Evolution and diversification of CaM/CML gene family in green plants

Systematic characterization of the calmodulin-like (CML) gene family in alfalfa and functional analysis of MsCML70 under salt stress

Calmodulin-like proteins (CMLs), which are widely involved in various abiotic stress responses, are important calcium ion sensors in plants. However, systematic identification and functional analysis of these proteins have not been performed in alfalfa. Here, a total of 211 MsCMLs were identified in the alfalfa genome. Conserved domain analysis revealed that most MsCMLs contained three EF-hand domains. A total of 17 tandem duplication events and 292 segmental duplication events were identified, indicating that segmental duplications were the major factor in the expansion of MsCMLs. There were 28, 36 and 18 MsCMLs that responded to drought, salt and cold stress, respectively, in alfalfa. In addition, MsCML70 overexpression significantly increased salt tolerance in Arabidopsis. MsCML70 participates in the plant salt stress response through various biological pathways, including transcriptional regulation, protein modification, plant hormone metabolism and secondary metabolism. Moreover, MsCML70 significantly increased the expression of HKT1 (high-affinity K+transporter 1), DREB19 (dehydration responsive element binding protein 19), PRX32 (peroxidase 32), JAL10 (jacalin-associated lectins 10), HB17 (homeobox 17), and NPF2.3 (nitrate transporter 2.3) under salt stress to promote tolerance to salt stress in Arabidopsis. The results of this study help elucidate the function of alfalfa CML genes and provide a new gene resource for the breeding of stress-resistant alfalfa.

Characterization of the Calmodulin-Like Protein Family in Chara braunii and their Conserved Interaction with the Calmodulin-Binding Transcription Activator Family

Calcium sensor proteins play important roles by detecting changes in intracellular calcium and relaying that information onto downstream targets through protein-protein interaction. Very little is known about calcium sensors from plant species that predate land colonization and the evolution of embryophytes. Here, we examined the genome of the multicellular algae, Chara braunii, for orthologs to the evolutionarily conserved calcium sensor calmodulin (CaM) and for CaM-like (CML) proteins. We identified one CaM and eight CML isoforms that range in size from 16.4 to 21.3 kDa and are predicted to have between two to four calcium-binding (EF-hand) domains. Using recombinant protein, we tested whether CbCaM and CbCML1-CbCML7 possess biochemical properties of typical calcium sensors. CbCaM and the CbCMLs all displayed high-affinity calcium binding with estimated global KD,app values in the physiological µM range. In response to calcium binding, CbCaM and the CbCMLs exhibited varying degrees of increase in exposed hydrophobicity, suggesting that different calcium-induced conformational changes occur among isoforms. We found many examples of putative CaM targets encoded in the C. braunii genome and explored the ability of CbCaM and CbCMLs to interact in planta with a representative putative target, a C. braunii CaM-binding transcription factor (CbCAMTA1). CbCaM, CbCML2 and CbCML4 each associated with the C-terminal region of CbCAMTA1. Collectively, our data support the hypothesis that complex calcium signaling and sensing networks involving CaM and CMLs evolved early in the green lineage. Similarly, it seems likely that calcium-mediated regulation of transcription occurs in C. braunii via CAMTAs and is an ancient trait predating embryophytic emergence.

Identifying Calmodulin and Calmodulin-like Protein Members in Canavalia rosea and Exploring Their Potential Roles in Abiotic Stress Tolerance

Calmodulins (CaMs) and calmodulin-like proteins (CMLs) belong to families of calcium-sensors that act as calcium ion (Ca2+) signal-decoding proteins and regulate downstream target proteins. As a tropical halophyte, Canavalia rosea shows great resistance to multiple abiotic stresses, including high salinity/alkalinity, extreme drought, heat, and intense sunlight. However, investigations of calcium ion signal transduction involved in the stress responses of C. rosea are limited. The CaM and CML gene families have been identified and characterized in many other plant species. Nevertheless, there is limited available information about these genes in C. rosea. In this study, a bioinformatic analysis, including the gene structures, conserved protein domains, phylogenetic relationships, chromosome distribution, and gene synteny, was comprehensively performed to identify and characterize CrCaMs and CrCMLs. A spatio-temporal expression assay in different organs and environmental conditions was then conducted using the RNA sequencing technique. Additionally, several CrCaM and CrCML members were then cloned and functionally characterized using the yeast heterogeneous expression system, and some of them were found to change the tolerance of yeast to heat, salt, alkalinity, and high osmotic stresses. The results of this study provide a foundation for understanding the possible roles of the CrCaM and CrCML genes, especially for halophyte C. rosea's natural ecological adaptability for its native habitats. This study also provides a theoretical basis for further study of the physiological and biochemical functions of plant CaMs and CMLs that are involved in tolerance to multiple abiotic stresses.

Integrated transcriptomics and metabolomics provide insights into the biosynthesis of militarine in the cell suspension culture system of Bletilla striata

Militarine is a monomer molecule with abundant and distinctive biological properties, also the lead member of secondary metabolites in Bletilla striata, while its biosynthesis mechanism is still unknown. To improve the production efficiency of militarine, sodium acetate and salicylic acid (SA) were introduced as elicitors into the suspension-cultured callus of B. striata. Subsequently, samples were taken from callus at different culturing stages to investigate the synthesis mechanisms of militarine in B. striata through integrated metabolomics and transcriptomics. Metabolomics analysis revealed that acetate ions promoted militarine synthesis, while SA had an inhibitory effect. Additionally, regulators such as ferulic acid, 2-hydroxy-3-phenylpropionic acid, and cis-beta-D-Glucosyl-2-hydroxycinnamate were identified as influencing militarine synthesis. Transcriptomics analysis indicated that the expression levels of genes involved in phenylalanine metabolism, phenylpropanoid biosynthesis, and tyrosine metabolism were correlated with militarine content. This study sheds light on the regulatory mechanism of militarine biosynthesis in plants. The results suggested that acetate ions and SA impact militarine synthesis through specific metabolic pathways and gene expression changes. This knowledge serves as a foundation for future research on militarine biosynthesis and its industrial production.

A Genome-Wide Analysis of the Jasmonic Acid Biosynthesis Gene Families in Peanut Reveals Their Crucial Roles in Growth and Abiotic Stresses

Abiotic stress is a limiting factor in peanut production. Peanut is an important oil crop and cash crop in China. Peanut yield is vulnerable to abiotic stress due to its seeds grown underground. Jasmonic acid (JA) is essential for plant growth and defense against adversity stresses. However, the regulation and mechanism of the jasmonic acid biosynthesis pathway on peanut defense against abiotic stresses are still limitedly understood. In this study, a total of 64 genes encoding key enzymes of JA biosynthesis were identified and classified into lipoxygenases (AhLOXs), alleno oxide synthases (AhAOSs), allene oxide cyclases (AhAOCs), and 12-oxo-phytodienoic acid reductases (AhOPRs) according to gene structure, conserved motif, and phylogenetic feature. A cis-regulatory element analysis indicated that some of the genes contained stress responsive and hormone responsive elements. In addition to proteins involved in JA biosynthesis and signaling, they also interacted with proteins involved in lipid biosynthesis and stress response. Sixteen putative Ah-miRNAs were identified from four families targeting 35 key genes of JA biosynthesis. A tissue expression pattern analysis revealed that AhLOX2 was the highest expressed in leaf tissues, and AhLOX32 was the highest expressed in shoot, root, and nodule tissues. AhLOX16, AhOPR1, and AhOPR3 were up-regulated under drought stress. AhLOX16, AhAOS3, AhOPR1, and AhAOC4 had elevated transcript levels in response to cold stress. AhLOX5, AhLOX16, AhAOC3, AhOPR1, and AhOPR3 were up-regulated for expression under salt stress. Our study could provide a reference for the study of the abiotic stress resistance mechanism in peanut.

Genome-Wide Identification and Expression Analysis of Calmodulin and Calmodulin-like Genes, Revealing CaM3 and CML13 Participating in Drought Stress in Phoebe bournei

Calmodulin (CaM) and calmodulin-like (CML) proteins are major Ca2+ sensors involved in the regulation of plant development and stress responses by converting Ca2+ signals into appropriate cellular responses. However, characterization and expression analyses of CaM/CML genes in the precious species, Phoebe bournei, remain limited. In this study, five PbCaM and sixty PbCML genes were identified that only had EF-hand motifs with no other functional domains. The phylogenetic tree was clustered into 11 subgroups, including a unique clade of PbCaMs. The PbCaMs were intron-rich with four EF-hand motifs, whereas PbCMLs had two to four EF-hands and were mostly intronless. PbCaMs/CMLs were unevenly distributed across the 12 chromosomes of P. bournei and underwent purifying selection. Fragment duplication was the main driving force for the evolution of the PbCaM/CML gene family. Cis-acting element analysis indicated that PbCaMs/CMLs might be related to hormones, growth and development, and stress response. Expression analysis showed that PbCaMs were generally highly expressed in five different tissues and under drought stress, whereas PbCMLs showed specific expression patterns. The expression levels of 11 candidate PbCaMs/CMLs were responsive to ABA and MeJA, suggesting that these genes might act through multiple signaling pathways. The overexpression of PbCaM3/CML13 genes significantly increased the tolerance of yeast cells to drought stress. The identification and characterization of the CaM/CML gene family in P. bournei laid the foundation for future functional studies of these genes.