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Doan-Nguyen TP, Aunkham A, Preedanorawut P, Chanpong T, Schulte A, Crespy D, Suginta W. Nanodots functionalized with chitooligosaccharides for blocking chitoporins. Colloids Surf B Biointerfaces 2024; 245:114284. [PMID: 39395215 DOI: 10.1016/j.colsurfb.2024.114284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2024] [Revised: 09/26/2024] [Accepted: 09/29/2024] [Indexed: 10/14/2024]
Abstract
We report the synthesis of functionalized nanodots as potential powerful blockers of solute transport through a chitoporin. Ultrasmall silica nanocapsules with a diameter of ∼ 6 nm were coated with chitooligosaccharides to be used as a "lid" binding to the opening of the chitoporin VhChiP of Vibrio campbellii. Efficient blocking is attributed to the adequate size of the nanodots and their functionalization with oligochitosan, which has strong affinity towards the Vibrio chitoporin. This strategy paves the way towards the development of nanomaterials for blocking other porins.
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Affiliation(s)
- Thao P Doan-Nguyen
- Department of Materials Science and Engineering, School of Molecular Science and Engineering (MSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand
| | - Anuwat Aunkham
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand
| | - Patitta Preedanorawut
- Department of Materials Science and Engineering, School of Molecular Science and Engineering (MSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand
| | - Thanida Chanpong
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand
| | - Albert Schulte
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand
| | - Daniel Crespy
- Department of Materials Science and Engineering, School of Molecular Science and Engineering (MSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand.
| | - Wipa Suginta
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand.
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2
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Meunier L, Costa R, Keller-Costa T, Cannella D, Dechamps E, George IF. Selection of marine bacterial consortia efficient at degrading chitin leads to the discovery of new potential chitin degraders. Microbiol Spectr 2024:e0088624. [PMID: 39315806 DOI: 10.1128/spectrum.00886-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 07/13/2024] [Indexed: 09/25/2024] Open
Abstract
Chitin degradation is a keystone process in the oceans, mediated by marine microorganisms with the help of several enzymes, mostly chitinases. Sediment, seawater, and filter-feeding marine invertebrates, such as sponges, are known to harbor chitin-degrading bacteria and are presumably hotspots for chitin turnover. Here, we employed an artificial selection process involving enrichment cultures derived from microbial communities associated with the marine sponge Hymeniacidon perlevis, its surrounding seawater and sediment, to select bacterial consortia capable of degrading raw chitin. Throughout the artificial selection process, chitin degradation rates and the taxonomic composition of the four successive enrichment cultures were followed. To the best of our knowledge, chitin degradation was characterized for the first time using size exclusion chromatography, which revealed significant shifts in the numbered average chitin molecular weight, strongly suggesting the involvement of endo-chitinases in the breakdown of the chitin polymer during the enrichment process. Concomitantly with chitin degradation, the enrichment cultures exhibited a decrease in alpha diversity compared with the environmental samples. Notably, some of the dominant taxa in the enriched communities, such as Motilimonas, Arcobacter, and Halarcobacter, were previously unknown to be involved in chitin degradation. In particular, the analysis of published genomes of these genera suggests a pivotal role of Motilimonas in the hydrolytic cleavage of chitin. This study provides context to the microbiome of the marine sponge Hymeniacidon perlevis in light of its environmental surroundings and opens new ground to the future discovery and characterization of novel enzymes of marine origin involved in chitin degradation processes.IMPORTANCEChitin is the second most abundant biopolymer on Earth after cellulose, and the most abundant in the marine environment. At present, industrial processes for the conversion of seafood waste into chitin, chitosan, and chitooligosaccharide (COS) rely on the use of high amounts of concentrated acids or strong alkali at high temperature. Developing bio-based methods to transform available chitin into valuable compounds, such as chitosan and COS, holds promise in promoting a more sustainable, circular bioeconomy. By employing an artificial selection procedure based on chitin as a sole C and N source, we discovered microorganisms so-far unknown to metabolize chitin in the rare microbial biosphere of several marine biotopes. This finding represents a first important step on the path towards characterizing and exploiting potentially novel enzymes of marine origin with biotechnological interest, since products of chitin degradation may find applications across several sectors, such as agriculture, pharmacy, and waste management.
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Affiliation(s)
- Laurence Meunier
- Laboratory of Ecology of Aquatic Systems, Brussels Bioengineering School, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Rodrigo Costa
- Institute for Bioengineering and Biosciences (iBB) and Institute for Health and Bioeconomy (i4HB), Instituto Superior Técnico (IST), Universidade de Lisboa, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico (IST), Universidade de Lisboa, Lisbon, Portugal
| | - Tina Keller-Costa
- Institute for Bioengineering and Biosciences (iBB) and Institute for Health and Bioeconomy (i4HB), Instituto Superior Técnico (IST), Universidade de Lisboa, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico (IST), Universidade de Lisboa, Lisbon, Portugal
| | - David Cannella
- PhotoBioCatalysis Unit, Crop Nutrition and Biostimulation Lab (CPBL) and Biomass Transformation Lab (BTL), Brussels Bioengineering School, Université Libre de Bruxelles, Brussels, Belgium
| | - Etienne Dechamps
- Laboratory of Ecology of Aquatic Systems, Brussels Bioengineering School, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Isabelle F George
- Laboratory of Ecology of Aquatic Systems, Brussels Bioengineering School, Université Libre de Bruxelles (ULB), Brussels, Belgium
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3
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Guseva K, Mohrlok M, Alteio L, Schmidt H, Pollak S, Kaiser C. Bacteria face trade-offs in the decomposition of complex biopolymers. PLoS Comput Biol 2024; 20:e1012320. [PMID: 39116194 PMCID: PMC11364420 DOI: 10.1371/journal.pcbi.1012320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 08/30/2024] [Accepted: 07/12/2024] [Indexed: 08/10/2024] Open
Abstract
Although depolymerization of complex carbohydrates is a growth-limiting bottleneck for microbial decomposers, we still lack understanding about how the production of different types of extracellular enzymes affect individual microbes and in turn the performance of whole decomposer communities. In this work we use a theoretical model to evaluate the potential trade-offs faced by microorganisms in biopolymer decomposition which arise due to the varied biochemistry of different depolymerizing enzyme classes. We specifically consider two broad classes of depolymerizing extracellular enzymes, which are widespread across microbial taxa: exo-enzymes that cleave small units from the ends of polymer chains and endo-enzymes that act at random positions generating degradation products of varied sizes. Our results demonstrate a fundamental trade-off in the production of these enzymes, which is independent of system's complexity and which appears solely from the intrinsically different temporal depolymerization dynamics. As a consequence, specialists that produce either exo- or only endo-enzymes limit their growth to high or low substrate conditions, respectively. Conversely, generalists that produce both enzymes in an optimal ratio expand their niche and benefit from the synergy between the two enzymes. Finally, our results show that, in spatially-explicit environments, consortia composed of endo- and exo-specialists can only exist under oligotrophic conditions. In summary, our analysis demonstrates that the (evolutionary or ecological) selection of a depolymerization pathway will affect microbial fitness under low or high substrate conditions, with impacts on the ecological dynamics of microbial communities. It provides a possible explanation why many polysaccharide degraders in nature show the genetic potential to produce both of these enzyme classes.
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Affiliation(s)
- Ksenia Guseva
- Centre for Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Moritz Mohrlok
- Centre for Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Lauren Alteio
- Centre for Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
- FFoQSI GmbH - Austrian Competence Centre for Feed and Food Quality, Safety and innovation, Tulln, Austria
| | - Hannes Schmidt
- Centre for Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Shaul Pollak
- Centre for Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Christina Kaiser
- Centre for Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
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4
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Ohnuma T, Tsujii J, Kataoka C, Yoshimoto T, Takeshita D, Lampela O, Juffer AH, Suginta W, Fukamizo T. Periplasmic chitooligosaccharide-binding protein requires a three-domain organization for substrate translocation. Sci Rep 2023; 13:20558. [PMID: 37996461 PMCID: PMC10667598 DOI: 10.1038/s41598-023-47253-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 11/10/2023] [Indexed: 11/25/2023] Open
Abstract
Periplasmic solute-binding proteins (SBPs) specific for chitooligosaccharides, (GlcNAc)n (n = 2, 3, 4, 5 and 6), are involved in the uptake of chitinous nutrients and the negative control of chitin signal transduction in Vibrios. Most translocation processes by SBPs across the inner membrane have been explained thus far by two-domain open/closed mechanism. Here we propose three-domain mechanism of the (GlcNAc)n translocation based on experiments using a recombinant VcCBP, SBP specific for (GlcNAc)n from Vibrio cholerae. X-ray crystal structures of unliganded or (GlcNAc)3-liganded VcCBP solved at 1.2-1.6 Å revealed three distinct domains, the Upper1, Upper2 and Lower domains for this protein. Molecular dynamics simulation indicated that the motions of the three domains are independent and that in the (GlcNAc)3-liganded state the Upper2/Lower interface fluctuated more intensively, compared to the Upper1/Lower interface. The Upper1/Lower interface bound two GlcNAc residues tightly, while the Upper2/Lower interface appeared to loosen and release the bound sugar molecule. The three-domain mechanism proposed here was fully supported by binding data obtained by thermal unfolding experiments and ITC, and may be applicable to other translocation systems involving SBPs belonging to the same cluster.
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Affiliation(s)
- Takayuki Ohnuma
- Department of Advanced Bioscience, Kindai University, 3327-204 Nakamachi, Nara, 631-8505, Japan.
- Agricultural Technology and Innovation Research Institute (ATIRI), Kindai University, 3327-204, Nakamachi, Nara, 631-8505, Japan.
| | - Jun Tsujii
- Department of Advanced Bioscience, Kindai University, 3327-204 Nakamachi, Nara, 631-8505, Japan
| | - Chikara Kataoka
- Department of Advanced Bioscience, Kindai University, 3327-204 Nakamachi, Nara, 631-8505, Japan
| | - Teruki Yoshimoto
- Department of Advanced Bioscience, Kindai University, 3327-204 Nakamachi, Nara, 631-8505, Japan
| | - Daijiro Takeshita
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba-Shi, Ibaraki, 305-8566, Japan
| | - Outi Lampela
- Biocenter Oulu, University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland
| | - André H Juffer
- Biocenter Oulu, University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O.Box 5000, FI-90014, Oulu, Finland
| | - Wipa Suginta
- School of Biomolecular Science & Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley 555 Moo 1 Payupnai, Wangchan, Rayong, 21210, Thailand
| | - Tamo Fukamizo
- Department of Advanced Bioscience, Kindai University, 3327-204 Nakamachi, Nara, 631-8505, Japan.
- School of Biomolecular Science & Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley 555 Moo 1 Payupnai, Wangchan, Rayong, 21210, Thailand.
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5
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Chumjan W, Sangchalee A, Somwang C, Mookda N, Yaikeaw S, Somsakeesit LO. Outer membrane protein N expressed in Gram-negative bacterial strain of Escherichia coli BL21 (DE3) Omp8 Rosetta strains under osmoregulation by salts, sugars, and pHs. PLoS One 2023; 18:e0288096. [PMID: 37535641 PMCID: PMC10399875 DOI: 10.1371/journal.pone.0288096] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 06/19/2023] [Indexed: 08/05/2023] Open
Abstract
This study presented the expression of the outer membrane protein N in E. coli BL21 (DE3) Omp8 Rosetta under its growth condition and by osmoregulation. The effects of osmotic stress caused by salts, sugars, or pH values on the survival of the target Gram-negative bacterial strain of E. coli BL21 (DE3) Omp8 Rosetta and OmpN expression remain unknown. Here, tryptone yeast extract with varied salts and concentrations was initially used to generate an LB broth medium. To show how salts and concentration affect bacterial growth, the optical density at 600 nm was measured. The findings supported the hypothesis that salts and concentrations control bacterial growth. Moreover, a Western blotting study revealed that OmpN overexpression was present in all tested salts after stimulation with both glucose and fructose after being treated individually with anti-OmpN and anti-histidine tag polyclonal antibodies on transferred nitrocellulose membrane containing crude OmpN. Following the presence of the plasmid pET21b(+)/ompN-BOR into E. coli BL21 (DE3) Omp8 Rosetta, which was expressed in the recombinant OmpN protein (BOR), OmpN expression was demonstrated for all monovalent cations as well as MgCl2. All of the tested salts, except for BaCl2, NaH2PO4, and KH2PO4, showed overexpression of recombinant BOR after Isopropyl β-D-1-thiogalactopyranoside (IPTG) induction. Using CH3COONa, both with and without IPTG induction, there was very little bacterial growth and no OmpN expression. With NaCl, a pH value of 7 was suitable for bacterial development, whereas KCl required a pH value of 8. According to this research, bacterial growth in addition to salts, sugars, and pH values influences how the OmpN protein is produced.
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Affiliation(s)
- Watcharin Chumjan
- Department of Chemistry, Rajamangala University of Technology Isan Khon Kaen Campus, Khon Kaen, Thailand
| | - Akira Sangchalee
- Department of Chemistry, Rajamangala University of Technology Isan Khon Kaen Campus, Khon Kaen, Thailand
| | - Cholthicha Somwang
- Department of Chemistry, Rajamangala University of Technology Isan Khon Kaen Campus, Khon Kaen, Thailand
| | - Nattida Mookda
- Department of Chemistry, Rajamangala University of Technology Isan Khon Kaen Campus, Khon Kaen, Thailand
| | - Sriwannee Yaikeaw
- Department of Chemistry, Rajamangala University of Technology Isan Khon Kaen Campus, Khon Kaen, Thailand
| | - La-Or Somsakeesit
- Department of Chemistry, Rajamangala University of Technology Isan Khon Kaen Campus, Khon Kaen, Thailand
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6
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Sanram S, Aunkham A, Robinson R, Suginta W. Structural displacement model of chitooligosaccharide transport through chitoporin. J Biol Chem 2023; 299:105000. [PMID: 37394001 PMCID: PMC10406626 DOI: 10.1016/j.jbc.2023.105000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/04/2023] Open
Abstract
VhChiP is a chitooligosaccharide-specific porin identified in the outer membrane of Vibrio campbellii type strain American Type Culture Collection BAA 1116. VhChiP contains three identical subunits, and in each subunit, the 19-amino acid N-terminal segment serves as a molecular plug (the "N-plug") that controls the closed/open dynamics of the neighboring pores. In this study, the crystal structures of VhChiP lacking the N-plug were determined in the absence and presence of chitohexaose. Binding studies of sugar-ligand interactions by single-channel recordings and isothermal microcalorimetry experiments suggested that the deletion of the N-plug peptide significantly weakened the sugar-binding affinity due to the loss of hydrogen bonds around the central affinity sites. Steered molecular dynamic simulations revealed that the movement of the sugar chain along the sugar passage triggered the ejection of the N-plug, while the H-bonds transiently formed between the reducing end GlcNAc units of the sugar chain with the N-plug peptide may help to facilitate sugar translocation. The findings enable us to propose the structural displacement model, which enables us to understand the molecular basis of chitooligosaccharide uptake by marine Vibrio bacteria.
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Affiliation(s)
- Surapoj Sanram
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Anuwat Aunkham
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Robert Robinson
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Wipa Suginta
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand.
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7
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Ran L, Wang X, He X, Guo R, Wu Y, Zhang P, Zhang XH. Genomic analysis and chitinase characterization of Vibrio harveyi WXL538: insight into its adaptation to the marine environment. Front Microbiol 2023; 14:1121720. [PMID: 37465025 PMCID: PMC10350509 DOI: 10.3389/fmicb.2023.1121720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 06/05/2023] [Indexed: 07/20/2023] Open
Abstract
Chitin, the most abundant bio-polymer in seawater, may be utilized by various microorganisms as a carbon source. Vibrios have been regarded as one of the main groups of chitin consumers in the marine carbon cycle and chitinase producers. The organisms are widely distributed in the aquatic environment. However, the co-working mechanism between their chitinases, and whether the chitinase's diversity contributes to their adaption to the environment, needs to be further elucidated. Here, we obtained a chitinolytic strain, Vibrio harveyi WXL538 with eight putative chitinase-coding genes. Five of the genes, i.e., Chi4733, Chi540, Chi4668, Chi5174, and Chi4963, were overexpressed and validated, in which Chi4668, Chi4733 and Chi540 were purified and characterized. The result of Chi4668 was described in our previous study. Endo-chitinase Chi4733 degraded colloidal chitin to produce (GlcNAc)2 and minor (GlcNAc)3. The enzymatic activity of Chi4733 was 175.5 U mg-1 and Kcat/Km was 54.9 s-1 M-1. Chi4733 had its maximum activity at 50°C and pH 4-6, activated by Sr2+, Co2+, Ca2+, and Mg2+ and inhibited by Al3+, Zn2+, Cu2+, Ni2+, and SDS. Exo-chitinase Chi540 degraded colloidal chitin to (GlcNAc)2. The enzymatic activity of Chi540 was 134.5 U mg-1 and Kcat/Km was 54.9 s-1 M-1. Chi540 had its maximum activity at 60°C and pH 6-8, was activated by Sr2+, Ca2+, and Mg2+ but inhibited by K+, Ba2+, Zn2+, Cu2+, Ni2+, SDS and urea. Whole genome analysis of V. harveyi WXL538 and characterization of its chitinase can provide a better understanding of its adaptability to the changing marine environment.
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Affiliation(s)
- Lingman Ran
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiaolei Wang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xinxin He
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Ruihong Guo
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yanhong Wu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Pingping Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiao-Hua Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
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8
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Soysa HSM, Kumsaoad S, Amornloetwattana R, Watanabe T, Suginta W. Single-channel characterization of the chitooligosaccharide transporter chitoporin (SmChiP) from the opportunistic pathogen Serratia marcescens. J Biol Chem 2022; 298:102487. [PMID: 36113582 PMCID: PMC9582717 DOI: 10.1016/j.jbc.2022.102487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 09/08/2022] [Accepted: 09/10/2022] [Indexed: 11/25/2022] Open
Abstract
Serratia marcescens is an opportunistic pathogen that can utilize chitin as a carbon source, through its ability to produce chitin-degrading enzymes to digest chitin and membrane transporters to transport the degradation products (chitooligosaccharides) into the cells. Further characterization of these proteins is important to understand details of chitin metabolism. Here, we investigate the properties and function of the S. marcescens chitoporin, namely SmChiP, a chitooligosaccharide transporter. We show that SmChiP is a monomeric porin that forms a stable channel in artificial phospholipid membranes, with an average single-channel conductance of 0.5 ± 0.02 nS in 1 M KCl electrolyte. Additionally, we demonstrated that SmChiP allowed the passage of small molecules with a size exclusion limit of <300 Da and exhibited substrate specificity toward chitooligosaccharides, both in membrane and detergent-solubilized forms. We found that SmChiP interacted strongly with chitopentaose (Kd = 23 ± 2.0 μM) and chitohexaose (Kd = 17 ± 0.6 μM) but did not recognize nonchitose oligosaccharides (maltohexaose and cellohexaose). Given that S. marcescens can use chitin as a primary energy source, SmChiP may serve as a target for further development of nutrient-based antimicrobial therapies directed against multidrug antibiotic-resistant S. marcescens infections.
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Affiliation(s)
- H Sasimali M Soysa
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Sawitree Kumsaoad
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Tumbol Payupnai, Wangchan District, Rayong, Thailand 21210
| | - Rawiporn Amornloetwattana
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Tumbol Payupnai, Wangchan District, Rayong, Thailand 21210
| | - Takeshi Watanabe
- Faculty of Agro-Food Science, Department of Agro-Food Science, Niigata Agro-Food University, Tainai-shi, Niigata 959-2702, Japan
| | - Wipa Suginta
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Tumbol Payupnai, Wangchan District, Rayong, Thailand 21210.
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9
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Suginta W, Sanram S, Aunkham A, Winterhalter M, Schulte A. The C2 entity of chitosugars is crucial in molecular selectivity of the Vibrio campbellii chitoporin. J Biol Chem 2021; 297:101350. [PMID: 34715124 PMCID: PMC8608610 DOI: 10.1016/j.jbc.2021.101350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 12/14/2022] Open
Abstract
The marine bacterium Vibrio campbellii expresses a chitooligosaccharide-specific outer-membrane channel (chitoporin) for the efficient uptake of nutritional chitosugars that are externally produced through enzymic degradation of environmental host shell chitin. However, the principles behind the distinct substrate selectivity of chitoporins are unclear. Here, we employed black lipid membrane (BLM) electrophysiology, which handles the measurement of the flow of ionic current through porins in phospholipid bilayers for the assessment of porin conductivities, to investigate the pH dependency of chitosugar-chitoporin interactions for the bacterium's natural substrate chitohexaose and its deacetylated form, chitosan hexaose. We show that efficient passage of the N-acetylated chitohexaose through the chitoporin is facilitated by its strong affinity for the pore. In contrast, the deacetylated chitosan hexaose is impermeant; however, protonation of the C2 amino entities of chitosan hexaose allows it to be pulled through the channel in the presence of a transmembrane electric field. We concluded from this the crucial role of C2-substitution as the determining factor for chitoporin entry. A change from N-acetylamino- to amino-substitution effectively abolished the ability of approaching molecules to enter the chitoporin, with deacetylation leading to loss of the distinctive structural features of nanopore opening and pore access of chitosugars. These findings provide further understanding of the multistep pathway of chitin utilization by marine Vibrio bacteria and may guide the development of solid-state or genetically engineered biological nanopores for relevant technological applications.
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Affiliation(s)
- Wipa Suginta
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand.
| | - Surapoj Sanram
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Anuwat Aunkham
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Albert Schulte
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand.
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10
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Kitaoku Y, Fukamizo T, Kumsaoad S, Ubonbal P, Robinson RC, Suginta W. A structural model for (GlcNAc) 2 translocation via a periplasmic chitooligosaccharide-binding protein from marine Vibrio bacteria. J Biol Chem 2021; 297:101071. [PMID: 34400168 PMCID: PMC8449061 DOI: 10.1016/j.jbc.2021.101071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 08/04/2021] [Accepted: 08/10/2021] [Indexed: 11/25/2022] Open
Abstract
VhCBP is a periplasmic chitooligosaccharide-binding protein mainly responsible for translocation of the chitooligosaccharide (GlcNAc)2 across the double membranes of marine bacteria. However, structural and thermodynamic understanding of the sugar-binding/-release processes of VhCBP is relatively less. VhCBP displayed the greatest affinity toward (GlcNAc)2, with lower affinity for longer-chain chitooligosaccharides [(GlcNAc)3–4]. (GlcNAc)4 partially occupied the closed sugar-binding groove, with two reducing-end GlcNAc units extending beyond the sugar-binding groove and barely characterized by weak electron density. Mutation of three conserved residues (Trp363, Asp365, and Trp513) to Ala resulted in drastic decreases in the binding affinity toward the preferred substrate (GlcNAc)2, indicating their significant contributions to sugar binding. The structure of the W513A–(GlcNAc)2 complex in a ‘half-open’ conformation unveiled the intermediary step of the (GlcNAc)2 translocation from the soluble CBP in the periplasm to the inner membrane–transporting components. Isothermal calorimetry data suggested that VhCBP adopts the high-affinity conformation to bind (GlcNAc)2, while its low-affinity conformation facilitated sugar release. Thus, chitooligosaccharide translocation, conferred by periplasmic VhCBP, is a crucial step in the chitin catabolic pathway, allowing Vibrio bacteria to thrive in oceans where chitin is their major source of nutrients.
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Affiliation(s)
- Yoshihito Kitaoku
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Tamo Fukamizo
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand.
| | - Sawitree Kumsaoad
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Prakayfun Ubonbal
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Robert C Robinson
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand; Research Institute of Interdisciplinary Science (RIIS), Okayama University, Okayama, Japan.
| | - Wipa Suginta
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand.
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11
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Golubchik A, Lopes LC, Singh V, Kuss S. Pharma‐molecule Transport across Bacterial Membranes: Detection and Quantification Approaches by Electrochemistry and Bioanalytical Methods. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Alon Golubchik
- Department Chemistry University of Manitoba Winnipeg R3T 2N2 Canada
| | | | - Vikram Singh
- Department Chemistry University of Manitoba Winnipeg R3T 2N2 Canada
| | - Sabine Kuss
- Department Chemistry University of Manitoba Winnipeg R3T 2N2 Canada
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12
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Aunkham A, Suginta W. Probing the physiological roles of the extracellular loops of chitoporin from Vibrio campbellii. Biophys J 2021; 120:2124-2137. [PMID: 33812846 PMCID: PMC8390830 DOI: 10.1016/j.bpj.2021.03.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 03/11/2021] [Accepted: 03/19/2021] [Indexed: 12/20/2022] Open
Abstract
VhChiP, a sugar-specific porin found on the outer membrane of Vibrio campbellii, is responsible for the transport of chitooligosaccharides, allowing the bacterium to thrive in aquatic environments using chitin as a nutrient. We previously showed that VhChiP is composed of three identical subunits, each containing a 16-stranded β-barrel connected by eight extracellular loops and eight short periplasmic turns. This study is focused on the specific roles of three prominent extracellular loops of VhChiP-L2, L3, and L8. The deletion of L2 completely disrupted the L2-L2 interactions, thus destabilizing the protein trimers as well as the integrity of the secondary structure. The deletion of L3 caused a drastic loss in the binding affinity for sugar substrates because of the absence of a cluster of key amino acid residues that form the affinity sites. The removal of L8 induced pronounced gating, which is highly responsive to elevated potentials. Our data provide further information on the important roles of the three prominent loops of VhChiP: loop L2 maintains the trimeric structure and the integrity of secondary structure, loop L3 controls the binding affinity for sugar substrates, and loop L8 retains the stably open state of the channel.
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Affiliation(s)
- Anuwat Aunkham
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Wipa Suginta
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand.
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13
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Golubchik A, Lopes LC, Singh V, Kuss S. Pharma-molecule Transport across Bacterial Membranes: Detection and Quantification Approaches by Electrochemistry and Bioanalytical Methods. Angew Chem Int Ed Engl 2021; 60:22112-22124. [PMID: 33979000 DOI: 10.1002/anie.202101055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Indexed: 11/07/2022]
Abstract
Antibiotic resistance is a significant challenge encountered by healthcare systems on a global scale. Knowledge about membrane transport of antibiotics and other pharmacologically relevant molecules in bacteria is crucial towards understanding and overcoming antibiotic resistance, as drug resistance often depends on drug transport. This comprehensive literature review discusses the detection and quantification of membrane transport of pharma-molecules in bacteria and highlights the importance of molecule transport to antibiotic resistance. This review emphasizes electrochemical and electrophysiological methods of detection and quantification. The results of this literature review reveal a substantial diversity in methods and types of quantitative information collected.
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Affiliation(s)
- Alon Golubchik
- Department Chemistry, University of Manitoba, Winnipeg, R3T 2N2, Canada
| | | | - Vikram Singh
- Department Chemistry, University of Manitoba, Winnipeg, R3T 2N2, Canada
| | - Sabine Kuss
- Department Chemistry, University of Manitoba, Winnipeg, R3T 2N2, Canada
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14
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Meekrathok P, Bürger M, Porfetye AT, Kumsaoad S, Aunkham A, Vetter IR, Suginta W. Structural basis of chitin utilization by a GH20 β-N-acetylglucosaminidase from Vibrio campbellii strain ATCC BAA-1116. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2021; 77:674-689. [PMID: 33950022 PMCID: PMC8098473 DOI: 10.1107/s2059798321002771] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 03/15/2021] [Indexed: 12/03/2022]
Abstract
Crystal structures of a GH20 β-N-acetylglucosaminidase from V. campbellii reveal substrate specificity in chitin utilization. Vibrio species play a crucial role in maintaining the carbon and nitrogen balance between the oceans and the land through their ability to employ chitin as a sole source of energy. This study describes the structural basis for the action of the GH20 β-N-acetylglucosaminidase (VhGlcNAcase) in chitin metabolism by Vibrio campbellii (formerly V. harveyi) strain ATCC BAA-1116. Crystal structures of wild-type VhGlcNAcase in the absence and presence of the sugar ligand, and of the unliganded D437A mutant, were determined. VhGlcNAcase contains three distinct domains: an N-terminal carbohydrate-binding domain linked to a small α+β domain and a C-terminal (β/α)8 catalytic domain. The active site of VhGlcNAcase has a narrow, shallow pocket that is suitable for accommodating a small chitooligosaccharide. VhGlcNAcase is a monomeric enzyme of 74 kDa, but its crystal structures show two molecules of enzyme per asymmetric unit, in which Gln16 at the dimeric interface of the first molecule partially blocks the entrance to the active site of the neighboring molecule. The GlcNAc unit observed in subsite −1 makes exclusive hydrogen bonds to the conserved residues Arg274, Tyr530, Asp532 and Glu584, while Trp487, Trp546, Trp582 and Trp505 form a hydrophobic wall around the −1 GlcNAc. The catalytic mutants D437A/N and E438A/Q exhibited a drastic loss of GlcNAcase activity, confirming the catalytic role of the acidic pair (Asp437–Glu438).
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Affiliation(s)
- Piyanat Meekrathok
- Biochemistry-Electrochemistry Research Unit, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Marco Bürger
- Max-Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Arthur T Porfetye
- Max-Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Sawitree Kumsaoad
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), 555 Payupnai, Wangchan, Rayong 21210, Thailand
| | - Anuwat Aunkham
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), 555 Payupnai, Wangchan, Rayong 21210, Thailand
| | - Ingrid R Vetter
- Max-Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Wipa Suginta
- Biochemistry-Electrochemistry Research Unit, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
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15
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Amornloetwattana R, Robinson RC, Soysa HSM, van den Berg B, Suginta W. Chitoporin from Serratia marcescens: recombinant expression, purification and crystallization. Acta Crystallogr F Struct Biol Commun 2020; 76:536-543. [PMID: 33135672 PMCID: PMC7605108 DOI: 10.1107/s2053230x20013874] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 10/18/2020] [Indexed: 11/10/2022] Open
Abstract
Serratia marcescens is an opportunistic pathogen that commonly causes hospital-acquired infections and can utilize chitin-enriched nutrients as an alternative energy source. This study reports the identification of a chitoporin (ChiP), termed SmChiP, from the outer membrane of S. marcescens. Sequence alignment with genetically characterized ChiPs suggests that SmChiP is more closely related to the monomeric EcChiP from Escherichia coli than to the trimeric VhChiP from Vibrio campbellii. A single crystal of SmChiP grown under the condition 22%(w/v) PEG 8000, 0.1 M calcium acetate, 0.1 M MES pH 6.0 diffracted X-ray synchrotron radiation to 1.85 Å resolution. SmChiP co-crystallized with chitohexaose under the condition 19%(w/v) PEG 1500, 2 M ammonium phosphate monobasic, 0.1 M HEPES pH 7.0 diffracted X-rays to 2.70 Å resolution. Preliminary crystallographic analysis shows that both SmChiP crystal forms contain one molecule per asymmetric unit and that they belong to the tetragonal space groups P42212 and P41212, respectively. The SmChiP crystal has unit-cell parameters a = 82.97, b = 82.97, c = 189.53 Å, α = β = γ = 90°, while the crystal of SmChiP in complex with chitohexaose has unit-cell parameters a = 73.24, b = 73.24, c = 213.46 Å, α = β = γ = 90°. Initial assessment of the complex structure clearly revealed electron density for the sugar ligand. Structure determination of SmChiP in the absence and presence of chitohexaose should reveal the molecular basis of chitin utilization by S. marcescens.
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Affiliation(s)
- Rawiporn Amornloetwattana
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology, Payupnai, Wangchan, Rayong 21210, Thailand
| | - Robert C. Robinson
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology, Payupnai, Wangchan, Rayong 21210, Thailand
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
| | - Hannadige Sasimali Madusanka Soysa
- Department of Physical Sciences and Technology, Faculty of Applied Sciences, Sabaragamuwa University of Sri Lanka, Belihuloya 70140, Sri Lanka
| | - Bert van den Berg
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Wipa Suginta
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology, Payupnai, Wangchan, Rayong 21210, Thailand
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16
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Regulation of Chitin-Dependent Growth and Natural Competence in Vibrio parahaemolyticus. Microorganisms 2020; 8:microorganisms8091303. [PMID: 32859005 PMCID: PMC7564644 DOI: 10.3390/microorganisms8091303] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 02/06/2023] Open
Abstract
Vibrios can degrade chitin surfaces to soluble N-acetyl glucosamine oligosaccharides (GlcNAcn) that can be utilized as a carbon source and also induce a state of natural genetic competence. In this study, we characterized chitin-dependent growth and natural competence in Vibrio parahaemolyticus and its regulation. We found that growth on chitin was regulated through chitin sensors ChiS (sensor histidine kinase) and TfoS (transmembrane transcriptional regulator) by predominantly controlling the expression of chitinase VPA0055 (ChiA2) in a TfoX-dependent manner. The reduced growth of ΔchiA2, ΔchiS and ΔtfoS mutants highlighted the critical role played by ChiA2 in chitin breakdown. This growth defect of ΔchiA2 mutant could be recovered when chitin oligosaccharides GlcNAc2 or GlcNAc6 were supplied instead of chitin. The ΔtfoS mutant was also able to grow on GlcNAc2 but the ΔchiS mutant could not, which indicates that GlcNAc2 catabolic operon is dependent on ChiS and independent of TfoS. However, the ΔtfoS mutant was unable to utilize GlcNAc6 because the periplasmic enzymes required for the breakdown of GlcNAc6 were found to be downregulated at the mRNA level. We also showed that natural competence can be induced only by GlcNAc6, not GlcNAc2, because the expression of competence genes was significantly higher in the presence of GlcNAc6 compared to GlcNAc2. Moreover, this might be an indication that GlcNAc2 and GlcNAc6 were detected by different receptors. Therefore, we speculate that GlcNAc2-dependent activation of ChiS and GlcNAc6-dependent activation of TfoS might be crucial for the induction of natural competence in V. parahaemolyticus through the upregulation of the master competence regulator TfoX.
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17
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Aunkham A, Schulte A, Sim WC, Chumjan W, Suginta W. Vibrio campbellii chitoporin: Thermostability study and implications for the development of therapeutic agents against Vibrio infections. Int J Biol Macromol 2020; 164:3508-3522. [PMID: 32858106 DOI: 10.1016/j.ijbiomac.2020.08.188] [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: 06/30/2020] [Revised: 08/22/2020] [Accepted: 08/23/2020] [Indexed: 02/02/2023]
Abstract
Vibrio campbellii (formerly Vibrio harveyi) is a bacterial pathogen that causes vibriosis, which devastates fisheries and aquaculture worldwide. V. campbellii expresses chitinolytic enzymes and chitin binding/transport proteins, which serve as excellent targets for antimicrobial agent development. We previously characterized VhChiP, a chitooligosaccharide-specific porin from the outer membrane of V. campbellii BAA-1116. This study employed far-UV circular dichroism and tryptophan fluorescence spectroscopy, together with single channel electrophysiology to demonstrate that the strong binding of chitoligosaccharides enhanced thermal stability of VhChiP. The alanine substitution of Trp136 at the center of the affinity sites caused a marked decrease in the binding affinity and decreased the thermal stability of VhChiP. Tryptophan fluorescence titrations over a range of temperatures showed greater free-energy changes on ligand binding (ΔG°binding) with increasing chain length of the chitooligosaccharides. Our findings suggest the possibility of designing stable channel-blockers, using sugar-based analogs that serve as antimicrobial agents, active against Vibrio infection.
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Affiliation(s)
- Anuwat Aunkham
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Payupnai, Wangchan, Rayong 21210, Thailand; School of Chemistry, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Albert Schulte
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Payupnai, Wangchan, Rayong 21210, Thailand
| | - Wei Chung Sim
- School of Chemistry, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Watcharin Chumjan
- School of Chemistry, Faculty of Engineering, Rajamangala University of Technology, Khon Kaen 40000, Thailand
| | - Wipa Suginta
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Payupnai, Wangchan, Rayong 21210, Thailand.
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18
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Soysa HSM, Aunkham A, Schulte A, Suginta W. Single-channel properties, sugar specificity, and role of chitoporin in adaptive survival of Vibrio cholerae type strain O1. J Biol Chem 2020; 295:9421-9432. [PMID: 32409576 PMCID: PMC7363139 DOI: 10.1074/jbc.ra120.012921] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 05/12/2020] [Indexed: 11/06/2022] Open
Abstract
Vibrio cholerae is a Gram-negative, facultative anaerobic bacterial species that causes serious disease and can grow on various carbon sources, including chitin polysaccharides. In saltwater, its attachment to chitin surfaces not only serves as the initial step of nutrient recruitment but is also a crucial mechanism underlying cholera epidemics. In this study, we report the first characterization of a chitooligosaccharide-specific chitoporin, VcChiP, from the cell envelope of the V. cholerae type strain O1. We modeled the structure of VcChiP, revealing a trimeric cylinder that forms single channels in phospholipid bilayers. The membrane-reconstituted VcChiP channel was highly dynamic and voltage induced. Substate openings O1', O2', and O3', between the fully open states O1, O2, and O3, were polarity selective, with nonohmic conductance profiles. Results of liposome-swelling assays suggested that VcChiP can transport monosaccharides, as well as chitooligosaccharides, but not other oligosaccharides. Of note, an outer-membrane porin (omp)-deficient strain of Escherichia coli expressing heterologous VcChiP could grow on M9 minimal medium supplemented with small chitooligosaccharides. These results support a crucial role of chitoporin in the adaptive survival of bacteria on chitinous nutrients. Our findings also suggest a promising means of vaccine development based on surface-exposed outer-membrane proteins and the design of novel anticholera agents based on chitooligosaccharide-mimicking analogs.
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Affiliation(s)
| | - Anuwat Aunkham
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Payupnai, Rayong, Thailand
| | - Albert Schulte
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Payupnai, Rayong, Thailand
| | - Wipa Suginta
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Payupnai, Rayong, Thailand
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19
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Meekrathok P, Stubbs KA, Aunkham A, Kaewmaneewat A, Kardkuntod A, Bulmer DM, Berg B, Suginta W. NAG‐thiazoline is a potent inhibitor of the
Vibrio campbellii
GH20 β‐
N
‐Acetylglucosaminidase. FEBS J 2020; 287:4982-4995. [DOI: 10.1111/febs.15283] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 02/15/2020] [Accepted: 03/04/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Piyanat Meekrathok
- School of Chemistry Suranaree University of Technology Nakhon Ratchasima Thailand
| | - Keith A. Stubbs
- School of Molecular Sciences The University of Western Australia Crawley WA Australia
| | - Anuwat Aunkham
- School of Biomolecular Science and Engineering (BSE) Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong Thailand
| | - Anuphon Kaewmaneewat
- School of Biomolecular Science and Engineering (BSE) Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong Thailand
| | - Apinya Kardkuntod
- School of Biomolecular Science and Engineering (BSE) Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong Thailand
| | - David M. Bulmer
- Institute for Cell and Molecular Biosciences Newcastle University UK
| | - Bert Berg
- Institute for Cell and Molecular Biosciences Newcastle University UK
| | - Wipa Suginta
- School of Biomolecular Science and Engineering (BSE) Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong Thailand
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20
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Chitin Heterodisaccharide, Released from Chitin by Chitinase and Chitin Oligosaccharide Deacetylase, Enhances the Chitin-Metabolizing Ability of Vibrio parahaemolyticus. J Bacteriol 2019; 201:JB.00270-19. [PMID: 31358611 DOI: 10.1128/jb.00270-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 07/24/2019] [Indexed: 11/20/2022] Open
Abstract
Vibrio parahaemolyticus RIMD2210633 secretes both chitinase and chitin oligosaccharide deacetylase and produces β-N-acetyl-d-glucosaminyl-(1,4)-d-glucosamine (GlcNAc-GlcN) from chitin. Previously, we reported that GlcNAc-GlcN induces chitinase production by several strains of Vibrio harboring chitin oligosaccharide deacetylase genes (T. Hirano, K. Kadokura, T. Ikegami, Y. Shigeta, et al., Glycobiology 19:1046-1053, 2009). The metabolism of chitin by Vibrio was speculated on the basis of the findings of previous studies, and the role of chitin oligosaccharide produced from chitin has been well studied. However, the role of GlcNAc-GlcN in the Vibrio chitin degradation system, with the exception of the above-mentioned function as an inducer of chitinase production, remains unclear. N,N'-Diacetylchitobiose, a homodisaccharide produced from chitin, is known to induce the expression of genes encoding several proteins involved in chitin metabolism in Vibrio strains (K. L. Meibom, X. B. Li, A. Nielsen, C. Wu, et al., Proc Natl Acad Sci U S A 101:2524-2529, 2004). We therefore hypothesized that GlcNAc-GlcN also affects the expression of enzymes involved in chitin metabolism in the same manner. In this study, we examined the induction of protein expression by several sugars released from chitin using peptide mass fingerprinting and confirmed the expression of genes encoding enzymes involved in chitin metabolism using real-time quantitative PCR analysis. We then confirmed that GlcNAc-GlcN induces the expression of genes encoding many soluble enzymes involved in chitin degradation in Vibrio parahaemolyticus Here, we demonstrate that GlcNAc-GlcN enhances the chitin-metabolizing ability of V. parahaemolyticus IMPORTANCE We demonstrate that β-N-acetyl-d-glucosaminyl-(1,4)-d-glucosamine (GlcNAc-GlcN) enhances the chitin-metabolizing ability of V. parahaemolyticus Members of the genus Vibrio are chitin-degrading bacteria, and some species of this genus are associated with diseases affecting fish and animals, including humans (F. L. Thompson, T. Iida, and J. Swings, Microbiol Mol Biol Rev 68:403-431, 2004; M. Y. Ina-Salwany, N. Al-Saari, A. Mohamad, F.-A. Mursidi, et al., J Aquat Anim Health 31:3-22, 2019). Studies on Vibrio are considered important, as they may facilitate the development of solutions related to health, food, and aquaculture problems attributed to this genus. This report enhances the current understanding of chitin degradation by Vibrio bacteria.
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21
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Effects of H-bonds on sugar binding to chitoporin from Vibrio harveyi. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:610-618. [PMID: 30576623 DOI: 10.1016/j.bbamem.2018.12.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 12/15/2018] [Accepted: 12/17/2018] [Indexed: 11/24/2022]
Abstract
BACKGROUND VhChiP is a sugar-specific-porin present in the outer membrane of the marine bacterium Vibrio harveyi and responsible for chitin uptake, with a high selectivity for chitohexaose. METHODS VhChiP and its mutants were expressed and purified from BL21 (DE3) Omp8 Rosetta strain. After reconstitution into planar lipid bilayers, the ion current fluctuations caused by chitohexaose entering the channel were measured in deuterium oxide and in water. RESULTS The role of hydrogen-bonding in sugar binding was investigated by comparing channel occlusion by chitohexaose in buffers containing H2O and D2O. The BLM results revealed the significant contribution of hydrogen bonding to the binding of chitohexaose in the constriction zone of VhChiP. Replacing H2O as solvent by D2O significantly decreased the on- and off-rates of sugar penetration into the channel. The importance of hydrogen bonding inside the channel was more noticeable when the hydrophobicity of the constriction zone was diminished by replacing Trp136 with the charged residues Asp or Arg. The on- and off-rates decreased up to 2.5-fold and 4-fold when Trp136 was replaced by Arg, or 5-fold and 3-fold for Trp136 replacement by Asp, respectively. Measuring the on-rate at different temperatures and for different channel mutants revealed the activation energy for chitohexaose entrance into VhChiP channel. CONCLUSIONS Hydrogen-bonds contribute to sugar permeation.
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22
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Fukamizo T, Kitaoku Y, Suginta W. Periplasmic solute-binding proteins: Structure classification and chitooligosaccharide recognition. Int J Biol Macromol 2019; 128:985-993. [PMID: 30771387 DOI: 10.1016/j.ijbiomac.2019.02.064] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 01/12/2019] [Accepted: 02/11/2019] [Indexed: 12/17/2022]
Abstract
Periplasmic solute-binding proteins (SBPs) serve as molecular shuttles that assist the transport of small solutes from the outer membrane to the inner membrane of all Gram-negative bacteria. Based on the available crystal structures, SBPs are classified into seven clusters, A-G, and are further divided into subclusters, IV. This minireview is focused on the classification, structure and substrate specificity of a distinct class of SBPs specific for chitooligosaccharides (CBPs). To date, only two structures of CBP homologues, VhCBP and VcCBP, have been reported in the marine Vibrio species, with exposition of their limited function. The Vibrio CBPs are structurally classified as cluster C/subcluster IV SBPs that exclusively recognize β-1,4- or β-1,3-linked linear oligosaccharides. The overall structural feature of the Vibrios CBPs is most similar to the cellobiose-binding orthologue from the hyperthermophilic bacterium Thermotoga maritima. This similarity provides an opportunity to engineer the substrate specificity of the proteins and to control the uptake of chitinous and cellulosic nutrients in marine bacteria.
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Affiliation(s)
- Tamo Fukamizo
- Biochemistry and Electrochemistry Research Unit and School of Chemistry, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Yoshihito Kitaoku
- Biochemistry and Electrochemistry Research Unit and School of Chemistry, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Wipa Suginta
- Biochemistry and Electrochemistry Research Unit and School of Chemistry, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand; School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Payupnai, Wangchan, Rayong 21210, Thailand.
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Meekrathok P, Stubbs KA, Suginta W. Potent inhibition of a GH20 exo-β-N-acetylglucosaminidase from marine Vibrio bacteria by reaction intermediate analogues. Int J Biol Macromol 2018; 115:1165-1173. [DOI: 10.1016/j.ijbiomac.2018.04.193] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/14/2018] [Accepted: 04/30/2018] [Indexed: 02/04/2023]
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Soysa HSM, Suginta W, Moonsap W, Smith MF. Chitosugar translocation by an unexpressed monomeric protein channel. Phys Rev E 2018; 97:052417. [PMID: 29906877 DOI: 10.1103/physreve.97.052417] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Indexed: 12/14/2022]
Abstract
The outer membrane protein channel EcChiP, associated with a silent gene in E. coli, is a monomeric chitoporin. In a glucose-deficient environment, E. coli can express the ChiP gene to exploit chitin degradation products. Single-channel small ion current measurements, which reveal the dynamics of single sugar molecules trapped in channel, are used here to study the exotic transport of chitosugars by E. coli. Molecules escape from the channel on multiple timescales. Voltage-dependent trapping rates observed for charged chitosan molecules, as well as model calculations, indicate that the rapid escape processes are those in which the molecule escapes back to the side of the membrane from which it originated. The probability that a sugar molecule is translocated through the membrane is thus estimated from the current data and the dependence of this translocation probability on the length of the chitosugar molecule and the applied voltage analyzed. The described method for obtaining the translocation probability and related molecular translocation current is applicable to other transport channels.
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Affiliation(s)
- H Sasimali M Soysa
- Biochemistry-Electrochemistry Research Unit, School of Chemistry, Institute of Science, Center of Excellence in Advanced Functional Materials, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Wipa Suginta
- Biochemistry-Electrochemistry Research Unit, School of Chemistry, Institute of Science, Center of Excellence in Advanced Functional Materials, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Watcharaporn Moonsap
- School of Physics, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - M F Smith
- School of Physics, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
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Suginta W, Sritho N, Ranok A, Bulmer DM, Kitaoku Y, van den Berg B, Fukamizo T. Structure and function of a novel periplasmic chitooligosaccharide-binding protein from marine Vibrio bacteria. J Biol Chem 2018; 293:5150-5159. [PMID: 29444825 DOI: 10.1074/jbc.ra117.001012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Revised: 02/11/2018] [Indexed: 12/11/2022] Open
Abstract
Periplasmic solute-binding proteins in bacteria are involved in the active transport of nutrients into the cytoplasm. In marine bacteria of the genus Vibrio, a chitooligosaccharide-binding protein (CBP) is thought to be the major solute-binding protein controlling the rate of chitin uptake in these bacteria. However, the molecular mechanism of the CBP involvement in chitin metabolism has not been elucidated. Here, we report the structure and function of a recombinant chitooligosaccharide-binding protein from Vibrio harveyi, namely VhCBP, expressed in Escherichia coli Isothermal titration calorimetry revealed that VhCBP strongly binds shorter chitooligosaccharides ((GlcNAc) n , where n = 2, 3, and 4) with affinities that are considerably greater than those for glycoside hydrolase family 18 and 19 chitinases but does not bind longer ones, including insoluble chitin polysaccharides. We also found that VhCBP comprises two domains with flexible linkers and that the domain-domain interface forms the sugar-binding cleft, which is not long extended but forms a small cavity. (GlcNAc)2 bound to this cavity, apparently triggering a closed conformation of VhCBP. Trp-363 and Trp-513, which stack against the two individual GlcNAc rings, likely make a major contribution to the high affinity of VhCBP for (GlcNAc)2 The strong chitobiose binding, followed by the conformational change of VhCBP, may facilitate its interaction with an active-transport system in the inner membrane of Vibrio species.
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Affiliation(s)
- Wipa Suginta
- From the Biochemistry-Electrochemistry Research Unit, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand,
| | - Natchanok Sritho
- From the Biochemistry-Electrochemistry Research Unit, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Araya Ranok
- Rajamangala University of Technology Isan, Nakhon Ratchasima 30000, Thailand
| | - David Michael Bulmer
- the Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom, and
| | - Yoshihito Kitaoku
- the Department of Advanced Bioscience, Kindai University, Nara 631-8505 Japan
| | - Bert van den Berg
- the Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom, and
| | - Tamo Fukamizo
- From the Biochemistry-Electrochemistry Research Unit, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand.,the Department of Advanced Bioscience, Kindai University, Nara 631-8505 Japan
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Structural basis for chitin acquisition by marine Vibrio species. Nat Commun 2018; 9:220. [PMID: 29335469 PMCID: PMC5768706 DOI: 10.1038/s41467-017-02523-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 12/07/2017] [Indexed: 11/18/2022] Open
Abstract
Chitin, an insoluble polymer of N-acetylglucosamine, is one of the most abundant biopolymers on Earth. By degrading chitin, chitinolytic bacteria such as Vibrio harveyi are critical for chitin recycling and maintenance of carbon and nitrogen cycles in the world’s oceans. A decisive step in chitin degradation is the uptake of chito-oligosaccharides by an outer membrane protein channel named chitoporin (ChiP). Here, we report X-ray crystal structures of ChiP from V. harveyi in the presence and absence of chito-oligosaccharides. Structures without bound sugar reveal a trimeric assembly with an unprecedented closing of the transport pore by the N-terminus of a neighboring subunit. Substrate binding ejects the pore plug to open the transport channel. Together with molecular dynamics simulations, electrophysiology and in vitro transport assays our data provide an explanation for the exceptional affinity of ChiP for chito-oligosaccharides and point to an important role of the N-terminal gate in substrate transport. Chitin degrading bacteria are important for marine ecosystems. Here the authors structurally and functionally characterize the Vibrio harveyi outer membrane diffusion channel chitoporin and give mechanistic insights into chito-oligosaccharide uptake.
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Chitinase Expression in Listeria monocytogenes Is Influenced by lmo0327, Which Encodes an Internalin-Like Protein. Appl Environ Microbiol 2017; 83:AEM.01283-17. [PMID: 28887418 PMCID: PMC5666140 DOI: 10.1128/aem.01283-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 08/23/2017] [Indexed: 02/02/2023] Open
Abstract
The chitinolytic system of Listeria monocytogenes thus far comprises two chitinases, ChiA and ChiB, and a lytic polysaccharide monooxygenase, Lmo2467. The role of the system in the bacterium appears to be pleiotropic, as besides mediating the hydrolysis of chitin, the second most ubiquitous carbohydrate in nature, the chitinases have been deemed important for the colonization of unicellular molds, as well as mammalian hosts. To identify additional components of the chitinolytic system, we screened a transposon mutant library for mutants exhibiting impaired chitin hydrolysis. The screening yielded a mutant with a transposon insertion in a locus corresponding to lmo0327 of the EGD-e strain. lmo0327 encodes a large (1,349 amino acids [aa]) cell wall-associated protein that has been proposed to possess murein hydrolase activity. The single inactivation of lmo0327, as well as of lmo0325 that codes for a putative transcriptional regulator functionally related to lmo0327, led to an almost complete abolishment of chitinolytic activity. The effect could be traced at the transcriptional level, as both chiA and chiB transcripts were dramatically decreased in the lmo0327 mutant. In accordance with that, we could barely detect ChiA and ChiB in the culture supernatants of the mutant strain. Our results provide new information regarding the function of the lmo0325-lmo0327 locus in L. monocytogenes and link it to the expression of chitinolytic activity. IMPORTANCE Many bacteria from terrestrial and marine environments express chitinase activities enabling them to utilize chitin as the sole source of carbon and nitrogen. Interestingly, several bacterial chitinases may also be involved in host pathogenesis. For example, in the important foodborne pathogen Listeria monocytogenes, the chitinases ChiA and ChiB and the lytic polysaccharide monooxygenase Lmo2467 are implicated in chitin assimilation but also act as virulence factors during the infection of mammalian hosts. Therefore, it is important to identify their regulators and induction cues to understand how the different roles of the chitinolytic system are controlled and mediated. Here, we provide evidence for the importance of lmo0327 and lmo0325, encoding a putative internalin/autolysin and a putative transcriptional activator, respectively, in the efficient expression of chitinase activity in L. monocytogenes and thereby provide new information regarding the function of the lmo0325-lmo0327 locus.
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Soysa HSM, Schulte A, Suginta W. Functional analysis of an unusual porin-like channel that imports chitin for alternative carbon metabolism in Escherichia coli. J Biol Chem 2017; 292:19328-19337. [PMID: 28972167 DOI: 10.1074/jbc.m117.812321] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 09/22/2017] [Indexed: 12/15/2022] Open
Abstract
Escherichia coli have the genetic potential to use chitin as a carbon source in the absence of glucose, importing it via the chitin-uptake channel EcChiP for processing by the glucosamine catabolic pathway. The chip gene is usually not expressed when E. coli are grown on glucose-enriched nutrients, providing a general regulatory mechanism for the pathway. EcChiP is unusual in that it is homologous to porins and monomeric instead of trimeric, the typical form of sugar-specific channels, making it unclear how this channel operates. We recently reported that EcChiP could form a stable channel in lipid membranes and that the channel is specific for chitooligosaccharides. This report describes the biophysical nature of sugar-channel interactions and the kinetics of sugar association and dissociation. Titrating EcChiP with chitohexaose resulted in protein fluorescence enhancement in a concentration-dependent manner, yielding a binding constant of 2.9 × 105 m-1, consistent with the value of 2.5 × 105 m-1 obtained from isothermal titration microcalorimetry. Analysis of the integrated heat change suggested that the binding process was endothermic and driven by entropy. Single-channel recordings confirmed the voltage dependence of the penetration of chitohexaose molecules into and their release from EcChiP. Once inside the pore, the sugar release rate (koff) from the affinity site increased with elevated voltage, regardless of the side of sugar addition. Our findings revealed distinct thermodynamic and kinetic features of the activity of sugar-specific EcChiP and advance our knowledge of the physiological possibility of chitin utilization by non-chitinolytic bacteria.
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Affiliation(s)
- H Sasimali M Soysa
- From the Biochemistry-Electrochemistry Research Unit, Institute of Science and
| | - Albert Schulte
- the School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology, Rayong 21210, Thailand
| | - Wipa Suginta
- From the Biochemistry-Electrochemistry Research Unit, Institute of Science and .,the Center of Excellence in Advanced Functional Materials, Suranaree University of Technology Nakhon Ratchasima 30000, Thailand and
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Suginta W, Winterhalter M, Smith MF. Correlated trapping of sugar molecules by the trimeric protein channel chitoporin. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:3032-3040. [PMID: 27638174 DOI: 10.1016/j.bbamem.2016.09.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 09/02/2016] [Accepted: 09/09/2016] [Indexed: 10/21/2022]
Abstract
The protein channel chitoporin (ChiP), which is used by marine bacteria to translocate selected sugar molecules through the outer cell membrane, is studied via single channel current measurements in water and heavy water sugar solutions. The dynamic trapping and escape probabilities of sugar molecules from different monomers in the trimeric channel are characterized, including their dependence on channel orientation and sensitivity to a deuterium isotope effect. A detailed analysis of stochastic current fluctuations reveals that the trapping properties of chitoporin exhibit memory effects: the rate of trapping transitions depends on the previous sequence of transitions; and intermonomer correlations: the average trapping rate of an unblocked monomer is larger when its neighboring monomers are blocked. The latter, likely resulting from rapid re-trapping of recently escaped sugar molecules, is considered as a possible design strategy to enhance sugar transport.
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Affiliation(s)
- Wipa Suginta
- Biochemistry-Electrochemistry Research Unit, School of Chemistry, Institute of Science, Center of Excellence in Advanced Functional Materials, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | | | - M F Smith
- School of Physics, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand.
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Soysa HSM, Suginta W. Identification and Functional Characterization of a Novel OprD-like Chitin Uptake Channel in Non-chitinolytic Bacteria. J Biol Chem 2016; 291:13622-33. [PMID: 27226611 DOI: 10.1074/jbc.m116.728881] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Indexed: 11/06/2022] Open
Abstract
Chitoporin from the chitinolytic marine Vibrio has been characterized as a trimeric OmpC-like channel responsible for effective chitin uptake. In this study we describe the identification and characterization of a novel OprD-like chitoporin (so-called EcChiP) from Escherichia coli The gene was identified, cloned, and functionally expressed in the Omp-deficient E. coli BL21 (Omp8) Rosetta strain. On size exclusion chromatography, EcChiP had an apparent native molecular mass of 50 kDa, as predicted by amino acid sequencing and mass analysis, confirming that the protein is a monomer. Black lipid membrane reconstitution demonstrated that EcChiP could readily form stable, monomeric channels in artificial phospholipid membranes, with an average single channel conductance of 0.55 ± 0.01 nanosiemens and a slight preference for cations. Single EcChiP channels showed strong specificity, interacting with long chain chitooligosaccharides but not with maltooligosaccharides. Liposome swelling assays indicated the bulk permeation of neutral monosaccharides and showed the size exclusion limit of EcChiP to be ∼200-300 Da for small permeants that pass through by general diffusion while allowing long chain chitooligosaccharides to pass through by a facilitated diffusion process. Taking E. coli as a model, we offer the first evidence that non-chitinolytic bacteria can activate a quiescent ChiP gene to express a functional chitoporin, enabling them to take up chitooligosaccharides for metabolism as an immediate source of energy.
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Affiliation(s)
- H Sasimali M Soysa
- From the Biochemistry-Electrochemistry Research Unit and School of Chemistry, Institute of Science and
| | - Wipa Suginta
- From the Biochemistry-Electrochemistry Research Unit and School of Chemistry, Institute of Science and Center of Excellence in Advanced Functional Materials, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
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Abstract
Members of the genus Vibrio are known to interact with phyto- and zooplankton in aquatic environments. These interactions have been proven to protect the bacterium from various environmental stresses, serve as a nutrient source, facilitate exchange of DNA, and to serve as vectors of disease transmission. This review highlights the impact of Vibrio-zooplankton interactions at the ecosystem scale and the importance of studies focusing on a wide range of Vibrio-zooplankton interactions. The current knowledge on chitin utilization (i.e., chemotaxis, attachment, and degradation) and the role of these factors in attachment to nonchitinous zooplankton is also presented.
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Meekrathok P, Suginta W. Probing the Catalytic Mechanism of Vibrio harveyi GH20 β-N-Acetylglucosaminidase by Chemical Rescue. PLoS One 2016; 11:e0149228. [PMID: 26870945 PMCID: PMC4752478 DOI: 10.1371/journal.pone.0149228] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Accepted: 01/28/2016] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Vibrio harveyi GH20 β-N-acetylglucosaminidase (VhGlcNAcase) is a chitinolytic enzyme responsible for the successive degradation of chitin fragments to GlcNAc monomers, activating the onset of the chitin catabolic cascade in marine Vibrios. METHODS Two invariant acidic pairs (Asp303-Asp304 and Asp437-Glu438) of VhGlcNAcase were mutated using a site-directed mutagenesis strategy. The effects of these mutations were examined and the catalytic roles of these active-site residues were elucidated using a chemical rescue approach. Enhancement of the enzymic activity of the VhGlcNAcase mutants was evaluated by a colorimetric assay using pNP-GlcNAc as substrate. RESULTS Substitution of Asp303, Asp304, Asp437 or Glu438 with Ala/Asn/Gln produced a dramatic loss of the GlcNAcase activity. However, the activity of the inactive D437A mutant was recovered in the presence of sodium formate. Our kinetic data suggest that formate ion plays a nucleophilic role by mimicking the β-COO-side chain of Asp437, thereby stabilizing the reaction intermediate during both the glycosylation and the deglycosylation steps. CONCLUSIONS Chemical rescue of the inactive D437A mutant of VhGlcNAcase by an added nucleophile helped to identify Asp437 as the catalytic nucleophile/base, and hence its acidic partner Glu438 as the catalytic proton donor/acceptor. GENERAL SIGNIFICANCE Identification of the catalytic nucleophile of VhGlcNAcases supports the proposal of a substrate-assisted mechanism of GH20 GlcNAcases, requiring the catalytic pair Asp437-Glu438 for catalysis. The results suggest the mechanistic basis of the participation of β-N-acetylglucosaminidase in the chitin catabolic pathway of marine Vibrios.
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Affiliation(s)
- Piyanat Meekrathok
- Biochemistry-Electrochemistry Research Unit and School of Biochemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Wipa Suginta
- Biochemistry-Electrochemistry Research Unit and School of Biochemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
- Center of Excellence in Advanced Functional Materials, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
- * E-mail:
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Sirimontree P, Fukamizo T, Suginta W. Azide anions inhibit GH-18 endochitinase and GH-20 Exo β-N-acetylglucosaminidase from the marine bacterium Vibrio harveyi. J Biochem 2015; 159:191-200. [PMID: 26330565 DOI: 10.1093/jb/mvv087] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 08/02/2015] [Indexed: 11/14/2022] Open
Abstract
Vibrio harveyi is a bioluminescent marine bacterium that utilizes chitin as its sole source of energy. In the course of chitin degradation, the bacterium primarily secretes an endochitinase A (VhChiA) to hydrolyze chitin, generating chitooligosaccharide fragments that are readily transported into the cell and broken down to GlcNAc monomers by an exo β-N-acetylglucosaminidase (VhGlcNAcase). Here we report that sodium salts, especially sodium azide, inhibit two classes of these chitin-degrading enzymes (VhChiA and VhGlcNAcase) with distinct modes of action. Kinetic analysis of the enzymatic hydrolysis of pNP-glycoside substrates reveals that sodium azide inhibition of VhChiA has a mixed-type mode, but that it inhibits VhGlcNAcase competitively. We propose that azide anions inhibit chitinase activity by acting as strong nucleophiles that attack Cγ of the catalytic Glu or Cβ of the neighbouring Asp residues. Azide anions may bind not only to the catalytic centre, but also to the other subsites in the substrate-binding cleft of VhChiA. In contrast, azide anions may merely occupy the small-binding pocket of VhGlcNAcase, thereby blocking the accessibility of its active site by short-chain substrates.
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Affiliation(s)
- Paknisa Sirimontree
- Biochemistry-Electrochemistry Research Unit, School of Biochemistry, Suranaree University of Technology, Nakhon Ratchasima, Thailand and
| | - Tamo Fukamizo
- Department of Advanced Biosciences, Kinki University, Nara, Japan
| | - Wipa Suginta
- Biochemistry-Electrochemistry Research Unit, School of Biochemistry, Suranaree University of Technology, Nakhon Ratchasima, Thailand and
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Chumjan W, Winterhalter M, Schulte A, Benz R, Suginta W. Chitoporin from the Marine Bacterium Vibrio harveyi: PROBING THE ESSENTIAL ROLES OF TRP136 AT THE SURFACE OF THE CONSTRICTION ZONE. J Biol Chem 2015; 290:19184-96. [PMID: 26082491 DOI: 10.1074/jbc.m115.660530] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Indexed: 11/06/2022] Open
Abstract
VhChiP is a sugar-specific porin present in the outer membrane of the marine bacterium Vibrio harveyi. VhChiP is responsible for the uptake of chitin oligosaccharides, with particular selectivity for chitohexaose. In this study, we employed electrophysiological and biochemical approaches to demonstrate that Trp(136), located at the mouth of the VhChiP pore, plays an essential role in controlling the channel's ion conductivity, chitin affinity, and permeability. Kinetic analysis of sugar translocation obtained from single channel recordings indicated that the Trp(136) mutations W136A, W136D, W136R, and W136F considerably reduce the binding affinity of the protein channel for its best substrate, chitohexaose. Liposome swelling assays confirmed that the Trp(136) mutations decreased the rate of bulk chitohexaose permeation through the VhChiP channel. Notably, all of the mutants show increases in the off-rate for chitohexaose of up to 20-fold compared with that of the native channel. Furthermore, the cation/anion permeability ratio Pc/Pa is decreased in the W136R mutant and increased in the W136D mutant. This demonstrates that the negatively charged surface at the interior of the protein lumen preferentially attracts cationic species, leading to the cation selectivity of this trimeric channel.
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Affiliation(s)
- Watcharin Chumjan
- From the Biochemistry-Electrochemistry Research Unit, the School of Biochemistry, and
| | - Mathias Winterhalter
- the Department of Life Sciences and Chemistry, Jacobs University Bremen, D-28759 Bremen, Germany
| | - Albert Schulte
- From the Biochemistry-Electrochemistry Research Unit, the School of Chemistry, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand and
| | - Roland Benz
- the Department of Life Sciences and Chemistry, Jacobs University Bremen, D-28759 Bremen, Germany
| | - Wipa Suginta
- From the Biochemistry-Electrochemistry Research Unit, the School of Biochemistry, and
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Meekrathok P, Bürger M, Porfetye AT, Vetter IR, Suginta W. Expression, purification, crystallization and preliminary crystallographic analysis of a GH20 β-N-acetylglucosaminidase from the marine bacterium Vibrio harveyi. Acta Crystallogr F Struct Biol Commun 2015; 71:427-33. [PMID: 25849504 PMCID: PMC4388178 DOI: 10.1107/s2053230x1500415x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Accepted: 02/27/2015] [Indexed: 11/10/2022] Open
Abstract
Vibrio harveyi β-N-acetylglucosaminidase (VhGlcNAcase) is a new member of the GH20 glycoside hydrolase family responsible for the complete degradation of chitin fragments, with N-acetylglucosamine (GlcNAc) monomers as the final products. In this study, the crystallization and preliminary crystallographic data of wild-type VhGlcNAcase and its catalytically inactive mutant D437A in the absence and the presence of substrate are reported. Crystals of wild-type VhGlcNAcase were grown in 0.1 M sodium acetate pH 4.6, 1.4 M sodium malonate, while crystals of the D437A mutant were obtained in 0.1 M bis-tris pH 7.5, 0.1 M sodium acetate, 20% PEG 3350. X-ray data from the wild-type and the mutant crystals were collected at a synchrotron-radiation light source and were complete to a resolution of 2.5 Å. All crystals were composed of the same type of dimer, with the substrate N,N'-diacetylglucosamine (GlcNAc₂ or diNAG) used for soaking was cleaved by the active enzyme, leaving only a single GlcNAc molecule bound to the protein.
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Affiliation(s)
- Piyanat Meekrathok
- Biochemistry–Electrochemistry Research Unit, School of Biochemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Marco Bürger
- Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | | | - Ingrid R. Vetter
- Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Wipa Suginta
- Biochemistry–Electrochemistry Research Unit, School of Biochemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
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Porin involvement in cephalosporin and carbapenem resistance of Burkholderia pseudomallei. PLoS One 2014; 9:e95918. [PMID: 24788109 PMCID: PMC4006797 DOI: 10.1371/journal.pone.0095918] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 04/01/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Burkholderia pseudomallei (Bps) is a Gram-negative bacterium that causes frequently lethal melioidosis, with a particularly high prevalence in the north and northeast of Thailand. Bps is highly resistant to many antimicrobial agents and this resistance may result from the low drug permeability of outer membrane proteins, known as porins. PRINCIPAL FINDINGS Microbiological assays showed that the clinical Bps strain was resistant to most antimicrobial agents and sensitive only to ceftazidime and meropenem. An E. coli strain defective in most porins, but expressing BpsOmp38, exhibited considerably lower antimicrobial susceptibility than the control strain. In addition, mutation of Tyr119, the most prominent pore-lining residue in BpsOmp38, markedly altered membrane permeability, substitution with Ala (mutant BpsOmp38Y119A) enhanced uptake of the antimicrobial agents, while substitution with Phe (mutant BpsOmp38Y119F) inhibited uptake. Channel recordings of BpsOmp38 reconstituted in a planar black lipid membrane (BLM) suggested that the higher permeability of BpsOmp38Y119A was caused by widening of the pore interior through removal of the bulky side chain. In contrast, the lower permeability of BpsOmp38Y119F was caused by introduction of the hydrophobic side chain (Phe), increasing the 'greasiness' of the pore lumen. Significantly, liposome swelling assays showed no permeation through the BpsOmp38 channel by antimicrobial agents to which Bps is resistant (cefoxitin, cefepime, and doripenem). In contrast, high permeability to ceftazidime and meropenem was observed, these being agents to which Bps is sensitive. CONCLUSION/SIGNIFICANCE Our results, from both in vivo and in vitro studies, demonstrate that membrane permeability associated with BpsOmp38 expression correlates well with the antimicrobial susceptibility of the virulent bacterium B. pseudomallei, especially to carbapenems and cephalosporins. In addition, substitution of the residue Tyr119 affects the permeability of the BpsOmp38 channel to neutral sugars and antimicrobial agents.
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Takanao S, Honma S, Miura T, Ogawa C, Sugimoto H, Suzuki K, Watanabe T. Construction and basic characterization of deletion mutants of the genes involved in chitin utilization by Serratia marcescens 2170. Biosci Biotechnol Biochem 2014; 78:524-32. [DOI: 10.1080/09168451.2014.882755] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Abstract
In order to elucidate the roles of ChiP, ChiQ, and ChiX in chitin utilization by Serratia marcescens 2170, the construction of single-gene deletion mutants of the chiP, chiQ, and chiX genes was attempted by allelic exchange mutagenesis. ΔchiP formed smaller clearing zones and ΔchiX formed larger ones than wild-type 2170 on an agar plate containing colloidal chitin. ΔchiP grew slowly on the lower concentration of (GlcNAc)2, and there was essentially no growth on chitin oligosaccharides larger than (GlcNAc)3. The gene product of chiP was detected in the outer membrane fraction, consistently with the hypothesis that chiP encodes outer membrane chitoporin. Deletion of chiQ decreased and that of chiX increased the growth rates on chitin oligosaccharides. These observations strongly suggest that all three genes are involved in chitin utilization and that the deletion mutants obtained in this study might prove useful tools to clarify the details of the chitin utilization system of this bacterium.
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Affiliation(s)
- Shinya Takanao
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Syouta Honma
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Takuma Miura
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Chisana Ogawa
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Hayuki Sugimoto
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
- Faculty of Agriculture, Department of Applied Biological Chemistry, Niigata University, Niigata, Japan
| | - Kazushi Suzuki
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
- Faculty of Agriculture, Department of Applied Biological Chemistry, Niigata University, Niigata, Japan
| | - Takeshi Watanabe
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
- Faculty of Agriculture, Department of Applied Biological Chemistry, Niigata University, Niigata, Japan
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Suginta W, Smith MF. Single-molecule trapping dynamics of sugar-uptake channels in marine bacteria. PHYSICAL REVIEW LETTERS 2013; 110:238102. [PMID: 25167532 DOI: 10.1103/physrevlett.110.238102] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Indexed: 06/03/2023]
Abstract
Stochastic fluctuations of ion current through one chitoporin (ChiP) channel within a bilayer lipid membrane in sugar solution are analyzed. These reflect single-molecule dynamics, which indicate that ChiP has multiple binding sites for sugar and exploits interactions between bound molecules to direct sugar passage. Since ChiP is used by marine bacteria, this is likely an adaptive strategy to enhance sugar translocation from rough water.
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Affiliation(s)
- Wipa Suginta
- Biochemistry-Electrochemistry Research Unit, Schools of Chemistry and Biochemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - M F Smith
- School of Physics, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand and Thailand Center of Excellence in Physics (ThEP), Commission of Higher Education, Ministry of Education, Bangkok 10400, Thailand
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Suginta W, Khunkaewla P, Schulte A. Electrochemical Biosensor Applications of Polysaccharides Chitin and Chitosan. Chem Rev 2013; 113:5458-79. [DOI: 10.1021/cr300325r] [Citation(s) in RCA: 341] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Wipa Suginta
- Biochemistry and Electrochemistry
Research Unit, Schools
of Chemistry and Biochemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima
30000, Thailand
| | - Panida Khunkaewla
- Biochemistry and Electrochemistry
Research Unit, Schools
of Chemistry and Biochemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima
30000, Thailand
| | - Albert Schulte
- Biochemistry and Electrochemistry
Research Unit, Schools
of Chemistry and Biochemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima
30000, Thailand
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Suginta W, Chumjan W, Mahendran KR, Schulte A, Winterhalter M. Chitoporin from Vibrio harveyi, a channel with exceptional sugar specificity. J Biol Chem 2013; 288:11038-46. [PMID: 23447539 DOI: 10.1074/jbc.m113.454108] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Chitoporin (VhChiP) is a sugar-specific channel responsible for the transport of chitooligosaccharides through the outer membrane of the marine bacterium Vibrio harveyi. Single channel reconstitution into black lipid membrane allowed single chitosugar binding events in the channel to be resolved. VhChiP has an exceptionally high substrate affinity, with a binding constant of K = 5.0 × 10(6) M(-1) for its best substrate (chitohexaose). The on-rates of chitosugars depend on applied voltages, as well as the side of the sugar addition, clearly indicating the inherent asymmetry of the VhChiP lumen. The binding affinity of VhChiP for chitohexaose is 1-5 orders of magnitude larger than that of other known sugar-specific porins for their preferred substrates. Thus, VhChiP is the most potent sugar-specific channel reported to date, with its high efficiency presumably reflecting the need for the bacterium to take up chitin-containing nutrients promptly under turbulent aquatic conditions to exploit them efficiently as its sole source of energy.
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Affiliation(s)
- Wipa Suginta
- Biochemistry-Electrochemistry Research Unit, School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand.
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