Homopeptide and homocodon levels across fungi are coupled to GC/AT-bias and intrinsic disorder, with unique behaviours for some amino acids

Abstract Homopeptides (runs of one amino-acid type) are evolutionarily important since they are prone to expand/contract during DNA replication, recombination and repair. To gain insight into the genomic/proteomic traits driving their variation, we analyzed how homopeptides and homocodons (which are...

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Autores principales:	Yue Wang, Paul M. Harrison
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/15ecc4a3f15742828f9ba305fd375273
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spelling	oai:doaj.org-article:15ecc4a3f15742828f9ba305fd3752732021-12-02T16:58:09ZHomopeptide and homocodon levels across fungi are coupled to GC/AT-bias and intrinsic disorder, with unique behaviours for some amino acids10.1038/s41598-021-89650-12045-2322https://doaj.org/article/15ecc4a3f15742828f9ba305fd3752732021-05-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-89650-1https://doaj.org/toc/2045-2322Abstract Homopeptides (runs of one amino-acid type) are evolutionarily important since they are prone to expand/contract during DNA replication, recombination and repair. To gain insight into the genomic/proteomic traits driving their variation, we analyzed how homopeptides and homocodons (which are pure codon repeats) vary across 405 Dikarya, and probed their linkage to genome GC/AT bias and other factors. We find that amino-acid homopeptide frequencies vary diversely between clades, with the AT-rich Saccharomycotina trending distinctly. As organisms evolve, homocodon and homopeptide numbers are majorly coupled to GC/AT-bias, exhibiting a bi-furcated correlation with degree of AT- or GC-bias. Mid-GC/AT genomes tend to have markedly fewer simply because they are mid-GC/AT. Despite these trends, homopeptides tend to be GC-biased relative to other parts of coding sequences, even in AT-rich organisms, indicating they absorb AT bias less or are inherently more GC-rich. The most frequent and most variable homopeptide amino acids favour intrinsic disorder, and there are an opposing correlation and anti-correlation versus homopeptide levels for intrinsic disorder and structured-domain content respectively. Specific homopeptides show unique behaviours that we suggest are linked to inherent slippage probabilities during DNA replication and recombination, such as poly-glutamine, which is an evolutionarily very variable homopeptide with a codon repertoire unbiased for GC/AT, and poly-lysine whose homocodons are overwhelmingly made from the codon AAG.Yue WangPaul M. HarrisonNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-15 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Yue Wang Paul M. Harrison Homopeptide and homocodon levels across fungi are coupled to GC/AT-bias and intrinsic disorder, with unique behaviours for some amino acids
description	Abstract Homopeptides (runs of one amino-acid type) are evolutionarily important since they are prone to expand/contract during DNA replication, recombination and repair. To gain insight into the genomic/proteomic traits driving their variation, we analyzed how homopeptides and homocodons (which are pure codon repeats) vary across 405 Dikarya, and probed their linkage to genome GC/AT bias and other factors. We find that amino-acid homopeptide frequencies vary diversely between clades, with the AT-rich Saccharomycotina trending distinctly. As organisms evolve, homocodon and homopeptide numbers are majorly coupled to GC/AT-bias, exhibiting a bi-furcated correlation with degree of AT- or GC-bias. Mid-GC/AT genomes tend to have markedly fewer simply because they are mid-GC/AT. Despite these trends, homopeptides tend to be GC-biased relative to other parts of coding sequences, even in AT-rich organisms, indicating they absorb AT bias less or are inherently more GC-rich. The most frequent and most variable homopeptide amino acids favour intrinsic disorder, and there are an opposing correlation and anti-correlation versus homopeptide levels for intrinsic disorder and structured-domain content respectively. Specific homopeptides show unique behaviours that we suggest are linked to inherent slippage probabilities during DNA replication and recombination, such as poly-glutamine, which is an evolutionarily very variable homopeptide with a codon repertoire unbiased for GC/AT, and poly-lysine whose homocodons are overwhelmingly made from the codon AAG.
format	article
author	Yue Wang Paul M. Harrison
author_facet	Yue Wang Paul M. Harrison
author_sort	Yue Wang
title	Homopeptide and homocodon levels across fungi are coupled to GC/AT-bias and intrinsic disorder, with unique behaviours for some amino acids
title_short	Homopeptide and homocodon levels across fungi are coupled to GC/AT-bias and intrinsic disorder, with unique behaviours for some amino acids
title_full	Homopeptide and homocodon levels across fungi are coupled to GC/AT-bias and intrinsic disorder, with unique behaviours for some amino acids
title_fullStr	Homopeptide and homocodon levels across fungi are coupled to GC/AT-bias and intrinsic disorder, with unique behaviours for some amino acids
title_full_unstemmed	Homopeptide and homocodon levels across fungi are coupled to GC/AT-bias and intrinsic disorder, with unique behaviours for some amino acids
title_sort	homopeptide and homocodon levels across fungi are coupled to gc/at-bias and intrinsic disorder, with unique behaviours for some amino acids
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/15ecc4a3f15742828f9ba305fd375273
work_keys_str_mv	AT yuewang homopeptideandhomocodonlevelsacrossfungiarecoupledtogcatbiasandintrinsicdisorderwithuniquebehavioursforsomeaminoacids AT paulmharrison homopeptideandhomocodonlevelsacrossfungiarecoupledtogcatbiasandintrinsicdisorderwithuniquebehavioursforsomeaminoacids
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Homopeptide and homocodon levels across fungi are coupled to GC/AT-bias and intrinsic disorder, with unique behaviours for some amino acids

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