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Barla RJ, Raghuvanshi S, Gupta S. Reforming CO 2 bio-mitigation utilizing Bacillus cereus from hypersaline realms in pilot-scale bubble column bioreactor. Sci Rep 2024; 14:6354. [PMID: 38491100 PMCID: PMC10943127 DOI: 10.1038/s41598-024-56965-8] [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: 01/19/2024] [Accepted: 03/13/2024] [Indexed: 03/18/2024] Open
Abstract
The bubble column reactor of 10 and 20 L capacity was designed to bio-mitigate 10% CO2 (g) with 90% air utilizing thermophilic bacteria (Bacillus cereus SSLMC2). The maximum biomass yield during the growth phase was obtained as 9.14 and 10.78 g L-1 for 10 and 20 L capacity, respectively. The maximum removal efficiency for CO2 (g) was obtained as 56% and 85% for the 10 and 20 L reactors, respectively. The FT-IR and GC-MS examination of the extracellular and intracellular samples identified value-added products such as carboxylic acid, fatty alcohols, and hydrocarbons produced during the process. The total carbon balance for CO2 utilization in different forms confirmed that B. cereus SSLMC2 utilized 1646.54 g C in 10 L and 1587 g of C in 20 L reactor out of 1696.13 g of total carbon feed. The techno-economic assessment established that the capital investment required was $286.21 and $289.08 per reactor run of 11 days and $0.167 and $0.187 per gram of carbon treated for 10 and 20 L reactors, respectively. The possible mechanism pathways for bio-mitigating CO2 (g) by B. cereus SSLMC2 were also presented utilizing the energy reactions. Hence, the work presents the novelty of utilizing thermophilic bacteria and a bubble column bioreactor for CO2 (g) bio-mitigation.
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Affiliation(s)
- Rachael J Barla
- Faculty Division-1, Department of Chemical Engineering, Birla Institute of Technology and Science (BITS), BITS PILANI, Pilani, 333031, Rajasthan, India
| | - Smita Raghuvanshi
- Faculty Division-1, Department of Chemical Engineering, Birla Institute of Technology and Science (BITS), BITS PILANI, Pilani, 333031, Rajasthan, India.
| | - Suresh Gupta
- Faculty Division-1, Department of Chemical Engineering, Birla Institute of Technology and Science (BITS), BITS PILANI, Pilani, 333031, Rajasthan, India
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2
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Recent Advances In Microbe-Photocatalyst Hybrid Systems for Production of Bulk Chemicals: A Review. Appl Biochem Biotechnol 2023; 195:1574-1588. [PMID: 36346559 DOI: 10.1007/s12010-022-04169-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2022] [Indexed: 11/11/2022]
Abstract
Solar-driven biocatalysis technologies can combine inorganic photocatalytic materials with biological catalysts to convert CO2, light, and water into chemicals, offering the promise of high energy efficiency and a broader product scope than that of natural photosynthesis. Solar energy is the most abundant renewable energy source on earth, but it cannot be directly utilized by current industrial microorganisms. Therefore, the establishment of a solar-driven bio-catalysis platform, a bridge between solar energy and heterotrophic microorganisms, can dramatically increase carbon flux in biomanufacturing systems and consequently may revolutionize the biorefinery. This review first discusses the main applications of microbe-photocatalyst hybrid (MPH) systems in biorefinery processes. Then, various strategies to improve the electron transfer by microorganisms at the inorganic photocatalytic material interface are discussed, especially biohybrid systems based on autotrophic or heterotrophic bacteria and photocatalytic materials. Finally, we discuss the current challenges and offer potential solutions for the development of MPH systems.
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Al'Abri IS, Haller DJ, Li Z, Crook N. Inducible directed evolution of complex phenotypes in bacteria. Nucleic Acids Res 2022; 50:e58. [PMID: 35150576 PMCID: PMC9177967 DOI: 10.1093/nar/gkac094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 12/22/2021] [Accepted: 02/01/2022] [Indexed: 11/15/2022] Open
Abstract
Directed evolution is a powerful method for engineering biology in the absence of detailed sequence-function relationships. To enable directed evolution of complex phenotypes encoded by multigene pathways, we require large library sizes for DNA sequences >5–10 kb in length, elimination of genomic hitchhiker mutations, and decoupling of diversification and screening steps. To meet these challenges, we developed Inducible Directed Evolution (IDE), which uses a temperate bacteriophage to package large plasmids and transfer them to naive cells after intracellular mutagenesis. To demonstrate IDE, we evolved a 5-gene pathway from Bacillus licheniformis that accelerates tagatose catabolism in Escherichia coli, resulting in clones with 65% shorter lag times during growth on tagatose after only two rounds of evolution. Next, we evolved a 15.4 kb, 10-gene pathway from Bifidobacterium breve UC2003 that aids E. coli’s utilization of melezitose. After three rounds of IDE, we isolated evolved pathways that both reduced lag time by more than 2-fold and enabled 150% higher final optical density. Taken together, this work enhances the capacity and utility of a whole pathway directed evolution approach in E. coli.
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Affiliation(s)
- Ibrahim S Al'Abri
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Daniel J Haller
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Zidan Li
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Nathan Crook
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
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4
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Muthukrishnan L. Bio‐engineering of microalgae: Challenges and future prospects toward industrial and environmental applications. J Basic Microbiol 2022; 62:310-329. [DOI: 10.1002/jobm.202100417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 12/28/2021] [Accepted: 01/08/2022] [Indexed: 01/29/2023]
Affiliation(s)
- Lakshmipathy Muthukrishnan
- Department of Conservative Dentistry and Endodontics, Saveetha Dental College and Hospitals Saveetha Institute of Medical and Technical Sciences Chennai Tamil Nadu India
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5
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Wiatrowski M, Klein BC, Davis RW, Quiroz-Arita C, Tan ECD, Hunt RW, Davis RE. Techno-economic assessment for the production of algal fuels and value-added products: opportunities for high-protein microalgae conversion. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:8. [PMID: 35418157 PMCID: PMC8764804 DOI: 10.1186/s13068-021-02098-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 12/24/2021] [Indexed: 11/10/2022]
Abstract
BACKGROUND Microalgae possess numerous advantages for use as a feedstock in producing renewable fuels and products, with techno-economic analysis (TEA) frequently used to highlight the economic potential and technical challenges of utilizing this biomass in a biorefinery context. However, many historical TEA studies have focused on the conversion of biomass with elevated levels of carbohydrates and lipids and lower levels of protein, incurring substantial burdens on the ability to achieve high cultivation productivity rates relative to nutrient-replete, high-protein biomass. Given a strong dependence of algal biomass production costs on cultivation productivity, further TEA assessment is needed to understand the economic potential for utilizing potentially lower-cost but lower-quality, high-protein microalgae for biorefinery conversion. RESULTS In this work, we conduct rigorous TEA modeling to assess the economic viability of two conceptual technology pathways for processing proteinaceous algae into a suite of fuels and products. One approach, termed mild oxidative treatment and upgrading (MOTU), makes use of a series of thermo-catalytic operations to upgrade solubilized proteins and carbohydrates to hydrocarbon fuels, while another alternative focuses on the biological conversion of those substrates to oxygenated fuels in the form of mixed alcohols (MA). Both pathways rely on the production of polyurethanes from unsaturated fatty acids and valorization of unconverted solids for use as a material for synthesizing bioplastics. The assessment found similar, albeit slightly higher fuel yields and lower costs for the MA pathway, translating to a residual solids selling price of $899/ton for MA versus $1033/ton for MOTU as would be required to support a $2.50/gallon gasoline equivalent (GGE) fuel selling price. A variation of the MA pathway including subsequent upgrading of the mixed alcohols to hydrocarbon fuels (MAU) reflected a required solids selling price of $975/ton. CONCLUSION The slight advantages observed for the MA pathway are partially attributed to a boundary that stops at oxygenated fuels versus fungible drop-in hydrocarbon fuels through a more complex MOTU configuration, with more comparable results obtained for the MAU scenario. In either case, it was shown that an integrated algal biorefinery can be economical through optimal strategies to utilize and valorize all fractions of the biomass.
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Affiliation(s)
- Matthew Wiatrowski
- Catalytic Carbon Transformation and Scale-up Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA.
| | - Bruno C Klein
- Catalytic Carbon Transformation and Scale-up Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Ryan W Davis
- Biomass Science and Conversion Technologies, Sandia National Laboratories, Livermore, CA, 94550, USA
| | - Carlos Quiroz-Arita
- Biomass Science and Conversion Technologies, Sandia National Laboratories, Livermore, CA, 94550, USA
| | - Eric C D Tan
- Catalytic Carbon Transformation and Scale-up Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Ryan W Hunt
- Algix, 5168 Water Tower Rd, Meridian, MS, 39301, USA
| | - Ryan E Davis
- Catalytic Carbon Transformation and Scale-up Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
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6
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Ataeian M, Vadlamani A, Haines M, Mosier D, Dong X, Kleiner M, Strous M, Hawley AK. Proteome and strain analysis of cyanobacterium Candidatus "Phormidium alkaliphilum" reveals traits for success in biotechnology. iScience 2021; 24:103405. [PMID: 34877483 PMCID: PMC8633866 DOI: 10.1016/j.isci.2021.103405] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/27/2021] [Accepted: 11/03/2021] [Indexed: 11/18/2022] Open
Abstract
Cyanobacteria encompass a diverse group of photoautotrophic bacteria with important roles in nature and biotechnology. Here we characterized Candidatus “Phormidium alkaliphilum,” an abundant member in alkaline soda lake microbial communities globally. The complete, circular whole-genome sequence of Ca. “P. alkaliphilum” was obtained using combined Nanopore and Illumina sequencing of a Ca. “P. alkaliphilum” consortium. Strain-level diversity of Ca. “P. alkaliphilum” was shown to contribute to photobioreactor robustness under different operational conditions. Comparative genomics of closely related species showed that adaptation to high pH was not attributed to specific genes. Proteomics at high and low pH showed only minimal changes in gene expression, but higher productivity in high pH. Diverse photosystem antennae proteins, and high-affinity terminal oxidase, compared with other soda lake cyanobacteria, appear to contribute to the success of Ca. “P. alkaliphilum” in photobioreactors and biotechnology applications. Closed genome of the cyanobacteria Ca. P. alkaliphilum from high-pH photobioreactor Genetic factors lead this Phormidium to outcompete other cyanobacteria in photobioreactor Adaptation to high pH and alkalinity is not linked to specific genes Strain-level diversity contributes Ca. P. alkaliphilum success in changing conditions
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Affiliation(s)
- Maryam Ataeian
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | | | - Marianne Haines
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Damon Mosier
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Xiaoli Dong
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Marc Strous
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Alyse K. Hawley
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
- School of Engineering, University of British Columbia Okanagan, Kelowna, BC, Canada
- Corresponding author
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7
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Cao Y, Tian R, Lv X, Li J, Liu L, Du G, Chen J, Liu Y. Inducible Population Quality Control of Engineered Bacillus subtilis for Improved N-Acetylneuraminic Acid Biosynthesis. ACS Synth Biol 2021; 10:2197-2209. [PMID: 34404207 DOI: 10.1021/acssynbio.1c00086] [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] [Indexed: 12/29/2022]
Abstract
Biosynthesis by microorganisms using renewable feedstocks is an important approach for realizing sustainable chemical manufacturing. However, cell-to-cell variation in biosynthesis capability during fermentation restricts the robustness and efficiency of bioproduction, hampering the industrialization of biosynthesis. Herein, we developed an inducible population quality control system (iPopQC) for dynamically modulating the producing and nonproducing subpopulations of engineered Bacillus subtilis, which was constructed via inducible promoter- and metabolite-responsive biosensor-based genetic circuit for regulating essential genes. Moreover, iPopQC achieved a 1.97-fold increase in N-acetylneuraminic acid (NeuAc) titer by enriching producing cell subpopulation during cultivation, representing 52% higher than that of previous PopQC. Strains with double-output iPopQC cocoupling the expression of double essential genes with NeuAc production improved production robustness further, retaining NeuAc production throughout 96 h of fermentation, upon which the strains cocoupling one essential gene expression with NeuAc production abolished the production ability.
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Affiliation(s)
- Yanting Cao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Rongzhen Tian
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Jian Chen
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
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8
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Catalyst derived from wastes for biofuel production: a critical review and patent landscape analysis. APPLIED NANOSCIENCE 2021. [DOI: 10.1007/s13204-021-01948-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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9
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Chukwuma OB, Rafatullah M, Tajarudin HA, Ismail N. A Review on Bacterial Contribution to Lignocellulose Breakdown into Useful Bio-Products. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:6001. [PMID: 34204975 PMCID: PMC8199887 DOI: 10.3390/ijerph18116001] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/28/2021] [Accepted: 05/28/2021] [Indexed: 12/15/2022]
Abstract
Discovering novel bacterial strains might be the link to unlocking the value in lignocellulosic bio-refinery as we strive to find alternative and cleaner sources of energy. Bacteria display promise in lignocellulolytic breakdown because of their innate ability to adapt and grow under both optimum and extreme conditions. This versatility of bacterial strains is being harnessed, with qualities like adapting to various temperature, aero tolerance, and nutrient availability driving the use of bacteria in bio-refinery studies. Their flexible nature holds exciting promise in biotechnology, but despite recent pointers to a greener edge in the pretreatment of lignocellulose biomass and lignocellulose-driven bioconversion to value-added products, the cost of adoption and subsequent scaling up industrially still pose challenges to their adoption. However, recent studies have seen the use of co-culture, co-digestion, and bioengineering to overcome identified setbacks to using bacterial strains to breakdown lignocellulose into its major polymers and then to useful products ranging from ethanol, enzymes, biodiesel, bioflocculants, and many others. In this review, research on bacteria involved in lignocellulose breakdown is reviewed and summarized to provide background for further research. Future perspectives are explored as bacteria have a role to play in the adoption of greener energy alternatives using lignocellulosic biomass.
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Affiliation(s)
| | - Mohd Rafatullah
- Division of Environmental Technology, School of Industrial Technology, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia; (O.B.C.); (H.A.T.); (N.I.)
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10
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Sakhuja D, Ghai H, Rathour RK, Kumar P, Bhatt AK, Bhatia RK. Cost-effective production of biocatalysts using inexpensive plant biomass: a review. 3 Biotech 2021; 11:280. [PMID: 34094799 DOI: 10.1007/s13205-021-02847-z] [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] [Received: 04/02/2021] [Accepted: 05/11/2021] [Indexed: 12/12/2022] Open
Abstract
Enzymes are the complex protein moieties, catalyze the rate of chemical reactions by transforming various substrates to specific products and play an integral part in multiple biochemical cycles. Advancement in enzyme research and its integration with industries have reformed the biotech industries. It provides a superior monetary and ecological exchange to traditional material measures in an efficient and environmentally sustainable manner. The cost-effective production of pure and highly active enzymes is still a challenge for the biocatalyst industries. The use of high purity substrates further raises the cost of a typical biocatalyst. The use of low-cost plant-based biomasses as an enticing and sustainable substrate for enzyme production is the most cost-effective approach to these problems. Given the relevance of biomass as a substrate for enzyme development, this review article focuses on the key source, composition and major enzyme generated using various biomass residues. Furthermore, the difficulties associated with the use of biomass as a substrate and technical developments in this area, are also addressed. The use of waste biomass as a substrate lowers the ultimate cost for the production of biocatalysts while simultaneously reduces the waste burden from the environment.
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11
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Wang XN, Niu MT, Fan JX, Chen QW, Zhang XZ. Photoelectric Bacteria Enhance the In Situ Production of Tetrodotoxin for Antitumor Therapy. NANO LETTERS 2021; 21:4270-4279. [PMID: 33955768 DOI: 10.1021/acs.nanolett.1c00408] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Engineered bacteria are promising bioagents to synthesize antitumor drugs at tumor sites with the advantages of avoiding drug leakage and degradation during delivery. Here, we report an optically controlled material-assisted microbial system by biosynthesizing gold nanoparticles (AuNPs) on the surface of Shewanella algae K3259 (S. algae) to obtain Bac@Au. Leveraging the dual directional electron transport mechanism of S. algae, the hybrid biosystem enhances in situ synthesis of antineoplastic tetrodotoxin (TTX) for a promising antitumor effect. Because of tumor hypoxia-targeting feature of facultative anaerobic S. algae, Bac@Au selectively target and colonize at tumor. Upon light irradiation, photoelectrons produced by AuNPs deposited on bacterial surface are transferred into bacterial cytoplasm and participate in accelerated cell metabolism to increase the production of TTX for antitumor therapy. The optically controlled material-assisted microbial system enhances the efficiency of bacterial drug synthesis in situ and provides an antitumor strategy that could broaden conventional therapy boundaries.
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Affiliation(s)
- Xia-Nan Wang
- Key Laboratory of Biomedical Polymers of Ministry of Education and Department of Chemistry, Wuhan University, Wuhan 430072, P.R. China
| | - Mei-Ting Niu
- Key Laboratory of Biomedical Polymers of Ministry of Education and Department of Chemistry, Wuhan University, Wuhan 430072, P.R. China
| | - Jin-Xuan Fan
- Key Laboratory of Biomedical Polymers of Ministry of Education and Department of Chemistry, Wuhan University, Wuhan 430072, P.R. China
| | - Qi-Wen Chen
- Key Laboratory of Biomedical Polymers of Ministry of Education and Department of Chemistry, Wuhan University, Wuhan 430072, P.R. China
| | - Xian-Zheng Zhang
- Key Laboratory of Biomedical Polymers of Ministry of Education and Department of Chemistry, Wuhan University, Wuhan 430072, P.R. China
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12
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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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13
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Li NN, Li W, Feng JX, Zhang WW, Zhang R, Du SH, Liu SY, Xue GH, Yan C, Cui JH, Zhao HQ, Feng YL, Gan L, Zhang Q, Chen C, Liu D, Yuan J. High alcohol-producing Klebsiella pneumoniae causes fatty liver disease through 2,3-butanediol fermentation pathway in vivo. Gut Microbes 2021; 13:1979883. [PMID: 34632939 PMCID: PMC8510565 DOI: 10.1080/19490976.2021.1979883] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 08/26/2021] [Accepted: 08/30/2021] [Indexed: 02/08/2023] Open
Abstract
High alcohol-producing Klebsiella pneumoniae (HiAlc Kpn) in the gut microbiota had been demonstrated to be the causative agent of fatty liver disease (FLD). However, the catabolic pathways for alcohol production in vivo remain unclear. Here, we characterized the genome of HiAlc and medium alcohol-producing (MedAlc) Kpn and constructed an adh (an essential gene encoding alcohol dehydrogenase) knock-out HiAlc Kpn W14 strain (W14Δadh) using CRISPR-Cas9 system. Subsequently, we established the mouse model via gavage administration of HiAlc Kpn W14 and W14 Δadh strains, respectively. Proteome and metabolome analysis showed that 10 proteins and six major metabolites involved in the 2,3-butanediol fermentation pathway exhibited at least a three-fold change or greater during intestinal growth. Compared with HiAlc Kpn W14-fed mice, W14Δadh-fed mice with weak alcohol-producing ability did not show apparent pathological changes at 4 weeks, although some steatotic hepatocytes were observed at 12 weeks. Our data demonstrated that carbohydrate substances are catabolized to produce alcohol and 2,3-butanediol via the 2,3-butanediol fermentation pathway in HiAlc Kpn, which could be a promising clinical diagnostic marker. The production of high amounts of endogenous alcohol is responsible for the observed steatosis effects in hepatocytes in vivo.
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Affiliation(s)
- Nan-Nan Li
- Bacteriology Laboratory, Capital Institute of Pediatrics, Beijing, China
- Graduate School of Peking Union Medical College, Beijing, China
| | - Wei Li
- Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China, Beijing, China
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China, Beijing, China
| | - Jun-Xia Feng
- Bacteriology Laboratory, Capital Institute of Pediatrics, Beijing, China
| | - Wei-Wei Zhang
- Bacteriology Laboratory, Capital Institute of Pediatrics, Beijing, China
| | - Rui Zhang
- Bacteriology Laboratory, Capital Institute of Pediatrics, Beijing, China
| | - Shu-Heng Du
- Bacteriology Laboratory, Capital Institute of Pediatrics, Beijing, China
| | - Shi-Yu Liu
- Bacteriology Laboratory, Capital Institute of Pediatrics, Beijing, China
| | - Guan-Hua Xue
- Bacteriology Laboratory, Capital Institute of Pediatrics, Beijing, China
| | - Chao Yan
- Bacteriology Laboratory, Capital Institute of Pediatrics, Beijing, China
| | - Jing-Hua Cui
- Bacteriology Laboratory, Capital Institute of Pediatrics, Beijing, China
| | - Han-Qing Zhao
- Bacteriology Laboratory, Capital Institute of Pediatrics, Beijing, China
| | - Yan-Ling Feng
- Bacteriology Laboratory, Capital Institute of Pediatrics, Beijing, China
| | - Lin Gan
- Bacteriology Laboratory, Capital Institute of Pediatrics, Beijing, China
| | - Qun Zhang
- Bacteriology Laboratory, Capital Institute of Pediatrics, Beijing, China
| | - Chen Chen
- Biomedical inovation center, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Di Liu
- Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China, Beijing, China
| | - Jing Yuan
- Bacteriology Laboratory, Capital Institute of Pediatrics, Beijing, China
- Graduate School of Peking Union Medical College, Beijing, China
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14
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Passarini MRZ, E Silva TR, Bernal SPF, Cecchet NL, Sartoratto A, Boroski M, Duarte AWF, Ottoni JR, Rosa LH, de Oliveira VM. Undecane production by cold-adapted bacteria from Antarctica. Extremophiles 2020; 24:863-873. [PMID: 32944821 DOI: 10.1007/s00792-020-01200-1] [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: 05/20/2020] [Accepted: 09/03/2020] [Indexed: 11/27/2022]
Abstract
In the last decades, efforts to reduce the use of fossil fuels have increased the search for alternative sustainable sources of renewable energy. In this scenario, hydrocarbons derived from fatty acids are among the compounds that have been drawing attention. The intracellular production of hydrocarbons by bacteria derived from cold environments such as the Antarctic continent is currently poorly investigated, as extremophilic microorganisms provide a great range of metabolic capabilities and may represent a key tool in the production of biofuels. The aim of this study was to explore the ability of bacterial cells derived from extreme environments to produce hydrocarbons with potential for further use as biofuels. Seven bacteria isolated from Antarctic samples were evaluated for hydrocarbon production using GC-MS approaches. Two isolates, identified as Arthrobacter livingstonensis 593 and Pseudoalteromonas arctica 628, were able to produce the hydrocarbon undecane (CH3-(CH2)9-CH3) in concentrations of 1.39 mg L-1 and 1.81 mg L-1, respectively. Results from the present work encourage further research focusing on the optimization of hydrocarbon production by the isolates identified as producers, which may be used in further aircraft biofuel production. This is the first report on the production of the undecane compound by bacteria isolated from waterlogged soil and sponge from Antarctica.
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Affiliation(s)
- Michel Rodrigo Zambrano Passarini
- UNILA-Universidade Federal da Integração Latino-Americana. Laboratório de Biotecnologia Ambiental, Av. Tarquínio Joslin dos Santos, 1000-Jd Universitário, Foz do Iguaçu, PR, 85870-650, Brazil.
| | - Tiago Rodrigues E Silva
- CPQBA/UNICAMP-Divisão de Recursos Microbianos, Rua Alexandre Caselatto 999, Vila Betel, CP 6171, Campinas, SP, 13083-970, Brazil
| | - Suzan Prado Fernandes Bernal
- UNILA-Universidade Federal da Integração Latino-Americana. Laboratório de Biotecnologia Ambiental, Av. Tarquínio Joslin dos Santos, 1000-Jd Universitário, Foz do Iguaçu, PR, 85870-650, Brazil
| | - Nathália Luana Cecchet
- UNILA-Universidade Federal da Integração Latino-Americana. Laboratório de Biotecnologia Ambiental, Av. Tarquínio Joslin dos Santos, 1000-Jd Universitário, Foz do Iguaçu, PR, 85870-650, Brazil
| | - Adilson Sartoratto
- CPQBA/UNICAMP-Divisão de Química Orgânica e Farmacêutica, Rua Alexandre Caselatto 999, Vila Betel, CP 6171, Campinas, SP, 13083-970, Brazil
| | - Marcela Boroski
- UNILA-Universidade Federal da Integração Latino-Americana. Laboratório de Química, Av. Tancredo Neves 6731- Conjunto B, Foz do Iguaçu, PR, 85867-970, Brazil
| | - Alysson Wagner Fernandes Duarte
- UFAL-Universidade Federal de Alagoas, Av. Manoel Severino Barbosa-Rodovia AL-115, Bom Sucesso, Arapiraca, AL, 57309-005, Brazil
| | - Júlia Ronzella Ottoni
- UDC-Centro Universitário Dinâmica das Cataratas, Rua Castelo Branco, 349, Centro, Foz do Iguaçu, PR, Brazil
| | - Luiz Henrique Rosa
- UFMG-Departamento de Microbiologia, Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte, MG, 31270-901, Brazil
| | - Valéria Maia de Oliveira
- CPQBA/UNICAMP-Divisão de Recursos Microbianos, Rua Alexandre Caselatto 999, Vila Betel, CP 6171, Campinas, SP, 13083-970, Brazil
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15
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Rubinstein GM, Lipscomb GL, Williams-Rhaesa AM, Schut GJ, Kelly RM, Adams MWW. Engineering the cellulolytic extreme thermophile Caldicellulosiruptor bescii to reduce carboxylic acids to alcohols using plant biomass as the energy source. J Ind Microbiol Biotechnol 2020; 47:585-597. [PMID: 32783103 DOI: 10.1007/s10295-020-02299-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 07/27/2020] [Indexed: 01/13/2023]
Abstract
Caldicellulosiruptor bescii is the most thermophilic cellulolytic organism yet identified (Topt 78 °C). It grows on untreated plant biomass and has an established genetic system thereby making it a promising microbial platform for lignocellulose conversion to bio-products. Here, we investigated the ability of engineered C. bescii to generate alcohols from carboxylic acids. Expression of aldehyde ferredoxin oxidoreductase (aor from Pyrococcus furiosus) and alcohol dehydrogenase (adhA from Thermoanaerobacter sp. X514) enabled C. bescii to generate ethanol from crystalline cellulose and from biomass by reducing the acetate produced by fermentation. Deletion of lactate dehydrogenase in a strain expressing the AOR-Adh pathway increased ethanol production. Engineered strains also converted exogenously supplied organic acids (isobutyrate and n-caproate) to the corresponding alcohol (isobutanol and hexanol) using both crystalline cellulose and switchgrass as sources of reductant for alcohol production. This is the first instance of an acid to alcohol conversion pathway in a cellulolytic microbe.
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Affiliation(s)
- Gabriel M Rubinstein
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Gina L Lipscomb
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | | | - Gerrit J Schut
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA.
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16
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Cyanobacterial sigma factors: Current and future applications for biotechnological advances. Biotechnol Adv 2020; 40:107517. [DOI: 10.1016/j.biotechadv.2020.107517] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 01/07/2020] [Accepted: 01/09/2020] [Indexed: 11/15/2022]
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17
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Eiben CB, Tian T, Thompson MG, Mendez-Perez D, Kaplan N, Goyal G, Chiniquy J, Hillson NJ, Lee TS, Keasling JD. Adenosine Triphosphate and Carbon Efficient Route to Second Generation Biofuel Isopentanol. ACS Synth Biol 2020; 9:468-474. [PMID: 32149502 DOI: 10.1021/acssynbio.9b00402] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Climate change necessitates the development of CO2 neutral or negative routes to chemicals currently produced from fossil carbon. In this paper we demonstrate a pathway from the renewable resource glucose to next generation biofuel isopentanol by pairing the isovaleryl-CoA biosynthesis pathway from Myxococcus xanthus and a butyryl-CoA reductase from Clostridium acetobutylicum. The best plasmid and Escherichia coli strain combination makes 80.50 ± 8.08 (SD) mg/L of isopentanol after 36 h under microaerobic conditions with an oleyl alcohol overlay. In addition, the system also shows a strong preference for isopentanol production over prenol in microaerobic conditions. Finally, the pathway requires zero adenosine triphosphate and can be paired theoretically with nonoxidative glycolysis, the combination being redox balanced from glucose thus avoiding unnecessary carbon loss as CO2. These pathway properties make the isovaleryl-CoA pathway an attractive isopentanol production route for further optimization.
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Affiliation(s)
- Christopher B. Eiben
- Department of Bioengineering, University of California, Berkeley, Berkeley, California 94270, United States
- Department of Bioengineering, University of California, San Francisco, California 94143, United States
| | - Tian Tian
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Mitchell G. Thompson
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California 94270, United States
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Daniel Mendez-Perez
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Nurgul Kaplan
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Agile BioFoundry, Emeryville, California 94608, United States
| | - Garima Goyal
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Agile BioFoundry, Emeryville, California 94608, United States
| | - Jennifer Chiniquy
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Agile BioFoundry, Emeryville, California 94608, United States
| | - Nathan J. Hillson
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Agile BioFoundry, Emeryville, California 94608, United States
| | - Taek Soon Lee
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jay D. Keasling
- Department of Bioengineering, University of California, Berkeley, Berkeley, California 94270, United States
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94270, United States
- Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California 94270, United States
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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18
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Kahn A, Moraïs S, Chung D, Sarai NS, Hengge NN, Kahn A, Himmel ME, Bayer EA, Bomble YJ. Glycosylation of hyperthermostable designer cellulosome components yields enhanced stability and cellulose hydrolysis. FEBS J 2020; 287:4370-4388. [DOI: 10.1111/febs.15251] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 01/06/2020] [Accepted: 02/14/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Amaranta Kahn
- Department of Biomolecular Sciences The Weizmann Institute of Science Rehovot Israel
| | - Sarah Moraïs
- Department of Biomolecular Sciences The Weizmann Institute of Science Rehovot Israel
- Faculty of Natural Sciences Ben‐Gurion University of the Negev Beer‐Sheva Israel
| | - Daehwan Chung
- Biosciences Center National Renewable Energy Laboratory Golden CO USA
| | - Nicholas S. Sarai
- Biosciences Center National Renewable Energy Laboratory Golden CO USA
| | - Neal N. Hengge
- Biosciences Center National Renewable Energy Laboratory Golden CO USA
| | - Audrey Kahn
- Department of Biomolecular Sciences The Weizmann Institute of Science Rehovot Israel
| | - Michael E. Himmel
- Biosciences Center National Renewable Energy Laboratory Golden CO USA
| | - Edward A. Bayer
- Department of Biomolecular Sciences The Weizmann Institute of Science Rehovot Israel
| | - Yannick J. Bomble
- Biosciences Center National Renewable Energy Laboratory Golden CO USA
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19
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Li S, Huang L, Ke C, Pang Z, Liu L. Pathway dissection, regulation, engineering and application: lessons learned from biobutanol production by solventogenic clostridia. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:39. [PMID: 32165923 PMCID: PMC7060580 DOI: 10.1186/s13068-020-01674-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 02/04/2020] [Indexed: 06/01/2023]
Abstract
The global energy crisis and limited supply of petroleum fuels have rekindled the interest in utilizing a sustainable biomass to produce biofuel. Butanol, an advanced biofuel, is a superior renewable resource as it has a high energy content and is less hygroscopic than other candidates. At present, the biobutanol route, employing acetone-butanol-ethanol (ABE) fermentation in Clostridium species, is not economically competitive due to the high cost of feedstocks, low butanol titer, and product inhibition. Based on an analysis of the physiological characteristics of solventogenic clostridia, current advances that enhance ABE fermentation from strain improvement to product separation were systematically reviewed, focusing on: (1) elucidating the metabolic pathway and regulation mechanism of butanol synthesis; (2) enhancing cellular performance and robustness through metabolic engineering, and (3) optimizing the process of ABE fermentation. Finally, perspectives on engineering and exploiting clostridia as cell factories to efficiently produce various chemicals and materials are also discussed.
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Affiliation(s)
- Shubo Li
- College of Light Industry and Food Engineering, Guangxi University, Nanning, 530004 China
| | - Li Huang
- College of Light Industry and Food Engineering, Guangxi University, Nanning, 530004 China
| | - Chengzhu Ke
- College of Light Industry and Food Engineering, Guangxi University, Nanning, 530004 China
| | - Zongwen Pang
- College of Life Science and Technology, Guangxi University, Nanning, 530005 China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122 China
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20
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Enhanced Production of Fatty Acid Ethyl Ester with Engineered fabHDG Operon in Escherichia coli. Microorganisms 2019; 7:microorganisms7110552. [PMID: 31717929 PMCID: PMC6920873 DOI: 10.3390/microorganisms7110552] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/23/2019] [Accepted: 11/05/2019] [Indexed: 12/16/2022] Open
Abstract
Biodiesel, or fatty acid ethyl ester (FAEE), is an environmentally safe, next-generation biofuel. Conventionally, FAEE is produced by the conversion of oil/fats, obtained from plants, animals, and microorganisms, by transesterification. Recently, metabolic engineering of bacteria for ready-to-use biodiesel was developed. In Escherichia coli, it is produced by fatty acyl-carrier proteins and ethanol, with the help of thioesterase (TesB) and wax synthase (WS) enzymes. One of the foremost barriers in microbial FAEE production is the feedback inhibition of the fatty acid (FA) operon (fabHDG). Here, we studied the effect of biodiesel biosynthesis in E. coli with an engineered fabHDG operon. With a basic FAEE producing BD1 strain harboring tes and ws genes, biodiesel of 32 mg/L were produced. Optimal FAEE biosynthesis was achieved in the BD2 strain that carries an overexpressed operon (fabH, fabD, and fabG genes) and achieved up to 1291 mg/L of biodiesel, a 40-fold rise compared to the BD1 strain. The composition of FAEE obtained from the BD2 strain was 65% (C10:C2, decanoic acid ethyl ester) and 35% (C12:C2, dodecanoic acid ethyl ester). Our findings indicate that overexpression of the native FA operon, along with FAEE biosynthesis enzymes, improved biodiesel biosynthesis in E. coli.
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21
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Zhou L, Ren J, Li Z, Nie J, Wang C, Zeng AP. Characterization and Engineering of a Clostridium Glycine Riboswitch and Its Use To Control a Novel Metabolic Pathway for 5-Aminolevulinic Acid Production in Escherichia coli. ACS Synth Biol 2019; 8:2327-2335. [PMID: 31550137 DOI: 10.1021/acssynbio.9b00137] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A riboswitch, a regulatory RNA that controls gene expression by specifically binding a ligand, is an attractive genetic element for the control of conditional gene expression and metabolic pathways. In this study, we identified a glycine riboswitch located in the 5'-untranslated regions of a glycine:proton symporter gene in Clostridium pasteurianum. The glycine riboswitch is shown to contain two tandem aptamers and to function as an activator of expression of genes fused to its expression platform. Results of singlet aptamer experiments indicated that aptamer-2 has a much higher impact on regulating gene expression than aptamer-1. Further, we successfully obtained synthetic glycine-OFF riboswitches using a dual selection approach, and one of them repressed gene expression up to 10.2-fold with an improved dynamic range. The specific glycine-OFF riboswitch can function as an independent repressor in the presence of glycine, and its repression mechanism is inferred from predicted secondary structure. The selected glycine-OFF riboswitch was used to dynamically control the biosynthesis of 5-aminolevulinic acid (5-ALA) in Escherichia coli with an unnatural 5-ALA synthetic pathway, in which glycine plays a key role. It is demonstrated that the use of a synthetic Clostridium glycine-OFF riboswitch can lead to a significant increase (11%) of 5-ALA in E. coli harboring an unnatural biosynthetic pathway.
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Affiliation(s)
- Libang Zhou
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering , Beijing University of Chemical Technology , North Third Ring Road 15 , Chaoyang District, Beijing 100029 , China
- College of Food Science and Technology , Nanjing Agricultural University , Weigang 1 , Nanjing 210095 , PR China
| | - Jie Ren
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering , Beijing University of Chemical Technology , North Third Ring Road 15 , Chaoyang District, Beijing 100029 , China
| | - Zhidong Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering , Beijing University of Chemical Technology , North Third Ring Road 15 , Chaoyang District, Beijing 100029 , China
| | - Jinglei Nie
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering , Beijing University of Chemical Technology , North Third Ring Road 15 , Chaoyang District, Beijing 100029 , China
| | - Chuang Wang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering , Beijing University of Chemical Technology , North Third Ring Road 15 , Chaoyang District, Beijing 100029 , China
| | - An-Ping Zeng
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering , Beijing University of Chemical Technology , North Third Ring Road 15 , Chaoyang District, Beijing 100029 , China
- Institute of Bioprocess and Biosystems Engineering , Hamburg University of Technology , Denickestrasse 15 , D-21073 Hamburg , Germany
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22
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Production of nonnatural straight-chain amino acid 6-aminocaproate via an artificial iterative carbon-chain-extension cycle. Metab Eng 2019; 55:23-32. [DOI: 10.1016/j.ymben.2019.06.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 06/13/2019] [Accepted: 06/15/2019] [Indexed: 12/23/2022]
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23
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Phototrophic Lactate Utilization by Rhodopseudomonas palustris Is Stimulated by Coutilization with Additional Substrates. Appl Environ Microbiol 2019; 85:AEM.00048-19. [PMID: 30902855 DOI: 10.1128/aem.00048-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 03/14/2019] [Indexed: 01/09/2023] Open
Abstract
The phototrophic purple nonsulfur bacterium Rhodopseudomonas palustris is known for its metabolic versatility and is of interest for various industrial and environmental applications. Despite decades of research on R. palustris growth under diverse conditions, patterns of R. palustris growth and carbon utilization with mixtures of carbon substrates remain largely unknown. R. palustris readily utilizes most short-chain organic acids but cannot readily use lactate as a sole carbon source. Here we investigated the influence of mixed-substrate utilization on phototrophic lactate consumption by R. palustris We found that lactate was simultaneously utilized with a variety of other organic acids and glycerol in time frames that were insufficient for R. palustris growth on lactate alone. Thus, lactate utilization by R. palustris was expedited by its coutilization with additional substrates. Separately, experiments using carbon pairs that did not contain lactate revealed acetate-mediated inhibition of glycerol utilization in R. palustris This inhibition was specific to the acetate-glycerol pair, as R. palustris simultaneously utilized acetate or glycerol when either was paired with succinate or lactate. Overall, our results demonstrate that (i) R. palustris commonly employs simultaneous mixed-substrate utilization, (ii) mixed-substrate utilization expands the spectrum of readily utilized organic acids in this species, and (iii) R. palustris has the capacity to exert carbon catabolite control in a substrate-specific manner.IMPORTANCE Bacterial carbon source utilization is frequently assessed using cultures provided single carbon sources. However, the utilization of carbon mixtures by bacteria (i.e., mixed-substrate utilization) is of both fundamental and practical importance; it is central to bacterial physiology and ecology, and it influences the utility of bacteria as biotechnology. Here we investigated mixed-substrate utilization by the model organism Rhodopseudomonas palustris Using mixtures of organic acids and glycerol, we show that R. palustris exhibits an expanded range of usable carbon substrates when provided substrates in mixtures. Specifically, coutilization enabled the prompt consumption of lactate, a substrate that is otherwise not readily used by R. palustris Additionally, we found that R. palustris utilizes acetate and glycerol sequentially, revealing that this species has the capacity to use some substrates in a preferential order. These results provide insights into R. palustris physiology that will aid the use of R. palustris for industrial and commercial applications.
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24
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Volatile Compounds Produced by Cyanobacteria Isolated from Mangrove Environment. Curr Microbiol 2019; 76:575-582. [DOI: 10.1007/s00284-019-01658-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 02/22/2019] [Indexed: 10/27/2022]
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25
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Liu S, Liu YJ, Feng Y, Li B, Cui Q. Construction of consolidated bio-saccharification biocatalyst and process optimization for highly efficient lignocellulose solubilization. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:35. [PMID: 30820245 PMCID: PMC6378752 DOI: 10.1186/s13068-019-1374-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/07/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND The industrial conversion of biomass to high-value biofuels and biochemical is mainly restricted by lignocellulose solubilization. Consolidated bio-saccharification (CBS) is considered a promising process for lignocellulose solubilization depending on whole-cell biocatalysts that simultaneously perform effective cellulase production and hydrolysis. However, it usually takes a long time to reach a high saccharification level using the current CBS biocatalyst and process. RESULTS To promote the saccharification efficiency and reduce the cost, a Clostridium thermocellum recombinant strain ∆pyrF::KBm was constructed as a new CBS biocatalyst in this study. The key CBS factors, including the medium, inoculum size and cultivation, and substrate load, were investigated and optimized. The saccharification process was also stimulated by adding free hemicellulases, suggesting the need to further enhance hemicellulase activity of the whole-cell catalyst. Under the optimal conditions, the CBS process was shortened by 50% with pretreated wheat straw as the substrate. The sugar yield reached 0.795 g/g and the saccharification level was 89.3%. CONCLUSIONS This work provided a new biocatalyst and an optimized process of CBS and confirmed that CBS is a feasible strategy for cost-efficient solubilization of lignocellulose, which will greatly promote the industrial utilization of lignocellulosic biomass.
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Affiliation(s)
- Shiyue Liu
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Dalian National Laboratory for Clean Energy, Chinese Academy of Sciences, Dalian, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Ya-Jun Liu
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Dalian National Laboratory for Clean Energy, Chinese Academy of Sciences, Dalian, China
| | - Yingang Feng
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Dalian National Laboratory for Clean Energy, Chinese Academy of Sciences, Dalian, China
| | - Bin Li
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Dalian National Laboratory for Clean Energy, Chinese Academy of Sciences, Dalian, China
| | - Qiu Cui
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Dalian National Laboratory for Clean Energy, Chinese Academy of Sciences, Dalian, China
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26
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Acedos MG, de la Torre I, Santos VE, Garcia-Ochoa F. Kinetic Modeling of the Isobutanol Production from Glucose Using Shimwellia blattae (p424IbPSO) Strain: Effect of Initial Substrate Concentration. Ind Eng Chem Res 2019. [DOI: 10.1021/acs.iecr.8b05121] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Miguel G. Acedos
- Chemical & Materials Engineering Department, Universidad Complutense, 28040 Madrid, Spain
| | - Isabel de la Torre
- Chemical & Materials Engineering Department, Universidad Complutense, 28040 Madrid, Spain
| | - Victoria E. Santos
- Chemical & Materials Engineering Department, Universidad Complutense, 28040 Madrid, Spain
| | - Felix Garcia-Ochoa
- Chemical & Materials Engineering Department, Universidad Complutense, 28040 Madrid, Spain
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27
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Wang J, Lu A, Liu J, Huang W, Wang J, Cai Z, Zhao G. iCatch: a new strategy for capturing large DNA fragments using homing endonucleases. Acta Biochim Biophys Sin (Shanghai) 2019; 51:97-103. [PMID: 30452545 DOI: 10.1093/abbs/gmy139] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 10/21/2018] [Indexed: 11/15/2022] Open
Abstract
Natural genetic materials contain many biosynthetic gene clusters encoding potentially valuable natural products, many of which can be used directly without codon optimization or other manipulations. With the development of synthetic biology, several DNA assembly standards have been proposed, conveniently facilitating the reuse of natural materials. Among these standards, the iBrick assembly standard was developed by our laboratory to manipulate large DNA fragments, employing two homing endonucleases. Considering the difficulty of cloning large iBrick parts using conventional endonuclease-mediated restriction and ligation methods, we herein present a new method, known as iCatch, which readily captures biosynthetic gene clusters. As the clusters cloned by iCatch have the prefix and suffix of the iBrick standard, they serve as new iBrick parts and are therefore conducive to further editing and assembly with the iBrick standard. iCatch employs the natural homologous recombination system to flank the region of interest with I-SceI and PI-PspI recognition sites, after which the genome is digested with I-SceI or PI-PspI and the fragments are then self-ligated to clone the target DNA fragments. We used this method to successfully capture the actinorhodin biosynthetic cluster from Streptomyces coelicolor and then heterologously expressed this cluster in a thermophilic Streptomyces strain. We propose that iCatch can be used for the cloning of DNA sequences that are dozens of kilobases in length, facilitating the heterologous expression of microbial natural products. Moreover, this cloning methodology can be a complementary tool for the iBrick standard, especially in applications requiring the manipulation of large DNA fragments.
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Affiliation(s)
- Jingman Wang
- Carson International Cancer Center, Shenzhen University School of Medicine, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Anrui Lu
- Carson International Cancer Center, Shenzhen University School of Medicine, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Jiakun Liu
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Weiren Huang
- Carson International Cancer Center, Shenzhen University School of Medicine, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology, Urogenital Tumors, Shenzhen, China
| | - Jin Wang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Zhiming Cai
- Carson International Cancer Center, Shenzhen University School of Medicine, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology, Urogenital Tumors, Shenzhen, China
| | - Guoping Zhao
- Carson International Cancer Center, Shenzhen University School of Medicine, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
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28
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Horinouchi T, Maeda T, Furusawa C. Understanding and engineering alcohol-tolerant bacteria using OMICS technology. World J Microbiol Biotechnol 2018; 34:157. [PMID: 30341456 PMCID: PMC6208762 DOI: 10.1007/s11274-018-2542-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/13/2018] [Indexed: 12/16/2022]
Abstract
Microbes are capable of producing alcohols, making them an important source of alternative energy that can replace fossil fuels. However, these alcohols can be toxic to the microbes themselves, retaring or inhibiting cell growth and decreasing the production yield. One solution is improving the alcohol tolerance of such alcohol-producing organisms. Advances in omics technologies, including transcriptomic, proteomic, metabolomic, and genomic technologies, have helped us understand the complex mechanisms underlying alcohol toxicity, and such advances could assist in devising strategies for engineering alcohol-tolerant strains. This review highlights these advances and discusses strategies for improving alcohol tolerance using omics analyses.
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Affiliation(s)
- Takaaki Horinouchi
- Center for Biosystems Dynamics Research (BDR), RIKEN, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan.
| | - Tomoya Maeda
- Center for Biosystems Dynamics Research (BDR), RIKEN, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
| | - Chikara Furusawa
- Center for Biosystems Dynamics Research (BDR), RIKEN, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan.
- Universal Biology Institute, The University of Tokyo, 7-3-1 Hongo, Tokyo, 113-0033, Japan.
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29
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Long-Term Biogas Production from Glycolate by Diverse and Highly Dynamic Communities. Microorganisms 2018; 6:microorganisms6040103. [PMID: 30287755 PMCID: PMC6313629 DOI: 10.3390/microorganisms6040103] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 09/25/2018] [Accepted: 09/29/2018] [Indexed: 12/19/2022] Open
Abstract
Generating chemical energy carriers and bulk chemicals from solar energy by microbial metabolic capacities is a promising technology. In this long-term study of over 500 days, methane was produced by a microbial community that was fed by the mono-substrate glycolate, which was derived from engineered algae. The microbial community structure was measured on the single cell level using flow cytometry. Abiotic and operational reactor parameters were analyzed in parallel. The R-based tool flowCyBar facilitated visualization of community dynamics and indicated sub-communities involved in glycolate fermentation and methanogenesis. Cell sorting and amplicon sequencing of 16S rRNA and mcrA genes were used to identify the key organisms involved in the anaerobic conversion process. The microbial community allowed a constant fermentation, although it was sensitive to high glycolate concentrations in the feed. A linear correlation between glycolate loading rate and biogas amount was observed (R2 = 0.99) for glycolate loading rates up to 1.81 g L−1 day−1 with a maximum in biogas amount of 3635 mL day−1 encompassing 45% methane. The cytometric diversity remained high during the whole cultivation period. The dominating bacterial genera were Syntrophobotulus, Clostridia genus B55_F, Aminobacterium, and Petrimonas. Methanogenesis was almost exclusively performed by the hydrogenotrophic genus Methanobacterium.
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30
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Acedos MG, Santos VE, Garcia-Ochoa F. Resting cells isobutanol production by Shimwellia blattae (p424IbPSO): Influence of growth culture conditions. Biotechnol Prog 2018; 34:1073-1080. [PMID: 30281946 DOI: 10.1002/btpr.2705] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/31/2018] [Accepted: 08/08/2018] [Indexed: 01/19/2023]
Abstract
Isobutanol is a promising gasoline additive and could even be a potential substitute used directly as combustible. In this work, the production of isobutanol from glucose by Shimwellia blattae (p424IbPSO) in resting cell cultures is studied. This production has two stages, involving a resting cell phase that has not been studied before. The cell growth was carried out under different operating conditions: temperature and medium composition (YE, ammonium, and IPTG concentrations), looking for the highest isobutanol production. Moreover, the cells were collected at three different growth times checking their isobutanol production capacity. The best operating conditions have been determined as: 30°C of temperature, a medium containing 1.5 g L-1 YE and 1.4 g L-1 of ammonium as nitrogen sources, adding 0.5 mM IPTG as inducer. The cells collected at early growth times are significantly more active. The use of S. blattae (p424IbPSO) in resting cells is a good strategy for the production of isobutanol from glucose yielding better results than in batch growth cultures, a yield of 60% attainment of theoretical maximum yield is obtained under optimal conditions. In addition, it has been demonstrated that if the cells are cultured at higher temperatures and with high IPTG concentrations, inclusion bodies are formed in the cytoplasm inhibiting the isobutanol production in the resting cell stage.
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Affiliation(s)
- Miguel G Acedos
- Dept. of Chemical and Materials Engineering, Universidad Complutense, Madrid, 28040, Spain
| | - Victoria E Santos
- Dept. of Chemical and Materials Engineering, Universidad Complutense, Madrid, 28040, Spain
| | - Felix Garcia-Ochoa
- Dept. of Chemical and Materials Engineering, Universidad Complutense, Madrid, 28040, Spain
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31
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Yao R, Liu D, Jia X, Zheng Y, Liu W, Xiao Y. CRISPR-Cas9/Cas12a biotechnology and application in bacteria. Synth Syst Biotechnol 2018; 3:135-149. [PMID: 30345399 PMCID: PMC6190536 DOI: 10.1016/j.synbio.2018.09.004] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 09/24/2018] [Accepted: 09/25/2018] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas technologies have greatly reshaped the biology field. In this review, we discuss the CRISPR-Cas with a particular focus on the associated technologies and applications of CRISPR-Cas9 and CRISPR-Cas12a, which have been most widely studied and used. We discuss the biological mechanisms of CRISPR-Cas as immune defense systems, recently-discovered anti-CRISPR-Cas systems, and the emerging Cas variants (such as xCas9 and Cas13) with unique characteristics. Then, we highlight various CRISPR-Cas biotechnologies, including nuclease-dependent genome editing, CRISPR gene regulation (including CRISPR interference/activation), DNA/RNA base editing, and nucleic acid detection. Last, we summarize up-to-date applications of the biotechnologies for synthetic biology and metabolic engineering in various bacterial species.
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Affiliation(s)
- Ruilian Yao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Di Liu
- Department of Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, CA 94551, USA
| | - Xiao Jia
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yuan Zheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wei Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yi Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
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32
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Zhang H, Liu H, Tian Z, Lu D, Yu Y, Cestellos-Blanco S, Sakimoto KK, Yang P. Bacteria photosensitized by intracellular gold nanoclusters for solar fuel production. NATURE NANOTECHNOLOGY 2018; 13:900-905. [PMID: 30275495 DOI: 10.1038/s41565-018-0267-z] [Citation(s) in RCA: 245] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 08/23/2018] [Indexed: 06/08/2023]
Abstract
The demand for renewable and sustainable fuel has prompted the rapid development of advanced nanotechnologies to effectively harness solar power. The construction of photosynthetic biohybrid systems (PBSs) aims to link preassembled biosynthetic pathways with inorganic light absorbers. This strategy inherits both the high light-harvesting efficiency of solid-state semiconductors and the superior catalytic performance of whole-cell microorganisms. Here, we introduce an intracellular, biocompatible light absorber, in the form of gold nanoclusters (AuNCs), to circumvent the sluggish kinetics of electron transfer for existing PBSs. Translocation of these AuNCs into non-photosynthetic bacteria enables photosynthesis of acetic acid from CO2. The AuNCs also serve as inhibitors of reactive oxygen species (ROS) to maintain high bacterium viability. With the dual advantages of light absorption and biocompatibility, this new generation of PBS can efficiently harvest sunlight and transfer photogenerated electrons to cellular metabolism, realizing CO2 fixation continuously over several days.
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Affiliation(s)
- Hao Zhang
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Hao Liu
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Zhiquan Tian
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, P. R. China
| | - Dylan Lu
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Chemistry Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yi Yu
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Stefano Cestellos-Blanco
- Department of Materials Science and Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Kelsey K Sakimoto
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Peidong Yang
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
- Chemistry Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Materials Science and Engineering, University of California, Berkeley, Berkeley, CA, USA.
- Kavli Energy NanoSciences Institute, Berkeley, CA, USA.
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33
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Marcella AM, Barb AW. Acyl-coenzyme A:(holo-acyl carrier protein) transacylase enzymes as templates for engineering. Appl Microbiol Biotechnol 2018; 102:6333-6341. [PMID: 29858956 DOI: 10.1007/s00253-018-9114-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 05/16/2018] [Accepted: 05/17/2018] [Indexed: 01/18/2023]
Abstract
This review will cover the structure, enzymology, and related aspects that are important for structure-based engineering of the transacylase enzymes from fatty acid biosynthesis and polyketide synthesis. Furthermore, this review will focus on in vitro characteristics and not cover engineering of the upstream or downstream reactions or strategies to manipulate metabolic flux in vivo. The malonyl-coenzyme A(CoA)-holo-acyl-carrier protein (holo-ACP) transacylase (FabD) from Escherichia coli serves as a model for this enzyme with thorough descriptions of structure, enzyme mechanism, and effects of mutation on substrate binding presented in the literature. Here, we discuss multiple practical and theoretical considerations regarding engineering transacylase enzymes to accept non-cognate substrates and form novel acyl-ACPs for downstream reactions.
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Affiliation(s)
- Aaron M Marcella
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, 2437 Pammel Drive, Molecular Biology Building, rm 4210, Ames, IA, 50011, USA
| | - Adam W Barb
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, 2437 Pammel Drive, Molecular Biology Building, rm 4210, Ames, IA, 50011, USA.
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34
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Methods for enhancing cyanobacterial stress tolerance to enable improved production of biofuels and industrially relevant chemicals. Appl Microbiol Biotechnol 2018; 102:1617-1628. [DOI: 10.1007/s00253-018-8755-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 01/03/2018] [Accepted: 01/04/2018] [Indexed: 10/18/2022]
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35
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Tan LR, Xia PF, Li Q, Yuan XZ, Wang SG. Micelle-mediated transport disturbance providing extracellular strategy for alleviating n-butanol stress on Escherichia coli. Bioprocess Biosyst Eng 2017; 41:443-447. [PMID: 29209846 DOI: 10.1007/s00449-017-1872-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 11/27/2017] [Indexed: 10/18/2022]
Abstract
One barrier inhibiting further progress in biofuel production is the toxicity of biofuels towards their producers. It is promising to apply gene-based intracellular techniques to engineer better strains with higher organic solvent tolerance. These methods are, however, complex. In the present study, we developed a simple, manageable, and commercial extracellular prototypal strategy to alleviate n-butanol (n-BuOH) stress on Escherichia coli via a micelle-mediated transport disturbance. When the concentration of sodium dodecyl sulfate, a typical anionic surfactant, is high enough to form micelles, n-BuOH will be trapped into/onto the micelles, and the negative charge prevents the n-BuOH from approaching the cells. Our study provides an extracellular strategy to relieve the stress from n-BuOH, and it also exhibits a new angle to advance microbial factories through extracellular routines.
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Affiliation(s)
- Lin-Rui Tan
- School of Environmental Science and Engineering, Shandong University, 27 Shanda Nanlu, Jinan, 250100, China
| | - Peng-Fei Xia
- School of Environmental Science and Engineering, Shandong University, 27 Shanda Nanlu, Jinan, 250100, China
| | - Qian Li
- School of Environmental Science and Engineering, Shandong University, 27 Shanda Nanlu, Jinan, 250100, China
| | - Xian-Zheng Yuan
- School of Environmental Science and Engineering, Shandong University, 27 Shanda Nanlu, Jinan, 250100, China
| | - Shu-Guang Wang
- School of Environmental Science and Engineering, Shandong University, 27 Shanda Nanlu, Jinan, 250100, China.
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36
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Liu H, Cheng T, Zou H, Zhang H, Xu X, Sun C, Aboulnaga E, Cheng Z, Zhao G, Xian M. High titer mevalonate fermentation and its feeding as a building block for isoprenoids (isoprene and sabinene) production in engineered Escherichia coli. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.07.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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37
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Marcella AM, Barb AW. The R117A variant of the Escherichia coli transacylase FabD synthesizes novel acyl-(acyl carrier proteins). Appl Microbiol Biotechnol 2017; 101:8431-8441. [DOI: 10.1007/s00253-017-8586-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 08/29/2017] [Accepted: 10/09/2017] [Indexed: 11/24/2022]
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38
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Yim SS, Choi JW, Lee SH, Jeon EJ, Chung WJ, Jeong KJ. Engineering of Corynebacterium glutamicum for Consolidated Conversion of Hemicellulosic Biomass into Xylonic Acid. Biotechnol J 2017; 12. [PMID: 28799725 DOI: 10.1002/biot.201700040] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 08/05/2017] [Indexed: 12/12/2022]
Abstract
Xylonic acid is a promising platform chemical with various applications in the fields of food, pharmaceuticals, and agriculture. However, in the current process, xylonic acid is mainly produced by the conversion of xylose, whose preparation requires substantial cost and time. Here, Corynebacterium glutamicum is engineered for the consolidated bioconversion of hemicellulosic biomass (xylan) into xylonic acid in a single cultivation. First, for the efficient conversion of xylose to xylonic acid, xylose dehydrogenase (Xdh) and xylonolactonase (XylC) from Caulobacter crescentus are evaluated together with a previously optimized xylose transporter module (XylE of Escherichia coli), and cells expressing xdh and xylE genes with an optimized expression system can produce xylonic acid from xylose with 100% conversion yield. Next, to directly process xylan as a substrate, an engineered xylan-degrading module is introduced, in which two xylan-degrading enzymes (endoxylanase and xylosidase) are secreted into the culture medium. The engineered C. glutamicum successfully produce 6.23 g L-1 of xylonic acid from 20 g L-1 of xylan. This is the first report on xylonic acid production in C. glutamicum and this robust system will contribute to development of an industrially relevant platform for production of xylonic acid from raw biomass.
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Affiliation(s)
- Sung Sun Yim
- Department of Chemical and Biomolecular Engineering, BK21 Plus Program, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141,, Republic of Korea
| | - Jae Woong Choi
- Department of Chemical and Biomolecular Engineering, BK21 Plus Program, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141,, Republic of Korea
| | - Se Hwa Lee
- Department of Chemical and Biomolecular Engineering, BK21 Plus Program, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141,, Republic of Korea
| | - Eun Jung Jeon
- Department of Chemical and Biomolecular Engineering, BK21 Plus Program, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141,, Republic of Korea
| | - Wook-Jin Chung
- Energy and Environment Fusion Technology Center (E2FTC), Myongji University, Yongin City, Gyeonggi Province, Republic of Korea
| | - Ki Jun Jeong
- Department of Chemical and Biomolecular Engineering, BK21 Plus Program, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141,, Republic of Korea.,Institute for the BioCentury, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141,, Republic of Korea
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39
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Microbial Production of Amino Acid-Related Compounds. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2017; 159:255-269. [PMID: 27872963 DOI: 10.1007/10_2016_34] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Corynebacterium glutamicum is the workhorse of the production of proteinogenic amino acids used in food and feed biotechnology. After more than 50 years of safe amino acid production, C. glutamicum has recently also been engineered for the production of amino acid-derived compounds, which find various applications, e.g., as synthons for the chemical industry in several markets including the polymer market. The amino acid-derived compounds such as non-proteinogenic ω-amino acids, α,ω-diamines, and cyclic or hydroxylated amino acids have similar carbon backbones and functional groups as their amino acid precursors. Decarboxylation of amino acids may yield ω-amino acids such as β-alanine, γ-aminobutyrate, and δ-aminovalerate as well as α,ω-diamines such as putrescine and cadaverine. Since transamination is the final step in several amino acid biosynthesis pathways, 2-keto acids as immediate amino acid precursors are also amenable to production using recombinant C. glutamicum strains. Approaches for metabolic engineering of C. glutamicum for production of amino acid-derived compounds will be described, and where applicable, production from alternative carbon sources or use of genome streamline will be referred to. The excellent large-scale fermentation experience with C. glutamicum offers the possibility that these amino acid-derived speciality products may enter large-volume markets.
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40
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Guo H, Zheng B, Jiang D, Qin W. Overexpression of a Laccase with Dye Decolorization Activity from Bacillus sp. Induced in Escherichia coli. J Mol Microbiol Biotechnol 2017; 27:217-227. [DOI: 10.1159/000478859] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 06/14/2017] [Indexed: 12/19/2022] Open
Abstract
Laccases from bacteria have been widely studied in the past 2 decades due to the higher growth rate of bacteria and their excellent thermal and alkaline pH stability. In this study, a novel laccase gene was cloned from<i> Bacillus</i> sp., analyzed, and functionally expressed in<i> Escherichia coli</i>. The laccase was highly induced in the <i>E. coli</i> expression system with a maximum intracellular activity of 16 U mg<sup>-1</sup> protein. The optimal temperature and pH of the purified laccase were 40°C and 4.6, respectively, when ABTS (2,2'-azino-bis[3-ethylbenzothiazoline-6-sulfonate]) was used as the substrate. The purified laccase showed high stability in the pH range of 3.0-9.0, and retained more than 70% of its activity after 24 h of incubation at 40°C with a pH value of 9.0. Furthermore, the enzyme exhibited extremely high temperature and ion metal tolerance. The half-life of the purified laccase at 70°C was 15.9 h. The purified laccase could efficiently decolorize 3 chemical dyes, especially in the presence of ABTS as a mediator. The high production of this laccase in<i> E. coli</i> and exceptional characteristics of the recombinant enzyme protein make it a promising candidate for industrial applications.
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41
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Schlecht U, Mok J, Dallett C, Berka J. ConcatSeq: A method for increasing throughput of single molecule sequencing by concatenating short DNA fragments. Sci Rep 2017; 7:5252. [PMID: 28701704 PMCID: PMC5507877 DOI: 10.1038/s41598-017-05503-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 05/30/2017] [Indexed: 12/26/2022] Open
Abstract
Single molecule sequencing (SMS) platforms enable base sequences to be read directly from individual strands of DNA in real-time. Though capable of long read lengths, SMS platforms currently suffer from low throughput compared to competing short-read sequencing technologies. Here, we present a novel strategy for sequencing library preparation, dubbed ConcatSeq, which increases the throughput of SMS platforms by generating long concatenated templates from pools of short DNA molecules. We demonstrate adaptation of this technique to two target enrichment workflows, commonly used for oncology applications, and feasibility using PacBio single molecule real-time (SMRT) technology. Our approach is capable of increasing the sequencing throughput of the PacBio RSII platform by more than five-fold, while maintaining the ability to correctly call allele frequencies of known single nucleotide variants. ConcatSeq provides a versatile new sample preparation tool for long-read sequencing technologies.
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Affiliation(s)
- Ulrich Schlecht
- Roche Sequencing Solutions, 4300 Hacienda Drive, Pleasanton, CA, 94588, USA.
| | - Janine Mok
- Roche Sequencing Solutions, 4300 Hacienda Drive, Pleasanton, CA, 94588, USA
| | - Carolina Dallett
- Roche Sequencing Solutions, 4300 Hacienda Drive, Pleasanton, CA, 94588, USA
| | - Jan Berka
- Roche Sequencing Solutions, 4300 Hacienda Drive, Pleasanton, CA, 94588, USA
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42
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Horinouchi T, Sakai A, Kotani H, Tanabe K, Furusawa C. Improvement of isopropanol tolerance of Escherichia coli using adaptive laboratory evolution and omics technologies. J Biotechnol 2017. [PMID: 28645581 DOI: 10.1016/j.jbiotec.2017.06.408] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Isopropanol (IPA) is the secondary alcohol that can be dehydrated to yield propylene. To produce IPA using microorganisms, a significant issue is that the toxicity of IPA causes retardation or inhibition of cell growth, decreasing the yield. One possible strategy to overcome this problem is to improve IPA tolerance of production organisms. For the understanding of tolerance to IPA, we performed parallel adaptive laboratory evolution (ALE) of Escherichia coli under IPA stress. To identify the genotypic change during ALE, we performed genome re-sequencing analyses of obtained tolerant strains. To verify which mutations were contributed to IPA tolerance, we constructed the mutant strains and quantify the IPA tolerance of the constructed mutants. From these analyses, we found that five mutations (relA, marC, proQ, yfgO, and rraA) provided the increase of IPA tolerance. To understand the phenotypic change during ALE, we performed transcriptome analysis of tolerant strains. From transcriptome analysis, we found that expression levels of genes related to biosynthetic pathways of amino acids, iron ion homeostasis, and energy metabolisms were changed in the tolerant strains. Results from these experiments provide fundamental bases for designing IPA tolerant strains for industrial purposes.
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Affiliation(s)
- Takaaki Horinouchi
- Quantitative Biology Center, RIKEN, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan.
| | - Aki Sakai
- Quantitative Biology Center, RIKEN, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan
| | - Hazuki Kotani
- Quantitative Biology Center, RIKEN, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan
| | - Kumi Tanabe
- Quantitative Biology Center, RIKEN, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan
| | - Chikara Furusawa
- Quantitative Biology Center, RIKEN, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan; Universal Biology Institute, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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43
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Obst U, Lu TK, Sieber V. A Modular Toolkit for Generating Pichia pastoris Secretion Libraries. ACS Synth Biol 2017; 6:1016-1025. [PMID: 28252957 DOI: 10.1021/acssynbio.6b00337] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Yeasts are powerful eukaryotic hosts for the production of recombinant proteins due to their rapid growth to high cell densities and ease of genetic modification. For large-scale industrial production, secretion of a protein offers the advantage of simple and efficient downstream purification that avoids costly cell rupture, denaturation and refolding. The methylotrophic yeast Pichia pastoris (Komagataella phaffi) is a well-established expression host that has the ability to perform post-translational modifications and is generally regarded as safe (GRAS). Nevertheless, optimization of protein secretion in this host remains a challenge due to the multiple steps involved during secretion and a lack of genetic tools to tune this process. Here, we developed a toolkit of standardized regulatory elements specific for Pichia pastoris allowing the tuning of gene expression and choice of protein secretion tag. As protein secretion is a complex process, these parts are compatible with a hierarchical assembly method to enable the generation of large and diverse secretion libraries in order to explore a wide range of secretion constructs, achieve successful secretion, and better understand the regulatory factors of importance to specific proteins of interest. To assess the performance of these parts, we built and characterized the expression and secretion efficiency of 124 constructs that combined different regulatory elements with two fluorescent reporter proteins (RFP, yEGFP). Intracellular expression from our promoters was comparatively independent of whether RFP or yEGFP, and whether plasmid-based expression or genomically integrated expression, was used. In contrast, secretion efficiency significantly varied for different genes expressed using identical regulatory elements, with differences in secretion efficiency of >10-fold observed. These results highlight the importance of generating diverse secretion libraries when searching for optimal expression conditions, and demonstrate that our toolkit is a valuable asset for the creation of efficient microbial cell factories.
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Affiliation(s)
- Ulrike Obst
- Straubing Centre of Science, 94315 Straubing, Germany
| | - Timothy K. Lu
- Biophysics
Program, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Volker Sieber
- Catalysis
Research Center, Technical University of Munich, 85748 Garching, Germany
- Fraunhofer IGB, Straubing Branch Bio, Electro, and
Chemocatalysis BioCat, 94315 Straubing, Germany
- Straubing Centre of Science, 94315 Straubing, Germany
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Ishida Y, Nguyen TTM, Izawa S. The yeast ADH7 promoter enables gene expression under pronounced translation repression caused by the combined stress of vanillin, furfural, and 5-hydroxymethylfurfural. J Biotechnol 2017; 252:65-72. [DOI: 10.1016/j.jbiotec.2017.04.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 04/03/2017] [Accepted: 04/21/2017] [Indexed: 11/30/2022]
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Zhang J, Liu S, Li R, Hong W, Xiao Y, Feng Y, Cui Q, Liu YJ. Efficient whole-cell-catalyzing cellulose saccharification using engineered Clostridium thermocellum. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:124. [PMID: 28507596 PMCID: PMC5429504 DOI: 10.1186/s13068-017-0796-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 04/19/2017] [Indexed: 05/26/2023]
Abstract
BACKGROUND Cost-efficient saccharification is one of the main bottlenecks for industrial lignocellulose conversion. Clostridium thermocellum naturally degrades lignocellulose efficiently using the cellulosome, a multiprotein supermolecular complex, and thus can be potentially used as a low-cost catalyst for lignocellulose saccharification. The industrial use of C. thermocellum is restrained due largely to the inhibition of the hydrolysate cellobiose to its cellulosome. Although the supplementation of beta-glucosidase may solve the problem, the production of the enzymes greatly complicates the process and may also increase the cost of saccharification. RESULTS To conquer the feedback inhibition and establish an efficient whole-cell catalyst for highly efficient cellulose saccharification, we constructed a recombinant strain of C. thermocellum ∆pyrF::CaBglA which produced a secretory exoglucanase CelS-bearing heterologous BGL using a newly developed seamless genome editing system. Without the extra addition of enzymes, the relative saccharification level of ∆pyrF::CaBglA was stimulated by over twofolds compared to its parent strain ∆pyrF through a two-stage saccharification process with 100 g/L Avicel as the carbon source. The production of reducing sugars and the relative saccharification level were further enhanced to 490 mM and 79.4%, respectively, with increased cell density. CONCLUSIONS The high cellulose-degrading ability and sugar productivity suggested that the whole-cell-catalysis strategy for cellulose saccharification is promising, and the C. thermocellum strain ∆pyrF::CaBglA could be potentially used as an efficient whole-cell catalyst for industrial cellulose saccharification.
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Affiliation(s)
- Jie Zhang
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Shiyue Liu
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Renmin Li
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Wei Hong
- Key Laboratory of Endemic and Ethnic Diseases (Guizhou Medical University), Ministry of Education, Guiyang, 550000 People’s Republic of China
| | - Yan Xiao
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
| | - Yingang Feng
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
| | - Qiu Cui
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
| | - Ya-Jun Liu
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
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Blumer-Schuette SE, Zurawski JV, Conway JM, Khatibi P, Lewis DL, Li Q, Chiang VL, Kelly RM. Caldicellulosiruptor saccharolyticus transcriptomes reveal consequences of chemical pretreatment and genetic modification of lignocellulose. Microb Biotechnol 2017; 10:1546-1557. [PMID: 28322023 PMCID: PMC5658599 DOI: 10.1111/1751-7915.12494] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Revised: 11/28/2016] [Accepted: 11/29/2016] [Indexed: 11/28/2022] Open
Abstract
Recalcitrance of plant biomass is a major barrier for commercially feasible cellulosic biofuel production. Chemical and enzymatic assays have been developed to measure recalcitrance and carbohydrate composition; however, none of these assays can directly report which polysaccharides a candidate microbe will sense during growth on these substrates. Here, we propose using the transcriptomic response of the plant biomass‐deconstructing microbe, Caldicellulosiruptor saccharolyticus, as a direct measure of how suitable a sample of plant biomass may be for fermentation based on the bioavailability of polysaccharides. Key genes were identified using the global gene response of the microbe to model plant polysaccharides and various types of unpretreated, chemically pretreated and genetically modified plant biomass. While the majority of C. saccharolyticus genes responding were similar between plant biomasses; subtle differences were discernable, most importantly between chemically pretreated or genetically modified biomass that both exhibit similar levels of solubilization by the microbe. Furthermore, the results here present a new paradigm for assessing plant–microbe interactions that can be deployed as a biological assay to report on the complexity and recalcitrance of plant biomass.
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Affiliation(s)
- Sara E Blumer-Schuette
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Jeffrey V Zurawski
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Jonathan M Conway
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Piyum Khatibi
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Derrick L Lewis
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Quanzi Li
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA
| | - Vincent L Chiang
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
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Identification of residues important for the activity of aldehyde-deformylating oxygenase through investigation into the structure-activity relationship. BMC Biotechnol 2017; 17:31. [PMID: 28302170 PMCID: PMC5356278 DOI: 10.1186/s12896-017-0351-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 03/08/2017] [Indexed: 12/24/2022] Open
Abstract
Background Aldehyde-deformylating oxygenase (ADO) is a key enzyme involved in the biosynthetic pathway of fatty alk(a/e)nes in cyanobacteria. However, cADO (cyanobacterial ADO) showed extreme low activity with the kcat value below 1 min−1, which would limit its application in biofuel production. To identify the activity related key residues of cADO is urgently required. Results The amino acid residues which might affect cADO activity were identified based on the crystal structures and sequence alignment of cADOs, including the residues close to the di-iron center (Tyr39, Arg62, Gln110, Tyr122, Asp143 of cADO-1593), the protein surface (Trp 178 of cADO-1593), and those involved in two important hydrogen bonds (Gln49, Asn123 of cADO-1593, and Asp49, Asn123 of cADO-sll0208) and in the oligopeptide whose conformation changed in the absence of the di-iron center (Leu146, Asn149, Phe150 of cADO-1593, and Thr146, Leu148, Tyr150 of cADO-sll0208). The variants of cADO-1593 from Synechococcus elongatus PCC7942 and cADO-sll0208 from Synechocystis sp. PCC6803 were constructed, overexpressed, purified and kinetically characterized. The kcat values of L146T, Q49H/N123H/F150Y and W178R of cADO-1593 and L148R of cADO-sll0208 were increased by more than two-fold, whereas that of R62A dropped by 91.1%. N123H, Y39F and D143A of cADO-1593, and Y150F of cADO-sll0208 reduced activities by ≤ 20%. Conclusions Some important amino acids, which exerted some effects on cADO activity, were identified. Several enzyme variants exhibited greatly reduced activity, while the kcat values of several mutants are more than two-fold higher than the wild type. This study presents the report on the relationship between amino acid residues and enzyme activity of cADOs, and the information will provide a guide for enhancement of cADO activity through protein engineering. Electronic supplementary material The online version of this article (doi:10.1186/s12896-017-0351-8) contains supplementary material, which is available to authorized users.
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Cheng T, Liu H, Zou H, Chen N, Shi M, Xie C, Zhao G, Xian M. Enzymatic process optimization for the in vitro production of isoprene from mevalonate. Microb Cell Fact 2017; 16:8. [PMID: 28068985 PMCID: PMC5223365 DOI: 10.1186/s12934-016-0622-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 12/27/2016] [Indexed: 11/26/2022] Open
Abstract
Background As an important bulk chemical for synthetic rubber, isoprene can be biosynthesized by robust microbes. But rational engineering and optimization are often demanded to make the in vivo process feasible due to the complexities of cellular metabolism. Alternative synthetic biochemistry strategies are in fast development to produce isoprene or isoprenoids in vitro. Results This study set up an in vitro enzyme synthetic chemistry process using 5 enzymes in the lower mevalonate pathway to produce isoprene from mevalonate. We found the level and ratio of individual enzymes would significantly affect the efficiency of the whole system. The optimized process using 10 balanced enzyme unites (5.0 µM of MVK, PMK, MVD; 10.0 µM of IDI, 80.0 µM of ISPS) could produce 6323.5 µmol/L/h (430 mg/L/h) isoprene in a 2 ml in vitro system. In a scale up process (50 ml) only using 1 balanced enzyme unit (0.5 µM of MVK, PMK, MVD; 1.0 µM of IDI, 8.0 µM of ISPS), the system could produce 302 mg/L isoprene in 40 h, which showed higher production rate and longer reaction phase with comparison of the in vivo control. Conclusions By optimizing the enzyme levels of lower MVA pathway, synthetic biochemistry methods could be set up for the enzymatic production of isoprene or isoprenoids from mevalonate.
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Affiliation(s)
- Tao Cheng
- CAS Key Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Laoshan District, Qingdao, 266101, China.,State Key Laboratory Base of Eco-Chemical Engineering, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Hui Liu
- CAS Key Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Laoshan District, Qingdao, 266101, China
| | - Huibin Zou
- CAS Key Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Laoshan District, Qingdao, 266101, China. .,College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China.
| | - Ningning Chen
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Mengxun Shi
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Congxia Xie
- State Key Laboratory Base of Eco-Chemical Engineering, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Guang Zhao
- CAS Key Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Laoshan District, Qingdao, 266101, China.
| | - Mo Xian
- CAS Key Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Laoshan District, Qingdao, 266101, China.
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Loder AJ, Zeldes BM, Conway JM, Counts JA, Straub CT, Khatibi PA, Lee LL, Vitko NP, Keller MW, Rhaesa AM, Rubinstein GM, Scott IM, Lipscomb GL, Adams MW, Kelly RM. Extreme Thermophiles as Metabolic Engineering Platforms: Strategies and Current Perspective. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Andrew J. Loder
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Benjamin M. Zeldes
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Jonathan M. Conway
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - James A. Counts
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Christopher T. Straub
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Piyum A. Khatibi
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Laura L. Lee
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Nicholas P. Vitko
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Matthew W. Keller
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Amanda M. Rhaesa
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Gabe M. Rubinstein
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Israel M. Scott
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Gina L. Lipscomb
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Michael W.W. Adams
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Robert M. Kelly
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
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Shaw AJ, Lam FH, Hamilton M, Consiglio A, MacEwen K, Brevnova EE, Greenhagen E, LaTouf WG, South CR, van Dijken H, Stephanopoulos G. Metabolic engineering of microbial competitive advantage for industrial fermentation processes. Science 2016; 353:583-6. [PMID: 27493184 DOI: 10.1126/science.aaf6159] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 06/22/2016] [Indexed: 01/23/2023]
Abstract
Microbial contamination is an obstacle to widespread production of advanced biofuels and chemicals. Current practices such as process sterilization or antibiotic dosage carry excess costs or encourage the development of antibiotic resistance. We engineered Escherichia coli to assimilate melamine, a xenobiotic compound containing nitrogen. After adaptive laboratory evolution to improve pathway efficiency, the engineered strain rapidly outcompeted a control strain when melamine was supplied as the nitrogen source. We additionally engineered the yeasts Saccharomyces cerevisiae and Yarrowia lipolytica to assimilate nitrogen from cyanamide and phosphorus from potassium phosphite, and they outcompeted contaminating strains in several low-cost feedstocks. Supplying essential growth nutrients through xenobiotic or ecologically rare chemicals provides microbial competitive advantage with minimal external risks, given that engineered biocatalysts only have improved fitness within the customized fermentation environment.
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Affiliation(s)
- A Joe Shaw
- Novogy, 85 Bolton Street, Cambridge, MA 02140, USA
| | - Felix H Lam
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | | | - Kyle MacEwen
- Novogy, 85 Bolton Street, Cambridge, MA 02140, USA
| | - Elena E Brevnova
- Novogy, 85 Bolton Street, Cambridge, MA 02140, USA. Total New Energies USA, 5858 Horton Street, Emeryville, CA 94608, USA
| | | | | | | | | | - Gregory Stephanopoulos
- Novogy, 85 Bolton Street, Cambridge, MA 02140, USA. Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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