OsLYP4 and OsLYP6 play critical roles in rice defense signal transduction

Mining of disease-resistance genes in Crocus sativus based on transcriptome sequencing

Introduction: Crocus sativus L. has an important medicinal and economic value in traditional perennial Chinese medicine. However, due to its unique growth characteristics, during cultivation it is highly susceptible to disease. The absence of effective resistance genes restricts us to breed new resistant varieties of C. sativus. Methods: In present study, comprehensive transcriptome sequencing was introduced to explore the disease resistance of the candidate gene in healthy and corm rot-infected C. sativus. Results and discussion: Totally, 43.72 Gb of clean data was obtained from the assembly to generate 65,337 unigenes. By comparing the gene expression levels, 7,575 differentially expressed genes (DEGs) were primarily screened. A majority of the DEGs were completely in charge of defense and metabolism, and 152 of them were annotated as pathogen recognition genes (PRGs) based on the PGRdb dataset. The expression of some transcription factors including NAC, MYB, and WRKY members, changed significantly based on the dataset of transcriptome sequencing. Therefore, this study provides us some valuable information for exploring candidate genes involved in the disease resistance in C. sativus.

LysM-containing proteins function in the resistance of Litopenaeus vannamei against Vibrio parahaemolyticus infection

Lysin motif (LysM) is a functional domain that can bind to peptidoglycans, chitin and their derivatives. The LysM-containing proteins participate in multiple biological processes, such as the hydrolysis of bacterial cell walls and the perception of PAMPs in plants and high animals. In the present study, two genes encoding LysM-containing proteins, designated as LvLysM1 and LvLysM2, were identified in the Pacific white shrimp, Litopenaeus vannamei, and their functions during Vibrio infection were analyzed. The open-reading frame (ORF) of LvLysM1 was 795 bp, only encoding a LysM domain at the N-terminal region. The ORF of LvLysM2 was 834 bp, encoding a LysM domain at the central region and a transmembrane region at the C-terminal region. Both LvLysM1 and LvLysM2 were widely transcribed in all tested shrimp tissues. Enzyme-linked immunosorbent assay (ELISA) showed that the recombinant protein of LvLysM2 could bind to different bacterial polysaccharides, while LvLysM1 showed no direct binding activity. The transcripts of LvLysMs in gills increased significantly after infection with Vibrio parahaemolyticus. When LvLysM1 or LvLysM2 was knocked down by dsRNA, the mortality of shrimp was significantly increased after infection with Vibrio parahaemolyticus. Interestingly, some SNPs existed in these two genes were apparently correlated with the VpAHPND resistance of shrimp. These results suggested that LvLysM1 and LvLysM2 might contribute to the disease resistance of shrimp. The data provide new knowledge about the function of LysM-containing proteins in shrimp and potential genetic markers for disease resistance breeding.

Plant lectins: Classical molecules with emerging roles in stress tolerance

Biotic and abiotic stresses impose adverse effects on plant's development, growth, and production. For the past many years, researchers are trying to understand the stress induced responses in plants and decipher strategies to produce stress tolerant crops. It has been demonstrated that molecular networks encompassing an array of genes and functional proteins play a key role in generating responses to combat different stresses. Newly, there has been a resurgence of interest to explore the role of lectins in modulating various biological responses in plants. Lectins are naturally occurring proteins that form reversible linkages with their respective glycoconjugates. To date, several plant lectins have been recognized and functionally characterized. However, their involvement in stress tolerance is yet to be comprehensively analyzed in greater detail. The availability of biological resources, modern experimental tools, and assay systems has provided a fresh impetus for plant lectin research. Against this backdrop, the present review provides background information on plant lectins and recent knowledge on their crosstalks with other regulatory mechanisms, which play a remarkable role in plant stress amelioration. It also highlights their versatile role and suggests that adding more information to this under-explored area will usher in a new era of crop improvement.

The grapevine LysM receptor-like kinase VvLYK5-1 recognizes chitin oligomers through its association with VvLYK1-1

The establishment of defense reactions to protect plants against pathogens requires the recognition of invasion patterns (IPs), mainly detected by plasma membrane-bound pattern recognition receptors (PRRs). Some IPs, also termed elicitors, are used in several biocontrol products that are gradually being developed to reduce the use of chemicals in agriculture. Chitin, the major component of fungal cell walls, as well as its deacetylated derivative, chitosan, are two elicitors known to activate plant defense responses. However, recognition of chitooligosaccharides (COS) in Vitis vinifera is still poorly understood, hampering the improvement and generalization of protection tools for this important crop. In contrast, COS perception in the model plant Arabidopsis thaliana is well described and mainly relies on a tripartite complex formed by the cell surface lysin motif receptor-like kinases (LysM-RLKs) AtLYK1/CERK1, AtLYK4 and AtLYK5, the latter having the strongest affinity for COS. In grapevine, COS perception has for the moment only been demonstrated to rely on two PRRs VvLYK1-1 and VvLYK1-2. Here, we investigated additional players by overexpressing in Arabidopsis the two putative AtLYK5 orthologs from grapevine, VvLYK5-1 and VvLYK5-2. Expression of VvLYK5-1 in the atlyk4/5 double mutant background restored COS sensitivity, such as chitin-induced MAPK activation, defense gene expression, callose deposition and conferred non-host resistance to grapevine downy mildew (Erysiphe necator). Protein-protein interaction studies conducted in planta revealed a chitin oligomer-triggered interaction between VvLYK5-1 and VvLYK1-1. Interestingly, our results also indicate that VvLYK5-1 mediates the perception of chitin but not chitosan oligomers showing a part of its specificity.

Genome-wide analysis of LysM gene family members and their expression in response to Colletotrichum fructicola infection in Octoploid strawberry(Fragaria × ananassa)

The cultivated octoploid strawberry (Fragaria × ananassa) is an economically important fruit that is planted worldwide. The lysin motif (LysM) protein family is composed of the major class of plant pattern recognition receptors, which play important roles in sensing pathogen-associated molecular patterns (PAMPs), and subsequently triggers downstream plant immunity. In the present study, a comprehensive, genome-wide analysis of F. × ananassa LysM (FaLysM) genes was performed to investigate gene structures, phylogenic relationships, chromosome location, collinear relationships, transcription factor binding sites, and protein model analysis. We aimed to identify the LysM genes involved in the defense against plant pathogens. A total of 14 FaLysM genes were identified in the F. × ananassa genome and divided into 2 subgroups (LYP and LYK) on the basis of the phylogenetic analysis. The Ka/Ks ratio for the duplicated pair of most FaLysM genes was less than 1, which indicates that the selection pressure was mostly subject to the purifying selection during evolution. The protein model analysis revealed that FaLysM2-10 contain conserved mode of chitin binding, which suggest the potential role of FaLysM2-10 in pathogen perception and plant immunity. The RNA-Seq results showed the differential regulation of 14 FaLysM genes in response to Colletotrichum fructicola infection, implying the complex interaction between C. fructicola and strawberry. Knockout of candidate effector gene CfLysM2, which was previously proved to be highly expressed during C. fructicola infection, resulted in the up-regulation of six FaLysM genes (FaLysM1, FaLysM2, FaLysM3, FaLysM7, FaLysM8, and FaLysM12), indicating the competitive relations between CfLysM2 and FaLysM genes. Overall, this study provides fundamental information on the roles of LysM proteins in octoploid strawberry and its interaction with C. fructicola, laying useful information for further investigation on the C. fructicola-strawberry interaction and strawberry resistance breeding.

Bulked segregant transcriptome analysis in pea identifies key expression markers for resistance to Peyronellaea pinodes

Peyronellaea pinodes is a devastating pathogen of pea crop. Quantitative trait loci (QTL) associated with resistance have been identified, as well as genes differentially expressed between resistant and susceptible pea lines. The key question is which of these many genes located into these QTLs, or differentially expressed, are the key genes that distinguish resistant from susceptible plants and could be used as markers. To identify these key genes, in the present study we applied MACE (Massive Analysis of cDNA Ends) -Seq to a whole Recombinant Inbred Line population segregating for resistance to this disease and their parental lines and identified those genes which expression was more correlated with the level of resistance. We also compared gene expression profiles between the most resistant and the most susceptible families of the RIL population. A total of 6780 transcripts were differentially expressed between the parental lines after inoculation. Of them, 803 showed the same expression pattern in the bulks formed by the most resistant and most susceptible RIL families. These genes, showing a consistent expression pattern, could be used as expression markers to distinguish resistant from susceptible plants. The analysis of these genes also discovered the crucial mechanisms acting against P. pinodes.

Transcriptome-wide analysis of North-East Indian rice cultivars in response to Bipolaris oryzae infection revealed the importance of early response to the pathogen in suppressing the disease progression

Brown spot disease (BSD) of rice (Oryza sativa L.) caused by Bipolaris oryzae is one of the major and neglected fungal diseases worldwide affecting rice production. Despite its significance, very limited knowledge on genetics and genomics of rice in response to B. oryzae available. Our study firstly identified moderately resistant (Gitesh) and susceptible (Shahsarang) North-East Indian rice cultivars in response to a native Bipolaris oryzae isolate BO1. Secondly, a systematic comparative RNA seq was performed for both cultivars at four different time points viz. 12, 24, 48, and 72 hours post infestation (hpi). Differential gene expression analysis revealed the importance of early response to the pathogen in suppressing disease progression. The pathogen negatively regulates the expression of photosynthetic-related genes at early stages in both cultivars. Of the cell wall modification enzymes, cellulose synthase and callose synthase are important for signal transduction and defense. Cell wall receptors OsLYP6, OsWAK80 might positively and OsWAK25 negatively regulate disease resistance. Jasmonic acid and/or abscisic acid signaling pathways are presumably involved in disease resistance, whereas salicylic acid pathway, and an ethylene response gene OsEBP-89 in promoting disease. Surprisingly, pathogenesis-related proteins showed no antimicrobial impact on the pathogen. Additionally, transcription factors OsWRKY62 and OsWRKY45 together might negatively regulate resistance to the pathogen. Taken together, our study has identified and provide key regulatory genes involved in response to B. oryzae which serve as potential resources for functional genetic analysis to develop genetic tolerance to BSD of rice.

Receptors in the Induction of the Plant Innate Immunity

Plants adjust amplitude and duration of immune responses via different strategies to maintain growth, development, and resistance to pathogens. Pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and effector-triggered immunity (ETI) play vital roles. Pattern recognition receptors, comprising a large number of receptor-like protein kinases and receptor-like proteins, recognize related ligands and trigger immunity. PTI is the first layer of the innate immune system, and it recognizes PAMPs at the plasma membrane to prevent infection. However, pathogens exploit effector proteins to bypass or directly inhibit the PTI immune pathway. Consistently, plants have evolved intracellular nucleotide-binding domain and leucine-rich repeat-containing proteins to detect pathogenic effectors and trigger a hypersensitive response to activate ETI. PTI and ETI work together to protect plants from infection by viruses and other pathogens. Diverse receptors and the corresponding ligands, especially several pairs of well-studied receptors and ligands in PTI immunity, are reviewed to illustrate the dynamic process of PTI response here.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Lysin Motif (LysM) Proteins: Interlinking Manipulation of Plant Immunity and Fungi

The proteins with lysin motif (LysM) are carbohydrate-binding protein modules that play a critical role in the host-pathogen interactions. The plant LysM proteins mostly function as pattern recognition receptors (PRRs) that sense chitin to induce the plant's immunity. In contrast, fungal LysM blocks chitin sensing or signaling to inhibit chitin-induced host immunity. In this review, we provide historical perspectives on plant and fungal LysMs to demonstrate how these proteins are involved in the regulation of plant's immune response by microbes. Plants employ LysM proteins to recognize fungal chitins that are then degraded by plant chitinases to induce immunity. In contrast, fungal pathogens recruit LysM proteins to protect their cell wall from hydrolysis by plant chitinase to prevent activation of chitin-induced immunity. Uncovering this coevolutionary arms race in which LysM plays a pivotal role in manipulating facilitates a greater understanding of the mechanisms governing plant-fungus interactions.

Recognition Pattern, Functional Mechanism and Application of Chitin and Chitosan Oligosaccharides in Sustainable Agriculture

Background:

Application of chitin attracts much attention in the past decades as the second abundant polysaccharides in the world after cellulose. Chitin oligosaccharides (CTOS) and its deacetylated derivative chitosan oligosaccharides (COS) were shown great potentiality in agriculture by enhancing plant resistance to abiotic or biotic stresses, promoting plant growth and yield, improving fruits quality and storage, etc. Those applications have already served huge economic and social benefits for many years. However, the recognition mode and functional mechanism of CTOS and COS on plants have gradually revealed just in recent years.

Objective:

Recognition pattern and functional mechanism of CTOS and COS in plant together with application status of COS in agricultural production will be well described in this review. By which we wish to promote further development and application of CTOS and COS–related products in the field.

A lysin motif-containing protein (SpLysMD3) functions as a PRR involved in the antibacterial responses of mud crab, Scylla paramamosain

Lysin motif (LysM)-containing proteins function as pattern-recognition receptors in plants to recognize different N-acetylglucosamine-containing ligands, thereby triggering specific defense responses against pathogens. However, the biological functions of these proteins in animals remain unclear. In this study, we characterized a novel LysM protein, designated as SpLysMD3, in mud crab Scylla paramamosain. The cDNA sequence of SpLysMD3 had 1058 bp with an open reading frame of 840 bp encoding a protein with 279 amino acid residues. The deduced protein contained a LysM domain and a transmembrane region. SpLysMD3 was highly expressed in gills, intestine, muscle, and hemocytes and upregulated after challenges with bacteria, suggesting that it may be involved in antibacterial defense. Binding assay showed that SpLysMD3 possessed specific binding activities to all tested microorganisms as well as bacterial cell wall components lipopolysaccharide (LPS) and peptidoglycan (PGN), indicating that SpLysMD3 was an important LPS- and PGN-binding protein in mud crab. Bacterial clearance assay revealed that coating bacteria with SpLysMD3 accelerated bacterial clearance in vivo. The promotion of bacterial clearance by SpLysMD3 was further determined by using SpLysMD3-silenced crabs injected with S. aureus or V. parahemolyticus. Silencing SpLysMD3 dramatically suppressed the bacterial clearance. Meanwhile, knockdown of SpLysMD3 also severely impaired the expression of a specific set of antimicrobial peptides (AMPs); moreover, SpLysMD3 overexpression can enhance the promoter activity of SpALF2. These results suggested that SpLysMD3 affected bacterial clearance by regulating AMPs. Collectively, all the results demonstrated that SpLysMD3 may function as a potential receptor involved in innate immunity by binding to LPS and PGN and by regulating AMPs to eliminate invading pathogen. This study provided new insights into the biological functions of LysM proteins in animals and the mechanisms underlying the antibacterial activity of crustaceans.

Molecular identification and expression analysis of four Lysin motif (LysM) domain-containing proteins from turbot (Scophthalmus maximus)

Lysin motif (LysM) is involved in chitin, peptidoglycan and other structurally-related oligosaccharides recognition and binding, and it is important for the biological processes of responsing to bacterial and viral infections and pathogen defense. LysM is also a widely spread protein, ranging from prokaryotes to eukaryotes, including bacteria, plants and mammals. However, research of LysM in teleosts especially in marine fish was rarely scarce. In the present study, four novel LysM domain-containing proteins in turbot (Scophthalmus maximus), named as SmLysMd1, SmLysMd2, SmLysMd3, and SmLysMd4, were cloned and identified firstly. The full-length cDNA of SmLysMd1 was 1235 bp with a 678 bp ORF, capable of encoding a peptide of 225 amino acids. The complete cDNA sequence of SmLysMd2 was 1273 bp, and contained a 675 bp ORF, encoding a predicted protein of 224 amino acids. The full-length of SmLysMd3 cDNA was 2132 bp, containing a ORF of 987 bp, with a ORF of encoding 328 amino acids. The full-length SmLysMd4 cDNA was 1115 bp contained a 888 bp ORF, encoding 295 amino acids. And all the four predicated proteins contained a specific LYSM domain. Moreover, SmLysMd1 and SmLysMd2 belong to the intracellular non-secretory types, and SmLysMd3 and SmLysMd4 belong to the anchored transmembrane types. In addition, the four SmLysMd were ubiquitously expressed in all the examined tissues. Moreover, the SmLysMds levels were up-regulated in muscle and liver, and had a reduce tendency immediately in different degree following Vibrio vulnificus challenge, indicating that the turbot LysM could be participant in the immune responses to bacterial infections. The present result of LysM in turbot for the first time in a marine fish will provide foundation knowledge for the functions studies of LysM in immune responses. Further studies should be carried out to better understand their immune mechanism in turbot and other teleosts.

Tomato LysM Receptor-Like Kinase SlLYK12 Is Involved in Arbuscular Mycorrhizal Symbiosis

Arbuscular mycorrhiza (AM) is a widespread symbiotic relationship between plants and fungi (Glomeromycota), which improves the supply of water and nutrients to host plants. AM symbiosis is set in motion by fungal chitooligosaccharides and lipochitooligosaccharides, which are perceived by plant-specific LysM-type receptor kinases (LYK). In rice this involves OsCERK1, a LYK also essential for chitin triggered innate immunity. In contrast in legumes, the CERK1 homologous gene experienced duplication events resulting in subfunctionalization. However, it remains unknown whether this subfunctionalization is legume-specific, or has occurred also in other dicot plant species. We identified four CERK1 homologs in tomato (SlLYK1, SlLYK11, SlLYK12, and SlLYK13) and investigated their roles in chitin signaling and AM symbiosis. We found that knockdown of SlLYK12 in tomato significantly reduced AM colonization, whereas chitin-induced responses were unaffected. In contrast, knockdown of SlLYK1 resulted in reduced responses to chitin, but did not alter responses to AM fungi. Moreover, ectopic overexpression of SlLYK1 and SlLYK13 in Nicotiana benthamiana induced cell death, whereas SlLYK12 overexpression did not. Based on our results and comparison with rice OsCERK1, we hypothesize that OsCERK1 orthologs in tomato underwent gene duplication, leading to the subfunctionalization of immunity and symbiosis.

From Chaos to Harmony: Responses and Signaling upon Microbial Pattern Recognition

Pathogen- or microbe-associated molecular patterns (PAMPs/MAMPs) are detected as nonself by host pattern recognition receptors (PRRs) and activate pattern-triggered immunity (PTI). Microbial invasions often trigger the production of host-derived endogenous signals referred to as danger- or damage-associated molecular patterns (DAMPs), which are also perceived by PRRs to modulate PTI responses. Collectively, PTI contributes to host defense against infections by a broad range of pathogens. Remarkable progress has been made toward demonstrating the cellular and physiological responses upon pattern recognition, elucidating the molecular, biochemical, and genetic mechanisms of PRR activation, and dissecting the complex signaling networks that orchestrate PTI responses. In this review, we present an update on the current understanding of how plants recognize and respond to nonself patterns, a process from which the seemingly chaotic responses form into a harmonic defense.

The Role of Plant Innate Immunity in the Legume-Rhizobium Symbiosis

A classic view of the evolution of mutualism is that it derives from a pathogenic relationship that attenuated over time to a situation in which both partners can benefit. If this is the case for rhizobia, then one might uncover features of the symbiosis that reflect this earlier pathogenic state. For example, as with plant pathogens, it is now generally assumed that rhizobia actively suppress the host immune response to allow infection and symbiosis establishment. Likewise, the host has retained mechanisms to control the nutrient supply to the symbionts and the number of nodules so that they do not become too burdensome. The open question is whether such events are strictly ancillary to the central symbiotic nodulation factor signaling pathway or are essential for rhizobial host infection. Subsequent to these early infection events, plant immune responses can also be induced inside nodules and likely play a role in, for example, nodule senescence. Thus, a balanced regulation of innate immunity is likely required throughout rhizobial infection, symbiotic establishment, and maintenance. In this review, we discuss the significance of plant immune responses in the regulation of symbiotic associations with rhizobia, as well as rhizobial evasion of the host immune system.

Involvement of a LysM and putative peptidoglycan-binding domain-containing protein in the antibacterial immune response of kuruma shrimp Marsupenaeus japonicus

Lysin motif (LysM) is a peptidoglycan and chitin-binding motif with multiple functions in bacteria, plants, and animals. In this study, a novel LysM and putative peptidoglycan-binding domain-containing protein was cloned from kuruma shrimp (Marsupenaeus japonicus) and named as MjLPBP. The cDNA of MjLPBP contained 1010 nucleotides with an open reading frame of 834 nucleotides encoding a protein of 277 amino acid residues. The deduced protein contained a Lysin motif and a transmembrane region, with a calculated molecular mass of 31.54 kDa and isoelectric point of 8.61. MjLPBP was ubiquitously distributed in different tissues of shrimp at the mRNA level. Time course expression assay showed that MjLPBP was upregulated in hemocytes of shrimp challenged with Vibrio anguillarum or Staphylococcus aureus. MjLPBP was also upregulated in hepatopancreas after white spot syndrome virus and bacteria challenge. The recombinant protein of MjLPBP could bind to some Gram-positive and Gram-negative bacteria and yeast. Further study found that rMjLPBP bound to bacterial cell wall components, including peptidoglycans, lipoteichoic acid, lipopolysaccharide, and chitin. The induction of several antimicrobial peptide genes and phagocytosis-related gene, such as anti-lipopolysaccharide factors and myosin, was depressed after knockdown of MjLPBP. MjLPBP could facilitate V. anguillarum clearance in vivo. All the results indicated that MjLPBP might play an important role in the innate immunity of shrimp.

OsCERK1 and OsRLCK176 play important roles in peptidoglycan and chitin signaling in rice innate immunity

Microbe-associated molecular pattern (MAMP)-triggered immunity plays critical roles in the basal resistance defense response in plants. Chitin and peptidoglycan (PGN) are major molecular patterns for fungi and bacteria, respectively. Two rice (Oryza sativa) lysin motif-containing proteins, OsLYP4 and OsLYP6, function as receptors that sense bacterial PGN and fungal chitin. These membrane receptors, which lack intracellular kinase domains, likely contain another component for transmembrane immune signal transduction. Here, we demonstrate that the rice LysM receptor-like kinase OsCERK1, a key component of the chitin elicitor signaling pathway, also plays an important role in PGN-triggered immunity in rice. Silencing of OsCERK1 suppressed PGN-induced (and chitin-induced) immunity responses, including reactive oxygen species generation, defense gene expression, and callose deposition, indicating that OsCERK1 is essential for both PGN and chitin signaling initiated by OsLYP4 and OsLYP6. OsLYP4 associated with OsLYP6 and the rice chitin receptor chitin oligosaccharide elicitor-binding protein (CEBiP) in the absence of PGN or chitin, and treatment with PGN or chitin led to their disassociation in vivo. OsCERK1 associated with OsLYP4 or OsLYP6 when induced by PGN but it associated with OsLYP4, OsLYP6, or CEBiP under chitin treatment, suggesting the presence of different patterns of ligand-induced heterooligomeric receptor complexes. Furthermore, the receptor-like cytoplasmic kinase OsRLCK176 functions downstream of OsCERK1 in the PGN and chitin signaling pathways, suggesting that these MAMPs share overlapping intracellular signaling components. Therefore, OsCERK1 plays dual roles in PGN and chitin signaling in rice innate immunity and as an adaptor involved in signal transduction at the plasma membrane in conjunction with OsLYP4 and OsLYP6.