Calmodulin as a versatile calcium signal transducer in plants

Wheat Tae-MIR1118 Constitutes a Functional Module With Calmodulin TaCaM2-1 and MYB Member TaMYB44 to Modulate Plant Low-N Stress Response

Distinct target genes are modulated by microRNA members and affect various biological processes associated with abiotic stress responses in plants. In this study, we characterized a functional module comprising miRNA/target and a downstream MYB transcription factor partner, Tae-MIR1118/TaCaM2/TaMYB44, in Triticum aestivum to mediate the plant low-nitrogen (N) stress response. Dual luciferase (LUC) assay and expression analysis indicated that TaCaM2 is regulated by Tae-MIR1118 through a posttranscriptional cleavage mechanism. Reporter LUC activity in N. benthamiana leaves co-transformed with effector CaMV35S::Tae-MIR1118 and reporter TaCaM2::LUC was significantly reduced, and the transcripts of Tae-MIR1118 and TaCaM2 in tissues exhibited converse expression patterns under varying N levels. Specifically, the transcripts of Tae-MIR1118 decreased, whereas those of TaCaM2 increased under low-N stress in a temporal-dependent manner. Yeast two-hybrid, bimolecular fluorescence complementation (BiFC) and co-immunoprecipitation (Co-IP) assays indicated that TaCaM2 interacted with the MYB transcription factor TaMYB44. Transgene analysis revealed the negative roles of Tae-MIR1118 and the positive functions of TaCaM2 and TaMYB44 in regulating plants for low-N stress adaptation by modulating glutamine synthetase activity, N uptake capacity, and root morphology. Yeast one-hybrid, transcriptional activation, and chromatin immunoprecipitation-quantitative polymerase chain reaction (ChIP-PCR) assays indicated that TaMYB44 could bind to the promoters of genes TaGS2.2, TaNRT2.1, and TaPIN4 and induce transcription of these stress-defensive genes. Knockdown of these three genes reduced GS activity, N accumulation, and root growth traits in plants subjected to N starvation. The yield in the wheat variety panel was highly correlated with the transcripts of Tae-MIR1118, TaCaM2, and TaMYB44 in plants cultured under N-deprived field conditions. A major haplotype of Tae-MIR1118, TaMIR1118-Hap1, enhanced the low-N stress tolerance of plants. Our findings indicate that the Tae-MIR1118/TaCaM2/TaMYB44 pathway primarily affects the low-N response of plants by modulating associated physiological processes.

Improvement of salt tolerance in Vicia faba (L.) seedlings: a comprehensive investigation of the effects of exogenous calcium chloride

BACKGROUND

This study investigated the effects of the different concentrations of CaCl2 (10 and 15 mol m-3) on the growth, physiology, and cytological characteristics of salt-stressed Vicia faba (L.) seedlings grown under greenhouse conditions.

RESULTS

Salinity stress (150 mol m-3 NaCl) had detrimental effects on all measured growth parameters, increased the micronucleus count number (MCN) by 26.6 micronuclei/1000 cells, decreased the mitotic index (MI) by 66.6%, and caused various chromosomal aberrations, nuclear alterations, and chromatin bridges in salt-stressed seedlings compared to the untreated plant. Nevertheless, the seed priming with CaCl2 (10 and 15 mol m-3) significantly alleviated the toxic effects induced by salinity stress, improved growth parameters, total chlorophyll (TChl), proline, and total soluble sugar (TSS) contents in salt-stressed faba bean seedling compared with seedlings germinated from non-primed seeds. The antioxidative system of salt-stressed faba bean was highly stimulated by increasing the activity of catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD) enzymes as well as phenolics and flavonoids were increased in all salt-stressed seedlings germinated from seeds primed with CaCl2 (10 and 15 mol m-3) indicating an improved tolerance of faba bean plant to salinity stress. Notably, the pretreatment with CaCl2 (10 mol m-3) reduced the micronuclei number per 1000 cells by 91.3% and decreased the abnormality index by 58.9% more effectively than CaCl2 (15 mol m-3). SDS-PAGE profiling revealed the presence of 16 proteins with different molecular weights, including two peptides, induced by CaCl2 (10 mol m-3) in response to salinity stress.

CONCLUSIONS

This study showed that 10 mol m-3 CaCl2 significantly improved salt tolerance in treated faba bean plants mitigating the antagonistic effects of salt stress on several physiological and cytological parameters.

The concerted function of a novel class of transcription factors, ZBFs, in light, jasmonate, and abscisic acid signaling pathways

Several classes of transcription factors have been investigated in light signaling pathways that bind to the light-responsive elements (LREs) present in the promoters of light regulatory genes for transcriptional regulation. Some of these transcription factors have been shown to bind to numerous promoters through genome-wide ChIP-on-chip (ChIP-chip) studies. Furthermore, through the integration of ChIP-seq and RNA-seq techniques, it has been demonstrated that a transcription factor modifies the expression of numerous genes with which it interacts. However, the mode of action of these transcription factors and their dependency on other regulators in the pathway has just started to be unraveled. In this review, we focus on a particular class of transcription factors, ZBFs (Z-box-binding factors), and their associated partners within the same or other classes of transcription factors and regulatory proteins during photomorphogenesis. Moreover, we have further made an attempt to summarize the crosstalk of these transcription factors with jasmonic acid-, abscisic acid-, and salicylic acid-mediated defense signaling pathways. This review offers an in-depth insight into the manner in which ZBFs and their interactors reshape cellular functions and plant behavior. The underlying principles not only contribute to a comprehensive understanding but also establish a framework for analyzing the interplay between early developmental events and hormone signaling, a regulation orchestrated by the ZBF family.

Comprehensive in-silico characterization and expression pattern of calmodulin genes under various abiotic and biotic stresses in Indian mustard (Brassica juncea)

Calcium (Ca2⁺) as a secondary messenger has a multidimensional role, including the growth and development of plants and the adaptive response to stress conditions. Calmodulin (CaM), a calcium-binding protein, uniquely binds with these Ca2⁺ ions and transmits Ca2⁺ signals. Calmodulin proteins have been well-reported in various plants for playing a role in abiotic and biotic stress signaling; however, a comprehensive analysis of the CaM genes of Indian mustard (Brassica juncea) has not been studied much. This study reports their chromosome placements, phylogenetic relations, the presence of protein motifs and cis-acting elements, and their expression patterns under stress due to salt, heat, cadmium, Xanthomonas campestris, and Alternaria brassicae. We identified 23 BjCaM genes coding for eight BjCaM proteins possessing the signature EF-hand domains. Chromosome locations, intron-exon structure, and in-silico protein characterization pointed toward genetic diversification. Phylogenetic analysis revealed a close relationship with previously characterized CaM proteins from Arabidopsis and rice. Cis-acting elements in the promoter regions suggested the potential role of BjCaM candidates in hormone signaling and various stress-responsive regulatory mechanisms. qRT-PCR analysis showed differential expression patterns, of which BjCaM17 and BjCaM19 showed higher expression under all stresses. The seven selected BjCaM genes were sensitive to cadmium stress. Interestingly, despite translating to same protein, BjCaM15, BjCaM17, and BjCaM19 showed differential expressions under the same stresses. This research represents the first genome-wide analysis of calmodulin genes in Indian mustard, providing a valuable reference for decoding calcium signaling via calmodulin and its potential exploitation to improve crop resistance to stress conditions.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-025-01561-x.

The calcium sensor AtCML8 contributes to Arabidopsis plant cell growth by modulating the brassinosteroid signaling pathway

Calcium signaling plays an essential role in integrating plant responses to diverse stimuli and regulating growth and development. While some signaling components and their roles are well-established, such as the ubiquitous calmodulin (CaM) sensor, plants possess a broader repertoire of calcium sensors. Notably, CaM-like proteins (CMLs) represent a poorly characterized class for which interacting partners and biological functions remain largely elusive. Our work investigates the role of Arabidopsis thaliana CML8 that exhibits a unique expression profile in seedlings. A reverse genetic approach revealed a function of CML8 in regulating root growth and hypocotyl elongation. RNA-seq analyses highlighted CML8 association with the regulation of numerous genes involved in growth and brassinosteroid (BR) signaling. Using co-immunoprecipitation experiments, we demonstrated that CML8 interacts with the BR receptor, BRI1, in planta in a ligand-dependent manner. This finding suggests the existence of a novel regulatory step in the BR pathway, involving calcium signaling.

Genome-wide identification and characterization of Calcium-Dependent Protein Kinase (CDPK) gene family in autotetraploid cultivated alfalfa (Medicago sativa subsp. sativa) and expression analysis under abiotic stresses

BACKGROUND

Calcium-dependent protein kinases (CDPKs), play multiple roles in plant development, growth and response to bio- or abiotic stresses. Calmodulin-like domains typically contain four EF-hand motifs for Ca²⁺ binding. The CDPK gene family can be divided into four subgroups in Arabidopsis, and it has been identified in many plants, such as rice, tomato, but has not been investigated in alfalfa (Medicago sativa subsp. sativa) yet.

RESULTS

In our study, 38 non-redundant MsCDPK genes were identified from the "XinJiangDaYe" alfalfa genome. They can be divided into four subgroups which is the same as in Arabidopsis and Medicago truncatula, and there were 15, 12,10 and 1 in CDPK I, II, III and IV, respectively. RNA-seq analysis revealed tissue-specificity of 38 MsCDPK genes. After researching the transcriptome data, we found these 38 MsCDPK members responsive to drought, salt, and cold stress treatments. Further analysis showed that the expression of almost all the MsCDPKs is regulated by abiotic stresses. In addition, we chose MsCDPK03, MsCDPK26, MsCDPK31 and MsCDPK36 for RT-qPCR validation which was from CDPK I-IV subgroups respectively. The result showed that the expression of these four genes was significantly induced by drought, salt and cold treatments. The subcellular location experiment showed that these four proteins were all located in nucleus.

CONCLUSION

In our study, we identified 38 distinct MsCDPK genes within the alfalfa genome, which were classified into four groups. We conducted a comprehensive analysis of various gene features, including physicochemical properties, phylogenetic relationships, exon-intron structures, conserved motifs, chromosomal locations, gene duplication events, cis-regulatory elements, 3D structures, and tissue-specific expression patterns, as well as responses to drought, salt, and cold stresses. These results also provide a solid foundation for further investigations into the functions of MsCDPKs aimed at improving drought tolerance in autotetraploid cultivated alfalfa through genetic engineering.

The Role of Glutamate Metabolism and the GABA Shunt in Bypassing the Tricarboxylic Acid Cycle in the Light

Glutamate is an essential amino acid in both the energy and biosynthetic processes in plant cells. The aim of this work was to study changes in glutamate metabolism upon irradiation of maize (Zea mays L.) leaves with light of different spectral compositions, as well as to identify mechanisms regulating the work of enzymes involved in the studied process. A study was conducted of light-induced changes in glutamate metabolism in maize leaves, mediated by redirecting the glutamate flow to the γ-aminobutyric acid (GABA) shunt. Glutamate dehydrogenase (GDH) was more active in darkness, and the irradiation by red light inhibited the expression of both the Gdh1 and Gdh2 genes. EGTA and ruthenium red abolished the effects of light, indicating the participation of Ca2+ ions in phytochrome signal transduction. Contrary to GDH, glutamate decarboxylase (GAD) activity was moderately higher in the light, stimulated by red light, while far-red light reversed the effect. The effect of light on Gad expression was more pronounced than on GAD activity. Irradiation by red light also resulted in the increase in activity of GABA transaminase (GTA), which was abolished by far-red light. The third enzyme of the GABA shunt, succinic semialdehyde dehydrogenase (SSADH), was also activated by light. The effect of light on the expression of Ssadh1, but not on Ssadh2, was phytochrome-dependent. It is concluded that irradiation by light shifts glutamate metabolism from GDH to GAD with the activation of GABA transaminase and SSADH. This suggests that the GABA pathway plays a role in the maintenance of the tricarboxylic acid cycle in the light via bypassing its reactions when the 2-oxoglutarate dehydrogenase complex is inhibited and the cycle switches to the open mode.

The Vital Role of the CAMTA Gene Family in Phoebe bournei in Response to Drought, Heat, and Light Stress

The calmodulin-binding transcriptional activator (CAMTA) is a small, conserved gene family in plants that plays a crucial role in regulating growth, development, and responses to various abiotic stress. Given the significance of the CAMTA gene family, various studies have been dedicated to uncovering its functional characteristics. In this study, genome-wide identification and bioinformatics analysis were conducted to explore CAMTAs in Phoebe bournei. A total of 17 CAMTA genes, each containing at least one domain from CG-1, TIG, ANK, or IQ, were identified in the P. bournei genome. The diversity of PbCAMTAs could be varied depending on their subcellular localization. An analysis of protein motifs, domains, and gene structure revealed that members within the same subgroup exhibited similar organization, supporting the results of the phylogenetic analysis. Gene duplications occurred among members of the PbCAMTA gene family. According to the cis-regulatory element prediction and protein-protein interaction network analysis, eight genes were subjected to qRT-PCR under drought, heat, and light stresses. The expression profiles indicated that PbCAMTAs, particularly PbCAMTA2, PbCAMTA12, and PbCAMTA16, were induced by abiotic stress. This study provides profound insights into the functions of CAMTAs in P. bournei.

Characterization of Arabidopsis aldolases AtFBA4, AtFBA5, and their inhibition by morin and interaction with calmodulin

Fructose bisphosphate aldolases (FBAs) catalyze the reversible cleavage of fructose 1,6-bisphosphate into dihydroxyacetone phosphate and glyceraldehyde 3-phosphate. We analyzed two previously uncharacterized cytosolic Arabidopsis FBAs, AtFBA4 and AtFBA5. Based on a recent report, we examined the interaction of AtFBA4 with calmodulin (CaM)-like protein 11 (AtCML11). AtFBA4 did not bind AtCML11; however, we found that CaM bound AtFBA5 in a Ca2+-dependent manner with high specificity and affinity (KD ~ 190 nm) and enhanced its stability. AtFBA4 and AtFBA5 exhibited Michaelis-Menten kinetics with Km and Vmax values of 180 μm and 4.9 U·mg-1 for AtFBA4, and 6.0 μm and 0.30 U·mg-1 for AtFBA5, respectively. The flavonoid morin inhibited both isozymes. Our study suggests that Ca2+ signaling and flavanols may influence plant glycolysis/gluconeogenesis.

BcWRKY1 confers Botrytis cinerea susceptibility via inhibiting JA biosynthesis

WRKYs play important roles in plant stress resistance. However, the role of WRKYs in non-heading Chinese cabbage (Brassica campestris ssp. chinensis) against Botrytis cinerea (B. cinerea) remains poorly understood. Herein, the expression of BcWRKY1 was induced by B. cinerea. Further, the role of BcWRKY1 in B. cinerea infection was identified. Silencing of BcWRKY1 in non-heading Chinese cabbage enhanced plant resistance to B. cinerea. After B. cinerea inoculation, BcWRKY1-silencing plants exhibited lower reactive oxygen species (ROS) content, higher jasmonic acid (JA) content, and the expression level of JA biosynthesis genes, BcOPR3, BcLOX3-1 and BcLOX3-2 were upregulated. Overexpression of BcWRKY1 in Arabidopsis exhibited a complementary phenotype. By directly targeting W-boxes in the promoter of BcLOX3-2, BcWRKY1 inhibited the transcription of this gene. In addition, 13 candidate interacting proteins of BcWRKY1 were identified by yeast two-hybrid (Y2H) screening, and the interaction between BcWRKY1 and BcCaM6 weakened the inhibition of BcLOX3-2. In summary, our findings suggest that BcWRKY1 interacts with BcCaM6 to negatively regulate disease resistance.

Stripe rust effector Pst03724 modulates host immunity by inhibiting NAD kinase activation by a calmodulin

Puccinia striiformis f. sp. tritici (Pst) secretes effector proteins that enter plant cells to manipulate host immune processes. In this report, we present an important Pst effector, Pst03724, whose mRNA expression level increases during Pst infection of wheat (Triticum aestivum). Silencing of Pst03724 reduced the growth and development of Pst. Pst03724 targeted the wheat calmodulin TaCaM3-2B, a positive regulator of wheat immunity. Subsequent investigations revealed that Pst03724 interferes with the TaCaM3-2B-NAD kinase (NADK) TaNADK2 association and thus inhibits the enzyme activity of TaNADK2 activated by TaCaM3-2B. Knocking down TaNADK2 expression by virus-mediated gene silencing significantly increased fungal growth and development, suggesting a decrease in resistance against Pst infection. In conclusion, our findings indicate that Pst effector Pst03724 inhibits the activity of NADK by interfering with the TaCaM3-2B-TaNADK2 association, thereby facilitating Pst infection.

Genome-wide identification of the CNGC gene family and negative regulation of drought tolerance by HvCNGC3 and HvCNGC16 in transgenic Arabidopsis thaliana

Cyclic nucleotide-gated ion channels (CNGCs), as non-selective cation channels, play essential roles in plant growth and stress responses. However, they have not been identified in Qingke (Hordeum vulgare L.). Here, we performed a comprehensive genome-wide identification and function analysis of the HvCNGC gene family to determine its role in drought tolerance. Phylogenetic analysis showed that 27 HvCNGC genes were divided into four groups and unevenly located on seven chromosomes. Transcription analysis revealed that two closely related members of HvCNGC3 and HvCNGC16 were highly induced and the expression of both genes were distinctly different in two extremely drought-tolerant materials. Transient expression revealed that the HvCNGC3 and HvCNGC16 proteins both localized to the plasma membrane and karyotheca. Overexpression of HvCNGC3 and HvCNGC16 in Arabidopsis thaliana led to impaired seed germination and seedling drought tolerance, which was accompanied by higher hydrogen peroxide (H2O2), malondialdehyde (MDA), proline accumulation and increased cell damage. In addition, HvCNGC3 and HvCNGC16-overexpression lines reduced ABA sensitivity, as well as lower expression levels of some ABA biosynthesis and stress-related gene in transgenic lines. Furthermore, Yeast two hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays revealed that HvCNGC3 and HvCNGC16 interacted with calmodulin/calmodulin-like proteins (CaM/CML), which, as calcium sensors, participate in the perception and decoding of intracellular calcium signaling. Thus, this study provides information on the CNGC gene family and provides insight into the function and potential regulatory mechanism of HvCNGC3 and HvCNGC16 in drought tolerance in Qingke.

Arabidopsis Calmodulin-like Proteins CML13 and CML14 Interact with Calmodulin-Binding Transcriptional Activators and Function in Salinity Stress Response

Eukaryotic cells use calcium ions (Ca2+) as second messengers, particularly in response to abiotic and biotic stresses. These signals are detected by Ca2+ sensor proteins, such as calmodulin (CaM), which regulate the downstream target proteins. Plants also possess many CaM-like proteins (CMLs), most of which remain unstudied. We recently demonstrated that Arabidopsis CML13 and CML14 interact with proteins containing isoleucine/glutamine (IQ) domains, including CaM-binding transcriptional activators (CAMTAs). Here, we show that CaM, CML13 and CML14 bind all six members of the Arabidopsis CAMTA family. Using a combination of in planta and in vitro protein-interaction assays, we tested 11 members of the CaM/CML family and demonstrated that only CaM, CML13 and CML14 bind to CAMTA IQ domains. CaM, CML13 and CML14 showed Ca2+-independent binding to the IQ region of CAMTA6 and CAMTA3, and CAMTA6 in vitro exhibited some specificity toward individual IQ domains within CAMTA6 in split-luciferase in planta assays. We show that cml13 mutants exhibited enhanced salinity tolerance during germination compared to wild-type plants, a phenotype similar to camta6 mutants. In contrast, plants overexpressing CML13-GFP or CML14-GFP in the wild-type background showed increased NaCl sensitivity. Under mannitol stress, cml13 mutants were more susceptible than camta6 mutants or wild-type plants. The phenotype of cml13 mutants could be rescued with the wild-type CML13 gene. Several salinity-marker genes under CAMTA6 control were similarly misregulated in both camta6 and cml13 mutants, further supporting a role for CML13 in CAMTA6 function. Collectively, our data suggest that CML13 and CML14 participate in abiotic stress signaling as CAMTA effectors.

Genome-wide analyses of calmodulin and calmodulin-like proteins in the halophyte Nitraria sibirica reveal their involvement in response to salinity, drought and cold stress

The calmodulin (CaM) and calmodulin-like (CML) proteins are major calcium sensors that play a critical role in environmental stimulus response in plants. Nevertheless, the CaM/CML proteins from the specific plants with extreme tolerance to abiotic stresses remained so far uncharacterized. In this study, 66 candidate proteins (three NsCaMs and sixty-three NsCMLs) were identified from the halophyte Nitraria sibirica, which can withstand an extreme salinity. Bioinformatic analysis of upstream cis-acting elements predicted the potential involvement of NsCaM/CMLs in abiotic stress responses and various hormone responses. Additionally, the Nitraria sibirica transcriptome revealed that 17 and 7 NsCMLs were significantly upregulated under 100 mM or 400 mM NaCl treatment. Transcription of most salt-responsive genes was similarly upregulated under cold stress, yet downregulated under drought treatment. Moreover, predictive subcellular localization analysis suggested that the stress-responsive NsCML proteins mainly localize at the cellular membrane and within the nucleus. Furthermore, transgenic overexpression of two NsCMLs (NISI03G1136 and NISI01G1645) was found to mitigate H2O2 accumulation caused by salt stress. These results provide insights into the potential function of Nitraria sibirica CaM/CML proteins, which could aid the investigation of molecular mechanisms of extreme tolerance to abiotic stresses in halophytes.

Genome-Wide Identification and Expression Analysis of Catalase Gene Families in Triticeae

Aerobic metabolism in plants results in the production of hydrogen peroxide (H2O2), a significant and comparatively stable non-radical reactive oxygen species (ROS). H2O2 is a signaling molecule that regulates particular physiological and biological processes (the cell cycle, photosynthesis, plant growth and development, and plant responses to environmental challenges) at low concentrations. Plants may experience oxidative stress and ultimately die from cell death if excess H2O2 builds up. Triticum dicoccoides, Triticum urartu, and Triticum spelta are different ancient wheat species that present different interesting characteristics, and their importance is becoming more and more clear. In fact, due to their interesting nutritive health, flavor, and nutritional values, as well as their resistance to different parasites, the cultivation of these species is increasingly important. Thus, it is important to understand the mechanisms of plant tolerance to different biotic and abiotic stresses by studying different stress-induced gene families such as catalases (CAT), which are important H2O2-metabolizing enzymes found in plants. Here, we identified seven CAT-encoding genes (TdCATs) in Triticum dicoccoides, four genes in Triticum urartu (TuCATs), and eight genes in Triticum spelta (TsCATs). The accuracy of the newly identified wheat CAT gene members in different wheat genomes is confirmed by the gene structures, phylogenetic relationships, protein domains, and subcellular location analyses discussed in this article. In fact, our analysis showed that the identified genes harbor the following two conserved domains: a catalase domain (pfam00199) and a catalase-related domain (pfam06628). Phylogenetic analyses showed that the identified wheat CAT proteins were present in an analogous form in durum wheat and bread wheat. Moreover, the identified CAT proteins were located essentially in the peroxisome, as revealed by in silico analyses. Interestingly, analyses of CAT promoters in those species revealed the presence of different cis elements related to plant development, maturation, and plant responses to different environmental stresses. According to RT-qPCR, Triticum CAT genes showed distinctive expression designs in the studied organs and in response to different treatments (salt, heat, cold, mannitol, and ABA). This study completed a thorough analysis of the CAT genes in Triticeae, which advances our knowledge of CAT genes and establishes a framework for further functional analyses of the wheat gene family.

Role of calcium in regulating key steps in phytochrome-induced signaling pathways

A major focus in the field of signal transduction pathways in plants has been the role of calcium ions in mediating diverse sensory responses. Among these responses, those initiated by the red-light activated photoreceptor, phytochrome have received increasing attention in recent years. Although not all phytochrome responses are mediated by calcium, many of them are, and a number of recent publications have clarified just how calcium helps to transduce some of the transcriptomic changes induced by phytochrome. Many of these publications reference Dr. Sopory's laboratory as an important contributor to the initial data documenting that an early step in the signaling pathways induced by phytochrome was an increased uptake of calcium into cells. This review summarizes the strong evidence that calcium-dependent steps play a major role in transducing phytochrome-initiated responses, and it updates the latest reports on specific steps in some phytochrome responses that are dependent on the mediation of calcium-binding protein kinases and calmodulin.

The role of arbuscular mycorrhizal fungi in the alleviation of cadmium stress in cereals: A multilevel meta-analysis

The symbiotic relationships between crop species and arbuscular mycorrhizal fungi (AMF) are crucial for plant health, productivity, and environmental sustainability. The roles of AMF in reducing crop stress caused by cadmium (Cd) toxicity and in the remediation of Cd-contaminated soil are not fully understood. Here we report on a meta-analysis that sought to identify the functions of AMF in cereals under Cd stress. A total of 54 articles published between January 1992 and September 2022 were used to create the dataset, which provided 7216 data sets on mycorrhizal cereals under Cd stress examined. AMF effects on colonization rate, biomass, physiological level, nutritional level, and plant Cd level were measured using the logarithmic response ratio (Ln R). The results showed that AMF overall greatly reduced 5.14 - 33.6 % Cd stress on cereals in greenhouse experiments under controlled conditions. AMF colonization significantly stimulated crop biomass by 65.7 %, boosted the formation of photosynthetic pigments (23.2 %), and greatly increased plant nitrogen (24.8 %) and phosphorus (58.4 %) uptake. The dilution effect of mycorrhizal plants made the Cd concentration decline by 25.2 % in AMF plants compared to non-mycorrhizal ones. AMF also alleviated Cd stress by improving osmotic regulators (soluble protein, sugar, and total proline, from 14.8 to 36.0 %) and lowering the membrane lipid peroxidation product (MDA, 12.9 %). Importantly, the results from the random forest and model selection analysis demonstrated that crop type, soil characteristics, chemical form, and Cd levels were the main factors determining the function of AMF in alleviating Cd stress. Additionally, there was a significant interaction between AMF colonization rate and Cd addition, but their interactive effect was less than the colonization rate alone. This meta-analysis demonstrated that AMF inoculation could be considered as a promising strategy for mitigation of Cd stress in cereals.

Genome-Wide Investigation and Expression Analysis of the Catalase Gene Family in Oat Plants (Avena sativa L.)

Through the degradation of reactive oxygen species (ROS), different antioxidant enzymes, such as catalase (CAT), defend organisms against oxidative stress. These enzymes are crucial to numerous biological functions, like plant development and defense against several biotic and abiotic stresses. However, despite the major economic importance of Avena sativa around the globe, little is known about the CAT gene's structure and organization in this crop. Thus, a genome-wide investigation of the CAT gene family in oat plants has been carried out to characterize the potential roles of those genes under different stressors. Bioinformatic approaches were used in this study to predict the AvCAT gene's structure, secondary and tertiary protein structures, physicochemical properties, phylogenetic tree, and expression profiling under diverse developmental and biological conditions. A local Saudi oat variety (AlShinen) was used in this work. Here, ten AvCAT genes that belong to three groups (Groups I-III) were identified. All identified CATs harbor the two conserved domains (pfam00199 and pfam06628), a heme-binding domain, and a catalase activity motif. Moreover, identified AvCAT proteins were located in different compartments in the cell, such as the peroxisome, mitochondrion, and cytoplasm. By analyzing their promoters, different cis-elements were identified as being related to plant development, maturation, and response to different environmental stresses. Gene expression analysis revealed that three different AvCAT genes belonging to three different subgroups showed noticeable modifications in response to various stresses, such as mannitol, salt, and ABA. As far as we know, this is the first report describing the genome-wide analysis of the oat catalase gene family, and these data will help further study the roles of catalase genes during stress responses, leading to crop improvement.

Phosphorylation of MdCYTOKININ RESPONSE FACTOR4 suppresses ethylene biosynthesis during apple fruit ripening

The plant hormone ethylene plays a central role in the ripening of climacteric fruits, such as apple (Malus domestica). Ethylene biosynthesis in apple fruit can be suppressed by calcium ions (Ca2+); however, the underlying mechanism is largely unknown. In this study, we identified an apple APETALA2/ETHYLENE-RESPONSIVE FACTOR (AP2/ERF) transcription factor, MdCYTOKININ RESPONSE FACTOR4 (MdCRF4), which functions as a transcriptional activator of ethylene biosynthesis- and signaling-related genes, including Md1-AMINOCYCLOPROPANE-1-CARBOXYLIC ACID SYNTHASE1 (MdACS1) and MdETHYLENE-RESPONSIVE FACTOR3 (MdERF3), as a partner of the calcium sensor, calmodulin. Ca2+ promoted the Ca2+/CaM2-mediated phosphorylation of MdCRF4, resulting in MdCRF4 recognition by the E3 ubiquitin ligase MdXB3 ORTHOLOG 1 IN ARABIDOPSIS THALIANA (MdXBAT31), and consequently its ubiquitination and degradation via the 26S proteasome pathway. This in turn resulted in lower expression of MdACS1 and MdERF3 and reduced ethylene biosynthesis. Transiently overexpressing various MdCRF4 proteins with specific mutated phosphorylation sites revealed that the phosphorylation state of MdCRF4 affects the ripening of apple fruit. The results reveal that a Ca2+/CaM-MdCRF4-MdXBAT31 module is involved in Ca2+-suppressed ethylene biosynthesis, which delays apple fruit ripening. This provides insights into fruit ripening that may result in strategies for extending fruit shelf life.

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.

Genome-Wide Identification of the SUN Gene Family in Melon (Cucumis melo) and Functional Characterization of Two CmSUN Genes in Regulating Fruit Shape Variation

Melon (Cucumis melo) is an important economic crop cultivated worldwide. A unique SUN gene family plays a crucial role in regulating plant growth and fruit development, but many SUN family genes and their function have not been well-characterized in melon. In the present study, we performed genome-wide identification and bioinformatics analysis and identified 24 CmSUN family genes that contain integrated and conserved IQ67 domain in the melon genome. Transcriptome data analysis and qRT-PCR results showed that most CmSUNs are specifically enriched in melon reproductive organs, such as young flowers and ovaries. Through genetic transformation in melons, we found that overexpression of CmSUN23-24 and CmSUN25-26-27c led to an increased fruit shape index, suggesting that they act as essential regulators in melon fruit shape variation. Subcellular localization revealed that the CmSUN23-24 protein is located in the cytoplasmic membrane. A direct interaction between CmSUN23-24 and a Calmodulin protein CmCaM5 was found by yeast two-hybrid assay, which indicated their participation in the calcium signal transduction pathway in regulating plant growth. These findings revealed the molecular characteristics, expression profile, and functional pattern of the CmSUN genes, and may provide the theoretical basis for the genetic improvement of melon fruit breeding.

Tobacco mosaic virus hijacks its coat protein-interacting protein IP-L to inhibit NbCML30, a calmodulin-like protein, to enhance its infection

Calcium is an important plant immune signal that is essential for activating host resistance, but how RNA viruses manipulate calcium signals to promote their infections remains largely unknown. Here, we demonstrated that tobacco mosaic virus (TMV) coat protein (CP)-interacting protein L (IP-L) associates with calmodulin-like protein 30 (NbCML30) in the cytoplasm and nucleus, and can suppress its expression at the nucleic acid and protein levels. NbCML30, which lacks the EF-hand conserved domain and cannot bind to Ca²⁺ , was located in the cytoplasm and nucleus and was downregulated by TMV infection. NbCML30 silencing promoted TMV infection, while its overexpression inhibited TMV infection by activating Ca²⁺ -dependent oxidative stress in plants. NbCML30-mediated resistance to TMV mainly depends on IP-L regulation as the facilitation of TMV infection by silencing NbCML30 was canceled by co-silencing NbCML30 and IP-L. Overall, these findings indicate that in the absence of any reported silencing suppressor activity, TMV CP manipulates IP-L to inhibit NbCML30, influencing its Ca²⁺ -dependent role in the oxidative stress response. These results lay a theoretical foundation that will enable us to engineer tobacco (Nicotiana spp.) with improved TMV resistance in the future.

Sequence Characteristics and Expression Analysis of GhCIPK23 Gene in Upland Cotton (Gossypium hirsutum L.)

CIPK (calcineurin B-like-interacting protein kinase) is a kind of serine/threonine protein kinase widely existing in plants, and it plays an important role in plant growth and development and stress response. To better understand the biological functions of the GhCIPK23 gene in upland cotton, the coding sequence (CDS) of the GhCIPK23 gene was cloned in upland cotton, and its protein sequence, evolutionary relationship, subcellular localization, expression pattern and cis-acting elements in the promoter region were analyzed. Our results showed that the full-length CDS of GhCIPK23 was 1368 bp, encoding a protein with 455 amino acids. The molecular weight and isoelectric point of this protein were 50.83 KDa and 8.94, respectively. The GhCIPK23 protein contained a conserved N-terminal protein kinase domain and C-terminal regulatory domain of the CIPK gene family member. Phylogenetic tree analysis demonstrated that GhCIPK23 had a close relationship with AtCIPK23, followed by OsCIPK23, and belonged to Group A with AtCIPK23 and OsCIPK23. The subcellular localization experiment indicated that GhCIPK23 was located in the plasma membrane. Tissue expression analysis showed that GhCIPK23 had the highest expression in petals, followed by sepals, and the lowest in fibers. Stress expression analysis showed that the expression of the GhCIPK23 gene was in response to drought, salt, low-temperature and exogenous abscisic acid (ABA) treatment, and had different expression patterns under different stress conditions. Further cis-acting elements analysis showed that the GhCIPK23 promoter region had cis-acting elements in response to abiotic stress, phytohormones and light. These results established a foundation for understanding the function of GhCIPK23 and breeding varieties with high-stress tolerance in cotton.

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.

CML8 and GAD4 function in (Z)-3-hexenol-mediated defense by regulating γ-aminobutyric acid accumulation in Arabidopsis

(Z)-3-hexenol, a small gaseous molecule, is produced in plants under biotic stress and induces defense responses in neighboring plants. However, little is known about how (Z)-3-hexenol induces plant defense-related signaling. In this study, we uncovered how (Z)-3-hexenol treatment enhances plant resistance to insect attacks by increasing γ-aminobutyric acid (GABA) contents in Arabidopsis leaves. First, (Z)-3-hexenol increases the intracellular content of calcium as secondary messenger in Arabidopsis leaf mesophyll cells. Both intracellular and extracellular calcium stores regulate changes in calcium content. Then, CML8 and GAD4 transmit calcium signaling to affect (Z)-3-hexenol induced GABA content and plant resistance. Herein, CML8 interaction with GAD4 was examined via yeast two-hybrid assays, firefly luciferase complementation imaging, and GST pull-down assays. These results indicate that (Z)-3-hexenol treatment increased the GABA contents in Arabidopsis leaves based on CML8 and GAD4, thus increasing plant resistance to the insect Plutella xylostella. This study revealed the mechanism of activating plant insect defense induced by (Z)-3-hexenol, which guides the study of volatiles as biological pest control.

Ectopic expression of BrIQD35 promotes drought stress tolerance in Nicotiana benthamiana

The plant IQD gene family is responsive to a variety of stresses. In this study, we studied the structural features and functions of the gene BrIQD35 in Chinese cabbage, a member of the IQD gene family. BrIQD35 was cloned and shown to contain an IQ motif. Transient expression of BrIQD35 indicated that it was localized on the plasma membrane and was significantly upregulated under drought and salt stress in Chinese cabbage. To further identify the function of BrIQD35, it was heterologously overexpressed in Nicotiana benthamiana. Although there was no significant difference between BrIQD35-overexpressed and wild-type (WT) plants under salt stress, WT N. benthamiana showed more wilting than the BrIQD35-overexpressed plants under drought stress. Since the IQ motif has been annotated as a CaM binding site, yeast two-hybrid assays were used to explore the interaction between BrIQD35 and CaM. The results indicated that BrIQD35 interacts weakly with CaMb, but not with CaMa, suggesting that BrIQD35 may function through the Ca2+ -CaMb pathway. The findings reveal a novel gene involved in drought tolerance, which is important for plant breeding and quality improvement for Chinese cabbage.

The Activity of the Durum Wheat (Triticum durum L.) Catalase 1 (TdCAT1) Is Modulated by Calmodulin

Plant catalases (CAT) are involved in the cellular scavenging of the reactive oxygen species during developmental processes and in response to abiotic and biotic stresses. However, little is known about the regulation of the CAT activity to ensure efficient antioxidant function. Using bioinformatic analyses, we showed that durum wheat catalase 1 (TdCAT1) harbors highly conserved cation-binding and calmodulin binding (CaMBD) domains which are localized at different positions of the protein. As a result, the catalytic activity of TdCAT1 is enhanced in vitro by the divalent cations Mn²⁺ and Fe²⁺ and to a lesser extent by Cu²⁺, Zn²⁺, and Mg²⁺. Moreover, the GST-pull down assays performed here revealed that TdCAT1 bind to the wheat CaM (TdCaM1.3) in a Ca²⁺-independent manner. Furthermore, the TdCaM1.3/Ca²⁺ complex is stimulated in a CaM-dose-dependent manner by the catalytic activity of TdCAT1, which is further increased in the presence of Mn²⁺ cations. The catalase activity of TdCAT1 is enhanced by various divalent cations and TdCaM1.3 in a Ca-dependent manner. Such effects are not reported so far and raise a possible role of CaM and cations in the function of CATs during cellular response to oxidative stress.

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.

Identification of Candidate Genes Regulating Drought Tolerance in Pearl Millet

Pearl millet is an important crop of the arid and semi-arid ecologies to sustain food and fodder production. The greater tolerance to drought stress attracts us to examine its cellular and molecular mechanisms via functional genomics approaches to augment the grain yield. Here, we studied the drought response of 48 inbreds representing four different maturity groups at the flowering stage. A set of 74 drought-responsive genes were separated into five major phylogenic groups belonging to eight functional groups, namely ABA signaling, hormone signaling, ion and osmotic homeostasis, TF-mediated regulation, molecular adaptation, signal transduction, physiological adaptation, detoxification, which were comprehensively studied. Among the conserved motifs of the drought-responsive genes, the protein kinases and MYB domain proteins were the most conserved ones. Comparative in-silico analysis of the drought genes across millet crops showed foxtail millet had most orthologs with pearl millet. Of 698 haplotypes identified across millet crops, MyC2 and Myb4 had maximum haplotypes. The protein–protein interaction network identified ABI2, P5CS, CDPK, DREB, MYB, and CYP707A3 as major hub genes. The expression assay showed the presence of common as well as unique drought-responsive genes across maturity groups. Drought tolerant genotypes in respective maturity groups were identified from the expression pattern of genes. Among several gene families, ABA signaling, TFs, and signaling proteins were the prospective contributors to drought tolerance across maturity groups. The functionally validated genes could be used as promising candidates in backcross breeding, genomic selection, and gene-editing schemes in pearl millet and other millet crops to increase the yield in drought-prone arid and semi-arid ecologies.

Characterization of the Calmodulin/Calmodulin-like Protein (CAM/CML) Family in Ginkgo biloba, and the Influence of an Ectopically Expressed GbCML Gene (Gb_30819) on Seedling and Fruit Development of Transgenic Arabidopsis

Calmodulins (CAMs) and calmodulin-like proteins (CMLs) can participate in the regulation of various physiological processes via sensing and decoding Ca²⁺ signals. To reveal the characteristics of the CAM/CML family in Ginkgo biloba, a comprehensive analysis was performed at the genome-wide level. A total of 26 CAMs/CMLs, consisting of 5 GbCAMs and 21 GbCMLs, was identified on 11 out of 12 chromosomes in G. biloba. They displayed a certain degree of multiplicity in their sequences, albeit with conserved EF hands. Collinearity analysis suggested that tandem rather than segmental or whole-genome duplications were likely to play roles in the evolution of the Ginkgo CAM/CML family. Furthermore, GbCAMs/GbCMLs were grouped into higher, lower, and moderate expression in magnitude. The cis-acting regulatory elements involved in phytohormone-responsiveness within GbCAM/GbCML promotors may explain their varied expression profiles. The ectopic expression of a GbCML gene (Gb_30819) in transgenic Arabidopsis led to phenotypes with significantly shortened root length and seedling height, and decreased yields of both pods and seeds. Moreover, an electrophoresis mobility shift assay demonstrated the Ca²⁺-binding activity of Gb_30819 in vitro. Altogether, these results contribute to insights into the characteristics of the evolution and expression of GbCAMs/GbCMLs, as well as evidence for Ca²⁺-CAM/CML pathways functioning within the ancient gymnosperm G. biloba.

Identification of the Wheat (Triticum aestivum) IQD Gene Family and an Expression Analysis of Candidate Genes Associated with Seed Dormancy and Germination

The IQ67 Domain (IQD) gene family plays important roles in plant developmental processes and stress responses. Although IQDs have been characterized in model plants, little is known about their functions in wheat (Triticum aestivum), especially their roles in the regulation of seed dormancy and germination. Here, we identified 73 members of the IQD gene family from the wheat genome and phylogenetically separated them into six major groups. Gene structure and conserved domain analyses suggested that most members of each group had similar structures. A chromosome positional analysis showed that TaIQDs were unevenly located on 18 wheat chromosomes. A synteny analysis indicated that segmental duplications played significant roles in TaIQD expansion, and that the IQD gene family underwent strong purifying selection during evolution. Furthermore, a large number of hormone, light, and abiotic stress response elements were discovered in the promoters of TaIQDs, implying their functional diversity. Microarray data for 50 TaIQDs showed different expression levels in 13 wheat tissues. Transcriptome data and a quantitative real-time PCR analysis of wheat varieties with contrasting seed dormancy and germination phenotypes further revealed that seven genes (TaIQD4/-28/-32/-58/-64/-69/-71) likely participated in seed dormancy and germination through the abscisic acid-signaling pathway. The study results provide valuable information for cloning and a functional investigation of candidate genes controlling wheat seed dormancy and germination; consequently, they increase our understanding of the complex regulatory networks affecting these two traits.

Differential Gene Expression Analysis of SoCBL Family Calcineurin B-like Proteins: Potential Involvement in Sugarcane Cold Stress

Sugarcan e is a major crop for sugar and biofuel production and is cultivated in tropical and subtropical areas worldwide. Sugarcane growth is constrained because of winter’s low-temperature stress, and cold resistance is an important limitation in sugarcane growth enhancement. Therefore, in this study, we identified a gene involved in the low-temperature stress response of sugarcane. Calcineurin B-like (CBL) protein is a calcium signal receptor involved in the cold stress response. Five sugarcane CBL genes were cloned, sequenced, and named SoCBL1, SoCBL3, SoCBL5, SoCBL6, and SoCBL9. The protein sequences of these genes were analyzed. The calculated molecular weight of these proteins was 24.5, 25.9, 25.2, 25.6, and 26.3 kD, respectively. Subcellular localization analysis revealed that SoCBL1, SoCBL3, SoCBL6, and SoCBL9 were situated in the cytoplasm, while SoCBL5 was present in mitochondria. Secondary structure analysis showed that these five CBL proteins had similar secondary structures. Conserved domain analysis displayed that each sugarcane CBL protein contained three conserved EF domains. According to the self-expanding values of the phylogenetic tree, the CBL gene family was divided into four groups. The CBL1 and CBL9 genes were classified into one group, illustrating that these two genes might possess a similar function. The expression analysis of the SoCBL gene under low temperatures showed that SoCBL3 and SoCBL5 were affected significantly, while SoCBL1 and SoCBL9 were less affected. These results demonstrate that the CBL genes in sugarcane have similar characteristics and present differences in genetic diversity and gene expression response to low temperatures. Therefore, these genes might be novel candidates for fighting cold stress in sugarcane.

Molecular mechanisms of N-acyl homoserine lactone signals perception by plants

N-acyl homoserine lactones (AHLs) belong to the class of bacterial quorum sensing signal molecules involved in distance signal transduction between Gram-negative bacteria colonizers of the rhizosphere, as well as bacteria and plants. AHLs synchronize the activity of genes from individual cells, allowing the bacterial population to act as a multicellular organism, and establish a symbiotic or antagonistic relationship with the host plant. Although the effect of AHLs on plants has been studied for more than ten years, the mechanisms of plant perception of AHL signals are not fully understood. The specificity of the reactions caused by AHL indicates the existence of appropriate mechanisms for their perception by plants. In the current review, we summarize available data on the molecular mechanisms of AHL-signal perception in plants, its effect on plant growth, development, and stress resistance. We describe the latest research demonstrating direct (on plants) and indirect (on rhizosphere microflora) effects of AHLs, as well as the prospects of using these compounds in biotechnology to increase plant resistance to biotic and abiotic stresses.

Molecular Evolution of Calcium Signaling and Transport in Plant Adaptation to Abiotic Stress

Adaptation to unfavorable abiotic stresses is one of the key processes in the evolution of plants. Calcium (Ca2+) signaling is characterized by the spatiotemporal pattern of Ca2+ distribution and the activities of multi-domain proteins in integrating environmental stimuli and cellular responses, which are crucial early events in abiotic stress responses in plants. However, a comprehensive summary and explanation for evolutionary and functional synergies in Ca2+ signaling remains elusive in green plants. We review mechanisms of Ca2+ membrane transporters and intracellular Ca2+ sensors with evolutionary imprinting and structural clues. These may provide molecular and bioinformatics insights for the functional analysis of some non-model species in the evolutionarily important green plant lineages. We summarize the chronological order, spatial location, and characteristics of Ca2+ functional proteins. Furthermore, we highlight the integral functions of calcium-signaling components in various nodes of the Ca2+ signaling pathway through conserved or variant evolutionary processes. These ultimately bridge the Ca2+ cascade reactions into regulatory networks, particularly in the hormonal signaling pathways. In summary, this review provides new perspectives towards a better understanding of the evolution, interaction and integration of Ca2+ signaling components in green plants, which is likely to benefit future research in agriculture, evolutionary biology, ecology and the environment.

Evolution Analyses of CAMTA Transcription Factor in Plants and Its Enhancing Effect on Cold-tolerance

The calmodulin binding transcription activator (CAMTA) is a transcription factor that is widely present in eukaryotes with conserved structure. It contributes to the response to biotic and abiotic stresses and promotes the growth and development of plants. Although previous studies have investigated the number and function of CAMTAs in some species, there is still a lack of comprehensive understanding of the evolutionary process, phylogenetic relationship, expression patterns, and functions of CAMTAs in plants. Here we identified 465 CMATA genes from 112 plants and systematically studied the origin of CAMTA family, gene expansion, functional differentiation, gene structure, and conservative motif distribution. Based on these analyses, we presented the evidence that CAMTA family was originated from chlorophyta, and we speculated that CAMTA might experience obvious structure variation during its early evolution, and that the number of CAMTA genes might gradually increase in higher plants. To reveal potential functions of CAMTA genes, we analyzed the expression patterns of 12 representative species and found significant species specificity, tissue specificity, and developmental stage specificity of CAMTAs. The results also indicated that the CAMTA genes might promote the maturation and senescence. The expression levels and regulatory networks of CAMTAs revealed that CAMTAs could enhance cold tolerance of rice by regulating carbohydrate metabolism-related genes to accumulate carbohydrates or by modulating target genes together with other transcription factors. Our study provides an insight into the molecular evolution of CAMTA family and lays a foundation for further study of related biological functions.

The CBL1/9-CIPK23-AKT1 complex is essential for low potassium response in cassava

Cassava is a food crop and an important energy crop worldwide. However, its yield and quality are easily affected by low K+ stress, and the molecular mechanism of potassium channel is unknown in cassava. Herein, we revealed that calcineurin B-like 1/9 (MeCBL1/9)-CBL-interacting protein kinase 23 (MeCIPK23)-K+ TRANSPORTER1 (MeAKT1) complex plays an important role in low potassium response in cassava. Firstly, this study verified the in vivo role of MeAKT1 in K+ uptake in yeast. Secondly, we found that MeCBL1, MeCBL9, MeCIPK23 and MeAKT1 are involved in the absorption of K+ in cassava, and MeCBL1/9-CIPK23 complex is essential for MeAKT1-mediated K+ uptake. Moreover, MeCBL1/9-MeCIPK23-MeAKT1 showed different expression in different cassava varieties contrasting in the resistance to low K+ stress. Taken together, this study provides new insights into further improvement of K+ uptake in cassava.

Overexpression of NtCBL5A Leads to Necrotic Lesions by Enhancing Na+ Sensitivity of Tobacco Leaves Under Salt Stress

Many tobacco (Nicotiana tabacum) cultivars are salt-tolerant and thus are potential model plants to study the mechanisms of salt stress tolerance. The CALCINEURIN B-LIKE PROTEIN (CBL) is a vital family of plant calcium sensor proteins that can transmit Ca²⁺ signals triggered by environmental stimuli including salt stress. Therefore, assessing the potential of NtCBL for genetic improvement of salt stress is valuable. In our studies on NtCBL members, constitutive overexpression of NtCBL5A was found to cause salt supersensitivity with necrotic lesions on leaves. NtCBL5A-overexpressing (OE) leaves tended to curl and accumulated high levels of reactive oxygen species (ROS) under salt stress. The supersensitivity of NtCBL5A-OE leaves was specifically induced by Na⁺, but not by Cl^-, osmotic stress, or drought stress. Ion content measurements indicated that NtCBL5A-OE leaves showed sensitivity to the Na⁺ accumulation levels that wild-type leaves could tolerate. Furthermore, transcriptome profiling showed that many immune response-related genes are significantly upregulated and photosynthetic machinery-related genes are significantly downregulated in salt-stressed NtCBL5A-OE leaves. In addition, the expression of several cation homeostasis-related genes was also affected in salt-stressed NtCBL5A-OE leaves. In conclusion, the constitutive overexpression of NtCBL5A interferes with the normal salt stress response of tobacco plants and leads to Na⁺-dependent leaf necrosis by enhancing the sensitivity of transgenic leaves to Na⁺. This Na⁺ sensitivity of NtCBL5A-OE leaves might result from the abnormal Na⁺ compartmentalization, plant photosynthesis, and plant immune response triggered by the constitutive overexpression of NtCBL5A. Identifying genes and pathways involved in this unusual salt stress response can provide new insights into the salt stress response of tobacco plants.

Calmodulin7: recent insights into emerging roles in plant development and stress

Analyses of the function of Arabidopsis Calmodulin7 (CAM7) in concert with multiple regulatory proteins involved in various signal transduction processes. Calmodulin (CaM) plays various regulatory roles in multiple signaling pathways in eukaryotes. Arabidopsis CALMODULIN 7 (CAM7) is a unique member of the CAM family that works as a transcription factor in light signaling pathways. CAM7 works in concert with CONSTITUTIVE PHOTOMORPHOGENIC 1 and ELONGATED HYPOCOTYL 5, and plays an important role in seedling development. Further, it is involved in the regulation of the activity of various Ca²⁺-gated channels such as cyclic nucleotide gated channel 6 (CNGC6), CNGC14 and auto-inhibited Ca²⁺ ATPase 8. Recent studies further indicate that CAM7 is also an integral part of multiple signaling pathways including hormone, immunity and stress. Here, we review the recent advances in understanding the multifaceted role of CAM7. We highlight the open-ended questions, and also discuss the diverse aspects of CAM7 characterization that need to be addressed for comprehensive understanding of its cellular functions.

A forward genetics approach integrating genome-wide association study and expression quantitative trait locus mapping to dissect leaf development in maize (Zea mays)

The characterization of the genetic basis of maize (Zea mays) leaf development may support breeding efforts to obtain plants with higher vigor and productivity. In this study, a mapping panel of 197 biparental and multiparental maize recombinant inbred lines (RILs) was analyzed for multiple leaf traits at the seedling stage. RNA sequencing was used to estimate the transcription levels of 29 573 gene models in RILs and to derive 373 769 single nucleotide polymorphisms (SNPs), and a forward genetics approach combining these data was used to pinpoint candidate genes involved in leaf development. First, leaf traits were correlated with gene expression levels to identify transcript-trait correlations. Then, leaf traits were associated with SNPs in a genome-wide association (GWA) study. An expression quantitative trait locus mapping approach was followed to associate SNPs with gene expression levels, prioritizing candidate genes identified based on transcript-trait correlations and GWAs. Finally, a network analysis was conducted to cluster all transcripts in 38 co-expression modules. By integrating forward genetics approaches, we identified 25 candidate genes highly enriched for specific functional categories, providing evidence supporting the role of vacuolar proton pumps, cell wall effectors, and vesicular traffic controllers in leaf growth. These results tackle the complexity of leaf trait determination and may support precision breeding in maize.

Gamma-aminobutyric acid improves phenanthrene phytotoxicity tolerance in cucumber through the glutathione-dependent system of antioxidant defense

Phenanthrene (PHE), a typical organic pollutant, has drawn attention in recent years due to its toxicity to plants and human health. Gamma-aminobutyric acid (GABA) induce plant tolerance to diverse stresses. However, the role and regulatory mechanisms of GABA in PHE stress responses in plants remains largely uncharacterized. Here, we showed that GABA content increased by 44.5%, 89.2%, 160% and 39.2% under 50, 100, 200 and 300 µM PHE treatment, respectively compared with mock. GABA treatment alleviated PHE-induced growth inhibition in a dose-dependent manner, with the most effective concentration of 50 mM GABA. Although exogenous GABA could not influence the accumulation of PHE in cucumber, it significantly mitigated photosynthetic inhibition and enhanced the transcripts and activities of the antioxidant enzymes such as ascorbate peroxidase (APX), catalase (CAT), peroxidase (POD) and superoxide dismutase (SOD), resulting in less accumulation of hydrogen peroxide (H₂O₂) and superoxide (O₂^.-). Importantly, timecourse analyses of glutathione (GSH) homeostasis showed that GABA markedly increased GSH content and GR activity as well as the transcripts of GSH biosynthesis-related genes GSH1, GSH2 and GR during PHE stress. Conversely, pretreatment with GSH biosynthesis inhibitor buthionine sulfoximine (BSO) abolished the GABA-induced changes in PHE stress. Together, these results suggest that GABA enhances tolerance to PHE stress via a GSH-dependent system of antioxidant defense in cucumber.

The Ca2+-CaM Signaling Pathway Mediates Potassium Uptake by Regulating Reactive Oxygen Species Homeostasis in Tobacco Roots Under Low-K+ Stress

Potassium (K⁺) deficiency severely threatens crop growth and productivity. Calcium (Ca²⁺) signaling and its sensors play a central role in the response to low-K⁺ stress. Calmodulin (CaM) is an important Ca²⁺ sensor. However, the mechanism by which Ca²⁺ signaling and CaM mediate the response of roots to low-K⁺ stress remains unclear. In this study, we found that the K⁺ concentration significantly decreased in both shoots and roots treated with Ca²⁺ channel blockers, a Ca²⁺ chelator, and CaM antagonists. Under low-K⁺ stress, reactive oxygen species (ROS) accumulated, and the activity of antioxidant enzymes, NAD kinase (NADK), and NADP phosphatase (NADPase) decreased. This indicates that antioxidant enzymes, NADK, and NADPase might be downstream target proteins in the Ca²⁺-CaM signaling pathway, which facilitates K⁺ uptake in plant roots by mediating ROS homeostasis under low-K⁺ stress. Moreover, the expression of NtCNGC3, NtCNGC10, K⁺ channel genes, and transporter genes was significantly downregulated in blocker-treated, chelator-treated, and antagonist-treated plant roots in the low K⁺ treatment, suggesting that the Ca²⁺-CaM signaling pathway may mediate K⁺ uptake by regulating the expression of these genes. Overall, this study shows that the Ca²⁺-CaM signaling pathway promotes K⁺ absorption by regulating ROS homeostasis and the expression of K⁺ uptake-related genes in plant roots under low-K⁺ stress.

StCaM2, a calcium binding protein, alleviates negative effects of salinity and drought stress in tobacco

KEY MESSAGE

Overexpression of StCaM2 in tobacco promotes plant growth and confers increased salinity and drought tolerance by enhancing the photosynthetic efficiency, ROS scavenging, and recovery from membrane injury. Calmodulins (CaMs) are important Ca2+ sensors that interact with effector proteins and drive a network of signal transduction pathways involved in regulating the growth and developmental pattern of plants under stress. Herein, using in silico analysis, we identified 17 CaM isoforms (StCaM) in potato. Expression profiling revealed different temporal and spatial expression patterns of these genes, which were modulated under abiotic stress. Among the identified StCaM genes, StCaM2 was found to have the largest number of abiotic stress responsive promoter elements. In addition, StCaM2 was upregulated in response to some of the selected abiotic stress in potato tissues. Overexpression of StCaM2 in transgenic tobacco plants enhanced their tolerance to salinity and drought stress. Accumulation of reactive oxygen species was remarkably decreased in transgenic lines compared to that in wild type plants. Chlorophyll a fluorescence analysis suggested better performance of photosystem II in transgenic plants under stress compared to that in wild type plants. The increase in salinity stress tolerance in StCaM2-overexpressing plants was also associated with a favorable K+/Na+ ratio. The enhanced tolerance to abiotic stresses correlated with the increase in the activities of anti-oxidative enzymes in transgenic tobacco plants. Overall, our results suggest that StCaM2 can be a novel candidate for conferring salt and drought tolerance in plants.

A soybean calcineurin B-like protein-interacting protein kinase, GmPKS4, regulates plant responses to salt and alkali stresses

Calcineurin B-like protein-interacting protein kinases (CIPKs) are key elements of plant abiotic stress signaling pathways. CIPKs are SOS2 (Salt Overly Sensitive 2)-like proteins (protein kinase S [PKS] proteins) which all contain a putative FISL motif. It seems that the FISL motif is found only in the SOS2 subfamily of protein kinases. In this study, the full-length cDNA of a soybean CIPK gene (GmPKS4) was isolated and was revealed to have an important role in abiotic stress responses. A qRT-PCR analysis indicated that GmPKS4 expression is upregulated under saline conditions or when exposed to alkali, salt-alkali, drought, or abscisic acid (ABA). A subcellular localization assay revealed the presence of GmPKS4 in the nucleus and cytoplasm. Further studies on the GmPKS4 promoter suggested it affects soybean resistance to various stresses. Transgenic Arabidopsis thaliana and soybean hairy roots overexpressing GmPKS4 had increased proline content as well as high antioxidant enzyme activities but decreased malondialdehyde levels following salt and salt-alkali stress treatments. Additionally, GmPKS4 overexpression activated reactive oxygen species scavenging systems, thereby minimizing damages due to oxidative and osmotic stresses. Moreover, upregulated stress-related gene expression levels were detected in lines overexpressing GmPKS4 under stress conditions. In conclusion, GmPKS4 improves soybean tolerance to salt and salt-alkali stresses. The overexpression of GmPKS4 enhances the scavenging of reactive oxygen species, osmolyte synthesis, and the transcriptional regulation of stress-related genes.

Calmodulin binding transcription activators: An interplay between calcium signalling and plant stress tolerance

In plants, next to the secondary messengers lies an array of signal relaying molecules among which Calmodulins convey the unequivocal alarms of calcium influxes to Calmodulin-Binding Transcription Activators (CAMTA). Upon reception, CAMTA transcription factors decode the calcium signatures by transcribing the genes corresponding to the specific stimulus, thus have direct/indirect engagement in the complex signalling crosstalk. CAMTA transcription factors make an important contribution to the genome of all eukaryotes, including plants, from Brassica napus (18) to Carica papaya (2), the number of CAMTA genes varies across the plant species, however they exhibit a similar evolutionarily conserved domain organization including a DNA-Binding Domain (CG-1), a Transcription Factor Immunoglobulin Binding Domain (TIG), a Calmodulin-Binding Domain (CaMBD/IQ) and several Ankyrin repeats. The regulatory region of CAMTA genes possess multiple stress-responsive cis motifs including ABRE, SARE, G-box, W-box, AuXRE, DRE and others. CAMTA TFs in Arabidopsis have been studied extensively, however in other plants (with a few exceptions), the evidence merely bases upon expression analyses. CAMTAs are reported to orchestrate biotic as well as abiotic stresses including those occurring due to water and temperature fluctuations as well as heavy metals, light and salinity. Through CG-1 domain, CAMTA TFs bind the CG-box in the promoter of their target genes and modulate their expression under adverse conditions. Here we present a glimpse of how calcium signatures are coded and decoded and translated into necessary responses. In addition, we have emphasized on exploitation of the multiple-stress responsive nature of CAMTAs in engineering plants with desired traits.

Physiological, Biochemical, and Transcriptomic Responses of Neolamarckia cadamba to Aluminum Stress

Aluminum is the most abundant metal of the Earth's crust accounting for 7% of its mass, and release of toxic Al3+ in acid soils restricts plant growth. Neolamarckia cadamba, a fast-growing tree, only grows in tropical regions with acidic soils. In this study, N. cadamba was treated with high concentrations of aluminum under acidic condition (pH 4.5) to study its physiological, biochemical, and molecular response mechanisms against high aluminum stress. High aluminum concentration resulted in significant inhibition of root growth with time in N. cadamba. The concentration of Al3+ ions in the root tip increased significantly and the distribution of absorbed Al3+ was observed in the root tip after Al stress. Meanwhile, the concentration of Ca, Mg, Mn, and Fe was significantly decreased, but P concentration increased. Aluminum stress increased activities of antioxidant enzymes such as superoxide dismutase (SOD), catalase from micrococcus lysodeiktic (CAT), and peroxidase (POD) in the root tip, while the content of MDA was decreased. Transcriptome analysis showed 37,478 differential expression genes (DEGs) and 4096 GOs terms significantly associated with treatments. The expression of genes regulating aluminum transport and abscisic acid synthesis was significantly upregulated; however, the genes involved in auxin synthesis were downregulated. Of note, the transcripts of several key enzymes affecting lignin monomer synthesis in phenylalanine pathway were upregulated. Our results shed light on the physiological and molecular mechanisms of aluminum stress tolerance in N. cadamba.

Ca2+/Calmodulin Complex Triggers CAMTA Transcriptional Machinery Under Stress in Plants: Signaling Cascade and Molecular Regulation

Calcium (Ca2+) ion is a critical ubiquitous intracellular second messenger, acting as a lead currency for several distinct signal transduction pathways. Transient perturbations in free cytosolic Ca2+ ([Ca2+]cyt) concentrations are indispensable for the translation of signals into adaptive biological responses. The transient increase in [Ca2+]cyt levels is sensed by an array of Ca2+ sensor relay proteins such as calmodulin (CaM), eventually leading to conformational changes and activation of CaM. CaM, in a Ca2+-dependent manner, regulates several transcription factors (TFs) that are implicated in various molecular, physiological, and biochemical functions in cells. CAMTA (calmodulin-binding transcription activator) is one such member of the Ca2+-loaded CaM-dependent family of TFs. The present review focuses on Ca2+ as a second messenger, its interaction with CaM, and Ca2+/CaM-mediated CAMTA transcriptional regulation in plants. The review recapitulates the molecular and physiological functions of CAMTA in model plants and various crops, confirming its probable involvement in stress signaling pathways and overall plant development. Studying Ca2+/CaM-mediated CAMTA TF will help in answering key questions concerning signaling cascades and molecular regulation under stress conditions and plant growth, thus improving our knowledge for crop improvement.

Regulation mechanisms of humic acid on Pb stress in tea plant (Camellia sinensis L.)

Though the interaction between humic acid (HA) and heavy metals has been widely reported, the effects of HA on the toxicity of heavy metals to plants are still in debate. In this study, the regulation mechanisms of HA on Pb stress in tea plant (Camellia sinensis L.) was investigated through hydroponic experiments, and the experimental results were explained by using transmission electron microscope (TEM), scanning transmission X-ray microscopes (STXM) and isobaric tags for relative and absolute quantitation (iTRAQ) differential proteomics. Significant alleviation of Pb stress was found with HA coexistence. TEM results showed that HA greatly mitigated the damage of cells caused by Pb stress. Compared with sole Pb treatment, the addition of HA increased the contents of pectin and pectic acid in the cell wall by 10.5% and 30.5%, while arabinose (Ara) and galactose (Gal) decreased by 20.5% and 15.9%, respectively, which were beneficial for increasing Pb adsorption capacity of the cell wall and promoting cell elongation. Moreover, iTRAQ differential proteomics analysis proved that HA strengthened the antioxidant system, promoted the synthesis of cell wall, and stabilized protein and sulfur-containing substance metabolism in molecular level. Notably, the concentration of calcium (Ca) in the cell wall of HA coexistence treatment was 47.4% higher than Pb treatment. STXM results also indicated that the distribution of Ca in the cell wall was restored with the presence of HA. This might promote the formation of the egg-box model, thus alleviating Pb stress in cells. Our results reveal the regulation mechanisms of HA on Pb detoxification in plants and provide useful information for improving the safety of agricultural products.

Functional characterisation of the transcriptome from leaf tissue of the fluoroacetate-producing plant, Dichapetalum cymosum, in response to mechanical wounding

Dichapetalum cymosum produces the toxic fluorinated metabolite, fluoroacetate, presumably as a defence mechanism. Given the rarity of fluorinated metabolites in nature, the biosynthetic origin and function of fluoroacetate have been of particular interest. However, the mechanism for fluorination in D. cymosum was never elucidated. More importantly, there is a severe lack in knowledge on a genetic level for fluorometabolite-producing plants, impeding research on the subject. Here, we report on the first transcriptome for D. cymosum and investigate the wound response for insights into fluorometabolite production. Mechanical wounding studies were performed and libraries of the unwounded (control) and wounded (30 and 60 min post wounding) plant were sequenced using the Illumina HiSeq platform. A combined reference assembly generated 77,845 transcripts. Using the SwissProt, TrEMBL, GO, eggNOG, KEGG, Pfam, EC and PlantTFDB databases, a 69% annotation rate was achieved. Differential expression analysis revealed the regulation of 364 genes in response to wounding. The wound responses in D. cymosum included key mechanisms relating to signalling cascades, phytohormone regulation, transcription factors and defence-related secondary metabolites. However, the role of fluoroacetate in inducible wound responses remains unclear. Bacterial fluorinases were searched against the D. cymosum transcriptome but transcripts with homology were not detected suggesting the presence of a potentially different fluorinating enzyme in plants. Nevertheless, the transcriptome produced in this study significantly increases genetic resources available for D. cymosum and will assist with future research into fluorometabolite-producing plants.

Plant Cyclophilins: Multifaceted Proteins With Versatile Roles

Cyclophilins constitute a family of ubiquitous proteins that bind cyclosporin A (CsA), an immunosuppressant drug. Several of these proteins possess peptidyl-prolyl cis-trans isomerase (PPIase) activity that catalyzes the cis-trans isomerization of the peptide bond preceding a proline residue, essential for correct folding of the proteins. Compared to prokaryotes and other eukaryotes studied until now, the cyclophilin gene families in plants exhibit considerable expansion. With few exceptions, the role of the majority of these proteins in plants is still a matter of conjecture. However, recent studies suggest that cyclophilins are highly versatile proteins with multiple functionalities, and regulate a plethora of growth and development processes in plants, ranging from hormone signaling to the stress response. The present review discusses the implications of cyclophilins in different facets of cellular processes, particularly in the context of plants, and provides a glimpse into the molecular mechanisms by which these proteins fine-tune the diverse physiological pathways.