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Zhang W, Shao ZQ, Wang ZX, Ye YF, Li SF, Wang YJ. Advances in aldo-keto reductases immobilization for biocatalytic synthesis of chiral alcohols. Int J Biol Macromol 2024; 274:133264. [PMID: 38901517 DOI: 10.1016/j.ijbiomac.2024.133264] [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: 02/23/2024] [Revised: 06/13/2024] [Accepted: 06/17/2024] [Indexed: 06/22/2024]
Abstract
Chiral alcohols are essential building blocks of numerous pharmaceuticals and fine chemicals. Aldo-keto reductases (AKRs) constitute a superfamily of oxidoreductases that catalyze the reduction of aldehydes and ketones to their corresponding alcohols using NAD(P)H as a coenzyme. Knowledge about the crucial roles of AKRs immobilization in the biocatalytic synthesis of chiral alcohols is expanding. Herein, we reviewed the characteristics of various AKRs immobilization approaches, the applications of different immobilization materials, and the prospects of continuous flow bioreactor construction by employing these immobilized biocatalysts for synthesizing chiral alcohols. Finally, the opportunities and ongoing challenges for AKR immobilization are discussed and the outlook for this emerging area is analyzed.
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Affiliation(s)
- Wen Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Zi-Qing Shao
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Zhi-Xiu Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Yuan-Fan Ye
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Shu-Fang Li
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Ya-Jun Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, PR China.
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Malhotra H, Dhamale T, Kaur S, Kasarlawar ST, Phale PS. Metabolic engineering of Pseudomonas bharatica CSV86 T to degrade Carbaryl (1-naphthyl- N-methylcarbamate) via the salicylate-catechol route. Microbiol Spectr 2024:e0028424. [PMID: 38869268 DOI: 10.1128/spectrum.00284-24] [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: 02/06/2024] [Accepted: 04/22/2024] [Indexed: 06/14/2024] Open
Abstract
Pseudomonas bharatica CSV86T displays the unique property of preferential utilization of aromatic compounds over simple carbon sources like glucose and glycerol and their co-metabolism with organic acids. Well-characterized growth conditions, aromatic compound metabolic pathways and their regulation, genome sequence, and advantageous eco-physiological traits (indole acetic acid production, alginate production, fusaric acid resistance, organic sulfur utilization, and siderophore production) make it an ideal host for metabolic engineering. Strain CSV86T was engineered for Carbaryl (1-naphthyl-N-methylcarbamate) degradation via salicylate-catechol route by expression of a Carbaryl hydrolase (CH) and a 1-naphthol 2-hydroxylase (1NH). Additionally, the engineered strain exhibited faster growth on Carbaryl upon expression of the McbT protein (encoded by the mcbT gene, a part of Carbaryl degradation upper operon of Pseudomonas sp. C5pp). Bioinformatic analyses predict McbT to be an outer membrane protein, and Carbaryl-dependent expression suggests its probable role in Carbaryl uptake. Enzyme activity and protein analyses suggested periplasmic localization of CH (carrying transmembrane domain plus signal peptide sequence at the N-terminus) and 1NH, enabling compartmentalization of the pathway. Enzyme activity, whole-cell oxygen uptake, spent media analyses, and qPCR results suggest that the engineered strain preferentially utilizes Carbaryl over glucose. The plasmid-encoded degradation property was stable for 75-90 generations even in the absence of selection pressure (kanamycin or Carbaryl). These results indicate the utility of P. bharatica CSV86T as a potential host for engineering various aromatic compound degradation pathways.IMPORTANCEThe current study describes engineering of Carbaryl metabolic pathway in Pseudomonas bharatica CSV86T. Carbaryl, a naphthalene-derived carbamate pesticide, is known to act as an endocrine disruptor, mutagen, cytotoxin, and carcinogen. Removal of xenobiotics from the environment using bioremediation faces challenges, such as slow degradation rates, instability of the degradation phenotype, and presence of simple carbon sources in the environment. The engineered CSV86-MEC2 overcomes these disadvantages as Carbaryl was degraded preferentially over glucose. Furthermore, the plasmid-borne degradation phenotype is stable, and presence of glucose and organic acids does not repress Carbaryl metabolism in the strain. The study suggests the role of outer membrane protein McbT in Carbaryl transport. This work highlights the suitability of P. bharatica CSV86T as an ideal host for engineering aromatic pollutant degradation pathways.
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Affiliation(s)
- Harshit Malhotra
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
| | - Tushar Dhamale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
| | - Sukhjeet Kaur
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
| | - Sravanti T Kasarlawar
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
| | - Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
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Stack TMM, Li W, Johnson WH, Zhang YJ, Whitman CP. Inactivation of 4-Oxalocrotonate Tautomerase by 5-Halo-2-hydroxy-2,4-pentadienoates. Biochemistry 2018; 57:1012-1021. [PMID: 29303557 DOI: 10.1021/acs.biochem.7b00899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
5-Halo-2-hydroxy-2,4-pentadienoates (5-halo-HPDs) are reportedly generated in the bacterial catabolism of halogenated aromatic hydrocarbons by the meta-fission pathway. The 5-halo-HPDs, where the halogen can be bromide, chloride, or fluoride, result in the irreversible inactivation of 4-oxalocrotonate tautomerase (4-OT), which precedes the enzyme that generates them. The loss of activity is due to the covalent modification of the nucleophilic amino-terminal proline. Mass spectral and crystallographic analysis of the modified enzymes indicates that inactivation of 4-OT by 5-chloro- and 5-bromo-2-hydroxy-2,4-pentadienoate follows a mechanism different from that for the inactivation of 4-OT by 5-fluoro-2-hydroxy-2,4-pentadienoate. The 5-chloro and 5-bromo derivatives undergo 4-OT-catalyzed tautomerization to their respective α,β-unsaturated ketones followed by attack at C5 (by the prolyl nitrogen) with concomitant loss of the halide. For the 5-fluoro species, the presence of a small amount of the α,β-unsaturated ketone could result in a Michael addition of the prolyl nitrogen to C4 followed by protonation at C3. The fluoride is not eliminated. These observations suggest that the inactivation of 4-OT by a downstream metabolite could hamper the efficacy of the pathway, which is the first time that such a bottleneck has been reported for the meta-fission pathway.
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Affiliation(s)
- Tyler M M Stack
- Department of Molecular Biosciences, The University of Texas at Austin , Austin, Texas 78712, United States.,Institute for Cellular and Molecular Biology, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Wenzong Li
- Department of Molecular Biosciences, The University of Texas at Austin , Austin, Texas 78712, United States.,Institute for Cellular and Molecular Biology, The University of Texas at Austin , Austin, Texas 78712, United States
| | - William H Johnson
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Yan Jessie Zhang
- Department of Molecular Biosciences, The University of Texas at Austin , Austin, Texas 78712, United States.,Institute for Cellular and Molecular Biology, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Christian P Whitman
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
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Dvořák P, Nikel PI, Damborský J, de Lorenzo V. Bioremediation 3 . 0 : Engineering pollutant-removing bacteria in the times of systemic biology. Biotechnol Adv 2017; 35:845-866. [DOI: 10.1016/j.biotechadv.2017.08.001] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 08/01/2017] [Accepted: 08/04/2017] [Indexed: 01/07/2023]
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Bench scale synthesis of p-hydroxybenzoic acid using whole-cell nitrilase of Gordonia terrae mutant E9. Bioprocess Biosyst Eng 2015; 38:1267-79. [DOI: 10.1007/s00449-015-1367-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 01/19/2015] [Indexed: 12/26/2022]
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Luque A, Sebai SC, Sauveplane V, Ramaen O, Pandjaitan R. In vivo evolution of metabolic pathways: Assembling old parts to build novel and functional structures. Bioengineered 2014; 5:347-56. [PMID: 25482082 PMCID: PMC4601399 DOI: 10.4161/bioe.34347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In our recent article "In vivo evolution of metabolic pathways by homeologous recombination in mitotic cells" we proposed a useful alternative to directed evolution methods that permits the generation of yeast cell libraries containing recombinant metabolic pathways from counterpart genes. The methodology was applied to generate single mosaic genes and intragenic mosaic pathways. We used flavonoid metabolism genes as a working model to assembly and express evolved pathways in DNA repair deficient cells. The present commentary revises the principles of gene and pathway mosaicism and explores the scope and perspectives of our results as an additional tool for synthetic biology.
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Rao MA, Scelza R, Acevedo F, Diez MC, Gianfreda L. Enzymes as useful tools for environmental purposes. CHEMOSPHERE 2014; 107:145-162. [PMID: 24411841 DOI: 10.1016/j.chemosphere.2013.12.059] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 12/02/2013] [Accepted: 12/13/2013] [Indexed: 06/03/2023]
Abstract
In the environment enzymes may play important and different roles at least in three cases: as main agents (as isolated, cell-bound or immobilized enzymes) in charge of either the transformation and/or degradation of compounds polluting the environment and the restoration of the polluted environment; as reliable and sensitive tools to detect and measure the amount and concentration of pollutants before, during and after the restoration process; as reliable, easy and sensitive indicators of quality and health status of the environment subjected to the restoration process. To our knowledge papers or reviews integrating findings on these three functions of enzymes are missing in literature. Therefore the main scope of the present paper is to briefly encompass general and specific concepts about roles of enzymes as decontaminating agents, pollutant assaying agents and indicators of environment safety. Examples chosen among those published very recently, supporting and confirming peculiarities, features, and performance of enzymatic agents will be illustrated.
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Affiliation(s)
- M A Rao
- Dipartimento di Agraria, Università di Napoli Federico II, Portici, Napoli, Italy.
| | - R Scelza
- Dipartimento di Agraria, Università di Napoli Federico II, Portici, Napoli, Italy
| | - F Acevedo
- Centre of Food Biotechnology and Bioseparations, BIOREN, Universidad de La Frontera, Temuco, Chile
| | - M C Diez
- Environmental Biotechnology Center, BIOREN, Universidad de La Frontera, Temuco, Chile
| | - L Gianfreda
- Dipartimento di Agraria, Università di Napoli Federico II, Portici, Napoli, Italy
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In vivo evolution of metabolic pathways by homeologous recombination in mitotic cells. Metab Eng 2014; 23:123-35. [DOI: 10.1016/j.ymben.2014.02.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 01/27/2014] [Accepted: 02/12/2014] [Indexed: 12/29/2022]
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Biochemical methane potential (BMP) test for thickened sludge using anaerobic granular sludge at different inoculum/substrate ratios. BIOTECHNOL BIOPROC E 2013. [DOI: 10.1007/s12257-012-0465-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Dror A, Fishman A. Engineering non-heme mono- and dioxygenases for biocatalysis. Comput Struct Biotechnol J 2012; 2:e201209011. [PMID: 24688652 PMCID: PMC3962191 DOI: 10.5936/csbj.201209011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2012] [Revised: 10/02/2012] [Accepted: 10/12/2012] [Indexed: 11/25/2022] Open
Abstract
Oxygenases are ubiquitous enzymes that catalyze the introduction of one or two oxygen atoms to unreactive chemical compounds. They require reduction equivalents from NADH or NADPH and comprise metal ions, metal ion complexes, or coenzymes in their active site. Thus, for industrial purposes, oxygenases are most commonly employed using whole cell catalysis, to alleviate the need for co-factor regeneration. Biotechnological applications include bioremediation, chiral synthesis, biosensors, fine chemicals, biofuels, pharmaceuticals, food ingredients and polymers. Controlling activity and selectivity of oxygenases is therefore of great importance and of growing interest to the scientific community. This review focuses on protein engineering of non-heme monooxygenases and dioxygenases for generating improved or novel functionalities. Rational mutagenesis based on x-ray structures and sequence alignment, as well as random methods such as directed evolution, have been utilized. It is concluded that knowledge-based protein engineering accompanied with targeted libraries, is most efficient for the design and tuning of biocatalysts towards novel substrates and enhanced catalytic activity while minimizing the screening efforts.
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Affiliation(s)
- Adi Dror
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Ayelet Fishman
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, 32000, Israel
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An Y, Sun S, Lv S, Chen L. Digestion-after-shuffling: A method for combinatorial library construction. Anal Biochem 2011; 416:138-40. [DOI: 10.1016/j.ab.2011.04.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Revised: 04/03/2011] [Accepted: 04/15/2011] [Indexed: 11/28/2022]
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An Y, Chen L, Sun S, Lv A, Wu W. QuikChange shuffling: a convenient and robust method for site-directed mutagenesis and random recombination of homologous genes. N Biotechnol 2011; 28:320-5. [DOI: 10.1016/j.nbt.2011.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 02/12/2011] [Accepted: 03/02/2011] [Indexed: 11/25/2022]
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Jez JM. Toward protein engineering for phytoremediation: possibilities and challenges. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2011; 13 Suppl 1:77-89. [PMID: 22046752 DOI: 10.1080/15226514.2011.568537] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The combination of rational protein engineering and directed evolution techniques allow for the redesign of enzymes with tailored properties for use in environmental remediation. This review summarizes current molecular methods for either altering or improving protein function and highlights examples of how these methods can address bioremediation problems. Although much of the protein engineering applied to environmental clean-up employs microbial systems, there is great potential for and significant challenges to translating these approaches to plant systems for phytoremediation purposes. Protein engineering technologies combined with genomic information and metabolic engineering strategies hold promise for the design of plants and microbes to remediate organic and inorganic pollutants.
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Affiliation(s)
- Joseph M Jez
- Department of Biology, Washington University, St. Louis, Missouri 63130, USA.
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Librando V, Alparone A. The role of electronic properties to the mutagenic activity of 1,6- and 3,6-dinitrobenzo[a]pyrene isomers. JOURNAL OF HAZARDOUS MATERIALS 2009; 161:1338-1346. [PMID: 18571843 DOI: 10.1016/j.jhazmat.2008.04.095] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2008] [Revised: 04/22/2008] [Accepted: 04/23/2008] [Indexed: 05/26/2023]
Abstract
Equilibrium geometries, infrared spectra, vertical first ionization potential (IP), electronic affinity (EA), dipole moment (mu) and electronic dipole polarizability (alpha) of 1,6- and 3,6-dinitrobenzo[a]pyrene isomers (1,6-DNBaP and 3,6-DNBaP) were evaluated by means of Density Functional Theory (DFT) and recent semiempirical PM6 method. Structural, energetic and vibrational properties of DNBaP isomers are substantially similar to each other. Calculated IP, EA and alpha values of these isomers are practically identical, while mu of 3,6-DNBaP (8.2 D at DFT level) is predicted to be ca. 4 times the value of 1,6-DNBaP isomer (1.9 D at DFT level), owing to favorable mutual orientation of the individual nitro group vectors. Higher direct-mutagenic activities of 3,6-DNBaP with respect to 1,6-DNBaP isomer by 1-2 orders of magnitude might be determined by its peculiar electronic charge distribution, which through stronger electrostatic and inductive interactions, can promote much more effectively binding to active-site of enzymes involved in mutagenic pathways. On the other hand, orientation of the nitro substituents relatively to the plane of the aromatic moiety, molecular sizes, as well as nitroreduction and oxidation reactions seem not to have a key role in the determination of the different mutagenic behaviour of these isomers.
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Affiliation(s)
- Vito Librando
- Research Centre for Analysis, Monitoring and Minimization Methods of Environmental Risk and Department of Chemistry, University of Catania, viale A. Doria 8, I-95125 Catania, Italy.
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Librando V, Alparone A, Tomaselli G. Electronic properties of some nitrobenzo[a]pyrene isomers: a possible relationship to mutagenic activity. J Mol Model 2008; 14:489-97. [DOI: 10.1007/s00894-008-0297-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Accepted: 02/18/2008] [Indexed: 11/29/2022]
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Bertin PN, Médigue C, Normand P. Advances in environmental genomics: towards an integrated view of micro-organisms and ecosystems. MICROBIOLOGY-SGM 2008; 154:347-359. [PMID: 18227239 DOI: 10.1099/mic.0.2007/011791-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Microbial genome sequencing has, for the first time, made accessible all the components needed for both the elaboration and the functioning of a cell. Associated with other global methods such as protein and mRNA profiling, genomics has considerably extended our knowledge of physiological processes and their diversity not only in human, animal and plant pathogens but also in environmental isolates. At a higher level of complexity, the so-called meta approaches have recently shown great promise in investigating microbial communities, including uncultured micro-organisms. Combined with classical methods of physico-chemistry and microbiology, these endeavours should provide us with an integrated view of how micro-organisms adapt to particular ecological niches and participate in the dynamics of ecosystems.
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Affiliation(s)
- Philippe N Bertin
- Génétique Moléculaire, Génomique et Microbiologie, Université Louis Pasteur, UMR7156 CNRS, Strasbourg, France
| | | | - Philippe Normand
- Ecologie Microbienne, Université Claude Bernard - Lyon 1, UMR5557 CNRS, Villeurbanne, France
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Taly V, Urban P, Truan G, Pompon D. A combinatorial approach to substrate discrimination in the P450 CYP1A subfamily. Biochim Biophys Acta Gen Subj 2007; 1770:446-57. [PMID: 16996693 DOI: 10.1016/j.bbagen.2006.08.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2006] [Revised: 07/22/2006] [Accepted: 08/08/2006] [Indexed: 11/21/2022]
Abstract
A comparison of all known mammalian CYP1A sequences identifies nineteen sequence regions that are conserved within all 1A1s or within all 1A2s but at the same time systematically differ between any 1A1 and any 1A2. The purpose of this study was to explore links between these specific CYP1A sequence signatures and substrate specificity shift through the kinetic analysis of combinatorial variants of increasing complexity. The less complex variants correspond to multiple mutations within a short segment of their sequence. The more complex variants correspond to mosaic P450s recombining 1A1 and 1A2 sequences (up to 5 crossovers per sequence). Fifty-eight such functional CYP1A variants and parental wild-type enzymes were expressed in yeast and assayed with 7-alkoxyresorufins and ethoxyflurorescein ethyl ester as substrates. Observed kinetic data were analyzed by multivariate statistical analyses and hierarchical clustering in order to highlight correlations and identify potential sequence-activity relationships within the three-dimensional function space investigated. Several variants are outliers in these representations and show a redistribution of their substrate specificity compared to wild-type CYP1As. Some combinations of sequence elements were identified that significantly discriminate between 1A1 and 1A2 for these three substrates. The comparison of this combinatorial approach with previous results of site-directed mutagenesis is discussed.
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Affiliation(s)
- Valérie Taly
- Centre de Génétique Moléculaire, Centre National de la Recherche Scientifique, UPR2167, Avenue de la Terrasse, 91190 Gif-sur-Yvette, France
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de la Peña Mattozzi M, Tehara SK, Hong T, Keasling JD. Mineralization of paraoxon and its use as a sole C and P source by a rationally designed catabolic pathway in Pseudomonas putida. Appl Environ Microbiol 2006; 72:6699-706. [PMID: 17021221 PMCID: PMC1610300 DOI: 10.1128/aem.00907-06] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Organophosphate compounds, which are widely used as pesticides and chemical warfare agents, are cholinesterase inhibitors. These synthetic compounds are resistant to natural degradation and threaten the environment. We constructed a strain of Pseudomonas putida that can efficiently degrade a model organophosphate, paraoxon, and use it as a carbon, energy, and phosphorus source. This strain was engineered with the pnp operon from Pseudomonas sp. strain ENV2030, which encodes enzymes that transform p-nitrophenol into beta-ketoadipate, and with a synthetic operon encoding an organophosphate hydrolase (encoded by opd) from Flavobacterium sp. strain ATCC 27551, a phosphodiesterase (encoded by pde) from Delftia acidovorans, and an alkaline phosphatase (encoded by phoA) from Pseudomonas aeruginosa HN854 under control of a constitutive promoter. The engineered strain can efficiently mineralize up to 1 mM (275 mg/liter) paraoxon within 48 h, using paraoxon as the sole carbon and phosphorus source and an inoculum optical density at 600 nm of 0.03. Because the organism can utilize paraoxon as a sole carbon, energy, and phosphorus source and because one of the intermediates in the pathway (p-nitrophenol) is toxic at high concentrations, there is no need for selection pressure to maintain the heterologous pathway.
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Chiu WC, You JY, Liu JS, Hsu SK, Hsu WH, Shih CH, Hwang JK, Wang WC. Structure-stability-activity relationship in covalently cross-linked N-carbamoyl D-amino acid amidohydrolase and N-acylamino acid racemase. J Mol Biol 2006; 359:741-53. [PMID: 16650857 DOI: 10.1016/j.jmb.2006.03.063] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2006] [Revised: 03/27/2006] [Accepted: 03/30/2006] [Indexed: 11/24/2022]
Abstract
N-Acylamino acid racemase (NAAAR) and N-carbamoyl-D-amino-acid amidohydrolase (D-NCAase) are important biocatalysts for producing enantiopure alpha-amino acids. NAAAR forms an octameric assembly and displays induced fit movements upon substrate binding, while D-NCAase is a tetramer that does not change conformation in the presence of a ligand. To investigate the effects of introducing potentially stabilizing S-S bridges in these different multimeric enzymes, cysteine residues predicted to form inter or intra-subunit disulfide bonds were introduced by site-directed mutagenesis. Inter-subunit S-S bonds were formed in two NAAAR variants (A68C-D72C and P60C-Y100C) and two d-NCAase variants (A302C and P295C-F304C). Intra-subunit S-S bonds were formed in two additional NAAAR variants (E149C-A182C and V265C). Crystal structures of NAAARs variants show limited deviations from the wild-type overall tertiary structure. An apo A68C-D72C subunit differs from the wild-type enzyme, in which it has an ordered lid loop, resembling ligand-bound NAAAR. The structures of A222C and A302C D-NCAases are nearly identical to the wild-type enzyme. All mutants with inter-subunit bridges had increases in thermostability. Compared with the wild-type enzyme, A68C-D72C NAAAR showed similar kcat/Km ratios, whereas mutant D-NCAases demonstrated increased kcat/Km ratios at high temperatures (A302C: 4.2-fold at 65 degrees C). Furthermore, molecular dynamic simulations reveal that A302C substantially sustains the fine-tuned catalytic site as temperature increases, achieving enhanced activity.
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Affiliation(s)
- Wei-Chun Chiu
- Institute of Molecular and Cellular Biology & Department of Life Science, National Tsing Hua University, HsinChu, Taiwan, 30013, ROC
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