Genome-wide investigation of SnRK2 gene family in two jute species: Corchorus olitorius and Corchorus capsularis

Abstract

Background Sucrose non-fermenting-1 (SNF1)-related protein kinase 2 (SnRK2), a plant-specific serine/threonine kinase family, is associated with metabolic responses, including abscisic acid signaling under biotic and abiotic stresses. So far, no information on a genome-wide investigation and stress-mediated expression profiling of jute SnRK2 is available. Recent whole-genome sequencing of two Corchorus species prompted to identify and characterize this SnRK2 gene family. Result We identified seven SnRK2 genes of each of Corchorus olitorius (Co) and C. capsularis (Cc) genomes, with similar physico-molecular properties and sub-group patterns of other models and related crops. In both species, the SnRK2 gene family showed an evolutionarily distinct trend. Highly variable C-terminal and conserved N-terminal regions were observed. Co- and CcSnRK2.3, Co- and CcSnRk2.5, Co- and CcSnRk2.7, and Co- and CcSnRK2.8 were upregulated in response to drought and salinity stresses. In waterlogging conditions, Co- and CcSnRk2.6 and Co- and CcSnRK2.8 showed higher activity when exposed to hypoxic conditions. Expression analysis in different plant parts showed that SnRK2.5 in both Corchorus species is highly expressed in fiber cells providing evidence of the role of fiber formation. Conclusion This is the first comprehensive study of SnRK2 genes in both Corchorus species. All seven genes identified in this study showed an almost similar pattern of gene structures and molecular properties. Gene expression patterns of these genes varied depending on the plant parts and in response to abiotic stresses.

Structural and functional characterization of genes PYL-PP2C-SnRK2s in the ABA signalling pathway of Cucurbita pepo

“…Some conclusions were drawn from leaf exposure to ABA and cold. Genes within the same family responded differently to ABA and cold, which is consistent with the specific regulation of ABA genes under different stresses in other plants [ 21 , 61 , 62 , 64 ].…”

“…Furthermore, all motifs, except motif 9, were conserved in the three subfamilies. Common motifs are likely to preserve the more relevant functions of these proteins, including the N-terminal motif 1 with the active site signature of serine/threonine protein kinases, the N-terminal motif 5, which is an ATP binding signature [ 63 , 64 ], and the C-terminal domains I (SnRK2 box) (motif 6) and II (ABA box) (motifs 8 and 10), which are required to respond to osmotic stress and ABA, respectively [ 66 ]. The presence of these domains and motifs indicates that all squash CpSnRK2 identified in this work are functional and ABA dependent.…”