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Put H, Gerstmans H, Vande Capelle H, Fauvart M, Michiels J, Masschelein J. Bacillus subtilis as a host for natural product discovery and engineering of biosynthetic gene clusters. Nat Prod Rep 2024; 41:1113-1151. [PMID: 38465694 DOI: 10.1039/d3np00065f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Covering: up to October 2023Many bioactive natural products are synthesized by microorganisms that are either difficult or impossible to cultivate under laboratory conditions, or that produce only small amounts of the desired compound. By transferring biosynthetic gene clusters (BGCs) into alternative host organisms that are more easily cultured and engineered, larger quantities can be obtained and new analogues with potentially improved biological activity or other desirable properties can be generated. Moreover, expression of cryptic BGCs in a suitable host can facilitate the identification and characterization of novel natural products. Heterologous expression therefore represents a valuable tool for natural product discovery and engineering as it allows the study and manipulation of their biosynthetic pathways in a controlled setting, enabling innovative applications. Bacillus is a genus of Gram-positive bacteria that is widely used in industrial biotechnology as a host for the production of proteins from diverse origins, including enzymes and vaccines. However, despite numerous successful examples, Bacillus species remain underexploited as heterologous hosts for the expression of natural product BGCs. Here, we review important advantages that Bacillus species offer as expression hosts, such as high secretion capacity, natural competence for DNA uptake, and the increasing availability of a wide range of genetic tools for gene expression and strain engineering. We evaluate different strain optimization strategies and other critical factors that have improved the success and efficiency of heterologous natural product biosynthesis in B. subtilis. Finally, future perspectives for using B. subtilis as a heterologous host are discussed, identifying research gaps and promising areas that require further exploration.
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Affiliation(s)
- Hanne Put
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
| | - Hans Gerstmans
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- Laboratory for Biomolecular Discovery & Engineering, KU Leuven, 3001 Leuven, Belgium
- Biosensors Group, KU Leuven, 3001 Leuven, Belgium
| | - Hanne Vande Capelle
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- Laboratory for Biomolecular Discovery & Engineering, KU Leuven, 3001 Leuven, Belgium
| | - Maarten Fauvart
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- imec, 3001 Leuven, Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
| | - Joleen Masschelein
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- Laboratory for Biomolecular Discovery & Engineering, KU Leuven, 3001 Leuven, Belgium
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Iqbal S, Begum F, Rabaan AA, Aljeldah M, Al Shammari BR, Alawfi A, Alshengeti A, Sulaiman T, Khan A. Classification and Multifaceted Potential of Secondary Metabolites Produced by Bacillus subtilis Group: A Comprehensive Review. Molecules 2023; 28:molecules28030927. [PMID: 36770594 PMCID: PMC9919246 DOI: 10.3390/molecules28030927] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 12/31/2022] [Accepted: 01/04/2023] [Indexed: 01/19/2023] Open
Abstract
Despite their remarkable biosynthetic potential, Bacillus subtilis have been widely overlooked. However, their capability to withstand harsh conditions (extreme temperature, Ultraviolet (UV) and γ-radiation, and dehydration) and the promiscuous metabolites they synthesize have created increased commercial interest in them as a therapeutic agent, a food preservative, and a plant-pathogen control agent. Nevertheless, the commercial-scale availability of these metabolites is constrained due to challenges in their accessibility via synthesis and low fermentation yields. In the context of this rising in interest, we comprehensively visualized the antimicrobial peptides produced by B. subtilis and highlighted their prospective applications in various industries. Moreover, we proposed and classified these metabolites produced by the B. subtilis group based on their biosynthetic pathways and chemical structures. The biosynthetic pathway, bioactivity, and chemical structure are discussed in detail for each class. We believe that this review will spark a renewed interest in the often disregarded B. subtilis and its remarkable biosynthetic capabilities.
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Affiliation(s)
- Sajid Iqbal
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
- Correspondence: or
| | - Farida Begum
- Department of Biochemistry, Abdul Wali Khan University Mardan (AWKUM), Mardan 23200, Pakistan
| | - Ali A. Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
| | - Mohammed Aljeldah
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, Hafr Al Batin 39831, Saudi Arabia
| | - Basim R. Al Shammari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, Hafr Al Batin 39831, Saudi Arabia
| | - Abdulsalam Alawfi
- Department of Pediatrics, College of Medicine, Taibah University, Al-Madinah 41491, Saudi Arabia
| | - Amer Alshengeti
- Department of Pediatrics, College of Medicine, Taibah University, Al-Madinah 41491, Saudi Arabia
- Department of Infection Prevention and Control, Prince Mohammad Bin Abdulaziz Hospital, National Guard Health Affairs, Al-Madinah 41491, Saudi Arabia
| | - Tarek Sulaiman
- Infectious Diseases Section, Medical Specialties Department, King Fahad Medical City, Riyadh 12231, Saudi Arabia
| | - Alam Khan
- Department of Life Sciences, Abasyn University Islamabad Campus, Islamabad 44000, Pakistan
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Sheldon RA, Brady D. Green Chemistry, Biocatalysis, and the Chemical Industry of the Future. CHEMSUSCHEM 2022; 15:e202102628. [PMID: 35026060 DOI: 10.1002/cssc.202102628] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/11/2022] [Indexed: 06/14/2023]
Abstract
In the movement to decarbonize our economy and move away from fossil fuels we will need to harness the waste products of our activities, such as waste lignocellulose, methane, and carbon dioxide. Our wastes need to be integrated into a circular economy where used products are recycled into a manufacturing carbon cycle. Key to this will be the recycling of plastics at the resin and monomer levels. Biotechnology is well suited to a future chemical industry that must adapt to widely distributed and diverse biological chemical feedstocks. Our increasing mastery of biotechnology is allowing us to develop enzymes and organisms that can synthesize a widening selection of desirable bulk chemicals, including plastics, at commercially viable productivities. Integration of bioreactors with electrochemical systems will permit new production opportunities with enhanced productivities and the advantage of using a low-carbon electricity from renewable and sustainable sources.
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Affiliation(s)
- Roger A Sheldon
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, 1 Jan Smuts Avenue, Braamfontein, Johannesburg, 2000, South Africa
- Department of Biotechnology, Delft University of Technology, Section BOC, van der Maasweg 9, 2629 HZ, Delft, Netherlands
| | - Dean Brady
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, 1 Jan Smuts Avenue, Braamfontein, Johannesburg, 2000, South Africa
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Abstract
Dextran is an exopolysaccharide (EPS) synthesized by lactic acid bacteria (LAB) or their enzymes in the presence of sucrose. Dextran is composed of a linear chain of d-glucoses linked by α-(1→6) bonds, with possible branches of d-glucoses linked by α-(1→4), α-(1→3), or α-(1→2) bonds, which can be low (<40 kDa) or high molecular weight (>40 kDa). The characteristics of dextran in terms of molecular weight and branches depend on the producing strain, so there is a great variety in its properties. Dextran has commercial interest because its solubility, viscosity, and thermal and rheological properties allow it to be used in food, pharmaceutical, and research areas. The aim of this review article is to compile the latest research (in the past decade) using LAB to synthesize high or low molecular weight dextran. In addition, studies using modified enzymes to produce dextran with specific structural characteristics (molecular weights and branches) are addressed. On the other hand, special attention is paid to LAB extracted from unconventional sources to expose their capacities as dextran producers and their possible application to compete with the only commercial strain (Leuconostoc mesenteroides NRRL B512).
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Schalck T, den Bergh BV, Michiels J. Increasing Solvent Tolerance to Improve Microbial Production of Alcohols, Terpenoids and Aromatics. Microorganisms 2021; 9:249. [PMID: 33530454 PMCID: PMC7912173 DOI: 10.3390/microorganisms9020249] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/14/2021] [Accepted: 01/20/2021] [Indexed: 12/16/2022] Open
Abstract
Fuels and polymer precursors are widely used in daily life and in many industrial processes. Although these compounds are mainly derived from petrol, bacteria and yeast can produce them in an environment-friendly way. However, these molecules exhibit toxic solvent properties and reduce cell viability of the microbial producer which inevitably impedes high product titers. Hence, studying how product accumulation affects microbes and understanding how microbial adaptive responses counteract these harmful defects helps to maximize yields. Here, we specifically focus on the mode of toxicity of industry-relevant alcohols, terpenoids and aromatics and the associated stress-response mechanisms, encountered in several relevant bacterial and yeast producers. In practice, integrating heterologous defense mechanisms, overexpressing native stress responses or triggering multiple protection pathways by modifying the transcription machinery or small RNAs (sRNAs) are suitable strategies to improve solvent tolerance. Therefore, tolerance engineering, in combination with metabolic pathway optimization, shows high potential in developing superior microbial producers.
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Affiliation(s)
- Thomas Schalck
- VIB Center for Microbiology, Flanders Institute for Biotechnology, B-3001 Leuven, Belgium; (T.S.); (B.V.d.B.)
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Bram Van den Bergh
- VIB Center for Microbiology, Flanders Institute for Biotechnology, B-3001 Leuven, Belgium; (T.S.); (B.V.d.B.)
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Jan Michiels
- VIB Center for Microbiology, Flanders Institute for Biotechnology, B-3001 Leuven, Belgium; (T.S.); (B.V.d.B.)
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
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Wu JQ, Xu XM, Wang DL, Long NB, Zhang RF. Immobilization of phospholipase D on macroporous SiO 2/cationic polymer nano-composited support for the highly efficient synthesis of phosphatidylserine. Enzyme Microb Technol 2020; 142:109696. [PMID: 33220874 DOI: 10.1016/j.enzmictec.2020.109696] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 10/15/2020] [Accepted: 10/17/2020] [Indexed: 11/26/2022]
Abstract
Novel nano-composites were prepared by coating epoxy resin-based cationic polymer in nano-thickness via in-situ curing on the nano-wall of macroporous SiO2 with pore size of 0.5∼1 μm. By changing the thickness of polymer coating the specific surface area and porosity varied in range of 115∼74 m2/g and 90.4∼83.9 %, respectively. Through ion exchange phospholipase D (PLD, from Streptomyces sp) was efficiently immobilized on the nano-composites as support and the immobilized PLD was applied for the highly efficient synthesis of phosphatidylserine (PS). The loading amount of PLD on the nano-composited support reached to a maximum of 90.2 mg/gsupport, 4 times as high as that on the pure macroporous silica. The specific activity of the immobilized PLD reached as high as 16,230 U/gprotein, while that of free PLD was 18,780 U/gprotein. Under a wide range of temperature and pH the stability and activity of the immobilized PLD were greatly improved as compared with the free ones. Under optimized conditions at 45 °C and pH 7.0, the PS yield reached as high as 96.2 % within 40 min. After 28 days storage the immobilized PLD retained 82.2 % of original activity, and after 12 cycling reuses it retained 79.3 % of PS yield, which indicated that the immobilized PLD exhibited good stability.
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Affiliation(s)
- Jia-Qin Wu
- Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, PR China
| | - Xiao-Mei Xu
- Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, PR China
| | - Ding-Lin Wang
- Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, PR China
| | - Neng-Bing Long
- Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, PR China
| | - Rui-Feng Zhang
- Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, PR China.
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Zhang S, Wakai S, Sasakura N, Tsutsumi H, Hata Y, Ogino C, Kondo A. Pyruvate metabolism redirection for biological production of commodity chemicals in aerobic fungus Aspergillus oryzae. Metab Eng 2020; 61:225-237. [DOI: 10.1016/j.ymben.2020.06.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 06/03/2020] [Accepted: 06/22/2020] [Indexed: 01/31/2023]
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Piñero-Lambea C, Garcia-Ramallo E, Martinez S, Delgado J, Serrano L, Lluch-Senar M. Mycoplasma pneumoniae Genome Editing Based on Oligo Recombineering and Cas9-Mediated Counterselection. ACS Synth Biol 2020; 9:1693-1704. [PMID: 32502342 PMCID: PMC7372593 DOI: 10.1021/acssynbio.0c00022] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Mycoplasma species
share a set of features, such as lack of a cell
wall, streamlined genomes, simplified metabolism, and the use of a
deviant genetic code, that make them attractive approximations of
what a chassis strain should ideally be. Among them, Mycoplasma
pneumoniae arises as a candidate for synthetic biology projects,
as it is one of the most deeply characterized bacteria. However, the
historical paucity of tools for editing Mycoplasma genomes has precluded
the establishment of M. pneumoniae as a suitable
chassis strain. Here, we developed an oligonucleotide recombineering
method for this strain based on GP35, a ssDNA recombinase originally
encoded by a Bacillus subtilis-associated phage.
GP35-mediated oligo recombineering is able to carry out point mutations
in the M. pneumoniae genome with an efficiency as
high as 2.7 × 10–2, outperforming oligo recombineering
protocols developed for other bacteria. Gene deletions of different
sizes showed a decreasing power trend between efficiency and the scale
of the attempted edition. However, the editing rates for all modifications
increased when CRISPR/Cas9 was used to counterselect nonedited cells.
This allowed edited clones carrying chromosomal deletions of up to
1.8 kb to be recovered with little to no screening of survivor cells.
We envision this technology as a major step toward the use of M. pneumoniae, and possibly other Mycoplasmas, as synthetic
biology chassis strains.
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Affiliation(s)
- Carlos Piñero-Lambea
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Eva Garcia-Ramallo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Sira Martinez
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Javier Delgado
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- ICREA, Pg. Lluis Companys 23, Barcelona 08010, Spain
| | - Maria Lluch-Senar
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
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Karagoz P, Mandair R, Manayil JC, Lad J, Chong K, Kyriakou G, Lee AF, Wilson K, Bill RM. Purification and immobilization of engineered glucose dehydrogenase: a new approach to producing gluconic acid from breadwaste. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:100. [PMID: 32514312 PMCID: PMC7268246 DOI: 10.1186/s13068-020-01735-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 05/18/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Platform chemicals are essential to industrial processes. Used as starting materials for the manufacture of diverse products, their cheap availability and efficient sourcing are an industrial requirement. Increasing concerns about the depletion of natural resources and growing environmental consciousness have led to a focus on the economics and ecological viability of bio-based platform chemical production. Contemporary approaches include the use of immobilized enzymes that can be harnessed to produce high-value chemicals from waste. RESULTS In this study, an engineered glucose dehydrogenase (GDH) was optimized for gluconic acid (GA) production. Sulfolobus solfataricus GDH was expressed in Escherichia coli. The K m and V max values for recombinant GDH were calculated as 0.87 mM and 5.91 U/mg, respectively. Recombinant GDH was immobilized on a hierarchically porous silica support (MM-SBA-15) and its activity was compared with GDH immobilized on three commercially available supports. MM-SBA-15 showed significantly higher immobilization efficiency (> 98%) than the commercial supports. After 5 cycles, GDH activity was at least 14% greater than the remaining activity on commercial supports. Glucose in bread waste hydrolysate was converted to GA by free-state and immobilized GDH. After the 10th reuse cycle on MM-SBA-15, a 22% conversion yield was observed, generating 25 gGA/gGDH. The highest GA production efficiency was 47 gGA/gGDH using free-state GDH. CONCLUSIONS This study demonstrates the feasibility of enzymatically converting BWH to GA: immobilizing GDH on MM-SBA-15 renders the enzyme more stable and permits its multiple reuse.
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Affiliation(s)
- Pinar Karagoz
- School of Life and Health Sciences, Aston University, Birmingham, B4 7ET UK
| | - Ravneet Mandair
- School of Life and Health Sciences, Aston University, Birmingham, B4 7ET UK
| | | | - Jai Lad
- European Bioenergy Research Institute (EBRI), Aston University, Birmingham, B4 7ET UK
| | - Katie Chong
- European Bioenergy Research Institute (EBRI), Aston University, Birmingham, B4 7ET UK
| | - Georgios Kyriakou
- Department of Chemical Engineering, University of Patras, 265 04 Patras, Greece
| | - Adam F. Lee
- Applied Chemistry & Environmental Science, School of Science, RMIT University, Melbourne, VIC 3000 Australia
| | - Karen Wilson
- Applied Chemistry & Environmental Science, School of Science, RMIT University, Melbourne, VIC 3000 Australia
| | - Roslyn M. Bill
- School of Life and Health Sciences, Aston University, Birmingham, B4 7ET UK
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Hara KY, Saito M, Kato H, Morikawa K, Kikukawa H, Nomura H, Fujimoto T, Hirono-Hara Y, Watanabe S, Kanamaru K, Kondo A. 5-Aminolevulinic acid fermentation using engineered Saccharomyces cerevisiae. Microb Cell Fact 2019; 18:194. [PMID: 31699086 PMCID: PMC6839092 DOI: 10.1186/s12934-019-1242-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 10/24/2019] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND 5'-Aminolevulinic acid (ALA) is widely used in the pharmaceutical industry, healthcare, and food production, and is a substrate for the biosynthesis of heme, which is required for respiration and photosynthesis. Enhancement of ALA biosynthesis has never been developed in Saccharomyces cerevisiae, which is a well-known model microorganism used for bioproduction of many value-added compounds. RESULTS We demonstrated that metabolic engineering significantly improved ALA production in S. cerevisiae. First, we found that overexpression of HEM1, which encodes ALA synthetase, increased ALA production. Furthermore, addition of an optimal amount of glycine, a substrate for ALA biosynthesis, or levulinic acid, an inhibitor of ALA dehydrogenase, effectively increased ALA production. Next, we developed an assay for multiple metabolites including ALA and found that aconitase, encoded by ACO1 and ACO2, is the rate-limiting enzyme of ALA biosynthesis when sufficient glycine is supplied. Overexpression of ACO2 further enhanced ALA production in S. cerevisiae overexpressing HEM1. CONCLUSIONS In this study, ALA production in S. cerevisiae was enhanced by metabolic engineering. This study also shows a strategy to identify the rate-limiting step of a target synthetic pathway by assay for multiple metabolites alongside the target product. This strategy can be applied to improve production of other valuable products in the well-studied and well-industrialized microorganism S. cerevisiae.
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Affiliation(s)
- Kiyotaka Y Hara
- Department of Environmental and Life Sciences, School of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga, Shizuoka, 422-8526, Japan.
- Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501, Japan.
| | - Masaru Saito
- Cosmo Oil Co., Ltd., 1-1-1 Shibaura, Minato-ku, Tokyo, 105-8528, Japan
| | - Hiroko Kato
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, 657-8501, Japan
| | - Kana Morikawa
- Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501, Japan
| | - Hiroshi Kikukawa
- Department of Environmental and Life Sciences, School of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga, Shizuoka, 422-8526, Japan
| | - Hironari Nomura
- Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501, Japan
- Department of Applied Chemistry in Bioscience, Graduate School of Agricultural Science, Kobe University, Kobe, 657-8501, Japan
| | - Takanori Fujimoto
- Cosmo Oil Co., Ltd., 1-1-1 Shibaura, Minato-ku, Tokyo, 105-8528, Japan
| | - Yoko Hirono-Hara
- Department of Environmental and Life Sciences, School of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga, Shizuoka, 422-8526, Japan
| | | | - Kengo Kanamaru
- Department of Applied Chemistry in Bioscience, Graduate School of Agricultural Science, Kobe University, Kobe, 657-8501, Japan
| | - Akihiko Kondo
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, 657-8501, Japan.
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501, Japan.
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501, Japan.
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Kaspar F, Neubauer P, Gimpel M. Bioactive Secondary Metabolites from Bacillus subtilis: A Comprehensive Review. JOURNAL OF NATURAL PRODUCTS 2019; 82:2038-2053. [PMID: 31287310 DOI: 10.1021/acs.jnatprod.9b00110] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Bacillus subtilis is widely underappreciated for its inherent biosynthetic potential. This report comprehensively summarizes the known bioactive secondary metabolites from B. subtilis and highlights potential applications as plant pathogen control agents, drugs, and biosurfactants. B. subtilis is well known for the production of cyclic lipopeptides exhibiting strong surfactant and antimicrobial activities, such as surfactins, iturins, and fengycins. Several polyketide-derived macrolides as well as nonribosomal peptides, dihydroisocoumarins, and linear lipopeptides with antimicrobial properties have been reported, demonstrating the biosynthetic arsenal of this bacterium. Promising efforts toward the application of B. subtilis strains and their natural products in areas of agriculture and medicine are underway. However, industrial-scale availability of these compounds is currently limited by low fermentation yields and challenging accessibility via synthesis, necessitating the development of genetically engineered strains and optimized cultivation processes. We hope that this review will attract renewed interest in this often-overlooked bacterium and its impressive biosynthetic skill set.
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Affiliation(s)
- Felix Kaspar
- Institute of Biotechnology , Technical University of Berlin , Ackerstraße 76 , 13355 Berlin , Germany
| | - Peter Neubauer
- Institute of Biotechnology , Technical University of Berlin , Ackerstraße 76 , 13355 Berlin , Germany
| | - Matthias Gimpel
- Institute of Biotechnology , Technical University of Berlin , Ackerstraße 76 , 13355 Berlin , Germany
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Silva M, Vieira B, Ottens M. Preferential crystallization for the purification of similar hydrophobic polyphenols. JOURNAL OF CHEMICAL TECHNOLOGY AND BIOTECHNOLOGY (OXFORD, OXFORDSHIRE : 1986) 2018; 93:1997-2010. [PMID: 30008507 PMCID: PMC6033112 DOI: 10.1002/jctb.5526] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 11/22/2017] [Accepted: 11/22/2017] [Indexed: 06/08/2023]
Abstract
BACKGROUND Preferential crystallization is a common technique used in the purification of enantiomers, proving that crystallization may also be applied to the purification of very similar molecules by seeding the solution with the desired compound. Nonetheless, its application to other organic molecules is less widely documented in the literature. Knowing that chemically related polyphenols are generally co-produced by fermentation and their purification can be too expensive for their market value, this technique may contribute to developing a downstream process with less expensive steps. The goal of this work is to show the applicability of the preferential crystallization concept to the purification of similar polyphenols - naringenin and trans-resveratrol - with either single or coupled crystallizers. RESULTS After developing the required crystallization kinetic models, an experiment using two coupled vessels was devised, where a 63% yield of naringenin and 44% yield of trans-resveratrol was obtained, with ≥98% purity in both cases. When the vessels were working independently, 81% of pure trans-resveratrol (started 60% pure) and 70% of pure naringenin (started 68% pure) were recovered. CONCLUSION The experiments performed show the possibility of separately purifying two similar molecules (from 60% to roughly 100%) with promising yields, despite their similar solubility. This method, which can be significantly improved, might provide an economically attractive way for the production of low added value products. © 2017 The Authors. Journal of Chemical Technology & Biotechnology published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Marcelo Silva
- Delft University of TechnologyDepartment of BiotechnologyDelftThe Netherlands
| | - Briana Vieira
- Delft University of TechnologyDepartment of BiotechnologyDelftThe Netherlands
| | - Marcel Ottens
- Delft University of TechnologyDepartment of BiotechnologyDelftThe Netherlands
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Oliva-Arancibia B, Órdenes-Aenishanslins N, Bruna N, Ibarra PS, Zacconi FC, Pérez-Donoso JM, Poblete-Castro I. Co-synthesis of medium-chain-length polyhydroxyalkanoates and CdS quantum dots nanoparticles in Pseudomonas putida KT2440. J Biotechnol 2017; 264:29-37. [PMID: 29056529 DOI: 10.1016/j.jbiotec.2017.10.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 10/17/2017] [Accepted: 10/18/2017] [Indexed: 12/15/2022]
Abstract
Microbial polymers and nanomaterials production is a promising alternative for sustainable bioeconomics. To this end, we used Pseudomonas putida KT2440 as a cell factory in batch cultures to coproduce two important nanotechnology materials- medium-chain-length (MCL)-polyhydroxyalkanoates (PHAs) and CdS fluorescent nanoparticles (i.e. quantum dots [QDots]). Due to high cadmium resistance, biomass and PHA yields were almost unaffected by coproduction conditions. Fluorescent nanocrystal biosynthesis was possible only in presence of cysteine. Furthermore, this process took place exclusively in the cell, displaying the classical emission spectra of CdS QDots under UV-light exposure. Cell fluorescence, zeta potential values, and particles size of QDots depended on cadmium concentration and exposure time. Using standard PHA-extraction procedures, the biosynthesized QDots remained associated with the biomass, and the resulting PHAs presented no traces of CdS QDots. Transmission electron microscopy located the synthesized PHAs in the cell cytoplasm, whereas CdS nanocrystals were most likely located within the periplasmic space, exhibiting no apparent interaction. This is the first report presenting the microbial coproduction of MCL-PHAs and CdS QDots in P. putida KT2440, thus constituting a foundation for further bioprocess developments and strain engineering towards the efficient synthesis of these highly relevant bioproducts for nanotechnology.
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Affiliation(s)
- Barbara Oliva-Arancibia
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology (CBIB), Faculty of Biological Sciences, Universidad Andres Bello, República 239, 8370146 Santiago, Chile
| | - Nicolás Órdenes-Aenishanslins
- BioNanotechnology and Microbiology Laboratory, Center for Bioinformatics and Integrative Biology (CBIB), Faculty of Biological Sciences, Universidad Andres Bello, República 239, 8370146 Santiago, Chile
| | - Nicolas Bruna
- BioNanotechnology and Microbiology Laboratory, Center for Bioinformatics and Integrative Biology (CBIB), Faculty of Biological Sciences, Universidad Andres Bello, República 239, 8370146 Santiago, Chile
| | - Paula S Ibarra
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology (CBIB), Faculty of Biological Sciences, Universidad Andres Bello, República 239, 8370146 Santiago, Chile
| | - Flavia C Zacconi
- Departamento de Química Orgánica, Facultad de Química, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Macul, 78204336 Santiago, Chile
| | - José M Pérez-Donoso
- BioNanotechnology and Microbiology Laboratory, Center for Bioinformatics and Integrative Biology (CBIB), Faculty of Biological Sciences, Universidad Andres Bello, República 239, 8370146 Santiago, Chile
| | - Ignacio Poblete-Castro
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology (CBIB), Faculty of Biological Sciences, Universidad Andres Bello, República 239, 8370146 Santiago, Chile.
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15
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Yoshimoto S, Ohara Y, Nakatani H, Hori K. Reversible bacterial immobilization based on the salt-dependent adhesion of the bacterionanofiber protein AtaA. Microb Cell Fact 2017; 16:123. [PMID: 28720107 PMCID: PMC5516326 DOI: 10.1186/s12934-017-0740-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 07/10/2017] [Indexed: 01/05/2023] Open
Abstract
Background Immobilization of microbial cells is an important strategy for the efficient use of whole-cell catalysts because it simplifies product separation, enables the cell concentration to be increased, stabilizes enzymatic activity, and permits repeated or continuous biocatalyst use. However, conventional immobilization methods have practical limitations, such as limited mass transfer in the inner part of a gel, gel fragility, cell leakage from the support matrix, and adverse effects on cell viability and catalytic activity. We previously showed a new method for bacterial cell immobilization using AtaA, a member of the trimeric autotransporter adhesin family found in Acinetobacter sp. Tol 5. This approach is expected to solve the drawbacks of conventional immobilization methods. However, similar to all other immobilization methods, the use of support materials increases the cost of bioprocesses and subsequent waste materials. Results We found that the stickiness of the AtaA molecule isolated from Tol 5 cells is drastically diminished at ionic strengths lower than 10 mM and that it cannot adhere in deionized water, which also inhibits cell adhesion mediated by AtaA. Cells immobilized on well plates and polyurethane foam in a salt solution were detached in deionized water by rinsing and shaking, respectively. The detached cells regained their adhesiveness in a salt solution and could rapidly be re-immobilized. The cells expressing the ataA gene maintained their adhesiveness throughout four repeated immobilization and detachment cycles and could be repeatedly immobilized to polyurethane foam by a 10-min shake in a flask. We also demonstrated that both bacterial cells and a support used in a reaction could be reused for a different type of reaction after detachment of the initially immobilized cells from the support and a subsequent immobilization step. Conclusions We invented a unique reversible immobilization method based on the salt-dependent adhesion of the AtaA molecule that allows us to reuse bacterial cells and supports by a simple manipulation involving a deionized water wash. This mitigates problems caused by the use of support materials and greatly helps to enhance the efficiency and productivity of microbial production processes. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0740-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shogo Yoshimoto
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Yuki Ohara
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Hajime Nakatani
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Katsutoshi Hori
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan.
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16
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Oesterle S, Wuethrich I, Panke S. Toward Genome-Based Metabolic Engineering in Bacteria. ADVANCES IN APPLIED MICROBIOLOGY 2017; 101:49-82. [PMID: 29050667 DOI: 10.1016/bs.aambs.2017.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Prokaryotes modified stably on the genome are of great importance for production of fine and commodity chemicals. Traditional methods for genome engineering have long suffered from imprecision and low efficiencies, making construction of suitable high-producer strains laborious. Here, we review the recent advances in discovery and refinement of molecular precision engineering tools for genome-based metabolic engineering in bacteria for chemical production, with focus on the λ-Red recombineering and the clustered regularly interspaced short palindromic repeats/Cas9 nuclease systems. In conjunction, they enable the integration of in vitro-synthesized DNA segments into specified locations on the chromosome and allow for enrichment of rare mutants by elimination of unmodified wild-type cells. Combination with concurrently developing improvements in important accessory technologies such as DNA synthesis, high-throughput screening methods, regulatory element design, and metabolic pathway optimization tools has resulted in novel efficient microbial producer strains and given access to new metabolic products. These new tools have made and will likely continue to make a big impact on the bioengineering strategies that transform the chemical industry.
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17
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Review of sample preparation strategies for MS-based metabolomic studies in industrial biotechnology. Anal Chim Acta 2016; 938:18-32. [DOI: 10.1016/j.aca.2016.07.033] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 07/22/2016] [Accepted: 07/26/2016] [Indexed: 02/08/2023]
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18
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Carbonell P, Gök A, Shapira P, Faulon JL. Mapping the patent landscape of synthetic biology for fine chemical production pathways. Microb Biotechnol 2016; 9:687-95. [PMID: 27489206 PMCID: PMC4993189 DOI: 10.1111/1751-7915.12401] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 07/13/2016] [Indexed: 12/01/2022] Open
Abstract
A goal of synthetic biology bio‐foundries is to innovate through an iterative design/build/test/learn pipeline. In assessing the value of new chemical production routes, the intellectual property (IP) novelty of the pathway is important. Exploratory studies can be carried using knowledge of the patent/IP landscape for synthetic biology and metabolic engineering. In this paper, we perform an assessment of pathways as potential targets for chemical production across the full catalogue of reachable chemicals in the extended metabolic space of chassis organisms, as computed by the retrosynthesis‐based algorithm RetroPath. Our database for reactions processed by sequences in heterologous pathways was screened against the PatSeq database, a comprehensive collection of more than 150M sequences present in patent grants and applications. We also examine related patent families using Derwent Innovations. This large‐scale computational study provides useful insights into the IP landscape of synthetic biology for fine and specialty chemicals production.
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Affiliation(s)
- Pablo Carbonell
- Manchester Centre for Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Abdullah Gök
- Manchester Centre for Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.,Manchester Institute of Innovation Research, Alliance Manchester Business School, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Philip Shapira
- Manchester Centre for Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.,Manchester Institute of Innovation Research, Alliance Manchester Business School, University of Manchester, Oxford Road, Manchester, M13 9PL, UK.,School of Public Policy, Georgia Institute of Technology, 685 Cherry Street, Atlanta, GA, 30332-0345, USA
| | - Jean-Loup Faulon
- Manchester Centre for Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.,MICALIS Institute, INRA, Domaine de Vilvert, 78352, Jouy en Josas Cedex, France
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19
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CRISPR interference as a titratable, trans-acting regulatory tool for metabolic engineering in the cyanobacterium Synechococcus sp. strain PCC 7002. Metab Eng 2016; 38:170-179. [PMID: 27481676 DOI: 10.1016/j.ymben.2016.07.007] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 07/18/2016] [Accepted: 07/21/2016] [Indexed: 11/22/2022]
Abstract
Trans-acting regulators provide novel opportunities to study essential genes and regulate metabolic pathways. We have adapted the clustered regularly interspersed palindromic repeats (CRISPR) system from Streptococcus pyogenes to repress genes in trans in the cyanobacterium Synechococcus sp. strain PCC 7002 (hereafter PCC 7002). With this approach, termed CRISPR interference (CRISPRi), transcription of a specific target sequence is repressed by a catalytically inactive Cas9 protein recruited to the target DNA by base-pair interactions with a single guide RNA that is complementary to the target sequence. We adapted this system for PCC 7002 and achieved conditional and titratable repression of a heterologous reporter gene, yellow fluorescent protein. Next, we demonstrated the utility of finely tuning native gene expression by downregulating the abundance of phycobillisomes. In addition, we created a conditional auxotroph by repressing synthesis of the carboxysome, an essential component of the carbon concentrating mechanism cyanobacteria use to fix atmospheric CO2. Lastly, we demonstrated a novel strategy for increasing central carbon flux by conditionally downregulating a key node in nitrogen assimilation. The resulting cells produced 2-fold more lactate than a baseline engineered cell line, representing the highest photosynthetically generated productivity to date. This work is the first example of titratable repression in cyanobacteria using CRISPRi, enabling dynamic regulation of essential processes and manipulation of flux through central carbon metabolism. This tool facilitates the study of essential genes of unknown function and enables groundbreaking metabolic engineering capability, by providing a straightforward approach to redirect metabolism and carbon flux in the production of high-value chemicals.
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20
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Costa TM, Tavares LBB, de Oliveira D. Fungi as a source of natural coumarins production. Appl Microbiol Biotechnol 2016; 100:6571-6584. [PMID: 27364626 DOI: 10.1007/s00253-016-7660-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 05/29/2016] [Accepted: 05/31/2016] [Indexed: 10/21/2022]
Abstract
Natural coumarins and derivatives are compounds that occur naturally in several organisms (plant, bacteria, and fungi) consisting of fused benzene and α-pyrone rings. These compounds show high technological potential applications in agrochemical, food, pharmaceuticals, and cosmetics industries. Therefore, the need for bulk production of coumarins and the advancement of the chemical and pharmaceutical industries led to the development of synthetic coumarin. However, biotransformation process, synthetic bioengineering, metabolic engineering, and bioinformatics have proven effective in the production of natural products. Today, these biological systems are recognized as green chemistry innovation and business strategy. This review article aims to report the potential of fungi for synthesis of coumarin. These microorganisms are described as a source of natural products capable of synthesizing many bioactive metabolites. The features, classification, properties, and industrial applications of natural coumarins as well as new molecules obtained by basidiomycetes and ascomycetes fungi are reported in order to explore a topic not yet discussed in the scientific literature.
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Affiliation(s)
- Tania Maria Costa
- Department of Chemical Engineering, Federal University of Santa Catarina, Trindade, Florianópolis, Santa Catarina, CEP 88040-900, Brazil
| | - Lorena Benathar Ballod Tavares
- Environmental Engineering Postgraduate, Regional University of Blumenau, Itoupava Seca, Blumenau, Santa Catarina, CEP 89030-080, Brazil
| | - Débora de Oliveira
- Department of Chemical Engineering, Federal University of Santa Catarina, Trindade, Florianópolis, Santa Catarina, CEP 88040-900, Brazil.
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21
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The potential of Synechococcus elongatus UTEX 2973 for sugar feedstock production. Appl Microbiol Biotechnol 2016; 100:7865-75. [DOI: 10.1007/s00253-016-7510-z] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 03/25/2016] [Accepted: 03/29/2016] [Indexed: 02/02/2023]
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22
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Hara KY, Kondo A. ATP regulation in bioproduction. Microb Cell Fact 2015; 14:198. [PMID: 26655598 PMCID: PMC4676173 DOI: 10.1186/s12934-015-0390-6] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/25/2015] [Indexed: 01/06/2023] Open
Abstract
Adenosine-5'-triphosphate (ATP) is consumed as a biological energy source by many intracellular reactions. Thus, the intracellular ATP supply is required to maintain cellular homeostasis. The dependence on the intracellular ATP supply is a critical factor in bioproduction by cell factories. Recent studies have shown that changing the ATP supply is critical for improving product yields. In this review, we summarize the recent challenges faced by researchers engaged in the development of engineered cell factories, including the maintenance of a large ATP supply and the production of cell factories. The strategies used to enhance ATP supply are categorized as follows: addition of energy substrates, controlling pH, metabolic engineering of ATP-generating or ATP-consuming pathways, and controlling reactions of the respiratory chain. An enhanced ATP supply generated using these strategies improves target production through increases in resource uptake, cell growth, biosynthesis, export of products, and tolerance to toxic compounds.
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Affiliation(s)
- Kiyotaka Y Hara
- Department of Environmental Sciences, Graduate School of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan.
| | - Akihiko Kondo
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, 657-8501, Japan.
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23
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Abstract
Synthetic biology (SB) is an emerging discipline, which is slowly reorienting the field of drug discovery. For thousands of years, living organisms such as plants were the major source of human medicines. The difficulty in resynthesizing natural products, however, often turned pharmaceutical industries away from this rich source for human medicine. More recently, progress on transformation through genetic manipulation of biosynthetic units in microorganisms has opened the possibility of in-depth exploration of the large chemical space of natural products derivatives. Success of SB in drug synthesis culminated with the bioproduction of artemisinin by microorganisms, a tour de force in protein and metabolic engineering. Today, synthetic cells are not only used as biofactories but also used as cell-based screening platforms for both target-based and phenotypic-based approaches. Engineered genetic circuits in synthetic cells are also used to decipher disease mechanisms or drug mechanism of actions and to study cell-cell communication within bacteria consortia. This review presents latest developments of SB in the field of drug discovery, including some challenging issues such as drug resistance and drug toxicity.
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Affiliation(s)
| | - Pablo Carbonell
- Faculty of Life Sciences, SYNBIOCHEM Centre, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
- Department of Experimental and Health Sciences (DCEXS), Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Universitat Pompeu Fabra (UPF), Barcelona, Spain
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24
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Montella S, Amore A, Faraco V. Metagenomics for the development of new biocatalysts to advance lignocellulose saccharification for bioeconomic development. Crit Rev Biotechnol 2015; 36:998-1009. [PMID: 26381035 DOI: 10.3109/07388551.2015.1083939] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The world economy is moving toward the use of renewable and nonedible lignocellulosic biomasses as substitutes for fossil sources in order to decrease the environmental impact of manufacturing processes and overcome the conflict with food production. Enzymatic hydrolysis of the feedstock is a key technology for bio-based chemical production, and the identification of novel, less expensive and more efficient biocatalysts is one of the main challenges. As the genomic era has shown that only a few microorganisms can be cultured under standard laboratory conditions, the extraction and analysis of genetic material directly from environmental samples, termed metagenomics, is a promising way to overcome this bottleneck. Two screening methodologies can be used on metagenomic material: the function-driven approach of expression libraries and sequence-driven analysis based on gene homology. Both techniques have been shown to be useful for the discovery of novel biocatalysts for lignocellulose conversion, and they enabled identification of several (hemi)cellulases and accessory enzymes involved in (hemi)cellulose hydrolysis. This review summarizes the latest progress in metagenomics aimed at discovering new enzymes for lignocellulose saccharification.
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Affiliation(s)
- Salvatore Montella
- a Department of Chemical Sciences , University of Naples "Federico II", Complesso Universitario Monte S. Angelo , Naples , Italy
| | - Antonella Amore
- a Department of Chemical Sciences , University of Naples "Federico II", Complesso Universitario Monte S. Angelo , Naples , Italy
| | - Vincenza Faraco
- a Department of Chemical Sciences , University of Naples "Federico II", Complesso Universitario Monte S. Angelo , Naples , Italy
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25
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Improvement of oxidized glutathione fermentation by thiol redox metabolism engineering in Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2015; 99:9771-8. [DOI: 10.1007/s00253-015-6847-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 07/10/2015] [Accepted: 07/15/2015] [Indexed: 02/02/2023]
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26
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Sasaki K, Hara KY, Kawaguchi H, Sazuka T, Ogino C, Kondo A. Nanofiltration concentration of extracellular glutathione produced by engineered Saccharomyces cerevisiae. J Biosci Bioeng 2015; 121:96-100. [PMID: 26105794 DOI: 10.1016/j.jbiosc.2015.05.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 05/15/2015] [Accepted: 05/19/2015] [Indexed: 10/23/2022]
Abstract
This study aimed to optimize extracellular glutathione production by a Saccharomyces cerevisiae engineered strain and to concentrate the extracellular glutathione by membrane separation processes, including ultrafiltration (UF) and nanofiltration (NF). Synthetic defined (SD) medium containing 20 g L(-1) glucose was fermented for 48 h; the fermentation liquid was passed through an UF membrane to remove macromolecules. Glutathione in this permeate was concentrated for 48 h to 545.1 ± 33.6 mg L(-1) using the NF membrane; this was a significantly higher concentration than that obtained with yeast extract peptone dextrose (YPD) medium following 96 h NF concentration (217.9 ± 57.4 mg L(-1)). This higher glutathione concentration results from lower cellular growth in SD medium (final OD600 = 6.9 ± 0.1) than in YPD medium (final OD600 = 11.0 ± 0.6) and thus higher production of extracellular glutathione (16.0 ± 1.3 compared to 9.2 ± 2.1 mg L(-1) in YPD medium, respectively). Similar fermentation and membrane processing of sweet sorghum juice containing 20 g L(-1) total sugars provided 240.3 ± 60.6 mg L(-1) glutathione. Increased extracellular production of glutathione by this engineered strain in SD medium and subsequent UF permeation and NF concentration in shortend time may help realize industrial recovery of extracellular glutathione.
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Affiliation(s)
- Kengo Sasaki
- Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, Hyogo 675-8501, Japan
| | - Kiyotaka Y Hara
- Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, Hyogo 675-8501, Japan
| | - Hideo Kawaguchi
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Takashi Sazuka
- Bioscience and Biotechnology Center, Nagoya University, Furo, Chikusa, Nagoya 464-8601, Japan
| | - Chiaki Ogino
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Akihiko Kondo
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, Hyogo 657-8501, Japan; Biomass Engineering Program, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
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