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Fousek J, Dušek J, Hoffmeisterová H, Čeřovská N, Kundu JK, Moravec T. Quantitative Estimation of Promoter Activity in Cannabis sativa Using Agroinfiltration-Based Transient Gene Expression. Methods Mol Biol 2024; 2787:245-253. [PMID: 38656494 DOI: 10.1007/978-1-0716-3778-4_16] [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] [Indexed: 04/26/2024]
Abstract
To properly assess promoter activity, which is critical for understanding biosynthetic pathways in different plant species, we use agroinfiltration-based transient gene expression assay. We compare the activity of several known promoters in Nicotiana benthamiana with their activity in Cannabis sativa (both hemp and medicinal cannabis), which has attracted much attention in recent years for its industrial, medicinal, and recreational properties. Here we describe an optimized protocol for transient expression in Cannabis combined with a ratiometric GUS reporter system that allows more accurate evaluation of promoter activity and reduces the effects of variable infiltration efficiency.
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Affiliation(s)
- Jan Fousek
- Laboratory of Virology, Centre for Plant Virus Research, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jakub Dušek
- Laboratory of Virology, Centre for Plant Virus Research, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czech Republic
| | - Hana Hoffmeisterová
- Laboratory of Virology, Centre for Plant Virus Research, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czech Republic
| | - Noemi Čeřovská
- Laboratory of Virology, Centre for Plant Virus Research, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jiban Kumar Kundu
- Laboratory of Virology, Centre for Plant Virus Research, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czech Republic
- Plant Virus and Vector Interactions, Centre for Plant Virus Research, Crop Research Institute, Prague, Czech Republic
| | - Tomáš Moravec
- Laboratory of Virology, Centre for Plant Virus Research, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czech Republic.
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Zhu B, Qian C, Tang H, Kitaguchi T, Ueda H. Creating a Thermostable β-Glucuronidase Switch for Homogeneous Immunoassay by Disruption of Conserved Salt Bridges at Diagonal Interfaces. Biochemistry 2023; 62:309-317. [PMID: 35849118 DOI: 10.1021/acs.biochem.2c00165] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Escherichia coli β-glucuronidase (GUS) has been used as a reporter enzyme in molecular biology and engineered as an enzyme switch for the development of homogeneous biosensors. In this study, we developed a thermostable GUS enzyme switch based on the thermostable GUS mutant TR3337 by disrupting a conserved salt bridge (H514-E523) between the diagonal subunits of its homotetramer. A combinatorial library (240 variants) was screened using a novel high-throughput strategy, which led to the identification of mutant DLW (H514D/M516L/Y517W) as a functional enzyme switch in a caffeine-recognizing immunosensor. Molecular dynamics simulations were performed to predict the topology change around position 514, and a side-chain flip of D514 (repulsion with E523) was observed in the DLW mutant. Up to 1.8-fold of signal-to-background ratio was confirmed when measured at up to 45 °C, thereby highlighting the DLW mutant as a versatile tool for developing thermostable immunosensors for in vitro and in cellulo applications.
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Affiliation(s)
- Bo Zhu
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Cheng Qian
- Graduate School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Haoxuan Tang
- Graduate School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Tetsuya Kitaguchi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Hiroshi Ueda
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
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Han B, Hou Y, Jiang T, Lv B, Zhao L, Feng X, Li C. Computation-Aided Rational Deletion of C-Terminal Region Improved the Stability, Activity, and Expression Level of GH2 β-Glucuronidase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:11380-11389. [PMID: 30296070 DOI: 10.1021/acs.jafc.8b03449] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In this study, computation-aided design on the basis of structural analysis was employed to rationally identify a highly dynamic C-terminal region that regulates the stability, expression level, and activity of a GH2 fungal glucuronidase from Aspergillus oryzae Li-3 (PGUS). Then, four mutants with a precisely truncated C-terminal region in different lengths were constructed; among them, mutant D591-604 with a 3.8-fold increase in half-life at 65 °C and a 6.8 kJ/mol increase in Gibbs free energy showed obviously improved kinetic and thermodynamic stability in comparison to PGUS. Mutants D590-604 and D591-604 both showed approximately 2.4-fold increases in the catalytic efficiency kcat/ Km and 1.8-fold increases in the expression level. Additionally, the expression level of PGUS was doubled through a C-terminal region swap with bacterial GUS from E. coli (EGUS). Finally, the robust PGUS mutants D590-604 and D591-604 were applied in the preparation of glycyrrhetinic acid with 4.0- and 4.4-fold increases in concentration through glycyrrhizin hydrolysis by a fed-batch process.
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Affiliation(s)
- Beijia Han
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , People's Republic of China
| | - Yuhui Hou
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , People's Republic of China
| | - Tian Jiang
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , People's Republic of China
| | - Bo Lv
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , People's Republic of China
| | - Lina Zhao
- Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety , Institute of High Energy Physics, Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
| | - Xudong Feng
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , People's Republic of China
| | - Chun Li
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , People's Republic of China
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Briciu-Burghina C, Heery B, Regan F. Protocol for the recovery and detection of Escherichia coli in environmental water samples. Anal Chim Acta 2017; 964:178-186. [DOI: 10.1016/j.aca.2017.02.035] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/27/2017] [Accepted: 02/24/2017] [Indexed: 10/24/2022]
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5
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Yeom SJ, Han GH, Kim M, Kwon KK, Fu Y, Kim H, Lee H, Lee DH, Jung H, Lee SG. Controlled Aggregation and Increased Stability of β-Glucuronidase by Cellulose Binding Domain Fusion. PLoS One 2017; 12:e0170398. [PMID: 28099480 PMCID: PMC5242468 DOI: 10.1371/journal.pone.0170398] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 01/04/2017] [Indexed: 11/18/2022] Open
Abstract
Cellulose-binding domains (CBDs) are protein domains with cellulose-binding activity, and some act as leaders in the localization of cellulosomal scaffoldin proteins to the hydrophobic surface of crystalline cellulose. In this study, we found that a CBD fusion enhanced and improved soluble β-glucuronidase (GusA) enzyme properties through the formation of an artificially oligomeric state. First, a soluble CBD fused to the C-terminus of GusA (GusA-CBD) was obtained and characterized. Interestingly, the soluble GusA-CBD showed maximum activity at higher temperatures (65°C) and more acidic pH values (pH 6.0) than free GusA did (60°C and pH 7.5). Moreover, the GusA-CBD enzyme showed higher thermal and pH stabilities than the free GusA enzyme did. Additionally, GusA-CBD showed higher enzymatic activity in the presence of methanol than free GusA did. Evaluation of the protease accessibility of both enzymes revealed that GusA-CBD retained 100% of its activity after 1 h incubation in 0.5 mg/ml protease K, while free GusA completely lost its activity. Simple fusion of CBD as a single domain may be useful for tunable enzyme states to improve enzyme stability in industrial applications.
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Affiliation(s)
- Soo-Jin Yeom
- Synthetic Biology & Bioengineering Research Center, KRIBB, Yuseong-gu, Daejeon, Korea
| | - Gui Hwan Han
- Synthetic Biology & Bioengineering Research Center, KRIBB, Yuseong-gu, Daejeon, Korea
| | - Moonjung Kim
- Synthetic Biology & Bioengineering Research Center, KRIBB, Yuseong-gu, Daejeon, Korea
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, Korea
| | - Kil Koang Kwon
- Synthetic Biology & Bioengineering Research Center, KRIBB, Yuseong-gu, Daejeon, Korea
| | - Yaoyao Fu
- Synthetic Biology & Bioengineering Research Center, KRIBB, Yuseong-gu, Daejeon, Korea
| | - Haseong Kim
- Synthetic Biology & Bioengineering Research Center, KRIBB, Yuseong-gu, Daejeon, Korea
| | - Hyewon Lee
- Synthetic Biology & Bioengineering Research Center, KRIBB, Yuseong-gu, Daejeon, Korea
| | - Dae-Hee Lee
- Synthetic Biology & Bioengineering Research Center, KRIBB, Yuseong-gu, Daejeon, Korea
- Biosystems & Bioengineering, University of Science & Technology, Yuseong-gu, Daejeon, Korea
| | - Heungchae Jung
- Synthetic Biology & Bioengineering Research Center, KRIBB, Yuseong-gu, Daejeon, Korea
| | - Seung-Goo Lee
- Synthetic Biology & Bioengineering Research Center, KRIBB, Yuseong-gu, Daejeon, Korea
- Biosystems & Bioengineering, University of Science & Technology, Yuseong-gu, Daejeon, Korea
- * E-mail:
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Zhuang J, Li MY, Wu B, Liu YJ, Xiong AS. Arg156 in the AP2-Domain Exhibits the Highest Binding Activity among the 20 Individuals to the GCC Box in BnaERF-B3-hy15, a Mutant ERF Transcription Factor from Brassica napus. FRONTIERS IN PLANT SCIENCE 2016; 7:1603. [PMID: 27833627 PMCID: PMC5081391 DOI: 10.3389/fpls.2016.01603] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 10/11/2016] [Indexed: 05/29/2023]
Abstract
To develop mutants of the ERF factor with more binding activities to the GCC box, we performed in vitro directed evolution by using DNA shuffling and screened mutants through yeast one-hybrid assay. Here, a series of mutants were obtained and used to reveal key amino acids that induce changes in the DNA binding activity of the BnaERF-B3 protein. With the BnaERF-B3-hy15 as the template, we produced 12 mutants which host individual mutation of potential key residues. We found that amino acid 156 is the key site, and the other 18 mutants host the 18 corresponding individual amino acid residues at site 156. Among the 20 individuals comprising WT (Gly156), Mu3 (Arg156), and 18 mutants with other 18 amino acid residues, Arg156 in the AP2-domain is the amino acid residue with the highest binding activity to the GCC box. The structure of the α-helix in the AP2-domain affects the binding activity. Other residues within AP2-domain modulated binding activity of ERF protein, suggesting that these positions are important for binding activity. Comparison of the mutant and wild-type transcription factors revealed the relationship of protein function and sequence modification. Our result provides a potential useful resource for understanding the trans-activation of ERF proteins.
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Large scale analysis of the mutational landscape in β-glucuronidase: A major player of mucopolysaccharidosis type VII. Gene 2015; 576:36-44. [PMID: 26415878 DOI: 10.1016/j.gene.2015.09.062] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 08/17/2015] [Accepted: 09/23/2015] [Indexed: 11/22/2022]
Abstract
The lysosomal storage disorders are a group of 50 unique inherited diseases characterized by unseemly lipid storage in lysosomes. These malfunctions arise due to genetic mutations that result in deficiency or reduced activities of the lysosomal enzymes, which are responsible for catabolism of biological macromolecules. Sly syndrome or mucopolysaccharidosis type VII is a lysosomal storage disorder associated with the deficiency of β-glucuronidase (EC 3.2.1.31) that catalyzes the hydrolysis of β-D-glucuronic acid residues from the non-reducing terminal of glycosaminoglycan. The effects of the disease causing mutations on the framework of the sequences and structure of β-glucuronidase (GUSBp) were analyzed utilizing a variety of bioinformatic tools. These analyses showed that 211 mutations may result in alteration of the biological activity of GUSBp, including previously experimentally validated mutations. Finally, we refined 90 disease causing mutations, which presumably cause a significant impact on the structure, function, and stability of GUSBp. Stability analyses showed that mutations p.Phe208Pro, p.Phe539Gly, p.Leu622Gly, p.Ile499Gly and p.Ile586Gly caused the highest impact on GUSBp stability and function because of destabilization of the protein structure. Furthermore, structures of wild type and mutant GUSBp were subjected to molecular dynamics simulation to examine the relative structural behaviors in the explicit conditions of water. In a broader view, the use of in silico approaches provided a useful understanding of the effect of single point mutations on the structure-function relationship of GUSBp.
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Rochelet M, Solanas S, Betelli L, Chantemesse B, Vienney F, Hartmann A. Rapid amperometric detection of Escherichia coli in wastewater by measuring β-D glucuronidase activity with disposable carbon sensors. Anal Chim Acta 2015; 892:160-6. [PMID: 26388487 DOI: 10.1016/j.aca.2015.08.023] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 08/11/2015] [Accepted: 08/19/2015] [Indexed: 11/30/2022]
Abstract
An assay on the indirect amperometric quantification of the β-D-Glucuronidase (GLUase) activity was developed for the rapid and specific detection of Escherichia coli (E. coli) in complex environmental samples. The p-aminophenyl β-D-glucopyranoside (PAPG) was selected as an electrochemical substrate for GLUase measurement and the p-aminophenol (PAP) released during the enzymatic hydrolysis was monitored by cyclic voltammetry with disposable carbon screen-printed sensors. The intensity of the measured anodic peak current was proportional to the amount of GLUase, and therefore to the number of E. coli in the tested sample. Once the substrate concentration and pH values optimized, a GLUase detection limit of 10 ng mL(-1) was achieved. Using a procedure involving a filtration step of the bacteria followed by their incubation with the substrate solution containing both the nonionic detergent Triton X-100 as permeabilization agent and the culture media Luria broth to monitor the growth, filtered bacterial cells ranging from 5 × 10(4) to 10(8) UFC/membrane were detected within 3 h. The amperometric assay was applied to the determination of fecal contamination in raw and treated wastewater samples and it was successfully compared with conventional bacterial plating methods and uidA gene quantitative PCR. Owing to its ability to perform measurements in turbid media, the GLUase amperometric method is a reliable tool for the rapid and decentralized quantification of viable but also nonculturable E. coli in complex environmental samples.
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Affiliation(s)
- Murielle Rochelet
- Université Bourgogne Franche-Comté, UMR1347 Agroécologie, 17 Rue Sully, 21000 Dijon, France.
| | - Sébastien Solanas
- Université Bourgogne Franche-Comté, UMR1347 Agroécologie, 17 Rue Sully, 21000 Dijon, France
| | - Laetitia Betelli
- Université Bourgogne Franche-Comté, UMR1347 Agroécologie, 17 Rue Sully, 21000 Dijon, France
| | - Benoît Chantemesse
- Université Bourgogne Franche-Comté, UMR1347 Agroécologie, 17 Rue Sully, 21000 Dijon, France
| | - Fabienne Vienney
- Université Bourgogne Franche-Comté, UMR1347 Agroécologie, 17 Rue Sully, 21000 Dijon, France
| | - Alain Hartmann
- INRA, UMR1347 Agroécologie, 17 Rue Sully, 21000 Dijon, France
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9
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Liebherr RB, Renner M, Gorris HH. A single molecule perspective on the functional diversity of in vitro evolved β-glucuronidase. J Am Chem Soc 2014; 136:5949-55. [PMID: 24684619 DOI: 10.1021/ja412379p] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mechanisms that drive the evolution of new enzyme activity have been investigated by comparing the kinetics of wild-type and in vitro evolved β-glucuronidase (GUS) at the single molecule level. Several hundred single GUS molecules were separated in large arrays of 62,500 ultrasmall reaction chambers etched into the surface of a fused silica slide to observe their individual substrate turnover rates in parallel by fluorescence microscopy. Individual GUS molecules feature long-lived but divergent activity states, and their mean activity is consistent with classic Michaelis-Menten kinetics. The large number of single molecule substrate turnover rates is representative of the activity distribution within an entire enzyme population. Partially evolved GUS displays a much broader activity distribution among individual enzyme molecules than wild-type GUS. The broader activity distribution indicates a functional division of work between individual molecules in a population of partially evolved enzymes that-as so-called generalists-are characterized by their promiscuous activity with many different substrates.
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Affiliation(s)
- Raphaela B Liebherr
- Institute of Analytical Chemistry, Chemo- and Biosensors and ‡Institute of Biophysics and Physical Biochemistry, University of Regensburg , 93040 Regensburg, Germany
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Expression and function of a modified AP2/ERF transcription factor from Brassica napus enhances cold tolerance in transgenic Arabidopsis. Mol Biotechnol 2013; 53:198-206. [PMID: 22351429 DOI: 10.1007/s12033-012-9515-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
One of the most rapid and effective defensive mechanisms plants have for protecting themselves, from a variety of biotic and abiotic stresses, is the regulation of plant signal transcription factors. AP2/ERF factors play an important role in plant development as well as in hormonal regulation and cold response. Directed evolution is a powerful tool to modify proteins, improving their properties, and for studying their structure-function relations. Here, the transgenic Arabidopsis plants over-expressed a mutant gene, BnaERF-B3-hy15-mu3, which encoded for a factor that exhibited more binding activity with the GCC box element than the wild-type gene BnaERF-B3-hy15 encode factor, and exhibited more freezing tolerance than transgenic plants containing the original BnaERF-B3-hy15 gene. Real-time PCR analyses also revealed that the expression levels of several stress-regulated genes were altered in the over-expressed BnaERF-B3-hy15-mu3 transgenic lines. The BnaERF-B3-hy15 responded to exogenous ABA. Using RT-PCR analysis, the expression of BnaERF-B3-hy15 at different stages and stress treatments were also analyzed.
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Tian YS, Xu H, Xu J, Peng RH, Yao QH. Heterologous extracellular expression and initial characterization of the peroxisomal catalase from the methylotrophic yeast Hansenula polymorpha in Pichia pastoris. APPL BIOCHEM MICRO+ 2013. [DOI: 10.1134/s0003683813050141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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12
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Xiong AS, Peng RH, Zhuang J, Chen JM, Zhang B, Zhang J, Yao QH. A thermostable β-glucuronidase obtained by directed evolution as a reporter gene in transgenic plants. PLoS One 2011; 6:e26773. [PMID: 22096498 PMCID: PMC3212524 DOI: 10.1371/journal.pone.0026773] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Accepted: 10/03/2011] [Indexed: 11/18/2022] Open
Abstract
A β-glucuronidase variant, GUS-TR3337, that was obtained by directed evolution exhibited higher thermostability than the wild-type enzyme, GUS-WT. In this study, the utility of GUS-TR337 as an improved reporter was evaluated. The corresponding gus-tr3337 and gus-wt genes were independently cloned in a plant expression vector and introduced into Arabidopsis thaliana. With 4-MUG as a substrate, plants containing the gus-wt gene showed no detectable β-glucuronidase activity after exposure to 60°C for 10 min, while those hosting the gus-tr3337 gene retained 70% or 50% activity after exposure to 80°C for 10 min or 30 min, respectively. Similarly, in vivo β-glucuronidase activity could be demonstrated by using X-GLUC as a substrate in transgenic Arabidopsis plants hosting the gus-tr3337 gene that were exposed to 80°C for up to 30 min. Thus, the thermostability of GUS-TR3337 can be exploited to distinguish between endogenous and transgenic β-glucuronidase activity, which is a welcome improvement in its use as a reporter.
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Affiliation(s)
- Ai-Sheng Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, China
- * E-mail: ,cn (A-SX); (JZ); (Q-HY)
| | - Ri-He Peng
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jing Zhuang
- Alberta Innovates-Technology Futures, Vegreville, Alberta, Canada
| | - Jian-Min Chen
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Bin Zhang
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jian Zhang
- Alberta Innovates-Technology Futures, Vegreville, Alberta, Canada
- * E-mail: ,cn (A-SX); (JZ); (Q-HY)
| | - Quan-Hong Yao
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
- * E-mail: ,cn (A-SX); (JZ); (Q-HY)
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Xiong AS, Peng RH, Zhuang J, Davies J, Zhang J, Yao QH. Advances in directed molecular evolution of reporter genes. Crit Rev Biotechnol 2011; 32:133-42. [DOI: 10.3109/07388551.2011.593503] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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14
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Hydrolysis of the soluble fluorescent molecule carboxyumbelliferyl-beta-d-glucuronide by E. coli beta-glucuronidase as applied in a rugged, in situ optical sensor. Enzyme Microb Technol 2011; 49:6-10. [DOI: 10.1016/j.enzmictec.2011.03.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Revised: 08/30/2010] [Accepted: 03/19/2011] [Indexed: 11/18/2022]
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15
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Directed in vitro evolution of reporter genes based on semi-rational design and high-throughput screening. Methods Mol Biol 2010; 634:239-56. [PMID: 20676989 DOI: 10.1007/978-1-60761-652-8_18] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Marker genes, such as gusA, lacZ, and gfp, have been applied comprehensively in biological studies. Directed in vitro evolution provides a powerful tool for modifying genes and for studying gene structure, expression, and function. Here, we describe a strategy for directed in vitro evolution of reporter genes based on semi-rational design and high-throughput screening. The protocol involves two processes of DNA shuffling and screening. The first DNA shuffling and screening process involves eight steps: (1) amplifying the target gene by PCR, (2) cutting the product into random fragments with DNase I, (3) purification of 50-100 bp fragments, (4) reassembly of the fragments in a primerless PCR, (5) amplification of the reassembled product by primer PCR, (6) cloning into expression vector, (7) transformation of E. coli by electroporation, and (8) screening the target mutants using a nitrocellulose filter. The second DNA shuffling and screening process also involves the same eight steps, except that degenerate oligonucleotide primers are based on the sequence of the selected mutant.
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Xu H, Xiong AS, Zhao W, Tian YS, Peng RH, Chen JM, Yao QH. Characterization of a Glucose-, Xylose-, Sucrose-, and d-Galactose-Stimulated β-Glucosidase from the Alkalophilic Bacterium Bacillus halodurans C-125. Curr Microbiol 2010; 62:833-9. [DOI: 10.1007/s00284-010-9766-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Accepted: 09/08/2010] [Indexed: 09/29/2022]
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17
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Simultaneous mutations up to six distal sites using a phosphorylation-free and ligase-free polymerase chain reaction-based mutagenesis. Anal Biochem 2010; 401:315-7. [DOI: 10.1016/j.ab.2010.03.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2009] [Revised: 03/08/2010] [Accepted: 03/08/2010] [Indexed: 11/20/2022]
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18
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Montanucci L, Fariselli P, Martelli PL, Casadio R. Predicting protein thermostability changes from sequence upon multiple mutations. Bioinformatics 2008; 24:i190-5. [PMID: 18586713 PMCID: PMC2718644 DOI: 10.1093/bioinformatics/btn166] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Motivation: A basic question in protein science is to which extent mutations affect protein thermostability. This knowledge would be particularly relevant for engineering thermostable enzymes. In several experimental approaches, this issue has been serendipitously addressed. It would be therefore convenient providing a computational method that predicts when a given protein mutant is more thermostable than its corresponding wild-type. Results: We present a new method based on support vector machines that is able to predict whether a set of mutations (including insertion and deletions) can enhance the thermostability of a given protein sequence. When trained and tested on a redundancy-reduced dataset, our predictor achieves 88% accuracy and a correlation coefficient equal to 0.75. Our predictor also correctly classifies 12 out of 14 experimentally characterized protein mutants with enhanced thermostability. Finally, it correctly detects all the 11 mutated proteins whose increase in stability temperature is >10°C. Availability: The dataset and the list of protein clusters adopted for the SVM cross-validation are available at the web site http://lipid.biocomp.unibo.it/~ludovica/thermo-meso-MUT. Contact:casadio@alma.unibo.it
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Affiliation(s)
- Ludovica Montanucci
- Department of Biology, University of Bologna, via Irnerio 42, 40126 Bologna, Italy
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Xiong AS, Peng RH, Zhuang J, Gao F, Li Y, Cheng ZM, Yao QH. Chemical gene synthesis: strategies, softwares, error corrections, and applications. FEMS Microbiol Rev 2008; 32:522-40. [DOI: 10.1111/j.1574-6976.2008.00109.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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Xiong AS, Peng RH, Zhuang J, Liu JG, Gao F, Xu F, Cai B, Yao QH. A semi-rational design strategy of directed evolution combined with chemical synthesis of DNA sequences. Biol Chem 2008; 388:1291-300. [PMID: 18020945 DOI: 10.1515/bc.2007.153] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Directed evolution in vitro is a powerful molecular tool for the creation of new biological phenotypes. It is unclear whether it is more efficient to mutate an enzyme randomly or to mutate just the active sites or key sites. In this study, the strategy of a semi-rational design of directed evolution combined with whole sequence and sites was developed. The 1553 bp gene encoding the thermostable beta-galactosidase of Pyrococcus woesei was chemically synthesized and optimized for G+C content and mRNA secondary structures. The synthesized gene product was used as a template or as a wild-type control. On the basis of the first round of DNA shuffling, library construction and screening, one mutant of YH6754 was isolated with higher activity. Eight potential key sites were deduced from the sequence of the shuffled gene, and 16 degenerate oligonucleotides were designed according to those eight amino acids. Two variants of YG6765 and YG8252 were screened in the second part of DNA shuffling, library construction and screening. For comparison, one mutant of YH8757 was screened through the same routine rounds of directed evolution with YH6754 as template. The purified beta-galactosidase from YH8757 exhibited a lower specific activity at 25 degrees C than those purified from mutated YG6755 and YG8252.
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Affiliation(s)
- Ai-Sheng Xiong
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai 201106, China
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Xiong AS, Peng RH, Zhuang J, Li X, Xue Y, Liu JG, Gao F, Cai B, Chen JM, Yao QH. Directed evolution of a beta-galactosidase from Pyrococcus woesei resulting in increased thermostable beta-glucuronidase activity. Appl Microbiol Biotechnol 2007; 77:569-78. [PMID: 17876575 DOI: 10.1007/s00253-007-1182-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2007] [Revised: 08/10/2007] [Accepted: 08/23/2007] [Indexed: 11/29/2022]
Abstract
We performed directed evolution on a chemically synthesized 1,533-bp recombinant beta-galactosidase gene from Pyrococcus woesei. More than 200,000 variant colonies in each round of directed evolution were screened using the pYPX251 vector and host strain Rosetta-Blue (DE3). One shifted beta-galactosidase to beta-glucuronidase mutant, named YG6762, was obtained after four rounds of directed evolution and screening. This mutant had eight mutated amino acid residues. T29A, V213I, L217M, N277H, I387V, R491C, and N496D were key mutations for high beta-glucuronidase activity, while E414D was not essential because the mutation did not lead to a change in beta-glucuronidase activity. The amino acid site 277 was the most essential because mutating H back to N resulted in a 50% decrease in beta-glucuronidase activity at 37 degrees C. We also demonstrated that amino acid 277 was the most essential site, as the mutation from N to H resulted in a 1.5-fold increase in beta-glucuronidase activity at 37 degrees C. Although most single amino acid changes lead to less than a 20% increase in beta-glucuronidase activity, the YG6762 variant, which was mutated at all eight amino acid sites, had a beta-glucuronidase activity that was about five and seven times greater than the wild-type enzyme at 37 and 25 degrees C, respectively.
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Affiliation(s)
- Ai-Sheng Xiong
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, 201106, China
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