1
|
Heine V, Meinert-Berning C, Lück J, Mikowsky N, Voigt B, Riedel K, Steinbüchel A. The catabolism of 3,3'-thiodipropionic acid in Variovorax paradoxus strain TBEA6: A proteomic analysis. PLoS One 2019; 14:e0211876. [PMID: 30742653 PMCID: PMC6370202 DOI: 10.1371/journal.pone.0211876] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/23/2019] [Indexed: 01/11/2023] Open
Abstract
Variovorax paradoxus strain TBEA6 is one of the few organisms known to utilize 3,3'-thiodipropionate (TDP) as the only source of carbon and energy. It cleaves TDP to 3-mercaptopropionate (3MP), which is a direct precursor for polythioester synthesis. To establish this process in V. paradoxus TBEA6, it is crucial to unravel its TDP metabolism. Therefore, a proteomic approach with subsequent deletion of interesting genes in the bacterium was chosen. Cells were cultivated with D-gluconate, TDP or 3-sulfinopropionate as the only carbon sources. Proteins with high abundances in gels of cells cultivated with either of the organic sulfur compounds were analyzed further. Thereby, we did not only confirm parts of the already postulated TDP metabolism, but also eight new protein candidates for TDP degradation were detected. Deletions of the corresponding genes (two enoyl-CoA hydratases (Ech-20 and Ech-30), an FK506-binding protein, a putative acetolactate synthase, a carnitinyl-CoA dehydratase, and a putative crotonase family protein) were obtained. Only the deletions of both Ech-20 and Ech-30 led to a TDP negative phenotype. The deletion mutant of VPARA_05510, which encodes the putative crotonase family protein showed reduced growth with TDP. The three genes are located in one cluster with genes proven to be involved in TDP metabolism. Thermal shift assays showed an increased stability of Ech-20 with TDP-CoA but not with TDP. These results indicate that Ech-20 uses TDP-CoA as a substrate instead of TDP. Hence, we postulate a new putative pathway for TDP metabolism. Ech-30 interacts with neither TDP-CoA nor TDP but might interact with other CoA-activated intermediates of the proposed pathway. Further enzyme characterization is necessary to unravel the complete pathway from TDP to 3MP.
Collapse
Affiliation(s)
- Viktoria Heine
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany
| | - Christina Meinert-Berning
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany
| | - Janina Lück
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany
| | - Nadine Mikowsky
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany
| | - Birgit Voigt
- Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, Greifswald, Germany
| | - Katharina Riedel
- Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, Greifswald, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany
- Environmental Science Department, King Abdulaziz University, Jeddah, Saudi Arabia
| |
Collapse
|
2
|
Cao HY, Wang P, Xu F, Li PY, Xie BB, Qin QL, Zhang YZ, Li CY, Chen XL. Molecular Insight into the Acryloyl-CoA Hydration by AcuH for Acrylate Detoxification in Dimethylsulfoniopropionate-Catabolizing Bacteria. Front Microbiol 2017; 8:2034. [PMID: 29089943 PMCID: PMC5651017 DOI: 10.3389/fmicb.2017.02034] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 10/05/2017] [Indexed: 11/13/2022] Open
Abstract
Microbial cleavage of dimethylsulfoniopropionate (DMSP) producing dimethyl sulfide (DMS) and acrylate is an important step in global sulfur cycling. Acrylate is toxic for cells, and thus should be metabolized effectively for detoxification. There are two proposed pathways for acrylate metabolism in DMSP-catabolizing bacteria, the AcuN-AcuK pathway and the PrpE-AcuI pathway. AcuH is an acryloyl-CoA hydratase in DMSP-catabolizing bacteria and can catalyze the hydration of toxic acryloyl-CoA to produce 3-hydroxypropionyl-CoA (3-HP-CoA) in both the AcuN-AcuK pathway and the side path of the PrpE-AcuI pathway. However, the structure and catalytic mechanism of AcuH remain unknown. Here, we cloned a putative acuH gene from Roseovarius nubinhibens ISM, a typical DMSP-catabolizing bacterium, and expressed it (RdAcuH) in Escherichia coli. The activity of RdAcuH toward acryloyl-CoA was detected by liquid chromatography-mass spectrometry (LC-MS), which suggests that RdAcuH is a functional acryloyl-CoA hydratase. Then we solved the crystal structure of RdAcuH. Each asymmetric unit in the crystal of RdAcuH contains a dimer of trimers and each RdAcuH monomer contains an N-terminal domain (NTD) and a C-terminal domain (CTD). There are three active centers in each trimer and each active center is located between the NTD of a subunit and the CTD of the neighboring subunit. Site-directed mutagenesis analysis indicates that two highly conserved glutamates, Glu112 and Glu132, in the active center are essential for catalysis. Based on our results and previous research, we analyzed the catalytic mechanism of AcuH to hydrate acryloyl-CoA, in which Glu132 acts as the catalytic base. This study sheds light on the mechanism of acrylate detoxification in DMSP-catabolizing bacteria.
Collapse
Affiliation(s)
- Hai-Yan Cao
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, China
| | - Peng Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, China
| | - Fei Xu
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, China
| | - Ping-Yi Li
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, China
| | - Bin-Bin Xie
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, China
| | - Qi-Long Qin
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Chun-Yang Li
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, China
| |
Collapse
|
3
|
Putting bioactivation reactions to work: Targeting antioxidants to mitochondria. Chem Biol Interact 2011; 192:8-13. [DOI: 10.1016/j.cbi.2010.10.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Revised: 10/08/2010] [Accepted: 10/14/2010] [Indexed: 01/01/2023]
|
4
|
Abstract
Acyl-CoA dehydrogenases constitute a family of flavoproteins that catalyze the alpha,beta-dehydrogenation of fatty acid acyl-CoA conjugates. While they differ widely in their specificity, they share the same basic chemical mechanism of alpha,beta-dehydrogenation. Medium chain acyl-CoA dehydrogenase is probably the best-studied member of the class and serves as a model for the study of catalytic mechanisms. Based on medium chain acyl-CoA dehydrogenase we discuss the main factors that bring about catalysis, promote specificity and determine the selective transfer of electrons to electron transferring flavoprotein. The mechanism of alpha,beta-dehydrogenation is viewed as a process in which the substrate alphaC-H and betaC-H bonds are ruptured concertedly, the first hydrogen being removed by the active center base Glu376-COO- as an H+, the second being transferred as a hydride to the flavin N(5) position. Hereby the pKa of the substrate alphaC-H is lowered from > 20 to approximately 8 by the effect of specific hydrogen bonds. Concomitantly, the pKa of Glu376-COO- is also raised to 8-9 due to the decrease in polarity brought about by substrate binding. The kinetic sequence of medium chain acyl-CoA dehydrogenase is rather complex and involves several intermediates. A prominent one is the molecular complex of reduced enzyme with the enoyl-CoA product that is characterized by an intense charge transfer absorption and serves as the point of transfer of electrons to the electron transferring flavoprotein. These views are also discussed in the context of the accompanying paper on the three-dimensional properties of acyl-CoA dehydrogenases.
Collapse
Affiliation(s)
- Sandro Ghisla
- Department of Biology, University of Konstanz, Germany.
| | | |
Collapse
|
5
|
Abstract
Enoyl-CoA hydratase (ECH) catalyzes the second step in the physiologically important beta-oxidation pathway of fatty acid metabolism. This enzyme facilitates the syn-addition of a water molecule across the double bond of a trans-2-enoyl-CoA thioester, resulting in the formation of a beta-hydroxyacyl-CoA thioester. The catalytic mechanism of this proficient enzyme has been studied in great depth through a combination of kinetic, spectroscopic, and structural techniques, and is proposed to occur via the formation of a single transition state. Sequence alignment and mutagenesis studies have implicated the key residues important for catalysis: Gly-141, Glu-144, and Glu-164 (rat liver ECH numbering). The two catalytic glutamic acid residues are believed to act in concert to activate a water molecule, while Gly-141 is proposed to be involved in substrate activation. Recently, two potent inhibitors of ECH have been reported in the literature, which result in the irreversible inactivation of the enzyme via covalent adduct formation. This review summarizes studies on the structure, mechanism, and inhibition of ECH.
Collapse
Affiliation(s)
- Gautam Agnihotri
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas, Austin 78712, USA
| | | |
Collapse
|
6
|
Mursula AM, van Aalten DM, Hiltunen JK, Wierenga RK. The crystal structure of delta(3)-delta(2)-enoyl-CoA isomerase. J Mol Biol 2001; 309:845-53. [PMID: 11399063 DOI: 10.1006/jmbi.2001.4671] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The active-site geometry of the first crystal structure of a Delta(3)-Delta(2)-enoyl-coenzyme A (CoA) isomerase (the peroxisomal enzyme from the yeast Saccharomyces cerevisiae) shows that only one catalytic base, Glu158, is involved in shuttling the proton from the C2 carbon atom of the substrate, Delta(3)-enoyl-CoA, to the C4 atom of the product, Delta(2)-enoyl-CoA. Site-directed mutagenesis has been performed to confirm that this glutamate residue is essential for catalysis. This Delta(3)-Delta(2)-enoyl-CoA isomerase is a hexameric enzyme, consisting of six identical subunits. It belongs to the hydratase/isomerase superfamily of enzymes which catalyze a wide range of CoA-dependent reactions. The members of the hydratase/ isomerase superfamily have only a low level of sequence identity. Comparison of the crystal structure of the Delta(3)-Delta(2)-enoyl-CoA isomerase with the other structures of this superfamily shows only one region of large structural variability, which is in the second turn of the spiral fold and which is involved in defining the shape of the binding pocket.
Collapse
Affiliation(s)
- A M Mursula
- Biocenter Oulu and Department of Biochemistry, University of Oulu, FIN-90014, Finland
| | | | | | | |
Collapse
|