Widespread stop-codon recoding in bacteriophages may regulate translation of lytic genes

Borges, Adair L.; Lou, Yue Clare; Sachdeva, Rohan; Al-Shayeb, Basem; Penev, Petar I.; Jaffe, Alexander L.; Lei, Shufei; Santini, Joanne M.; Banfield, Jillian F.

doi:10.1038/s41564-022-01128-6

Cited by 38 publications

(64 citation statements)

References 75 publications

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“…In order to represent the gut virome as comprehensively as possible, we incorporated genomes from existing viral databases [3, 23-31] (Table 2) into the analysis. To avoid redundancy, both the viral genomes from the databases and the virus-like contigs identified in the four Dutch cohorts were clustered into virus operational taxonomic units (vOTUs) together.…”

Section: Resultsmentioning

confidence: 99%

“…Only 7% of the vOTUs were assigned to such groups based on the presence of previously classified genomes within the vOTUs (Figure 3, Table S1). Extending assignment by finding the most recent common ancestor (MRCA) of all vOTUs assigned to a group on the TerL-based phylogenetic tree, and then placing all descendants of the MRCA into the group, resulted in 11% of vOTUs being taxonomically assigned: family Autographiviridae (4 vOTUs), family Drexlerviridae (2 vOTUs), Flandersviridae (also known as Gubaphages, 32 vOTUs) [2, 24, 27], Gratiaviridae (16 vOTUs) [24], crAss-like phages (135 vOTUs), group Topaz (18 vOTUs) and group Garnet (1 vOTU) [31].…”

Section: Resultsmentioning

confidence: 99%

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Diversity and ecology of Caudoviricetes phages with genome terminal repeats in fecal metagenomes from four Dutch cohorts

Gulyaeva

Garmaeva

Kurilshikov

et al. 2022

Preprint

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The human gut harbors numerous viruses infecting the human host, microbes and other inhabitants of the gastrointestinal tract. Most of these viruses remain undiscovered, and their influence on human health is unknown. Here we characterize viral genomes in gut metagenomic data from 1,950 individuals from four population and patient cohorts. We focus on a subset of viruses that is highly abundant in the gut, remains largely uncharacterized, and allows confident complete genome identification - phages that belong to the class Caudoviricetes and possess genome terminal repeats. We detect 1,899 species-level units belonging to this subset, 19% of which do not have complete representative genomes in major public gut virome databases. These units display diverse genomic features, are predicted to infect a wide range of microbial hosts, and on average account for < 1% of metagenomic reads. Analysis of longitudinal data from 338 individuals shows that the composition of this fraction of the virome remained relatively stable over a period of 4 years. We also demonstrate that 54 species-level units are highly prevalent (detected in > 5% of individuals in a cohort). Finally, we find 34 associations between highly prevalent phages and human phenotypes, 24 of which can be explained by the relative abundance of potential hosts.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Diversity and ecology of Caudoviricetes phages with genome terminal repeats in fecal metagenomes from four Dutch cohorts

Gulyaeva

Garmaeva

Kurilshikov

et al. 2022

Preprint

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“…Viral genomes observed within bacterial genome fragments were identified as lysogenic. Viral hosts were identified using a combination of gene homologies, the presence of tRNAs, and CRISPR (clustered regularly interspaced short palindromic repeats) spacers (Coutinho et al , 2017; Borges et al , 2022). (I) Sequence homology matches were made from the phages identified from Lime Blue and Poison Lake to databases generated from PSB/GSB genomes retrieved from NCBI, and MAGs generated in this study using BLASTn (Camacho et al , 2009).…”

Section: Methodsmentioning

confidence: 99%

Genomics of viruses infecting green and purple sulfur bacteria in two euxinic lakes

Hesketh-Best

Bosco-Santos

Garcia

et al. 2022

Preprint

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Viral infections of marine bacteria modulate the rates of primary production and the cycling of organic and inorganic matter in the world's oceans. Here, we investigated the hypothesis that viral infections influence the ecology of purple and green sulfur bacteria (PSB and GSB) in anoxic and sulfidic (euxinic) lakes, modern analogs of early Earth oceans. Over 200 high and medium quality viral contigs were identified in long-read metagenomes from the sediments and water column of Lime Blue and Poison Lake, respectively. We compared these sequences with 94 predicted prophages identified in the complete genomes of PSB (n = 213) and GSB (n = 33). Viral genomes carrying psbA, encoding the small subunit of photosystem II protein, were present in all three datasets (sediment, water column, and complete genomes). The ubiquity of these genes suggests that PSB and GSB viruses interfere with the light reactions of sulfur-oxidizing autotrophs in a process similar to viral modulation of photosynthesis in Cyanobacteria. Viruses predicted to infect PSB and GSB also encoded auxiliary metabolic genes involved in reductive sulfur assimilation as cysteine, a pathway not yet described in these sulfur bacteria, as well as genes involved in pigment production (crtF) and carbon fixation (CP12, zwf, PGD). These observations highlight the potential for viral modulation of metabolic markers used as proxies to interpret biogeochemical processes in early Earth oceans.

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“…To account for the possibility of alternatively-coded phages, predictions were made in genetic codes 11, 15, and 4, and coding density was compared. If an 'alternate' code (15 or 4) displayed an increase in coding density ≥10% relative to standard (11) code for a given phage [77], protein predictions in that code were retained. Otherwise, protein predictions in standard code were retained.…”

Section: Phage-related Analysesmentioning

confidence: 99%

Variable impact of geochemical gradients on the functional potential of bacteria, archaea, and phages from the permanently stratified Lac Pavin

Jaffe

Bardot

Jeune

et al. 2022

Preprint

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Permanently stratified lakes contain diverse microbial communities that vary with depth, and so serve as useful models for studying the relationships between microbial community structure and geochemistry. Recent work has shown that these lakes can also harbor numerous bacteria and archaea from novel lineages, including those from the Candidate Phyla Radiation (CPR). However, the extent to which geochemical stratification differentially impacts carbon metabolism and overall genetic potential in CPR bacteria compared to other organisms is not well defined. Here, we determine the distribution of microbial lineages along an oxygen gradient in Lac Pavin, a deep, stratified lake in central France, and examine the influence of this gradient on their metabolism. Genome-based analyses revealed an enrichment of distinct C1 and CO2 fixation pathways in the oxic lake interface and anoxic zone/sediments, suggesting that oxygen likely plays a role in structuring metabolic strategies in non-CPR bacteria and archaea. Notably, we find that oxidation of methane and its byproducts is largely spatially separated from methane production, which is mediated by diverse communities of sediment methanogens that vary on the centimeter scale. In contrast, we detected evidence for RuBisCO throughout the water column and sediments, including form II/III and form III-related enzymes encoded by CPR bacteria in the water column and DPANN archaea in the sediments. Overall, CPR bacteria and phages did not show strong signals of gene content differentiation by depth, despite the fact that distinct species groups populate different lake and sediment compartments. Thus, environmental gradients in Lac Pavin probably select for the capacities of CPR bacteria and phages to a lesser extent than other bacteria and archaea, possibly because selection on the former groups is indirect and depends on host characteristics.

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Widespread stop-codon recoding in bacteriophages may regulate translation of lytic genes

Cited by 38 publications

References 75 publications

Diversity and ecology of Caudoviricetes phages with genome terminal repeats in fecal metagenomes from four Dutch cohorts

Diversity and ecology of Caudoviricetes phages with genome terminal repeats in fecal metagenomes from four Dutch cohorts

Genomics of viruses infecting green and purple sulfur bacteria in two euxinic lakes

Variable impact of geochemical gradients on the functional potential of bacteria, archaea, and phages from the permanently stratified Lac Pavin

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