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Ding Q, Liu L. Reprogramming cellular metabolism to increase the efficiency of microbial cell factories. Crit Rev Biotechnol 2024; 44:892-909. [PMID: 37380349 DOI: 10.1080/07388551.2023.2208286] [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: 11/17/2022] [Accepted: 04/11/2023] [Indexed: 06/30/2023]
Abstract
Recent studies are increasingly focusing on advanced biotechnological tools, self-adjusting smart microorganisms, and artificial intelligent networks, to engineer microorganisms with various functions. Microbial cell factories are a vital platform for improving the bioproduction of medicines, biofuels, and biomaterials from renewable carbon sources. However, these processes are significantly affected by cellular metabolism, and boosting the efficiency of microbial cell factories remains a challenge. In this review, we present a strategy for reprogramming cellular metabolism to enhance the efficiency of microbial cell factories for chemical biosynthesis, which improves our understanding of microbial physiology and metabolic control. Current methods are mainly focused on synthetic pathways, metabolic resources, and cell performance. This review highlights the potential biotechnological strategy to reprogram cellular metabolism and provide novel guidance for designing more intelligent industrial microbes with broader applications in this growing field.
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Affiliation(s)
- Qiang Ding
- School of Life Sciences, Anhui University, Hefei, China
- Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
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2
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Zhang Y, Meng W, He Y, Chen Y, Shao M, Yuan J. Multidimensional optimization for accelerating light-powered biocatalysis in Rhodopseudomonas palustris. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:160. [PMID: 37891652 PMCID: PMC10612212 DOI: 10.1186/s13068-023-02410-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023]
Abstract
BACKGROUND Whole-cell biocatalysis has been exploited to convert a variety of substrates into high-value bulk or chiral fine chemicals. However, the traditional whole-cell biocatalysis typically utilizes the heterotrophic microbes as the biocatalyst, which requires carbohydrates to power the cofactor (ATP, NAD (P)H) regeneration. RESULTS In this study, we sought to harness purple non-sulfur photosynthetic bacterium (PNSB) as the biocatalyst to achieve light-driven cofactor regeneration for cascade biocatalysis. We substantially improved the performance of Rhodopseudomonas palustris-based biocatalysis using a highly active and conditional expression system, blocking the side-reactions, controlling the feeding strategy, and attenuating the light shading effect. Under light-anaerobic conditions, we found that 50 mM ferulic acid could be completely converted to vanillyl alcohol using the recombinant strain with 100% efficiency, and > 99.9% conversion of 50 mM p-coumaric acid to p-hydroxybenzyl alcohol was similarly achieved. Moreover, we examined the isoprenol utilization pathway for pinene synthesis and 92% conversion of 30 mM isoprenol to pinene was obtained. CONCLUSIONS Taken together, these results suggested that R. palustris could be a promising host for light-powered biotransformation, which offers an efficient approach for synthesizing value-added chemicals in a green and sustainable manner.
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Affiliation(s)
- Yang Zhang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, 361102, China
- Shenzhen Research Institute of Xiamen University, Shenzhen, 518057, China
| | - Wenchang Meng
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, 361102, China
| | - Yuting He
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, 361102, China
| | - Yuhui Chen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, 361102, China
| | - Mingyu Shao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, 361102, China
| | - Jifeng Yuan
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, 361102, China.
- Shenzhen Research Institute of Xiamen University, Shenzhen, 518057, China.
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3
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Mengele AK, Weixler D, Amthor S, Eikmanns BJ, Seibold GM, Rau S. Transforming Escherichia coli Proteomembranes into Artificial Chloroplasts Using Molecular Photocatalysis. Angew Chem Int Ed Engl 2022; 61:e202114842. [PMID: 34932847 PMCID: PMC9306768 DOI: 10.1002/anie.202114842] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Indexed: 12/01/2022]
Abstract
During the light-dependent reaction of photosynthesis, green plants couple photoinduced cascades of redox reactions with transmembrane proton translocations to generate reducing equivalents and chemical energy in the form of NADPH (nicotinamide adenine dinucleotide phosphate) and ATP (adenosine triphosphate), respectively. We mimic these basic processes by combining molecular ruthenium polypyridine-based photocatalysts and inverted vesicles derived from Escherichia coli. Upon irradiation with visible light, the interplay of photocatalytic nicotinamide reduction and enzymatic membrane-located respiration leads to the simultaneous formation of two biologically active cofactors, NADH (nicotinamide adenine dinucleotide) and ATP, respectively. This inorganic-biologic hybrid system thus emulates the cofactor delivering function of an active chloroplast.
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Affiliation(s)
- Alexander K. Mengele
- Institute of Inorganic Chemistry IMaterials and CatalysisUlm UniversityAlbert-Einstein-Allee 1189081UlmGermany
| | - Dominik Weixler
- Institute of Microbiology and BiotechnologyUlm UniversityAlbert-Einstein-Allee 1189081UlmGermany
| | - Sebastian Amthor
- Institute of Inorganic Chemistry IMaterials and CatalysisUlm UniversityAlbert-Einstein-Allee 1189081UlmGermany
| | - Bernhard J. Eikmanns
- Institute of Microbiology and BiotechnologyUlm UniversityAlbert-Einstein-Allee 1189081UlmGermany
| | - Gerd M. Seibold
- Institute of Microbiology and BiotechnologyUlm UniversityAlbert-Einstein-Allee 1189081UlmGermany
- Section of Synthetic BiologyDepartment of Biotechnology and BioengineeringTechnical University of DenmarkSøltoftsplads2800Kongens LyngbyDenmark
| | - Sven Rau
- Institute of Inorganic Chemistry IMaterials and CatalysisUlm UniversityAlbert-Einstein-Allee 1189081UlmGermany
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Production of Vitamin K by Wild-Type and Engineered Microorganisms. Microorganisms 2022; 10:microorganisms10030554. [PMID: 35336129 PMCID: PMC8954062 DOI: 10.3390/microorganisms10030554] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/23/2022] [Accepted: 03/01/2022] [Indexed: 12/14/2022] Open
Abstract
Vitamin K is a fat-soluble vitamin that mainly exists as phylloquinone or menaquinone in nature. Vitamin K plays an important role in blood clotting and bone health in humans. For use as a nutraceutical, vitamin K is produced by natural extraction, chemical synthesis, and microbial fermentation. Natural extraction and chemical synthesis methods for vitamin K production have limitations, such as low yield of products and environmental concerns. Microbial fermentation is a more sustainable process for industrial production of natural vitamin K than two other methods. Recent advanced genetic technology facilitates industrial production of vitamin K by increasing the yield and productivity of microbial host strains. This review covers (i) general information about vitamin K and microbial host, (ii) current titers of vitamin K produced by wild-type microorganisms, and (iii) vitamin K production by engineered microorganisms, including the details of strain engineering strategies. Finally, current limitations and future directions for microbial production of vitamin K are also discussed.
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Mengele AK, Weixler D, Amthor S, Eikmanns BJ, Seibold GM, Rau S. Transforming
Escherichia coli
Proteomembranes into Artificial Chloroplasts Using Molecular Photocatalysis. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202114842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Alexander K. Mengele
- Institute of Inorganic Chemistry I Materials and Catalysis Ulm University Albert-Einstein-Allee 11 89081 Ulm Germany
| | - Dominik Weixler
- Institute of Microbiology and Biotechnology Ulm University Albert-Einstein-Allee 11 89081 Ulm Germany
| | - Sebastian Amthor
- Institute of Inorganic Chemistry I Materials and Catalysis Ulm University Albert-Einstein-Allee 11 89081 Ulm Germany
| | - Bernhard J. Eikmanns
- Institute of Microbiology and Biotechnology Ulm University Albert-Einstein-Allee 11 89081 Ulm Germany
| | - Gerd M. Seibold
- Institute of Microbiology and Biotechnology Ulm University Albert-Einstein-Allee 11 89081 Ulm Germany
- Section of Synthetic Biology Department of Biotechnology and Bioengineering Technical University of Denmark Søltoftsplads 2800 Kongens Lyngby Denmark
| | - Sven Rau
- Institute of Inorganic Chemistry I Materials and Catalysis Ulm University Albert-Einstein-Allee 11 89081 Ulm Germany
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Genome Mining Reveals Two Missing CrtP and AldH Enzymes in the C30 Carotenoid Biosynthesis Pathway in Planococcus faecalis AJ003 T. Molecules 2020; 25:molecules25245892. [PMID: 33322786 PMCID: PMC7764019 DOI: 10.3390/molecules25245892] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/02/2020] [Accepted: 12/10/2020] [Indexed: 11/19/2022] Open
Abstract
Planococcus faecalis AJ003T produces glycosyl-4,4′-diaponeurosporen-4′-ol-4-oic acid as its main carotenoid. Five carotenoid pathway genes were presumed to be present in the genome of P. faecalis AJ003T; however, 4,4-diaponeurosporene oxidase (CrtP) was non-functional, and a gene encoding aldehyde dehydrogenase (AldH) was not identified. In the present study, a genome mining approach identified two missing enzymes, CrtP2 and AldH2454, in the glycosyl-4,4′-diaponeurosporen-4′-ol-4-oic acid biosynthetic pathway. Moreover, CrtP2 and AldH enzymes were functional in heterologous Escherichia coli and generated two carotenoid aldehydes (4,4′-diapolycopene-dial and 4,4′-diaponeurosporene-4-al) and two carotenoid carboxylic acids (4,4′-diaponeurosporenoic acid and 4,4′-diapolycopenoic acid). Furthermore, the genes encoding CrtP2 and AldH2454 were located at a distance the carotenoid gene cluster of P. faecalis.
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Abstract
The utilization of light energy to power organic-chemical transformations is a fundamental strategy of the terrestrial energy cycle. Inspired by the elegance of natural photosynthesis, much interdisciplinary research effort has been devoted to the construction of simplified cell mimics based on artificial vesicles to provide a novel tool for biocatalytic cascade reactions with energy-demanding steps. By inserting natural or even artificial photosynthetic systems into liposomes or polymersomes, the light-driven proton translocation and the resulting formation of electrochemical gradients have become possible. This is the basis for the conversion of photonic into chemical energy in form of energy-rich molecules such as adenosine triphosphate (ATP), which can be further utilized by energy-dependent biocatalytic reactions, e.g. carbon fixation. This review compares liposomes and polymersomes as artificial compartments and summarizes the types of light-driven proton pumps that have been employed in artificial photosynthesis so far. We give an overview over the methods affecting the orientation of the photosystems within the membranes to ensure a unidirectional transport of molecules and highlight recent examples of light-driven biocatalysis in artificial vesicles. Finally, we summarize the current achievements and discuss the next steps needed for the transition of this technology from the proof-of-concept status to preparative applications.
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Dann M, Leister D. Enhancing (crop) plant photosynthesis by introducing novel genetic diversity. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0380. [PMID: 28808099 DOI: 10.1098/rstb.2016.0380] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2017] [Indexed: 12/22/2022] Open
Abstract
Although some elements of the photosynthetic light reactions might appear to be ideal, the overall efficiency of light conversion to biomass has not been optimized during evolution. Because crop plants are depleted of genetic diversity for photosynthesis, efforts to enhance its efficiency with respect to light conversion to yield must generate new variation. In principle, three sources of natural variation are available: (i) rare diversity within extant higher plant species, (ii) photosynthetic variants from algae, and (iii) reconstruction of no longer extant types of plant photosynthesis. Here, we argue for a novel approach that outsources crop photosynthesis to a cyanobacterium that is amenable to adaptive evolution. This system offers numerous advantages, including a short generation time, virtually unlimited population sizes and high mutation rates, together with a versatile toolbox for genetic manipulation. On such a synthetic bacterial platform, 10 000 years of (crop) plant evolution can be recapitulated within weeks. Limitations of this system arise from its unicellular nature, which cannot reproduce all aspects of crop photosynthesis. But successful establishment of such a bacterial host for crop photosynthesis promises not only to enhance the performance of eukaryotic photosynthesis but will also reveal novel facets of the molecular basis of photosynthetic flexibility.This article is part of the themed issue 'Enhancing photosynthesis in crop plants: targets for improvement'.
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Affiliation(s)
- Marcel Dann
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians University of Munich, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany
| | - Dario Leister
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians University of Munich, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany
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9
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Complete genome sequence of Planococcus faecalis AJ003 T, the type species of the genus Planococcus and a microbial C30 carotenoid producer. J Biotechnol 2018; 266:72-76. [PMID: 29237561 DOI: 10.1016/j.jbiotec.2017.12.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 12/06/2017] [Accepted: 12/06/2017] [Indexed: 11/23/2022]
Abstract
A novel type strain, Planococcus faecalis AJ003T, isolated from the feces of Antarctic penguins, synthesizes a rare C30 carotenoid, glycosyl-4,4'-diaponeurosporen-4'-ol-4-oic acid. The complete genome of P. faecalis AJ003T comprises a single circular chromosome (3,495,892 bp; 40.9% G + C content). Annotation analysis has revealed 3511 coding DNA sequences and 99 RNAs; seven genes associated with the MEP pathway and five genes involved in the carotenoid pathway have been identified. The functionality and complementation of 4,4'-diapophytoene synthase (CrtM) and two copies of heterologous 4,4'-diapophytoene desaturase (CrtN) involved in carotenoid biosynthesis were analyzed in Escherichia coli.
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10
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Wu G, Yan Q, Jones JA, Tang YJ, Fong SS, Koffas MA. Metabolic Burden: Cornerstones in Synthetic Biology and Metabolic Engineering Applications. Trends Biotechnol 2016; 34:652-664. [DOI: 10.1016/j.tibtech.2016.02.010] [Citation(s) in RCA: 365] [Impact Index Per Article: 45.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 02/18/2016] [Accepted: 02/19/2016] [Indexed: 01/23/2023]
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12
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Bourcier de Carbon C, Thurotte A, Wilson A, Perreau F, Kirilovsky D. Biosynthesis of soluble carotenoid holoproteins in Escherichia coli. Sci Rep 2015; 5:9085. [PMID: 25765842 PMCID: PMC4358027 DOI: 10.1038/srep09085] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 02/16/2015] [Indexed: 01/23/2023] Open
Abstract
Carotenoids are widely distributed natural pigments that are excellent antioxidants acting in photoprotection. They are typically solubilized in membranes or attached to proteins. In cyanobacteria, the photoactive soluble Orange Carotenoid Protein (OCP) is involved in photoprotective mechanisms as a highly active singlet oxygen and excitation energy quencher. Here we describe a method for producing large amounts of holo-OCP in E.coli. The six different genes involved in the synthesis of holo-OCP were introduced into E. coli using three different plasmids. The choice of promoters and the order of gene induction were important: the induction of genes involved in carotenoid synthesis must precede the induction of the ocp gene in order to obtain holo-OCPs. Active holo-OCPs with primary structures derived from several cyanobacterial strains and containing different carotenoids were isolated. This approach for rapid heterologous synthesis of large quantities of carotenoproteins is a fundamental advance in the production of antioxidants of great interest to the pharmaceutical and cosmetic industries.
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Affiliation(s)
- Céline Bourcier de Carbon
- 1] Commissariat à l'Energie Atomique (CEA), Institut de Biologie et Technologies de Saclay (iBiTec-S), 91191 Gif sur Yvette, France [2] Centre National de la Recherche Scientifique (CNRS), UMR 8221, 91191 Gif sur Yvette, France [3] Phycosource, 13 boulevard de l'Hautil, 95092 Cergy Cedex, France
| | - Adrien Thurotte
- 1] Commissariat à l'Energie Atomique (CEA), Institut de Biologie et Technologies de Saclay (iBiTec-S), 91191 Gif sur Yvette, France [2] Centre National de la Recherche Scientifique (CNRS), UMR 8221, 91191 Gif sur Yvette, France
| | - Adjélé Wilson
- 1] Commissariat à l'Energie Atomique (CEA), Institut de Biologie et Technologies de Saclay (iBiTec-S), 91191 Gif sur Yvette, France [2] Centre National de la Recherche Scientifique (CNRS), UMR 8221, 91191 Gif sur Yvette, France
| | - François Perreau
- 1] INRA, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France [2] AgroParisTech, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France
| | - Diana Kirilovsky
- 1] Commissariat à l'Energie Atomique (CEA), Institut de Biologie et Technologies de Saclay (iBiTec-S), 91191 Gif sur Yvette, France [2] Centre National de la Recherche Scientifique (CNRS), UMR 8221, 91191 Gif sur Yvette, France
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Hara KY, Araki M, Okai N, Wakai S, Hasunuma T, Kondo A. Development of bio-based fine chemical production through synthetic bioengineering. Microb Cell Fact 2014; 13:173. [PMID: 25494636 PMCID: PMC4302092 DOI: 10.1186/s12934-014-0173-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 11/23/2014] [Indexed: 01/23/2023] Open
Abstract
Fine chemicals that are physiologically active, such as pharmaceuticals, cosmetics, nutritional supplements, flavoring agents as well as additives for foods, feed, and fertilizer are produced by enzymatically or through microbial fermentation. The identification of enzymes that catalyze the target reaction makes possible the enzymatic synthesis of the desired fine chemical. The genes encoding these enzymes are then introduced into suitable microbial hosts that are cultured with inexpensive, naturally abundant carbon sources, and other nutrients. Metabolic engineering create efficient microbial cell factories for producing chemicals at higher yields. Molecular genetic techniques are then used to optimize metabolic pathways of genetically and metabolically well-characterized hosts. Synthetic bioengineering represents a novel approach to employ a combination of computer simulation and metabolic analysis to design artificial metabolic pathways suitable for mass production of target chemicals in host strains. In the present review, we summarize recent studies on bio-based fine chemical production and assess the potential of synthetic bioengineering for further improving their productivity.
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Affiliation(s)
- Kiyotaka Y Hara
- Organization of Advanced Science and Technology, Kobe University, Nada, Kobe, Japan.
| | - Michihiro Araki
- Organization of Advanced Science and Technology, Kobe University, Nada, Kobe, Japan.
| | - Naoko Okai
- Organization of Advanced Science and Technology, Kobe University, Nada, Kobe, Japan.
| | - Satoshi Wakai
- Organization of Advanced Science and Technology, Kobe University, Nada, Kobe, Japan.
| | - Tomohisa Hasunuma
- Organization of Advanced Science and Technology, Kobe University, Nada, Kobe, Japan.
| | - Akihiko Kondo
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada, Kobe, 657-8501, Japan.
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Tikh IB, Quin MB, Schmidt-Dannert C. A tale of two reductases: extending the bacteriochlorophyll biosynthetic pathway in E. coli. PLoS One 2014; 9:e89734. [PMID: 24586995 PMCID: PMC3931815 DOI: 10.1371/journal.pone.0089734] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 01/23/2014] [Indexed: 12/23/2022] Open
Abstract
The creation of a synthetic microbe that can harvest energy from sunlight to drive its metabolic processes is an attractive approach to the economically viable biosynthetic production of target compounds. Our aim is to design and engineer a genetically tractable non-photosynthetic microbe to produce light-harvesting molecules. Previously we created a modular, multienzyme system for the heterologous production of intermediates of the bacteriochlorophyll (BChl) pathway in E. coli. In this report we extend this pathway to include a substrate promiscuous 8-vinyl reductase that can accept multiple intermediates of BChl biosynthesis. We present an informative comparative analysis of homologues of 8-vinyl reductase from the model photosynthetic organisms Rhodobacter sphaeroides and Chlorobaculum tepidum. The first purification of the enzymes leads to their detailed biochemical and biophysical characterization. The data obtained reveal that the two 8-vinyl reductases are substrate promiscuous, capable of reducing the C8-vinyl group of Mg protoporphyrin IX, Mg protoporphyrin IX methylester, and divinyl protochlorophyllide. However, activity is dependent upon the presence of chelated Mg2+ in the porphyrin ring, with no activity against non-Mg2+ chelated intermediates observed. Additionally, CD analyses reveal that the two 8-vinyl reductases appear to bind the same substrate in a different fashion. Furthermore, we discover that the different rates of reaction of the two 8-vinyl reductases both in vitro, and in vivo as part of our engineered system, results in the suitability of only one of the homologues for our BChl pathway in E. coli. Our results offer the first insights into the different functionalities of homologous 8-vinyl reductases. This study also takes us one step closer to the creation of a nonphotosynthetic microbe that is capable of harvesting energy from sunlight for the biosynthesis of molecules of choice.
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Affiliation(s)
- Ilya B. Tikh
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Maureen B. Quin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Claudia Schmidt-Dannert
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota, United States of America
- * E-mail:
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15
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Shen Y. Carbon dioxide bio-fixation and wastewater treatment via algae photochemical synthesis for biofuels production. RSC Adv 2014. [DOI: 10.1039/c4ra06441k] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Utilizing the energy, nutrients and CO2held within residual waste materials to provide all necessary inputs except for sunlight, the cultivation of algae becomes a closed-loop engineered ecosystem. Developing this green biotechnology is a tangible step towards a waste-free sustainable society.
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Affiliation(s)
- Yafei Shen
- Department of Environmental Science and Technology
- Interdisciplinary Graduate School of Science and Engineering
- Tokyo Institute of Technology
- Yokohama, Japan
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16
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Claassens NJ, Volpers M, dos Santos VAPM, van der Oost J, de Vos WM. Potential of proton-pumping rhodopsins: engineering photosystems into microorganisms. Trends Biotechnol 2013; 31:633-42. [PMID: 24120288 DOI: 10.1016/j.tibtech.2013.08.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Revised: 08/19/2013] [Accepted: 08/27/2013] [Indexed: 01/04/2023]
Abstract
A wide range of proton-pumping rhodopsins (PPRs) have been discovered in recent years. Using a synthetic biology approach, PPR photosystems with different features can be easily introduced in nonphotosynthetic microbial hosts. PPRs can provide hosts with the ability to harvest light and drive the sustainable production of biochemicals or biofuels. PPRs use light energy to generate an outward proton flux, and the resulting proton motive force can subsequently power cellular processes. Recently, the introduction of PPRs in microbial production hosts has successfully led to light-driven biotechnological conversions. In this review, we discuss relevant features of natural PPRs, evaluate reported biotechnological applications of microbial production hosts equipped with PPRs, and provide an outlook on future developments.
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Affiliation(s)
- Nico J Claassens
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
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17
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Chisti Y. Constraints to commercialization of algal fuels. J Biotechnol 2013; 167:201-14. [DOI: 10.1016/j.jbiotec.2013.07.020] [Citation(s) in RCA: 510] [Impact Index Per Article: 46.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 07/12/2013] [Accepted: 07/12/2013] [Indexed: 01/01/2023]
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18
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Heo J, Kim SH, Lee PC. New insight into the cleavage reaction of Nostoc sp. strain PCC 7120 carotenoid cleavage dioxygenase in natural and nonnatural carotenoids. Appl Environ Microbiol 2013; 79:3336-45. [PMID: 23524669 PMCID: PMC3648047 DOI: 10.1128/aem.00071-13] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 03/15/2013] [Indexed: 01/13/2023] Open
Abstract
Carotenoid cleavage dioxygenases (CCDs) are enzymes that catalyze the oxidative cleavage of carotenoids at a specific double bond to generate apocarotenoids. In this study, we investigated the activity and substrate preferences of NSC3, a CCD of Nostoc sp. strain PCC 7120, in vivo and in vitro using natural and nonnatural carotenoid structures. NSC3 cleaved β-apo-8'-carotenal at 3 positions, C-13 C-14, C-15 C-15', and C-13' C-14', revealing a unique cleavage pattern. NSC3 cleaves the natural structure of carotenoids 4,4'-diaponeurosporene, 4,4'-diaponeurosporen-4'-al, 4,4'-diaponeurosporen-4'-oic acid, 4,4'-diapotorulene, and 4,4'-diapotorulen-4'-al to generate novel cleavage products (apo-14'-diaponeurosporenal, apo-13'-diaponeurosporenal, apo-10'-diaponeurosporenal, apo-14'-diapotorulenal, and apo-10'-diapotorulenal, respectively). The study of carotenoids with natural or nonnatural structures produced by using synthetic modules could provide information valuable for understanding the cleavage reactions or substrate preferences of other CCDs in vivo and in vitro.
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Affiliation(s)
- Jinsol Heo
- Department of Molecular Science and Technology and Department of Applied Chemistry and Biological Engineering, Ajou University, Woncheon-Dong, Yeongtong-gu, Suwon, South Korea
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Lee SJ, Lee SJ, Lee DW. Design and development of synthetic microbial platform cells for bioenergy. Front Microbiol 2013; 4:92. [PMID: 23626588 PMCID: PMC3630320 DOI: 10.3389/fmicb.2013.00092] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 04/03/2013] [Indexed: 12/26/2022] Open
Abstract
The finite reservation of fossil fuels accelerates the necessity of development of renewable energy sources. Recent advances in synthetic biology encompassing systems biology and metabolic engineering enable us to engineer and/or create tailor made microorganisms to produce alternative biofuels for the future bio-era. For the efficient transformation of biomass to bioenergy, microbial cells need to be designed and engineered to maximize the performance of cellular metabolisms for the production of biofuels during energy flow. Toward this end, two different conceptual approaches have been applied for the development of platform cell factories: forward minimization and reverse engineering. From the context of naturally minimized genomes,non-essential energy-consuming pathways and/or related gene clusters could be progressively deleted to optimize cellular energy status for bioenergy production. Alternatively, incorporation of non-indigenous parts and/or modules including biomass-degrading enzymes, carbon uptake transporters, photosynthesis, CO2 fixation, and etc. into chassis microorganisms allows the platform cells to gain novel metabolic functions for bioenergy. This review focuses on the current progress in synthetic biology-aided pathway engineering in microbial cells and discusses its impact on the production of sustainable bioenergy.
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Affiliation(s)
- Sang Jun Lee
- Systems and Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology Daejeon, South Korea
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Maurino VG, Weber APM. Engineering photosynthesis in plants and synthetic microorganisms. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:743-51. [PMID: 23028016 DOI: 10.1093/jxb/ers263] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Photosynthetic organisms, such as cyanobacteria, algae, and plants, sustain life on earth by converting light energy, water, and CO(2) into chemical energy. However, due to global change and a growing human population, arable land is becoming scarce and resources, including water and fertilizers, are becoming exhausted. It will therefore be crucial to design innovative strategies for sustainable plant production to maintain the food and energy bases of human civilization. Several different strategies for engineering improved photosynthesis in crop plants and introducing novel photosynthetic capacity into microorganisms have been reviewed.
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Affiliation(s)
- Veronica G Maurino
- Plant Molecular Physiology and Biotechnology, Institute of Plant Developmental and Molecular Biology, Center of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
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Kim SH, Lee PC. Functional expression and extension of staphylococcal staphyloxanthin biosynthetic pathway in Escherichia coli. J Biol Chem 2012; 287:21575-83. [PMID: 22535955 DOI: 10.1074/jbc.m112.343020] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The biosynthetic pathway for staphyloxanthin, a C(30) carotenoid biosynthesized by Staphylococcus aureus, has previously been proposed to consist of five enzymes (CrtO, CrtP, CrtQ, CrtM, and CrtN). Here, we report a missing sixth enzyme, 4,4'-diaponeurosporen-aldehyde dehydrogenase (AldH), in the staphyloxanthin biosynthetic pathway and describe the functional expression of the complete staphyloxanthin biosynthetic pathway in Escherichia coli. When we expressed the five known pathway enzymes through artificial synthetic operons and the wild-type operon (crtOPQMN) in E. coli, carotenoid aldehyde intermediates such as 4,4'-diaponeurosporen-4-al accumulated without being converted into staphyloxanthin or other intermediates. We identified an aldH gene located 670 kilobase pairs from the known staphyloxanthin gene cluster in the S. aureus genome and an aldH gene in the non-staphyloxanthin-producing Staphylococcus carnosus genome. These two putative enzymes catalyzed the missing oxidation reaction to convert 4,4'-diaponeurosporen-4-al into 4,4'-diaponeurosporenoic acid in E. coli. Deletion of the aldH gene in S. aureus abolished staphyloxanthin biosynthesis and caused accumulation of 4,4'-diaponeurosporen-4-al, confirming the role of AldH in staphyloxanthin biosynthesis. When the complete staphyloxanthin biosynthetic pathway was expressed using an artificial synthetic operon in E. coli, staphyloxanthin-like compounds, which contained altered fatty acid acyl chains, and novel carotenoid compounds were produced, indicating functional expression and coordination of the six staphyloxanthin pathway enzymes.
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Affiliation(s)
- Se Hyeuk Kim
- Department of Molecular Science and Technology, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon 443-749, South Korea
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Anemaet IG, Bekker M, Hellingwerf KJ. Algal photosynthesis as the primary driver for a sustainable development in energy, feed, and food production. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2010; 12:619-29. [PMID: 20640935 PMCID: PMC2991177 DOI: 10.1007/s10126-010-9311-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2010] [Accepted: 06/30/2010] [Indexed: 05/11/2023]
Abstract
High oil prices and global warming that accompany the use of fossil fuels are an incentive to find alternative forms of energy supply. Photosynthetic biofuel production represents one of these since for this, one uses renewable resources. Sunlight is used for the conversion of water and CO₂ into biomass. Two strategies are used in parallel: plant-based production via sugar fermentation into ethanol and biodiesel production through transesterification. Both, however, exacerbate other problems, including regional nutrient balancing and the world's food supply, and suffer from the modest efficiency of photosynthesis. Maximizing the efficiency of natural and engineered photosynthesis is therefore of utmost importance. Algal photosynthesis is the system of choice for this particularly for energy applications. Complete conversion of CO₂ into biomass is not necessary for this. Innovative methods of synthetic biology allow one to combine photosynthetic and fermentative metabolism via the so-called Photanol approach to form biofuel directly from Calvin cycle intermediates through use of the naturally transformable cyanobacterium Synechocystis sp. PCC 6803. Beyond providing transport energy and chemical feedstocks, photosynthesis will continue to be used for food and feed applications. Also for this application, arguments of efficiency will become more and more important as the size of the world population continues to increase. Photosynthetic cells can be used for food applications in various innovative forms, e.g., as a substitute for the fish proteins in the diet supplied to carnivorous fish or perhaps--after acid hydrolysis--as a complex, animal-free serum for growth of mammalian cells in vitro.
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Affiliation(s)
- Ida G. Anemaet
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands
| | - Martijn Bekker
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands
| | - Klaas J. Hellingwerf
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands
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Wen J, Tsukatani Y, Cui W, Zhang H, Gross ML, Bryant DA, Blankenship RE. Structural model and spectroscopic characteristics of the FMO antenna protein from the aerobic chlorophototroph, Candidatus Chloracidobacterium thermophilum. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1807:157-64. [PMID: 20875391 DOI: 10.1016/j.bbabio.2010.09.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Revised: 09/15/2010] [Accepted: 09/17/2010] [Indexed: 11/17/2022]
Abstract
The Fenna-Matthews-Olson protein (FMO) binds seven or eight bacteriochlorophyll a (BChl a) molecules and is an important model antenna system for understanding pigment-protein interactions and mechanistic aspects of photosynthetic light harvesting. FMO proteins of green sulfur bacteria (Chlorobiales) have been extensively studied using a wide range of spectroscopic and theoretical approaches because of their stability, the spectral resolution of their pigments, their water-soluble nature, and the availability of high-resolution structural data. We obtained new structural and spectroscopic insights by studying the FMO protein from the recently discovered, aerobic phototrophic acidobacterium, Candidatus Chloracidobacterium thermophilum. Native C. thermophilum FMO is a trimer according to both analytical gel filtration and native-electrospray mass spectrometry. Furthermore, the mass of intact FMO trimer is consistent with the presence of 21-24 BChl a in each. Homology modeling of the C. thermophilum FMO was performed by using the structure of the FMO protein from Chlorobaculum tepidum as a template. C. thermophilum FMO differs from C. tepidum FMO in two distinct regions: the baseplate, CsmA-binding region and a region that is proposed to bind the reaction center subunit, PscA. C. thermophilum FMO has two fluorescence emission peaks at room temperature but only one at 77K. Temperature-dependent fluorescence spectroscopy showed that the two room-temperature emission peaks result from two excited-state BChl a populations that have identical fluorescence lifetimes. Modeling of the data suggests that the two populations contain 1-2 BChl and 5-6 BChl a molecules and that thermal equilibrium effects modulate the relative population of the two emitting states.
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Affiliation(s)
- Jianzhong Wen
- Department of Biology, Washington University in St. Louis, St. Louis MO 63130, USA
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Walter JM, Greenfield D, Liphardt J. Potential of light-harvesting proton pumps for bioenergy applications. Curr Opin Biotechnol 2010; 21:265-70. [DOI: 10.1016/j.copbio.2010.03.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Revised: 03/09/2010] [Accepted: 03/09/2010] [Indexed: 10/19/2022]
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Enhancement of survival and electricity production in an engineered bacterium by light-driven proton pumping. Appl Environ Microbiol 2010; 76:4123-9. [PMID: 20453141 DOI: 10.1128/aem.02425-09] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Microorganisms can use complex photosystems or light-dependent proton pumps to generate membrane potential and/or reduce electron carriers to support growth. The discovery that proteorhodopsin is a light-dependent proton pump that can be expressed readily in recombinant bacteria enables development of new strategies to probe microbial physiology and to engineer microbes with new light-driven properties. Here, we describe functional expression of proteorhodopsin and light-induced changes in membrane potential in the bacterium Shewanella oneidensis strain MR-1. We report that there were significant increases in electrical current generation during illumination of electrochemical chambers containing S. oneidensis expressing proteorhodopsin. We present evidence that an engineered strain is able to consume lactate at an increased rate when it is illuminated, which is consistent with the hypothesis that proteorhodopsin activity enhances lactate uptake by increasing the proton motive force. Our results demonstrate that there is coupling of a light-driven process to electricity generation in a nonphotosynthetic engineered bacterium. Expression of proteorhodopsin also preserved the viability of the bacterium under nutrient-limited conditions, providing evidence that fulfillment of basic energy needs of organisms may explain the widespread distribution of proteorhodopsin in marine environments.
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Abstract
Solar fuels from water and CO2 are a topic of current large scientific and industrial interest. Research advances on bioroutes, concentrated solar thermal and low-temperature conversion using semiconductors and a photoelectrocatalytic (PEC) approach, are critically discussed and compared in an attempt to define challenges and current limits and to identify the priorities on which focus research and development (R&D). The need to produce fuels that are easy to transport and store, which can be integrated into the existing energy infrastructure, is emphasized. The role of solar fuels produced from CO2 in comparison with solar H2 is analyzed. Solar fuels are complementary to solar to electrical energy conversion, but they still need intensified R&D before possible commercialization.
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Affiliation(s)
- Gabriele Centi
- Dipartimento di Chimica Industriale ed Ingegneria dei Materiali, University of Messina and INSTM/CASPE (Laboratory of Catalysis for Sustainable Production and Energy), Salita Sperone 31, 98166 Messina, Italy.
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