Distribution of mutational fitness effects and of epistasis in the 5’ untranslated region of a plant RNA virusReport as inadecuate




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BMC Evolutionary Biology

, 15:274

Experimental evolution

Abstract

BackgroundUnderstanding the causes and consequences of phenotypic variability is a central topic of evolutionary biology. Mutations within non-coding cis-regulatory regions are thought to be of major effect since they affect the expression of downstream genes. To address the evolutionary potential of mutations affecting such regions in RNA viruses, we explored the fitness properties of mutations affecting the 5’-untranslated region UTR of a prototypical member of the picorna-like superfamily, Tobacco etch virus TEV. This 5’ UTR acts as an internal ribosomal entry site IRES and is essential for expression of all viral genes.

ResultsWe determined in vitro the folding of 5’ UTR using the selective 2’-hydroxyl acylation analyzed by primer extension SHAPE technique. Then, we created a collection of single-nucleotide substitutions on this region and evaluated the statistical properties of their fitness effects in vivo. We found that, compared to random mutations affecting coding sequences, mutations at the 5’ UTR were of weaker effect. We also created double mutants by combining pairs of these single mutations and found variation in the magnitude and sign of epistatic interactions, with an enrichment of cases of positive epistasis. A correlation exists between the magnitude of fitness effects and the size of the perturbation made in the RNA folding structure, suggesting that the larger the departure from the predicted fold, the more negative impact in viral fitness.

ConclusionsEvidence that mutational fitness effects on the short 5’ UTR regulatory sequence of TEV are weaker than those affecting its coding sequences have been found. Epistasis among pairs of mutations on the 5’ UTR ranged between the extreme cases of synthetic lethal and compensatory. A plausible hypothesis to explain all these observations is that the interaction between the 5’ UTR and the host translational machinery was shaped by natural selection to be robust to mutations, thus ensuring the homeostatic expression of viral genes even at high mutation rates.

KeywordsDistribution of mutational fitness effects Plant virus Potyvirus RNA regulatory sequences RNA folding Virus evolution AbbreviationsBexperimental block

CIREcap-independent regulatory element

DMFEdistribution of mutational fitness effects

GLMgeneral linear model

HEPES4-2-hydroxyethyl-1-piperazineethanesulfonic acid

HIV-1Human immunodeficiency virus type 1

IRESinternal ribosomal entry site

LRTlikelihood ratio test

Mmutant genotype

MEmagnitude epistasis

MFESSminimum free energy secondary structure

NMIAN-methylisatoic anhydride

Pplant replicate

RNAribonucleic acid

RSEreciprocal sign epistasis

RSVRous sarcoma virus

SEsign epistasis

SEMstandard error of the mean

SHAPEselective 2’-hydroxyl acylation analyzed by primer extension

TEVTobacco etch virus

UTRuntranslated region

VPggenome-linked viral protein

Wrelative fitness

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Author: Guillermo P. Bernet - Santiago F. Elena

Source: https://link.springer.com/



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