The expansion of amino-acid repeats is not associated to adaptive evolution in mammalian genes

Cruz, Fernando; Roux, Julien; Robinson‐Rechavi, Marc

doi:10.1186/1471-2164-10-619

Cited by 6 publications

(8 citation statements)

References 49 publications

(78 reference statements)

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“…For example, Cruz et al . 45 suggested that hydrophobic and acidic amino acids are more likely to be used in LCRs compared to amino acids belonging to other Lehninger categories. However, our results do not show this preference as Asn and Lys belong to the “polar uncharged” and “basic” categories, respectively.…”

Section: Discussionmentioning

confidence: 99%

Comparative analysis of low complexity regions in Plasmodia

Chaudhry

Lwin

Phelan

et al. 2018

Sci Rep

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Low complexity regions (LCRs) are a common feature shared by many genomes, but their evolutionary and functional significance remains mostly unknown. At the core of the uncertainty is a poor understanding of the mechanisms that regulate their retention in genomes, whether driven by natural selection or neutral evolution. Applying a comparative approach of LCRs to multiple strains and species is a powerful approach to identify patterns of conservation in these regions. Using this method, we investigate the evolutionary history of LCRs in the genus Plasmodium based on orthologous protein coding genes shared by 11 species and strains from primate and rodent-infecting pathogens. We find multiple lines of evidence in support of natural selection as a major evolutionary force shaping the composition and conservation of LCRs through time and signatures that their evolutionary paths are species specific. Our findings add a comparative analysis perspective to the debate on the evolution of LCRs and harness the power of sequence comparisons to identify potential functionally important LCR candidates.

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Section: Discussionmentioning

confidence: 99%

Comparative analysis of low complexity regions in Plasmodia

Chaudhry

Lwin

Phelan

et al. 2018

Sci Rep

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“…The causal factors underlying this variation are still a matter of dispute [13,17], and some have attributed them to GC content bias [16,18,23]. In plants, repetitive DNA is widely used as a genetic marker, and its variation among transcripts has been observed [24].…”

Section: Introductionmentioning

confidence: 99%

“…This AAR was suggested to control circadian period length [ 12 ]. Large-scale analyses indicate that AARs tend to participate in the regulation of transcription [ 8 , 13 , 14 ] and are frequently involved in protein-protein interactions [ 15 ].…”

Section: Introductionmentioning

confidence: 99%

Comprehensive analysis of tandem amino acid repeats from ten angiosperm genomes

et al. 2011

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BackgroundThe presence of tandem amino acid repeats (AARs) is one of the signatures of eukaryotic proteins. AARs were thought to be frequently involved in bio-molecular interactions. Comprehensive studies that primarily focused on metazoan AARs have suggested that AARs are evolving rapidly and are highly variable among species. However, there is still controversy over causal factors of this inter-species variation. In this work, we attempted to investigate this topic mainly by comparing AARs in orthologous proteins from ten angiosperm genomes.ResultsAngiosperm AAR content is positively correlated with the GC content of the protein coding sequence. However, based on observations from fungal AARs and insect AARs, we argue that the applicability of this kind of correlation is limited by AAR residue composition and species' life history traits. Angiosperm AARs also tend to be fast evolving and structurally disordered, supporting the results of comprehensive analyses of metazoans. The functions of conserved long AARs are summarized. Finally, we propose that the rapid mRNA decay rate, alternative splicing and tissue specificity are regulatory processes that are associated with angiosperm proteins harboring AARs.ConclusionsOur investigation suggests that GC content is a predictor of AAR content in the protein coding sequence under certain conditions. Although angiosperm AARs lack conservation and 3D structure, a fraction of the proteins that contain AARs may be functionally important and are under extensive regulation in plant cells.

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“…Finding more glutamine than any other amino acid in repeats despite using a criterion that sampled far fewer repeats, i.e. less than 25% of repeats have 9 or more codons in Drosophila [ 46 , 47 ], suggests that glutamine may be particularly prone to repeat formation in flies. Indeed, Faux et al [ 28 ] found that glutamine was also the most common amino acid among repeats in Anopheles gambiae , although it was only 1/6 as common as in D. melanogaster .…”

Section: Discussionmentioning

confidence: 99%

Length polymorphism and head shape association among genes with polyglutamine repeats in the stalk-eyed fly, Teleopsis dalmanni

et al. 2010

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BackgroundPolymorphisms of single amino acid repeats (SARPs) are a potential source of genetic variation for rapidly evolving morphological traits. Here, we characterize variation in and test for an association between SARPs and head shape, a trait under strong sexual selection, in the stalk-eyed fly, Teleopsis dalmanni. Using an annotated expressed sequence tag database developed from eye-antennal imaginal disc tissues in T. dalmanni we identified 98 genes containing nine or more consecutive copies of a single amino acid. We then quantify variation in length and allelic diversity for 32 codon and 15 noncodon repeat regions in a large outbred population. We also assessed the frequency with which amino acid repeats are either gained or lost by identifying sequence similarities between T. dalmanni SARP loci and their orthologs in Drosophila melanogaster. Finally, to identify SARP containing genes that may influence head development we conducted a two-generation association study after assortatively mating for extreme relative eyespan.ResultsWe found that glutamine repeats occur more often than expected by amino acid abundance among 3,400 head development genes in T. dalmanni and D. melanogaster. Furthermore, glutamine repeats occur disproportionately in transcription factors. Loci with glutamine repeats exhibit heterozygosities and allelic diversities that do not differ from noncoding dinucleotide microsatellites, including greater variation among X-linked than autosomal regions. In the majority of cases, repeat tracts did not overlap between T. dalmanni and D. melanogaster indicating that large glutamine repeats are gained or lost frequently during Dipteran evolution. Analysis of covariance reveals a significant effect of parental genotype on mean progeny eyespan, with body length as a covariate, at six SARP loci [CG33692, ptip, band4.1 inhibitor LRP interactor, corto, 3531953:1, and ecdysone-induced protein 75B (Eip75B)]. Mixed model analysis of covariance using the eyespan of siblings segregating for repeat length variation confirms that significant genotype-phenotype associations exist for at least one sex at five of these loci and for one gene, CG33692, longer repeats were associated with longer relative eyespan in both sexes.ConclusionAmong genes expressed during head development in stalk-eyed flies, long codon repeats typically contain glutamine, occur in transcription factors and exhibit high levels of heterozygosity. Furthermore, the presence of significant associations within families between repeat length and head shape indicates that six genes, or genes linked to them, contribute genetic variation to the development of this extremely sexually dimorphic trait.

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The expansion of amino-acid repeats is not associated to adaptive evolution in mammalian genes

Cited by 6 publications

References 49 publications

Comparative analysis of low complexity regions in Plasmodia

Comparative analysis of low complexity regions in Plasmodia

Comprehensive analysis of tandem amino acid repeats from ten angiosperm genomes

Length polymorphism and head shape association among genes with polyglutamine repeats in the stalk-eyed fly, Teleopsis dalmanni

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