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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: 1.8] [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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Ega SL, Drendel G, Petrovski S, Egidi E, Franks AE, Muddada S. Comparative Analysis of Structural Variations Due to Genome Shuffling of Bacillus Subtilis VS15 for Improved Cellulase Production. Int J Mol Sci 2020; 21:ijms21041299. [PMID: 32075107 PMCID: PMC7072954 DOI: 10.3390/ijms21041299] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 10/29/2019] [Accepted: 10/29/2019] [Indexed: 12/23/2022] Open
Abstract
Cellulose is one of the most abundant and renewable biomass products used for the production of bioethanol. Cellulose can be efficiently hydrolyzed by Bacillus subtilis VS15, a strain isolate obtained from decomposing logs. A genome shuffling approach was implemented to improve the cellulase activity of Bacillus subtilis VS15. Mutant strains were created using ethyl methyl sulfonate (EMS), N-Methyl-N′ nitro-N-nitrosoguanidine (NTG), and ultraviolet light (UV) followed by recursive protoplast fusion. After two rounds of shuffling, the mutants Gb2, Gc8, and Gd7 were produced that had an increase in cellulase activity of 128%, 148%, and 167%, respectively, in comparison to the wild type VS15. The genetic diversity of the shuffled strain Gd7 and wild type VS15 was compared at whole genome level. Genomic-level comparisons identified a set of eight genes, consisting of cellulase and regulatory genes, of interest for further analyses. Various genes were identified with insertions and deletions that may be involved in improved celluase production in Gd7. Strain Gd7 maintained the capability of hydrolyzing wheatbran to glucose and converting glucose to ethanol by fermentation with Saccharomyces cerevisiae of the wild type VS17. This ability was further confirmed by the acidified potassium dichromate (K2Cr2O7) method.
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Affiliation(s)
| | - Gene Drendel
- Department of Physiology, Anatomy and Microbiology, College of Science, Health and Engineering, La Trobe University, Melbourne, Victoria 3086, Australia; (G.D.); (S.P.); (E.E.); (A.E.F.)
| | - Steve Petrovski
- Department of Physiology, Anatomy and Microbiology, College of Science, Health and Engineering, La Trobe University, Melbourne, Victoria 3086, Australia; (G.D.); (S.P.); (E.E.); (A.E.F.)
| | - Eleonora Egidi
- Department of Physiology, Anatomy and Microbiology, College of Science, Health and Engineering, La Trobe University, Melbourne, Victoria 3086, Australia; (G.D.); (S.P.); (E.E.); (A.E.F.)
- Hawkesbury Institute for the Environment, Western Sydney University, Sydney, NSW 2750, Australia
| | - Ashley E. Franks
- Department of Physiology, Anatomy and Microbiology, College of Science, Health and Engineering, La Trobe University, Melbourne, Victoria 3086, Australia; (G.D.); (S.P.); (E.E.); (A.E.F.)
- Centre for Future Landscapes, College of Science, Health and Engineering, La Trobe University, Melbourne, VI 3086, Australia
| | - Sudhamani Muddada
- Department of Biotechnology, K L E F University, Guntur 522 502, India;
- Correspondence: ; Tel.: +91-970-3470-598
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Huang QG, Zeng BD, Liang L, Wu SG, Huang JZ. Genome shuffling and high-throughput screening of Brevibacterium flavum MDV1 for enhanced L-valine production. World J Microbiol Biotechnol 2018; 34:121. [PMID: 30039311 DOI: 10.1007/s11274-018-2502-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 07/10/2018] [Indexed: 11/25/2022]
Abstract
L-valine is an essential branched-amino acid that is widely used in multiple areas such as pharmaceuticals and special dietary products and its use is increasing. As the world market for L-valine grows rapidly, there is an increasing interest to develop an efficient L-valine-producing strain. In this study, a simple, sensitive, efficient, and consistent screening procedure termed 96 well plate-PC-HPLC (96-PH) was developed for the rapid identification of high-yield L-valine strains to replace the traditional L-valine assay. L-valine production by Brevibacterium flavum MDV1 was increased by genome shuffling. The starting strains were obtained using ultraviolet (UV) irradiation and binary ethylenimine treatment followed by preparation of protoplasts, UV irradiation inactivation, multi-cell fusion, and fusion of the inactivated protoplasts to produce positive colonies. After two rounds of genome shuffling and the 96-PH method, six L-valine high-yielding mutants were selected. One genetically stable mutant (MDVR2-21) showed an L-valine yield of 30.1 g/L during shake flask fermentation, 6.8-fold higher than that of MDV1. Under fed-batch conditions in a 30 L automated fermentor, MDVR2-21 accumulated 70.1 g/L of L-valine (0.598 mol L-valine per mole of glucose; 38.9% glucose conversion rate). During large-scale fermentation using a 120 m3 fermentor, this strain produced > 66.8 g/L L-valine (36.5% glucose conversion rate), reflecting a very productive and stable industrial enrichment fermentation effect. Genome shuffling is an efficient technique to improve production of L-valine by B. flavum MDV1. Screening using 96-PH is very economical, rapid, efficient, and well-suited for high-throughput screening.
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Affiliation(s)
- Qin-Geng Huang
- Engineering Research Center of Industrial Microbiology, Ministry of Education, College of Life Sciences, Fujian Normal University, No. 1, Science & Technology Road, Fuzhou, 350108, Fujian, People's Republic of China
| | - Bang-Ding Zeng
- Engineering Research Center of Industrial Microbiology, Ministry of Education, College of Life Sciences, Fujian Normal University, No. 1, Science & Technology Road, Fuzhou, 350108, Fujian, People's Republic of China
| | - Ling Liang
- Engineering Research Center of Industrial Microbiology, Ministry of Education, College of Life Sciences, Fujian Normal University, No. 1, Science & Technology Road, Fuzhou, 350108, Fujian, People's Republic of China
| | - Song-Gang Wu
- Engineering Research Center of Industrial Microbiology, Ministry of Education, College of Life Sciences, Fujian Normal University, No. 1, Science & Technology Road, Fuzhou, 350108, Fujian, People's Republic of China
| | - Jian-Zhong Huang
- Engineering Research Center of Industrial Microbiology, Ministry of Education, College of Life Sciences, Fujian Normal University, No. 1, Science & Technology Road, Fuzhou, 350108, Fujian, 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: 1.4] [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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Yu J, Zhang Y, Cui H, Hu P, Yu X, Ye Z. An efficient genetic manipulation protocol for Ustilago esculenta. FEMS Microbiol Lett 2015; 362:fnv087. [PMID: 26038251 DOI: 10.1093/femsle/fnv087] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2015] [Indexed: 11/14/2022] Open
Abstract
Ustilago esculenta grows within the flowering stem of the aquatic grass Zizania latifolia, resembling a fungal endophyte. The fungus colonizes Z. latifolia and induces swelling which results in the formation of galls near the base of the plant. Due to their unique flavor and textures these galls are considered as a delicacy in southern China. Efficient genetic manipulation is required to determine the relationship between U. esculenta and Z. latifolia. In this study, we report a protoplast-based transformation system for this unique fungal species. We have explored various factors (enzyme digesting conditions, osmotic pressure stabilizers, vectors and selection agents) that might impact protoplast yield and high frequencies of transformation. A haploid strain (UeT55) of U. esculenta was found to produce higher yields of protoplasts when treating with 15 mg mL(-1) lywallzyme in a sucrose-containing solution at 30°C for 3 h. The transformation frequencies were higher when fungal strain was transformed with a linear plasmid harboring hygromycin or carboxin resistance gene and regenerated on a sucrose-containing medium. A UeICL gene (coding isocitrate lyase) was disrupted and an EGFP (coding enhanced green fluorescent protein) gene was overexpressed successfully in the UeT55 strain using the developed conditions. The genetic manipulation system reported in this study will open up new opportunities for forward and reverse genetics in U. esculenta.
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Affiliation(s)
- Jiajia Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang 310018, China
| | - Yafen Zhang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang 310018, China
| | - Haifeng Cui
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang 310018, China
| | - Peng Hu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang 310018, China
| | - Xiaoping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang 310018, China
| | - Zihong Ye
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang 310018, China
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Guerriero G, Hausman JF, Strauss J, Ertan H, Siddiqui KS. Destructuring plant biomass: focus on fungal and extremophilic cell wall hydrolases. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 234:180-93. [PMID: 25804821 PMCID: PMC4937988 DOI: 10.1016/j.plantsci.2015.02.010] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 02/17/2015] [Accepted: 02/18/2015] [Indexed: 05/05/2023]
Abstract
The use of plant biomass as feedstock for biomaterial and biofuel production is relevant in the current bio-based economy scenario of valorizing renewable resources. Fungi, which degrade complex and recalcitrant plant polymers, secrete different enzymes that hydrolyze plant cell wall polysaccharides. The present review discusses the current research trends on fungal, as well as extremophilic cell wall hydrolases that can withstand extreme physico-chemical conditions required in efficient industrial processes. Secretomes of fungi from the phyla Ascomycota, Basidiomycota, Zygomycota and Neocallimastigomycota are presented along with metabolic cues (nutrient sensing, coordination of carbon and nitrogen metabolism) affecting their composition. We conclude the review by suggesting further research avenues focused on the one hand on a comprehensive analysis of the physiology and epigenetics underlying cell wall degrading enzyme production in fungi and on the other hand on the analysis of proteins with unknown function and metagenomics of extremophilic consortia. The current advances in consolidated bioprocessing, altered secretory pathways and creation of designer plants are also examined. Furthermore, recent developments in enhancing the activity, stability and reusability of enzymes based on synergistic, proximity and entropic effects, fusion enzymes, structure-guided recombination between homologous enzymes and magnetic enzymes are considered with a view to improving saccharification.
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Affiliation(s)
- Gea Guerriero
- Environmental Research and Innovation (ERIN), Luxembourg Institute of Science and Technology (LIST), Esch/Alzette, Luxembourg.
| | - Jean-Francois Hausman
- Environmental Research and Innovation (ERIN), Luxembourg Institute of Science and Technology (LIST), Esch/Alzette, Luxembourg
| | - Joseph Strauss
- Department of Applied Genetics and Cell Biology, Fungal Genetics and Genomics Unit, University of Natural Resources and Life Sciences Vienna (BOKU), University and Research Center Campus Tulln-Technopol, Tulln/Donau, Austria; Health and Environment Department, Austrian Institute of Technology GmbH - AIT, University and Research Center Campus Tulln-Technopol, Tulln/Donau, Austria
| | - Haluk Ertan
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia; Department of Molecular Biology and Genetics, Istanbul University, Turkey
| | - Khawar Sohail Siddiqui
- Biology Department, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran, Saudi Arabia.
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