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Sánchez-Vallet A, Saleem-Batcha R, Kombrink A, Hansen G, Valkenburg DJ, Thomma BPHJ, Mesters JR. Fungal effector Ecp6 outcompetes host immune receptor for chitin binding through intrachain LysM dimerization. eLife 2013; 2:e00790. [PMID: 23840930 DOI: 10.7554/elife.00790.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Accepted: 05/30/2013] [Indexed: 05/23/2023] Open
Abstract
While host immune receptors detect pathogen-associated molecular patterns to activate immunity, pathogens attempt to deregulate host immunity through secreted effectors. Fungi employ LysM effectors to prevent recognition of cell wall-derived chitin by host immune receptors, although the mechanism to compete for chitin binding remained unclear. Structural analysis of the LysM effector Ecp6 of the fungal tomato pathogen Cladosporium fulvum reveals a novel mechanism for chitin binding, mediated by intrachain LysM dimerization, leading to a chitin-binding groove that is deeply buried in the effector protein. This composite binding site involves two of the three LysMs of Ecp6 and mediates chitin binding with ultra-high (pM) affinity. Intriguingly, the remaining singular LysM domain of Ecp6 binds chitin with low micromolar affinity but can nevertheless still perturb chitin-triggered immunity. Conceivably, the perturbation by this LysM domain is not established through chitin sequestration but possibly through interference with the host immune receptor complex. DOI:http://dx.doi.org/10.7554/eLife.00790.001.
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Affiliation(s)
- Andrea Sánchez-Vallet
- Centro de Biotecnología y Genómica de Plantas , Universidad Politécnica de Madrid , Madrid , Spain ; Laboratory of Phytopathology , Wageningen University , Wageningen , Netherlands
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52
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Li WJ, Li DF, Hu YL, Zhang XE, Bi LJ, Wang DC. Crystal structure of L,D-transpeptidase LdtMt2 in complex with meropenem reveals the mechanism of carbapenem against Mycobacterium tuberculosis. Cell Res 2013; 23:728-31. [PMID: 23588382 DOI: 10.1038/cr.2013.53] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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53
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Lecoq L, Dubée V, Triboulet S, Bougault C, Hugonnet JE, Arthur M, Simorre JP. Structure of Enterococcus faeciuml,d-transpeptidase acylated by ertapenem provides insight into the inactivation mechanism. ACS Chem Biol 2013; 8:1140-6. [PMID: 23574509 DOI: 10.1021/cb4001603] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The maintenance of bacterial cell shape and integrity is largely attributed to peptidoglycan, a biopolymer highly cross-linked through d,d-transpeptidation. Peptidoglycan cross-linking is catalyzed by penicillin-binding proteins (PBPs) that are the essential target of β-lactam antibiotics. PBPs are functionally replaced by l,d-transpeptidases (Ldts) in ampicillin-resistant mutants of Enterococcus faecium and in wild-type Mycobacterium tuberculosis. Ldts are inhibited in vivo by a single class of β-lactams, the carbapenems, which act as a suicide substrate. We present here the first structure of a carbapenem-acylated l,d-transpeptidase, E. faecium Ldtfm acylated by ertapenem, which revealed key contacts between the carbapenem core and residues of the catalytic cavity of the enzyme. Significant reorganization of the antibiotic conformation occurs upon enzyme acylation. These results, together with the analysis of protein-to-carbapenem proton transfers, provide new insights into the mechanism of Ldt acylation by carbapenems.
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Affiliation(s)
- Lauriane Lecoq
- CEA, Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075, Grenoble,
France
- CNRS, Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075,
Grenoble, France
- Université
Joseph Fourier−Grenoble
1, Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075, Grenoble, France
| | - Vincent Dubée
- Centre de Recherche des Cordeliers,
LRMA, Equipe 12, Université Pierre et Marie Curie−Paris 6, UMR S 872, Paris, France
- INSERM, U872, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, UMR S 872, Paris,
France
| | - Sébastien Triboulet
- Centre de Recherche des Cordeliers,
LRMA, Equipe 12, Université Pierre et Marie Curie−Paris 6, UMR S 872, Paris, France
- INSERM, U872, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, UMR S 872, Paris,
France
| | - Catherine Bougault
- CEA, Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075, Grenoble,
France
- CNRS, Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075,
Grenoble, France
- Université
Joseph Fourier−Grenoble
1, Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075, Grenoble, France
| | - Jean-Emmanuel Hugonnet
- Centre de Recherche des Cordeliers,
LRMA, Equipe 12, Université Pierre et Marie Curie−Paris 6, UMR S 872, Paris, France
- INSERM, U872, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, UMR S 872, Paris,
France
| | - Michel Arthur
- Centre de Recherche des Cordeliers,
LRMA, Equipe 12, Université Pierre et Marie Curie−Paris 6, UMR S 872, Paris, France
- INSERM, U872, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, UMR S 872, Paris,
France
| | - Jean-Pierre Simorre
- CEA, Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075, Grenoble,
France
- CNRS, Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075,
Grenoble, France
- Université
Joseph Fourier−Grenoble
1, Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075, Grenoble, France
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54
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Yoon JY, Kim J, An DR, Lee SJ, Kim HS, Im HN, Yoon HJ, Kim JY, Kim SJ, Han BW, Suh SW. Structural and functional characterization of HP0377, a thioredoxin-fold protein from Helicobacter pylori. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:735-46. [PMID: 23633582 DOI: 10.1107/s0907444913001236] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 01/12/2013] [Indexed: 12/16/2022]
Abstract
Maturation of cytochrome c is carried out in the bacterial periplasm, where specialized thiol-disulfide oxidoreductases provide the correct reduction of oxidized apocytochrome c before covalent haem attachment. HP0377 from Helicobacter pylori is a thioredoxin-fold protein that has been implicated as a component of system II for cytochrome c assembly and shows limited sequence similarity to Escherichia coli DsbC, a disulfide-bond isomerase. To better understand the role of HP0377, its crystal structures have been determined in both reduced and partially oxidized states, which are highly similar to each other. Sedimentation-equilibrium experiments indicate that HP0377 is monomeric in solution. HP0377 adopts a thioredoxin fold but shows distinctive variations as in other thioredoxin-like bacterial periplasmic proteins. The active site of HP0377 closely resembles that of E. coli DsbC. A reductase assay suggests that HP0377 may play a role as a reductase in the biogenesis of holocytochrome c553 (HP1227). Binding experiments indicate that it can form a covalent complex with HP0518, a putative L,D-transpeptidase with a catalytic cysteine residue, via a disulfide bond. Furthermore, physicochemical properties of HP0377 and its R86A variant have been determined. These results suggest that HP0377 may perform multiple functions as a reductase in H. pylori.
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Affiliation(s)
- Ji Young Yoon
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea
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55
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Kim HS, Kim J, Im HN, Yoon JY, An DR, Yoon HJ, Kim JY, Min HK, Kim SJ, Lee JY, Han BW, Suh SW. Structural basis for the inhibition of Mycobacterium tuberculosis L,D-transpeptidase by meropenem, a drug effective against extensively drug-resistant strains. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:420-31. [PMID: 23519417 PMCID: PMC3605043 DOI: 10.1107/s0907444912048998] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 11/29/2012] [Indexed: 01/17/2023]
Abstract
Difficulty in the treatment of tuberculosis and growing drug resistance in Mycobacterium tuberculosis (Mtb) are a global health issue. Carbapenems inactivate L,D-transpeptidases; meropenem, when administered with clavulanate, showed in vivo activity against extensively drug-resistant Mtb strains. LdtMt2 (Rv2518c), one of two functional L,D-transpeptidases in Mtb, is predominantly expressed over LdtMt1 (Rv0116c). Here, the crystal structure of N-terminally truncated LdtMt2 (residues Leu131-Ala408) is reported in both ligand-free and meropenem-bound forms. The structure of meropenem-inhibited LdtMt2 provides a detailed structural view of the interactions between a carbapenem drug and Mtb L,D-transpeptidase. The structures revealed that the catalytic L,D-transpeptidase domain of LdtMt2 is preceded by a bacterial immunogloblin-like Big_5 domain and is followed by an extended C-terminal tail that interacts with both domains. Furthermore, it is shown using mass analyses that meropenem acts as a suicide inhibitor of LdtMt2. Upon acylation of the catalytic Cys354 by meropenem, the `active-site lid' undergoes a large conformational change to partially cover the active site so that the bound meropenem is accessible to the bulk solvent via three narrow paths. This work will facilitate structure-guided discovery of L,D-transpeptidase inhibitors as novel antituberculosis drugs against drug-resistant Mtb.
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Affiliation(s)
- Hyoun Sook Kim
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Jieun Kim
- Department of Biophysics and Chemical Biology, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea
| | - Ha Na Im
- Department of Biophysics and Chemical Biology, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea
| | - Ji Young Yoon
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea
| | - Doo Ri An
- Department of Biophysics and Chemical Biology, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea
| | - Hye Jin Yoon
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea
| | - Jin Young Kim
- Division of Mass Spectrometry, Korea Basic Science Institute, Ochang-eup Yeongudangiro 162, Cheongwon-gun, Chungbuk 363-883, Republic of Korea
| | - Hye Kyeoung Min
- Division of Mass Spectrometry, Korea Basic Science Institute, Ochang-eup Yeongudangiro 162, Cheongwon-gun, Chungbuk 363-883, Republic of Korea
| | - Soon-Jong Kim
- Department of Chemistry, Mokpo National University, Chonnam 534-729, Republic of Korea
| | - Jae Young Lee
- Department of Life Science, Dongguk University Seoul, Seoul 100-712, Republic of Korea
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Se Won Suh
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea
- Department of Biophysics and Chemical Biology, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea
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56
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Böth D, Steiner EM, Stadler D, Lindqvist Y, Schnell R, Schneider G. Structure of LdtMt2, an L,D-transpeptidase from Mycobacterium tuberculosis. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:432-41. [PMID: 23519418 PMCID: PMC3605044 DOI: 10.1107/s0907444912049268] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 11/30/2012] [Indexed: 05/12/2023]
Abstract
The transpeptidase LtdMt2 catalyzes the formation of the (3-3) cross-links characteristic of the peptidoglycan layer in the Mycobacterium tuberculosis cell wall. Bioinformatics analysis suggests that the extramembrane part of the enzyme consists of three domains: two smaller domains (denoted as A and B domains) and a transpeptidase domain (the C domain) at the C-terminus. The crystal structures of two fragments comprising the AB domains and the BC domains have been determined. The structure of the BC module, which was determined to 1.86 Å resolution using Se-SAD phasing, consists of the B domain with an immunoglobulin-related fold and the catalytic domain belonging to the ErfK/YbiS/YbnG fold family. The structure of the AB-domain fragment, which was solved by molecular replacement to 1.45 Å resolution, reveals that despite a lack of overall sequence identity the A domain is structurally very similar to the B domain. Combining the structures of the two fragments provides a view of the complete three-domain extramembrane part of LdtMt2 and shows that the protein extends at least 80-100 Å from the plasma membrane into the peptidoglycan layer and thus defines the maximal distance at which cross-links are formed by this enzyme. The LdtMt-related transpeptidases contain one or two immunoglobulin domains, which suggests that these might serve as extender units to position the catalytic domain at an appropriate distance from the membrane in the peptidoglycan layer.
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Affiliation(s)
- Dominic Böth
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-17 177 Stockholm, Sweden
| | - Eva Maria Steiner
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-17 177 Stockholm, Sweden
| | - Daniela Stadler
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-17 177 Stockholm, Sweden
| | - Ylva Lindqvist
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-17 177 Stockholm, Sweden
| | - Robert Schnell
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-17 177 Stockholm, Sweden
| | - Gunter Schneider
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-17 177 Stockholm, Sweden
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57
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Erdemli SB, Gupta R, Bishai WR, Lamichhane G, Amzel LM, Bianchet MA. Targeting the cell wall of Mycobacterium tuberculosis: structure and mechanism of L,D-transpeptidase 2. Structure 2012; 20:2103-15. [PMID: 23103390 DOI: 10.1016/j.str.2012.09.016] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 09/26/2012] [Accepted: 09/26/2012] [Indexed: 01/08/2023]
Abstract
With multidrug-resistant cases of tuberculosis increasing globally, better antibiotic drugs and novel drug targets are becoming an urgent need. Traditional β-lactam antibiotics that inhibit D,D-transpeptidases are not effective against mycobacteria, in part because mycobacteria rely mostly on L,D-transpeptidases for biosynthesis and maintenance of their peptidoglycan layer. This reliance plays a major role in drug resistance and persistence of Mycobacterium tuberculosis (Mtb) infections. The crystal structure at 1.7 Å resolution of the Mtb L,D-transpeptidase Ldt(Mt2) containing a bound peptidoglycan fragment, reported here, provides information about catalytic site organization as well as substrate recognition by the enzyme. Based on our structural, kinetic, and calorimetric data, we propose a catalytic mechanism for Ldt(Mt2) in which both acyl-acceptor and acyl-donor substrates reach the catalytic site from the same, rather than different, entrances. Together, this information provides vital insights to facilitate development of drugs targeting this validated yet unexploited enzyme.
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Affiliation(s)
- Sabri B Erdemli
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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58
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Lecoq L, Bougault C, Kern T, Hugonnet JE, Veckerlé C, Pessey O, Arthur M, Simorre JP. Backbone and side-chain 1H, 15N and 13C assignment of apo- and imipenem-acylated L,D-transpeptidase from Bacillus subtilis. BIOMOLECULAR NMR ASSIGNMENTS 2012; 6:205-208. [PMID: 22278298 DOI: 10.1007/s12104-012-9358-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 01/17/2012] [Indexed: 05/31/2023]
Abstract
The D,D-transpeptidase activity of Penicillin Binding Proteins (PBPs) is essential to maintain cell wall integrity. PBPs catalyze the final step of the peptidoglycan synthesis by forming 4 → 3 cross-links between two peptide stems. Recently, a novel β-lactam resistance mechanism involving L,D-transpeptidases has been identified in Enterococcus faecium and Mycobacterium tuberculosis. In this resistance pathway, the classical 4 → 3 cross-links are replaced by 3 → 3 cross-links, whose formation are catalyzed by the L,D-transpeptidases. To date, only one class of the entire β-lactam family, the carbapenems, is able to inhibit the L,D-transpeptidase activity. Nevertheless, the specificity of this inactivation is still not understood. Hence, the study of this new transpeptidase family is of considerable interest in order to understand the mechanism of the L,D-transpeptidases inhibition by carbapenems. In this context, we present herein the backbone and side-chain (1)H, (15)N and (13)C NMR assignment of the L,D-transpeptidase from Bacillus subtilis (Ldt(Bs)) in the apo and in the acylated form with a carbapenem, the imipenem.
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Affiliation(s)
- L Lecoq
- CEA, Institut de Biologie Structurale Jean-Pierre Ebel, 41, rue Jules Horowitz, 38027 Grenoble, France
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59
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Lecoq L, Bougault C, Hugonnet JE, Veckerlé C, Pessey O, Arthur M, Simorre JP. Dynamics induced by β-lactam antibiotics in the active site of Bacillus subtilis L,D-transpeptidase. Structure 2012; 20:850-61. [PMID: 22579252 DOI: 10.1016/j.str.2012.03.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 02/29/2012] [Accepted: 03/05/2012] [Indexed: 11/18/2022]
Abstract
β-lactams inhibit peptidoglycan polymerization by acting as suicide substrates of essential d,d-transpeptidases. Bypass of these enzymes by unrelated l,d-transpeptidases results in β-lactam resistance, although carbapenems remain unexpectedly active. To gain insight into carbapenem specificity of l,d-transpeptidases (Ldts), we solved the nuclear magnetic resonance (NMR) structures of apo and imipenem-acylated Bacillus subtilis Ldt and show that the cysteine nucleophile is present as a neutral imidazole-sulfhydryl pair in the substrate-free enzyme. NMR relaxation dispersion does not reveal any preexisting conformational exchange in the apoenzyme, and change in flexibility is not observed upon noncovalent binding of β-lactams (K(D) > 37.5 mM). In contrast, covalent modification of active cysteine by both carbapenems and 2-nitro-5-thiobenzoate induces backbone flexibility that does not result from disruption of the imidazole-sulfhydryl proton interaction or steric hindrance. The chemical step of the reaction determines enzyme specificity since no differences in drug affinity were observed.
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Affiliation(s)
- Lauriane Lecoq
- CEA, DSV, Institut de Biologie Structurale (IBS), Grenoble F-38027, France
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60
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Monitoring lysin motif–ligand interactions via tryptophan analog fluorescence spectroscopy. Anal Biochem 2012; 428:111-8. [DOI: 10.1016/j.ab.2012.06.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 05/13/2012] [Accepted: 06/08/2012] [Indexed: 12/14/2022]
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61
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Gust AA, Willmann R, Desaki Y, Grabherr HM, Nürnberger T. Plant LysM proteins: modules mediating symbiosis and immunity. TRENDS IN PLANT SCIENCE 2012; 17:495-502. [PMID: 22578284 DOI: 10.1016/j.tplants.2012.04.003] [Citation(s) in RCA: 141] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Revised: 04/05/2012] [Accepted: 04/11/2012] [Indexed: 05/18/2023]
Abstract
Microbial glycans, such as bacterial peptidoglycans, fungal chitin or rhizobacterial Nod factors (NFs), are important signatures for plant immune activation or for the establishment of beneficial symbioses. Plant lysin motif (LysM) domain proteins serve as modules mediating recognition of these different N-acetylglucosamine (GlcNAc)-containing ligands, suggesting that this class of proteins evolved from an ancient sensor for GlcNAc. During early plant evolution, these glycans probably served as immunogenic patterns activating LysM protein receptor-mediated plant immunity and stopping microbial infection. The biochemical potential of plant LysM proteins for sensing microbial GlcNAc-containing glycans has probably since favored the evolution of receptors facilitating microbial infection and symbiosis.
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Affiliation(s)
- Andrea A Gust
- Department of Plant Biochemistry, ZMBP, University of Tübingen, 72076 Tübingen, Germany.
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Zhang D, de Souza RF, Anantharaman V, Iyer LM, Aravind L. Polymorphic toxin systems: Comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics. Biol Direct 2012; 7:18. [PMID: 22731697 PMCID: PMC3482391 DOI: 10.1186/1745-6150-7-18] [Citation(s) in RCA: 364] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 05/31/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Proteinaceous toxins are observed across all levels of inter-organismal and intra-genomic conflicts. These include recently discovered prokaryotic polymorphic toxin systems implicated in intra-specific conflicts. They are characterized by a remarkable diversity of C-terminal toxin domains generated by recombination with standalone toxin-coding cassettes. Prior analysis revealed a striking diversity of nuclease and deaminase domains among the toxin modules. We systematically investigated polymorphic toxin systems using comparative genomics, sequence and structure analysis. RESULTS Polymorphic toxin systems are distributed across all major bacterial lineages and are delivered by at least eight distinct secretory systems. In addition to type-II, these include type-V, VI, VII (ESX), and the poorly characterized "Photorhabdus virulence cassettes (PVC)", PrsW-dependent and MuF phage-capsid-like systems. We present evidence that trafficking of these toxins is often accompanied by autoproteolytic processing catalyzed by HINT, ZU5, PrsW, caspase-like, papain-like, and a novel metallopeptidase associated with the PVC system. We identified over 150 distinct toxin domains in these systems. These span an extraordinary catalytic spectrum to include 23 distinct clades of peptidases, numerous previously unrecognized versions of nucleases and deaminases, ADP-ribosyltransferases, ADP ribosyl cyclases, RelA/SpoT-like nucleotidyltransferases, glycosyltranferases and other enzymes predicted to modify lipids and carbohydrates, and a pore-forming toxin domain. Several of these toxin domains are shared with host-directed effectors of pathogenic bacteria. Over 90 families of immunity proteins might neutralize anywhere between a single to at least 27 distinct types of toxin domains. In some organisms multiple tandem immunity genes or immunity protein domains are organized into polyimmunity loci or polyimmunity proteins. Gene-neighborhood-analysis of polymorphic toxin systems predicts the presence of novel trafficking-related components, and also the organizational logic that allows toxin diversification through recombination. Domain architecture and protein-length analysis revealed that these toxins might be deployed as secreted factors, through directed injection, or via inter-cellular contact facilitated by filamentous structures formed by RHS/YD, filamentous hemagglutinin and other repeats. Phyletic pattern and life-style analysis indicate that polymorphic toxins and polyimmunity loci participate in cooperative behavior and facultative 'cheating' in several ecosystems such as the human oral cavity and soil. Multiple domains from these systems have also been repeatedly transferred to eukaryotes and their viruses, such as the nucleo-cytoplasmic large DNA viruses. CONCLUSIONS Along with a comprehensive inventory of toxins and immunity proteins, we present several testable predictions regarding active sites and catalytic mechanisms of toxins, their processing and trafficking and their role in intra-specific and inter-specific interactions between bacteria. These systems provide insights regarding the emergence of key systems at different points in eukaryotic evolution, such as ADP ribosylation, interaction of myosin VI with cargo proteins, mediation of apoptosis, hyphal heteroincompatibility, hedgehog signaling, arthropod toxins, cell-cell interaction molecules like teneurins and different signaling messengers.
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Affiliation(s)
- Dapeng Zhang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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63
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Zeng L, Velásquez AC, Munkvold KR, Zhang J, Martin GB. A tomato LysM receptor-like kinase promotes immunity and its kinase activity is inhibited by AvrPtoB. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 69:92-103. [PMID: 21880077 PMCID: PMC3240704 DOI: 10.1111/j.1365-313x.2011.04773.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Resistance in tomato (Solanum lycopersicum) to infection by Pseudomonas syringae involves both detection of pathogen-associated molecular patterns (PAMPs) and recognition by the host Pto kinase of pathogen effector AvrPtoB which is translocated into the host cell and interferes with PAMP-triggered immunity (PTI). The N-terminal portion of AvrPtoB is sufficient for its virulence activity and for recognition by Pto. An amino acid substitution in AvrPtoB, F173A, abolishes these activities. To investigate the mechanisms of AvrPtoB virulence, we screened for tomato proteins that interact with AvrPtoB and identified Bti9, a LysM receptor-like kinase. Bti9 has the highest amino acid similarity to Arabidopsis CERK1 among the tomato LysM receptor-like kinases (RLKs) and belongs to a clade containing three other tomato proteins, SlLyk11, SlLyk12, and SlLyk13, all of which interact with AvrPtoB. The F173A substitution disrupts the interaction of AvrPtoB with Bti9 and SlLyk13, suggesting that these LysM-RLKs are its virulence targets. Two independent tomato lines with RNAi-mediated reduced expression of Bti9 and SlLyk13 were more susceptible to P. syringae. Bti9 kinase activity was inhibited in vitro by the N-terminal domain of AvrPtoB in an F173-dependent manner. These results indicate Bti9 and/or SlLyk13 play a role in plant immunity and the N-terminal domain of AvrPtoB may have evolved to interfere with their kinase activity. Finally, we found that Bti9 and Pto interact with AvrPtoB in a structurally similar although not identical fashion, suggesting that Pto may have evolved as a molecular mimic of LysM-RLK kinase domains.
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Affiliation(s)
- Lirong Zeng
- Boyce Thompson Institute for Plant Research, Ithaca, NY
| | - André C. Velásquez
- Boyce Thompson Institute for Plant Research, Ithaca, NY
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY
| | | | - Jingwei Zhang
- Boyce Thompson Institute for Plant Research, Ithaca, NY
| | - Gregory B. Martin
- Boyce Thompson Institute for Plant Research, Ithaca, NY
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY
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Ligands of RLKs and RLPs Involved in Defense and Symbiosis. SIGNALING AND COMMUNICATION IN PLANTS 2012. [DOI: 10.1007/978-3-642-23044-8_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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65
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Murein and pseudomurein cell wall binding domains of bacteria and archaea--a comparative view. Appl Microbiol Biotechnol 2011; 92:921-8. [PMID: 22012341 PMCID: PMC3210951 DOI: 10.1007/s00253-011-3637-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2011] [Revised: 09/29/2011] [Accepted: 10/07/2011] [Indexed: 02/02/2023]
Abstract
The cell wall, a major barrier protecting cells from their environment, is an essential compartment of both bacteria and archaea. It protects the organism from internal turgor pressure and gives a defined shape to the cell. The cell wall serves also as an anchoring surface for various proteins and acts as an adhesion platform for bacteriophages. The walls of bacteria and archaea are mostly composed of murein and pseudomurein, respectively. Cell wall binding domains play a crucial role in the non-covalent attachment of proteins to cell walls. Here, we give an overview of the similarities and differences in the biochemical and functional properties of the two major murein and pseudomurein cell wall binding domains, i.e., the Lysin Motif (LysM) domain (Pfam PF01476) and the pseudomurein binding (PMB) domain (Pfam PF09373) of bacteria and archaea, respectively.
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66
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Distinct pathways for modification of the bacterial cell wall by non-canonical D-amino acids. EMBO J 2011; 30:3442-53. [PMID: 21792174 DOI: 10.1038/emboj.2011.246] [Citation(s) in RCA: 211] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Accepted: 06/28/2011] [Indexed: 02/02/2023] Open
Abstract
Production of non-canonical D-amino acids (NCDAAs) in stationary phase promotes remodelling of peptidoglycan (PG), the polymer that comprises the bacterial cell wall. Impairment of NCDAAs production leads to excessive accumulation of PG and hypersensitivity to osmotic shock; however, the mechanistic bases for these phenotypes were not previously determined. Here, we show that incorporation of NCDAAs into PG is a critical means by which NCDAAs control PG abundance and strength. We identified and reconstituted in vitro two (of at least three) distinct processes that mediate NCDAA incorporation. Diverse bacterial phyla incorporate NCDAAs into their cell walls, either through periplasmic editing of the mature PG or via incorporation into PG precursor subunits in the cytosol. Production of NCDAAs in Vibrio cholerae requires the stress response sigma factor RpoS, suggesting that NCDAAs may aid bacteria in responding to varied environmental challenges. The widespread capacity of diverse bacteria, including non-producers, to incorporate NCDAAs suggests that these amino acids may serve as both autocrine- and paracrine-like regulators of chemical and physical properties of the cell wall in microbial communities.
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67
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Peltier J, Courtin P, El Meouche I, Lemée L, Chapot-Chartier MP, Pons JL. Clostridium difficile has an original peptidoglycan structure with a high level of N-acetylglucosamine deacetylation and mainly 3-3 cross-links. J Biol Chem 2011; 286:29053-29062. [PMID: 21685382 DOI: 10.1074/jbc.m111.259150] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The structure of the vegetative cell wall peptidoglycan of Clostridium difficile was determined by analysis of its constituent muropeptides with a combination of reverse-phase high pressure liquid chromatography separation of muropeptides, amino acid analysis, mass spectrometry and tandem mass spectrometry. The structures assigned to 36 muropeptides evidenced several original features in C. difficile vegetative cell peptidoglycan. First, it is characterized by a strikingly high level of N-acetylglucosamine deacetylation. In addition, the majority of dimers (around 75%) contains A(2)pm(3) → A(2)pm(3) (A(2)pm, 2,6-diaminopimelic acid) cross-links and only a minority of the more classical Ala(4) → A(2)pm(3) cross-links. Moreover, a significant amount of muropeptides contains a modified tetrapeptide stem ending in Gly instead of D-Ala(4). Two L,D-transpeptidases homologues encoding genes present in the genome of C. difficile 630 and named ldt(cd1) and ldt(cd2), were inactivated. The inactivation of either ldt(cd1) or ldt(cd2) significantly decreased the abundance of 3-3 cross-links, leading to a marked decrease of peptidoglycan reticulation and demonstrating that both ldt(cd1)-and ldt(cd2)-encoded proteins have a redundant L,D-transpeptidase activity. The contribution of 3-3 cross-links to peptidoglycan synthesis increased in the presence of ampicillin, indicating that this drug does not inhibit the L,D-transpeptidation pathway in C. difficile.
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Affiliation(s)
- Johann Peltier
- Laboratoire G.R.A.M., EA 2656 IFR 23, Rouen University Hospital, 22 Boulevard Gambetta, 76183 Rouen Cedex, France
| | - Pascal Courtin
- Institut National de la Recherche Agronomique, UMR1319 Micalis, F-78350 Jouy-en-Josas, France, and; AgroParisTech, UMR Michalis, F-78350 Jouy-en-Josas, France
| | - Imane El Meouche
- Laboratoire G.R.A.M., EA 2656 IFR 23, Rouen University Hospital, 22 Boulevard Gambetta, 76183 Rouen Cedex, France
| | - Ludovic Lemée
- Laboratoire G.R.A.M., EA 2656 IFR 23, Rouen University Hospital, 22 Boulevard Gambetta, 76183 Rouen Cedex, France
| | - Marie-Pierre Chapot-Chartier
- Institut National de la Recherche Agronomique, UMR1319 Micalis, F-78350 Jouy-en-Josas, France, and; AgroParisTech, UMR Michalis, F-78350 Jouy-en-Josas, France
| | - Jean-Louis Pons
- Laboratoire G.R.A.M., EA 2656 IFR 23, Rouen University Hospital, 22 Boulevard Gambetta, 76183 Rouen Cedex, France,.
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68
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Bramkamp M. The putative Bacillus subtilis L,D-transpeptidase YciB is a lipoprotein that localizes to the cell poles in a divisome-dependent manner. Arch Microbiol 2009; 192:57-68. [PMID: 20013255 DOI: 10.1007/s00203-009-0532-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2009] [Revised: 11/20/2009] [Accepted: 12/01/2009] [Indexed: 11/25/2022]
Abstract
Cell wall synthesis in bacteria is spatially organized by cytoskeletal structures. Common to all cell wall-bearing bacteria, the cytokinetic machinery localizes the cell wall synthesis to the site of septation. Recently, MinJ, a new component of the cytokinetic machinery, or divisome, of Bacillus subtilis has been described. MinJ is part of the division site selection system but also essential for correct assembly of the divisome. Here, I used the isolated PDZ domain of MinJ for co-elution experiments. One of the proteins that co-eluted was the so far uncharacterized, putative L,D-transpeptidase protein YciB. Evidence is shown that YciB localizes to the cell poles. YciB localization depends on the existence of a mature divisome, suggesting that L,D-transpeptidases are, like penicillin-binding proteins, part of the divisome.
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Affiliation(s)
- Marc Bramkamp
- Institute for Biochemistry, University of Cologne, Zülpicher Strasse 47, Cologne, Germany.
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69
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Zhang XC, Cannon SB, Stacey G. Evolutionary genomics of LysM genes in land plants. BMC Evol Biol 2009; 9:183. [PMID: 19650916 PMCID: PMC2728734 DOI: 10.1186/1471-2148-9-183] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2009] [Accepted: 08/03/2009] [Indexed: 11/23/2022] Open
Abstract
Background The ubiquitous LysM motif recognizes peptidoglycan, chitooligosaccharides (chitin) and, presumably, other structurally-related oligosaccharides. LysM-containing proteins were first shown to be involved in bacterial cell wall degradation and, more recently, were implicated in perceiving chitin (one of the established pathogen-associated molecular patterns) and lipo-chitin (nodulation factors) in flowering plants. However, the majority of LysM genes in plants remain functionally uncharacterized and the evolutionary history of complex LysM genes remains elusive. Results We show that LysM-containing proteins display a wide range of complex domain architectures. However, only a simple core architecture is conserved across kingdoms. Each individual kingdom appears to have evolved a distinct array of domain architectures. We show that early plant lineages acquired four characteristic architectures and progressively lost several primitive architectures. We report plant LysM phylogenies and associated gene, protein and genomic features, and infer the relative timing of duplications of LYK genes. Conclusion We report a domain architecture catalogue of LysM proteins across all kingdoms. The unique pattern of LysM protein domain architectures indicates the presence of distinctive evolutionary paths in individual kingdoms. We describe a comparative and evolutionary genomics study of LysM genes in plant kingdom. One of the two groups of tandemly arrayed plant LYK genes likely resulted from an ancient genome duplication followed by local genomic rearrangement, while the origin of the other groups of tandemly arrayed LYK genes remains obscure. Given the fact that no animal LysM motif-containing genes have been functionally characterized, this study provides clues to functional characterization of plant LysM genes and is also informative with regard to evolutionary and functional studies of animal LysM genes.
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Affiliation(s)
- Xue-Cheng Zhang
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO 65211, USA.
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70
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Fungal LysM effectors: extinguishers of host immunity? Trends Microbiol 2009; 17:151-7. [PMID: 19299132 DOI: 10.1016/j.tim.2009.01.002] [Citation(s) in RCA: 158] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2008] [Revised: 12/20/2008] [Accepted: 01/15/2009] [Indexed: 01/19/2023]
Abstract
Lysin motifs (LysMs) have been recognized in prokaryotes and plants as carbohydrate-binding protein modules. Recently, a novel virulence factor with LysMs was characterized from the plant pathogenic fungus Cladosporium fulvum. Here, we present a survey of public sequence data of 70 fungal species to demonstrate that putatively secreted LysM-containing proteins are widespread in the fungal kingdom, as they are found in mammalian and plant pathogenic species, in addition to saprophytes. We propose that these putative LysM effectors might have a role in sequestration of chitin oligosaccharides - breakdown products of fungal cell walls that are released during invasion and act as triggers of host immunity - to dampen host defence.
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71
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Ohnuma T, Onaga S, Murata K, Fukamizo T, Taira T, Katoh E. Structure and Function of Family 50 Carbohydrate Binding Modules (LysM Domains) from Pteris ryukyuensis Chitinase-A. J Appl Glycosci (1999) 2009. [DOI: 10.5458/jag.56.97] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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72
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C2 domain protein MIN1 promotes eyespot organization in Chlamydomonas reinhardtii. EUKARYOTIC CELL 2008; 7:2100-12. [PMID: 18849467 DOI: 10.1128/ec.00118-08] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Assembly and asymmetric localization of the photosensory eyespot in the biflagellate, unicellular green alga Chlamydomonas reinhardtii requires coordinated organization of photoreceptors in the plasma membrane and pigment granule/thylakoid membrane layers in the chloroplast. min1 (mini-eyed) mutant cells contain abnormally small, disorganized eyespots in which the chloroplast envelope and plasma membrane are no longer apposed. The MIN1 gene, identified here by phenotypic rescue, encodes a protein with an N-terminal C2 domain and a C-terminal LysM domain separated by a transmembrane sequence. This novel domain architecture led to the hypothesis that MIN1 is in the plasma membrane or the chloroplast envelope, where membrane association of the C2 domain promotes proper eyespot organization. Mutation of conserved C2 domain loop residues disrupted association of the MIN1 C2 domain with the chloroplast envelope in moss cells but did not abolish eyespot assembly in Chlamydomonas. In min1 null cells, channelrhodopsin-1 (ChR1) photoreceptor levels were reduced, indicating a role for MIN1 in ChR1 expression and/or stability. However, ChR1 localization was only minimally disturbed during photoautotrophic growth of min1 cells, conditions under which the pigment granule layers are disorganized. The data are consistent with the hypothesis that neither MIN1 nor proper organization of the plastidic components of the eyespot is essential for localization of ChR1.
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73
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Ragumani S, Kumaran D, Burley SK, Swaminathan S. Crystal structure of a putative lysostaphin peptidase from Vibrio cholerae. Proteins 2008; 72:1096-103. [PMID: 18498110 PMCID: PMC3614409 DOI: 10.1002/prot.22095] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Sugadev Ragumani
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973
| | - Desigan Kumaran
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973
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74
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Buist G, Steen A, Kok J, Kuipers OP. LysM, a widely distributed protein motif for binding to (peptido)glycans. Mol Microbiol 2008; 68:838-47. [PMID: 18430080 DOI: 10.1111/j.1365-2958.2008.06211.x] [Citation(s) in RCA: 430] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Bacteria retain certain proteins at their cell envelopes by attaching them in a non-covalent manner to peptidoglycan, using specific protein domains, such as the prominent LysM (Lysin Motif) domain. More than 4000 (Pfam PF01476) proteins of both prokaryotes and eukaryotes have been found to contain one or more Lysin Motifs. Notably, this collection contains not only truly secreted proteins, but also (outer-)membrane proteins, lipoproteins or proteins bound to the cell wall in a (non-)covalent manner. The motif typically ranges in length from 44 to 65 amino acid residues and binds to various types of peptidoglycan and chitin, most likely recognizing the N-acetylglucosamine moiety. Most bacterial LysM-containing proteins are peptidoglycan hydrolases with various cleavage specificities. Binding of certain LysM proteins to cells of Gram-positive bacteria has been shown to occur at specific sites, as binding elsewhere is hindered by the presence of other cell wall components such as lipoteichoic acids. Interestingly, LysM domains of certain plant kinases enable the plant to recognize its symbiotic bacteria or sense and induce resistance against fungi. This interaction is triggered by chitin-like compounds that are secreted by the symbiotic bacteria or released from fungi, demonstrating an important sensing function of LysMs.
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Affiliation(s)
- Girbe Buist
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
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75
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Identification of the L,D-transpeptidases for peptidoglycan cross-linking in Escherichia coli. J Bacteriol 2008; 190:4782-5. [PMID: 18456808 DOI: 10.1128/jb.00025-08] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Three active-site cysteine L,D-transpeptidases can individually anchor the Braun lipoprotein to the Escherichia coli peptidoglycan. We show here that two additional enzymes of the same family form peptide bonds between the third residues of peptidoglycan stems, generating meso-DAP(3)-->meso-DAP(3) unusual cross-links. This activity partially replaces the D,D-transpeptidase activity of penicillin-binding proteins.
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76
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Bolton MD, van Esse HP, Vossen JH, de Jonge R, Stergiopoulos I, Stulemeijer IJE, van den Berg GCM, Borrás-Hidalgo O, Dekker HL, de Koster CG, de Wit PJGM, Joosten MHAJ, Thomma BPHJ. The novel Cladosporium fulvum lysin motif effector Ecp6 is a virulence factor with orthologues in other fungal species. Mol Microbiol 2008; 69:119-36. [PMID: 18452583 DOI: 10.1111/j.1365-2958.2008.06270.x] [Citation(s) in RCA: 195] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
During tomato leaf colonization, the biotrophic fungus Cladosporium fulvum secretes several effector proteins into the apoplast. Eight effectors have previously been characterized and show no significant homology to each other or to other fungal genes. To discover novel C. fulvum effectors that might play a role in virulence, we utilized two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) to visualize proteins secreted during C. fulvum-tomato interactions. Three novel C. fulvum proteins were identified: CfPhiA, Ecp6 and Ecp7. CfPhiA shows homology to proteins found on fungal sporogenous cells called phialides. Ecp6 contains lysin motifs (LysM domains) that are recognized as carbohydrate-binding modules. Ecp7 encodes a small, cysteine-rich protein with no homology to known proteins. Heterologous expression of Ecp6 significantly increased the virulence of the vascular pathogen Fusarium oxysporum on tomato. Furthermore, by RNA interference (RNAi)-mediated gene silencing we demonstrate that Ecp6 is instrumental for C. fulvum virulence on tomato. Hardly any allelic variation was observed in the Ecp6 coding region of a worldwide collection of C. fulvum strains. Although none of the C. fulvum effectors identified so far have obvious orthologues in other organisms, conserved Ecp6 orthologues were identified in various fungal species. Homology-based modelling suggests that the LysM domains of C. fulvum Ecp6 may be involved in chitin binding.
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Affiliation(s)
- Melvin D Bolton
- Laboratory of Phytopathology, Wageningen University, Binnenhaven 5, Wageningen, The Netherlands
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77
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Dramsi S, Magnet S, Davison S, Arthur M. Covalent attachment of proteins to peptidoglycan. FEMS Microbiol Rev 2008; 32:307-20. [PMID: 18266854 DOI: 10.1111/j.1574-6976.2008.00102.x] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Bacterial surface proteins are key players in host-symbiont or host-pathogen interactions. How these proteins are targeted and displayed at the cell surface are challenging issues of both fundamental and clinical relevance. While surface proteins of Gram-negative bacteria are assembled in the outer membrane, Gram-positive bacteria predominantly utilize their thick cell wall as a platform to anchor their surface proteins. This surface display involves both covalent and noncovalent interactions with either the peptidoglycan or secondary wall polymers such as teichoic acid or lipoteichoic acid. This review focuses on the role of enzymes that covalently link surface proteins to the peptidoglycan, the well-known sortases in Gram-positive bacteria, and the recently characterized l,d-transpeptidases in Gram-negative bacteria.
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Affiliation(s)
- Shaynoor Dramsi
- Unité de Biologie des Bactéries Pathogènes à Gram-positif, Institut Pasteur, Paris, France.
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78
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Ohnuma T, Onaga S, Murata K, Taira T, Katoh E. LysM Domains from Pteris ryukyuensis Chitinase-A. J Biol Chem 2008; 283:5178-87. [DOI: 10.1074/jbc.m707156200] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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79
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Goldschmidt L, Cooper DR, Derewenda ZS, Eisenberg D. Toward rational protein crystallization: A Web server for the design of crystallizable protein variants. Protein Sci 2007; 16:1569-76. [PMID: 17656576 PMCID: PMC2203352 DOI: 10.1110/ps.072914007] [Citation(s) in RCA: 206] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Growing well-diffracting crystals constitutes a serious bottleneck in structural biology. A recently proposed crystallization methodology for "stubborn crystallizers" is to engineer surface sequence variants designed to form intermolecular contacts that could support a crystal lattice. This approach relies on the concept of surface entropy reduction (SER), i.e., the replacement of clusters of flexible, solvent-exposed residues with residues with lower conformational entropy. This strategy minimizes the loss of conformational entropy upon crystallization and renders crystallization thermodynamically favorable. The method has been successfully used to crystallize more than 15 novel proteins, all stubborn crystallizers. But the choice of suitable sites for mutagenesis is not trivial. Herein, we announce a Web server, the surface entropy reduction prediction server (SERp server), designed to identify mutations that may facilitate crystallization. Suggested mutations are predicted based on an algorithm incorporating a conformational entropy profile, a secondary structure prediction, and sequence conservation. Minor considerations include the nature of flanking residues and gaps between mutation candidates. While designed to be used with default values, the server has many user-controlled parameters allowing for considerable flexibility. Within, we discuss (1) the methodology of the server, (2) how to interpret the results, and (3) factors that must be considered when selecting mutations. We also attempt to benchmark the server by comparing the server's predictions with successful SER structures. In most cases, the structure yielding mutations were easily identified by the SERp server. The server can be accessed at http://www.doe-mbi.ucla.edu/Services/SER.
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Affiliation(s)
- Lukasz Goldschmidt
- Howard Hughes Medical Institute, University of California, Los Angeles-DOE Institute of Genomics and Proteomics, Los Angeles, California 90095-1570, USA
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80
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Derewenda ZS. Protein crystallization in drug design: towards a rational approach. Expert Opin Drug Discov 2007; 2:1329-40. [PMID: 23484529 DOI: 10.1517/17460441.2.10.1329] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
X-ray crystallography is the method of choice for the detailed characterization of stereochemistry of interactions of drug leads and potential chemotherapeutics with their protein targets. The resulting atomic models allow for rational enhancement of the lead properties and consequently for the design of high-affinity inhibitors. However, a major bottleneck of the technique is the requirement for the protein and its complexes to yield high quality single crystals. Furthermore, it is highly desirable that such crystals diffract to high resolution, preferably ≥ 1.2 Å, revealing the structures in atomic detail. Unfortunately, only a small portion of proteins readily crystallize in that fashion. New approaches are being developed to circumvent this problem. One proposed option includes rational protein surface engineering to systematically improve the crystallizability of the protein. This is accomplished by creating surface patches readily mediating weak, but specific, intermolecular interactions that take on the role of crystal contacts during nucleation and crystal growth phase.
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Affiliation(s)
- Zygmunt S Derewenda
- University of Virginia, Integrated Center for Structure and Function Innovation (PSI2), Departments of Molecular Physiology and Biological Physics, PO Box 800736, Jordan Hall, Charlottesville, VA 22908-0736, USA +1 434 243 6842 ; +1 434 982 1616 ;
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81
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Abstract
Bacterial peptidoglycan amidases are a large and diverse group of enzymes. During the last few years, genomic sequence information has accumulated to an extent such that lists of proven or predicted peptidoglycan amidases can now be expected to be fairly complete. Moreover, representative crystal structures for most groups of phylogenetically related peptidoglycan amidases have been solved. Here, sequence and structural information is combined with published biochemical findings to demonstrate that (a) peptidoglycan amidases have evolved for almost every bond that occurs in peptidoglycan, (b) there are enzymes that share the fold, yet cleave different bonds and (c) there are enzymes that have entirely different folds and must have evolved independently, and yet cleave the same peptide bond. It is shown that despite these complications, some rules can be deduced from the available biochemical and structural information that can be useful to predict the specificity of hypothetical peptidoglycan hydrolases, for which only sequence information is available.
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Affiliation(s)
- Małgorzata Firczuk
- International Institute of Molecular and Cell Biology, Warsaw, Poland; and Max-Planck-Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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82
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Zhang XC, Wu X, Findley S, Wan J, Libault M, Nguyen HT, Cannon SB, Stacey G. Molecular evolution of lysin motif-type receptor-like kinases in plants. PLANT PHYSIOLOGY 2007; 144:623-36. [PMID: 17449649 PMCID: PMC1914208 DOI: 10.1104/pp.107.097097] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The lysin motif (LysM) domain is an ancient and ubiquitous protein module that binds peptidoglycan and structurally related molecules. A genomic survey in a large number of species spanning all kingdoms reveals that the combination of LysM and receptor kinase domains is present exclusively in plants. However, the particular biological functions and molecular evolution of this gene family remain largely unknown. We show that LysM domains in plant LysM proteins are highly diversified and that a minimum of six distinct types of LysM motifs exist in plant LysM kinase proteins and five additional types of LysM motifs exist in nonkinase plant LysM proteins. Further, motif similarities suggest that plant LysM motifs are ancient. Although phylogenetic signals are not sufficient to resolve the earliest relationships, plant LysM motifs may have arisen through common ancestry with LysM motifs in other kingdoms. Within plants, the gene family has evolved through local and segmental duplications. The family has undergone further duplication and diversification in legumes, where some LysM kinase genes function as receptors for bacterial nodulation factor. Two pairs of homeologous regions were identified in soybean (Glycine max) based on microsynteny and fluorescence in situ hybridization. Expression data show that most plant LysM kinase genes are expressed predominantly in the root and that orthologous LysM kinase genes share similar tissue expression patterns. We also examined synteny around plant LysM kinase genes to help reconstruct scenarios for the evolution of this important gene family.
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Affiliation(s)
- Xue-Cheng Zhang
- Division of Plant Sciences and National Center for Soybean Biotechnology , University of Missouri, Columbia, Missouri 65211, USA.
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83
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Magnet S, Arbeloa A, Mainardi JL, Hugonnet JE, Fourgeaud M, Dubost L, Marie A, Delfosse V, Mayer C, Rice LB, Arthur M. Specificity of L,D-transpeptidases from gram-positive bacteria producing different peptidoglycan chemotypes. J Biol Chem 2007; 282:13151-9. [PMID: 17311917 DOI: 10.1074/jbc.m610911200] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We report here the first direct assessment of the specificity of a class of peptidoglycan cross-linking enzymes, the L,D-transpeptidases, for the highly diverse structure of peptidoglycan precursors of Gram-positive bacteria. The lone functionally characterized member of this new family of active site cysteine peptidases, Ldt(fm) from Enterococcus faecium, was previously shown to bypass the D,D-transpeptidase activity of the classical penicillin-binding proteins leading to high level cross-resistance to glycopeptide and beta-lactam antibiotics. Ldt(fm) homologues from Bacillus subtilis (Ldt(Bs)) and E. faecalis (Ldt(fs)) were found here to cross-link their cognate disaccharide-peptide subunits containing meso-diaminopimelic acid (mesoDAP(3)) and L-Lys(3)-L-Ala-L-Ala at the third position of the stem peptide, respectively, instead of L-Lys(3)-d-iAsn in E. faecium. Ldt(fs) differed from Ldt(fm) and Ldt(Bs) by its capacity to hydrolyze the L-Lys(3)-D-Ala(4) bond of tetrapeptide (L,D-carboxypeptidase activity) and pentapeptide (L,D-endopeptidase activity) stems, in addition to the common cross-linking activity. The three enzymes were specific for their cognate acyl acceptors in the cross-linking reaction. In contrast to Ldt(fs), which was also specific for its cognate acyl donor, Ldt(fm) tolerated substitution of L-Lys(3)-D-iAsn by L-Lys(3)-L-Ala-L-Ala. Likewise, Ldt(Bs) tolerated substitution of mesoDAP(3) by L-Lys(3)-D-iAsn and L-Lys(3)-L-Ala-L-Ala in the acyl donor. Thus, diversification of the structure of peptidoglycan precursors associated with speciation has led to a parallel evolution of the substrate specificity of the L,D-transpeptidases affecting mainly the recognition of the acyl acceptor. Blocking the assembly of the side chain could therefore be used to combat antibiotic resistance involving L,D-transpeptidases.
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Mulder L, Lefebvre B, Cullimore J, Imberty A. LysM domains of Medicago truncatula NFP protein involved in Nod factor perception. Glycosylation state, molecular modeling and docking of chitooligosaccharides and Nod factors. Glycobiology 2006; 16:801-9. [PMID: 16723404 DOI: 10.1093/glycob/cwl006] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The establishment of the symbiosis between legume plants and rhizobial bacteria depends on the production of rhizobial lipo-chitooligosaccharidic signals (the Nod factors) that are specifically recognized by roots of the host plant. In Medicago truncatula, specific recognition of Sinorhizobium meliloti and its Nod factors requires the NFP (Nod factor perception) gene, which encodes a putative serine/threonine receptor-like kinase (RLK). The extracellular region of this protein contains three tandem lysin motifs (LysMs), a short peptide domain that is implicated in peptidoglycan or chitin binding in various bacterial or eukaryotic proteins, respectively. We report here the homology modeling of the three LysM domains of M. truncatula NFP based on the structure of a LysM domain of the Escherichia coli membrane-bound lytic murein transglycosidase D (MltD). Expression of NFP in a homologous system (M. truncatula roots) revealed that the protein is highly N-glycosylated, probably with both high-mannose and complex glycans. Surface analysis and docking calculations performed on the models of the three domains were used to predict the most favored binding modes for chitooligosaccharides and Nod factors. A convergent model can be proposed where the sulfated, O-acetylated lipo-chitooligosaccharidic Nod factor of S. meliloti binds in similar orientation to the three LysM domains of M. truncatula NFP. N-glycosylation is not expected to interfere with Nod factor binding in this orientation.
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Affiliation(s)
- Lonneke Mulder
- Centre de Recherches sur les Macromolécules Végétales, CNRS (affiliated with Université Joseph Fourier), 601 rue de la Chimie, BP 53, 38041 Grenoble Cedex 9, France
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Biarrotte-Sorin S, Hugonnet JE, Delfosse V, Mainardi JL, Gutmann L, Arthur M, Mayer C. Crystal structure of a novel beta-lactam-insensitive peptidoglycan transpeptidase. J Mol Biol 2006; 359:533-8. [PMID: 16647082 DOI: 10.1016/j.jmb.2006.03.014] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2006] [Revised: 03/02/2006] [Accepted: 03/08/2006] [Indexed: 11/29/2022]
Abstract
During the final stages of cell-wall synthesis in bacteria, penicillin-binding proteins (PBPs) catalyse the cross-linking of peptide chains from adjacent glycan strands of nascent peptidoglycan. We have recently shown that this step can be bypassed by an L,D-transpeptidase, which confers high-level beta-lactam-resistance in Enterococcus faecium. The resistance bypass leads to replacement of D-Ala4-->D-Asx-L-Lys3 cross-links generated by the PBPs by L-Lys3-->D-Asx-L-Lys3 cross-links generated by the L,D-transpeptidase. As the first structure of a member of this new transpeptidase family, we have determined the crystal structure of a fragment of the L,D-transpeptidase from E.faecium (Ldt(fm217)) at 2.4A resolution. Ldt(fm217) consists of two domains, the N-terminal domain, a new mixed alpha-beta fold, and the ErfK_YbiS_YhnG C-terminal domain, a representative of the mainly beta class of protein structures. Residue Cys442 of the C-terminal domain has been proposed to be the catalytic residue implicated in the cleavage of the L-Lys-D-Ala peptide bond. Surface analysis of Ldt(fm217) reveals that residue Cys442 is localized in a buried pocket and is accessible by two paths on different sides of the protein. We propose that the two paths to the catalytic residue Cys442 are the binding sites for the acceptor and donor substrates of the L,D-transpeptidase.
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Affiliation(s)
- Sabrina Biarrotte-Sorin
- INSERM, U655-LRMA, Université Pierre et Marie Curie-Paris 6, Université Paris-Descartes, Faculté de Médecine Pitié Salpêtrière and Centre de Recherches Biomédicales des Cordeliers, 91 boulevard de l'Hôpital, 75634 Paris Cedex 13, France
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