Gene mining and characterization of intrinsically disordered regions of circadian clock components in Fungi

DIEGO LIBKIND; MICAELA PARRA; NICOLAS BELLORA

Mendoza

Congreso; A2B2C 2019 - Congreso Argentino de Bioinformática y Biología Computacional; 2019

Asociación Argentina de Bioinformática y Biología Computacional

The presence of endogenous circadian rhythms, regulated by a molecular clock, is almost universal in the tree of life, conferring an adaptive advantage by anticipating daily variations of the environment, especially for wild organisms. Although these rhythms have been described in many fungi, molecular clock components have not yet been found in many species other than Neurospora crassa. A previous study, based on a BLAST analysis of five circadian clock proteins on 64 fungal proteomes, suggests that the machinery required for a FRQ-WC-dependent circadian oscillator is taxonomically restricted within Ascomycetes. This raises the question of whether those core proteins are really absent in most species, or if traditional methods are ineffective for finding them. In this study, we extended previous research in three ways: by expanding the phylogenetic chart (including more species: fungal and amoebal (because of new evidence regarding its closely related ancestry)), adding more genes, and employing alternative gene mining methods. Because we expanded the phylogenetic chart, it was necessary to generate new hidden Markov models using alignments provided by Pfam. Additionally, since it has been reported that some clock- (e.g. FRQ) and clock-related-proteins (e.g. FF7) have intrinsically disordered regions (IDRs), we will measure the dependence between residues using Mutual Information. Also, since it is known that some clock proteins have unique architectures incertain lineages, we will search for conservative motifs using MEME. In this study, we trace the evolutionary history of fungal homologs of seven of N. crassa's clock proteins and fourteen of its light related genes in over 100 genomes pulled from FungiDB. Since there is a bias in the databases towards human and crop pathogens, we decided to also include wild Patagonian strains: Saccharomyces eubayanus, the ancestor of hybrid lager-brewing yeasts, and Aureobasidium pullulans CRUB 1823, which we have been studying and have proposed as a new model for studying circadian rhythms and regulation of secondary metabolite production. The characterization of the components of its molecular clock could potentially be useful for improving yields of industrial-level bio-synthetic productions and will provide informative insights into the IDR conservation and evolution of circadian mechanisms in fungus.