Do Viruses Exchange Genes across Superkingdoms of Life?

Malik, Shahana Seher; Azem-e-Zahra, Syeda; Kim, Kyung Mo; Caetano‐Anollés, Gustavo; Nasir, Arshan

doi:10.3389/fmicb.2017.02110

Cited by 28 publications

(29 citation statements)

References 77 publications

(118 reference statements)

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“…Building on previous ideas [ 26 ], new intelligent definitions of viruses have been proposed (e.g., the virocell and virion-factory concepts discussed below) [ 4 , 27 ] that highlight the distinction between viruses and virions [ 7 , 28 ]. In parallel, we and others have integrated the genomes of giant viruses into phylogenetic and phylogenomic studies to investigate their origin, evolution, and co-evolution with their hosts [ 3 , 9 , 11 , 14 , 29 – 33 ], some fueled by the appreciation of the importance of protein structure [ 34 , 35 ].…”

Section: Virology In the Era Of Giant Virusesmentioning

confidence: 99%

“…Here, we summarize our phylogenomic effort, which spans over a decade of investigations [ 3 , 8 – 10 , 29 , 36 ]. Unlike traditional approaches, our strategy focuses on protein structural domains grouped by conserved three-dimensional structural backbones [ 35 ].…”

Section: Virology In the Era Of Giant Virusesmentioning

confidence: 99%

“…The negligible presence of capsid/coat proteins in cells uncovered by our analysis supports the role of virus-to-cell horizontal gene transfer events that mediate molecular innovation. Capsid/coat-related proteins are hallmark virus proteins that point to genetic innovation in viruses [ 29 ]. The cellular distribution of 37 FFs related to capsid/coat FSFs (identified using data from Nasir and Caetano-Anollés [ 9 ]) attests to this innovation.…”

Section: Virus-specific Genes and Virus-to-cell Gene Transfermentioning

confidence: 99%

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The origin and evolution of viruses inferred from fold family structure

2020

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The canonical frameworks of viral evolution describe viruses as cellular predecessors, reduced forms of cells, or entities that escaped cellular control. The discovery of giant viruses has changed these standard paradigms. Their genetic, proteomic and structural complexities resemble those of cells, prompting a redefinition and reclassification of viruses. In a previous genome-wide analysis of the evolution of structural domains in proteomes, with domains defined at the fold superfamily level, we found the origins of viruses intertwined with those of ancient cells. Here, we extend these data-driven analyses to the study of fold families confirming the co-evolution of viruses and ancient cells and the genetic ability of viruses to foster molecular innovation. The results support our suggestion that viruses arose by genomic reduction from ancient cells and validate a co-evolutionary 'symbiogenic' model of viral origins.

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Section: Virology In the Era Of Giant Virusesmentioning

confidence: 99%

Section: Virology In the Era Of Giant Virusesmentioning

confidence: 99%

Section: Virus-specific Genes and Virus-to-cell Gene Transfermentioning

confidence: 99%

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The origin and evolution of viruses inferred from fold family structure

2020

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“…Viruses infect all living things from three domains of life (Bacteria, Archaea, and Eukarya), and they represent the most abundant and ubiquitous biological entities on the planet (1–3). As mandatory intracellular parasites, viruses evolve in close physical contact with their hosts and drive the evolution of the host via gene transfer (4–6) and coevolutionary arms races (7–10). The major virological discoveries of the last few decades are the successive discoveries of the diverse nature of the virosphere with respect to virion structures (3, 11–13), genetic repertoire (14–16), and various replication strategies in the cell (17–19).…”

Section: Introductionmentioning

confidence: 99%

Medusavirus, a Novel Large DNA Virus Discovered from Hot Spring Water

Yoshikawa

Blanc-Mathieu

Song

et al. 2019

J Virol

141

210

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Recent discoveries of new large DNA viruses reveal high diversity in their morphologies, genetic repertoires, and replication strategies. Here, we report the novel features of medusavirus, a large DNA virus newly isolated from hot spring water in Japan. Medusavirus, with a diameter of 260 nm, shows a T=277 icosahedral capsid with unique spherical-headed spikes on its surface. It has a 381-kb genome encoding 461 putative proteins, 86 of which have their closest homologs in Acanthamoeba, whereas 279 (61%) are orphan genes. The virus lacks the genes encoding DNA topoisomerase II and RNA polymerase, showing that DNA replication takes place in the host nucleus, whereas the progeny virions are assembled in the cytoplasm. Furthermore, the medusavirus genome harbored genes for all five types of histones (H1, H2A, H2B, H3, and H4) and one DNA polymerase, which are phylogenetically placed at the root of the eukaryotic clades. In contrast, the host amoeba encoded many medusavirus homologs, including the major capsid protein. These facts strongly suggested that amoebae are indeed the most promising natural hosts of medusavirus, and that lateral gene transfers have taken place repeatedly and bidirectionally between the virus and its host since the early stage of their coevolution. Medusavirus reflects the traces of direct evolutionary interactions between the virus and eukaryotic hosts, which may be caused by sharing the DNA replication compartment and by evolutionarily long lasting virus-host relationships. Based on its unique morphological characteristics and phylogenomic relationships with other known large DNA viruses, we propose that medusavirus represents a new family, Medusaviridae. IMPORTANCE We have isolated a new nucleocytoplasmic large DNA virus (NCLDV) from hot spring water in Japan, named medusavirus. This new NCLDV is phylogenetically placed at the root of the eukaryotic clades based on the phylogenies of several key genes, including that encoding DNA polymerase, and its genome surprisingly encodes the full set of histone homologs. Furthermore, its laboratory host, Acanthamoeba castellanii, encodes many medusavirus homologs in its genome, including the major capsid protein, suggesting that the amoeba is the genuine natural host from ancient times of this newly described virus and that lateral gene transfers have repeatedly occurred between the virus and amoeba. These results suggest that medusavirus is a unique NCLDV preserving ancient footprints of evolutionary interactions with its hosts, thus providing clues to elucidate the evolution of NCLDVs, eukaryotes, and virus-host interaction. Based on the dissimilarities with other known NCLDVs, we propose that medusavirus represents a new viral family, Medusaviridae.

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“…Viruses swap genes among a great number of organisms beyond their common hosts. These infections contribute to the diversity of genetic tools in cells that they are not typically known to infect as virus hallmark genes [ 136 ].…”

Section: Variations In Multicellular Organismsmentioning

confidence: 99%

Non-Random Genome Editing and Natural Cellular Engineering in Cognition-Based Evolution

Miller

Enguita

Leitão

2021

Cells

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Neo-Darwinism presumes that biological variation is a product of random genetic replication errors and natural selection. Cognition-Based Evolution (CBE) asserts a comprehensive alternative approach to phenotypic variation and the generation of biological novelty. In CBE, evolutionary variation is the product of natural cellular engineering that permits purposive genetic adjustments as cellular problem-solving. CBE upholds that the cornerstone of biology is the intelligent measuring cell. Since all biological information that is available to cells is ambiguous, multicellularity arises from the cellular requirement to maximize the validity of available environmental information. This is best accomplished through collective measurement purposed towards maintaining and optimizing individual cellular states of homeorhesis as dynamic flux that sustains cellular equipoise. The collective action of the multicellular measurement and assessment of information and its collaborative communication is natural cellular engineering. Its yield is linked cellular ecologies and mutualized niche constructions that comprise biofilms and holobionts. In this context, biological variation is the product of collective differential assessment of ambiguous environmental cues by networking intelligent cells. Such concerted action is enabled by non-random natural genomic editing in response to epigenetic impacts and environmental stresses. Random genetic activity can be either constrained or deployed as a ‘harnessing of stochasticity’. Therefore, genes are cellular tools. Selection filters cellular solutions to environmental stresses to assure continuous cellular-organismal-environmental complementarity. Since all multicellular eukaryotes are holobionts as vast assemblages of participants of each of the three cellular domains (Prokaryota, Archaea, Eukaryota) and the virome, multicellular variation is necessarily a product of co-engineering among them.

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Do Viruses Exchange Genes across Superkingdoms of Life?

Cited by 28 publications

References 77 publications

The origin and evolution of viruses inferred from fold family structure

The origin and evolution of viruses inferred from fold family structure

Medusavirus, a Novel Large DNA Virus Discovered from Hot Spring Water

Non-Random Genome Editing and Natural Cellular Engineering in Cognition-Based Evolution

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