BIOINFORMATIC ANALYSIS OF THE CODING SEQUENCES OF NICOTIANA SYLVESTRIS sHSP
DOI:
https://doi.org/10.31861/biosystems2024.01.031Keywords:
abiotic stress, bioinformatic analysis, genetic polymorphism, molecular genomics, molecular evolution, multigene family, α-crystallin domain, sHSP, N. sylvestrisAbstract
During the evolution, plants have developed defense mechanisms against temperature stress associated with the synthesis of protective proteins, among which molecular chaperones predominate, in particular low molecular weight heat stress proteins (sHSPs). Despite the important role these proteins play in the defense response to high temperature stress, they are still poorly studied for many taxonomic groups of plants. In particular, almost nothing is known about the organization and diversity of heat shock genes/proteins in representatives of such an important genus as Nicotiana (tobacco). The article presents the results of a bioinformatic analysis of the multigene/multiprotein sHSP family in N. sylvestris, an important model object in plant physiology, biochemistry, molecular genetics and cell biotechnology.
The GenBank database was used to search for homologous sequences using the BLAST algorithm. Amino acid sequences were aligned using the L-INS-I method on the MAFFT server. Phylogenetic analysis was performed by the maximum likelihood method using the PhyML plugin for Geneious Prime 2023.2.1. Statistical support of branches was calculated using the aLRT-Chi2 method.
It was found that within the compared amino acid sequences of N. sylvestris sHSP, three parts can be distinguished: the variable N-terminal region, the conserved α-crystallin domain (ACD), and the C-terminal region. Based on the alignment of the sHSP amino acid sequences, a similarity dendrogram was constructed, on which several clades with high statistical support are visualized.
The results of the comparative analysis of the amino acid sequences show that sHSPs of N. sylvestris belong to 10 structural classes. Proteins of seven classes are believed to be localized in the cytoplasm and/or nucleus, while the rest are located in the endoplasmic reticulum, mitochondria, plastids and peroxisomes.
In total, according to the results of bioinformatic analysis, 24 genes encoding sHSP were found in the genome of N. sylvestris, as well as one pseudogene in which the fragment encoding the N-terminal region has been lost. Since the sequence of the pseudogene differs slightly from the closest representatives of this group, it can be assumed that the conversion of this region into a pseudogene is a relatively recent evolutionary event.
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