1
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Chiu T, Li Y. Polygalacturonase-inhibiting proteins as an exogenously applied natural solution for prevention of postharvest fungal infections. Synth Syst Biotechnol 2024; 9:481-493. [PMID: 38651095 PMCID: PMC11035021 DOI: 10.1016/j.synbio.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 03/19/2024] [Accepted: 04/02/2024] [Indexed: 04/25/2024] Open
Abstract
Polygalacturonase inhibiting proteins (PGIPs) are plant proteins involved in the inhibition of polygalacturonases (PGs), cell-wall degrading enzymes often secreted by phytopathogenic fungi. Previously, we confirmed that PGIP2 from Phaseolus vulgaris (PvPGIP2) can inhibit the growth of Aspergillus niger and Botrytis cinerea on agar plate. In this study, we further validated the feasibility of using PGIP as an environmental and ecological friendly agent to prevent fungal infection post-harvest. We found that application of either purified PGIP (full length PvPGIP2 or truncated tPvPGIP2_5-8), or PGIP-secreting Saccharomyces cerevisiae strains can effectively inhibit fungal growth and necrotic lesions on tobacco leaf. We also examined the effective amount and thermostability of PGIP when applied on plants. A concentration of 0.75 mg/mL or higher can significantly reduce the area of B. cinerea lesions. The activity of full-length PvPGIPs is not affected after incubation at various temperatures ranging from -20 to 42 °C for 24 h, while truncated tPvPGIP2_5-8 lost some efficacy after incubation at 42 °C. Furthermore, we have also examined the efficacy of PGIP on tomato fruit. When the purified PvPGIP2 proteins were applied to tomato fruit inoculated with B. cinerea at a concentration of roughly 1.0 mg/mL, disease incidence and area of disease had reduced by more than half compared to the controls without PGIP treatment. This study explores the potential of PGIPs as exogenously applied, eco-friendly fungal control agents on fruit and vegetables post-harvest.
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Affiliation(s)
- Tiffany Chiu
- Graduate Program in Genetics, Genomics, and Bioinformatics, 1140 Batchelor Hall, University of California Riverside, California, 92521, USA
| | - Yanran Li
- Program of Chemical Engineering, Department of Nanoengineering, University of California, San Diego, CA, 92521, USA
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2
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Furumizu C, Aalen RB. Peptide signaling through leucine-rich repeat receptor kinases: insight into land plant evolution. THE NEW PHYTOLOGIST 2023; 238:977-982. [PMID: 36811171 DOI: 10.1111/nph.18827] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Multicellular organisms need mechanisms for communication between cells so that they can fulfill their purpose in the organism as a whole. Over the last two decades, several small post-translationally modified peptides (PTMPs) have been identified as components of cell-to-cell signaling modules in flowering plants. Such peptides most often influence growth and development of organs not universally conserved among land plants. PTMPs have been matched to subfamily XI leucine-rich repeat receptor-like kinases with > 20 repeats. Phylogenetic analyses, facilitated by recently published genomic sequences of non-flowering plants, have identified seven clades of such receptors with a history back to the common ancestor of bryophytes and vascular plants. This raises a number of questions: When did peptide signaling arise during land plant evolution? Have orthologous peptide-receptor pairs preserved their biological functions? Has peptide signaling contributed to major innovations, such as stomata, vasculature, roots, seeds, and flowers? Using genomic, genetic, biochemical, and structural data and non-angiosperm model species, it is now possible to address these questions. The vast number of peptides that have not yet found their partners suggests furthermore that we have far more to learn about peptide signaling in the coming decades.
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Affiliation(s)
- Chihiro Furumizu
- Natural Science Center for Basic Research and Development, Hiroshima University, 1-4-2 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8527, Japan
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8530, Japan
| | - Reidunn Birgitta Aalen
- Department of Biosciences, University of Oslo, PO Box 1066, Blindern, Oslo, 0316, Norway
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3
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Prapong S, Tansiri Y, Sritrakul T, Sripattanakul S, Sopitthummakhun A, Katzenmeier G, Hsieh CL, McDonough SP, Prapong T, Chang YF. Leptospira borgpetersenii Leucine-Rich Repeat Proteins Provide Strong Protective Efficacy as Novel Leptospiral Vaccine Candidates. Trop Med Infect Dis 2022; 8:tropicalmed8010006. [PMID: 36668913 PMCID: PMC9863753 DOI: 10.3390/tropicalmed8010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Leucine-rich repeat (LRR) proteins are advocated for being assessed in vaccine development. Leptospiral LRR proteins were identified recently in silico from the genome of Leptospira borgpetersenii serogroup Sejroe, the seroprevalence of leptospiral infections of cattle in Thailand. Two LRR recombinant proteins, rKU_Sej_LRR_2012M (2012) and rhKU_Sej_LRR_2271 (2271), containing predicted immunogenic epitopes, were investigated for their cross-protective efficacies in an acute leptospirosis model with heterologous Leptospira serovar Pomona, though, strains from serogroup Sejroe are host-adapted to bovine, leading to chronic disease. Since serovar Pomona is frequently reported as seropositive in cattle, buffaloes, pigs, and dogs in Thailand and causes acute and severe leptospirosis in cattle by incidental infection, the serogroup Sejroe LRR proteins were evaluated for their cross-protective immunity. The protective efficacies were 37.5%, 50.0%, and 75.0% based on the survival rate for the control, 2012, and 2271 groups, respectively. Sera from 2012-immunized hamsters showed weak bactericidal action compared to sera from 2271-immunized hamsters (p < 0.05). Therefore, bacterial tissue clearances, inflammatory responses, and humoral and cell-mediated immune (HMI and CMI) responses were evaluated only in 2271-immunized hamsters challenged with virulent L. interrogans serovar Pomona. The 2271 protein induced prompt humoral immune responses (p < 0.05) and leptospiral tissue clearance, reducing tissue inflammation in immunized hamsters. In addition, protein 2271 and its immunogenic peptides stimulated splenocyte lymphoproliferation and stimulated both HMI and CMI responses by activating Th1 and Th2 cytokine gene expression in vaccinated hamsters. Our data suggest that the immunogenic potential renders rhKU_Sej_LRR_2271 protein a promising candidate for the development of a novel cross-protective vaccine against animal leptospirosis.
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Affiliation(s)
- Siriwan Prapong
- Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand
- The Interdisciplinary Graduate Program in Genetic Engineering, The Graduate School, Kasetsart University, Bangkok 10900, Thailand
- Center for Advanced Studies for Agriculture and Food (CASAF), Kasetsart University, Bangkok 10900, Thailand
- Correspondence: ; Tel.: +66-871-264-148
| | - Yada Tansiri
- Faculty of Medicine, King Mongkut’s Institute of Technology Ladkrabang, Bangkok 10520, Thailand
| | - Tepyuda Sritrakul
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Kasetsart University, Kamphaengsaen Campus, Nakorn Pathom 73140, Thailand
| | - Sineenat Sripattanakul
- Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand
- The Interdisciplinary Graduate Program in Genetic Engineering, The Graduate School, Kasetsart University, Bangkok 10900, Thailand
| | - Aukkrimapann Sopitthummakhun
- Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand
- Center for Advanced Studies for Agriculture and Food (CASAF), Kasetsart University, Bangkok 10900, Thailand
| | - Gerd Katzenmeier
- Akkhraratchakumari Veterinary College, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Chin-Lin Hsieh
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Sean P. McDonough
- Department of Biomedical Science, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Teerasak Prapong
- Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand
| | - Yung-Fu Chang
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
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4
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Chiu T, Behari A, Chartron JW, Putman A, Li Y. Exploring the potential of engineering polygalacturonase-inhibiting protein as an ecological, friendly, and nontoxic pest control agent. Biotechnol Bioeng 2021; 118:3200-3214. [PMID: 34050940 DOI: 10.1002/bit.27845] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 05/03/2021] [Accepted: 05/22/2021] [Indexed: 11/11/2022]
Abstract
In plants, polygalacturonase-inhibiting proteins (PGIPs) play critical roles for resistance to fungal disease by inhibiting the pectin-depolymerizing activity of endopolygalacturonases (PGs), one type of enzyme secreted by pathogens that compromises plant cell walls and leaves the plant susceptible to disease. Here, the interactions between PGIPs from Phaseolus vulgaris (PvPGIP1 and PvPGIP2) and PGs from Aspergillus niger (AnPG2), Botrytis cinerea (BcPG1 and BcPG2), and Fusarium moniliforme (FmPG3) were reconstituted through a yeast two hybrid (Y2H) system to investigate the inhibition efficiency of various PvPGIP1 and 2 truncations and mutants. We found that tPvPGIP2_5-8, which contains LRR5 to LRR8 and is only one-third the size of the full length peptide, exhibits the same level of interactions with AnPG and BcPGs as the full length PvPGIP2 via Y2H. The inhibitory activities of tPvPGIP2_5-8 on the growth of A. niger and B. cinerea were then examined and confirmed on pectin agar. On pectin assays, application of both full length PvPGIP2 and tPvPGIP2_5-8 clearly slows down the growth of A. niger and B. cinerea. Investigation on the sequence-function relationships of PGIP utilizing a combination of site directed mutagenesis and a variety of peptide truncations suggests that LRR5 could have the most essential structural feature for the inhibitory activities, and may be a possible target for the future engineering of PGIP with enhanced activity. This study highlights the potential of plant-derived PGIPs as a candidate for future in planta evaluation as a pest control agent.
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Affiliation(s)
- Tiffany Chiu
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, California, USA
| | - Anita Behari
- Department of Microbiology and Plant Pathology, University of California Riverside, Revierside, California, USA
| | - Justin W Chartron
- Department of Bioengineering, University of California Riverside, Riverside, California, USA
| | - Alexander Putman
- Department of Microbiology and Plant Pathology, University of California Riverside, Revierside, California, USA
| | - Yanran Li
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, California, USA
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5
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Pijuan J, Ortigoza-Escobar JD, Ortiz J, Alcalá A, Calvo MJ, Cubells M, Hernando-Davalillo C, Palau F, Hoenicka J. PLXNA2 and LRRC40 as candidate genes in autism spectrum disorder. Autism Res 2021; 14:1088-1100. [PMID: 33749153 DOI: 10.1002/aur.2502] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/10/2021] [Indexed: 12/12/2022]
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disability with high heritability yet the genetic etiology remains elusive. Therefore, it is necessary to elucidate new genotype-phenotype relationships for ASD to improve both the etiological knowledge and diagnosis. In this work, a copy-number variant and whole-exome sequencing analysis were performed in an ASD patient with a complex neurobehavioral phenotype with epilepsy and attention deficit hyperactivity disorder. We identified rare recessive single nucleotide variants in the two genes, PLXNA2 encoding Plexin A2 that participates in neurodevelopment, and LRRC40, which encodes Leucine-rich repeat containing protein 40, a protein of unknown function. PLXNA2 showed the heterozygous missense variants c.614G>A (p.Arg205Gln) and c.4904G>A (p.Arg1635Gln) while LRRC40 presented the homozygous missense variant c.1461G>T (p.Leu487Phe). In silico analysis predicted that these variants could be pathogenic. We studied PLXNA2 and LRRC40 mRNA and proteins in fibroblasts from the patient and controls. We observed a significant PlxnA2 subcellular delocalization and very low levels of LRRC40 in the patient. Moreover, we found a novel interaction between PlxnA2 and LRRC40 suggesting that participate in a common neural pathway. This interaction was significant decreased in the patient's fibroblasts. In conclusion, our results identified PLXNA2 and LRRC40 genes as candidates in ASD providing novel clues for the pathogenesis. Further attention to these genes is warranted in genetic studies of patients with neurodevelopmental disorders, particularly ASD. LAY SUMMARY: Genomics is improving the knowledge and diagnosis of patients with autism spectrum disorder (ASD) yet the genetic etiology remains elusive. Here, using genomic analysis together with experimental functional studies, we identified in an ASD complex patient the PLXNA2 and LRRC40 recessive genes as ASD candidates. Furthermore, we found that the proteins of these genes interact in a common neural network. Therefore, more attention to these genes is warranted in genetic studies of patients with neurodevelopmental disorders, particularly ASD.
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Affiliation(s)
- Jordi Pijuan
- Laboratory of Neurogenetics and Molecular Medicine - IPER, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
| | - Juan Darío Ortigoza-Escobar
- Movement Disorders Unit, Department of Pediatric Neurology, Institut de Recerca Sant Joan de Déu, CIBERER-ISCIII and European Reference Network for Rare Neurological Diseases (ERN-RND), Barcelona, Spain
| | - Juan Ortiz
- Department of Child Psychiatry, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Adrián Alcalá
- Department of Genetic Medicine - IPER, Hospital Sant Joan de Déu, Barcelona, Spain
| | - María José Calvo
- Department of Pediatric Neurology, Hospital San Jorge de Huesca, Huesca, Spain
| | - Mariona Cubells
- Laboratory of Neurogenetics and Molecular Medicine - IPER, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
| | | | - Francesc Palau
- Laboratory of Neurogenetics and Molecular Medicine - IPER, Institut de Recerca Sant Joan de Déu, Barcelona, Spain.,Department of Genetic Medicine - IPER, Hospital Sant Joan de Déu, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain.,Clinic Institute of Medicine and Dermatology (ICMiD), Hospital Clínic, Barcelona, Spain.,Division of Pediatrics, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
| | - Janet Hoenicka
- Laboratory of Neurogenetics and Molecular Medicine - IPER, Institut de Recerca Sant Joan de Déu, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
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6
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Wyżewski Z, Gradowski M, Krysińska M, Dudkiewicz M, Pawłowski K. A novel predicted ADP-ribosyltransferase-like family conserved in eukaryotic evolution. PeerJ 2021; 9:e11051. [PMID: 33854844 PMCID: PMC7955679 DOI: 10.7717/peerj.11051] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 02/11/2021] [Indexed: 01/12/2023] Open
Abstract
The presence of many completely uncharacterized proteins, even in well-studied organisms such as humans, seriously hampers full understanding of the functioning of the living cells. ADP-ribosylation is a common post-translational modification of proteins; also nucleic acids and small molecules can be modified by the covalent attachment of ADP-ribose. This modification, important in cellular signalling and infection processes, is usually executed by enzymes from the large superfamily of ADP-ribosyltransferases (ARTs). Here, using bioinformatics approaches, we identify a novel putative ADP-ribosyltransferase family, conserved in eukaryotic evolution, with a divergent active site. The hallmark of these proteins is the ART domain nestled between flanking leucine-rich repeat (LRR) domains. LRRs are typically involved in innate immune surveillance. The novel family appears as putative novel ADP-ribosylation-related actors, most likely pseudoenzymes. Sequence divergence and lack of clearly detectable “classical” ART active site suggests the novel domains are pseudoARTs, yet atypical ART activity, or alternative enzymatic activity cannot be excluded. We propose that this family, including its human member LRRC9, may be involved in an ancient defense mechanism, with analogies to the innate immune system, and coupling pathogen detection to ADP-ribosyltransfer or other signalling mechanisms.
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Affiliation(s)
- Zbigniew Wyżewski
- Institute of Biological Sciences, Cardinal Stefan Wyszynski University in Warsaw, Warszawa, Poland
| | - Marcin Gradowski
- Department of Biochemistry and Microbiology, Warsaw University of Life Sciences - SGGW, Warszawa, Poland
| | - Marianna Krysińska
- Department of Biochemistry and Microbiology, Warsaw University of Life Sciences - SGGW, Warszawa, Poland
| | - Małgorzata Dudkiewicz
- Department of Biochemistry and Microbiology, Warsaw University of Life Sciences - SGGW, Warszawa, Poland
| | - Krzysztof Pawłowski
- Department of Biochemistry and Microbiology, Warsaw University of Life Sciences - SGGW, Warszawa, Poland.,Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, United States.,Department of Translational Medicine, Lund University, Lund, Sweden
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7
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Poretsky E, Dressano K, Weckwerth P, Ruiz M, Char SN, Shi D, Abagyan R, Yang B, Huffaker A. Differential activities of maize plant elicitor peptides as mediators of immune signaling and herbivore resistance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:1582-1602. [PMID: 33058410 DOI: 10.1111/tpj.15022] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 08/13/2020] [Accepted: 09/01/2020] [Indexed: 05/27/2023]
Abstract
Plant elicitor peptides (Peps) are conserved regulators of defense responses and models for the study of damage-associated molecular pattern-induced immunity. Although present as multigene families in most species, the functional relevance of these multigene families remains largely undefined. While Arabidopsis Peps appear largely redundant in function, previous work examining Pep-induced responses in maize (Zm) implied specificity of function. To better define the function of individual ZmPeps and their cognate receptors (ZmPEPRs), activities were examined by assessing changes in defense-associated phytohormones, specialized metabolites and global gene expression patterns, in combination with heterologous expression assays and analyses of CRISPR/Cas9-generated knockout plants. Beyond simply delineating individual ZmPep and ZmPEPR activities, these experiments led to a number of new insights into Pep signaling mechanisms. ZmPROPEP and other poaceous precursors were found to contain multiple active Peps, a phenomenon not previously observed for this family. In all, seven new ZmPeps were identified and the peptides were found to have specific activities defined by the relative magnitude of their response output rather than by uniqueness. A striking correlation was observed between individual ZmPep-elicited changes in levels of jasmonic acid and ethylene and the magnitude of induced defense responses, indicating that ZmPeps may collectively regulate immune output through rheostat-like tuning of phytohormone levels. Peptide structure-function studies and ligand-receptor modeling revealed structural features critical to the function of ZmPeps and led to the identification of ZmPep5a as a potential antagonist peptide able to competitively inhibit the activity of other ZmPeps, a regulatory mechanism not previously observed for this family.
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Affiliation(s)
- Elly Poretsky
- Division of Biology, University of California San Diego, La Jolla, CA, USA
| | - Keini Dressano
- Division of Biology, University of California San Diego, La Jolla, CA, USA
| | - Philipp Weckwerth
- Division of Biology, University of California San Diego, La Jolla, CA, USA
| | - Miguel Ruiz
- Division of Biology, University of California San Diego, La Jolla, CA, USA
| | - Si Nian Char
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Da Shi
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Ruben Abagyan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Bing Yang
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Alisa Huffaker
- Division of Biology, University of California San Diego, La Jolla, CA, USA
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8
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LRRpredictor-A New LRR Motif Detection Method for Irregular Motifs of Plant NLR Proteins Using an Ensemble of Classifiers. Genes (Basel) 2020; 11:genes11030286. [PMID: 32182725 PMCID: PMC7140858 DOI: 10.3390/genes11030286] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 02/28/2020] [Accepted: 03/04/2020] [Indexed: 12/17/2022] Open
Abstract
Leucine-rich-repeats (LRRs) belong to an archaic procaryal protein architecture that is widely involved in protein-protein interactions. In eukaryotes, LRR domains developed into key recognition modules in many innate immune receptor classes. Due to the high sequence variability imposed by recognition specificity, precise repeat delineation is often difficult especially in plant NOD-like Receptors (NLRs) notorious for showing far larger irregularities. To address this problem, we introduce here LRRpredictor, a method based on an ensemble of estimators designed to better identify LRR motifs in general but particularly adapted for handling more irregular LRR environments, thus allowing to compensate for the scarcity of structural data on NLR proteins. The extrapolation capacity tested on a set of annotated LRR domains from six immune receptor classes shows the ability of LRRpredictor to recover all previously defined specific motif consensuses and to extend the LRR motif coverage over annotated LRR domains. This analysis confirms the increased variability of LRR motifs in plant and vertebrate NLRs when compared to extracellular receptors, consistent with previous studies. Hence, LRRpredictor is able to provide novel insights into the diversification of LRR domains and a robust support for structure-informed analyses of LRRs in immune receptor functioning.
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9
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Calderan-Rodrigues MJ, Guimarães Fonseca J, de Moraes FE, Vaz Setem L, Carmanhanis Begossi A, Labate CA. Plant Cell Wall Proteomics: A Focus on Monocot Species, Brachypodium distachyon, Saccharum spp. and Oryza sativa. Int J Mol Sci 2019; 20:E1975. [PMID: 31018495 PMCID: PMC6514655 DOI: 10.3390/ijms20081975] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/06/2019] [Accepted: 03/07/2019] [Indexed: 12/13/2022] Open
Abstract
Plant cell walls mostly comprise polysaccharides and proteins. The composition of monocots' primary cell walls differs from that of dicots walls with respect to the type of hemicelluloses, the reduction of pectin abundance and the presence of aromatic molecules. Cell wall proteins (CWPs) differ among plant species, and their distribution within functional classes varies according to cell types, organs, developmental stages and/or environmental conditions. In this review, we go deeper into the findings of cell wall proteomics in monocot species and make a comparative analysis of the CWPs identified, considering their predicted functions, the organs analyzed, the plant developmental stage and their possible use as targets for biofuel production. Arabidopsis thaliana CWPs were considered as a reference to allow comparisons among different monocots, i.e., Brachypodium distachyon, Saccharum spp. and Oryza sativa. Altogether, 1159 CWPs have been acknowledged, and specificities and similarities are discussed. In particular, a search for A. thaliana homologs of CWPs identified so far in monocots allows the definition of monocot CWPs characteristics. Finally, the analysis of monocot CWPs appears to be a powerful tool for identifying candidate proteins of interest for tailoring cell walls to increase biomass yield of transformation for second-generation biofuels production.
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Affiliation(s)
- Maria Juliana Calderan-Rodrigues
- Department of Genetics, Max Feffer Laboratory of Plant Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, CP 83, 13400-970 Piracicaba, SP, Brazil.
| | - Juliana Guimarães Fonseca
- Department of Genetics, Max Feffer Laboratory of Plant Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, CP 83, 13400-970 Piracicaba, SP, Brazil.
| | - Fabrício Edgar de Moraes
- Department of Genetics, Max Feffer Laboratory of Plant Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, CP 83, 13400-970 Piracicaba, SP, Brazil.
| | - Laís Vaz Setem
- Department of Genetics, Max Feffer Laboratory of Plant Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, CP 83, 13400-970 Piracicaba, SP, Brazil.
| | - Amanda Carmanhanis Begossi
- Department of Genetics, Max Feffer Laboratory of Plant Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, CP 83, 13400-970 Piracicaba, SP, Brazil.
| | - Carlos Alberto Labate
- Department of Genetics, Max Feffer Laboratory of Plant Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, CP 83, 13400-970 Piracicaba, SP, Brazil.
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10
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Biglycan is a new high-affinity ligand for CD14 in macrophages. Matrix Biol 2019; 77:4-22. [DOI: 10.1016/j.matbio.2018.05.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 05/15/2018] [Accepted: 05/15/2018] [Indexed: 02/06/2023]
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11
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Karki S, Paudel P, Sele C, Shkumatov AV, Kajander T. The structure of SALM5 suggests a dimeric assembly for the presynaptic RPTP ligand recognition. Protein Eng Des Sel 2019; 31:147-157. [PMID: 29897575 DOI: 10.1093/protein/gzy012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 05/15/2018] [Indexed: 12/28/2022] Open
Abstract
Synaptic adhesion molecules play a crucial role in the regulation of synapse development and maintenance. Recently, several families of leucine-rich repeat (LRR) domain-containing neuronal adhesion molecules have been characterised, including netrin-G ligands, LRRTMs and the synaptic adhesion-like molecule (SALM) family proteins. Most of these are expressed at the excitatory glutamatergic synapses, and dysfunctions of these genes are genetically linked with cognitive disorders, such as autism spectrum disorders and schizophrenia. The SALM family proteins SALM3 and SALM5, similar to SLITRKs, have been shown to bind to the presynaptic receptor protein tyrosine phosphatase (RPTP) family ligands. Here, we present the 3.1 Å crystal structure of the SALM5 LRR-Ig-domain construct and biophysical studies that verify the crystallographic results. We show that SALM1, SALM3 and SALM5 form similar dimeric structures, in which the LRR domains form the dimer interface. Both SALM3 and SALM5 bind to RPTP immunoglobulin domains with micromolar affinity. SALM3 shows a clear preference for the RPTP ligands with the meB splice insert. Our structural studies and sequence conservation analysis suggests a ligand-binding site and mechanism for RPTP binding via the dimeric LRR domain region.
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Affiliation(s)
- Sudeep Karki
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Prodeep Paudel
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Celeste Sele
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Alexander V Shkumatov
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels 1050, Belgium.,VIB-VUB Center for Structural Biology, Brussels 1050, Belgium
| | - Tommi Kajander
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
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12
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Eshghi A, Gaultney RA, England P, Brûlé S, Miras I, Sato H, Coburn J, Bellalou J, Moriarty TJ, Haouz A, Picardeau M. An extracellular Leptospira interrogans leucine-rich repeat protein binds human E- and VE-cadherins. Cell Microbiol 2018; 21:e12949. [PMID: 30171791 DOI: 10.1111/cmi.12949] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 08/20/2018] [Accepted: 08/24/2018] [Indexed: 01/07/2023]
Abstract
Pathogenic Leptospira bacteria are the causative agents of leptospirosis, a zoonotic disease affecting animals and humans worldwide. These pathogenic species have the ability to rapidly cross host tissue barriers by a yet unknown mechanism. A comparative analysis of pathogens and saprophytes revealed a higher abundance of genes encoding proteins with leucine-rich repeat (LRR) domains in the genomes of pathogens. In other bacterial pathogens, proteins with LRR domains have been shown to be involved in mediating host cell attachment and invasion. One protein from the pathogenic species Leptospira interrogans, LIC10831, has been previously analysed via X-ray crystallography, with findings suggesting it may be an important bacterial adhesin. Herein we show that LIC10831 elicits an antibody response in infected animals, is actively secreted by the bacterium, and binds human E- and VE-cadherins. These results provide biochemical and cellular evidences of LRR protein-mediated host-pathogen interactions and identify a new multireceptor binding protein from this infectious Leptospira species.
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Affiliation(s)
- Azad Eshghi
- Unité de Biologie des Spirochètes, Institut Pasteur, Paris, France.,University of Victoria - Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, Victoria, British Columbia, Canada
| | | | - Patrick England
- Plate-forme de Biophysique Moléculaire, Institut Pasteur, CNRS-UMR 3528, Paris, France
| | - Sébastien Brûlé
- Plate-forme de Biophysique Moléculaire, Institut Pasteur, CNRS-UMR 3528, Paris, France
| | - Isabelle Miras
- Plate-forme de Cristallographie, Institut Pasteur, CNRS-UMR 3528, Paris, France
| | - Hiromi Sato
- Center for Infectious Disease Research, Department of Medicine (Division of Infectious Diseases), Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Jenifer Coburn
- Center for Infectious Disease Research, Department of Medicine (Division of Infectious Diseases), Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Jacques Bellalou
- Plate-forme de Protéines Recombinantes, Institut Pasteur, CNRS-UMR 3528, Paris, France
| | - Tara J Moriarty
- Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada.,Faculty of Medicine (Department of Laboratory Medicine and Pathobiology), University of Toronto, Toronto, Ontario, Canada
| | - Ahmed Haouz
- Plate-forme de Cristallographie, Institut Pasteur, CNRS-UMR 3528, Paris, France
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13
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Yuan N, Rai KM, Balasubramanian VK, Upadhyay SK, Luo H, Mendu V. Genome-wide identification and characterization of LRR-RLKs reveal functional conservation of the SIF subfamily in cotton (Gossypium hirsutum). BMC PLANT BIOLOGY 2018; 18:185. [PMID: 30189845 PMCID: PMC6128003 DOI: 10.1186/s12870-018-1395-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/27/2018] [Indexed: 05/12/2023]
Abstract
BACKGROUND As one of the largest subfamilies of the receptor-like protein kinases (RLKs) in plants, Leucine Rich Repeats-RLKs (LRR-RLKs) are involved in many critical biological processes including growth, development and stress responses in addition to various physiological roles. Arabidopsis contains 234 LRR-RLKs, and four members of Stress Induced Factor (SIF) subfamily (AtSIF1-AtSIF4) which are involved in abiotic and biotic stress responses. Herein, we aimed at identification and functional characterization of SIF subfamily in cultivated tetraploid cotton Gossypium hirsutum. RESULTS Genome-wide analysis of cotton LRR-RLK gene family identified 543 members and phylogenetic analysis led to the identification of 6 cotton LRR-RLKs with high homology to Arabidopsis SIFs. Of the six SIF homologs, GhSIF1 is highly conserved exhibiting 46-47% of homology with AtSIF subfamily in amino acid sequence. The GhSIF1 was transiently silenced using Virus-Induced Gene Silencing system specifically targeting the 3' Untranslated Region. The transiently silenced cotton seedlings showed enhanced salt tolerance compared to the control plants. Further, the transiently silenced plants showed better growth, lower electrolyte leakage, and higher chlorophyll and biomass contents. CONCLUSIONS Overall, 543 LRR-RLK genes were identified using genome-wide analysis in cultivated tetraploid cotton G. hirsutum. The present investigation also demonstrated the conserved salt tolerance function of SIF family member in cotton. The GhSIF1 gene can be knocked out using genome editing technologies to improve salt tolerance in cotton.
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Affiliation(s)
- Ning Yuan
- Fiber and Biopolymer Research Institute (FBRI), Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409 USA
| | - Krishan Mohan Rai
- Fiber and Biopolymer Research Institute (FBRI), Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409 USA
| | - Vimal Kumar Balasubramanian
- Fiber and Biopolymer Research Institute (FBRI), Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409 USA
| | | | - Hong Luo
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634 USA
| | - Venugopal Mendu
- Fiber and Biopolymer Research Institute (FBRI), Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409 USA
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14
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Basavanhally T, Fonseca R, Uversky VN. Born This Way: Using Intrinsic Disorder to Map the Connections between SLITRKs, TSHR, and Male Sexual Orientation. Proteomics 2018; 18:e1800307. [PMID: 30156382 DOI: 10.1002/pmic.201800307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 08/03/2018] [Indexed: 12/15/2022]
Abstract
Recently, genome-wide association study reveals a significant association between specific single nucleotide polymorphisms (SNPs) in men and their sexual orientation. These SNPs (rs9547443 and rs1035144) reside in the intergenic region between the SLITRK5 and SLITRK6 genes and in the intronic region of the TSHR gene and might affect functionality of SLITRK5, SLITRK6, and TSHR proteins that are engaged in tight control of key developmental processes, such as neurite outgrowth and modulation, cellular differentiation, and hormonal regulation. SLITRK5 and SLITRK6 are single-pass transmembrane proteins, whereas TSHR is a heptahelical G protein-coupled receptor (GPCR). Mutations in these proteins are associated with various diseases and are linked to phenotypes found at a higher rate in homosexual men. A bioinformatics analysis of SLITRK5, SLITRK6, and TSHR proteins is conducted to look at their structure, protein interaction networks, and propensity for intrinsic disorder. It is assumed that this information might improve understanding of the roles that SLITRK5, SLITRK6, and TSHR play within neuronal and thyroidal tissues and give insight into the phenotypes associated with male homosexuality.
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Affiliation(s)
- Tara Basavanhally
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Renée Fonseca
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.,USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.,Protein Research Group, Institute for Biological Instrumentation of the Russian Academy of Sciences, 142290, Pushchino, Moscow, Russia
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15
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In Silico Prediction of Ligand-Binding Sites of Plant Receptor Kinases Using Conservation Mapping. Methods Mol Biol 2018; 1621:93-105. [PMID: 28567646 DOI: 10.1007/978-1-4939-7063-6_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Plasma membrane-bound plant receptor-like kinases (RLKs) can be categorized based on their ligand-binding extracellular domain. The largest group encompasses RLKs having ectodomains with leucine-rich repeats (LRRs). The LRR-RLKs can further be assigned to classes mainly based on the number of LRRs. Many of the receptors of the classes X and XI with more than 20 LRRs are activated by small secreted peptide ligands. To understand how peptide signaling works, it is of interest to identify the amino acids of the receptor that are directly involved in ligand interaction. Such residues have most likely been conserved over evolutionary time and can therefore be predicted to be conserved in receptor orthologues of different plant species. Here we present an in silico method to identify such residues. This involves a simplified method for identification of orthologues and a web-based program for identifying the most conserved amino acids aside from the leucines that structure the ectodomain. The method has been validated for the LRR-RLKs HAESA (HAE) and PHYTOSULFOKINE RECEPTOR1 (PSKR1) for which conservation-mapping results closely matched recent structure-based identification of ligand and co-receptor-interacting residues.
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16
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Hong JK, Hwang IS, Hwang BK. Functional roles of the pepper leucine-rich repeat protein and its interactions with pathogenesis-related and hypersensitive-induced proteins in plant cell death and immunity. PLANTA 2017; 246:351-364. [PMID: 28508261 DOI: 10.1007/s00425-017-2709-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 05/06/2017] [Indexed: 05/25/2023]
Abstract
Pepper leucine-rich repeat protein (CaLRR1) interacts with defense response proteins to regulate plant cell death and immunity. This review highlights the current understanding of the molecular functions of CaLRR1 and its interactor proteins. Plant cell death and immune responses to microbial pathogens are controlled by complex and tightly regulated molecular signaling networks. Xanthomonas campestris pv. vesicatoria (Xcv)-inducible pepper (Capsicum annuum) leucine-rich repeat protein 1 (CaLRR1) serves as a molecular marker for plant cell death and immunity signaling. In this review, we discuss recent advances in elucidating the functional roles of CaLRR1 and its interacting plant proteins, and understanding how they are involved in the cell death and defense responses. CaLRR1 physically interacts with pepper pathogenesis-related proteins (CaPR10 and CaPR4b) and hypersensitive-induced reaction protein (CaHIR1) to regulate plant cell death and defense responses. CaLRR1 is produced in the cytoplasm and trafficked to the extracellular matrix. CaLRR1 binds to CaPR10 in the cytoplasm and CaPR4b and CaHIR1 at the plasma membrane. CaLRR1 synergistically accelerates CaPR10-triggered hypersensitive cell death, but negatively regulates CaPR4b- and CaHIR1-triggered cell death. CaHIR1 interacts with Xcv filamentous hemagglutinin (Fha1) to trigger disease-associated cell death. The subcellular localization and cellular function of these CaLRR1 interactors during plant cell death and defense responses were elucidated by Agrobacterium-mediated transient expression, virus-induced gene silencing, and transgenic overexpression studies. CaPR10, CaPR4b, and CaHIR1 positively regulate defense signaling mediated by salicylic acid and reactive oxygen species, thereby activating hypersensitive cell death and disease resistance. A comprehensive understanding of the molecular functions of CaLRR1 and its interacting protein partners in cell death and defense responses will provide valuable information for the molecular genetics of plant disease resistance, which could be exploited as a sustainable disease management strategy.
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Affiliation(s)
- Jeum Kyu Hong
- Laboratory of Plant Pathology and Protection, Department of Horticultural Science, College of Biosciences, Gyeongnam National University of Science and Technology, Jinju, 52725, Republic of Korea
| | - In Sun Hwang
- Department of Horticultural Biotechnology, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Byung Kook Hwang
- Laboratory of Molecular Plant Pathology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea.
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17
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Rapid cloning of genes in hexaploid wheat using cultivar-specific long-range chromosome assembly. Nat Biotechnol 2017; 35:793-796. [PMID: 28504667 DOI: 10.1038/nbt.3877] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 04/11/2017] [Indexed: 11/08/2022]
Abstract
Cereal crops such as wheat and maize have large repeat-rich genomes that make cloning of individual genes challenging. Moreover, gene order and gene sequences often differ substantially between cultivars of the same crop species. A major bottleneck for gene cloning in cereals is the generation of high-quality sequence information from a cultivar of interest. In order to accelerate gene cloning from any cropping line, we report 'targeted chromosome-based cloning via long-range assembly' (TACCA). TACCA combines lossless genome-complexity reduction via chromosome flow sorting with Chicago long-range linkage to assemble complex genomes. We applied TACCA to produce a high-quality (N50 of 9.76 Mb) de novo chromosome assembly of the wheat line CH Campala Lr22a in only 4 months. Using this assembly we cloned the broad-spectrum Lr22a leaf-rust resistance gene, using molecular marker information and ethyl methanesulfonate (EMS) mutants, and found that Lr22a encodes an intracellular immune receptor homologous to the Arabidopsis thaliana RPM1 protein.
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18
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Helft L, Thompson M, Bent AF. Directed Evolution of FLS2 towards Novel Flagellin Peptide Recognition. PLoS One 2016; 11:e0157155. [PMID: 27270917 PMCID: PMC4894583 DOI: 10.1371/journal.pone.0157155] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 05/25/2016] [Indexed: 12/20/2022] Open
Abstract
Microbe-associated molecular patterns (MAMPs) are molecules, or domains within molecules, that are conserved across microbial taxa and can be recognized by a plant or animal immune system. Although MAMP receptors have evolved to recognize conserved epitopes, the MAMPs in some microbial species or strains have diverged sufficiently to render them unrecognizable by some host immune systems. In this study, we carried out in vitro evolution of the Arabidopsis thaliana flagellin receptor FLAGELLIN-SENSING 2 (FLS2) to isolate derivatives that recognize one or more flagellin peptides from bacteria for which the wild-type Arabidopsis FLS2 confers little or no response. A targeted approach generated amino acid variation at FLS2 residues in a region previously implicated in flagellin recognition. The primary screen tested for elevated response to the canonical flagellin peptide from Pseudomonas aeruginosa, flg22. From this pool, we then identified five alleles of FLS2 that confer modest (quantitatively partial) recognition of an Erwinia amylovora flagellin peptide. Use of this Erwinia-based flagellin peptide to stimulate Arabidopsis plants expressing the resulting FLS2 alleles did not lead to a detectable reduction of virulent P. syringae pv. tomato growth. However, combination of two identified mutations into a single allele further increased FLS2-mediated responses to the E. amylovora flagellin peptide. These studies demonstrate the potential to raise the sensitivity of MAMP receptors toward particular targets.
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Affiliation(s)
- Laura Helft
- Department of Plant Pathology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Cellular and Molecular Biology Program, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Mikayla Thompson
- Department of Plant Pathology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Andrew F. Bent
- Department of Plant Pathology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- * E-mail:
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19
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Ivaschuk BV, Samofalova DO, Pirko YV, Fedak G, Blume YB. The homologous identification of the stem rust resistance genes Rpg5, Adf3 and RGA1 in the relatives of barley. CYTOL GENET+ 2016. [DOI: 10.3103/s0095452716020055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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20
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Wang K, Remigi P, Anisimova M, Lonjon F, Kars I, Kajava A, Li CH, Cheng CP, Vailleau F, Genin S, Peeters N. Functional assignment to positively selected sites in the core type III effector RipG7 from Ralstonia solanacearum. MOLECULAR PLANT PATHOLOGY 2016; 17:553-64. [PMID: 26300048 PMCID: PMC6638336 DOI: 10.1111/mpp.12302] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The soil-borne pathogen Ralstonia solanacearum causes bacterial wilt in a broad range of plants. The main virulence determinants of R. solanacearum are the type III secretion system (T3SS) and its associated type III effectors (T3Es), translocated into the host cells. Of the conserved T3Es among R. solanacearum strains, the Fbox protein RipG7 is required for R. solanacearum pathogenesis on Medicago truncatula. In this work, we describe the natural ripG7 variability existing in the R. solanacearum species complex. We show that eight representative ripG7 orthologues have different contributions to pathogenicity on M. truncatula: only ripG7 from Asian or African strains can complement the absence of ripG7 in GMI1000 (Asian reference strain). Nonetheless, RipG7 proteins from American and Indonesian strains can still interact with M. truncatula SKP1-like/MSKa protein, essential for the function of RipG7 in virulence. This indicates that the absence of complementation is most likely a result of the variability in the leucine-rich repeat (LRR) domain of RipG7. We identified 11 sites under positive selection in the LRR domains of RipG7. By studying the functional impact of these 11 sites, we show the contribution of five positively selected sites for the function of RipG7CMR15 in M. truncatula colonization. This work reveals the genetic and functional variation of the essential core T3E RipG7 from R. solanacearum. This analysis is the first of its kind on an essential disease-controlling T3E, and sheds light on the co-evolutionary arms race between the bacterium and its hosts.
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Affiliation(s)
- Keke Wang
- INRA, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR441, CS52627 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR2594, CS52627 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France
| | - Philippe Remigi
- INRA, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR441, CS52627 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR2594, CS52627 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France
| | - Maria Anisimova
- Institute of Applied Simulations, School of Life Sciences and Facility Management, Zürich University of Applied Sciences, Gruenalstrasse 14, 8820, Wädesnwil, Switzerland
| | - Fabien Lonjon
- INRA, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR441, CS52627 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR2594, CS52627 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France
| | - Ilona Kars
- INRA, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR441, CS52627 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR2594, CS52627 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France
| | - Andrey Kajava
- Centre de Recherche de Biochimie Macromoléculaire, CNRS, UMR5237, 1919 Route de Mende, 34000, Montpellier, France
| | - Chien-Hui Li
- Institute of Plant Biology, National Taiwan University, Taipei, 11529, Taiwan, R.O.C
| | - Chiu-Ping Cheng
- Institute of Plant Biology, National Taiwan University, Taipei, 11529, Taiwan, R.O.C
| | - Fabienne Vailleau
- INRA, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR441, CS52627 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR2594, CS52627 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France
- Université de Toulouse, INP, ENSAT, 18 Chemin de Borde Rouge, Castanet-Tolosan, 31326, France
| | - Stéphane Genin
- INRA, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR441, CS52627 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR2594, CS52627 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France
| | - Nemo Peeters
- INRA, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR441, CS52627 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR2594, CS52627 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France
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21
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Liu PL, Xie LL, Li PW, Mao JF, Liu H, Gao SM, Shi PH, Gong JQ. Duplication and Divergence of Leucine-Rich Repeat Receptor-Like Protein Kinase ( LRR-RLK) Genes in Basal Angiosperm Amborella trichopoda. FRONTIERS IN PLANT SCIENCE 2016; 7:1952. [PMID: 28066499 PMCID: PMC5179525 DOI: 10.3389/fpls.2016.01952] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 12/08/2016] [Indexed: 05/22/2023]
Abstract
Leucine-rich repeat receptor-like protein kinases (LRR-RLKs) are the largest group of receptor-like kinases, which are one of the largest protein superfamilies in plants, and play crucial roles in development and stress responses. Although the evolution of LRR-RLK families has been investigated in some eudicot and monocot plants, no comprehensive evolutionary studies have been performed for these genes in basal angiosperms like Amborella trichopoda. In this study, we identified 94 LRR-RLK genes in the genome of A. trichopoda. The number of LRR-RLK genes in the genome of A. trichopoda is only 17-50% of that of several eudicot and monocot species. Tandem duplication and whole-genome duplication have made limited contributions to the expansion of LRR-RLK genes in A. trichopoda. According to the phylogenetic analysis, all A. trichopoda LRR-RLK genes can be organized into 18 subfamilies, which roughly correspond to the LRR-RLK subfamilies defined in Arabidopsis thaliana. Most LRR-RLK subfamilies are characterized by highly conserved protein structures, motif compositions, and gene structures. The unique gene structure, protein structures, and protein motif compositions of each subfamily provide evidence for functional divergence among LRR-RLK subfamilies. Moreover, the expression data of LRR-RLK genes provided further evidence for the functional diversification of them. In addition, selection analyses showed that most LRR-RLK protein sites are subject to purifying selection. Our results contribute to a better understanding of the evolution of LRR-RLK gene family in angiosperm and provide a framework for further functional investigation on A. trichopoda LRR-RLKs.
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Affiliation(s)
- Ping-Li Liu
- College of Biological Sciences and Biotechnology, Beijing Forestry UniversityBeijing, China
- *Correspondence: Ping-Li Liu
| | - Lu-Lu Xie
- Department of Chinese Cabbage, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Peng-Wei Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Jian-Feng Mao
- College of Biological Sciences and Biotechnology, Beijing Forestry UniversityBeijing, China
| | - Hui Liu
- College of Biological Sciences and Biotechnology, Beijing Forestry UniversityBeijing, China
| | - Shu-Min Gao
- College of Biological Sciences and Biotechnology, Beijing Forestry UniversityBeijing, China
| | - Peng-Hao Shi
- College of Biological Sciences and Biotechnology, Beijing Forestry UniversityBeijing, China
| | - Jun-Qing Gong
- College of Biological Sciences and Biotechnology, Beijing Forestry UniversityBeijing, China
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22
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Martin T, Rönnberg-Wästljung AC, Stenlid J, Samils B. Identification of a Differentially Expressed TIR-NBS-LRR Gene in a Major QTL Associated to Leaf Rust Resistance in Salix. PLoS One 2016; 11:e0168776. [PMID: 28002449 PMCID: PMC5176316 DOI: 10.1371/journal.pone.0168776] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 12/06/2016] [Indexed: 11/25/2022] Open
Abstract
An earlier identified major quantitative trait locus for resistance towards the willow leaf rust fungus Melampsora larici-epitea in a Salix viminalis x (S. viminalis × S. schwerinii) population was used to identify potential resistance genes to the rust pathogen. Screening a genomic bacterial artificial chromosome library with markers from the peak position of the QTL region revealed one gene with TIR-NBS-LRR (Toll Interleukin1 Receptor-Nucleotide Binding Site-Leucine-Rich Repeat) domain structure indicative of a resistance gene. The resistance gene analog was denoted RGA1 and further analysis revealed a number of non-synonymous single nucleotide polymorphisms in the LRR domain between the resistant and susceptible Salix genotypes. Gene expression levels under controlled conditions showed a significantly lower constitutive expression of RGA1 in the susceptible genotype. In addition, the susceptible genotype showed a significantly reduced expression level of the RGA1 gene at 24 hours post inoculation with M. larici-epitea. This indicates that the pathogen may actively suppress RGA1 gene expression allowing a compatible plant-pathogen interaction and causing infection.
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Affiliation(s)
- Tom Martin
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Jan Stenlid
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Berit Samils
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
- * E-mail:
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23
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Brody MJ, Feng L, Grimes AC, Hacker TA, Olson TM, Kamp TJ, Balijepalli RC, Lee Y. LRRC10 is required to maintain cardiac function in response to pressure overload. Am J Physiol Heart Circ Physiol 2015; 310:H269-78. [PMID: 26608339 DOI: 10.1152/ajpheart.00717.2014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 11/18/2015] [Indexed: 01/08/2023]
Abstract
We previously reported that the cardiomyocyte-specific leucine-rich repeat containing protein (LRRC)10 has critical functions in the mammalian heart. In the present study, we tested the role of LRRC10 in the response of the heart to biomechanical stress by performing transverse aortic constriction on Lrrc10-null (Lrrc10(-/-)) mice. Mild pressure overload induced severe cardiac dysfunction and ventricular dilation in Lrrc10(-/-) mice compared with control mice. In addition to dilation and cardiomyopathy, Lrrc10(-/-) mice showed a pronounced increase in heart weight with pressure overload stimulation and a more dramatic loss of cardiac ventricular performance, collectively suggesting that the absence of LRRC10 renders the heart more disease prone with greater hypertrophy and structural remodeling, although rates of cardiac fibrosis and myocyte dropout were not different from control mice. Lrrc10(-/-) cardiomyocytes also exhibited reduced contractility in response to β-adrenergic stimulation, consistent with loss of cardiac ventricular performance after pressure overload. We have previously shown that LRRC10 interacts with actin in the heart. Here, we show that His(150) of LRRC10 was required for an interaction with actin, and this interaction was reduced after pressure overload, suggesting an integral role for LRRC10 in the response of the heart to mechanical stress. Importantly, these experiments demonstrated that LRRC10 is required to maintain cardiac performance in response to pressure overload and suggest that dysregulated expression or mutation of LRRC10 may greatly sensitize human patients to more severe cardiac disease in conditions such as chronic hypertension or aortic stenosis.
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Affiliation(s)
- Matthew J Brody
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin; Molecular and Environmental Toxicology Center, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin
| | - Li Feng
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin; and
| | - Adrian C Grimes
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin; and
| | - Timothy A Hacker
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin; and
| | - Timothy M Olson
- Cardiovascular Genetics Research Laboratory and Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota
| | - Timothy J Kamp
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin; Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin; and
| | - Ravi C Balijepalli
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin; and
| | - Youngsook Lee
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin; Molecular and Environmental Toxicology Center, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin;
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Stø IM, Orr RJS, Fooyontphanich K, Jin X, Knutsen JMB, Fischer U, Tranbarger TJ, Nordal I, Aalen RB. Conservation of the abscission signaling peptide IDA during Angiosperm evolution: withstanding genome duplications and gain and loss of the receptors HAE/HSL2. FRONTIERS IN PLANT SCIENCE 2015; 6:931. [PMID: 26579174 PMCID: PMC4627355 DOI: 10.3389/fpls.2015.00931] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 10/15/2015] [Indexed: 11/13/2022]
Abstract
The peptide INFLORESCENCE DEFICIENT IN ABSCISSION (IDA), which signals through the leucine-rich repeat receptor-like kinases HAESA (HAE) and HAESA-LIKE2 (HSL2), controls different cell separation events in Arabidopsis thaliana. We hypothesize the involvement of this signaling module in abscission processes in other plant species even though they may shed other organs than A. thaliana. As the first step toward testing this hypothesis from an evolutionarily perspective we have identified genes encoding putative orthologs of IDA and its receptors by BLAST searches of publically available protein, nucleotide and genome databases for angiosperms. Genes encoding IDA or IDA-LIKE (IDL) peptides and HSL proteins were found in all investigated species, which were selected as to represent each angiosperm order with available genomic sequences. The 12 amino acids representing the bioactive peptide in A. thaliana have virtually been unchanged throughout the evolution of the angiosperms; however, the number of IDL and HSL genes varies between different orders and species. The phylogenetic analyses suggest that IDA, HSL2, and the related HSL1 gene, were present in the species that gave rise to the angiosperms. HAE has arisen from HSL1 after a genome duplication that took place after the monocot-eudicots split. HSL1 has also independently been duplicated in the monocots, while HSL2 has been lost in gingers (Zingiberales) and grasses (Poales). IDA has been duplicated in eudicots to give rise to functionally divergent IDL peptides. We postulate that the high number of IDL homologs present in the core eudicots is a result of multiple whole genome duplications (WGD). We substantiate the involvement of IDA and HAE/HSL2 homologs in abscission by providing gene expression data of different organ separation events from various species.
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Affiliation(s)
- Ida M Stø
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo Oslo, Norway
| | - Russell J S Orr
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo Oslo, Norway
| | - Kim Fooyontphanich
- UMR Diversité et Adaptation et Développement des Plantes, Institut de Recherche pour le Développement Montpellier, France
| | - Xu Jin
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences Umeå, Sweden
| | - Jonfinn M B Knutsen
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo Oslo, Norway
| | - Urs Fischer
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences Umeå, Sweden
| | - Timothy J Tranbarger
- UMR Diversité et Adaptation et Développement des Plantes, Institut de Recherche pour le Développement Montpellier, France
| | - Inger Nordal
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo Oslo, Norway
| | - Reidunn B Aalen
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo Oslo, Norway
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Miras I, Saul F, Nowakowski M, Weber P, Haouz A, Shepard W, Picardeau M. Structural characterization of a novel subfamily of leucine-rich repeat proteins from the human pathogen Leptospira interrogans. ACTA ACUST UNITED AC 2015; 71:1351-9. [PMID: 26057675 DOI: 10.1107/s139900471500704x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 04/08/2015] [Indexed: 12/26/2022]
Abstract
Pathogenic Leptospira spp. are the agents of leptospirosis, an emerging zoonotic disease. Analyses of Leptospira genomes have shown that the pathogenic leptospires (but not the saprophytes) possess a large number of genes encoding proteins containing leucine-rich repeat (LRR) domains. In other pathogenic bacteria, proteins with LRR domains have been shown to be involved in mediating host-cell attachment and invasion, but their functions remain unknown in Leptospira. To gain insight into the potential function of leptospiral LRR proteins, the crystal structures of four LRR proteins that represent a novel subfamily with consecutive stretches of a 23-amino-acid LRR repeat motif have been solved. The four proteins analyzed adopt the characteristic α/β-solenoid horseshoe fold. The exposed residues of the inner concave surfaces of the solenoid, which constitute a putative functional binding site, are not conserved. The various leptospiral LRR proteins could therefore recognize distinct structural motifs of different host proteins and thus serve separate and complementary functions in the physiology of these bacteria.
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Affiliation(s)
- Isabelle Miras
- Institut Pasteur, Plate-forme de Cristallographie, CNRS-UMR 3528, Paris, France
| | - Frederick Saul
- Institut Pasteur, Plate-forme de Cristallographie, CNRS-UMR 3528, Paris, France
| | - Mireille Nowakowski
- Institut Pasteur, Plate-forme Protéines Recombinantes, CNRS-UMR 3528, Paris, France
| | - Patrick Weber
- Institut Pasteur, Plate-forme de Cristallographie, CNRS-UMR 3528, Paris, France
| | - Ahmed Haouz
- Institut Pasteur, Plate-forme de Cristallographie, CNRS-UMR 3528, Paris, France
| | - William Shepard
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin, BP48, Gif-sur-Yvette, France
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Kalunke RM, Tundo S, Benedetti M, Cervone F, De Lorenzo G, D'Ovidio R. An update on polygalacturonase-inhibiting protein (PGIP), a leucine-rich repeat protein that protects crop plants against pathogens. FRONTIERS IN PLANT SCIENCE 2015; 6:146. [PMID: 25852708 PMCID: PMC4367531 DOI: 10.3389/fpls.2015.00146] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 02/23/2015] [Indexed: 05/20/2023]
Abstract
Polygalacturonase inhibiting proteins (PGIPs) are cell wall proteins that inhibit the pectin-depolymerizing activity of polygalacturonases secreted by microbial pathogens and insects. These ubiquitous inhibitors have a leucine-rich repeat structure that is strongly conserved in monocot and dicot plants. Previous reviews have summarized the importance of PGIP in plant defense and the structural basis of PG-PGIP interaction; here we update the current knowledge about PGIPs with the recent findings on the composition and evolution of pgip gene families, with a special emphasis on legume and cereal crops. We also update the information about the inhibition properties of single pgip gene products against microbial PGs and the results, including field tests, showing the capacity of PGIP to protect crop plants against fungal, oomycetes and bacterial pathogens.
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Affiliation(s)
- Raviraj M. Kalunke
- Dipartimento di Scienze e Tecnologie per l'Agricoltura, le Foreste, la Natura e l'Energia, Università della TusciaViterbo, Italy
| | - Silvio Tundo
- Dipartimento di Scienze e Tecnologie per l'Agricoltura, le Foreste, la Natura e l'Energia, Università della TusciaViterbo, Italy
| | - Manuel Benedetti
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di RomaRoma, Italy
| | - Felice Cervone
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di RomaRoma, Italy
| | - Giulia De Lorenzo
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di RomaRoma, Italy
- Giulia De Lorenzo, Dipartimento di Biologia e Biotecnologie “Charles Darwin,” Sapienza Università di Roma, Roma, Italy
| | - Renato D'Ovidio
- Dipartimento di Scienze e Tecnologie per l'Agricoltura, le Foreste, la Natura e l'Energia, Università della TusciaViterbo, Italy
- *Correspondence: Renato D'Ovidio, Dipartimento di Scienze e Tecnologie per l'Agricoltura, le Foreste, la Natura e l'Energia, Università Degli Studi Della Tuscia, 01100 Viterbo, Italy
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Koller T, Bent AF. FLS2-BAK1 extracellular domain interaction sites required for defense signaling activation. PLoS One 2014; 9:e111185. [PMID: 25356676 PMCID: PMC4214723 DOI: 10.1371/journal.pone.0111185] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Accepted: 09/27/2014] [Indexed: 11/19/2022] Open
Abstract
Signaling initiation by receptor-like kinases (RLKs) at the plasma membrane of plant cells often requires regulatory leucine-rich repeat (LRR) RLK proteins such as SERK or BIR proteins. The present work examined how the microbe-associated molecular pattern (MAMP) receptor FLS2 builds signaling complexes with BAK1 (SERK3). We first, using in vivo methods that validate separate findings by others, demonstrated that flg22 (flagellin epitope) ligand-initiated FLS2-BAK1 extracellular domain interactions can proceed independent of intracellular domain interactions. We then explored a candidate SERK protein interaction site in the extracellular domains (ectodomains; ECDs) of the significantly different receptors FLS2, EFR (MAMP receptors), PEPR1 (damage-associated molecular pattern (DAMP) receptor), and BRI1 (hormone receptor). Repeat conservation mapping revealed a cluster of conserved solvent-exposed residues near the C-terminus of models of the folded LRR domains. However, site-directed mutagenesis of this conserved site in FLS2 did not impair FLS2-BAK1 ECD interactions, and mutations in the analogous site of EFR caused receptor maturation defects. Hence this conserved LRR C-terminal region apparently has functions other than mediating interactions with BAK1. In vivo tests of the subsequently published FLS2-flg22-BAK1 ECD co-crystal structure were then performed to functionally evaluate some of the unexpected configurations predicted by that crystal structure. In support of the crystal structure data, FLS2-BAK1 ECD interactions were no longer detected in in vivo co-immunoprecipitation experiments after site-directed mutagenesis of the FLS2 BAK1-interaction residues S554, Q530, Q627 or N674. In contrast, in vivo FLS2-mediated signaling persisted and was only minimally reduced, suggesting residual FLS2-BAK1 interaction and the limited sensitivity of co-immunoprecipitation data relative to in vivo assays for signaling outputs. However, Arabidopsis plants expressing FLS2 with the Q530A+Q627A double mutation were impaired both in detectable interaction with BAK1 and in FLS2-mediated responses, lending overall support to current models of FLS2 structure and function.
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Affiliation(s)
- Teresa Koller
- Department of Plant Pathology, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
| | - Andrew F Bent
- Department of Plant Pathology, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
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Tsai YC, Teng YN, Hung JH, Wu CH, Kuo YT, Kuo PL, Chiu CC, Huang B. Correlation between leucine rich domain and the stability of LRWD1 protein in human NT2/D1 cells. Adv Med Sci 2014; 59:266-72. [PMID: 25170821 DOI: 10.1016/j.advms.2014.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 06/13/2014] [Accepted: 07/23/2014] [Indexed: 10/24/2022]
Abstract
PURPOSE LRWD1 is a protein that contains LRR and WDs domains and is important in regulating spermatogenesis. However, the roles of LRR or WDs domains in the expression of LRWD1 remain unclear. MATERIALS AND METHODS The NT2/D1 cells separately transfected with full length of LRWD1 gene (LRWD(WT)) or genes with deleted sequences in the LRR domain (LRWD1(ΔLRR)), WD1 domain (LRWD1(ΔWD1)), WD2 domain (LRWD1(ΔWD2)), WD3 domain (LRWD1(ΔWD3)) and entire three WD domains (LRWD1(Δ3×WD)) were applied to investigate the expression levels of LRWD1 protein by either Western blot or flow cytometry. The associated proteins in these mutated LRWD1 proteins were identified by mass spectrometry. RESULTS Deletion of the LRR domain significantly decreased the expression of LRWD1 protein. With the treatment of MG132, the LRR domain may functions in preventing LRWD1 protein from proteasome-mediated degradation. In the co-immunoprecipitation analysis, protein receptor of tumor necrosis factor 2 (TNFR2) was specifically observed to be associated with LRR-deficient LRWD1 protein. CONCLUSIONS The LRR domain is significantly correlated to the stability of LRWD1 protein. Determining if the stability is modulated by TNFR2 is worthy of further study.
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Aalen RB. Maturing peptides open for communication. JOURNAL OF EXPERIMENTAL BOTANY 2014; 64:5231-5. [PMID: 24259454 DOI: 10.1093/jxb/ert378] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Abstract
Despite being sessile organisms constantly exposed to potential pathogens and pests, plants are surprisingly resilient to infections. Plants can detect invaders via the recognition of pathogen-associated molecular patterns (PAMPs) by pattern recognition receptors (PRRs). Plant PRRs are surface-localized receptor-like kinases, which comprise a ligand-binding ectodomain and an intracellular kinase domain, or receptor-like proteins, which do not exhibit any known intracellular signaling domain. In this review, we summarize recent discoveries that shed light on the molecular mechanisms underlying ligand perception and subsequent activation of plant PRRs. Notably, plant PRRs appear as central components of multiprotein complexes at the plasma membrane that contain additional transmembrane and cytosolic kinases required for the initiation and specificity of immune signaling. PRR complexes are under tight control by protein phosphatases, E3 ligases, and other regulatory proteins, illustrating the exquisite and complex regulation of these molecular machines whose proper activation underlines a crucial layer of plant immunity.
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Affiliation(s)
- Alberto P Macho
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, UK
| | - Cyril Zipfel
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, UK.
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Morrill GA, Kostellow AB, Gupta RK. A computational analysis of non-genomic plasma membrane progestin binding proteins: signaling through ion channel-linked cell surface receptors. Steroids 2013; 78:1233-44. [PMID: 24012561 DOI: 10.1016/j.steroids.2013.08.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 08/13/2013] [Accepted: 08/20/2013] [Indexed: 12/18/2022]
Abstract
A number of plasma membrane progestin receptors linked to non-genomic events have been identified. These include: (1) α1-subunit of the Na(+)/K(+)-ATPase (ATP1A1), (2) progestin binding PAQR proteins, (3) membrane progestin receptor alpha (mPRα), (4) progesterone receptor MAPR proteins and (5) the association of nuclear receptor (PRB) with the plasma membrane. This study compares: the pore-lining regions (ion channels), transmembrane (TM) helices, caveolin binding (CB) motifs and leucine-rich repeats (LRRs) of putative progesterone receptors. ATP1A1 contains 10 TM helices (TM-2, 4, 5, 6 and 8 are pores) and 4 CB motifs; whereas PAQR5, PAQR6, PAQR7, PAQRB8 and fish mPRα each contain 8 TM helices (TM-3 is a pore) and 2-4 CB motifs. MAPR proteins contain a single TM helix but lack pore-lining regions and CB motifs. PRB contains one or more TM helices in the steroid binding region, one of which is a pore. ATP1A1, PAQR5/7/8, mPRα, and MAPR-1 contain highly conserved leucine-rich repeats (LRR, common to plant membrane proteins) that are ligand binding sites for ouabain-like steroids associated with LRR kinases. LRR domains are within or overlap TM helices predicted to be ion channels (pore-lining regions), with the variable LRR sequence either at the C-terminus (PAQR and MAPR-1) or within an external loop (ATP1A1). Since ouabain-like steroids are produced by animal cells, our findings suggest that ATP1A1, PAQR5/7/8 and mPRα represent ion channel-linked receptors that respond physiologically to ouabain-like steroids (not progestin) similar to those known to regulate developmental and defense-related processes in plants.
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Affiliation(s)
- Gene A Morrill
- Department of Physiology & Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA.
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A molecular model of the full-length human NOD-like receptor family CARD domain containing 5 (NLRC5) protein. BMC Bioinformatics 2013; 14:275. [PMID: 24044430 PMCID: PMC3848420 DOI: 10.1186/1471-2105-14-275] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 08/30/2013] [Indexed: 11/25/2022] Open
Abstract
Background Pattern recognition receptors of the immune system have key roles in the regulation of pathways after the recognition of microbial- and danger-associated molecular patterns in vertebrates. Members of NOD-like receptor (NLR) family typically function intracellularly. The NOD-like receptor family CARD domain containing 5 (NLRC5) is the largest member of this family that also contains the largest number of leucine-rich repeats (LRRs). Due to the lack of crystal structures of full-length NLRs, projects have been initiated with the aim to model certain or all members of the family, but systematic studies did not model the full-length NLRC5 due to its unique domain architecture. Our aim was to analyze the LRR sequences of NLRC5 and some NLRC5-related proteins and to build a model for the full-length human NLRC5 by homology modeling. Results LRR sequences of NLRC5 were aligned and were compared with the consensus pattern of ribonuclease inhibitor protein (RI)-like LRR subfamily. Two types of alternating consensus patterns previously identified for RI repeats were also found in NLRC5. A homology model for full-length human NLRC5 was prepared and, besides the closed conformation of monomeric NLRC5, a heptameric platform was also modeled for the opened conformational NLRC5 monomers. Conclusions Identification of consensus patterns of leucine-rich repeat sequences helped to identify LRRs in NLRC5 and to predict their number and position within the protein. In spite of the lack of fully adequate template structures, the presence of an untypical CARD domain and unusually high number of LRRs in NLRC5, we were able to construct a homology model for both the monomeric and homo-heptameric full-length human NLRC5 protein.
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Identification of Functional Regulatory Residues of the β -Lactam Inducible Penicillin Binding Protein in Methicillin-Resistant Staphylococcus aureus. CHEMOTHERAPY RESEARCH AND PRACTICE 2013; 2013:614670. [PMID: 23984067 PMCID: PMC3745919 DOI: 10.1155/2013/614670] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Revised: 06/19/2013] [Accepted: 07/03/2013] [Indexed: 11/30/2022]
Abstract
Resistance to methicillin by Staphylococcus aureus is a persistent clinical problem worldwide. A mechanism for resistance has been proposed in which methicillin resistant Staphylococcus aureus (MRSA) isolates acquired a new protein called β-lactam inducible penicillin binding protein (PBP-2′). The PBP-2′ functions by substituting other penicillin binding proteins which have been inhibited by β-lactam antibiotics. Presently, there is no structural and regulatory information on PBP-2′ protein. We conducted a complete structural and functional regulatory analysis of PBP-2′ protein. Our analysis revealed that the PBP-2′ is very stable with more hydrophilic amino acids expressing antigenic sites. PBP-2′ has three striking regulatory points constituted by first penicillin binding site at Ser25, second penicillin binding site at Ser405, and finally a single metallic ligand binding site at Glu657 which binds to Zn2+ ions. This report highlights structural features of PBP-2′ that can serve as targets for developing new chemotherapeutic agents and conducting site direct mutagenesis experiments.
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Robatzek S, Wirthmueller L. Mapping FLS2 function to structure: LRRs, kinase and its working bits. PROTOPLASMA 2013; 250:671-81. [PMID: 23053766 DOI: 10.1007/s00709-012-0459-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 09/21/2012] [Indexed: 05/26/2023]
Abstract
The plasma membrane-localised FLAGELLIN SENSING 2 (FLS2) receptor is an important component of plant immunity against potentially pathogenic bacteria, acting to recognise the conserved flg22 peptide of flagellin. FLS2 shares the common structure of transmembrane receptor kinases with a receptor-like ectodomain composed of leucine-rich repeats (LRR) and an active intracellular kinase domain. Upon ligand binding, FLS2 dimerises with the regulatory LRR-receptor kinase BRI1-associated kinase 1, which in turn triggers downstream signalling cascades. Although lacking crystal structure data, recent advances have been made in our understanding of flg22 recognition based on structural and functional analyses of FLS2. These studies have revealed critical regions/residues of FLS2 and post-translational modifications that regulate the abundance and activity of this receptor. In this review, we present the current knowledge on the structural mechanism of the FLS2-flg22 interaction and subsequent receptor-mediated signalling.
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Affiliation(s)
- Silke Robatzek
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK.
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35
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Identification and characterization of a unique leucine-rich repeat protein (LRRC33) that inhibits Toll-like receptor-mediated NF-κB activation. Biochem Biophys Res Commun 2013; 434:28-34. [PMID: 23545260 DOI: 10.1016/j.bbrc.2013.03.071] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 03/18/2013] [Indexed: 12/30/2022]
Abstract
Toll-like receptors (TLRs) are important initiators in innate immune responses against pathogenic microbes such as viruses, intracellular bacteria or parasites. Although the innate immune system is designed to fight infectious pathogens, excessive activation of TLR signaling may lead to unwarranted inflammation with hazardous outcomes. Mechanisms of restraining excessive inflammation and controlling homeostasis for innate immunity are the focus of intense study. Here we showed that LRRC33, a novel member of leucine-rich repeat (LRR) protein family, plays a critical role in desensitizing TLR signaling. LRRC33 is TLR homolog that contains 17 putative LRRs in the extracellular region but lacks a cytoplasmic Toll/IL-1 receptor (TIR) domain. Expression of LRRC33 appears to be ubiquitous with high level of expression found in bone marrow, thymus, liver, lung, intestine and spleen. The LRRs of LRRC33 is required for the interaction with TLR and its inhibitory effect on NF-κB and AP-1 activation as well as cytokine production. Our study sheds new insight into the TLR signaling and inflammatory response in development and human diseases.
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Does Computational Biology Help us to Understand the Molecular Phylogenetics and Evolution of Cluster of Differentiation (CD) Proteins? Protein J 2013; 32:143-54. [DOI: 10.1007/s10930-013-9466-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Abstract
The last decades have seen numerous approaches being used to decipher biological phenomena, notably the strategies we employ to defend ourselves against pathogenic attacks. From microarrays to genetics to computing technologies, all have supported a better but not yet comprehensive understanding of the pathways regulating our immune system. Limitations are notably exemplified by cases of immune deficiencies in humans that often result in high susceptibility to infections or even death, without the genetic cause being evident. To provide further insight into the mechanisms by which pathogen detection and eradication occur, several in vivo strategies can be used. The current review focuses on one of them, namely germline mutagenesis in the mouse. After describing the main technical aspects of this forward genetic approach, we will discuss particular germline mutants that have all been instrumental in deciphering innate or adaptive immune responses. Mutations in previously uncharacterized genes in the mouse, like Unc93B or Themis, have demonstrated the impartiality of forward genetics and led to the identification of new crucial immunity actors. Some mutants, like PanR1, have informed us on particular protein domains and their specific functions. Finally, certain mutations identified by this non-hypothesis-driven method have revealed previously unknown gene functions, as recently illustrated by memi, which links a particular nucleoside salvage enzyme to cell proliferation and apoptosis.
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Affiliation(s)
- Onjee Choi
- National Heart and Lung Institute, Imperial College London, London, UK
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Takken FLW, Goverse A. How to build a pathogen detector: structural basis of NB-LRR function. CURRENT OPINION IN PLANT BIOLOGY 2012; 15:375-84. [PMID: 22658703 DOI: 10.1016/j.pbi.2012.05.001] [Citation(s) in RCA: 169] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 04/27/2012] [Accepted: 05/02/2012] [Indexed: 05/20/2023]
Abstract
Many plant disease resistance (R) proteins belong to the family of nucleotide-binding-leucine rich repeat (NB-LRR) proteins. NB-LRRs mediate recognition of pathogen-derived effector molecules and subsequently activate host defence. Their multi-domain structure allows these pathogen detectors to simultaneously act as sensor, switch and response factor. Structure-function analyses and the recent elucidation of the 3D structures of subdomains have provided new insight in how these different functions are combined and what the contribution is of the individual subdomains. Besides interdomain contacts, interactions with chaperones, the proteasome and effector baits are required to keep NB-LRRs in a signalling-competent, yet auto-inhibited state. In this review we explore operational models of NB-LRR functioning based on recent advances in understanding their structure.
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Affiliation(s)
- Frank L W Takken
- University of Amsterdam, SILS, Molecular Plant Pathology, Science Park 904, 1098 XH Amsterdam, The Netherlands.
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Schwessinger B, Ronald PC. Plant innate immunity: perception of conserved microbial signatures. ANNUAL REVIEW OF PLANT BIOLOGY 2012; 63:451-82. [PMID: 22404464 DOI: 10.1146/annurev-arplant-042811-105518] [Citation(s) in RCA: 218] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Plants and animals sense conserved microbial signatures through receptors localized to the plasma membrane and cytoplasm. These receptors typically carry or associate with non-arginine-aspartate (non-RD) kinases that initiate complex signaling networks cumulating in robust defense responses. In plants, coregulatory receptor kinases have been identified that not only are critical for the innate immune response but also serve an essential function in other regulatory signaling pathways.
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