The coevolution of large and small terminases of bacteriophages is a result of purifying selection leading to phenotypic stabilization

Wangchuk, Jigme; Chatterjee, Anirvan; Patil, Supriya; Madugula, Santhosh Kumar; Kondabagil, Kiran

doi:10.1016/j.virol.2021.09.004

Cited by 5 publications

(1 citation statement)

References 97 publications

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“…In the absence of a genomic taxonomy for viruses, we have referred to those phages that encode members of the same terminase family as members of the same phage family 35 . This notation is predicated on previous studies, including our own 36 , that have shown no significant sequence similarity between terminase sequences of unrelated phages 37,38 as well as studies that have used the terminases to build phage phylogenetic trees 39,40 . Moreover, we focused our search on terminases because they are among the most functionally-conserved genes in double-stranded DNA phage genomes 41,42 .…”

Section: Introductionmentioning

confidence: 99%

Machine learning models can identify individuals based on a resident oral bacteriophage family

Mahmoudabadi,

Homyk,

Catching

et al. 2024

Preprint

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Metagenomic studies have revolutionized the study of novel phages. However these studies trade depth of coverage for breadth. We show that the targeted sequencing of a small region of a phage terminase family can provide sufficient sequence diversity to serve as an individual-specific barcode or a phageprint, defined as the relative abundance profile of the variants within a terminase family. By collecting ~700 oral samples from ~100 individuals living on multiple continents, we found a consistent trend wherein each individual harbors one or two dominant variants that coexist with numerous low-abundance variants. By tracking phageprints over the span of a month across ten individuals, we observed that phageprints were generally stable, and found instances of concordant temporal fluctuations of variants shared between partners. To quantify these patterns further, we built machine learning models that, with high precision and recall, distinguished individuals even when we eliminated the most abundant variants and further downsampled phageprints to 2% of the remaining variants. Except between partners, phageprints are dissimilar between individuals, and neither country-of-residence, genetics, diet nor cohabitation seem to play a role in the relatedness of phageprints across individuals. By sampling from six different oral sites, we were able to study the impact of millimeters to a few centimeters of separation on an individual's phageprint and found that such limited spatial separation results in site-specific phageprints.

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Section: Introductionmentioning

confidence: 99%

Machine learning models can identify individuals based on a resident oral bacteriophage family

Mahmoudabadi,

Homyk,

Catching

et al. 2024

Preprint

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Comparative Analyses of Bacteriophage Genomes

Rossi,

Flores,

Uceda-Campos

et al. 2024

Methods in Molecular Biology

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Prokaryotic morphological features and maintenance activities governed by seasonal productivity conditions

Verma,

Amnebrink,

Lee

et al. 2024

FEMS Microbiology Ecology

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Prokaryotic maintenance respiration and associated metabolic activities constitute a considerable proportion of the total respiration of carbon to CO2 in the ocean's mixed layer. However, seasonal influences on prokaryotic maintenance activities in terms of morphological and metabolic adaptations at low (winter) and high productivity (summer) are still unclear. To address this, we examined the natural prokaryotic communities at the mesocosm scale to analyse the differences in their morphological features and gene expression at low and high maintenance respiration, experimentally manipulated with the specific growth rate. Here, we showed that morphological features including membrane blebbing, membrane vesicles and cell‒cell connections occurred under high productivity. Metabolic adaptations associated with maintenance activities were observed under low productivity. Several Kyoto Encyclopedia of Genes and Genomes categories related to signal transduction, energy metabolism, and translational machinery supported maintenance activities under simulated winter conditions. Differential abundances of genes related to transporters, osmoregulation, nitrogen metabolism, ribosome biogenesis, and cold stress were observed. Our results demonstrate how specific growth rate in different seasons can influence resource allocation at the levels of morphological features and metabolic adaptations. This motivates further study of morphological features and their ecological role during high productivity, while investigations of metabolic adaptations during low productivity can advance our knowledge about maintenance activities.

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The coevolution of large and small terminases of bacteriophages is a result of purifying selection leading to phenotypic stabilization

Cited by 5 publications

References 97 publications

Machine learning models can identify individuals based on a resident oral bacteriophage family

Machine learning models can identify individuals based on a resident oral bacteriophage family

Comparative Analyses of Bacteriophage Genomes

Prokaryotic morphological features and maintenance activities governed by seasonal productivity conditions

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