Genome-wide identification of sucrose nonfermenting-1-related protein kinase (SnRK) genes in barley and RNA-seq analyses of their expression in response to abscisic acid treatment

Abstract

Background Sucrose nonfermenting-1 (SNF1)-related protein kinases (SnRKs) play important roles in regulating metabolism and stress responses in plants, providing a conduit for crosstalk between metabolic and stress signalling, in some cases involving the stress hormone, abscisic acid (ABA). The burgeoning and divergence of the plant gene family has led to the evolution of three subfamilies, SnRK1, SnRK2 and SnRK3, of which SnRK2 and SnRK3 are unique to plants. Therefore, the study of SnRKs in crops may lead to the development of strategies for breeding crop varieties that are more resilient under stress conditions. In the present study, we describe the SnRK gene family of barley (Hordeum vulgare), the widespread cultivation of which can be attributed to its good adaptation to different environments. Results The barley HvSnRK gene family was elucidated in its entirety from publicly-available genome data and found to comprise 50 genes. Phylogenetic analyses assigned six of the genes to the HvSnRK1 subfamily, 10 to HvSnRK2 and 34 to HvSnRK3. The search was validated by applying it to Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) genome data, identifying 50 SnRK genes in rice (four OsSnRK1, 11 OsSnRK2 and 35 OsSnRK3) and 39 in Arabidopsis (three AtSnRK1, 10 AtSnRK2 and 26 AtSnRK3). Specific motifs were identified in the encoded barley proteins, and multiple putative regulatory elements were found in the gene promoters, with light-regulated elements (LRE), ABA response elements (ABRE) and methyl jasmonate response elements (MeJa) the most common. RNA-seq analysis showed that many of the HvSnRK genes responded to ABA, some positively, some negatively and some with complex time-dependent responses. Conclusions The barley HvSnRK gene family is large, comprising 50 members, subdivided into HvSnRK1 (6 members), HvSnRK2 (10 members) and HvSnRK3 (34 members), showing differential positive and negative responses to ABA.

Barley GRIK1‐SnRK1 kinases subvert a viral virulence protein to upregulate antiviral RNAi and inhibit infection

“…So another question worthy of future investigation is to examine whether other types of SnRK proteins may also interact with BYDV 17K and take part in its phosphorylation. In a preliminary experiment, we found that HvPKABA1, a SnRK2 protein (Holappa & Walker‐Simmons, 1995 ; Chen et al , 2021a , 2021b ), interacted with 17K in both Y2H and LC assays; but HvCIPK1, a SnRK3 protein (Hrabak et al , 2003 ; Chen et al , 2021a , 2021b ), failed to do so in the same tests (Appendix Fig S9 A and B). Notably, compared with HvCIPK1, HvPKABA1 exhibited lower amino acid sequence identities with HvSnRK1 in both full‐length protein and kinase domain (Appendix Fig S9 C and D); hence, we speculate that BYDV 17K may interact with additional SnRK proteins in a highly selective manner in host cells, and that HvPKABA1 may also participate in 17K phosphorylation during BYDV infection.…”

“…It is well known that the SNF1‐related kinase family of higher plants has multiple members with diverse functions (Halford & Hey, 2009 ; Chen et al , 2021b ). So another question worthy of future investigation is to examine whether other types of SnRK proteins may also interact with BYDV 17K and take part in its phosphorylation.…”

Genome-Wide Identification and Expression Analysis of SnRK Gene Family under Abiotic Stress in Cucumber (Cucumis sativus L.)

“…However, SnRKs as a type of Ser/Thr protein kinase represent an interface between stress and ABA signal transduction [39]. It has been shown that 39, 48, 50 and 44 SnRK genes were identified in Oryza sativa, Brachypodium distachyon [3], Arabidopsis thaliana [40] and Hordeum vulgare [41], respectively. In this study, we were the first to comprehensively identified SnRK members of cucumber genome, which will provide crucial information to research their functions in the future.…”

The Role of GmSnRK1-GmNodH Module in Regulating Soybean Nodulation Capacity

“…SnRK1 is not only an important regulator of plant carbon metabolism, but also an important regulator of plant nitrogen metabolism. The fact that SnRK1 phosphorylates and inactivates nitrate reductase provides a route through which SnRK1 can affect nitrogen metabolism [ 35 ]. The regulation of nitrogen absorption is closely related to SnRK1 [ 8 ].…”