Characterization of the soybean KRP gene family reveals a key role for GmKRP2a in root development

Abstract

Kip-related proteins (KRPs), as inhibitory proteins of cyclin-dependent kinases, are involved in the growth and development of plants by regulating the activity of the CYC-CDK complex to control cell cycle progression. The KRP gene family has been identified in several plants, and several KRP proteins from Arabidopsis thaliana have been functionally characterized. However, there is little research on KRP genes in soybean, which is an economically important crop. In this study, we identified nine GmKRP genes in the Glycine max genome using HMM modeling and BLASTP searches. Protein subcellular localization and conserved motif analysis showed soybean KRP proteins located in the nucleus, and the C-terminal protein sequence was highly conserved. By investigating the expression patterns in various tissues, we found that all GmKRPs exhibited transcript abundance, while several showed tissue-specific expression patterns. By analyzing the promoter region, we found that light, low temperature, an anaerobic environment, and hormones-related cis-elements were abundant. In addition, we performed a co-expression analysis of the GmKRP gene family, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) set enrichment analysis. The co-expressing genes were mainly involved in RNA synthesis and modification and energy metabolism. Furthermore, the GmKRP2a gene, a member of the soybean KRP family, was cloned for further functional analysis. GmKRP2a is located in the nucleus and participates in root development by regulating cell cycle progression. RNA-seq results indicated that GmKRP2a is involved in cell cycle regulation through ribosome regulation, cell expansion, hormone response, stress response, and plant pathogen response pathways. To our knowledge, this is the first study to identify and characterize the KRP gene family in soybean.

Genomic organization and expression profiles of nitrogen assimilation genes in Glycine max

“…To impose drought-nitrate (D-N) stress, the seedlings were subjected to the specified above nitrate concentrations for 5 days after that the 15% PEG6000 was added to each nitrate treatments over 2 days ( Yang et al, 2023 ). Furthermore, for salt stress experiments, the seedlings were exposed to 150 mM NaCl for 24 and 48 h ( Guo et al, 2023 ). The control treatment exclusively utilized MS medium.…”

The SIAMESE family of cell-cycle inhibitors in the response of plants to environmental stresses

“…Regulation of CKIs is believed to primarily take place posttranscriptionally, with secondary regulatory mechanisms operating at the transcriptional level (Liu et al, 2008;Ren et al, 2008;Jun et al, 2013;Kumar and Larkin, 2017;Guo et al, 2023). It is probable that SMRs undergo post-transcriptional activation following the initiation of the S phase.…”