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Bonin M, Irion AL, Jürß A, Pascual S, Cord-Landwehr S, Planas A, Moerschbacher BM. Engineering of a chitin deacetylase to generate tailor-made chitosan polymers. PLoS Biol 2024; 22:e3002459. [PMID: 38236907 PMCID: PMC10796014 DOI: 10.1371/journal.pbio.3002459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 12/04/2023] [Indexed: 01/22/2024] Open
Abstract
Chitin deacetylases (CDAs) emerge as a valuable tool to produce chitosans with a nonrandom distribution of N-acetylglucosamine (GlcNAc) and glucosamine (GlcN) units. We hypothesized before that CDAs tend to bind certain sequences within the substrate matching their subsite preferences for either GlcNAc or GlcN units. Thus, they deacetylate or N-acetylate their substrates at nonrandom positions. To understand the molecular basis of these preferences, we analyzed the binding site of a CDA from Pestalotiopsis sp. (PesCDA) using a detailed activity screening of a site-saturation mutagenesis library. In addition, molecular dynamics simulations were conducted to get an in-depth view of crucial interactions along the binding site. Besides elucidating the function of several amino acids, we were able to show that only 3 residues are responsible for the highly specific binding of PesCDA to oligomeric substrates. The preference to bind a GlcNAc unit at subsite -2 and -1 can mainly be attributed to N75 and H199, respectively. Whereas an exchange of N75 at subsite -2 eliminates enzyme activity, H199 can be substituted with tyrosine to increase the GlcN acceptance at subsite -1. This change in substrate preference not only increases enzyme activity on certain substrates and changes composition of oligomeric products but also significantly changes the pattern of acetylation (PA) when N-acetylating polyglucosamine. Consequently, we could clearly show how subsite preferences influence the PA of chitosans produced with CDAs.
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Affiliation(s)
- Martin Bonin
- Institute for Biology and Biotechnology of Plants, University of Münster, Münster, Germany
- Laboratory of Biochemistry, Institut Químic de Sarrià, University Ramon Llull, Barcelona, Spain
| | - Antonia L. Irion
- Institute for Biology and Biotechnology of Plants, University of Münster, Münster, Germany
| | - Anika Jürß
- Institute for Biology and Biotechnology of Plants, University of Münster, Münster, Germany
| | - Sergi Pascual
- Laboratory of Biochemistry, Institut Químic de Sarrià, University Ramon Llull, Barcelona, Spain
| | - Stefan Cord-Landwehr
- Institute for Biology and Biotechnology of Plants, University of Münster, Münster, Germany
| | - Antoni Planas
- Laboratory of Biochemistry, Institut Químic de Sarrià, University Ramon Llull, Barcelona, Spain
| | - Bruno M. Moerschbacher
- Institute for Biology and Biotechnology of Plants, University of Münster, Münster, Germany
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Muñoz-Escudero D, Breazeale SD, Lee M, Guan Z, Raetz CRH, Sousa MC. Structure and Function of ArnD. A Deformylase Essential for Lipid A Modification with 4-Amino-4-deoxy-l-arabinose and Polymyxin Resistance. Biochemistry 2023; 62:2970-2981. [PMID: 37782650 PMCID: PMC10914315 DOI: 10.1021/acs.biochem.3c00293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Covalent modification of lipid A with 4-deoxy-4-amino-l-arabinose (Ara4N) mediates resistance to cationic antimicrobial peptides and polymyxin antibiotics in Gram-negative bacteria. The proteins required for Ara4N biosynthesis are encoded in the pmrE and arnBCADTEF loci, with ArnT ultimately transferring the amino sugar from undecaprenyl-phospho-4-deoxy-4-amino-l-arabinose (C55P-Ara4N) to lipid A. However, Ara4N is N-formylated prior to its transfer to undecaprenyl-phosphate by ArnC, requiring a deformylase activity downstream in the pathway to generate the final C55P-Ara4N donor. Here, we show that deletion of the arnD gene in an Escherichia coli mutant that constitutively expresses the arnBCADTEF operon leads to accumulation of the formylated ArnC product undecaprenyl-phospho-4-deoxy-4-formamido-l-arabinose (C55P-Ara4FN), suggesting that ArnD is the downstream deformylase. Purification of Salmonella typhimurium ArnD (stArnD) shows that it is membrane-associated. We present the crystal structure of stArnD revealing a NodB homology domain structure characteristic of the metal-dependent carbohydrate esterase family 4 (CE4). However, ArnD displays several distinct features: a 44 amino acid insertion, a C-terminal extension in the NodB fold, and sequence divergence in the five motifs that define the CE4 family, suggesting that ArnD represents a new family of carbohydrate esterases. The insertion is responsible for membrane association as its deletion results in a soluble ArnD variant. The active site retains a metal coordination H-H-D triad, and in the presence of Co2+ or Mn2+, purified stArnD efficiently deformylates C55P-Ara4FN confirming its role in Ara4N biosynthesis. Mutations D9N and H233Y completely inactivate stArnD implicating these two residues in a metal-assisted acid-base catalytic mechanism.
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Affiliation(s)
- Daniel Muñoz-Escudero
- Department of Molecular Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309
| | - Steven D. Breazeale
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710
| | - Myeongseon Lee
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309
| | - Ziqiang Guan
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710
| | | | - Marcelo C. Sousa
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309
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Liu L, Xia Y, Li Y, Zhou Y, Su X, Yan X, Wang Y, Liu W, Cheng H, Wang Y, Yang Q. Inhibition of chitin deacetylases to attenuate plant fungal diseases. Nat Commun 2023; 14:3857. [PMID: 37385996 PMCID: PMC10310857 DOI: 10.1038/s41467-023-39562-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 06/20/2023] [Indexed: 07/01/2023] Open
Abstract
Phytopathogenic fungi secrete chitin deacetylase (CDA) to escape the host's immunological defense during infection. Here, we showed that the deacetylation activity of CDA toward chitin is essential for fungal virulence. Five crystal structures of two representative and phylogenetically distant phytopathogenic fungal CDAs, VdPDA1 from Verticillium dahliae and Pst_13661 from Puccinia striiformis f. sp. tritici, were obtained in ligand-free and inhibitor-bound forms. These structures suggested that both CDAs have an identical substrate-binding pocket and an Asp-His-His triad for coordinating a transition metal ion. Based on the structural identities, four compounds with a benzohydroxamic acid (BHA) moiety were obtained as phytopathogenic fungal CDA inhibitors. BHA exhibited high effectiveness in attenuating fungal diseases in wheat, soybean, and cotton. Our findings revealed that phytopathogenic fungal CDAs share common structural features, and provided BHA as a lead compound for the design of CDA inhibitors aimed at attenuating crop fungal diseases.
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Affiliation(s)
- Lin Liu
- School of Bioengineering, Dalian University of Technology, 116024, Dalian, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518000, Shenzhen, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 100193, Beijing, China
| | - Yeqiang Xia
- Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, 210095, Nanjing, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, 210095, Nanjing, China
| | - Yingchen Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 100193, Beijing, China
| | - Yong Zhou
- School of Software, Dalian University of Technology, 116024, Dalian, China
| | - Xiaofeng Su
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaojing Yan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 100193, Beijing, China
| | - Yan Wang
- Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, 210095, Nanjing, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, 210095, Nanjing, China
| | - Wende Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 100193, Beijing, China
| | - Hongmei Cheng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China.
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, 210095, Nanjing, China.
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, 210095, Nanjing, China.
| | - Qing Yang
- School of Bioengineering, Dalian University of Technology, 116024, Dalian, China.
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518000, Shenzhen, China.
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 100193, Beijing, China.
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Yin L, Wang Q, Sun J, Mao X. Expression and Molecular Modification of Chitin Deacetylase from Streptomyces bacillaris. MOLECULES (BASEL, SWITZERLAND) 2022; 28:molecules28010113. [PMID: 36615307 PMCID: PMC9822392 DOI: 10.3390/molecules28010113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/19/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
Chitin deacetylase can be used in the green and efficient preparation of chitosan from chitin. Herein, a novel chitin deacetylase SbCDA from Streptomyces bacillaris was heterologously expressed and comprehensively characterized. SbDNA exhibits its highest deacetylation activity at 35 °C and pH 8.0. The enzyme activity is enhanced by Mn2+ and prominently inhibited by Zn2+, SDS, and EDTA. SbCDA showed better deacetylation activity on colloidal chitin, (GlcNAc)5, and (GlcNAc)6 than other forms of the substrate. Molecular modification of SbCDA was conducted based on sequence alignment and homology modeling. A mutant SbCDA63G with higher activity and better temperature stability was obtained. The deacetylation activity of SbCDA63G was increased by 133% compared with the original enzyme, and the optimal reaction temperature increased from 35 to 40 °C. The half-life of SbCDA63G at 40 °C is 15 h, which was 5 h longer than that of the original enzyme. The improved characteristics of the chitin deacetylase SbCDA63G make it a potential candidate to industrially produce chitosan from chitin.
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Affiliation(s)
- Lili Yin
- Qingdao Key Laboratory of Food Biotechnology, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
- Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, Qingdao 266404, China
| | - Qi Wang
- Qingdao Key Laboratory of Food Biotechnology, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
- Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, Qingdao 266404, China
| | - Jianan Sun
- Qingdao Key Laboratory of Food Biotechnology, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
- Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, Qingdao 266404, China
- Correspondence: (J.S.); (X.M.); Tel.: +86-532-82031360 (J.S.); +86-532-82032660 (X.M.)
| | - Xiangzhao Mao
- Qingdao Key Laboratory of Food Biotechnology, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
- Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, Qingdao 266404, China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Correspondence: (J.S.); (X.M.); Tel.: +86-532-82031360 (J.S.); +86-532-82032660 (X.M.)
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2019-2020. MASS SPECTROMETRY REVIEWS 2022:e21806. [PMID: 36468275 DOI: 10.1002/mas.21806] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2020. Also included are papers that describe methods appropriate to analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. The review is basically divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of arrays. (2) Applications to various structural types such as oligo- and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other areas such as medicine, industrial processes and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. The reported work shows increasing use of incorporation of new techniques such as ion mobility and the enormous impact that MALDI imaging is having. MALDI, although invented nearly 40 years ago is still an ideal technique for carbohydrate analysis and advancements in the technique and range of applications show little sign of diminishing.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
- Department of Chemistry, University of Oxford, Oxford, Oxfordshire, United Kingdom
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Xia H, Yang H, Yan N, Hou W, Wang H, Wang X, Wang H, Zhou M. Bacteriostatic effects of phage F23s1 and its endolysin on Vibrio parahaemolyticus. J Basic Microbiol 2022; 62:963-974. [PMID: 35662075 DOI: 10.1002/jobm.202200056] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/01/2022] [Accepted: 05/14/2022] [Indexed: 11/06/2022]
Abstract
Vibrio parahaemolyticus is a common foodborne pathogenic bacterium and drug-resistant strains are now widespread. Phages led by drug-resistant V. parahaemolyticus strains are promising means to decrease the pressure on public health. We isolated a V. parahaemolyticus-specific bacteriophage F23s1 that was active at wide ranges of temperature (30-60°C) and pH (4-10). Phage F23s1 exhibited a specific host range; in that, only 13 of the 23 V. parahaemolyticus strains were lysed. F23s1 effectively inhibited the growth of V. parahaemolyticus strain F23 in shrimp at 25°C within 12 h at a multiplicity of infection of 1000. We sequenced the genome of phage F23s1 which comprised a 76,648-bp DNA with 105 open reading frames (ORFs) and identified an endolysin gene ORF52 that was then cloned and successfully expressed in Escherichia coli. The recombinant ORF52 protein significantly decreased OD600 nm of V. parahaemolyticus F23 from 0.978 to 0.249 when used at 20 µmol/L within 60 min. The endolysin also showed lytic activity against a panel of 23 drug-resistant V. parahaemolyticus and 12 Salmonella strains with a higher lytic ability for V. parahaemolyticus. The phage F23s1 and its endolysin will be useful for preventing and controlling V. parahaemolyticus in food safety.
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Affiliation(s)
- Hai Xia
- Department of Food Quality and Safety, School of Food Science and Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Houji Yang
- Department of Food Quality and Safety, School of Food Science and Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Na Yan
- Department of Food Quality and Safety, School of Food Science and Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Wenfu Hou
- Department of Food Quality and Safety, School of Food Science and Engineering, Wuhan Polytechnic University, Wuhan, China.,Hubei Industrial Technology Research Institute of Jingchu Special Foods, Jingzhou, China
| | - Huajuan Wang
- Department of Food Quality and Safety, School of Food Science and Engineering, Wuhan Polytechnic University, Wuhan, China.,Hubei Industrial Technology Research Institute of Jingchu Special Foods, Jingzhou, China
| | - Xiaohong Wang
- Department of Food Quality and Safety, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hongxun Wang
- Department of Food Quality and Safety, School of Food Science and Engineering, Wuhan Polytechnic University, Wuhan, China.,Hubei Industrial Technology Research Institute of Jingchu Special Foods, Jingzhou, China
| | - Min Zhou
- Department of Food Quality and Safety, School of Food Science and Engineering, Wuhan Polytechnic University, Wuhan, China.,Hubei Industrial Technology Research Institute of Jingchu Special Foods, Jingzhou, China
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7
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The WalR-WalK signaling pathway modulates the activities of both CwlO and LytE through control of the peptidoglycan deacetylase PdaC in Bacillus subtilis. J Bacteriol 2021; 204:e0053321. [PMID: 34871030 PMCID: PMC8846395 DOI: 10.1128/jb.00533-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The WalR-WalK two component signaling system in Bacillus subtilis functions in the homeostatic control of the peptidoglycan (PG) hydrolases LytE and CwlO that are required for cell growth. When the activities of these enzymes are low, WalR activates transcription of lytE and cwlO and represses transcription of iseA, a secreted inhibitor of LytE. Conversely, when PG hydrolases activity is too high, WalR-dependent expression of lytE and cwlO is reduced and iseA is de-repressed. In a screen for additional factors that regulate this signaling pathway, we discovered that over-expression of the membrane-anchored PG deacetylase PdaC increases WalR-dependent gene expression. We show that increased expression of PdaC, but not catalytic mutants, prevents cell wall cleavage by both LytE and CwlO, explaining the WalR activation. Importantly, the pdaC gene, like iseA, is repressed by active WalR. We propose that de-repression of pdaC when PG hydrolase activity is too high results in modification of the membrane-proximal layers of the PG, protecting the wall from excessive cleavage by the membrane-tethered CwlO. Thus, the WalR-WalK system homeostatically controls the levels and activities of both elongation-specific cell wall hydrolases. Importance: Bacterial growth and division requires a delicate balance between the synthesis and remodeling of the cell wall exoskeleton. How bacteria regulate the potentially autolytic enzymes that remodel the cell wall peptidoglycan remains incompletely understood. Here, we provide evidence that the broadly conserved WalR-WalK two-component signaling system homeostatically controls both the levels and activities of two cell wall hydrolases that are critical for cell growth.
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Sasamoto K, Himiyama T, Moriyoshi K, Ohmoto T, Uegaki K, Nishiya Y, Nakamura T. Crystal structure of acetylxylan esterase from Caldanaerobacter subterraneus subsp. tengcongensis. Acta Crystallogr F Struct Biol Commun 2021; 77:399-406. [PMID: 34726178 PMCID: PMC8561816 DOI: 10.1107/s2053230x21009675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/17/2021] [Indexed: 11/10/2022] Open
Abstract
The acetylxylan esterases (AXEs) classified into carbohydrate esterase family 4 (CE4) are metalloenzymes that catalyze the deacetylation of acetylated carbohydrates. AXE from Caldanaerobacter subterraneus subsp. tengcongensis (TTE0866), which belongs to CE4, is composed of three parts: a signal sequence (residues 1-22), an N-terminal region (NTR; residues 23-135) and a catalytic domain (residues 136-324). TTE0866 catalyzes the deacetylation of highly substituted cellulose acetate and is expected to be useful for industrial applications in the reuse of resources. In this study, the crystal structure of TTE0866 (residues 23-324) was successfully determined. The crystal diffracted to 1.9 Å resolution and belonged to space group I212121. The catalytic domain (residues 136-321) exhibited a (β/α)7-barrel topology. However, electron density was not observed for the NTR (residues 23-135). The crystal packing revealed the presence of an intermolecular space without observable electron density, indicating that the NTR occupies this space without a defined conformation or was truncated during the crystallization process. Although the active-site conformation of TTE0866 was found to be highly similar to those of other CE4 enzymes, the orientation of its Trp264 side chain near the active site was clearly distinct. The unique orientation of the Trp264 side chain formed a different-shaped cavity within TTE0866, which may contribute to its reactivity towards highly substituted cellulose acetate.
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Affiliation(s)
- Kohei Sasamoto
- Division of Life Science, Graduate School of Science and Engineering, Setsunan University, 17-8 Ikeda-Nakamachi, Neyagawa, Osaka 572-8508, Japan
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577, Japan
| | - Tomoki Himiyama
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577, Japan
| | - Kunihiko Moriyoshi
- Osaka Research Institute of Industrial Science and Technology, 1-6-50 Morinomiya, Joto-ku, Osaka 536-8553, Japan
| | - Takashi Ohmoto
- Osaka Research Institute of Industrial Science and Technology, 1-6-50 Morinomiya, Joto-ku, Osaka 536-8553, Japan
| | - Koichi Uegaki
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, 3327-204 Nakamachi, Nara 631-8505, Japan
- Agricultural Technology and Innovation Research Institute, Kindai University, 3327-204 Nakamachi, Nara 631-8505, Japan
| | - Yoshiaki Nishiya
- Division of Life Science, Graduate School of Science and Engineering, Setsunan University, 17-8 Ikeda-Nakamachi, Neyagawa, Osaka 572-8508, Japan
| | - Tsutomu Nakamura
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577, Japan
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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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10
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In silico and in vitro analysis of an Aspergillus niger chitin deacetylase to decipher its subsite sugar preferences. J Biol Chem 2021; 297:101129. [PMID: 34478709 PMCID: PMC8488497 DOI: 10.1016/j.jbc.2021.101129] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/21/2021] [Accepted: 08/26/2021] [Indexed: 11/29/2022] Open
Abstract
Chitin deacetylases (CDAs) are found in many different organisms ranging from marine bacteria to fungi and insects. These enzymes catalyze the removal of acetyl groups from chitinous substrates generating various chitosans, linear copolymers consisting of N-acetylglucosamine (GlcNAc) and glucosamine. CDAs influence the degree of acetylation of chitosans as well as their pattern of acetylation, a parameter that was recently shown to influence the physicochemical properties and biological activities of chitosans. The binding site of CDAs typically consists of around four subsites, each accommodating a single sugar unit of the substrate. It has been hypothesized that the subsite preferences for GlcNAc or glucosamine units play a crucial role in the acetylation pattern they generate, but so far, this characteristic was largely ignored and still lacks structural data on the involved residues. Here, we determined the crystal structure of an Aspergillus niger CDA. Then, we used molecular dynamics simulations, backed up with a variety of in vitro activity assays using different well-defined polymeric and oligomeric substrates, to study this CDA in detail. We found that Aspergillus niger CDA strongly prefers a GlcNAc sugar unit at its −1 subsite and shows a weak GlcNAc preference at the other noncatalytic subsites, which was apparent both when deacetylating and N-acetylating oligomeric substrates. Overall, our results show that the combination of in vitro and in silico methods used here enables the detailed analysis of CDAs, including their subsite preferences, which could influence their substrate targets and the characteristics of chitosans produced by these species.
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Buscaill P, van der Hoorn RAL. Defeated by the nines: nine extracellular strategies to avoid microbe-associated molecular patterns recognition in plants. THE PLANT CELL 2021; 33:2116-2130. [PMID: 33871653 PMCID: PMC8364246 DOI: 10.1093/plcell/koab109] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 04/07/2021] [Indexed: 05/13/2023]
Abstract
Recognition of microbe-associated molecular patterns (MAMPs) by cell-surface receptors is pivotal in host-microbe interactions. Both pathogens and symbionts establish plant-microbe interactions using fascinating intricate extracellular strategies to avoid recognition. Here we distinguish nine different extracellular strategies to avoid recognition by the host, acting at three different levels. To avoid the accumulation of MAMP precursors (Level 1), microbes take advantage of polymorphisms in both MAMP proteins and glycans, or downregulate MAMP production. To reduce hydrolytic MAMP release (Level 2), microbes shield MAMP precursors with proteins or glycans and inhibit or degrade host-derived hydrolases. And to prevent MAMP perception directly (Level 3), microbes degrade or sequester MAMPs before they are perceived. We discuss examples of these nine strategies and envisage three additional extracellular strategies to avoid MAMP perception in plants.
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Affiliation(s)
- Pierre Buscaill
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, OX1 3RB Oxford, UK
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12
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Preparation of Defined Chitosan Oligosaccharides Using Chitin Deacetylases. Int J Mol Sci 2020; 21:ijms21217835. [PMID: 33105791 PMCID: PMC7660110 DOI: 10.3390/ijms21217835] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 10/19/2020] [Indexed: 12/13/2022] Open
Abstract
During the past decade, detailed studies using well-defined 'second generation' chitosans have amply proved that both their material properties and their biological activities are dependent on their molecular structure, in particular on their degree of polymerisation (DP) and their fraction of acetylation (FA). Recent evidence suggests that the pattern of acetylation (PA), i.e., the sequence of acetylated and non-acetylated residues along the linear polymer, is equally important, but chitosan polymers with defined, non-random PA are not yet available. One way in which the PA will influence the bioactivities of chitosan polymers is their enzymatic degradation by sequence-dependent chitosan hydrolases present in the target tissues. The PA of the polymer substrates in conjunction with the subsite preferences of the hydrolases determine the type of oligomeric products and the kinetics of their production and further degradation. Thus, the bioactivities of chitosan polymers will at least in part be carried by the chitosan oligomers produced from them, possibly through their interaction with pattern recognition receptors in target cells. In contrast to polymers, partially acetylated chitosan oligosaccharides (paCOS) can be fully characterised concerning their DP, FA, and PA, and chitin deacetylases (CDAs) with different and known regio-selectivities are currently emerging as efficient tools to produce fully defined paCOS in quantities sufficient to probe their bioactivities. In this review, we describe the current state of the art on how CDAs can be used in forward and reverse mode to produce all of the possible paCOS dimers, trimers, and tetramers, most of the pentamers and many of the hexamers. In addition, we describe the biotechnological production of the required fully acetylated and fully deacetylated oligomer substrates, as well as the purification and characterisation of the paCOS products.
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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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Pascual S, Planas A. Carbohydrate de-N-acetylases acting on structural polysaccharides and glycoconjugates. Curr Opin Chem Biol 2020; 61:9-18. [PMID: 33075728 DOI: 10.1016/j.cbpa.2020.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/06/2020] [Accepted: 09/08/2020] [Indexed: 12/14/2022]
Abstract
Deacetylation of N-acetylhexosamine residues in structural polysaccharides and glycoconjugates is catalyzed by different families of carbohydrate esterases that, despite different structural folds, share a common metal-assisted acid/base mechanism with the metal cation coordinated with a conserved Asp-His-His triad. These enzymes serve diverse biological functions in the modification of cell-surface polysaccharides in bacteria and fungi as well as in the metabolism of hexosamines in the biosynthesis of cellular glycoconjugates. Focusing on carbohydrate de-N-acetylases, this article summarizes the background of the different families from a structural and functional viewpoint and covers advances in the characterization of novel enzymes over the last 2-3 years. Current research is addressed to the identification of new deacetylases and unravel their biological functions as they are candidate targets for the design of antimicrobials against pathogenic bacteria and fungi. Likewise, some families are also used as biocatalysts for the production of defined glycostructures with diverse applications.
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Affiliation(s)
- Sergi Pascual
- 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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