Phylogenomic analysis of MKKs and MAPKs from 16 legumes and detection of interacting pairs in chickpea divulge MAPK signalling modules

YuPingFengSan ameliorates LPS-induced acute lung injury and gut barrier dysfunction in mice

ETHNOPHARMACOLOGICAL RELEVANCE

Yupingfengsan (YPFS) is a traditional Chinese medicine decoction. YPFS comprises Astragalus mongholicus Bunge (Huangqi), Atractylodes rubra Dekker (Baizhu), and Saposhnikovia divaricata (Turcz.ex Ledeb.) Schischk (Fangfeng). YPFS is commonly used to treat chronic obstructive pulmonary disease, asthma, respiratory infections, and pneumonia, but the mechanism of action remains unclear.

AIM OF THE STUDY

Acute lung injury (ALI) and its severe form of acute respiratory distress syndrome (ARDS) cause morbidity and mortality in critical patients. YPFS is a commonly used herbal soup to treat respiratory and immune system diseases. Nevertheless, the effect of YPFS on ALI remains unclear. This study aimed to investigate the effect of YPFS on lipopolysaccharide (LPS)-induced ALI in mice and elucidate its potential molecular mechanisms.

MATERIALS AND METHODS

The major components of YPFS were detected by High-performance liquid chromatography (HPLC). C57BL/6J mice were given YPFS for seven days and then treated with LPS. IL-1β, IL-6, TNF-α, IL-8, iNOS, NLRP3, PPARγ, HO-1, ZO-1, Occludin, Claudin-1, AQP3, AQP4, AQP5, ENaCα, ENaCβ, EnaCγ mRNA in lung and ZO-1, Occludin, Claudin-1, AQP3, AQP4, AQP5, ENaCα, ENaCβ, and EnaCγ mRNA in colon tissues were measured by Real-Time Quantitative PCR (RT-qPCR). The expressions of TLR4, MyD88, NOD-like receptor thermal protein domain associated protein 3 (NLRP3), ASC, MAPK signaling pathway, Nrf2, and HO-1 in the lung were detected by Western blot. Plasma inflammatory factors Interleukin (IL)-1β, IL-6, and Tumor Necrosis Factor-α (TNF-α) were determined by Enzyme-linked Immunosorbent Assay (ELISA). Lung tissues were processed for H & E staining, and colon tissues for HE, WGA-FITC, and Alcian Blue staining.

RESULTS

The results showed that YPFS administration alleviated lung injury and suppressed the production of inflammatory factors, including IL-1β, IL-6, and TNF-α. Additionally, YPFS reduced pulmonary edema by promoting the expressions of aquaporin and sodium channel-related genes (AQP3, AQP4, AQP5, ENaCα, ENaCβ, and EnaCγ). Further, YPFS intervention exhibited a therapeutic effect on ALI by inhibiting the activation of the NLRP3 inflammasome and MAPK signaling pathways. Finally, YPFS improved gut barrier integrity and suppressed intestinal inflammation in LPS-challenged mice.

CONCLUSIONS

YPFS protected mice against LPS-induced ALI by attenuating lung and intestinal tissue damage. This study sheds light on the potential application of YPFS to treat ALI/ARDS.

Genomics-assisted genetics of complex region from chickpea chromosome 4 reveals two candidate genes for Ascochyta blight resistance

Ascochyta blight (AB) disease caused by the fungus Ascochyta rabiei is a major threat to global chickpea production. Molecular breeding for improved AB resistance requires the identification of robust fine-mapped QTLs/candidate genes and associated markers. Earlier, we identified three QTLs (qABR4.1, qABR4.2, and qABR4.3) for AB resistance on chickpea chromosome 4 by employing multiple quantitative trait loci sequencing strategy on an intra-specific (FLIP84-92C x PI359075) and an inter-specific (FLIP84-92C x PI599072) crosses derived recombinant inbred lines. Here, we report the identification of AB resistance providing candidate genes under the fine mapped qABR4.2 and qABR4.3 genomic region by combining genetic mapping, haplotype block inheritance, and expression analysis. The qABR4.2 region was narrowed down from 5.94Mb to ~800kb. Among 34 predicted gene models, a secreted class III peroxidase encoding gene showed higher expression in AB resistant parent after A. rabiei conidia inoculation. Under qABR4.3, we identified a frame-shift mutation in a cyclic nucleotide-gated channel CaCNGC1 gene leading to the truncated N-terminal domain in resistant accession of chickpea. This N-terminal domain of CaCNGC1 interacts with chickpea calmodulin. Thus, our analysis has revealed narrowed genomic regions and their associated polymorphic markers, CaNIP43 and CaCNGCPD1. These co-dominant markers significantly associate with AB resistance on qABR4.2 and qABR4.3 regions. Our genetic analysis revealed that the presence of resistant alleles for two major QTLs (qABR4.1 and qABR4.2) together provide AB resistance in the field while minor QTL qABR4.3 determines the degree of resistance. The identified candidate genes and their diagnostic markers will help in biotechnological and AB resistance introgression into farmers adapted local chickpea varieties.

Physiological Roles and Mechanisms of Action of Class I TCP Transcription Factors

TEOSINTE BRANCHED1, CYCLOIDEA, PROLIFERATING CELL FACTOR 1 and 2 (TCP) proteins constitute a plant-specific transcription factors family exerting effects on multiple aspects of plant development, such as germination, embryogenesis, leaf and flower morphogenesis, and pollen development, through the recruitment of other factors and the modulation of different hormonal pathways. They are divided into two main classes, I and II. This review focuses on the function and regulation of class I TCP proteins (TCPs). We describe the role of class I TCPs in cell growth and proliferation and summarize recent progresses in understanding the function of class I TCPs in diverse developmental processes, defense, and abiotic stress responses. In addition, their function in redox signaling and the interplay between class I TCPs and proteins involved in immunity and transcriptional and posttranslational regulation is discussed.

Simultaneously monitoring endogenous MAPK members in single living cells by multi-channel fluorescence correlation spectroscopy

The mitogen-activated protein kinase (MAPK) pathway is a major module for cellular signal transduction. The dysregulation of the MAPK pathway has been involved in the pathogenesis of multiple diseases ranging from cancers to chronic inflammations. So far, we have not fully understood the influences of external factors and signaling networks on the MAPK pathway due to the lack of in situ methods for simultaneous detection of multiple kinases in the pathway in living cells. Herein, we present a new strategy for in situ and simultaneously monitoring MAPK pathway kinases in single living cells combining multi-channel fluorescence correlation spectroscopy (FCS) with affinity fluorescent probes. We chose rapidly growing fibrosarcoma kinase (RAF), mitogen-activated protein kinase (MEK), and extracellular signal-regulated kinase (ERK) as representative members in the MAPK pathway. We designed and synthesized three fluorescent affinity probes and experimental results demonstrated that the three probes specifically targeted endogenous BRAF, MEK1/2, and ERK1/2 in living cells. Based on the multi-channel FCS system, we studied the influences of biological substances, drugs and oxidative stress on the activities of endogenous MAPK kinases and the cross-talk between the MAPK and PI3K-mTOR pathways. We have found that serum, sorafenib, and hydrogen peroxide can regulate multiple MAPK kinases and the effects of external stimuli can transmit to the MAPK pathway; furthermore, we have observed that the MAPK pathway can be activated by modulating the PI3K-mTOR pathway. Our results illustrated the complexity of a cellular signal network and the necessity of in situ and simultaneous determination of biomolecules in living cells.

CaMPK9 increases the stability of CaWRKY40 transcription factor which triggers defense response in chickpea upon Fusarium oxysporum f. sp. ciceri Race1 infection

Physical interaction and phosphorylation by CaMPK9 protects the degradation of CaWRKY40 that induces resistance response in chickpea to Fusarium wilt disease by modulating the transcription of defense responsive genes. WRKY transcription factors (TFs) are the global regulators of plant defense signaling that modulate immune responses in host plants by regulating transcription of downstream target genes upon challenged by pathogens. However, very little is known about immune responsive role of Cicer arietinum L. (Ca) WRKY TFs particularly. Using two contrasting chickpea genotypes with respect to resistance against Fusarium oxysporum f. sp. ciceri Race1 (Foc1), we demonstrate transcript accumulation of different CaWRKYs under multiple stresses and establish that CaWRKY40 triggers defense. CaWRKY40 overexpressing chickpea mounts resistance to Foc1 by positively modulating the defense related gene expression. EMSA, ChIP assay and real-time PCR analyses suggest CaWRKY40 binds at the promoters and positively regulates transcription of CaDefensin and CaWRKY33. Further studies revealed that mitogen Activated Protein Kinase9 (CaMPK9) phosphorylates CaWRKY40 by directly interacting with its two canonical serine residues. Interestingly, CaMPK9 is unable to interact with CaWRKY40 when the relevant two serine residues were replaced by alanine. Overexpression of serine mutated WRKY40 isoform in chickpea fails to provide resistance against Foc1. Mutated WRKY40^{Ser.224/225 to AA} overexpressing chickpea resumes its ability to confer resistance against Foc1 after application of 26S proteasomal inhibitor MG132, suggests that phosphorylation is essential to protect CaWRKY40 from proteasomal degradation. CaMPK9 silencing also led to susceptibility in chickpea to Foc1. Altogether, our results elucidate positive regulatory roles of CaMPK9 and CaWRKY40 in modulating defense response in chickpea upon Foc1 infection.

Defense responses of lentil (Lens culinaris) genotypes carrying non-allelic ascochyta blight resistance genes to Ascochyta lentis infection

Ascochyta blight of lentil is an important fungal disease in many lentil-producing regions of the world causing major yield and grain quality losses. Quick shifts in aggressiveness of the population of the causal agent Ascochyta lentis mandates developing germplasm with novel and durable resistance. In the absence of complete resistance, lentil genotypes CDC Robin and 964a-46 have frequently been used as sources of partial resistance to ascochyta blight and carry non-allelic ascochyta blight resistance genes. RNA-seq analysis was conducted to identify differences in the transcriptome of CDC Robin, 964a-46 and the susceptible check Eston after inoculation with A. lentis. Candidate defense genes differentially expressed among the genotypes had hypothetical functions in various layers of plant defense, including pathogen recognition, phytohormone signaling pathways and downstream defense responses. CDC Robin and 964a-46 activated cell surface receptors (e.g. receptor like kinases) tentatively associated with pathogen-associated molecular patterns (PAMP) recognition and nucleotide-binding site leucine-rich repeat (NBS-LRR) receptors associated with intracellular effector recognition upon A. lentis infection, and differed in their activation of salicylic acid, abscisic acid and jasmonic acid / ethylene signal transduction pathways. These differences were reflected in the differential expression of downstream defense responses such as pathogenesis-related proteins, and genes associated with the induction of cell death and cell-wall reinforcement. A significant correlation between expression levels of a selection of genes based on quantitative real-time PCR and their expression levels estimated through RNA-seq demonstrated the technical and analytical accuracy of RNA-seq for identification of genes differentially expressed among genotypes. The presence of different resistance mechanisms in 964a-46 and CDC Robin indicates their value for pyramiding gene leading to more durable resistance to ascochyta blight.

mQTL-seq and classical mapping implicates the role of an AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED (AHL) family gene in Ascochyta blight resistance of chickpea

Ascochyta blight (AB) caused by the fungal pathogen Ascochyta rabiei is a serious foliar disease of chickpea (Cicer arietinum L.). Despite many genetic studies on chickpea-Ascochyta interaction, genome-wide scan of chickpea for the identification of AB-associated quantitative trait loci (QTLs) and their gene(s) has not been accomplished. To elucidate narrow QTLs for AB resistance, here, we report the use of multiple QTL-sequencing approach on 2 sets of extreme AB phenotype bulks derived from Cicer intraspecific and interspecific crosses. Two major QTLs, qABR4.1 and qABR4.2, and a minor QTL, qABR4.3, were identified on assembled chickpea pseudomolecule 4. We narrowed qABR4.1 to a "robust region" at 4.568-4.618 Mb through mapping on a larger intraspecific cross-derived population and comparative analysis. Among 4 genes, the CaAHL18 gene showed higher expression under Ascochyta stress in AB resistant parent suggesting that it is the candidate gene under "robust qABR4.1." Dual-luciferase assay with CaAHL18 polymorphic cis-regulatory sequences showed that allelic variation is associated with higher expression. Thus, our findings on chickpea-Ascochyta interaction have narrowed down AB resistance associated QTLs on chickpea physical map. The narrowed QTLs and gene-associated markers will help in biotechnological and breeding programs for chickpea improvement.

Current advances in chickpea genomics: applications and future perspectives

Chickpea genomics promises to illuminate our understanding of genome organization, structural variations, evolutionary and domestication-related insights and fundamental biology of legume crops. Unprecedented advancements of next generation sequencing (NGS) technologies have enabled in decoding of multiple chickpea genome sequences and generating huge genomic resources in chickpea both at functional and structural level. This review is aimed to update the current progress of chickpea genomics ranging from high density linkage map development, genome-wide association studies (GWAS), functional genomics resources for various traits, emerging role of abiotic stress responsive coding and non-coding RNAs after the completion of draft chickpea genome sequences. Additionally, the current efforts of whole genome re-sequencing (WGRS) approach of global chickpea germplasm to capture the global genetic diversity existing in the historically released varieties across the world and increasing the resolution of the previously identified candidate gene(s) of breeding importance have been discussed. Thus, the outcomes of these genomics resources will assist in genomics-assisted selection and facilitate breeding of climate-resilient chickpea cultivars for sustainable agriculture.