Cyclic nucleotide gated channel and Ca²⁺-mediated signal transduction during plant senescence signaling

Genome-wide identification and expression analysis of the cyclic nucleotide-gated ion channel (CNGC) gene family in Saccharum spontaneum

BACKGROUND

Cyclic nucleotide-gated ion channels (CNGCs) are nonselective cation channels that are ubiquitous in eukaryotic organisms. As Ca²⁺ channels, some CNGCs have also proven to be K⁺-permeable and involved in plant development and responses to environmental stimuli. Sugarcane is an important sugar and energy crop worldwide. However, reports on CNGC genes in sugarcane are limited.

RESULTS

In this study, 16 CNGC genes and their alleles were identified from Saccharum spontaneum and classified into 5 groups based on phylogenetic analysis. Investigation of gene duplication and syntenic relationships between S. spontaneum and both rice and Arabidopsis demonstrated that the CNGC gene family in S. spontaneum expanded primarily by segmental duplication events. Many SsCNGCs showed variable expression during growth and development as well as in tissues, suggesting functional divergence. Light-responsive cis-acting elements were discovered in the promoters of all the identified SsCNGCs, and the expression of most of the SsCNGCs showed a diurnal rhythm. In sugarcane, the expression of some SsCNGCs was regulated by low-K⁺ treatment. Notably, SsCNGC13 may be involved in both sugarcane development and its response to environmental stimuli, including response to low-K⁺ stress.

CONCLUSION

This study identified the CNGC genes in S. spontaneum and provided insights into the transcriptional regulation of these SsCNGCs during development, circadian rhythm and under low-K⁺ stress. These findings lay a theoretical foundation for future investigations of the CNGC gene family in sugarcane.

Establishment of a Landscape of UPL5-Ubiquitinated on Multiple Subcellular Components of Leaf Senescence Cell in Arabidopsis

Catabolism of macromolecules is a major event in senescent cells, especially involving proteolysis of organelles and abnormally aggregated proteins, circulation of nutrients, and precise control of intracellular environmental balance. Proteasomes are distributed in the nucleus and cytoplasm; however, proteasomes in organelles are limited. In this study, multi-omics proteomic analyses of ubiquitinated proteins enriched by using antibody against “di-Gly-Lys” via a free labeling were used to investigate the global changes of protein levels and ubiquitination modification levels of upl5 mutant relative to wild-type plant; subcellular localization analysis of UPL5 was found to be located in the nucleus, cytoplasm, and plastid within the cell; and the direct lysine site patterns of UPL5 were screened by the H89R substitution in the tagged ubiquitinated assay. It suggests that UPL5 acting as a candidate of organelle E3 ligase either in the nucleus or cytoplasm or plastid modifies numerous targets related to nuclear transcription and plastid photosynthesis involving in Ca²⁺ and hormone signaling pathway in plant senescence and in response to (a)biotic stress protection.

Characterization of the Gene Expression Profile Response to Drought Stress in Populus ussuriensis Using PacBio SMRT and Illumina Sequencing

In this study, we characterized the gene expression profile in the roots of Populus ussuriensis at 0, 6, 12, 24, 48 and 120 h after the start of polyethylene glycol (PEG)-induced drought stress using PacBio single-molecule real-time sequencing (SMRT-seq) and Illumina RNA sequencing. Compared to the control, 2244 differentially expressed genes (DEGs) were identified, and many of these DEGs were associated with the signal transduction, antioxidant system, ion accumulation and drought-inducing proteins. Changes in certain physiological and biochemical indexes, such as antioxidant activity and the contents of Ca²⁺, proline, and total soluble sugars, were further confirmed in P. ussuriensis roots. Furthermore, most of the differentially expressed transcription factors were members of the AP2/ERF, C2H2, MYB, NAC, C2C2 and WRKY families. Additionally, based on PacBio SMRT-seq results, 5955 long non-coding RNAs and 700 alternative splicing events were identified. Our results provide a global view of the gene expression profile that contributes to drought resistance in P. ussuriensis and meaningful information for genetic engineering research in the future.

Comparative genomics and evolutionary analysis of plant CNGCs

Comparative genomics and computational biology offer powerful research tools for studying evolutionary mechanisms of organisms, and the identification and characterization of conserved/distant genes and gene families. The plant CNGC gene family encodes evolutionary conserved ion channel proteins involved in important signaling pathways and biological functions. The fundamental ideas and standard procedures for genome-wide identification and evolutionary analysis of plant cyclic nucleotide-gated ion channels employing various software, tools, and online servers have been discussed. In particular, this developed method focused on practical procedures involving the comparative analysis of paralogs and orthologs of CNGC genes in different plant species at different levels including phylogenetic analysis, nomenclature and classification, gene structure, molecular protein evolution, and duplication events as mechanisms of gene family expansion and synteny.

BrCNGC gene family in field mustard: genome-wide identification, characterization, comparative synteny, evolution and expression profiling

CNGCs are ligand-gated calcium signaling channels, which participate in important biological processes in eukaryotes. However, the CNGC gene family is not well-investigated in Brassica rapa L. (i.e., field mustard) that is economically important and evolutionary model crop. In this study, we systematically identified 29 member genes in BrCNGC gene family, and studied their physico-chemical properties. The BrCNGC family was classified into four major and two sub phylogenetic groups. These genes were randomly localized on nine chromosomes, and dispersed into three sub-genomes of B. rapa L. Both whole-genome triplication and gene duplication (i.e., segmental/tandem) events participated in the expansion of the BrCNGC family. Using in-silico bioinformatics approaches, we determined the gene structures, conserved motif compositions, protein interaction networks, and revealed that most BrCNGCs can be regulated by phosphorylation and microRNAs of diverse functionality. The differential expression patterns of BrCNGC genes in different plant tissues, and in response to different biotic, abiotic and hormonal stress types, suggest their strong role in plant growth, development and stress tolerance. Notably, BrCNGC-9, 27, 18 and 11 exhibited highest responses in terms of fold-changes against club-root pathogen Plasmodiophora brassicae, Pseudomonas syringae pv. maculicola, methyl-jasmonate, and trace elements. These results provide foundation for the selection of candidate BrCNGC genes for future breeding of field mustard.

Abiotic Stresses Intervene with ABA Signaling to Induce Destructive Metabolic Pathways Leading to Death: Premature Leaf Senescence in Plants

Abiotic stresses trigger premature leaf senescence by affecting some endogenous factors, which is an important limitation for plant growth and grain yield. Among these endogenous factors that regulate leaf senescence, abscisic acid (ABA) works as a link between the oxidase damage of cellular structure and signal molecules responding to abiotic stress during leaf senescence. Considering the importance of ABA, we collect the latest findings related to ABA biosynthesis, ABA signaling, and its inhibitory effect on chloroplast structure destruction, chlorophyll (Chl) degradation, and photosynthesis reduction. Post-translational changes in leaf senescence end with the exhaustion of nutrients, yellowing of leaves, and death of senescent tissues. In this article, we review the literature on the ABA-inducing leaf senescence mechanism in rice and Arabidopsis starting from ABA synthesis, transport, signaling receptors, and catabolism. We also predict the future outcomes of investigations related to other plants. Before changes in translation occur, ABA signaling that mediates the expression of NYC, bZIP, and WRKY transcription factors (TFs) has been investigated to explain the inducing effect on senescence-associated genes. Various factors related to calcium signaling, reactive oxygen species (ROS) production, and protein degradation are elaborated, and research gaps and potential prospects are presented. Examples of gene mutation conferring the delay or induction of leaf senescence are also described, and they may be helpful in understanding the inhibitory effect of abiotic stresses and effective measures to tolerate, minimize, or resist their inducing effect on leaf senescence.

Electrophysiological Studies Revealed CaM1-Mediated Regulation of the Arabidopsis Calcium Channel CNGC12

The Arabidopsis cyclic nucleotide-gated channel (CNGC) family consists of 20 members, which have been reported to participate in various physiological processes, such as pathogen defense, development, and thermotolerance. Although CNGC11 and CNGC12 have been identified a decade ago and their role in programmed cell death is well studied, their precise channel regulation has not been studied electrophysiologically. Here, we determined the channel activities of CNGC11 and CNGC12 utilizing the two-electrode voltage-clamp technique in the Xenopus laevis oocyte heterologous expression system. Our results suggest that CNGC12 but not CNGC11 functions as an active calcium channel. Furthermore, the cyclic nucleotide monophosphates (cNMPs) did not affect the activities of CNGC11 nor CNGC12 in Xenopus oocytes. Interestingly, while the activity of CNGC11 was not affected by co-expression with calmodulin (CaM), the activity of CNGC12 was significantly enhanced when CaM1 was co-expressed in oocytes. This study reveals that the channel activities and the mechanisms of regulation by CaM are different between CNGC11 and CNGC12.

Comprehensive genomic analysis of the CNGC gene family in Brassica oleracea: novel insights into synteny, structures, and transcript profiles

Background

The cyclic nucleotide-gated ion channel (CNGC) family affects the uptake of cations, growth, pathogen defence, and thermotolerance in plants. However, the systematic identification, origin and function of this gene family has not been performed in Brassica oleracea, an important vegetable crop and genomic model organism.

Results

In present study, we identified 26 CNGC genes in B. oleracea genome, which are non-randomly localized on eight chromosomes, and classified into four major (I-IV) and two sub-groups (i.e., IV-a and IV-b). The BoCNGC family is asymmetrically fractioned into the following three sub-genomes: least fractionated (14 genes), most fractionated-I (10), and most fractionated-II (2). The syntenic map of BoCNGC genes exhibited strong relationships with the model Arabidopsis thaliana and B. rapa CNGC genes and provided markers for defining the regions of conserved synteny among the three genomes. Both whole-genome triplication along with segmental and tandem duplications contributed to the expansion of this gene family. We predicted the characteristics of BoCNGCs regarding exon-intron organisations, motif compositions and post-translational modifications, which diversified their structures and functions. Using orthologous Arabidopsis CNGCs as a reference, we found that most CNGCs were associated with various protein–protein interaction networks involving CNGCs and other signalling and stress related proteins. We revealed that five microRNAs (i.e., bol-miR5021, bol-miR838d, bol-miR414b, bol-miR4234, and bol-miR_new2) have target sites in nine BoCNGC genes. The BoCNGC genes were differentially expressed in seven B. oleracea tissues including leaf, stem, callus, silique, bud, root and flower. The transcript abundance levels quantified by qRT-PCR assays revealed that BoCNGC genes from phylogenetic Groups I and IV were particularly sensitive to cold stress and infections with bacterial pathogen Xanthomonas campestris pv. campestris, suggesting their importance in abiotic and biotic stress responses.

Conclusion

Our comprehensive genome-wide analysis represents a rich data resource for studying new plant gene families. Our data may also be useful for breeding new B. oleracea cultivars with improved productivity, quality, and stress resistance.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4244-y) contains supplementary material, which is available to authorized users.

Role of Cyclic Nucleotide Gated Channels in Stress Management in Plants

Tolerance of plants to a number of biotic and abiotic stresses such as pathogen and herbivore attack, drought, salinity, cold and nutritional limitations is ensued by complex multimodule signaling pathways. The outcome of this complex signaling pathways results in adaptive responses by restoring the cellular homeostasis and thus promoting survival. Functions of many plant cation transporter and channel protein families such as glutamate receptor homologs (GLRs), cyclic nucleotide-gated ion channel (CNGC) have been implicated in providing biotic and abiotic stress tolerance. Ion homeostasis regulated by several transporters and channels is one of the crucial parameters for the optimal growth, development and survival of all living organisms. The CNGC family members are known to be involved in the uptake of cations such as Na(+), K(+) and Ca(2+) and regulate plant growth and development. Detail functional genomics approaches have given an emerging picture of CNGCs wherein these protein are believed to play crucial role in pathways related to cellular ion homeostasis, development and as a 'guard' in defense against biotic and abiotic challenges. Here, we discuss the current knowledge of role of CNGCs in mediating stress management and how they aid plants in survival under adverse conditions.

Abscisic Acid as an Internal Integrator of Multiple Physiological Processes Modulates Leaf Senescence Onset in Arabidopsis thaliana

Many studies have shown that exogenous abscisic acid (ABA) promotes leaf abscission and senescence. However, owing to a lack of genetic evidence, ABA function in plant senescence has not been clearly defined. Here, two-leaf early-senescence mutants (eas) that were screened by chlorophyll fluorescence imaging and named eas1-1 and eas1-2 showed high photosynthetic capacity in the early stage of plant growth compared with the wild type. Gene mapping showed that eas1-1 and eas1-2 are two novel ABA2 allelic mutants. Under unstressed conditions, the eas1 mutations caused plant dwarf, early germination, larger stomatal apertures, and early leaf senescence compared with those of the wild type. Flow cytometry assays showed that the cell apoptosis rate in eas1 mutant leaves was higher than that of the wild type after day 30. A significant increase in the transcript levels of several senescence-associated genes, especially SAG12, was observed in eas1 mutant plants in the early stage of plant growth. More importantly, ABA-activated calcium channel activity in plasma membrane and induced the increase of cytoplasmic calcium concentration in guard cells are suppressed due to the mutation of EAS1. In contrast, the eas1 mutants lost chlorophyll and ion leakage significant faster than in the wild type under treatment with calcium channel blocker. Hence, our results indicate that endogenous ABA level is an important factor controlling the onset of leaf senescence through Ca(2+) signaling.

Molecular cloning and characterization of a novel adenylyl cyclase gene, HpAC1, involved in stress signaling in Hippeastrum x hybridum

Adenylyl cyclases (ACs) are enzymes that generate cyclic AMP, which is involved in different physiological and developmental processes in a number of organisms. Here, we report the cloning and characterization of a new plant adenylyl cyclases (AC) gene, designated HpAC1, from Hippeastrum x hybridum. This gene encodes a protein of 206 amino acids with a calculated molecular mass of 23 kD and an isoelectric point of 5.07. The predicted amino acid sequence contains all the typical features of and shows high identity with putative plant ACs. The purified, recombinant HpAC1 is able to convert ATP to cAMP. The complementation test that was performed to analyze the ability of HpAC1 to compensate for the AC deficiency in the Escherichia coli SP850 strain revealed that HpAC1 functions as an adenylyl cyclase and produces cyclic AMP. Moreover, it was shown that the transcript level of HpAC1 and cyclic AMP concentration changed during certain stress conditions. Both mechanical damage and Phoma narcissi infection lead to two sharp increases in HpAC1 mRNA levels during a 72-h test cycle. Changes in intracellular cAMP level were also observed. These results may indicate the participation of a cAMP-dependent pathway both in rapid and systemic reactions induced after disruption of symplast and apoplast continuity.

Senescence and programmed cell death in plants: polyamine action mediated by transglutaminase

Research on polyamines (PAs) in plants laps a long way of about 50 years and many roles have been discovered for these aliphatic cations. PAs regulate cell division, differentiation, organogenesis, reproduction, dormancy-break and senescence, homeostatic adjustments in response to external stimuli and stresses. Nevertheless, the molecular mechanisms of their multiple activities are still matter of research. PAs are present in free and bound forms and interact with several important cell molecules; some of these interactions may occur by covalent linkages catalyzed by transglutaminase (TGase), giving rise to "cationization" or cross-links among specific proteins. Senescence and programmed cell death (PCD) can be delayed by PAs; in order to re-interpret some of these effects and to obtain new insights into their molecular mechanisms, their conjugation has been revised here. The TGase-mediated interactions between proteins and PAs are the main target of this review. After an introduction on the characteristics of this enzyme, on its catalysis and role in PCD in animals, the plant senescence and PCD models in which TGase has been studied, are presented: the corolla of naturally senescing or excised flowers, the leaves senescing, either excised or not, the pollen during self-incompatible pollination, the hypersensitive response and the tuber storage parenchyma during dormancy release. In all the models examined, TGase appears to be involved by a similar molecular mechanism as described during apoptosis in animal cells, even though several substrates are different. Its effect is probably related to the type of PCD, but mostly to the substrate to be modified in order to achieve the specific PCD program. As a cross-linker of PAs and proteins, TGase is an important factor involved in multiple, sometimes controversial, roles of PAs during senescence and PCD.

Identification of cyclic GMP-activated nonselective Ca2+-permeable cation channels and associated CNGC5 and CNGC6 genes in Arabidopsis guard cells

Cytosolic Ca(2+) in guard cells plays an important role in stomatal movement responses to environmental stimuli. These cytosolic Ca(2+) increases result from Ca(2+) influx through Ca(2+)-permeable channels in the plasma membrane and Ca(2+) release from intracellular organelles in guard cells. However, the genes encoding defined plasma membrane Ca(2+)-permeable channel activity remain unknown in guard cells and, with some exceptions, largely unknown in higher plant cells. Here, we report the identification of two Arabidopsis (Arabidopsis thaliana) cation channel genes, CNGC5 and CNGC6, that are highly expressed in guard cells. Cytosolic application of cyclic GMP (cGMP) and extracellularly applied membrane-permeable 8-Bromoguanosine 3',5'-cyclic monophosphate-cGMP both activated hyperpolarization-induced inward-conducting currents in wild-type guard cells using Mg(2+) as the main charge carrier. The cGMP-activated currents were strongly blocked by lanthanum and gadolinium and also conducted Ba(2+), Ca(2+), and Na(+) ions. cngc5 cngc6 double mutant guard cells exhibited dramatically impaired cGMP-activated currents. In contrast, mutations in CNGC1, CNGC2, and CNGC20 did not disrupt these cGMP-activated currents. The yellow fluorescent protein-CNGC5 and yellow fluorescent protein-CNGC6 proteins localize in the cell periphery. Cyclic AMP activated modest inward currents in both wild-type and cngc5cngc6 mutant guard cells. Moreover, cngc5 cngc6 double mutant guard cells exhibited functional abscisic acid (ABA)-activated hyperpolarization-dependent Ca(2+)-permeable cation channel currents, intact ABA-induced stomatal closing responses, and whole-plant stomatal conductance responses to darkness and changes in CO2 concentration. Furthermore, cGMP-activated currents remained intact in the growth controlled by abscisic acid2 and abscisic acid insensitive1 mutants. This research demonstrates that the CNGC5 and CNGC6 genes encode unique cGMP-activated nonselective Ca(2+)-permeable cation channels in the plasma membrane of Arabidopsis guard cells.

Phytohormones and microRNAs as sensors and regulators of leaf senescence: assigning macro roles to small molecules

Ageing or senescence is an intricate and highly synchronized developmental phase in the life of plant parts including leaf. Senescence not only means death of a plant part, but during this process, different macromolecules undergo degradation and the resulting components are transported to other parts of the plant. During the period from when a leaf is young and green to the stage when it senesces, a multitude of factors such as hormones, environmental factors and senescence associated genes (SAGs) are involved. Plant hormones including salicylic acid, abscisic acid, jasmonic acid and ethylene advance leaf senescence, whereas others like cytokinins, gibberellins, and auxins delay this process. The environmental factors which generally affect plant development and growth, can hasten senescence, the examples being nutrient dearth, water stress, pathogen attack, radiations, high temperature and light intensity, waterlogging, and air, water or soil contamination. Other important influences include carbohydrate accumulation and high carbon/nitrogen level. To date, although several genes involved in this complex process have been identified, still not much information exists in the literature on the signalling mechanism of leaf senescence. Now, the Arabidopsis mutants have paved our way and opened new vistas to elucidate the signalling mechanism of leaf senescence for which various mutants are being utilized. Recent studies demonstrating the role of microRNAs in leaf senescence have reinforced our knowledge of this intricate process. This review provides a comprehensive and critical analysis of the information gained particularly on the roles of several plant growth regulators and microRNAs in regulation of leaf senescence.