Abstract
BackgroundSucrose 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.ResultsThe 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.ConclusionsThe 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.
Highlights
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)
Genome-wide identification of the Sucrose nonfermenting-1-related protein kinase (SnRK) gene family members in barley In total, 50 HvSnRKs were found to be encoded in the barley genome (Table 1), of which six were classed as SnRK1s by Pfams analysis and called HvSnRK1.1 – HvSnRK1.6
Thirty-four proteins were assigned to the SnRK3/CBL-interacting protein kinase (CIPK) group based on the presence of a NAF domain (PF03822), a 24 amino acid domain required for binding to calcineurin B-like protein (CBL) [64]
Summary
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). Sucrose nonfermenting-1 (SNF1)-related protein kinases (SnRKs) are related to SNF1 of fungi and AMP-activated protein kinase (AMPK) of mammals (see [1] for review) These protein kinases play important roles in regulating metabolism in all three systems, but in plants the SnRK family has expanded and diverged into three subfamilies, SnRK1 (structurally and functionally the most similar to SNF1 and AMPK), SnRK2 and SnRK3 [2]. The study of SnRKs in crops may lead to the development of strategies for breeding crop varieties that are more resilient under stress conditions This is important in the face of climate change and the prediction that extreme weather events are likely to become more frequent and more severe in the coming decades, with the potential for serious impacts on crop yield and quality
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