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Kordesedehi R, Shahpiri A, Asadollahi MA, Biria D, Nikel PI. Enhanced chaotrope tolerance and (S)-2-hydroxypropiophenone production by recombinant Pseudomonas putida engineered with Pprl from Deinococcus radiodurans. Microb Biotechnol 2024; 17:e14448. [PMID: 38498302 PMCID: PMC10946676 DOI: 10.1111/1751-7915.14448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/20/2024] Open
Abstract
Pseudomonas putida is a soil bacterium with multiple uses in fermentation and biotransformation processes. P. putida ATCC 12633 can biotransform benzaldehyde and other aldehydes into valuable α-hydroxyketones, such as (S)-2-hydroxypropiophenone. However, poor tolerance of this strain toward chaotropic aldehydes hampers efficient biotransformation processes. To circumvent this problem, we expressed the gene encoding the global regulator PprI from Deinococcus radiodurans, an inducer of pleiotropic proteins promoting DNA repair, in P. putida. Fine-tuned gene expression was achieved using an expression plasmid under the control of the LacIQ /Ptrc system, and the cross-protective role of PprI was assessed against multiple stress treatments. Moreover, the stress-tolerant P. putida strain was tested for 2-hydroxypropiophenone production using whole resting cells in the presence of relevant aldehyde substrates. P. putida cells harbouring the global transcriptional regulator exhibited high tolerance toward benzaldehyde, acetaldehyde, ethanol, butanol, NaCl, H2 O2 and thermal stress, thereby reflecting the multistress protection profile conferred by PprI. Additionally, the engineered cells converted aldehydes to 2-hydroxypropiophenone more efficiently than the parental P. putida strain. 2-Hydroxypropiophenone concentration reached 1.6 g L-1 upon a 3-h incubation under optimized conditions, at a cell concentration of 0.033 g wet cell weight mL-1 in the presence of 20 mM benzaldehyde and 600 mM acetaldehyde. Product yield and productivity were 0.74 g 2-HPP g-1 benzaldehyde and 0.089 g 2-HPP g cell dry weight-1 h-1 , respectively, 35% higher than the control experiments. Taken together, these results demonstrate that introducing PprI from D. radiodurans enhances chaotrope tolerance and 2-HPP production in P. putida ATCC 12633.
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Affiliation(s)
- Reihaneh Kordesedehi
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Azar Shahpiri
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Mohammad Ali Asadollahi
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Davoud Biria
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Pablo Iván Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
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2
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Jomrit J, Suhardi S, Summpunn P. Effects of Signal Peptide and Chaperone Co-Expression on Heterologous Protein Production in Escherichia coli. Molecules 2023; 28:5594. [PMID: 37513466 PMCID: PMC10384211 DOI: 10.3390/molecules28145594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Various host systems have been employed to increase the yield of recombinant proteins. However, some recombinant proteins were successfully produced at high yields but with no functional activities. To achieve both high protein yield and high activities, molecular biological strategies have been continuously developed. This work describes the effect of signal peptide (SP) and co-expression of molecular chaperones on the production of active recombinant protein in Escherichia coli. Extracellular enzymes from Bacillus subtilis, including β-1,4-xylanase, β-1,4-glucanase, and β-mannanase constructed with and without their signal peptides and intracellular enzymes from Pseudomonas stutzeri ST201, including benzoylformate decarboxylase (BFDC), benzaldehyde dehydrogenase (BADH), and d-phenylglycine aminotransferase (d-PhgAT) were cloned and overexpressed in E. coli BL21(DE3). Co-expression of molecular chaperones with all enzymes studied was also investigated. Yields of β-1,4-xylanase (Xyn), β-1,4-glucanase (Cel), and β-mannanase (Man), when constructed without their N-terminal signal peptides, increased 1112.61-, 1.75-, and 1.12-fold, respectively, compared to those of spXyn, spCel, and spMan, when constructed with their signal peptides. For the natural intracellular enzymes, the chaperones, GroEL-GroES complex, increased yields of active BFDC, BADH, and d-PhgAT, up to 1.31-, 4.94- and 37.93-fold, respectively, and also increased yields of Man and Xyn up to 1.53- and 3.46-fold, respectively, while other chaperones including DnaK-DnaJ-GrpE and Trigger factor (Tf) showed variable effects with these enzymes. This study successfully cloned and overexpressed extracellular and intracellular enzymes in E. coli BL21(DE3). When the signal peptide regions of the secretory enzymes were removed, yields of active enzymes were higher than those with intact signal peptides. In addition, a higher yield of active enzymes was obtained, in general, when these enzymes were co-expressed with appropriate chaperones. Therefore, E. coli can produce cytoplasmic and secretory enzymes effectively if only the enzyme coding sequence without its signal peptide is used and appropriate chaperones are co-expressed to assist in correct folding.
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Affiliation(s)
- Juntratip Jomrit
- School of Pharmacy, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Suhardi Suhardi
- Department of Animal Science, Faculty of Agriculture, Mulawarman University, Samarinda 75123, Indonesia
| | - Pijug Summpunn
- Food Technology and Innovation Research Center of Excellence, School of Agricultural Technology and Food industry, Walailak University, Nakhon Si Thammarat 80160, Thailand
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3
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Kordesedehi R, Asadollahi MA, Shahpiri A, Biria D, Nikel PI. Optimized enantioselective (S)-2-hydroxypropiophenone synthesis by free- and encapsulated-resting cells of Pseudomonas putida. Microb Cell Fact 2023; 22:89. [PMID: 37131175 PMCID: PMC10155308 DOI: 10.1186/s12934-023-02073-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 03/25/2023] [Indexed: 05/04/2023] Open
Abstract
BACKGROUND Aromatic α-hydroxy ketones, such as S-2-hydroxypropiophenone (2-HPP), are highly valuable chiral building blocks useful for the synthesis of various pharmaceuticals and natural products. In the present study, enantioselective synthesis of 2-HPP was investigated by free and immobilized whole cells of Pseudomonas putida ATCC 12633 starting from readily-available aldehyde substrates. Whole resting cells of P. putida, previously grown in a culture medium containing ammonium mandelate, are a source of native benzoylformate decarboxylase (BFD) activity. BFD produced by induced P. putida resting cells is a highly active biocatalyst without any further treatment in comparison with partially purified enzyme preparations. These cells can convert benzaldehyde and acetaldehyde into the acyloin compound 2-HPP by BFD-catalyzed enantioselective cross-coupling reaction. RESULTS The reaction was carried out in the presence of exogenous benzaldehyde (20 mM) and acetaldehyde (600 mM) as substrates in 6 mL of 200 mM phosphate buffer (pH 7) for 3 h. The optimal biomass concentration was assessed to be 0.006 g dry cell weight (DCW) mL- 1. 2-HPP titer, yield and productivity using the free cells were 1.2 g L- 1, 0.56 g 2-HPP/g benzaldehyde (0.4 mol 2-HPP/mol benzaldehyde), 0.067 g 2-HPP g- 1 DCW h- 1, respectively, under optimized biotransformation conditions (30 °C, 200 rpm). Calcium alginate (CA)-polyvinyl alcohol (PVA)-boric acid (BA)-beads were used for cell entrapment. Encapsulated whole-cells were successfully employed in four consecutive cycles for 2-HPP production under aerobic conditions without any noticeable beads degradation. Moreover, there was no production of benzyl alcohol as an unwanted by-product. CONCLUSIONS Bioconversion by whole P. putida resting cells is an efficient strategy for the production of 2-HPP and other α-hydroxyketones.
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Affiliation(s)
- Reihaneh Kordesedehi
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Mohammad Ali Asadollahi
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
| | - Azar Shahpiri
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Davoud Biria
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Pablo Iván Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
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Genomic Features of Pseudomonas putida PCL1760: A Biocontrol Agent Acting via Competition for Nutrient and Niche. Appl Microbiol 2022. [DOI: 10.3390/applmicrobiol2040057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Pseudomonasputida strain PCL1760 is a biocontrol agent protecting plants from pathogens via the mechanism of competition for nutrients and niches (CNN). To confirm this mechanism as well as to adapt the strain for biotechnological applications, full genome analysis was compared with the known biotechnological model, P. putida S12, and other related species, which were analyzed on different genomic databases. Moreover, the antibacterial activity of PCL1760 was tested against Staphylococcus aureus, Pseudomonas aeruginosa, and Pseudomonas syringae. No genetic systems involved in antibiosis were revealed among the secondary metabolite clusters of the strain of PCL1760. The only antagonistic effect was observed against P. syringae, which might be because of siderophore (yellow-greenish fluorescence), although less than 19% pyoverdin biosynthesis clusters were predicted using the AntiSMASH server. P. putida PCL1760 in comparison with the Pseudomonas simiae strain PCL1751, another biocontrol agent acting solely via CNN, which lost its ‘luxury’ genes necessary for antibiosis or parasitism/predation mechanisms, but carries genetic systems providing motility. Interestingly, immunity genes (CRISPR/Cas and prophages) showed PCL1760 to be robust in comparison with S12, while annotation on OrthoVenn2 showed PCL1760 to be amenable for genetic manipulations. It is tempting to state that rhizobacteria using the mechanism of CNN are distinguishable from biocontrol agents acting via antibiosis or parasitism/predation at the genomic level. This confirms the CNN of PCL1760 as the sole mechanism for biocontrol and we suggest the strain as a new model for genetic engineering.
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Liu Y, Tan Y, Huang J, Wu C, Fan X, Stalin A, Lu S, Wang H, Zhang J, Zhang F, Wu Z, Li B, Huang Z, Chen M, Cheng G, Mou Y, Wu J. Revealing the Mechanism of Huazhi Rougan Granule in the Treatment of Nonalcoholic Fatty Liver Through Intestinal Flora Based on 16S rRNA, Metagenomic Sequencing and Network Pharmacology. Front Pharmacol 2022; 13:875700. [PMID: 35559233 PMCID: PMC9086680 DOI: 10.3389/fphar.2022.875700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 03/16/2022] [Indexed: 12/12/2022] Open
Abstract
Background: The incidence of Nonalcoholic Fatty Liver (NAFL) is increasing year by year, growing evidence suggests that the intestinal flora plays a causative role in NAFL. Huazhi Rougan Granule (HRG) is commonly used in the clinical treatment of NAFL. It is reported that it can reduce lipids and protect the liver, but no research has confirmed whether the drug's effect is related to the intestinal flora. Therefore, we investigated whether the effect of HRG is related to the regulation of intestinal flora to further explore the mechanism of HRG in the treatment of NAFL through intestinal flora. Methods: In this study, C57BL/6J mice were fed a high-fat diet for 8 weeks, and the high-fat diet plus HRG or polyene phosphatidylcholine capsules were each administered by gavage for 4 weeks. High-throughput sequencing, network pharmacology, and molecular docking were used to explore the mechanism of HRG in the treatment of NAFL through intestinal flora. Results: HRG treatment can reduce body weight gain, lipid accumulation in liver and lipogenesis and reduce serum biochemical indexes in high-fat-fed mice. Analysis of intestinal flora showed that HRG changed the composition of intestinal flora, which was characterized by a decrease in the Firmicutes/Bacteroidetes ratio. Moreover, the species distribution was significantly correlated with AKP, HDL-C, and TG. Metagenetic analysis showed that HRG altered the functional composition and functional diversity of microorganisms, which was mainly characterized by an increase in the abundance of metabolic pathways. The network pharmacology results show that the mechanism of HRG in the treatment of NAFL through intestinal flora is mainly reflected in the biological process of gene function and related to infectious diseases, immune systems, and signal transduction pathways, such as cytokine-cytokine receptor interaction, Chagas disease, IL-17 signaling pathway and other signaling pathways. Conclusion: These results strongly suggest that HRG may alleviate NAFL by preventing IFD.
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Affiliation(s)
- Yingying Liu
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Yingying Tan
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Jiaqi Huang
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Chao Wu
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Xiaotian Fan
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Antony Stalin
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
| | - Shan Lu
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Haojia Wang
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Jingyuan Zhang
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Fanqin Zhang
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Zhishan Wu
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Bing Li
- State Key Laboratory of Generic Manufacture Technology of Chinese Traditional Medicine, Linyi, China
| | - Zhihong Huang
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Meilin Chen
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Guoliang Cheng
- State Key Laboratory of Generic Manufacture Technology of Chinese Traditional Medicine, Linyi, China
| | - Yanfang Mou
- State Key Laboratory of Generic Manufacture Technology of Chinese Traditional Medicine, Linyi, China
| | - Jiarui Wu
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
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Wang Q, Geng S, Wang L, Wen Z, Sun X, Huang H. Bacterial mandelic acid degradation pathway and its application in biotechnology. J Appl Microbiol 2022; 133:273-286. [PMID: 35294082 DOI: 10.1111/jam.15529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 12/22/2021] [Accepted: 03/09/2022] [Indexed: 11/28/2022]
Abstract
Mandelic acid and its derivatives are an important class of chemical synthetic blocks, which is widely used in drug synthesis and stereochemistry research. In nature, mandelic acid degradation pathway has been widely identified and analyzed as a representative pathway of aromatic compounds degradation. The most studied mandelic acid degradation pathway from Pseudomonas putida consists of mandelate racemase, S-mandelate dehydrogenase, benzoylformate decarboxylase, benzaldehyde dehydrogenase and downstream benzoic acid degradation pathways. Because of the ability to catalyze various reactions of aromatic substrates, pathway enzymes have been widely used in biocatalysis, kinetic resolution, chiral compounds synthesis or construction of new metabolic pathways. In this paper, the physiological significance and the existing range of the mandelic acid degradation pathway were introduced first. Then each of the enzymes in the pathway is reviewed one by one, including the researches on enzymatic properties and the applications in biotechnology as well as efforts that have been made to modify the substrate specificity or improving catalytic activity by enzyme engineering to adapt different applications. The composition of the important metabolic pathway of bacterial mandelic acid degradation pathway as well as the researches and applications of pathway enzymes is summarized in this review for the first time.
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Affiliation(s)
- Qingzhuo Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2# Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - Shanshan Geng
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2# Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - Lingru Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2# Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - Zhiqiang Wen
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2# Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - Xiaoman Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2# Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2# Xuelin Road, Qixia District, Nanjing, People's Republic of China.,College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, People's Republic of China
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7
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Highly Stable, Cold-Active Aldehyde Dehydrogenase from the Marine Antarctic Flavobacterium sp. PL002. FERMENTATION 2021. [DOI: 10.3390/fermentation8010007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Stable aldehyde dehydrogenases (ALDH) from extremophilic microorganisms constitute efficient catalysts in biotechnologies. In search of active ALDHs at low temperatures and of these enzymes from cold-adapted microorganisms, we cloned and characterized a novel recombinant ALDH from the psychrotrophic Flavobacterium PL002 isolated from Antarctic seawater. The recombinant enzyme (F-ALDH) from this cold-adapted strain was obtained by cloning and expressing of the PL002 aldH gene (1506 bp) in Escherichia coli BL21(DE3). Phylogeny and structural analyses showed a high amino acid sequence identity (89%) with Flavobacterium frigidimaris ALDH and conservation of all active site residues. The purified F-ALDH by affinity chromatography was homotetrameric, preserving 80% activity at 4 °C for 18 days. F-ALDH used both NAD+ and NADP+ and a broad range of aliphatic and aromatic substrates, showing cofactor-dependent compensatory KM and kcat values and the highest catalytic efficiency (0.50 µM−1 s−1) for isovaleraldehyde. The enzyme was active in the 4–60 °C-temperature interval, with an optimal pH of 9.5, and a preference for NAD+-dependent reactions. Arrhenius plots of both NAD(P)+-dependent reactions indicated conformational changes occurring at 30 °C, with four(five)-fold lower activation energy at high temperatures. The high thermal stability and substrate-specific catalytic efficiency of this novel cold-active ALDH favoring aliphatic catalysis provided a promising catalyst for biotechnological and biosensing applications.
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8
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Luo ZW, Lee SY. Metabolic engineering of Escherichia coli for the production of benzoic acid from glucose. Metab Eng 2020; 62:298-311. [DOI: 10.1016/j.ymben.2020.10.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/25/2020] [Accepted: 10/05/2020] [Indexed: 12/19/2022]
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9
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Zhou Y, Sekar BS, Wu S, Li Z. Benzoic acid production via cascade biotransformation and coupled fermentation‐biotransformation. Biotechnol Bioeng 2020; 117:2340-2350. [DOI: 10.1002/bit.27366] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 04/22/2020] [Accepted: 04/26/2020] [Indexed: 12/31/2022]
Affiliation(s)
- Yi Zhou
- Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences InstituteNational University of Singapore Singapore Singapore
| | - Balaji Sundara Sekar
- Department of Chemical and Biomolecular EngineeringNational University of Singapore Singapore Singapore
| | - Shuke Wu
- Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences InstituteNational University of Singapore Singapore Singapore
- Department of Chemical and Biomolecular EngineeringNational University of Singapore Singapore Singapore
| | - Zhi Li
- Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences InstituteNational University of Singapore Singapore Singapore
- Department of Chemical and Biomolecular EngineeringNational University of Singapore Singapore Singapore
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10
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Zahniser MPD, Prasad S, Kneen MM, Kreinbring CA, Petsko GA, Ringe D, McLeish MJ. Structure and mechanism of benzaldehyde dehydrogenase from Pseudomonas putida ATCC 12633, a member of the Class 3 aldehyde dehydrogenase superfamily. Protein Eng Des Sel 2017; 30:271-278. [PMID: 28338942 DOI: 10.1093/protein/gzx015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 02/23/2017] [Indexed: 11/14/2022] Open
Abstract
Benzaldehyde dehydrogenase from Pseudomonas putida (PpBADH) belongs to the Class 3 aldehyde dehydrogenase (ALDH) family. The Class 3 ALDHs are unusual in that they are generally dimeric (rather than tetrameric), relatively non-specific and utilize both NAD+ and NADP+. To date, X-ray structures of three Class 3 ALDHs have been determined, of which only two have cofactor bound, both in the NAD+ form. Here we report the crystal structure of PpBADH in complex with NADP+ and a thioacyl intermediate adduct. The overall architecture of PpBADH resembles that of most other members of the ALDH superfamily, and the cofactor binding residues are well conserved. Conversely, the pattern of cofactor binding for the rat Class 3 ALDH differs from that of PpBADH and other ALDHs. This has been interpreted in terms of a different mechanism for the rat enzyme. Comparison with the PpBADH structure, as well as multiple sequence alignments, suggest that one of two conserved glutamates, at positions 215 (209 in rat) and 337 (333 in rat), would act as the general base necessary to hydrolyze the thioacyl intermediate. While the latter is the general base in the rat Class 3 ALDH, site-specific mutagenesis indicates that Glu215 is the likely candidate for PpBADH, a result more typical of the Class 1 and 2 ALDH families. Finally, this study shows that hydride transfer is not rate limiting, lending further credence to the suggestion that PpBADH is more similar to the Class 1 and 2 ALDHs than it is to other Class 3 ALDHs.
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Affiliation(s)
- Megan P D Zahniser
- Department of Biochemistry, Brandeis University, 415 South St., Waltham, MA 02454,USA
| | - Shreenath Prasad
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 N. Blackford Street, Indianapolis, IN 46202,USA
| | - Malea M Kneen
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 N. Blackford Street, Indianapolis, IN 46202,USA
| | - Cheryl A Kreinbring
- Department of Biochemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA.,Rosenstiel Basic Medical Sciences Research Center, MS029, 415 South Street, Waltham, MA 02454, USA
| | - Gregory A Petsko
- Department of Biochemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA.,Rosenstiel Basic Medical Sciences Research Center, MS029, 415 South Street, Waltham, MA 02454, USA
| | - Dagmar Ringe
- Department of Biochemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA.,Rosenstiel Basic Medical Sciences Research Center, MS029, 415 South Street, Waltham, MA 02454, USA.,Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA
| | - Michael J McLeish
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 N. Blackford Street, Indianapolis, IN 46202,USA
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11
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Ruan LT, Zheng RC, Zheng YG. Mining and characterization of two amidase signature family amidases from Brevibacterium epidermidis ZJB-07021 by an efficient genome mining approach. Protein Expr Purif 2016; 126:16-25. [DOI: 10.1016/j.pep.2016.05.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 05/02/2016] [Accepted: 05/10/2016] [Indexed: 11/28/2022]
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12
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Andrews FH, Horton JD, Shin D, Yoon HJ, Logsdon MG, Malik AM, Rogers MP, Kneen MM, Suh SW, McLeish MJ. The kinetic characterization and X-ray structure of a putative benzoylformate decarboxylase from M. smegmatis highlights the difficulties in the functional annotation of ThDP-dependent enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1001-9. [DOI: 10.1016/j.bbapap.2015.04.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 04/05/2015] [Accepted: 04/23/2015] [Indexed: 10/23/2022]
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13
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González-Segura L, Riveros-Rosas H, Julián-Sánchez A, Muñoz-Clares RA. Residues that influence coenzyme preference in the aldehyde dehydrogenases. Chem Biol Interact 2015; 234:59-74. [PMID: 25601141 DOI: 10.1016/j.cbi.2014.12.039] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 12/12/2014] [Accepted: 12/31/2014] [Indexed: 11/25/2022]
Abstract
To find out the residues that influence the coenzyme preference of aldehyde dehydrogenases (ALDHs), we reviewed, analyzed and correlated data from their known crystal structures and amino-acid sequences with their published kinetic parameters for NAD(P)(+). We found that the conformation of the Rossmann-fold loops participating in binding the adenosine ribose is very conserved among ALDHs, so that coenzyme specificity is mainly determined by the nature of the residue at position 195 (human ALDH2 numbering). Enzymes with glutamate or proline at 195 prefer NAD(+) because the side-chains of these residues electrostatically and/or sterically repel the 2'-phosphate group of NADP(+). But contrary to the conformational rigidity of proline, the conformational flexibility of glutamate may allow NADP(+)-binding in some enzymes by moving the carboxyl group away from the 2'-phosphate group, which is possible if a small neutral residue is located at position 224, and favored if the residue at position 53 interacts with Glu195 in a NADP(+)-compatible conformation. Of the residues found at position 195, only glutamate interacts with the NAD(+)-adenosine ribose; glutamine and histidine cannot since their side-chain points are opposite to the ribose, probably because the absence of the electrostatic attraction by the conserved nearby Lys192, or its electrostatic repulsion, respectively. The shorter side-chains of other residues-aspartate, serine, threonine, alanine, valine, leucine, or isoleucine-are distant from the ribose but leave room for binding the 2'-phosphate group. Generally, enzymes having a residue different from Glu bind NAD(+) with less affinity, but they can also bind NADP(+) even sometimes with higher affinity than NAD(+), as do enzymes containing Thr/Ser/Gln195. Coenzyme preference is a variable feature within many ALDH families, consistent with being mainly dependent on a single residue that apparently has no other structural or functional roles, and therefore can easily be changed through evolution and selected in response to physiological needs.
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Affiliation(s)
- Lilian González-Segura
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, México D. F. 04510, Mexico
| | - Héctor Riveros-Rosas
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, México D. F. 04510, Mexico
| | - Adriana Julián-Sánchez
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, México D. F. 04510, Mexico
| | - Rosario A Muñoz-Clares
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, México D. F. 04510, Mexico.
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14
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Patten CL, Blakney AJC, Coulson TJD. Activity, distribution and function of indole-3-acetic acid biosynthetic pathways in bacteria. Crit Rev Microbiol 2012; 39:395-415. [PMID: 22978761 DOI: 10.3109/1040841x.2012.716819] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The capacity to produce the phytohormone indole-3-acetic acid (IAA) is widespread among bacteria that inhabit diverse environments such as soils, fresh and marine waters, and plant and animal hosts. Three major pathways for bacterial IAA synthesis have been characterized that remove the amino and carboxyl groups from the α-carbon of tryptophan via the intermediates indolepyruvate, indoleacetamide, or indoleacetonitrile; the oxidized end product IAA is typically secreted. The enzymes in these pathways often catabolize a broad range of substrates including aromatic amino acids and in some cases the branched chain amino acids. Moreover, expression of some of the genes encoding key IAA biosynthetic enzymes is induced by all three aromatic amino acids. The broad distribution and substrate specificity of the enzymes suggests a role for these pathways beyond plant-microbe interactions in which bacterial IAA has been best studied.
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Affiliation(s)
- Cheryl L Patten
- Department of Biology, University of New Brunswick , Fredericton, New Brunswick , Canada
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15
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Yep A, McLeish MJ. Engineering the Substrate Binding Site of Benzoylformate Decarboxylase. Biochemistry 2009; 48:8387-95. [DOI: 10.1021/bi9008402] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alejandra Yep
- College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109
| | - Michael J. McLeish
- College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109
- Department of Chemistry and Chemical Biology, IUPUI, Indianapolis, Indiana 46202
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16
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Wang PF, Yep A, Kenyon GL, McLeish MJ. Using directed evolution to probe the substrate specificity of mandelamide hydrolase. Protein Eng Des Sel 2008; 22:103-10. [DOI: 10.1093/protein/gzn073] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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17
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Wenzel SC, Bode HB, Kochems I, Müller R. A Type I/Type III Polyketide Synthase Hybrid Biosynthetic Pathway for the Structurally UniqueansaCompound Kendomycin. Chembiochem 2008; 9:2711-21. [DOI: 10.1002/cbic.200800456] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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18
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Yeung CK, Yep A, Kenyon GL, McLeish MJ. Physical, kinetic and spectrophotometric studies of a NAD(P)-dependent benzaldehyde dehydrogenase from Pseudomonas putida ATCC 12633. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:1248-55. [PMID: 18498778 DOI: 10.1016/j.bbapap.2008.04.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2007] [Revised: 04/15/2008] [Accepted: 04/16/2008] [Indexed: 11/24/2022]
Abstract
The mandelate pathway of Pseudomonas putida ATCC 12633 comprises five enzymes and catalyzes the conversion of R- and S-mandelamide to benzoic acid which subsequently enters the beta-ketoadipate pathway. Although the first four enzymes have been extensively characterized the terminal enzyme, a NAD(P)+-dependent benzaldehyde dehydrogenase (BADH), remains largely undescribed. Here we report that BADH is a dimer in solution, and that DTT is necessary both to maintain the activity of BADH and to prevent oligimerization of the enzyme. Site-directed mutagenesis confirms that Cys249 is the catalytic cysteine and identifies Cys140 as the cysteine likely to be involved in inter-monomer disulfide formation. BADH can utilize a range of aromatic substrates and will also operate efficiently with cyclohexanal as well as medium-chain aliphatic aldehydes. The logV and logV/K pH-rate profiles for benzaldehyde with either NAD+ or NADP+ as the coenzyme are both bell-shaped. The pKa values on the ascending limb range from 6.2 to 7.1 while those on the descending limb range from 9.6 to 9.9. A spectrophotometric approach was used to show that the pKa of Cys249 was 8.4, i.e., Cys249 is not responsible for the pKas observed in the pH-rate profiles.
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Affiliation(s)
- Catherine K Yeung
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, MI 48109, USA
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19
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Saehuan C, Rojanarata T, Wiyakrutta S, McLeish MJ, Meevootisom V. Isolation and characterization of a benzoylformate decarboxylase and a NAD+/NADP+-dependent benzaldehyde dehydrogenase involved in D-phenylglycine metabolism in Pseudomonas stutzeri ST-201. Biochim Biophys Acta Gen Subj 2007; 1770:1585-92. [PMID: 17916405 DOI: 10.1016/j.bbagen.2007.08.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2007] [Revised: 08/07/2007] [Accepted: 08/08/2007] [Indexed: 11/16/2022]
Abstract
Following induction with D-phenylglycine both d-phenylglycine aminotransferase activity and benzoylformate decarboxylase activity were observed in cultures of Pseudomonas stutzeri ST-201. Induction with benzoylformate, on the other hand, induced only benzoylformate decarboxylase activity. Purification of the benzoylformate decarboxylase, followed by N-terminal sequencing, enabled the design of probes for hybridization with P. stutzeri ST-201 genomic DNA libraries. Sequencing of two overlapping genomic DNA restriction fragments revealed two open reading frames which were denoted dpgB and dpgC. Sequence alignments suggested that the genes encoded a thiamin-diphosphate-dependent decarboxylase and an aldehyde dehydrogenase, respectively. Both genes were isolated and expressed in Escherichia coli. The dpgB gene product was confirmed as a benzoylformate decarboxylase while the dpgC gene product was characterized as a NAD+/NADP+-dependent benzaldehyde dehydrogenase. In keeping with their high sequence identities (both greater than 85%) the kinetic properties of the two enzymes were similar to those of the homologous enzymes in the mandelate pathway of Pseudomonas putida ATCC 12633. However, Pseudomonas stutzeri ST-201 was unable to grow on either isomer of mandelate, and sequencing indicated that the dpgB gene did not form part of an operon. Thus it appears that the two enzymes form part of a d-phenylglycine, rather than mandelate, degrading pathway.
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Affiliation(s)
- Choedchai Saehuan
- Department of Microbiology, Faculty of Science, Mahidol University, Thailand
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20
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Hirano JI, Miyamoto K, Ohta H. Purification and characterization of aldehyde dehydrogenase with a broad substrate specificity originated from 2-phenylethanol-assimilating Brevibacterium sp. KU1309. Appl Microbiol Biotechnol 2007; 76:357-63. [PMID: 17619188 DOI: 10.1007/s00253-007-1004-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2007] [Revised: 04/11/2007] [Accepted: 04/12/2007] [Indexed: 10/23/2022]
Abstract
Phenylacetaldehyde dehydrogenase (PADH) was purified and characterized from Brevibacterium sp. KU1309, which can grow on the medium containing 2-phenylethanol as the sole carbon source. This enzyme was a homotetrameric protein with a subunit of 61 kDa. The enzyme catalyzed the oxidation of aryl (benzaldehyde, phenylacetaldehyde, 3-phenylpropionaldehyde) and aliphatic (hexanal, octanal, decanal) aldehydes to the corresponding carboxylic acids using NAD(+) as the electron acceptor. The PADH activity was enhanced by several divalent cationic ions such as Mg(2+), Ca(2+), and Mn(2+). On the other hand, it was inhibited by SH reagents (Hg(2+), p-chloromercuribenzoate, iodoacetamide, and N-ethylmaleinimide). The substrate specificity of the enzyme is compared with those of various aldehyde dehydrogenases.
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Affiliation(s)
- Jun-ichiro Hirano
- Department of Biosciences and Informatics, Center for Bioscience and Informatics, Keio University, 3-14-1 Hiyoshi, Yokohama 223-8522, Japan
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21
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Kiziak C, Conradt D, Stolz A, Mattes R, Klein J. Nitrilase from Pseudomonas fluorescens EBC191: cloning and heterologous expression of the gene and biochemical characterization of the recombinant enzyme. MICROBIOLOGY-SGM 2005; 151:3639-3648. [PMID: 16272385 DOI: 10.1099/mic.0.28246-0] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The gene encoding an enantioselective arylacetonitrilase was identified on a 3.8 kb DNA fragment from the genomic DNA of Pseudomonas fluorescens EBC191. The gene was isolated, sequenced and cloned into the L-rhamnose-inducible expression vector pJOE2775. The nitrilase was produced in large quantities and purified as a histidine-tagged enzyme from crude extracts of L-rhamnose-induced cells of Escherichia coli JM109. The purified nitrilase was significantly stabilized during storage by the addition of 1 M ammonium sulfate. The temperature optimum (50 degrees C), pH optimum (pH 6.5), and specific activity of the recombinant nitrilase were similar to those of the native enzyme from P. fluorescens EBC191. The enzyme hydrolysed various phenylacetonitriles with different substituents in the 2-position and also heterocyclic and bicyclic arylacetonitriles to the corresponding carboxylic acids. The conversion of most arylacetonitriles was accompanied by the formation of different amounts of amides as by-products. The relative amounts of amides formed from different nitriles increased with an increasing negative inductive effect of the substituent in the 2-position. The acids and amides that were formed from chiral nitriles demonstrated in most cases opposite enantiomeric excesses. Thus mandelonitrile was converted by the nitrilase preferentially to R-mandelic acid and S-mandelic acid amide. The nitrilase gene is physically linked in the genome of P. fluorescens with genes encoding the degradative pathway for mandelic acid. This might suggest a natural function of the nitrilase in the degradation of mandelonitrile or similar naturally occurring hydroxynitriles.
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Affiliation(s)
- Christoph Kiziak
- Institut für Mikrobiologie, Universität Stuttgart, Allmandring 31, D-70569 Stuttgart, Germany
- Institut für Industrielle Genetik, Universität Stuttgart, Allmandring 31, D-70569 Stuttgart, Germany
| | - Doris Conradt
- Institut für Industrielle Genetik, Universität Stuttgart, Allmandring 31, D-70569 Stuttgart, Germany
| | - Andreas Stolz
- Institut für Mikrobiologie, Universität Stuttgart, Allmandring 31, D-70569 Stuttgart, Germany
| | - Ralf Mattes
- Institut für Industrielle Genetik, Universität Stuttgart, Allmandring 31, D-70569 Stuttgart, Germany
| | - Joachim Klein
- Institut für Industrielle Genetik, Universität Stuttgart, Allmandring 31, D-70569 Stuttgart, Germany
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22
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Abstract
Fatty acid amide hydrolase (FAAH) is a mammalian integral membrane enzyme that degrades the fatty acid amide family of endogenous signaling lipids, which includes the endogenous cannabinoid anandamide and the sleep-inducing substance oleamide. FAAH belongs to a large and diverse class of enzymes referred to as the amidase signature (AS) family. Investigations into the structure and function of FAAH, in combination with complementary studies of other AS enzymes, have engendered provocative molecular models to explain how this enzyme integrates into cell membranes and terminates fatty acid amide signaling in vivo. These studies, as well as their biological and therapeutic implications, are the subject of this review.
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Affiliation(s)
- Michele K McKinney
- Departments of Cell Biology and Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA.
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23
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Gopalakrishna KN, Stewart BH, Kneen MM, Andricopulo AD, Kenyon GL, McLeish MJ. Mandelamide hydrolase from Pseudomonas putida: characterization of a new member of the amidase signature family. Biochemistry 2004; 43:7725-35. [PMID: 15196015 DOI: 10.1021/bi049907q] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A recently discovered enzyme in the mandelate pathway of Pseudomonas putida, mandelamide hydrolase (MAH), catalyzes the hydrolysis of mandelamide to mandelic acid and ammonia. Sequence analysis suggests that MAH is a member of the amidase signature family, which is widespread in nature and contains a novel Ser-cis-Ser-Lys catalytic triad. Here we report the expression in Escherichia coli, purification, and characterization of both wild-type and His(6)-tagged MAH. The recombinant enzyme was stable, exhibited a pH optimum of 7.8, and was able to hydrolyze both enantiomers of mandelamide with little enantiospecificity. The His-tagged variant showed no significant change in kinetic constants. Phenylacetamide was found to be the best substrate, with changes in chain length or replacement of the phenyl group producing greatly decreased values of k(cat)/K(m). As with another member of this family, fatty acid amide hydrolase, MAH has the uncommon ability to hydrolyze esters and amides at similar rates. MAH is even more unusual in that it will only hydrolyze esters and amides with little steric bulk. Ethyl and larger esters and N-ethyl and larger amides are not substrates, suggesting that the MAH active site is very sterically hindered. Mutation of each residue in the putative catalytic triad to alanine resulted in total loss of activity for S204A and K100A, while S180A exhibited a 1500-fold decrease in k(cat) and significant increases in K(m) values. Overall, the MAH data are similar to those of fatty acid amide hydrolase and support the suggestion that there are two distinct subgroups within the amidase signature family.
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Affiliation(s)
- Kota N Gopalakrishna
- College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109-1065, USA
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