Genome-Wide Identification of Wild Soybean Mitochondrial Calcium Uniporter Family Genes and Their Responses to Cold and Carbonate Alkaline Stresses

Abstract

The mitochondrial calcium uniporter (MCU), as an important component of the Ca2+ channel uniporter complex, plays a regulatory role in intracellular Ca2+ signal transduction. However, only a few studies to date have investigated plant MCU genes. In this study, we identified the MCU family genes in wild soybean and investigated their expression under cold and carbonate alkaline stresses. Eleven Glycine soja MCU genes (GsMCUs) were identified and clustered into two subgroups (subgroups I and II), and subgroup II could be further divided into two branches (MCU5 and MCU6). A total of 21 pairs of GsMCUs were characterized as duplicated genes, and displayed a similar exon-intron architecture. All GsMCU proteins contained one conserved MCU domain, within which two transmembrane domains were found. An analysis of the conserved motifs further supported that the GsMCUs showed high conservation in protein sequence and structure. Moreover, we found that all GsMCUs were expressed ubiquitously in different tissues and organs, and GsMCUs from the same subgroup displayed varied tissue expression profiles. In addition, based on RNA-seq and qRT-PCR assays, six and nine GsMCUs were differentially expressed under cold and carbonate alkaline stress, respectively. Promoter analysis also uncovered the existence of two canonical cold-related cis-acting elements, LTR and DRE/CRT, as well as stress-related phytohormone-responsive elements. Our results provide valuable information about the MCU family in soybean responses to cold and carbonate alkaline stress, which will be helpful in further characterizing their biological roles in response to abiotic stress.

An advanced systems biology framework of feature engineering for cold tolerance genes discovery from integrated omics and non-omics data in soybean

“…Robison et al (2019) reviewed Yamasaki and Randall's results (2016) and conducted RNA-seq analysis to confirm the ethylene-mediated signaling pathway has negative impacts on CBF/DREB-regulated cold responses in soybean underlying different scenarios of cold treatments. Li et al (2022) later conducted genome-wide analysis of homologs using proteins sequences to identify mitochondrial calcium uniporter family genes, and validated by RT-PCR assays under cold treatment (harvested and measured gene expression after 0, 1, and 24 hr cold treatment at 4°C), which echo Yamasaki and Randall's results (2016) results . These evidenced that the whole genome RNA-seq databases can be a basis of cold-tolerant responses in soybean for further validation, evaluation, and experiments.…”

“…All experiments were performed in triplicate. Because of the comprehensive and large-scale of databases, their results were frequently used to confirm soybean's physiological experiments (Robison et al, 2019;Li et al, 2022). Robison et al (2019) reviewed Yamasaki and Randall's results (2016) and conducted RNA-seq analysis to confirm the ethylene-mediated signaling pathway has negative impacts on CBF/DREB-regulated cold responses in soybean underlying different scenarios of cold treatments.…”

Comparative analysis of physiological variations and genetic architecture for cold stress response in soybean germplasm

“…At the genetic level soybean plant respond to cold stress by activating the various cold-responsive genes including GmDREB3 (Chen et al, 2009), novel MYB transcription factor GmMYBJ1 (Su et al, 2014), GmDREB1 (Yamasaki & Randall, 2016), NIMA-related kinase GmNEK1 (Pan et al, 2017) and mitochondrial calcium uniporter GsMCU (Li et al, 2022). The GmSCOF1 genes responded to cold stress conditions and have been functionally validated by stable ectopic overexpression in Arabidopsis (Liao et al, 2008).…”