Abstract
BackgroundAlba (Acetylation lowers binding affinity) proteins are an ancient family of nucleic acid-binding proteins that function in gene regulation, RNA metabolism, mRNA translatability, developmental processes, and stress adaptation. However, comprehensive bioinformatics analysis on the Alba gene family of Solanum lycopersicum has not been reported previously.ResultsIn the present study, we undertook the first comprehensive genome-wide characterization of the Alba gene family in tomato (Solanum lycopersicum L.). We identified eight tomato Alba genes, which were classified into two groups: genes containing a single Alba domain and genes with a generic Alba domain and RGG/RG repeat motifs. Cis-regulatory elements and target sites for miRNAs, which function in plant development and stress responses, were prevalent in SlAlba genes. To explore the structure-function relationships of tomato Alba proteins, we predicted their 3D structures, highlighting their likely interactions with several putative ligands. Confocal microscopy revealed that SlAlba–GFP fusion proteins were localized to the nucleus and cytoplasm, consistent with putative roles in various signalling cascades. Expression profiling revealed the differential expression patterns of most SlAlba genes across diverse organs. SlAlba1 and SlAlba2 were predominantly expressed in flowers, whereas SlAlba5 expression peaked in 1 cm-diameter fruits. The SlAlba genes were differentially expressed (up- or downregulated) in response to different abiotic stresses. All but one of these genes were induced by abscisic acid treatment, pointing to their possible regulatory roles in stress tolerance via an abscisic acid-dependent pathway. Furthermore, co-expression of SlAlba genes with multiple genes related to several metabolic pathways spotlighted their crucial roles in various biological processes and signalling.ConclusionsOur characterization of SlAlba genes should facilitate the discovery of additional genes associated with organ and fruit development as well as abiotic stress adaptation in tomato.
Highlights
Alba (Acetylation lowers binding affinity) proteins are an ancient family of nucleic acid-binding pro‐ teins that function in gene regulation, RNA metabolism, mRNA translatability, developmental processes, and stress adaptation
The likely involvement of these SlAlba genes in diverse signalling pathways, developmental cascades, and plant stress responses is underscored by the presence of development- and stress response-associated cis-regulatory elements and miRNA target sites in their sequences, their dual localization to the cytoplasm and nucleus, and their putative binding to several ligands including DNA, RNA, and peptides
Expression profiling revealed that most SlAlba genes are differentially expressed across various organs and in response to different stimuli
Summary
Alba (Acetylation lowers binding affinity) proteins are an ancient family of nucleic acid-binding pro‐ teins that function in gene regulation, RNA metabolism, mRNA translatability, developmental processes, and stress adaptation. Wai et al BMC Plant Biology (2021) 21:530 of archaea and eukaryotes and are widely distributed in most kingdoms of life [1, 2]. These small, basic proteins interact with DNA and RNA as homodimers or heterodimers [3,4,5,6] and contain a conserved nucleic acid-binding Alba domain with an IF3-C fold [1]. The RGG/RG repeat motifs are thought to have roles in DNA damage signalling, snRNP biogenesis, the regulation of apoptosis, transcription, pre-mRNA splicing, and translation, many of which are at least partly controlled by the arginine methylation of RGG/ RG repeats [16]
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