Genes codificando quitinases de Arabidopsis thaliana e espécies relacionadas: um estudo in silico da variabilidade das estruturas primárias das enzimas, suas relações filogenéticas e diversidade de organização de domínios

Abstract

Chitinases (EC 3.2.1.14) are glycosyl hydrolases that act on chitin, a structural polysaccharide present in fungi and arthropods. These enzymes are divided into two main families in plants: GH18 (which includes classes III and V) and GH19 (which includes classes I, II, IV, VI, and VII). Each class possesses specific differences in its primary structure and domain architecture. Studying the distribution of chitinases in Arabidopsis thaliana and related genomes is a representative way to evaluate the diversity of domain organization in plant chitinases and to infer phylogenetic reasoning that helps in the understanding of the gene group encoding these enzymes, in addition to the scientific interest in understanding the function and dynamics of their encoded proteins in plant metabolism. The sequences were obtained from the GenBank, Phytozome, Ensembl Plants, and Plants Gramene databases. Subsequently, the presence of signal peptides, subcellular localization, and conserved domains (CDDs) were predicted in the protein sequences. Alignments were performed via MAFFT, and phylogenetic trees via IQ-TREE, with images generated in MEGA. The alignments for the trees were submitted to synonymous and non-synonymous substitution rate inference using the aBSREL and FEL tests from DataMonkey. With the Genes_on_Chr package, the chromosomal localizations of the studied genes were inferred for Arabidopsis thaliana, Arabidopsis arenosa, and for the allotetraploid originated from the crossing of the two mentioned species, Arabidopsis suecica. Arabidopsis thaliana possesses 24 genes that encode chitinases, grouped into classes I (one chitinase), II (two), III (one), IV (eight), V (nine), VI (two), and VII (one), in addition to the Chitinase-like-proteins (CLP) CLP1, CLP2, and CLP3, with one unity each. With the exception of Arabidopsis suecica, all other studied species presented a lower or equal number of chitinases encoded in the genome, with the relative halophyte Eutrema salsugineum not presenting class VII chitinases. Substitution rate analyses revealed purifying pressure in class I, II, III, VI, and VII chitinases and diversifying pressure for class IV and V chitinases. This reveals that for members of classes IV and V, there is a greater influence of mutations accumulated in their polypeptide sequences, aligning with the fact that proteins of these classes are located in tandem on the chromosomes, being the origin of duplication events, which relates to mechanisms of senescence, germination, and plant development, and not directly to plant defense, unlike classes I, II, III, and VI. The absence of class VII chitinases in the genome of Eutrema salsugineum may indicate loss of function of enzymes of this class.