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

MICAELA PARRA; DIEGO LIBKIND; NICOLÁS BELLORA

Mendoza

Congreso; Congreso Argentino de Bioinformática y Biología Computacional; 2019

The presence of endogenous circadian rhythms, regulated by a molecular clock, is almost universal inthe 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, molecularclock components have not yet been found in many species other than Neurospora crassa. A previousstudy, based on a BLAST analysis of five circadian clock proteins on 64 fungal proteomes, suggeststhat the machinery required for a FRQ-WC-dependent circadian oscillator is taxonomically restrictedwithin Ascomycetes. This raises the question of whether those core proteins are really absent in mostspecies, or if traditional methods are ineffective for finding them. In this study, we extended previousresearch in three ways: by expanding the phylogenetic chart (including more species: fungal andamoebal (because of new evidence regarding its closely related ancestry)), adding more genes, andemploying alternative gene mining methods. Because we expanded the phylogenetic chart, it wasnecessary 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) haveintrinsically disordered regions (IDRs), we will measure the dependence between residues usingMutual 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 theevolutionary history of fungal homologs of seven of N. crassa?s clock proteins and fourteen of its lightrelated genes in over 100 genomes pulled from FungiDB. Since there is a bias in the databases towardshuman and crop pathogens, we decided to also include wild Patagonian strains: Saccharomyceseubayanus, 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 andregulation of secondary metabolite production. The characterization of the components of its molecularclock could potentially be useful for improving yields of industrial-level bio-synthetic productions andwill provide informative insights into the IDR conservation and evolution of circadian mechanisms infungus.