OsDSR-1, a calmodulin-like gene, improves drought tolerance through scavenging of reactive oxygen species in rice (Oryza sativa L.)

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.

The involvement of a novel calmodulin-like protein isoform from oyster Crassostrea gigas in transcription factor regulation provides new insight into acclimation to ocean acidification

Marine organisms need to adapt to improve organismal fitness under ocean acidification (OA). Recent studies have shown that marine calcifiers can achieve acclimation by stimulating calcium binding/signaling pathways. Here, a CaM-like gene (CgCaLP-2) from oyster Crassostrea gigas which typically responded to long-term CO₂ exposure (two months) rather than short-term exposure (one week) was characterized. The cloned cDNA was 678 bp and was shorter than the retrieved sequence from NCBI (1125 bp). The two sequences, designated as CgCaLP-2-v1 and CgCaLP-2-v2, were demonstrated to be different splice variants by the genome sequence analysis. Western blotting analysis revealed two bands of 23 kD and 43 kD in mantle and hemocytes, corresponding to predicted molecular weight of CgCaLP-2-v1 and CgCaLP-2-v2, respectively. The isoform CgCaLP-2-v1 (the 23 kD band) was highly stimulated in response to long-term CO₂ exposure (42-day and 56-day treatment) in hemocytes and mantle tissue. The fluorescence signal of CgCaLP-2 in mantle and hemocytes became more intensive after long-term CO₂ exposure. Besides, in hemocytes, CgCaLP-2 presented a higher localization on the nuclear membrane after long-term CO₂ exposure (56 d). The target gene network of CgCaLP-2 was predicted, and a transcription factor (TF) gene annotated as Homeobox protein SIX4 (CgSIX4) showed a similar expressive trend to CgCaLP-2 during CO₂ exposure. Suppression of CgCaLP-2 via RNA interference significantly reduced the mRNA expression of CgSIX4. The results suggested that CgCaLP-2 might mediate the Ca²⁺-CaLP-TF signal transduction pathway under long-term CO₂ exposure. This study serves as an example to reveal that alternative splicing is an important mechanism for generation multiple protein isoforms and thus shape the plastic responses under CO₂ exposure, providing new insight into the potential acclimation ability of marine calcifiers to future OA.

New insights on the regulatory network of drought-responsive key genes in Arabidopsis thaliana

Drought stress is complex abiotic stress that seriously affects crop productivity and yield. Many genes with various functions are induced in response to drought stress. The present study aimed to identify drought-responsive hub genes and their related regulation network in Arabidopsis thaliana under drought stress. In this study, RNA-sequencing data of well-watered and drought treatment samples of Arabidopsis were analyzed, and differential expression genes were identified. The gene ontology enrichment and protein-protein interaction network analyses were performed for differential expression genes. Then, the most important hub genes, gene ontology enrichment, co-expression network, and prediction of related miRNAs of hub genes were investigated by in silico approaches. A total of 2462 genes were expressed differentially, of which 1926 transcripts were up-regulated under drought stress, and the rest were down-regulated. WRKY33, WRKY40, AT1G19020, STZ, SYP122, CNI1, CML37, BCS1, AT3G02840, and AT5G54490 were identified as hub genes in drought stress. The gene ontology analysis showed that hub genes significantly enriched in response to hypoxia, chitin, wounding, and salicylic acid-mediated signaling pathway. The hub genes were co-expressed with important drought-responsive genes such as WRKY46, WRKY60, CML38, ERF6, ERF104, and ERF1A. They were regulated by many stress-responsive miRNAs, such as ath-miR5021, miR413, miR5998, and miR162, that could be used as candidate miRNAs for regulating key genes under drought stress. It seems that the regulation network was involved in signaling pathways and protein degradation under drought stress, and it consists of several important genes and miRNAs that are potential candidates for plant improvement and breeding programs.

IPA1 improves drought tolerance by activating SNAC1 in rice

Drought is a major abiotic stress to rice (Oryza sativa) during growth. Ideal Plant Architecture (IPA1), the first cloned gene controlling the ideal plant type in rice, has been reported to function in both ideal rice plant architecture and biotic resistance. Here, we report that the IPA1/OsSPL14, encoding a transcriptional factor, positively regulates drought tolerance in rice. The IPA1 is constitutively expressed and regulated by H₂O₂, abscisic acid, NaCl and polyethylene glycol 6000 treatments in rice. Furthermore, the IPA1-knockout plants showed much greater accumulation of H₂O₂ as measured by 3,3'-diaminobenzidine staining in leaves compared with WT plants. Yeast one-hybrid, dual-luciferase and electrophoretic mobility shift assays indicated that the IPA1 directly activates the promoter of SNAC1. Expression of SNAC1 is significantly down-regulated in IPA1 knockout plants. Further investigation indicated that the IPA1 plays a positive role in drought-stress tolerance by inducing reactive oxygen species scavenging in rice. Together, these findings indicated that the IPA1 played important roles in drought tolerance by regulating SNAC1, thus activating the antioxidant system in rice.

Calcium decoders and their targets: The holy alliance that regulate cellular responses in stress signaling

Calcium (Ca²⁺) signaling is versatile communication network in the cell. Stimuli perceived by cells are transposed through Ca²⁺-signature, and are decoded by plethora of Ca²⁺ sensors present in the cell. Calmodulin, calmodulin-like proteins, Ca²⁺-dependent protein kinases and calcineurin B-like proteins are major classes of proteins that decode the Ca²⁺ signature and serve in the propagation of signals to different parts of cells by targeting downstream proteins. These decoders and their targets work together to elicit responses against diverse stress stimuli. Over a period of time, significant attempts have been made to characterize as well as summarize elements of this signaling machinery. We begin with a structural overview and amalgamate the newly identified Ca²⁺ sensor protein in plants. Their ability to bind Ca²⁺, undergo conformational changes, and how it facilitates binding to a wide variety of targets is further embedded. Subsequently, we summarize the recent progress made on the functional characterization of Ca²⁺ sensing machinery and in particular their target proteins in stress signaling. We have focused on the physiological role of Ca²⁺, the Ca²⁺ sensing machinery, and the mode of regulation on their target proteins during plant stress adaptation. Additionally, we also discuss the role of these decoders and their mode of regulation on the target proteins during abiotic, hormone signaling and biotic stress responses in plants. Finally, here, we have enumerated the limitations and challenges in the Ca²⁺ signaling. This article will greatly enable in understanding the current picture of plant response and adaptation during diverse stimuli through the lens of Ca²⁺ signaling.

Identification of the OsCML4 Gene in Rice Related to Salt Stress Using QTL Analysis

Soil salinity is a major abiotic stress that causes disastrous losses in crop yields. To identify favorable alleles that enhance the salinity resistance of rice (Oryza sativa L.) crops, a set of 120 Cheongcheong Nagdong double haploid (CNDH) lines derived from a cross between the Indica variety Cheongcheong and the Japonica variety Nagdong were used. A total of 23 QTLs for 8 different traits related to salinity resistance on chromosomes 1–3 and 5–12 were identified at the seedling stage. A QTL related to the salt injury score (SIS), qSIS-3b, had an LOD score of six within the interval RM3525–RM15904 on chromosome 3, and a phenotypic variation of 31% was further examined for the candidate genes. Among all the CNDH populations, five resistant lines (CNDH 27, CNDH 34-1, CNDH 64, CNDH 78, and CNDH 112), five susceptible lines (CNDH 52-1, CNDH 67, CNDH 69, CNDH 109, and CNDH 110), and the parent lines Cheongcheong and Nagdong were selected for relative gene expression analysis. Among all the genes, two candidate genes were highly upregulated in resistant lines, including the auxin-responsive protein IAA13 (Os03g0742900) and the calmodulin-like protein 4 (Os03g0743500-1). The calmodulin-like protein 4 (Os03g0743500-1) showed a higher expression in all the resistant lines than in the susceptible lines and a high similarity with other species in sequence alignment and phylogenetic tree, and it also showed a protein–protein interaction with other important proteins. The genes identified in our study will provide new genetic resources for improving salt resistance in rice using molecular breeding strategies in the future.

Changes in physiological responses of OsCaM1-1 overexpression in the transgenic rice under dehydration stress

Calmodulin, a primary calcium sensor in eukaryotes, binds calcium and regulates the activity of effector proteins in response to calcium signals that evoked in response to abiotic and biotic stress. To identify physiological responses associated with improved tolerance under dehydration stress that may be regulated by calmodulin in rice, the transgenic rice overexpressing OsCaM1-1, the control and the wild-type KDML105 differing in their dehydration tolerance were compared 24 h after exposure to dehydration stress. The results demonstrated a greater increase in relative water content, relative growth rate, abscisic acid, photosynthetic pigment and proline contents, and antioxidant activities in the transgenic rice plants, whereas Na/K and Na/Ca ratio, lipid peroxidation, and electrolytic leakage decreased. The OsCaM1-1 gene overexpression in the transgenic rice showed greater tolerance to dehydration stress than non-transgenic rice, suggesting that OsCaM1-1 might play an important role in mitigating dehydration stress.

Pinpointing genomic regions associated with root system architecture in rice through an integrative meta-analysis approach

Applying an integrated meta-analysis approach led to identification of meta-QTLs/ candidate genes associated with rice root system architecture, which can be used in MQTL-assisted breeding/ genetic engineering of root traits. Root system architecture (RSA) is an important factor for facilitating water and nutrient uptake from deep soils and adaptation to drought stress conditions. In the present research, an integrated meta-analysis approach was employed to find candidate genes and genomic regions involved in rice RSA traits. A whole-genome meta-analysis was performed for 425 initial QTLs reported in 34 independent experiments controlling RSA traits under control and drought stress conditions in the previous twenty years. Sixty-four consensus meta-QTLs (MQTLs) were detected, unevenly distributed on twelve rice chromosomes. The confidence interval (CI) of the identified MQTLs was obtained as 0.11-14.23 cM with an average of 3.79 cM, which was 3.88 times narrower than the mean CI of the original QTLs. Interestingly, 52 MQTLs were co-located with SNP peak positions reported in rice genome-wide association studies (GWAS) for root morphological traits. The genes located in these RSA-related MQTLs were detected and explored to find the drought-responsive genes in the rice root based on the RNA-seq and microarray data. Multiple RSA and drought tolerance-associated genes were found in the MQTLs including the genes involved in auxin biosynthesis or signaling (e.g. YUCCA, WOX, AUX/IAA, ARF), root angle (DRO1-related genes), lateral root development (e.g. DSR, WRKY), root diameter (e.g. OsNAC5), plant cell wall (e.g. EXPA), and lignification (e.g. C4H, PAL, PRX and CAD). The genes located within both the SNP peak positions and the QTL-overview peaks for RSA are suggested as novel candidate genes for further functional analysis. The promising candidate genes and MQTLs can be used as basis for genetic engineering and MQTL-assisted breeding of root phenotypes to improve yield potential, stability and performance in a water-stressed environment.

Calmodulin and calmodulin-like gene family in barley: Identification, characterization and expression analyses

Calmodulin (CaM) and calmodulin-like (CML) proteins are Ca²⁺ relays and play diverse and multiple roles in plant growth, development and stress responses. However, CaM/CML gene family has not been identified in barley (Hordeum vulgare). In the present study, 5 HvCaMs and 80 HvCMLs were identified through a genome-wide analysis. All HvCaM proteins possessed 4 EF-hand motifs, whereas HvCMLs contained 1 to 4 EF-hand motifs. HvCaM2, HvCaM3 and HvCaM5 coded the same polypeptide although they differed in nucleotide sequence, which was identical to the polypeptides coded by OsCaM1-1, OsCaM1-2 and OsCaM1-3. HvCaMs/CMLs were unevenly distributed over barley 7 chromosomes, and could be phylogenetically classified into 8 groups. HvCaMs/CMLs differed in gene structure, cis-acting elements and tissue expression patterns. Segmental and tandem duplication were observed among HvCaMs/CMLs during evolution. HvCML16, HvCML18, HvCML50 and HvCML78 were dispensable genes and the others were core genes in barley pan-genome. In addition, 14 HvCaM/CML genes were selected to examine their responses to salt, osmotic and low potassium stresses by qRT-PCR, and their expression were stress-and time-dependent. These results facilitate our understanding and further functional identification of HvCaMs/CMLs.

RNA Interference and CRISPR/Cas Gene Editing for Crop Improvement: Paradigm Shift towards Sustainable Agriculture

With the rapid population growth, there is an urgent need for innovative crop improvement approaches to meet the increasing demand for food. Classical crop improvement approaches involve, however, a backbreaking process that cannot equipoise with increasing crop demand. RNA-based approaches i.e., RNAi-mediated gene regulation and the site-specific nuclease-based CRISPR/Cas9 system for gene editing has made advances in the efficient targeted modification in many crops for the higher yield and resistance to diseases and different stresses. In functional genomics, RNA interference (RNAi) is a propitious gene regulatory approach that plays a significant role in crop improvement by permitting the downregulation of gene expression by small molecules of interfering RNA without affecting the expression of other genes. Gene editing technologies viz. the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (CRISPR/Cas) have appeared prominently as a powerful tool for precise targeted modification of nearly all crops' genome sequences to generate variation and accelerate breeding efforts. In this regard, the review highlights the diverse roles and applications of RNAi and CRISPR/Cas9 system as powerful technologies to improve agronomically important plants to enhance crop yields and increase tolerance to environmental stress (biotic or abiotic). Ultimately, these technologies can prove to be important in view of global food security and sustainable agriculture.

ROS Homeostasis in Abiotic Stress Tolerance in Plants

Climate change-induced abiotic stress results in crop yield and production losses. These stresses result in changes at the physiological and molecular level that affect the development and growth of the plant. Reactive oxygen species (ROS) is formed at high levels due to abiotic stress within different organelles, leading to cellular damage. Plants have evolved mechanisms to control the production and scavenging of ROS through enzymatic and non-enzymatic antioxidative processes. However, ROS has a dual function in abiotic stresses where, at high levels, they are toxic to cells while the same molecule can function as a signal transducer that activates a local and systemic plant defense response against stress. The effects, perception, signaling, and activation of ROS and their antioxidative responses are elaborated in this review. This review aims to provide a purview of processes involved in ROS homeostasis in plants and to identify genes that are triggered in response to abiotic-induced oxidative stress. This review articulates the importance of these genes and pathways in understanding the mechanism of resistance in plants and the importance of this information in breeding and genetically developing crops for resistance against abiotic stress in plants.

Drought and heat stress-related proteins: an update about their functional relevance in imparting stress tolerance in agricultural crops

We describe here the recent developments about the involvement of diverse stress-related proteins in sensing, signaling, and defending the cells in plants in response to drought or/and heat stress. In the current era of global climate drift, plant growth and productivity are often limited by various environmental stresses, especially drought and heat. Adaptation to abiotic stress is a multigenic process involving maintenance of homeostasis for proper survival under adverse environment. It has been widely observed that a series of proteins respond to heat and drought conditions at both transcriptional and translational levels. The proteins are involved in various signaling events, act as key transcriptional activators and saviors of plants under extreme environments. A detailed insight about the functional aspects of diverse stress-responsive proteins may assist in unraveling various stress resilience mechanisms in plants. Furthermore, by identifying the metabolic proteins associated with drought and heat tolerance, tolerant varieties can be produced through transgenic/recombinant technologies. A large number of regulatory and functional stress-associated proteins are reported to participate in response to heat and drought stresses, such as protein kinases, phosphatases, transcription factors, and late embryogenesis abundant proteins, dehydrins, osmotins, and heat shock proteins, which may be similar or unique to stress treatments. Few studies have revealed that cellular response to combined drought and heat stresses is distinctive, compared to their individual treatments. In this review, we would mainly focus on the new developments about various stress sensors and receptors, transcription factors, chaperones, and stress-associated proteins involved in drought or/and heat stresses, and their possible role in augmenting stress tolerance in crops.

Growth, physiology, and transcriptional analysis of Two contrasting Carex rigescens genotypes under Salt stress reveals salt-tolerance mechanisms

Salt stress is a major abiotic stress threatening plant growth and development throughout the world. In this study, we investigated the salt stress adaptation mechanism of Carex rigescens (Franch.) V. Krecz, a stress-tolerant turfgrass species with a wide distribution in northern China. Specifically, we analyzed the growth, physiology, and transcript expression patterns of two C. rigescens genotypes (Huanghua and Lvping No.1) exposed to salt stress. Results show that Huanghua demonstrated better growth performance, and higher turf quality (TQ), photochemical efficiency (Fv/Fm), relative water content (RWC), proline content, and lower relative electrolyte leakage (REL) during seven days of salt treatment compared to Lvping No.1, suggesting that Huanghua is more salt tolerant. Significant differences in reactive oxygen species (ROS), Malondialdehyde (MDA), melatonin, non-enzymatic antioxidants, lignin, and flavonoid content, as well as in antioxidant activity between Huanghua and Lvping No.1 after salt stress indicate the diverse regulation involved in salt stress adaptation in C. rigescens. These results, combined with those of the transcript expression pattern of involved genes, suggest that Huanghua is more active and efficient in ROS scavenging, Ca²⁺ binding, and its phytohormone response than Lvping No.1. Meanwhile, Lvping No.1 showed relatively higher phenylpropanoid synthesis, using flavonoid and lignin as supplements for the inadequate ROS-scavenging capacity and the development of vascular tissues, respectively. These performances illustrate the differences between the two genotypes in multifaceted and sophisticated actions contributing to the tolerance mechanism of salt stress in C. rigescens. In addition, the significantly higher content of melatonin and the rapid induction of Caffeic acid O-methyltransferase (COMT) highlight the role of melatonin in the salt stress response in Huanghua. The results of our study expand existing knowledge of the complexity of the salt stress response involving the antioxidant system, Ca²⁺ signaling, phytohormone response signaling, and phenylpropanoid pathways. It also provides a basis for further study of the underlying mechanism of salt tolerance in C. rigescens and other plant species.