1
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Jang H, Do H, Kim CM, Kim GE, Lee JH, Park HH. Molecular basis of dimerization of lytic transglycosylase revealed by the crystal structure of MltA from Acinetobacter baumannii. IUCRJ 2021; 8:921-930. [PMID: 34804545 PMCID: PMC8562663 DOI: 10.1107/s2052252521008666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 08/18/2021] [Indexed: 06/13/2023]
Abstract
Peptidoglycan digestion by murein-degrading enzymes is a critical process in bacterial cell growth and/or cell division. The membrane-bound lytic murein transglycosylase A (MltA) is a murein-degrading enzyme; it catalyzes the cleavage of the β-1,4-glycosidic linkage between N-acetylmuramic acid and N-acetylglucosamine in peptidoglycans. Although substrate recognition and cleavage by MltA have been examined by previous structural and mutagenesis studies, the overall mechanism of MltA in conjunction with other functionally related molecules on the outer membrane of bacterial cells for peptidoglycan degradation has remained elusive. In this study, the crystal structure of MltA from the virulent human pathogen Acinetobacter baumannii is characterized and presented. The study indicated that MltA from A. baumannii forms homodimers via an extra domain which is specific to this species. Furthermore, the working mechanism of MltA with various functionally related proteins on the bacterial outer membrane was modeled based on the structural and biochemical analysis.
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Affiliation(s)
- Hyunseok Jang
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul 06974, Republic of Korea
| | - Hackwon Do
- Unit of Research for Practical Application, Korea Polar Research Institute, Incheon 21990, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
| | - Chang Min Kim
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul 06974, Republic of Korea
| | - Gi Eob Kim
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul 06974, Republic of Korea
| | - Jun Hyuck Lee
- Unit of Research for Practical Application, Korea Polar Research Institute, Incheon 21990, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
| | - Hyun Ho Park
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul 06974, Republic of Korea
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2
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Pereira CS, Silveira RL, Skaf MS. QM/MM Simulations of Enzymatic Hydrolysis of Cellulose: Probing the Viability of an Endocyclic Mechanism for an Inverting Cellulase. J Chem Inf Model 2021; 61:1902-1912. [PMID: 33760586 PMCID: PMC8154253 DOI: 10.1021/acs.jcim.0c01380] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Glycoside hydrolases
(GH) cleave carbohydrate glycosidic bonds
and play pivotal roles in living organisms and in many industrial
processes. Unlike acid-catalyzed hydrolysis of carbohydrates in solution,
which can occur either via cyclic or acyclic oxocarbenium-like transition
states, it is widely accepted that GH-catalyzed hydrolysis proceeds
via a general acid mechanism involving a cyclic oxocarbenium-like
transition state with protonation of the glycosidic oxygen. The GH45
subfamily C inverting endoglucanase from Phanerochaete chrysosporium (PcCel45A) defies the classical inverting mechanism as its crystal
structure conspicuously lacks a general Asp or Glu base residue. Instead,
PcCel45A has an Asn residue, a notoriously weak base in solution,
as one of its catalytic residues at position 92. Moreover, unlike
other inverting GHs, the relative position of the catalytic residues
in PcCel45A impairs the proton abstraction from the nucleophilic water
that attacks the anomeric carbon, a key step in the classical mechanism.
Here, we investigate the viability of an endocyclic mechanism for
PcCel45A using hybrid quantum mechanics/molecular mechanics (QM/MM)
simulations, with the QM region treated with the self-consistent-charge
density-functional tight-binding level of theory. In this mechanism,
an acyclic oxocarbenium-like transition state is stabilized leading
to the opening of the glucopyranose ring and formation of an unstable
acyclic hemiacetal that can be readily decomposed into hydrolysis
product. In silico characterization of the Michaelis
complex shows that PcCel45A significantly restrains the sugar ring
to the 4C1 chair conformation at the −1
subsite of the substrate binding cleft, in contrast to the classical
exocyclic mechanism in which ring puckering is critical. We also show
that PcCel45A provides an environment where the catalytic Asn92 residue
in its standard amide form participates in a cooperative hydrogen
bond network resulting in its increased nucleophilicity due to an
increased negative charge on the oxygen atom. Our results for PcCel45A
suggest that carbohydrate hydrolysis catalyzed by GHs may take an
alternative route from the classical mechanism.
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Affiliation(s)
- Caroline S Pereira
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas-Unicamp, Campinas 13084-862, Sao Paulo, Brazil
| | - Rodrigo L Silveira
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas-Unicamp, Campinas 13084-862, Sao Paulo, Brazil.,Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro 21941-909, Rio de Janeiro, Brazil
| | - Munir S Skaf
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas-Unicamp, Campinas 13084-862, Sao Paulo, Brazil
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3
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Bharadwaj VS, Knott BC, Ståhlberg J, Beckham GT, Crowley MF. The hydrolysis mechanism of a GH45 cellulase and its potential relation to lytic transglycosylase and expansin function. J Biol Chem 2020; 295:4477-4487. [PMID: 32054684 DOI: 10.1074/jbc.ra119.011406] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 02/12/2020] [Indexed: 11/06/2022] Open
Abstract
Family 45 glycoside hydrolases (GH45) are endoglucanases that are integral to cellulolytic secretomes, and their ability to break down cellulose has been successfully exploited in textile and detergent industries. In addition to their industrial relevance, understanding the molecular mechanism of GH45-catalyzed hydrolysis is of fundamental importance because of their structural similarity to cell wall-modifying enzymes such as bacterial lytic transglycosylases (LTs) and expansins present in bacteria, plants, and fungi. Our understanding of the catalytic itinerary of GH45s has been incomplete because a crystal structure with substrate spanning the -1 to +1 subsites is currently lacking. Here we constructed and validated a putative Michaelis complex in silico and used it to elucidate the hydrolytic mechanism in a GH45, Cel45A from the fungus Humicola insolens, via unbiased simulation approaches. These molecular simulations revealed that the solvent-exposed active-site architecture results in lack of coordination for the hydroxymethyl group of the substrate at the -1 subsite. This lack of coordination imparted mobility to the hydroxymethyl group and enabled a crucial hydrogen bond with the catalytic acid during and after the reaction. This suggests the possibility of a nonhydrolytic reaction mechanism when the catalytic base aspartic acid is missing, as is the case in some LTs (murein transglycosylase A) and expansins. We calculated reaction free energies and demonstrate the thermodynamic feasibility of the hydrolytic and nonhydrolytic reaction mechanisms. Our results provide molecular insights into the hydrolysis mechanism in HiCel45A, with possible implications for elucidating the elusive catalytic mechanism in LTs and expansins.
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Affiliation(s)
- Vivek S Bharadwaj
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Brandon C Knott
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Jerry Ståhlberg
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, P. O. Box 7015, 750 07 Uppsala, Sweden
| | - Gregg T Beckham
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Michael F Crowley
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401
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4
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Weaver AI, Jiménez-Ruiz V, Tallavajhala SR, Ransegnola BP, Wong KQ, Dörr T. Lytic transglycosylases RlpA and MltC assist in Vibrio cholerae daughter cell separation. Mol Microbiol 2019; 112:1100-1115. [PMID: 31286580 DOI: 10.1111/mmi.14349] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2019] [Indexed: 12/21/2022]
Abstract
The cell wall is a crucial structural feature in the vast majority of bacteria and comprises a covalently closed network of peptidoglycan (PG) strands. While PG synthesis is important for survival under many conditions, the cell wall is also a dynamic structure, undergoing degradation and remodeling by 'autolysins', enzymes that break down PG. Cell division, for example, requires extensive PG remodeling, especially during separation of daughter cells, which depends heavily upon the activity of amidases. However, in Vibrio cholerae, we demonstrate that amidase activity alone is insufficient for daughter cell separation and that lytic transglycosylases RlpA and MltC both contribute to this process. MltC and RlpA both localize to the septum and are functionally redundant under normal laboratory conditions; however, only RlpA can support normal cell separation in low-salt media. The division-specific activity of lytic transglycosylases has implications for the local structure of septal PG, suggesting that there may be glycan bridges between daughter cells that cannot be resolved by amidases. We propose that lytic transglycosylases at the septum cleave PG strands that are crosslinked beyond the reach of the highly regulated activity of the amidase and clear PG debris that may block the completion of outer membrane invagination.
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Affiliation(s)
- Anna I Weaver
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA.,Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA
| | - Valeria Jiménez-Ruiz
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Srikar R Tallavajhala
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Brett P Ransegnola
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Kimberly Q Wong
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Tobias Dörr
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA.,Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA.,Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY, 14853, USA
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5
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Jenkins CH, Wallis R, Allcock N, Barnes KB, Richards MI, Auty JM, Galyov EE, Harding SV, Mukamolova GV. The lytic transglycosylase, LtgG, controls cell morphology and virulence in Burkholderia pseudomallei. Sci Rep 2019; 9:11060. [PMID: 31363151 PMCID: PMC6667503 DOI: 10.1038/s41598-019-47483-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 07/15/2019] [Indexed: 02/07/2023] Open
Abstract
Burkholderia pseudomallei is the causative agent of the tropical disease melioidosis. Its genome encodes an arsenal of virulence factors that allow it, when required, to switch from a soil dwelling bacterium to a deadly intracellular pathogen. With a high intrinsic resistance to antibiotics and the ability to overcome challenges from the host immune system, there is an increasing requirement for new antibiotics and a greater understanding into the molecular mechanisms of B. pseudomallei virulence and dormancy. The peptidoglycan remodeling enzymes, lytic transglycosylases (Ltgs) are potential targets for such new antibiotics. Ltgs cleave the glycosidic bonds within bacterial peptidoglycan allowing for the insertion of peptidoglycan precursors during cell growth and division, and cell membrane spanning structures such as flagella and secretion systems. Using bioinformatic analysis we have identified 8 putative Ltgs in B. pseudomallei K96243. We aimed to investigate one of these Ltgs, LtgG (BPSL3046) through the generation of deletion mutants and biochemical analysis. We have shown that LtgG is a key contributor to cellular morphology, division, motility and virulence in BALB/c mice. We have determined the crystal structure of LtgG and have identified various amino acids likely to be important in peptidoglycan binding and catalytic activity. Recombinant protein assays and complementation studies using LtgG containing a site directed mutation in aspartate 343, confirmed the essentiality of this amino acid in the function of LtgG.
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Affiliation(s)
- Christopher H Jenkins
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, UK.
- Defence Science and Technology Laboratory, Chemical, Biological and Radiological Division, Porton Down, Salisbury, Wiltshire, UK.
| | - Russell Wallis
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, UK
- The Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, Leicester, UK
| | - Natalie Allcock
- Electron Microscopy Facility, Core Biotechnology Services, University of Leicester, Leicester, UK
| | - Kay B Barnes
- Defence Science and Technology Laboratory, Chemical, Biological and Radiological Division, Porton Down, Salisbury, Wiltshire, UK
| | - Mark I Richards
- Defence Science and Technology Laboratory, Chemical, Biological and Radiological Division, Porton Down, Salisbury, Wiltshire, UK
| | - Joss M Auty
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Edouard E Galyov
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, UK
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Sarah V Harding
- Defence Science and Technology Laboratory, Chemical, Biological and Radiological Division, Porton Down, Salisbury, Wiltshire, UK
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Galina V Mukamolova
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, UK.
- Department of Respiratory Sciences, University of Leicester, Leicester, UK.
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6
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Lee M, Batuecas MT, Tomoshige S, Domínguez-Gil T, Mahasenan KV, Dik DA, Hesek D, Millán C, Usón I, Lastochkin E, Hermoso JA, Mobashery S. Exolytic and endolytic turnover of peptidoglycan by lytic transglycosylase Slt of Pseudomonas aeruginosa. Proc Natl Acad Sci U S A 2018; 115:4393-4398. [PMID: 29632171 PMCID: PMC5924928 DOI: 10.1073/pnas.1801298115] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
β-Lactam antibiotics inhibit cell-wall transpeptidases, preventing the peptidoglycan, the major constituent of the bacterial cell wall, from cross-linking. This causes accumulation of long non-cross-linked strands of peptidoglycan, which leads to bacterial death. Pseudomonas aeruginosa, a nefarious bacterial pathogen, attempts to repair this aberrantly formed peptidoglycan by the function of the lytic transglycosylase Slt. We document in this report that Slt turns over the peptidoglycan by both exolytic and endolytic reactions, which cause glycosidic bond scission from a terminus or in the middle of the peptidoglycan, respectively. These reactions were characterized with complex synthetic peptidoglycan fragments that ranged in size from tetrasaccharides to octasaccharides. The X-ray structure of the wild-type apo Slt revealed it to be a doughnut-shaped protein. In a series of six additional X-ray crystal structures, we provide insights with authentic substrates into how Slt is enabled for catalysis for both the endolytic and exolytic reactions. The substrate for the exolytic reaction binds Slt in a canonical arrangement and reveals how both the glycan chain and the peptide stems are recognized by the Slt. We document that the apo enzyme does not have a fully formed active site for the endolytic reaction. However, binding of the peptidoglycan at the existing subsites within the catalytic domain causes a conformational change in the protein that assembles the surface for binding of a more expansive peptidoglycan between the catalytic domain and an adjacent domain. The complexes of Slt with synthetic peptidoglycan substrates provide an unprecedented snapshot of the endolytic reaction.
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Affiliation(s)
- Mijoon Lee
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - María T Batuecas
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Rocasolano," Consejo Superior de Investigaciones Científicas, E-28006 Madrid, Spain
| | - Shusuke Tomoshige
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Teresa Domínguez-Gil
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Rocasolano," Consejo Superior de Investigaciones Científicas, E-28006 Madrid, Spain
| | - Kiran V Mahasenan
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - David A Dik
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Dusan Hesek
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Claudia Millán
- Structural Biology Unit, Institute of Molecular Biology of Barcelona, Consejo Superior de Investigaciones Científicas, E-08028 Barcelona, Spain
| | - Isabel Usón
- Structural Biology Unit, Institute of Molecular Biology of Barcelona, Consejo Superior de Investigaciones Científicas, E-08028 Barcelona, Spain
- Structural Biology Unit, Institució Catalana de Recerca i Estudis Avançats, E-08003 Barcelona, Spain
| | - Elena Lastochkin
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Rocasolano," Consejo Superior de Investigaciones Científicas, E-28006 Madrid, Spain;
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556;
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7
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Williams AH, Wheeler R, Rateau L, Malosse C, Chamot-Rooke J, Haouz A, Taha MK, Boneca IG. A step-by-step in crystallo guide to bond cleavage and 1,6-anhydro-sugar product synthesis by a peptidoglycan-degrading lytic transglycosylase. J Biol Chem 2018; 293:6000-6010. [PMID: 29483188 DOI: 10.1074/jbc.ra117.001095] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 02/12/2018] [Indexed: 01/13/2023] Open
Abstract
Lytic transglycosylases (LTs) are a class of enzymes important for the recycling and metabolism of peptidoglycan (PG). LTs cleave the β-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and GlcNAc in the PG glycan strand, resulting in the concomitant formation of 1,6-anhydro-N-acetylmuramic acid and GlcNAc. No LTs reported to date have utilized chitins as substrates, despite the fact that chitins are GlcNAc polymers linked via β-1,4-glycosidic bonds, which are the known site of chemical activity for LTs. Here, we demonstrate enzymatically that LtgA, a non-canonical, substrate-permissive LT from Neisseria meningitidis utilizes chitopentaose ((GlcNAc)5) as a substrate to produce three newly identified sugars: 1,6-anhydro-chitobiose, 1,6-anhydro-chitotriose, and 1,6-anhydro-chitotetraose. Although LTs have been widely studied, their complex reactions have not previously been visualized in the crystalline state because macromolecular PG is insoluble. Here, we visualized the cleavage of the glycosidic bond and the liberation of GlcNAc-derived residues by LtgA, followed by the synthesis of atypical 1,6-anhydro-GlcNAc derivatives. In addition to the newly identified anhydro-chitin products, we identified trapped intermediates, unpredicted substrate rearrangements, sugar distortions, and a conserved crystallographic water molecule bound to the catalytic glutamate of a high-resolution native LT. This study enabled us to propose a revised alternative mechanism for LtgA that could also be applicable to other LTs. Our work contributes to the understanding of the mechanisms of LTs in bacterial cell wall biology.
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Affiliation(s)
- Allison H Williams
- From the Institut Pasteur, Département de Microbiologie, Unité Biologie et Génétique de la Paroi Bactérienne, 75015 Paris, France, .,INSERM, 75015 Paris, France
| | - Richard Wheeler
- From the Institut Pasteur, Département de Microbiologie, Unité Biologie et Génétique de la Paroi Bactérienne, 75015 Paris, France.,INSERM, 75015 Paris, France.,the Gustave Roussy Comprehensive Cancer Center, Tumour Immunology and Immunotherapy, F-94805 Villejuif, France
| | - Lesly Rateau
- From the Institut Pasteur, Département de Microbiologie, Unité Biologie et Génétique de la Paroi Bactérienne, 75015 Paris, France.,INSERM, 75015 Paris, France
| | - Christian Malosse
- the Institut Pasteur, CNRS USR 2000, Unité des Spectrométrie de Masse Structurale et Proteomique, 75015 Paris, France
| | - Julia Chamot-Rooke
- the Institut Pasteur, CNRS USR 2000, Unité des Spectrométrie de Masse Structurale et Proteomique, 75015 Paris, France
| | - Ahmed Haouz
- the Institut Pasteur, Plate-forme de Cristallographie, CNRS-UMR3528, 75724 Paris, France, and
| | - Muhamed-Kheir Taha
- the Institut Pasteur, Département d'Infection et Epidémiologie, Unité des Infection Bactériennes Invasives, 75015 Paris, France
| | - Ivo Gomperts Boneca
- From the Institut Pasteur, Département de Microbiologie, Unité Biologie et Génétique de la Paroi Bactérienne, 75015 Paris, France, .,INSERM, 75015 Paris, France
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8
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Structural basis for chitin acquisition by marine Vibrio species. Nat Commun 2018; 9:220. [PMID: 29335469 PMCID: PMC5768706 DOI: 10.1038/s41467-017-02523-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 12/07/2017] [Indexed: 11/18/2022] Open
Abstract
Chitin, an insoluble polymer of N-acetylglucosamine, is one of the most abundant biopolymers on Earth. By degrading chitin, chitinolytic bacteria such as Vibrio harveyi are critical for chitin recycling and maintenance of carbon and nitrogen cycles in the world’s oceans. A decisive step in chitin degradation is the uptake of chito-oligosaccharides by an outer membrane protein channel named chitoporin (ChiP). Here, we report X-ray crystal structures of ChiP from V. harveyi in the presence and absence of chito-oligosaccharides. Structures without bound sugar reveal a trimeric assembly with an unprecedented closing of the transport pore by the N-terminus of a neighboring subunit. Substrate binding ejects the pore plug to open the transport channel. Together with molecular dynamics simulations, electrophysiology and in vitro transport assays our data provide an explanation for the exceptional affinity of ChiP for chito-oligosaccharides and point to an important role of the N-terminal gate in substrate transport. Chitin degrading bacteria are important for marine ecosystems. Here the authors structurally and functionally characterize the Vibrio harveyi outer membrane diffusion channel chitoporin and give mechanistic insights into chito-oligosaccharide uptake.
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9
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Dik DA, Marous DR, Fisher JF, Mobashery S. Lytic transglycosylases: concinnity in concision of the bacterial cell wall. Crit Rev Biochem Mol Biol 2017. [PMID: 28644060 DOI: 10.1080/10409238.2017.1337705] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The lytic transglycosylases (LTs) are bacterial enzymes that catalyze the non-hydrolytic cleavage of the peptidoglycan structures of the bacterial cell wall. They are not catalysts of glycan synthesis as might be surmised from their name. Notwithstanding the seemingly mundane reaction catalyzed by the LTs, their lytic reactions serve bacteria for a series of astonishingly diverse purposes. These purposes include cell-wall synthesis, remodeling, and degradation; for the detection of cell-wall-acting antibiotics; for the expression of the mechanism of cell-wall-acting antibiotics; for the insertion of secretion systems and flagellar assemblies into the cell wall; as a virulence mechanism during infection by certain Gram-negative bacteria; and in the sporulation and germination of Gram-positive spores. Significant advances in the mechanistic understanding of each of these processes have coincided with the successive discovery of new LTs structures. In this review, we provide a systematic perspective on what is known on the structure-function correlations for the LTs, while simultaneously identifying numerous opportunities for the future study of these enigmatic enzymes.
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Affiliation(s)
- David A Dik
- a Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , IN , USA
| | - Daniel R Marous
- a Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , IN , USA
| | - Jed F Fisher
- a Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , IN , USA
| | - Shahriar Mobashery
- a Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , IN , USA
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10
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Carbohydrate recognition and lysis by bacterial peptidoglycan hydrolases. Curr Opin Struct Biol 2017; 44:87-100. [PMID: 28109980 DOI: 10.1016/j.sbi.2017.01.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 12/23/2016] [Accepted: 01/02/2017] [Indexed: 01/26/2023]
Abstract
The major component of bacterial cell wall is peptidoglycan (PG), a complex polymer formed by long glycan chains cross-linked by peptide stems. PG is in constant equilibrium requiring well-orchestrated coordination between synthesis and degradation. The resulting cell-wall fragments can be recycled, act as messengers for bacterial communication, as effector molecules in immune response or as signaling molecules triggering antibiotics resistance. Tailoring and recycling of PG requires the cleavage of different covalent bonds of the PG sacculi by a diverse set of specific enzymes whose activities are strictly regulated. Here, we review the molecular mechanisms that govern PG remodeling focusing on the structural information available for the bacterial lytic enzymes and the mechanisms by which they recognize their substrates.
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11
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Gaber Y, Mekasha S, Vaaje-Kolstad G, Eijsink VG, Fraaije MW. Characterization of a chitinase from the cellulolytic actinomycete Thermobifida fusca. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1253-1259. [DOI: 10.1016/j.bbapap.2016.04.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 03/22/2016] [Accepted: 04/20/2016] [Indexed: 01/19/2023]
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12
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Domínguez-Gil T, Molina R, Alcorlo M, Hermoso JA. Renew or die: The molecular mechanisms of peptidoglycan recycling and antibiotic resistance in Gram-negative pathogens. Drug Resist Updat 2016; 28:91-104. [PMID: 27620957 DOI: 10.1016/j.drup.2016.07.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Antimicrobial resistance is one of the most serious health threats. Cell-wall remodeling processes are tightly regulated to warrant bacterial survival and in some cases are directly linked to antibiotic resistance. Remodeling produces cell-wall fragments that are recycled but can also act as messengers for bacterial communication, as effector molecules in immune response and as signaling molecules triggering antibiotic resistance. This review is intended to provide state-of-the-art information about the molecular mechanisms governing this process and gather structural information of the different macromolecular machineries involved in peptidoglycan recycling in Gram-negative bacteria. The growing body of literature on the 3D structures of the corresponding macromolecules reveals an extraordinary complexity. Considering the increasing incidence and widespread emergence of Gram-negative multidrug-resistant pathogens in clinics, structural information on the main actors of the recycling process paves the way for designing novel antibiotics disrupting cellular communication in the recycling-resistance pathway.
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Affiliation(s)
- Teresa Domínguez-Gil
- Department of Crystallography and Structural Biology, Inst. Química-Física "Rocasolano", CSIC, Serrano 119, 28006 Madrid, Spain
| | - Rafael Molina
- Department of Crystallography and Structural Biology, Inst. Química-Física "Rocasolano", CSIC, Serrano 119, 28006 Madrid, Spain
| | - Martín Alcorlo
- Department of Crystallography and Structural Biology, Inst. Química-Física "Rocasolano", CSIC, Serrano 119, 28006 Madrid, Spain
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Inst. Química-Física "Rocasolano", CSIC, Serrano 119, 28006 Madrid, Spain.
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13
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Lee M, Domínguez-Gil T, Hesek D, Mahasenan KV, Lastochkin E, Hermoso JA, Mobashery S. Turnover of Bacterial Cell Wall by SltB3, a Multidomain Lytic Transglycosylase of Pseudomonas aeruginosa. ACS Chem Biol 2016; 11:1525-31. [PMID: 27035839 DOI: 10.1021/acschembio.6b00194] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A family of 11 lytic transglycosylases in Pseudomonas aeruginosa, an opportunistic human pathogen, turn over the polymeric bacterial cell wall in the course of its recycling, repair, and maturation. The functions of these enzymes are not fully understood. We disclose herein that SltB3 of P. aeruginosa is an exolytic lytic transglycosylase. We characterize its reaction and its products by the use of peptidoglycan-based molecules. The enzyme recognizes a minimum of four sugars in its substrate but can process a substrate comprised of a peptidoglycan of 20 sugars. The ultimate product of the reaction is N-acetylglucosamine-1,6-anhydro-N-acetylmuramic acid. The X-ray structure of this enzyme is reported for the first time. The enzyme is comprised of four domains, arranged within an annular conformation. The polymeric linear peptidoglycan substrate threads through the opening of the annulus, as it experiences turnover.
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Affiliation(s)
- Mijoon Lee
- Department
of Chemistry and Biochemistry, University of Notre Dame, Nieuwland
Science Hall, Notre Dame, Indiana 46556, United States
| | - Teresa Domínguez-Gil
- Department
of Crystallography and Structural Biology, Inst. Química-Física “Rocasolano”, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Dusan Hesek
- Department
of Chemistry and Biochemistry, University of Notre Dame, Nieuwland
Science Hall, Notre Dame, Indiana 46556, United States
| | - Kiran V. Mahasenan
- Department
of Chemistry and Biochemistry, University of Notre Dame, Nieuwland
Science Hall, Notre Dame, Indiana 46556, United States
| | - Elena Lastochkin
- Department
of Chemistry and Biochemistry, University of Notre Dame, Nieuwland
Science Hall, Notre Dame, Indiana 46556, United States
| | - Juan A. Hermoso
- Department
of Crystallography and Structural Biology, Inst. Química-Física “Rocasolano”, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Shahriar Mobashery
- Department
of Chemistry and Biochemistry, University of Notre Dame, Nieuwland
Science Hall, Notre Dame, Indiana 46556, United States
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14
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Quay DHX, Cole AR, Cryar A, Thalassinos K, Williams MA, Bhakta S, Keep NH. Structure of the stationary phase survival protein YuiC from B.subtilis. BMC STRUCTURAL BIOLOGY 2015; 15:12. [PMID: 26163297 PMCID: PMC4499186 DOI: 10.1186/s12900-015-0039-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 07/02/2015] [Indexed: 11/23/2022]
Abstract
Background Stationary phase survival proteins (Sps) were found in Firmicutes as having analogous domain compositions, and in some cases genome context, as the resuscitation promoting factors of Actinobacteria, but with a different putative peptidoglycan cleaving domain. Results The first structure of a Firmicute Sps protein YuiC from B. subtilis, is found to be a stripped down version of the cell-wall peptidoglycan hydrolase MltA. The YuiC structures are of a domain swapped dimer, although some monomer is also found in solution. The protein crystallised in the presence of pentasaccharide shows a 1,6-anhydrodisaccharide sugar product, indicating that YuiC cleaves the sugar backbone to form an anhydro product at least on lengthy incubation during crystallisation. Conclusions The structural simplification of MltA in Sps proteins is analogous to that of the resuscitation promoting factor domains of Actinobacteria, which are stripped down versions of lysozyme and soluble lytic transglycosylase proteins. Electronic supplementary material The online version of this article (doi:10.1186/s12900-015-0039-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Doris H X Quay
- Institute for Structural and Molecular Biology, Crystallography, Department of Biological Sciences, Birkbeck University of London, Malet Street, London, WC1E 7HX, UK.
| | - Ambrose R Cole
- Institute for Structural and Molecular Biology, Crystallography, Department of Biological Sciences, Birkbeck University of London, Malet Street, London, WC1E 7HX, UK.
| | - Adam Cryar
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, UK.
| | - Konstantinos Thalassinos
- Institute for Structural and Molecular Biology, Crystallography, Department of Biological Sciences, Birkbeck University of London, Malet Street, London, WC1E 7HX, UK. .,Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, UK.
| | - Mark A Williams
- Institute for Structural and Molecular Biology, Crystallography, Department of Biological Sciences, Birkbeck University of London, Malet Street, London, WC1E 7HX, UK.
| | - Sanjib Bhakta
- Institute for Structural and Molecular Biology, Crystallography, Department of Biological Sciences, Birkbeck University of London, Malet Street, London, WC1E 7HX, UK.
| | - Nicholas H Keep
- Institute for Structural and Molecular Biology, Crystallography, Department of Biological Sciences, Birkbeck University of London, Malet Street, London, WC1E 7HX, UK.
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15
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Jorgenson MA, Chen Y, Yahashiri A, Popham DL, Weiss DS. The bacterial septal ring protein RlpA is a lytic transglycosylase that contributes to rod shape and daughter cell separation in Pseudomonas aeruginosa. Mol Microbiol 2014; 93:113-28. [PMID: 24806796 DOI: 10.1111/mmi.12643] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2014] [Indexed: 11/28/2022]
Abstract
Rare lipoprotein A (RlpA) is a widely conserved outer membrane protein of unknown function that has previously only been studied in Escherichia coli, where it localizes to the septal ring and scattered foci along the lateral wall, but mutants have no phenotypic change. Here we show rlpA mutants of Pseudomonas aeruginosa form chains of short, fat cells when grown in low osmotic strength media. These morphological defects indicate RlpA is needed for efficient separation of daughter cells and maintenance of rod shape. Analysis of peptidoglycan sacculi from an rlpA deletion mutant revealed increased tetra and hexasaccharides that lack stem peptides (hereafter called 'naked glycans'). Incubation of these sacculi with purified RlpA resulted in release of naked glycans containing 1,6-anhydro N-acetylmuramic acid ends. RlpA did not degrade sacculi from wild-type cells unless the sacculi were subjected to a limited digestion with an amidase to remove some of the stem peptides. Thus, RlpA is a lytic transglycosylase with a strong preference for naked glycan strands. We propose that RlpA activity is regulated in vivo by substrate availability, and that amidases and RlpA work in tandem to degrade peptidoglycan in the division septum and lateral wall.
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Affiliation(s)
- Matthew A Jorgenson
- Department of Microbiology, Carver College of Medicine, The University of Iowa, Iowa City, IA, 52242, USA
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16
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TraG encoded by the pIP501 type IV secretion system is a two-domain peptidoglycan-degrading enzyme essential for conjugative transfer. J Bacteriol 2013; 195:4436-44. [PMID: 23913323 DOI: 10.1128/jb.02263-12] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
pIP501 is a conjugative broad-host-range plasmid frequently present in nosocomial Enterococcus faecalis and Enterococcus faecium isolates. We focus here on the functional analysis of the type IV secretion gene traG, which was found to be essential for pIP501 conjugative transfer between Gram-positive bacteria. The TraG protein, which localizes to the cell envelope of E. faecalis harboring pIP501, was expressed and purified without its N-terminal transmembrane helix (TraGΔTMH) and shown to possess peptidoglycan-degrading activity. TraGΔTMH was inhibited by specific lytic transglycosylase inhibitors hexa-N-acetylchitohexaose and bulgecin A. Analysis of the TraG sequence suggested the presence of two domains which both could contribute to the observed cell wall-degrading activity: an N-terminal soluble lytic transglycosylase domain (SLT) and a C-terminal cysteine-, histidine-dependent amidohydrolases/peptidases (CHAP) domain. The protein domains were expressed separately, and both degraded peptidoglycan. A change of the conserved glutamate residue in the putative catalytic center of the SLT domain (E87) to glycine resulted in almost complete inactivity, which is consistent with this part of TraG being a predicted lytic transglycosylase. Based on our findings, we propose that TraG locally opens the peptidoglycan to facilitate insertion of the Gram-positive bacterial type IV secretion machinery into the cell envelope.
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17
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Smith LJ, Bowen AM, Di Paolo A, Matagne A, Redfield C. The Dynamics of Lysozyme from Bacteriophage Lambda in Solution Probed by NMR and MD Simulations. Chembiochem 2013; 14:1780-8. [DOI: 10.1002/cbic.201300193] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Indexed: 11/09/2022]
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18
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Abstract
Many Gram-negative and Gram-positive bacteria recycle a significant proportion of the peptidoglycan components of their cell walls during their growth and septation. In many--and quite possibly all--bacteria, the peptidoglycan fragments are recovered and recycled. Although cell-wall recycling is beneficial for the recovery of resources, it also serves as a mechanism to detect cell-wall-targeting antibiotics and to regulate resistance mechanisms. In several Gram-negative pathogens, anhydro-MurNAc-peptide cell-wall fragments regulate AmpC β-lactamase induction. In some Gram-positive organisms, short peptides derived from the cell wall regulate the induction of both β-lactamase and β-lactam-resistant penicillin-binding proteins. The involvement of peptidoglycan recycling with resistance regulation suggests that inhibitors of the enzymes involved in the recycling might synergize with cell-wall-targeted antibiotics. Indeed, such inhibitors improve the potency of β-lactams in vitro against inducible AmpC β-lactamase-producing bacteria. We describe the key steps of cell-wall remodeling and recycling, the regulation of resistance mechanisms by cell-wall recycling, and recent advances toward the discovery of cell-wall-recycling inhibitors.
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Affiliation(s)
- Jarrod W Johnson
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
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19
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Fibriansah G, Gliubich FI, Thunnissen AMWH. On the Mechanism of Peptidoglycan Binding and Cleavage by the endo-Specific Lytic Transglycosylase MltE from Escherichia coli. Biochemistry 2012; 51:9164-77. [DOI: 10.1021/bi300900t] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Guntur Fibriansah
- Laboratory
of Biophysical Chemistry, Groningen Biomolecular
Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Francesca I. Gliubich
- Laboratory
of Biophysical Chemistry, Groningen Biomolecular
Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Andy-Mark W. H. Thunnissen
- Laboratory
of Biophysical Chemistry, Groningen Biomolecular
Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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20
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Abstract
The review summarizes the abundant information on the 35 identified peptidoglycan (PG) hydrolases of Escherichia coli classified into 12 distinct families, including mainly glycosidases, peptidases, and amidases. An attempt is also made to critically assess their functions in PG maturation, turnover, elongation, septation, and recycling as well as in cell autolysis. There is at least one hydrolytic activity for each bond linking PG components, and most hydrolase genes were identified. Few hydrolases appear to be individually essential. The crystal structures and reaction mechanisms of certain hydrolases having defined functions were investigated. However, our knowledge of the biochemical properties of most hydrolases still remains fragmentary, and that of their cellular functions remains elusive. Owing to redundancy, PG hydrolases far outnumber the enzymes of PG biosynthesis. The presence of the two sets of enzymes acting on the PG bonds raises the question of their functional correlations. It is difficult to understand why E. coli keeps such a large set of PG hydrolases. The subtle differences in substrate specificities between the isoenzymes of each family certainly reflect a variety of as-yet-unidentified physiological functions. Their study will be a far more difficult challenge than that of the steps of the PG biosynthesis pathway.
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Affiliation(s)
- Jean van Heijenoort
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Bat 430, Université Paris-Sud, Orsay F-91405, France.
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21
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Artola-Recolons C, Carrasco-López C, Llarrull LI, Kumarasiri M, Lastochkin E, Martínez de Ilarduya I, Meindl K, Usón I, Mobashery S, Hermoso JA. High-resolution crystal structure of MltE, an outer membrane-anchored endolytic peptidoglycan lytic transglycosylase from Escherichia coli. Biochemistry 2011; 50:2384-6. [PMID: 21341761 DOI: 10.1021/bi200085y] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The crystal structure of the first endolytic peptidoglycan lytic transglycosylase MltE from Escherichia coli is reported here. The degradative activity of this enzyme initiates the process of cell wall recycling, which is an integral event in the existence of bacteria. The structure sheds light on how MltE recognizes its substrate, the cell wall peptidoglycan. It also explains the ability of this endolytic enzyme to cleave in the middle of the peptidoglycan chains. Furthermore, the structure reveals how the enzyme is sequestered on the inner leaflet of the outer membrane.
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Affiliation(s)
- Cecilia Artola-Recolons
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Rocasolano", CSIC, Serrano 119, 28006 Madrid, Spain
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22
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Artola-Recolons C, Llarrull LI, Lastochkin E, Mobashery S, Hermoso JA. Crystallization and preliminary X-ray diffraction analysis of the lytic transglycosylase MltE from Escherichia coli. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:161-3. [PMID: 21206052 PMCID: PMC3080000 DOI: 10.1107/s1744309110049171] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Accepted: 11/24/2010] [Indexed: 11/10/2022]
Abstract
MltE from Escherichia coli (193 amino acids, 21,380 Da) is a lytic transglycosylase that initiates the first step of cell-wall recycling. This enzyme is responsible for the cleavage of the cell-wall peptidoglycan at the β-1,4-glycosidic bond between the N-acetylglucosamine and N-acetylmuramic acid units. At the end this reaction generates a disaccharide that is internalized and initiates the recycling process. To obtain insights into the biological functions of MltE, crystallization trials were performed and crystals of MltE protein that were suitable for X-ray diffraction analysis were obtained. The MltE protein of E. coli was crystallized using the hanging-drop vapour-diffusion method at 291 K. Crystals grew from a mixture consisting of 28% polyethylene glycol 4000, 0.1 M Tris pH 8.4 and 0.2 M magnesium chloride. Further optimization was performed using the microbatch technique. Single crystals were obtained that belonged to the orthorhombic space group C222(1), with unit-cell parameters a=123.32, b=183.93, c=35.29 Å, and diffracted to a resolution of 2.1 Å.
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Affiliation(s)
- Cecilia Artola-Recolons
- Department of Crystallography and Structural Biology, Instituto de Química-Física ‘Rocasolano’, Consejo Superior de Investigaciones Científicas, Serrano 119, Madrid 28006, Spain
| | - Leticia I. Llarrull
- Department of Chemistry and Biochemistry, Nieuwland Science Hall, Notre Dame, Indiana 46556, USA
| | - Elena Lastochkin
- Department of Chemistry and Biochemistry, Nieuwland Science Hall, Notre Dame, Indiana 46556, USA
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, Nieuwland Science Hall, Notre Dame, Indiana 46556, USA
| | - Juan A. Hermoso
- Department of Crystallography and Structural Biology, Instituto de Química-Física ‘Rocasolano’, Consejo Superior de Investigaciones Científicas, Serrano 119, Madrid 28006, Spain
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Bacillus subtilis CwlQ (previous YjbJ) is a bifunctional enzyme exhibiting muramidase and soluble-lytic transglycosylase activities. Biochem Biophys Res Commun 2010; 398:606-12. [PMID: 20609359 DOI: 10.1016/j.bbrc.2010.07.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Accepted: 07/01/2010] [Indexed: 11/22/2022]
Abstract
CwlQ (previous YjbJ) is one of the putative cell wall hydrolases in Bacillus subtilis. Its domain has an amino acid sequence similar to the soluble-lytic transglycosylase (SLT) of Escherichia coli Slt70 and also goose lysozyme (muramidase). To characterize the enzyme, the domain of CwlQ was cloned and expressed in E. coli. The purified CwlQ protein exhibited cell wall hydrolytic activity. Surprisingly, RP-HPLC, mass spectrometry (MS), and MS/MS analyses showed that CwlQ produces two products, 1,6-anhydro-N-acetylmuramic acid and N-acetylmuramic acid, thus indicating that CwlQ is a bifunctional enzyme. The site-directed mutagenesis revealed that glutamic acid 85 (Glu-85) is an amino acid residue essential to both activities.
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24
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Madoori PK, Thunnissen AMWH. Purification, crystallization and preliminary X-ray diffraction analysis of the lytic transglycosylase MltF from Escherichia coli. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:534-8. [PMID: 20445253 PMCID: PMC2864686 DOI: 10.1107/s1744309110010596] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2009] [Accepted: 03/21/2010] [Indexed: 11/10/2022]
Abstract
The lytic transglycosylase MltF from Escherichia coli is an outer-membrane-bound periplasmic protein with two domains: a C-terminal catalytic domain with a lysozyme-like fold and an N-terminal domain of unknown function that is homologous to the periplasmic substrate-binding proteins of ABC transporters. In order to investigate its structure and function, a soluble form of full-length MltF (sMltF) containing both domains and a soluble fragment containing only the N-terminal domain (sMltF-NTD) were purified and crystallized. Crystals of sMltF belonged to space group P4(3)2(1)2 or P4(1)2(1)2, with unit-cell parameters a = b = 110.8, c = 163.5 A and one or two molecules per asymmetric unit. A complete data set was collected to 3.5 A resolution. Crystals of sMltF-NTD belonged to space group P3(1)21, with unit-cell parameters a = b = 82.4, c = 75.2 A and one molecule per asymmetric unit. For sMltF-NTD, a complete native data set was collected to 2.20 A resolution. In addition, for phasing purposes, a three-wavelength MAD data set was collected to 2.5 A resolution using a bromide-soaked sMltF-NTD crystal. Using phases derived from the Br-MAD data, it was possible to build a partial model of sMltF-NTD.
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Affiliation(s)
- Pramod K. Madoori
- Department of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Andy-Mark W. H. Thunnissen
- Department of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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25
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Clair G, Roussi S, Armengaud J, Duport C. Expanding the known repertoire of virulence factors produced by Bacillus cereus through early secretome profiling in three redox conditions. Mol Cell Proteomics 2010; 9:1486-98. [PMID: 20368289 DOI: 10.1074/mcp.m000027-mcp201] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The pathogen Bacillus cereus causes diarrheal disease in humans. In the small intestine, B. cereus has to deal with anaerobiosis, low oxidoreduction potential, and carbohydrate limitation conditions. To gain insight into the virulence potential of low density B. cereus cells in such an environment, we cultured bacteria in low and high oxidoreduction potential anoxic conditions and in fully oxic conditions and compared their full secretomes. A unique pattern of proteins assigned to virulence factors was revealed. Among the 57 virulence-related factors, 31 were found for the first time in the B. cereus secretome. The putative fourth component of hemolysin BL (HblB'), enterotoxin FM, hemolysin II, and three new putative conserved enterotoxins were uncovered. Cross-comparison of the relative abundance of secreted proteins reveals that a restricted set comprising 19 proteins showed significant changes in response to redox condition changes. We complemented these results with transcriptomics data and confirmed the cytotoxicity of the B. cereus secretome toward Caco-2 human epithelial cells. Our data suggest that (i) the redox-dependent regulatory pathway may modulate the expression of a subset of virulence factors to ensure an appropriate response in a specific redox environment, and (ii) an early growth phase-dependent pathway could regulate the expression of several virulence factors, allowing B. cereus to infect a host whatever the redox conditions. This early growth phase-dependent pathway may function, at least partially, independently of the pleiotropic virulence gene regulator PlcR and may therefore be more specific to the B. cereus group.
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Affiliation(s)
- Gérémy Clair
- UMR408, Université d'Avignon et des Pays de Vaucluse, F-84000 Avignon, France
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26
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Morlot C, Uehara T, Marquis KA, Bernhardt TG, Rudner DZ. A highly coordinated cell wall degradation machine governs spore morphogenesis in Bacillus subtilis. Genes Dev 2010; 24:411-22. [PMID: 20159959 DOI: 10.1101/gad.1878110] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
How proteins catalyze morphogenesis is an outstanding question in developmental biology. In bacteria, morphogenesis is intimately linked to remodeling the cell wall exoskeleton. Here, we investigate the mechanisms by which the mother cell engulfs the prospective spore during sporulation in Bacillus subtilis. A membrane-anchored protein complex containing two cell wall hydrolases plays a central role in this morphological process. We demonstrate that one of the proteins (SpoIIP) has both amidase and endopeptidase activities, such that it removes the stem peptides from the cell wall and cleaves the cross-links between them. We further show that the other protein (SpoIID) is the founding member of a new family of lytic transglycosylases that degrades the glycan strands of the peptidoglycan into disaccharide units. Importantly, we show that SpoIID binds the cell wall, but will only cleave the glycan strands after the stem peptides have been removed. Finally, we demonstrate that SpoIID also functions as an enhancer of SpoIIP activity. Thus, this membrane-anchored enzyme complex is endowed with complementary, sequential, and stimulatory activities. These activities provide a mechanism for processive cell wall degradation, supporting a model in which circumferentially distributed degradation machines function as motors pulling the mother cell membranes around the forespore.
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Affiliation(s)
- Cecile Morlot
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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27
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Shah IM, Dworkin J. Induction and regulation of a secreted peptidoglycan hydrolase by a membrane Ser/Thr kinase that detects muropeptides. Mol Microbiol 2010; 75:1232-43. [PMID: 20070526 DOI: 10.1111/j.1365-2958.2010.07046.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Here, we report that the model Gram-positive organism, Bacillus subtilis, expresses and secretes a muralytic enzyme, YocH, in response to cell wall-derived muropeptides derived from growing cells but not lysed cells. This induction is dependent on PrkC, a membrane Ser/Thr kinase that binds to peptidoglycan and that belongs to a broadly conserved family including the essential PknB kinase of M. tuberculosis. YocH stimulates its own expression in a PrkC-dependent manner demonstrating the presence of an autoregulatory loop during growth. Cells lacking YocH display a survival defect in stationary phase but enzymes secreted by other cells in the culture rescue this defect. The essential translation factor EF-G is an in vivo substrate of PrkC and this phosphorylation occurs in response to muropeptides. Therefore, we hypothesize that YocH is used by the bacterium to digest peptidoglycan released by other bacteria in the milieu and that the presence of these fragments is detected by a membrane kinase that modifies a key regulator of translation as well as to stimulate its own expression.
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Affiliation(s)
- Ishita M Shah
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
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28
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Kövér KE, Szilágyi L, Batta G, Uhrín D, Jiménez-Barbero J. Biomolecular Recognition by Oligosaccharides and Glycopeptides: The NMR Point of View. COMPREHENSIVE NATURAL PRODUCTS II 2010:197-246. [DOI: 10.1016/b978-008045382-8.00193-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/27/2023]
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29
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Crystal structure and activity of Bacillus subtilis YoaJ (EXLX1), a bacterial expansin that promotes root colonization. Proc Natl Acad Sci U S A 2008; 105:16876-81. [PMID: 18971341 DOI: 10.1073/pnas.0809382105] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We solved the crystal structure of a secreted protein, EXLX1, encoded by the yoaJ gene of Bacillus subtilis. Its structure is remarkably similar to that of plant beta-expansins (group 1 grass pollen allergens), consisting of 2 tightly packed domains (D1, D2) with a potential polysaccharide-binding surface spanning the 2 domains. Domain D1 has a double-psi beta-barrel fold with partial conservation of the catalytic site found in family 45 glycosyl hydrolases and in the MltA family of lytic transglycosylases. Domain D2 has an Ig-like fold similar to group 2/3 grass pollen allergens, with structural features similar to a type A carbohydrate-binding domain. EXLX1 bound to plant cell walls, cellulose, and peptidoglycan, but it lacked lytic activity against a variety of plant cell wall polysaccharides and peptidoglycan. EXLX1 promoted plant cell wall extension similar to, but 10 times weaker than, plant beta-expansins, which synergistically enhanced EXLX1 activity. Deletion of the gene encoding EXLX1 did not affect growth or peptidoglycan composition of B. subtilis in liquid medium, but slowed lysis upon osmotic shock and greatly reduced the ability of the bacterium to colonize maize roots. The presence of EXLX1 homologs in a small but diverse set of plant pathogens further supports a role in plant-bacterial interactions. Because plant expansins have proved difficult to express in active form in heterologous systems, the discovery of a bacterial homolog opens the door for detailed structural studies of expansin function.
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Vollmer W, Joris B, Charlier P, Foster S. Bacterial peptidoglycan (murein) hydrolases. FEMS Microbiol Rev 2008; 32:259-86. [PMID: 18266855 DOI: 10.1111/j.1574-6976.2007.00099.x] [Citation(s) in RCA: 609] [Impact Index Per Article: 38.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Most bacteria have multiple peptidoglycan hydrolases capable of cleaving covalent bonds in peptidoglycan sacculi or its fragments. An overview of the different classes of peptidoglycan hydrolases and their cleavage sites is provided. The physiological functions of these enzymes include the regulation of cell wall growth, the turnover of peptidoglycan during growth, the separation of daughter cells during cell division and autolysis. Specialized hydrolases enlarge the pores in the peptidoglycan for the assembly of large trans-envelope complexes (pili, flagella, secretion systems), or they specifically cleave peptidoglycan during sporulation or spore germination. Moreover, peptidoglycan hydrolases are involved in lysis phenomena such as fratricide or developmental lysis occurring in bacterial populations. We will also review the current view on the regulation of autolysins and on the role of cytoplasm hydrolases in peptidoglycan recycling and induction of beta-lactamase.
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Affiliation(s)
- Waldemar Vollmer
- Institute for Cell and Molecular Biosciences, University of Newcastle upon Tyne, Newcastle upon Tyne, UK.
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Sureshan KM, Trusselle M, Tovey SC, Taylor CW, Potter BVL. 2-Position Base-Modified Analogues of Adenophostin A as High-Affinity Agonists of the d-myo-Inositol Trisphosphate Receptor: In Vitro Evaluation and Molecular Modeling. J Org Chem 2008; 73:1682-92. [DOI: 10.1021/jo702617c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kana M. Sureshan
- Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, U.K., and Department of Pharmacology, Tennis Court Road, University of Cambridge, Cambridge CB2 1PD, U.K
| | - Melanie Trusselle
- Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, U.K., and Department of Pharmacology, Tennis Court Road, University of Cambridge, Cambridge CB2 1PD, U.K
| | - Stephen C. Tovey
- Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, U.K., and Department of Pharmacology, Tennis Court Road, University of Cambridge, Cambridge CB2 1PD, U.K
| | - Colin W. Taylor
- Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, U.K., and Department of Pharmacology, Tennis Court Road, University of Cambridge, Cambridge CB2 1PD, U.K
| | - Barry V. L. Potter
- Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, U.K., and Department of Pharmacology, Tennis Court Road, University of Cambridge, Cambridge CB2 1PD, U.K
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