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Zhu Z, Ding X, Rang J, Xia L. Application and research progress of ARTP mutagenesis in actinomycetes breeding. Gene 2024; 929:148837. [PMID: 39127415 DOI: 10.1016/j.gene.2024.148837] [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: 04/17/2024] [Revised: 08/06/2024] [Accepted: 08/07/2024] [Indexed: 08/12/2024]
Abstract
Atmospheric and room temperature plasma (ARTP) is an emerging artificial mutagenesis breeding technology. In comparison to traditional physical and chemical methods, ARTP technology can induce DNA damage more effectively and obtain mutation strains with stable heredity more easily after screening. It possesses advantages such as simplicity, safety, non-toxicity, and cost-effectiveness, showing high application value in microbial breeding. This article focuses on ARTP mutagenesis breeding of actinomycetes, specifically highlighting the application of ARTP mutagenesis technology in improving the performance of strains and enhancing the biosynthetic capabilities of actinomycetes. We analyzed the advantages and challenges of ARTP technology in actinomycetes breeding and summarized the common features, specific mutation sites and metabolic pathways of ARTP mutagenic strains, which could give guidance for genetic modification. It suggested that the future research work should focus on the establishment of high throughput rapid screening methods and integrate transcriptomics, proteomics, metabonomics and other omics to delve into the genetic regulations and synthetic mechanisms of the bioactive substances in ARTP mutated actinomycetes. This article aims to provide new perspectives for actinomycetes breeding through the establishment and application of ARTP mutagenesis technology, thereby promoting source innovation and the sustainable industrial development of actinomycetes.
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Affiliation(s)
- Zirong Zhu
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410081, Hunan, China
| | - Xuezhi Ding
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410081, Hunan, China
| | - Jie Rang
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410081, Hunan, China
| | - Liqiu Xia
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410081, Hunan, 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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3
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Wang L, Lyu Y, Miao X, Yin X, Zhang C. Enhanced protein glutaminase production from Chryseobacterium proteolyticum combining physico-chemical mutagenesis and resistance screening and its application to soybean protein isolates. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:4562-4572. [PMID: 36853147 DOI: 10.1002/jsfa.12535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 02/22/2023] [Accepted: 02/28/2023] [Indexed: 06/06/2023]
Abstract
BACKGROUND Protein glutaminase (PG) is a novel protein modification biotechnology that is increasingly being used in the food industry. However, the current level of fermentation of PG-producing strains still does not meet the requirements of industrial production. To obtain the mutant strains with high PG production, the atmospheric and room temperature plasma (ARTP) combined with LiCl chemical mutagen were used in mutagenesis of a PG producing Chryseobacterium proteolyticum 1003. RESULTS A mutant strain (WG15) was successfully obtained based on malonic acid resistance screening after compound mutagenesis of the starting strain C. proteolyticum 1003 using ARTP with LiCl, and it was confirmed to be genetically stable in PG synthesis after 15 generations. The protein glutaminase production of WG15 was 2.91 U mL-1 after optimization of fermentation conditions, which is 48.69% higher than the original strain C. proteolyticum 1003. The PG obtained from fermentation showed good activities in deamidation of soy protein isolate. The solubility and foaming properties of the PG-treated soy protein isolate were significantly increased by 36.50% and 10.03%, respectively, when PG was added at the amount of 100 U mL-1 . In addition, the emulsifying activity and emulsion stability of the treated soy protein isolate were improved by 12.44% and 10.34%, respectively, on the addition of 10 U mL-1 PG. The secondary structure of the soy protein isolate changed after PG treatment, with an increased proportion of glutamate. CONCLUSION The results of the present study indicate that the PG produced by this mutant strain could improve the functional properties of soybean protein isolate and the C. proteolyticum mutant WG15 has great potential in food industry. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Lijuan Wang
- Laboratory of Food Industrial Enzyme Technology, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yunbin Lyu
- Laboratory of Food Industrial Enzyme Technology, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xing Miao
- Laboratory of Food Industrial Enzyme Technology, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | | | - Chong Zhang
- Laboratory of Food Industrial Enzyme Technology, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
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4
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Xu Z, Tian P. Rethinking Biosynthesis of Aclacinomycin A. Molecules 2023; 28:molecules28062761. [PMID: 36985733 PMCID: PMC10054333 DOI: 10.3390/molecules28062761] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/01/2023] [Accepted: 03/06/2023] [Indexed: 03/22/2023] Open
Abstract
Aclacinomycin A (ACM-A) is an anthracycline antitumor agent widely used in clinical practice. The current industrial production of ACM-A relies primarily on chemical synthesis and microbial fermentation. However, chemical synthesis involves multiple reactions which give rise to high production costs and environmental pollution. Microbial fermentation is a sustainable strategy, yet the current fermentation yield is too low to satisfy market demand. Hence, strain improvement is highly desirable, and tremendous endeavors have been made to decipher biosynthesis pathways and modify key enzymes. In this review, we comprehensively describe the reported biosynthesis pathways, key enzymes, and, especially, catalytic mechanisms. In addition, we come up with strategies to uncover unknown enzymes and improve the activities of rate-limiting enzymes. Overall, this review aims to provide valuable insights for complete biosynthesis of ACM-A.
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Abd Allah FM, Elhosiny AM, Mohamed HF, Farrag AA, Elmeleigy MA. Enhanced antimicrobial activity of lactic acid bacteria through genome shuffling and genetic variability among shuffled strains. World J Microbiol Biotechnol 2023; 39:114. [PMID: 36913158 DOI: 10.1007/s11274-023-03556-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 02/24/2023] [Indexed: 03/14/2023]
Abstract
In this investigation, lactic acid bacteria (LAB) isolated from milk were tested for their antibacterial properties and improved the antimicrobial activity of these isolates using genome shuffling. A total of sixty-one isolates were found in eleven samples, which were then tested using the agar diffusion method for their antibacterial activity against Staphylococcus aureus, Escherichia coli, Salmonella typhimurium, and Pseudomonas aeruginosa. Thirty-one strains exhibited antibacterial activity against at least one of the tested pathogens, with an inhibitory zone's diameter varying between 15.0 and 24.0 mm. Two isolates that showed the highest antimicrobial activity were identified as Lactobacillus plantarum CIP 103151 and Lactobacillus plantarum JCM 1149 according to 16S rRNA analysis. In the present study, applying genome shuffling approach significantly enhanced the antibacterial activity of L. plantarum. The initial populations were obtained via ultraviolet irradiation and were treated using the protoplast fusion method. The ideal condition for the production of protoplasts was 15 mg/ml of lysozyme and 10 μg/ml of mutanolysin. After two rounds of fusion, ten recombinants exhibited a significant increase in the inhibition zones versus S. aureus, S. typhimurium, P. aeruginosa, and E. coli, reaching up to 1.34, 1.31, 1.37, and 1.37-fold increase in inhibitory zone respectively. Random Amplified Polymorphic DNA results showed clear differences in DNA banding patterns among the wild strain of L. plantarum CIP 103151 and the three selected shuffled strains using primers 1283 & OPA09. On the other hand, no change was obtained using primers OPD03 neither among the wild strain and the three recombinant strains nor among the three shuffled strains.
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Affiliation(s)
- Fatema M Abd Allah
- Botany & Microbiology Department (Girls Branch), Faculty of Science, Al-Azhar University, Cairo, Egypt
| | - Asmaa M Elhosiny
- Botany & Microbiology Department (Girls Branch), Faculty of Science, Al-Azhar University, Cairo, Egypt
| | - Hala F Mohamed
- Botany & Microbiology Department (Girls Branch), Faculty of Science, Al-Azhar University, Cairo, Egypt. .,Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, People's Republic of China.
| | - Ayman A Farrag
- Al-Azhar Centre for Fermentation Biotechnology & Applied Microbiology, Al-Azhar University, Cairo, Egypt.,Botany & Microbiology Department (Boys Branch), Faculty of Science, Al-Azhar University, Cairo, Egypt
| | - Magda A Elmeleigy
- Botany & Microbiology Department (Girls Branch), Faculty of Science, Al-Azhar University, Cairo, Egypt.
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Kaur R, Kanotra M, Sood A, Abdellatif AAH, Bhatia S, Al-Harrasi A, Aleya L, Vargas-De-La-Cruz C, Behl T. Emergence of nutriments as a nascent complementary therapy against antimicrobial resistance. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:49568-49582. [PMID: 35589902 DOI: 10.1007/s11356-022-20775-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 05/08/2022] [Indexed: 06/15/2023]
Abstract
With these growing and evolving years, antimicrobial resistance has become a great subject of interest. The idea of using natural productive ways can be an effective measure against antimicrobial resistance. The growing prevalence of antimicrobial resistance indicates that advanced natural approaches are a topic of concern for fighting the resistance. Many natural products including essential oils, flavonoids, alkaloids and botanicals have been demonstrated as effective bactericidal agents. In this review, we will discuss in detail about the relevance of such natural products to tackle the problem of antimicrobial resistance, antibiotic adjuvants that aim towards non-essential bacterial targets to reduce the prevalence of resistant bacterial infections, latest bioinformatics approach towards antibacterial drug discovery along with an understanding of biogenic nanoparticles in antimicrobial activity.
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Affiliation(s)
- Rajwinder Kaur
- Chitkara College of Pharmacy, Chitkara University, Patiala, Punjab, India
| | - Muskan Kanotra
- Chitkara College of Pharmacy, Chitkara University, Patiala, Punjab, India
| | - Ankita Sood
- Chitkara College of Pharmacy, Chitkara University, Patiala, Punjab, India
| | - Ahmed A H Abdellatif
- Department of Pharmaceutics, College of Pharmacy, Qassim University, Buraydah, Saudi Arabia
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Al-Azhar University, Assiut, Egypt
| | - Saurabh Bhatia
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
- School of Health Science, University of Petroleum and Energy Studies, Dehradun, Uttarakhand, India
| | - Ahmed Al-Harrasi
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Lotfi Aleya
- Chrono-Environment Laboratory, UMR CNRS 6249, Bourgogne Franche-Comté University, Besancon, France
| | - Celia Vargas-De-La-Cruz
- Department of Pharmacology, Bromatology and Toxicology, Faculty of Pharmacy and Biochemistry, Universidad Nacional Mayor de San Marcos, Lima, Peru
- E-Health Research Center, Universidad de Ciencias Y Humanidades, Lima, Peru
| | - Tapan Behl
- Chitkara College of Pharmacy, Chitkara University, Patiala, Punjab, India.
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Kaari M, Manikkam R, Baskaran A. Exploring Newer Biosynthetic Gene Clusters in Marine Microbial Prospecting. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:448-467. [PMID: 35394575 DOI: 10.1007/s10126-022-10118-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
Marine microbes genetically evolved to survive varying salinity, temperature, pH, and other stress factors by producing different bioactive metabolites. These microbial secondary metabolites (SMs) are novel, have high potential, and could be used as lead molecule. Genome sequencing of microbes revealed that they have the capability to produce numerous novel bioactive metabolites than observed under standard in vitro culture conditions. Microbial genome has specific regions responsible for SM assembly, termed biosynthetic gene clusters (BGCs), possessing all the necessary genes to encode different enzymes required to generate SM. In order to augment the microbial chemo diversity and to activate these gene clusters, various tools and techniques are developed. Metagenomics with functional gene expression studies aids in classifying novel peptides and enzymes and also in understanding the biosynthetic pathways. Genome shuffling is a high-throughput screening approach to improve the development of SMs by incorporating genomic recombination. Transcriptionally silent or lower level BGCs can be triggered by artificially knocking promoter of target BGC. Additionally, bioinformatic tools like antiSMASH, ClustScan, NAPDOS, and ClusterFinder are effective in identifying BGCs of existing class for annotation in genomes. This review summarizes the significance of BGCs and the different approaches for detecting and elucidating BGCs from marine microbes.
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Affiliation(s)
- Manigundan Kaari
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600 119, Tamil Nadu, India
| | - Radhakrishnan Manikkam
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600 119, Tamil Nadu, India.
| | - Abirami Baskaran
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600 119, Tamil Nadu, India
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Huang A, Luo X, Xu Z, Huang L, Wang X, Xie S, Pan Y, Fang S, Liu Z, Yuan Z, Hao H. Optimal Regimens and Clinical Breakpoint of Avilamycin Against Clostridium perfringens in Swine Based on PK-PD Study. Front Pharmacol 2022; 13:769539. [PMID: 35281904 PMCID: PMC8908370 DOI: 10.3389/fphar.2022.769539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 01/14/2022] [Indexed: 11/21/2022] Open
Abstract
Clostridium perfringens causes significant morbidity and mortality in swine worldwide. Avilamycin showed no cross resistance and good activity for treatment of C. perfringens. The aim of this study was to formulate optimal regimens of avilamycin treatment for C. perfringens infection based on the clinical breakpoint (CBP). The wild-type cutoff value (COWT) was defined as 0.25 μg/ml, which was developed based on the minimum inhibitory concentration (MIC) distributions of 120 C. perfringens isolates and calculated using ECOFFinder. Pharmacokinetics–pharmacodynamics (PK-PD) of avilamycin in ileal content were analyzed based on the high-performance liquid chromatography method and WinNonlin software to set up the target of PK/PD index (AUC0–24h/MIC)ex based on sigmoid Emax modeling. The PK parameters of AUC0–24h, Cmax, and Tmax in the intestinal tract were 428.62 ± 14.23 h μg/mL, 146.30 ± 13.41 μg/ml,, and 4 h, respectively. The target of (AUC0–24h/MIC)ex for bactericidal activity in intestinal content was 36.15 h. The PK-PD cutoff value (COPD) was defined as 8 μg/ml and calculated by Monte Carlo simulation. The dose regimen designed from the PK-PD study was 5.2 mg/kg mixed feeding and administrated for the treatment of C. perfringens infection. Five respective strains with different MICs were selected as the infection pathogens, and the clinical cutoff value was defined as 0.125 μg/ml based on the relationship between MIC and the possibility of cure (POC) following nonlinear regression analysis, CART, and “Window” approach. The CBP was set to be 0.25 μg/ml and selected by the integrated decision tree recommended by the Clinical Laboratory of Standard Institute. The formulation of the optimal regimens and CBP is good for clinical treatment and to control drug resistance.
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Affiliation(s)
- Anxiong Huang
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA (Ministry of Agriculture) Key Laboratory for Detection of Veterinary Drug Residues, Wuhan, China.,MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan, China
| | - Xun Luo
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA (Ministry of Agriculture) Key Laboratory for Detection of Veterinary Drug Residues, Wuhan, China.,MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan, China
| | - Zihui Xu
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA (Ministry of Agriculture) Key Laboratory for Detection of Veterinary Drug Residues, Wuhan, China.,MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan, China
| | - Lingli Huang
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA (Ministry of Agriculture) Key Laboratory for Detection of Veterinary Drug Residues, Wuhan, China.,MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan, China
| | - Xu Wang
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA (Ministry of Agriculture) Key Laboratory for Detection of Veterinary Drug Residues, Wuhan, China.,MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan, China
| | - Shuyu Xie
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA (Ministry of Agriculture) Key Laboratory for Detection of Veterinary Drug Residues, Wuhan, China.,MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan, China
| | - Yuanhu Pan
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA (Ministry of Agriculture) Key Laboratory for Detection of Veterinary Drug Residues, Wuhan, China.,MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan, China
| | - Shiwei Fang
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA (Ministry of Agriculture) Key Laboratory for Detection of Veterinary Drug Residues, Wuhan, China.,MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan, China
| | - Zhenli Liu
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA (Ministry of Agriculture) Key Laboratory for Detection of Veterinary Drug Residues, Wuhan, China.,MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan, China
| | - Zonghui Yuan
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA (Ministry of Agriculture) Key Laboratory for Detection of Veterinary Drug Residues, Wuhan, China.,MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan, China
| | - Haihong Hao
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA (Ministry of Agriculture) Key Laboratory for Detection of Veterinary Drug Residues, Wuhan, China.,MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan, China
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Hussain MH, Mohsin MZ, Zaman WQ, Yu J, Zhao X, Wei Y, Zhuang Y, Mohsin A, Guo M. Multiscale engineering of microbial cell factories: A step forward towards sustainable natural products industry. Synth Syst Biotechnol 2022; 7:586-601. [PMID: 35155840 PMCID: PMC8816652 DOI: 10.1016/j.synbio.2021.12.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/08/2021] [Accepted: 12/30/2021] [Indexed: 01/09/2023] Open
Abstract
Microbial cell factories (bacteria and fungi) are the leading producers of beneficial natural products such as lycopene, carotene, herbal medicine, and biodiesel etc. These microorganisms are considered efficient due to their effective bioprocessing strategy (monoculture- and consortial-based approach) under distinct processing conditions. Meanwhile, the advancement in genetic and process optimization techniques leads to enhanced biosynthesis of natural products that are known functional ingredients with numerous applications in the food, cosmetic and medical industries. Natural consortia and monoculture thrive in nature in a small proportion, such as wastewater, food products, and soils. In similitude to natural consortia, it is possible to engineer artificial microbial consortia and program their behaviours via synthetic biology tools. Therefore, this review summarizes the optimization of genetic and physicochemical parameters of the microbial system for improved production of natural products. Also, this review presents a brief history of natural consortium and describes the functional properties of monocultures. This review focuses on synthetic biology tools that enable new approaches to design synthetic consortia; and highlights the syntropic interactions that determine the performance and stability of synthetic consortia. In particular, the effect of processing conditions and advanced genetic techniques to improve the productibility of both monoculture and consortial based systems have been greatly emphasized. In this context, possible strategies are also discussed to give an insight into microbial engineering for improved production of natural products in the future. In summary, it is concluded that the coupling of genomic modifications with optimum physicochemical factors would be promising for producing a robust microbial cell factory that shall contribute to the increased production of natural products.
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Affiliation(s)
- Muhammad Hammad Hussain
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Muhammad Zubair Mohsin
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Waqas Qamar Zaman
- Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National University of Sciences and Technology (NUST), Sector H-12, Islamabad, 44000, Pakistan
| | - Junxiong Yu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Xueli Zhao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Yanlong Wei
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Ali Mohsin
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
- Corresponding author. East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237, PR China.
| | - Meijin Guo
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
- Corresponding author. P.O. box 329#, East China University of Science and Technology, 130 Meilong Rd., Shanghai, 200237, PR China.
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10
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Avilamycin production enhancement by mutagenesis and fermentation optimization in Streptomyces viridochromogenes. World J Microbiol Biotechnol 2022; 38:50. [DOI: 10.1007/s11274-021-03191-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 11/14/2021] [Indexed: 12/12/2022]
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11
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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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Combination of atmospheric and room temperature plasma (ARTP) mutagenesis, genome shuffling and dimethyl sulfoxide (DMSO) feeding to improve FK506 production in Streptomyces tsukubaensis. Biotechnol Lett 2021; 43:1809-1820. [PMID: 34160747 DOI: 10.1007/s10529-021-03154-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 06/08/2021] [Indexed: 12/30/2022]
Abstract
FK506 is a clinically important macrocyclic polyketide with immunosuppressive activity produced by Streptomyces tsukubaensis. However, the production capacity of the strain is very low. To improve production, atmospheric and room temperature plasma (ARTP) mutagenesis was adopted to get the initial strains used in genome shuffling (GS). After three rounds of GS, S. tsukubaensis R3-C4 was the most productive strain, resulting in a FK506 concentration of 335 μg/mL, 2.6 times than that of the original wild-type strain. Moreover, exogenous DMSO 4% (v/v) addition could induce efflux of FK506 and increased FK506 production by 27.9% to 429 μg/mL. Finally, analyses of the differences in morphology, fermentation characteristics and specific gene expression levels between S. tsukubaensis R3-C4 and the wild-type strain revealed that R3-C4 strain: has hampered spore differentiation, thicker mycelia and more red pigment, which are likely related to the downregulation of bldD and cdgB expression. In addition, the expression levels of fkbO, fkbP, dahp, pccB and prpE all showed up-regulation at diverse degrees compared to the wild-type S. tsukubaensis. Overall, these results show that a combined approach involving classical random mutation and exogenous feeding can be applied to increase FK506 biosynthesis and may be applied also to the improvement of other important secondary metabolites.
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Wawro A. Improvement of Acetic Acid Tolerance in Saccharomyces cerevisiae by Novel Genome Shuffling. APPL BIOCHEM MICRO+ 2021. [DOI: 10.1134/s0003683821020198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Genome shuffling based on different types of ribosome engineering mutants for enhanced production of 10-membered enediyne tiancimycin-A. Appl Microbiol Biotechnol 2020; 104:4359-4369. [PMID: 32236679 DOI: 10.1007/s00253-020-10583-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/15/2020] [Accepted: 03/23/2020] [Indexed: 12/21/2022]
Abstract
Tiancimycin-A (TNM-A) is an anthraquinone-fused ten-membered enediyne produced by Streptomyces sp. CB03234, which is very promising for the development of anticancer antibody-drug conjugates (ADCs). To improve the titer of TNM-A, we have generated high-producing mutants CB03234-S and CB03234-R through ribosome engineering, but still not sufficient for pilot production of TNM-A. As the follow-up work, gentamycin-induced ribosome engineering was further adopted here to generate the mutant CB03234-G, which produced similar level of TNM-A as in CB03234-S and CB03234-R. Benefiting from the distinct antibiotic resistances of three ribosome engineering mutants, genome shuffling between any two of them was respectively carried out, and finally obtained the recombinant CB03234-GS26. Under optimal conditions, CB03234-GS26 produced 40.6 ± 1.0 mg/L TNM-A in shaking flasks and 20.8 ± 0.4 mg/L in a scaled-up 30-L fermentor. Comparing with the parental high-producing mutants, the over 1.6-fold titer improvement of CB03234-GS26 in fermentor was more promising for pilot production of TNM-A. Besides the distinctive morphological features, genetic characterization revealed that CB03234-GS26 possessed 1.8 kb rsmG related deletion just the same as CB03234-S, but no mutation was found in rpsL. Subsequent knockouts proved that rsmG was unrelated to titer improvement of TNM-A, which implied other genomic variations and mechanisms rather than ribosome engineering to enhance the biosynthesis of TNM-A. Therefore, CB03234-GS26 provided a basis to locate potential novel genetic targets, and explore the interactions between complex metabolic network and TNM biosynthetic pathway, which shall promote future construction of high-yielding systems for TNM-A and other anthraquinone-fused enediynes.Key Points •United genome shuffling and ribosome engineering help further strain improvement. •CB03234-GS26 with improved titer is practical for the pilot production of TNM-A. •Enhanced TNM-A production should attribute to novel genetic features/mechanisms.
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The Application of Ribosome Engineering to Natural Product Discovery and Yield Improvement in Streptomyces. Antibiotics (Basel) 2019; 8:antibiotics8030133. [PMID: 31480298 PMCID: PMC6784132 DOI: 10.3390/antibiotics8030133] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/10/2019] [Accepted: 08/27/2019] [Indexed: 12/23/2022] Open
Abstract
Microbial natural product drug discovery and development has entered a new era, driven by microbial genomics and synthetic biology. Genome sequencing has revealed the vast potential to produce valuable secondary metabolites in bacteria and fungi. However, many of the biosynthetic gene clusters are silent under standard fermentation conditions. By rational screening for mutations in bacterial ribosomal proteins or RNA polymerases, ribosome engineering is a versatile approach to obtain mutants with improved titers for microbial product formation or new natural products through activating silent biosynthetic gene clusters. In this review, we discuss the mechanism of ribosome engineering and its application to natural product discovery and yield improvement in Streptomyces. Our analysis suggests that ribosome engineering is a rapid and cost-effective approach and could be adapted to speed up the discovery and development of natural product drug leads in the post-genomic era.
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Pham JV, Yilma MA, Feliz A, Majid MT, Maffetone N, Walker JR, Kim E, Cho HJ, Reynolds JM, Song MC, Park SR, Yoon YJ. A Review of the Microbial Production of Bioactive Natural Products and Biologics. Front Microbiol 2019; 10:1404. [PMID: 31281299 PMCID: PMC6596283 DOI: 10.3389/fmicb.2019.01404] [Citation(s) in RCA: 244] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 06/04/2019] [Indexed: 12/24/2022] Open
Abstract
A variety of organisms, such as bacteria, fungi, and plants, produce secondary metabolites, also known as natural products. Natural products have been a prolific source and an inspiration for numerous medical agents with widely divergent chemical structures and biological activities, including antimicrobial, immunosuppressive, anticancer, and anti-inflammatory activities, many of which have been developed as treatments and have potential therapeutic applications for human diseases. Aside from natural products, the recent development of recombinant DNA technology has sparked the development of a wide array of biopharmaceutical products, such as recombinant proteins, offering significant advances in treating a broad spectrum of medical illnesses and conditions. Herein, we will introduce the structures and diverse biological activities of natural products and recombinant proteins that have been exploited as valuable molecules in medicine, agriculture and insect control. In addition, we will explore past and ongoing efforts along with achievements in the development of robust and promising microorganisms as cell factories to produce biologically active molecules. Furthermore, we will review multi-disciplinary and comprehensive engineering approaches directed at improving yields of microbial production of natural products and proteins and generating novel molecules. Throughout this article, we will suggest ways in which microbial-derived biologically active molecular entities and their analogs could continue to inspire the development of new therapeutic agents in academia and industry.
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Affiliation(s)
- Janette V. Pham
- Geisinger Commonwealth School of Medicine, Scranton, PA, United States
- Baruch S. Blumberg Institute, Doylestown, PA, United States
| | - Mariamawit A. Yilma
- Geisinger Commonwealth School of Medicine, Scranton, PA, United States
- Baruch S. Blumberg Institute, Doylestown, PA, United States
| | - Adriana Feliz
- Geisinger Commonwealth School of Medicine, Scranton, PA, United States
- Baruch S. Blumberg Institute, Doylestown, PA, United States
| | - Murtadha T. Majid
- Geisinger Commonwealth School of Medicine, Scranton, PA, United States
- Baruch S. Blumberg Institute, Doylestown, PA, United States
| | - Nicholas Maffetone
- Geisinger Commonwealth School of Medicine, Scranton, PA, United States
- Baruch S. Blumberg Institute, Doylestown, PA, United States
| | - Jorge R. Walker
- Geisinger Commonwealth School of Medicine, Scranton, PA, United States
- Baruch S. Blumberg Institute, Doylestown, PA, United States
| | - Eunji Kim
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, South Korea
| | - Hyo Je Cho
- School of Life Sciences and Biotechnology, Kyungpook National University, Daegu, South Korea
| | - Jared M. Reynolds
- Geisinger Commonwealth School of Medicine, Scranton, PA, United States
- Baruch S. Blumberg Institute, Doylestown, PA, United States
| | - Myoung Chong Song
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, South Korea
| | - Sung Ryeol Park
- Geisinger Commonwealth School of Medicine, Scranton, PA, United States
- Baruch S. Blumberg Institute, Doylestown, PA, United States
- Natural Products Discovery Institute, Doylestown, PA, United States
| | - Yeo Joon Yoon
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, South Korea
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18
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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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Chandra Mohana N, Yashavantha Rao H, Rakshith D, Mithun P, Nuthan B, Satish S. Omics based approach for biodiscovery of microbial natural products in antibiotic resistance era. J Genet Eng Biotechnol 2018; 16:1-8. [PMID: 30647697 PMCID: PMC6296576 DOI: 10.1016/j.jgeb.2018.01.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 01/25/2018] [Accepted: 01/30/2018] [Indexed: 01/01/2023]
Abstract
The need for a new antibiotic pipeline to confront threat imposed by resistant pathogens has become a major global concern for human health. To confront the challenge there is a need for discovery and development of new class of antibiotics. Nature which is considered treasure trove, there is re-emerged interest in exploring untapped microbial to yield novel molecules, due to their wide array of negative effects associated with synthetic drugs. Natural product researchers have developed many new techniques over the past few years for developing diverse compounds of biopotential. Taking edge in the advancement of genomics, genetic engineering, in silico drug design, surface modification, scaffolds, pharmacophores and target-based approach is necessary. These techniques have been economically sustainable and also proven efficient in natural product discovery. This review will focus on recent advances in diverse discipline approach from integrated Bioinformatics predictions, genetic engineering and medicinal chemistry for the synthesis of natural products vital for the discovery of novel antibiotics having potential application.
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Affiliation(s)
- N. Chandra Mohana
- Microbial Drugs Laboratory, Department of Studies in Microbiology, Manasagangotri, University of Mysore, Mysore 570006, Karnataka, India
| | - H.C. Yashavantha Rao
- Microbial Drugs Laboratory, Department of Studies in Microbiology, Manasagangotri, University of Mysore, Mysore 570006, Karnataka, India
| | - D. Rakshith
- Microbial Drugs Laboratory, Department of Studies in Microbiology, Manasagangotri, University of Mysore, Mysore 570006, Karnataka, India
| | - P.R. Mithun
- Department of Life Sciences, Christ University, Bengaluru 560029, Karnataka, India
| | - B.R. Nuthan
- Microbial Drugs Laboratory, Department of Studies in Microbiology, Manasagangotri, University of Mysore, Mysore 570006, Karnataka, India
| | - S. Satish
- Microbial Drugs Laboratory, Department of Studies in Microbiology, Manasagangotri, University of Mysore, Mysore 570006, Karnataka, India
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20
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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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21
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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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22
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Luna‐Flores CH, Palfreyman RW, Krömer JO, Nielsen LK, Marcellin E. Improved production of propionic acid using genome shuffling. Biotechnol J 2016; 12. [DOI: 10.1002/biot.201600120] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 09/22/2016] [Accepted: 09/23/2016] [Indexed: 11/05/2022]
Affiliation(s)
- Carlos H Luna‐Flores
- Australian Institute for Bioengineering and Nanotechnology (AIBN) The University of Queensland Brisbane Qld Australia
| | - Robin W Palfreyman
- Australian Institute for Bioengineering and Nanotechnology (AIBN) The University of Queensland Brisbane Qld Australia
| | - Jens O Krömer
- Australian Institute for Bioengineering and Nanotechnology (AIBN) The University of Queensland Brisbane Qld Australia
| | - Lars K Nielsen
- Australian Institute for Bioengineering and Nanotechnology (AIBN) The University of Queensland Brisbane Qld Australia
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology (AIBN) The University of Queensland Brisbane Qld Australia
- Dow Centre for Sustainable Engineering and Innovation The University of Queensland Brisbane Qld Australia
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23
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Zhu Z, Wu X, Lv B, Wu G, Wang J, Jiang W, Li P, He J, Chen J, Chen M, Bao D, Zhang J, Tan Q, Tang X. A new approach for breeding low-temperature-resistantVolvariella volvaceastrains: Genome shuffling in edible fungi. Biotechnol Appl Biochem 2016; 63:605-615. [DOI: 10.1002/bab.1420] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 05/15/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Ziping Zhu
- Biotechnology Research Institute; Shanghai Academy of Agricultural Sciences; Shanghai People's Republic of China
- School of Life Science; Taizhou University; Taizhou People's Republic of China
| | - Xiao Wu
- Biotechnology Research Institute; Shanghai Academy of Agricultural Sciences; Shanghai People's Republic of China
- Key Laboratory of Agricultural Genetics and Breeding; Shanghai Academy of Agricultural Sciences; Shanghai People's Republic of China
| | - Beibei Lv
- Biotechnology Research Institute; Shanghai Academy of Agricultural Sciences; Shanghai People's Republic of China
- Key Laboratory of Agricultural Genetics and Breeding; Shanghai Academy of Agricultural Sciences; Shanghai People's Republic of China
| | - Guogan Wu
- Biotechnology Research Institute; Shanghai Academy of Agricultural Sciences; Shanghai People's Republic of China
- Key Laboratory of Agricultural Genetics and Breeding; Shanghai Academy of Agricultural Sciences; Shanghai People's Republic of China
| | - Jinbin Wang
- Biotechnology Research Institute; Shanghai Academy of Agricultural Sciences; Shanghai People's Republic of China
- Key Laboratory of Agricultural Genetics and Breeding; Shanghai Academy of Agricultural Sciences; Shanghai People's Republic of China
| | - Wei Jiang
- Biotechnology Research Institute; Shanghai Academy of Agricultural Sciences; Shanghai People's Republic of China
- Key Laboratory of Agricultural Genetics and Breeding; Shanghai Academy of Agricultural Sciences; Shanghai People's Republic of China
| | - Peng Li
- Biotechnology Research Institute; Shanghai Academy of Agricultural Sciences; Shanghai People's Republic of China
- Key Laboratory of Agricultural Genetics and Breeding; Shanghai Academy of Agricultural Sciences; Shanghai People's Republic of China
| | - Jianhua He
- Biotechnology Research Institute; Shanghai Academy of Agricultural Sciences; Shanghai People's Republic of China
- Key Laboratory of Agricultural Genetics and Breeding; Shanghai Academy of Agricultural Sciences; Shanghai People's Republic of China
| | - Jianzhong Chen
- Biotechnology Research Institute; Shanghai Academy of Agricultural Sciences; Shanghai People's Republic of China
- Key Laboratory of Agricultural Genetics and Breeding; Shanghai Academy of Agricultural Sciences; Shanghai People's Republic of China
| | - Mingjie Chen
- National Engineering Research Center of Edible Fungi; Shanghai People's Republic of China
| | - Dapeng Bao
- National Engineering Research Center of Edible Fungi; Shanghai People's Republic of China
| | - Jinsong Zhang
- National Engineering Research Center of Edible Fungi; Shanghai People's Republic of China
| | - Qi Tan
- National Engineering Research Center of Edible Fungi; Shanghai People's Republic of China
| | - Xueming Tang
- Biotechnology Research Institute; Shanghai Academy of Agricultural Sciences; Shanghai People's Republic of China
- Key Laboratory of Agricultural Genetics and Breeding; Shanghai Academy of Agricultural Sciences; Shanghai People's Republic of China
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24
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Zhang MM, Wang Y, Ang EL, Zhao H. Engineering microbial hosts for production of bacterial natural products. Nat Prod Rep 2016; 33:963-87. [PMID: 27072804 PMCID: PMC4963277 DOI: 10.1039/c6np00017g] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Covering up to end 2015Microbial fermentation provides an attractive alternative to chemical synthesis for the production of structurally complex natural products. In most cases, however, production titers are low and need to be improved for compound characterization and/or commercial production. Owing to advances in functional genomics and genetic engineering technologies, microbial hosts can be engineered to overproduce a desired natural product, greatly accelerating the traditionally time-consuming strain improvement process. This review covers recent developments and challenges in the engineering of native and heterologous microbial hosts for the production of bacterial natural products, focusing on the genetic tools and strategies for strain improvement. Special emphasis is placed on bioactive secondary metabolites from actinomycetes. The considerations for the choice of host systems will also be discussed in this review.
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Affiliation(s)
- Mingzi M Zhang
- Metabolic Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology and Research, Singapore
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25
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Zeng W, Chen G, Wu H, Wang J, Liu Y, Guo Y, Liang Z. Improvement of Bacillus subtilis for poly-γ-glutamic acid production by genome shuffling. Microb Biotechnol 2016; 9:824-833. [PMID: 27562078 PMCID: PMC5072198 DOI: 10.1111/1751-7915.12405] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 07/18/2016] [Accepted: 07/24/2016] [Indexed: 12/03/2022] Open
Abstract
Poly‐γ‐glutamic acid (γ‐PGA) is a promising microbial polymer with potential applications in industry, agriculture and medicine. The use of high γ‐PGA‐producing strains is an effective approach to improve productivity of γ‐PGA. In this study, we developed a mutant, F3‐178, from Bacillus subtilis GXA‐28 using genome shuffling. The morphological characteristics of F3‐178 and GXA‐28 were not identical. Compared with GXA‐28 (18.4 ± 0.8 g l−1), the yield of γ‐PGA was 1.9‐fold higher in F3‐178 (34.3 ± 1.2 g l−1). Results from batch fermentation in 3.7 l fermenter showed that F3‐178 was satisfactory for industrial production of γ‐PGA. Metabolic studies suggested that the higher γ‐PGA yield in F3‐178 could be attributed to increased intracellular flux and uptake of extracellular glutamate. Real‐time PCR indicated that mRNA level of pgsB in F3‐178 was 18.8‐fold higher than in GXA‐28, suggesting the higher yield might be related to the overexpression of genes involved in γ‐PGA production. This study demonstrated that genome shuffling can be used for rapid improvement of γ‐PGA strains, and the possible mechanism for the improved phenotype was also explored at the metabolic and transcriptional levels.
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Affiliation(s)
- Wei Zeng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, Guangxi, 530004, China.,Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, Guangxi University, Nanning, Guangxi, 530004, China.,College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
| | - Guiguang Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, Guangxi, 530004, China.,Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, Guangxi University, Nanning, Guangxi, 530004, China.,College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
| | - Hao Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, Guangxi, 530004, China.,Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, Guangxi University, Nanning, Guangxi, 530004, China.,College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
| | - Jun Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, Guangxi, 530004, China.,Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, Guangxi University, Nanning, Guangxi, 530004, China.,College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
| | - Yanliao Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, Guangxi, 530004, China.,Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, Guangxi University, Nanning, Guangxi, 530004, China.,College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
| | - Ye Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, Guangxi, 530004, China.,Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, Guangxi University, Nanning, Guangxi, 530004, China.,College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
| | - Zhiqun Liang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, Guangxi, 530004, China. .,Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, Guangxi University, Nanning, Guangxi, 530004, China. .,College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China.
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26
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Insights into microbial cryptic gene activation and strain improvement: principle, application and technical aspects. J Antibiot (Tokyo) 2016; 70:25-40. [PMID: 27381522 DOI: 10.1038/ja.2016.82] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 05/22/2016] [Accepted: 06/06/2016] [Indexed: 12/22/2022]
Abstract
As bacteria and fungi have been found to contain genes encoding enzymes that synthesize a plethora of potential secondary metabolites, interest has grown in the activation of these cryptic pathways. Homologous and heterologous expression of these cryptic secondary metabolite-biosynthetic genes, often silent under ordinary laboratory fermentation conditions, may lead to the discovery of novel secondary metabolites. This review addresses current progress in the activation of these pathways, describing methods for activating silent genes. It especially focuses on genetic manipulation of transcription and translation (ribosome engineering), the utilization of elicitors, metabolism remodeling and co-cultivation. In particular, the principles and technical points of ribosome engineering and the significance of S-adenosylmethionine in bacterial physiology, especially secondary metabolism, are described in detail.
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27
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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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Improved antibiotic production and silent gene activation in Streptomyces diastatochromogenes by ribosome engineering. J Antibiot (Tokyo) 2015; 69:406-10. [DOI: 10.1038/ja.2015.123] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 10/22/2015] [Accepted: 10/28/2015] [Indexed: 11/08/2022]
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29
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Wang Z, Zang N, Shi J, Feng W, Liu Y, Liang X. Comparative Proteome of Acetobacter pasteurianus Ab3 During the High Acidity Rice Vinegar Fermentation. Appl Biochem Biotechnol 2015; 177:1573-88. [PMID: 26369782 DOI: 10.1007/s12010-015-1838-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 09/07/2015] [Indexed: 01/20/2023]
Abstract
As a traditional Asian food for several centuries, vinegar is known to be produced by acetic acid bacteria. The Acetobacter species is the primary starter for vinegar fermentation and has evolutionarily acquired acetic acid resistance, in which Acetobacter pasteurianus Ab3 is routinely used for industrial production of rice vinegar with a high acidity (9 %, w/v). In contrast to the documented short-term and low acetic acid effects on A. pasteurianus, here we investigated the molecular and cellular signatures of long-term and high acetic acid responses by proteomic profiling with bidimensional gel electrophoresis and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI TOF/MS) analyses. Protein spots of interest were selected based on the threshold ANOVA p value of 0.05 and minimal twofold of differential expression, leading to the identification of 26 proteins that are functionally enriched in oxidoreductase activity, cell membrane, and metabolism. The alterations in protein functioning in respiratory chain and protein denaturation may underlay cellular modifications at the outer membrane. Significantly, we found that at higher acidity fermentation phase, the A. pasteurianus Ab3 cells would adapt to distinct physiological processes from that of an ordinary vinegar fermentation with intermediate acidity, indicating increasing energy requirement and dependency of membrane integrity during the transition of acetic acid production. Together, our study provided new insights into the adaptation mechanisms in A. pasteurianus to high acetic acid environments and yield novel regulators and key pathways during the development of acetic acid resistance.
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Affiliation(s)
- Zhe Wang
- Department of Biochemical Engineering, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Ning Zang
- Medical Scientific Research Center, Guangxi Medical University, Nanning, 530021, China
| | - Jieyan Shi
- Department of Biochemical Engineering, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Wei Feng
- Hangzhou Xihu Brewing Company, Hangzhou, 310012, China
| | - Ye Liu
- Hangzhou Xihu Brewing Company, Hangzhou, 310012, China
| | - Xinle Liang
- Department of Biochemical Engineering, Zhejiang Gongshang University, Hangzhou, 310018, China.
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Breeding High Producers of Enduracidin from Streptomyces fungicidicus by Combination of Various Mutation Treatments. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/978-3-662-45657-6_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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31
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Wang H, Xue W, He YM, Peng RH, Yao QH. Improvement of the ability to produce spinosad in Saccharopolyspora spinosa through the acquisition of drug resistance and genome shuffling. ANN MICROBIOL 2014. [DOI: 10.1007/s13213-014-0917-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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32
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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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Du W, Huang D, Xia M, Wen J, Huang M. Improved FK506 production by the precursors and product-tolerant mutant of Streptomyces tsukubaensis based on genome shuffling and dynamic fed-batch strategies. J Ind Microbiol Biotechnol 2014; 41:1131-43. [PMID: 24788378 DOI: 10.1007/s10295-014-1450-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 04/18/2014] [Indexed: 01/09/2023]
Abstract
FK506, a secondary metabolite produced by Streptomyces tsukubaensis, is well known for its immunosuppressant properties to prevent rejection of transplanted organs and treat autoimmune diseases. However, the low titer of FK506 in the original producer strain limits the further industrialization efforts and restricts its clinical applications. To address this issue, a highly efficient method combined genome shuffling and dynamic fed-batch strategies was systematically performed in this work. Firstly, after five rounds of genome shuffling based on precursors and product resistances, a higher yielding strain TJ-P325 was successfully acquired, whose production reached 365.6 mg/L, 11-fold increase compared with the original strain. Then, the possible mechanism of different production capabilities between TJ-P325 and the wild type was explored through comparative gene expression analysis of key genes. Results showed that the transcription level of key genes was altered significantly in the mutant. Moreover, precursors addition enhanced the FK506 production by 28 %, as well as reduced the by-products biosynthesis. Finally, the disodium malonate and disodium methylmalonate dynamic fed-batch strategies dramatically led to the production of 514.5 mg/L in a 7.5-L bioreactor. These results demonstrated that genome shuffling and dynamic fed-batch strategies could be successfully applied to generate high-yield strains with value-added natural products during industrial microbial fermentation.
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Affiliation(s)
- Wenjie Du
- Department of Biological Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
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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 Streptomyces roseosporus for Improving Daptomycin Production. Appl Biochem Biotechnol 2014; 172:2661-9. [DOI: 10.1007/s12010-013-0687-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 12/18/2013] [Indexed: 11/26/2022]
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36
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Zheng DQ, Chen J, Zhang K, Gao KH, Li O, Wang PM, Zhang XY, Du FG, Sun PY, Qu AM, Wu S, Wu XC. Genomic structural variations contribute to trait improvement during whole-genome shuffling of yeast. Appl Microbiol Biotechnol 2013; 98:3059-70. [PMID: 24346281 DOI: 10.1007/s00253-013-5423-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 11/17/2013] [Accepted: 11/18/2013] [Indexed: 11/24/2022]
Abstract
Whole-genome shuffling (WGS) is a powerful technology of improving the complex traits of many microorganisms. However, the molecular mechanisms underlying the altered phenotypes in isolates were less clarified. Isolates with significantly enhanced stress tolerance and ethanol titer under very-high-gravity conditions were obtained after WGS of the bioethanol Saccharomyces cerevisiae strain ZTW1. Karyotype analysis and RT-qPCR showed that chromosomal rearrangement occurred frequently in genome shuffling. Thus, the phenotypic effects of genomic structural variations were determined in this study. RNA-Seq and physiological analyses revealed the diverse transcription pattern and physiological status of the isolate S3-110 and ZTW1. Our observations suggest that the improved stress tolerance of S3-110 can be largely attributed to the copy number variations in large DNA regions, which would adjust the ploidy of yeast cells and expression levels of certain genes involved in stress response. Overall, this work not only constructed shuffled S. cerevisiae strains that have potential industrial applications but also provided novel insights into the molecular mechanisms of WGS and enhanced our knowledge on this useful breeding strategy.
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Affiliation(s)
- Dao-Qiong Zheng
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang Province, China
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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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39
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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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