Does Sequence Conservation Provide Evidence for Biological Function?

Omer, Seila; Harlow, Timothy J.; Gogarten, J. Peter

doi:10.1016/j.tim.2016.09.010

Cited by 14 publications

(7 citation statements)

References 33 publications

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“…For example, Bobay and coauthors have detected different prophage sequences in the whole genome of 20 strains of S. enterica and classified them based on their sequence similarity in order to understand prophage integration patterns and their genetic adaptation to host genomes (Bobay et al, 2013 ). These sequence variants may arise from modular exchange with other prophage DNA, mutation, adaptational shift, and/or drift (Brüssow et al, 2004 ; Boyd et al, 2012 ; Omer et al, 2017 ) and these changes can be expected to have evolutionary implications (Diard et al, 2017 ). To that end, prophage diversity within bacterial strains does not only rely on the presence or absence of a certain prophage, but also on the conservation of the prophage sequences.…”

Section: Discussionmentioning

confidence: 99%

Salmonella enterica Prophage Sequence Profiles Reflect Genome Diversity and Can Be Used for High Discrimination Subtyping

et al. 2018

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Non-typhoidal Salmonella is a leading cause of foodborne illness worldwide. Prompt and accurate identification of the sources of Salmonella responsible for disease outbreaks is crucial to minimize infections and eliminate ongoing sources of contamination. Current subtyping tools including single nucleotide polymorphism (SNP) typing may be inadequate, in some instances, to provide the required discrimination among epidemiologically unrelated Salmonella strains. Prophage genes represent the majority of the accessory genes in bacteria genomes and have potential to be used as high discrimination markers in Salmonella. In this study, the prophage sequence diversity in different Salmonella serovars and genetically related strains was investigated. Using whole genome sequences of 1,760 isolates of S. enterica representing 151 Salmonella serovars and 66 closely related bacteria, prophage sequences were identified from assembled contigs using PHASTER. We detected 154 different prophages in S. enterica genomes. Prophage sequences were highly variable among S. enterica serovars with a median ± interquartile range (IQR) of 5 ± 3 prophage regions per genome. While some prophage sequences were highly conserved among the strains of specific serovars, few regions were lineage specific. Therefore, strains belonging to each serovar could be clustered separately based on their prophage content. Analysis of S. Enteritidis isolates from seven outbreaks generated distinct prophage profiles for each outbreak. Taken altogether, the diversity of the prophage sequences correlates with genome diversity. Prophage repertoires provide an additional marker for differentiating S. enterica subtypes during foodborne outbreaks.

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Section: Discussionmentioning

confidence: 99%

Salmonella enterica Prophage Sequence Profiles Reflect Genome Diversity and Can Be Used for High Discrimination Subtyping

et al. 2018

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“…The results are supported by the analyses of 58 nucleotide sequences of isolates of the three known species whose P15 amino acid sequences cover a spectrum of identity ranging from 14 to 100%. The main predictions have been obtained by integrating the results of different computational methods because of the premise that each of these elements taken in isolation does not allow to draw solid conclusions about the activity and function of a given protein (Omer et al, 2017;Ponting, 2017;Ravantti et al, 2020). Taken them together, we posit a theory that partially describes the evolution of the cilevirus genomes that involves elements denoting the likely close interplay during the coevolutionary history of Brevipalpus-transmitted viruses.…”

Section: Discussionmentioning

confidence: 99%

Poorly Conserved P15 Proteins of Cileviruses Retain Elements of Common Ancestry and Putative Functionality: A Theoretical Assessment on the Evolution of Cilevirus Genomes

et al. 2021

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The genus Cilevirus groups enveloped single-stranded (+) RNA virus members of the family Kitaviridae, order Martellivirales. Proteins P15, scarcely conserved polypeptides encoded by cileviruses, have no apparent homologs in public databases. Accordingly, the open reading frames (ORFs) p15, located at the 5′-end of the viral RNA2 molecules, are considered orphan genes (ORFans). In this study, we have delved into ORFs p15 and the relatively poorly understood biochemical properties of the proteins P15 to posit their importance for viruses across the genus and theorize on their origin. We detected that the ORFs p15 are under purifying selection and that, in some viral strains, the use of synonymous codons is biased, which might be a sign of adaptation to their plant hosts. Despite the high amino acid sequence divergence, proteins P15 show the conserved motif [FY]-L-x(3)-[FL]-H-x-x-[LIV]-S-C-x-C-x(2)-C-x-G-x-C, which occurs exclusively in members of this protein family. Proteins P15 also show a common predicted 3D structure that resembles the helical scaffold of the protein ORF49 encoded by radinoviruses and the phosphoprotein C-terminal domain of mononegavirids. Based on the 3D structural similarities of P15, we suggest elements of common ancestry, conserved functionality, and relevant amino acid residues. We conclude by postulating a plausible evolutionary trajectory of ORFans p15 and the 5′-end of the RNA2 of cileviruses considering both protein fold superpositions and comparative genomic analyses with the closest kitaviruses, negeviruses, nege/kita-like viruses, and unrelated viruses that share the ecological niches of cileviruses.

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“…Is it more likely that RNAi evolved as a defense against parasitic genetic elements at the cost of disrupting or altering gene regulation, or as a multifunctional process that can regulate gene expression, favor heterochromatin formation, and inhibit TEs and viruses? When addressing this fundamental question, one should bear in mind that biological complexity can emerge by neutral events and may become essential even if it is useless [ 19 , 22 , 113 – 116 ]; that a specific function can originate from exaptation of a trait that was selected for a different function [ 79 ]; and that the characteristics of most biological entities may produce important physiological and evolutionary by-products [ 1 ]. Furthermore, macromolecules are also dynamically interconnected inside the crowded cellular environment [ 21 ], with an incredible number of possible interactions and activities, most of which will have no effect on fitness [ 19 , 115 ].…”

Section: Introductionmentioning

confidence: 99%

The origin of RNA interference: Adaptive or neutral evolution?

et al. 2022

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The origin of RNA interference (RNAi) is usually explained by a defense-based hypothesis, in which RNAi evolved as a defense against transposable elements (TEs) and RNA viruses and was already present in the last eukaryotic common ancestor (LECA). However, since RNA antisense regulation and double-stranded RNAs (dsRNAs) are ancient and widespread phenomena, the origin of defensive RNAi should have occurred in parallel with its regulative functions to avoid imbalances in gene regulation. Thus, we propose a neutral evolutionary hypothesis for the origin of RNAi in which qualitative system drift from a prokaryotic antisense RNA gene regulation mechanism leads to the formation of RNAi through constructive neutral evolution (CNE). We argue that RNAi was already present in the ancestor of LECA before the need for a new defense system arose and that its presence helped to shape eukaryotic genomic architecture and stability.

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Does Sequence Conservation Provide Evidence for Biological Function?

Cited by 14 publications

References 33 publications

Salmonella enterica Prophage Sequence Profiles Reflect Genome Diversity and Can Be Used for High Discrimination Subtyping

Salmonella enterica Prophage Sequence Profiles Reflect Genome Diversity and Can Be Used for High Discrimination Subtyping

Poorly Conserved P15 Proteins of Cileviruses Retain Elements of Common Ancestry and Putative Functionality: A Theoretical Assessment on the Evolution of Cilevirus Genomes

The origin of RNA interference: Adaptive or neutral evolution?

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