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Huang Z, Gu Z, Abuduwupuer X, Qin D, Liu Y, Guo Z, Gao R. Engineering non-conservative substrate recognition sites of extradiol dioxygenase: Computation guided design to diversify and accelerate degradation of aromatic compounds. Int J Biol Macromol 2024; 264:130739. [PMID: 38460639 DOI: 10.1016/j.ijbiomac.2024.130739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/16/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024]
Abstract
Extradiol dioxygenases (EDOs) catalyzing meta-cleavage of catecholic compounds promise an effective way to detoxify aromatic pollutants. This work reported a novel scenario to engineer our recently identified Type I EDO from Tcu3516 for a broader substrate scope and enhanced activity, which was based on 2,3-dihydroxybiphenyl (2,3-DHB)-liganded molecular docking of Tcu3516 and multiple sequence alignment with other 22 Type I EDOs. 11 non-conservative residues of Tcu3516 within 6 Å distance to the 2,3-DHB ligand center were selected as potential hotspots and subjected to semi-rational design using 6 catecholic analogues as substrates; the mutants V186L and V212N returned with progressive evolution in substrate scope and catalytic activity. Both mutants were combined with D285A for construction of double mutants and final triple mutant V186L/V212N/D285A. Except for 2,3-DHB (the mutant V186L/D285A gave the best catalytic performance), the triple mutant prevailed all other 5 catecholic compounds for their degradation; affording the catalytic efficiency kcat/Km value increase by 10-30 folds, protein Tm (structural rigidity) increase by 15 °C and the half-life time enhancement by 10 times compared to the wild type Tcu3516. The molecular dynamic simulation suggested that a stabler core and a more flexible entrance are likely accounting for enhanced catalytic activity and stability of enzymes.
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Affiliation(s)
- Zihao Huang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Zhenyu Gu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Xiemuxinuer Abuduwupuer
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Deyuan Qin
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Yuchen Liu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Zheng Guo
- Department of Biological and Chemical Engineering, Faculty of Technical Sciences, Aarhus University, Gustav Wieds Vej 10, Aarhus 8000, Denmark.
| | - Renjun Gao
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China.
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Han JT, Zhang SP, Jia WJ, Zhang Z, Wang Y, He YX. Discovery and structural analysis of a phloretin hydrolase from the opportunistic human pathogen Mycobacterium abscessus. FEBS J 2019; 286:1959-1971. [PMID: 30784195 DOI: 10.1111/febs.14792] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 01/25/2019] [Accepted: 02/18/2019] [Indexed: 11/28/2022]
Abstract
The family of PhlG proteins catalyses the hydrolysis of carbon-carbon bonds and is widely distributed across diverse bacterial species. Two members of the PhlG family have been separately identified as 2,4-diacetylphloroglucinol (2,4-DAPG) hydrolase and phloretin hydrolase; however, the extent of functional divergence and catalytic substrates for most members of this family is still unknown. Here, using sequence similarity network and gene co-occurrence analysis, we categorized PhlG proteins into several subgroups and inferred that PhlG proteins from Mycobacterium abscessus (MaPhlG) are likely to be functionally equivalent to phloretin hydrolase. Indeed, we confirmed the hydrolytic activity of MaPhlG towards phloretin and its analog monoacetylphloroglucinol (MAPG), and the crystal structure of MaPhlG in complex with MAPG revealed the key residues involved in catalysis and substrate binding. Through mutagenesis and enzymatic assays, we demonstrated that H160, I162, A213 and Q266, which are substituted in 2,4-DAPG hydrolase, are essential for the activity towards phloretin. Based on the conservation of these residues, potential phloretin hydrolases were identified from Frankia, Colletotrichum tofieldiae and Magnaporthe grisea, which are rhizosphere inhabitants. These enzymes may be important for rhizosphere adaptation of the producing microbes by providing a carbon source through anaerobic degradation of flavonoids. Taken together, our results provided a framework for understanding the mechanism of functional divergence of PhlG proteins.
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Affiliation(s)
- Jian-Ting Han
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, China
| | - Si-Ping Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, China
| | - Wen-Juan Jia
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, China
| | - Zhang Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, China
| | - Yong Wang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, China
| | - Yong-Xing He
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, China
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Duan Y, Liu Y, Huang T, Zou Y, Huang T, Hu K, Deng Z, Lin S. Divergent biosynthesis of indole alkaloids FR900452 and spiro-maremycins. Org Biomol Chem 2018; 16:5446-5451. [DOI: 10.1039/c8ob01181h] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
FR900452 was demonstrated to be biosynthesized by the gene cluster of maremycin G and diversified by SnoaL-like protein MarP.
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Affiliation(s)
- Yingyi Duan
- State Key Laboratory of Microbial Metabolism
- Joint International Laboratory of Metabolic & Developmental Sciences
- School of Life Sciences & Biotechnology
- Shanghai Jiao Tong University
- Shanghai
| | - Yanyan Liu
- State Key Laboratory of Microbial Metabolism
- Joint International Laboratory of Metabolic & Developmental Sciences
- School of Life Sciences & Biotechnology
- Shanghai Jiao Tong University
- Shanghai
| | - Tao Huang
- Kunming Institute of Botany
- Chinese Academy of Science
- Kunming
- P. R. China
| | - Yi Zou
- College of Pharmaceutical Science and Chinese Medicine
- Southwest University
- Chongqing
- P. R. China
| | - Tingting Huang
- State Key Laboratory of Microbial Metabolism
- Joint International Laboratory of Metabolic & Developmental Sciences
- School of Life Sciences & Biotechnology
- Shanghai Jiao Tong University
- Shanghai
| | - Kaifeng Hu
- Kunming Institute of Botany
- Chinese Academy of Science
- Kunming
- P. R. China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism
- Joint International Laboratory of Metabolic & Developmental Sciences
- School of Life Sciences & Biotechnology
- Shanghai Jiao Tong University
- Shanghai
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism
- Joint International Laboratory of Metabolic & Developmental Sciences
- School of Life Sciences & Biotechnology
- Shanghai Jiao Tong University
- Shanghai
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George KW, Hay AG. Bacterial strategies for growth on aromatic compounds. ADVANCES IN APPLIED MICROBIOLOGY 2016; 74:1-33. [PMID: 21459192 DOI: 10.1016/b978-0-12-387022-3.00005-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Although the biodegradation of aromatic compounds has been studied for over 40 years, there is still much to learn about the strategies bacteria employ for growth on novel substrates. Elucidation of these strategies is crucial for predicting the environmental fate of aromatic pollutants and will provide a framework for the development of engineered bacteria and degradation pathways. In this chapter, we provide an overview of studies that have advanced our knowledge of bacterial adaptation to aromatic compounds. We have divided these strategies into three broad categories: (1) recruitment of catabolic genes, (2) expression of "repair" or detoxification proteins, and (3) direct alteration of enzymatic properties. Specific examples from the literature are discussed, with an eye toward the molecular mechanisms that underlie each strategy.
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Affiliation(s)
- Kevin W George
- Field of Environmental Toxicology, Cornell University Ithaca, New York, USA; Department of Microbiology, Wing Hall, Cornell University Ithaca, New York, USA
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Chakka D, Gudla R, Madikonda AK, Pandeeti EVP, Parthasarathy S, Nandavaram A, Siddavattam D. The Organophosphate Degradation (opd) Island-borne Esterase-induced Metabolic Diversion in Escherichia coli and Its Influence on p-Nitrophenol Degradation. J Biol Chem 2015; 290:29920-30. [PMID: 26453310 DOI: 10.1074/jbc.m115.661249] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Indexed: 02/04/2023] Open
Abstract
In previous studies of the organophosphate degradation gene cluster, we showed that expression of an open reading frame (orf306) present within the cluster in Escherichia coli allowed growth on p-nitrophenol (PNP) as sole carbon source. We have now shown that expression of orf306 in E. coli causes a dramatic up-regulation in genes coding for alternative carbon catabolism. The propionate, glyoxylate, and methylcitrate cycle pathway-specific enzymes are up-regulated along with hca (phenylpropionate) and mhp (hydroxyphenylpropionate) degradation operons. These hca and mhp operons play a key role in degradation of PNP, enabling E. coli to grow using it as sole carbon source. Supporting growth experiments, PNP degradation products entered central metabolic pathways and were incorporated into the carbon backbone. The protein and RNA samples isolated from E. coli (pSDP10) cells grown in (14)C-labeled PNP indicated incorporation of (14)C carbon, suggesting Orf306-dependent assimilation of PNP in E. coli cells.
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Affiliation(s)
- Deviprasanna Chakka
- From the Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India
| | - Ramurthy Gudla
- From the Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India
| | - Ashok Kumar Madikonda
- From the Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India
| | - Emmanuel Vijay Paul Pandeeti
- From the Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India
| | - Sunil Parthasarathy
- From the Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India
| | - Aparna Nandavaram
- From the Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India
| | - Dayananda Siddavattam
- From the Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India
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Hajizadeh N, Sefidi Heris Y, Zununi Vahed S, Vallipour J, Hejazi MA, Golabi SM, Asadpour-Zeynali K, Hejazi MS. Biodegradation of Para Amino Acetanilide by Halomonas sp. TBZ3. Jundishapur J Microbiol 2015; 8:e18622. [PMID: 26495103 PMCID: PMC4609326 DOI: 10.5812/jjm.18622] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 06/04/2014] [Accepted: 06/14/2014] [Indexed: 12/07/2022] Open
Abstract
BACKGROUND Aromatic compounds are known as a group of highly persistent environmental pollutants. Halomonas sp. TBZ3 was isolated from the highly salty Urmia Lake of Iran. In this study, characterization of a new Halomonas isolate called Halomonas sp. TBZ3 and its employment for biodegradation of para-amino acetanilide (PAA), as an aromatic environmental pollutant, is described. OBJECTIVES This study aimed to characterize the TBZ3 isolate and to elucidate its ability as a biodegradative agent that decomposes PAA. MATERIALS AND METHODS Primarily, DNA-DNA hybridization between TBZ3, Halomonas denitrificans DSM18045T and Halomonas saccharevitans LMG 23976T was carried out. Para-amino acetanilide biodegradation was assessed using spectrophotometry and confirmed by gas chromatography-mass spectroscopy (GC-MS). Parameters effective on biodegradation of PAA were optimized by the Response Surface Methodology (RSM). RESULTS The DNA-DNA hybridization experiments between isolate TBZ3, H. denitrificans and H. saccharevitans revealed relatedness levels of 57% and 65%, respectively. According to GC-MS results, TBZ3 degrades PAA to benzene, hexyl butanoate, 3-methyl-1-heptanol and hexyl hexanoate. Temperature 32.92°C, pH 6.76, and salinity 14% are the optimum conditions for biodegradation with a confidence level of 95% (at level α = 0.05). CONCLUSIONS According to our results, Halomonas sp. TBZ3 could be considered as a biological agent for bioremediation of PAA and possibly other similar aromatic compounds.
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Affiliation(s)
- Nader Hajizadeh
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, IR Iran
- Department of Microbiology, Zanjan Branch, Islamic Azad University, Zanjan, IR Iran
| | - Youssof Sefidi Heris
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, IR Iran
- Department of Microbiology, Zanjan Branch, Islamic Azad University, Zanjan, IR Iran
| | - Sepideh Zununi Vahed
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, IR Iran
- Faculty of Advanced Biomedical Sciences, Tabriz University of Medical Sciences, Tabriz, IR Iran
| | - Javad Vallipour
- Department of Analytical Chemistry, Faculty of Chemistry, University of Tabriz, Tabriz, IR Iran
| | - Mohammad Amin Hejazi
- Branch for the Northwest and West Region, Agriculture Biotechnology Research Institute of Iran (ABRII), Tabriz, IR Iran
| | - Sayyed Mahdi Golabi
- Department of Analytical Chemistry, Faculty of Chemistry, University of Tabriz, Tabriz, IR Iran
| | - Karim Asadpour-Zeynali
- Department of Analytical Chemistry, Faculty of Chemistry, University of Tabriz, Tabriz, IR Iran
| | - Mohammad Saeid Hejazi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, IR Iran
- Faculty of Advanced Biomedical Sciences, Tabriz University of Medical Sciences, Tabriz, IR Iran
- Corresponding author: Mohammad Saeid Hejazi, Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, IR Iran. Tel: +98-4133372256, Fax: +98-413334 4798, E-mail:
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Catalytic properties of 2,3-dihydroxybiphenyl 1,2-dioxygenase from Dyella Ginsengisoli LA-4 immobilized on mesoporous silica SBA-15. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2013.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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8
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Lucey KS, Leadbetter JR. Catechol 2,3-dioxygenase and othermeta-cleavage catabolic pathway genes in the ‘anaerobic’ termite gut spirocheteTreponema primitia. Mol Ecol 2013; 23:1531-1543. [DOI: 10.1111/mec.12598] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 11/17/2013] [Accepted: 11/18/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Kaitlyn S. Lucey
- Ronald and Maxine Linde Center for Global Environmental Science; California Institute of Technology; Mail Code 100-23 Pasadena CA 91125 USA
| | - Jared R. Leadbetter
- Ronald and Maxine Linde Center for Global Environmental Science; California Institute of Technology; Mail Code 100-23 Pasadena CA 91125 USA
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10
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Zhou H, Qu Y, Kong C, Shen E, Wang J, Zhang X, Ma Q, Zhou J. The key role of a non-active-site residue Met148 on the catalytic efficiency of meta-cleavage product hydrolase BphD. Appl Microbiol Biotechnol 2013; 97:10399-411. [PMID: 23494625 DOI: 10.1007/s00253-013-4814-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 02/21/2013] [Accepted: 02/26/2013] [Indexed: 11/26/2022]
Abstract
meta-Cleavage product (MCP) hydrolases (EC 3.7.1.9) can catalyze a specific C-C bond fission during the microbial aerobic degradation of aromatics. The previous studies on structure-function relationship of MCP hydrolases mainly focus on the active site residues by site-directed mutagenesis. However, the information about the role of the non-active-site residues is still unclear. In this study, a non-active-site residue Met148 of MCP hydrolase BphD was selected as the mutagenesis site according to the sequence alignments, structure superimpose and the tunnel analysis, which underwent the saturation mutagenesis resulting 19 mutants. The catalytic efficiencies of the mutants on 6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) were all decreased compared with the wild-type one except for the M148D mutant. Especially, the M148P mutant exhibited 290-fold lower k cat/K m than that of the wild-type BphD. Transient kinetic analyses of M148P showed the reciprocal relaxation time corresponded to C-C bond cleavage and product release steps (9.6 s(-1)) was 4.08-fold lower than BphD WT (39.2 s(-1)). Tunnel cluster analysis of BphD WT, M148P and M148W demonstrated that only the bulky Trp148 could block tunnel T2 in the BphD WT, but it exhibited slight effects on the catalytic efficiency (0.94-fold of BphD WT). Therefore, product release was not the main reason for the efficiency decrease of M148P. On the other hand, molecular dynamics simulations on the BphD WT and BphD M148P in complex with HOPDA indicated that the dramatic decrease of the catalytic efficiencies of BphD M148P should be due to the unproductive binding of HOPDA. The study demonstrated the catalytic efficiency of MCP hydrolase can be engineered by modification of non-active site residue.
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Affiliation(s)
- Hao Zhou
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
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Tuning the substrate selectivity of meta-cleavage product hydrolase by domain swapping. Appl Microbiol Biotechnol 2012; 97:5343-50. [DOI: 10.1007/s00253-012-4405-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 08/29/2012] [Accepted: 09/04/2012] [Indexed: 10/27/2022]
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12
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Zhou H, Qu Y, Bu Y, Li X, Kong C, Ma Q, Zhang Q, Zhang X, Zhou J. Molecular-Simulation-Assisted Immobilization and Catalytic Performance of CC Hydrolase MfphA on SBA-15 Mesoporous Silica. Chempluschem 2012. [DOI: 10.1002/cplu.201100041] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Zhang Q, Qu Y, Zhou J, Zhang X, Zhou H, Ma Q, Li X. Optimization of 2,3-dihydroxybiphenyl 1,2-dioxygenase expression and its application for biosensor. BIORESOURCE TECHNOLOGY 2011; 102:10553-10560. [PMID: 21924604 DOI: 10.1016/j.biortech.2011.08.071] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 07/14/2011] [Accepted: 08/17/2011] [Indexed: 05/31/2023]
Abstract
In this study, two statistical experimental designs, Plackett-Burman design (PBD) and response surface methodology (RSM), were employed to enhance the expression of 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC_LA-4), which was subsequently used for the construction of catechol biosensor. Ten important factors were evaluated by PBD, and four significant parameters were then optimized by RSM. Under the favorable fermentation conditions, the maximal specific activity of BphC_LA-4 was about 0.58U/mg with catechol as substrate. Meanwhile, homology modeling and molecular docking were utilized to help understand the interaction between BphC_LA-4 and catecholic substrates, which illustrated that BphC_LA-4 presented lower binding affinity towards 4-methylcatechol in comparison with 3-methylcatechol and catechol. Interestingly, the BphC_LA-4 enzyme electrode prepared by SiO2 sol-gel showed good response to all these three catecholic compounds. The differences of selectivity to 4-methylcatechol between free and immobilized enzyme implied that the introduction of electro-catalysis might have an effect on the enzyme-catalysis process.
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Affiliation(s)
- Qiang Zhang
- State Key Laboratory of Fine Chemicals and Industrial Ecology and Environmental Engineering, Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
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Zhang Q, Qu Y, Zhang X, Zhou J, Wang H. Extradiol dioxygenase-SiO₂ sol-gel modified electrode for catechol and its derivatives detection. Biosens Bioelectron 2011; 26:4362-7. [PMID: 21592766 DOI: 10.1016/j.bios.2011.04.042] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 04/06/2011] [Accepted: 04/21/2011] [Indexed: 11/26/2022]
Abstract
A feasible and sensitive biosensor for catechol and its derivatives using 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC)-modified glassy carbon electrode was successfully constructed by polyvinyl alcohol-modified SiO₂ sol-gel method. The as-prepared biosensor was characterized by electrochemical impedance spectroscopy, and the surface topography of the film was imaged by atomic force microscope. Liquid chromatography-tandem mass spectrometry was applied to reveal the catalytic mechanism. BphC embedded in SiO₂ gel maintained its bioactivity well and exhibited excellent eletrocatalytical response to both catechol and some of its derivatives (such as 3-methylcatechol and 4-methylcatechol). The biosensor showed a linear amperometric response range between 0.002 mM and 0.8 mM catechol. And the sensitivity was 1.268 mA/(mM cm²) with a detection limit of 0.428 μM for catechol (S/N = 3). Furthermore, the BphC biosensor exhibited perfect selectivity for catechol in the mixtures of catechol and phenol. It was suggested that this flexible protocol would open up a new avenue for designing other ring-cleavage enzyme biosensors, which could be widely used for monitoring various kinds of environmental pollutants.
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Affiliation(s)
- Qiang Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian 116024, PR China
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Kourist R, Jochens H, Bartsch S, Kuipers R, Padhi SK, Gall M, Böttcher D, Joosten HJ, Bornscheuer UT. The alpha/beta-hydrolase fold 3DM database (ABHDB) as a tool for protein engineering. Chembiochem 2010; 11:1635-43. [PMID: 20593436 DOI: 10.1002/cbic.201000213] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Robert Kourist
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Strasse 4, 17487 Greifswald, Germany
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16
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Li A, Qu Y, Zhou J, Ma F, Zhou H, Shi S. Characterization of a novel meta-fission product hydrolase from Dyella ginsengisoli LA-4. Process Biochem 2010. [DOI: 10.1016/j.procbio.2009.08.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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17
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Pandeeti EVP, Chinnaboina MR, Siddavattam D. Benzoate-mediated changes on expression profile of soluble proteins in Serratia sp. DS001. Lett Appl Microbiol 2009; 48:566-71. [PMID: 19291211 DOI: 10.1111/j.1472-765x.2009.02564.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIM To assess differences in protein expression profile associated with shift in carbon source from succinate to benzoate in Serratia sp. DS001 using a proteomics approach. METHODS AND RESULTS A basic proteome map was generated for the soluble proteins extracted from Serratia sp. DS001 grown in succinate and benzoate. The differently and differentially expressed proteins were identified using ImageMaster 2D Platinum software (GE Healthcare). The identity of the proteins was determined by employing MS or MS/MS. Important enzymes such as Catechol 1,2 dioxygenase and transcriptional regulators that belong to the LysR superfamily were identified. CONCLUSIONS Nearly 70 proteins were found to be differentially expressed when benzoate was used as carbon source. Based on the protein identity and degradation products generated from benzoate it is found that ortho pathway is operational in Serratia sp. DS001. SIGNIFICANCE AND IMPACT OF THE STUDY Expression profile of the soluble proteins associated with shift in carbon source was mapped. The study also elucidates degradation pathway of benzoate in Serratia sp. DS001 by correlating the proteomics data with the catabolites of benzoate.
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Affiliation(s)
- E V P Pandeeti
- Department of Animal Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
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