The rice SnRK family: biological roles and cell signaling modules

A cystathionine beta-synthase domain containing protein, OsCBSCBS4, interacts with OsSnRK1A and OsPKG and functions in abiotic stress tolerance in rice

The Cystathionine-β-Synthase (CBS) domain-containing proteins (CDCPs) constitute a functionally diverse protein superfamily, sharing an evolutionary conserved CBS domain either in pair or quad. Rice genome (Oryza sativa subsp. indica) encodes 42 CDCPs; their functions remain largely unexplored. This study examines OsCBSCBS4, a quadruple CBS domain containing protein towards its role in regulating the abiotic stress tolerance in rice. Gene expression analyses revealed upregulation of OsCBSCBS4 in response to diverse abiotic stresses. Further, the cytoplasm-localised OsCBSCBS4 showed interaction with two different kinases, a cytoplasmic localised cGMP-dependant protein kinase (OsPKG) and the nucleo-cytoplasmic catalytic subunit of sucrose-nonfermentation 1-related protein kinase 1 (OsSnRK1A). The interaction with the latter assisted in trafficking of OsCBSCBS4 to the nucleus as well. Overexpression of OsCBSCBS4 in rice resulted in enhanced tolerance to drought and salinity stress, via maintaining better physiological parameters and antioxidant activity. Additionally, OsCBSCBS4-overexpressing rice plants exhibited reduced yield penalty under stress conditions. The in silico docking and in vitro binding analyses of OsCBSCBS4 with ATP suggest its involvement in cellular energy balance. Overall, this study provides novel insight into the unexplored functions of OsCBSCBS4 and demonstrates it as a new promising target for augmenting crop resilience.

Genomic signatures of SnRKs highlighted conserved evolution within orchids and stress responses through ABA signaling in the Cymbidium ensifolium

Sucrose non-fermenting 1-related protein kinases (SnRKs) are crucial for modulating plant responses to abiotic stresses, linking metabolism with stress signaling pathways. Investigating the roles and stress responses of SnRKs in plants paves the way for developing stress-tolerant strategies in orchid species. Here, 362 SnRK members were identified from nine current orchid genomes, highlighting the conservation of these genes in evolution. Among these, 33 CeSnRKs were found across 20 chromosomes of C. ensifolium genome. Multiple duplication events increased the complexity of CeSnRKs during independent evolution. Moreover, distinct functional domains beyond the kinase domain differentiated the subfamilies. These multi-copy members existed tissue specific expressions falling into 6 main trends, especially CeSnRK1, CeCIPK9, CeCIPK23 displayed a strict floral expression. ABA-related elements were enriched in the promoters of CeSnRKs, and stress-related miRNA binding sites were identified on partial CeSnRKs. Consequently, most CeSnRKs exhibited up-regulated expression during ABA treatment. Several genes, such as CeSnRK2.1 and CeCIPK28 involved growth and development at different times and various tissues. The up-regulation of SnRK2.1, along with high expression of SnRK1 and CIPK27 under drought stress, and the differential expression patterns of CeSnRKs under cold stress, underscore the involvement of CeSnRK genes in different stress responses. Additionally, the diverse interactions of CeSnRKs with proteins highlighted a multifaceted functional network.These findings offer valuable insights for the future functional characterization formation of CeSnRKs and the adaptive evolution of genes in orchids.

Genome-wide identification of ZmMYC2 binding sites and target genes in maize

BACKGROUND

Jasmonate (JA) is the important phytohormone to regulate plant growth and adaption to stress signals. MYC2, an bHLH transcription factor, is the master regulator of JA signaling. Although MYC2 in maize has been identified, its function remains to be clarified.

RESULTS

To understand the function and regulatory mechanism of MYC2 in maize, the joint analysis of DAP-seq and RNA-seq is conducted to identify the binding sites and target genes of ZmMYC2. A total of 3183 genes are detected both in DAP-seq and RNA-seq data, potentially as the directly regulating genes of ZmMYC2. These genes are involved in various biological processes including plant growth and stress response. Besides the classic cis-elements like the G-box and E-box that are bound by MYC2, some new motifs are also revealed to be recognized by ZmMYC2, such as nGCATGCAnn, AAAAAAAA, CACGTGCGTGCG. The binding sites of many ZmMYC2 regulating genes are identified by IGV-sRNA.

CONCLUSIONS

All together, abundant target genes of ZmMYC2 are characterized with their binding sites, providing the basis to construct the regulatory network of ZmMYC2 and better understanding for JA signaling in maize.