Variable absorption of mutational trends by prion-forming domains during Saccharomycetes evolution

fLPS 2.0: rapid annotation of compositionally-biased regions in biological sequences

Compositionally-biased (CB) regions in biological sequences are enriched for a subset of sequence residue types. These can be shorter regions with a concentrated bias (i.e., those termed ‘low-complexity’), or longer regions that have a compositional skew. These regions comprise a prominent class of the uncharacterized ‘dark matter’ of the protein universe. Here, I report the latest version of the fLPS package for the annotation of CB regions, which includes added consideration of DNA sequences, to label the eight possible biased regions of DNA. In this version, the user is now able to restrict analysis to a specified subset of residue types, and also to filter for previously annotated domains to enable detection of discontinuous CB regions. A ‘thorough’ option has been added which enables the labelling of subtler biases, typically made from a skew for several residue types. In the output, protein CB regions are now labelled with bias classes reflecting the physico-chemical character of the biasing residues. The fLPS 2.0 package is available from: https://github.com/pmharrison/flps2 or in a Supplemental File of this paper.

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

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.