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Wang ZJ, Chen F, Xu YQ, Huang P, Liu SS. Protein Model and Function Analysis in Quorum-Sensing Pathway of Vibrio qinghaiensis sp.-Q67. BIOLOGY 2021; 10:638. [PMID: 34356493 PMCID: PMC8301110 DOI: 10.3390/biology10070638] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 07/03/2021] [Accepted: 07/05/2021] [Indexed: 01/08/2023]
Abstract
Bioluminescent bacteria are mainly found in marine habitats. Vibrio qinghaiensis sp.-Q67 (Q67), a nonpathogenic freshwater bacterium, has been a focus due to its wide use in the monitoring of environmental pollution and the assessment of toxicity. However, the lack of available crystal structures limits the elucidation of the structures of the functional proteins of the quorum-sensing (QS) system that regulates bacterial luminescence in Q67. In this study, 19 functional proteins were built through monomer and oligomer modeling based on their coding proteins in the QS system of Q67 using MODELLER. Except for the failure to construct LuxM due to the lack of a suitable template, 18 functional proteins were successfully constructed. Furthermore, the relationships between the function and predicted structures of 19 functional proteins were explored one by one according to the three functional classifications: autoinducer synthases and receptors, signal transmission proteins (phosphotransferases, an RNA chaperone, and a transcriptional regulator), and enzymes involved in bacterial bioluminescence reactions. This is the first analysis of the whole process of bioluminescence regulation from the perspective of nonpathogenic freshwater bacteria at the molecular level. It provides a theoretical basis for the explanation of applications of Q67 in which luminescent inhibition is used as the endpoint.
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Affiliation(s)
- Ze-Jun Wang
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; (Z.-J.W.); (Y.-Q.X.)
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China;
| | - Fu Chen
- Department of Environmental Engineering, School of Environmental and Geographical Science, Shanghai Normal University, Shanghai 200234, China;
| | - Ya-Qian Xu
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; (Z.-J.W.); (Y.-Q.X.)
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Peng Huang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China;
- Department of Environmental Engineering, School of Environmental and Geographical Science, Shanghai Normal University, Shanghai 200234, China;
| | - Shu-Shen Liu
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; (Z.-J.W.); (Y.-Q.X.)
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China;
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
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Fan L, Huang Y, Huang T, Zhao K, Zhang YN, Li C, Zhao YH. Photolysis and photo-induced toxicity of pyraclostrobin to Vibrio fischeri: Pathway and toxic mechanism. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2020; 220:105417. [PMID: 31958710 DOI: 10.1016/j.aquatox.2020.105417] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 12/16/2019] [Accepted: 01/12/2020] [Indexed: 06/10/2023]
Abstract
Pyraclostrobin is a fungicide used widely across the world. However, its photolysis pathway and toxic mechanism is unclear. In this study, photolysis and photo-induced toxicity of pyraclostrobin to Vibrio fischeri were determined. The results showed that direct photolysis dominated the degradation of pyraclostrobin. Gas Chromatography-Mass spectrometry and quantum chemical calculation revealed that the pyraclostrobin was firstly photo-degraded into Methyl N-phenyl-carbamate and 1-(4-chlorophenyl)-3-hydroxy-1H-pyrzole, synthetic intermediates of pyraclostrobin, then into aniline, benzoquinone and acids. Toxicity assay showed that bioluminescent inhibition rate to V. fischeri fluctuated with radiation/illumination time and the toxicity curve can be classified into three phases (Phase I: 0-10 min, incline; Phase II: 10-60 min, decline; Phase III: 60-120 min, incline). The up-and-down curve indicates the change of parent compound during the photolysis. Simulation of molecular docking showed that the CDOCKER interaction energy of pyraclostrobin (-44.71) lower than other intermediate products (>-30.00), indicating that the parent compound is more toxic than its intermediates. An increased toxicity observed in the toxicity curve was attributed to the generation of benzoquinone with log1/EC50 of 6.73, which can greatly change structure of target luciferase in Vibrio fischeri. In addition, the addition of radical scavengers can inhibit the bioluminescence of the tested solutions, indicating the involvement of radicals in the transformation of intermediates. This paper reveals that one of photochemical transformation products of pyraclostrobin can cause more toxic than its parent compound to bacteria. Environmental risk assessment should consider not only the parent compound, but also its metabolites.
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Affiliation(s)
- Lingyun Fan
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Changchun 130117, China
| | - Ying Huang
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Changchun 130117, China
| | - Tao Huang
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Changchun 130117, China
| | - Kun Zhao
- Key Laboratory of Industrial Ecology and Environmental Engineering, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Ya-Nan Zhang
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Changchun 130117, China
| | - Chao Li
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Changchun 130117, China
| | - Yuan Hui Zhao
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Changchun 130117, China.
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Campbell ZT, Weichsel A, Montfort WR, Baldwin TO. Crystal structure of the bacterial luciferase/flavin complex provides insight into the function of the beta subunit. Biochemistry 2009; 48:6085-94. [PMID: 19435287 PMCID: PMC6481928 DOI: 10.1021/bi900003t] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacterial luciferase from Vibrio harveyi is a heterodimer composed of a catalytic alpha subunit and a homologous but noncatalytic beta subunit. Despite decades of enzymological investigation, structural evidence defining the active center has been elusive. We report here the crystal structure of V. harveyi luciferase bound to flavin mononucleotide (FMN) at 2.3 A. The isoalloxazine ring is coordinated by an unusual cis-Ala-Ala peptide bond. The reactive sulfhydryl group of Cys106 projects toward position C-4a, the site of flavin oxygenation. This structure also provides the first data specifying the conformations of a mobile loop that is crystallographically disordered in both prior crystal structures [(1995) Biochemistry 34, 6581-6586; (1996) J. Biol. Chem. 271, 21956 21968]. This loop appears to be a boundary between solvent and the active center. Within this portion of the protein, a single contact was observed between Phe272 of the alpha subunit, not seen in the previous structures, and Tyr151 of the beta subunit. Substitutions at position 151 on the beta subunit caused reductions in activity and total quantum yield. Several of these mutants were found to have decreased affinity for reduced flavin mononucleotide (FMNH(2)). These findings partially address the long-standing question of how the beta subunit stabilizes the active conformation of the alpha subunit, thereby participating in the catalytic mechanism.
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Affiliation(s)
- Zachary T. Campbell
- Department of Biochemistry and Molecular Biophysics, University of Arizona, 1041 East Lowell Street, Biological Sciences West, Tucson, Arizona 85721-0088
| | - Andrzej Weichsel
- Department of Biochemistry and Molecular Biophysics, University of Arizona, 1041 East Lowell Street, Biological Sciences West, Tucson, Arizona 85721-0088
| | - William R. Montfort
- Department of Biochemistry and Molecular Biophysics, University of Arizona, 1041 East Lowell Street, Biological Sciences West, Tucson, Arizona 85721-0088
| | - Thomas O. Baldwin
- Department of Biochemistry and Molecular Biophysics, University of Arizona, 1041 East Lowell Street, Biological Sciences West, Tucson, Arizona 85721-0088
- Department of Biochemistry, University of California, Riverside, California 92521
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Isupov MN, Lebedev AA. NCS-constrained exhaustive search using oligomeric models. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2007; 64:90-8. [PMID: 18094472 PMCID: PMC2394828 DOI: 10.1107/s0907444907053802] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2007] [Accepted: 10/29/2007] [Indexed: 11/10/2022]
Abstract
The efficiency of the cross-rotation function step of molecular replacement (MR) is intrinsically limited as it uses only a fraction of the Patterson vectors. Along with general techniques extending the boundaries of the method, there are approaches that utilize specific features of a given structure. In special cases, where the directions of noncrystallographic symmetry axes can be unambiguously derived from the self-rotation function and the structure of the homologue protein is available in a related oligomeric state, the cross-rotation function step of MR can be omitted. In such cases, a small number of yet unknown parameters defining the orientation of the oligomer and/or its internal organization can be optimized using an exhaustive search. Three difficult MR cases are reported in which these parameters were determined and the oligomer was positioned according to the maximal value of the correlation coefficient in a series of translation searches.
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Affiliation(s)
- Michail N Isupov
- Henry Wellcome Building for Biocatalysis, School of Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England.
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Hamelryck T. Efficient identification of side-chain patterns using a multidimensional index tree. Proteins 2003; 51:96-108. [PMID: 12596267 DOI: 10.1002/prot.10338] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Convergent evolution often produces similar functional sites in nonhomologous proteins. The identification of these sites can make it possible to infer function from structure, to pinpoint the location of a functional site, to identify enzymes with similar enzymatic mechanisms, or to discover putative functional sites. In this article, a novel method is presented that (a) queries a database of protein structures for the occurrence of a given side chain pattern and (b) identifies interesting side-chain patterns in a given structure. For efficiency and to make a robust statistical evaluation of the significance of a similarity possible, patterns of three residues (or triads) are considered. Each triad is encoded as a high-dimensional vector and stored in an SR (Sphere/Rectangle) tree, an efficient multidimensional index tree. Identifying similar triads can then be reformulated as identifying neighboring vectors. The method deals with many features that otherwise complicate the identification of meaningful patterns: shifted backbone positions, conservative substitutions, various atom label ambiguities and mirror imaged geometries. The combined treatment of these features leads to the identification of previously unidentified patterns. In particular, the identification of mirror imaged side-chain patterns is unique to the here-described method. Interesting triads in a given structure can be identified by extracting all triads and comparing them with a database of triads involved in ligand binding. The approach was tested by an all-against-all comparison of unique representatives of all SCOP superfamilies. New findings include mirror imaged metal binding and active sites, and a putative active site in bacterial luciferase.
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Affiliation(s)
- Thomas Hamelryck
- ULTR Department, Vrije Universiteit Brussel (VUB), Vlaams Interuniversitair Instituut voor Biotechnologie (VIB), Brussel, Belgium.
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Wei CJ, Lei B, Tu SC. Characterization of the binding of Photobacterium phosphoreum P-flavin by Vibrio harveyi Luciferase. Arch Biochem Biophys 2001; 396:199-206. [PMID: 11747297 DOI: 10.1006/abbi.2001.2612] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The isolated Photobacterium phosphoreum luciferase is associated with a bound flavin designated P-flavin and tentatively identified as 6-(3"-myristic acid)-FMN. Since FMN and myristic acid are products of the normal luciferase reaction, we explored the possibility that P-flavin can also be bound by luciferase from other luminous bacteria and serve as an active site probe. P-flavin has never been detected in Vibrio harveyi cells. We found that the V. harveyi luciferase binds P. phosphoreum P-flavin, at a ratio of 1 P-flavin per luciferase alphabeta dimer, and with concomitant absorption spectral perturbation of P-flavin, fluorescence quenching of P-flavin and luciferase, and activity inhibition of luciferase. Isolated P-flavin can be fully reduced photochemically. V. harveyi luciferase bound the oxidized P-flavin with a K(d) (or K(i) competitively against decanal) of 0.1-0.16 microM, which is three orders of magnitude lower than the K(d) for FMN binding but similar to that of reduced FMN binding. The reduced P-flavin exhibited a K(i) (competitively against the reduced FMN substrate) of 0.16 microM, also similar to the K(d) for reduced FMN. Hence, the covalent attachment of myristic acid to FMN greatly and preferentially enhanced the binding of oxidized P-flavin. The dissociation of P-flavin was slow in comparison with the binding of reduced FMN and decanal substrates. Modification of the alphaCys106 near the active site by N-ethylmaleimide can be retarded by P-flavin. These findings indicate that P-flavin is potentially a superb active site probe for luciferase. We hypothesize that P-flavin is a by-product of luciferase generated by a side reaction which is trivial with the V. harveyi luciferase but significant in the P. phosphoreum luciferase-catalyzed reaction.
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Affiliation(s)
- C J Wei
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204-5001, USA
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Abstract
Although mechanisms of metabolite channeling have been extensively studied, the nature of reduced flavin transfer from donor to acceptor enzymes remains essentially unexplored. In this review, identities and properties of reduced flavin-producing enzymes (namely flavin reductases) and reduced flavin-requiring processes and enzymes are summarized. By using flavin reductase-luciferase enzyme couples from luminous bacteria, two types of reduced flavin channeling were observed involving the differential transfers of the reduced flavin cofactor and the reduced flavin product of reductase to luciferase. The exact mode of transfer is controlled by the specific makeup of the constituent enzymes within the reductase-luciferase couple. The plausible physiological significance of the monomer-dimer equilibrium of the NADPH-specific flavin reductase from Vibrio harveyi is also discussed.
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Affiliation(s)
- S C Tu
- Department of Biology and Biochemistry, University of Houston, TX 77204-5513, USA.
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Metzler DE, Metzler CM, Sauke DJ. Light and Life. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50026-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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