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Choi JW, Song NE, Hong SP, Rhee YK, Hong HD, Cho CW. Engineering Bacillus subtilis J46 for efficient utilization of galactose through adaptive laboratory evolution. AMB Express 2024; 14:14. [PMID: 38282124 PMCID: PMC10822834 DOI: 10.1186/s13568-024-01666-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 01/08/2024] [Indexed: 01/30/2024] Open
Abstract
Efficient utilization of galactose by microorganisms can lead to the production of valuable bio-products and improved metabolic processes. While Bacillus subtilis has inherent pathways for galactose metabolism, there is potential for enhancement via evolutionary strategies. This study aimed to boost galactose utilization in B. subtilis using adaptive laboratory evolution (ALE) and to elucidate the genetic and metabolic changes underlying the observed enhancements. The strains of B. subtilis underwent multiple rounds of adaptive laboratory evolution (approximately 5000 generations) in an environment that favored the use of galactose. This process resulted in an enhanced specific growth rate of 0.319 ± 0.005 h-1, a significant increase from the 0.03 ± 0.008 h-1 observed in the wild-type strains. Upon selecting the evolved strain BSGA14, a comprehensive whole-genome sequencing revealed the presence of 63 single nucleotide polymorphisms (SNPs). Two of them, located in the coding sequences of the genes araR and glcR, were found to be the advantageous mutations after reverse engineering. The strain with these two accumulated mutations, BSGALE4, exhibited similar specific growth rate on galactose to the evolved strain BSGA14 (0.296 ± 0.01 h-1). Furthermore, evolved strain showed higher productivity of protease and β-galactosidase in mock soybean biomass medium. ALE proved to be a potent tool for enhancing galactose metabolism in B. subtilis. The findings offer valuable insights into the potential of evolutionary strategies in microbial engineering and pave the way for industrial applications harnessing enhanced galactose conversion.
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Affiliation(s)
- Jae Woong Choi
- Research Group of Traditional Food, Korea Food Research Institute, 245, Nongsaengmyeong-ro, Iseo-myeon, Wanju-gun, 55365, Republic of Korea
| | - Nho-Eul Song
- Research Group of Traditional Food, Korea Food Research Institute, 245, Nongsaengmyeong-ro, Iseo-myeon, Wanju-gun, 55365, Republic of Korea
| | - Sang-Pil Hong
- Research Group of Traditional Food, Korea Food Research Institute, 245, Nongsaengmyeong-ro, Iseo-myeon, Wanju-gun, 55365, Republic of Korea
| | - Young Kyoung Rhee
- Research Group of Traditional Food, Korea Food Research Institute, 245, Nongsaengmyeong-ro, Iseo-myeon, Wanju-gun, 55365, Republic of Korea
| | - Hee-Do Hong
- Research Group of Traditional Food, Korea Food Research Institute, 245, Nongsaengmyeong-ro, Iseo-myeon, Wanju-gun, 55365, Republic of Korea
| | - Chang-Won Cho
- Research Group of Traditional Food, Korea Food Research Institute, 245, Nongsaengmyeong-ro, Iseo-myeon, Wanju-gun, 55365, Republic of Korea.
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Koehle AP, Brumwell SL, Seto EP, Lynch AM, Urbaniak C. Microbial applications for sustainable space exploration beyond low Earth orbit. NPJ Microgravity 2023; 9:47. [PMID: 37344487 DOI: 10.1038/s41526-023-00285-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 05/25/2023] [Indexed: 06/23/2023] Open
Abstract
With the construction of the International Space Station, humans have been continuously living and working in space for 22 years. Microbial studies in space and other extreme environments on Earth have shown the ability for bacteria and fungi to adapt and change compared to "normal" conditions. Some of these changes, like biofilm formation, can impact astronaut health and spacecraft integrity in a negative way, while others, such as a propensity for plastic degradation, can promote self-sufficiency and sustainability in space. With the next era of space exploration upon us, which will see crewed missions to the Moon and Mars in the next 10 years, incorporating microbiology research into planning, decision-making, and mission design will be paramount to ensuring success of these long-duration missions. These can include astronaut microbiome studies to protect against infections, immune system dysfunction and bone deterioration, or biological in situ resource utilization (bISRU) studies that incorporate microbes to act as radiation shields, create electricity and establish robust plant habitats for fresh food and recycling of waste. In this review, information will be presented on the beneficial use of microbes in bioregenerative life support systems, their applicability to bISRU, and their capability to be genetically engineered for biotechnological space applications. In addition, we discuss the negative effect microbes and microbial communities may have on long-duration space travel and provide mitigation strategies to reduce their impact. Utilizing the benefits of microbes, while understanding their limitations, will help us explore deeper into space and develop sustainable human habitats on the Moon, Mars and beyond.
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Affiliation(s)
- Allison P Koehle
- Department of Plant Science, Pennsylvania State University, University Park, PA, USA
| | - Stephanie L Brumwell
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON, Canada
| | | | - Anne M Lynch
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA
| | - Camilla Urbaniak
- ZIN Technologies Inc, Middleburg Heights, OH, USA.
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA.
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3
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Averesch NJH, Berliner AJ, Nangle SN, Zezulka S, Vengerova GL, Ho D, Casale CA, Lehner BAE, Snyder JE, Clark KB, Dartnell LR, Criddle CS, Arkin AP. Microbial biomanufacturing for space-exploration-what to take and when to make. Nat Commun 2023; 14:2311. [PMID: 37085475 PMCID: PMC10121718 DOI: 10.1038/s41467-023-37910-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 04/05/2023] [Indexed: 04/23/2023] Open
Abstract
As renewed interest in human space-exploration intensifies, a coherent and modernized strategy for mission design and planning has become increasingly crucial. Biotechnology has emerged as a promising approach to increase resilience, flexibility, and efficiency of missions, by virtue of its ability to effectively utilize in situ resources and reclaim resources from waste streams. Here we outline four primary mission-classes on Moon and Mars that drive a staged and accretive biomanufacturing strategy. Each class requires a unique approach to integrate biomanufacturing into the existing mission-architecture and so faces unique challenges in technology development. These challenges stem directly from the resources available in a given mission-class-the degree to which feedstocks are derived from cargo and in situ resources-and the degree to which loop-closure is necessary. As mission duration and distance from Earth increase, the benefits of specialized, sustainable biomanufacturing processes also increase. Consequentially, we define specific design-scenarios and quantify the usefulness of in-space biomanufacturing, to guide techno-economics of space-missions. Especially materials emerged as a potentially pivotal target for biomanufacturing with large impact on up-mass cost. Subsequently, we outline the processes needed for development, testing, and deployment of requisite technologies. As space-related technology development often does, these advancements are likely to have profound implications for the creation of a resilient circular bioeconomy on Earth.
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Affiliation(s)
- Nils J H Averesch
- Center for the Utilization of Biological Engineering in Space (CUBES), Berkeley, CA, USA.
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA.
| | - Aaron J Berliner
- Center for the Utilization of Biological Engineering in Space (CUBES), Berkeley, CA, USA.
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA.
| | - Shannon N Nangle
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.
- Circe Bioscience Inc., Somerville, MA, USA.
| | - Spencer Zezulka
- Center for the Utilization of Biological Engineering in Space (CUBES), Berkeley, CA, USA
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
- School of Information, University of California Berkeley, Berkeley, CA, USA
| | - Gretchen L Vengerova
- Center for the Utilization of Biological Engineering in Space (CUBES), Berkeley, CA, USA
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
| | - Davian Ho
- Center for the Utilization of Biological Engineering in Space (CUBES), Berkeley, CA, USA
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
| | - Cameran A Casale
- Center for the Utilization of Biological Engineering in Space (CUBES), Berkeley, CA, USA
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
| | - Benjamin A E Lehner
- Department of Bionanoscience, Delft University of Technology, Delft, South Holland, Netherlands
| | | | - Kevin B Clark
- Cures Within Reach, Chicago, IL, USA
- Champions Program, eXtreme Science and Engineering Discovery Environment (XSEDE), Urbana, IL, USA
| | - Lewis R Dartnell
- Department of Life Sciences, University of Westminster, London, UK
| | - Craig S Criddle
- Center for the Utilization of Biological Engineering in Space (CUBES), Berkeley, CA, USA
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - Adam P Arkin
- Center for the Utilization of Biological Engineering in Space (CUBES), Berkeley, CA, USA
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
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Sun Y, Kokko M, Vassilev I. Anode-assisted electro-fermentation with Bacillus subtilis under oxygen-limited conditions. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:6. [PMID: 36627716 PMCID: PMC9832610 DOI: 10.1186/s13068-022-02253-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 12/20/2022] [Indexed: 01/12/2023]
Abstract
BACKGROUND Bacillus subtilis is generally regarded as a ubiquitous facultative anaerobe. Oxygen is the major electron acceptor of B. subtilis, and when oxygen is absent, B. subtilis can donate electrons to nitrate or perform fermentation. An anode electrode can also be used by microorganisms as the electron sink in systems called anodic electro-fermentation. The facultative anaerobic character of B. subtilis makes it an excellent candidate to explore with different electron acceptors, such as an anode. This study aimed to optimise industrial aerobic bioprocesses using alternative electron acceptors. In particular, different end product spectrum of B. subtilis with various electron acceptors, including anode from the electro-fermentation system, was investigated. RESULTS B. subtilis was grown using three electron acceptors, i.e. oxygen, nitrate and anode (poised at a potential of 0.7 V vs. standard hydrogen electrode). The results showed oxygen had a crucial role for cells to remain metabolically active. When nitrate or anode was applied as the sole electron acceptor anaerobically, immediate cell lysis and limited glucose consumption were observed. In anode-assisted electro-fermentation with a limited aeration rate, acetoin, as the main end product showed the highest yield of 0.78 ± 0.04 molproduct/molglucose, two-fold higher than without poised potential (0.39 ± 0.08 molproduct/molglucose). CONCLUSIONS Oxygen controls B. subtilis biomass growth, alternative electron acceptors utilisation and metabolites formation. Limited oxygen/air supply enabled the bacteria to donate excess electrons to nitrate or anode, leading to steered product spectrum. The anode-assisted electro-fermentation showed its potential to boost acetoin production for future industrial biotechnology applications.
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Affiliation(s)
- Yu Sun
- grid.502801.e0000 0001 2314 6254Faculty of Engineering and Natural Sciences, Tampere University, Korkeakoulunkatu 8, 33720 Tampere, Finland
| | - Marika Kokko
- grid.502801.e0000 0001 2314 6254Faculty of Engineering and Natural Sciences, Tampere University, Korkeakoulunkatu 8, 33720 Tampere, Finland
| | - Igor Vassilev
- grid.502801.e0000 0001 2314 6254Faculty of Engineering and Natural Sciences, Tampere University, Korkeakoulunkatu 8, 33720 Tampere, Finland
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Aliivibrio fischeri L-Asparaginase production by engineered Bacillus subtilis: a potential new biopharmaceutical. Bioprocess Biosyst Eng 2022; 45:1635-1644. [PMID: 35974197 DOI: 10.1007/s00449-022-02769-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/04/2022] [Indexed: 11/02/2022]
Abstract
L-Asparaginase (L-ASNase) is an enzyme applied in the treatment of lymphoid malignancies. However, an innovative L-ASNase with high yield and lower side effects than the commercially available preparations are still a market requirement. Here, a new-engineered Bacillus subtilis strain was evaluated for Aliivibrio fischeri L-ASNase II production, being the bioprocess development and the enzyme characterization studied. The pBS0E plasmid replicative in Bacillus sp and containing PxylA promoter inducible by xylose and its repressive molecule sequence (XylR) was used for the genetic modification. Initially, cultivations were carried out in orbital shaker, and then the process was scaled up to stirred tank bioreactor (STB). After the bioprocess, the cells were recovered and submitted to ultrasound sonication for cells disruption and intracellular enzyme recovery. The enzymatic extract was characterized to assess its biochemical, kinetic and thermal properties using L-Asparagine and L-Glutamine as substrates. The results indicated the potential enzyme production in STB achieving L-ASNase activity up to 1.539 U mL-1. The enzymatic extract showed an optimum pH of 7.5, high L-Asparagine affinity (Km = 1.2275 mmol L-1) and low L-Glutaminase activity (0.568-0.738 U mL-1). In addition, thermal inactivation was analyzed by two different Kinect models to elucidate inactivation mechanisms, low kinetic thermal inactivation constants for 25 ºC and 37 ºC (0.128 and 0.148 h-1, respectively) indicate an elevated stability. The findings herein show that the produced recombinant L-ASNase has potential to be applied for pharmaceutical purposes.
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6
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Averesch NJH, Shunk GK, Kern C. Cultivation of the Dematiaceous Fungus Cladosporium sphaerospermum Aboard the International Space Station and Effects of Ionizing Radiation. Front Microbiol 2022; 13:877625. [PMID: 35865919 PMCID: PMC9294542 DOI: 10.3389/fmicb.2022.877625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/17/2022] [Indexed: 12/03/2022] Open
Abstract
In Space, cosmic radiation is a strong, ubiquitous form of energy with constant flux, and the ability to harness it could greatly enhance the energy-autonomy of expeditions across the solar system. At the same time, radiation is the greatest permanent health risk for humans venturing into deep space. To protect astronauts beyond Earth's magnetosphere, advanced shielding against ionizing as well as non-ionizing radiation is highly sought after. In search of innovative solutions to these challenges, biotechnology appeals with suitability for in situ resource utilization (ISRU), self-regeneration, and adaptability. Where other organisms fail, certain microscopic fungi thrive in high-radiation environments on Earth, showing high radioresistance. The adaptation of some of these molds to areas, such as the Chernobyl Exclusion Zone has coined the terms positive "radiotropism" and "radiotrophy", reflecting the affinity to and stimulation by radiation, and sometimes even enhanced growth under ionizing conditions. These abilities may be mediated by the pigment melanin, many forms of which also have radioprotective properties. The expectation is that these capabilities are extendable to radiation in space. To study its growth in space, an experiment cultivating Cladosporium sphaerospermum Penzig ATCC® 11289™ aboard the International Space Station (ISS) was conducted while monitoring radiation beneath the formed biomass in comparison to a no-growth negative control. A qualitative growth advantage in space was observable. Quantitatively, a 1.21 ± 0.37-times higher growth rate than in the ground control was determined, which might indicate a radioadaptive response to space radiation. In addition, a reduction in radiation compared to the negative control was discernable, which is potentially attributable to the fungal biomass.
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Affiliation(s)
- Nils J. H. Averesch
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, United States
- Center for the Utilization of Biological Engineering in Space, Berkeley, CA, United States
| | - Graham K. Shunk
- Physics Department, North Carolina School of Science and Mathematics, Durham, NC, United States
- Higher Orbits “Go for Launch!” Program, Leesburg, VA, United States
| | - Christoph Kern
- Department of Statistics, Ludwig Maximilian University of Munich, Munich, Germany
- School of Social Sciences, University of Mannheim, Mannheim, Germany
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7
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Absence of increased genomic variants in the cyanobacterium Chroococcidiopsis exposed to Mars-like conditions outside the space station. Sci Rep 2022; 12:8437. [PMID: 35589950 PMCID: PMC9120168 DOI: 10.1038/s41598-022-12631-5] [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: 01/08/2022] [Accepted: 05/06/2022] [Indexed: 11/08/2022] Open
Abstract
Despite the increasing interest in using microbial-based technologies to support human space exploration, many unknowns remain not only on bioprocesses but also on microbial survivability and genetic stability under non-Earth conditions. Here the desert cyanobacterium Chroococcidiopsis sp. CCMEE 029 was investigated for robustness of the repair capability of DNA lesions accumulated under Mars-like conditions (UV radiation and atmosphere) simulated in low Earth orbit using the EXPOSE-R2 facility installed outside the International Space Station. Genomic alterations were determined in a space-derivate of Chroococcidiopsis sp. CCMEE 029 obtained upon reactivation on Earth of the space-exposed cells. Comparative analysis of whole-genome sequences showed no increased variant numbers in the space-derivate compared to triplicates of the reference strain maintained on the ground. This result advanced cyanobacteria-based technologies to support human space exploration.
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8
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Yang H, Yang J, Liu C, Lv X, Liu L, Li J, Du G, Chen J, Liu Y. High-Level 5-Methyltetrahydrofolate Bioproduction in Bacillus subtilis by Combining Modular Engineering and Transcriptomics-Guided Global Metabolic Regulation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:5849-5859. [PMID: 35521920 DOI: 10.1021/acs.jafc.2c01252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
5-Methyltetrahydrofolate (5-MTHF) is the predominant folate form in human plasma, which has been widely used as a nutraceutical. However, the microbial synthesis of 5-MTHF is currently inefficient, limiting green and sustainable 5-MTHF production. In this study, the Generally Regarded As Safe (GRAS) microorganism Bacillus subtilis was engineered as the 5-MTHF production host. Three precursor supply modules were first optimized by modular engineering for strengthening the supply of guanosine-5-triphosphate (GTP) and p-aminobenzoic acid (pABA). Next, the impact of genome-wide gene expression on 5-MTHF biosynthesis was evaluated using transcriptome analyses, which identified key genes for 5-MTHF production. The effects of potential genes on 5-MTHF synthesis were verified by observing the genes' up-regulated by strong promoter P566 and those down-regulated by inhibition through the clustered regularly interspaced short palindromic repeat interference (CRISPRi). Finally, a key gene for improved 5-MTHF biosynthesis, comGC, was integrated into the genome of modular engineered strain B89 for its overexpression and facilitating efficient 5-MTHF synthesis, reaching 3.41 ± 0.10 mg/L with a productivity of 0.21 mg/L/h, which was the highest level achieved by microbial synthesis. The engineered 5-MTHF-producing B. subtilis developed in this work lays the foundation of further enhancing 5-MTHF production by microbial fermentation, which can be used for isolation and purification of 5-MTHF as food and nutraceutical ingredients.
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Affiliation(s)
- Han Yang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jinning Yang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Cheng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jian Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
- Qingdao Special Food Research Institute, Qingdao 266109, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
- Qingdao Special Food Research Institute, Qingdao 266109, China
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Pierrel F, Burgardt A, Lee JH, Pelosi L, Wendisch VF. Recent advances in the metabolic pathways and microbial production of coenzyme Q. World J Microbiol Biotechnol 2022; 38:58. [PMID: 35178585 PMCID: PMC8854274 DOI: 10.1007/s11274-022-03242-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/30/2022] [Indexed: 12/13/2022]
Abstract
Coenzyme Q (CoQ) serves as an electron carrier in aerobic respiration and has become an interesting target for biotechnological production due to its antioxidative effect and benefits in supplementation to patients with various diseases. Here, we review discovery of the pathway with a particular focus on its superstructuration and regulation, and we summarize the metabolic engineering strategies for overproduction of CoQ by microorganisms. Studies in model microorganisms elucidated the details of CoQ biosynthesis and revealed the existence of multiprotein complexes composed of several enzymes that catalyze consecutive reactions in the CoQ pathways of Saccharomyces cerevisiae and Escherichia coli. Recent findings indicate that the identity and the total number of proteins involved in CoQ biosynthesis vary between species, which raises interesting questions about the evolution of the pathway and could provide opportunities for easier engineering of CoQ production. For the biotechnological production, so far only microorganisms have been used that naturally synthesize CoQ10 or a related CoQ species. CoQ biosynthesis requires the aromatic precursor 4-hydroxybenzoic acid and the prenyl side chain that defines the CoQ species. Up to now, metabolic engineering strategies concentrated on the overproduction of the prenyl side chain as well as fine-tuning the expression of ubi genes from the ubiquinone modification pathway, resulting in high CoQ yields. With expanding knowledge about CoQ biosynthesis and exploration of new strategies for strain engineering, microbial CoQ production is expected to improve.
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Affiliation(s)
- Fabien Pierrel
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000, Grenoble, France.
| | - Arthur Burgardt
- Genetics of Prokaryotes, Faculty of Biology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Jin-Ho Lee
- Department of Food Science & Biotechnology, Kyungsung University, Busan, South Korea
| | - Ludovic Pelosi
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000, Grenoble, France
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany.
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10
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Design and construction of an artificial pathway for biosynthesis of acetaminophen in Escherichia coli. Metab Eng 2021; 68:26-33. [PMID: 34487838 DOI: 10.1016/j.ymben.2021.09.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/17/2021] [Accepted: 09/01/2021] [Indexed: 11/23/2022]
Abstract
Acetaminophen (AAP) is one of the most commonly used drug ingredients that possesses antipyretic and analgesic effects. As an unnatural chemical, AAP is commercially produced by chemical processes using petroleum-derived carbohydrates, such as phenol, as raw materials, which is unsustainable and eco-unfriendly. In this study, we report design and construction of an artificial biosynthetic pathway for de novo production of AAP from simple carbon source. By exploring and expanding the substrate repertoire of natural enzymes, we identified and characterized a novel p-aminobenzoic acid (p-ABA) monooxygenase and an p-aminophenol (p-AP) N-acetyltransferase, which enabled the bacterial production of AAP from p-ABA. Then, we constructed an p-ABA over-producer by screening of p-ABA synthases and enhancing glutamine availability, resulting in 836.43 mg/L p-ABA in shake flasks in E. coli. Subsequent assembly of the entire biosynthetic pathway permitted the de novo production of AAP from glycerol for the first time. Finally, pathway engineering by dynamically regulating the expression of pathway genes via a temperature-inducible controller enabled production enhancement of AAP with a titer of 120.03 mg/L. This work not only constructs a microbial platform for AAP production, but also demonstrates design and construction of artificial biosynthetic pathways via discovering novel bioreactions based on existing enzymes.
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11
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Díaz-Rullo J, Rodríguez-Valdecantos G, Torres-Rojas F, Cid L, Vargas IT, González B, González-Pastor JE. Mining for Perchlorate Resistance Genes in Microorganisms From Sediments of a Hypersaline Pond in Atacama Desert, Chile. Front Microbiol 2021; 12:723874. [PMID: 34367123 PMCID: PMC8343002 DOI: 10.3389/fmicb.2021.723874] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 06/18/2021] [Indexed: 11/15/2022] Open
Abstract
Perchlorate is an oxidative pollutant toxic to most of terrestrial life by promoting denaturation of macromolecules, oxidative stress, and DNA damage. However, several microorganisms, especially hyperhalophiles, are able to tolerate high levels of this compound. Furthermore, relatively high quantities of perchlorate salts were detected on the Martian surface, and due to its strong hygroscopicity and its ability to substantially decrease the freezing point of water, perchlorate is thought to increase the availability of liquid brine water in hyper-arid and cold environments, such as the Martian regolith. Therefore, perchlorate has been proposed as a compound worth studying to better understanding the habitability of the Martian surface. In the present work, to study the molecular mechanisms of perchlorate resistance, a functional metagenomic approach was used, and for that, a small-insert library was constructed with DNA isolated from microorganisms exposed to perchlorate in sediments of a hypersaline pond in the Atacama Desert, Chile (Salar de Maricunga), one of the regions with the highest levels of perchlorate on Earth. The metagenomic library was hosted in Escherichia coli DH10B strain and exposed to sodium perchlorate. This technique allowed the identification of nine perchlorate-resistant clones and their environmental DNA fragments were sequenced. A total of seventeen ORFs were predicted, individually cloned, and nine of them increased perchlorate resistance when expressed in E. coli DH10B cells. These genes encoded hypothetical conserved proteins of unknown functions and proteins similar to other not previously reported to be involved in perchlorate resistance that were related to different cellular processes such as RNA processing, tRNA modification, DNA protection and repair, metabolism, and protein degradation. Furthermore, these genes also conferred resistance to UV-radiation, 4-nitroquinoline-N-oxide (4-NQO) and/or hydrogen peroxide (H2O2), other stress conditions that induce oxidative stress, and damage in proteins and nucleic acids. Therefore, the novel genes identified will help us to better understand the molecular strategies of microorganisms to survive in the presence of perchlorate and may be used in Mars exploration for creating perchlorate-resistance strains interesting for developing Bioregenerative Life Support Systems (BLSS) based on in situ resource utilization (ISRU).
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Affiliation(s)
- Jorge Díaz-Rullo
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
- Polytechnic School, University of Alcalá, Alcalá de Henares, Spain
| | - Gustavo Rodríguez-Valdecantos
- Faculty of Engineering and Sciences, Universidad Adolfo Ibáñez, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Faculty of Biological Sciences, Pontifical Catholic University of Chile, Santiago, Chile
| | - Felipe Torres-Rojas
- Department of Hydraulic and Environmental Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Luis Cid
- Faculty of Engineering and Sciences, Universidad Adolfo Ibáñez, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Faculty of Biological Sciences, Pontifical Catholic University of Chile, Santiago, Chile
| | - Ignacio T. Vargas
- Department of Hydraulic and Environmental Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
- Centro de Desarrollo Urbano Sustentable (CEDEUS), Santiago, Chile
| | - Bernardo González
- Faculty of Engineering and Sciences, Universidad Adolfo Ibáñez, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Faculty of Biological Sciences, Pontifical Catholic University of Chile, Santiago, Chile
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12
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Production of proteins and commodity chemicals using engineered Bacillus subtilis platform strain. Essays Biochem 2021; 65:173-185. [PMID: 34028523 DOI: 10.1042/ebc20210011] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 05/02/2021] [Accepted: 05/06/2021] [Indexed: 12/19/2022]
Abstract
Currently, increasing demand of biochemicals produced from renewable resources has motivated researchers to seek microbial production strategies instead of traditional chemical methods. As a microbial platform, Bacillus subtilis possesses many advantages including the generally recognized safe status, clear metabolic networks, short growth cycle, mature genetic editing methods and efficient protein secretion systems. Engineered B. subtilis strains are being increasingly used in laboratory research and in industry for the production of valuable proteins and other chemicals. In this review, we first describe the recent advances of bioinformatics strategies during the research and applications of B. subtilis. Secondly, the applications of B. subtilis in enzymes and recombinant proteins production are summarized. Further, the recent progress in employing metabolic engineering and synthetic biology strategies in B. subtilis platform strain to produce commodity chemicals is systematically introduced and compared. Finally, the major limitations for the further development of B. subtilis platform strain and possible future directions for its research are also discussed.
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13
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Vassilev I, Averesch NJH, Ledezma P, Kokko M. Anodic electro-fermentation: Empowering anaerobic production processes via anodic respiration. Biotechnol Adv 2021; 48:107728. [PMID: 33705913 DOI: 10.1016/j.biotechadv.2021.107728] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 01/31/2021] [Accepted: 03/03/2021] [Indexed: 11/24/2022]
Abstract
In nature as well as in industrial microbiology, all microorganisms need to achieve redox balance. Their redox state and energy conservation highly depend on the availability of a terminal electron acceptor, for example oxygen in aerobic production processes. Under anaerobic conditions in the absence of an electron acceptor, redox balance is achieved via the production of reduced carbon-compounds (fermentation). An alternative strategy to artificially stabilize microbial redox and energy state is the use of anodic electro-fermentation (AEF). This emerging biotechnology empowers respiration under anaerobic conditions using the anode of a bioelectrochemical system as an undepletable terminal electron acceptor. Electrochemical control of redox metabolism and energy conservation via AEF can steer the carbon metabolism towards a product of interest and avoid the need for continuous and cost-inefficient supply of oxygen as well as the production of mixed reduced by-products, as is the case in aerobic production and fermentation processes, respectively. The great challenge for AEF is to establish efficient extracellular electron transfer (EET) from the microbe to the anode and link it to central carbon metabolism to enhance the synthesis of a target product. This article reviews the advantages and challenges of AEF, EET mechanisms, microbial energy gain, and discusses the rational choice of substrate-product couple as well as the choice of microbial catalyst. Besides, it discusses the potential of the industrial model-organism Bacillus subtilis as a promising candidate for AEF, which has not been yet considered for such an application. This prospective review contributes to a better understanding of how industrial microbiology can benefit from AEF and analyses key-factors required to successfully implement AEF processes. Overall, this work aims to advance the young research field especially by critically revisiting the fundamental aspects of AEF.
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Affiliation(s)
- Igor Vassilev
- Faculty of Engineering and Natural Sciences, Tampere University, Tampere, Finland.
| | - Nils J H Averesch
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, United States.
| | - Pablo Ledezma
- Advanced Water Management Centre, The University of Queensland, Brisbane, QLD, Australia.
| | - Marika Kokko
- Faculty of Engineering and Natural Sciences, Tampere University, Tampere, Finland.
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14
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Engineering Bacillus subtilis Cells as Factories: Enzyme Secretion and Value-added Chemical Production. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-020-0104-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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15
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Xiang M, Kang Q, Zhang D. Advances on systems metabolic engineering of Bacillus subtilis as a chassis cell. Synth Syst Biotechnol 2020; 5:245-251. [PMID: 32775709 PMCID: PMC7394859 DOI: 10.1016/j.synbio.2020.07.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 07/22/2020] [Accepted: 07/23/2020] [Indexed: 12/15/2022] Open
Abstract
The Gram-positive model bacterium Bacillus subtilis, has been broadly applied in various fields because of its low pathogenicity and strong protein secretion ability, as well as its well-developed fermentation technology. B. subtilis is considered as an attractive host in the field of metabolic engineering, in particular for protein expression and secretion, so it has been well studied and applied in genetic engineering. In this review, we discussed why B. subtilis is a good chassis cell for metabolic engineering. We also summarized the latest research progress in systematic biology, synthetic biology and evolution-based engineering of B. subtilis, and showed systemic metabolic engineering expedite the harnessing B. subtilis for bioproduction.
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Affiliation(s)
- Mengjie Xiang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Qian Kang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
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16
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Common problems associated with the microbial productions of aromatic compounds and corresponding metabolic engineering strategies. Biotechnol Adv 2020; 41:107548. [DOI: 10.1016/j.biotechadv.2020.107548] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 04/06/2020] [Accepted: 04/08/2020] [Indexed: 01/06/2023]
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17
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Shin SK, Ko YJ, Hyeon JE, Han SO. Studies of advanced lignin valorization based on various types of lignolytic enzymes and microbes. BIORESOURCE TECHNOLOGY 2019; 289:121728. [PMID: 31277889 DOI: 10.1016/j.biortech.2019.121728] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 06/26/2019] [Accepted: 06/28/2019] [Indexed: 06/09/2023]
Abstract
Lignin is a robust material that is considered useless because it has an inhibitory effect on microbes and acts as a physical barrier for cellulose degradation. Therefore, it has been removed from cellulosic biomass to produce high-value materials. However, lignin monomers can be converted to value-added chemicals such as biodegradable plastics and food additives by appropriately engineered microbes. Lignin degradation through peroxidase, laccase and other proteins with auxiliary activity is the first step in lignin valorization. Metabolic engineering of microorganisms for increased tolerance and production yield is the second step for lignin valorization. Here, this review offers a summary of current biotechnologies using various enzymatic activities, synergistic enzyme mixtures and metabolic engineering for lignin valorization in biorefinery.
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Affiliation(s)
- Sang Kyu Shin
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Young Jin Ko
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Jeong Eun Hyeon
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea; Department of Food Science and Biotechnology, College of Knowledge-Based Services Engineering, Sungshin Women's University, Seoul 01133, Republic of Korea; Department of Food and Nutrition, College of Health & Wellness, Sungshin Women's University, Seoul 01133, Republic of Korea
| | - Sung Ok Han
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea.
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18
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Averesch NJH, Rothschild LJ. Metabolic engineering of Bacillus subtilis for production of para-aminobenzoic acid - unexpected importance of carbon source is an advantage for space application. Microb Biotechnol 2019; 12:703-714. [PMID: 30980511 PMCID: PMC6559200 DOI: 10.1111/1751-7915.13403] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 03/08/2019] [Accepted: 03/08/2019] [Indexed: 01/28/2023] Open
Abstract
High-strength polymers, such as aramid fibres, are important materials in space technology. To obtain these materials in remote locations, such as Mars, biological production is of interest. The aromatic polymer precursor para-aminobenzoic acid (pABA) can be derived from the shikimate pathway through metabolic engineering of Bacillus subtilis, an organism suited for space synthetic biology. Our engineering strategy included repair of the defective indole-3-glycerol phosphate synthase (trpC), knockout of one chorismate mutase isozyme (aroH) and overexpression of the aminodeoxychorismate synthase (pabAB) and aminodeoxychorismate lyase (pabC) from the bacteria Corynebacterium callunae and Xenorhabdus bovienii respectively. Further, a fusion-protein enzyme (pabABC) was created for channelling of the carbon flux. Using adaptive evolution, mutants of the production strain, able to metabolize xylose, were created, to explore and compare pABA production capacity from different carbon sources. Rather than the efficiency of the substrate or performance of the biochemical pathway, the product toxicity, which was strongly dependent on the pH, appeared to be the overall limiting factor. The highest titre achieved in shake flasks was 3.22 g l-1 with a carbon yield of 12.4% [C-mol/C-mol] from an amino sugar. This promises suitability of the system for in situ resource utilization (ISRU) in space biotechnology, where feedstocks that can be derived from cyanobacterial cell lysate play a role.
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Affiliation(s)
- Nils J. H. Averesch
- Universities Space Research AssociationMountain ViewCA94043USA
- NASA Ames Research CenterMoffett FieldCA94035USA
- Present address:
Stanford UniversityStanfordCA94305USA
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