Análises in silico da família ABC transporters em feijão comum

Abstract

Common bean (Phaseolus vulgaris L.) is an important legume worldwide. However, its cultivation is affected by biotic and abiotic stresses. Transmembrane proteins ABC transporters (ATP-binding cassette) play a key role plant's tolerance response to stresses. However, little is known about ABC transporters in common bean. Thus, the aim of this study was to identify and characterize in silico the PvABC genes and proteins (ABC transporters of P. vulgaris). For protein identification, ABC transporters of Arabidopsis thaliana were subjected to BLASTp (e-value < e-10) in the P. vulgaris proteome hosted at NCBI. The identified peptide sequences were submitted to HMMER and InterProScan for domain confirmation. Molecular weights and isoelectric points, as well as transmembrane helices, conserved motifs and subcellular localization, were predicted using ExPASy, TMHMM, MEME, DeepLoc and Wolf PSORT software, respectively. MAFFT and IQTree software were used for phylogenetic analysis. PvABC genes were characterized regarding exon-intron structures by GSDS and chromosomal localization by TBtools. The promoter sequences of PvABC genes were submitted to PlantCARE to predict cis-regulatory elements. In total, 180 ABC proteins (size between 72 and 1,945 aa) corresponding to 164 P. vulgaris genes were identified. The isoelectric point of PvABC proteins ranged from 5.57 (PvABCI114) to 10.86 (PvABCI162), while the molecular weight ranged from 7,919.25 (PvABCC134) to 210,122.4 Da (PvABCB58). The prediction of transmembrane helices revealed the presence of 0 to 17 helices, with the majority of PvABC proteins having 06 transmembrane helices and being predicted mainly in the plasma membrane. The MEME analysis revealed 10 conserved motifs in the PvABC family, with motif 01 being the most conserved, being present in 157 (87.2%) of the PvABC proteins. Phylogenetic analysis distributed PvABC proteins into 07 subfamilies, PvABCA (06), PvABCB (32), PvABCC (32), PvABCD (05), PvABCF (07), PvABCG (80) and PvABCI (18). Chromosomal localization revealed 161 PvABC genes distributed in the 11 chromosomes of P. vulgaris, except for one mitochondrial gene (PvABCI162) and two genes (PvABCC163 and PvABCG164) with unidentified locus. Chromosome 01 had the largest number of mapped genes, with 38 PvABC genes. The number of exons and introns ranged from 1 to 36 and 0 to 35, respectively. A total of 112 cis-regulatory elements were identified in the promoter regions of the 162 PvABC genes, and 49 elements were categorized into three functional groups: stress-responsive elements (07), hormone-responsive elements (12), and light-responsive elements (30). Some of the main cis-regulatory elements identified were the elements involved in anaerobic induction (ARE), ABRE, and Box 4. Several studies carried out in other plant species reveal a variety of functions of ABC proteins related to development and stress tolerance. Therefore, our results provide a basis for further research on the function of PvABC genes with potential for application in the genetic improvement of P. vulgaris.