Genome‐wide identification and characterization of SNW/SKIP domain‐containing proteins in plants

• Published in: Plant biology (Stuttgart, Germany) Vol. 26; no. 5; pp. 705 - 714
• Main Authors: Silva, S. A., Bezerra, V. B. F., Teixeira, F. C., Roque, E. M. S., Nascimento, J. I. B., Aguiar, A. M., Carvalho, H. H., Alves, M. S.
• Format: Journal Article
• Language: English
• Published: England Wiley Subscription Services, Inc 01-08-2024
• Subjects: Amino acid sequence; Bioinformatics; Chemical properties; Cluster analysis; Environmental changes; Environmental effects; Eukaryotes; Evolutionary genetics; Gene expression; Gene family evolution; Gene regulation; Genomes; genome‐wide comparative analysis; Introns; Localization; Phylogenetics; Phylogeny; Physicochemical properties; Plant species; protein interaction network; protein physicochemical parameters; Protein structure; Proteins; Sessile species; Ski protein; Skip protein; Stimuli; stress tolerance; Structural analysis; protein physicochemical parameters; genome‐wide comparative analysis; stress tolerance; protein interaction network; Gene family evolution
• ISSN: 1435-8603; 1438-8677; 1438-8677
• DOI: 10.1111/plb.13676

Sessile organisms, such as plants, developed various ways to sense and respond to external and internal stimuli to maximize their fitness through evolutionary time. Transcripts and protein regulation are, among many, the main mechanisms that plants use to respond to environmental changes. SKIP protein is one such, presenting an SNKW interacting domain, which is highly conserved among eukaryotes, where SKI interacting protein acts in regulating key processes.
In the present work, many bioinformatics tools, such as phylogenetic relationships, gene structure, physical–chemical properties, conserved motifs, prediction of regulatory cis‐elements, chromosomal localization, and protein–protein interaction network, were used to better understand the genome‐wide SNW/SKIP domain‐containing proteins.
In total, 28 proteins containing the SNW/SKIP domain were identified in different plant species, including plants of agronomic interest. Two main protein clusters were formed in phylogenetic analysis, and gene structure analysis revealed that, in general, the coding region had no introns. Also, expression of these genes is possibly induced by abiotic stress stimuli. Primary structure analysis of the proteins revealed the existence of an evolutionarily conserved functional unit. But physicochemical properties show that proteins containing the SNW/SKIP domain are commonly unstable under in vivo conditions.
In addition, the protein network, demonstrated that SKIP homologues could act by modulating plant fitness through gene expression regulation at the transcriptional and post‐transcriptional levels. This could be corroborated by the expression number of gene copies of SKIP proteins in many species, highlighting it's crucial role in plant development and tolerance through the course of evolution.
Genome‐wide analysis of plant SNW/SKIP domain‐containing proteins revealed an evolutionarily conserved functional unit, suggesting that SKIP homologues can modulate plant fitness through regulation of gene expression at transcriptional and post‐transcriptional levels.