1
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Kariyazono R, Osanai T. CyAbrB2 is a nucleoid-associated protein in Synechocystis controlling hydrogenase expression during fermentation. eLife 2024; 13:RP94245. [PMID: 39221912 PMCID: PMC11368403 DOI: 10.7554/elife.94245] [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] [Indexed: 09/04/2024] Open
Abstract
The hox operon in Synechocystis sp. PCC 6803, encoding bidirectional hydrogenase responsible for H2 production, is transcriptionally upregulated under microoxic conditions. Although several regulators for hox transcription have been identified, their dynamics and higher-order DNA structure of hox region in microoxic conditions remain elusive. We focused on key regulators for the hox operon: cyAbrB2, a conserved regulator in cyanobacteria, and SigE, an alternative sigma factor. Chromatin immunoprecipitation sequencing revealed that cyAbrB2 binds to the hox promoter region under aerobic conditions, with its binding being flattened in microoxic conditions. Concurrently, SigE exhibited increased localization to the hox promoter under microoxic conditions. Genome-wide analysis revealed that cyAbrB2 binds broadly to AT-rich genome regions and represses gene expression. Moreover, we demonstrated the physical interactions of the hox promoter region with its distal genomic loci. Both the transition to microoxic conditions and the absence of cyAbrB2 influenced the chromosomal interaction. From these results, we propose that cyAbrB2 is a cyanobacterial nucleoid-associated protein (NAP), modulating chromosomal conformation, which blocks RNA polymerase from the hox promoter in aerobic conditions. We further infer that cyAbrB2, with altered localization pattern upon microoxic conditions, modifies chromosomal conformation in microoxic conditions, which allows SigE-containing RNA polymerase to access the hox promoter. The coordinated actions of this NAP and the alternative sigma factor are crucial for the proper hox expression in microoxic conditions. Our results highlight the impact of cyanobacterial chromosome conformation and NAPs on transcription, which have been insufficiently investigated.
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2
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Feng X, Sun Y, Fan Y, Zhang Q, Bu X, Gao D. Integrated physiological, transcriptomics and metabolomics analysis revealed the molecular mechanism of Bupleurum chinense seedlings to drought stress. PLoS One 2024; 19:e0304503. [PMID: 38843246 PMCID: PMC11156411 DOI: 10.1371/journal.pone.0304503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 05/14/2024] [Indexed: 06/09/2024] Open
Abstract
Drought stress is a prominent abiotic factor that adversely influences the growth and development of Bupleurum chinense during its seedling stage, negatively impacting biomass and secondary metabolite production, thus affecting yield and quality. To investigate the molecular mechanism underlying the response of B. chinense seedlings under drought stress, this study employed comprehensive physiological, transcriptomic, and metabolomic analyses. The results revealed that under drought stress, the root soluble sugar and free proline content in B. chinense seedlings significantly increased, while the activities of SOD, POD, and CAT increased in the leaves. These findings indicate the presence of distinct response mechanisms in B. chinense to cope with drought stress. Integrated analysis further identified significant correlations between genes and metabolites related to amino acid biosynthesis in the leaves, as well as genes and metabolites associated with acetaldehyde and dicarboxylic acid metabolism. In the roots, genes and metabolites related to plant hormone signaling and the tricarboxylic acid (TCA) cycle showed significant correlations. These findings provide vital views into the molecular-level response mechanisms of B. chinense under drought stress. Moreover, this study establishes the groundwork for identifying drought-tolerant genes and breeding drought-resistant varieties, which could improve the drought tolerance of medicinal plants and have broader implications for agriculture and crop production in water-scarce areas.
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Affiliation(s)
- Xiaohan Feng
- School of Pharmacy, Shandong University of Traditional Chinese Medicine (TCM), Jinan, China
| | - Yan Sun
- School of Pharmacy, Shandong University of Traditional Chinese Medicine (TCM), Jinan, China
| | - Ya Fan
- School of Pharmacy, Shandong University of Traditional Chinese Medicine (TCM), Jinan, China
| | - Quanfang Zhang
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Xun Bu
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Demin Gao
- School of Pharmacy, Shandong University of Traditional Chinese Medicine (TCM), Jinan, China
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3
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Li Z, Li S, Chen L, Sun T, Zhang W. Fast-growing cyanobacterial chassis for synthetic biology application. Crit Rev Biotechnol 2024; 44:414-428. [PMID: 36842999 DOI: 10.1080/07388551.2023.2166455] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 11/19/2022] [Accepted: 12/28/2022] [Indexed: 02/28/2023]
Abstract
Carbon neutrality by 2050 has become one of the most urgent challenges the world faces today. To address the issue, it is necessary to develop and promote new technologies related with CO2 recycling. Cyanobacteria are the only prokaryotes performing oxygenic photosynthesis, capable of fixing CO2 into biomass under sunlight and serving as one of the most important primary producers on earth. Notably, recent progress on synthetic biology has led to utilizing model cyanobacteria such as Synechocystis sp. PCC 6803 and Synechococcus elongatus PCC 7942 as chassis for "light-driven autotrophic cell factories" to produce several dozens of biofuels and various fine chemicals directly from CO2. However, due to the slow growth rate and low biomass accumulation in the current chassis, the productivity for most products is still lower than the threshold necessary for large-scale commercial application, raising the importance of developing high-efficiency cyanobacterial chassis with fast growth and/or higher biomass accumulation capabilities. In this article, we critically reviewed recent progresses on identification, systems biology analysis, and engineering of fast-growing cyanobacterial chassis. Specifically, fast-growing cyanobacteria identified in recent years, such as S. elongatus UTEX 2973, S. elongatus PCC 11801, S. elongatus PCC 11802 and Synechococcus sp. PCC 11901 was comparatively analyzed. In addition, the progresses on their recent application in converting CO2 into chemicals, and genetic toolboxes developed for these new cyanobacterial chassis were discussed. Finally, the article provides insights into future challenges and perspectives on the synthetic biology application of cyanobacterial chassis.
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Affiliation(s)
- Zhixiang Li
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, P.R. China
| | - Shubin Li
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, P.R. China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, P.R. China
| | - Tao Sun
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, P.R. China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, P.R. China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, P.R. China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, P.R. China
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4
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Ito S, Watanabe A, Osanai T. Regulation of L-aspartate oxidase contributes to NADP+ biosynthesis in Synechocystis sp. PCC 6803. PLANT PHYSIOLOGY 2024; 194:945-957. [PMID: 37936332 DOI: 10.1093/plphys/kiad580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/11/2023] [Accepted: 10/16/2023] [Indexed: 11/09/2023]
Abstract
Cyanobacteria have been promoted as a biomass resource that can contribute to carbon neutrality. Synechocystis sp. PCC 6803 is a model cyanobacterium that is widely used in various studies. NADP+ and NAD+ are electron receptors involved in energy metabolism. The NADP+/NAD+ ratio in Synechocystis sp. PCC 6803 is markedly higher than that in the heterotrophic bacterium Escherichia coli. In Synechocystis sp. PCC 6803, NADP+ primarily functions as an electron receptor during the light reaction of photosynthesis, and NADP+ biosynthesis is essential for photoautotrophic growth. Generally, the regulatory enzyme of NADP+ biosynthesis is NAD kinase, which catalyzes the phosphorylation of NAD+. However, a previous study suggested that the regulation of another enzyme contributes to NADP+ biosynthesis in Synechocystis sp. PCC 6803 under photoautotrophic conditions. L-Aspartate oxidase is the first enzyme in NAD(P)+ biosynthesis. In this study, we biochemically characterized Synechocystis sp. PCC 6803 L-aspartate oxidase and determined the phenotype of a Synechocystis sp. PCC 6803 mutant overexpressing L-aspartate oxidase. The catalytic efficiency of L-aspartate oxidase from Synechocystis sp. PCC 6803 was lower than that of L-aspartate oxidases and NAD kinases from other organisms. L-Aspartate oxidase activity was affected by different metabolites such as NADP+ and ATP. The L-aspartate oxidase-overexpressing strain grew faster than the wild-type strain under photoautotrophic conditions. The L-aspartate oxidase-overexpressing strain accumulated NADP+ under photoautotrophic conditions. These results indicate that the regulation of L-aspartate oxidase contributes to NADP+ biosynthesis in Synechocystis sp. PCC 6803 under photoautotrophic conditions. These findings provide insight into the regulatory mechanism of cyanobacterial NADP+ biosynthesis.
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Affiliation(s)
- Shoki Ito
- School of Agriculture, Meiji University, 1-1-1, Higashimita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - Atsuko Watanabe
- School of Agriculture, Meiji University, 1-1-1, Higashimita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - Takashi Osanai
- School of Agriculture, Meiji University, 1-1-1, Higashimita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
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Saito S, Kobayashi I, Hoshina M, Uenaka E, Sakurai A, Imamura S, Shimada T. Regulatory Role of GgaR (YegW) for Glycogen Accumulation in Escherichia coli K-12. Microorganisms 2024; 12:115. [PMID: 38257942 PMCID: PMC10819704 DOI: 10.3390/microorganisms12010115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 12/31/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Glycogen, the stored form of glucose, accumulates upon growth arrest in the presence of an excess carbon source in Escherichia coli and other bacteria. Chromatin immunoprecipitation screening for the binding site of a functionally unknown GntR family transcription factor, YegW, revealed that the yegTUV operon was a single target of the E. coli genome. Although none of the genes in the yegTUV operon have a clear function, a previous study suggested their involvement in the production of ADP-glucose (ADPG), a glycogen precursor. Various validation through in vivo and in vitro experiments showed that YegW is a single-target transcription factor that acts as a repressor of yegTUV, with an intracellular concentration of consistently approximately 10 molecules, and senses ADPG as an effector. Further analysis revealed that YegW repressed glycogen accumulation in response to increased glucose concentration, which was not accompanied by changes in the growth phase. In minimal glucose medium, yegW-deficient E. coli promoted glycogen accumulation, at the expense of poor cell proliferation. We concluded that YegW is a single-target transcription factor that senses ADPG and represses glycogen accumulation in response to the amount of glucose available to the cell. We propose renaming YegW to GgaR (repressor of glycogen accumulation).
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Affiliation(s)
- Shunsuke Saito
- School of Agriculture, Meiji University, 1-1-1 Kawasaki-Shi, Kanagawa 214-8571, Japan
| | - Ikki Kobayashi
- School of Agriculture, Meiji University, 1-1-1 Kawasaki-Shi, Kanagawa 214-8571, Japan
| | - Motoki Hoshina
- Research and Development Section, Diagnostics Division, YAMASA Corporation, 2-10-1 Araoicho, Choshi, Chiba 288-0056, Japan
| | - Emi Uenaka
- School of Agriculture, Meiji University, 1-1-1 Kawasaki-Shi, Kanagawa 214-8571, Japan
- Space Environment and Energy Laboratories, Nippon Telegraph and Telephone Corporation, Musashino-shi, Tokyo 180-8585, Japan
| | - Atsushi Sakurai
- Space Environment and Energy Laboratories, Nippon Telegraph and Telephone Corporation, Musashino-shi, Tokyo 180-8585, Japan
| | - Sousuke Imamura
- Space Environment and Energy Laboratories, Nippon Telegraph and Telephone Corporation, Musashino-shi, Tokyo 180-8585, Japan
| | - Tomohiro Shimada
- School of Agriculture, Meiji University, 1-1-1 Kawasaki-Shi, Kanagawa 214-8571, Japan
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6
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Akiyama M, Osanai T. Regulation of organic acid and hydrogen production by NADH/NAD + ratio in Synechocystis sp. PCC 6803. Front Microbiol 2024; 14:1332449. [PMID: 38249449 PMCID: PMC10797119 DOI: 10.3389/fmicb.2023.1332449] [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: 11/03/2023] [Accepted: 12/12/2023] [Indexed: 01/23/2024] Open
Abstract
Cyanobacteria serve as useful hosts in the production of substances to support a low-carbon society. Specifically, the unicellular cyanobacterium Synechocystis sp. PCC 6803 (Synechocystis 6803) can produce organic acids, such as acetate, lactate, and succinate, as well as hydrogen, under dark, anaerobic conditions. The efficient production of these compounds appears to be closely linked to the regulation of intracellular redox balance. Notably, alterations in intracellular redox balance have been believed to influence the production of organic acids and hydrogen. To achieve these alterations, genetic manipulations involved overexpressing malate dehydrogenase (MDH), knocking out d-lactate dehydrogenase (DDH), or knocking out acetate kinase (AK), which subsequently modified the quantities and ratios of organic acids and hydrogen under dark, anaerobic conditions. Furthermore, the mutants generated displayed changes in the oxidation of reducing powers and the nicotinamide adenine dinucleotide hydrogen (NADH)/NAD+ ratio when compared to the parental wild-type strain. These findings strongly suggest that intracellular redox balance, especially the NADH/NAD+ ratio, plays a pivotal role in the production of organic acids and hydrogen in Synechocystis 6803.
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Affiliation(s)
| | - Takashi Osanai
- School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
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7
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Treece TR, Tessman M, Pomeroy RS, Mayfield SP, Simkovsky R, Atsumi S. Fluctuating pH for efficient photomixotrophic succinate production. Metab Eng 2023; 79:118-129. [PMID: 37499856 DOI: 10.1016/j.ymben.2023.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 07/15/2023] [Accepted: 07/23/2023] [Indexed: 07/29/2023]
Abstract
Cyanobacteria are attracting increasing attention as a photosynthetic chassis organism for diverse biochemical production, however, photoautotrophic production remains inefficient. Photomixotrophy, a method where sugar is used to supplement baseline autotrophic metabolism in photosynthetic hosts, is becoming increasingly popular for enhancing sustainable bioproduction with multiple input energy streams. In this study, the commercially relevant diacid, succinate, was produced photomixotrophically. Succinate is an important industrial chemical that can be used for the production of a wide array of products, from pharmaceuticals to biopolymers. In this system, the substrate, glucose, is transported by a proton symporter and the product, succinate, is hypothesized to be transported by another proton symporter, but in the opposite direction. Thus, low pH is required for the import of glucose and high pH is required for the export of succinate. Succinate production was initiated in a pH 7 medium containing bicarbonate. Glucose was efficiently imported at around neutral pH. Utilization of bicarbonate by CO2 fixation raised the pH of the medium. As succinate, a diacid, was produced, the pH of the medium dropped. By repeating this cycle with additional pH adjustment, those contradictory requirements for transport were overcome. pH affects a variety of biological factors and by cycling from high pH to neutral pH processes such as CO2 fixation rates and CO2 solubility can vary. In this study the engineered strains produced succinate during fluctuating pH conditions, achieving a titer of 5.0 g L-1 after 10 days under shake flask conditions. These results demonstrate the potential for photomixotrophic production as a viable option for the large-scale production of succinate.
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Affiliation(s)
- Tanner R Treece
- Department of Chemistry, University of California, Davis, Davis, CA, 95616, USA
| | | | - Robert S Pomeroy
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Stephen P Mayfield
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093, USA; California Center for Algae Biotechnology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Ryan Simkovsky
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093, USA; California Center for Algae Biotechnology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Shota Atsumi
- Department of Chemistry, University of California, Davis, Davis, CA, 95616, USA.
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8
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Yamane M, Osanai T. Nondiazotrophic cyanobacteria metabolic engineering for succinate and lactate production. ALGAL RES 2023. [DOI: 10.1016/j.algal.2023.103088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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9
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Engineering Microorganisms to Produce Bio-Based Monomers: Progress and Challenges. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9020137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Bioplastics are polymers made from sustainable bio-based feedstocks. While the potential of producing bio-based monomers in microbes has been investigated for decades, their economic feasibility is still unsatisfactory compared with petroleum-derived methods. To improve the overall synthetic efficiency of microbial cell factories, three main strategies were summarized in this review: firstly, implementing approaches to improve the microbial utilization ability of cheap and abundant substrates; secondly, developing methods at enzymes, pathway, and cellular levels to enhance microbial production performance; thirdly, building technologies to enhance microbial pH, osmotic, and metabolites stress tolerance. Moreover, the challenges of, and some perspectives on, exploiting microorganisms as efficient cell factories for producing bio-based monomers are also discussed.
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10
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Sukkasam N, Leksingto J, Incharoensakdi A, Monshupanee T. Chemical Triggering Cyanobacterial Glycogen Accumulation: Methyl Viologen Treatment Increases Synechocystis sp. PCC 6803 Glycogen Storage by Enhancing Levels of Gene Transcript and Substrates in Glycogen Synthesis. PLANT & CELL PHYSIOLOGY 2023; 63:2027-2041. [PMID: 36197756 DOI: 10.1093/pcp/pcac136] [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: 07/12/2022] [Revised: 09/26/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Two-stage cultivation is effective for glycogen production by cyanobacteria. Cells were first grown under adequate nitrate supply (BG11) to increase biomass and subsequently transferred to nitrogen deprivation (-N) to stimulate glycogen accumulation. However, the two-stage method is time-consuming and requires extensive energy. Thus, one-stage cultivation that enables both cell growth and glycogen accumulation is advantageous. Such one-stage method could be achieved using a chemical triggering glycogen storage. However, there is a limited study on such chemicals. Here, nine compounds previously reported to affect cyanobacterial cellular functions were examined in Synechocystis sp. PCC 6803. 2-Phenylethanol, phenoxyethanol, 3-(3,4-dichlorophenyl)-1,1-dimethylurea and methyl viologen can stimulate glycogen accumulation. The oxidative stress agent, methyl viologen significantly increased glycogen levels up to 57% and 69% [w/w dry weight (DW)] under BG11 and -N cultivation, respectively. One-stage cultivation where methyl viologen was directly added to the pre-grown culture enhanced glycogen storage to 53% (w/w DW), compared to the 10% (w/w DW) glycogen level of the control cells without methyl viologen. Methyl viologen treatment reduced the contents of total proteins (including phycobiliproteins) but caused increased transcript levels of glycogen synthetic genes and elevated levels of metabolite substrates for glycogen synthesis. Metabolomic results suggested that upon methyl viologen treatment, proteins degraded to amino acids, some of which could be used as a carbon source for glycogen synthesis. Results of oxygen evolution and metabolomic analysis suggested that photosynthesis and carbon fixation were not completely inhibited upon methyl viologen treatment, and these two processes may partially generate upstream metabolites required for glycogen synthesis.
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Affiliation(s)
- Nannaphat Sukkasam
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Jidapa Leksingto
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Aran Incharoensakdi
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Academy of Science, Royal Society of Thailand, Bangkok 10300, Thailand
| | - Tanakarn Monshupanee
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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11
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Chen AY, Ku JT, Tsai TP, Hung JJ, Hung BC, Lan EI. Metabolic Engineering Design Strategies for Increasing Carbon Fluxes Relevant for Biosynthesis in Cyanobacteria. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 183:105-144. [PMID: 37093259 DOI: 10.1007/10_2023_218] [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: 04/25/2023]
Abstract
Cyanobacteria are promising microbial cell factories for the direct production of biochemicals and biofuels from CO2. Through genetic and metabolic engineering, they can be modified to produce a variety of both natural and non-natural compounds. To enhance the yield of these products, various design strategies have been developed. In this chapter, strategies used to enhance metabolic fluxes towards common precursors used in biosynthesis, including pyruvate, acetyl-CoA, malonyl-CoA, TCA cycle intermediates, and aromatics, are discussed. Additionally, strategies related to cofactor availability and mixotrophic conditions for bioproduction are also summarize.
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Affiliation(s)
- Arvin Y Chen
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu City, Taiwan
| | - Jason T Ku
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu City, Taiwan
| | - Teresa P Tsai
- Institute of Biomedical Engineering, National Yang Ming Chiao Tung University, Hsinchu City, Taiwan
| | - Jenny J Hung
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu City, Taiwan
| | - Billy C Hung
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu City, Taiwan
| | - Ethan I Lan
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu City, Taiwan.
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12
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Hidese R, Matsuda M, Kajikawa M, Osanai T, Kondo A, Hasunuma T. Metabolic and Microbial Community Engineering for Four-Carbon Dicarboxylic Acid Production from CO 2-Derived Glycogen in the Cyanobacterium Synechocystis sp. PCC6803. ACS Synth Biol 2022; 11:4054-4064. [PMID: 36445137 DOI: 10.1021/acssynbio.2c00379] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The four-carbon (C4) dicarboxylic acids, fumarate, malate, and succinate, are the most valuable targets that must be exploited for CO2-based chemical production in the move to a sustainable low-carbon future. Cyanobacteria excrete high amounts of C4 dicarboxylic acids through glycogen fermentation in a dark anoxic environment. The enhancement of metabolic flux in the reductive TCA branch in the Cyanobacterium Synechocystis sp. PCC6803 is a key issue in the C4 dicarboxylic acid production. To improve metabolic flux through the anaplerotic pathway, we have created the recombinant strain PCCK, which expresses foreign ATP-forming phosphoenolpyruvate carboxykinase (PEPck) concurrent with intrinsic phosphoenolpyruvate carboxylase (Ppc) overexpression. Expression of PEPck concurrent with Ppc led to an increase in C4 dicarboxylic acids by autofermentation. Metabolome analysis revealed that PEPck contributed to an increase in carbon flux from hexose and pentose phosphates into the TCA reductive branch. To enhance the metabolic flux in the reductive TCA branch, we examined the effect of corn-steep liquor (CSL) as a nutritional supplement on C4 dicarboxylic acid production. Surprisingly, the addition of sterilized CSL enhanced the malate production in the PCCK strain. Thereafter, the malate and fumarate excreted by the PCCK strain are converted into succinate by the CSL-settling microorganisms. Finally, high-density cultivation of cells lacking the acetate kinase gene showed the highest production of malate and fumarate (3.2 and 2.4 g/L with sterilized CSL) and succinate (5.7 g/L with non-sterile CSL) after 72 h cultivation. The present microbial community engineering is useful for succinate production by one-pot fermentation under dark anoxic conditions.
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Affiliation(s)
- Ryota Hidese
- Graduate School of Science, Innovation and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan.,Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Mami Matsuda
- Graduate School of Science, Innovation and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Mamiko Kajikawa
- Graduate School of Science, Innovation and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Takashi Osanai
- School of Agriculture, Meiji University, 1-1-1 Higashimita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - Akihiko Kondo
- Graduate School of Science, Innovation and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan.,Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan.,Research Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Tomohisa Hasunuma
- Graduate School of Science, Innovation and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan.,Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan.,Research Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
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13
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Alfaro-Sayes DA, Amoah J, Aikawa S, Matsuda M, Hasunuma T, Kondo A, Ogino C. Alginate immobilization as a strategy for improving succinate production during autofermentation using cyanobacteria Synechocystis sp. PCC 6803. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108681] [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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14
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Lai MJ, Tsai JC, Lan EI. CRISPRi-enhanced direct photosynthetic conversion of carbon dioxide to succinic acid by metabolically engineered cyanobacteria. BIORESOURCE TECHNOLOGY 2022; 366:128131. [PMID: 36252759 DOI: 10.1016/j.biortech.2022.128131] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/09/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Engineering photoautotrophic microorganisms to directly convert carbon dioxide into platform chemicals is an attractive approach for chemical sustainability and carbon mitigation. Here, an engineered cyanobacterium Synechococcus elongatus PCC 7942 was developed to produce succinic acid directly from ambient carbon dioxide. Inhibition of succinate dehydrogenase and glycogen synthase by CRIPSR interference increased carbon flux towards succinic acid. Dual inhibition of these two genes led to an 82 % increase in titer. The resulting strain produced 4.8 g/L of succinic acid in a 28-days cultivation. However, cells after the 28-days cultivation became non-viable and cannot continue production. This issue was addressed by re-inoculation with fresh cells into the production medium. This strategy enabled continuous succinic acid accumulation, reaching a final titer of 8.9 g/L. This study provides a sustainable route to succinic acid directly from carbon dioxide and a potential method to overcome the low titer limitation of cyanobacterial-based bioproduction for practical applications.
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Affiliation(s)
- Martin J Lai
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, 1001 Daxue Road, Hsinchu City 300, Taiwan
| | - Jemmy C Tsai
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, 1001 Daxue Road, Hsinchu City 300, Taiwan
| | - Ethan I Lan
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, 1001 Daxue Road, Hsinchu City 300, Taiwan.
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Fitriana HN, Lee S, Kim HS, Lee J, Lee Y, Lee JS, Park H, Ko CH, Lim SY, Lee SY. Enhanced CO 2 electroconversion of Rhodobacter sphaeroides by cobalt-phosphate complex assisted water oxidation. Bioelectrochemistry 2022; 145:108102. [PMID: 35338862 DOI: 10.1016/j.bioelechem.2022.108102] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 03/10/2022] [Accepted: 03/18/2022] [Indexed: 01/02/2023]
Abstract
CO2 can be a next generation feedstock for electricity-driven bioproduction due to its abundance and availability. Microbial electrosynthesis (MES), a promising technique for CO2 electroconversion, provides an attractive route for the production of valuable products from CO2, but issues surrounding efficiency and reasonable productivity should be resolved. Improving the anode performance for water oxidation under neutral pH is one of the most important aspects to advance current MES. Here, we introduce cobalt-phosphate (Co-Pi) assisted water oxidation at the counter electrode (i.e., anode) to upgrade the MES performance at pH 7.0. We show that CO2 can be converted by photochemoautotrophic bacterium, Rhodobacter sphaeroides into organic acids and carotenoids in the MES reactor. Planktonic cells of R. sphareroides in the Co-Pi anode equipped MES reactor was ca. 1.5-fold higher than in the control condition (w/o Co-Pi). The faradaic efficiency of the Co-Pi anode equipped MES reactor was remarkably higher (58.3%) than that of the bare anode (27.8%). While the system can improve the CO2 electroconversion nonetheless there are some further optimizations are necessary.
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Affiliation(s)
- Hana Nur Fitriana
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research, 61003 Gwangju, South Korea
| | - Sangmin Lee
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research, 61003 Gwangju, South Korea
| | - Hui Su Kim
- Department of Advanced Chemicals & Engineering, Chonnam National University, 61186 Gwangju, South Korea
| | - Jiye Lee
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research, 61003 Gwangju, South Korea
| | - Yurim Lee
- Interdisciplinary Program of Agriculture and Life Science, Chonnam National University, 61186 Gwangju, South Korea
| | - Jin-Suk Lee
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research, 61003 Gwangju, South Korea
| | - Hyojung Park
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research, 61003 Gwangju, South Korea; Bioremediation Team, National Institute of Agricultural Sciences, 55365 Jeollabuk-do, South Korea
| | - Chang Hyun Ko
- Department of Advanced Chemicals & Engineering, Chonnam National University, 61186 Gwangju, South Korea; School of Chemical Engineering, Chonnam National University, 61186 Gwangju, South Korea
| | - Sung Yul Lim
- Department of Chemistry, Kyung Hee University, 02447 Seoul, South Korea
| | - Soo Youn Lee
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research, 61003 Gwangju, South Korea.
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Liu J, Liu J, Guo L, Liu J, Chen X, Liu L, Gao C. Advances in microbial synthesis of bioplastic monomers. ADVANCES IN APPLIED MICROBIOLOGY 2022; 119:35-81. [DOI: 10.1016/bs.aambs.2022.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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17
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Kato Y, Inabe K, Hidese R, Kondo A, Hasunuma T. Metabolomics-based engineering for biofuel and bio-based chemical production in microalgae and cyanobacteria: A review. BIORESOURCE TECHNOLOGY 2022; 344:126196. [PMID: 34710610 DOI: 10.1016/j.biortech.2021.126196] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/18/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
Metabolomics, an essential tool in modern synthetic biology based on the design-build-test-learn platform, is useful for obtaining a detailed understanding of cellular metabolic mechanisms through comprehensive analyses of the metabolite pool size and its dynamic changes. Metabolomics is critical to the design of a rational metabolic engineering strategy by determining the rate-limiting reaction and assimilated carbon distribution in a biosynthetic pathway of interest. Microalgae and cyanobacteria are promising photosynthetic producers of biofuels and bio-based chemicals, with high potential for developing a bioeconomic society through bio-based carbon neutral manufacturing. Metabolomics technologies optimized for photosynthetic organisms have been developed and utilized in various microalgal and cyanobacterial species. This review provides a concise overview of recent achievements in photosynthetic metabolomics, emphasizing the importance of microalgal and cyanobacterial cell factories that satisfy industrial requirements.
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Affiliation(s)
- Yuichi Kato
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Kosuke Inabe
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Ryota Hidese
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; Graduate School of Science, Innovation and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Akihiko Kondo
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; Graduate School of Science, Innovation and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Tomohisa Hasunuma
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; Graduate School of Science, Innovation and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan.
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Japhalekar K, Srinivasan S, Viswanathan G, Venkatesh K. Flux balance analysis for overproduction of organic acids by Synechocystis sp. PCC 6803 under dark anoxic condition. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2021.108297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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