Comprehensive Analysis of the CDPK-SnRK Superfamily Genes in Chinese Cabbage and Its Evolutionary Implications in Plants

In silico analysis of the wheat BBX gene family and identification of candidate genes for seed dormancy and germination

BACKGROUND

B-box (BBX) proteins are a type of zinc finger proteins containing one or two B-box domains. They play important roles in development and diverse stress responses of plants, yet their roles in wheat remain unclear.

RESULTS

In this study, 96 BBX genes were identified in the wheat genome and classified into five subfamilies. Subcellular localization prediction results showed that 68 TaBBXs were localized in the nucleus. Protein interaction prediction analysis indicated that interaction was one way that these proteins exerted their functions. Promoter analysis indicated that TaBBXs may play important roles in light signal, hormone, and stress responses. qRT-PCR analysis revealed that 14 TaBBXs were highly expressed in seeds compared with other tissues. These were probably involved in seed dormancy and germination, and their expression patterns were investigated during dormancy acquisition and release in the seeds of wheat varieties Jing 411 and Hongmangchun 21, showing significant differences in seed dormancy and germination phenotypes. Subcellular localization analysis confirmed that the three candidates TaBBX2-2 A, TaBBX4-2 A, and TaBBX11-2D were nuclear proteins. Transcriptional self-activation experiments further demonstrated that TaBBX4-2A was transcriptionally active, but TaBBX2-2A and TaBBX11-2D were not. Protein interaction analysis revealed that TaBBX2-2A, TaBBX4-2A, and TaBBX11-2D had no interaction with each other, while TaBBX2-2A and TaBBX11-2D interacted with each other, indicating that TaBBX4-2A may regulate seed dormancy and germination by transcriptional regulation, and TaBBX2-2A and TaBBX11-2D may regulate seed dormancy and germination by forming a homologous complex.

CONCLUSIONS

In this study, the wheat BBX gene family was identified and characterized at the genomic level by bioinformatics analysis. These observations provide a theoretical basis for future studies on the functions of BBXs in wheat and other species.

Genome-wide characterization and expression analysis of MADS-box transcription factor gene family in Perilla frutescens

MADS-box transcription factors are widely involved in the regulation of plant growth, developmental processes, and response to abiotic stresses. Perilla frutescens, a versatile plant, is not only used for food and medicine but also serves as an economical oil crop. However, the MADS-box transcription factor family in P. frutescens is still largely unexplored. In this study, a total of 93 PfMADS genes were identified in P. frutescens genome. These genes, including 37 Type I and 56 Type II members, were randomly distributed across 20 chromosomes and 2 scaffold regions. Type II PfMADS proteins were found to contain a greater number of motifs, indicating more complex structures and diverse functions. Expression analysis revealed that most PfMADS genes (more than 76 members) exhibited widely expression model in almost all tissues. The further analysis indicated that there was strong correlation between some MIKCC-type PfMADS genes and key genes involved in lipid synthesis and flavonoid metabolism, which implied that these PfMADS genes might play important regulatory role in the above two pathways. It was further verified that PfMADS47 can effectively mediate the regulation of lipid synthesis in Chlamydomonas reinhardtii transformants. Using cis-acting element analysis and qRT-PCR technology, the potential functions of six MIKCC-type PfMADS genes in response to abiotic stresses, especially cold and drought, were studied. Altogether, this study is the first genome-wide analysis of PfMADS. This result further supports functional and evolutionary studies of PfMADS gene family and serves as a benchmark for related P. frutescens breeding studies.

Comprehensive identification and expression analyses of the SnRK gene family in Casuarina equisetifolia in response to salt stress

BACKGROUND

Sucrose nonfermenting-1 (SNF1)-related protein kinases (SnRKs) play crucial roles in plant signaling pathways and stress adaptive responses by activating protein phosphorylation pathways. However, there have been no comprehensive studies of the SnRK gene family in the widely planted salt-tolerant tree species Casuarina equisetifolia. Here, we comprehensively analyze this gene family in C. equisetifolia using genome-wide identification, characterization, and profiling of expression changes in response to salt stress.

RESULTS

A total of 26 CeqSnRK genes were identified, which were divided into three subfamilies (SnRK1, SnRK2, and SnRK3). The intron-exon structures and protein‑motif compositions were similar within each subgroup but differed among groups. Ka/Ks ratio analysis indicated that the CeqSnRK family has undergone purifying selection, and cis-regulatory element analysis suggested that these genes may be involved in plant development and responses to various environmental stresses. A heat map was generated using quantitative real‑time PCR (RT-qPCR) data from 26 CeqSnRK genes, suggesting that they were expressed in different tissues. We also examined the expression of all CeqSnRK genes under exposure to different salt concentrations using RT-qPCR, finding that most CeqSnRK genes were regulated by different salt treatments. Moreover, co-expression network analysis revealed synergistic effects among CeqSnRK genes.

CONCLUSIONS

Several CeqSnRK genes (CeqSnRK3.7, CeqSnRK3.16, CeqSnRK3.17) were up-regulated following salt treatment. Among them, CeqSnRK3.16 expression was significantly up-regulated under various salt treatments, identifying this as a candidate gene salt stress tolerance gene. In addition, CeqSnRK3.16 showed significant expression change correlations with multiple genes under salt stress, indicating that it might exhibit synergistic effects with other genes in response to salt stress. This comprehensive analysis will provide a theoretical reference for CeqSnRK gene functional verification and the role of these genes in salt tolerance.

Genome-wide identification and functional analysis of Dof transcription factor family in Camelina sativa

BACKGROUND

Dof transcription factors (TFs) containing C₂-C₂ zinc finger domains are plant-specific regulatory proteins, playing crucial roles in a variety of biological processes. However, little is known about Dof in Camelina sativa, an important oil crop worldwide, with high stress tolerance. In this study, a genome-wide characterization of Dof proteins is performed to examine their basic structural characteristics, phylogenetics, expression patterns, and functions to identify the regulatory mechanism underlying lipid/oil accumulation and the candidate Dofs mediating stress resistance regulation in C. sativa.

RESULTS

Total of 103 CsDof genes unevenly distributed on 20 chromosomes were identified from the C. sativa genome, and they were classified into four groups (A, B, C and D) based on the classification of Arabidopsis Dof gene family. All of the CsDof proteins contained the highly-conserved typic CX₂C-X₂₁-CX₂C structure. Segmental duplication and purifying selection were detected for CsDof genes. 61 CsDof genes were expressed in multiple tissues, and 20 of them showed tissue-specific expression patterns, suggesting that CsDof genes functioned differentially in different tissues of C. sativa. Remarkably, a set of CsDof members were detected to be possible involved in regulation of oil/lipid biosynthesis in C. sativa. Six CsDof genes exhibited significant expression changes in seedlings under salt stress treatment.

CONCLUSIONS

The present data reveals that segmental duplication is the key force responsible for the expansion of CsDof gene family, and a strong purifying pressure plays a crucial role in CsDofs' evolution. Several CsDof TFs may mediate lipid metabolism and stress responses in C. sativa. Several CsDof TFs may mediate lipid metabolism and stress responses in C. sativa. Collectively, our findings provide a foundation for deep understanding the roles of CsDofs and genetic improvements of oil yield and salt stress tolerance in this species and the related crops.

The role of CDPKs in plant development, nutrient and stress signaling

The second messenger calcium (Ca2+) is a ubiquitous intracellular signaling molecule found in eukaryotic cells. In plants, the multigene family of calcium-dependent protein kinases (CDPKs) plays an important role in regulating plant growth, development, and stress tolerance. CDPKs sense changes in intracellular Ca2+ concentration and translate them into phosphorylation events that initiate downstream signaling processes. Several functional and expression studies on different CDPKs and their encoding genes have confirmed their multifunctional role in stress. Here, we provide an overview of the signal transduction mechanisms and functional roles of CDPKs. This review includes details on the regulation of secondary metabolites, nutrient uptake, regulation of flower development, hormonal regulation, and biotic and abiotic stress responses.

Identification and Expression Analysis of Calcium-Dependent Protein Kinases Gene Family in Potato Under Drought Stress

Calcium-dependent protein kinases (CDPKs) are a class of serine/threonine protein kinases encoded by several gene families that play key roles in stress response and plant growth and development. In this study, the BLAST method was used to search for protein sequences of the potato Calcium-dependent protein kinase gene family. The chromosome location, phylogeny, gene structures, gene duplication, cis-acting elements, protein-protein interaction, and expression profiles were analyzed. Twenty-five CDPK genes in the potato genome were identified based on RNA-seq data and were clustered into four groups (I-IV) based on their structural features and phylogenetic analysis. The result showed the composition of the promoter region of the StCDPKs gene, including light-responsive elements such as Box4, hormone-responsive elements such as ABRE, and stress-responsive elements such as MBS. Four pairs of segmental duplications were found in StCDPKs genes and the Ka/Ks ratios were below 1, indicating a purifying selection of the genes. The protein-protein interaction network revealed defense-related proteins such as; respiratory burst oxidase homologs (RBOHs) interacting with potato CDPKs. Transcript abundance was measured via RT-PCR between the two cultivars and their relative expression of CDPK genes was analyzed after 15, 20, and 25 days of drought. There were varied expression patterns of StCDPK3/13/21 and 23, between the two potato cultivars under mannitol induced-drought conditions. Correlation analysis showed that StCDPK21/22 and StCDPK3 may be the major differentially expressed genes involved in the regulation of malondialdehyde (MDA) and proline content in response to drought stress, opening a new research direction for genetic improvement of drought resistance in potato.

Molecular Characterization Reveals the Involvement of Calcium Dependent Protein Kinases in Abiotic Stress Signaling and Development in Chickpea (Cicer arietinum)

Calcium-dependent protein kinases (CDPKs) are a major group of calcium (Ca²⁺⁾ sensors in plants. CDPKs play a dual function of "Ca²⁺ sensor and responder." These sensors decode the "Ca²⁺ signatures" generated in response to adverse growth conditions such as drought, salinity, and cold and developmental processes. However, knowledge of the CDPK family in the legume crop chickpea is missing. Here, we have identified a total of 22 CDPK genes in the chickpea genome. The phylogenetic analysis of the chickpea CDPK family with other plants revealed their evolutionary conservation. Protein homology modeling described the three-dimensional structure of chickpea CDPKs. Defined arrangements of α-helix, β-strands, and transmembrane-helix represent important structures like kinase domain, inhibitory junction domain, N and C-lobes of EF-hand motifs. Subcellular localization analysis revealed that CaCDPK proteins are localized mainly at the cytoplasm and in the nucleus. Most of the CaCDPK promoters had abiotic stress and development-related cis-regulatory elements, suggesting the functional role of CaCDPKs in abiotic stress and development-related signaling. RNA sequencing (RNA-seq) expression analysis indicated the role of the CaCDPK family in various developmental stages, including vegetative, reproductive development, senescence stages, and during seed stages of early embryogenesis, late embryogenesis, mid and late seed maturity. The real-time quantitative PCR (qRT-PCR) analysis revealed that several CaCDPK genes are specifically as well as commonly induced by drought, salt, and Abscisic acid (ABA). Overall, these findings indicate that the CDPK family is probably involved in abiotic stress responses and development in chickpeas. This study provides crucial information on the CDPK family that will be utilized in generating abiotic stress-tolerant and high-yielding chickpea varieties.

Comparison of the Distinct, Host-Specific Response of Three Solanaceae Hosts Induced by Phytophthora infestans

Three Solanaceae hosts (TSHs), S. tuberosum, N. benthamiana and S. lycopersicum, represent the three major phylogenetic clades of Solanaceae plants infected by Phytophthora infestans, which causes late blight, one of the most devastating diseases seriously affecting crop production. However, details regarding how different Solanaceae hosts respond to P. infestans are lacking. Here, we conducted RNA-seq to analyze the transcriptomic data from the TSHs at 12 and 24 h post P. infestans inoculation to capture early expression effects. Macroscopic and microscopic observations showed faster infection processes in S. tuberosum than in N. benthamiana and S. lycopersicum under the same conditions. Analysis of the number of genes and their level of expression indicated that distinct response models were adopted by the TSHs in response to P. infestans. The host-specific infection process led to overlapping but distinct in GO terms and KEGG pathways enriched for differentially expressed genes; many were tightly linked to the immune response in the TSHs. S. tuberosum showed the fastest response and strongest accumulation of reactive oxygen species compared with N. benthamiana and S. lycopersicum, which also had similarities and differences in hormone regulation. Collectively, our study provides an important reference for a better understanding of late blight response mechanisms of different Solanaceae host interactions.

Genome-wide identification of sucrose nonfermenting-1-related protein kinase (SnRK) genes in barley and RNA-seq analyses of their expression in response to abscisic acid treatment

Background

Sucrose nonfermenting-1 (SNF1)-related protein kinases (SnRKs) play important roles in regulating metabolism and stress responses in plants, providing a conduit for crosstalk between metabolic and stress signalling, in some cases involving the stress hormone, abscisic acid (ABA). The burgeoning and divergence of the plant gene family has led to the evolution of three subfamilies, SnRK1, SnRK2 and SnRK3, of which SnRK2 and SnRK3 are unique to plants. Therefore, the study of SnRKs in crops may lead to the development of strategies for breeding crop varieties that are more resilient under stress conditions. In the present study, we describe the SnRK gene family of barley (Hordeum vulgare), the widespread cultivation of which can be attributed to its good adaptation to different environments.

Results

The barley HvSnRK gene family was elucidated in its entirety from publicly-available genome data and found to comprise 50 genes. Phylogenetic analyses assigned six of the genes to the HvSnRK1 subfamily, 10 to HvSnRK2 and 34 to HvSnRK3. The search was validated by applying it to Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) genome data, identifying 50 SnRK genes in rice (four OsSnRK1, 11 OsSnRK2 and 35 OsSnRK3) and 39 in Arabidopsis (three AtSnRK1, 10 AtSnRK2 and 26 AtSnRK3). Specific motifs were identified in the encoded barley proteins, and multiple putative regulatory elements were found in the gene promoters, with light-regulated elements (LRE), ABA response elements (ABRE) and methyl jasmonate response elements (MeJa) the most common. RNA-seq analysis showed that many of the HvSnRK genes responded to ABA, some positively, some negatively and some with complex time-dependent responses.

Conclusions

The barley HvSnRK gene family is large, comprising 50 members, subdivided into HvSnRK1 (6 members), HvSnRK2 (10 members) and HvSnRK3 (34 members), showing differential positive and negative responses to ABA.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07601-6.

Cytological Observation and Transcriptome Comparative Analysis of Self-Pollination and Cross-Pollination in Dendrobium Officinale

Dendrobium officinale is a rare and traditional medicinal plant with high pharmacological and nutritional value. The self-incompatibility mechanism of D. officinale reproductive isolation was formed in the long-term evolution process, but intraspecific hybridization of different germplasm resources leads to a large gap in the yield, quality, and medicinal value of D. officinale. To investigate the biological mechanism of self-incompatibility in D. officinale, cytological observation and the transcriptome analysis was carried out on the samples of self-pollination and cross-pollination in D. officinale. Results for self-pollination showed that the pollen tubes could grow in the style at 2 h, but most of pollen tubes stopped growing at 4 h, while a large number of cross-pollinated pollen tubes grew along the placental space to the base of ovary, indicating that the self-incompatibility of D. officinale may be gametophyte self-incompatibility. A total of 63.41 G basesum of D. officinale style samples from non-pollinated, self-pollination, and cross-pollination by RNA-seq were obtained, and a total of 1944, 1758, and 475 differentially expressed genes (DEGs) in the comparison of CK (non-pollinated) vs. HF (cross-pollination sample), CK vs. SF (self-pollination sample) and SF vs. HF were identified, respectively. Forty-one candidate genes related to self-incompatibility were found by function annotation of DEGs, including 6 Ca²⁺ signal genes, 4 armed repeat containing (ARC) related genes, 11 S-locus receptor kinase (SRK) related genes, 2 Exo70 family genes, 9 ubiquitin related genes, 1 fatty acid related gene, 6 amino acid-related genes, 1 pollen-specific leucine-rich repeat extensin-like protein (LRX) related gene and 1 lectin receptor-like kinases (RLKs) related gene, showed that self-incompatibility mechanism of D. officinale involves the interaction of multiple genes and pathways. The results can provide a basis for the study of the self-incompatibility mechanism of D. officinale, and provide ideas for the preservation and utilization of high-quality resources of D. officinale.

Genome-wide identification and characterization of the OFP gene family in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

Ovate family proteins (OFPs) are a class of proteins with a conserved OVATE domain that contains approximately 70 amino acid residues. OFP proteins are plant-specific transcription factors that participate in regulating plant growth and development and are widely distributed in many plants. Little is known about OFPs in Brassica rapa to date. We identified 29 OFP genes in Brassica rapa and found that they were unevenly distributed on 10 chromosomes. Intron gain events may have occurred during the structural evolution of BraOFP paralogues. Syntenic analysis verified Brassica genome triplication, and whole genome duplication likely contributed to the expansion of the OFP gene family. All BraOFP genes had light responsive- and phytohormone-related cis-acting elements. Expression analysis from RNA-Seq data indicated that there were obvious changes in the expression levels of six OFP genes in the Brassica rapa hybrid, which may contribute to the formation of heterosis. Finally, we found that the paralogous genes had different expression patterns among the hybrid and its parents. These results provide the theoretical basis for the further analysis of the biological functions of OFP genes across the Brassica species.

Genome-wide identification and expression pattern of SnRK gene family under several hormone treatments and its role in floral scent emission in Hedychium coronarium

The SnRK (Snf1-Related protein Kinase) gene family plays crucial roles in various plant signaling pathways and stress-adaptive responses including biotic and abiotic stresses via activating protein phosphorylation pathways. However, there is no information available on the role of the SnRK gene family in Hedychium coronarium. H. coronarium is an important crop widely cultivated as an ornamental plant, herb, spice, or condiment. In this study, 60 HcSnRK genes were identified from the H. coronarium genomic and transcriptome data. Phylogenetic and gene structure analysis showed that the HcSnRK genes were divided into three groups (HcSnRK1, HcSnRK2 and HcSnRK3) and among them HcSnRK3 subfamily was further subdivided into two clades according to the number of introns. Chromosome localization analysis showed that HcSnRK genes were unevenly mapped onto all chromosomes, and the Ka/Ks ratio of 24 paralogues includes four tandems and 20 segmental duplications indicated that the HcSnRK gene family underwent a purifying selection. Cis-regulatory elements analysis suggested that the HcSnRK genes respond to multiple hormones and other stresses. The responsiveness of HcSnRK genes to several hormones was analyzed by quantitative real-time PCR. Based on the different transcriptome data, two candidates HcSnRK genes (HcSnRK2.2 and HcSnRK2.9) were screened out for further characterization . The subcellular localization experiment revealed that both genes were located in the nucleus and cytoplasm. Moreover, virus-induced gene silencing (VIGS) of HcSnRK2.2 and HcSnRK2.9 significantly reduced the floral volatile contents by suppressing the expression of terpene synthase genes (HcTPS1, HcTPS3, and HcTPS5), indicating that HcSnRK2.2 and HcSnRK2.9 genes play an important role in the regulatory mechanism of floral aroma. These results will provide novel insights into the functional dissection of H. coronarium SnRK gene family.

Genome-Wide Identification and Characterization of Calcium-Dependent Protein Kinase (CDPK) and CDPK-Related Kinase (CRK) Gene Families in Medicago truncatula

Calcium-dependent protein kinase (CDPK or CPK) and CDPK-related kinase (CRK) play an important role in plant growth, development, and adaptation to environmental stresses. However, their gene families had been yet inadequately investigated in Medicago truncatula. In this study, six MtCRK genes were computationally identified, they were classified into five groups with MtCDPKs based on phylogenetic relationships. Six pairs of segmental duplications were observed in MtCDPK and MtCRK genes and the Ka/Ks ratio, an indicator of selection pressure, was below 0.310, indicating that these gene pairs underwent strong purifying selection. Cis-acting elements of morphogenesis, multiple hormone responses, and abiotic stresses were predicted in the promoter region. The spatial expression of MtCDPKs and MtCRKs displays diversity. The expression of MtCDPKs and MtCRKs could be regulated by various stresses. MtCDPK4, 14, 16, 22, and MtCRK6 harbor both N-myristoylation site and palmitoylation site and were anchored on plasma membrane, while MtCDPK7, 9, and 15 contain no or only one N-acylation site and were distributed in cytosol and nucleus, suggesting that the N-terminal acylation sites play a key role in subcellular localization of MtCDPKs and MtCRKs. In summary, comprehensive characterization of MtCDPKs and MtCRKs provide a subset of candidate genes for further functional analysis and genetic improvement against drought, cold, salt and biotic stress.

Expression, Subcellular Localization, and Interactions of CPK Family Genes in Maize

Calcium-dependent protein kinase (CPKs) is a key player in the calcium signaling pathway to decode calcium signals into various physiological responses. cDNA sequences of 9 ZmCPK genes were successfully cloned from all four phylogenetic groups in maize. qRT-PCR analysis showed the expression variation of these selected genes under abscisic acid (ABA) and calcium chloride (CaCl2) treatment. Due to the presence of N-myristoylation/palmitoylation sites, the selected ZmCPK members were localized in a plasma membrane. To clarify whether ZmCPK, a key player in calcium signaling, interacts with key players of ABA, protein phosphatase 2Cs (PP2Cs) and the SNF1-related protein kinase 2s (SnRK2s) and mitogen-activated protein kinase (MAPK) signaling pathways in maize, we examined the interaction between 9 CPKs, 8 PP2Cs, 5 SnRKs, and 20 members of the MPK family in maize by using yeast two-hybrid assay. Our results showed that three ZmCPKs interact with three different members of ZmSnRKs while four ZmCPK members had a positive interaction with 13 members of ZmMPKs in different combinations. These four ZmCPK proteins are from three different groups in maize. These findings of physical interactions between ZmCPKs, ZmSnRKs, and ZmMPKs suggested that these signaling pathways do not only have indirect influence but also have direct crosstalk that may involve the defense mechanism in maize. The present study may improve the understanding of signal transduction in plants.

Identification, Expression, and Interaction Network Analyses of the CDPK Gene Family Reveal Their Involvement in the Development, Ripening, and Abiotic Stress Response in Banana

Calcium-dependent protein kinases (CDPKs) play vital roles in the regulation of plant growth, development, and tolerance to various abiotic stresses. However, little information is available for this gene family in banana. In this study, 44 CDPKs were identified in banana and were classified into four groups based on phylogenetic, gene structure, and conserved motif analyses. The majority of MaCDPKs generally exhibited similar expression patterns in the different tissues. Transcriptome analyses revealed that many CDPKs showed strong transcript accumulation at the early stages of fruit development and postharvest ripening in both varieties. Interaction network and co-expression analysis further identified some CDPKs-mediated network that was potentially active at the early stages of fruit development. Comparative expression analysis suggested that the high levels of CDPK expression in FJ might be related to its fast ripening characteristic. CDPK expression following the abiotic stress treatments indicated a significant transcriptional response to osmotic, cold, and salt treatment, as well as differential expression profiles, between BX and FJ. The findings of this study elucidate the transcriptional control of CDPKs in development, ripening, and the abiotic stress response in banana. Some tissue-specific, development/ripening-dependent, and abiotic stress-responsive candidate MaCDPK genes were identified for further genetic improvement of banana.

Genome-Wide Identification, Evolution, and Transcriptional Profiling of PP2C Gene Family in Brassica rapa

The type 2C protein which belongs to the major group of protein phosphatases (PP2C) plays a vital role in abscisic acid (ABA) signaling and signal transductions processes. In the present study, 131 PP2C genes were identified in total in Brassica rapa and categorized into thirteen subgroups based on their phylogenetic relationships. These B. rapa PP2C are structurally conserved based on amino acid sequence alignment, phylogenetic analysis, and conserved domains. Moreover, we utilized previously reported RNA-sequence data on various tissues (root, stem, leaf, flower, and silique), which suggests overlapping expression pattern in 29 paralogous gene pairs. The qRT-PCR validation of 15 paralogous gene pairs depicts distinct expression patterns in response to various abiotic stresses, such as heat, cold, ABA, and drought. Interestingly, stress-responsive BraPP2C candidate genes were also identified, suggesting their significance in stress-tolerance mechanism in B. rapa. The evolutionary analysis for 15 paralogous gene pairs suggested that only three pairs have the positive selection and remaining were purifying in nature. The presented results of this study hasten our understanding of the molecular evolution of the PP2C gene family in B. rapa. Thus, it will be ultimately helping in future research for facilitating the functional characterization of BraPP2C genes in developing the abiotic stress tolerant plants.

Genome-wide identification and characterization of CKIN/SnRK gene family in Chlamydomonas reinhardtii

The SnRK (Snf1-Related protein Kinase) gene family plays an important role in energy sensing and stress-adaptive responses in plant systems. In this study, Chlamydomonas CKIN family (SnRK in Arabidopsis) was defined after a genome-wide analysis of all sequenced Chlorophytes. Twenty-two sequences were defined as plant SnRK orthologs in Chlamydomonas and classified into two subfamilies: CKIN1 and CKIN2. While CKIN1 subfamily is reduced to one conserved member and a close protein (CKIN1L), a large CKIN2 subfamily clusters both plant-like and algae specific CKIN2s. The responsiveness of these genes to abiotic stress situations was tested by RT-qPCR. Results showed that almost all elements were sensitive to osmotic stress while showing different degrees of sensibility to other abiotic stresses, as occurs in land plants, revealing their specialization and the family pleiotropy for some elements. The regulatory pathway of this family may differ from land plants since these sequences shows unique regulatory features and some of them are sensitive to ABA, despite conserved ABA receptors (PYR/PYL/RCAR) and regulatory domains are not present in this species. Core Chlorophytes and land plant showed divergent stress signalling, but SnRKs/CKINs share the same role in cell survival and stress response and adaption including the accumulation of specific biomolecules. This fact places the CKIN family as well-suited target for bioengineering-based studies in microalgae (accumulation of sugars, lipids, secondary metabolites), while promising new findings in stress biology and specially in the evolution of ABA-signalling mechanisms.

GmSnRK1.1, a Sucrose Non-fermenting-1(SNF1)-Related Protein Kinase, Promotes Soybean Resistance to Phytophthora sojae

Phytophthora root and stem rot, a destructive disease of soybean [Glycine max (L.) Merr.], is caused by the oomycete Phytophthora sojae. However, how the disease resistance mechanisms of soybean respond to P. sojae infection remains unclear. Previously, we showed that GmWRKY31, which interacts with a sucrose non-fermenting-1(SNF1)-related protein kinase (SnRK), enhances resistance to P. sojae in soybean. Here, we report that the membrane-localized SnRK GmSnRK1.1 is involved in the soybean host response to P. sojae. The overexpression of GmSnRK1.1 (GmSnRK1.1-OE) increased soybean resistance to P. sojae, and the RNA interference (RNAi)-mediated silencing of GmSnRK1.1 (GmSnRK1.1-R) reduced resistance to P. sojae. Moreover, the activities and transcript levels of the antioxidant enzymes superoxide dismutase and peroxidase were markedly higher in the GmSnRK1.1-OE transgenic soybean plants than in the wild type (WT), but were reduced in the GmSnRK1.1-R plants. Several isoflavonoid phytoalexins related genes GmPAL, GmIFR, Gm4CL and GmCHS were significantly higher in "Suinong 10" and GmSnRK1.1-OE lines than these in "Dongnong 50," and were significantly lower in GmSnRK1.1-R lines. In addition, the accumulation of salicylic acid (SA) and the expression level of the SA biosynthesis-related gene were significantly higher in the GmSnRK1.1-OE plants than in the WT and GmSnRK1.1-R plants, moreover, SA biosynthesis inhibitor treated GmSnRK1.1-R lines plants displayed clearly increased pathogen biomass compared with H₂O-treated plants after 24 h post-inoculation. These results showed that GmSnRK1.1 positively regulates soybean resistance to P. sojae, potentially functioning via effects on the expression of SA-related genes and increased accumulation of SA.

Comparative Analysis of CDPK Family in Maize, Arabidopsis, Rice, and Sorghum Revealed Potential Targets for Drought Tolerance Improvement

Calcium dependent protein kinases (CDPKs) play significant role in regulation of plant growth and development in response to various stresses including drought. A set of 32 CDPK genes identified in maize were further used for searching of orthologs in the model plant Arabidopsis (72) and major food crops such as rice (78) and sorghum (91). We comprehensively studied the phylogenetic relationship, annotations, gene duplications, gene structure, divergence time, 3-D protein structures and tissue-specific drought induced expression of CDPK genes in all four species. Variation in intron frequency in the studied species was one of the reasons for the functional diversity of CDPK genes to various stress responses. Protein kinase and protein kinase C phosphorylation site domains were the most conserved motifs identified in all species. Four groups were identified from the sequence-based phylogenetic analysis, in which maize CDPKs were clustered in group III. Expression data showed that the CDPK genes were highly expressed in leaf of maize, rice, and sorghum whereas in Arabidopsis the maximum expression was observed in root. The expression assay showed 5, 6, 11, and 9 were the commonly and differentially expressed drought-related orthologous genes in maize, Arabidopsis, rice, and sorghum, respectively. 3-D protein structure were predicted for the nine genes (Arabidopsis: 2, maize: 2, rice: 3, and sorghum: 2) showing differential expression in at least three species. The predicted 3-D structures were further evaluated and validated by Ramachandran plot, ANOLEA, ProSA, and Verify-3D. The superimposed 3-D structure of drought-related orthologous proteins retained similar folding pattern owing to their conserved nature. Functional annotation revealed the involvement of CDPK genes in various pathways such as osmotic homeostasis, cell protection, and root growth. The interactions of CDPK genes in various pathways play crucial role in imparting drought tolerance through different ABA and MAPK signaling cascades. These selected candidate genes could be targeted in development of drought tolerant genotypes in maize, rice, and sorghum through appropriate breeding approaches. Our comparative experiments of CDPK genes could also be extended in the drought stress breeding programmes of the related species.

Genome-wide identification and expression analysis of calmodulin-like (CML) genes in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

BACKGROUND

Calmodulin-like (CML) proteins are a primary family of plant-specific Ca2+ sensors that specifically bind to Ca2+ and deliver a Ca2+ signal. CML proteins have been identified and characterized in many plant species, such as the model plant Arabidopsis and rice. Based on considerable evidence, the roles of CML proteins are crucial in plant growth and development and in the response to various external stimuli. Nevertheless, the characterization and expression profiling of CML genes in Chinese cabbage (Brassica rapa L. ssp. pekinensis) remain limited.

RESULTS

In this study, a genome-wide search and comprehensive analysis were performed, and a total of 79 BrCML genes were identified in Chinese cabbage. Gene structure analysis revealed that these BrCML genes contained two to four conserved EF-hand motifs. Phylogenetic analysis showed that CML homologs between Chinese cabbage and Arabidopsis shared close relationships. The identified BrCML genes were located across ten chromosomes and three different subgenomes of Chinese cabbage. Moreover, 126 pairs of orthologous CML genes were found among Chinese cabbage, Arabidopsis and Brassica oleracea. Expression analysis revealed that the expression of some BrCML genes was tissue-specific and that of some was susceptible to temperature stress. A putative interaction network of BrCML proteins was proposed, which suggested that BrCML2, BrCML6, BrCML15 and BrCML25 were co-expressed and might play roles in flower development and other relevant biological processes of Chinese cabbage.

CONCLUSIONS

The results of this study increased the understanding and characterization of BrCML genes in Chinese cabbage, and will be a rich resource for further studies to investigate BrCML protein function in various developmental processes of Chinese cabbage.

Recent advances in understanding the roles of whole genome duplications in evolution

Ancient whole-genome duplications (WGDs)- paleopolyploidy events-are key to solving Darwin's 'abominable mystery' of how flowering plants evolved and radiated into a rich variety of species. The vertebrates also emerged from their invertebrate ancestors via two WGDs, and genomes of diverse gymnosperm trees, unicellular eukaryotes, invertebrates, fishes, amphibians and even a rodent carry evidence of lineage-specific WGDs. Modern polyploidy is common in eukaryotes, and it can be induced, enabling mechanisms and short-term cost-benefit assessments of polyploidy to be studied experimentally. However, the ancient WGDs can be reconstructed only by comparative genomics: these studies are difficult because the DNA duplicates have been through tens or hundreds of millions of years of gene losses, mutations, and chromosomal rearrangements that culminate in resolution of the polyploid genomes back into diploid ones (rediploidisation). Intriguing asymmetries in patterns of post-WGD gene loss and retention between duplicated sets of chromosomes have been discovered recently, and elaborations of signal transduction systems are lasting legacies from several WGDs. The data imply that simpler signalling pathways in the pre-WGD ancestors were converted via WGDs into multi-stranded parallelised networks. Genetic and biochemical studies in plants, yeasts and vertebrates suggest a paradigm in which different combinations of sister paralogues in the post-WGD regulatory networks are co-regulated under different conditions. In principle, such networks can respond to a wide array of environmental, sensory and hormonal stimuli and integrate them to generate phenotypic variety in cell types and behaviours. Patterns are also being discerned in how the post-WGD signalling networks are reconfigured in human cancers and neurological conditions. It is fascinating to unpick how ancient genomic events impact on complexity, variety and disease in modern life.