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Zhang Y, Zheng Y, Hu Q, Hu Z, Sun J, Cheng P, Rao X, Jiang XR. Simultaneous multiplex genome loci editing of Halomonas bluephagenesis using an engineered CRISPR-guided base editor. Synth Syst Biotechnol 2024; 9:586-593. [PMID: 38720820 PMCID: PMC11076302 DOI: 10.1016/j.synbio.2024.04.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/15/2024] [Accepted: 04/23/2024] [Indexed: 05/12/2024] Open
Abstract
Halomonas bluephagenesis TD serves as an exceptional chassis for next generation industrial biotechnology to produce various products. However, the simultaneous editing of multiple loci in H. bluephagenesis TD remains a significant challenge. Herein, we report the development of a multiple loci genome editing system, named CRISPR-deaminase-assisted base editor (CRISPR-BE) in H. bluephagenesis TD. This system comprises two components: a cytidine (CRISPR-cBE) and an adenosine (CRISPR-aBE) deaminase-based base editor. CRISPR-cBE can introduce a cytidine to thymidine mutation with an efficiency of up to 100 % within a 7-nt editing window in H. bluephagenesis TD. Similarly, CRISPR-aBE demonstrates an efficiency of up to 100 % in converting adenosine to guanosine mutation within a 7-nt editing window. CRISPR-cBE has been further validated and successfully employed for simultaneous multiplexed editing in H. bluephagenesis TD. Our findings reveal that CRISPR-cBE efficiently inactivated all six copies of the IS1086 gene simultaneously by introducing stop codon. This system achieved an editing efficiency of 100 % and 41.67 % in inactivating two genes and three genes, respectively. By substituting the Pcas promoter with the inducible promoter PMmp1, we optimized CRISPR-cBE system and ultimately achieved 100 % editing efficiency in inactivating three genes. In conclusion, our research offers a robust and efficient method for concurrently modifying multiple loci in H. bluephagenesis TD, opening up vast possibilities for industrial applications in the future.
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Affiliation(s)
- Yulin Zhang
- Medical Research Institute, Southwest University, Chongqing, 400716, China
| | - Yang Zheng
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Chongqing, 400038, China
| | - Qiwen Hu
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Chongqing, 400038, China
| | - Zhen Hu
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Chongqing, 400038, China
| | - Jiyuan Sun
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Chongqing, 400038, China
| | - Ping Cheng
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Chongqing, 400038, China
| | - Xiancai Rao
- Medical Research Institute, Southwest University, Chongqing, 400716, China
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Chongqing, 400038, China
| | - Xiao-Ran Jiang
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Chongqing, 400038, China
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Gu S, Zhu F, Zhang L, Wen J. Mid-Long Chain Dicarboxylic Acid Production via Systems Metabolic Engineering: Progress and Prospects. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:5555-5573. [PMID: 38442481 DOI: 10.1021/acs.jafc.4c00002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Mid-to-long-chain dicarboxylic acids (DCAi, i ≥ 6) are organic compounds in which two carboxylic acid functional groups are present at the terminal position of the carbon chain. These acids find important applications as structural components and intermediates across various industrial sectors, including organic compound synthesis, food production, pharmaceutical development, and agricultural manufacturing. However, conventional petroleum-based DCA production methods cause environmental pollution, making sustainable development challenging. Hence, the demand for eco-friendly processes and renewable raw materials for DCA production is rising. Owing to advances in systems metabolic engineering, new tools from systems biology, synthetic biology, and evolutionary engineering can now be used for the sustainable production of energy-dense biofuels. Here, we explore systems metabolic engineering strategies for DCA synthesis in various chassis via the conversion of different raw materials into mid-to-long-chain DCAs. Subsequently, we discuss the future challenges in this field and propose synthetic biology approaches for the efficient production and successful commercialization of these acids.
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Affiliation(s)
- Shanna Gu
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072,China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072,China
- SINOPEC Dalian Research Institute of Petroleum and Petrochemicals Co., Ltd, Dalian 116045, China
| | - Fuzhou Zhu
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072,China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072,China
| | - Lin Zhang
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072,China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072,China
- SINOPEC Dalian Research Institute of Petroleum and Petrochemicals Co., Ltd, Dalian 116045, China
| | - Jianping Wen
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072,China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072,China
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Neoh SZ, Tan HT, Trakunjae C, Chek MF, Vaithanomsat P, Hakoshima T, Sudesh K. N-terminal truncation of PhaC BP-M-CPF4 and its effect on PHA production. Microb Cell Fact 2024; 23:52. [PMID: 38360657 PMCID: PMC10867992 DOI: 10.1186/s12934-024-02329-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/07/2024] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND Among the polyhydroxyalkanoate (PHA), poly[(R)-3-hydroxybutyrate-co-(R)-3-hydroxyhexanoate] [P(3HB-co-3HHx)] is reported to closely resemble polypropylene and low-density polyethylene. Studies have shown that PHA synthase (PhaC) from mangrove soil (PhaCBP-M-CPF4) is an efficient PhaC for P(3HB-co-3HHx) production and N-termini of PhaCs influence its substrate specificity, dimerization, granule morphology, and molecular weights of PHA produced. This study aims to further improve PhaCBP-M-CPF4 through N-terminal truncation. RESULTS The N-terminal truncated mutants of PhaCBP-M-CPF4 were constructed based on the information of the predicted secondary and tertiary structures using PSIPRED server and AlphaFold2 program, respectively. The N-terminal truncated PhaCBP-M-CPF4 mutants were evaluated in C. necator mutant PHB-4 based on the cell dry weight, PHA content, 3HHx molar composition, molecular weights, and granule morphology of the PHA granules. The results showed that most transformants harbouring the N-terminal truncated PhaCBP-M-CPF4 showed a reduction in PHA content and cell dry weight except for PhaCBP-M-CPF4 G8. PhaCBP-M-CPF4 G8 and A27 showed an improved weight-average molecular weight (Mw) of PHA produced due to lower expression of the truncated PhaCBP-M-CPF4. Transformants harbouring PhaCBP-M-CPF4 G8, A27, and T74 showed a reduction in the number of granules. PhaCBP-M-CPF4 G8 produced higher Mw PHA in mostly single larger PHA granules with comparable production as the full-length PhaCBP-M-CPF4. CONCLUSION This research showed that N-terminal truncation had effects on PHA accumulation, substrate specificity, Mw, and granule morphology. This study also showed that N-terminal truncation of the amino acids that did not adopt any secondary structure can be an alternative to improve PhaCs for the production of PHA with higher Mw in mostly single larger granules.
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Affiliation(s)
- Soon Zher Neoh
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800 USM, Pulau Pinang, Penang, Malaysia
| | - Hua Tiang Tan
- Structural Biology Laboratory, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Chanaporn Trakunjae
- Kasetsart Agricultural and Agro-Industrial Product Improvement Institute (KAPI), Kasetsart University, Bangkok, 10900, Thailand
| | - Min Fey Chek
- Structural Biology Laboratory, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Pilanee Vaithanomsat
- Kasetsart Agricultural and Agro-Industrial Product Improvement Institute (KAPI), Kasetsart University, Bangkok, 10900, Thailand
| | - Toshio Hakoshima
- Structural Biology Laboratory, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Kumar Sudesh
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800 USM, Pulau Pinang, Penang, Malaysia.
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Diankristanti PA, Lin YC, Yi YC, Ng IS. Polyhydroxyalkanoates bioproduction from bench to industry: Thirty years of development towards sustainability. BIORESOURCE TECHNOLOGY 2024; 393:130149. [PMID: 38049017 DOI: 10.1016/j.biortech.2023.130149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/06/2023]
Abstract
The pursuit of carbon neutrality goals has sparked considerable interest in expanding bioplastics production from microbial cell factories. One prominent class of bioplastics, polyhydroxyalkanoates (PHA), is generated by specific microorganisms, serving as carbon and energy storage materials. To begin with, a native PHA producer, Cupriavidus necator (formerly Ralstonia eutropha) is extensively studied, covering essential topics such as carbon source selection, cultivation techniques, and accumulation enhancement strategies. Recently, various hosts including archaea, bacteria, cyanobacteria, yeast, and plants have been explored, stretching the limit of microbial PHA production. This review provides a comprehensive overview of current advancements in PHA bioproduction, spanning from the native to diversified cell factories. Recovery and purification techniques are discussed, and the current status of industrial applications is assessed as a critical milestone for startups. Ultimately, it concludes by addressing contemporary challenges and future prospects, offering insights into the path towards reduced carbon emissions and sustainable development goals.
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Affiliation(s)
| | - Yu-Chieh Lin
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Ying-Chen Yi
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan; Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, USA
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan.
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Zhang J, Yan X, Park H, Scrutton NS, Chen T, Chen GQ. Nonsterile microbial production of chemicals based on Halomonas spp. Curr Opin Biotechnol 2024; 85:103064. [PMID: 38262074 DOI: 10.1016/j.copbio.2023.103064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 10/09/2023] [Accepted: 12/30/2023] [Indexed: 01/25/2024]
Abstract
The use of extremophile organisms such as Halomomas spp. can eliminate the need for fermentation sterilization, significantly reducing process costs. Microbial fermentation is considered a pivotal strategy to reduce reliance on fossil fuel resources; however, sustainable processes continue to incur higher costs than their chemical industry counterparts. Most organisms require equipment sterilization to prevent contamination, a practice that introduces complexity and financial strain. Fermentations involving extremophile organisms can eliminate the sterilization process, relying instead on conditions that are conductive solely to the growth of the desired organism. This review discusses current challenges in pilot- and industrial-scale bioproduction when using the extremophile bacteria Halomomas spp. under nonsterile conditions.
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Affiliation(s)
- Jing Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin 300072, China
| | - Xu Yan
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Helen Park
- School of Life Sciences, Tsinghua University, Beijing 100084, China; EPSRC/BBSRC Future Biomanufacturing Research Hub, BBSRC Synthetic Biology Research Centre, SYNBIOCHEM, Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Sciences, The University of Manchester, Manchester, UK
| | - Nigel S Scrutton
- EPSRC/BBSRC Future Biomanufacturing Research Hub, BBSRC Synthetic Biology Research Centre, SYNBIOCHEM, Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Sciences, The University of Manchester, Manchester, UK
| | - Tao Chen
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin 300072, China.
| | - Guo-Qiang Chen
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; MOE Key Lab for Industrial Biocatalysis, Dept Chemical Engineering, Tsinghua University, Beijing 100084, China.
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6
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Cywar RM, Ling C, Clarke RW, Kim DH, Kneucker CM, Salvachúa D, Addison B, Hesse SA, Takacs CJ, Xu S, Demirtas MU, Woodworth SP, Rorrer NA, Johnson CW, Tassone CJ, Allen RD, Chen EYX, Beckham GT. Elastomeric vitrimers from designer polyhydroxyalkanoates with recyclability and biodegradability. SCIENCE ADVANCES 2023; 9:eadi1735. [PMID: 37992173 PMCID: PMC10664982 DOI: 10.1126/sciadv.adi1735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 10/23/2023] [Indexed: 11/24/2023]
Abstract
Cross-linked elastomers are stretchable materials that typically are not recyclable or biodegradable. Medium-chain-length polyhydroxyalkanoates (mcl-PHAs) are soft and ductile, making these bio-based polymers good candidates for biodegradable elastomers. Elasticity is commonly imparted by a cross-linked network structure, and covalent adaptable networks have emerged as a solution to prepare recyclable thermosets via triggered rearrangement of dynamic covalent bonds. Here, we develop biodegradable and recyclable elastomers by chemically installing the covalent adaptable network within biologically produced mcl-PHAs. Specifically, an engineered strain of Pseudomonas putida was used to produce mcl-PHAs containing pendent terminal alkenes as chemical handles for postfunctionalization. Thiol-ene chemistry was used to incorporate boronic ester (BE) cross-links, resulting in PHA-based vitrimers. mcl-PHAs cross-linked with BE at low density (<6 mole %) affords a soft, elastomeric material that demonstrates thermal reprocessability, biodegradability, and denetworking at end of life. The mechanical properties show potential for applications including adhesives and soft, biodegradable robotics and electronics.
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Affiliation(s)
- Robin M. Cywar
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- BOTTLE Consortium, Golden, CO 80401, USA
| | - Chen Ling
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- Agile BioFoundry, Golden, CO 80401, USA
| | - Ryan W. Clarke
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- BOTTLE Consortium, Golden, CO 80401, USA
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523-1872, USA
| | - Dong Hyun Kim
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- Agile BioFoundry, Golden, CO 80401, USA
| | - Colin M. Kneucker
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- Agile BioFoundry, Golden, CO 80401, USA
| | - Davinia Salvachúa
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- Agile BioFoundry, Golden, CO 80401, USA
| | - Bennett Addison
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Sarah A. Hesse
- BOTTLE Consortium, Golden, CO 80401, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Christopher J. Takacs
- BOTTLE Consortium, Golden, CO 80401, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Shu Xu
- Applied Materials Division, Argonne National Laboratory, Lemont, IL 60439, USA
- Northwestern Argonne Institute of Science and Engineering, 2205 Tech Drive, Suite 1160, Evanston, IL 60208, USA
| | | | - Sean P. Woodworth
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- BOTTLE Consortium, Golden, CO 80401, USA
| | - Nicholas A. Rorrer
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- BOTTLE Consortium, Golden, CO 80401, USA
| | - Christopher W. Johnson
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- Agile BioFoundry, Golden, CO 80401, USA
| | - Christopher J. Tassone
- BOTTLE Consortium, Golden, CO 80401, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Robert D. Allen
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- BOTTLE Consortium, Golden, CO 80401, USA
| | - Eugene Y.-X. Chen
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523-1872, USA
| | - Gregg T. Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- BOTTLE Consortium, Golden, CO 80401, USA
- Agile BioFoundry, Golden, CO 80401, USA
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7
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Ye JW, Lin YN, Yi XQ, Yu ZX, Liu X, Chen GQ. Synthetic biology of extremophiles: a new wave of biomanufacturing. Trends Biotechnol 2023; 41:342-357. [PMID: 36535816 DOI: 10.1016/j.tibtech.2022.11.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/12/2022] [Accepted: 11/25/2022] [Indexed: 12/23/2022]
Abstract
Microbial biomanufacturing, powered by the advances of synthetic biology, has attracted growing interest for the production of diverse products. In contrast to conventional microbes, extremophiles have shown better performance for low-cost production owing to their outstanding growth and synthesis capacity under stress conditions, allowing unsterilized fermentation processes. We review increasing numbers of products already manufactured utilizing extremophiles in recent years. In addition, genetic parts, molecular tools, and manipulation approaches for extremophile engineering are also summarized, and challenges and opportunities are predicted for non-conventional chassis. Next-generation industrial biotechnology (NGIB) based on engineered extremophiles promises to simplify biomanufacturing processes and achieve open and continuous fermentation, without sterilization, and utilizing low-cost substrates, making NGIB an attractive green process for sustainable manufacturing.
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Affiliation(s)
- Jian-Wen Ye
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China; Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China; Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Yi-Na Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China; Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China; Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Xue-Qing Yi
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhuo-Xuan Yu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Xu Liu
- PhaBuilder Biotech Company, Shunyi District, Zhaoquan Ying, Beijing 101309, China
| | - Guo-Qiang Chen
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; Ministry of Education (MOE) Laboratory of Industrial Biocatalysis, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing, China.
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8
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Liu W, Cong B, Lin J, Zhao L, Liu S. Complete genome sequencing and comparison of two nitrogen-metabolizing bacteria isolated from Antarctic deep-sea sediment. BMC Genomics 2022; 23:713. [PMID: 36261793 PMCID: PMC9580203 DOI: 10.1186/s12864-022-08942-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 10/13/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bacteria are an essential component of the earth`s biota and affect circulation of matters through their metabolic activity. They also play an important role in the carbon and nitrogen cycle in the deep-sea environment. In this paper, two strains from deep-sea sediments were investigated in order to understand nitrogen cycling involved in the deep-sea environment. RESULTS In this paper, the basic genomic information of two strains was obtained by whole genome sequencing. The Cobetia amphilecti N-80 and Halomonas profundus 13 genome sizes are 4,160,095 bp with a GC content of 62.5% and 5,251,450 bp with a GC content of 54.84%. Through a comparison of functional analyses, we predicted the possible C and N metabolic pathways of the two strains and determined that Halomonas profundus 13 could use more carbon sources than Cobetia amphilecti N-80. The main genes associated with N metabolism in Halomonas profundus 13 are narG, narY, narI, nirS, norB, norC, nosZ, and nirD. On the contrast, nirD, using NH4+ for energy, plays a main role in Cobetia amphilecti N-80. Both of them have the same genes for fixing inorganic carbon: icd, ppc, fdhA, accC, accB, accD, and accA. CONCLUSION In this study, the whole genomes of two strains were sequenced to clarify the basic characteristics of their genomes, laying the foundation for further studying nitrogen-metabolizing bacteria. Halomonas profundus 13 can utilize more carbon sources than Cobetia amphilecti N-80, as indicated by API as well as COG and KEGG prediction results. Finally, through the analysis of the nitrification and denitrification abilities as well as the inorganic carbon fixation ability of the two strains, the related genes were identified, and the possible metabolic pathways were predicted. Together, these results provide molecular markers and theoretical support for the mechanisms of inorganic carbon fixation by deep-sea microorganisms.
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Affiliation(s)
- Wenqi Liu
- School of Advanced Manufacturing, Fuzhou University, Fuzhou, 350108, China
| | - Bailin Cong
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China.
| | - Jing Lin
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Linlin Zhao
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Shenghao Liu
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
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9
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Halomonas spp., as chassis for low-cost production of chemicals. Appl Microbiol Biotechnol 2022; 106:6977-6992. [PMID: 36205763 DOI: 10.1007/s00253-022-12215-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 11/02/2022]
Abstract
Halomonas spp. are the well-studied platform organisms or chassis for next-generation industrial biotechnology (NGIB) due to their contamination-resistant nature combined with their fast growth property. Several Halomonas spp. have been studied regarding their genomic information and molecular engineering approaches. Halomonas spp., especially Halomonas bluephagenesis, have been engineered to produce various biopolyesters such as polyhydroxyalkanoates (PHA), proteins including surfactants and enzymes, small molecular compounds including amino acids and derivates, as well as organic acids. This paper reviews all the progress reported in the last 10 years regarding this robust microbial cell factory. KEY POINTS: • Halomonas spp. are robust chassis for low-cost production of chemicals • Genomic information of some Halomonas spp. has been revealed • Molecular tools and approaches for Halomonas spp. have been developed • Halomonas spp. are becoming more and more important for biotechnology.
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10
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Zhou Y, Kumar V, Harirchi S, Vigneswaran VS, Rajendran K, Sharma P, Wah Tong Y, Binod P, Sindhu R, Sarsaiya S, Balakrishnan D, Mofijur M, Zhang Z, Taherzadeh MJ, Kumar Awasthi M. Recovery of value-added products from biowaste: A review. BIORESOURCE TECHNOLOGY 2022; 360:127565. [PMID: 35788392 DOI: 10.1016/j.biortech.2022.127565] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
This review provides an update on the state-of-the art technologies for the valorization of solid waste and its mechanism to generate various bio-products. The organic content of these wastes can be easily utilized by the microbes and produce value-added compounds. Microbial fermentation techniques can be utilized for developing waste biorefinery processes. The utilization of lignocellulosic and plastics wastes for the generation of carbon sources for microbial utilization after pre-processing steps will make the process a multi-product biorefinery. The C1 and C2 gases generated from different industries could also be utilized by various microbes, and this will help to control global warming. The review seeks to expand expertise about the potential application through several perspectives, factors influencing remediation, issues, and prospects.
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Affiliation(s)
- Yuwen Zhou
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Vinay Kumar
- Department of Biotechnology, Indian Institute of Technology (IIT) Roorkee, Roorkee 247667, Uttarakhand, India
| | - Sharareh Harirchi
- Swedish Centre for Resource Recovery, University of Borås, Borås 50190, Sweden
| | - V S Vigneswaran
- Department of Environmental Science and Engineering, School of Engineering and Sciences, SRM University-AP, Amaravati, Andhra Pradesh 522240, India
| | - Karthik Rajendran
- Department of Environmental Science and Engineering, School of Engineering and Sciences, SRM University-AP, Amaravati, Andhra Pradesh 522240, India
| | - Pooja Sharma
- Environmental Research Institute, National University of Singapore, 1 Create Way, 138602, Singapore; Energy and Environmental Sustainability for Megacities (E2S2) Phase II, Campus for Research Excellence and Technology Enterprise (CREATE), 1 CREATE Way, Singapore 138602, Singapore
| | - Yen Wah Tong
- Environmental Research Institute, National University of Singapore, 1 Create Way, 138602, Singapore; Energy and Environmental Sustainability for Megacities (E2S2) Phase II, Campus for Research Excellence and Technology Enterprise (CREATE), 1 CREATE Way, Singapore 138602, Singapore; Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive, 117585, Singapore
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695 019, Kerala, India
| | - Raveendran Sindhu
- Department of Food Technology, TKM Institute of Technology, Kollam 691505, Kerala, India
| | - Surendra Sarsaiya
- Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, China
| | - Deepanraj Balakrishnan
- Department of Mechanical Engineering, College of Engineering, Prince Mohammad Bin Fahd University, Al Khobar, 31952, Saudi Arabia
| | - M Mofijur
- Faculty of Engineering and IT, University of Technology Sydney, NSW 2007, Australia; Mechanical Engineering Department, Prince Mohammad Bin Fahd University, Al Khobar 31952, Saudi Arabia
| | - Zengqiang Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | | | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China.
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11
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Baseline proteomics characterisation of the emerging host biomanufacturing organism Halomonas bluephagenesis. Sci Data 2022; 9:492. [PMID: 35963929 PMCID: PMC9376085 DOI: 10.1038/s41597-022-01610-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 08/03/2022] [Indexed: 11/12/2022] Open
Abstract
Despite its greener credentials, biomanufacturing remains financially uncompetitive compared with the higher carbon emitting, hydrocarbon-based chemical industry. Replacing traditional chassis such as E. coli with novel robust organisms, are a route to cost reduction for biomanufacturing. Extremophile bacteria such as the halophilic Halomonas bluephagenesis TD01 exemplify this potential by thriving in environments inherently inimical to other organisms, so reducing sterilisation costs. Novel chassis are inevitably less well annotated than established organisms. Rapid characterisation along with community data sharing will facilitate adoption of such organisms for biomanufacturing. The data record comprises a newly sequenced genome for the organism and evidence via LC-MS based proteomics for expression of 1160 proteins (30% of the proteome) including baseline quantification of 1063 proteins (27% of the proteome), and a spectral library enabling re-use for targeted LC-MS proteomics assays. Protein data are annotated with KEGG Orthology, enabling rapid matching of quantitative data to pathways of interest to biomanufacturing. Measurement(s) | Genome • Proteomic Profile | Technology Type(s) | PacBio Sequel System • nanoflow liquid chromatography-electrospray ionisation mass spectrometry | Sample Characteristic - Organism | Halomonas sp. TD01 |
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12
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Biopolymer production in microbiology by application of metabolic engineering. Polym Bull (Berl) 2022. [DOI: 10.1007/s00289-021-03820-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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13
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Gao Q, Yang H, Wang C, Xie XY, Liu KX, Lin Y, Han SY, Zhu M, Neureiter M, Lin Y, Ye JW. Advances and trends in microbial production of polyhydroxyalkanoates and their building blocks. Front Bioeng Biotechnol 2022; 10:966598. [PMID: 35928942 PMCID: PMC9343942 DOI: 10.3389/fbioe.2022.966598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 07/01/2022] [Indexed: 11/13/2022] Open
Abstract
With the rapid development of synthetic biology, a variety of biopolymers can be obtained by recombinant microorganisms. Polyhydroxyalkanoates (PHA) is one of the most popular one with promising material properties, such as biodegradability and biocompatibility against the petrol-based plastics. This study reviews the recent studies focusing on the microbial synthesis of PHA, including chassis engineering, pathways engineering for various substrates utilization and PHA monomer synthesis, and PHA synthase modification. In particular, advances in metabolic engineering of dominant workhorses, for example Halomonas, Ralstonia eutropha, Escherichia coli and Pseudomonas, with outstanding PHA accumulation capability, were summarized and discussed, providing a full landscape of diverse PHA biosynthesis. Meanwhile, we also introduced the recent efforts focusing on structural analysis and mutagenesis of PHA synthase, which significantly determines the polymerization activity of varied monomer structures and PHA molecular weight. Besides, perspectives and solutions were thus proposed for achieving scale-up PHA of low cost with customized material property in the coming future.
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Affiliation(s)
- Qiang Gao
- Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, QH, China
| | - Hao Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Chi Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Xin-Ying Xie
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Kai-Xuan Liu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Ying Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Shuang-Yan Han
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Mingjun Zhu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Markus Neureiter
- Institute for Environmental Biotechnology, Department of Agrobiotechnology, University of Natural Resources and Life Sciences, Tulln, Austria
- *Correspondence: Markus Neureiter, ; Yina Lin, ; Jian-Wen Ye,
| | - Yina Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
- *Correspondence: Markus Neureiter, ; Yina Lin, ; Jian-Wen Ye,
| | - Jian-Wen Ye
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
- *Correspondence: Markus Neureiter, ; Yina Lin, ; Jian-Wen Ye,
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14
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From Organic Wastes and Hydrocarbons Pollutants to Polyhydroxyalkanoates: Bioconversion by Terrestrial and Marine Bacteria. SUSTAINABILITY 2022. [DOI: 10.3390/su14148241] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The use of fossil-based plastics has become unsustainable because of the polluting production processes, difficulties for waste management sectors, and high environmental impact. Polyhydroxyalkanoates (PHA) are bio-based biodegradable polymers derived from renewable resources and synthesized by bacteria as intracellular energy and carbon storage materials under nutrients or oxygen limitation and through the optimization of cultivation conditions with both pure and mixed culture systems. The PHA properties are affected by the same principles of oil-derived polyolefins, with a broad range of compositions, due to the incorporation of different monomers into the polymer matrix. As a consequence, the properties of such materials are represented by a broad range depending on tunable PHA composition. Producing waste-derived PHA is technically feasible with mixed microbial cultures (MMC), since no sterilization is required; this technology may represent a solution for waste treatment and valorization, and it has recently been developed at the pilot scale level with different process configurations where aerobic microorganisms are usually subjected to a dynamic feeding regime for their selection and to a high organic load for the intracellular accumulation of PHA. In this review, we report on studies on terrestrial and marine bacteria PHA-producers. The available knowledge on PHA production from the use of different kinds of organic wastes, and otherwise, petroleum-polluted natural matrices coupling bioremediation treatment has been explored. The advancements in these areas have been significant; they generally concern the terrestrial environment, where pilot and industrial processes are already established. Recently, marine bacteria have also offered interesting perspectives due to their advantageous effects on production practices, which they can relieve several constraints. Studies on the use of hydrocarbons as carbon sources offer evidence for the feasibility of the bioconversion of fossil-derived plastics into bioplastics.
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15
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Borrero‐de Acuña JM, Poblete‐Castro I. Rational engineering of natural polyhydroxyalkanoates producing microorganisms for improved synthesis and recovery. Microb Biotechnol 2022; 16:262-285. [PMID: 35792877 PMCID: PMC9871526 DOI: 10.1111/1751-7915.14109] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 06/14/2022] [Indexed: 01/27/2023] Open
Abstract
Microbial production of biopolymers derived from renewable substrates and waste streams reduces our heavy reliance on petrochemical plastics. One of the most important biodegradable polymers is the family of polyhydroxyalkanoates (PHAs), naturally occurring intracellular polyoxoesters produced for decades by bacterial fermentation of sugars and fatty acids at the industrial scale. Despite the advances, PHA production still suffers from heavy costs associated with carbon substrates and downstream processing to recover the intracellular product, thus restricting market positioning. In recent years, model-aided metabolic engineering and novel synthetic biology approaches have spurred our understanding of carbon flux partitioning through competing pathways and cellular resource allocation during PHA synthesis, enabling the rational design of superior biopolymer producers and programmable cellular lytic systems. This review describes these attempts to rationally engineering the cellular operation of several microbes to elevate PHA production on specific substrates and waste products. We also delve into genome reduction, morphology, and redox cofactor engineering to boost PHA biosynthesis. Besides, we critically evaluate engineered bacterial strains in various fermentation modes in terms of PHA productivity and the period required for product recovery.
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Affiliation(s)
| | - Ignacio Poblete‐Castro
- Biosystems Engineering LaboratoryDepartment of Chemical and Bioprocess EngineeringUniversidad de Santiago de Chile (USACH)SantiagoChile
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16
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Xu M, Chang Y, Zhang Y, Wang W, Hong J, Zhao J, Lu X, Tan D. Development and Application of Transcription Terminators for Polyhydroxylkanoates Production in Halophilic Halomonas bluephagenesis TD01. Front Microbiol 2022; 13:941306. [PMID: 35832813 PMCID: PMC9271916 DOI: 10.3389/fmicb.2022.941306] [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: 05/11/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Halomonas bluephagenesis TD01 is one of the ideal chassis for low-cost industrial production based on “Next Generation Industrial Biotechnology,” yet the limited genetically regulatory parts such as transcriptional terminators, which are crucial for tuned regulations on gene expression, have hampered the engineering and applications of the strain. In this study, a series of intrinsic Rho-independent terminators were developed by either genome mining or rational design, and seven of them proved to exhibit higher efficiencies than the canonical strong T7 terminator, among which three terminators displayed high efficiencies over 90%. A preliminary modeling on the sequence-efficiency relationship of the terminators suggested that the poly U sequence regularity, the length and GC content of the stem, and the number and the size of hairpin loops remarkably affected the termination efficiency (TE). The rational and de novo designs of novel synthetic terminators based on the sequence-efficiency relationship and the “main contributor” engineering strategy proved to be effective, and fine-tuned polyhydroxylkanoates production was also achieved by the regulation of these native or synthetic terminators with different efficiencies. Furthermore, a perfectly positive correlation between the promoter activity and the TE was revealed in our study. The study enriches our knowledge of transcriptional termination via its sequence–strength relationship and enables the precise regulation of gene expression and PHA synthesis by intrinsic terminators, contributing to the extensive applications of H. bluephagenesis TD01 in the low-cost production of various chemicals.
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17
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Hammami K, Souissi Y, Souii A, Ouertani A, El-Hidri D, Jabberi M, Chouchane H, Mosbah A, Masmoudi AS, Cherif A, Neifar M. Extremophilic Bacterium Halomonas desertis G11 as a Cell Factory for Poly-3-Hydroxybutyrate-co-3-Hydroxyvalerate Copolymer’s Production. Front Bioeng Biotechnol 2022; 10:878843. [PMID: 35677302 PMCID: PMC9168272 DOI: 10.3389/fbioe.2022.878843] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/06/2022] [Indexed: 11/13/2022] Open
Abstract
Microbial polyhydroxyalkanoates (PHA) are biodegradable and biocompatible bio-based polyesters, which are used in various applications including packaging, medical and coating materials. In this study, an extremophilic hydrocarbonoclastic bacterium, previously isolated from saline sediment in the Tunisian desert, has been investigated for PHA production. The accumulation of intracellular PHA granules in Halomonas desertis G11 was detected by Nile blue A staining of the colonies. To achieve maximum PHA yield by the strain G11, the culture conditions were optimized through response surface methodology (RSM) employing a Box-Behnken Design (BBD) with three independent variables, namely, substrate concentration (1–5%), inoculum size (1–5%) and incubation time (5–15 days). Under optimized conditions, G11 strain produced 1.5 g/L (68% of DCW) of PHA using glycerol as a substrate. Application of NMR (1H and 13C) and FTIR spectroscopies showed that H. desertis accumulated PHA is a poly-3-hydroxybutyrate-co-3-hydroxyvalerate (PHBV). The genome analysis revealed the presence of typical structural genes involved in PHBV metabolism including phaA, phaB, phaC, phaP, phaZ, and phaR, coding for acetyl-CoA acetyltransferase, acetoacetyl-CoA reductase, class I polyhydroxyalkanoates synthases, phasin, polyhydroxyalkanoates depolymerase and polyhydroxyalkanoates synthesis repressor, respectively. Glycerol can be metabolized to 1) acetyl-CoA through the glycolysis pathway and subsequently converted to the 3HB monomer, and 2) to propionyl-CoA via the threonine biosynthetic pathway and subsequently converted to the 3HV monomer. In silico analysis of PhaC1 from H. desertis G11 indicated that this enzyme belongs to Class I PHA synthase family with a “lipase box”-like sequence (SYCVG). All these characteristics make the extremophilic bacterium H. desertis G11 a promising cell factory for the conversion of bio-renewable glycerol to high-value PHBV.
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Affiliation(s)
- Khouloud Hammami
- BVBGR-LR11ES31, Higher Institute of Biotechnology of Sidi Thabet (ISBST), University of Manouba, Ariana, Tunisia
| | - Yasmine Souissi
- BVBGR-LR11ES31, Higher Institute of Biotechnology of Sidi Thabet (ISBST), University of Manouba, Ariana, Tunisia
- Department of Engineering, German University of Technology in Oman, Muscat, Oman
| | - Amal Souii
- BVBGR-LR11ES31, Higher Institute of Biotechnology of Sidi Thabet (ISBST), University of Manouba, Ariana, Tunisia
| | - Awatef Ouertani
- BVBGR-LR11ES31, Higher Institute of Biotechnology of Sidi Thabet (ISBST), University of Manouba, Ariana, Tunisia
| | - Darine El-Hidri
- BVBGR-LR11ES31, Higher Institute of Biotechnology of Sidi Thabet (ISBST), University of Manouba, Ariana, Tunisia
| | - Marwa Jabberi
- BVBGR-LR11ES31, Higher Institute of Biotechnology of Sidi Thabet (ISBST), University of Manouba, Ariana, Tunisia
| | - Habib Chouchane
- BVBGR-LR11ES31, Higher Institute of Biotechnology of Sidi Thabet (ISBST), University of Manouba, Ariana, Tunisia
| | - Amor Mosbah
- BVBGR-LR11ES31, Higher Institute of Biotechnology of Sidi Thabet (ISBST), University of Manouba, Ariana, Tunisia
| | - Ahmed Slaheddine Masmoudi
- BVBGR-LR11ES31, Higher Institute of Biotechnology of Sidi Thabet (ISBST), University of Manouba, Ariana, Tunisia
| | - Ameur Cherif
- BVBGR-LR11ES31, Higher Institute of Biotechnology of Sidi Thabet (ISBST), University of Manouba, Ariana, Tunisia
| | - Mohamed Neifar
- BVBGR-LR11ES31, Higher Institute of Biotechnology of Sidi Thabet (ISBST), University of Manouba, Ariana, Tunisia
- APVA-LR16ES20, National School of Engineers of Sfax (ENIS), University of Sfax, Sfax, Tunisia
- *Correspondence: Mohamed Neifar,
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18
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Adaptive Laboratory Evolution of Halomonas bluephagenesis Enhances Acetate Tolerance and Utilization to Produce Poly(3-hydroxybutyrate). Molecules 2022; 27:molecules27093022. [PMID: 35566371 PMCID: PMC9103988 DOI: 10.3390/molecules27093022] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/02/2022] [Accepted: 05/06/2022] [Indexed: 11/17/2022] Open
Abstract
Acetate is a promising economical and sustainable carbon source for bioproduction, but it is also a known cell-growth inhibitor. In this study, adaptive laboratory evolution (ALE) with acetate as selective pressure was applied to Halomonas bluephagenesis TD1.0, a fast-growing and contamination-resistant halophilic bacterium that naturally accumulates poly(3-hydroxybutyrate) (PHB). After 71 transfers, the evolved strain, B71, was isolated, which not only showed better fitness (in terms of tolerance and utilization rate) to high concentrations of acetate but also produced a higher PHB titer compared with the parental strain TD1.0. Subsequently, overexpression of acetyl-CoA synthetase (ACS) in B71 resulted in a further increase in acetate utilization but a decrease in PHB production. Through whole-genome resequencing, it was speculated that genetic mutations (single-nucleotide variation (SNV) in phaB, mdh, and the upstream of OmpA, and insertion of TolA) in B71 might contribute to its improved acetate adaptability and PHB production. Finally, in a 5 L bioreactor with intermittent feeding of acetic acid, B71 was able to produce 49.79 g/L PHB and 70.01 g/L dry cell mass, which were 147.2% and 82.32% higher than those of TD1.0, respectively. These results highlight that ALE provides a reliable method to harness H. bluephagenesis to metabolize acetate for the production of PHB or other high-value chemicals more efficiently.
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19
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Ma Y, Zheng X, Lin Y, Zhang L, Yuan Y, Wang H, Winterburn J, Wu F, Wu Q, Ye JW, Chen GQ. Engineering an oleic acid-induced system for Halomonas, E. coli and Pseudomonas. Metab Eng 2022; 72:325-336. [PMID: 35513297 DOI: 10.1016/j.ymben.2022.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 03/11/2022] [Accepted: 04/20/2022] [Indexed: 11/17/2022]
Abstract
Ligand-induced system plays an important role for microbial engineering due to its tunable gene expression control over timings and levels. An oleic acid (OA)-induced system was recently constructed based on protein FadR, a transcriptional regulator involved in fatty acids metabolism, for metabolic control in Escherichia coli. In this study, we constructed a synthetic FadR-based OA-induced systems in Halomonas bluephagenesis by hybridizing the porin promoter core region and FadR-binding operator (fadO). The dynamic control range was optimized over 150-fold, and expression leakage was significantly reduced by tuning FadR expression and positioning fadO, forming a series of OA-induced systems with various expression strengths, respectively. Additionally, ligand orthogonality and cross-species portability were also studied and showed highly linear correlation among Halomonas spp., Escherichia coli and Pseudomonas spp. Finally, OA-induced systems with medium- and small-dynamic control ranges were employed to dynamically control the expression levels of morphology associated gene minCD, and monomer precursor 4-hydroxybutyrate-CoA (4HB-CoA) synthesis pathway for polyhydroxyalkanoates (PHA), respectively, in the presence of oleic acid as an inducer. As a result, over 10 g/L of poly-3-hydroxybutyrate (PHB) accumulated by elongated cell sizes, and 6 g/L of P(3HB-co-9.57 mol% 4HB) were obtained by controlling the dose and induction time of oleic acid only. This study provides a systematic approach for ligand-induced system engineering, and demonstrates an alternative genetic tool for dynamic control of industrial biotechnology.
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Affiliation(s)
- Yueyuan Ma
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xiangrui Zheng
- School of Life Sciences, Tsinghua University, Beijing, 100084, China; Department of Chemical Engineering and Analytical Science, The University of Manchester, Manchester, M13 9PL, United Kingdom
| | - Yina Lin
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Lizhan Zhang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yiping Yuan
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Huan Wang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - James Winterburn
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Manchester, M13 9PL, United Kingdom
| | - Fuqing Wu
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Qiong Wu
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jian-Wen Ye
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China; Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China; Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China.
| | - Guo-Qiang Chen
- School of Life Sciences, Tsinghua University, Beijing, 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China; MOE Key Laboratory for Industrial Biocatalysts, Dept Chemical Engineering, Tsinghua University, Beijing, 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing, China.
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20
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Luo CB, Li HC, Li DQ, Nawaz H, You TT, Xu F. Efficiently unsterile polyhydroxyalkanoate production from lignocellulose by using alkali-halophilic Halomonas alkalicola M2. BIORESOURCE TECHNOLOGY 2022; 351:126919. [PMID: 35240276 DOI: 10.1016/j.biortech.2022.126919] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 06/14/2023]
Abstract
The alkali-halophilic Halomonas alkalicola M2 was isolated and developed for an open unsterile polyhydroxyalkanoate (PHA) fermentation from lignocellulose at pH 10.0 and NaCl 70 g/L. The alkaline pretreatment liquid (APL) was converted into PHA by the strain, which was significantly affected by the cultural conditions, including pH, NaCl concentration, nitrogen source, and APL concentration. The extracted PHA was composed of three monomers and similar in physicochemical properties to conventional short chain-length PHA. A record yield of 2.1 and 5.9 g of PHA was accumulated from 100 g dry bamboo powder (BP) by using APL and APL combined with hydrolysate during a 48-h open unsterile fermentation process, respectively. In summary, the alkali-halophilic H. alkalicola M2 achieved the open unsterile fermentation for lignocellulose efficient bioconversion into PHA under high alkalinity and salinity conditions and would be an ideal producer in the field.
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Affiliation(s)
- Chao-Bing Luo
- Beijing Key Laboratory of Lignocellulosic Chemistry, Beijing Forestry University, Beijing 100083, PR China.
| | - Hai-Chao Li
- Beijing Key Laboratory of Lignocellulosic Chemistry, Beijing Forestry University, Beijing 100083, PR China.
| | - De-Qiang Li
- Beijing Key Laboratory of Lignocellulosic Chemistry, Beijing Forestry University, Beijing 100083, PR China.
| | - Haq Nawaz
- Beijing Key Laboratory of Lignocellulosic Chemistry, Beijing Forestry University, Beijing 100083, PR China.
| | - Ting-Ting You
- Beijing Key Laboratory of Lignocellulosic Chemistry, Beijing Forestry University, Beijing 100083, PR China.
| | - Feng Xu
- Beijing Key Laboratory of Lignocellulosic Chemistry, Beijing Forestry University, Beijing 100083, PR China; Shandong Key Laboratory of Paper Science & Technology, Qilu University of Technology, Jinan 250353, PR China.
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21
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Control of D-lactic acid content in P(LA-3HB) copolymer in the yeast Saccharomyces cerevisiae using a synthetic gene expression system. Metab Eng Commun 2022; 14:e00199. [PMID: 35571351 PMCID: PMC9095885 DOI: 10.1016/j.mec.2022.e00199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/26/2022] [Accepted: 04/22/2022] [Indexed: 11/22/2022] Open
Abstract
The fully biobased polyhydroxyalkanoate (PHA) polymers provide interesting alternatives for petrochemical derived plastic materials. The mechanical properties of some PHAs, including the common poly(3-hydroxybutyrate) (PHB), are limited, but tunable by addition of other monomers into the polymer chain. In this study we present a precise synthetic biology method to adjust lactate monomer fraction of a polymer by controlling the monomer formation in vivo at gene expression level, independent of cultivation conditions. We used the modified doxycycline-based Tet-On approach to adjust the expression of the stereospecific D-lactate dehydrogenase gene (ldhA) from Leuconostoc mesenteroides to control D-lactic acid formation in yeast Saccharomyces cerevisiae. The synthetic Tet-On transcription factor with a VP16 activation domain was continuously expressed and its binding to a synthetic promoter with eight transcription factor specific binding sites upstream of the ldhA gene was controlled with the doxycycline concentration in the media. The increase in doxycycline concentration correlated positively with ldhA expression, D-lactic acid production, poly(D-lactic acid) (PDLA) accumulation in vivo, and D-lactic acid content in the poly(D-lactate-co-3-hydroxybutyrate) P(LA-3HB) copolymer. We demonstrated that the D-lactic acid content of the P(LA-3HB) copolymer can be adjusted linearly from 6 mol% to 93 mol% in vivo in S. cerevisiae. These results highlight the power of controlling gene expression and monomer formation in the tuning of the polymer composition. In addition, we obtained 5.6% PDLA and 19% P(LA-3HB) of the cell dry weight (CDW), which are over two- and five-fold higher accumulation levels, respectively, than reported in the previous studies with yeast. We also compared two engineered PHA synthases and discovered that in S. cerevisiae the PHA synthase PhaC1437Ps6-19 produced P(LA-3HB) copolymers with lower D-lactic acid content, but with higher molecular weight, in comparison to the PHA synthase PhaC1Pre. P(LA-3HB) monomer structure was adjusted with controlled gene expression. Expression of D-lactate dehydrogenase (ldhA) was controlled with Tet-On approach. Lactic acid content in copolymer P(LA-3HB) was adjusted from 6 mol% up to 93 mol%. 5.6% PDLA and 19% P(LA-3HB) of cell dry weight (CDW) were obtained in S. cerevisiae. PhaC1437Ps6-19 P(LA-3HB) had lower D-lactic acid % than PhaC1Pre P(LA-3HB).
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22
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Yan X, Liu X, Yu LP, Wu F, Jiang XR, Chen GQ. Biosynthesis of diverse α,ω-diol-derived polyhydroxyalkanoates by engineered Halomonas bluephagenesis. Metab Eng 2022; 72:275-288. [DOI: 10.1016/j.ymben.2022.04.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/07/2022] [Accepted: 04/09/2022] [Indexed: 01/08/2023]
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23
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Zhang X, Liu XY, Yang H, Chen JN, Lin Y, Han SY, Cao Q, Zeng HS, Ye JW. A Polyhydroxyalkanoates-Based Carrier Platform of Bioactive Substances for Therapeutic Applications. Front Bioeng Biotechnol 2022; 9:798724. [PMID: 35071207 PMCID: PMC8767415 DOI: 10.3389/fbioe.2021.798724] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/02/2021] [Indexed: 12/13/2022] Open
Abstract
Bioactive substances (BAS), such as small molecule drugs, proteins, RNA, cells, etc., play a vital role in many therapeutic applications, especially in tissue repair and regeneration. However, the therapeutic effect is still a challenge due to the uncontrollable release and instable physico-chemical properties of bioactive components. To address this, many biodegradable carrier systems of micro-nano structures have been rapidly developed based on different biocompatible polymers including polyhydroxyalkanoates (PHA), the microbial synthesized polyesters, to provide load protection and controlled-release of BAS. We herein highlight the developments of PHA-based carrier systems in recent therapeutic studies, and give an overview of its prospective applications in various disease treatments. Specifically, the biosynthesis and material properties of diverse PHA polymers, designs and fabrication of micro- and nano-structure PHA particles, as well as therapeutic studies based on PHA particles, are summarized to give a comprehensive landscape of PHA-based BAS carriers and applications thereof. Moreover, recent efforts focusing on novel-type BAS nano-carriers, the functionalized self-assembled PHA granules in vivo, was discussed in this review, proposing the underlying innovations of designs and fabrications of PHA-based BAS carriers powered by synthetic biology. This review outlines a promising and applicable BAS carrier platform of novelty based on PHA particles for different medical uses.
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Affiliation(s)
- Xu Zhang
- Department of Chemical Engineering, Tsinghua University, Beijing, China
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, China
- Tsinghua-Peking Center of Life Sciences, Beijing, China
| | - Xin-Yi Liu
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Hao Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Jiang-Nan Chen
- Tsinghua-Peking Center of Life Sciences, Beijing, China
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Ying Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Shuang-Yan Han
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Qian Cao
- China Manned Space Agency, Beijing, China
| | - Han-Shi Zeng
- Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Jian-Wen Ye
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
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24
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Nanda S, Patra BR, Patel R, Bakos J, Dalai AK. Innovations in applications and prospects of bioplastics and biopolymers: a review. ENVIRONMENTAL CHEMISTRY LETTERS 2022; 20:379-395. [PMID: 34867134 PMCID: PMC8629338 DOI: 10.1007/s10311-021-01334-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 09/23/2021] [Indexed: 05/22/2023]
Abstract
Non-biodegradable plastics are continually amassing landfills and oceans worldwide while creating severe environmental issues and hazards to animal and human health. Plastic pollution has resulted in the death of millions of seabirds and aquatic animals. The worldwide production of plastics in 2020 has increased by 36% since 2010. This has generated significant interest in bioplastics to supplement global plastic demands. Bioplastics have several advantages over conventional plastics in terms of biodegradability, low carbon footprint, energy efficiency, versatility, unique mechanical and thermal characteristics, and societal acceptance. Bioplastics have huge potential to replace petroleum-based plastics in a wide range of industries from automobiles to biomedical applications. Here we review bioplastic polymers such as polyhydroxyalkanoate, polylactic acid, poly-3-hydroxybutyrate, polyamide 11, and polyhydroxyurethanes; and cellulose-based, starch-based, protein-based and lipid-based biopolymers. We discuss economic benefits, market scenarios, chemistry and applications of bioplastic polymers.
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Affiliation(s)
- Sonil Nanda
- Titan Clean Energy Projects Corporation, Craik, SK Canada
| | - Biswa R. Patra
- Department of Chemical and Biological Engineering, University of Saskatchewan, Saskatoon, SK Canada
| | - Ravi Patel
- Department of Chemical and Biological Engineering, University of Saskatchewan, Saskatoon, SK Canada
| | - Jamie Bakos
- Titan Clean Energy Projects Corporation, Craik, SK Canada
| | - Ajay K. Dalai
- Department of Chemical and Biological Engineering, University of Saskatchewan, Saskatoon, SK Canada
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25
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Obruča S, Dvořák P, Sedláček P, Koller M, Sedlář K, Pernicová I, Šafránek D. Polyhydroxyalkanoates synthesis by halophiles and thermophiles: towards sustainable production of microbial bioplastics. Biotechnol Adv 2022; 58:107906. [DOI: 10.1016/j.biotechadv.2022.107906] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/15/2021] [Accepted: 01/07/2022] [Indexed: 01/10/2023]
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Zhang J, Jin B, Hong K, Lv Y, Wang Z, Chen T. Cell Catalysis of Citrate to Itaconate by Engineered Halomonas bluephagenesis. ACS Synth Biol 2021; 10:3017-3027. [PMID: 34704752 DOI: 10.1021/acssynbio.1c00320] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Itaconic acid (IA), an important five-carbon unsaturated dicarboxylic acid, is one of the top 12 renewable chemicals with an urgent need to reduce industrial production costs. Halomonas bluephagenesis, which possesses the potential for cost-effective bioproduction of chemicals and organic acids due to its ability to grow under open nonsterile conditions and high tolerance to organic acid salts, was genetically engineered and used to produce IA from citrate by a cell catalytic strategy. Here, two essential genes (cis-aconitate decarboxylase encoding gene cadA and aconitase (ACN) encoding gene acn) were introduced into H. bluephagenesis to construct an IA biosynthesis pathway. Further engineering modifications including coexpression of molecular chaperones GroESL, increasing the copy number of the gene encoding rate-limiting enzyme ACN, and weakening the competing pathway were implemented. Under the optimized condition for the cell catalytic system, the engineered strain TAZI-08 produced 451.45 mM (58.73 g/L) IA from 500 mM citrate, with 93.24% conversion in 36 h and a productivity of 1.63 g/(L h). An intermittent feeding strategy further increased the IA titer to 488.86 mM (63.60 g/L). The IA titer and citrate conversion in H. bluephagenesis are the highest among heterologous hosts reported so far, demonstrating that this strain is a suitable chassis for hyperproduction of IA.
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Affiliation(s)
- Jing Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, China
| | - Biao Jin
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, China
| | - Kunqiang Hong
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, China
| | - You Lv
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Zhiwen Wang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, China
| | - Tao Chen
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, China
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27
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Zhang G, Ren X, Liang X, Wang Y, Feng D, Zhang Y, Xian M, Zou H. Improving the Microbial Production of Amino Acids: From Conventional Approaches to Recent Trends. BIOTECHNOL BIOPROC E 2021. [DOI: 10.1007/s12257-020-0390-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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28
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Halomonas as a chassis. Essays Biochem 2021; 65:393-403. [PMID: 33885142 PMCID: PMC8314019 DOI: 10.1042/ebc20200159] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/24/2021] [Accepted: 03/26/2021] [Indexed: 01/04/2023]
Abstract
With the rapid development of systems and synthetic biology, the non-model bacteria, Halomonas spp., have been developed recently to become a cost-competitive platform for producing a variety of products including polyesters, chemicals and proteins owing to their contamination resistance and ability of high cell density growth at alkaline pH and high salt concentration. These salt-loving microbes can partially solve the challenges of current industrial biotechnology (CIB) which requires high energy-consuming sterilization to prevent contamination as CIB is based on traditional chassis, typically, Escherichia coli, Bacillus subtilis, Pseudomonas putida and Corynebacterium glutamicum. The advantages and current status of Halomonas spp. including their molecular biology and metabolic engineering approaches as well as their applications are reviewed here. Moreover, a systematic strain engineering streamline, including product-based host development, genetic parts mining, static and dynamic optimization of modularized pathways and bioprocess-inspired cell engineering are summarized. All of these developments result in the term called next-generation industrial biotechnology (NGIB). Increasing efforts are made to develop their versatile cell factories powered by synthetic biology to demonstrate a new biomanufacturing strategy under open and continuous processes with significant cost-reduction on process complexity, energy, substrates and fresh water consumption.
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29
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Lhamo P, Behera SK, Mahanty B. Process optimization, metabolic engineering interventions and commercialization of microbial polyhydroxyalkanoates production - A state-of-the art review. Biotechnol J 2021; 16:e2100136. [PMID: 34132046 DOI: 10.1002/biot.202100136] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/29/2021] [Accepted: 06/03/2021] [Indexed: 12/31/2022]
Abstract
Microbial polyhydroxyalkanoates (PHAs) produced using renewable resources could be the best alternative for conventional plastics. Despite their incredible potential, commercial production of PHAs remains very low. Nevertheless, sincere attempts have been made by researchers to improve the yield and economic viability of PHA production by utilizing low-cost agricultural or industrial wastes. In this context, the use of efficient microbial culture or consortia, adoption of experimental design to trace ideal growth conditions, nutritional requirements, and intervention of metabolic engineering tools have gained significant attention. This review has been structured to highlight the important microbial sources for PHA production, use of conventional and non-conventional substrates, product optimization using experimental design, metabolic engineering strategies, and global players in the commercialization of PHA in the past two decades. The challenges about PHA recovery and analysis have also been discussed which possess indirect hurdle while expanding the horizon of PHA-based bioplastics. Selection of appropriate microorganism and substrate plays a vital role in improving the productivity and characteristics of PHAs. Experimental design-based bioprocess, use of metabolic engineering tools, and optimal product recovery techniques are invaluable in this dimension. Optimization strategies, which are being explored in isolation, need to be logically integrated for the successful commercialization of microbial PHAs.
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Affiliation(s)
- Pema Lhamo
- Department of Biotechnology, Karunya Institute of Technology and Sciences, Coimbatore, Tamil Nadu, India
| | - Shishir Kumar Behera
- Industrial Ecology Research Group, School of Chemical Engineering, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Biswanath Mahanty
- Department of Biotechnology, Karunya Institute of Technology and Sciences, Coimbatore, Tamil Nadu, India
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Bedade DK, Edson CB, Gross RA. Emergent Approaches to Efficient and Sustainable Polyhydroxyalkanoate Production. Molecules 2021; 26:3463. [PMID: 34200447 PMCID: PMC8201374 DOI: 10.3390/molecules26113463] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 05/25/2021] [Accepted: 05/27/2021] [Indexed: 11/16/2022] Open
Abstract
Petroleum-derived plastics dominate currently used plastic materials. These plastics are derived from finite fossil carbon sources and were not designed for recycling or biodegradation. With the ever-increasing quantities of plastic wastes entering landfills and polluting our environment, there is an urgent need for fundamental change. One component to that change is developing cost-effective plastics derived from readily renewable resources that offer chemical or biological recycling and can be designed to have properties that not only allow the replacement of current plastics but also offer new application opportunities. Polyhydroxyalkanoates (PHAs) remain a promising candidate for commodity bioplastic production, despite the many decades of efforts by academicians and industrial scientists that have not yet achieved that goal. This article focuses on defining obstacles and solutions to overcome cost-performance metrics that are not sufficiently competitive with current commodity thermoplastics. To that end, this review describes various process innovations that build on fed-batch and semi-continuous modes of operation as well as methods that lead to high cell density cultivations. Also, we discuss work to move from costly to lower cost substrates such as lignocellulose-derived hydrolysates, metabolic engineering of organisms that provide higher substrate conversion rates, the potential of halophiles to provide low-cost platforms in non-sterile environments for PHA formation, and work that uses mixed culture strategies to overcome obstacles of using waste substrates. We also describe historical problems and potential solutions to downstream processing for PHA isolation that, along with feedstock costs, have been an Achilles heel towards the realization of cost-efficient processes. Finally, future directions for efficient PHA production and relevant structural variations are discussed.
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Affiliation(s)
- Dattatray K. Bedade
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA;
| | - Cody B. Edson
- New York State Center for Polymer Synthesis, Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA;
| | - Richard A. Gross
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA;
- New York State Center for Polymer Synthesis, Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA;
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31
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Lee SM, Lee HJ, Kim SH, Suh MJ, Cho JY, Ham S, Song HS, Bhatia SK, Gurav R, Jeon JM, Yoon JJ, Choi KY, Kim JS, Lee SH, Yang YH. Engineering of Shewanella marisflavi BBL25 for biomass-based polyhydroxybutyrate production and evaluation of its performance in electricity production. Int J Biol Macromol 2021; 183:1669-1675. [PMID: 34023371 DOI: 10.1016/j.ijbiomac.2021.05.105] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 04/27/2021] [Accepted: 05/15/2021] [Indexed: 01/13/2023]
Abstract
Polyhydroxybutyrate (PHB) is a biodegradable plastic with physical properties similar to petrochemically derived plastics. Here, Shewanella marisflavi BBL25 was engineered by inserting the pLW487 vector containing polyhydroxyalkanoates synthesis genes from Ralstonia eutropha H16. Under optimal conditions, the engineered S. marisflavi BBL25 produced 1.99 ± 0.05 g/L PHB from galactose. The strain showed high tolerance to various inhibitors and could utilize lignocellulosic biomass for PHB production. When barley straw hydrolysates were used as a carbon source, PHB production was 3.27 ± 0.19 g/L. In addition, PHB production under the microbial fuel cell system was performed to confirm electricity coproduction. The maximum electricity current output density was 1.71 mA/cm2, and dry cell weight (DCW) and PHB production were 11.4 g/L and 6.31 g/L, respectively. Our results demonstrated PHB production using various lignocellulosic biomass and the feasibility of PHB and electricity production, simultaneously, and it is the first example of PHB production in engineered Shewanella.
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Affiliation(s)
- Sun Mi Lee
- Department of Biological Engineering, College of Engineering, Konkuk University, Republic of Korea
| | - Hong-Ju Lee
- Department of Biological Engineering, College of Engineering, Konkuk University, Republic of Korea
| | - Sang Hyun Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Republic of Korea
| | - Min Ju Suh
- Department of Biological Engineering, College of Engineering, Konkuk University, Republic of Korea
| | - Jang Yeon Cho
- Department of Biological Engineering, College of Engineering, Konkuk University, Republic of Korea
| | - Sion Ham
- Department of Biological Engineering, College of Engineering, Konkuk University, Republic of Korea
| | - Hun-Suk Song
- Department of Biological Engineering, College of Engineering, Konkuk University, Republic of Korea
| | - Shashi Kant Bhatia
- Department of Biological Engineering, College of Engineering, Konkuk University, Republic of Korea
| | - Ranjit Gurav
- Department of Biological Engineering, College of Engineering, Konkuk University, Republic of Korea
| | - Jong-Min Jeon
- Green & Sustainable Materials R&D Department, Research Institute of Clean Manufacturing System, Korea Institute of Industrial Technology (KITECH), Republic of Korea
| | - Jeong-Jun Yoon
- Green & Sustainable Materials R&D Department, Research Institute of Clean Manufacturing System, Korea Institute of Industrial Technology (KITECH), Republic of Korea
| | - Kwon-Young Choi
- Department of Environmental and Safety Engineering, College of Engineering, Ajou University, Republic of Korea
| | - Jae-Seok Kim
- Department of Laboratory Medicine, Kangdong Sacred Heart Hospital, Hallym University College of Medicine, Republic of Korea
| | - Sang Ho Lee
- Department of Pharmacy, College of Pharmacy, Jeju National University, Republic of Korea
| | - Yung-Hun Yang
- Department of Biological Engineering, College of Engineering, Konkuk University, Republic of Korea.
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32
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Li HL, Deng RX, Wang W, Liu KQ, Hu HB, Huang XQ, Zhang XH. Biosynthesis and Characterization of Medium-Chain-Length Polyhydroxyalkanoate with an Enriched 3-Hydroxydodecanoate Monomer from a Pseudomonas chlororaphis Cell Factory. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:3895-3903. [PMID: 33759523 DOI: 10.1021/acs.jafc.1c00500] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Polyhydroxyalkanoates (PHAs) have been reported with agricultural and medical applications in virtue of their biodegradable and biocompatible properties. Here, we systematically engineered three modules for the enhanced biosynthesis of medium-chain-length polyhydroxyalkanoate (mcl-PHA) in Pseudomonas chlororaphis HT66. The phzE, fadA, and fadB genes were deleted to block the native phenazine pathway and weaken the fatty acid β-oxidation pathway. Additionally, a PHA depolymerase gene phaZ was knocked out to prevent the degradation of mcl-PHA. Three genes involved in the mcl-PHA biosynthesis pathway were co-overexpressed to increase carbon flux. The engineered strain HT4Δ::C1C2J exhibited an 18.2 g/L cell dry weight with 84.9 wt % of mcl-PHA in a shake-flask culture, and the 3-hydroxydodecanoate (3HDD) monomer was increased to 71.6 mol %. Thermophysical and mechanical properties of mcl-PHA were improved with an enriched ratio of 3HDD. This study demonstrated a rational metabolic engineering approach to enhance the production of mcl-PHA with the enriched dominant monomer and improved material properties.
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Affiliation(s)
- Hui-Ling Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ru-Xiang Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Kai-Quan Liu
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong 250353, China
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong 250353, China
| | - Hong-Bo Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- National Experimental Teaching Center for Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xian-Qing Huang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xue-Hong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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33
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Jiang XR, Yan X, Yu LP, Liu XY, Chen GQ. Hyperproduction of 3-hydroxypropionate by Halomonas bluephagenesis. Nat Commun 2021; 12:1513. [PMID: 33686068 PMCID: PMC7940609 DOI: 10.1038/s41467-021-21632-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 02/02/2021] [Indexed: 01/31/2023] Open
Abstract
3-Hydroxypropionic acid (3HP), an important three carbon (C3) chemical, is designated as one of the top platform chemicals with an urgent need for improved industrial production. Halomonas bluephagenesis shows the potential as a chassis for competitive bioproduction of various chemicals due to its ability to grow under an open, unsterile and continuous process. Here, we report the strategy for producing 3HP and its copolymer poly(3-hydroxybutyrate-co-3-hydroxypropionate) (P3HB3HP) by the development of H. bluephagenesis. The transcriptome analysis reveals its 3HP degradation and synthesis pathways involving endogenous synthetic enzymes from 1,3-propanediol. Combing the optimized expression of aldehyde dehydrogenase (AldDHb), an engineered H. bluephagenesis strain of whose 3HP degradation pathway is deleted and that overexpresses alcohol dehydrogenases (AdhP) on its genome under a balanced redox state, is constructed with an enhanced 1.3-propanediol-dependent 3HP biosynthetic pathway to produce 154 g L-1 of 3HP with a yield and productivity of 0.93 g g-1 1,3-propanediol and 2.4 g L-1 h-1, respectively. Moreover, the strain could also accumulate 60% poly(3-hydroxybutyrate-co-32-45% 3-hydroxypropionate) in the dry cell mass, demonstrating to be a suitable chassis for hyperproduction of 3HP and P3HB3HP.
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Affiliation(s)
- Xiao-Ran Jiang
- Department of Microbiology, Army Medical University, Chongqing, China
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Xu Yan
- School of Life Sciences, Tsinghua University, Beijing, China
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Lin-Ping Yu
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Xin-Yi Liu
- School of Life Sciences, Tsinghua University, Beijing, China
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Guo-Qiang Chen
- School of Life Sciences, Tsinghua University, Beijing, China.
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China.
- MOE Key Lab for Industrial Biocatalysis, Department of Chemical Engineering, Tsinghua University, Beijing, China.
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34
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Tan D, Wang Y, Tong Y, Chen GQ. Grand Challenges for Industrializing Polyhydroxyalkanoates (PHAs). Trends Biotechnol 2021; 39:953-963. [PMID: 33431229 DOI: 10.1016/j.tibtech.2020.11.010] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 11/17/2020] [Accepted: 11/17/2020] [Indexed: 02/06/2023]
Abstract
Polyhydroxyalkanoates (PHAs) are a diverse family of sustainable bioplastics synthesized by various bacteria, but their high production cost and unstable material properties make them challenging to use in commercial applications. Current industrial biotechnology (CIB) employs conventional microbial chassis, leading to high production costs. However, next-generation industrial biotechnology (NGIB) approaches, based on fast-growing and contamination-resistant extremophilic Halomonas spp., allow stable continuous processing and thus economical production of PHAs with stable properties. Halomonas spp. designed and constructed using synthetic biology not only produce low-cost intracellular PHAs but also secrete extracellular soluble products for improved process economics. Next-generation industrial biotechnology is expected to reduce the bioproduction cost and process complexity, leading to successful commercial production of PHAs.
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Affiliation(s)
- Dan Tan
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Ying Wang
- Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Yi Tong
- National Engineering Research Center for Corn Deep Processing, COFCO, Changchun 130033, Jilin, China
| | - Guo-Qiang Chen
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; MOE Key Lab on Industrial Biocatalyst, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China.
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35
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McAdam B, Brennan Fournet M, McDonald P, Mojicevic M. Production of Polyhydroxybutyrate (PHB) and Factors Impacting Its Chemical and Mechanical Characteristics. Polymers (Basel) 2020; 12:polym12122908. [PMID: 33291620 PMCID: PMC7761907 DOI: 10.3390/polym12122908] [Citation(s) in RCA: 135] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 01/02/2023] Open
Abstract
Plastic pollution is fueling the grave environmental threats currently facing humans, the animal kingdom, and the planet. The pursuit of renewable resourced biodegradable materials commenced in the 1970s with the need for carbon neutral fully sustainable products driving important progress in recent years. The development of bioplastic materials is highlighted as imperative to the solutions to our global environment challenges and to the restoration of the wellbeing of our planet. Bio-based plastics are becoming increasingly sustainable and are expected to substitute fossil-based plastics. Bioplastics currently include both, nondegradable and biodegradable compositions, depending on factors including the origins of production and post-use management and conditions. Among the most promising materials being developed and evaluated is polyhydroxybutyrate (PHB), a microbial bioprocessed polyester belonging to the polyhydroxyalkanoate (PHA) family. This biocompatible and non-toxic polymer is biosynthesized and accumulated by a number of specialized bacterial strains. The favorable mechanical properties and amenability to biodegradation when exposed to certain active biological environments, earmark PHB as a high potential replacement for petrochemical based polymers such as ubiquitous high density polyethylene (HDPE). To date, high production costs, minimal yields, production technology complexities, and difficulties relating to downstream processing are limiting factors for its progression and expansion in the marketplace. This review examines the chemical, mechanical, thermal, and crystalline characteristics of PHB, as well as various fermentation processing factors which influence the properties of PHB materials.
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36
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Trisrivirat D, Hughes JMX, Hoeven R, Faulkner M, Toogood H, Chaiyen P, Scrutton NS. Promoter engineering for microbial bio-alkane gas production. Synth Biol (Oxf) 2020; 5:ysaa022. [PMID: 33263086 PMCID: PMC7680561 DOI: 10.1093/synbio/ysaa022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 12/29/2022] Open
Abstract
Successful industrial biotechnological solutions to biofuels and other chemicals production rely on effective competition with existing lower-cost natural sources and synthetic chemistry approaches enabled by adopting low-cost bioreactors and processes. This is achievable by mobilizing Halomonas as a next generation industrial chassis, which can be cultivated under non-sterile conditions. To increase the cost effectiveness of an existing sustainable low carbon bio-propane production strategy, we designed and screened a constitutive promoter library based on the known strong porin promoter from Halomonas. Comparative studies were performed between Escherichia coli and Halomonas using the reporter gene red fluorescent protein (RFP). Later studies with a fatty acid photodecarboxylase-RFP fusion protein demonstrated tuneable propane production in Halomonas and E. coli, with an ∼8-fold improvement in yield over comparable isopropyl-β-D-thiogalactoside-inducible systems. This novel set of promoters is a useful addition to the synthetic biology toolbox for future engineering of Halomonas to make chemicals and fuels.
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Affiliation(s)
- Duangthip Trisrivirat
- Department of Chemistry, School of Natural Sciences, EPSRC/BBSRC Future Biomanufacturing Research Hub, BBSRC/EPSRC Synthetic Biology Research Centre SYNBIOCHEM Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK.,School of Biomolecular Science and Engineering, Vidyasirimedhi Inistitute of Science and Technology (VISTEC), Rayong 21210, Thailand.,Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - John M X Hughes
- Department of Chemistry, School of Natural Sciences, EPSRC/BBSRC Future Biomanufacturing Research Hub, BBSRC/EPSRC Synthetic Biology Research Centre SYNBIOCHEM Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK
| | - Robin Hoeven
- Department of Chemistry, School of Natural Sciences, EPSRC/BBSRC Future Biomanufacturing Research Hub, BBSRC/EPSRC Synthetic Biology Research Centre SYNBIOCHEM Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK
| | - Matthew Faulkner
- Department of Chemistry, School of Natural Sciences, EPSRC/BBSRC Future Biomanufacturing Research Hub, BBSRC/EPSRC Synthetic Biology Research Centre SYNBIOCHEM Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK
| | - Helen Toogood
- Department of Chemistry, School of Natural Sciences, EPSRC/BBSRC Future Biomanufacturing Research Hub, BBSRC/EPSRC Synthetic Biology Research Centre SYNBIOCHEM Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Inistitute of Science and Technology (VISTEC), Rayong 21210, Thailand
| | - Nigel S Scrutton
- Department of Chemistry, School of Natural Sciences, EPSRC/BBSRC Future Biomanufacturing Research Hub, BBSRC/EPSRC Synthetic Biology Research Centre SYNBIOCHEM Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK.,School of Biomolecular Science and Engineering, Vidyasirimedhi Inistitute of Science and Technology (VISTEC), Rayong 21210, Thailand
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Liu L, Zhou S, Deng Y. The 3-ketoacyl-CoA thiolase: an engineered enzyme for carbon chain elongation of chemical compounds. Appl Microbiol Biotechnol 2020; 104:8117-8129. [PMID: 32830293 DOI: 10.1007/s00253-020-10848-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 08/09/2020] [Accepted: 08/17/2020] [Indexed: 01/03/2023]
Abstract
Because of their function of catalyzing the rearrangement of the carbon chains, thiolases have attracted increasing attentions over the past decades. The 3-ketoacyl-CoA thiolase (KAT) is a member of the thiolase, which is capable of catalyzing the Claisen condensation reaction between the two acyl-CoAs, thereby achieving carbon chain elongation. In this way, diverse value-added compounds might be synthesized starting from simple small CoA thioesters. However, most KATs are hampered by low stability and poor substrate specificity, which has hindered the development of large-scale biosynthesis. In this review, the common characteristics in the three-dimensional structure of KATs from different sources are summarized. Moreover, structure-guided rational engineering is discussed as a strategy for enhancing the performance of KATs. Finally, we reviewed the metabolic engineering applications of KATs for producing various energy-storage molecules, such as n-butanol, fatty acids, dicarboxylic acids, and polyhydroxyalkanoates. KEY POINTS: • Summarize the structural characteristics and catalyzation mechanisms of KATs. • Review on the rational engineering to enhance the performance of KATs. • Discuss the applications of KATs for producing energy-storage molecules.
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Affiliation(s)
- Lixia Liu
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, People's Republic of China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, People's Republic of China
| | - Shenghu Zhou
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, People's Republic of China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, People's Republic of China
| | - Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, People's Republic of China. .,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, People's Republic of China.
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