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Biniek-Antosiak K, Bejger M, Śliwiak J, Baranowski D, Mohammed ASA, Svergun DI, Rypniewski W. Structural, Thermodynamic and Enzymatic Characterization of N, N-Diacetylchitobiose Deacetylase from Pyrococcus chitonophagus. Int J Mol Sci 2022; 23:ijms232415736. [PMID: 36555375 PMCID: PMC9779004 DOI: 10.3390/ijms232415736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/29/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Chitin is a major source of energy and macroelements for many organisms. An important step in its degradation is the deacetylation of chitin or its fragments. Deacetylase from the extremophile Pyrococcus chitonophagus has been analyzed by X-ray crystallography, small-angle X-ray scattering, differential scanning calorimetry, isothermal titration calorimetry and NMR to determine its structure, thermodynamics and enzymatic properties. It is a hexameric, zinc-containing metalloenzyme that retains its structural integrity up to temperatures slightly exceeding 100 °C. It removes the acetyl group specifically from the non-reducing end of the sugar substrate. Its main substrate is N,N-diacetylchitobiose but it also active, at a reduced level, toward N-acetyl-d-glucosamine or a trimer of N-acetyl-d-glucosamine units. Crystallographic analysis includes the structure of the enzyme with its main substrate approaching the active site in a monodentate manner, replacing the single water molecule that is bound at the Zn2+ cation when the ligand is absent. The Zn2+ cation remains tetrahedrally coordinated, with three of its ligands provided by the protein's conserved His-Asp-His triad. The crystal structures are consistent with the reaction mechanism proceeding via an anhydride intermediate. Hydrolysis as the first step cannot be ruled out in a hydrated environment but no defined 'hydrolytic water' site can be identified in the analyzed structures.
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Affiliation(s)
- Katarzyna Biniek-Antosiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12-14, 61-704 Poznań, Poland
| | - Magdalena Bejger
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12-14, 61-704 Poznań, Poland
| | - Joanna Śliwiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12-14, 61-704 Poznań, Poland
| | - Daniel Baranowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12-14, 61-704 Poznań, Poland
| | - Ahmed S. A. Mohammed
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, DESY, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, DESY, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Wojciech Rypniewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12-14, 61-704 Poznań, Poland
- Correspondence:
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Metabolic Adaptation to Sulfur of Hyperthermophilic Palaeococcus pacificus DY20341 T from Deep-Sea Hydrothermal Sediments. Int J Mol Sci 2020; 21:ijms21010368. [PMID: 31935923 PMCID: PMC6981617 DOI: 10.3390/ijms21010368] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 12/26/2019] [Accepted: 12/29/2019] [Indexed: 11/30/2022] Open
Abstract
The hyperthermo-piezophilic archaeon Palaeococcus pacificus DY20341T, isolated from East Pacific hydrothermal sediments, can utilize elemental sulfur as a terminal acceptor to simulate growth. To gain insight into sulfur metabolism, we performed a genomic and transcriptional analysis of Pa. pacificus DY20341T with/without elemental sulfur as an electron acceptor. In the 2001 protein-coding sequences of the genome, transcriptomic analysis showed that 108 genes increased (by up to 75.1 fold) and 336 genes decreased (by up to 13.9 fold) in the presence of elemental sulfur. Palaeococcus pacificus cultured with elemental sulfur promoted the following: the induction of membrane-bound hydrogenase (MBX), NADH:polysulfide oxidoreductase (NPSOR), NAD(P)H sulfur oxidoreductase (Nsr), sulfide dehydrogenase (SuDH), connected to the sulfur-reducing process, the upregulation of iron and nickel/cobalt transfer, iron–sulfur cluster-carrying proteins (NBP35), and some iron–sulfur cluster-containing proteins (SipA, SAM, CobQ, etc.). The accumulation of metal ions might further impact on regulators, e.g., SurR and TrmB. For growth in proteinous media without elemental sulfur, cells promoted flagelin, peptide/amino acids transporters, and maltose/sugar transporters to upregulate protein and starch/sugar utilization processes and riboflavin and thiamin biosynthesis. This indicates how strain DY20341T can adapt to different living conditions with/without elemental sulfur in the hydrothermal fields.
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Machałowski T, Wysokowski M, Tsurkan MV, Galli R, Schimpf C, Rafaja D, Brendler E, Viehweger C, Żółtowska-Aksamitowska S, Petrenko I, Czaczyk K, Kraft M, Bertau M, Bechmann N, Guan K, Bornstein SR, Voronkina A, Fursov A, Bejger M, Biniek-Antosiak K, Rypniewski W, Figlerowicz M, Pokrovsky O, Jesionowski T, Ehrlich H. Spider Chitin: An Ultrafast Microwave-Assisted Method for Chitin Isolation from Caribena versicolor Spider Molt Cuticle. Molecules 2019; 24:E3736. [PMID: 31623238 PMCID: PMC6833065 DOI: 10.3390/molecules24203736] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/07/2019] [Accepted: 10/14/2019] [Indexed: 01/07/2023] Open
Abstract
Chitin, as a fundamental polysaccharide in invertebrate skeletons, continues to be actively investigated, especially with respect to new sources and the development of effective methods for its extraction. Recent attention has been focused on marine crustaceans and sponges; however, the potential of spiders (order Araneae) as an alternative source of tubular chitin has been overlooked. In this work, we focused our attention on chitin from up to 12 cm-large Theraphosidae spiders, popularly known as tarantulas or bird-eating spiders. These organisms "lose" large quantities of cuticles during their molting cycle. Here, we present for the first time a highly effective method for the isolation of chitin from Caribena versicolor spider molt cuticle, as well as its identification and characterization using modern analytical methods. We suggest that the tube-like molt cuticle of this spider can serve as a naturally prefabricated and renewable source of tubular chitin with high potential for application in technology and biomedicine.
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Affiliation(s)
- Tomasz Machałowski
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, 60965 Poznan, Poland.
- Institute of Electronics and Sensor Materials, TU Bergakademie Freiberg, 09599 Freiberg, Germany.
| | - Marcin Wysokowski
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, 60965 Poznan, Poland.
- Institute of Electronics and Sensor Materials, TU Bergakademie Freiberg, 09599 Freiberg, Germany.
| | - Mikhail V Tsurkan
- Leibniz Institute of Polymer Research Dresden, Dresden 01069, Germany.
| | - Roberta Galli
- Clinical Sensoring and Monitoring, Department of Anesthesiology and Intensive Care Medicine, Faculty of Medicine, TU Dresden, 01307 Dresden, Germany.
| | - Christian Schimpf
- Institute of Materials Science, TU Bergakademie Freiberg, 09599 Freiberg, Germany.
| | - David Rafaja
- Institute of Materials Science, TU Bergakademie Freiberg, 09599 Freiberg, Germany.
| | - Erica Brendler
- Institute of Analytical Chemistry, TU Bergakademie Freiberg, 09599 Freiberg, Germany.
| | - Christine Viehweger
- Institute of Analytical Chemistry, TU Bergakademie Freiberg, 09599 Freiberg, Germany.
| | - Sonia Żółtowska-Aksamitowska
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, 60965 Poznan, Poland.
- Institute of Electronics and Sensor Materials, TU Bergakademie Freiberg, 09599 Freiberg, Germany.
| | - Iaroslav Petrenko
- Institute of Electronics and Sensor Materials, TU Bergakademie Freiberg, 09599 Freiberg, Germany.
| | - Katarzyna Czaczyk
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, 60637 Poznan, Poland.
| | - Michael Kraft
- Institute of Chemical Technology, TU Bergakademie Freiberg, 09599 Freiberg, Germany.
| | - Martin Bertau
- Institute of Chemical Technology, TU Bergakademie Freiberg, 09599 Freiberg, Germany.
| | - Nicole Bechmann
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany.
| | - Kaomei Guan
- Institute of Pharmacology and Toxicology, TU Dresden, 01307 Dresden, Germany.
| | - Stefan R Bornstein
- Center for Regenerative Therapies Dresden, TU Dresden, 01307 Dresden, Germany.
- Department of Medicine III, University Hospital Carl Gustav Carus Dresden, TU Dresden, 01307 Dresden, Germany.
| | - Alona Voronkina
- Department of Pharmacy, National Pirogov Memorial Medical University, 21018 Vinnytsia, Ukraine.
| | - Andriy Fursov
- Institute of Electronics and Sensor Materials, TU Bergakademie Freiberg, 09599 Freiberg, Germany.
| | - Magdalena Bejger
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61704 Poznan, Poland.
| | | | - Wojciech Rypniewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61704 Poznan, Poland.
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61704 Poznan, Poland.
| | - Oleg Pokrovsky
- Geoscience and Environment Toulouse, UMR 5563 CNRS, 31400 Toulouse, France.
- BIO-GEO-CLIM Laboratory, Tomsk State University, Lenina St. 36, 634050 Tomsk, Russia.
| | - Teofil Jesionowski
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, 60965 Poznan, Poland.
| | - Hermann Ehrlich
- Institute of Electronics and Sensor Materials, TU Bergakademie Freiberg, 09599 Freiberg, Germany.
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Nishitani Y, Horiuchi A, Aslam M, Kanai T, Atomi H, Miki K. Crystal structures of an archaeal chitinase ChiD and its ligand complexes. Glycobiology 2018; 28:418-426. [PMID: 29800365 DOI: 10.1093/glycob/cwy024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 03/20/2018] [Indexed: 11/13/2022] Open
Abstract
Chitinase D (designated as Pc-ChiD) was found in a hyperthermophilic archaeon, Pyrococcus chitonophagus (previously described as Thermococcus chitonophagus), that was isolated from media containing only chitin as carbon source. Pc-ChiD displays chitinase activity and is thermostable at temperatures up to 95°C, suggesting its potential for industrial use. Pc-ChiD has a secretion signal peptide and two chitin-binding domains (ChBDs) in the N-terminal domain. However, the C-terminal domain shares no sequence similarity with previously identified saccharide-degrading enzymes and does not contain the DXDXE motif conserved in the glycoside hydrolase (GH) 18 family chitinases. To elucidate its overall structure and reaction mechanism, we determined the first crystal structures of Pc-ChiD, both in the ligand-free form and in complexes with substrates. Structure analyses revealed that the C-terminal domain of Pc-ChiD, Pc-ChiD(ΔBD), consists of a third putative substrate-binding domain, which cannot be predicted from the amino acid sequence, and a catalytic domain structurally similar to that found in not the GH18 family but the GH23 family. Based on the similarity with GH23 family chitinase, the catalytic residues of Pc-ChiD were predicted and confirmed by mutagenesis analyses. Moreover, the specific C-terminal 100 residues of Pc-ChiD are important to fix the putative substrate-binding domain next to the catalytic domain, contributing to the structure stability as well as the long chitin chain binding. Our findings reveal the structure of a unique archaeal chitinase that is distinct from previously known members of the GH23 family.
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Affiliation(s)
- Yuichi Nishitani
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Ayumi Horiuchi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Mehwish Aslam
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Tamotsu Kanai
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.,JST, CREST, Gobancho 7, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Haruyuki Atomi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.,JST, CREST, Gobancho 7, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Kunio Miki
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.,JST, CREST, Gobancho 7, Chiyoda-ku, Tokyo 102-0076, Japan
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Aslam M, Takahashi N, Matsubara K, Imanaka T, Kanai T, Atomi H. Identification of the glucosamine kinase in the chitinolytic pathway of Thermococcus kodakarensis. J Biosci Bioeng 2018; 125:320-326. [DOI: 10.1016/j.jbiosc.2017.10.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 10/07/2017] [Accepted: 10/10/2017] [Indexed: 01/13/2023]
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Luo H, Quan CL, Peng C, Gao F. Recent development of Ori-Finder system and DoriC database for microbial replication origins. Brief Bioinform 2018; 20:1114-1124. [DOI: 10.1093/bib/bbx174] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 12/04/2017] [Indexed: 01/28/2023] Open
Abstract
Abstract
DNA replication begins at replication origins in all three domains of life. Identification and characterization of replication origins are important not only in providing insights into the structure and function of the replication origins but also in understanding the regulatory mechanisms of the initiation step in DNA replication. The Z-curve method has been used in the identification of replication origins in archaeal genomes successfully since 2002. Furthermore, the Web servers of Ori-Finder and Ori-Finder 2 have been developed to predict replication origins in both bacterial and archaeal genomes based on the Z-curve method, and the replication origins with manual curation have been collected into an online database, DoriC. Ori-Finder system and DoriC database are currently used in the research field of DNA replication origins in prokaryotes, including: (i) identification of oriC regions in bacterial and archaeal genomes; (ii) discovery and analysis of the conserved sequences within oriC regions; and (iii) strand-biased analysis of bacterial genomes.
Up to now, more and more predicted results by Ori-Finder system were supported by subsequent experiments, and Ori-Finder system has been used to identify the replication origins in > 100 newly sequenced prokaryotes in their genome reports. In addition, the data in DoriC database have been widely used in the large-scale analyses of replication origins and strand bias in prokaryotic genomes. Here, we review the development of Ori-Finder system and DoriC database as well as their applications. Some future directions and aspects for extending the application of Ori-Finder and DoriC are also presented.
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Engineering of the Hyperthermophilic Archaeon Thermococcus kodakarensis for Chitin-Dependent Hydrogen Production. Appl Environ Microbiol 2017; 83:AEM.00280-17. [PMID: 28550062 DOI: 10.1128/aem.00280-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 05/16/2017] [Indexed: 11/20/2022] Open
Abstract
Thermococcus kodakarensis is a hyperthermophilic archaeon that harbors a complete set of genes for chitin degradation to fructose 6-phosphate. However, wild-type T. kodakarensis KOD1 does not display growth on chitin. In this study, we developed a T. kodakarensis strain that can grow on chitin via genetic and adaptive engineering. First, a chitinase overproduction strain (KC01) was constructed by replacing the chitinase gene promoter with a strong promoter from the cell surface glycoprotein gene, resulting in increased degradation of swollen chitin and accumulation of N-,N'-diacetylchitobiose in the medium. To enhance N-,N'-diacetylchitobiose assimilation in KC01, genes encoding diacetylchitobiose deacetylase, exo-β-d-glucosaminidase, and glucosamine-6-phosphate deaminase were also overexpressed to obtain strain KC04. To strengthen the glycolytic flux of KC04, the gene encoding Tgr (transcriptional repressor of glycolytic genes) was disrupted to obtain strain KC04Δt. In both KC04 and KC04Δt strains, degradation of swollen chitin was further enhanced. In the culture broth of these strains, the accumulation of glucosamine was observed. KC04Δt was repeatedly inoculated in a swollen-chitin-containing medium for 13 cultures. This adaptive engineering strategy resulted in the isolation of a strain (KC04ΔtM1) that showed almost complete degradation of 0.4% (wt/vol) swollen chitin after 90 h. The strain produced high levels of acetate and ammonium in the culture medium, and, moreover, molecular hydrogen was generated. This strongly suggests that strain KC04ΔtM1 has acquired the ability to convert chitin to fructose 6-phosphate via deacetylation and deamination and further convert fructose 6-phosphate to acetate via glycolysis coupled to hydrogen generation.IMPORTANCE Chitin is a linear homopolymer of β-1,4-linked N-acetylglucosamine and is the second most abundant biomass next to cellulose. Compared to the wealth of research focused on the microbial degradation and conversion of cellulose, studies addressing microbial chitin utilization are still limited. In this study, using the hyperthermophilic archaeon Thermococcus kodakarensis as a host, we have constructed a strain that displays chitin-dependent hydrogen generation. The apparent hydrogen yield per unit of sugar consumed was slightly higher with swollen chitin than with starch. As gene manipulation in T. kodakarensis is relatively simple, the strain constructed in this study can also be used as a parent strain for the development and expansion of chitin-dependent biorefinery, in addition to its capacity to produce hydrogen.
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