Caracterização in silico da família MC (Mitochondrial carrier) em Phaseolus vulgaris

Abstract

The common bean (Phaseolus vulgaris L.) is a legume of great economic importance, widely cultivated and consumed in various regions of the world. However, its cultivation faces challenges due to exposure to various types of stresses, such as drought, salinity, and pests, which can compromise its productivity and quality. The MC (mitochondrial carrier) gene family is essential in the plant's response to abiotic stresses, such as drought, salinity, and cold. However, there is a lack of information on the MC family in P. vulgaris. Therefore, we aimed to identify and characterize MC genes and proteins in the genome and proteome of the common bean using bioinformatics tools. These proteins were identified via BLASTp (e-value < e-10) in the P. vulgaris proteome hosted at NCBI. The identified peptide sequences were analyzed in HMMER and InterProScan to confirm the protein domain. The molecular weight and isoelectric point were determined in ExPASy, while the subcellular localization was performed in DeepLoc. Gene characterization involved the determination of the number of exons and the chromosomal localization was performed via NCBI and TbTools, the protein motifs were predicted in MEME. The phylogenetic analysis with the MC proteins of A. thaliana and P. vulgaris was performed in the MAFFT and IQTree software. Eighty PvMC proteins (size between 127 and 812 aa) were identified, corresponding to 74 P. vulgaris genes. The molecular weight ranged from 14,100.39 (PvMC 64) to 39,790.21 Da (PvMC 4), and the isoelectric point ranged from 5.44 (PvMC 61a) to 9.99 (PvMC 25). Most PvMC proteins (97.5%) are found in mitochondria, although one was predicted to occur in the peroxisome and another in the plastid. PvMC genes have 1 to 13 exons and are distributed throughout all P. vulgaris chromosomes. The number of genes per chromosome ranged from 3 (chromosome 11) to 14 (chromosome 2). PvMCs had between 0 and 8 transmembrane regions. The MEME analysis identified 10 conserved motifs, with motifs 2, 1, and 3 being the most conserved, and motif 10 being the least conserved. Phylogenetic analysis was performed using 74 P. vulgaris MC proteins and 25 characterized A. thaliana MC proteins. In the phylogenetic tree, the proteins were divided into four main subfamilies: nucleotides and dinucleotides; di-/tri-carboxylates and ketoacids; amino acids; and other substrates and subdivided into 10 subgroups: AAC, APC, NDT, ORNITHINE, DIC, DTC, UCP, SFC, SAMC, and MRS. Several characterized MCs from A. thaliana and other species are involved in essential functions as well as in the plant response to biotic and abiotic stresses. Thus, the identification and characterization of the MC family presented here provides useful information for P. vulgaris breeding programs.