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Hilário S, Gonçalves MFM, Matos I, Rangel LF, Sousa JA, Santos MJ, Ayra-Pardo C. Comparative genomics reveals insights into the potential of Lysinibacillus irui as a plant growth promoter. Appl Microbiol Biotechnol 2024; 108:370. [PMID: 38861018 PMCID: PMC11166776 DOI: 10.1007/s00253-024-13210-6] [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] [Received: 03/05/2024] [Revised: 05/23/2024] [Accepted: 05/28/2024] [Indexed: 06/12/2024]
Abstract
Members of the genus Lysinibacillus attract attention for their mosquitocidal, bioremediation, and plant growth-promoting abilities. Despite this interest, comprehensive studies focusing on genomic traits governing plant growth and stress resilience in this genus using whole-genome sequencing are still scarce. Therefore, we sequenced and compared the genomes of three endophytic Lysinibacillus irui strains isolated from Canary Island date palms with the ex-type strain IRB4-01. Overall, the genomes of these strains consist of a circular chromosome with an average size of 4.6 Mb and a GC content of 37.2%. Comparative analysis identified conserved gene clusters within the core genome involved in iron acquisition, phosphate solubilization, indole-3-acetic acid biosynthesis, and volatile compounds. In addition, genome analysis revealed the presence of genes encoding carbohydrate-active enzymes, and proteins that confer resistance to oxidative, osmotic, and salinity stresses. Furthermore, pathways of putative novel bacteriocins were identified in all genomes. This illustrates possible common plant growth-promoting traits shared among all strains of L. irui. Our findings highlight a rich repertoire of genes associated with plant lifestyles, suggesting significant potential for developing inoculants to enhance plant growth and resilience. This study is the first to provide insights into the overall genomic signatures and mechanisms of plant growth promotion and biocontrol in the genus Lysinibacillus. KEY POINTS: • Pioneer study in elucidating plant growth promoting in L. irui through comparative genomics. • Genome mining identified biosynthetic pathways of putative novel bacteriocins. • Future research directions to develop L. irui-based biofertilizers for sustainable agriculture.
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Affiliation(s)
- Sandra Hilário
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal.
- GreenUPorto, Sustainable Agrifood Production Research Centre/Inov4Agro, DGAOT, Faculty of Sciences, University of Porto, Campus de Vairão, 747, 4485-646, Vila do Conde, Portugal.
| | - Micael F M Gonçalves
- Department of Biology, Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Inês Matos
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal
| | - Luis F Rangel
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal
| | - José A Sousa
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal
- Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, FC4, 4169-007, Porto, Portugal
| | - Maria J Santos
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal
- Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, FC4, 4169-007, Porto, Portugal
| | - Camilo Ayra-Pardo
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal.
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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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Gonçalves MFM, Hilário S, Tacão M, Van de Peer Y, Alves A, Esteves AC. Genome and Metabolome MS-Based Mining of a Marine Strain of Aspergillus affinis. J Fungi (Basel) 2021; 7:1091. [PMID: 34947073 PMCID: PMC8709101 DOI: 10.3390/jof7121091] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/17/2021] [Accepted: 12/17/2021] [Indexed: 01/09/2023] Open
Abstract
Aspergillus section Circumdati encompasses several species that express both beneficial (e.g., biochemical transformation of steroids and alkaloids, enzymes and metabolites) and harmful compounds (e.g., production of ochratoxin A (OTA)). Given their relevance, it is important to analyze the genetic and metabolic diversity of the species of this section. We sequenced the genome of Aspergillus affinis CMG 70, isolated from sea water, and compared it with the genomes of species from section Circumdati, including A. affinis's strain type. The A. affinis genome was characterized considering secondary metabolites biosynthetic gene clusters (BGCs), carbohydrate-active enzymes (CAZymes), and transporters. To uncover the biosynthetic potential of A. affinis CMG 70, an untargeted metabolomics (LC-MS/MS) approach was used. Cultivating the fungus in the presence and absence of sea salt showed that A. affinis CMG 70 metabolite profiles are salt dependent. Analyses of the methanolic crude extract revealed the presence of both unknown and well-known Aspergillus compounds, such as ochratoxin A, anti-viral (e.g., 3,5-Di-tert-butyl-4-hydroxybenzoic acid and epigallocatechin), anti-bacterial (e.g., 3-Hydroxybenzyl alcohol, l-pyroglutamic acid, lecanoric acid), antifungal (e.g., lpyroglutamic acid, 9,12,13-Trihydroxyoctadec-10-enoic acid, hydroxyferulic acid), and chemotherapeutic (e.g., daunomycinone, mitoxantrone) related metabolites. Comparative analysis of 17 genomes from 16 Aspergillus species revealed abundant CAZymes (568 per species), secondary metabolite BGCs (73 per species), and transporters (1359 per species). Some BGCs are highly conserved in this section (e.g., pyranonigrin E and UNII-YC2Q1O94PT (ACR toxin I)), while others are incomplete or completely lost among species (e.g., bikaverin and chaetoglobosins were found exclusively in series Sclerotiorum, while asperlactone seemed completely lost). The results of this study, including genome analysis and metabolome characterization, emphasize the molecular diversity of A. affinis CMG 70, as well as of other species in the section Circumdati.
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Affiliation(s)
- Micael F. M. Gonçalves
- CESAM, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (M.F.M.G.); (S.H.); (M.T.); (A.C.E.)
| | - Sandra Hilário
- CESAM, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (M.F.M.G.); (S.H.); (M.T.); (A.C.E.)
| | - Marta Tacão
- CESAM, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (M.F.M.G.); (S.H.); (M.T.); (A.C.E.)
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Artur Alves
- CESAM, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (M.F.M.G.); (S.H.); (M.T.); (A.C.E.)
| | - Ana C. Esteves
- CESAM, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (M.F.M.G.); (S.H.); (M.T.); (A.C.E.)
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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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Huang X, Zhang R, Qiu Y, Wu H, Xiang Q, Yu X, Zhao K, Zhang X, Chen Q, Penttinen P, Gu Y. RNA-seq Profiling Showed Divergent Carbohydrate-Active Enzymes (CAZymes) Expression Patterns in Lentinula edodes at Brown Film Formation Stage Under Blue Light Induction. Front Microbiol 2020; 11:1044. [PMID: 32536907 PMCID: PMC7267012 DOI: 10.3389/fmicb.2020.01044] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 04/27/2020] [Indexed: 12/12/2022] Open
Abstract
Lentinula edodes (shiitake mushroom) is one of the most important edible mushrooms worldwide. The L. edodes cultivation cycle includes a unique developing stage called brown film formation that directly affects the development of primordium and the quality of fruiting body. Brown film formation is induced by light, especially blue light. To promote our understanding of the role of blue light in brown film formation mechanisms of L. edodes, we used RNA-seq and compared the transcriptomes of L. edodes grown under blue light and in dark, and validated the expression profiles using qRT-PCR. Blue light stimulated the formation of brown film and increased the content of polysaccharides in L. edodes. Blue light also promoted L. edodes to absorb more polysaccharides by enhancing the activities of enzymes. Among the 730 differentially expressed genes (DEGs), 433 genes were up-regulated and 297 were down-regulated. Most of the DEGs were in the oxidoreductase activity group. Pentose and glucuronic acid conversion and starch and sucrose metabolism were the most important pathways in the formation of brown film. A total of 79 genes of DEGs were identified as genes encoding carbohydrate-active enzymes (CAZymes). Fifty-one of the CAZymes genes were up-regulated, suggesting that CAZymes play important roles in brown film formation to provide sufficient nutrition for L. edodes. The results will facilitate future functional investigations of the genes involved in the developmental control of L. edodes.
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Affiliation(s)
- Xiying Huang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Runji Zhang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Yijie Qiu
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Haibing Wu
- Department of Livestock and Fisheries, Mianyang Academy of Agricultural University, Mianyang, China
| | - Quanju Xiang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Xiumei Yu
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Ke Zhao
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Xiaoping Zhang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Qiang Chen
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Petri Penttinen
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Yunfu Gu
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
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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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Liu L, Zhou Y, Qu M, Qiu Y, Guo X, Zhang Y, Liu T, Yang J, Yang Q. Structural and biochemical insights into the catalytic mechanisms of two insect chitin deacetylases of the carbohydrate esterase 4 family. J Biol Chem 2019; 294:5774-5783. [PMID: 30755482 PMCID: PMC6463723 DOI: 10.1074/jbc.ra119.007597] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 02/08/2019] [Indexed: 12/15/2022] Open
Abstract
Insect chitin deacetylases (CDAs) catalyze the removal of acetyl groups from chitin and modify this polymer during its synthesis and reorganization. CDAs are essential for insect survival and therefore represent promising targets for insecticide development. However, the structural and biochemical characteristics of insect CDAs have remained elusive. Here, we report the crystal structures of two insect CDAs from the silk moth Bombyx mori: BmCDA1, which may function in cuticle modification, and BmCDA8, which may act in modifying peritrophic membranes in the midgut. Both enzymes belong to the carbohydrate esterase 4 (CE4) family. Comparing their overall structures at 1.98–2.4 Å resolution with those from well-studied microbial CDAs, we found that two unique loop regions in BmCDA1 and BmCDA8 contribute to the distinct architecture of their substrate-binding clefts. These comparisons revealed that both BmCDA1 and BmCDA8 possess a much longer and wider substrate-binding cleft with a very open active site in the center than the microbial CDAs, including VcCDA from Vibrio cholerae and ArCE4A from Arthrobacter species AW19M34-1. Biochemical analyses indicated that BmCDA8 is an active enzyme that requires its substrates to occupy subsites 0, +1, and +2 for catalysis. In contrast, BmCDA1 also required accessory proteins for catalysis. To the best of our knowledge, our work is the first to unveil the structural and biochemical features of insect proteins belonging to the CE4 family.
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Affiliation(s)
- Lin Liu
- From the State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, Dalian 116024, China
| | - Yong Zhou
- From the State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, Dalian 116024, China
| | - Mingbo Qu
- From the State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, Dalian 116024, China
| | - Yu Qiu
- Department of Protein Engineering, Biologics Research, Sanofi, Bridgewater, New Jersey 08807
| | - Xingming Guo
- From the State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, Dalian 116024, China
| | - Yuebin Zhang
- the Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116024, China
| | - Tian Liu
- From the State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, Dalian 116024, China
| | - Jun Yang
- From the State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, Dalian 116024, China
| | - Qing Yang
- From the State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, Dalian 116024, China; the State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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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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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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Eminoğlu A, Ülker S, Sandallı C. Cloning, Purification and Characterization of Acetyl Xylane Esterase from Anoxybacillus flavithermus DSM 2641(T) with Activity on Low Molecular-Weight Acetates. Protein J 2016; 34:237-42. [PMID: 26126589 DOI: 10.1007/s10930-015-9618-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Family 4 carbohydrate esterases (CE-4) have deacetylate different forms of acetylated poly/oligosaccharides in nature. This family is recognized with a specific polysaccharide deacetylase domain assigned as NodB homology domain in their secondary structure. Most family 4 carbohydrate esterases have been structurally and biochemically characterized. However, this is the first study about the enzymological function of pdaB-like CE4s from thermophilic bacterium Anoxybacillus flavithermus DSM 2641(T). A. flavithermus WK1 genome harbors five putative CE4 family genes. One of them is 762 bp long and encodes a protein of 253 amino acids in length and it was used as reference sequence in this study. It was described as acetyl xylane esterase (AXE) in genome project and this AfAXE gene was amplified without signal sequence and cloned. The recombinant protein was expressed in E. coli BL21 (DE3), purified by nickel affinity chromatography and its purity was visualized on SDS-PAGE. The activity of the recombinant enzyme was shown by zymogram analysis with α-naphtyl acetate as a substrate. The enzyme was characterized spectrophotometrically using chromogenic p-nitrophenyl acetate. Optimum temperature and pH were determined as 50 °C and 7.5, respectively. Km and Vmax were determined as 0.43 mM and 3333.33 U/mg, respectively under optimum conditions. To our knowledge this is the first enzymological characterization of a pdaB-like family 4 carbohydrate esterase from the members of Anoxybacillus genus.
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Affiliation(s)
- Ayşenur Eminoğlu
- Department of Biology, Molecular Biology Research Laboratory, Recep Tayyip Erdogan University, 53100, Fener, Rize, Turkey
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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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Cuervo-Soto LI, Valdés-García G, Batista-García R, del Rayo Sánchez-Carbente M, Balcázar-López E, Lira-Ruan V, Pastor N, Folch-Mallol JL. Identification of a novel carbohydrate esterase from Bjerkandera adusta: structural and function predictions through bioinformatics analysis and molecular modeling. Proteins 2015; 83:533-46. [PMID: 25586442 DOI: 10.1002/prot.24760] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 12/19/2014] [Accepted: 12/31/2014] [Indexed: 11/07/2022]
Abstract
A new gene from Bjerkandera adusta strain UAMH 8258 encoding a carbohydrate esterase (designated as BacesI) was isolated and expressed in Pichia pastoris. The gene had an open reading frame of 1410 bp encoding a polypeptide of 470 amino acid residues, the first 18 serving as a secretion signal peptide. Homology and phylogenetic analyses showed that BaCesI belongs to carbohydrate esterases family 4. Three-dimensional modeling of the protein and normal mode analysis revealed a breathing mode of the active site that could be relevant for esterase activity. Furthermore, the overall negative electrostatic potential of this enzyme suggests that it degrades neutral substrates and will not act on negative substrates such as peptidoglycan or p-nitrophenol derivatives. The enzyme shows a specific activity of 1.118 U mg(-1) protein on 2-naphthyl acetate. No activity was detected on p-nitrophenol derivatives as proposed from the electrostatic potential data. The deacetylation activity of the recombinant BaCesI was confirmed by measuring the release of acetic acid from several substrates, including oat xylan, shrimp shell chitin, N-acetylglucosamine, and natural substrates such as sugar cane bagasse and grass. This makes the protein very interesting for the biofuels production industry from lignocellulosic materials and for the production of chitosan from chitin.
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Affiliation(s)
- Laura I Cuervo-Soto
- Department of Biochemistry and Molecular Biology, Facultad de Ciencias, Universidad Autónoma del Estado de Morelos. Av. Universidad 1001, Col., Chamilpa, Cuernavaca, Morelos México; Department of Environmental Biotechnology, Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos. Av. Universidad 1001, Col., Chamilpa, Cuernavaca, Morelos México
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14
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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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PelA deacetylase activity is required for Pel polysaccharide synthesis in Pseudomonas aeruginosa. J Bacteriol 2013; 195:2329-39. [PMID: 23504011 DOI: 10.1128/jb.02150-12] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Pel polysaccharide serves as an intercellular adhesin for the formation and maintenance of biofilms in the opportunistic pathogen Pseudomonas aeruginosa. Pel biosynthesis requires the products of a seven-gene operon, pelA-pelG, all of which are necessary for Pel-dependent biofilm formation and Pel-related phenotypes. One of the genes, pelA, encodes a protein with a predicted polysaccharide deacetylase domain. In this work, the role of the putative deacetylase domain in Pel production was examined. We first established that purified recombinant PelA hydrolyzed the pseudosubstrate p-nitrophenyl acetate in vitro, and site-specific mutations of predicted deacetylase active-site residues reduced activity greater than 10-fold. Additionally, these mutants were deficient in Pel-dependent biofilm formation and wrinkly colony morphology in vivo. Subcellular fractionation experiments demonstrate that PelA localizes to both the membrane and periplasmic fractions. Finally, antiserum against the Pel polysaccharide was generated, and PelA deacetylase mutants do not produce Pel-reactive material. Taken together, these results suggest that the deacetylase activity of PelA is important for the production of the Pel polysaccharide.
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Fadouloglou VE, Kapanidou M, Agiomirgianaki A, Arnaouteli S, Bouriotis V, Glykos NM, Kokkinidis M. Structure determination through homology modelling and torsion-angle simulated annealing: application to a polysaccharide deacetylase from Bacillus cereus. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:276-83. [PMID: 23385463 DOI: 10.1107/s0907444912045829] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 11/06/2012] [Indexed: 11/10/2022]
Abstract
The structure of BC0361, a polysaccharide deacetylase from Bacillus cereus, has been determined using an unconventional molecular-replacement procedure. Tens of putative models of the C-terminal domain of the protein were constructed using a multitude of homology-modelling algorithms, and these were tested for the presence of signal in molecular-replacement calculations. Of these, only the model calculated by the SAM-T08 server gave a consistent and convincing solution, but the resulting model was too inaccurate to allow phase determination to proceed to completion. The application of slow-cooling torsion-angle simulated annealing (started from a very high temperature) drastically improved this initial model to the point of allowing phasing through cycles of model building and refinement to be initiated. The structure of the protein is presented with emphasis on the presence of a C(α)-modified proline at its active site, which was modelled as an α-hydroxy-L-proline.
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Affiliation(s)
- Vasiliki E Fadouloglou
- Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, 68100 Alexandroupolis, Greece
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18
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Little DJ, Poloczek J, Whitney JC, Robinson H, Nitz M, Howell PL. The structure- and metal-dependent activity of Escherichia coli PgaB provides insight into the partial de-N-acetylation of poly-β-1,6-N-acetyl-D-glucosamine. J Biol Chem 2012; 287:31126-37. [PMID: 22810235 DOI: 10.1074/jbc.m112.390005] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Exopolysaccharides are required for the development and integrity of biofilms produced by a wide variety of bacteria. In Escherichia coli, partial de-N-acetylation of the exopolysaccharide poly-β-1,6-N-acetyl-D-glucosamine (PNAG) by the periplasmic protein PgaB is required for polysaccharide intercellular adhesin-dependent biofilm formation. To understand the molecular basis for PNAG de-N-acetylation, the structure of PgaB in complex with Ni(2+) and Fe(3+) have been determined to 1.9 and 2.1 Å resolution, respectively, and its activity on β-1,6-GlcNAc oligomers has been characterized. The structure of PgaB reveals two (β/α)(x) barrel domains: a metal-binding de-N-acetylase that is a member of the family 4 carbohydrate esterases (CE4s) and a domain structurally similar to glycoside hydrolases. PgaB displays de-N-acetylase activity on β-1,6-GlcNAc oligomers but not on the β-1,4-(GlcNAc)(4) oligomer chitotetraose and is the first CE4 member to exhibit this substrate specificity. De-N-acetylation occurs in a length-dependent manor, and specificity is observed for the position of de-N-acetylation. A key aspartic acid involved in de-N-acetylation, normally seen in other CE4s, is missing in PgaB, suggesting that the activity of PgaB is attenuated to maintain the low levels of de-N-acetylation of PNAG observed in vivo. The metal dependence of PgaB is different from most CE4s, because PgaB shows increased rates of de-N-acetylation with Co(2+) and Ni(2+) under aerobic conditions, and Co(2+), Ni(2+) and Fe(2+) under anaerobic conditions, but decreased activity with Zn(2+). The work presented herein will guide inhibitor design to combat biofilm formation by E. coli and potentially a wide range of medically relevant bacteria producing polysaccharide intercellular adhesin-dependent biofilms.
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Affiliation(s)
- Dustin J Little
- Program in Molecular Structure & Function, Research Institute, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
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Shi YW, Liu XQ, Shi P, Zhang XY. Characterization of zinc-binding properties of a novel imidase from Pseudomonas putida YZ-26. Arch Biochem Biophys 2009; 494:1-6. [PMID: 19931221 DOI: 10.1016/j.abb.2009.11.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Revised: 10/27/2009] [Accepted: 11/12/2009] [Indexed: 11/25/2022]
Abstract
The imidase from Pseudomonas putida YZ-26 consisting of 293-amino acid residues is a novel imidase with four subunits as the holo-enzyme and low molecular weight which is significantly different from known mammalian imidase. This study measured the zinc-binding properties of the imidase using inductively coupled plasma-atomic emission spectrometry and competition assay combined with activity determinations. Results show that each subunit of the imidase binds the zinc ion by 1:1 stoichiometry with apparent binding constant of 9.5 x 10(8)M(-1). The activity of the apo-imidase (20 microM) was recovered with the addition of zinc in the lower concentration (0-20 microM), whereas the enzymatic activity is decreased in the presence of high concentration of zinc (above 100 microM). The site-directed mutagenesis of His(247), His(86) or Cys(7), Cys(108) in imidase resulted in loss of activity and zinc-binding abilities at different degrees, showing that these residues may critically affect both enzymatic activity and conformation.
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Affiliation(s)
- Ya-Wei Shi
- Institute of Biotechnology, Key Laboratory of Chemical Biology and Molecular Engineering of Education Ministry, Shanxi University, Taiyuan, PR China.
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Ramazzina I, Cendron L, Folli C, Berni R, Monteverdi D, Zanotti G, Percudani R. Logical identification of an allantoinase analog (puuE) recruited from polysaccharide deacetylases. J Biol Chem 2008; 283:23295-304. [PMID: 18550550 DOI: 10.1074/jbc.m801195200] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The hydrolytic cleavage of the hydantoin ring of allantoin, catalyzed by allantoinase, is required for the utilization of the nitrogen present in purine-derived compounds. The allantoinase gene (DAL1), however, is missing in many completely sequenced organisms able to use allantoin as a nitrogen source. Here we show that an alternative allantoinase gene (puuE) can be precisely identified by analyzing its logic relationship with three other genes of the pathway. The novel allantoinase is annotated in structure and sequence data bases as polysaccharide deacetylase for its homology with enzymes that catalyze hydrolytic reactions on chitin or peptidoglycan substrates. The recombinant PuuE protein from Pseudomonas fluorescens exhibits metal-independent allantoinase activity and stereospecificity for the S enantiomer of allantoin. The crystal structures of the protein and of protein-inhibitor complexes reveal an overall similarity with the polysaccharide deacetylase beta/alpha barrel and remarkable differences in oligomeric assembly and active site geometry. The conserved Asp-His-His metal-binding triad is replaced by Glu-His-Trp, a configuration that is distinctive of PuuE proteins within the protein family. An extra domain at the top of the barrel offers a scaffold for protein tetramerization and forms a small substrate-binding cleft by hiding the large binding groove of polysaccharide deacetylases. Substrate positioning at the active site suggests an acid/base mechanism of catalysis in which only one member of the catalytic pair of polysaccharide deacetylases has been conserved. These data provide a structural rationale for the shifting of substrate specificity that occurred during evolution.
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Affiliation(s)
- Ileana Ramazzina
- Department of Biochemistry and Molecular Biology and Mathematics, University of Parma, 43100, Parma, Italy
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