |
MDPI AG |
series |
Viruses |
issn |
1999-4915 |
publishDate |
2021-01-01 |
description |
Jumbo phages have attracted much attention by virtue of their extraordinary genome size and unusual aspects of biology. By performing a comparative genomics analysis of 224 jumbo phages, we suggest an objective inclusion criterion based on genome size distributions and present a synthetic overview of their manifold adaptations across major biological systems. By means of clustering and principal component analysis of the phyletic patterns of conserved genes, all known jumbo phages can be classified into three higher-order groups, which include both myoviral and siphoviral morphologies indicating multiple independent origins from smaller predecessors. Our study uncovers several under-appreciated or unreported aspects of the DNA replication, recombination, transcription and virion maturation systems. Leveraging sensitive sequence analysis methods, we identify novel protein-modifying enzymes that might help hijack the host-machinery. Focusing on host–virus conflicts, we detect strategies used to counter different wings of the bacterial immune system, such as cyclic nucleotide- and NAD<sup>+</sup>-dependent effector-activation, and prevention of superinfection during pseudolysogeny. We reconstruct the RNA-repair systems of jumbo phages that counter the consequences of RNA-targeting host effectors. These findings also suggest that several jumbo phage proteins provide a snapshot of the systems found in ancient replicons preceding the last universal ancestor of cellular life. |
topic |
DNA viruses anti-phage systems nicotinamide dinucleotide DNA polymerases DNA polymerase III RNA polymerase |
url |
https://www.mdpi.com/1999-4915/13/1/63 |
work_keys_str_mv |
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