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Goswami L, Kushwaha A, Napathorn SC, Kim BS. Valorization of organic wastes using bioreactors for polyhydroxyalkanoate production: Recent advancement, sustainable approaches, challenges, and future perspectives. Int J Biol Macromol 2023; 247:125743. [PMID: 37423435 DOI: 10.1016/j.ijbiomac.2023.125743] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 06/23/2023] [Accepted: 07/06/2023] [Indexed: 07/11/2023]
Abstract
Microbial polyhydroxyalkanoates (PHA) are encouraging biodegradable polymers, which may ease the environmental problems caused by petroleum-derived plastics. However, there is a growing waste removal problem and the high price of pure feedstocks for PHA biosynthesis. This has directed to the forthcoming requirement to upgrade waste streams from various industries as feedstocks for PHA production. This review covers the state-of-the-art progress in utilizing low-cost carbon substrates, effective upstream and downstream processes, and waste stream recycling to sustain entire process circularity. This review also enlightens the use of various batch, fed-batch, continuous, and semi-continuous bioreactor systems with flexible results to enhance the productivity and simultaneously cost reduction. The life-cycle and techno-economic analyses, advanced tools and strategies for microbial PHA biosynthesis, and numerous factors affecting PHA commercialization were also covered. The review includes the ongoing and upcoming strategies viz. metabolic engineering, synthetic biology, morphology engineering, and automation to expand PHA diversity, diminish production costs, and improve PHA production with an objective of "zero-waste" and "circular bioeconomy" for a sustainable future.
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Affiliation(s)
- Lalit Goswami
- Department of Chemical Engineering, Chungbuk National University, Cheongju, Chungbuk 28644, Republic of Korea
| | - Anamika Kushwaha
- Department of Chemical Engineering, Chungbuk National University, Cheongju, Chungbuk 28644, Republic of Korea
| | | | - Beom Soo Kim
- Department of Chemical Engineering, Chungbuk National University, Cheongju, Chungbuk 28644, Republic of Korea.
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2
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Sakurai T, Mizuno S, Miyahara Y, Hiroe A, Taguchi S, Tsuge T. Optimization of Culture Conditions for Secretory Production of 3-Hydroxybutyrate Oligomers Using Recombinant Escherichia coli. Front Bioeng Biotechnol 2022; 10:829134. [PMID: 35284416 PMCID: PMC8914192 DOI: 10.3389/fbioe.2022.829134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 01/24/2022] [Indexed: 11/20/2022] Open
Abstract
Poly(3-hydroxybutyrate) [P(3HB)] is the most representative polyhydroxyalkanoate (PHA), which is a storage polyester for prokaryotic cells. P(3HB)-producing recombinant Escherichia coli secretes diethylene glycol (DEG)-terminated 3HB oligomers (3HBO-DEG) through a PHA synthase-mediated chain transfer and alcoholysis reactions with externally added DEG. The purpose of this study was to optimize the culture conditions for the secretory production of 3HBO-DEG with jar fermenters. First, the effects of culture conditions, such as agitation speed, culture temperature, culture pH, and medium composition on 3HBO-DEG production, were investigated in a batch culture using 250-ml mini jar fermenters. Based on the best culture conditions, a fed-batch culture was conducted by feeding glucose to further increase the 3HBO-DEG titer. Consequently, the optimized culture conditions were reproduced using a 2-L jar fermenter. This study successfully demonstrates a high titer of 3HBO-DEG, up to 34.8 g/L, by optimizing the culture conditions, showing the feasibility of a new synthetic strategy for PHA-based materials by combining secretory oligomer production and subsequent chemical reaction.
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Affiliation(s)
- Tetsuo Sakurai
- Department of Materials Science and Engineering, Tokyo Institute of Technology, Yokohama, Japan
- MIRAI, Japan Science and Technology Agency (JST), Saitama, Japan
| | - Shoji Mizuno
- Department of Materials Science and Engineering, Tokyo Institute of Technology, Yokohama, Japan
- MIRAI, Japan Science and Technology Agency (JST), Saitama, Japan
| | - Yuki Miyahara
- Department of Materials Science and Engineering, Tokyo Institute of Technology, Yokohama, Japan
- MIRAI, Japan Science and Technology Agency (JST), Saitama, Japan
| | - Ayaka Hiroe
- MIRAI, Japan Science and Technology Agency (JST), Saitama, Japan
- Department of Chemistry for Life Sciences and Agriculture, Faculty of Life Sciences, Tokyo University of Agriculture, Setagaya, Japan
| | - Seiichi Taguchi
- Department of Chemistry for Life Sciences and Agriculture, Faculty of Life Sciences, Tokyo University of Agriculture, Setagaya, Japan
| | - Takeharu Tsuge
- Department of Materials Science and Engineering, Tokyo Institute of Technology, Yokohama, Japan
- MIRAI, Japan Science and Technology Agency (JST), Saitama, Japan
- *Correspondence: Takeharu Tsuge,
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3
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Screening Method for Polyhydroxyalkanoate Synthase Mutants Based on Polyester Degree of Polymerization Using High-Performance Liquid Chromatography. Microorganisms 2021; 9:microorganisms9091949. [PMID: 34576844 PMCID: PMC8469876 DOI: 10.3390/microorganisms9091949] [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: 07/28/2021] [Revised: 09/08/2021] [Accepted: 09/08/2021] [Indexed: 11/29/2022] Open
Abstract
A high-throughput screening method based on the degree of polymerization (DP) of polyhydroxyalkanoate (PHA) was developed using high-performance liquid chromatography (HPLC). In this method, PHA production was achieved using recombinant Escherichia coli supplemented with benzyl alcohol as a chain terminal compound. The cultured cells containing benzyl alcohol-capped PHA were decomposed by alkaline treatment, and the peaks of the decomposed monomer and benzyl alcohol were detected using HPLC. The DP of PHA could be determined from the peak ratio of the decomposed monomer to terminal benzyl alcohol. The measured DP was validated by other instrumental analyses using purified PHA samples. Using this system, mutants of PHA synthase from Bacillus cereus YB-4 (PhaRCYB4) were screened, and some enzymes capable of producing PHA with higher DP than the wild-type enzyme were obtained. The PHA yields of two of these enzymes were equivalent to the yield of the wild-type enzyme. Therefore, this screening method is suitable for the selection of beneficial mutants that can produce high molecular weight PHAs.
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Li D, Ma X, Yin F, Qiu Y, Yan X. Creating biotransformation of volatile fatty acids and octanoate as co-substrate to high yield medium-chain-length polyhydroxyalkanoate. BIORESOURCE TECHNOLOGY 2021; 331:125031. [PMID: 33798859 DOI: 10.1016/j.biortech.2021.125031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 06/12/2023]
Abstract
Using mixed microbial consortium (MMC) to accumulate polyhydroxyalkanoate (PHA) is an effective strategy to solve high production cost and reduce the amount of excess sludge. In this study, a process for the production of short-chain-length and medium-chain-length PHA using volatile fatty acids (VFAs) from pretreated wood hydrolysate synergistic with octanoate as co-substrate was proposed. The effects of co-substrate ratios on PHA accumulation ability and physical properties were investigated. The incorporation of co-substrate accelerated the time of PHA and 3-hydroxyoctanoate reaching the maximum production (1834 and 280 mg COD/L). The highest PHA content was 53.0% (w/w), which was equivalent to that reported previously. The biopolymer films possessed high tensile strength, Young's modulus, and could be used in the field of water vapor barrier requirements. The accumulation strategy applied for converting fermentation products VFAs and octanoate co-substrate into high value and yield PHA could potentially demonstrate the valuable for low-cost large-scale production.
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Affiliation(s)
- Dongna Li
- College of Light Industry Science and Engineering, Tianjin University of Science & Technology, Tianjin 300222, PR China
| | - Xiaojun Ma
- College of Light Industry Science and Engineering, Tianjin University of Science & Technology, Tianjin 300222, PR China.
| | - Fen Yin
- College of Light Industry Science and Engineering, Tianjin University of Science & Technology, Tianjin 300222, PR China
| | - Yujuan Qiu
- College of Light Industry Science and Engineering, Tianjin University of Science & Technology, Tianjin 300222, PR China
| | - Xu Yan
- College of Light Industry Science and Engineering, Tianjin University of Science & Technology, Tianjin 300222, PR China
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5
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Mizuno S, Sakurai T, Nabasama M, Kawakami K, Hiroe A, Taguchi S, Tsuge T. The influence of medium composition on the microbial secretory production of hydroxyalkanoate oligomers. J GEN APPL MICROBIOL 2021; 67:134-141. [PMID: 33952784 DOI: 10.2323/jgam.2020.09.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
With the aid of a chain transfer (CT) reaction, hydroxyalkanoate (HA) oligomers can be secreted by recombinant Escherichia coli carrying the gene encoding a lactate-polymerizing enzyme (PhaC1PsSTQK) using Luria-Bertani (LB) medium supplemented with a carbon source and CT agent. In this study, HA oligomers were produced through microbial secretion using a mineral-based medium instead of LB medium, and the impact of medium composition on HA oligomer secretion was investigated. The focused targets were medium composition and NaCl concentration related to osmotic conditions. It was observed that 4.21 g/L HA oligomer was secreted by recombinant E. coli in LB medium, but the amount secreted in the mineral-based modified R (MR) medium was negligible. However, when the MR medium was supplemented with 5 g/L yeast extract, 3.75 g/L HA oligomer was secreted. This can be accounted for by the enhanced expression and activity of PhaC1PsSTQK upon supplementation with growth-activated nutrients as supplementation with yeast extract also promoted cell growth and intracellular growth-associated polymer accumulation. Furthermore, upon adding 10 g/L NaCl to the yeast extract-supplemented MR medium, HA oligomer secretion increased to 6.86 g/L, implying that NaCl-induced osmotic pressure promotes HA oligomer secretion. These findings may facilitate the secretory production of HA oligomers using an inexpensive medium.
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Affiliation(s)
- Shoji Mizuno
- Department of Materials Science and Engineering, Tokyo Institute of Technology.,MIRAI, JST
| | - Tetsuo Sakurai
- Department of Materials Science and Engineering, Tokyo Institute of Technology
| | - Mikito Nabasama
- Department of Materials Science and Engineering, Tokyo Institute of Technology
| | - Kyouhei Kawakami
- Department of Materials Science and Engineering, Tokyo Institute of Technology
| | - Ayaka Hiroe
- Department of Chemistry for Life Sciences and Agriculture, Faculty of Life Sciences, Tokyo University of Agriculture.,MIRAI, JST
| | - Seiichi Taguchi
- Department of Chemistry for Life Sciences and Agriculture, Faculty of Life Sciences, Tokyo University of Agriculture
| | - Takeharu Tsuge
- Department of Materials Science and Engineering, Tokyo Institute of Technology.,MIRAI, JST
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Chanthaset N, Ajiro H. Synthetic Biodegradable Polymers with Chain End Modification: Polylactide, Poly(butylene succinate), and Poly(hydroxyalkanoate). CHEM LETT 2021. [DOI: 10.1246/cl.200859] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Nalinthip Chanthaset
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Hiroharu Ajiro
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
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Nduko JM, Taguchi S. Microbial Production of Biodegradable Lactate-Based Polymers and Oligomeric Building Blocks From Renewable and Waste Resources. Front Bioeng Biotechnol 2021; 8:618077. [PMID: 33614605 PMCID: PMC7889595 DOI: 10.3389/fbioe.2020.618077] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/17/2020] [Indexed: 12/20/2022] Open
Abstract
Polyhydroxyalkanoates (PHAs) are naturally occurring biopolymers produced by microorganisms. PHAs have become attractive research biomaterials in the past few decades owing to their extensive potential industrial applications, especially as sustainable alternatives to the fossil fuel feedstock-derived products such as plastics. Among the biopolymers are the bioplastics and oligomers produced from the fermentation of renewable plant biomass. Bioplastics are intracellularly accumulated by microorganisms as carbon and energy reserves. The bioplastics, however, can also be produced through a biochemistry process that combines fermentative secretory production of monomers and/or oligomers and chemical synthesis to generate a repertoire of biopolymers. PHAs are particularly biodegradable and biocompatible, making them a part of today's commercial polymer industry. Their physicochemical properties that are similar to those of petrochemical-based plastics render them potential renewable plastic replacements. The design of efficient tractable processes using renewable biomass holds key to enhance their usage and adoption. In 2008, a lactate-polymerizing enzyme was developed to create new category of polyester, lactic acid (LA)-based polymer and related polymers. This review aims to introduce different strategies including metabolic and enzyme engineering to produce LA-based biopolymers and related oligomers that can act as precursors for catalytic synthesis of polylactic acid. As the cost of PHA production is prohibitive, the review emphasizes attempts to use the inexpensive plant biomass as substrates for LA-based polymer and oligomer production. Future prospects and challenges in LA-based polymer and oligomer production are also highlighted.
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Affiliation(s)
- John Masani Nduko
- Department of Dairy and Food Science and Technology, Faculty of Agriculture, Egerton University, Egerton, Kenya
| | - Seiichi Taguchi
- Department of Chemistry for Life Sciences and Agriculture, Faculty of Life Sciences and Agriculture, Tokyo University of Agriculture, Tokyo, Japan
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8
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Hiroe A, Sakurai T, Mizuno S, Miyahara Y, Goto S, Yamada M, Tsuge T, Taguchi S. Microbial oversecretion of (R)-3-hydroxybutyrate oligomer with diethylene glycol terminal as a macromonomer for polyurethane synthesis. Int J Biol Macromol 2020; 167:1290-1296. [PMID: 33202278 DOI: 10.1016/j.ijbiomac.2020.11.083] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/07/2020] [Accepted: 11/12/2020] [Indexed: 11/28/2022]
Abstract
Poly((R)-3-hydroxybutyrate) (P(3HB)) is a polyester that is synthesized and accumulated in many prokaryotic cells. Recently, a new culture method for the secretion of the intracellularly synthesized (R)-3-hydroxybutyrate oligomer (3HBO) from recombinant Escherichia coli cells was developed. In this study, we attempted to produce microbial 3HBO capped with a diethylene glycol terminal (3HBO-DEG) as a macromonomer for polymeric materials. First, we prepared recombinant E. coli strains harboring genes encoding various polyhydroxyalkanoate (PHA) synthases (PhaC, PhaEC or PhaRC) that can incorporate chain transfer (CT) agents such as DEG into the polymer's terminal and generate CT end-capped oligomers. To this end, each strain was cultivated under DEG supplemental conditions, and the synthesis of 3HBO-DEG was confirmed. As a result, the highest secretory production of 3HBO-DEG was observed for the PHA synthase derived from Bacillus cereus YB-4 (PhaRCYB4). To evaluate the usability of the secreted 3HBO-DEG as a macromonomer, 3HBO-DEG was purified from the culture medium and polymerized with 4,4'-diphenylmethane diisocyanate as a spacer compound. Characterization of the polymeric products revealed that 3HBO-based polyurethane was successfully obtained and was a flexible and transparent noncrystalline polymer, unlike P(3HB). These results suggested that microbial 3HBO-DEG is a promising platform building block for synthesizing polyurethane and various other polymers.
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Affiliation(s)
- Ayaka Hiroe
- Department of Chemistry for Life Sciences and Agriculture, Faculty of Life Sciences, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502, Japan; MIRAI, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Tetsuo Sakurai
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8502, Japan
| | - Shoji Mizuno
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8502, Japan; MIRAI, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Yuki Miyahara
- Department of Chemistry for Life Sciences and Agriculture, Faculty of Life Sciences, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502, Japan; MIRAI, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Saki Goto
- Department of Chemistry for Life Sciences and Agriculture, Faculty of Life Sciences, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502, Japan; MIRAI, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Mariko Yamada
- Department of Chemistry for Life Sciences and Agriculture, Faculty of Life Sciences, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502, Japan; MIRAI, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Takeharu Tsuge
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8502, Japan; MIRAI, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
| | - Seiichi Taguchi
- Department of Chemistry for Life Sciences and Agriculture, Faculty of Life Sciences, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502, Japan.
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9
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Liu LY, Xie GJ, Xing DF, Liu BF, Ding J, Ren NQ. Biological conversion of methane to polyhydroxyalkanoates: Current advances, challenges, and perspectives. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2020; 2:100029. [PMID: 36160923 PMCID: PMC9487992 DOI: 10.1016/j.ese.2020.100029] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/20/2020] [Accepted: 04/22/2020] [Indexed: 05/13/2023]
Abstract
Methane emissions and plastic pollution are critical global challenges. The biological conversion of methane to poly-β-hydroxybutyrate (PHB) not only mitigates methane emissions but also provides biodegradable polymer substitutes for petroleum-based materials used in plastics production. This work provides an early overview of the methane-based PHB advances and discusses challenges and related strategies. Recent advances of PHB, including PHB biosynthetic pathways, methanotrophs, bioreactors, and the performances of PHB materials are introduced. Major challenges of methane-based PHB production are discussed in detail; these include low efficiency of methanotrophs, low gas-liquid mass transfer efficiency, and poor material properties. To overcome these limitations, various approaches are also explored, such as feast-famine regimes, engineered microorganisms, gas-permeable membrane bioreactors, two-phase partitioning bioreactors, poly-β-hydroxybutyrate-co-hydroxyvalerate synthesis, and molecular weight manipulation.
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Miyahara Y, Hiroe A, Tsuge T, Taguchi S. Microbial Secretion Platform for 3‐Hydroxybutyrate Oligomer and Its End‐Capped Forms Using Chain Transfer Reaction‐Mediated Polyhydroxyalkanoate Synthases. Biotechnol J 2019; 14:e1900201. [DOI: 10.1002/biot.201900201] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 10/27/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Yuki Miyahara
- Department of Chemistry for Life Sciences and Agriculture, Faculty of Life Sciences Tokyo University of Agriculture 1‐1‐1 Sakuragaoka, Setagaya Tokyo 156–8502 Japan
- MIRAI, JST 4‐1‐8 Honcho Kawaguchi Saitama 332‐0012 Japan
| | - Ayaka Hiroe
- Department of Chemistry for Life Sciences and Agriculture, Faculty of Life Sciences Tokyo University of Agriculture 1‐1‐1 Sakuragaoka, Setagaya Tokyo 156–8502 Japan
- MIRAI, JST 4‐1‐8 Honcho Kawaguchi Saitama 332‐0012 Japan
| | - Takeharu Tsuge
- Department of Materials Science and Engineering, Major in Human Centered Science and Biomedical Engineering School of Materials and Chemical Technology, Tokyo Institute of Technology 4259 J2‐47 Nagatsuta‐cho, Midori‐ku Yokohama‐shi Kanagawa 226–8502 Japan
- MIRAI, JST 4‐1‐8 Honcho Kawaguchi Saitama 332‐0012 Japan
| | - Seiichi Taguchi
- Department of Chemistry for Life Sciences and Agriculture, Faculty of Life Sciences Tokyo University of Agriculture 1‐1‐1 Sakuragaoka, Setagaya Tokyo 156–8502 Japan
- CREST, JST 4‐1‐8 Honcho Kawaguchi Saitama 332‐0012 Japan
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Nambu Y, Ishii-Hyakutake M, Harada K, Mizuno S, Tsuge T. Expanded amino acid sequence of the PhaC box in the active center of polyhydroxyalkanoate synthases. FEBS Lett 2019; 594:710-716. [PMID: 31665820 DOI: 10.1002/1873-3468.13651] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 09/27/2019] [Accepted: 10/22/2019] [Indexed: 12/15/2022]
Abstract
Polyhydroxyalkanoate (PHA) synthases catalyze the polymerization reaction of the acyl moiety of hydroxyacyl-coenzyme A into polyester. The catalytic subunit PhaC of PHA synthase has the PhaC box sequence at the active site that is typically described as G-X-C-X-G-G (X is an arbitrary amino acid), and cysteine is an active center. In this study, an amino acid replacement was introduced into the PhaC box of the PHA synthase derived from Ralstonia eutropha (PhaCRe ) to investigate the importance of highly conserved residues in polymerizing activity. Point mutagenesis revealed that PhaCRe mutants with the expanded PhaC box sequence ([GAST]-X-C-X-[GASV]-[GA]) are functional PHA synthases. These findings highlight the low mutational robustness of the last glycine residue in the PhaC box as well as that of the active center cysteine.
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Affiliation(s)
- Yuka Nambu
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Manami Ishii-Hyakutake
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Yokohama, Japan.,Bioplastic Research Team, RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Ken Harada
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Shoji Mizuno
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Takeharu Tsuge
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Yokohama, Japan
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12
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Zheng Y, Chen JC, Ma YM, Chen GQ. Engineering biosynthesis of polyhydroxyalkanoates (PHA) for diversity and cost reduction. Metab Eng 2019; 58:82-93. [PMID: 31302223 DOI: 10.1016/j.ymben.2019.07.004] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 06/23/2019] [Accepted: 07/11/2019] [Indexed: 11/29/2022]
Abstract
PHA, a family of natural biopolymers aiming to replace non-degradable plastics for short-term usages, has been developed to include various structures such as short-chain-length (scl) and medium-chain-length (mcl) monomers as well as their copolymers. However, PHA market has been grown slowly since 1980s due to limited variety with good mechanical properties and the high production cost. Here, we review most updated strategies or approaches including metabolic engineering, synthetic biology and morphology engineering on expanding PHA diversity, reducing production cost and enhancing PHA production. The extremophilic Halomonas spp. are taken as examples to show the feasibility and challenges to develop next generation industrial biotechnology (NGIB) for producing PHA more competitively.
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Affiliation(s)
- Yang Zheng
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China; School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jin-Chun Chen
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China; School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yi-Ming Ma
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China; School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Guo-Qiang Chen
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China; School of Life Sciences, Tsinghua University, Beijing, 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China; Center for Nano- and Micro-Mechanics, Tsinghua University, Beijing, 100084, China; Dept of Chemical Engineering, Tsinghua University, Beijing, 100084, China.
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13
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Miyahara Y, Oota M, Tsuge T. NADPH supply for poly(3-hydroxybutyrate) synthesis concomitant with enzymatic oxidation of phosphite. J Biosci Bioeng 2018; 126:764-768. [PMID: 29910188 DOI: 10.1016/j.jbiosc.2018.05.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 05/28/2018] [Accepted: 05/29/2018] [Indexed: 01/07/2023]
Abstract
Acetoacetyl-CoA reductase (PhaB), involved in poly(3-hydroxybutyrate) [P(3HB)] biosynthesis, requires the coenzyme NADPH as a reducing agent. In this study, the effect of NADPH supply on P(3HB) production was investigated in vitro and in vivo using a phosphite dehydrogenase double mutant (PtxDEAAR), which catalyzes oxidation of phosphite to phosphate with the generation of NADH and NADPH. In an in vitro assay using purified enzymes, P(3HB) polymerization was observed only when phosphite and PtxDEAAR were present, confirming that NADPH was supplied to PhaB. In an in vivo assay using Escherichia coli as a production host for P(3HB), the presence of phosphite and PtxDEAAR did not influence the yield of P(3HB) under normal growth conditions. However, P(3HB) yield increased 3.2-fold in non-growing E. coli cells compared to the control, suggesting that PtxDEAAR-mediated NADPH generation is coupled with P(3HB) biosynthesis. This study confirmed the use of PtxDEAAR for supplying NADPH during P(3HB) synthesis in vitro and in vivo.
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Affiliation(s)
- Yuki Miyahara
- Department of Innovative and Engineered Materials, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Mino Oota
- Department of Innovative and Engineered Materials, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Takeharu Tsuge
- Department of Innovative and Engineered Materials, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan; Department of Materials Science and Engineering, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan.
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14
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Li D, Lv L, Chen JC, Chen GQ. Controlling microbial PHB synthesis via CRISPRi. Appl Microbiol Biotechnol 2017; 101:5861-5867. [PMID: 28620688 DOI: 10.1007/s00253-017-8374-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 05/25/2017] [Accepted: 05/28/2017] [Indexed: 12/20/2022]
Abstract
Microbial polyhydroxyalkanoates (PHA) are a family of biopolyesters with properties similar to petroleum plastics such as polyethylene (PE) or polypropylene (PP). Polyhydroxybutyrate (PHB) is the most common PHA known so far. Clustered regularly interspaced short palindromic repeats interference (CRISPRi), a technology recently developed to control gene expression levels in eukaryotic and prokaryotic genomes, was employed to regulate PHB synthase activity influencing PHB synthesis. Recombinant Escherichia coli harboring an operon of three PHB synthesis genes phaCAB cloned from Ralstonia eutropha, was transformed with various single guided RNA (sgRNA with its guide sequence of 20-23 bases) able to bind to various locations of the PHB synthase PhaC, respectively. Depending on the binding location and the number of sgRNA on phaC, CRISPRi was able to control the phaC transcription and thus PhaC activity. It was found that PHB content, molecular weight, and polydispersity were approximately in direct and reverse proportion to the PhaC activity, respectively. The higher the PhaC activity, the more the intracellular PHB accumulation, yet the less the PHB molecular weights and the wider the polydispersity. This study allowed the PHB contents to be controlled in the ranges of 1.47-75.21% cell dry weights, molecular weights from 2 to 6 millions Dalton and polydispersity of 1.2 to 1.43 in 48 h shake flask studies. This result will be very important for future development of ultrahigh molecular weight PHA useful to meet high strength application requirements.
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Affiliation(s)
- Dan Li
- Center for Synthetic and Systems Biology, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Li Lv
- Center for Synthetic and Systems Biology, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jin-Chun Chen
- Center for Synthetic and Systems Biology, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Guo-Qiang Chen
- Center for Synthetic and Systems Biology, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China.
- Center for Nano and Micro-Mechanics, Tsinghua University, Beijing, 100084, China.
- MOE Key Lab for Industrial Biocatalysis, Tsinghua University, Beijing, 100084, China.
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15
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Scheel RA, Ji L, Lundgren BR, Nomura CT. Enhancing poly(3-hydroxyalkanoate) production in Escherichia coli by the removal of the regulatory gene arcA. AMB Express 2016; 6:120. [PMID: 27878786 PMCID: PMC5120623 DOI: 10.1186/s13568-016-0291-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 11/09/2016] [Indexed: 11/18/2022] Open
Abstract
Recombinant Escherichia coli is a desirable platform for the production of many biological compounds including poly(3-hydroxyalkanoates), a class of naturally occurring biodegradable polyesters with promising biomedical and material applications. Although the controlled production of desirable polymers is possible with the utilization of fatty acid feedstocks, a central challenge to this biosynthetic route is the improvement of the relatively low polymer yield, a necessary factor of decreasing the production costs. In this study we sought to address this challenge by deleting arcA and ompR, two global regulators with the capacity to inhibit the uptake and activation of exogenous fatty acids. We found that polymer yields in a ΔarcA mutant increased significantly with respect to the parental strain. In the parental strain, PHV yields were very low but improved 64-fold in the ΔarcA mutant (1.92-124 mg L-1) The ΔarcA mutant also allowed for modest increases in some medium chain length polymer yields, while weight average molecular weights improved by approximately 1.5-fold to 12-fold depending on the fatty acid substrate utilized. These results were supported by an analysis of differential gene expression, which showed that the key genes (fadD, fadL, and fadE) encoding fatty acid degradation enzymes were all upregulated by 2-, 10-, and 31-fold in an ΔarcA mutant, respectively. Additionally, the short chain length fatty acid uptake genes atoA, atoE and atoD were upregulated by 103-, 119-, and 303-fold respectively, though these values are somewhat inflated due to low expression in the parental strain. Overall, this study demonstrates that arcA is an important target to improve PHA production from fatty acids.
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Affiliation(s)
- Ryan A. Scheel
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, 1 Forestry Drive, Syracuse, NY 13210 USA
| | - Liyuan Ji
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, 1 Forestry Drive, Syracuse, NY 13210 USA
| | - Benjamin R. Lundgren
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, 1 Forestry Drive, Syracuse, NY 13210 USA
| | - Christopher T. Nomura
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, 1 Forestry Drive, Syracuse, NY 13210 USA
- Center for Applied Microbiology, State University of New York College of Environmental Science and Forestry, 1 Forestry Drive, Syracuse, NY 13210 USA
- Hubei Collaborative Center for Green Transformation of Bio-Resources, College of Life Sciences, Hubei University, Wuhan, 430062 China
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16
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Tsuge T. Fundamental factors determining the molecular weight of polyhydroxyalkanoate during biosynthesis. Polym J 2016. [DOI: 10.1038/pj.2016.78] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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17
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Characterization of binding preference of polyhydroxyalkanoate biosynthesis-related multifunctional protein PhaM from Ralstonia eutropha. Appl Microbiol Biotechnol 2016; 100:4413-21. [DOI: 10.1007/s00253-015-7225-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 12/02/2015] [Accepted: 12/05/2015] [Indexed: 10/22/2022]
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18
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Hiroe A, Shiraishi M, Mizuno K, Tsuge T. Behavior of different polyhydroxyalkanoate synthases in response to the ethanol level in Escherichia coli cultures. Polym J 2015. [DOI: 10.1038/pj.2015.53] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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19
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Tsuge T, Hyakutake M, Mizuno K. Class IV polyhydroxyalkanoate (PHA) synthases and PHA-producing Bacillus. Appl Microbiol Biotechnol 2015; 99:6231-40. [PMID: 26135986 DOI: 10.1007/s00253-015-6777-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Revised: 06/11/2015] [Accepted: 06/17/2015] [Indexed: 12/28/2022]
Abstract
This review highlights the recent investigations of class IV polyhydroxyalkanoate (PHA) synthases, the newest classification of PHA synthases. Class IV synthases are prevalent in organisms of the Bacillus genus and are composed of a catalytic subunit PhaC (approximately 40 kDa), which has a PhaC box sequence ([GS]-X-C-X-[GA]-G) at the active site, and a second subunit PhaR (approximately 20 kDa). The representative PHA-producing Bacillus strains are Bacillus megaterium and Bacillus cereus; the nucleotide sequence of phaC and the genetic organization of the PHA biosynthesis gene locus are somewhat different between these two strains. It is generally considered that class IV synthases favor short-chain-length monomers such as 3-hydroxybutyrate (C4) and 3-hydroxyvalerate (C5) for polymerization, but can polymerize some unusual monomers as minor components. In Escherichia coli expressing PhaRC from B. cereus YB-4, the biosynthesized PHA undergoes synthase-catalyzed alcoholytic cleavage using endogenous and exogenous alcohols. This alcoholysis is thought to be shared among class IV synthases, and this reaction is useful not only for the regulation of PHA molecular weight but also for the modification of the PHA carboxy terminus. The novel properties of class IV synthases will open up the possibility for the design of new PHA materials.
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Affiliation(s)
- Takeharu Tsuge
- Department of Innovative and Engineered Materials, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8502, Japan,
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20
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Hyakutake M, Tomizawa S, Sugahara I, Murata E, Mizuno K, Abe H, Tsuge T. Carboxy-terminal modification of polyhydroxyalkanoate (PHA) via alcoholysis reaction catalyzed by Class IV PHA synthase. Polym Degrad Stab 2015. [DOI: 10.1016/j.polymdegradstab.2015.04.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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21
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Malik MR, Yang W, Patterson N, Tang J, Wellinghoff RL, Preuss ML, Burkitt C, Sharma N, Ji Y, Jez JM, Peoples OP, Jaworski JG, Cahoon EB, Snell KD. Production of high levels of poly-3-hydroxybutyrate in plastids of Camelina sativa seeds. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:675-88. [PMID: 25418911 DOI: 10.1111/pbi.12290] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 10/07/2014] [Indexed: 05/20/2023]
Abstract
Poly-3-hydroxybutyrate (PHB) production in plastids of Camelina sativa seeds was investigated by comparing levels of polymer produced upon transformation of plants with five different binary vectors containing combinations of five seed-specific promoters for expression of transgenes. Genes encoding PHB biosynthetic enzymes were modified at the N-terminus to encode a plastid targeting signal. PHB levels of up to 15% of the mature seed weight were measured in single sacrificed T1 seeds with a genetic construct containing the oleosin and glycinin promoters. A more detailed analysis of the PHB production potential of two of the best performing binary vectors in a Camelina line bred for larger seed size yielded lines containing up to 15% polymer in mature T2 seeds. Transmission electron microscopy showed the presence of distinct granules of PHB in the seeds. PHB production had varying effects on germination, emergence and survival of seedlings. Once true leaves formed, plants grew normally and were able to set seeds. PHB synthesis lowered the total oil but not the protein content of engineered seeds. A change in the oil fatty acid profile was also observed. High molecular weight polymer was produced with weight-averaged molecular weights varying between 600 000 and 1 500 000, depending on the line. Select lines were advanced to later generations yielding a line with 13.7% PHB in T4 seeds. The levels of polymer produced in this study are the highest reported to date in a seed and are an important step forward for commercializing an oilseed-based platform for PHB production.
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Affiliation(s)
| | - Wenyu Yang
- Donald Danforth Plant Science Center, Saint Louis, MO, USA
| | | | | | | | - Mary L Preuss
- Donald Danforth Plant Science Center, Saint Louis, MO, USA
- Department of Biological Sciences, Webster University, Saint Louis, MO, USA
| | | | | | - Yuanyuan Ji
- Metabolix Oilseeds Inc, Saskatoon, SK, Canada
| | - Joseph M Jez
- Donald Danforth Plant Science Center, Saint Louis, MO, USA
- Department of Biology, Washington University, Saint Louis, MO, USA
| | | | - Jan G Jaworski
- Donald Danforth Plant Science Center, Saint Louis, MO, USA
| | - Edgar B Cahoon
- Donald Danforth Plant Science Center, Saint Louis, MO, USA
- Center for Plant Science Innovation and Department of Biochemistry, University of Nebraska, Lincoln, NE, USA
| | - Kristi D Snell
- Metabolix Oilseeds Inc, Saskatoon, SK, Canada
- Metabolix Inc, Cambridge, MA, USA
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22
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Ushimaru K, Watanabe Y, Hiroe A, Tsuge T. A single-nucleotide substitution in phasin gene leads to enhanced accumulation of polyhydroxyalkanoate (PHA) in Escherichia coli harboring Aeromonas caviae PHA biosynthetic operon. J GEN APPL MICROBIOL 2015; 61:63-6. [DOI: 10.2323/jgam.61.63] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Kazunori Ushimaru
- Department of Innovative and Engineered Materials, Tokyo Institute of Technology
| | - Yoriko Watanabe
- Department of Innovative and Engineered Materials, Tokyo Institute of Technology
| | - Ayaka Hiroe
- Department of Innovative and Engineered Materials, Tokyo Institute of Technology
| | - Takeharu Tsuge
- Department of Innovative and Engineered Materials, Tokyo Institute of Technology
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23
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Fukui T, Mukoyama M, Orita I, Nakamura S. Enhancement of glycerol utilization ability of Ralstonia eutropha H16 for production of polyhydroxyalkanoates. Appl Microbiol Biotechnol 2014; 98:7559-68. [PMID: 24878751 DOI: 10.1007/s00253-014-5831-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 05/13/2014] [Accepted: 05/13/2014] [Indexed: 11/25/2022]
Abstract
Ralstonia eutropha H16 is a well-studied bacterium with respect to biosynthesis of polyhydroxyalkanoates (PHAs), which has attracted attentions as biodegradable bio-based plastics. However, this strain shows quite poor growth on glycerol of which bulk supply has been increasing as a major by-product of biodiesel industries. This study examined enhancement of glycerol assimilation ability of R. eutropha H16 by introduction of the genes of aquaglyceroporin (glpF) and glycerol kinase (glpK) from Escherichia coli. Although introduction of glpFK Ec into the strain H16 using a multi-copy vector was not successful, a recombinant strain possessing glpFK Ec within the chromosome showed much faster growth on glycerol than H16. Further analyses clarified that weak expression of glpK Ec alone allowed to establish efficient glycerol assimilation pathway, indicating that the poor growth of H16 on glycerol was caused by insufficient kination activity to glycerol, as well as this strain had a potential ability for uptake of extracellular glycerol. The engineered strains expressing glpFK Ec or glpK Ec produced large amounts of poly[(R)-3-hydroxybutyrate] [P(3HB)] from glycerol with much higher productivity than H16. Unlike other glycerol-utilizable wild strains of R. eutropha, the H16-derived engineered strains accumulated P(3HB) with no significant decrease in molecular weights on glycerol, and the polydispersity index of the glycerol-based P(3HB) synthesized by the strains expressing glpFK Ec was lower than those by the parent strains. The present study demonstrated possibility of R. eutropha H16-based platform for production of useful compounds from inexpensive glycerol.
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Affiliation(s)
- Toshiaki Fukui
- Department of Bioengineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan,
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24
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Alcoholytic cleavage of polyhydroxyalkanoate chains by class IV synthases induced by endogenous and exogenous ethanol. Appl Environ Microbiol 2013; 80:1421-9. [PMID: 24334666 DOI: 10.1128/aem.03576-13] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Polyhydroxyalkanoate (PHA)-producing Bacillus strains express class IV PHA synthase, which is composed of the subunits PhaR and PhaC. Recombinant Escherichia coli expressing PHA synthase from Bacillus cereus strain YB-4 (PhaRCYB-4) showed an unusual reduction of the molecular weight of PHA produced during the stationary phase of growth. Nuclear magnetic resonance analysis of the low-molecular-weight PHA revealed that its carboxy end structure was capped by ethanol, suggesting that the molecular weight reduction was the result of alcoholytic cleavage of PHA chains by PhaRCYB-4 induced by endogenous ethanol. This scission reaction was also induced by exogenous ethanol in both in vivo and in vitro assays. In addition, PhaRCYB-4 was observed to have alcoholysis activity for PHA chains synthesized by other synthases. The PHA synthase from Bacillus megaterium (PhaRCBm) from another subgroup of class IV synthases was also assayed and was shown to have weak alcoholysis activity for PHA chains. These results suggest that class IV synthases may commonly share alcoholysis activity as an inherent feature.
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