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Bai S, Luo H, Tong H, Wu Y, Yuan Y. Advances on transfer and maintenance of large DNA in bacteria, fungi, and mammalian cells. Biotechnol Adv 2024; 76:108421. [PMID: 39127411 DOI: 10.1016/j.biotechadv.2024.108421] [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: 03/24/2023] [Revised: 05/07/2024] [Accepted: 08/04/2024] [Indexed: 08/12/2024]
Abstract
Advances in synthetic biology allow the design and manipulation of DNA from the scale of genes to genomes, enabling the engineering of complex genetic information for application in biomanufacturing, biomedicine and other areas. The transfer and subsequent maintenance of large DNA are two core steps in large scale genome rewriting. Compared to small DNA, the high molecular weight and fragility of large DNA make its transfer and maintenance a challenging process. This review outlines the methods currently available for transferring and maintaining large DNA in bacteria, fungi, and mammalian cells. It highlights their mechanisms, capabilities and applications. The transfer methods are categorized into general methods (e.g., electroporation, conjugative transfer, induced cell fusion-mediated transfer, and chemical transformation) and specialized methods (e.g., natural transformation, mating-based transfer, virus-mediated transfection) based on their applicability to recipient cells. The maintenance methods are classified into genomic integration (e.g., CRISPR/Cas-assisted insertion) and episomal maintenance (e.g., artificial chromosomes). Additionally, this review identifies the major technological advantages and disadvantages of each method and discusses the development for large DNA transfer and maintenance technologies.
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Affiliation(s)
- Song Bai
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, China; Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Han Luo
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, China; Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Hanze Tong
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, China; Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Yi Wu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, China; Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China. @tju.edu.cn
| | - Yingjin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, China; Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
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Itakorode BO, Itakorode DI, Torimiro N, Okonji RE. Kinetic and thermodynamic investigation of Rhodanese synthesized by enhanced Klebsiella oxytoca JCM 1665 strain: a comparative between the free and immobilized enzyme entrapped in alginate beads. Prep Biochem Biotechnol 2024:1-10. [PMID: 38696619 DOI: 10.1080/10826068.2024.2347407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2024]
Abstract
Klebsiella oxytoca JCM 1665 was subjected to extracellular rhodanese production using a submerged fermentation technique. The organism was further engineered for higher cyanide tolerance and rhodanese yield using ethylmethanesulfonate as a mutagen. Mutagenesis resulted in an improved mutant with high cyanide tolerance (100 mM) and rhodanese yield (26.7 ± 0.67 U/mL). This yield was 4.34-fold higher than the wild strain (6.15 ± 0.65 U/mL). At temperatures ranging from 30 to 80 °C, the first-order thermal denaturation constant (Kd) for free enzyme increases from 0.00818 to 0.0333 min-1 while the immobilized enzyme increases from 0.003 to 0.0204 min-1. The equivalent half-life reduces from 99 to 21 minutes and 231 to 35 minutes, respectively. Residual activity tests were used to assess the thermodynamic parameters for both enzyme preparations. For the free enzyme, the parameters obtained were enthalpy (29.40 to 29.06 kJ.mol-1), entropy (-194.24 to -197.50 J.mol-1K-1) and Gibbs free energy (90.20 to 98.80 kJ.mol-1). In addition, for immobilized rhodanese, we obtained enthalpy (40.40 to 40.07 kJ.mol-1), entropy (-164.21 to - 165.20 J.mol-1K-1) and Gibbs free energy (91.80 to 98.40 kJ.mol-1. Regarding its operational stability, the enzyme was able to maintain 63% of its activity after being used for five cycles. Immobilized K. oxytoca rhodanese showed a marked resistance to heat inactivation compared to free enzyme forms; making it of utmost significance in many biotechnological applications.
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Affiliation(s)
- Babamotemi Oluwasola Itakorode
- Department of Biotechnology, Osun State University, Osogbo, Nigeria
- Department of Biochemistry and Molecular Biology, Obafemi Awolowo University Ile-Ife, Osun State, Nigeria
| | | | - Nkem Torimiro
- Department of Microbiology, Obafemi Awolowo University Ile-Ife, Osun state, Nigeria
| | - Raphael Emuebie Okonji
- Department of Biochemistry and Molecular Biology, Obafemi Awolowo University Ile-Ife, Osun State, Nigeria
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Liu Y, Wang K, Pan L, Chen X. Improved Production of ε-Poly-L-Lysine in Streptomyces albulus Using Genome Shuffling and Its High-Yield Mechanism Analysis. Front Microbiol 2022; 13:923526. [PMID: 35711770 PMCID: PMC9195005 DOI: 10.3389/fmicb.2022.923526] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 05/09/2022] [Indexed: 11/29/2022] Open
Abstract
ε-Poly-L-lysine (ε-PL), a natural food preservative, has recently gained interest and mainly produced by Streptomyces albulus. Lacking of efficient breeding methods limit ε-PL production improving, knockout byproducts and increase of main product flux strategies as a logical solution to increase yield. However, removing byproduct formation and improving main product synthesis has seen limited success due to the genetic background of ε-PL producing organism is not clear. To overcome this limitation, random mutagenesis continues to be the best way towards improving strains for ε-PL production. Recent advances in Illumina sequencing opened new avenues to understand improved strains. In this work, we used genome shuffling on strains obtained by ribosome engineering to generate a better ε-PL producing strain. The mutant strain SG-86 produced 144.7% more ε-PL than the parent strain M-Z18. Except that SG-86 displayed obvious differences in morphology and ATP compared to parent strain M-Z18. Using Illumina sequencing, we mapped the genomic changes leading to the improved phenotype. Sequencing two strains showed that the genome of the mutant strain was about 2.1 M less than that of the parent strain, including a large number of metabolic pathways, secondary metabolic gene clusters, and gene deletions. In addition, there are many SNPs (single nucleotide polymorphisms) and InDels (insertions and deletions) in the mutant strain. Based on the results of data analysis, a mechanism of ε-PL overproduction in S. albulus SG-86 was preliminarily proposed. This study is of great significance for improving the fermentation performance and providing theoretical guidance for the metabolic engineering construction of ε-PL producing strains.
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Affiliation(s)
- Yongjuan Liu
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,Shandong Energy Institute, Qingdao, China.,Qingdao New Energy Shandong Laboratory, Qingdao, China
| | - Kaifang Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Long Pan
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,College of Biological Engineering, Henan University of Technology, Zhengzhou, China
| | - Xusheng Chen
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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Hospet R, Thangadurai D, Cruz-Martins N, Sangeetha J, Anu Appaiah KA, Chowdhury ZZ, Bedi N, Soytong K, Al Tawahaj ARM, Jabeen S, Tallur MM. Genome shuffling for phenotypic improvement of industrial strains through recursive protoplast fusion technology. Crit Rev Food Sci Nutr 2021:1-10. [PMID: 34592865 DOI: 10.1080/10408398.2021.1983763] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Strains' improvement technology plays an essential role in enhancing the quality of industrial strains. Several traditional methods and modern techniques have been used to further improve strain engineering programs. The advances stated in strain engineering and the increasing demand for microbial metabolites leads to the invention of the genome shuffling technique, which ensures a specific phenotype improvement through inducing mutation and recursive protoplast fusion. In such technique, the selection of multi-parental strains with distinct phenotypic traits is crucial. In addition, as this evolutionary strain improvement technique involves combinative approaches, it does not require any gene sequence data for genome alteration and, therefore, strains developed by this elite technique will not be considered as genetically modified organisms. In this review, the different stages involved in the genome shuffling technique and its wide applications in various phenotype improvements will be addressed. Taken together, data discussed here highlight that the use of genome shuffling for strain improvement will be a plus for solving complex phenotypic traits and in promoting the rapid development of other industrially important strains.
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Affiliation(s)
| | | | - Natália Cruz-Martins
- Faculty of Medicine, University of Porto, Porto, Portugal.,Institute for Research and Innovation in Health (i3S), University of Porto, Porto, Portugal.,Institute of Research and Advanced Training in Health Sciences and Technologies (CESPU), Gandra PRD, Portugal
| | - Jeyabalan Sangeetha
- Department of Environmental Science, Central University of Kerala, Kasaragod, Kerala, India
| | - Konerira Aiyappa Anu Appaiah
- Department of Microbiology and Fermentation Technology, Central Food Technological Research Institute (CSIR), Mysore, Karnataka, India
| | - Zaira Zaman Chowdhury
- Nanotechnology and Catalysis Research Center (NANOCAT), Institute of Advanced Studies (IAS), University of Malaya, Kuala Lumpur, Malaysia
| | - Namita Bedi
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
| | - Kasem Soytong
- Department of Plant Production Technology, King Mongkut's Institute of Technology Ladkrabang (KMITL), Ladkrabang, Bangkok, Thailand
| | | | - Shoukat Jabeen
- Department of Botany, Karnatak University, Dharwad, Karnataka, India
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Sun J, Liu H, Dang L, Liu J, Wang J, Lu Z, Lu Y. Genome shuffling of Lactobacillus plantarum 163 enhanced antibacterial activity and usefulness in preserving orange juice. Lett Appl Microbiol 2021; 73:741-749. [PMID: 34562034 DOI: 10.1111/lam.13566] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/25/2021] [Accepted: 09/17/2021] [Indexed: 01/04/2023]
Abstract
Lactic acid bacteria have been used to inhibit the growth of spoilage bacteria in food and animal feeds. For instance, Lactobacillus plantarum 163 can inhibit efficiently the growth of both gram-positive and gram-negative bacteria. In our study, the antibacterial activity of L. plantarum 163 was further improved significantly by genome shuffling. The optimal conditions for protoplast formation and regeneration were 20 mg ml-1 lysozyme and 5 mg ml-1 mutanolysin for 30 min at 37°C using 0·5 mol l-1 sucrose as stabilizer. The protoplasts were inactivated under ultraviolet light for 120 s or heated at 58°C for 20 min. After two rounds of genome shuffling, the inhibitory activity of strain F2-14 was improved by 2·45- and 1·99-fold, respectively, as compared to their parent strains. The prepared antibacterial peptides supernatant (APS) was added to the orange juice to inhibit spores of Alicyclobacillus acidoterrestris (SAA) at 45 and 28°C. Results showed that the growth of A. acidoterrestris was significantly inhibited, and the decrease in total soluble solids, OD value and pH value was also delayed. After treatment with APS, the thermal sensitivity of spores was increased and its D value was reduced to 13·78, 3·87 and 1·47 min at 80, 90 and 95°C respectively.
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Affiliation(s)
- J Sun
- College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing, China
| | - H Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - L Dang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - J Liu
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University (BTBU), Beijing, China
| | - J Wang
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University (BTBU), Beijing, China
| | - Z Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Y Lu
- College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing, China
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Ghosh S, Dam B. Genome shuffling improves pigment and other bioactive compound production in Monascus purpureus. Appl Microbiol Biotechnol 2020; 104:10451-10463. [DOI: 10.1007/s00253-020-10987-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 10/05/2020] [Accepted: 10/28/2020] [Indexed: 11/25/2022]
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Baldwin EL, Karki B, Johnson TJ, Zahler JD, Gibbons J, Gibbons WR. Enhancing Cellulase Production in Aureobasidium pullulans by Genome Shuffling. Ind Biotechnol (New Rochelle N Y) 2020. [DOI: 10.1089/ind.2018.0011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Emily L. Baldwin
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Bishnu Karki
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Tylor J. Johnson
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
- Department of Microbiology, The University of Tennessee, Knoxville, TN, USA
| | - Jacob D. Zahler
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Jaimie Gibbons
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - William R. Gibbons
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
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CgCmk1 Activates CgRds2 To Resist Low-pH Stress in Candida glabrata. Appl Environ Microbiol 2020; 86:AEM.00302-20. [PMID: 32245757 DOI: 10.1128/aem.00302-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 03/27/2020] [Indexed: 02/07/2023] Open
Abstract
In Candida glabrata, the transcription factor CgRds2 has been previously characterized as a regulator of glycerophospholipid metabolism, playing a crucial role in the response to osmotic stress. Here, we report that CgRds2 is also involved in the response to pH 2.0 stress. At pH 2.0, the deletion of CgRDS2 led to reduced cell growth and survival, by 33% and 57%, respectively, compared with those of the wild-type strain. These adverse phenotypes resulted from the downregulation of genes related to energy metabolism in the Cgrds2Δ strain at pH 2.0, which led to a 34% reduction of the intracellular ATP content and a 24% decrease in membrane permeability. In contrast, the overexpression of CgRDS2 rescued the growth defect of the Cgrds2Δ strain and increased cell survival at pH 2.0 by 17% compared with that of the wild-type strain, and this effect was accompanied by significant increases in ATP content and membrane permeability, by 42% and 19%, respectively. Furthermore, we found that the calcium/calmodulin-dependent protein kinase (CaMK) CgCmk1 physically interacts with the PAS domain of CgRds2, and CgCmk1 is required for CgRds2 activation and translocation from the cytoplasm to the nucleus under pH 2.0 stress. Moreover, CgCmk1 is critical for CgRds2 function in resistance to pH 2.0 stress, because cells of the Cgrds2-pas strain with a disrupted CgCmk1-CgRds2 interaction exhibited impaired energy metabolism and membrane permeability at pH 2.0. Therefore, our results indicate that CgCmk1 positively regulates CgRds2 and suggest that they promote resistance to low-pH stress by enhancing energy metabolism and membrane permeability in C. glabrata IMPORTANCE An acidic environment is the main problem in the production of organic acids in C. glabrata The present study reports that the calcium/calmodulin-dependent protein kinase CgCmk1 positively regulates CgRds2 to increase intracellular ATP content, membrane permeability, and resistance to low-pH stress. Hence, the transcription factor CgRds2 may be a potential target for improving the acid stress tolerance of C. glabrata during the fermentation of organic acids. The present study also establishes a new link between the calcium signaling pathway and energy metabolism.
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Patel D, Buch A. Improvisation of a spectrophotometric method to quantify hydroxycitric acid. Anal Biochem 2019; 586:113412. [PMID: 31473244 DOI: 10.1016/j.ab.2019.113412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 08/18/2019] [Accepted: 08/28/2019] [Indexed: 11/16/2022]
Abstract
Existing spectrophotometric method to quantify hydroxycitric acid (HCA), although is specific and sensitive; finds limited use owing to poor stability of HCA-metavanadate complex. Present study describes improvisation of this method with respect to source of HCA standard and assay parameters. Assay system consisting of HCA and metavanadate reagent was modified to include 1 M NaOH to neutralize excess acidity. Resulting complex showed λmax at 485 nm, obeying Beer-Lambert's law within concentration range of 33-677 μg/ml, with linear calibration curve showing a good coefficient of determination (R2 = 0.998). Moreover, HCA-metavanadate complex showed enhanced stability retaining up to 70% absorbance even after 60 min of its formation. Similar consistency in scaled-down assay system renders the method suitable for high-throughput screening of HCA-producing microbes. Of the tested metabolites and media components, only tartrate interfered with the spectrophotometric estimation of HCA; a correction factor to eliminate which was also established. Accordingly measured HCA level in the culture supernatant of a bacterial isolate IT6 was comparable to that determined using the standardized HPLC method. The proposed procedure therefore is a convenient, sensitive, accurate and high-throughput method suitable for primary screening of HCA producing microbes; the only ecofriendly alternative source of optically pure HCA.
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Affiliation(s)
- Disha Patel
- Department of Biological Sciences, P D Patel Institute of Applied Sciences, Charotar University of Science and Technology, CHARUSAT Campus, Changa, 388 421, Dist. Anand, Gujarat, India.
| | - Aditi Buch
- Department of Biological Sciences, P D Patel Institute of Applied Sciences, Charotar University of Science and Technology, CHARUSAT Campus, Changa, 388 421, Dist. Anand, Gujarat, India.
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Zhang P, Lee Y, Wei X, Wu J, Liu Q, Wan S. Enhanced production of tanshinone IIA in endophytic fungi Emericella foeniculicola by genome shuffling. PHARMACEUTICAL BIOLOGY 2018; 56:357-362. [PMID: 30266071 PMCID: PMC6171462 DOI: 10.1080/13880209.2018.1481108] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 03/14/2018] [Accepted: 05/16/2018] [Indexed: 06/08/2023]
Abstract
CONTEXT Tanshinone IIA, commercially produced from Salvia miltiorrhiza Bunge (C.Y.Wu) (Labiatae), has various biological benefits. Currently, this compound is mainly extracted from plants. However, because of the long growth cycle and the unstable quality of plants, the market demands can barely be satisfied. OBJECTIVE The genomic shuffling technology is applied to screen the high-yield tanshinone IIA strain, which could be used to replace the plant S. miltiorrhiza for the production of tanshinone IIA. The change in the production of tanshinone IIA is clarified by comparing it with the original strain. MATERIALS AND METHODS Tanshinone IIA was extracted from Strains cells, which was prepared through 0.5 mL protoplast samples by using hypertonic solution I from two different strains. Then, it was analyzed by high-performance liquid chromatography at 30 °C and UV 270 nm. Total DNA from the strains was extracted for RAPD amplification and electrophoresis to isolate the product. RESULTS In this study, a high-yield tanshinone IIA strain F-3.4 was screened and the yield of tanshinone IIA was increased by 387.56 ± 0.02 mg/g, 11.07 times higher than that of the original strain TR21. DISCUSSION This study shows that the genetic basis of high-yield strains is achieved through genome shuffling, which proves that genome shuffling can shorten the breeding cycle and improve the mutagenesis efficiency in obtaining the strains with good traits and it is a useful method for the molecular breeding of industrial strains.
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Affiliation(s)
- Pengyu Zhang
- College of Life Sciences, Shaanxi Normal University, Chang’an Campus, Xi’an, Shaanxi, China
| | - Yiting Lee
- College of Life Sciences, Shaanxi Normal University, Chang’an Campus, Xi’an, Shaanxi, China
| | - Xiying Wei
- College of Life Sciences, Shaanxi Normal University, Chang’an Campus, Xi’an, Shaanxi, China
| | - Jinlan Wu
- College of Life Sciences, Shaanxi Normal University, Chang’an Campus, Xi’an, Shaanxi, China
| | - Qingmei Liu
- College of Life Sciences, Shaanxi Normal University, Chang’an Campus, Xi’an, Shaanxi, China
| | - Shanning Wan
- College of Life Sciences, Shaanxi Normal University, Chang’an Campus, Xi’an, Shaanxi, China
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Enhancement of Pyruvate Productivity in Candida glabrata by Deleting the CgADE13 Gene to Improve Acid Tolerance. BIOTECHNOL BIOPROC E 2018. [DOI: 10.1007/s12257-018-0201-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Shi J, Zhu X, Lu Y, Zhao H, Lu F, Lu Z. Improving Iturin A Production of Bacillus amyloliquefaciens by Genome Shuffling and Its Inhibition Against Saccharomyces cerevisiae in Orange Juice. Front Microbiol 2018; 9:2683. [PMID: 30467499 PMCID: PMC6236126 DOI: 10.3389/fmicb.2018.02683] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 10/19/2018] [Indexed: 11/13/2022] Open
Abstract
Genome shuffling is an effective method for the rapid improvement of the production of secondary metabolites. This study used the principle of gene shuffling to enhance the yield of iturin A produced by Bacillus amyloliquefaciens LZ-5. Improvements in lipopeptide yield were evident among four strains subjected to recursive protoplast fusion. The four strains were obtained through mutagenesis processes: nitrosoguanidine, ultraviolet irradiation, and atmospheric and room temperature plasma. A high yield strain with 179.22 mg/l of iturin A was obtained after two rounds of genome shuffling, which was a 2.03-fold increase compared with the wild strain. To evaluate the efficacy of iturin A for control of spoilage yeast in food, the anti-yeast efficacy of iturin A was evaluated in orange juice incubated with Saccharomyces cerevisiae. The juice treated with 0.76 mg/ml iturin A showed a significant (p < 0.05) control on yeast population during the storage, similar to that of the 0.30 mg/ml natamycin. In addition, iturin A showed a tiny effect on chemical-physical characteristics of orange juice. Our results provide a basis for the application of antimicrobial lipopeptide in juice products.
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Affiliation(s)
- Juran Shi
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xiaoyu Zhu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yingjian Lu
- Department of Nutrition and Food Science, University of Maryland, College Park, MD, United States
| | - Haizhen Zhao
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Fengxia Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
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Genome shuffling and high-throughput screening of Brevibacterium flavum MDV1 for enhanced l-valine production. World J Microbiol Biotechnol 2018; 34:121. [DOI: 10.1007/s11274-018-2502-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 07/10/2018] [Indexed: 11/25/2022]
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Xu F, Wang S, Li Y, Zheng M, Xi X, Cao H, Cui X, Guo H, Han C. Yield enhancement strategies of rare pharmaceutical metabolites from endophytes. Biotechnol Lett 2018; 40:797-807. [PMID: 29605937 DOI: 10.1007/s10529-018-2531-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 02/28/2018] [Indexed: 11/25/2022]
Abstract
Endophytes are barely untapped as vital sources in the medicine. They are microorganisms which mostly exist in plants. As they are exploited, it is accepted that endophytes can produce active metabolites that possess same function as their hosts such as taxol, podophyllotoxin, hypericin, and azadirachtin. These metabolites have been promising potential usefulness in safety and human health concerns. We are supposed to adopt measures to raise production for the low yield of metabolites. This paper summarizes the latest advances in various bioprocess optimization strategies. These techniques can overcome the limitations associated with rare pharmaceutical metabolite-producing endophytic fungi. These strategies include strain improvement, genome shuffling, medium optimization, fermentation conditions optimization, addition of specific factor, addition of solid sorbent, and co-culturing. It will enable endophytes to produce high and sustainable production of rare pharmaceutical metabolites.
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Affiliation(s)
- Fangxue Xu
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, 250355, People's Republic of China
| | - Shiyuan Wang
- School of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, 250355, People's Republic of China
| | - Yujuan Li
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, 250355, People's Republic of China
| | - Mengmeng Zheng
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, 250355, People's Republic of China
| | - Xiaozhi Xi
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, 250355, People's Republic of China
| | - Hui Cao
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, 250355, People's Republic of China
| | - Xiaowei Cui
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, 250355, People's Republic of China
| | - Hong Guo
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, 250355, People's Republic of China
| | - Chunchao Han
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, 250355, People's Republic of China.
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Tong QQ, Zhou YH, Chen XS, Wu JY, Wei P, Yuan LX, Yao JM. Genome shuffling and ribosome engineering of Streptomyces virginiae for improved virginiamycin production. Bioprocess Biosyst Eng 2018; 41:729-738. [DOI: 10.1007/s00449-018-1906-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 01/31/2018] [Indexed: 10/18/2022]
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Wu J, Luo Q, Liu J, Chen X, Liu L. Enhanced pyruvate production in Candida glabrata by overexpressing the CgAMD1 gene to improve acid tolerance. Biotechnol Lett 2017; 40:143-149. [PMID: 28983762 DOI: 10.1007/s10529-017-2452-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 09/27/2017] [Indexed: 10/18/2022]
Abstract
OBJECTIVES To enhance acid tolerance of Candida glabrata for pyruvate production by engineering AMP metabolism. RESULTS The physiological function of AMP deaminase in AMP metabolism from C. glabrata was investigated by deleting or overexpresseing the corresponding gene, CgAMD1. At pH 4, CgAMD1 overexpression resulted in 59 and 51% increases in biomass and cell viability compared to those of wild type strain, respectively. In addition, the intracellular ATP level of strain Cgamd1Δ/CgAMD1 was down-regulated by 22%, which led to a 94% increase in pyruvate production. Further, various strengths of CgAMD1 expression cassettes were designed, thus resulting in a 59% increase in pyruvate production at pH 4. Strain Cgamd1Δ/CgAMD1 (H) was grown in a 30 l batch bioreactor at pH 4, and pyruvate reached 46.1 g/l. CONCLUSION CgAMD1 overexpression plays an active role in improving acid tolerance and pyruvate fermentation performance of C. glabrata at pH 4.
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Affiliation(s)
- Jing Wu
- School of Pharmaceutical Science, Jiangnan University, Wuxi, 214122, China
| | - Qiuling Luo
- School of Pharmaceutical Science, Jiangnan University, Wuxi, 214122, China.,State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China. .,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
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Yin H, Liu M, Deng Y, Zhao J, Yu J, Dong J, Yang M. Reduced acetaldehyde production by genome shuffling of an industrial brewing yeast strain. JOURNAL OF THE INSTITUTE OF BREWING 2017. [DOI: 10.1002/jib.457] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Hua Yin
- State Key Laboratory of Biological Fermentation Engineering of Beer; Tsingtao Brewery Co. Ltd; Qingdao 266061 People's Republic of China
| | - Ming Liu
- China National Research Institute of Food and Fermentation Industries; Beijing 100015 People's Republic of China
| | - Yang Deng
- State Key Laboratory of Biological Fermentation Engineering of Beer; Tsingtao Brewery Co. Ltd; Qingdao 266061 People's Republic of China
| | - Junfeng Zhao
- College of Food Science and Engineering; Henan University of Science and Technology; Luoyang 471003 People's Republic of China
| | - Junhong Yu
- State Key Laboratory of Biological Fermentation Engineering of Beer; Tsingtao Brewery Co. Ltd; Qingdao 266061 People's Republic of China
| | - Jianjun Dong
- State Key Laboratory of Biological Fermentation Engineering of Beer; Tsingtao Brewery Co. Ltd; Qingdao 266061 People's Republic of China
| | - Mei Yang
- State Key Laboratory of Biological Fermentation Engineering of Beer; Tsingtao Brewery Co. Ltd; Qingdao 266061 People's Republic of China
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Zhao Y, Duan C, Gao L, Yu X, Niu C, Li S. Genome shuffling of Lactobacillus plantarum C88 improves adhesion. Biosci Biotechnol Biochem 2017; 81:184-193. [DOI: 10.1080/09168451.2016.1224637] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Abstract
Genome shuffling is an important method for rapid improvement in microbial strains for desired phenotypes. In this study, ultraviolet irradiation and nitrosoguanidine were used as mutagens to enhance the adhesion of the wild-type Lactobacillus plantarum C88. Four strains with better property were screened after mutagenesis to develop a library of parent strains for three rounds of genome shuffling. Fusants F3-1, F3-2, F3-3, and F3-4 were screened as the improved strains. The in vivo and in vitro tests results indicated that the population after three rounds of genome shuffling exhibited improved adhesive property. Random Amplified Polymorphic DNA results showed significant differences between the parent strain and recombinant strains at DNA level. These results suggest that the adhesive property of L. plantarum C88 can be significantly improved by genome shuffling. Improvement in the adhesive property of bacterial cells by genome shuffling enhances the colonization of probiotic strains which further benefits to exist probiotic function.
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Affiliation(s)
- Yujuan Zhao
- Institute of Agro-food Technology, Jilin Academy of Agricultural Sciences, Changchun, PR China
| | - Cuicui Duan
- Institute of Agro-food Technology, Jilin Academy of Agricultural Sciences, Changchun, PR China
| | - Lei Gao
- Institute of Agro-food Technology, Jilin Academy of Agricultural Sciences, Changchun, PR China
| | - Xue Yu
- Institute of Agro-food Technology, Jilin Academy of Agricultural Sciences, Changchun, PR China
| | - Chunhua Niu
- Institute of Agro-food Technology, Jilin Academy of Agricultural Sciences, Changchun, PR China
| | - Shengyu Li
- Institute of Agro-food Technology, Jilin Academy of Agricultural Sciences, Changchun, PR China
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Crz1p Regulates pH Homeostasis in Candida glabrata by Altering Membrane Lipid Composition. Appl Environ Microbiol 2016; 82:6920-6929. [PMID: 27663025 DOI: 10.1128/aem.02186-16] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Accepted: 09/02/2016] [Indexed: 12/17/2022] Open
Abstract
The asexual facultative aerobic haploid yeast Candida glabrata is widely used in the industrial production of various organic acids. To elucidate the physiological function of the C. glabrata transcription factor Crz1p (CgCrz1p) and its role in tolerance to acid stress, we deleted or overexpressed the corresponding gene, CgCRZ1 Deletion of CgCRZ1 resulted in a 60% decrease in the dry weight of cells (DCW) and a 50% drop in cell viability compared with those of the wild type at pH 2.0. Expression of lipid metabolism-associated genes was also significantly downregulated. Consequently, the proportion of C18:1 fatty acids, the ratio of unsaturated to saturated fatty acids, and the ergosterol content decreased by 30%, 46%, and 30%, respectively. Additionally, membrane integrity, fluidity, and H+-ATPase activity were reduced by 45%, 9%, and 50%, respectively. In contrast, overexpression of CgCrz1p increased C18:1 and ergosterol contents by 16% and 40%, respectively. Overexpression also enhanced membrane integrity, fluidity, and H+-ATPase activity by 31%, 6%, and 20%, respectively. Moreover, in the absence of pH buffering, the DCW and pyruvate titers increased by 48% and 60%, respectively, compared to that of the wild type. Together, these results suggest that CgCrz1p regulates tolerance to acidic conditions by altering membrane lipid composition in C. glabrataIMPORTANCE This study provides insight into the metabolism of Candida glabrata under acidic conditions, such as those encountered during the industrial production of organic acids. We found that overexpression of the transcription factor CgCrz1p improved viability, biomass, and pyruvate yields at a low pH. Analysis of plasma membrane lipid composition indicated that CgCrz1p might play an important role in its integrity and fluidity and that it enhanced the pumping of protons in acidic environments. We propose that altering the structure of the cell membrane may provide a successful strategy for increasing C. glabrata productivity at a low pH.
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20
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Genome shuffling of Saccharomyces cerevisiae for enhanced glutathione yield and relative gene expression analysis using fluorescent quantitation reverse transcription polymerase chain reaction. J Microbiol Methods 2016; 127:188-192. [DOI: 10.1016/j.mimet.2016.06.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 06/06/2016] [Accepted: 06/10/2016] [Indexed: 11/18/2022]
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21
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Optimization of genome shuffling for high-yield production of the antitumor deacetylmycoepoxydiene in an endophytic fungus of mangrove plants. Appl Microbiol Biotechnol 2016; 100:7491-8. [DOI: 10.1007/s00253-016-7457-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 03/01/2016] [Accepted: 03/05/2016] [Indexed: 11/26/2022]
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22
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Zhao J, Zhang C, Lu J, Lu Z. Enhancement of fengycin production in Bacillus amyloliquefaciens by genome shuffling and relative gene expression analysis using RT-PCR. Can J Microbiol 2016; 62:431-6. [PMID: 27035066 DOI: 10.1139/cjm-2015-0734] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Genome shuffling is an efficient approach for the rapid engineering of microbial strains with desirable industrial phenotypes. In this study, we used genome shuffling in an attempt to improve fengycin production of the wild-type strain Bacillus amyloliquefaciens ES-2-4. After 2 rounds of genome shuffling, a high-yield recombinant F2-72 (FMB72) strain that exhibited 8.30-fold increases in fengycin production was obtained. Comparative analysis of synthetase gene (fenA) expression was conducted between the initial and shuffled strains using fluorescent quantitation RT-PCR. Delta CT (threshold cycle) relative quantitation analysis revealed that fengycin synthetase gene (fenA) expression at the transcriptional level in the FMB72 strain was 12.77-fold greater than in the ES-2-4 wild type. The shuffled strain has a potential application in food and pharmaceutical industries. At the same time, the analysis of improved phenotypes will provide more valuable data for inverse metabolic engineering.
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Affiliation(s)
- Junfeng Zhao
- a College of Food Science and Engineering, Henan University of Science and Technology, Tianjing Road, Luoyang 471003, People's Republic of China
| | - Chong Zhang
- b College of Food Science and Technology, Nanjing Agricultural University, Jiangsu, Nanjing 210095, People's Republic of China
| | - Jing Lu
- b College of Food Science and Technology, Nanjing Agricultural University, Jiangsu, Nanjing 210095, People's Republic of China
| | - Zhaoxin Lu
- b College of Food Science and Technology, Nanjing Agricultural University, Jiangsu, Nanjing 210095, People's Republic of China
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23
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Li SB, Qian Y, Liang ZW, Guo Y, Zhao MM, Pang ZW. Enhanced butanol production from cassava with Clostridium acetobutylicum by genome shuffling. World J Microbiol Biotechnol 2016; 32:53. [DOI: 10.1007/s11274-016-2022-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 01/29/2016] [Indexed: 11/29/2022]
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24
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Genome shuffling of Lactobacillus brevis for enhanced production of thymidine phosphorylase. BIOTECHNOL BIOPROC E 2015. [DOI: 10.1007/s12257-014-0617-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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25
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Liu P, Zhu X, Tan Z, Zhang X, Ma Y. Construction of Escherichia Coli Cell Factories for Production of Organic Acids and Alcohols. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2015; 155:107-40. [PMID: 25577396 DOI: 10.1007/10_2014_294] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Production of bulk chemicals from renewable biomass has been proved to be sustainable and environmentally friendly. Escherichia coli is the most commonly used host strain for constructing cell factories for production of bulk chemicals since it has clear physiological and genetic characteristics, grows fast in minimal salts medium, uses a wide range of substrates, and can be genetically modified easily. With the development of metabolic engineering, systems biology, and synthetic biology, a technology platform has been established to construct E. coli cell factories for bulk chemicals production. In this chapter, we will introduce this technology platform, as well as E. coli cell factories successfully constructed for production of organic acids and alcohols.
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Affiliation(s)
- Pingping Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Xinna Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Zaigao Tan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Area, Tianjin, 300308, China.,University of Chinese Academy of Sciences, Tianjin, China
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China. .,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Area, Tianjin, 300308, China.
| | - Yanhe Ma
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
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26
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Da-Costa-Rocha I, Bonnlaender B, Sievers H, Pischel I, Heinrich M. Hibiscus sabdariffa L. – A phytochemical and pharmacological review. Food Chem 2014; 165:424-43. [DOI: 10.1016/j.foodchem.2014.05.002] [Citation(s) in RCA: 417] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Revised: 03/26/2014] [Accepted: 05/01/2014] [Indexed: 02/06/2023]
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27
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Ding S, Zhang Y, Zhang J, Zeng W, Yang Y, Guan J, Pan L, Li W. Enhanced deacidification activity in Schizosaccharomyces pombe by genome shuffling. Yeast 2014; 32:317-25. [PMID: 25377082 DOI: 10.1002/yea.3053] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 10/24/2014] [Accepted: 10/29/2014] [Indexed: 11/07/2022] Open
Abstract
A problem frequently occurring in making some kinds of wines, particularly Vitis quinquangularis Rehd wine, is the presence of malic acid at high concentrations, which is detrimental to the quality of wines. Thus, there is a need of the ways for effectively reducing the malic acid levels in wine. This study aimed to generate shuffled fusants of Schizosaccharomyces pombe with enhanced deacidification activity for reducing the excessive malic acid content in wine. Sz. pombe CGMCC 2.1628 was used as the original strain. The starting mutant population was generated by UV treatment. The mutants with higher deacidification activity were selected and subjected to recursive protoplast fusion. The resulting fusants were screened by using the indicator of malic acid concentration of fermentation supernatants on 96-well microtitre plates, measured with bromocresol green. After three rounds of genome shuffling, the best-performing fusant, named GS3-1, was obtained. Its deacidification activity (consumed 4.78 g/l malic acid within 10 days) was increased by 225.2% as compared to that of original strain. In the Vitis quinquangularis Rehd wine fermentation test, GS3-1 consumed 4.0 g/l malic acid during the whole cycle of fermentation, providing up to 185.7% improvement in malic acid consumption compared with that of the original strain. This study shows that GS3-1 has great potential for improving the quality of Vitis quinquangularis Rehd wine.
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Affiliation(s)
- Su Ding
- Xingjian College of Science and Liberal Arts, Guangxi University, People's Republic of China; Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, Guangxi University, People's Republic of China
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Direct ethanol production from lignocellulosic sugars and sugarcane bagasse by a recombinant Trichoderma reesei strain HJ48. ScientificWorldJournal 2014; 2014:798683. [PMID: 24995362 PMCID: PMC4060538 DOI: 10.1155/2014/798683] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 05/10/2014] [Indexed: 11/18/2022] Open
Abstract
Trichoderma reesei can be considered as a candidate for consolidated bioprocessing (CBP) microorganism. However, its ethanol yield needs to be improved significantly. Here the ethanol production of T. reesei CICC 40360 was improved by genome shuffling while simultaneously enhancing the ethanol resistance. The initial mutant population was generated by nitrosoguanidine treatment of the spores, and an improved population producing more than fivefold ethanol than wild type was obtained by genome shuffling. The results show that the shuffled strain HJ48 can efficiently convert lignocellulosic sugars to ethanol under aerobic conditions. Furthermore, it was able to produce ethanol directly from sugarcane bagasse, demonstrating that the shuffled strain HJ48 is a suitable microorganism for consolidated bioprocessing.
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Genome Shuffling and Ribosome Engineering of Streptomyces actuosus for High-Yield Nosiheptide Production. Appl Biochem Biotechnol 2014; 173:1553-63. [DOI: 10.1007/s12010-014-0948-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2013] [Accepted: 04/24/2014] [Indexed: 11/26/2022]
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30
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Evolutionary engineering by genome shuffling. Appl Microbiol Biotechnol 2014; 98:3877-87. [PMID: 24595425 DOI: 10.1007/s00253-014-5616-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 02/11/2014] [Accepted: 02/12/2014] [Indexed: 01/28/2023]
Abstract
An upsurge in the bioeconomy drives the need for engineering microorganisms with increasingly complex phenotypes. Gains in productivity of industrial microbes depend on the development of improved strains. Classical strain improvement programmes for the generation, screening and isolation of such mutant strains have existed for several decades. An alternative to traditional strain improvement methods, genome shuffling, allows the directed evolution of whole organisms via recursive recombination at the genome level. This review deals chiefly with the technical aspects of genome shuffling. It first presents the diversity of organisms and phenotypes typically evolved using this technology and then reviews available sources of genetic diversity and recombination methodologies. Analysis of the literature reveals that genome shuffling has so far been restricted to microorganisms, both prokaryotes and eukaryotes, with an overepresentation of antibiotics- and biofuel-producing microbes. Mutagenesis is the main source of genetic diversity, with few studies adopting alternative strategies. Recombination is usually done by protoplast fusion or sexual recombination, again with few exceptions. For both diversity and recombination, prospective methods that have not yet been used are also presented. Finally, the potential of genome shuffling for gaining insight into the genetic basis of complex phenotypes is also discussed.
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Genome Shuffling of Aspergillus niger for Improving Transglycosylation Activity. Appl Biochem Biotechnol 2013; 172:50-61. [DOI: 10.1007/s12010-013-0421-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 07/31/2013] [Indexed: 10/26/2022]
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Chaudhary AK, Dhakal D, Sohng JK. An insight into the "-omics" based engineering of streptomycetes for secondary metabolite overproduction. BIOMED RESEARCH INTERNATIONAL 2013; 2013:968518. [PMID: 24078931 PMCID: PMC3775442 DOI: 10.1155/2013/968518] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 07/26/2013] [Accepted: 07/28/2013] [Indexed: 11/25/2022]
Abstract
Microorganisms produce a range of chemical substances representing a vast diversity of fascinating molecular architectures not available in any other system. Among them, Streptomyces are frequently used to produce useful enzymes and a wide variety of secondary metabolites with potential biological activities. Streptomyces are preferred over other microorganisms for producing more than half of the clinically useful naturally originating pharmaceuticals. However, these compounds are usually produced in very low amounts (or not at all) under typical laboratory conditions. Despite the superiority of Streptomyces, they still lack well documented genetic information and a large number of in-depth molecular biological tools for strain improvement. Previous attempts to produce high yielding strains required selection of the genetic material through classical mutagenesis for commercial production of secondary metabolites, optimizing culture conditions, and random selection. However, a profound effect on the strategy for strain development has occurred with the recent advancement of whole-genome sequencing, systems biology, and genetic engineering. In this review, we demonstrate a few of the major issues related to the potential of "-omics" technology (genomics, transcriptomics, proteomics, and metabolomics) for improving streptomycetes as an intelligent chemical factory for enhancing the production of useful bioactive compounds.
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Affiliation(s)
- Amit Kumar Chaudhary
- Department of Pharmaceutical Engineering, Institute of Biomolecule Reconstruction, SunMoon University, 100 Kalsan-ri, Tangjeongmyeon, Asan-si, Chungnam 336-708, Republic of Korea
| | - Dipesh Dhakal
- Department of Pharmaceutical Engineering, Institute of Biomolecule Reconstruction, SunMoon University, 100 Kalsan-ri, Tangjeongmyeon, Asan-si, Chungnam 336-708, Republic of Korea
| | - Jae Kyung Sohng
- Department of Pharmaceutical Engineering, Institute of Biomolecule Reconstruction, SunMoon University, 100 Kalsan-ri, Tangjeongmyeon, Asan-si, Chungnam 336-708, Republic of Korea
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Streptomycin resistance-aided genome shuffling to improve doramectin productivity of Streptomyces avermitilis NEAU1069. ACTA ACUST UNITED AC 2013; 40:877-89. [DOI: 10.1007/s10295-013-1280-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 04/25/2013] [Indexed: 11/30/2022]
Abstract
Abstract
Genome shuffling is an efficient approach for the rapid engineering of microbial strains with desirable industrial phenotypes. In this study, a strategy of incorporating streptomycin resistance screening into genome shuffling (GS-SR) was applied for rapid improvement of doramectin production by Streptomyces avermitilis NEAU1069. The starting mutant population was generated through treatment of the spores with N-methyl-N’-nitro-N-nitrosoguanidine and ultraviolet (UV) irradiation, respectively, and five mutants with higher productivity of doramectin were selected as starting strains for GS-SR. Finally, a genetically stable strain F4-137 was obtained and characterized to be able to yield 992 ± 4.4 mg/l doramectin in a shake flask, which was 7.3-fold and 11.2-fold higher than that of the starting strain UV-45 and initial strain NEAU1069, respectively. The doramectin yield by F4-137 in a 50-l fermentor reached 930.3 ± 3.8 mg/l. Furthermore, the factors associated with the improved doramectin yield were investigated and the results suggested that mutations in ribosomal protein S12 and the enhanced production of cyclohexanecarboxylic coenzyme A may contribute to the improved performance of the shuffled strains. The random amplified polymorphic DNA analysis showed a genetic diversity among the shuffled strains, which confirmed the occurrence of genome shuffling. In conclusion, our results demonstrated that GS-SR is a powerful method for enhancing the production of secondary metabolites in Streptomyces.
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Wang H, Sun Y, Chen C, Sun Z, Zhou Y, Shen F, Zhang H, Dai Y. Genome shuffling of Lactobacillus plantarum for improving antifungal activity. Food Control 2013. [DOI: 10.1016/j.foodcont.2012.12.020] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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35
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Wang C, Wu G, Li Y, Huang Y, Zhang F, Liang X. Genome Shuffling of Penicillium citrinum for Enhanced Production of Nuclease P1. Appl Biochem Biotechnol 2013; 170:1533-45. [DOI: 10.1007/s12010-013-0297-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2013] [Accepted: 05/09/2013] [Indexed: 12/29/2022]
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Li S, Chen X, Dong C, Zhao F, Tang L, Mao Z. Combining Genome Shuffling and Interspecific Hybridization Among Streptomyces Improved ε-Poly-l-Lysine Production. Appl Biochem Biotechnol 2012. [DOI: 10.1007/s12010-012-9969-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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37
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Genome shuffling of Streptomyces viridochromogenes for improved production of avilamycin. Appl Microbiol Biotechnol 2012; 97:641-8. [DOI: 10.1007/s00253-012-4322-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Revised: 06/21/2012] [Accepted: 07/18/2012] [Indexed: 10/28/2022]
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38
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Kang YM, Kang TH, Yun HD, Cho KM. Enhancing the Enzymatic Activity of the Multifunctional β-Glycosyl Hydrolase (Cel44C-Man26AP558) from Paenibacillus polymyxa GS01 Using DNA Shuffling. ACTA ACUST UNITED AC 2012. [DOI: 10.7845/kjm.2012.48.2.073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Luo JM, Li JS, Liu D, Liu F, Wang YT, Song XR, Wang M. Genome shuffling of Streptomyces gilvosporeus for improving natamycin production. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2012; 60:6026-6036. [PMID: 22607399 DOI: 10.1021/jf300663w] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Improvement of natamycin production by Streptomyces gilvosporeus ATCC 13326 was performed by recursive protoplast fusion in a genome-shuffling format. After four rounds of genome shuffling, the best producer, GS 4-21, with genetic stability was obtained and its production of natamycin reached 4.69 ± 0.05 g/L in shaking flask after 96 h cultivation, which was increased by 97.1% and 379% in comparison with the highest parental strain pop-72A(r)07 and the initial strain ATCC 13326, respectively. Compared with the initial strain ATCC 13326, the recombinant GS 4-21 presented higher polymorphism. Fifty-four proteins showed differential expression levels between the recombinant GS 4-21 and initial strain ATCC 13326. Of these proteins, 34 proteins were upregulated and 20 proteins were downregulated. Of the upregulated proteins, one protein, glucokinase regulatory protein, was involved in natamycin biosynthesis. This comprehensive analysis would provide useful information for understanding the natamycin metabolic pathway in S. gilvosporeus.
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Affiliation(s)
- Jian-Mei Luo
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science and Technology), Ministry of Education, Tianjin Key Lab of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China
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El-Bondkly AMA. Molecular identification using ITS sequences and genome shuffling to improve 2-deoxyglucose tolerance and xylanase activity of marine-derived fungus, Aspergillus sp. NRCF5. Appl Biochem Biotechnol 2012; 167:2160-73. [PMID: 22684364 DOI: 10.1007/s12010-012-9763-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 05/30/2012] [Indexed: 11/28/2022]
Abstract
During the screening of xylanolytic enzyme from marine-derived fungi isolated from the inner tissue of Egyptian soft coral Rhytisma sp., one strain, NRCF5, exhibited high enzyme activity with 0.1 % (w/v) antimetabolite 2-deoxyglucose (2DG) tolerance. This fungal strain was identified as Aspergillus sp. NRCF5 based on its morphological characteristics and internal transcribed spacer (ITS) sequences. The ITS region of hyperactive xylanolytic strain (NRCF5) was amplified, sequenced, and submitted to GenBank (accession no. JQ277356). To apply the fundamental principles of genome shuffling in breeding of xylanase-producing fungi, marine-derived fungus Aspergillus sp. NRCF5 was used as starting strain in this work and applied for induction of genetic variability using different combinations and doses of mutagens. Five mutants with high xylanase activity and 0.25 % (w/v) antimetabolite 2DG tolerance were obtained from the populations generated by the mutation of combination between ultraviolet irradiation (UV, 5 min) and N-methyl-N-nitro-N-nitrosoguanidine (NTG, 100 μg/ml) for 30 (UNA) and 60 (UNB)min as well as NTG (100 μg/ml) and ethidium bromide (250 μg/ml) for 30 (NEA) and 60 (NEB)min. Then, they were subjected for recursive protoplast fusion. Seven hereditarily stable recombinants with high xylanase activity and 1.0 % (w/v) 2DG tolerance were obtained by four rounds of genome shuffling. Among them, a high xylanase-producing recombinant, R4/31, was obtained, which produced 427.5 U/ml xylanase. This value is 6.13-fold higher than that of the starting strain NRCF5 and 2.48-fold higher than that of the parent strain (mutant NEA51). The subculture experiments indicated that the high producer of marine Aspergillus sp. R4/31 fusant was stable.
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Zhao J, Li Y, Zhang C, Yao Z, Zhang L, Bie X, Lu F, Lu Z. Genome shuffling of Bacillus amyloliquefaciens for improving antimicrobial lipopeptide production and an analysis of relative gene expression using FQ RT-PCR. ACTA ACUST UNITED AC 2012; 39:889-96. [DOI: 10.1007/s10295-012-1098-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 01/12/2012] [Indexed: 11/24/2022]
Abstract
Abstract
Genome shuffling is an efficient approach for the rapid improvement of the yield of secondary metabolites. This study was undertaken to enhance the yield of surfactin produced by Bacillus amyloliquefaciens ES-2-4 using genome shuffling and to examine changes in SrfA expression of the improved phenotype at the transcriptional level. Six strains with subtle improvements in lipopeptide yield were obtained from populations generated by ultraviolet irradiation, nitrosoguanidine, and ion beam mutagenesis. These strains were then subjected to recursive protoplast fusion. A strain library that was likely to yield positive colonies was created by fusing the lethal protoplasts obtained from both ultraviolet irradiation and heat treatments. After two rounds of genome shuffling, a high-yield recombinant F2-38 strain that exhibited 3.5- and 10.3-fold increases in surfactin production in shake flask and fermenter respectively, was obtained. Comparative analysis of synthetase gene expression was conducted between the initial and shuffled strains using FQ (fluorescent quantitation) RT-PCR. Delta CT (threshold cycle) relative quantitation analysis revealed that surfactin synthetase gene (srfA) expression at the transcriptional level in the F2-38 strain was 15.7-fold greater than in the ES-2-4 wild-type. The shuffled strain has a potential application in food and pharmaceutical industries. At the same time, the analysis of improved phenotypes will provide more valuable data for inverse metabolic engineering.
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Affiliation(s)
- Junfeng Zhao
- grid.27871.3b 0000000097507019 College of Food Science and Technology Nanjing Agricultural University 210095 Nanjing Jiangsu People’s Republic of China
- grid.453074.1 0000000097970900 College of Food Science and Engineering Henan University of Science and Technology Tianjing Road 471003 Luoyang People’s Republic of China
| | - Yuanhong Li
- grid.27871.3b 0000000097507019 College of Food Science and Technology Nanjing Agricultural University 210095 Nanjing Jiangsu People’s Republic of China
| | - Chong Zhang
- grid.27871.3b 0000000097507019 College of Food Science and Technology Nanjing Agricultural University 210095 Nanjing Jiangsu People’s Republic of China
| | - Zhengying Yao
- grid.27871.3b 0000000097507019 College of Food Science and Technology Nanjing Agricultural University 210095 Nanjing Jiangsu People’s Republic of China
| | - Li Zhang
- grid.27871.3b 0000000097507019 College of Food Science and Technology Nanjing Agricultural University 210095 Nanjing Jiangsu People’s Republic of China
| | - Xiaomei Bie
- grid.27871.3b 0000000097507019 College of Food Science and Technology Nanjing Agricultural University 210095 Nanjing Jiangsu People’s Republic of China
| | - Fengxia Lu
- grid.27871.3b 0000000097507019 College of Food Science and Technology Nanjing Agricultural University 210095 Nanjing Jiangsu People’s Republic of China
| | - Zhaoxin Lu
- grid.27871.3b 0000000097507019 College of Food Science and Technology Nanjing Agricultural University 210095 Nanjing Jiangsu People’s Republic of China
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Enhanced thermotolerance and ethanol tolerance in Saccharomyces cerevisiae mutated by high-energy pulse electron beam and protoplast fusion. Bioprocess Biosyst Eng 2012; 35:1455-65. [DOI: 10.1007/s00449-012-0734-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Accepted: 03/27/2012] [Indexed: 10/28/2022]
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Cobb RE, Sun N, Zhao H. Directed evolution as a powerful synthetic biology tool. Methods 2012; 60:81-90. [PMID: 22465795 DOI: 10.1016/j.ymeth.2012.03.009] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Accepted: 03/09/2012] [Indexed: 01/31/2023] Open
Abstract
At the heart of synthetic biology lies the goal of rationally engineering a complete biological system to achieve a specific objective, such as bioremediation and synthesis of a valuable drug, chemical, or biofuel molecule. However, the inherent complexity of natural biological systems has heretofore precluded generalized application of this approach. Directed evolution, a process which mimics Darwinian selection on a laboratory scale, has allowed significant strides to be made in the field of synthetic biology by allowing rapid identification of desired properties from large libraries of variants. Improvement in biocatalyst activity and stability, engineering of biosynthetic pathways, tuning of functional regulatory systems and logic circuits, and development of desired complex phenotypes in industrial host organisms have all been achieved by way of directed evolution. Here, we review recent contributions of directed evolution to synthetic biology at the protein, pathway, network, and whole cell levels.
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Affiliation(s)
- Ryan E Cobb
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Liu L, Zhu Y, Li J, Wang M, Lee P, Du G, Chen J. Microbial production of propionic acid from propionibacteria: current state, challenges and perspectives. Crit Rev Biotechnol 2012; 32:374-81. [PMID: 22299651 DOI: 10.3109/07388551.2011.651428] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Propionic acid (PA) is an important building block chemical and finds a variety of applications in organic synthesis, food, feeding stuffs, perfume, paint and pharmaceutical industries. Presently, PA is mainly produced by petrochemical route. With the continuous increase in oil prices, public concern about environmental pollution, and the consumers' desire for bio-based natural and green ingredients in foods and pharmaceuticals, PA production from propionibacteria has attracted considerable attention, and substantial progresses have been made on microbial PA production. However, production of PA by propionibacteria is facing challenges such as severe inhibition of end-products during cell growth and the formation of by-products (acetic acid and succinic acid). The integration of reverse metabolic engineering and systematic metabolic engineering provides an opportunity to significantly improve the acid tolerance of propionibacteria and reduce the formation of by-products, and makes it feasible to strengthen the commercial competition of biotechnological PA production from propionibacteria to be comparable to the petrochemical route.
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Affiliation(s)
- Long Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
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Kumar M, Pratap Singh M, Kumar Tuli D. Genome Shuffling of <i>Pseudomonas</i> Sp. Ioca11 for Improving Degradation of Polycyclic Aromatic Hydrocarbons. ACTA ACUST UNITED AC 2012. [DOI: 10.4236/aim.2012.21004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Haleema S, Sasi PV, Ibnusaud I, Polavarapu PL, Kagan HB. Enantiomerically pure compounds related to chiral hydroxy acids derived from renewable resources. RSC Adv 2012. [DOI: 10.1039/c2ra21205f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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Li S, Li F, Chen XS, Wang L, Xu J, Tang L, Mao ZG. Genome Shuffling Enhanced ε-Poly-l-Lysine Production by Improving Glucose Tolerance of Streptomyces graminearus. Appl Biochem Biotechnol 2011; 166:414-23. [DOI: 10.1007/s12010-011-9437-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 10/26/2011] [Indexed: 12/01/2022]
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Ma C, Jiang D, Wei X. Mutation breeding of Emericella foeniculicola TR21 for improved production of tanshinone IIA. Process Biochem 2011. [DOI: 10.1016/j.procbio.2011.07.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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49
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Genome shuffling improves thermotolerance and glutamic acid production of Corynebacteria glutamicum. World J Microbiol Biotechnol 2011; 28:1035-43. [DOI: 10.1007/s11274-011-0902-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Accepted: 09/16/2011] [Indexed: 10/17/2022]
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Clermont N, Lerat S, Beaulieu C. Genome shuffling enhances biocontrol abilities of Streptomyces strains against two potato pathogens. J Appl Microbiol 2011; 111:671-82. [DOI: 10.1111/j.1365-2672.2011.05078.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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