Viruses as Winners in the Game of Life

Güemes, Ana Georgina Cobián; Youle, Merry; Cantu, Adrian; Felts, Ben; Nulton, James; Rohwer, Forest

doi:10.1146/annurev-virology-100114-054952

Cited by 222 publications

(154 citation statements)

References 84 publications

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“…In addition to the challenge of surviving in wide-ranging hostile niches, such as the human body and the depths of the ocean, microbes face a constant onslaught from viruses (1). Bacteriophages (phages)—viruses that infect bacteria—are the most abundant biological entities on the planet, with estimates of ~10 31 particles on Earth (2). Phages are intrinsically specific for the bacterial host that they infect, typically being restricted to a single bacterial species and even a subset of strains within that species.…”

Section: Antiphage Defensementioning

confidence: 99%

The Discovery, Mechanisms, and Evolutionary Impact of Anti-CRISPRs

2017

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Bacteria and archaea use CRISPR-Cas adaptive immune systems to defend themselves from infection by bacteriophages (phages). These RNA-guided nucleases are powerful weapons in the fight against foreign DNA, such as phages and plasmids, as well as a revolutionary gene editing tool. Phages are not passive bystanders in their interactions with CRISPR-Cas systems, however; recent discoveries have described phage genes that inhibit CRISPR-Cas function. More than 20 protein families, previously of unknown function, have been ascribed anti-CRISPR function. Here, we discuss how these CRISPR-Cas inhibitors were discovered and their modes of action elucidated. We also consider the potential impact of anti-CRISPRs on bacterial and phage evolution. Finally, we speculate about the future of this field.

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Section: Antiphage Defensementioning

confidence: 99%

The Discovery, Mechanisms, and Evolutionary Impact of Anti-CRISPRs

2017

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“…We must constantly remember that viruses and subviral infectious genetic parasites are the most abundant biological agents on the planet . They outnumber cellular life forms by 10 times, invade all cellular organisms, and serve as key agents in the generation of adaptive and innate immune systems, which are essential for the survival of cellular life forms since they are key for the capacity for self/nonself‐differentiation .…”

Section: Viruses and Their Relativesmentioning

confidence: 99%

That is life: communicating RNA networks from viruses and cells in continuous interaction

Villarreal

Witzany²

2019

Annals of the New York Academy of Sciences

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All the conserved detailed results of evolution stored in DNA must be read, transcribed, and translated via an RNA‐mediated process. This is required for the development and growth of each individual cell. Thus, all known living organisms fundamentally depend on these RNA‐mediated processes. In most cases, they are interconnected with other RNAs and their associated protein complexes and function in a strictly coordinated hierarchy of temporal and spatial steps (i.e., an RNA network). Clearly, all cellular life as we know it could not function without these key agents of DNA replication, namely rRNA, tRNA, and mRNA. Thus, any definition of life that lacks RNA functions and their networks misses an essential requirement for RNA agents that inherently regulate and coordinate (communicate to) cells, tissues, organs, and organisms. The precellular evolution of RNAs occurred at the core of the emergence of cellular life and the question remained of how both precellular and cellular levels are interconnected historically and functionally. RNA networks and RNA communication can interconnect these levels. With the reemergence of virology in evolution, it became clear that communicating viruses and subviral infectious genetic parasites are bridging these two levels by invading, integrating, coadapting, exapting, and recombining constituent parts in host genomes for cellular requirements in gene regulation and coordination aims. Therefore, a 21st century understanding of life is of an inherently social process based on communicating RNA networks, in which viruses and cells continuously interact.

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“…Viruses are the most abundant biological entities on Earth, with the number of virus-like particles (VLPs) being estimated to be $4.80 3 10 31 (Cobi an G€ uemes et al, 2016). The bacteriophages (phages) that infect bacterial cells represent the largest proportion of VLPs, and are present as 10-times more abundant than their hosts (Ignacio-Espinoza et al, 2013), bacteria.…”

Section: Introductionmentioning

confidence: 99%

“…In-depth studies on specific bacteriophages have also been performed and discovered cyanophages with photosystem genes to assist their host metabolism and enhance their reproductivity (Sharon et al, 2009) and pelagiphages and Puniceispirillum phage, the most abundant bacteriophages in the ocean that infect the SAR11 and SAR116 clades respectively (Kang et al, 2013;Zhao et al, 2013). However, most of the extensive studies on bacteriophage are confined to marine environments (Brum and Sullivan, 2015;Roux et al, 2016), still leaving unexplored spaces of bacteriophages in other biospheres, such as freshwater lakes (Cobi an G€ uemes et al, 2016). To our knowledge, no phage has been isolated that infects major freshwater heterotrophic bacterial groups, such as acI, acIV, LD12, Limnohabitans, Polynucleobacter and LD28.…”

Section: Introductionmentioning

confidence: 99%

Genome characteristics and environmental distribution of the first phage that infects the LD28 clade, a freshwater methylotrophic bacterial group

Moon

Kang

Kim

et al. 2017

Environmental Microbiology

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Bacteriophages infecting major groups of freshwater heterotrophic bacteria have been rarely isolated, hampering analyses of freshwater viromes. Here, we report the isolation and genomic characterization of P19250A, the first phage that infects the LD28 clade, an abundant freshwater methylotrophic bacterial group. P19250A was isolated from Lake Soyang, an oligotrophic reservoir, using an LD28 strain as a host. Morphological and genomic analyses revealed that P19250A is a lytic siphovirus with a ∼38.6-kb genome. To analyze the distribution of P19250A genome within its habitat, six seasonal viral metagenome (virome) samples were prepared from Lake Soyang. Through binning analysis of freshwater viromes, P19250A was shown to be the most highly assigned freshwater phage that infects heterotrophic bacteria (up to 8.21%) in five viromes. Furthermore, when freshwater virome data collected worldwide were analyzed, P19250A genome also showed high abundance, especially in Lough Neagh, UK, where P19250A genome was recorded as the most abundant bacteriophage. From metagenome analysis, the proportion of P19250A-assigned reads showed seasonal fluctuation following the abundance of the LD28 clade in Lake Soyang. These results showed that P19250A would be an essential resource for analyses of freshwater viromes, and also suggest that phages of other abundant freshwater bacteria need to be isolated for better understanding of freshwater viruses.

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Viruses as Winners in the Game of Life

Cited by 222 publications

References 84 publications

The Discovery, Mechanisms, and Evolutionary Impact of Anti-CRISPRs

The Discovery, Mechanisms, and Evolutionary Impact of Anti-CRISPRs

That is life: communicating RNA networks from viruses and cells in continuous interaction

Genome characteristics and environmental distribution of the first phage that infects the LD28 clade, a freshwater methylotrophic bacterial group

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