Genome-wide exploration of the molecular evolution and regulatory network of mitogen-activated protein kinase cascades upon multiple stresses in Brachypodium distachyon

Harnessing the role of mitogen-activated protein kinases against abiotic stresses in plants

Crop plants are vulnerable to various biotic and abiotic stresses, whereas plants tend to retain their physiological mechanisms by evolving cellular regulation. To mitigate the adverse effects of abiotic stresses, many defense mechanisms are induced in plants. One of these mechanisms is the mitogen-activated protein kinase (MAPK) cascade, a signaling pathway used in the transduction of extracellular stimuli into intercellular responses. This stress signaling pathway is activated by a series of responses involving MAPKKKs→MAPKKs→MAPKs, consisting of interacting proteins, and their functions depend on the collaboration and activation of one another by phosphorylation. These proteins are key regulators of MAPK in various crop plants under abiotic stress conditions and also related to hormonal responses. It is revealed that in response to stress signaling, MAPKs are characterized as multigenic families and elaborate the specific stimuli transformation as well as the antioxidant regulation system. This pathway is directed by the framework of proteins and stopping domains confer the related associates with unique structure and functions. Early studies of plant MAPKs focused on their functions in model plants. Based on the results of whole-genome sequencing, many MAPKs have been identified in plants, such as Arbodiposis, tomato, potato, alfalfa, poplar, rice, wheat, maize, and apple. In this review, we summarized the recent work on MAPK response to abiotic stress and the classification of MAPK cascade in crop plants. Moreover, we highlighted the modern research methodologies such as transcriptomics, proteomics, CRISPR/Cas technology, and epigenetic studies, which proposed, identified, and characterized the novel genes associated with MAPKs and their role in plants under abiotic stress conditions. In-silico-based identification of novel MAPK genes also facilitates future research on MAPK cascade identification and function in crop plants under various stress conditions.

U0126 and BAY11-7082 Inhibit the Progression of Endometriosis in a Rat Model by Suppressing the MEK/ERK/NF-κB Pathway

Endometriosis is an aggressive disease. It is the main cause of chronic pelvic pain, dysmenorrhea, and infertility, affecting the well-being of women. This study aimed to explore the role of U0126 and BAY11-7082 in endometriosis (EMs) treatment in rats by targeting the MEK/ERK/NF-κB pathway. The EMs model was generated and the rats were divided into model, dimethyl sulfoxide, U0126, BAY11-708, and control groups (Sham operation group). After 4 weeks of treatment, the rats were sacrificed. Compared with model group, U0126 and BAY11-7082 treatment significantly inhibited ectopic lesion growth, glandular hyperplasia, and interstitial inflammation. Compared to control group, PCNA and MMP9 levels were significantly increased in the eutopic and ectopic endometrial tissues of model group; the levels of MEK/ERK/NF-κB pathway proteins also increased significantly. Compared with model group, MEK, ERK, and NF-κB levels decreased significantly after U0126 treatment and NF-κB protein expression decreased significantly after BAY11-7082 treatment, with no significant difference in MEK and ERK levels. The proliferation and invasion activities of eutopic and ectopic endometrial cells also significantly decreased after U0126 and BAY11-7082 treatment. In summary, our results showed that U0126 and BAY11-7082 inhibited ectopic lesion growth, glandular hyperplasia, and interstitial inflammatory response in EMs rats by inhibiting the MEK/ERK/NF-κB signaling pathway.

Exogenous 24-epibrassinolide boosts plant growth under alkaline stress from physiological and transcriptomic perspectives: The case of broomcorn millet (Panicum miliaceum L.)

Land alkalization is an abiotic stress that affects global sustainable agricultural development and the balance of natural ecosystems. In this study, two broomcorn millet cultivars, T289 (alkaline-tolerant) and S223 (alkaline-sensitive), were selected to investigate the response of broomcorn millet to alkaline stress and the role of brassinolide (BR) in alkaline tolerance. Phenotypes, physiologies, and transcriptomes of T289 and S223 plants under only alkaline stress (AS) and alkaline stress with BR (AB) were compared. The results showed that alkaline stress inhibited growth, promoted the accumulation of soluble sugars and malondialdehyde, enhanced electrolyte leakage, and destroyed the integrity of broomcorn millet stomata. In contrast, BR lessened the negative effects of alkaline stress on plants. Transcriptome sequencing analysis showed that relative to control groups (CK, nutrient solution), in AS groups, 21,113 and 12,151 differentially expressed genes (DEGs) were identified in S223 and T289, respectively. Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed various terms and pathways related to metabolism. Compared to S223, alkaline stress strongly activated the brassinosteroid biosynthesis pathway in T289. Conversely, ARF, TF, and TCH4, associated with cell growth and elongation, were inhibited by alkaline stress in S223. Moreover, alkaline stress induced the activation of the mitogen-activated protein kinase (MAPK) pathway, the abscisic acid signaling pathway that initiates stomatal closure, as well as the starch and sucrose metabolism. The EG and BGL genes, which are associated with cellulose degradation, were notably activated. BR enhanced alkaline tolerance, thereby alleviating the transcriptional responses of the two cultivars. Cultivar T289 is better in alkalized regions. Taken together, these results reveal how broomcorn millet responds to alkaline stress and BR mitigates alkaline stress, thus promoting agriculture in alkalized regions.

Identification and Expression Analysis of MPK and MKK Gene Families in Pecan (Carya illinoinensis)

Mitogen-activated protein kinases consist of three kinase modules composed of MPKs, MKKs, and MPKKKs. As members of the protein kinase (PK) superfamily, they are involved in various processes, such as developmental programs, cell division, hormonal progression, and signaling responses to biotic and abiotic stresses. In this study, a total of 18 MPKs and 10 MKKs were annotated on the pecan genome, all of which could be classified into four subgroups, respectively. The gene structures and conserved sequences of family members in the same branch were relatively similar. All MPK proteins had a conserved motif TxY, and D(L/I/V)K and VGTxxYMSPER existed in all MKK proteins. Duplication events contributed largely to the expansion of the pecan MPK and MKK gene families. Phylogenetic analysis of protein sequences from six plants indicated that species evolution occurred in pecan. Organ-specific expression profiles of MPK and MKK showed functional diversity. Ka/Ks values indicated that all genes with duplicated events underwent strong negative selection. Seven CiPawMPK and four CiPawMKK genes with high expression levels were screened by transcriptomic data from different organs, and these candidates were validated by qRT-PCR analysis of hormone-treated and stressed samples.

Genome-Wide Identification and Expression Analysis of MAPK Gene Family in Lettuce (Lactuca sativa L.) and Functional Analysis of LsMAPK4 in High- Temperature-Induced Bolting

The mitogen-activated protein kinase (MAPK) pathway is a widely distributed signaling cascade in eukaryotes and is involved in regulating plant growth, development, and stress responses. High temperature, a frequently occurring environmental stressor, causes premature bolting in lettuce with quality decline and yield loss. However, whether MAPKs play roles in thermally induced bolting remains poorly understood. In this study, 17 LsMAPK family members were identified from the lettuce genome. The physical and chemical properties, subcellular localization, chromosome localization, phylogeny, gene structure, family evolution, cis-acting elements, and phosphorylation sites of the LsMAPK gene family were evaluated via in silico analysis. According to phylogenetic relationships, LsMAPKs can be divided into four groups, A, B, C, and D, which is supported by analyses of gene structure and conserved domains. The collinearity analysis showed that there were 5 collinearity pairs among LsMAPKs, 8 with AtMAPKs, and 13 with SlMAPKs. The predicted cis-acting elements and potential phosphorylation sites were closely associated with hormones, stress resistance, growth, and development. Expression analysis showed that most LsMAPKs respond to high temperatures, among which LsMAPK4 is significantly and continuously upregulated upon heat treatments. Under heat stress, the stem length of the LsMAPK4-knockdown lines was significantly shorter than that of the control plants, and the microscope observations demonstrated that the differentiation time of flower buds at the stem apex was delayed accordingly. Therefore, silencing of LsMAPK4 significantly inhibited the high- temperature-accelerated bolting in lettuce, indicating that LsMPAK4 might be a potential regulator of lettuce bolting. This study provides a theoretical basis for a better understanding of the molecular mechanisms underlying the MAPK genes in high-temperature-induced bolting.

Integrated Transcriptomic and Metabolomic Analyses of Cold-Tolerant and Cold-Sensitive Pepper Species Reveal Key Genes and Essential Metabolic Pathways Involved in Response to Cold Stress

Cold stress, triggered by particularly low temperatures, is one of the most severe forms of abiotic stress in pepper plants and a major constraint to the global pepper industry, threatening crop production and food security. To acclimatize to extreme conditions, the plant undergoes numerous modifications, including genetic and metabolic modulations. A thorough study of both the genetic and metabolic alterations of plants in response to cold stress is vital to understanding and developing the cold stress resistance mechanism. This study implemented transcriptome and metabolome analyses to evaluate the cold stress response in cold-tolerant and cold-sensitive pepper species. The weighted gene co-expression network revealed three significant modules related to cold stress tolerance in Capsicum pubescens. We identified 17 commonly enriched genes among both species at different time points in 10 different comparisons, including the AP2 transcription factor, LRR receptor-like serine, hypersensitivity-related 4-like protein, and uncharacterized novel.295 and novel.6172 genes. A pathway enrichment analysis indicated that these DEGs were mainly associated with the MAPK signaling pathway, hormone signaling pathway, and primary and secondary metabolism. Additionally, 21 significantly differentially accumulated metabolites (DAMs) were identified in both species after 6 h of cold stress. A transcriptome and metabolome integrated analysis revealed that 54 genes correlated with metabolites enriched in five different pathways. Most genes and metabolites involved in carbohydrate metabolism, the TCA cycle, and flavonoid biosynthesis pathways were upregulated in cold-tolerant plants under cold stress. Together, the results of this study provide a comprehensive gene regulatory and metabolic network in response to cold stress and identified some key genes and metabolic pathways involved in pepper cold tolerance. This study lays a foundation for the functional characterization and development of pepper cultivars with improved cold tolerance.

Genome-Wide Identification and Functional Analysis of Lysine Histidine Transporter (LHT) Gene Families in Maize

Amino acid transporters (AATs) are essential membrane proteins that transfer amino acids across cells. They are necessary for plant growth and development. The lysine histidine transporter (LHT) gene family in maize (Zea mays) has not yet been characterized. According to sequence composition and phylogenetic placement, this study found 15 LHT genes in the maize genome. The ZmLHT genes are scattered across the plasma membrane. The study also analyzed the evolutionary relationships, gene structures, conserved motifs, 3D protein structure, a transmembrane domain, and gene expression of the 15 LHT genes in maize. Comprehensive analyses of ZmLHT gene expression profiles revealed distinct expression patterns in maize LHT genes in various tissues. This study's extensive data will serve as a foundation for future ZmLHT gene family research. This study might make easier to understand how LHT genes work in maize and other crops.

Ectopic Expression of OsJAZs Alters Plant Defense and Development

A key step in jasmonic acid (JA) signaling is the ligand-dependent assembly of a coreceptor complex comprising the F-box protein COI1 and JAZ transcriptional repressors. The assembly of this receptor complex results in proteasome-mediated degradation of JAZ repressors, which in turn bind and repress MYC transcription factors. Many studies on JAZs have been performed in Arabidopsis thaliana, but the function of JAZs in rice is largely unknown. To systematically reveal the function of OsJAZs, in this study, we compared the various phenotypes resulting from 13 OsJAZs via ectopic expression in Arabidopsis thaliana and the phenotypes of 12 AtJAZs overexpression (OE) lines. Phylogenetic analysis showed that the 25 proteins could be divided into three major groups. Yeast two-hybrid (Y2H) assays revealed that most OsJAZ proteins could form homodimers or heterodimers. The statistical results showed that the phenotypes of the OsJAZ OE plants were quite different from those of AtJAZ OE plants in terms of plant growth, development, and immunity. As an example, compared with other JAZ OE plants, OsJAZ11 OE plants exhibited a JA-insensitive phenotype and enhanced resistance to Pst DC3000. The protein stability after JA treatment of OsJAZ11 emphasized the specific function of the protein. This study aimed to explore the commonalities and characteristics of different JAZ proteins functions from a genetic perspective, and to screen genes with disease resistance value. Overall, the results of this study provide insights for further functional analysis of rice JAZ family proteins.

Mitogen-Activated Protein Kinase and Substrate Identification in Plant Growth and Development

Mitogen-activated protein kinases (MAPKs) form tightly controlled signaling cascades that play essential roles in plant growth, development, and defense response. However, the molecular mechanisms underlying MAPK cascades are still very elusive, largely because of our poor understanding of how they relay the signals. The MAPK cascade is composed of MAPK, MAPKK, and MAPKKK. They transfer signals through the phosphorylation of MAPKKK, MAPKK, and MAPK in turn. MAPKs are organized into a complex network for efficient transmission of specific stimuli. This review summarizes the research progress in recent years on the classification and functions of MAPK cascades under various conditions in plants, especially the research status and general methods available for identifying MAPK substrates, and provides suggestions for future research directions.

Identification, expression, and functional analysis of Hsf and Hsp20 gene families in Brachypodium distachyon under heat stress

Background

The heat shock factor (Hsf) and small heat shock protein (sHsp, also called Hsp20) complex has been identified as a primary component in the protection of plant cells from ubiquitous stresses, particularly heat stress. Our study aimed to characterize and analyze the Hsf and Hsp genes in Brachypodium distachyon, an annual temperate grass and model plant in cereal and grass studies.

Results

We identified 24 Hsf and 18 Hsp20 genes in B. distachyon and explored their evolution in gene organization, sequence features, chromosomal localization, and gene duplication. Our phylogenetic analysis showed that BdHsfs could be divided into three categories and BdHsp20s into ten subfamilies. Further analysis showed that the 3’UTR length of BdHsp20 genes had a negative relationship with their expression under heat stress. Expression analyses indicated that BdHsp20s and BdHsfs were strongly and rapidly induced by high-temperature treatment. Additionally, we constructed a complex regulatory network based on their expression patterns under heat stress. Morphological analysis suggested that the overexpression of five BdHsp20 genes enhanced the seed germination rate and decreased cell death under high temperatures.

Conclusion

Ultimately, our study provided important evolutionary and functional characterizations for future research on the regulatory mechanisms of BdHsp20s and BdHsfs in herbaceous plants under environmental stress.

Comparative analysis of MAPK and MKK gene families reveals differential evolutionary patterns in Brachypodium distachyon inbred lines

BACKGROUND

Mitogen-activated protein kinase (MAPK) cascades are involved with signal transduction in almost every aspect of plant growth and development, as well as biotic and abiotic stress responses. The evolutionary analysis of MAPKs and MKKs in individual or entire plant species has been reported, but the evolutionary patterns in the diverse inbred lines of Brachypodium distachyon are still unclear.

RESULTS

We conducted the systematical molecular evolutionary analysis of B. distachyon. A total of 799 MAPKs and 618 MKKs were identified from 53 B. distachyon inbred lines. Remarkably, only three inbred lines had 16 MPKs and most of those inbred lines lacked MPK7-2 members, whereas 12 MKKs existed in almost all B. distachyon inbred lines. Phylogenetic analysis indicated that MAPKs and MKKs were divided into four groups as previously reported, grouping them in the same branch as corresponding members. MPK21-2 was the exception and fell into two groups, which may be due to their exon-intron patterns, especially the untranslated regions (UTRs). We also found that differential evolution patterns of MKK10 paralogues from ancient tandem duplicates may have undergone functional divergence. Expression analyses suggested that MAPKs and MKKs likely played different roles in different genetic contexts within various tissues and with abiotic stresses.

CONCLUSION

Our study revealed that UTRs affected the structure and evolution of MPK21-2 genes and the differential evolution of MKK10 paralogues with ancient tandem duplication might have functional divergences. Our findings provide new insights into the functional evolution of genes in closely inbred lines.

The Function of MAPK Cascades in Response to Various Stresses in Horticultural Plants

The mitogen-activated protein kinase (MAPK) cascade is a highly conserved signaling transduction module that transduces extracellular stimuli into intracellular responses in plants. Early studies of plant MAPKs focused on their functions in model plants. Based on the results of whole-genome sequencing, many MAPKs have been identified in horticultural plants, such as tomato and apple. Recent studies revealed that the MAPK cascade also plays crucial roles in the biotic and abiotic stress responses of horticultural plants. In this review, we summarize the composition and classification of MAPK cascades in horticultural plants and recent research on this cascade in responses to abiotic stresses (such as drought, extreme temperature and high salinity) and biotic stresses (such as pathogen infection). In addition, we discuss the most advanced research themes related to plant MAPK cascades, thus facilitating research on MAPK cascade functions in horticultural plants.

Genome-wide identification of mitogen-activated protein kinase (MAPK) cascade and expression profiling of CmMAPKs in melon (Cucumis melo L.)

Mitogen-activated protein kinase (MAPK) is a form of serine/threonine protein kinase that activated by extracellular stimulation acting through the MAPK cascade (MAPKKK-MAPKK-MAPK). The MAPK cascade gene family, an important family of protein kinases, plays a vital role in responding to various stresses and hormone signal transduction processes in plants. In this study, we identified 14 CmMAPKs, 6 CmMAPKKs and 64 CmMAPKKKs in melon genome. Based on structural characteristics and a comparison of phylogenetic relationships of MAPK gene families from Arabidopsis, cucumber and watermelon, CmMAPKs and CmMAPKKs were categorized into 4 groups, and CmMAPKKKs were categorized into 3 groups. Furthermore, chromosome location revealed an unevenly distribution on chromosomes of MAPK cascade genes in melon, respectively. Eventually, qRT-PCR analysis showed that all 14 CmMAPKs had different expression patterns under drought, salt, salicylic acid (SA), methyl jasmonate (MeJA), red light (RL), and Podosphaera xanthii (P. xanthii) treatments. Overall, the expression levels of CmMAPK3 and CmMAPK7 under different treatments were higher than those in control. Our study provides an important basis for future functional verification of MAPK genes in regulating responses to stress and signal substance in melon.

Identification of the MAPK Cascade and its Relationship with Nitrogen Metabolism in the Green Alga Chlamydomonas reinhardtii

The mitogen activated protein kinases (MAPKs) form part of a signaling cascade through phosphorylation reactions conserved in all eukaryotic organisms. The MAPK cascades are mainly composed by three proteins, MAPKKKs, MAPKKs and MAPKs. Some signals induce MAPKKK-mediated phosphorylation and activation of MAPKK that phosphorylate and activate MAPK. Afterward, MAPKs can act either in the cytoplasm or be imported into the nucleus to activate other proteins or transcription factors. In the green microalga Chlamydomonas reinhardtii the pathway for nitrogen (N) assimilation is well characterized, yet its regulation still has many unknown features. Nitric oxide (NO) is a fundamental signal molecule for N regulation, where nitrate reductase (NR) plays a central role in its synthesis. The MAPK cascades could be regulating N assimilation, since it has been described that the phosphorylation of NR by MAPK6 promotes NO production in Arabidopsis thaliana. We have identified the proteins involved in the MAPK cascades in Chlamydomonas reinhardtii, finding 17 MAPKs, 2 MAPKKs and 108 MAPKKKs (11 MEKK-, 94 RAF- and 3 ZIK-type) that have been structurally and phylogenetically characterized. The genetic expressions of MAPKs and the MAPKK were slightly regulated by N. However, the genetic expressions of MAPKKKs RAF14 and RAF79 showed a very strong repression by ammonium, which suggests that they may have a key role in the regulation of N assimilation, encouraging to further analyze in detail the role of MAPK cascades in the regulation of N metabolism.

Cloning, molecular and functional characterization by overexpression in Arabidopsis of MAPKK genes from grapevine (Vitis vinifera)

BACKGROUND

The mitogen-activated protein kinases (MAPKs), as a part of the MAPKKK-MAPKK-MAPK cascade, play crucial roles in plant development as an intracellular signal transduction pathway to respond various environmental signals. However, few MAPKK have been functionally characterized in grapevine.

RESULTS

In the study, five MAPKK (MKK) members were identified in grapevine (cultivar 'Pinot Noir'), cloned and designated as VvMKK1-VvMKK5. A phylogenetic analysis grouped them into four sub-families based on the similarity of their conserved motifs and gene structure to Arabidopsis MAPKK members. qRT-PCR results indicated that the expression of VvMKK1, VvMKK2, VvMKK4, and VvMKK5 were up-regulated in mature leaf and young blades, and roots, but exhibited low expression in leaf petioles. VvMKK2, VvMKK3, and VvMKK5 genes were differentially up-regulated when grapevine leaves were inoculated with spores of Erisyphe necator, or treated with salicylic acid (SA), ethylene (ETH), H2O2, or exposed to drought, indicating that these genes may be involved in a variety of signaling pathways. Over expression of VvMKK2 and VvMKK4 genes in transgenic Arabidopsis plants resulted in the production of seeds with a significantly higher germination and survival rate, and better seedling growth under stress conditions than wild-type plants. Overexpression of VvMKK2 in Arabidopsis improved salt and drought stress tolerance while overexpression of VvMKK4 only improved salt stress tolerance.

CONCLUSIONS

Results of the present investigation provide a better understanding of the interaction and function of MAPKKK-MAPKK-MAPK genes at the transcriptional level in grapevine and led to the identification of candidate genes for drought and salt stress in grapes.

Role of BRAF in Hepatocellular Carcinoma: A Rationale for Future Targeted Cancer Therapies

The few therapeutic strategies for advance hepatocellular carcinoma (HCC) on poor knowledge of its biology. For several years, sorafenib, a tyrosine kinase inhibitors (TKI) inhibitor, has been the approved treatment option, to date, for advanced HCC patients. Its activity is the inhibition of the retrovirus-associated DNA sequences protein (RAS)/Rapidly Accelerated Fibrosarcoma protein (RAF)/mitogen-activated and extracellular-signal regulated kinase (MEK)/extracellular-signal regulated kinases (ERK) signaling pathway. However, the efficacy of sorafenib is limited by the development of drug resistance, and the major neuronal isoform of RAF, BRAF and MEK pathways play a critical and central role in HCC escape from TKIs activity. Advanced HCC patients with a BRAF mutation display a multifocal and/or more aggressive behavior with resistance to TKI. Moreover, also long non-coding RNA (lnc-RNA) have been studied in epigenetic studies for BRAF aggressiveness in HCC. So far, lnc-RNA of BRAF could be another mechanism of cancer proliferation and TKI escape in HCC and the inhibition could become a possible strategy treatment for HCC. Moreover, recent preclinical studies and clinical trials evidence that combined treatments, involving alternative pathways, have an important role of therapy for HCC and they could bypass resistance to the following TKIs: MEK, ERKs/ribosomal protein S6 kinase 2 (RSK2), and phosphatidylinositol 3-kinase (PI3K)/mammalian target of rapamycin (mTOR). These initial data must be confirmed in clinical studies, which are currently ongoing. Translational research discoveries could create new strategies of targeted therapy combinations, including BRAF pathway, and they could eventually bring light in new treatment of HCC.

Genome-wide identification, expression profiles and regulatory network of MAPK cascade gene family in barley

BACKGROUND

Mitogen-activated protein kinase (MAPK) cascade is a conserved and universal signal transduction module in organisms. Although it has been well characterized in many plants, no systematic analysis has been conducted in barley.

RESULTS

Here, we identified 20 MAPKs, 6 MAPKKs and 156 MAPKKKs in barley through a genome-wide search against the updated reference genome. Then, phylogenetic relationship, gene structure and conserved protein motifs organization of them were systematically analyzed and results supported the predictions. Gene duplication analysis revealed that segmental and tandem duplication events contributed to the expansion of barley MAPK cascade genes and the duplicated gene pairs were found to undergone strong purifying selection. Expression profiles of them were further investigated in different organs and under diverse abiotic stresses using the available 173 RNA-seq datasets, and then the tissue-specific and stress-responsive candidates were found. Finally, co-expression regulatory network of MAPK cascade genes was constructed by WGCNA tool, resulting in a complicated network composed of a total of 72 branches containing 46 HvMAPK cascade genes and 46 miRNAs.

CONCLUSION

This study provides the targets for further functional study and also contribute to better understand the MAPK cascade regulatory network in barley and beyond.

Genome-wide characterization and phylogenetic analysis of GSK gene family in three species of cotton: evidence for a role of some GSKs in fiber development and responses to stress

BACKGROUND

The glycogen synthase kinase 3/shaggy kinase (GSK3) is a serine/threonine kinase with important roles in animals. Although GSK3 genes have been studied for more than 30 years, plant GSK genes have been studied only since the last decade. Previous research has confirmed that plant GSK genes are involved in diverse processes, including floral development, brassinosteroid signaling, and responses to abiotic stresses.

RESULT

In this study, 20, 15 (including 5 different transcripts) and 10 GSK genes were identified in G. hirsutum, G. raimondii and G. arboreum, respectively. A total of 65 genes from Arabidopsis, rice, and cotton were classified into 4 clades. High similarities were found in GSK3 protein sequences, conserved motifs, and gene structures, as well as good concordance in gene pairwise comparisons (G. hirsutum vs. G. arboreum, G. hirsutum vs. G. raimondii, and G. arboreum vs. G. raimondii) were observed. Whole genome duplication (WGD) within At and Dt sub-genomes has been central to the expansion of the GSK gene family. Furthermore, GhSK genes showed diverse expression patterns in various tissues. Additionally, the expression profiles of GhSKs under different stress treatments demonstrated that many are stress-responsive genes. However, none were induced by brassinolide treatment. Finally, nine co-expression sub-networks were observed for GhSKs and the functional annotations of these genes suggested that some GhSKs might be involved in cotton fiber development.

CONCLUSION

In this present work, we identified 45 GSK genes from three cotton species, which were divided into four clades. The gene features, muti-alignment, conversed motifs, and syntenic blocks indicate that they have been highly conserved during evolution. Whole genome duplication was determined to be the dominant factor for GSK gene family expansion. The analysis of co-expressed sub-networks and tissue-specific expression profiles suggested functions of GhSKs during fiber development. Moreover, their different responses to various abiotic stresses indicated great functional diversity amongst the GhSKs. Briefly, data presented herein may serve as the basis for future functional studies of GhSKs.

DAXX promotes ovarian cancer ascites cell proliferation and migration by activating the ERK signaling pathway

BACKGROUND

The death-domain-associated protein (DAXX) was originally identified as a protein that binds to the transmembrane death receptor FAS and enhances both FAS-induced and transforming growth factor-β-dependent apoptosis. In a previous study, we found that nude mice injected with DAXX-overexpressing cells (ES-2-DAXX) accumulated large concentrations of first-generation ascites cells (I ascites cells). The role of DAXX in the development of ascites is unknown. The aim of this study was to analyze the effect of DAXX on proliferation and migration of ascites cells in ovarian cancer in vitro and in vivo.

METHODS

Nude mice were housed in cages with a 14:10 h light:dark cycle; water and food were provided ad libitum. ES-2-DAXX cells (1×106) were injected intraperitoneally into athymic nude mice (8-week-old female mice). After 4 weeks, I ascites cells were collected. The I ascites cells were injected intraperitoneally into athymic nude mice (8-week-old female mice). After 4 weeks, II ascites cells were collected and cultured. Ascites cell survival, migration, and colony formation were measured using colony formation and cell growth assays. Immunofluorescent staining revealed the co-localization of DAXX and promyelocytic leukemia protein (PML) in ascites cell nuclei. Western blotting and immunohistochemistry showed that extracellular signal-related kinase (p-ERK) 1/2 and CEBP-β were highly expressed in tumor tissues formed by II ascites cells. Through immunoprecipitation, we also found that DAXX can interact with CEBP-β.

RESULTS

DAXX enhanced ascites cell survival, migration, and colony formation. DAXX and PML nuclear foci dramatically increased in a passage-dependent manner in ascites cells, DAXX promoted the tumor growth of ascites cells in vivo, increased ascites cell proliferation in vivo, and enhanced ascites cell survival and migration by activating the ERK signalling pathway and integrating with CEBP-β.

CONCLUSIONS

DAXX can interact with CEBP-β. DAXX can induce ovarian cancer ascites formation by activating the ERK signal pathway and binding to CEBP-β.

In silico-prediction of protein-protein interactions network about MAPKs and PP2Cs reveals a novel docking site variants in Brachypodium distachyon

Protein-protein interactions (PPIs) underlie the molecular mechanisms of most biological processes. Mitogen-activated protein kinases (MAPKs) can be dephosphorylated by MAPK-specific phosphatases such as PP2C, which are critical to transduce extracellular signals into adaptive and programmed responses. However, the experimental approaches for identifying PPIs are expensive, time-consuming, laborious and challenging. In response, many computational methods have been developed to predict PPIs. Yet, these methods have inherent disadvantages such as high false positive and negative results. Thus, it is crucial to develop in silico approaches for predicting PPIs efficiently and accurately. In this study, we identified PPIs among 16 BdMAPKs and 86 BdPP2Cs in B. distachyon using a novel docking approach. Further, we systematically investigated the docking site (D-site) of BdPP2C which plays a vital role for recognition and docking of BdMAPKs. D-site analysis revealed that there were 96 pairs of PPIs including all BdMAPKs and most BdPP2Cs, which indicated that BdPP2C may play roles in other signaling networks. Moreover, most BdPP2Cs have a D-site for BdMAPKs in our prediction results, which suggested that our method can effectively predict PPIs, as confirmed by their 3D structure. In addition, we validated this methodology with known Arabidopsis and yeast phosphatase-MAPK interactions from the STRING database. The results obtained provide a vital research resource for exploring an accurate network of PPIs between BdMAPKs and BdPP2Cs.

Comprehensive analysis of mitogen-activated protein kinase cascades in chrysanthemum

Background

Mitogen-activated protein kinase (MAPK) cascades, an important type of pathway in eukaryotic signaling networks, play a key role in plant defense responses, growth and development.

Methods

Phylogenetic analysis and conserved motif analysis of the MKK and MPK families in Arabidopsis thaliana, Helianthus annuus and Chrysanthemum morifolium classified MKK genes and MPK genes. qRT-PCR was used for the expression patterns of CmMPK and CmMKK genes, and yeast two-hybrid assay was applied to clear the interaction between CmMPKs and CmMKKs.

Results

We characterized six MKK genes and 11 MPK genes in chrysanthemum based on transcriptomic sequences and classified these genes into four groups. qRT-PCR analysis demonstrated that CmMKKs and CmMPKs exhibited various expression patterns in different organs of chrysanthemum and in response to abiotic stresses and phytohormone treatments. Furthermore, a yeast two-hybrid assay was applied to analyze the interaction between CmMKKs and CmMPKs and reveal the MAPK cascades in chrysanthemum.

Discussion

Our data led us to propose that CmMKK4-CmMPK13 and CmMKK2-CmMPK4 may be involved in regulating salt resistance and in the relationship between CmMKK9 and CmMPK6 and temperature stress.

Comparative analysis of plant MKK gene family reveals novel expansion mechanism of the members and sheds new light on functional conservation

Background

Mitogen-activated protein kinase (MAPK) cascades play critical functions in almost every aspect of plant growth and development, which regulates many physiological and biochemical processes. As a middle nodal point of the MAPK cascades, although evolutionary analysis of MKK from individual plant families had some reports, their evolutionary history in entire plants is still not clear.

Results

To better understand the evolution and function of plant MKKs, we performed systematical molecular evolutionary analysis of the MAPKK gene family and also surveyed their gene organizations, sequence features and expression patterns in different subfamilies. Phylogenetic analysis showed that plant MAPKK fall into five different groups (Group A–E). Majority orthology groups seemed to be a single or low-copy genes in all plant species analyzed in Group B, C and D, whereas group A MKKs undergo several duplication events, generating multiple gene copies. Further analysis showed that these duplication events were on account of whole genome duplications (WGDs) in plants and the duplicate genes maybe have undergone functional divergence. We also found that group E MKKs had mutation with one change of serine or theronine might lead to inactivity originated through the ancient tandem duplicates in monocots. Moreover, we also identified MKK3 integrated NTF2 domain that might have gradually lost the cytoplasmic-nuclear trafficking activity, which suggests that they may involve with the gene function more and more sophistication in the evolutionary process. Moreover, expression analyses indicated that plant MKK genes play probable roles in UV-B signaling.

Conclusion

In general, ancient gene and genome duplications are significantly conducive to the expansion of the plant MKK gene family. Our study reveals two distinct evolutionary patterns for plant MKK proteins and sheds new light on the functional evolution of this gene family.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4793-8) contains supplementary material, which is available to authorized users.

Identification on mitogen-activated protein kinase signaling cascades by integrating protein interaction with transcriptional profiling analysis in cotton

Plant mitogen-activated protein kinase (MAPK) cascades play important roles in development and stress responses. In previous studies, we have systematically investigated the mitogen-activated protein kinase kinase (MKK) and MAPK gene families in cotton. However, the complete interactions between MAPK gene family members in MAPK signaling cascade is poorly characterized. Herein, we investigated the mitogen-activated protein kinase kinase kinase (MAPKKK) family members and identified a total of 89 MAPKKK genes in the Gossypium raimondii genome. We cloned 51 MAPKKKs in G. hirsutum and investigated the interactions between MKK and MAPKKK proteins through yeast-two hybrid assays. A total of 18 interactive protein pairs involved in 14 MAPKKKs and six MKKs were found. Among these, 13 interactive pairs had not been reported previously. Gene expression patterns revealed that 12 MAPKKKs were involved in diverse signaling pathways triggered by hormone treatments or abiotic stresses. By combining the MKK-MAPK and MKK-MAPKKK protein interactions with gene expression patterns, 38 potential MAPK signaling modules involved in the complicated cross-talks were identified, which provide a basis on elucidating biological function of the MAPK cascade in response to hormonal and/or stress responses. The systematic investigation in MAPK signaling cascades will lay a foundation for understanding the functional roles of different MAPK cascades in signal transduction pathways, and for the improvement of various defense responses in cotton.

Mitogen-Activated Protein Kinase Cascades in Plant Hormone Signaling

Mitogen-activated protein kinase (MAPK) modules play key roles in the transduction of environmental and developmental signals through phosphorylation of downstream signaling targets, including other kinases, enzymes, cytoskeletal proteins or transcription factors, in all eukaryotic cells. A typical MAPK cascade consists of at least three sequentially acting serine/threonine kinases, a MAP kinase kinase kinase (MAPKKK), a MAP kinase kinase (MAPKK) and finally, the MAP kinase (MAPK) itself, with each phosphorylating, and hence activating, the next kinase in the cascade. Recent advances in our understanding of hormone signaling pathways have led to the discovery of new regulatory systems. In particular, this research has revealed the emerging role of crosstalk between the protein components of various signaling pathways and the involvement of this crosstalk in multiple cellular processes. Here we provide an overview of current models and mechanisms of hormone signaling with a special emphasis on the role of MAPKs in cell signaling networks. One-sentence summary: In this review we highlight the mechanisms of crosstalk between MAPK cascades and plant hormone signaling pathways and summarize recent findings on MAPK regulation and function in various cellular processes.

The MAPKKK gene family in cassava: Genome-wide identification and expression analysis against drought stress

Mitogen-activated protein kinase kinase kinases (MAPKKKs), an important unit of MAPK cascade, play crucial roles in plant development and response to various stresses. However, little is known concerning the MAPKKK family in the important subtropical and tropical crop cassava. In this study, 62 MAPKKK genes were identified in the cassava genome, and were classified into 3 subfamilies based on phylogenetic analysis. Most of MAPKKKs in the same subfamily shared similar gene structures and conserved motifs. The comprehensive transcriptome analysis showed that MAPKKK genes participated in tissue development and response to drought stress. Comparative expression profiles revealed that many MAPKKK genes were activated in cultivated varieties SC124 and Arg7 and the function of MeMAPKKKs in drought resistance may be different between SC124/Arg7 and W14. Expression analyses of the 7 selected MeMAPKKK genes showed that most of them were significantly upregulated by osmotic, salt and ABA treatments, whereas slightly induced by H₂O₂ and cold stresses. Taken together, this study identified candidate MeMAPKKK genes for genetic improvement of abiotic stress resistance and provided new insights into MAPKKK -mediated cassava resistance to drought stress.

Genome-Wide Identification and Analysis of MAPK and MAPKK Gene Families in Bread Wheat (Triticum aestivum L.)

The mitogen-activated protein kinase (MAPK) cascade is a universal signal transduction module that plays a vital role in regulating growth and development, as well as environmental stress responses in plants. Wheat is one of the most important crops worldwide. Although the MAPK kinase kinase (MAP3K) family in wheat has been investigated, the MAPK and MAPK kinase (MAP2K) gene families remain unknown at present. Here, 54 MAPK and 18 MAPKK genes were identified in wheat using recent genomic information. Phylogenetic analysis of Triticum aestivum L. MAPKs and MAPKKs (TaMAPKs and TaMAPKKs) together with homologous genes from other species classified them into four groups, and the clustering was consistent with the genomic exon/intron structures. Conserved motif analysis found that MAPK proteins contained a typical TXY phosphorylation site and MAPKK proteins contained an S/T-X5-S/T motif. RNA-seq data mapping analysis showed that MAPK and MAPKK genes in group IV had tissue-specific expression profiles, whereas each group I member showed relatively high expression in all organs. Expression patterns of TaMAPK and TaMAPKK genes under stress conditions were also investigated and stress-responsive candidates were identified. Co-expression network analysis identified 11 TaMAPK genes and 6 TaMAPKK genes involved in the interaction network pathway. Overall, this study provided useful information for evolutionary and functional surveys of MAPK and MAPKK gene families in wheat and beyond.

Targeting the Ras/Raf/MEK/ERK pathway in hepatocellular carcinoma

Although the biological basis of hepatocellular carcinoma (HCC) remains unclear, effective treatments and improvement of the survival rate remain worthwhile research goals. Abnormal protein signaling pathways contributing to uncontrolled cell proliferation, differentiation, survival and apoptosis are biomarkers of the carcinogenic process. Certain mutated components or overexpression of the rat sarcoma virus (Ras)/rapidly accelerated fibrosarcoma (Raf)/mitogen-activated protein kinase kinase (MEK)/extracellular signal-regulated kinase (ERK) signaling pathway are increasingly being studied in HCC carcinogenesis. The present review addresses the effect of the Ras/Raf/MEK/ERK signaling pathway on the pathogenesis of HCC, and provides an update on the preclinical and clinical development of various inhibitors targeting this core signaling pathway, which include various Ras inhibitors, Raf inhibitors and MEK inhibitors for HCC.

Genome-wide identification, phylogeny and expressional profiles of mitogen activated protein kinase kinase kinase (MAPKKK) gene family in bread wheat (Triticum aestivum L.)

BACKGROUND

Mitogen-activated protein kinase kinase kinases (MAPKKKs) are the important components of MAPK cascades, which play the crucial role in plant growth and development as well as in response to diverse stresses. Although this family has been systematically studied in many plant species, little is known about MAPKKK genes in wheat (Triticum aestivum L.), especially those involved in the regulatory network of stress processes.

RESULTS

In this study, we identified 155 wheat MAPKKK genes through a genome-wide search method based on the latest available wheat genome information, of which 29 belonged to MEKK, 11 to ZIK and 115 to Raf subfamily, respectively. Then, chromosome localization, gene structure and conserved protein motifs and phylogenetic relationship as well as regulatory network of these TaMAPKKKs were systematically investigated and results supported the prediction. Furthermore, a total of 11 homologous groups between A, B and D sub-genome and 24 duplication pairs among them were detected, which contributed to the expansion of wheat MAPKKK gene family. Finally, the expression profiles of these MAPKKKs during development and under different abiotic stresses were investigated using the RNA-seq data. Additionally, 10 tissue-specific and 4 salt-responsive TaMAPKKK genes were selected to validate their expression level through qRT-PCR analysis.

CONCLUSIONS

This study for the first time reported the genome organization, evolutionary features and expression profiles of the wheat MAPKKK gene family, which laid the foundation for further functional analysis of wheat MAPKKK genes, and contributed to better understanding the roles and regulatory mechanism of MAPKKKs in wheat.

Integration analysis of MKK and MAPK family members highlights potential MAPK signaling modules in cotton

Mitogen-activated protein kinase (MAPK) cascades play a crucial role in plant growth and development, as well as their biotic and abiotic stress responses. As a nodal point of the MAPK cascade, the MKK gene family has not been systematically studied in cotton. Here, we identified 11 putative MKK genes in the Gossypium raimondii genome. Phylogenetic analysis showed that the MKKs were supported by architectures of conserved protein motifs. Expression patterns of MKKs under hormone treatments or abiotic stresses revealed their diverse functions in stress responses. Based on a yeast two hybrid, a total of 63 interactive pairs of MKKs and MAPKs were identified in cotton. Among these, 40 interactive pairs were newly identified compared to that reported previously in Arabidopsis. Integration analysis of the interaction network and expression patterns of MKK and MAPK family members revealed 13 potential MAPK signaling modules that are involved in the complicated cross-talk between hormones and abiotic stresses. Taken together, our data enhance the understanding of the evolution and function of MAPK cascades in cotton, and lay the foundation for the improvement of various defense responses that use MAPK signaling modules in the future.

Genome-wide identification and evolutionary analyses of the PP2C gene family with their expression profiling in response to multiple stresses in Brachypodium distachyon

Background

The type-2C protein phosphatases (PP2Cs), negatively regulating ABA responses and MAPK cascade pathways, play important roles in stress signal transduction in plants. Brachypodium distachyon is a new model plant for exploring the functional genomics of temperate grasses, cereals and biofuel crops. To date, genome-wide identification and analysis of the PP2C gene family in B. distachyon have not been investigated.

Results

In this study, 86 PP2C genes in B. distachyon were identified. Domain-based analyses of PP2C proteins showed that they all contained the phosphatase domains featured as 11 conserved signature motifs. Although not all phosphatase domains of BdPP2C members included all 11 motifs, tertiary structure analysis showed that four residues contributing to magnesium/manganese ions (Mg²⁺/Mn²⁺) coordination were conserved, except for two noncanonical members. The analysis of their chromosomal localizations showed that most of the BdPP2C genes were located within the low CpG density region. Phylogenetic tree and synteny blocks analyses among B. distachyon, Arabidopsis thaliana and Oryza sativa revealed that all PP2C members from the three species can be phylogenetically categorized into 13 subgroups (A–M) and BdPP2Cs were evolutionarily more closely related to OsPP2Cs than to AtPP2Cs. Segmental duplications contributed particularly to the expansion of the BdPP2C gene family and all duplicated BdPP2Cs evolved mainly from purifying selection. Real-time quantitative reverse transcription PCR (qRT-PCR) analysis showed that BdPP2Cs were broadly expressed in disparate tissues. We also found that almost all members displayed up-regulation in response to abiotic stresses such as cold, heat, PEG and NaCl treatments, but down-regulation to biotic stresses such as Ph14, Guy11 and F0968 infection.

Conclusions

In the present study, a comprehensive analysis of genome-wide identification and characterization of protein domains, phylogenetic relationship, gene and protein structure, chromosome location and expression pattern of the PP2C gene family was carried out for the first time in a new model monocot, i.e., B. distachyon. Our results provide a reference for genome-wide identification of the PP2C gene family of other species and also provide a foundation for future functional research on PP2C genes in B. distachyon.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2526-4) contains supplementary material, which is available to authorized users.

Expansion and stress responses of AP2/EREBP superfamily in Brachypodium distachyon

APETALA2/ethylene-responsive element binding protein (AP2/EREBP) transcription factors constitute one of the largest and most conserved gene families in plant, and play essential roles in growth, development and stress response. Except a few members, the AP2/EREBP family has not been characterized in Brachypodium distachyon, a model plant of Poaceae. We performed a genome-wide study of this family in B. distachyon by phylogenetic analyses, transactivation assays and transcript profiling. A total of 149 AP2/EREBP genes were identified and divided into four subfamilies, i.e., ERF (ethylene responsive factor), DREB (dehydration responsive element binding gene), RAV (related to ABI3/VP) and AP2. Tandem duplication was a major force in expanding B. distachyon AP2/EREBP (BdAP2/EREBP) family. Despite a significant expansion, genomic organizations of BdAP2/EREBPs were monotonous as the majority of them, except those of AP2 subfamily, had no intron. An analysis of transcription activities of several closely related and duplicated BdDREB genes showed their functional divergence and redundancy in evolution. The expression of BdAP2/EREBPs in different tissues and the expression of DREB/ERF subfamilies in B. distachyon, wheat and rice under abiotic stresses were investigated by next-generation sequencing and microarray profiling. Our results are valuable for further function analysis of stress tolerant AP2/EREBP genes in B. distachyon.

Genome-Wide Identification, Evolution, and Co-expression Network Analysis of Mitogen-Activated Protein Kinase Kinase Kinases in Brachypodium distachyon

Mitogen-activated protein kinase (MAPK) cascades are the conserved and universal signal transduction modules in all eukaryotes, which play the vital roles in plant growth, development, and in response to multiple stresses. In this study, we used bioinformatics methods to identify 86 MAPKKK protein encoded by 73 MAPKKK genes in Brachypodium. Phylogenetic analysis of MAPKKK family from Arabidopsis, rice, and Brachypodium has classified them into three subfamilies, of which 28 belonged to MEKK, 52 to Raf, and 6 to ZIK subfamily, respectively. Conserved protein motif, exon-intron organization, and splicing intron phase in kinase domains supported the evolutionary relationships inferred from the phylogenetic analysis. And gene duplication analysis suggested the chromosomal segment duplication happened before the divergence of the rice and Brachypodium, while all of three tandem duplicated gene pairs happened after their divergence. We further demonstrated that the MAPKKKs have evolved under strong purifying selection, implying the conservation of them. The splicing transcripts expression analysis showed that the splicesome translating longest protein tended to be adopted. Furthermore, the expression analysis of BdMAPKKKs in different organs and development stages as well as heat, virus and drought stresses revealed that the MAPKKK genes were involved in various signaling pathways. And the circadian analysis suggested there were 41 MAPKKK genes in Brachypodium showing cycled expression in at least one condition, of which seven MAPKKK genes expressed in all conditions and the promoter analysis indicated these genes possessed many cis-acting regulatory elements involved in circadian and light response. Finally, the co-expression network of MAPK, MAPKK, and MAPKKK in Brachypodium was constructed using 144 microarray and RNA-seq datasets, and ten potential MAPK cascades pathway were predicted. To conclude, our study provided the important information for evolutionary and functional characterization of MAPKKK family in Brachypodium, which will facilitate the functional analysis of BdMAPKKK genes, and also will facilitate better understanding the MAPK signal pathway in Brachypodium and beyond.

Genome-wide identification and transcriptional expression analysis of mitogen-activated protein kinase and mitogen-activated protein kinase kinase genes in Capsicum annuum

The tripartite mitogen-activated protein kinase (MAPK) signaling cascades have been implicated in plant growth, development, and environment adaptation, but a comprehensive understanding of MAPK signaling at genome-wide level is limited in Capsicum annuum. Herein, genome-wide identification and transcriptional expression analysis of MAPK and MAPK kinase (MAPKK) were performed in pepper. A total of 19 pepper MAPK (CaMAPKs) genes and five MAPKK (CaMAPKKs) genes were identified. Phylogenetic analysis indicated that CaMAPKs and CaMAPKKs could be classified into four groups and each group contains similar exon-intron structures. However, significant divergences were also found. Notably, five members of the pepper MAPKK family were much less conserved than those found in Arabidopsis, and 9 Arabidopsis MAPKs did not have orthologs in pepper. Additionally, 7 MAPKs in Arabidopsis had either two or three orthologs in the pepper genome, and six pepper MAPKs and one MAPKK differing in sequence were found in three pepper varieties. Quantitative real-time RT-PCR analysis showed that the majority of MAPK and MAPKK genes were ubiquitously expressed and transcriptionally modified in pepper leaves after treatments with heat, salt, and Ralstonia solanacearum inoculation as well as exogenously applied salicylic acid, methyl jasmonate, ethephon, and abscisic acid. The MAPKK-MAPK interactome was tested by yeast two-hybrid assay, the results showed that one MAPKK might interact with multiple MAPKs, one MAPK might also interact with more than one MAPKKs, constituting MAPK signaling networks which may collaborate in transmitting upstream signals into appropriate downstream cellular responses and processes. These results will facilitate future functional characterization of MAPK cascades in pepper.