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Wang J, Gao C, Chen X, Liu L. Expanding the lysine industry: biotechnological production of l-lysine and its derivatives. ADVANCES IN APPLIED MICROBIOLOGY 2021; 115:1-33. [PMID: 34140131 DOI: 10.1016/bs.aambs.2021.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
l-lysine is an essential amino acid that contains various functional groups including α-amino, ω-amino, and α-carboxyl groups, exhibiting high reaction potential. The derivatization of these functional groups produces a series of value-added chemicals, such as cadaverine, glutarate, and d-lysine, that are widely applied in the chemical synthesis, cosmetics, food, and pharmaceutical industries. Here, we review recent advances in the biotechnological production of l-lysine and its derivatives and expatiate key technological strategies. Furthermore, we also discuss the existing challenges and potential strategies for more efficient production of these chemicals.
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Affiliation(s)
- Jiaping Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China.
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2
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Novel mutagenesis and screening technologies for food microorganisms: advances and prospects. Appl Microbiol Biotechnol 2020; 104:1517-1531. [DOI: 10.1007/s00253-019-10341-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 12/19/2019] [Accepted: 12/28/2019] [Indexed: 12/19/2022]
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3
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The evolving interface between synthetic biology and functional metagenomics. Nat Chem Biol 2018; 14:752-759. [DOI: 10.1038/s41589-018-0100-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 06/13/2018] [Indexed: 12/15/2022]
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4
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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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5
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van Rossum T, Muras A, Baur MJ, Creutzburg SC, van der Oost J, Kengen SW. A growth- and bioluminescence-based bioreporter for the in vivo detection of novel biocatalysts. Microb Biotechnol 2017; 10:625-641. [PMID: 28393499 PMCID: PMC5404197 DOI: 10.1111/1751-7915.12612] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 01/10/2017] [Accepted: 01/13/2017] [Indexed: 11/28/2022] Open
Abstract
The use of bioreporters in high-throughput screening for small molecules is generally laborious and/or expensive. The technology can be simplified by coupling the generation of a desired compound to cell survival, causing only positive cells to stay in the pool of generated variants. Here, a dual selection/screening system was developed for the in vivo detection of novel biocatalysts. The sensor part of the system is based on the transcriptional regulator AraC, which controls expression of both a selection reporter (LeuB or KmR; enabling growth) for rapid reduction of the initially large library size and a screening reporter (LuxCDABE; causing bioluminescence) for further quantification of the positive variants. Of four developed systems, the best system was the medium copy system with KmR as selection reporter. As a proof of principle, the system was tested for the selection of cells expressing an l-arabinose isomerase derived from mesophilic Escherichia coli or thermophilic Geobacillus thermodenitrificans. A more than a millionfold enrichment of cells with l-arabinose isomerase activity was demonstrated by selection and exclusion of false positives by screening. This dual selection/screening system is an important step towards an improved detection method for small molecules, and thereby for finding novel biocatalysts.
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Affiliation(s)
- Teunke van Rossum
- Laboratory of MicrobiologyWageningen University and ResearchStippeneng 46708WE WageningenThe Netherlands
| | - Aleksandra Muras
- Laboratory of MicrobiologyWageningen University and ResearchStippeneng 46708WE WageningenThe Netherlands
| | - Marco J.J. Baur
- Laboratory of MicrobiologyWageningen University and ResearchStippeneng 46708WE WageningenThe Netherlands
| | - Sjoerd C.A. Creutzburg
- Laboratory of MicrobiologyWageningen University and ResearchStippeneng 46708WE WageningenThe Netherlands
| | - John van der Oost
- Laboratory of MicrobiologyWageningen University and ResearchStippeneng 46708WE WageningenThe Netherlands
| | - Servé W.M. Kengen
- Laboratory of MicrobiologyWageningen University and ResearchStippeneng 46708WE WageningenThe Netherlands
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6
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Behrendorff JBYH, Gillam EMJ. Prospects for Applying Synthetic Biology to Toxicology: Future Opportunities and Current Limitations for the Repurposing of Cytochrome P450 Systems. Chem Res Toxicol 2016; 30:453-468. [DOI: 10.1021/acs.chemrestox.6b00396] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | - Elizabeth M. J. Gillam
- School
of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane 4072, Australia
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7
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Wang Y, Li Q, Zheng P, Guo Y, Wang L, Zhang T, Sun J, Ma Y. Evolving the L-lysine high-producing strain of Escherichia coli using a newly developed high-throughput screening method. J Ind Microbiol Biotechnol 2016; 43:1227-35. [PMID: 27369765 PMCID: PMC4983297 DOI: 10.1007/s10295-016-1803-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 06/22/2016] [Indexed: 12/30/2022]
Abstract
This study provided a new method which applied a selected L-lysine-inducible promoter for evolving lysine industrial strains of E. coli. According to the intracellular levels of the enhanced green fluorescent protein (EGFP) whose expression was controlled by the promoter, 186 strains were preliminarily selected using fluorescence-activated cell sorting from a 10-million-mutant library generated from a L-lysine high-producing E. coli strain. By subsequent multiple parameter evaluation of the 186 selected strains according to the concentration and the yield of lysine, the productivity per unit of cell in 96-deep-well blocks, two mutants MU-1 and MU-2 were obtained. They produced 136.51 ± 1.55 and 133.2 9 ± 1.42 g/L of lysine, respectively, in 5-L jars. Compared with the lysine concentration and the yield of the original strain, those of strain MU-1 improved by 21.00 and 9.05 %, respectively, and those of strain MU-2 improved by 18.14 and 10.41 %, respectively. The mutant selection and evaluation system newly established in our study should be useful for continuous improvement of the current E. coli strains in the lysine industry.
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Affiliation(s)
- Yan Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, People's Republic of China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China
| | - Qinggang Li
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China
| | - Ping Zheng
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China. .,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China.
| | - Yanmei Guo
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China
| | - Lixian Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China
| | - Tongcun Zhang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, People's Republic of China
| | - Jibin Sun
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China. .,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China.
| | - Yanhe Ma
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China
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8
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Wang Z, Cirino PC. New and improved tools and methods for enhanced biosynthesis of natural products in microorganisms. Curr Opin Biotechnol 2016; 42:159-168. [PMID: 27284635 DOI: 10.1016/j.copbio.2016.05.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 05/17/2016] [Accepted: 05/18/2016] [Indexed: 12/28/2022]
Abstract
Engineering efficient biosynthesis of natural products in microorganisms requires optimizing gene expression levels to balance metabolite flux distributions and to minimize accumulation of toxic intermediates. Such metabolic optimization is challenged with identifying the right gene targets, and then determining and achieving appropriate gene expression levels. After decades of having a relatively limited set of gene regulation tools available, metabolic engineers are recently enjoying an ever-growing repertoire of more precise and tunable gene expression platforms. Here we review recent applications of natural and designed transcriptional and translational regulatory machinery for engineering biosynthesis of natural products in microorganisms. Customized trans-acting RNAs (sgRNA, asRNA and sRNA), along with appropriate accessory proteins, are allowing for unparalleled tuning of gene expression. Meanwhile metabolite-responsive transcription factors and riboswitches have been implemented in strain screening and evolution, and in dynamic gene regulation. Further refinements and expansions on these platform technologies will circumvent many long-term obstacles in natural products biosynthesis.
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Affiliation(s)
- Zhiqing Wang
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204, USA
| | - Patrick C Cirino
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204, USA.
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9
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Frei CS, Wang Z, Qian S, Deutsch S, Sutter M, Cirino PC. Analysis of amino acid substitutions in AraC variants that respond to triacetic acid lactone. Protein Sci 2016; 25:804-14. [PMID: 26749125 DOI: 10.1002/pro.2873] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 01/04/2016] [Indexed: 12/21/2022]
Abstract
The Escherichia coli regulatory protein AraC regulates expression of ara genes in response to l-arabinose. In efforts to develop genetically encoded molecular reporters, we previously engineered an AraC variant that responds to the compound triacetic acid lactone (TAL). This variant (named "AraC-TAL1") was isolated by screening a library of AraC variants, in which five amino acid positions in the ligand-binding pocket were simultaneously randomized. Screening was carried out through multiple rounds of alternating positive and negative fluorescence-activated cell sorting. Here we show that changing the screening protocol results in the identification of different TAL-responsive variants (nine new variants). Individual substituted residues within these variants were found to primarily act cooperatively toward the gene expression response. Finally, X-ray diffraction was used to solve the crystal structure of the apo AraC-TAL1 ligand-binding domain. The resolved crystal structure confirms that this variant takes on a structure nearly identical to the apo wild-type AraC ligand-binding domain (root-mean-square deviation 0.93 Å), suggesting that AraC-TAL1 behaves similar to wild-type with regard to ligand recognition and gene regulation. Our results provide amino acid sequence-function data sets for training and validating AraC modeling studies, and contribute to our understanding of how to design new biosensors based on AraC.
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Affiliation(s)
- Christopher S Frei
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, 77204
| | - Zhiqing Wang
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, 77204
| | - Shuai Qian
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, 77204
| | - Samuel Deutsch
- Joint Genome Institute, 2800 Mitchell Drive Walnut Creek, California, 94598
| | - Markus Sutter
- Joint Genome Institute, 2800 Mitchell Drive Walnut Creek, California, 94598
| | - Patrick C Cirino
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, 77204
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10
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Building cellular pathways and programs enabled by the genetic diversity of allo-genomes and meta-genomes. Curr Opin Biotechnol 2015; 36:16-31. [DOI: 10.1016/j.copbio.2015.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 08/06/2015] [Accepted: 08/09/2015] [Indexed: 12/21/2022]
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11
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Liu D, Evans T, Zhang F. Applications and advances of metabolite biosensors for metabolic engineering. Metab Eng 2015; 31:35-43. [DOI: 10.1016/j.ymben.2015.06.008] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 06/23/2015] [Accepted: 06/23/2015] [Indexed: 01/01/2023]
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12
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Chen W, Zhang S, Jiang P, Yao J, He Y, Chen L, Gui X, Dong Z, Tang SY. Design of an ectoine-responsive AraC mutant and its application in metabolic engineering of ectoine biosynthesis. Metab Eng 2015; 30:149-155. [PMID: 26051748 DOI: 10.1016/j.ymben.2015.05.004] [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: 01/29/2015] [Revised: 05/22/2015] [Accepted: 05/26/2015] [Indexed: 01/27/2023]
Abstract
Advanced high-throughput screening methods for small molecules may have important applications in the metabolic engineering of the biosynthetic pathways of these molecules. Ectoine is an excellent osmoprotectant that has been widely used in cosmetics. In this study, the Escherichia coli regulatory protein AraC was engineered to recognize ectoine as its non-natural effector and to activate transcription upon ectoine binding. As an endogenous reporter of ectoine, the mutated AraC protein was successfully incorporated into high-throughput screening of ectoine hyper-producing strains. The ectoine biosynthetic cluster from Halomonas elongata was cloned into E. coli. By engineering the rate-limiting enzyme L-2,4-diaminobutyric acid (DABA) aminotransferase (EctB), ectoine production and the specific activity of the EctB mutant were increased. Thus, these results demonstrated the effectiveness of engineering regulatory proteins into sensitive and rapid screening tools for small molecules and highlighted the importance and efficacy of directed evolution strategies applied to the engineering of genetic components for yield improvement in the biosynthesis of small molecules.
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Affiliation(s)
- Wei Chen
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shan Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Peixia Jiang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jun Yao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongzhi He
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lincai Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiwu Gui
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, China
| | - Zhiyang Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Shuang-Yan Tang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
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13
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Novel screening methods--biosensors. Curr Opin Biotechnol 2015; 35:30-6. [PMID: 25578902 DOI: 10.1016/j.copbio.2014.12.021] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Revised: 12/19/2014] [Accepted: 12/19/2014] [Indexed: 02/06/2023]
Abstract
Biosensors offer exciting possibilities for improving cells or enzymes as biocatalysts for the synthesis of small molecules. We here review recent progress in the development and the screening applications of transcription-factor-based biosensors. An example is a cofactor-dependent biosensor which provides a generalizable screen for NADPH-dependent enzymes. Another example is the use of a biosensor in combination with recombineering for strain development, thereby expanding the genome engineering techniques to deliver directly bacteria producing small molecules of interest. Biosensor-based techniques in combination with fluorescence-activated cell sorting demonstrate that the gap regarding throughput capabilities of existing methods for the generation of genetic diversity and methods for the subsequent screening can be closed.
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14
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Frommer J, Appel B, Müller S. Ribozymes that can be regulated by external stimuli. Curr Opin Biotechnol 2014; 31:35-41. [PMID: 25146171 DOI: 10.1016/j.copbio.2014.07.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 07/30/2014] [Indexed: 12/20/2022]
Abstract
Ribozymes have been known for about 30 years, and nowadays are understood well enough to be turned into useful tools for a number of applications in vitro and in vivo. Allosteric ribozymes switch on and off their activity in response to a specific chemical (ligand) or physical (temperature, light) signal. The possibility of controlling ribozyme activity by external stimuli is of particular relevance for applications in different fields, such as environmental and medicinal diagnostics, molecular computing, control of gene expression and others. Herein, we review recent advances and describe selected examples of addressable ribozymes.
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Affiliation(s)
- Jennifer Frommer
- Ernst Moritz Arndt University Greifswald, Institute for Biochemistry, Felix Hausdorff Str. 4, D-17487 Greifswald, Germany
| | - Bettina Appel
- Ernst Moritz Arndt University Greifswald, Institute for Biochemistry, Felix Hausdorff Str. 4, D-17487 Greifswald, Germany
| | - Sabine Müller
- Ernst Moritz Arndt University Greifswald, Institute for Biochemistry, Felix Hausdorff Str. 4, D-17487 Greifswald, Germany.
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15
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Recent advances in engineering proteins for biocatalysis. Biotechnol Bioeng 2014; 111:1273-87. [DOI: 10.1002/bit.25240] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 02/10/2014] [Accepted: 03/19/2014] [Indexed: 01/14/2023]
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16
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Generation and selection of ribozyme variants with potential application in protein engineering and synthetic biology. Appl Microbiol Biotechnol 2014; 98:3389-99. [DOI: 10.1007/s00253-014-5528-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 01/06/2014] [Accepted: 01/07/2014] [Indexed: 12/22/2022]
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17
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Siedler S, Stahlhut SG, Malla S, Maury J, Neves AR. Novel biosensors based on flavonoid-responsive transcriptional regulators introduced into Escherichia coli. Metab Eng 2013; 21:2-8. [PMID: 24188962 DOI: 10.1016/j.ymben.2013.10.011] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 10/04/2013] [Accepted: 10/25/2013] [Indexed: 01/19/2023]
Abstract
This study describes the construction of two flavonoid biosensors, which can be applied for metabolic engineering of Escherichia coli strains. The biosensors are based on transcriptional regulators combined with autofluorescent proteins. The transcriptional activator FdeR from Herbaspirillum seropedicae SmR1 responds to naringenin, while the repressor QdoR from Bacillus subtilis is inactivated by quercetin and kaempferol. Both biosensors showed over a 7-fold increase of the fluorescent signal after addition of their specific effectors, and a linear correlation between the fluorescence intensity and externally added flavonoid concentration. The QdoR-biosensor was successfully applied for detection of kaempferol production in vivo at the single cell level by fluorescence-activated cell sorting. Furthermore, the amount of kaempferol produced highly correlated with the specific fluorescence of E. coli cells containing a flavonol synthase from Arabidopsis thaliana (fls1). We expect the designed biosensors to be applied for isolation of genes involved in flavonoid biosynthetic pathways.
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Affiliation(s)
- Solvej Siedler
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, 2970 Hørsholm, Denmark
| | - Steen G Stahlhut
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, 2970 Hørsholm, Denmark
| | - Sailesh Malla
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, 2970 Hørsholm, Denmark
| | - Jérôme Maury
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, 2970 Hørsholm, Denmark.
| | - Ana Rute Neves
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, 2970 Hørsholm, Denmark
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18
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Lv W, Chen Y, Li D, Chen X, Leszczynski J. Methyl-triclosan binding to human serum albumin: multi-spectroscopic study and visualized molecular simulation. CHEMOSPHERE 2013; 93:1125-30. [PMID: 23911262 DOI: 10.1016/j.chemosphere.2013.06.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2012] [Revised: 05/31/2013] [Accepted: 06/11/2013] [Indexed: 05/10/2023]
Abstract
Methyl-triclosan (MTCS), a transformation product and metabolite of triclosan, has been widely spread in environment through the daily use of triclosan which is a commonly used anti-bacterial and anti-fungal substance in consumer products. Once entering human body, MTCS could affect the conformation of human serum albumin (HSA) by forming MTCS-HSA complex and alter function of protein and endocrine in human body. To evaluate the potential toxicity of MTCS, the binding mechanism of HSA with MTCS was investigated by UV-vis absorption, circular dichroism and Fourier transform infrared spectroscopy. Binding constants, thermodynamic parameters, the binding forces and the specific binding site were studied in detail. Binding constant at room tempreture (T = 298K) is 6.32 × 10(3)L mol(-1); ΔH(0), ΔS(0) and ΔG(0) were 22.48 kJ mol(-1), 148.16 J mol(-1)K(-1) and -21.68 kJ mol(-1), respectively. The results showed that the interactions between MTCS and HSA are mainly hydrophobic forces. The effects of MTCS on HSA conformation were also discussed. The binding distance (r = 1.2 nm) for MTCS-HSA system was calculated by the efficiency of fluorescence resonance energy transfer. The visualized binding details were also exhibited by molecular modeling method and the results could agree well with that from the experimental study.
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Affiliation(s)
- Wenjuan Lv
- Department of Chemistry, Lanzhou University, Lanzhou 730000, China; Interdisciplinary Nanotoxicity Center, Department of Chemistry, Jackson State University, Jackson, MS 39217, United States.
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19
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Williams GJ. Engineering polyketide synthases and nonribosomal peptide synthetases. Curr Opin Struct Biol 2013; 23:603-12. [PMID: 23838175 DOI: 10.1016/j.sbi.2013.06.012] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 06/14/2013] [Accepted: 06/17/2013] [Indexed: 01/05/2023]
Abstract
Naturally occurring polyketides and nonribosomal peptides with broad and potent biological activities continue to inspire the discovery of new and improved analogs. The biosynthetic apparatus responsible for the construction of these natural products has been the target of intensive protein engineering efforts. Traditionally, engineering has focused on substituting individual enzymatic domains or entire modules with those of different building block specificity, or by deleting various enzymatic functions, in an attempt to generate analogs. This review highlights strategies based on site-directed mutagenesis of substrate binding pockets, semi-rational mutagenesis, and whole-gene random mutagenesis to engineer the substrate specificity, activity, and protein interactions of polyketide and nonribosomal peptide biosynthetic machinery.
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Affiliation(s)
- Gavin J Williams
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, United States.
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20
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Tang SY, Qian S, Akinterinwa O, Frei CS, Gredell JA, Cirino PC. Screening for Enhanced Triacetic Acid Lactone Production by Recombinant Escherichia coli Expressing a Designed Triacetic Acid Lactone Reporter. J Am Chem Soc 2013; 135:10099-103. [DOI: 10.1021/ja402654z] [Citation(s) in RCA: 153] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Shuang-Yan Tang
- Department of Chemical Engineering, Pennsylvania State University, 226A Fenske Laboratory,
University Park, Pennsylvania 16802, United States
| | - Shuai Qian
- Department of Chemical & Biomolecular Engineering, University of Houston, S222 Engineering Building 1, Houston, Texas 77204-4004, United States
| | - Olubolaji Akinterinwa
- Department of Chemical Engineering, Pennsylvania State University, 226A Fenske Laboratory,
University Park, Pennsylvania 16802, United States
| | - Christopher S. Frei
- Department of Chemical & Biomolecular Engineering, University of Houston, S222 Engineering Building 1, Houston, Texas 77204-4004, United States
| | - Joseph A. Gredell
- Department of Chemical & Biomolecular Engineering, University of Houston, S222 Engineering Building 1, Houston, Texas 77204-4004, United States
| | - Patrick C. Cirino
- Department of Chemical & Biomolecular Engineering, University of Houston, S222 Engineering Building 1, Houston, Texas 77204-4004, United States
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21
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van Rossum T, Kengen SWM, van der Oost J. Reporter-based screening and selection of enzymes. FEBS J 2013; 280:2979-96. [DOI: 10.1111/febs.12281] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 04/05/2013] [Accepted: 04/09/2013] [Indexed: 12/25/2022]
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Chen Z, Zeng AP. Protein design in systems metabolic engineering for industrial strain development. Biotechnol J 2013; 8:523-33. [PMID: 23589416 DOI: 10.1002/biot.201200238] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Revised: 01/24/2013] [Accepted: 02/27/2013] [Indexed: 12/20/2022]
Abstract
Accelerating the process of industrial bacterial host strain development, aimed at increasing productivity, generating new bio-products or utilizing alternative feedstocks, requires the integration of complementary approaches to manipulate cellular metabolism and regulatory networks. Systems metabolic engineering extends the concept of classical metabolic engineering to the systems level by incorporating the techniques used in systems biology and synthetic biology, and offers a framework for the development of the next generation of industrial strains. As one of the most useful tools of systems metabolic engineering, protein design allows us to design and optimize cellular metabolism at a molecular level. Here, we review the current strategies of protein design for engineering cellular synthetic pathways, metabolic control systems and signaling pathways, and highlight the challenges of this subfield within the context of systems metabolic engineering.
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Affiliation(s)
- Zhen Chen
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Hamburg, Germany
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23
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Affiliation(s)
- Eleftherios T. Papoutsakis
- Dept. of Chemical and Biomolecular Engineering, Dept. of Biological Sciences, and the Delaware Biotechnology Institute; University of Delaware; 15 Innovation Way; Newark; DE; 19711
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24
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Sung JH, Han D, Lee JB. Self-assembled DNA-based giant thrombin nanoparticles for controlled release. Biotechnol J 2013; 8:215-20. [PMID: 23297045 DOI: 10.1002/biot.201200312] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 11/13/2012] [Accepted: 11/26/2012] [Indexed: 01/08/2023]
Abstract
Protein-aptamer interactions have been used in a wide range of fields, including medical diagnosis and protein delivery. Herein, we report a method for thrombin delivery with thrombin-binding aptamer (TBA), which is one of the well-known aptamers for thrombin, by generating giant thrombin nanoparticles (GTNPs). GTNPs can be synthesized by crosslinking thrombin with DNA nanostructures that possess several TBA molecules. To generate GTNPs, two different DNA nanostructures were used. Y-shaped DNA with TBA and X-shaped DNA with TBA were used for 250 and 650 nm GTNPs, respectively. Controlled release of thrombin from GTNPs was performed by adding complementary DNA (cDNA) to TBA. To investigate thrombin release from GTNPs, the sizes of the GTNPs were measured using dynamic light scattering, atomic force microscopy (AFM), and scanning electron microscopy (SEM). We confirmed a decrease in the size of GTNPs with various concentrations of cDNA, suggesting the release of thrombin. Based on these results, we expect that our method can be used to control the amount of thrombin released effectively. Our method is also widely applicable for effective protein delivery.
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Affiliation(s)
- Jong Hwan Sung
- Department of Chemical Engineering, Hongik University, Seoul, South Korea
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25
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BiotecVisions 2012, June. Biotechnol J 2012. [DOI: 10.1002/biot.201200053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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26
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Binder S, Schendzielorz G, Stäbler N, Krumbach K, Hoffmann K, Bott M, Eggeling L. A high-throughput approach to identify genomic variants of bacterial metabolite producers at the single-cell level. Genome Biol 2012; 13:R40. [PMID: 22640862 PMCID: PMC3446293 DOI: 10.1186/gb-2012-13-5-r40] [Citation(s) in RCA: 179] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Revised: 05/16/2012] [Accepted: 05/28/2012] [Indexed: 12/23/2022] Open
Abstract
We present a novel method for visualizing intracellular metabolite concentrations within single cells of Escherichia coli and Corynebacterium glutamicum that expedites the screening process of producers. It is based on transcription factors and we used it to isolate new L-lysine producing mutants of C. glutamicum from a large library of mutagenized cells using fluorescence-activated cell sorting (FACS). This high-throughput method fills the gap between existing high-throughput methods for mutant generation and genome analysis. The technology has diverse applications in the analysis of producer populations and screening of mutant libraries that carry mutations in plasmids or genomes.
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Affiliation(s)
- Stephan Binder
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
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