1
|
The two-step electrochemical oxidation of alcohols using a novel recombinant PQQ alcohol dehydrogenase as a catalyst for a bioanode. Bioelectrochemistry 2013; 94:75-8. [DOI: 10.1016/j.bioelechem.2013.08.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 08/05/2013] [Accepted: 08/11/2013] [Indexed: 11/23/2022]
|
2
|
Arif MI, Samin G, van Leeuwen JGE, Oppentocht J, Janssen DB. Novel dehalogenase mechanism for 2,3-dichloro-1-propanol utilization in Pseudomonas putida strain MC4. Appl Environ Microbiol 2012; 78:6128-36. [PMID: 22752160 PMCID: PMC3416625 DOI: 10.1128/aem.00760-12] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 06/14/2012] [Indexed: 11/20/2022] Open
Abstract
A Pseudomonas putida strain (MC4) that can utilize 2,3-dichloro-1-propanol (DCP) and several aliphatic haloacids and haloalcohols as sole carbon and energy source for growth was isolated from contaminated soil. Degradation of DCP was found to start with oxidation and concomitant dehalogenation catalyzed by a 72-kDa monomeric protein (DppA) that was isolated from cell lysate. The dppA gene was cloned from a cosmid library and appeared to encode a protein equipped with a signal peptide and that possessed high similarity to quinohemoprotein alcohol dehydrogenases (ADHs), particularly ADH IIB and ADH IIG from Pseudomonas putida HK. This novel dehalogenating dehydrogenase has a broad substrate range, encompassing a number of nonhalogenated alcohols and haloalcohols. With DCP, DppA exhibited a k(cat) of 17 s(-1). (1)H nuclear magnetic resonance experiments indicated that DCP oxidation by DppA in the presence of 2,6-dichlorophenolindophenol (DCPIP) and potassium ferricyanide [K(3)Fe(CN)(6)] yielded 2-chloroacrolein, which was oxidized to 2-chloroacrylic acid.
Collapse
Affiliation(s)
- Muhammad Irfan Arif
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | | | | | | | | |
Collapse
|
3
|
Yu H, Peng Z, Zhan Y, Wang J, Yan Y, Chen M, Lu W, Ping S, Zhang W, Zhao Z, Li S, Takeo M, Lin M. Novel regulator MphX represses activation of phenol hydroxylase genes caused by a XylR/DmpR-type regulator MphR in Acinetobacter calcoaceticus. PLoS One 2011; 6:e17350. [PMID: 21455294 PMCID: PMC3063778 DOI: 10.1371/journal.pone.0017350] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Accepted: 01/31/2011] [Indexed: 11/18/2022] Open
Abstract
Acinetobacter calcoaceticus PHEA-2 utilizes phenol as its sole carbon and energy source and has a multi-component phenol hydroxylase-encoding gene operon (mphKLMNOP) for phenol degradation. Two additional genes, mphR and mphX, were found upstream and downstream of mphKLMNOP, respectively. The mphR gene encodes a XylR/DmpR-type regulator-like protein and is transcribed in the opposite direction to mphKLMNOP. The mphX gene is transcribed in the same direction as mphKLMNOP and encodes a protein with 293 amino acid residues showing weak identity with some unknown proteins encoded in the meta-cleavage pathway gene clusters for aromatic compound degradation. Disruption of mphR by homologous recombination resulted in the loss of phenol degradation while disruption of mphX caused significantly faster phenol degradation than in the wild type strain. Transcriptional assays for mphK, mphR, and mphX revealed that mphR activated mphKLMNOP transcription in the presence of phenol, but mphX partially repressed this activation. Gel mobility-shift assay demonstrated a direct interaction of MphR with the mphK promoter region. These results indicate the involvement of a novel repressor protein MphX in transcriptional regulation of phenol hydroxylase genes caused by a XylR/DmpR-type regulator MphR.
Collapse
Affiliation(s)
- Haiying Yu
- College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Crop Biotechnology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
| | - Zixin Peng
- Key Laboratory of Crop Biotechnology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Hyogo, Japan
| | - Yuhua Zhan
- Key Laboratory of Crop Biotechnology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
| | - Jin Wang
- Key Laboratory of Crop Biotechnology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
| | - Yongliang Yan
- Key Laboratory of Crop Biotechnology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
- National Centre for Plant Gene Research, Beijing, China
| | - Ming Chen
- Key Laboratory of Crop Biotechnology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
| | - Wei Lu
- Key Laboratory of Crop Biotechnology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
| | - Shuzhen Ping
- Key Laboratory of Crop Biotechnology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
| | - Wei Zhang
- Key Laboratory of Crop Biotechnology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
- National Centre for Plant Gene Research, Beijing, China
| | - Zhonglin Zhao
- Key Laboratory of Crop Biotechnology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
| | - Shuying Li
- Key Laboratory of Crop Biotechnology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
| | - Masahiro Takeo
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Hyogo, Japan
- * E-mail: (MT); (ML)
| | - Min Lin
- College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Crop Biotechnology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
- * E-mail: (MT); (ML)
| |
Collapse
|
4
|
Howden AJM, Rico A, Mentlak T, Miguet L, Preston GM. Pseudomonas syringae pv. syringae B728a hydrolyses indole-3-acetonitrile to the plant hormone indole-3-acetic acid. MOLECULAR PLANT PATHOLOGY 2009; 10:857-65. [PMID: 19849791 PMCID: PMC6640395 DOI: 10.1111/j.1364-3703.2009.00595.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Nitrilase enzymes catalyse the hydrolysis of nitrile compounds to the corresponding carboxylic acid and ammonia, and have been identified in plants, bacteria and fungi. There is mounting evidence to support a role for nitrilases in plant-microbe interactions, but the activity of these enzymes in plant pathogenic bacteria remains unexplored. The genomes of the plant pathogenic bacteria Pseudomonas syringae pv. syringae B728a and Pseudomonas syringae pv. tomato DC3000 contain nitrilase genes with high similarity to characterized bacterial arylacetonitrilases. In this study, we show that the nitrilase of P. syringae pv. syringae B728a is an arylacetonitrilase, which is capable of hydrolysing indole-3-acetonitrile to the plant hormone indole-3-acetic acid, and allows P. syringae pv. syringae B728a to use indole-3-acetonitrile as a nitrogen source. This enzyme may represent an additional mechanism for indole-3-acetic acid biosynthesis by P. syringae pv. syringae B728a, or may be used to degrade and assimilate aldoximes and nitriles produced during plant secondary metabolism. Nitrilase activity was not detected in P. syringae pv. tomato DC3000, despite the presence of a homologous nitrilase gene. This raises the interesting question of why nitrilase activity has been retained in P. syringae pv. syringae B728a and not in P. syringae pv. tomato DC3000.
Collapse
Affiliation(s)
- Andrew J M Howden
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | | | | | | | | |
Collapse
|
5
|
Promden W, Vangnai AS, Toyama H, Matsushita K, Pongsawasdi P. Analysis of the promoter activities of the genes encoding three quinoprotein alcohol dehydrogenases in Pseudomonas putida HK5. MICROBIOLOGY-SGM 2009; 155:594-603. [PMID: 19202108 DOI: 10.1099/mic.0.021956-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The transcriptional regulation of three distinct alcohol oxidation systems, alcohol dehydrogenase (ADH)-I, ADH-IIB and ADH-IIG, in Pseudomonas putida HK5 was investigated under various induction conditions. The promoter activities of the genes involved in alcohol oxidation were determined using a transcriptional lacZ fusion promoter-probe vector. Ethanol was the best inducer for the divergent promoters of qedA and qedC, encoding ADH-I and a cytochrome c, respectively. Primary and secondary C3 and C4 alcohols and butyraldehyde specifically induced the divergent promoters of qbdBA and aldA, encoding ADH-IIB and an NAD-dependent aldehyde dehydrogenase, respectively. The qgdA promoter of ADH-IIG responded well to (S)-(+)-1,2-propanediol induction. In addition, the roles of genes encoding the response regulators exaE and agmR, located downstream of qedA, were inferred from the properties of exaE- or agmR-disrupted mutants and gene complementation tests. The gene products of both exaE and agmR were strictly necessary for qedA transcription. The mutation and complementation studies also suggested a role for AgmR, but not ExaE, in the transcriptional regulation of qbdBA (ADH-IIB) and qgdA (AGH-IIG). A hypothetical scheme describing a regulatory network, which directs expression of the three distinct alcohol oxidation systems in P. putida HK5, was derived.
Collapse
Affiliation(s)
- Worrawat Promden
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Alisa S Vangnai
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Hirohide Toyama
- Department of Bioscience and Biotechnology, Faculty of Agriculture, University of the Ryukyus, Okinawa 903-0213, Japan
| | - Kazunobu Matsushita
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi 753-8515, Japan
| | - Piamsook Pongsawasdi
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| |
Collapse
|
6
|
Promden W, Vangnai AS, Pongsawasdi P, Adachi O, Matsushita K, Toyama H. Disruption of quinoprotein ethanol dehydrogenase gene and adjacent genes in Pseudomonas putida HK5. FEMS Microbiol Lett 2008; 280:203-9. [PMID: 18218017 DOI: 10.1111/j.1574-6968.2008.01060.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Pseudomonas putida HK5 produces three different quinoprotein alcohol dehydrogenases: ADH-I, ADH-IIB and ADH-IIG. Gene organization of qedA, the gene for ADH-I, and other 10 genes in the cluster was related to the genome sequences of five other Pseudomonas strains. Insertion mutations in either qedA, exaE or agmR eliminated ADH-I activity, although the mutants were still able to grow on ethanol but more slowly than the wild-type strain. Mutant analysis demonstrated the requirement of agmR and exaE in ADH-I expression, and the tentative involvement of agmR, but not exaE, in the induction of ADH-IIB and ADH-IIG activities.
Collapse
Affiliation(s)
- Worrawat Promden
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | | | | | | | | | | |
Collapse
|
7
|
Kato Y, Asano Y. Molecular and enzymatic analysis of the “aldoxime–nitrile pathway” in the glutaronitrile degrader Pseudomonas sp. K-9. Appl Microbiol Biotechnol 2006; 70:92-101. [PMID: 16003557 DOI: 10.1007/s00253-005-0044-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2005] [Revised: 04/29/2005] [Accepted: 05/30/2005] [Indexed: 12/01/2022]
Abstract
A gene cluster responsible for aldoxime metabolism in the glutaronitrile degrader Pseudomonas sp. K-9 was analyzed genetically and enzymatically. The cluster was composed of genes coding for aldoxime dehydratase (Oxd), nitrile hydratase (NHase), NHase activator, amidase, acyl-CoA ligase, and some regulatory and functionally unknown proteins, which were similar to proteins appearing in the "aldoxime-nitrile pathway" gene cluster from strains having Fe-containing NHase. A key enzyme in the cluster, OxdK, which has 32.7-90.3 % identity with known Oxds, was overexpressed in Escherichia coli cells under the control of a T7 promoter in its His(6)-tagged form, purified, and characterized. The enzyme showed similar characteristics with the known Oxds coexisting with an Fe-containing NHase in its subunit structure, substrate specificity, and effects on various compounds. The enzyme can be classified into a group of "aliphatic aldoxime dehydratase (EC 4.99.1.5)." The existence of a gene cluster of enzymes responsible for aldoxime metabolism via the aldoxime-nitrile pathway (aldoxime-->nitrile-->amide-->acid-->acyl-CoA) in Pseudomonas sp. K-9, and the fact that the proteins comprising the cluster are similar to those acting on aliphatic type substrates, evidently clarified the alkylaldoxime-degrading pathway in that strain.
Collapse
Affiliation(s)
- Yasuo Kato
- Biotechnology Research Center, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Kosugi, Toyama 939-0398, Japan
| | | |
Collapse
|
8
|
Toyama H, Chen ZW, Fukumoto M, Adachi O, Matsushita K, Mathews FS. Molecular Cloning and Structural Analysis of Quinohemoprotein Alcohol Dehydrogenase ADH-IIG from Pseudomonas putida HK5. J Mol Biol 2005; 352:91-104. [PMID: 16061256 DOI: 10.1016/j.jmb.2005.06.078] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2005] [Revised: 06/28/2005] [Accepted: 06/28/2005] [Indexed: 11/26/2022]
Abstract
Depending on the alcohols used as growth substrates, Pseudomonas putida HK5 produces two distinct quinohemoprotein alcohol dehydrogenases, ADH-IIB and ADH-IIG, both of which contain pyrroloquinoline quinone (PQQ) and heme c as the prosthetic groups but show different substrate specificities, especially for diol substrates. Molecular cloning of the gene of ADH-IIB and its crystal structure are already reported. Here, molecular cloning of the gene, qgdA, and solution of the three-dimensional structure of ADH-IIG are reported. The enzyme consists of 718 amino acid residues including a signal sequence of 29 amino acid residues. The PQQ domain is highly homologous to other quinoproteins, especially to quinohemoproteins. The crystal structure of ADH-IIG, determined at 2.2A resolution, shows that the overall structure and the amino acid residues involved in PQQ binding are quite similar to ADH-IIB and to another quinohemoprotein ADH, qhEDH from Comamonas testosteroni. However, the lengths of the linker regions connecting the PQQ and the cytochrome domains are different from each other, leading to a significant difference in orientation of the cytochrome domain with respect to the PQQ domain. Apart from ADH-IIB and qhEDH, ADH-IIG has an extra 12-residue helix within loop 3 in the PQQ domain and an extra 3(10) helix in the C terminus of the cytochrome domain, and both helices appear parallel and linked by a hydrogen bond. The amino acid residues contacting substrate/product in the crystal structures are also different among them. In the crystal structure of ADH-IIG with 1,2-propanediol, one of the hydroxyl groups of the substrate forms a hydrogen bond with O5 of PQQ and OD1 of Asp300, and the other interacts with a water molecule and with NE2 of Trp386, the corresponding residue of which is not found in ADH-IIB and qhEDH, and might be the residue responsible for making ADH-IIG prefer diol substrates.
Collapse
Affiliation(s)
- Hirohide Toyama
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi 753-8515, Japan.
| | | | | | | | | | | |
Collapse
|