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Chen X, Molenda O, Brown CT, Toth CRA, Guo S, Luo F, Howe J, Nesbø CL, He C, Montabana EA, Cate JHD, Banfield JF, Edwards EA. " Candidatus Nealsonbacteria" Are Likely Biomass Recycling Ectosymbionts of Methanogenic Archaea in a Stable Benzene-Degrading Enrichment Culture. Appl Environ Microbiol 2023; 89:e0002523. [PMID: 37098974 PMCID: PMC10231131 DOI: 10.1128/aem.00025-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/20/2023] [Indexed: 04/27/2023] Open
Abstract
The Candidate Phyla Radiation (CPR), also referred to as superphylum Patescibacteria, is a very large group of bacteria with no pure culture representatives discovered by 16S rRNA sequencing or genome-resolved metagenomic analyses of environmental samples. Within the CPR, candidate phylum Parcubacteria, previously referred to as OD1, is prevalent in anoxic sediments and groundwater. Previously, we had identified a specific member of the Parcubacteria (referred to as DGGOD1a) as an important member of a methanogenic benzene-degrading consortium. Phylogenetic analyses herein place DGGOD1a within the clade "Candidatus Nealsonbacteria." Because of its persistence over many years, we hypothesized that "Ca. Nealsonbacteria" DGGOD1a must play an important role in sustaining anaerobic benzene metabolism in the consortium. To try to identify its growth substrate, we amended the culture with a variety of defined compounds (pyruvate, acetate, hydrogen, DNA, and phospholipid), as well as crude culture lysate and three subfractions thereof. We observed the greatest (10-fold) increase in the absolute abundance of "Ca. Nealsonbacteria" DGGOD1a only when the consortium was amended with crude cell lysate. These results implicate "Ca. Nealsonbacteria" in biomass recycling. Fluorescence in situ hybridization and cryogenic transmission electron microscope images revealed that "Ca. Nealsonbacteria" DGGOD1a cells were attached to larger archaeal Methanothrix cells. This apparent epibiont lifestyle was supported by metabolic predictions from a manually curated complete genome. This is one of the first examples of bacterial-archaeal episymbiosis and may be a feature of other "Ca. Nealsonbacteria" found in anoxic environments. IMPORTANCE An anaerobic microbial enrichment culture was used to study members of candidate phyla that are difficult to grow in the lab. We were able to visualize tiny "Candidatus Nealsonbacteria" cells attached to a large Methanothrix cell, revealing a novel episymbiosis.
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Affiliation(s)
- Xu Chen
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Olivia Molenda
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Christopher T. Brown
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, California, USA
| | - Courtney R. A. Toth
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Shen Guo
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Fei Luo
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Jane Howe
- Department of Materials Science and Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Camilla L. Nesbø
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Christine He
- Innovative Genomics Institute, University of California, Berkeley, California, USA
| | - Elizabeth A. Montabana
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jamie H. D. Cate
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Chemistry, University of California, Berkeley, California, USA
| | - Jillian F. Banfield
- Innovative Genomics Institute, University of California, Berkeley, California, USA
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Earth and Planetary Science, University of California, Berkeley, California, USA
- Environmental Science, Policy and Management, University of California, Berkeley, California, USA
| | - Elizabeth A. Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
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Ejaz U, Saleem F, Rashid R, Hasan KA, Syed MN, Sohail M. Unveiling the genomic potential of a novel thermostable glycoside hydrolases producing Neobacillus sedimentimangrovi UE25. Antonie Van Leeuwenhoek 2023:10.1007/s10482-023-01835-y. [PMID: 37140754 DOI: 10.1007/s10482-023-01835-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 04/24/2023] [Indexed: 05/05/2023]
Abstract
Genetic and enzymatic potential of Neobacillus sedimentimangrovi has not been assembled to date. Here, we report a high-quality genome assembly of thermophilic bacterium Neobacillus sedimentimangrovi UE25 using Illumina Hi-seq 2500. The strain was isolated from a crocodile pond Manghopir, Karachi, Pakistan. QUAST quality parameters showed 37.75% GC content and exhibited the genome into 110 contigs, with a total size of 3,230,777 bases. Genome of N. sedimentimangrovi UE25 harbors phage mediated DNA through horizontal gene exchange from the phages, symbiotic and pathogenic bacteria. Most of the phage genome encodes for hypothetical proteins, protease, and phage assembly proteins. Gene clusters encoding the intrinsic resistance to glycopeptides, isoniazid, rifamycin, elfamycin, macrolide, aminoglycosides, tetracycline and fluoroquinolone were identified into the genome. Since, the strain has been reported for the production of many industrially important thermostable enzymes, therefore, the genomic data of thermostable enzymes might be helpful to employ this species in commercial sectors. Probing genes of multiple thermostable glycoside hydrolase enzymes especially xylanases of N. sedimentimangrovi UE25 showed genetic diversity among the genes and confer the industrial importance of this microorganism. Furthermore, the genome of N. sedimentimangrovi will greatly improve our understanding of its genetics and evolution.
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Affiliation(s)
- Uroosa Ejaz
- Department of Biosciences, Faculty of Life Sciences, Shaheed Zulfikar Ali Bhutto Institute of Science and Technology (SZABIST), Karachi, 75600, Pakistan
- Department of Microbiology, University of Karachi, Karachi, 75600, Pakistan
| | - Faizan Saleem
- Department of Biology, McMaster University, Hamilton, ON, L8S 4L8, Canada
| | - Rozina Rashid
- Department of Microbiology, University of Karachi, Karachi, 75600, Pakistan
- Department of Microbiology, University of Balochistan, Quetta, Pakistan
| | - Khwaja Ali Hasan
- Molecular and Structural Biology Research Unit, Department of Biochemistry, University of Karachi, Karachi, 75270, Pakistan
| | - Muhammad Noman Syed
- Nutritional Biochemistry Research Unit, Department of Biochemistry, University of Karachi, Karachi, 75270, Pakistan
| | - Muhammad Sohail
- Department of Microbiology, University of Karachi, Karachi, 75600, Pakistan.
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Functional Characterisation of Two Novel Deacetylases from Streptococcus pyogenes. MICROBIOLOGY RESEARCH 2022. [DOI: 10.3390/microbiolres13020025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Streptococcus pyogenes (Group A Streptococcus, GAS) is an exclusively human pathogen that causes a wide range of diseases. We have identified two novel proteins, Spy1094 and Spy1370, which show sequence similarity with peptidoglycan deacetylases (PGDAs) from other streptococcal species like S. pneumoniae and S. iniae, that represent important virulence factors. Recombinant Spy1094 and Spy1370 were active at a wide pH range (pH 4.0–9.0) and showed metal ion-dependence, with the highest activities observed in the presence of Mn2+, Mg2+and Zn2+. The enzymes showed typical Michaelis–Menten saturation kinetics with the pseudo-substrate GlcNAc3. Binding affinities for rSpy1094 and rSpy1370 were high (Km = 2.2 ± 0.9 μM and 3.1 ± 1.1 μM, respectively), but substrate turnover was low (Kcat = 0.0075/s and 0.0089/s, respectively) suggesting that peptidoglycan might not be the preferred target for deacetylation. Both enzymes were expressed during bacterial growth.
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Baggio G, Groves RA, Chignola R, Piacenza E, Presentato A, Lewis IA, Lampis S, Vallini G, Turner RJ. Untargeted Metabolomics Investigation on Selenite Reduction to Elemental Selenium by Bacillus mycoides SeITE01. Front Microbiol 2021; 12:711000. [PMID: 34603239 PMCID: PMC8481872 DOI: 10.3389/fmicb.2021.711000] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 08/16/2021] [Indexed: 12/02/2022] Open
Abstract
Bacillus mycoides SeITE01 is an environmental isolate that transforms the oxyanion selenite (SeO 3 2 - ) into the less bioavailable elemental selenium (Se0) forming biogenic selenium nanoparticles (Bio-SeNPs). In the present study, the reduction of sodium selenite (Na2SeO3) by SeITE01 strain and the effect ofSeO 3 2 - exposure on the bacterial cells was examined through untargeted metabolomics. A time-course approach was used to monitor both cell pellet and cell free spent medium (referred as intracellular and extracellular, respectively) metabolites in SeITE01 cells treated or not withSeO 3 2 - . The results show substantial biochemical changes in SeITE01 cells when exposed toSeO 3 2 - . The initial uptake ofSeO 3 2 - by SeITE01 cells (3h after inoculation) shows both an increase in intracellular levels of 4-hydroxybenzoate and indole-3-acetic acid, and an extracellular accumulation of guanosine, which are metabolites involved in general stress response adapting strategies. Proactive and defensive mechanisms againstSeO 3 2 - are observed between the end of lag (12h) and beginning of exponential (18h) phases. Glutathione and N-acetyl-L-cysteine are thiol compounds that would be mainly involved in Painter-type reaction for the reduction and detoxification ofSeO 3 2 - to Se0. In these growth stages, thiol metabolites perform a dual role, both acting against the toxic and harmful presence of the oxyanion and as substrate or reducing sources to scavenge ROS production. Moreover, detection of the amino acids L-threonine and ornithine suggests changes in membrane lipids. Starting from stationary phase (24 and 48h), metabolites related to the formation and release of SeNPs in the extracellular environment begin to be observed. 5-hydroxyindole acetate, D-[+]-glucosamine, 4-methyl-2-oxo pentanoic acid, and ethanolamine phosphate may represent signaling strategies following SeNPs release from the cytoplasmic compartment, with consequent damage to SeITE01 cell membranes. This is also accompanied by intracellular accumulation of trans-4-hydroxyproline and L-proline, which likely represent osmoprotectant activity. The identification of these metabolites suggests the activation of signaling strategies that would protect the bacterial cells fromSeO 3 2 - toxicity while it is converting into SeNPs.
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Affiliation(s)
- Greta Baggio
- Department of Biotechnology, University of Verona, Verona, Italy
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Ryan A. Groves
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Roberto Chignola
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Elena Piacenza
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
| | - Alessandro Presentato
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
| | - Ian A. Lewis
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Silvia Lampis
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Giovanni Vallini
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Raymond J. Turner
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
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Planas A. Peptidoglycan Deacetylases in Bacterial Cell Wall Remodeling and Pathogenesis. Curr Med Chem 2021; 29:1293-1312. [PMID: 34525907 DOI: 10.2174/0929867328666210915113723] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 07/24/2021] [Accepted: 07/26/2021] [Indexed: 11/22/2022]
Abstract
The bacterial cell wall peptidoglycan (PG) is a dynamic structure that is constantly synthesized, re-modeled and degraded during bacterial division and growth. Post-synthetic modifications modulate the action of endogenous autolysis during PG lysis and remodeling for growth and sporulation, but also they are a mechanism used by pathogenic bacteria to evade the host innate immune system. Modifica-tions of the glycan backbone are limited to the C-2 amine and the C-6 hydroxyl moieties of either Glc-NAc or MurNAc residues. This paper reviews the functional roles and properties of peptidoglycan de-N-acetylases (distinct PG GlcNAc and MurNAc deacetylases) and recent progress through genetic stud-ies and biochemical characterization to elucidate their mechanism of action, 3D structures, substrate specificities and biological functions. Since they are virulence factors in pathogenic bacteria, peptidogly-can deacetylases are potential targets for the design of novel antimicrobial agents.
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Affiliation(s)
- Antoni Planas
- Laboratory of Biochemistry, Institut Químic de Sarrià. University Ramon Llull, 08017 Barcelona. Spain
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6
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Abeysiriwardana-Arachchige I, Chapman G, Rosalez R, Soliz N, Cui Z, Munasinghe-Arachchige S, Delanka-Pedige H, Brewer C, Lammers P, Nirmalakhandan N. Mixotrophic algal system for centrate treatment and resource recovery. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.102087] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Assoni L, Milani B, Carvalho MR, Nepomuceno LN, Waz NT, Guerra MES, Converso TR, Darrieux M. Resistance Mechanisms to Antimicrobial Peptides in Gram-Positive Bacteria. Front Microbiol 2020; 11:593215. [PMID: 33193264 PMCID: PMC7609970 DOI: 10.3389/fmicb.2020.593215] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 09/03/2020] [Indexed: 02/06/2023] Open
Abstract
With the alarming increase of infections caused by pathogenic multidrug-resistant bacteria over the last decades, antimicrobial peptides (AMPs) have been investigated as a potential treatment for those infections, directly through their lytic effect or indirectly, due to their ability to modulate the immune system. There are still concerns regarding the use of such molecules in the treatment of infections, such as cell toxicity and host factors that lead to peptide inhibition. To overcome these limitations, different approaches like peptide modification to reduce toxicity and peptide combinations to improve therapeutic efficacy are being tested. Human defense peptides consist of an important part of the innate immune system, against a myriad of potential aggressors, which have in turn developed different ways to overcome the AMPs microbicidal activities. Since the antimicrobial activity of AMPs vary between Gram-positive and Gram-negative species, so do the bacterial resistance arsenal. This review discusses the mechanisms exploited by Gram-positive bacteria to circumvent killing by antimicrobial peptides. Specifically, the most clinically relevant genera, Streptococcus spp., Staphylococcus spp., Enterococcus spp. and Gram-positive bacilli, have been explored.
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Affiliation(s)
- Lucas Assoni
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, Brazil
| | - Barbara Milani
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, Brazil
| | - Marianna Ribeiro Carvalho
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, Brazil
| | - Lucas Natanael Nepomuceno
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, Brazil
| | - Natalha Tedeschi Waz
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, Brazil
| | - Maria Eduarda Souza Guerra
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, Brazil
| | - Thiago Rojas Converso
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, Brazil
| | - Michelle Darrieux
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, Brazil
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8
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Starke R, Morais D, Větrovský T, López Mondéjar R, Baldrian P, Brabcová V. Feeding on fungi: genomic and proteomic analysis of the enzymatic machinery of bacteria decomposing fungal biomass. Environ Microbiol 2020; 22:4604-4619. [PMID: 32743948 DOI: 10.1111/1462-2920.15183] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 07/21/2020] [Accepted: 07/31/2020] [Indexed: 11/29/2022]
Abstract
Dead fungal biomass is an abundant source of nutrition in both litter and soil of temperate forests largely decomposed by bacteria. Here, we have examined the utilization of dead fungal biomass by the five dominant bacteria isolated from the in situ decomposition of fungal mycelia using a multiOMIC approach. The genomes of the isolates encoded a broad suite of carbohydrate-active enzymes, peptidases and transporters. In the extracellular proteome, only Ewingella americana expressed chitinases while the two Pseudomonas isolates attacked chitin by lytic chitin monooxygenase, deacetylation and deamination. Variovorax sp. expressed enzymes acting on the side-chains of various glucans and the chitin backbone. Surprisingly, despite its genomic potential, Pedobacter sp. did not produce extracellular proteins to decompose fungal mycelia but presumably feeds on simple substrates. The ecological roles of the five individual strains exhibited complementary features for a fast and efficient decomposition of dead fungal biomass by the entire bacterial community.
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Affiliation(s)
- Robert Starke
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Daniel Morais
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Ruben López Mondéjar
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Vendula Brabcová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
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Soni A, Oey I, Silcock P, Ross IK, Bremer PJ. Effect of pulsed electric field with moderate heat (80°C) on inactivation, thermal resistance and differential gene expression in B. cereusspores. J FOOD PROCESS PRES 2020. [DOI: 10.1111/jfpp.14503] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Aswathi Soni
- Department of Food Science University of Otago Dunedin New Zealand
- AgResearch Palmerston North New Zealand
| | - Indrawati Oey
- Department of Food Science University of Otago Dunedin New Zealand
- Riddet Institute Palmerston North New Zealand
| | - Patrick Silcock
- Department of Food Science University of Otago Dunedin New Zealand
| | - Ian K. Ross
- Department of Food Science University of Otago Dunedin New Zealand
| | - Phil J. Bremer
- Department of Food Science University of Otago Dunedin New Zealand
- New Zealand Food Safety Science Research Centre Palmerston North New Zealand
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Amon JD, Yadav AK, Ramirez-Guadiana FH, Meeske AJ, Cava F, Rudner DZ. SwsB and SafA Are Required for CwlJ-Dependent Spore Germination in Bacillus subtilis. J Bacteriol 2020; 202:e00668-19. [PMID: 31871031 PMCID: PMC7043669 DOI: 10.1128/jb.00668-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 12/13/2019] [Indexed: 02/07/2023] Open
Abstract
When Bacillus subtilis spores detect nutrients, they exit dormancy through the processes of germination and outgrowth. A key step in germination is the activation of two functionally redundant cell wall hydrolases (SleB and CwlJ) that degrade the specialized cortex peptidoglycan that surrounds the spore. How these enzymes are regulated remains poorly understood. To identify additional factors that affect their activity, we used transposon sequencing to screen for synthetic germination defects in spores lacking SleB or CwlJ. Other than the previously characterized protein YpeB, no additional factors were found to be specifically required for SleB activity. In contrast, our screen identified SafA and YlxY (renamed SwsB) in addition to the known factors GerQ and CotE as proteins required for CwlJ function. SafA is a member of the spore's proteinaceous coat and we show that, like GerQ and CotE, it is required for accumulation and retention of CwlJ in the dormant spore. SwsB is broadly conserved among spore formers, and we show that it is required for CwlJ to efficiently degrade the cortex during germination. Intriguingly, SwsB resembles polysaccharide deacetylases, and its putative catalytic residues are required for its role in germination. However, we find no chemical signature of its activity on the spore cortex or in vitro While the precise, mechanistic role of SwsB remains unknown, we explore and discuss potential activities.IMPORTANCE Spore formation in Bacillus subtilis has been studied for over half a century, and virtually every step in this developmental process has been characterized in molecular detail. In contrast, how spores exit dormancy remains less well understood. A key step in germination is the degradation of the specialized cell wall surrounding the spore called the cortex. Two enzymes (SleB and CwlJ) specifically target this protective layer, but how they are regulated and whether additional factors promote their activity are unknown. Here, we identified the coat protein SafA and a conserved but uncharacterized protein YlxY as additional factors required for CwlJ-dependent degradation of the cortex. Our analysis provides a more complete picture of this essential step in the exit from dormancy.
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Affiliation(s)
- Jeremy D Amon
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Akhilesh K Yadav
- Laboratory for Molecular Infection Medicine, Department of Molecular Biology, Umeå University, Umeå, Sweden
- Analytical Chemistry Division, CSIR-Indian Institute of Toxicology Research, Lucknow, India
| | | | - Alexander J Meeske
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine, Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - David Z Rudner
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
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Grifoll-Romero L, Sainz-Polo MA, Albesa-Jové D, Guerin ME, Biarnés X, Planas A. Structure-function relationships underlying the dual N-acetylmuramic and N-acetylglucosamine specificities of the bacterial peptidoglycan deacetylase PdaC. J Biol Chem 2019; 294:19066-19080. [PMID: 31690626 DOI: 10.1074/jbc.ra119.009510] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 11/01/2019] [Indexed: 01/30/2023] Open
Abstract
Bacillus subtilis PdaC (BsPdaC) is a membrane-bound, multidomain peptidoglycan N-deacetylase acting on N-acetylmuramic acid (MurNAc) residues and conferring lysozyme resistance to modified cell wall peptidoglycans. BsPdaC contains a C-terminal family 4 carbohydrate esterase (CE4) catalytic domain, but unlike other MurNAc deacetylases, BsPdaC also has GlcNAc deacetylase activity on chitooligosaccharides (COSs), characteristic of chitin deacetylases. To uncover the molecular basis of this dual activity, here we determined the X-ray structure of the BsPdaC CE4 domain at 1.54 Å resolution and analyzed its mode of action on COS substrates. We found that the minimal substrate is GlcNAc3 and that activity increases with the degree of glycan polymerization. COS deacetylation kinetics revealed that BsPdaC operates by a multiple-chain mechanism starting at the internal GlcNAc units and leading to deacetylation of all but the reducing-end GlcNAc residues. Interestingly, BsPdaC shares higher sequence similarity with the peptidoglycan GlcNAc deacetylase SpPgdaA than with other MurNAc deacetylases. Therefore, we used ligand-docking simulations to analyze the dual GlcNAc- and MurNAc-binding specificities of BsPdaC and compared them with those of SpPgdA and BsPdaA, representing peptidoglycan deacetylases highly specific for GlcNAc or MurNAc residues, respectively. BsPdaC retains the conserved Asp-His-His metal-binding triad characteristic of CE4 enzymes acting on GlcNAc residues, differing from MurNAc deacetylases that lack the metal-coordinating Asp residue. BsPdaC contains short loops similar to those in SpPgdA, resulting in an open binding cleft that can accommodate polymeric substrates. We propose that PdaC is the first member of a new subclass of peptidoglycan MurNAc deacetylases.
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Affiliation(s)
- Laia Grifoll-Romero
- Laboratory of Biochemistry, Institut Químic de Sarrià, University Ramon Llull, 08017 Barcelona, Spain
| | - María Angela Sainz-Polo
- Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Bizkaia Technology Park, Ed. 801A, 48160 Derio, Spain
| | - David Albesa-Jové
- Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Bizkaia Technology Park, Ed. 801A, 48160 Derio, Spain.,Basque Foundation for Science (IKERBASQUE), 48011 Bilbao, Spain
| | - Marcelo E Guerin
- Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Bizkaia Technology Park, Ed. 801A, 48160 Derio, Spain.,Basque Foundation for Science (IKERBASQUE), 48011 Bilbao, Spain
| | - Xevi Biarnés
- Laboratory of Biochemistry, Institut Químic de Sarrià, University Ramon Llull, 08017 Barcelona, Spain
| | - Antoni Planas
- Laboratory of Biochemistry, Institut Químic de Sarrià, University Ramon Llull, 08017 Barcelona, Spain
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12
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Mayer C, Kluj RM, Mühleck M, Walter A, Unsleber S, Hottmann I, Borisova M. Bacteria's different ways to recycle their own cell wall. Int J Med Microbiol 2019; 309:151326. [PMID: 31296364 DOI: 10.1016/j.ijmm.2019.06.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 05/28/2019] [Accepted: 06/30/2019] [Indexed: 01/05/2023] Open
Abstract
The ability to recover components of their own cell wall is a common feature of bacteria. This was initially recognized in the Gram-negative bacterium Escherichia coli, which recycles about half of the peptidoglycan of its cell wall during one cell doubling. Moreover, E. coli was shown to grow on peptidoglycan components provided as nutrients. A distinguished recycling enzyme of E. coli required for both, recovery of the cell wall sugar N-acetylmuramic acid (MurNAc) of the own cell wall and for growth on external MurNAc, is the MurNAc 6-phosphate (MurNAc 6P) lactyl ether hydrolase MurQ. We revealed however, that most Gram-negative bacteria lack a murQ ortholog and instead harbor a pathway, absent in E. coli, that channels MurNAc directly to peptidoglycan biosynthesis. This "anabolic recycling pathway" bypasses the initial steps of peptidoglycan de novo synthesis, including the target of the antibiotic fosfomycin, thus providing intrinsic resistance to the antibiotic. The Gram-negative oral pathogen Tannerella forsythia is auxotrophic for MurNAc and apparently depends on the anabolic recycling pathway to synthesize its own cell wall by scavenging cell wall debris of other bacteria. In contrast, Gram-positive bacteria lack the anabolic recycling genes, but mostly contain one or two murQ orthologs. Quantification of MurNAc 6P accumulation in murQ mutant cells by mass spectrometry allowed us to demonstrate for the first time that Gram-positive bacteria do recycle their own peptidoglycan. This had been questioned earlier, since peptidoglycan turnover products accumulate in the spent media of Gram-positives. We showed, that these fragments are recovered during nutrient limitation, which prolongs starvation survival of Bacillus subtilis and Staphylococcus aureus. Peptidoglycan recycling in these bacteria however differs, as the cell wall is either cleaved exhaustively and monosaccharide building blocks are taken up (B. subtilis) or disaccharides are released and recycled involving a novel phosphomuramidase (MupG; S.aureus). In B. subtilis also the teichoic acids, covalently bound to the peptidoglycan (wall teichoic acids; WTAs), are recycled. During phosphate limitation, the sn-glycerol-3-phosphate phosphodiesterase GlpQ specifically degrades WTAs of B. subtilis. In S. aureus, in contrast, GlpQ is used to scavenge external teichoic acid sources. Thus, although bacteria generally recover their own cell wall, they apparently apply distinct strategies for breakdown and reutilization of cell wall fragments. This review summarizes our work on this topic funded between 2011 and 2019 by the DFG within the collaborative research center SFB766.
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Affiliation(s)
- Christoph Mayer
- Mikrobiologie/Biotechnologie, Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany.
| | - Robert Maria Kluj
- Mikrobiologie/Biotechnologie, Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Maraike Mühleck
- Mikrobiologie/Biotechnologie, Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Axel Walter
- Mikrobiologie/Biotechnologie, Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Sandra Unsleber
- Mikrobiologie/Biotechnologie, Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Isabel Hottmann
- Mikrobiologie/Biotechnologie, Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Marina Borisova
- Mikrobiologie/Biotechnologie, Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
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13
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Rossoni AW, Price DC, Seger M, Lyska D, Lammers P, Bhattacharya D, Weber APM. The genomes of polyextremophilic cyanidiales contain 1% horizontally transferred genes with diverse adaptive functions. eLife 2019; 8:e45017. [PMID: 31149898 PMCID: PMC6629376 DOI: 10.7554/elife.45017] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 05/30/2019] [Indexed: 01/08/2023] Open
Abstract
The role and extent of horizontal gene transfer (HGT) in eukaryotes are hotly disputed topics that impact our understanding of the origin of metabolic processes and the role of organelles in cellular evolution. We addressed this issue by analyzing 10 novel Cyanidiales genomes and determined that 1% of their gene inventory is HGT-derived. Numerous HGT candidates share a close phylogenetic relationship with prokaryotes that live in similar habitats as the Cyanidiales and encode functions related to polyextremophily. HGT candidates differ from native genes in GC-content, number of splice sites, and gene expression. HGT candidates are more prone to loss, which may explain the absence of a eukaryotic pan-genome. Therefore, the lack of a pan-genome and cumulative effects fail to provide substantive arguments against our hypothesis of recurring HGT followed by differential loss in eukaryotes. The maintenance of 1% HGTs, even under selection for genome reduction, underlines the importance of non-endosymbiosis related foreign gene acquisition.
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Affiliation(s)
- Alessandro W Rossoni
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS)Heinrich Heine UniversityDüsseldorfGermany
| | - Dana C Price
- Department of Plant BiologyRutgers UniversityNew BrunswickUnited States
| | - Mark Seger
- Arizona Center for Algae Technology and InnovationArizona State UniversityMesaUnited States
| | - Dagmar Lyska
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS)Heinrich Heine UniversityDüsseldorfGermany
| | - Peter Lammers
- Arizona Center for Algae Technology and InnovationArizona State UniversityMesaUnited States
| | | | - Andreas PM Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS)Heinrich Heine UniversityDüsseldorfGermany
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14
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Andreou A, Giastas P, Arnaouteli S, Tzanodaskalaki M, Tzartos SJ, Bethanis K, Bouriotis V, Eliopoulos EE. The putative polysaccharide deacetylase Ba0331: cloning, expression, crystallization and structure determination. Acta Crystallogr F Struct Biol Commun 2019; 75:312-320. [PMID: 30950833 PMCID: PMC6450525 DOI: 10.1107/s2053230x19001766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 01/30/2019] [Indexed: 11/10/2022] Open
Abstract
Ba0331 is a putative polysaccharide deacetylase from Bacillus anthracis, the etiological agent of the disease anthrax, that contributes to adaptation of the bacterium under extreme conditions and to maintenance of the cell shape. In the present study, the crystal structure of Ba0331 was determined at 2.6 Å resolution. The structure consists of two domains: a fibronectin type 3-like (Fn3-like) domain and a NodB catalytic domain. The latter is present in all carbohydrate esterase family 4 enzymes, while a comparative analysis of the Fn3-like domain revealed structural plasticity despite the retention of the conserved Fn3-like domain characteristics.
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Affiliation(s)
- Athena Andreou
- Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Petros Giastas
- Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
- Department of Neurobiology, Hellenic Pasteur Institute, Vasilissis Sofias 127, 11521 Athens, Greece
| | - Sofia Arnaouteli
- Department of Biology, Enzyme Biotechnology Group, University of Crete, Vasilika Vouton, 70013 Heraklion, Crete, Greece
| | - Mary Tzanodaskalaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Hellas N. Plastira 100, 70013 Heraklion, Crete, Greece
| | - Socrates J. Tzartos
- Department of Neurobiology, Hellenic Pasteur Institute, Vasilissis Sofias 127, 11521 Athens, Greece
| | - Kostas Bethanis
- Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Vassilis Bouriotis
- Department of Biology, Enzyme Biotechnology Group, University of Crete, Vasilika Vouton, 70013 Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Hellas N. Plastira 100, 70013 Heraklion, Crete, Greece
| | - Elias E. Eliopoulos
- Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
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15
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Yadav AK, Espaillat A, Cava F. Bacterial Strategies to Preserve Cell Wall Integrity Against Environmental Threats. Front Microbiol 2018; 9:2064. [PMID: 30233540 PMCID: PMC6127315 DOI: 10.3389/fmicb.2018.02064] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 08/13/2018] [Indexed: 12/18/2022] Open
Abstract
Bacterial cells are surrounded by an exoskeleton-like structure, the cell wall, composed primarily of the peptidoglycan (PG) sacculus. This structure is made up of glycan strands cross-linked by short peptides generating a covalent mesh that shapes bacteria and prevents their lysis due to their high internal osmotic pressure. Even though the PG is virtually universal in bacteria, there is a notable degree of diversity in its chemical structure. Modifications in both the sugars and peptides are known to be instrumental for bacteria to cope with diverse environmental challenges. In this review, we summarize and discuss the cell wall strategies to withstand biotic and abiotic environmental insults such as the effect of antibiotics targeting cell wall enzymes, predatory PG hydrolytic proteins, and PG signaling systems. Finally we will discuss the opportunities that species-specific PG variability might open to develop antimicrobial therapies.
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Affiliation(s)
- Akhilesh K Yadav
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Akbar Espaillat
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
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16
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Andreou A, Giastas P, Christoforides E, Eliopoulos EE. Structural and Evolutionary Insights within the Polysaccharide Deacetylase Gene Family of Bacillus anthracis and Bacillus cereus. Genes (Basel) 2018; 9:E386. [PMID: 30065210 PMCID: PMC6115787 DOI: 10.3390/genes9080386] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/24/2018] [Accepted: 07/25/2018] [Indexed: 02/06/2023] Open
Abstract
Functional and folding constraints impose interdependence between interacting sites along the protein chain that are envisaged through protein sequence evolution. Studying the influence of structure in phylogenetic models requires detailed and reliable structural models. Polysaccharide deacetylases (PDAs), members of the carbohydrate esterase family 4, perform mainly metal-dependent deacetylation of O- or N-acetylated polysaccharides such as peptidoglycan, chitin and acetylxylan through a conserved catalytic core termed the NodB homology domain. Genomes of Bacillus anthracis and its relative Bacillus cereus contain multiple genes of putative or known PDAs. A comparison of the functional domains of the recently determined PDAs from B. anthracis and B. cereus and multiple amino acid and nucleotide sequence alignments and phylogenetic analysis performed on these closely related species showed that there were distinct differences in binding site formation, despite the high conservation on the protein sequence, the folding level and the active site assembly. This may indicate that, subject to biochemical verification, the binding site-forming sequence fragments are under functionally driven evolutionary pressure to accommodate and recognize distinct polysaccharide residues according to cell location, use, or environment. Finally, we discuss the suggestion of the paralogous nature of at least two genes of B. anthracis, ba0330 and ba0331, via specific differences in gene sequence, protein structure, selection pressure and available localization patterns. This study may contribute to understanding the mechanisms under which sequences evolve in their structures and how evolutionary processes enable structural variations.
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Affiliation(s)
- Athena Andreou
- Department of Biotechnology, Laboratory of Genetics, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece.
| | - Petros Giastas
- Department of Neurobiology, Hellenic Pasteur Institute, Vasilissis Sofias 127, 11521 Athens, Greece.
| | - Elias Christoforides
- Department of Biotechnology, Laboratory of Genetics, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece.
| | - Elias E Eliopoulos
- Department of Biotechnology, Laboratory of Genetics, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece.
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17
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Polysaccharide deacetylases serve as new targets for the design of inhibitors against Bacillus anthracis and Bacillus cereus. Bioorg Med Chem 2018; 26:3845-3851. [DOI: 10.1016/j.bmc.2018.06.045] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 06/25/2018] [Accepted: 06/30/2018] [Indexed: 02/02/2023]
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18
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Substrate Recognition and Specificity of Chitin Deacetylases and Related Family 4 Carbohydrate Esterases. Int J Mol Sci 2018; 19:ijms19020412. [PMID: 29385775 PMCID: PMC5855634 DOI: 10.3390/ijms19020412] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 01/22/2018] [Accepted: 01/24/2018] [Indexed: 12/27/2022] Open
Abstract
Carbohydrate esterases family 4 (CE4 enzymes) includes chitin and peptidoglycan deacetylases, acetylxylan esterases, and poly-N-acetylglucosamine deacetylases that act on structural polysaccharides, altering their physicochemical properties, and participating in diverse biological functions. Chitin and peptidoglycan deacetylases are not only involved in cell wall morphogenesis and remodeling in fungi and bacteria, but they are also used by pathogenic microorganisms to evade host defense mechanisms. Likewise, biofilm formation in bacteria requires partial deacetylation of extracellular polysaccharides mediated by poly-N-acetylglucosamine deacetylases. Such biological functions make these enzymes attractive targets for drug design against pathogenic fungi and bacteria. On the other side, acetylxylan esterases deacetylate plant cell wall complex xylans to make them accessible to hydrolases, making them attractive biocatalysts for biomass utilization. CE4 family members are metal-dependent hydrolases. They are highly specific for their particular substrates, and show diverse modes of action, exhibiting either processive, multiple attack, or patterned deacetylation mechanisms. However, the determinants of substrate specificity remain poorly understood. Here, we review the current knowledge on the structure, activity, and specificity of CE4 enzymes, focusing on chitin deacetylases and related enzymes active on N-acetylglucosamine-containing oligo and polysaccharides.
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19
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Abstract
Bacterial endospores possess multiple integument layers, one of which is the cortex peptidoglycan wall. The cortex is essential for the maintenance of spore core dehydration and dormancy and contains structural modifications that differentiate it from vegetative cell peptidoglycan and determine its fate during spore germination. Following the engulfment stage of sporulation, the cortex is synthesized within the intermembrane space surrounding the forespore. Proteins responsible for cortex synthesis are produced in both the forespore and mother cell compartments. While some of these proteins also contribute to vegetative cell wall synthesis, others are sporulation specific. In order for the bacterial endospore to germinate and resume metabolism, the cortex peptidoglycan must first be degraded through the action of germination-specific lytic enzymes. These enzymes are present, yet inactive, in the dormant spore and recognize the muramic-δ-lactam modification present in the cortex. Germination-specific lytic enzymes across Bacillaceae and Clostridiaceae share this specificity determinant, which ensures that the spore cortex is hydrolyzed while the vegetative cell wall remains unharmed. Bacillus species tend to possess two redundant enzymes, SleB and CwlJ, capable of sufficient cortex degradation, while the clostridia have only one, SleC. Additional enzymes are often present that cannot initiate the cortex degradation process, but which can increase the rate of release of small fragments into the medium. Between the two families, the enzymes also differ in the enzymatic activities they possess and the mechanisms acting to restrict their activation until germination has been initiated.
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20
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Giastas P, Andreou A, Papakyriakou A, Koutsioulis D, Balomenou S, Tzartos SJ, Bouriotis V, Eliopoulos EE. Structures of the Peptidoglycan N-Acetylglucosamine Deacetylase Bc1974 and Its Complexes with Zinc Metalloenzyme Inhibitors. Biochemistry 2018; 57:753-763. [PMID: 29257674 DOI: 10.1021/acs.biochem.7b00919] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The cell wall peptidoglycan is recognized as a primary target of the innate immune system, and usually its disintegration results in bacterial lysis. Bacillus cereus, a close relative of the highly virulent Bacillus anthracis, contains 10 polysaccharide deacetylases. Among these, the peptidoglycan N-acetylglucosamine deacetylase Bc1974 is the highest homologue to the Bacillus anthracis Ba1977 that is required for full virulence and is involved in resistance to the host's lysozyme. These metalloenzymes belong to the carbohydrate esterase family 4 (CE4) and are attractive targets for the development of new anti-infective agents. Herein we report the first X-ray crystal structures of the NodB domain of Bc1974, the conserved catalytic core of CE4s, in the unliganded form and in complex with four known metalloenzyme inhibitors and two amino acid hydroxamates that target the active site metal. These structures revealed the presence of two conformational states of a catalytic loop known as motif-4 (MT4), which were not observed previously for peptidoglycan deacetylases, but were recently shown in the structure of a Vibrio clolerae chitin deacetylase. By employing molecular docking of a substrate model, we describe a catalytic mechanism that probably involves initial binding of the substrate in a receptive, more open state of MT4 and optimal catalytic activity in the closed state of MT4, consistent with the previous observations. The ligand-bound structures presented here, in addition to the five Bc1974 inhibitors identified, provide a valuable basis for the design of antibacterial agents that target the peptidoglycan deacetylase Ba1977.
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Affiliation(s)
- Petros Giastas
- Department of Biotechnology, Laboratory of Genetics, Agricultural University of Athens , Iera Odos 75, 11855 Athens, Greece.,Department of Neurobiology, Hellenic Pasteur Institute , Vasilissis Sofias 127, 11521 Athens, Greece
| | - Athena Andreou
- Department of Biotechnology, Laboratory of Genetics, Agricultural University of Athens , Iera Odos 75, 11855 Athens, Greece
| | - Athanasios Papakyriakou
- Department of Biotechnology, Laboratory of Genetics, Agricultural University of Athens , Iera Odos 75, 11855 Athens, Greece.,Institute of Biosciences and Applications, NCSR "Demokritos" , 15310 Aghia Paraskevi, Athens, Greece
| | - Dimitris Koutsioulis
- Institute of Molecular Biology and Biotechnology, FORTH , 70013 Heraklion, Crete, Greece
| | - Stavroula Balomenou
- Institute of Molecular Biology and Biotechnology, FORTH , 70013 Heraklion, Crete, Greece.,Department of Biology, Enzyme Biotechnology Group, University of Crete , Vasilika Vouton, 70013 Heraklion, Crete, Greece
| | - Socrates J Tzartos
- Department of Neurobiology, Hellenic Pasteur Institute , Vasilissis Sofias 127, 11521 Athens, Greece
| | - Vassilis Bouriotis
- Institute of Molecular Biology and Biotechnology, FORTH , 70013 Heraklion, Crete, Greece.,Department of Biology, Enzyme Biotechnology Group, University of Crete , Vasilika Vouton, 70013 Heraklion, Crete, Greece
| | - Elias E Eliopoulos
- Department of Biotechnology, Laboratory of Genetics, Agricultural University of Athens , Iera Odos 75, 11855 Athens, Greece
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21
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Fadouloglou VE, Balomenou S, Aivaliotis M, Kotsifaki D, Arnaouteli S, Tomatsidou A, Efstathiou G, Kountourakis N, Miliara S, Griniezaki M, Tsalafouta A, Pergantis SA, Boneca IG, Glykos NM, Bouriotis V, Kokkinidis M. Unusual α-Carbon Hydroxylation of Proline Promotes Active-Site Maturation. J Am Chem Soc 2017; 139:5330-5337. [DOI: 10.1021/jacs.6b12209] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
| | - Stavroula Balomenou
- Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
- Department
of Biology, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
| | - Michalis Aivaliotis
- Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
| | - Dina Kotsifaki
- Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
| | - Sofia Arnaouteli
- Department
of Biology, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
| | - Anastasia Tomatsidou
- Department
of Biology, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
| | - Giorgos Efstathiou
- Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
| | - Nikos Kountourakis
- Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
| | - Sofia Miliara
- Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
| | - Marianna Griniezaki
- Department
of Biology, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
| | - Aleka Tsalafouta
- Department
of Biology, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
| | - Spiros A. Pergantis
- Department
of Chemistry, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
| | - Ivo G. Boneca
- Biology
and Genetics of the Bacterial Cell Wall Unit, Institut Pasteur, 75015 Paris, France
- INSERM, Equipe Avenir, Paris, France
| | - Nicholas M. Glykos
- Department
of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, 68100 Alexandroupolis, Greece
| | - Vassilis Bouriotis
- Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
- Department
of Biology, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
| | - Michael Kokkinidis
- Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
- Department
of Biology, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
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22
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Fadouloglou VE, Stavrakoudis A, Bouriotis V, Kokkinidis M, Glykos NM. Molecular Dynamics Simulations of BcZBP, A Deacetylase from Bacillus cereus: Active Site Loops Determine Substrate Accessibility and Specificity. J Chem Theory Comput 2015; 5:3299-311. [PMID: 26602510 DOI: 10.1021/ct9002338] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BcZBP is an LmbE-like, homohexameric, zinc-dependent deacetylase from the opportunistic pathogen Bacillus cereus with three, thus far uncharacterized, homologues in B. anthracis. Although its specific substrate is still unknown, the enzyme has been shown to preferentially deacetylate N-acetylglucosamine and diacetylchitobiose via an active site based on a zinc-binding motif of the type HXDDXnH. In the crystal structure, the active site is located at a deep and partially blocked cleft formed at the interface between monomers related by the molecular 3-fold axis, although the major, in structural terms, building block of the enzyme is not the trimer, but the intertwined dimer. Here, we report results from a 50 ns molecular dynamics simulation of BcZBP in explicit solvent with full electrostatics and show that (i) the view of the intertwined dimer as the major structural and functional building block of this class of hexameric enzymes is possibly an oversimplification of the rather complex dynamics observed in the simulation, (ii) the most mobile (with respect to their atomic fluctuations) parts of the structure coincide with three surface loops surrounding the active site, and (iii) these mobile loops define the active site's accessibility, and may be implicated in the determination of the enzyme's specificity.
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Affiliation(s)
- Vasiliki E Fadouloglou
- Department of Molecular Biology and Genetics, Democritus University of Thrace, University campus, GR-68100, Alexandroupolis, Greece, Department of Biology, University of Crete, PO Box 2208, GR-71409, Heraklion, Crete, Greece, Department of Economics, University of Ioannina, GR-45110, Ioannina, Greece, and Institute of Molecular Biology and Biotechnology (IMBB), PO Box 1527, GR-71110, Heraklion, Crete, Greece
| | - Athanassios Stavrakoudis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, University campus, GR-68100, Alexandroupolis, Greece, Department of Biology, University of Crete, PO Box 2208, GR-71409, Heraklion, Crete, Greece, Department of Economics, University of Ioannina, GR-45110, Ioannina, Greece, and Institute of Molecular Biology and Biotechnology (IMBB), PO Box 1527, GR-71110, Heraklion, Crete, Greece
| | - Vassilis Bouriotis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, University campus, GR-68100, Alexandroupolis, Greece, Department of Biology, University of Crete, PO Box 2208, GR-71409, Heraklion, Crete, Greece, Department of Economics, University of Ioannina, GR-45110, Ioannina, Greece, and Institute of Molecular Biology and Biotechnology (IMBB), PO Box 1527, GR-71110, Heraklion, Crete, Greece
| | - Michael Kokkinidis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, University campus, GR-68100, Alexandroupolis, Greece, Department of Biology, University of Crete, PO Box 2208, GR-71409, Heraklion, Crete, Greece, Department of Economics, University of Ioannina, GR-45110, Ioannina, Greece, and Institute of Molecular Biology and Biotechnology (IMBB), PO Box 1527, GR-71110, Heraklion, Crete, Greece
| | - Nicholas M Glykos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, University campus, GR-68100, Alexandroupolis, Greece, Department of Biology, University of Crete, PO Box 2208, GR-71409, Heraklion, Crete, Greece, Department of Economics, University of Ioannina, GR-45110, Ioannina, Greece, and Institute of Molecular Biology and Biotechnology (IMBB), PO Box 1527, GR-71110, Heraklion, Crete, Greece
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23
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Arnaouteli S, Giastas P, Andreou A, Tzanodaskalaki M, Aldridge C, Tzartos SJ, Vollmer W, Eliopoulos E, Bouriotis V. Two Putative Polysaccharide Deacetylases Are Required for Osmotic Stability and Cell Shape Maintenance in Bacillus anthracis. J Biol Chem 2015; 290:13465-78. [PMID: 25825488 PMCID: PMC4505593 DOI: 10.1074/jbc.m115.640029] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Indexed: 11/26/2022] Open
Abstract
Membrane-anchored lipoproteins have a broad range of functions and play key roles in several cellular processes in Gram-positive bacteria. BA0330 and BA0331 are the only lipoproteins among the 11 known or putative polysaccharide deacetylases of Bacillus anthracis. We found that both lipoproteins exhibit unique characteristics. BA0330 and BA0331 interact with peptidoglycan, and BA0330 is important for the adaptation of the bacterium to grow in the presence of a high concentration of salt, whereas BA0331 contributes to the maintenance of a uniform cell shape. They appear not to alter the peptidoglycan structure and do not contribute to lysozyme resistance. The high resolution x-ray structure of BA0330 revealed a C-terminal domain with the typical fold of a carbohydrate esterase 4 and an N-terminal domain unique for this family, composed of a two-layered (4 + 3) β-sandwich with structural similarity to fibronectin type 3 domains. Our data suggest that BA0330 and BA0331 have a structural role in stabilizing the cell wall of B. anthracis.
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Affiliation(s)
- Sofia Arnaouteli
- From the Department of Biology, Enzyme Biotechnology Group, University of Crete, Vasilika Vouton, 70013 Heraklion, Crete, Greece
| | - Petros Giastas
- the Department of Neurobiology, Hellenic Pasteur Institute, Vasilissis Sofias 127, 11521 Athens, Greece
| | - Athina Andreou
- the Department of Biotechnology, Laboratory of Genetics, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Mary Tzanodaskalaki
- the Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
| | - Christine Aldridge
- the Institute for Cell and Molecular Biosciences, Centre for Bacterial Cell Biology, Newcastle University, NE2 4AX Newcastle upon Tyne, United Kingdom, and
| | - Socrates J Tzartos
- the Department of Neurobiology, Hellenic Pasteur Institute, Vasilissis Sofias 127, 11521 Athens, Greece, the Department of Pharmacy, University of Patras, 26504, Patras, Greece
| | - Waldemar Vollmer
- the Institute for Cell and Molecular Biosciences, Centre for Bacterial Cell Biology, Newcastle University, NE2 4AX Newcastle upon Tyne, United Kingdom, and
| | - Elias Eliopoulos
- the Department of Biotechnology, Laboratory of Genetics, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Vassilis Bouriotis
- From the Department of Biology, Enzyme Biotechnology Group, University of Crete, Vasilika Vouton, 70013 Heraklion, Crete, Greece, the Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece,
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Nawrocki KL, Crispell EK, McBride SM. Antimicrobial Peptide Resistance Mechanisms of Gram-Positive Bacteria. Antibiotics (Basel) 2014; 3:461-92. [PMID: 25419466 PMCID: PMC4239024 DOI: 10.3390/antibiotics3040461] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 09/25/2014] [Accepted: 09/28/2014] [Indexed: 01/09/2023] Open
Abstract
Antimicrobial peptides, or AMPs, play a significant role in many environments as a tool to remove competing organisms. In response, many bacteria have evolved mechanisms to resist these peptides and prevent AMP-mediated killing. The development of AMP resistance mechanisms is driven by direct competition between bacterial species, as well as host and pathogen interactions. Akin to the number of different AMPs found in nature, resistance mechanisms that have evolved are just as varied and may confer broad-range resistance or specific resistance to AMPs. Specific mechanisms of AMP resistance prevent AMP-mediated killing against a single type of AMP, while broad resistance mechanisms often lead to a global change in the bacterial cell surface and protect the bacterium from a large group of AMPs that have similar characteristics. AMP resistance mechanisms can be found in many species of bacteria and can provide a competitive edge against other bacterial species or a host immune response. Gram-positive bacteria are one of the largest AMP producing groups, but characterization of Gram-positive AMP resistance mechanisms lags behind that of Gram-negative species. In this review we present a summary of the AMP resistance mechanisms that have been identified and characterized in Gram-positive bacteria. Understanding the mechanisms of AMP resistance in Gram-positive species can provide guidelines in developing and applying AMPs as therapeutics, and offer insight into the role of resistance in bacterial pathogenesis.
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Affiliation(s)
- Kathryn L Nawrocki
- Department of Microbiology and Immunology, Emory University School of Medicine, 1510 Clifton Rd, Atlanta, GA 30322, USA; (K.L.N.); (E.K.C.)
| | - Emily K Crispell
- Department of Microbiology and Immunology, Emory University School of Medicine, 1510 Clifton Rd, Atlanta, GA 30322, USA; (K.L.N.); (E.K.C.)
| | - Shonna M McBride
- Department of Microbiology and Immunology, Emory University School of Medicine, 1510 Clifton Rd, Atlanta, GA 30322, USA; (K.L.N.); (E.K.C.)
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25
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Yang S, Zhang F, Kang J, Zhang W, Deng G, Xin Y, Ma Y. Mycobacterium tuberculosis Rv1096 protein: gene cloning, protein expression, and peptidoglycan deacetylase activity. BMC Microbiol 2014; 14:174. [PMID: 24975018 PMCID: PMC4087242 DOI: 10.1186/1471-2180-14-174] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 06/25/2014] [Indexed: 01/26/2023] Open
Abstract
Background Many bacteria modulate and evade the immune defenses of their hosts through peptidoglycan (PG) deacetylation. The PG deacetylases from Streptococcus pneumonia, Listeria monocytogenes and Lactococcus lactis have been characterized. However, thus far, the PG deacetylase of Mycobacterium tuberculosis has not been identified. Results In this study, we cloned the Rv1096 gene from the M. tuberculosis H37Rv strain and expressed Rv1096 protein in both Escherichia coli and M. smegmatis. The results showed that the purified Rv1096 protein possessed metallo-dependent PG deacetylase activity, which increased in the presence of Co2+. The kinetic parameters of the PG deacetylase towards M. smegmatis PG as a substrate were as follows: Km, 0.910 ± 0.007 mM; Vmax, 0.514 ± 0.038 μMmin-1; and Kcat = 0.099 ± 0.007 (S-1). Additionally, the viability of M. smegmatis in the presence of over-expressed Rv1096 protein was 109-fold higher than that of wild-type M. smegmatis after lysozyme treatment. Additionally, light microscopy and scanning electron microscopy showed that in the presence of over-expressed Rv1096 protein, M. smegmatis kept its regular shape, with an undamaged cell wall and smooth surface. These results indicate that Rv1096 caused deacetylation of cell wall PG, leading to lysozyme resistance in M. smegmatis. Conclusion We have determined that M. tuberculosis Rv1096 is a PG deacetylase. The PG deacetylase activity of Rv1096 contributed to lysozyme resistance in M. smegmatis. Our findings suggest that deacetylation of cell wall PG may be involved in evasion of host immune defenses by M. tuberculosis.
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Affiliation(s)
| | | | | | | | | | | | - Yufang Ma
- Department of Biochemistry and Molecular Biology, Dalian Medical University, 9 W Lushun South Road, Dalian 116044, China.
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26
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Chemical biology of peptidoglycan acetylation and deacetylation. Bioorg Chem 2014; 54:44-50. [DOI: 10.1016/j.bioorg.2014.03.010] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 03/25/2014] [Indexed: 12/16/2022]
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27
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Candela T, Balomenou S, Aucher W, Bouriotis V, Simore JP, Fouet A, Boneca IG. N-acetylglucosamine deacetylases modulate the anchoring of the gamma-glutamyl capsule to the cell wall of Bacillus anthracis. Microb Drug Resist 2014; 20:222-30. [PMID: 24833281 DOI: 10.1089/mdr.2014.0063] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Bacillus anthracis has a complex cell wall structure composed of a peptidoglycan (PG) layer to which major structures are anchored such as a neutral polysaccharide, an S-layer, and a poly-γ-D-glutamate (PDGA) capsule. Many of these structures have central roles in the biology of B. anthracis, particularly, in virulence. However, little attention has been devoted to structurally study the PG and how it is modified in the presence of these secondary cell wall components. We present here the fine structure of the PG of the encapsulated RPG1 strain harboring both pXO1 and pXO2 virulence plasmids. We show that B. anthracis has a high degree of cross-linking and its GlcNAc residues are highly modified by N-deacetylation. The PG composition is not dependent on the presence of either LPXTG proteins or the capsule. Using NMR analysis of the PG-PDGA complex, we provide evidence for the anchoring of the PDGA to the glucosamine residues. We show that anchoring of the PDGA capsule is impaired in two PG N-deacetylase mutants, Ba1961 and Ba3679. Thus, these multiple N-deactylase activities would constitute excellent drug targets in B. anthracis by simultaneously affecting its resistance to lysozyme and to phagocytosis impairing B. anthracis survival in the host.
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Affiliation(s)
- Thomas Candela
- 1 Institut Pasteur , Unité Toxines et Pathogénie Bactérienne, Paris, France
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28
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Clostridium difficile extracytoplasmic function σ factor σV regulates lysozyme resistance and is necessary for pathogenesis in the hamster model of infection. Infect Immun 2014; 82:2345-55. [PMID: 24664503 DOI: 10.1128/iai.01483-13] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Clostridium difficile is a clinically important pathogen and the most common cause of hospital-acquired infectious diarrhea. Expression of the C. difficile gene csfV, which encodes σ(V), an extracytoplasmic function σ factor, is induced by lysozyme, which damages the peptidoglycan of bacteria. Here we show that σ(V) is required for lysozyme resistance in C. difficile. Using microarray analysis, we identified the C. difficile genes whose expression is dependent upon σ(V) and is induced by lysozyme. Although the peptidoglycan of wild-type C. difficile is intrinsically highly deacetylated, we have found that exposure to lysozyme leads to additional peptidoglycan deacetylation. This lysozyme-induced deacetylation is dependent upon σ(V). Expression of pdaV, which encodes a putative peptidoglycan deacetylase, was able to increase lysozyme resistance of a csfV mutant. The csfV mutant strain is severely attenuated compared to wild-type C. difficile in a hamster model of C. difficile-associated disease. We conclude that the σ(V) signal transduction system, which senses the host innate immune defense enzyme lysozyme, is required for lysozyme resistance and is necessary during C. difficile infection.
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29
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Strunk RJ, Piemonte KM, Petersen NM, Koutsioulis D, Bouriotis V, Perry K, Cole KE. Structure determination of BA0150, a putative polysaccharide deacetylase from Bacillus anthracis. Acta Crystallogr F Struct Biol Commun 2014; 70:156-9. [PMID: 24637747 PMCID: PMC3936449 DOI: 10.1107/s2053230x13034262] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 12/19/2013] [Indexed: 11/10/2022] Open
Abstract
Polysaccharide deacetylases are bacterial enzymes that catalyze the deacetylation of acetylated sugars on the membranes of Gram-positive bacteria, allowing them to be unrecognized by host immune systems. Inhibition of these enzymes would disrupt such pathogenic defensive mechanisms and therefore offers a promising route for the development of novel antibiotic therapeutics. Here, the first X-ray crystal structure of BA0150, a putative polysaccharide deacetylase from Bacillus anthracis, is reported to 2.0 Å resolution. The overall structure maintains the conserved (α/β)8 fold that is characteristic of this family of enzymes. The lack of a catalytic metal ion and a distinctive metal-binding site, however, suggest that this enzyme is not a functional polysaccharide deacetylase.
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Affiliation(s)
- Robert J. Strunk
- Department of Chemistry, Ithaca College, 953 Danby Road, Ithaca, NY 14850, USA
| | - Katrina M. Piemonte
- Department of Chemistry, Ithaca College, 953 Danby Road, Ithaca, NY 14850, USA
| | - Natasha M. Petersen
- Department of Chemistry, Ithaca College, 953 Danby Road, Ithaca, NY 14850, USA
| | - Dimitris Koutsioulis
- Department of Biology, Enzyme Biotechnology Group, University of Crete, PO Box 2209, Vassilika Vouton, 71409 Heraklion, Crete, Greece
| | - Vassilis Bouriotis
- Department of Biology, Enzyme Biotechnology Group, University of Crete, PO Box 2209, Vassilika Vouton, 71409 Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, 70019 Heraklion, Crete, Greece
| | - Kay Perry
- Northeastern Collaborative Access Team (NE-CAT) and Department of Chemistry and Chemical Biology, Cornell University, Building 436E, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Kathryn E. Cole
- Department of Chemistry, Ithaca College, 953 Danby Road, Ithaca, NY 14850, USA
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Munan Shaik M, Bhattacharjee N, Bhattacharjee A, Field MJ, Zanotti G. Characterization of the divalent metal binding site of bacterial polysaccharide deacetylase using crystallography and quantum chemical calculations. Proteins 2014; 82:1311-8. [DOI: 10.1002/prot.24497] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 11/18/2013] [Accepted: 12/09/2013] [Indexed: 12/20/2022]
Affiliation(s)
- Md Munan Shaik
- PATBAC, Institut de Biologie Structurale-Jean-Pierre Ebel; Grenoble France
| | | | | | - Martin J. Field
- DYNAMOP, Institut de Biologie Structurale-Jean-Pierre Ebel; Grenoble France
| | - Giuseppe Zanotti
- Department of Biomedical Sciences; University of Padua; Padua Italy
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31
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Balomenou S, Fouet A, Tzanodaskalaki M, Couture-Tosi E, Bouriotis V, Boneca IG. Distinct functions of polysaccharide deacetylases in cell shape, neutral polysaccharide synthesis and virulence ofBacillus anthracis. Mol Microbiol 2013; 87:867-83. [DOI: 10.1111/mmi.12137] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2012] [Indexed: 11/27/2022]
Affiliation(s)
| | | | - Mary Tzanodaskalaki
- Institute of Molecular Biology and Biotechnology; 70013; Heraklion; Crete; Greece
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Liu M, Haenssler E, Uehara T, Losick VP, Park JT, Isberg RR. The Legionella pneumophila EnhC protein interferes with immunostimulatory muramyl peptide production to evade innate immunity. Cell Host Microbe 2013; 12:166-76. [PMID: 22901537 PMCID: PMC3678716 DOI: 10.1016/j.chom.2012.06.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Revised: 04/27/2012] [Accepted: 06/04/2012] [Indexed: 12/22/2022]
Abstract
Successful pathogens have evolved to evade innate immune recognition of microbial molecules by pattern recognition receptors (PRR), which control microbial growth in host tissues. Upon Legionella pneumophila infection of macrophages, the cytosolic PRR Nod1 recognizes anhydro-disaccharide-tetrapeptide (anhDSTP) generated by soluble lytic transglycosylase (SltL), the predominant bacterial peptidoglycan degrading enzyme, to activate NF-κB-dependent innate immune responses. We show that L. pneumophila periplasmic protein EnhC, which is uniquely required for bacterial replication within macrophages, interferes with SltL to lower anhDSTP production. L. pneumophila mutant strains lacking EnhC (ΔenhC) increase Nod1-dependent NF-κB activation in host cells, while reducing SltL activity in a ΔenhC strain restores intracellular bacterial growth. Further, L. pneumophila ΔenhC is specifically rescued in Nod1- but not Nod2-deficient macrophages, arguing that EnhC facilitates evasion from Nod1 recognition. These results indicate that a bacterial pathogen regulates peptidoglycan degradation to control the production of PRR ligands and evade innate immune recognition.
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Affiliation(s)
- Mingyu Liu
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02115, USA
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Helicobacter pylori peptidoglycan modifications confer lysozyme resistance and contribute to survival in the host. mBio 2012; 3:e00409-12. [PMID: 23221800 PMCID: PMC3517862 DOI: 10.1128/mbio.00409-12] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The prominent host muramidase lysozyme cleaves bacterial peptidoglycan (PG), and the enzyme is abundant in mucosal secretions. The lytic enzyme susceptibility of Gram-negative bacteria and mechanisms they use to thwart lytic enzyme activity are poorly studied. We previously characterized a Helicobacter pylori PG modification enzyme, an N-deacetylase (PgdA) involved in lysozyme resistance. In this study, another PG modification enzyme, a putative PG O-acetyltransferase (PatA), was identified. Mass spectral analysis of the purified PG demonstrated that a patA strain contained a greatly reduced amount of acetylated muropeptides, indicating a role for PatA in H. pylori PG O-acetylation. The PG modification mutant strains (pgdA, patA, or pgdA patA) were more susceptible to lysozyme killing than the parent, but this assay required high lysozyme levels (up to 50 mg/ml). However, addition of host lactoferrin conferred lysozyme sensitivity to H. pylori, at physiologically relevant concentrations of both host components (3 mg/ml lactoferrin plus 0.3 mg/ml lysozyme). The pgdA patA double mutant strain was far more susceptible to lysozyme/lactoferrin killing than the parent. Peptidoglycan purified from a pgdA patA mutant was five times more sensitive to lysozyme than PG from the parent strain, while PG from both single mutants displayed intermediate sensitivity. Both sensitivity assays for whole cells and for purified PGs indicated that the modifications mediated by PgdA and PatA have a synergistic effect, conferring lysozyme tolerance. In a mouse infection model, significant colonization deficiency was observed for the double mutant at 3 weeks postinoculation. The results show that PG modifications affect the survival of a Gram-negative pathogen. Importance Pathogenic bacteria evade host antibacterial enzymes by a variety of mechanisms, which include resisting lytic enzymes abundant in the host. Enzymatic modifications to peptidoglycan (PG, the site of action of lysozyme) are a known mechanism used by Gram-positive bacteria to protect against host lysozyme attack. However, Gram-negative bacteria contain a thin layer of PG and a recalcitrant outer membrane permeability barrier to resist lysis, so molecular modifications to cell wall structure in order to combat lysis remain largely unstudied. Here we show that two Helicobacter pylori PG modification enzymes (PgdA and PatA) confer a clear protective advantage to a Gram-negative bacterium. They protect the bacterium from lytic enzyme degradation, albeit via different PG modification activities. Many pathogens are Gram negative, so some would be expected to have a similar cell wall-modifying strategy. Understanding such strategies may be useful for combating pathogen growth. Pathogenic bacteria evade host antibacterial enzymes by a variety of mechanisms, which include resisting lytic enzymes abundant in the host. Enzymatic modifications to peptidoglycan (PG, the site of action of lysozyme) are a known mechanism used by Gram-positive bacteria to protect against host lysozyme attack. However, Gram-negative bacteria contain a thin layer of PG and a recalcitrant outer membrane permeability barrier to resist lysis, so molecular modifications to cell wall structure in order to combat lysis remain largely unstudied. Here we show that two Helicobacter pylori PG modification enzymes (PgdA and PatA) confer a clear protective advantage to a Gram-negative bacterium. They protect the bacterium from lytic enzyme degradation, albeit via different PG modification activities. Many pathogens are Gram negative, so some would be expected to have a similar cell wall-modifying strategy. Understanding such strategies may be useful for combating pathogen growth.
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34
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Both TLR2 and TRIF contribute to interferon-β production during Listeria infection. PLoS One 2012; 7:e33299. [PMID: 22432012 PMCID: PMC3303824 DOI: 10.1371/journal.pone.0033299] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 02/07/2012] [Indexed: 12/14/2022] Open
Abstract
Synthesis of interferon-β (IFN-β) is an innate response to cytoplasmic infection with bacterial pathogens. Our recent studies showed that Listeria monocytogenes limits immune detection and IFN-β synthesis via deacetylation of its peptidoglycan, which renders the bacterium resistant to lysozyme degradation. Here, we examined signaling requirements for the massive IFN-β production resulting from the infection of murine macrophages with a mutant strain of L. monocytogenes, ΔpgdA, which is unable to modify its peptidoglycan. We report the identification of unconventional signaling pathways to the IFN-β gene, requiring TLR2 and bacterial internalization. Induction of IFN-β was independent of the Mal/TIRAP adaptor protein but required TRIF and the transcription factors IRF3 and IRF7. These pathways were stimulated to a lesser degree by wild-type L. monocytogenes. They operated in both resident and inflammatory macrophages derived from the peritoneal cavity, but not in bone marrow-derived macrophages. The novelty of our findings thus lies in the first description of TLR2 and TRIF as two critical components leading to the induction of the IFN-β gene and in uncovering that individual macrophage populations adopt different strategies to link pathogen recognition signals to IFN-β gene expression.
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Kobayashi K, Sudiarta IP, Kodama T, Fukushima T, Ara K, Ozaki K, Sekiguchi J. Identification and characterization of a novel polysaccharide deacetylase C (PdaC) from Bacillus subtilis. J Biol Chem 2012; 287:9765-9776. [PMID: 22277649 DOI: 10.1074/jbc.m111.329490] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Cell wall metabolism and cell wall modification are very important processes that bacteria use to adjust to various environmental conditions. One of the main modifications is deacetylation of peptidoglycan. The polysaccharide deacetylase homologue, Bacillus subtilis YjeA (renamed PdaC), was characterized and found to be a unique deacetylase. The pdaC deletion mutant was sensitive to lysozyme treatment, indicating that PdaC acts as a deacetylase. The purified recombinant and truncated PdaC from Escherichia coli deacetylated B. subtilis peptidoglycan and its polymer, (-GlcNAc-MurNAc[-L-Ala-D-Glu]-)(n). Surprisingly, RP-HPLC and ESI-MS/MS analyses showed that the enzyme deacetylates N-acetylmuramic acid (MurNAc) not GlcNAc from the polymer. Contrary to Streptococcus pneumoniae PgdA, which shows high amino acid sequence similarity with PdaC and is a zinc-dependent GlcNAc deacetylase toward peptidoglycan, there was less dependence on zinc ion for deacetylation of peptidoglycan by PdaC than other metal ions (Mn(2+), Mg(2+), Ca(2+)). The kinetic values of the activity toward B. subtilis peptidoglycan were K(m) = 4.8 mM and k(cat) = 0.32 s(-1). PdaC also deacetylated N-acetylglucosamine (GlcNAc) oligomers with a K(m) = 12.3 mM and k(cat) = 0.24 s(-1) toward GlcNAc(4). Therefore, PdaC has GlcNAc deacetylase activity toward GlcNAc oligomers and MurNAc deacetylase activity toward B. subtilis peptidoglycan.
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Affiliation(s)
- Kaori Kobayashi
- Interdisciplinary Graduate School of Science and Technology, Shinshu University, 3-15-1 Tokida, Ueda, Nagano 386-8567, Japan
| | - I Putu Sudiarta
- Interdisciplinary Graduate School of Science and Technology, Shinshu University, 3-15-1 Tokida, Ueda, Nagano 386-8567, Japan
| | - Takeko Kodama
- Biological Science Laboratories, Kao Corporation, 2606 Akabane, Ichikai, Haga, Tochigi 321-3497, Japan
| | - Tatsuya Fukushima
- Division of Gene Research, Department of Life Sciences, Research Center for Human and Environmental Sciences, Shinshu University, 3-15-1 Tokida, Ueda, Nagano 386-8567, Japan and
| | - Katsutoshi Ara
- Biological Science Laboratories, Kao Corporation, 2606 Akabane, Ichikai, Haga, Tochigi 321-3497, Japan
| | - Katsuya Ozaki
- Biological Science Laboratories, Kao Corporation, 2606 Akabane, Ichikai, Haga, Tochigi 321-3497, Japan
| | - Junichi Sekiguchi
- Interdisciplinary Graduate School of Science and Technology, Shinshu University, 3-15-1 Tokida, Ueda, Nagano 386-8567, Japan.
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Kaoukab-Raji A, Biskri L, Bernardini ML, Allaoui A. Characterization of SfPgdA, a Shigella flexneri peptidoglycan deacetylase required for bacterial persistence within polymorphonuclear neutrophils. Microbes Infect 2012; 14:619-27. [PMID: 22307019 DOI: 10.1016/j.micinf.2012.01.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Revised: 01/12/2012] [Accepted: 01/13/2012] [Indexed: 12/31/2022]
Abstract
Peptidoglycan deacetylases protect the Gram-positive bacteria cell wall from host lysozymes by deacetylating peptidoglycan. Sequence analysis of the genome of Shigella flexneri predicts a putative polysaccharide deacetylase encoded by the plasmidic gene orf185, renamed here SfpgdA. We demonstrated a peptidoglycan deacetylase (PGD) activity with the purified SfPgdA in vitro. To investigate the role SfPgdA in virulence, we constructed a SfpgdA mutant and studied its phenotype in vitro. The mutant showed an increased sensitivity to lysozyme compared to the parental strain. Moreover, the mutant was rapidly killed by polymorphonuclear neutrophils (PMNs). Specific substitution of histidines residues 120 and 125, located within the PGD catalytic domain, by phenylalanine abolished SfPgdA function. SfPgdA expression is controlled by PhoP. Mutation of phoP increases sensitivity to lysozyme compared to the SfpgdA mutant. Here, we confirmed that SfPgdA expression is enhanced under low magnesium concentration and not produced by the phoP mutant. Ectopic expression of SfPgdA in the phoP mutant restored lysozyme resistance and parental bacterial persistence within PMNs. Together our results indicate that PG deacetylation mechanism likely contributes to Shigella persistence by subverting detection by the host immune system.
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Affiliation(s)
- Abdelmoughit Kaoukab-Raji
- Laboratoire de Bactériologie Moléculaire, Faculté de Médecine, Université Libre de Bruxelles, Route de Lennik 808, 1070 Bruxelles, Belgium
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The Bacillus subtilis extracytoplasmic function σ factor σ(V) is induced by lysozyme and provides resistance to lysozyme. J Bacteriol 2011; 193:6215-22. [PMID: 21856855 DOI: 10.1128/jb.05467-11] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Bacteria encounter numerous environmental stresses which can delay or inhibit their growth. Many bacteria utilize alternative σ factors to regulate subsets of genes required to overcome different extracellular assaults. The largest group of these alternative σ factors are the extracytoplasmic function (ECF) σ factors. In this paper, we demonstrate that the expression of the ECF σ factor σ(V) in Bacillus subtilis is induced specifically by lysozyme but not other cell wall-damaging agents. A mutation in sigV results in increased sensitivity to lysozyme killing, suggesting that σ(V) is required for lysozyme resistance. Using reverse transcription (RT)-PCR, we show that the previously uncharacterized gene yrhL (here referred to as oatA for O-acetyltransferase) is in a four-gene operon which includes sigV and rsiV. In quantitative RT-PCR experiments, the expression of oatA is induced by lysozyme stress. Lysozyme induction of oatA is dependent upon σ(V). Overexpression of oatA in a sigV mutant restores lysozyme resistance to wild-type levels. This suggests that OatA is required for σ(V)-dependent resistance to lysozyme. We also tested the ability of lysozyme to induce the other ECF σ factors and found that only the expression of sigV is lysozyme inducible. However, we found that the other ECF σ factors contributed to lysozyme resistance. We found that sigX and sigM mutations alone had very little effect on lysozyme resistance but when combined with a sigV mutation resulted in significantly greater lysozyme sensitivity than the sigV mutation alone. This suggests that sigV, sigX, and sigM may act synergistically to control lysozyme resistance. In addition, we show that two ECF σ factor-regulated genes, dltA and pbpX, are required for lysozyme resistance. Thus, we have identified three independent mechanisms which B. subtilis utilizes to avoid killing by lysozyme.
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Reith J, Mayer C. Peptidoglycan turnover and recycling in Gram-positive bacteria. Appl Microbiol Biotechnol 2011; 92:1-11. [PMID: 21796380 DOI: 10.1007/s00253-011-3486-x] [Citation(s) in RCA: 124] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Revised: 07/02/2011] [Accepted: 07/13/2011] [Indexed: 11/24/2022]
Abstract
Bacterial cells are protected by an exoskeleton, the stabilizing and shape-maintaining cell wall, consisting of the complex macromolecule peptidoglycan. In view of its function, it could be assumed that the cell wall is a static structure. In truth, however, it is steadily broken down by peptidoglycan-cleaving enzymes during cell growth. In this process, named cell wall turnover, in one generation up to half of the preexisting peptidoglycan of a bacterial cell is released from the wall. This would result in a massive loss of cell material, if turnover products were not be taken up and recovered. Indeed, in the Gram-negative model organism Escherichia coli, peptidoglycan recovery has been recognized as a complex pathway, named cell wall recycling. It involves about a dozen dedicated recycling enzymes that convey cell wall turnover products to peptidoglycan synthesis or energy pathways. Whether Gram-positive bacteria also recover their cell wall is currently questioned. Given the much larger portion of peptidoglycan in the cell wall of Gram-positive bacteria, however, recovery of the wall material would provide an even greater benefit in these organisms compared to Gram-negatives. Consistently, in many Gram-positives, orthologs of recycling enzymes were identified, indicating that the cell wall may also be recycled in these organisms. This mini-review provides a compilation of information about cell wall turnover and recycling in Gram-positive bacteria during cell growth and division, including recent findings relating to muropeptide recovery in Bacillus subtilis and Clostridium acetobutylicum from our group. Furthermore, the impact of cell wall turnover and recycling on biotechnological processes is discussed.
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Affiliation(s)
- Jan Reith
- Fachbereich Biologie, Molekulare Mikrobiologie, University of Konstanz, Germany
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Bui NK, Turk S, Buckenmaier S, Stevenson-Jones F, Zeuch B, Gobec S, Vollmer W. Development of screening assays and discovery of initial inhibitors of pneumococcal peptidoglycan deacetylase PgdA. Biochem Pharmacol 2011; 82:43-52. [DOI: 10.1016/j.bcp.2011.03.028] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Revised: 03/30/2011] [Accepted: 03/31/2011] [Indexed: 11/28/2022]
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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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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: an update for the period 2005-2006. MASS SPECTROMETRY REVIEWS 2011; 30:1-100. [PMID: 20222147 DOI: 10.1002/mas.20265] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
This review is the fourth update of the original review, published in 1999, on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2006. The review covers fundamental studies, fragmentation of carbohydrate ions, method developments, and applications of the technique to the analysis of different types of carbohydrate. Specific compound classes that are covered include carbohydrate polymers from plants, N- and O-linked glycans from glycoproteins, glycated proteins, glycolipids from bacteria, glycosides, and various other natural products. There is a short section on the use of MALDI-TOF mass spectrometry for the study of enzymes involved in glycan processing, a section on industrial processes, particularly the development of biopharmaceuticals and a section on the use of MALDI-MS to monitor products of chemical synthesis of carbohydrates. Large carbohydrate-protein complexes and glycodendrimers are highlighted in this final section.
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Affiliation(s)
- David J Harvey
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, Oxford OX1 3QU, UK.
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Deli A, Koutsioulis D, Fadouloglou VE, Spiliotopoulou P, Balomenou S, Arnaouteli S, Tzanodaskalaki M, Mavromatis K, Kokkinidis M, Bouriotis V. LmbE proteins from Bacillus cereus are de-N-acetylases with broad substrate specificity and are highly similar to proteins in Bacillus anthracis. FEBS J 2010; 277:2740-53. [DOI: 10.1111/j.1742-4658.2010.07691.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Milani CJE, Aziz RK, Locke JB, Dahesh S, Nizet V, Buchanan JT. The novel polysaccharide deacetylase homologue Pdi contributes to virulence of the aquatic pathogen Streptococcus iniae. MICROBIOLOGY-SGM 2009; 156:543-554. [PMID: 19762441 DOI: 10.1099/mic.0.028365-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The aquatic zoonotic pathogen Streptococcus iniae represents a threat to the worldwide aquaculture industry and poses a risk to humans who handle raw fish. Because little is known about the mechanisms of S. iniae pathogenesis or virulence factors, we established a high-throughput system combining whole-genome pyrosequencing and transposon mutagenesis that allowed us to identify virulence proteins, including Pdi, the polysaccharide deacetylase of S. iniae, that we describe here. Using bioinformatics tools, we identified a highly conserved signature motif in Pdi that is also conserved in the peptidoglycan deacetylase PgdA protein family. A Deltapdi mutant was attenuated for virulence in the hybrid striped bass model and for survival in whole fish blood. Moreover, Pdi was found to promote bacterial resistance to lysozyme killing and the ability to adhere to and invade epithelial cells. On the other hand, there was no difference in the autolytic potential, resistance to oxidative killing or resistance to cationic antimicrobial peptides between S. iniae wild-type and Deltapdi. In conclusion, we have demonstrated that pdi is involved in S. iniae adherence and invasion, lysozyme resistance and survival in fish blood, and have shown that pdi plays a role in the pathogenesis of S. iniae. Identification of Pdi and other S. iniae virulence proteins is a necessary initial step towards the development of appropriate preventive and therapeutic measures against diseases and economic losses caused by this pathogen.
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Affiliation(s)
- Carlo J E Milani
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, MC 0687, La Jolla, CA 92093-0687, USA
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, 11562 Cairo, Egypt
| | - Jeffrey B Locke
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, MC 0687, La Jolla, CA 92093-0687, USA
| | - Samira Dahesh
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, MC 0687, La Jolla, CA 92093-0687, USA
| | - Victor Nizet
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, MC 0657, La Jolla, CA 92093-0657, USA.,Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, MC 0687, La Jolla, CA 92093-0687, USA
| | - John T Buchanan
- Aqua Bounty Technologies, 8395 Camino Santa Fe, Suite E, San Diego, CA 92121, USA.,Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, MC 0687, La Jolla, CA 92093-0687, USA
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Emirian A, Fromentin S, Eckert C, Chau F, Dubost L, Delepierre M, Gutmann L, Arthur M, Mesnage S. Impact of peptidoglycan O-acetylation on autolytic activities of the Enterococcus faecalis N-acetylglucosaminidase AtlA and N-acetylmuramidase AtlB. FEBS Lett 2009; 583:3033-8. [PMID: 19686739 DOI: 10.1016/j.febslet.2009.08.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2009] [Revised: 08/10/2009] [Accepted: 08/10/2009] [Indexed: 11/18/2022]
Abstract
Autolysins are potentially lethal enzymes that partially hydrolyze peptidoglycan for incorporation of new precursors and septum cleavage after cell division. Here, we explored the impact of peptidoglycan O-acetylation on the enzymatic activities of Enterococcus faecalis major autolysins, the N-acetylglucosaminidase AtlA and the N-acetylmuramidase AtlB. We constructed isogenic strains with various O-acetylation levels and used them as substrates to assay E. faecalis autolysin activities. Peptidoglycan O-acetylation had a marginal inhibitory impact on the activities of these enzymes. In contrast, removal of cell wall glycopolymers increased the AtlB activity (37-fold), suggesting that these polymers negatively control the activity of this enzyme.
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Affiliation(s)
- Aurélie Emirian
- Centre de Recherche des Cordeliers, INSERM U872, 75006 Paris, France
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Fouet A. The surface of Bacillus anthracis. Mol Aspects Med 2009; 30:374-85. [PMID: 19607856 DOI: 10.1016/j.mam.2009.07.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2009] [Accepted: 07/08/2009] [Indexed: 11/25/2022]
Abstract
Bacillus anthracis is a Gram positive organism possessing a complex parietal structure. An S-layer, a bi-dimensional crystalline layer, and a peptidic capsule surround the thick peptidoglycan of bacilli harvested during infection. A review of the current literature indicates that elements from each of these three structures, as well as membrane components, have been studied. So-called cell-wall secondary polymers, be they attached to the cell-wall or to the membrane play important functions, either per se or because they permit the anchoring of proteins. Some surface proteins, whichever compartment they are attached to, play, as had been hypothesized, key roles in virulence. Others, of yet unknown function, are nevertheless expressed in vivo. This review will focus on well-studied polymers or proteins and indicate, when appropriate, the mechanisms by which they are targeted to their respective locations.
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Affiliation(s)
- Agnès Fouet
- Institut Pasteur, Unité Toxines et Pathogénie Bactérienne, CNRS, URA2172, F-75015 Paris, France.
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Franco AT, Friedman DB, Nagy TA, Romero-Gallo J, Krishna U, Kendall A, Israel DA, Tegtmeyer N, Washington MK, Peek RM. Delineation of a carcinogenic Helicobacter pylori proteome. Mol Cell Proteomics 2009; 8:1947-58. [PMID: 19470446 DOI: 10.1074/mcp.m900139-mcp200] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Helicobacter pylori is the strongest known risk factor for gastric adenocarcinoma, yet only a fraction of infected persons ever develop cancer. The extensive genetic diversity inherent to this pathogen has precluded comprehensive analyses of constituents that mediate carcinogenesis. We previously reported that in vivo adaptation of a non-carcinogenic H. pylori strain endowed the output derivative with the ability to induce adenocarcinoma, providing a unique opportunity to identify proteins selectively expressed by an oncogenic H. pylori strain. Using a global proteomics DIGE/MS approach, a novel missense mutation of the flagellar protein FlaA was identified that affects structure and function of this virulence-related organelle. Among 25 additional differentially abundant proteins, this approach also identified new proteins previously unassociated with gastric cancer, generating a profile of H. pylori proteins to use in vaccine development and for screening persons infected with strains most likely to induce severe disease.
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Affiliation(s)
- Aime T Franco
- Division of Gastroenterology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-2279, USA
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Abstract
Pathogen recognition and induction of immune responses are important for efficient elimination of infection. However, pathogens such as Listeria monocytogenes employ strategies to evade or modulate these defences, thus creating a more favourable environment that ensures their survival and pathogenesis. New insights into these strategies, particularly those targeting innate immunity, have recently emerged. L. monocytogenes is initially detected at the cell surface or in phagosomes by toll-like receptor 2 and in the cytosol by nuclear oligodimerization domain (NOD)-like receptors (NOD1, NOD2) and NALP3 and Ipaf. It carries out N-deacetylation of peptidoglycan to avoid this detection by toll-like receptor 2 and NOD-like receptors. L. monocytogenes modulates transcription of host immunity genes through modification of histones and chromatin remodelling. Furthermore, L. monocytogenes has recently been shown to avoid autophagy and induce apoptosis in immune effector cells. In this review we discuss some of these strategies, which have provided new insights into the interaction between L. monocytogenes and the immune response at a crucial stage of infection.
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Affiliation(s)
- Sinead C Corr
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland.
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Wang G, Olczak A, Forsberg LS, Maier RJ. Oxidative stress-induced peptidoglycan deacetylase in Helicobacter pylori. J Biol Chem 2009; 284:6790-800. [PMID: 19147492 DOI: 10.1074/jbc.m808071200] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Structural modification of peptidoglycan (PG) is one of the mechanisms that pathogenic bacteria use to evade the host innate immune system. For the noninvasive human gastric pathogen Helicobacter pylori, PG delivery to the host cells is one trigger of the immune response. H. pylori HP310 was markedly up-expressed upon cell exposure to oxidative stress. However, disruption of HP310 did not produce a phenotype distinguishable from the parent, including oxidative stress resistance characteristics. HP310 shows very weak homology to a known gene pgdA encoding PG deacetylase in Streptococcous pneumoniae. PGs from wild type H. pylori and the HP310 mutant were purified and analyzed by matrix-assisted laser desorption ionization time-of-flight and high pressure liquid chromatography. The parent strain PG is partially deacetylated, whereas several major PG-deacetylated muropeptides are absent or significantly reduced in the HP310 mutant. PG deacetylase activity was directly demonstrated by use of pure PG and HP310 protein by measuring the release of acetic acid. The Gram-negative bacterium H. pylori is highly resistant to lysozyme (up to 50 mg/ml), but the HP310 mutant is less resistant to lysozyme compared with the parent strain. Complementation of an hp310 strain with the wild type gene restored lysozyme resistance. The purified PG from the mutant is more susceptible to lysozyme (0.3 mg/ml) digestion than the wild type PG. The PG deacetylation appears to confer lysozyme resistance to escape immune detection. HP310 is representative of a new subfamily of bacterial PG deacetylases.
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Affiliation(s)
- Ge Wang
- Department of Microbiology, University of Georgia, Athens, Georgia 30602, USA
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Davis KM, Akinbi HT, Standish AJ, Weiser JN. Resistance to mucosal lysozyme compensates for the fitness deficit of peptidoglycan modifications by Streptococcus pneumoniae. PLoS Pathog 2008; 4:e1000241. [PMID: 19079576 PMCID: PMC2587705 DOI: 10.1371/journal.ppat.1000241] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Accepted: 11/17/2008] [Indexed: 11/18/2022] Open
Abstract
The abundance of lysozyme on mucosal surfaces suggests that successful colonizers must be able to evade its antimicrobial effects. Lysozyme has a muramidase activity that hydrolyzes bacterial peptidoglycan and a non-muramidase activity attributable to its function as a cationic antimicrobial peptide. Two enzymes (PgdA, a N-acetylglucosamine deacetylase, and Adr, an O-acetyl transferase) that modify different sites on the peptidoglycan of Streptococcus pneumoniae have been implicated in its resistance to lysozyme in vitro. Here we show that the antimicrobial effect of human lysozyme is due to its muramidase activity and that both peptidoglycan modifications are required for full resistance by pneumococci. To examine the contribution of lysozyme and peptidoglycan modifications during colonization of the upper respiratory tract, competition experiments were performed with wild-type and pgdAadr mutant pneumococci in lysozyme M-sufficient (LysM+/+) and -deficient (LysM−/−) mice. The wild-type strain out-competed the double mutant in LysM+/+, but not LysM−/− mice, indicating the importance of resistance to the muramidase activity of lysozyme during mucosal colonization. In contrast, strains containing single mutations in either pgdA or adr prevailed over the wild-type strain in both LysM+/+ and LysM−/− mice. Our findings demonstrate that individual peptidoglycan modifications diminish fitness during colonization. The competitive advantage of wild-type pneumococci in LysM+/+ but not LysM−/− mice suggests that the combination of peptidoglycan modifications reduces overall fitness, but that this is outweighed by the benefits of resistance to the peptidoglycan degrading activity of lysozyme. For many successful pathogens, their surfaces must be able to adapt to different host environments, or to avoid host immune components, to establish infection. Bacterial pathogens, for example, are known to modify their cell walls, which are comprised largely of peptidoglycan. Our study focuses on peptidoglycan modifications by Streptococcus pneumoniae, which initiates interaction with its host by colonizing the mucosal surface of the upper respiratory tract. Two proteins (PgdA and Adr) that modify the cell wall of S. pneumoniae have each been associated with resistance to lysozyme, which cleaves peptidoglycan and is one of the most abundant antimicrobial factors in the human respiratory tract. Using defined bacterial mutants together with mice that express or lack lysozyme, we show that the full resistance to lysozyme requires modifications by both proteins. These cell wall modifications each come at a significant fitness cost to the bacterium. This fitness cost, however, is outweighed by the benefits of lysozyme resistance in vivo. Our study, therefore, demonstrates the relationship between a bacterial pathogen and a host defense mechanism that imparts a substantial selective pressure on organisms that colonize the mucosal surface.
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Affiliation(s)
- Kimberly M Davis
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
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Characterization of the Caulobacter crescentus holdfast polysaccharide biosynthesis pathway reveals significant redundancy in the initiating glycosyltransferase and polymerase steps. J Bacteriol 2008; 190:7219-31. [PMID: 18757530 DOI: 10.1128/jb.01003-08] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Caulobacter crescentus cells adhere to surfaces by using an extremely strong polar adhesin called the holdfast. The polysaccharide component of the holdfast is comprised in part of oligomers of N-acetylglucosamine. The genes involved in the export of the holdfast polysaccharide and the anchoring of the holdfast to the cell were previously discovered. In this study, we identified a cluster of polysaccharide biosynthesis genes (hfsEFGH) directly adjacent to the holdfast polysaccharide export genes. Sequence analysis indicated that these genes are involved in the biosynthesis of the minimum repeat unit of the holdfast polysaccharide. HfsE is predicted to be a UDP-sugar lipid-carrier transferase, the glycosyltransferase that catalyzes the first step in polysaccharide biosynthesis. HfsF is predicted to be a flippase, HfsG is a glycosyltransferase, and HfsH is similar to a polysaccharide (chitin) deacetylase. In-frame hfsG and hfsH deletion mutants resulted in severe deficiencies both in surface adhesion and in binding to the holdfast-specific lectin wheat germ agglutinin. In contrast, hfsE and hfsF mutants exhibited nearly wild-type levels of adhesion and holdfast synthesis. We identified three paralogs to hfsE, two of which are redundant to hfsE for holdfast synthesis. We also identified a redundant paralog to the hfsC gene, encoding the putative polysaccharide polymerase, and present evidence that the hfsE and hfsC paralogs, together with the hfs genes, are absolutely required for proper holdfast synthesis.
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