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MURATA K, KAWAI S, HASHIMOTO W. Bacteria with a mouth: Discovery and new insights into cell surface structure and macromolecule transport. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2022; 98:529-552. [PMID: 36504195 PMCID: PMC9751261 DOI: 10.2183/pjab.98.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 10/13/2022] [Indexed: 06/17/2023]
Abstract
A bacterium with a "mouth"-like pit structure isolated for the first time in the history of microbiology was a Gram-negative rod, containing glycosphingolipids in the cell envelope, and named Sphingomonas sp. strain A1. The pit was dynamic, with repetitive opening and closing during growth on alginate, and directly included alginate concentrated around the pit, particularly by flagellins, an alginate-binding protein localized on the cell surface. Alginate incorporated into the periplasm was subsequently transferred to the cytoplasm by cooperative interactions of periplasmic solute-binding proteins and an ATP-binding cassette transporter in the cytoplasmic membrane. The mechanisms of assembly, functions, and interactions between the above-mentioned molecules were clarified using structural biology. The pit was transplanted into other strains of sphingomonads, and the pitted recombinant cells were effectively applied to the production of bioethanol, bioremediation for dioxin removal, and other tasks. Studies of the function of the pit shed light on the biological significance of cell surface structures and macromolecule transport in bacteria.
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Affiliation(s)
| | - Shigeyuki KAWAI
- Research Institute for Bioresource and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
| | - Wataru HASHIMOTO
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan
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2
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Zhang L, Li X, Zhang X, Li Y, Wang L. Bacterial alginate metabolism: an important pathway for bioconversion of brown algae. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:158. [PMID: 34275475 PMCID: PMC8286568 DOI: 10.1186/s13068-021-02007-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/04/2021] [Indexed: 06/13/2023]
Abstract
Brown macroalgae have attracted great attention as an alternative feedstock for biorefining. Although direct conversion of ethanol from alginates (major components of brown macroalgae cell walls) is not amenable for industrial production, significant progress has been made not only on enzymes involved in alginate degradation, but also on metabolic pathways for biorefining at the laboratory level. In this article, we summarise recent advances on four aspects: alginate, alginate lyases, different alginate-degrading systems, and application of alginate lyases and associated pathways. This knowledge will likely inspire sustainable solutions for further application of both alginate lyases and their associated pathways.
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Affiliation(s)
- Lanzeng Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Xue Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Xiyue Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Yingjie Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
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3
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MURATA K. Polyphosphate-dependent nicotinamide adenine dinucleotide (NAD) kinase: A novel missing link in human mitochondria. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2021; 97:479-498. [PMID: 34629356 PMCID: PMC8553519 DOI: 10.2183/pjab.97.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/16/2021] [Indexed: 06/13/2023]
Abstract
Polyphosphate [poly(P)] is described as a homopolymer of inorganic phosphates. Nicotinamide adenine dinucleotide kinase (NAD kinase) catalyzes the phosphorylation of NAD+ to NADP+ in the presence of ATP (ATP-NAD kinase). Novel NAD kinase that explicitly phosphorylates NAD+ to NADP+ using poly(P), besides ATP [ATP/poly(P)-NAD kinase], was found in bacteria, in particular, Gram-positive bacteria, and the gene encoding ATP/poly(P)-NAD kinase was also newly identified in Mycobacterium tuberculosis H37Rv. Both NAD kinases required multi-homopolymeric structures for activity expression. The enzymatic and genetic results, combined with their primary and tertiary structures, have led to the discovery of a long-awaited human mitochondrial NAD kinase. This discovery showed that the NAD kinase is a bacterial type of ATP/poly(P)-NAD kinase. These pioneering findings, i.e., ATP/poly(P)-NAD kinase, NAD kinase gene, and human mitochondrial NAD kinase, have significantly enhanced research on the biochemistry, molecular biology, and evolutionary biology of NAD kinase, mitochondria, and poly(P), including some biotechnological knowledge applicable to NADP+ production.
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Asaf S, Numan M, Khan AL, Al-Harrasi A. Sphingomonas: from diversity and genomics to functional role in environmental remediation and plant growth. Crit Rev Biotechnol 2020; 40:138-152. [PMID: 31906737 DOI: 10.1080/07388551.2019.1709793] [Citation(s) in RCA: 184] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The species belonging to the Sphingomonas genus possess multifaceted functions ranging from remediation of environmental contaminations to producing highly beneficial phytohormones, such as sphingan and gellan gum. Recent studies have shown an intriguing role of Sphingomonas species in the degradation of organometallic compounds. However, the actual biotechnological potential of this genus requires further assessment. Some of the species from the genus have also been noted to improve plant-growth during stress conditions such as drought, salinity, and heavy metals in agricultural soil. This role has been attributed to their potential to produce plant growth hormones e.g. gibberellins and indole acetic acid. However, the current literature is scattered, and some of the important areas, such as taxonomy, phylogenetics, genome mapping, and cellular transport systems, are still being overlooked in terms of elucidation of the mechanisms behind stress-tolerance and bioremediation. In this review, we elucidated the prospective role and function of this genus for improved utilization during environmental biotechnology.
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Affiliation(s)
- Sajjad Asaf
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Muhammad Numan
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Abdul Latif Khan
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Ahmed Al-Harrasi
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
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5
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Fujita M, Mori K, Hara H, Hishiyama S, Kamimura N, Masai E. A TonB-dependent receptor constitutes the outer membrane transport system for a lignin-derived aromatic compound. Commun Biol 2019; 2:432. [PMID: 31799434 PMCID: PMC6874591 DOI: 10.1038/s42003-019-0676-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Accepted: 11/04/2019] [Indexed: 12/23/2022] Open
Abstract
TonB-dependent receptors (TBDRs) mediate substrate-specific transport across the outer membrane, utilizing energy derived from the proton motive force transmitted from the TonB-ExbB-ExbD complex located in the inner membrane (TonB system). Although a number of TonB systems involved in the uptake of siderophores, vitamin B12 and saccharides have been identified, their involvement in the uptake and catabolism of aromatic compounds was previously unknown. Here, we show that the outer membrane transport of a biphenyl compound derived from lignin is mediated by the TonB system in a Gram-negative bacterium capable of degrading lignin-derived aromatic compounds, Sphingobium sp. strain SYK-6. Furthermore, we found that overexpression of the corresponding TBDR gene enhanced the uptake of this biphenyl compound, contributing to the improved rate of platform chemical production. Our results will provide an important basis for establishing engineered strains optimized for use in lignin valorisation.
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Affiliation(s)
- Masaya Fujita
- 1Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata Japan
| | - Kosuke Mori
- 1Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata Japan
| | - Hirofumi Hara
- 2Department of Chemical Process Engineering, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia, Kuala Lumpur, Malaysia
| | - Shojiro Hishiyama
- 3Forestry and Forest Products Research Institute, Tsukuba, Ibaraki Japan
| | - Naofumi Kamimura
- 1Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata Japan
| | - Eiji Masai
- 1Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata Japan
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Maruyama Y, Hashimoto W, Murata K. Structural studies on bacterial system used in the recognition and uptake of the macromolecule alginate. Biosci Biotechnol Biochem 2019; 83:794-802. [PMID: 30744540 DOI: 10.1080/09168451.2019.1578642] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Alginate is an acidic heteropolysaccharide produced by brown seaweed and certain kinds of bacteria. The cells of Sphingomonas sp. strain A1, a gram-negative bacterium, have several alginate-degrading enzymes in their cytoplasm and efficiently utilize this polymer for their growth. Sphingomonas sp. strain A1 cells can directly incorporate alginate into their cytoplasm through a transport system consisting of a "pit" on their cell surface, substrate-binding proteins in their periplasm, and an ATP-binding cassette transporter in their inner membrane. This review deals with the structural and functional aspects of bacterial systems necessary for the recognition and uptake of alginate.
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Affiliation(s)
- Yukie Maruyama
- a Division of Food Science and Biotechnology , Graduate School of Agriculture, Kyoto University , Uji, Kyoto , Japan.,b Department of Life Science, Faculty of Science and Engineering , Setsunan University , Neyagawa, Osaka , Japan
| | - Wataru Hashimoto
- a Division of Food Science and Biotechnology , Graduate School of Agriculture, Kyoto University , Uji, Kyoto , Japan
| | - Kousaku Murata
- a Division of Food Science and Biotechnology , Graduate School of Agriculture, Kyoto University , Uji, Kyoto , Japan.,b Department of Life Science, Faculty of Science and Engineering , Setsunan University , Neyagawa, Osaka , Japan
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7
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Gatheru Waigi M, Sun K, Gao Y. Sphingomonads in Microbe-Assisted Phytoremediation: Tackling Soil Pollution. Trends Biotechnol 2017; 35:883-899. [DOI: 10.1016/j.tibtech.2017.06.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 06/18/2017] [Accepted: 06/22/2017] [Indexed: 12/24/2022]
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8
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“Living” dynamics of filamentous bacteria on an adherent surface under hydrodynamic exposure. Biointerphases 2017; 12:02C410. [DOI: 10.1116/1.4983150] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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9
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Song WS, Jeon YJ, Namgung B, Hong M, Yoon SI. A conserved TLR5 binding and activation hot spot on flagellin. Sci Rep 2017; 7:40878. [PMID: 28106112 PMCID: PMC5247705 DOI: 10.1038/srep40878] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 12/12/2016] [Indexed: 11/26/2022] Open
Abstract
Flagellin is a bacterial protein that polymerizes into the flagellar filament and is essential for bacterial motility. When flagellated bacteria invade the host, flagellin is recognized by Toll-like receptor 5 (TLR5) as a pathogen invasion signal and eventually evokes the innate immune response. Here, we provide a conserved structural mechanism by which flagellins from Gram-negative γ-proteobacteria and Gram-positive Firmicutes bacteria bind and activate TLR5. The comparative structural analysis using our crystal structure of a complex between Bacillus subtilis flagellin (bsflagellin) and TLR5 at 2.1 Å resolution, combined with the alanine scanning analysis of the binding interface, reveals a common hot spot in flagellin for TLR5 activation. An arginine residue (bsflagellin R89) of the flagellin D1 domain and its adjacent residues (bsflagellin E114 and L93) constitute a hot spot that provides shape and chemical complementarity to a cavity generated by the loop of leucine-rich repeat 9 in TLR5. In addition to the flagellin D1 domain, the D0 domain also contributes to TLR5 activity through structurally dispersed regions, but not a single focal area. These results establish the groundwork for the future design of flagellin-based therapeutics.
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Affiliation(s)
- Wan Seok Song
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Ye Ji Jeon
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Byeol Namgung
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Minsun Hong
- Division of Biological Science and Technology, Yonsei University, Wonju 26493, Republic of Korea
| | - Sung-Il Yoon
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea.,Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 24341, Republic of Korea
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Kobayashi M, Konishi H, Maruyama Y, Murata K, Hashimoto W. Lateral-typed flagellin responsible for formation of a polar flagellum but not of lateral flagella in Sphingomonas sp. strain A1. Microbiology (Reading) 2016; 162:2042-2052. [DOI: 10.1099/mic.0.000385] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Masahiro Kobayashi
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Hidenori Konishi
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Yukie Maruyama
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Kousaku Murata
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Wataru Hashimoto
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
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Tavafi H, Abdi-Ali A, Ghadam P, Gharavi S. Screening of Alginate Lyase-Producing Bacteria and Optimization of Media Compositions for Extracellular Alginate Lyase Production. IRANIAN BIOMEDICAL JOURNAL 2016; 21:48-56. [PMID: 27432784 PMCID: PMC5141254 DOI: 10.6091/.21.1.48] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Background: Alginate is a linear polysaccharide consisting of guluronate (polyG) and mannuronate (polyM) subunits. Methods: In the initial screening of alginate-degrading bacteria from soil, 10 isolates were able to grow on minimal medium containing alginate. The optimization of cell growth and alginate lyase (algL) production was carried out by the addition of 0.8% alginate and 0.2-0.3 M NaCl to the culture medium. Of 10 isolates, one was selected based on its fast growth rate on minimal 9 medium containing 0.4% sodium alginate. The selected bacterium, identified based on morphological and biochemical characteristics, as well as 16S rDNA sequence data, was confirmed to be an isolate belonging to the genus Bacillus and designated as Bacillus sp. TAG8. Results: The results showed the ability of Bacillus sp. TAG8 in utilizing alginate as a sole carbon source. Bacillus sp. TAG8 growth and algL production were augmented with an increase in sodium alginate concentration and also by the addition of 0.2-0.3 M NaCl. Molecular analysis of TAG8 algL gene showed 99% sequence identity with algL of Pseudomonasaeruginosa PAO1. The algL produced by Bacillus sp. TAG8 cleaved both polyM and polyG blocks in alginate molecule, as well as acetylated alginate residues, confirming the bifunctionality of the isolated lyase. Conclusion: The identification of novel algL genes from microbial communities constitutes a new approach for exploring lyases with specific activity against bacterial alginates and may thus contribute to the eradication of persistent biofilms from clinical samples.
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Affiliation(s)
- Hadis Tavafi
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
| | - Ahya Abdi-Ali
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
| | - Parinaz Ghadam
- Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
| | - Sara Gharavi
- Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
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Abstract
Proteinaceous components of the biofilm matrix include secreted extracellular proteins, cell surface adhesins, and protein subunits of cell appendages such as flagella and pili. Biofilm matrix proteins play diverse roles in biofilm formation and dissolution. They are involved in attaching cells to surfaces, stabilizing the biofilm matrix via interactions with exopolysaccharide and nucleic acid components, developing three-dimensional biofilm architectures, and dissolving biofilm matrix via enzymatic degradation of polysaccharides, proteins, and nucleic acids. In this article, we will review functions of matrix proteins in a selected set of microorganisms, studies of the matrix proteomes of Vibrio cholerae and Pseudomonas aeruginosa, and roles of outer membrane vesicles and of nucleoid-binding proteins in biofilm formation.
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13
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Maruyama Y, Kobayashi M, Murata K, Hashimoto W. Formation of a single polar flagellum by two distinct flagellar gene sets in Sphingomonas sp. strain A1. MICROBIOLOGY-SGM 2015; 161:1552-1560. [PMID: 26018545 DOI: 10.1099/mic.0.000119] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Gram-negative Sphingomonas sp. strain A1, originally identified as a non-motile and aflagellate bacterium, possesses two sets of genes required for flagellar formation. In this study, we characterized the flagellar genes and flagellum formation in strain A1. Flagellar gene cluster set I contained 35 flagellar genes, including one flagellin gene (p6), where the gene assembly structure resembled that required for the formation of lateral flagella in gammaproteobacteria. The set II flagellar genes were arranged in eight shorter clusters with 46 flagellar genes, including two flagellin genes (p5 and p5') and flhF, which is required for polar flagella. Our molecular phylogenetic analysis of the bacterial flagellins also demonstrated that, in contrast to p5 and p5', p6 was categorized as a lateral flagellin group. The motile phenotype appeared in strain A1 cells when they were subcultured on semisolid media. The motile strain A1 cells produced a single flagellum at the cell pole. DNA microarray analyses using non-motile and motile strain A1 cells indicated that flagellar formation was accompanied by increased transcription of both flagellar gene sets. The two flagellins p5 and p6 were major components of the flagellar filaments isolated from motile strain A1 cells, indicating that the polar flagellum is formed by lateral and non-lateral flagellins.
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Affiliation(s)
- Yukie Maruyama
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Masahiro Kobayashi
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Kousaku Murata
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Wataru Hashimoto
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
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14
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Structural insights into alginate binding by bacterial cell-surface protein. Carbohydr Res 2015; 404:39-45. [DOI: 10.1016/j.carres.2014.11.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 11/05/2014] [Accepted: 11/17/2014] [Indexed: 11/21/2022]
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15
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Shin JW, Lee OK, Park HH, Kim HS, Lee EY. Molecular characterization of a novel oligoalginate lyase consisting of AlgL- and heparinase II/III-like domains from Stenotrophomonas maltophilia KJ-2 and its application to alginate saccharification. KOREAN J CHEM ENG 2015. [DOI: 10.1007/s11814-014-0282-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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Hou X, McMillan M, Coumans JVF, Poljak A, Raftery MJ, Pereg L. Cellular responses during morphological transformation in Azospirillum brasilense and Its flcA knockout mutant. PLoS One 2014; 9:e114435. [PMID: 25502569 PMCID: PMC4264754 DOI: 10.1371/journal.pone.0114435] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 11/10/2014] [Indexed: 01/25/2023] Open
Abstract
FlcA is a response regulator controlling flocculation and the morphological transformation of Azospirillum cells from vegetative to cyst-like forms. To understand the cellular responses of Azospirillum to conditions that cause morphological transformation, proteins differentially expressed under flocculation conditions in A. brasilense Sp7 and its flcA knockout mutant were investigated. Comparison of 2-DE protein profiles of wild-type (Sp7) and a flcA deletion mutant (Sp7-flcAΔ) revealed a total of 33 differentially expressed 2-DE gel spots, with 22 of these spots confidently separated to allow protein identification. Analysis of these spots by liquid chromatography-tandem mass spectrometry (LC-MS/MS) and MASCOT database searching identified 48 proteins (≥10% emPAI in each spot). The functional characteristics of these proteins included carbon metabolism (beta-ketothiolase and citrate synthase), nitrogen metabolism (Glutamine synthetase and nitric oxide synthase), stress tolerance (superoxide dismutase, Alkyl hydroperoxidase and ATP-dependent Clp protease proteolytic subunit) and morphological transformation (transducer coupling protein). The observed differences between Sp7 wild-type and flcA− strains enhance our understanding of the morphological transformation process and help to explain previous phenotypical observations. This work is a step forward in connecting the Azospirillum phenome and genome.
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Affiliation(s)
- Xingsheng Hou
- School of Science and Technology, University of New England, Armidale, New South Wales, Australia
- Department of Microbiology and Immunology, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Mary McMillan
- School of Science and Technology, University of New England, Armidale, New South Wales, Australia
| | - Joëlle V. F. Coumans
- School of Science and Technology, University of New England, Armidale, New South Wales, Australia
- School of Rural Medicine, University of New England, Armidale, New South Wales, Australia
| | - Anne Poljak
- Bioanalytical Mass Spectrometry Facility, Analytical Centre, University of New South Wales, Sydney, New South Wales, Australia
- The School of Medical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Mark J. Raftery
- Bioanalytical Mass Spectrometry Facility, Analytical Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Lily Pereg
- School of Science and Technology, University of New England, Armidale, New South Wales, Australia
- * E-mail: mailto:
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Song WS, Yoon SI. Crystal structure of FliC flagellin from Pseudomonas aeruginosa and its implication in TLR5 binding and formation of the flagellar filament. Biochem Biophys Res Commun 2014; 444:109-15. [PMID: 24434155 DOI: 10.1016/j.bbrc.2014.01.008] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Accepted: 01/07/2014] [Indexed: 01/24/2023]
Abstract
Pseudomonas aeruginosa is one of leading opportunistic pathogens in humans and its movement is driven by a flagellar filament that is constituted through the polymerization of a single protein, FliC flagellin (paFliC). paFliC is an essential virulence factor for the colonization of P. aeruginosa. paFliC activates innate immune responses via its recognition by Toll-like receptor 5 (TLR5) and adaptive immunity in the host. Thus, paFliC has been a vaccine candidate to prevent P. aeruginosa infection, particularly for cystic fibrosis patients. To provide structural information on paFliC and its flagellar filament, we have determined the crystal structure of paFliC, which contains the conserved D1 and variable D2 domains, at 2.1 Å resolution. As observed for Salmonella FliC, the paFliC D1 domain is folded into a rod-shaped structure, and paFliC was demonstrated by gel filtration and native PAGE analyses to directly interact with TLR5. Moreover, a structural model of the paFliC-TLR5 complex suggests that paFliC D1 would provide major TLR5-binding sites, similar to Salmonella FliC. In contrast to the D1 domain, the paFliC D2 domain exhibits a unique structure of two β-sheets and one α-helix that has not been found in other flagellins. An in silico construction of a flagellar filament based on the packing of paFliC in the crystal suggests that the D2 domain would be exposed to solution and could play an important role in immunogenicity. Our biophysical and structure-based modeling study on paFliC, the paFliC-TLR5 complex, and the paFliC filament could contribute to the improvement of vaccine design to control P. aeruginosa infection.
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Affiliation(s)
- Wan Seok Song
- Department of Systems Immunology and Institute of Antibody Research, College of Biomedical Science, Kangwon National University, Chuncheon 200-701, Republic of Korea
| | - Sung-il Yoon
- Department of Systems Immunology and Institute of Antibody Research, College of Biomedical Science, Kangwon National University, Chuncheon 200-701, Republic of Korea.
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Sorokin DY, Gumerov VM, Rakitin AL, Beletsky AV, Damsté JSS, Muyzer G, Mardanov AV, Ravin NV. Genome analysis of Chitinivibrio alkaliphilus gen. nov., sp. nov., a novel extremely haloalkaliphilic anaerobic chitinolytic bacterium from the candidate phylum Termite Group 3. Environ Microbiol 2013; 16:1549-65. [PMID: 24112708 DOI: 10.1111/1462-2920.12284] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 07/29/2013] [Accepted: 09/09/2013] [Indexed: 11/30/2022]
Abstract
Anaerobic enrichments from hypersaline soda lakes with chitin as substrate yielded five closely related anaerobic haloalkaliphilic isolates growing on insoluble chitin by fermentation at pH 10 and salinities up to 3.5 M. The chitinolytic activity was exclusively cell associated. To better understand the biology and evolutionary history of this novel bacterial lineage, the genome of the type strain ACht1 was sequenced. Analysis of the 2.6 Mb draft genome revealed enzymes of chitin-degradation pathways, including secreted cell-bound chitinases. The reconstructed central metabolism revealed pathways enabling the fermentation of polysaccharides, while it lacks the genes needed for aerobic or anaerobic respiration. The Rnf-type complex, oxaloacetate decarboxylase and sodium-transporting V-type adenosine triphosphatase were identified among putative membrane-bound ion pumps. According to 16S ribosomal RNA analysis, the isolates belong to the candidate phylum Termite Group 3, representing its first culturable members. Phylogenetic analysis using ribosomal proteins and taxonomic distribution analysis of the whole proteome supported a class-level classification of ACht1 most probably affiliated to the phylum Fibribacteres. Based on phylogenetic, phenotypic and genomic analyses, the novel bacteria are proposed to be classified as Chitinivibrio alkaliphilus gen. nov., sp. nov., within a novel class Chitinivibrione.
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Affiliation(s)
- Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-let Oktyabrya, bld. 7-2, 117312, Moscow, Russia; Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
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Zhou J, Cai M, Jiang T, Zhou W, Shen W, Zhou X, Zhang Y. Mixed carbon source control strategy for enhancing alginate lyase production by marine Vibrio sp. QY102. Bioprocess Biosyst Eng 2013; 37:575-84. [DOI: 10.1007/s00449-013-1024-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 07/22/2013] [Indexed: 11/30/2022]
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Park HH, Kam N, Lee EY, Kim HS. Cloning and characterization of a novel oligoalginate lyase from a newly isolated bacterium Sphingomonas sp. MJ-3. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2012; 14:189-202. [PMID: 21826589 DOI: 10.1007/s10126-011-9402-7] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Accepted: 07/12/2011] [Indexed: 05/28/2023]
Abstract
A bacterium possessing alginate-degrading activity was isolated from marine brown seaweed soup liquefied by salted and fermented anchovy. The isolated strain was designated as Sphingomonas sp. MJ-3 based on the analyses of 16S ribosomal DNA sequences, 16S-23S internal transcribed spacer region sequences, biochemical characteristics, and cellular fatty acid composition. A novel alginate lyase gene was cloned from genomic DNA library and then expressed in Escherichia coli. When the deduced amino acid sequence was compared with the sequences on the databases, interestingly, the cloned gene product was predicted to consist of AlgL (alginate lyase L)-like and heparinase-like protein domain. The MJ-3 alginate lyase gene shared below 27.0% sequence identity with exolytic alginate lyase of Sphingomonas sp. A1. The optimal pH and temperature for the recombinant MJ-3 alginate lyase were 6.5 and 50°C, respectively. The final degradation products of alginate oligosaccharides were analyzed by electrospray ionization mass spectrometry and proved to be alginate monosaccharides. Based on the results, the recombinant alginate lyase from Sphingomonas sp. MJ-3 is regarded as an oligoalginate lyase that can degrade oligoalginate and alginate into alginate monosaccharides.
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Affiliation(s)
- Hwan Hee Park
- Department of Food Science and Biotechnology, Kyungsung University, Busan 608-736, South Korea
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Nagata Y, Natsui S, Endo R, Ohtsubo Y, Ichikawa N, Ankai A, Oguchi A, Fukui S, Fujita N, Tsuda M. Genomic organization and genomic structural rearrangements of Sphingobium japonicum UT26, an archetypal γ-hexachlorocyclohexane-degrading bacterium. Enzyme Microb Technol 2011; 49:499-508. [DOI: 10.1016/j.enzmictec.2011.10.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 10/28/2011] [Accepted: 10/28/2011] [Indexed: 11/27/2022]
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Suen G, Weimer PJ, Stevenson DM, Aylward FO, Boyum J, Deneke J, Drinkwater C, Ivanova NN, Mikhailova N, Chertkov O, Goodwin LA, Currie CR, Mead D, Brumm PJ. The complete genome sequence of Fibrobacter succinogenes S85 reveals a cellulolytic and metabolic specialist. PLoS One 2011; 6:e18814. [PMID: 21526192 PMCID: PMC3079729 DOI: 10.1371/journal.pone.0018814] [Citation(s) in RCA: 147] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2010] [Accepted: 03/11/2011] [Indexed: 11/17/2022] Open
Abstract
Fibrobacter succinogenes is an important member of the rumen microbial community that converts plant biomass into nutrients usable by its host. This bacterium, which is also one of only two cultivated species in its phylum, is an efficient and prolific degrader of cellulose. Specifically, it has a particularly high activity against crystalline cellulose that requires close physical contact with this substrate. However, unlike other known cellulolytic microbes, it does not degrade cellulose using a cellulosome or by producing high extracellular titers of cellulase enzymes. To better understand the biology of F. succinogenes, we sequenced the genome of the type strain S85 to completion. A total of 3,085 open reading frames were predicted from its 3.84 Mbp genome. Analysis of sequences predicted to encode for carbohydrate-degrading enzymes revealed an unusually high number of genes that were classified into 49 different families of glycoside hydrolases, carbohydrate binding modules (CBMs), carbohydrate esterases, and polysaccharide lyases. Of the 31 identified cellulases, none contain CBMs in families 1, 2, and 3, typically associated with crystalline cellulose degradation. Polysaccharide hydrolysis and utilization assays showed that F. succinogenes was able to hydrolyze a number of polysaccharides, but could only utilize the hydrolytic products of cellulose. This suggests that F. succinogenes uses its array of hemicellulose-degrading enzymes to remove hemicelluloses to gain access to cellulose. This is reflected in its genome, as F. succinogenes lacks many of the genes necessary to transport and metabolize the hydrolytic products of non-cellulose polysaccharides. The F. succinogenes genome reveals a bacterium that specializes in cellulose as its sole energy source, and provides insight into a novel strategy for cellulose degradation.
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Affiliation(s)
- Garret Suen
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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Heterosubunit composition and crystal structures of a novel bacterial M16B metallopeptidase. J Mol Biol 2011; 407:180-92. [PMID: 21262231 DOI: 10.1016/j.jmb.2011.01.038] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Revised: 01/14/2011] [Accepted: 01/17/2011] [Indexed: 11/20/2022]
Abstract
Three subfamilies of metallopeptidase family M16 enzymes--M16A, M16B, and M16C--are widely distributed among eukaryotes and prokaryotes. SPH2681, a periplasmic M16B protein found in Sphingomonas sp. strain A1, contains an HXXEH motif essential for Zn(2+) binding and catalytic activity. SPH2682 is another member of M16B, which lacks the metal-binding motif but conserves an active-site R/Y pair commonly found in the C-terminal half of M16 enzymes. Two genes coding for SPH2681 and SPH2682 assemble into a single operon in the bacterial genome. This study determined SPH2681 to be constitutively expressed in strain A1 cells grown on different carbon sources, suggesting a more general cellular function. SPH2681 and SPH2681/SPH2682 were overexpressed in Escherichia coli, purified, and characterized. SPH2681 was found to associate with SPH2682, forming a heterosubunit enzyme with peptidase activity, while SPH2681 alone exhibited no enzymatic activity. X-ray crystallography of the SPH2681/SPH2682 complex revealed two conformations (open and closed heterodimeric forms) within the same crystal. Compared with the closed form, the open form contains two subunits rotated away from each other by approximately 8°, increasing the distance between the zinc ion and active-site residues by up to 8 Å. In addition, many hydrogen bonds are formed or broken on change between the conformations of the heterodimers, suggesting that subunit dynamics is a prerequisite for catalysis. To our knowledge, this is the first report on both conformational forms of the same M16 peptidase, providing a unique insight into the general proteolytic mechanism of M16 proteases.
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Maruyama Y, Ochiai A, Mikami B, Hashimoto W, Murata K. Crystal structure of bacterial cell-surface alginate-binding protein with an M75 peptidase motif. Biochem Biophys Res Commun 2011; 405:411-6. [PMID: 21238429 DOI: 10.1016/j.bbrc.2011.01.043] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2010] [Accepted: 01/11/2011] [Indexed: 10/18/2022]
Abstract
A gram-negative Sphingomonas sp. A1 directly incorporates alginate polysaccharide into the cytoplasm via the cell-surface pit and ABC transporter. A cell-surface alginate-binding protein, Algp7, functions as a concentrator of the polysaccharide in the pit. Based on the primary structure and genetic organization in the bacterial genome, Algp7 was found to be homologous to an M75 peptidase motif-containing EfeO, a component of a ferrous ion transporter. Despite the presence of an M75 peptidase motif with high similarity, the Algp7 protein purified from recombinant Escherichia coli cells was inert on insulin B chain and N-benzoyl-Phe-Val-Arg-p-nitroanilide, both of which are substrates for a typical M75 peptidase, imelysin, from Pseudomonas aeruginosa. The X-ray crystallographic structure of Algp7 was determined at 2.10Å resolution by single-wavelength anomalous diffraction. Although a metal-binding motif, HxxE, conserved in zinc ion-dependent M75 peptidases is also found in Algp7, the crystal structure of Algp7 contains no metal even at the motif. The protein consists of two structurally similar up-and-down helical bundles as the basic scaffold. A deep cleft between the bundles is sufficiently large to accommodate macromolecules such as alginate polysaccharide. This is the first structural report on a bacterial cell-surface alginate-binding protein with an M75 peptidase motif.
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Affiliation(s)
- Yukie Maruyama
- Laboratory of Basic and Applied Molecular Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
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Kahnt J, Aguiluz K, Koch J, Treuner-Lange A, Konovalova A, Huntley S, Hoppert M, Søgaard-Andersen L, Hedderich R. Profiling the outer membrane proteome during growth and development of the social bacterium Myxococcus xanthus by selective biotinylation and analyses of outer membrane vesicles. J Proteome Res 2010; 9:5197-208. [PMID: 20687614 DOI: 10.1021/pr1004983] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Social behavior in the bacterium Myxococcus xanthus relies on contact-dependent activities involving cell-cell and cell-substratum interactions. To identify outer membrane proteins that have a role in these activities, we profiled the outer membrane proteome of growing and starving cells using two strategies. First, outer membrane proteins were enriched by biotinylation of intact cells using the reagent NHS (N-hydroxysuccinimide)-PEO(12) (polyethylene oxide)-biotin with subsequent membrane solubilization and affinity chromatography. Second, the proteome of outer membrane vesicles (OMV) was determined. Comparisons of detected proteins show that these methods have different detection profiles and together provide a comprehensive view of the outer membrane proteome. From 362 proteins identified, 274 (76%) were cell envelope proteins including 64 integral outer membrane proteins and 85 lipoproteins. The majority of these proteins were of unknown function. Among integral outer membrane proteins with homologues of known function, TonB-dependent transporters comprise the largest group. Our data suggest novel functions for these transporters. Among lipoproteins with homologues of known function, proteins with hydrolytic functions comprise the largest group. The luminal load of OMV was enriched for proteins with hydrolytic functions. Our data suggest that OMV have functions in predation and possibly in transfer of intercellular signaling molecules between cells.
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Affiliation(s)
- Jörg Kahnt
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str., Marburg, Germany
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Hashimoto W, Kawai S, Murata K. Bacterial supersystem for alginate import/metabolism and its environmental and bioenergy applications. Bioeng Bugs 2009; 1:97-109. [PMID: 21326935 DOI: 10.4161/bbug.1.2.10322] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2009] [Revised: 10/13/2009] [Accepted: 10/14/2009] [Indexed: 11/19/2022] Open
Abstract
Distinct from most alginate-assimilating bacteria that secrete polysaccharide lyases extracellularly, a gram-negative bacterium, Sphingomonas sp. A1 (strain A1), can directly incorporate alginate into its cytoplasm, without degradation, through a "superchannel" consisting of a mouth-like pit on the cell surface, periplasmic binding proteins, and a cytoplasmic membrane-bound ATP-binding cassette transporter. Flagellin homologues function as cell surface alginate receptors essential for expressing the superchannel. Cytoplasmic alginate lyases with different substrate specificities and action modes degrade the polysaccharide to its constituent monosaccharides. The resultant monosaccharides, α-keto acids, are converted to a reduced form by NADPH-dependent reductase, and are finally metabolized in the TCA cycle. Transplantation of the strain A1 superchannel to xenobiotic-degrading sphingomonads enhances bioremediation through the propagation of bacteria with an elevated transport activity. Furthermore, strain A1 cells transformed with Zymomonas mobilis genes for pyruvate decarboxylase and alcohol dehydrogenase II produce considerable amounts of biofuel ethanol from alginate when grown statically.
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Affiliation(s)
- Wataru Hashimoto
- Laboratory of Basic and Applied Molecular Biotechnology,; Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan
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Hashimoto W, Ochiai A, He J, Itoh T, Mikami B, Murata K. Crystallization and preliminary crystallographic analysis of the cell-surface alginate-binding protein Algp7 isolated from Sphingomonas sp. A1. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:515-7. [PMID: 19407391 DOI: 10.1107/s1744309109013669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2009] [Accepted: 04/11/2009] [Indexed: 11/11/2022]
Abstract
Sphingomonas sp. A1, a Gram-negative bacterium, directly internalizes alginate macromolecules through a mouth-like pit that is present on its cell surface. The alginate-binding protein Algp7, which was found to be localized on the cell surface, contributes to the accumulation of alginate in the pit. Algp7 was crystallized at 293 K by means of the sitting-drop vapour-diffusion method with polyethylene glycol 3350 as a crystallizing agent. Preliminary X-ray analysis showed that the Algp7 crystal belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 50.1, b = 98.0, c = 100.1 A, and that it diffracted to 2.8 A resolution.
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Hashimoto W, Ochiai A, Momma K, Itoh T, Mikami B, Maruyama Y, Murata K. Crystal structure of the glycosidase family 73 peptidoglycan hydrolase FlgJ. Biochem Biophys Res Commun 2009; 381:16-21. [PMID: 19351587 DOI: 10.1016/j.bbrc.2009.01.186] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Accepted: 01/27/2009] [Indexed: 10/21/2022]
Abstract
Glycoside hydrolase (GH) categorized into family 73 plays an important role in degrading bacterial cell wall peptidoglycan. The flagellar protein FlgJ contains N- and C-terminal domains responsible for flagellar rod assembly and peptidoglycan hydrolysis, respectively. A member of family GH-73, the C-terminal domain (SPH1045-C) of FlgJ from Sphingomonas sp. strain A1 was expressed in Escherichia coli, purified, and characterized. SPH1045-C exhibited bacterial cell lytic activity most efficiently at pH 6.0 and 37 degrees C. The X-ray crystallographic structure of SPH1045-C was determined at 1.74 A resolution by single-wavelength anomalous diffraction. The enzyme consists of two lobes, alpha and beta. A deep cleft located between the two lobes can accommodate polymer molecules, suggesting that the active site is located in the cleft. Although SPH1045-C shows a structural homology with family GH-22 and GH-23 lysozymes, the arrangement of the nucleophile/base residue in the active site is specific to each peptidoglycan hydrolase.
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Affiliation(s)
- Wataru Hashimoto
- Laboratory of Basic and Applied Molecular Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
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Structure, function, and evolution of bacterial ATP-binding cassette systems. Microbiol Mol Biol Rev 2008; 72:317-64, table of contents. [PMID: 18535149 DOI: 10.1128/mmbr.00031-07] [Citation(s) in RCA: 938] [Impact Index Per Article: 58.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
SUMMARY ATP-binding cassette (ABC) systems are universally distributed among living organisms and function in many different aspects of bacterial physiology. ABC transporters are best known for their role in the import of essential nutrients and the export of toxic molecules, but they can also mediate the transport of many other physiological substrates. In a classical transport reaction, two highly conserved ATP-binding domains or subunits couple the binding/hydrolysis of ATP to the translocation of particular substrates across the membrane, through interactions with membrane-spanning domains of the transporter. Variations on this basic theme involve soluble ABC ATP-binding proteins that couple ATP hydrolysis to nontransport processes, such as DNA repair and gene expression regulation. Insights into the structure, function, and mechanism of action of bacterial ABC proteins are reported, based on phylogenetic comparisons as well as classic biochemical and genetic approaches. The availability of an increasing number of high-resolution structures has provided a valuable framework for interpretation of recent studies, and realistic models have been proposed to explain how these fascinating molecular machines use complex dynamic processes to fulfill their numerous biological functions. These advances are also important for elucidating the mechanism of action of eukaryotic ABC proteins, because functional defects in many of them are responsible for severe human inherited diseases.
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Blanvillain S, Meyer D, Boulanger A, Lautier M, Guynet C, Denancé N, Vasse J, Lauber E, Arlat M. Plant carbohydrate scavenging through tonB-dependent receptors: a feature shared by phytopathogenic and aquatic bacteria. PLoS One 2007; 2:e224. [PMID: 17311090 PMCID: PMC1790865 DOI: 10.1371/journal.pone.0000224] [Citation(s) in RCA: 243] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2006] [Accepted: 01/26/2007] [Indexed: 01/12/2023] Open
Abstract
TonB-dependent receptors (TBDRs) are outer membrane proteins mainly known for the active transport of iron siderophore complexes in Gram-negative bacteria. Analysis of the genome of the phytopathogenic bacterium Xanthomonas campestris pv. campestris (Xcc), predicts 72 TBDRs. Such an overrepresentation is common in Xanthomonas species but is limited to only a small number of bacteria. Here, we show that one Xcc TBDR transports sucrose with a very high affinity, suggesting that it might be a sucrose scavenger. This TBDR acts with an inner membrane transporter, an amylosucrase and a regulator to utilize sucrose, thus defining a new type of carbohydrate utilization locus, named CUT locus, involving a TBDR for the transport of substrate across the outer membrane. This sucrose CUT locus is required for full pathogenicity on Arabidopsis, showing its importance for the adaptation to host plants. A systematic analysis of Xcc TBDR genes and a genome context survey suggested that several Xcc TBDRs belong to other CUT loci involved in the utilization of various plant carbohydrates. Interestingly, several Xcc TBDRs and CUT loci are conserved in aquatic bacteria such as Caulobacter crescentus, Colwellia psychrerythraea, Saccharophagus degradans, Shewanella spp., Sphingomonas spp. or Pseudoalteromonas spp., which share the ability to degrade a wide variety of complex carbohydrates and display TBDR overrepresentation. We therefore propose that TBDR overrepresentation and the presence of CUT loci designate the ability to scavenge carbohydrates. Thus CUT loci, which seem to participate to the adaptation of phytopathogenic bacteria to their host plants, might also play a very important role in the biogeochemical cycling of plant-derived nutrients in marine environments. Moreover, the TBDRs and CUT loci identified in this study are clearly different from those characterized in the human gut symbiont Bacteroides thetaiotaomicron, which allow glycan foraging, suggesting a convergent evolution of TBDRs in Proteobacteria and Bacteroidetes.
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Affiliation(s)
- Servane Blanvillain
- Laboratoire des Interactions Plantes-Microorganismes, Centre National de la Recherche Scientifique (CNRS)/Institut National de la Recherche Agronomique (INRA) UMR2594/441, Castanet-Tolosan, France
| | - Damien Meyer
- Laboratoire des Interactions Plantes-Microorganismes, Centre National de la Recherche Scientifique (CNRS)/Institut National de la Recherche Agronomique (INRA) UMR2594/441, Castanet-Tolosan, France
| | - Alice Boulanger
- Laboratoire des Interactions Plantes-Microorganismes, Centre National de la Recherche Scientifique (CNRS)/Institut National de la Recherche Agronomique (INRA) UMR2594/441, Castanet-Tolosan, France
| | - Martine Lautier
- Laboratoire des Interactions Plantes-Microorganismes, Centre National de la Recherche Scientifique (CNRS)/Institut National de la Recherche Agronomique (INRA) UMR2594/441, Castanet-Tolosan, France
- Université Paul Sabatier, Toulouse III, Toulouse, France
| | - Catherine Guynet
- Laboratoire des Interactions Plantes-Microorganismes, Centre National de la Recherche Scientifique (CNRS)/Institut National de la Recherche Agronomique (INRA) UMR2594/441, Castanet-Tolosan, France
| | - Nicolas Denancé
- Laboratoire des Interactions Plantes-Microorganismes, Centre National de la Recherche Scientifique (CNRS)/Institut National de la Recherche Agronomique (INRA) UMR2594/441, Castanet-Tolosan, France
| | - Jacques Vasse
- Laboratoire des Interactions Plantes-Microorganismes, Centre National de la Recherche Scientifique (CNRS)/Institut National de la Recherche Agronomique (INRA) UMR2594/441, Castanet-Tolosan, France
| | - Emmanuelle Lauber
- Laboratoire des Interactions Plantes-Microorganismes, Centre National de la Recherche Scientifique (CNRS)/Institut National de la Recherche Agronomique (INRA) UMR2594/441, Castanet-Tolosan, France
- * To whom correspondence should be addressed. E-mail: (EL); (MA)
| | - Matthieu Arlat
- Laboratoire des Interactions Plantes-Microorganismes, Centre National de la Recherche Scientifique (CNRS)/Institut National de la Recherche Agronomique (INRA) UMR2594/441, Castanet-Tolosan, France
- Université Paul Sabatier, Toulouse III, Toulouse, France
- * To whom correspondence should be addressed. E-mail: (EL); (MA)
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Tani A, Charoenpanich J, Mori T, Takeichi M, Kimbara K, Kawai F. Structure and conservation of a polyethylene glycol-degradative operon in sphingomonads. Microbiology (Reading) 2007; 153:338-346. [PMID: 17259605 DOI: 10.1099/mic.0.2006/000992-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sphingopyxis terrae, and Sphingopyxis macrogoltabida strains 103 and 203, can degrade polyethylene glycols (PEGs). They differ in the following respects: (i) different substrate specificities (chain length) of assimilable PEG, (ii) PEG-inducible or constitutive PEG-degradative proteins, and (iii) symbiotic or axenic degradation of PEG. S. terrae was able to incorporate PEG 6000, but strain 103 could not incorporate more than PEG 4000, suggesting that the difference in assimilable PEG chain length depends on the ability to take up substrate. PEG-degradative genes (pegB, C, D, A, E and R) from these strains were cloned. Their primary structures shared a high homology of more than 99 %. The peg genes encode a TonB-dependent receptor (pegB), a PEG-aldehyde dehydrogenase (pegC), a permease (pegD), a PEG dehydrogenase (pegA) and an acyl-CoA ligase (pegE), and in the opposite orientation, an AraC-type transcription regulator (pegR). The peg operon was flanked by two different sets of transposases. These three strains contained large plasmids and the operon was located in one of the large plasmids in S. terrae. The peg genes could be detected in other PEG-degrading sphingomonads. These results suggest that the peg genes have evolved in a plasmid-mediated manner. An insertion of a transposon gene (pegF) between pegD and pegA in strain 203 was found, which caused the constitutive expression of pegA in this strain.
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Affiliation(s)
- Akio Tani
- Institute for Bioresources, Okayama University, 2-20-1 Chuo, Kurashiki 710-0046, Okayama, Japan
| | - Jittima Charoenpanich
- Institute for Bioresources, Okayama University, 2-20-1 Chuo, Kurashiki 710-0046, Okayama, Japan
| | - Terumi Mori
- Institute for Bioresources, Okayama University, 2-20-1 Chuo, Kurashiki 710-0046, Okayama, Japan
| | - Mayuko Takeichi
- Institute for Bioresources, Okayama University, 2-20-1 Chuo, Kurashiki 710-0046, Okayama, Japan
| | - Kazuhide Kimbara
- Institute for Bioresources, Okayama University, 2-20-1 Chuo, Kurashiki 710-0046, Okayama, Japan
| | - Fusako Kawai
- Institute for Bioresources, Okayama University, 2-20-1 Chuo, Kurashiki 710-0046, Okayama, Japan
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Ochiai A, Hashimoto W, Murata K. A biosystem for alginate metabolism in Agrobacterium tumefaciens strain C58: molecular identification of Atu3025 as an exotype family PL-15 alginate lyase. Res Microbiol 2006; 157:642-9. [PMID: 16545947 DOI: 10.1016/j.resmic.2006.02.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2005] [Revised: 02/01/2006] [Accepted: 02/09/2006] [Indexed: 11/30/2022]
Abstract
The Gram-negative bacterium Sphingomonas sp. strain A1 (strain A1) has a peculiar biosystem to directly import and depolymerize a macromolecule, alginate, which is encoded by a cluster of genes on the genome. We identified five clustered ORFs homologous to some genes of the strain A1 cluster in the genome of Agrobacterium tumefaciens strain C58 (strain C58). These ORFs are Atu3021, Atu3022, Atu3023, and Atu3024, encoding a putative sugar ABC transporter system and Atu3025, which encodes a putative alginate lyase. We analyzed the involvement of this gene cluster in alginate metabolism. Strain C58 cells grew significantly on low-molecular-weight (LMW) alginate (average molecular weight, 1000), and we detected specific alginate-induced expression of Atu3024 and Atu3025. This strain does not grow on alginate (average molecular weight, 25,600), suggesting that the strain C58 gene cluster is involved in importing and degrading LMW alginate. One protein, Atu3025, purified from strain C58, was identified as an alginate lyase, and the enzyme overexpressed in Escherichia coli was further characterized. Atu3025 released monosaccharides specifically from alginate most efficiently at pH 7.3 and 30 degrees C through a beta-elimination reaction, indicating that Atu3025 is an exotype alginate lyase potentially involved in the assimilation of LMW alginate in strain C58.
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Affiliation(s)
- Akihito Ochiai
- Laboratory of Basic and Applied Molecular Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
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Aso Y, Miyamoto Y, Harada KM, Momma K, Kawai S, Hashimoto W, Mikami B, Murata K. Engineered membrane superchannel improves bioremediation potential of dioxin-degrading bacteria. Nat Biotechnol 2006; 24:188-9. [PMID: 16415854 DOI: 10.1038/nbt1181] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2005] [Accepted: 11/21/2005] [Indexed: 11/10/2022]
Abstract
Sphingomonas sp. A1 possesses specialized membrane structures termed 'superchannels' that enable the direct incorporation of macromolecules into the cell. We have engineered two related sphingomonads, the dioxin-degrading S. wittichii RW1 and the polypropylene glycol-degrading S. subarctica IFO 16058(T), to incorporate this superchannel into their cell membranes. In both cases the bioremediation capability of the organisms was substantially increased pointing at the potential of this approach as a general strategy to improve bacterial degradation of hazardous compounds in the environment.
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Affiliation(s)
- Yuji Aso
- Laboratory of Basic and Applied Molecular Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
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Abstract
We identified 1113 articles (103 reviews, 1010 primary research articles) published in 2005 that describe experiments performed using commercially available optical biosensors. While this number of publications is impressive, we find that the quality of the biosensor work in these articles is often pretty poor. It is a little disappointing that there appears to be only a small set of researchers who know how to properly perform, analyze, and present biosensor data. To help focus the field, we spotlight work published by 10 research groups that exemplify the quality of data one should expect to see from a biosensor experiment. Also, in an effort to raise awareness of the common problems in the biosensor field, we provide side-by-side examples of good and bad data sets from the 2005 literature.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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