1
|
Tiwari D, Kumar N, Bongirwar R, Shukla P. Nutraceutical prospects of genetically engineered cyanobacteria- technological updates and significance. World J Microbiol Biotechnol 2024; 40:263. [PMID: 38980547 DOI: 10.1007/s11274-024-04064-1] [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: 05/10/2024] [Accepted: 06/23/2024] [Indexed: 07/10/2024]
Abstract
Genetically engineered cyanobacterial strains that have improved growth rate, biomass productivity, and metabolite productivity could be a better option for sustainable bio-metabolite production. The global demand for biobased metabolites with nutraceuticals and health benefits has increased due to their safety and plausible therapeutic and nutritional utility. Cyanobacteria are solar-powered green cellular factories that can be genetically tuned to produce metabolites with nutraceutical and pharmaceutical benefits. The present review discusses biotechnological endeavors for producing bioprospective compounds from genetically engineered cyanobacteria and discusses the challenges and troubleshooting faced during metabolite production. This review explores the cyanobacterial versatility, the use of engineered strains, and the techno-economic challenges associated with scaling up metabolite production from cyanobacteria. Challenges to produce cyanobacterial bioactive compounds with remarkable nutraceutical values have been discussed. Additionally, this review also summarises the challenges and future prospects of metabolite production from genetically engineered cyanobacteria as a sustainable approach.
Collapse
Affiliation(s)
- Deepali Tiwari
- Enzyme Technology and Protein Bioinformatics Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India
| | - Niwas Kumar
- Enzyme Technology and Protein Bioinformatics Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India
| | - Riya Bongirwar
- Enzyme Technology and Protein Bioinformatics Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India.
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Yun L, Zegarac R, Ducat DC. Impact of irradiance and inorganic carbon availability on heterologous sucrose production in Synechococcus elongatus PCC 7942. FRONTIERS IN PLANT SCIENCE 2024; 15:1378573. [PMID: 38650707 PMCID: PMC11033428 DOI: 10.3389/fpls.2024.1378573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 03/27/2024] [Indexed: 04/25/2024]
Abstract
Cyanobacteria have been proposed as a potential alternative carbohydrate feedstock and multiple species have been successfully engineered to secrete fermentable sugars. To date, the most productive cyanobacterial strains are those designed to secrete sucrose, yet there exist considerable differences in reported productivities across different model species and laboratories. In this study, we investigate how cultivation conditions (specifically, irradiance, CO2, and cultivator type) affect the productivity of sucrose-secreting Synechococcus elongatus PCC 7942. We find that S. elongatus produces the highest sucrose yield in irradiances far greater than what is often experimentally utilized, and that high light intensities are tolerated by S. elongatus, especially under higher density cultivation where turbidity may attenuate the effective light experienced in the culture. By increasing light and inorganic carbon availability, S. elongatus cscB/sps produced a total of 3.8 g L-1 of sucrose and the highest productivity within that period being 47.8 mg L-1 h-1. This study provides quantitative description of the impact of culture conditions on cyanobacteria-derived sucrose that may assist to standardize cross-laboratory comparisons and demonstrates a significant capacity to improve productivity via optimizing cultivation conditions.
Collapse
Affiliation(s)
- Lisa Yun
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
- Department of Energy-Michigan State University Plant Research Laboratories, Michigan State University, East Lansing, MI, United States
| | - Robert Zegarac
- Department of Energy-Michigan State University Plant Research Laboratories, Michigan State University, East Lansing, MI, United States
| | - Daniel C. Ducat
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
- Department of Energy-Michigan State University Plant Research Laboratories, Michigan State University, East Lansing, MI, United States
| |
Collapse
|
4
|
Sengupta A, Bandyopadhyay A, Sarkar D, Hendry JI, Schubert MG, Liu D, Church GM, Maranas CD, Pakrasi HB. Genome streamlining to improve performance of a fast-growing cyanobacterium Synechococcus elongatus UTEX 2973. mBio 2024; 15:e0353023. [PMID: 38358263 PMCID: PMC10936165 DOI: 10.1128/mbio.03530-23] [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: 01/09/2024] [Accepted: 01/22/2024] [Indexed: 02/16/2024] Open
Abstract
Cyanobacteria are photosynthetic organisms that have garnered significant recognition as potential hosts for sustainable bioproduction. However, their complex regulatory networks pose significant challenges to major metabolic engineering efforts, thereby limiting their feasibility as production hosts. Genome streamlining has been demonstrated to be a successful approach for improving productivity and fitness in heterotrophs but is yet to be explored to its full potential in phototrophs. Here, we present the systematic reduction of the genome of the cyanobacterium exhibiting the fastest exponential growth, Synechococcus elongatus UTEX 2973. This work, the first of its kind in a photoautotroph, involved an iterative process using state-of-the-art genome-editing technology guided by experimental analysis and computational tools. CRISPR-Cas3 enabled large, progressive deletions of predicted dispensable regions and aided in the identification of essential genes. The large deletions were combined to obtain a strain with 55-kb genome reduction. The strains with streamlined genome showed improvement in growth (up to 23%) and productivity (by 22.7%) as compared to the wild type (WT). This streamlining strategy not only has the potential to develop cyanobacterial strains with improved growth and productivity traits but can also facilitate a better understanding of their genome-to-phenome relationships.IMPORTANCEGenome streamlining is an evolutionary strategy used by natural living systems to dispense unnecessary genes from their genome as a mechanism to adapt and evolve. While this strategy has been successfully borrowed to develop synthetic heterotrophic microbial systems with desired phenotype, it has not been extensively explored in photoautotrophs. Genome streamlining strategy incorporates both computational predictions to identify the dispensable regions and experimental validation using genome-editing tool, and in this study, we have employed a modified strategy with the goal to minimize the genome size to an extent that allows optimal cellular fitness under specified conditions. Our strategy has explored a novel genome-editing tool in photoautotrophs, which, unlike other existing tools, enables large, spontaneous optimal deletions from the genome. Our findings demonstrate the effectiveness of this modified strategy in obtaining strains with streamlined genome, exhibiting improved fitness and productivity.
Collapse
Affiliation(s)
- Annesha Sengupta
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | | | - Debolina Sarkar
- Department of Chemical Engineering, Pennsylvania State University, State College, Pennsylvania, USA
| | - John I. Hendry
- Department of Chemical Engineering, Pennsylvania State University, State College, Pennsylvania, USA
| | - Max G. Schubert
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA
| | - Deng Liu
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | - George M. Church
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Costas D. Maranas
- Department of Chemical Engineering, Pennsylvania State University, State College, Pennsylvania, USA
| | | |
Collapse
|
5
|
Hudson EP. The Calvin Benson cycle in bacteria: New insights from systems biology. Semin Cell Dev Biol 2024; 155:71-83. [PMID: 37002131 DOI: 10.1016/j.semcdb.2023.03.007] [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: 10/18/2022] [Revised: 02/21/2023] [Accepted: 03/16/2023] [Indexed: 03/31/2023]
Abstract
The Calvin Benson cycle in phototrophic and chemolithoautotrophic bacteria has ecological and biotechnological importance, which has motivated study of its regulation. I review recent advances in our understanding of how the Calvin Benson cycle is regulated in bacteria and the technologies used to elucidate regulation and modify it, and highlight differences between and photoautotrophic and chemolithoautotrophic models. Systems biology studies have shown that in oxygenic phototrophic bacteria, Calvin Benson cycle enzymes are extensively regulated at post-transcriptional and post-translational levels, with multiple enzyme activities connected to cellular redox status through thioredoxin. In chemolithoautotrophic bacteria, regulation is primarily at the transcriptional level, with effector metabolites transducing cell status, though new methods should now allow facile, proteome-wide exploration of biochemical regulation in these models. A biotechnological objective is to enhance CO2 fixation in the cycle and partition that carbon to a product of interest. Flux control of CO2 fixation is distributed over multiple enzymes, and attempts to modulate gene Calvin cycle gene expression show a robust homeostatic regulation of growth rate, though the synthesis rates of products can be significantly increased. Therefore, de-regulation of cycle enzymes through protein engineering may be necessary to increase fluxes. Non-canonical Calvin Benson cycles, if implemented with synthetic biology, could have reduced energy demand and enzyme loading, thus increasing the attractiveness of these bacteria for industrial applications.
Collapse
Affiliation(s)
- Elton P Hudson
- Department of Protein Science, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden.
| |
Collapse
|
6
|
Hasan R, Kasera N, Beck AE, Hall SG. Potential of Synechococcus elongatus UTEX 2973 as a feedstock for sugar production during mixed aquaculture and swine wastewater bioremediation. Heliyon 2024; 10:e24646. [PMID: 38314264 PMCID: PMC10837500 DOI: 10.1016/j.heliyon.2024.e24646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 12/14/2023] [Accepted: 01/11/2024] [Indexed: 02/06/2024] Open
Abstract
The demand for protein is increasing with an expanding world population and is influencing the rapid growth of fish and animal agriculture. These sectors are becoming a significant source of water pollution and need to develop environmentally sustainable techniques that are cost-effective, ideally with potential for downstream value-added production. This study investigated the potential of one of the fastest-growing cyanobacterial species, Synechococcus elongatus UTEX 2973, for bioremediation of mixed wastewater (combination of sturgeon and swine wastewater). Three different mixing ratios (25:75, 50:50, and 75:25 sturgeon:swine) were compared to find a suitable combination for the growth of S. elongatus as well as carbohydrate accumulation in biomass. The final biomass production was found to be 0.65 ± 0.03 g Dry cell Weight (DW)/L for 75%-25 %, 0.90 ± 0.004 g DW/L for 50%-50 %, and 0.71 ± 0.04 g DW/L for 25%-75 % sturgeon-swine wastewater combination. Cyanobacteria cultivated in 50%-50 % sturgeon-swine wastewater also accumulated 70 % total carbohydrate of DW, whereas 75%-25 % sturgeon-swine and 25%-75 % sturgeon-swine accumulated 53 % and 45 %, respectively. Subsequently, the S. elongatus cells were grown in a separate batch of 50%-50 % sturgeon-swine wastewater and compared with cells grown in BG11 synthetic growth media. Cultivation in BG11 resulted in higher biomass production but lower carbohydrate accumulation than 50%-50 % mixed wastewater. Final biomass production was 0.85 ± 0.08 g DW/L for BG11 and 0.65 ± 0.04 g DW/L for 50%-50 % sturgeon-swine wastewater. Total carbohydrate accumulated was 75 % and 64 % of DW for 50%-50 % sturgeon-swine mixed wastewater and BG11 growth media, respectively, where glycogen was the main carbohydrate component (90 %). The nutrient removal efficiencies of S. elongatus were 67.15 % for orthophosphate, 93.39 % for nitrate-nitrite, and 97.98 % for ammonia. This study suggested that S. elongatus is a promising candidate for enabling simultaneous bioremediation of mixed wastewater and the production of value-added biochemicals.
Collapse
Affiliation(s)
- Rifat Hasan
- Department of Biological and Agricultural Engineering, North Carolina State University, Raleigh, NC, USA
| | - Nitesh Kasera
- Department of Biological and Agricultural Engineering, North Carolina State University, Raleigh, NC, USA
| | - Ashley E. Beck
- Department of Biological and Environmental Sciences, Carroll College, Helena, MT, USA
| | - Steven G. Hall
- Department of Biological and Agricultural Engineering, North Carolina State University, Raleigh, NC, USA
| |
Collapse
|
7
|
Srivastava A, Thapa S, Chakdar H, Babele PK, Shukla P. Cyanobacterial myxoxanthophylls: biotechnological interventions and biological implications. Crit Rev Biotechnol 2024; 44:63-77. [PMID: 36137567 DOI: 10.1080/07388551.2022.2117682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 07/09/2022] [Accepted: 08/06/2022] [Indexed: 11/03/2022]
Abstract
Cyanobacteria safeguard their photosynthetic machinery from oxidative damage caused by adverse environmental factors such as high-intensity light. Together with many photoprotective compounds, they contain myxoxanthophylls, a rare group of glycosidic carotenoids containing a high number of conjugated double bonds. These carotenoids have been shown to: have strong photoprotective effects, contribute to the integrity of the thylakoid membrane, and upregulate in cyanobacteria under a variety of stress conditions. However, their metabolic potential has not been fully utilized in the stress biology of cyanobacteria and the pharmaceutical industry due to a lack of mechanistic understanding and their insufficient biosynthesis. This review summarizes current knowledge on: biological function, genetic regulation, biotechnological production, and pharmaceutical potential of myxoxanthophyll, with a focus on strain engineering and parameter optimization strategies for increasing their cellular content. The summarized knowledge can be utilized in cyanobacterial metabolic engineering to improve the stress tolerance of useful strains and enhance the commercial-scale synthesis of myxoxanthophyll for pharmaceutical uses.
Collapse
Affiliation(s)
- Amit Srivastava
- Department of Chemistry, Purdue University, West Lafayette, United States of America
| | - Shobit Thapa
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, India
| | - Hillol Chakdar
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, India
| | | | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
| |
Collapse
|
8
|
Lee SY, Lee JS, Sim SJ. Cost-effective production of bioplastic polyhydroxybutyrate via introducing heterogeneous constitutive promoter and elevating acetyl-Coenzyme A pool of rapidly growing cyanobacteria. BIORESOURCE TECHNOLOGY 2024; 394:130297. [PMID: 38185449 DOI: 10.1016/j.biortech.2023.130297] [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: 11/28/2023] [Revised: 12/31/2023] [Accepted: 12/31/2023] [Indexed: 01/09/2024]
Abstract
Bioplastic production using cyanobacteria can be an effective strategy to cope with environmental problems caused by using petroleum-based plastics. Synechococcus elongatus UTEX 2973 with heterogeneous phaCAB can produce bioplastic polyhydroxybutyrate (PHB) with a high CO2 uptake rate. For cost-effective production of PHB in S. elongatus UTEX 2973, phaCAB was expressed by the constitutive Pcpc560, resulting in the production of 226 mg/L of PHB by only photoautotrophic cultivation without the addition of inducer. Several culture conditions were applied to increase PHB productivity, and when acetate was supplied at a concentration of 1 g/L as an organic carbon source, productivity significantly increased resulting in 607.2 mg/L of PHB and additive cost reduction of more than 300 times was achieved compared to IPTG. Consequently, these results suggest the possibility of cyanobacteria as an agent that can economically produce PHB and as a solution to the problem of petroleum-based plastics.
Collapse
Affiliation(s)
- So Young Lee
- Department of Chemical and Biological Engineering, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Jeong Seop Lee
- Department of Chemical and Biological Engineering, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Sang Jun Sim
- Department of Chemical and Biological Engineering, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea.
| |
Collapse
|
9
|
Liang Y, Li X, Lei F, Yang R, Bai W, Yang Q, Zhang D. Transcriptome Profiles Reveals ScDREB10 from Syntrichia caninervis Regulated Phenylpropanoid Biosynthesis and Starch/Sucrose Metabolism to Enhance Plant Stress Tolerance. PLANTS (BASEL, SWITZERLAND) 2024; 13:205. [PMID: 38256758 PMCID: PMC10820175 DOI: 10.3390/plants13020205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 12/28/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024]
Abstract
Desiccation is a kind of extreme form of drought stress and desiccation tolerance (DT) is an ancient trait of plants that allows them to survive tissue water potentials reaching -100 MPa or lower. ScDREB10 is a DREB A-5 transcription factor gene from a DT moss named Syntrichia caninervis, which has strong comprehensive tolerance to osmotic and salt stresses. This study delves further into the molecular mechanism of ScDREB10 stress tolerance based on the transcriptome data of the overexpression of ScDREB10 in Arabidopsis under control, osmotic and salt treatments. The transcriptional analysis of weight gene co-expression network analysis (WGCNA) showed that "phenylpropanoid biosynthesis" and "starch and sucrose metabolism" were key pathways in the network of cyan and yellow modules. Meanwhile, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of differentially expressed genes (DEGs) also showed that "phenylpropanoid biosynthesis" and "starch and sucrose metabolism" pathways demonstrate the highest enrichment in response to osmotic and salt stress, respectively. Quantitative real-time PCR (qRT-PCR) results confirmed that most genes related to phenylpropanoid biosynthesis" and "starch and sucrose metabolism" pathways in overexpressing ScDREB10 Arabidopsis were up-regulated in response to osmotic and salt stresses, respectively. In line with the results, the corresponding lignin, sucrose, and trehalose contents and sucrose phosphate synthase activities were also increased in overexpressing ScDREB10 Arabidopsis under osmotic and salt stress treatments. Additionally, cis-acting promoter element analyses and yeast one-hybrid experiments showed that ScDREB10 was not only able to bind with classical cis-elements, such as DRE and TATCCC (MYBST1), but also bind with unknown element CGTCCA. All of these findings suggest that ScDREB10 may regulate plant stress tolerance by effecting phenylpropanoid biosynthesis, and starch and sucrose metabolism pathways. This research provides insights into the molecular mechanisms underpinning ScDREB10-mediated stress tolerance and contributes to deeply understanding the A-5 DREB regulatory mechanism.
Collapse
Affiliation(s)
- Yuqing Liang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (Y.L.)
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838008, China
- Conservation and Utilization of Plant Gene Resources, Key Laboratory of Xinjiang, Urumqi 830011, China
| | - Xiaoshuang Li
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (Y.L.)
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838008, China
- Conservation and Utilization of Plant Gene Resources, Key Laboratory of Xinjiang, Urumqi 830011, China
| | - Feiya Lei
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (Y.L.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruirui Yang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (Y.L.)
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838008, China
- Conservation and Utilization of Plant Gene Resources, Key Laboratory of Xinjiang, Urumqi 830011, China
| | - Wenwan Bai
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (Y.L.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qilin Yang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (Y.L.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Daoyuan Zhang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (Y.L.)
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838008, China
- Conservation and Utilization of Plant Gene Resources, Key Laboratory of Xinjiang, Urumqi 830011, China
| |
Collapse
|
10
|
Song X, Ju Y, Chen L, Zhang W. Construction of Xylose-Utilizing Cyanobacterial Chassis for Bioproduction Under Photomixotrophic Conditions. Methods Mol Biol 2024; 2760:57-75. [PMID: 38468082 DOI: 10.1007/978-1-0716-3658-9_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Xylose is a major component of lignocellulose and the second most abundant sugar present in nature after glucose; it, therefore, has been considered to be a promising renewable resource for the production of biofuels and chemicals. However, no natural cyanobacterial strain is known capable of utilizing xylose. Here, we take the fast-growing cyanobacteria Synechococcus elongatus UTEX 2973 as an example to develop the synthetic biology-based methodology of constructing a new xylose-utilizing cyanobacterial chassis with increased acetyl-CoA for bioproduction.
Collapse
Affiliation(s)
- Xinyu Song
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, People's Republic of China
- Key Laboratory of Systems Bioengineering and Frontier Science Center of Synthetic Biology, The Ministry of Education of China, Tianjin University, Tianjin, People's Republic of China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, People's Republic of China
| | - Yue Ju
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, People's Republic of China
- Key Laboratory of Systems Bioengineering and Frontier Science Center of Synthetic Biology, The Ministry of Education of China, Tianjin University, Tianjin, People's Republic of China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, People's Republic of China
- Key Laboratory of Systems Bioengineering and Frontier Science Center of Synthetic Biology, The Ministry of Education of China, Tianjin University, Tianjin, People's Republic of China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, People's Republic of China.
- Key Laboratory of Systems Bioengineering and Frontier Science Center of Synthetic Biology, The Ministry of Education of China, Tianjin University, Tianjin, People's Republic of China.
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, People's Republic of China.
| |
Collapse
|
11
|
Goswami SK, Kashyap AS, Kumar R, Gujjar RS, Singh A, Manzar N. Harnessing Rhizospheric Microbes for Eco-friendly and Sustainable Crop Production in Saline Environments. Curr Microbiol 2023; 81:14. [PMID: 38006515 DOI: 10.1007/s00284-023-03538-z] [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: 07/31/2023] [Accepted: 10/24/2023] [Indexed: 11/27/2023]
Abstract
Soil salinization is a global issue that negatively impacts crop yield and has become a prime concern for researchers worldwide. Many important crop plants are susceptible to salinity-induced stresses, including ionic and osmotic stress. Approximately, 20% of the world's cultivated and 33% of irrigated land is affected by salt. While various agricultural practices have been successful in alleviating salinity stress, they can be costly and not environment-friendly. Therefore, there is a need for cost-effective and eco-friendly practices to improve soil health. One promising approach involves utilizing microbes found in the vicinity of plant roots to mitigate the effects of salinity stress and enhance plant growth as well as crop yield. By exploiting the salinity tolerance of plants and their associated rhizospheric microorganisms, which have plant growth-promoting properties, it is possible to reduce the adverse effects of salt stress on crop plants. The soil salinization is a common problem in the world, due to which we are unable to use the saline land. To make proper use of this land for different crops, microorganisms can play an important role. Looking at the increasing population of the world, this will be an appreciated effort to make the best use of the wasted land for food security. The updated information on this issue is needed. In this context, this article provides a concise review of the latest research on the use of salt-tolerant rhizospheric microorganisms to mitigate salinity stress in crop plants.
Collapse
Affiliation(s)
- Sanjay K Goswami
- ICAR-Indian Institute of Sugarcane Research, Rai Bareli Road, Dilkusha, Lucknow, Uttar Pradesh, 220026, India
| | - Abhijeet S Kashyap
- ICAR-National Bureau of Agriculturally Important Microorganism, Mau, 275103, India
| | - Rajeev Kumar
- ICAR-Indian Institute of Sugarcane Research, Rai Bareli Road, Dilkusha, Lucknow, Uttar Pradesh, 220026, India
| | - Ranjit Singh Gujjar
- ICAR-Indian Institute of Sugarcane Research, Rai Bareli Road, Dilkusha, Lucknow, Uttar Pradesh, 220026, India.
| | - Arjun Singh
- ICAR-CSSRI Regional Research Station, Rai Bareli Road, Dilkusha, Lucknow, Uttar Pradesh, 220026, India
| | - Nazia Manzar
- ICAR-National Bureau of Agriculturally Important Microorganism, Mau, 275103, India
| |
Collapse
|
12
|
Wang B, Zuniga C, Guarnieri MT, Zengler K, Betenbaugh M, Young JD. Metabolic engineering of Synechococcus elongatus 7942 for enhanced sucrose biosynthesis. Metab Eng 2023; 80:12-24. [PMID: 37678664 DOI: 10.1016/j.ymben.2023.09.002] [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: 05/02/2023] [Revised: 07/28/2023] [Accepted: 09/03/2023] [Indexed: 09/09/2023]
Abstract
The capability of cyanobacteria to produce sucrose from CO2 and light has a remarkable societal and biotechnological impact since sucrose can serve as a carbon and energy source for a variety of heterotrophic organisms and can be converted into value-added products. However, most metabolic engineering efforts have focused on understanding local pathway alterations that drive sucrose biosynthesis and secretion in cyanobacteria rather than analyzing the global flux re-routing that occurs following induction of sucrose production by salt stress. Here, we investigated global metabolic flux alterations in a sucrose-secreting (cscB-overexpressing) strain relative to its wild-type Synechococcus elongatus 7942 parental strain. We used targeted metabolomics, 13C metabolic flux analysis (MFA), and genome-scale modeling (GSM) as complementary approaches to elucidate differences in cellular resource allocation by quantifying metabolic profiles of three cyanobacterial cultures - wild-type S. elongatus 7942 without salt stress (WT), wild-type with salt stress (WT/NaCl), and the cscB-overexpressing strain with salt stress (cscB/NaCl) - all under photoautotrophic conditions. We quantified the substantial rewiring of metabolic fluxes in WT/NaCl and cscB/NaCl cultures relative to WT and identified a metabolic bottleneck limiting carbon fixation and sucrose biosynthesis. This bottleneck was subsequently mitigated through heterologous overexpression of glyceraldehyde-3-phosphate dehydrogenase in an engineered sucrose-secreting strain. Our study also demonstrates that combining 13C-MFA and GSM is a useful strategy to both extend the coverage of MFA beyond central metabolism and to improve the accuracy of flux predictions provided by GSM.
Collapse
Affiliation(s)
- Bo Wang
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, 37235, USA
| | - Cristal Zuniga
- Department of Pediatrics, University of California, San Diego, CA, 92093, USA; Department of Biology, San Diego State University, San Diego, CA, 92182, USA
| | - Michael T Guarnieri
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Karsten Zengler
- Department of Pediatrics, University of California, San Diego, CA, 92093, USA; Department of Bioengineering, University of California, San Diego, CA, 92093, USA; Center for Microbiome Innovation, University of California, San Diego, CA, 92093, USA
| | - Michael Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Jamey D Young
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, 37235, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37235, USA.
| |
Collapse
|
13
|
Sun J, Zhang Z, Zhang S, Dan Y, Sun H, Wu Y, Luan G, Lu X. Engineering Cyanobacterial Cell Factories for Photosynthetic Production of Fructose. ACS Synth Biol 2023; 12:3008-3019. [PMID: 37728873 DOI: 10.1021/acssynbio.3c00338] [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] [Indexed: 09/21/2023]
Abstract
Fructose is an important monosaccharide product widely applied in the food, medicine, and chemical industries. Currently, fructose is mainly manufactured with plant biomass-sourced polysaccharides through multiple steps of digestion, conversion, separation, and purification. The development of cyanobacterial metabolic engineering provides an attractive alternative route for the one-step direct production of fructose utilizing carbon dioxide and solar energy. In this work, we developed a paradigm for engineering cyanobacterial chassis cells into efficient cell factories for the photosynthetic production of fructose. In a representative cyanobacterial strain, Synechococcus elongatus PCC 7942, knockout of fructokinase effectively activated the synthesis and secretion of fructose in hypersaline conditions, independent of any heterologous transporters. The native sucrose synthesis pathway was identified as playing a primary role in fructose synthesis. Through combinatory optimizations on the levels of metabolism, physiology, and cultivation, the fructose yield of the Synechococcus cell factories was stepwise improved to 3.9 g/L. Such a paradigm was also adopted to engineer another Synechococcus strain, the marine species Synechococcus sp. PCC 7002, and facilitated an even higher fructose yield of over 6 g/L. Finally, the fructose synthesized and secreted by the cyanobacterial photosynthetic cell factories was successfully extracted and prepared from the culture broth in the form of products with 86% purity through multistep separation-purification operations. This work demonstrated a paradigm for systematically engineering cyanobacteria for photosynthetic production of desired metabolites, and it also confirmed the feasibility and potential of cyanobacterial photosynthetic biomanufacturing as a simple and efficient route for fructose production.
Collapse
Affiliation(s)
- Jiahui Sun
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, China
- Shandong Energy Institute, No. 189 Songling Road, Qingdao, Shandong 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China
- College of Life Science, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Zhichao Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, China
- Shandong Energy Institute, No. 189 Songling Road, Qingdao, Shandong 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China
| | - Shanshan Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, China
- Shandong Energy Institute, No. 189 Songling Road, Qingdao, Shandong 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China
- College of Life Science, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Yu Dan
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, China
- Shandong Energy Institute, No. 189 Songling Road, Qingdao, Shandong 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China
| | - Huili Sun
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, China
- Shandong Energy Institute, No. 189 Songling Road, Qingdao, Shandong 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China
- College of Life Science, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Yannan Wu
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, China
- Shandong Energy Institute, No. 189 Songling Road, Qingdao, Shandong 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China
| | - Guodong Luan
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, China
- Shandong Energy Institute, No. 189 Songling Road, Qingdao, Shandong 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China
- College of Life Science, University of Chinese Academy of Sciences, 100049 Beijing, China
- Dalian National Laboratory for Clean Energy, Dalian, Liaoning 116023, China
| | - Xuefeng Lu
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, China
- Shandong Energy Institute, No. 189 Songling Road, Qingdao, Shandong 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China
- College of Life Science, University of Chinese Academy of Sciences, 100049 Beijing, China
- Dalian National Laboratory for Clean Energy, Dalian, Liaoning 116023, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
| |
Collapse
|
14
|
Jaiswal D, Nenwani M, Wangikar PP. Isotopically non-stationary 13 C metabolic flux analysis of two closely related fast-growing cyanobacteria, Synechococcus elongatus PCC 11801 and 11802. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:558-573. [PMID: 37219374 DOI: 10.1111/tpj.16316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 05/10/2023] [Accepted: 05/18/2023] [Indexed: 05/24/2023]
Abstract
Synechococcus elongatus PCC 11801 and 11802 are closely related cyanobacterial strains that are fast-growing and tolerant to high light and temperature. These strains hold significant promise as chassis for photosynthetic production of chemicals from carbon dioxide. A detailed quantitative understanding of the central carbon pathways would be a reference for future metabolic engineering studies with these strains. We conducted isotopic non-stationary 13 C metabolic flux analysis to quantitively assess the metabolic potential of these two strains. This study highlights key similarities and differences in the central carbon flux distribution between these and other model/non-model strains. The two strains demonstrated a higher Calvin-Benson-Bassham (CBB) cycle flux coupled with negligible flux through the oxidative pentose phosphate pathway and the photorespiratory pathway and lower anaplerosis fluxes under photoautotrophic conditions. Interestingly, PCC 11802 shows the highest CBB cycle and pyruvate kinase flux values among those reported in cyanobacteria. The unique tricarboxylic acid (TCA) cycle diversion in PCC 11801 makes it ideal for the large-scale production of TCA cycle-derived chemicals. Additionally, dynamic labeling transients were measured for intermediates of amino acid, nucleotide, and nucleotide sugar metabolism. Overall, this study provides the first detailed metabolic flux maps of S. elongatus PCC 11801 and 11802, which may aid metabolic engineering efforts in these strains.
Collapse
Affiliation(s)
- Damini Jaiswal
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Minal Nenwani
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Pramod P Wangikar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| |
Collapse
|
15
|
Li C, Zheng H, Li H, Liu L, Wang J, Ni J. Synthetic Light-Driven Consortia for Carbon-Negative Biosynthesis. Chembiochem 2023; 24:e202300122. [PMID: 37401840 DOI: 10.1002/cbic.202300122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/07/2023] [Accepted: 07/03/2023] [Indexed: 07/05/2023]
Abstract
Synthetic light-driven consortia composed of phototrophs and heterotrophs have attracted increasing attention owing to their potential to be used in sustainable biotechnology. In recent years, synthetic phototrophic consortia have been used to produce bulk chemicals, biofuels, and other valuable bioproducts. In addition, autotrophic-heterotrophic symbiosis systems have potential applications in wastewater treatment, bioremediation, and as a method for phytoplankton bloom control. Here, we discuss progress made on the biosynthesis of phototrophic microbial consortia. In addition, strategies for optimizing the synthetic light-driven consortia are summarized. Moreover, we highlight current challenges and future research directions for the development of robust and controllable synthetic light-driven consortia.
Collapse
Affiliation(s)
- Chaofeng Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Haotian Zheng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hengrun Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Liangxu Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiawei Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jun Ni
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| |
Collapse
|
16
|
Sengupta A, Bandyopadhyay A, Schubert MG, Church GM, Pakrasi HB. Antenna Modification in a Fast-Growing Cyanobacterium Synechococcus elongatus UTEX 2973 Leads to Improved Efficiency and Carbon-Neutral Productivity. Microbiol Spectr 2023; 11:e0050023. [PMID: 37318337 PMCID: PMC10433846 DOI: 10.1128/spectrum.00500-23] [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: 02/01/2023] [Accepted: 05/19/2023] [Indexed: 06/16/2023] Open
Abstract
Our planet is sustained by sunlight, the primary energy source made accessible to all life forms by photoautotrophs. Photoautotrophs are equipped with light-harvesting complexes (LHCs) that enable efficient capture of solar energy, particularly when light is limiting. However, under high light, LHCs can harvest photons in excess of the utilization capacity of cells, causing photodamage. This damaging effect is most evident when there is a disparity between the amount of light harvested and carbon available. Cells strive to circumvent this problem by dynamically adjusting the antenna structure in response to the changing light signals, a process known to be energetically expensive. Much emphasis has been laid on elucidating the relationship between antenna size and photosynthetic efficiency and identifying strategies to synthetically modify antennae for optimal light capture. Our study is an effort in this direction and investigates the possibility of modifying phycobilisomes, the LHCs present in cyanobacteria, the simplest of photoautotrophs. We systematically truncate the phycobilisomes of Synechococcus elongatus UTEX 2973, a widely studied, fast-growing model cyanobacterium and demonstrate that partial truncation of its antenna can lead to a growth advantage of up to 36% compared to the wild type and an increase in sucrose titer of up to 22%. In contrast, targeted deletion of the linker protein which connects the first phycocyanin rod to the core proved detrimental, indicating that the core alone is not enough, and it is essential to maintain a minimal rod-core structure for efficient light harvest and strain fitness. IMPORTANCE Light energy is essential for the existence of life on this planet, and only photosynthetic organisms, equipped with light-harvesting antenna protein complexes, can capture this energy, making it readily accessible to all other life forms. However, these light-harvesting antennae are not designed to function optimally under extreme high light, a condition which can cause photodamage and significantly reduce photosynthetic productivity. In this study, we attempt to assess the optimal antenna structure for a fast-growing, high-light tolerant photosynthetic microbe with the goal of improving its productivity. Our findings provide concrete evidence that although the antenna complex is essential, antenna modification is a viable strategy to maximize strain performance under controlled growth conditions. This understanding can also be translated into identifying avenues to improve light harvesting efficiency in higher photoautotrophs.
Collapse
Affiliation(s)
- Annesha Sengupta
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | | | - Max G. Schubert
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | | |
Collapse
|
17
|
Lu KJ, Chang CW, Wang CH, Chen FYH, Huang IY, Huang PH, Yang CH, Wu HY, Wu WJ, Hsu KC, Ho MC, Tsai MD, Liao JC. An ATP-sensitive phosphoketolase regulates carbon fixation in cyanobacteria. Nat Metab 2023; 5:1111-1126. [PMID: 37349485 PMCID: PMC10365998 DOI: 10.1038/s42255-023-00831-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 05/25/2023] [Indexed: 06/24/2023]
Abstract
Regulation of CO2 fixation in cyanobacteria is important both for the organism and global carbon balance. Here we show that phosphoketolase in Synechococcus elongatus PCC7942 (SeXPK) possesses a distinct ATP-sensing mechanism, where a drop in ATP level allows SeXPK to divert precursors of the RuBisCO substrate away from the Calvin-Benson-Bassham cycle. Deleting the SeXPK gene increased CO2 fixation particularly during light-dark transitions. In high-density cultures, the Δxpk strain showed a 60% increase in carbon fixation and unexpectedly resulted in sucrose secretion without any pathway engineering. Using cryo-EM analysis, we discovered that these functions were enabled by a unique allosteric regulatory site involving two subunits jointly binding two ATP, which constantly suppresses the activity of SeXPK until the ATP level drops. This magnesium-independent ATP allosteric site is present in many species across all three domains of life, where it may also play important regulatory functions.
Collapse
Affiliation(s)
- Kuan-Jen Lu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chiung-Wen Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chun-Hsiung Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | | | - Irene Y Huang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Pin-Hsuan Huang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Cheng-Han Yang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Hsiang-Yi Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Wen-Jin Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Kai-Cheng Hsu
- Graduate Institute of Cancer Biology and Drug Discovery, Taipei Medical University, Taipei, Taiwan
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Ming-Daw Tsai
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan.
| | - James C Liao
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.
| |
Collapse
|
18
|
Cantrell M, Cano M, Sebesta J, Paddock T, Xiong W, Chou KJ, Yu J. Manipulation of glycogen and sucrose synthesis increases photosynthetic productivity in cyanobacteria. Front Microbiol 2023; 14:1124274. [PMID: 37275163 PMCID: PMC10233058 DOI: 10.3389/fmicb.2023.1124274] [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: 12/14/2022] [Accepted: 05/05/2023] [Indexed: 06/07/2023] Open
Abstract
Photosynthetic productivity is limited by low energy conversion efficiency in naturally evolved photosynthetic organisms, via multiple mechanisms that are not fully understood. Here we show evidence that extends recent findings that cyanobacteria use "futile" cycles in the synthesis and degradation of carbon compounds to dissipate ATP. Reduction of the glycogen cycle or the sucrose cycle in the model cyanobacterium Synechocystis 6803 led to redirection of cellular energy toward faster growth under simulated outdoor light conditions in photobioreactors that was accompanied by higher energy charge [concentration ratio of ATP/(ATP + ADP)]. Such manipulation of energy metabolism may have potential in engineering microalgal chassis cells to increase productivity of biomass or target metabolites.
Collapse
|
19
|
Goodchild-Michelman IM, Church GM, Schubert MG, Tang TC. Light and carbon: Synthetic biology toward new cyanobacteria-based living biomaterials. Mater Today Bio 2023; 19:100583. [PMID: 36846306 PMCID: PMC9945787 DOI: 10.1016/j.mtbio.2023.100583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 01/30/2023] [Accepted: 02/10/2023] [Indexed: 02/13/2023] Open
Abstract
Cyanobacteria are ideal candidates to use in developing carbon neutral and carbon negative technologies; they are efficient photosynthesizers and amenable to genetic manipulation. Over the past two decades, researchers have demonstrated that cyanobacteria can make sustainable, useful biomaterials, many of which are engineered living materials. However, we are only beginning to see such technologies applied at an industrial scale. In this review, we explore the ways in which synthetic biology tools enable the development of cyanobacteria-based biomaterials. First we give an overview of the ecological and biogeochemical importance of cyanobacteria and the work that has been done using cyanobacteria to create biomaterials so far. This is followed by a discussion of commonly used cyanobacteria strains and synthetic biology tools that exist to engineer cyanobacteria. Then, three case studies-bioconcrete, biocomposites, and biophotovoltaics-are explored as potential applications of synthetic biology in cyanobacteria-based materials. Finally, challenges and future directions of cyanobacterial biomaterials are discussed.
Collapse
Affiliation(s)
- Isabella M. Goodchild-Michelman
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Max G. Schubert
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Tzu-Chieh Tang
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| |
Collapse
|
20
|
Feng J, Li J, Liu D, Xin Y, Sun J, Yin WB, Li T. Generation and comprehensive analysis of Synechococcus elongatus-Aspergillus nidulans co-culture system for polyketide production. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:32. [PMID: 36859469 PMCID: PMC9979520 DOI: 10.1186/s13068-023-02283-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 02/16/2023] [Indexed: 03/03/2023]
Abstract
BACKGROUND Artificial microbial consortia composed of heterotrophic and photoautotrophic organisms represent a unique strategy for converting light energy and carbon dioxide into high-value bioproducts. Currently, the types of desired bioproducts are still limited, and microbial fitness benefit rendered by paired partner generally needs to be intensified. Exploring novel artificial microbial consortia at a laboratory scale is an essential step towards addressing this unmet need. This study aimed to conduct and analyze an artificial consortium composed of cyanobacterium Synechococcus elongatus FL130 with the filamentous fungus Aspergillus nidulans TWY1.1 for producing fungi-derived secondary metabolite of polyketide neosartoricin B. RESULTS Polyketide-producing A. nidulans TWY1.1 substantially ameliorated the growth and the survival of sucrose-secreting cyanobacterium S. elongatus FL130 in salt-stressed environments. Besides sucrose, comparable amounts of other carbohydrates were released from axenically cultured FL130 cells, which could be efficiently consumed by TWY1.1. Relative to axenically cultured FL130, less glycogen was accumulated in FL130 cells co-cultured with TWY1.1, and the glycogen phosphorylase gene catalyzing the first step for glycogen degradation had two-fold expression. Different from axenically cultured filamentous fungi, abundant vacuoles were observed in fungal hyphae of TWY1.1 co-cultured with cyanobacterium FL130. Meanwhile, FL130 cells displayed a characteristic pattern of interacting with its heterotrophic partner, densely dispersing along certain hyphae of TWY1.1. Finally, polyketide neosartoricin B was produced from TWY1.1 in FL130-TWY1.1 co-cultures, which was tightly adjusted by nitrogen level. CONCLUSION Overall, the results thoroughly proved the concept of pairing cyanobacteria with filamentous fungi to build artificial consortia for producing fungi-derived biomolecules.
Collapse
Affiliation(s)
- Jie Feng
- grid.32566.340000 0000 8571 0482School of Basic Medical Sciences, Lanzhou University, Lanzhou, 730000 China
| | - Jingwei Li
- grid.32566.340000 0000 8571 0482School of Basic Medical Sciences, Lanzhou University, Lanzhou, 730000 China
| | - Dongxia Liu
- grid.32566.340000 0000 8571 0482School of Basic Medical Sciences, Lanzhou University, Lanzhou, 730000 China
| | - Yuxian Xin
- grid.32566.340000 0000 8571 0482School of Basic Medical Sciences, Lanzhou University, Lanzhou, 730000 China
| | - Jingrong Sun
- grid.32566.340000 0000 8571 0482School of Basic Medical Sciences, Lanzhou University, Lanzhou, 730000 China
| | - Wen-Bing Yin
- grid.9227.e0000000119573309State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 People’s Republic of China
| | - Tingting Li
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, 730000, China.
| |
Collapse
|
21
|
Wu Y, Sun J, Xu X, Mao S, Luan G, Lu X. Engineering cyanobacteria for converting carbon dioxide into isomaltulose. J Biotechnol 2023; 364:1-4. [PMID: 36702257 DOI: 10.1016/j.jbiotec.2023.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 01/19/2023] [Accepted: 01/22/2023] [Indexed: 01/25/2023]
Abstract
Isomaltulose is a promising functional sweetener with broad application prospects in the food industry. Currently, isomaltulose is mainly produced through bioconversion processes based on the isomerization of sucrose, the economic feasibility of which is influenced by the cost of sucrose feedstocks, the biocatalyst preparation, and product purification. Cyanobacterial photosynthetic production utilizing solar energy and carbon dioxide represents a promising route for the supply of sugar products, which can promote both carbon reduction and green production. Previously, some cyanobacteria strains have been successfully engineered for synthesis of sucrose, the main feedstock for isomaltulose production. In this work, we introduced different sucrose isomerases into Synechococcus elongatus PCC 7942 and successfully achieved the isomaltulose synthesis and accumulation in the recombinant strains. Combinatory expression of an Escherichia coli sourced sucrose permease CscB with the sucrose isomerases led to efficient secretion of isomaltulose and significantly elevated the final titer. During a 6-day cultivation, 777 mg/L of isomaltulose was produced by the engineered Synechococcus cell factory. This work demonstrated a new route for isomaltulose biosynthesis utilizing carbon dioxide as the substrate, and provided novel understandings for the plasticity of cyanobacterial photosynthetic metabolism network.
Collapse
Affiliation(s)
- Yannan Wu
- Hunan Provincial Key Laboratory for Forestry Biotechnology, College of Life Science and Technology, Central South University of Forestry and Technology, Changsha, China
| | - Jiahui Sun
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Xuejing Xu
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Shaoming Mao
- Hunan Provincial Key Laboratory for Forestry Biotechnology, College of Life Science and Technology, Central South University of Forestry and Technology, Changsha, China.
| | - Guodong Luan
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; College of Life Science, University of Chinese Academy of Sciences, Beijing, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Xuefeng Lu
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; College of Life Science, University of Chinese Academy of Sciences, Beijing, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| |
Collapse
|
22
|
Santos-Merino M, Yun L, Ducat DC. Cyanobacteria as cell factories for the photosynthetic production of sucrose. Front Microbiol 2023; 14:1126032. [PMID: 36865782 PMCID: PMC9971976 DOI: 10.3389/fmicb.2023.1126032] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 01/24/2023] [Indexed: 02/16/2023] Open
Abstract
Biofuels and other biologically manufactured sustainable goods are growing in popularity and demand. Carbohydrate feedstocks required for industrial fermentation processes have traditionally been supplied by plant biomass, but the large quantities required to produce replacement commodity products may prevent the long-term feasibility of this approach without alternative strategies to produce sugar feedstocks. Cyanobacteria are under consideration as potential candidates for sustainable production of carbohydrate feedstocks, with potentially lower land and water requirements relative to plants. Several cyanobacterial strains have been genetically engineered to export significant quantities of sugars, especially sucrose. Sucrose is not only naturally synthesized and accumulated by cyanobacteria as a compatible solute to tolerate high salt environments, but also an easily fermentable disaccharide used by many heterotrophic bacteria as a carbon source. In this review, we provide a comprehensive summary of the current knowledge of the endogenous cyanobacterial sucrose synthesis and degradation pathways. We also summarize genetic modifications that have been found to increase sucrose production and secretion. Finally, we consider the current state of synthetic microbial consortia that rely on sugar-secreting cyanobacterial strains, which are co-cultivated alongside heterotrophic microbes able to directly convert the sugars into higher-value compounds (e.g., polyhydroxybutyrates, 3-hydroxypropionic acid, or dyes) in a single-pot reaction. We summarize recent advances reported in such cyanobacteria/heterotroph co-cultivation strategies and provide a perspective on future developments that are likely required to realize their bioindustrial potential.
Collapse
Affiliation(s)
- María Santos-Merino
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
| | - Lisa Yun
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Daniel C. Ducat
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| |
Collapse
|
23
|
Satta A, Esquirol L, Ebert BE. Current Metabolic Engineering Strategies for Photosynthetic Bioproduction in Cyanobacteria. Microorganisms 2023; 11:microorganisms11020455. [PMID: 36838420 PMCID: PMC9964548 DOI: 10.3390/microorganisms11020455] [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: 12/12/2022] [Revised: 02/04/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
Cyanobacteria are photosynthetic microorganisms capable of using solar energy to convert CO2 and H2O into O2 and energy-rich organic compounds, thus enabling sustainable production of a wide range of bio-products. More and more strains of cyanobacteria are identified that show great promise as cell platforms for the generation of bioproducts. However, strain development is still required to optimize their biosynthesis and increase titers for industrial applications. This review describes the most well-known, newest and most promising strains available to the community and gives an overview of current cyanobacterial biotechnology and the latest innovative strategies used for engineering cyanobacteria. We summarize advanced synthetic biology tools for modulating gene expression and their use in metabolic pathway engineering to increase the production of value-added compounds, such as terpenoids, fatty acids and sugars, to provide a go-to source for scientists starting research in cyanobacterial metabolic engineering.
Collapse
Affiliation(s)
- Alessandro Satta
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
- Department of Biology, University of Padua, 35100 Padua, Italy
| | - Lygie Esquirol
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Natha, QLD 4111, Australia
| | - Birgitta E. Ebert
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
- Correspondence:
| |
Collapse
|
24
|
Li C, Wang R, Wang J, Liu L, Li H, Zheng H, Ni J. A Highly Compatible Phototrophic Community for Carbon-Negative Biosynthesis. Angew Chem Int Ed Engl 2023; 62:e202215013. [PMID: 36378012 DOI: 10.1002/anie.202215013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/09/2022] [Accepted: 11/14/2022] [Indexed: 11/17/2022]
Abstract
CO2 sequestration engineering is promising for carbon-negative biosynthesis, and artificial communities can solve more complex problems than monocultures. However, obtaining an ideal photosynthetic community is still a great challenge. Herein, we describe the development of a highly compatible photosynthetic community (HCPC) by integrating a sucrose-producing CO2 sequestration module and a super-coupled module. The cyanobacteria CO2 sequestration module was obtained using stepwise metabolic engineering and then coupled with the efficient sucrose utilization module Vibrio natriegens. Integrated omics analysis indicated that enhanced photosynthetic electron transport and extracellular vesicles promote intercellular communication. Additionally, the HCPC was used to channel CO2 into valuable chemicals, enabling the overall release of -22.27 to -606.59 kgCO2 e kg-1 in the end products. This novel light-driven community could facilitate circular economic implementation in the future.
Collapse
Affiliation(s)
- Chaofeng Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.,Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ruoyu Wang
- School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiawei Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.,Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Liangxu Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.,Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hengrun Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.,Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Haotian Zheng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.,Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jun Ni
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.,Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| |
Collapse
|
25
|
Burnap RL. Cyanobacterial Bioenergetics in Relation to Cellular Growth and Productivity. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 183:25-64. [PMID: 36764956 DOI: 10.1007/10_2022_215] [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: 02/12/2023]
Abstract
Cyanobacteria, the evolutionary originators of oxygenic photosynthesis, have the capability to convert CO2, water, and minerals into biomass using solar energy. This process is driven by intricate bioenergetic mechanisms that consist of interconnected photosynthetic and respiratory electron transport chains coupled. Over the last few decades, advances in physiochemical analysis, molecular genetics, and structural analysis have enabled us to gain a more comprehensive understanding of cyanobacterial bioenergetics. This includes the molecular understanding of the primary energy conversion mechanisms as well as photoprotective and other dissipative mechanisms that prevent photodamage when the rates of photosynthetic output, primarily in the form of ATP and NADPH, exceed the rates that cellular assimilatory processes consume these photosynthetic outputs. Despite this progress, there is still much to learn about the systems integration and the regulatory circuits that control expression levels for optimal cellular abundance and activity of the photosynthetic complexes and the cellular components that convert their products into biomass. With an improved understanding of these regulatory principles and mechanisms, it should be possible to optimally modify cyanobacteria for enhanced biotechnological purposes.
Collapse
Affiliation(s)
- Robert L Burnap
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA.
| |
Collapse
|
26
|
Tóth GS, Siitonen V, Nikkanen L, Sovic L, Kallio P, Kourist R, Kosourov S, Allahverdiyeva Y. Photosynthetically produced sucrose by immobilized Synechocystis sp. PCC 6803 drives biotransformation in E. coli. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:146. [PMID: 36575466 PMCID: PMC9795604 DOI: 10.1186/s13068-022-02248-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 12/14/2022] [Indexed: 12/28/2022]
Abstract
BACKGROUND Whole-cell biotransformation is a promising emerging technology for the production of chemicals. When using heterotrophic organisms such as E. coli and yeast as biocatalysts, the dependence on organic carbon source impairs the sustainability and economic viability of the process. As a promising alternative, photosynthetic cyanobacteria with low nutrient requirements and versatile metabolism, could offer a sustainable platform for the heterologous production of organic compounds directly from sunlight and CO2. This strategy has been applied for the photoautotrophic production of sucrose by a genetically engineered cyanobacterium, Synechocystis sp. PCC 6803 strain S02. As the key concept in the current work, this can be further used to generate organic carbon compounds for different heterotrophic applications, including for the whole-cell biotransformation by yeast and bacteria. RESULTS Entrapment of Synechocystis S02 cells in Ca2+-cross-linked alginate hydrogel beads improves the specific sucrose productivity by 86% compared to suspension cultures during 7 days of cultivation under salt stress. The process was further prolonged by periodically changing the medium in the vials for up to 17 days of efficient production, giving the final sucrose yield slightly above 3000 mg l-1. We successfully demonstrated that the medium enriched with photosynthetically produced sucrose by immobilized Synechocystis S02 cells supports the biotransformation of cyclohexanone to ε-caprolactone by the E. coli WΔcscR Inv:Parvi strain engineered to (i) utilize low concentrations of sucrose and (ii) perform biotransformation of cyclohexanone to ε-caprolactone. CONCLUSION We conclude that cell entrapment in Ca2+-alginate beads is an effective method to prolong sucrose production by the engineered cyanobacteria, while allowing efficient separation of the cells from the medium. This advantage opens up novel possibilities to create advanced autotroph-heterotroph coupled cultivation systems for solar-driven production of chemicals via biotransformation, as demonstrated in this work by utilizing the photosynthetically produced sucrose to drive the conversion of cyclohexanone to ε-caprolactone by engineered E. coli.
Collapse
Affiliation(s)
- Gábor Szilveszter Tóth
- grid.1374.10000 0001 2097 1371Molecular Plant Biology, Department of Life Technologies, University of Turku, 20014 Turku, Finland
| | - Vilja Siitonen
- grid.1374.10000 0001 2097 1371Molecular Plant Biology, Department of Life Technologies, University of Turku, 20014 Turku, Finland
| | - Lauri Nikkanen
- grid.1374.10000 0001 2097 1371Molecular Plant Biology, Department of Life Technologies, University of Turku, 20014 Turku, Finland
| | - Lucija Sovic
- grid.410413.30000 0001 2294 748XCell and Protein Engineering, Institute of Molecular Biotechnology, Graz University of Technology, 8010 Graz, Austria
| | - Pauli Kallio
- grid.1374.10000 0001 2097 1371Molecular Plant Biology, Department of Life Technologies, University of Turku, 20014 Turku, Finland
| | - Robert Kourist
- grid.410413.30000 0001 2294 748XCell and Protein Engineering, Institute of Molecular Biotechnology, Graz University of Technology, 8010 Graz, Austria
| | - Sergey Kosourov
- grid.1374.10000 0001 2097 1371Molecular Plant Biology, Department of Life Technologies, University of Turku, 20014 Turku, Finland
| | - Yagut Allahverdiyeva
- grid.1374.10000 0001 2097 1371Molecular Plant Biology, Department of Life Technologies, University of Turku, 20014 Turku, Finland
| |
Collapse
|
27
|
Photobiological production of high-value pigments via compartmentalized co-cultures using Ca-alginate hydrogels. Sci Rep 2022; 12:22163. [PMID: 36550285 PMCID: PMC9780300 DOI: 10.1038/s41598-022-26437-y] [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: 09/23/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
Engineered cyanobacterium Synechococcus elongatus can use light and CO2 to produce sucrose, making it a promising candidate for use in co-cultures with heterotrophic workhorses. However, this process is challenged by the mutual stresses generated from the multispecies microbial culture. Here we demonstrate an ecosystem where S. elongatus is freely grown in a photo-bioreactor (PBR) containing an engineered heterotrophic workhorse (either β-carotene-producing Yarrowia lipolytica or indigoidine-producing Pseudomonas putida) encapsulated in calcium-alginate hydrogel beads. The encapsulation prevents growth interference, allowing the cyanobacterial culture to produce high sucrose concentrations enabling the production of indigoidine and β-carotene in the heterotroph. Our experimental PBRs yielded an indigoidine titer of 7.5 g/L hydrogel and a β-carotene titer of 1.3 g/L hydrogel, amounts 15-22-fold higher than in a comparable co-culture without encapsulation. Moreover, 13C-metabolite analysis and protein overexpression tests indicated that the hydrogel beads provided a favorable microenvironment where the cell metabolism inside the hydrogel was comparable to that in a free culture. Finally, the heterotroph-containing hydrogels were easily harvested and dissolved by EDTA for product recovery, while the cyanobacterial culture itself could be reused for the next batch of immobilized heterotrophs. This co-cultivation and hydrogel encapsulation system is a successful demonstration of bioprocess optimization under photobioreactor conditions.
Collapse
|
28
|
Tan C, Xu P, Tao F. Carbon-negative synthetic biology: challenges and emerging trends of cyanobacterial technology. Trends Biotechnol 2022; 40:1488-1502. [PMID: 36253158 DOI: 10.1016/j.tibtech.2022.09.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/05/2022] [Accepted: 09/20/2022] [Indexed: 11/06/2022]
Abstract
Global warming and climate instability have spurred interest in using renewable carbon resources for the sustainable production of chemicals. Cyanobacteria are ideal cellular factories for carbon-negative production of chemicals owing to their great potentials for directly utilizing light and CO2 as sole energy and carbon sources, respectively. However, several challenges in adapting cyanobacterial technology to industry, such as low productivity, poor tolerance, and product harvesting difficulty, remain. Synthetic biology may finally address these challenges. Here, we summarize recent advances in the production of value-added chemicals using cyanobacterial cell factories, particularly in carbon-negative synthetic biology and emerging trends in cyanobacterial applications. We also propose several perspectives on the future development of cyanobacterial technology for commercialization.
Collapse
Affiliation(s)
- Chunlin Tan
- The State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ping Xu
- The State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Fei Tao
- The State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| |
Collapse
|
29
|
Ma J, Guo T, Ren M, Chen L, Song X, Zhang W. Cross-feeding between cyanobacterium Synechococcus and Escherichia coli in an artificial autotrophic–heterotrophic coculture system revealed by integrated omics analysis. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:69. [PMID: 35733176 PMCID: PMC9219151 DOI: 10.1186/s13068-022-02163-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 06/04/2022] [Indexed: 01/21/2023]
Abstract
Background Light-driven consortia, which consist of sucrose-secreting cyanobacteria and heterotrophic species, have attracted considerable attention due to their capability for the sustainable production of valuable chemicals directly from CO2. In a previous study, we achieved a one-step conversion of sucrose secreted from cyanobacteria to fine chemicals by constructing an artificial coculture system consisting of sucrose-secreting Synechococcus elongateus cscB+ and 3-hydroxypropionic acid (3-HP) producing Escherichia coli ABKm. Analyses of the coculture system showed that the cyanobacterial cells grew better than their corresponding axenic cultures. To explore the underlying mechanism and to identify the metabolic nodes with the potential to further improve the coculture system, we conducted integrated transcriptomic, proteomic and metabolomic analyses. Results We first explored how the relieved oxidative stress affected cyanobacterial cell growth in a coculture system by supplementing additional ascorbic acid to CoBG-11 medium. We found that the cell growth of cyanobacteria was clearly improved with an additional 1 mM ascorbic acid under axenic culture; however, its growth was still slower than that in the coculture system, suggesting that the improved growth of Synechococcus cscB+ may be caused by multiple factors, including reduced oxidative stress. To further explore the cellular responses of cyanobacteria in the system, quantitative transcriptomics, proteomics and metabolomics were applied to Synechococcus cscB+. Analyses of differentially regulated genes/proteins and the abundance change of metabolites in the photosystems revealed that the photosynthesis of the cocultured Synechococcus cscB+ was enhanced. The decreased expression of the CO2 transporter suggested that the heterotrophic partner in the system might supplement additional CO2 to support the cell growth of Synechococcus cscB+. In addition, the differentially regulated genes and proteins involved in the nitrogen and phosphate assimilation pathways suggested that the supply of phosphate and nitrogen in the Co-BG11 medium might be insufficient. Conclusion An artificial coculture system capable of converting CO2 to fine chemicals was established and then analysed by integrated omics analysis, which demonstrated that in the coculture system, the relieved oxidative stress and increased CO2 availability improved the cell growth of cyanobacteria. In addition, the results also showed that the supply of phosphate and nitrogen in the Co-BG11 medium might be insufficient, which paves a new path towards the optimization of the coculture system in the future. Taken together, these results from the multiple omics analyses provide strong evidence that beneficial interactions can be achieved from cross-feeding and competition between phototrophs and prokaryotic heterotrophs and new guidelines for engineering more intelligent artificial consortia in the future. Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02163-5.
Collapse
|
30
|
Mai DHA, Nguyen LT, Lee EY. TSSNote-CyaPromBERT: Development of an integrated platform for highly accurate promoter prediction and visualization of Synechococcus sp. and Synechocystis sp. through a state-of-the-art natural language processing model BERT. Front Genet 2022; 13:1067562. [PMID: 36523764 PMCID: PMC9745317 DOI: 10.3389/fgene.2022.1067562] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/17/2022] [Indexed: 07/30/2023] Open
Abstract
Since the introduction of the first transformer model with a unique self-attention mechanism, natural language processing (NLP) models have attained state-of-the-art (SOTA) performance on various tasks. As DNA is the blueprint of life, it can be viewed as an unusual language, with its characteristic lexicon and grammar. Therefore, NLP models may provide insights into the meaning of the sequential structure of DNA. In the current study, we employed and compared the performance of popular SOTA NLP models (i.e., XLNET, BERT, and a variant DNABERT trained on the human genome) to predict and analyze the promoters in freshwater cyanobacterium Synechocystis sp. PCC 6803 and the fastest growing cyanobacterium Synechococcus elongatus sp. UTEX 2973. These freshwater cyanobacteria are promising hosts for phototrophically producing value-added compounds from CO2. Through a custom pipeline, promoters and non-promoters from Synechococcus elongatus sp. UTEX 2973 were used to train the model. The trained model achieved an AUROC score of 0.97 and F1 score of 0.92. During cross-validation with promoters from Synechocystis sp. PCC 6803, the model achieved an AUROC score of 0.96 and F1 score of 0.91. To increase accessibility, we developed an integrated platform (TSSNote-CyaPromBERT) to facilitate large dataset extraction, model training, and promoter prediction from public dRNA-seq datasets. Furthermore, various visualization tools have been incorporated to address the "black box" issue of deep learning and feature analysis. The learning transfer ability of large language models may help identify and analyze promoter regions for newly isolated strains with similar lineages.
Collapse
|
31
|
Vermaas JV, Crowley MF, Beckham GT. Molecular simulation of lignin-related aromatic compound permeation through gram-negative bacterial outer membranes. J Biol Chem 2022; 298:102627. [PMID: 36273587 PMCID: PMC9720347 DOI: 10.1016/j.jbc.2022.102627] [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: 04/04/2022] [Revised: 10/14/2022] [Accepted: 10/15/2022] [Indexed: 12/12/2022] Open
Abstract
Lignin, an abundant aromatic heteropolymer in secondary plant cell walls, is the single largest source of renewable aromatics in the biosphere. Leveraging this resource for renewable bioproducts through targeted microbial action depends on lignin fragment uptake by microbial hosts and subsequent enzymatic action to obtain the desired product. Recent computational work has emphasized that bacterial inner membranes are permeable to many aromatic compounds expected from lignin depolymerization processes. In this study, we expand on these findings through simulations for 42 lignin-related compounds across a gram-negative bacterial outer membrane model. Unbiased simulation trajectories indicate that spontaneous crossing for the full outer membrane is relatively rare at molecular simulation timescales, primarily due to preferential membrane partitioning and slow diffusion within the lipopolysaccharide layer within the outer membrane. Membrane partitioning and permeability coefficients were determined through replica exchange umbrella sampling simulations to overcome sampling limitations. We find that the glycosylated lipopolysaccharides found in the outer membrane increase the permeation barrier to many lignin-related compounds, particularly the most hydrophobic compounds. However, the effect is relatively modest; at industrially relevant concentrations, uncharged lignin-related compounds will readily diffuse across the outer membrane without the need for specific porins. Together, our results provide insight into the permeability of the bacterial outer membrane for assessing lignin fragment uptake and the future production of renewable bioproducts.
Collapse
Affiliation(s)
- Josh V. Vermaas
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA,National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA,MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA,For correspondence: Josh V. Vermaas; Michael F. Crowley; Gregg T. Beckham
| | - Michael F. Crowley
- Renewable Resources and Enabling Sciences Center, National Renewable Energy, Laboratory, Golden, Colorado, USA,For correspondence: Josh V. Vermaas; Michael F. Crowley; Gregg T. Beckham
| | - Gregg T. Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy, Laboratory, Golden, Colorado, USA,For correspondence: Josh V. Vermaas; Michael F. Crowley; Gregg T. Beckham
| |
Collapse
|
32
|
Light-Driven Synthetic Biology: Progress in Research and Industrialization of Cyanobacterial Cell Factory. LIFE (BASEL, SWITZERLAND) 2022; 12:life12101537. [PMID: 36294972 PMCID: PMC9605453 DOI: 10.3390/life12101537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/21/2022] [Accepted: 09/29/2022] [Indexed: 11/07/2022]
Abstract
Light-driven synthetic biology refers to an autotrophic microorganisms-based research platform that remodels microbial metabolism through synthetic biology and directly converts light energy into bio-based chemicals. This technology can help achieve the goal of carbon neutrality while promoting green production. Cyanobacteria are photosynthetic microorganisms that use light and CO2 for growth and production. They thus possess unique advantages as "autotrophic cell factories". Various fuels and chemicals have been synthesized by cyanobacteria, indicating their important roles in research and industrial application. This review summarized the progresses and remaining challenges in light-driven cyanobacterial cell factory. The choice of chassis cells, strategies used in metabolic engineering, and the methods for high-value CO2 utilization will be discussed.
Collapse
|
33
|
Dan Y, Sun J, Zhang S, Wu Y, Mao S, Luan G, Lu X. Manipulating the Expression of Glycogen Phosphorylase in Synechococcus elongatus PCC 7942 to Mobilize Glycogen Storage for Sucrose Synthesis. Front Bioeng Biotechnol 2022; 10:925311. [PMID: 35845416 PMCID: PMC9284946 DOI: 10.3389/fbioe.2022.925311] [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: 04/21/2022] [Accepted: 05/11/2022] [Indexed: 11/23/2022] Open
Abstract
Cyanobacteria are a promising photosynthetic chassis to produce biofuels, biochemicals, and pharmaceuticals at the expense of CO2 and light energy. Glycogen accumulation represents a universal carbon sink mechanism among cyanobacteria, storing excess carbon and energy from photosynthesis and may compete with product synthesis. Therefore, the glycogen synthesis pathway is often targeted to increase cyanobacterial production of desired carbon-based products. However, these manipulations caused severe physiological and metabolic impairments and often failed to optimize the overall performance of photosynthetic production. Here, in this work, we explored to mobilize the glycogen storage by strengthening glycogen degradation activities. In Synechococcus elongatus PCC 7942, we manipulated the abundances of glycogen phosphorylase (GlgP) with a theophylline dose-responsive riboswitch approach, which holds control over the cyanobacterial glycogen degradation process and successfully regulated the glycogen contents in the recombinant strain. Taking sucrose synthesis as a model, we explored the effects of enhanced glycogen degradation on sucrose production and glycogen storage. It is confirmed that under non-hypersaline conditions, the overexpressed glgP facilitated the effective mobilization of glycogen storage and resulted in increased secretory sucrose production. The findings in this work provided fresh insights into the area of cyanobacteria glycogen metabolism engineering and would inspire the development of novel metabolic engineering approaches for efficient photosynthetic biosynthesis.
Collapse
Affiliation(s)
- Yu Dan
- College of Life Science and Technology, Central South University of Forestry and Technology, Changsha, China
- Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry and Technology, Changsha, China
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Jiahui Sun
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Shandong Energy Institute, Qingdao, China
- Qingdao New Energy Shandong Laboratory, Qingdao, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Shanshan Zhang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Shandong Energy Institute, Qingdao, China
- Qingdao New Energy Shandong Laboratory, Qingdao, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yannan Wu
- College of Life Science and Technology, Central South University of Forestry and Technology, Changsha, China
- Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry and Technology, Changsha, China
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Shaoming Mao
- College of Life Science and Technology, Central South University of Forestry and Technology, Changsha, China
- Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry and Technology, Changsha, China
- *Correspondence: Shaoming Mao, ; Guodong Luan, ; Xuefeng Lu,
| | - Guodong Luan
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Shandong Energy Institute, Qingdao, China
- Qingdao New Energy Shandong Laboratory, Qingdao, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Shaoming Mao, ; Guodong Luan, ; Xuefeng Lu,
| | - Xuefeng Lu
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Shandong Energy Institute, Qingdao, China
- Qingdao New Energy Shandong Laboratory, Qingdao, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- *Correspondence: Shaoming Mao, ; Guodong Luan, ; Xuefeng Lu,
| |
Collapse
|
34
|
Gao H, Manishimwe C, Yang L, Wang H, Jiang Y, Jiang W, Zhang W, Xin F, Jiang M. Applications of synthetic light-driven microbial consortia for biochemicals production. BIORESOURCE TECHNOLOGY 2022; 351:126954. [PMID: 35288267 DOI: 10.1016/j.biortech.2022.126954] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
Synthetic microbial consortia provide a versatile and efficient platform for biochemicals production through the labor division. Especially, microbial communities composed of phototrophs and heterotrophs offer a promising alternative, as they can directly convert carbon dioxide (CO2) into chemicals. Within this system, photoautotrophic microbes can convert CO2 into organic carbon for microbial growth and metabolites synthesis by the heterotrophic partners. In return, heterotrophs can provide additional CO2 to support the growth of photoautotrophic microbes. However, the unmatched growing conditions, low stability and production efficiency of synthetic microbial consortia hinder their further applications. Thus, design and construction of mutualistic and stable synthetic light-driven microbial consortia are urgently needed. In this review, the progress of synthetic light-driven microbial consortia for chemicals production was comprehensively summarized. In addition, space-efficient synthetic light-driven microbial consortia in hydrogel system were reviewed. Perspectives on orderly distribution of light-driven microbial consortia associated with 3D printing technology in biomanufacturing were also addressed.
Collapse
Affiliation(s)
- Hao Gao
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Clarisse Manishimwe
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Lu Yang
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Hanxiao Wang
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Yujia Jiang
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Wankui Jiang
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Wenming Zhang
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, PR China
| | - Fengxue Xin
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, PR China.
| | - Min Jiang
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, PR China
| |
Collapse
|
35
|
Yao J, Wang J, Ju Y, Dong Z, Song X, Chen L, Zhang W. Engineering a Xylose-Utilizing Synechococcus elongatus UTEX 2973 Chassis for 3-Hydroxypropionic Acid Biosynthesis under Photomixotrophic Conditions. ACS Synth Biol 2022; 11:678-688. [PMID: 35119824 DOI: 10.1021/acssynbio.1c00364] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Photomixotrophic cultivation of cyanobacteria is considered a promising strategy to achieve both high cell density and product accumulation, since cyanobacteria can obtain carbon and energy sources from organic matter in addition to those obtained from CO2 and sunlight. Acetyl coenzyme A (acetyl-CoA) is a key precursor used for the biosynthesis of a wide variety of important value-added chemicals. However, the acetyl-CoA content in cyanobacteria is typically low under photomixotrophic conditions, which limits the productivity of the derived chemicals. In this study, a xylose utilization pathway from Escherichia coli was first engineered into fast-growing Synechococcus elongatus UTEX 2973 (hereafter Synechococcus 2973), enabling the xylose based photomixotrophy. Metabolomics analysis of the engineered strain showed that the utilization of xylose enhanced the carbon flow to the oxidative pentose phosphate (OPP) pathway, along with an increase in the intracellular abundance of metabolites such as fructose-6-phosphate (F6P), fructose-1,6-bisphosphate (FBP), ribose-5-phosphate (R5P), erythrose-4-phosphate (E4P), and glyceraldehyde-3-phosphate (G3P). Then, the native glycolytic pathway was rewired via heterologous phosphoketolase (Pkt) gene expression, combined with phosphofructokinase (Pfk) gene knockout and fructose-1,6-bisphosphatase (Fbp) gene overexpression, to drive more carbon flux from xylose to acetyl-CoA. Finally, a heterologous 3-hydroxypropionic acid (3-HP) biosynthetic pathway was introduced. The results showed that 3-HP biosynthesis was improved by up to approximately 4.1-fold (from 22.5 mg/L to 91.3 mg/L) compared with the engineered strain without a rewired metabolism under photomixotrophic conditions and up to approximately 14-fold compared with the strain under photoautotrophic conditions. Using 3-HP as a "proof-of-molecule", our results demonstrated that this strategy could be applied to improve the intracellular pool of acetyl-CoA for the photomixotrophic production of value-added chemicals that require acetyl-CoA as a precursor in a cyanobacterial chassis.
Collapse
Affiliation(s)
- Jiaqi Yao
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, PR China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, PR China
| | - Jin Wang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, PR China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, PR China
| | - Yue Ju
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, PR China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, PR China
| | - Zhengxin Dong
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, PR China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, PR China
| | - Xinyu Song
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, PR China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, PR China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin 300072, PR China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, PR China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, PR China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, PR China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, PR China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin 300072, PR China
| |
Collapse
|
36
|
Sengupta A, Liu D, Pakrasi HB. CRISPR-Cas mediated genome engineering of cyanobacteria. Methods Enzymol 2022; 676:403-432. [DOI: 10.1016/bs.mie.2022.07.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
37
|
Dookeran ZA, Nielsen DR. Systematic Engineering of Synechococcus elongatus UTEX 2973 for Photosynthetic Production of l-Lysine, Cadaverine, and Glutarate. ACS Synth Biol 2021; 10:3561-3575. [PMID: 34851612 DOI: 10.1021/acssynbio.1c00492] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amino acids and related targets are typically produced by well-characterized heterotrophs including Corynebacterium glutamicum and Escherichia coli. Cyanobacteria offer an opportunity to supplant these sugar-intensive processes by instead directly utilizing atmospheric CO2 and sunlight. Synechococcus elongatus UTEX 2973 (hereafter UTEX 2973) is a particularly promising photoautotrophic platform due to its fast growth rate. Here, we first engineered UTEX 2973 to overproduce l-lysine (hereafter lysine), after which both cadaverine and glutarate production were achieved through further pathway engineering. To facilitate metabolic engineering, the relative activities of a subset of previously uncharacterized promoters were investigated, in each case, while also comparing the effects of both chromosomal (from neutral site NS3) and episomal (from pAM4788) expressions. Using these parts, lysine overproduction in UTEX 2973 was engineered by introducing a feedback-resistant copy of aspartate kinase (encoded by lysCfbr) and a lysine exporter (encoded by ybjE), both from E. coli. While chromosomal expression resulted in lysine production up to just 325.3 ± 14.8 mg/L after 120 h, this was then increased to 556.3 ± 62.3 mg/L via plasmid-based expression, also surpassing prior reports of photoautotrophic lysine bioproduction. Lastly, additional products of interest were then targeted by modularly extending the lysine pathway to glutarate and cadaverine, two 5-carbon, bioplastic monomers. By this approach, glutarate has so far been produced at final titers reaching 67.5 ± 2.2 mg/L by 96 h, whereas cadaverine has been produced at up to 55.3 ± 6.7 mg/L. Overcoming pathway and/or transport bottlenecks, meanwhile, will be important to improving upon these initial outputs.
Collapse
Affiliation(s)
- Zachary A. Dookeran
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, P.O. Box 876106, Tempe, Arizona 85287-6106, United States
| | - David R. Nielsen
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, P.O. Box 876106, Tempe, Arizona 85287-6106, United States
| |
Collapse
|
38
|
Taylor GM, Hitchcock A, Heap JT. Combinatorial assembly platform enabling engineering of genetically stable metabolic pathways in cyanobacteria. Nucleic Acids Res 2021; 49:e123. [PMID: 34554258 PMCID: PMC8643660 DOI: 10.1093/nar/gkab791] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 08/18/2021] [Accepted: 09/02/2021] [Indexed: 11/13/2022] Open
Abstract
Cyanobacteria are simple, efficient, genetically-tractable photosynthetic microorganisms which in principle represent ideal biocatalysts for CO2 capture and conversion. However, in practice, genetic instability and low productivity are key, linked problems in engineered cyanobacteria. We took a massively parallel approach, generating and characterising libraries of synthetic promoters and RBSs for the cyanobacterium Synechocystis sp. PCC 6803, and assembling a sparse combinatorial library of millions of metabolic pathway-encoding construct variants. Genetic instability was observed for some variants, which is expected when variants cause metabolic burden. Surprisingly however, in a single combinatorial round without iterative optimisation, 80% of variants chosen at random and cultured photoautotrophically over many generations accumulated the target terpenoid lycopene from atmospheric CO2, apparently overcoming genetic instability. This large-scale parallel metabolic engineering of cyanobacteria provides a new platform for development of genetically stable cyanobacterial biocatalysts for sustainable light-driven production of valuable products directly from CO2, avoiding fossil carbon or competition with food production.
Collapse
Affiliation(s)
- George M Taylor
- Imperial College Centre for Synthetic Biology, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Andrew Hitchcock
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - John T Heap
- Imperial College Centre for Synthetic Biology, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.,School of Life Sciences, The University of Nottingham, Biodiscovery Institute, University Park, Nottingham NG7 2RD, UK
| |
Collapse
|
39
|
Sengupta S, Sahasrabuddhe D, Wangikar PP. Transporter engineering for the development of cyanobacteria as cell factories: A text analytics guided survey. Biotechnol Adv 2021; 54:107816. [PMID: 34411662 DOI: 10.1016/j.biotechadv.2021.107816] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 08/10/2021] [Accepted: 08/13/2021] [Indexed: 11/28/2022]
Abstract
Cyanobacteria are attractive candidates for photoautotrophic production of platform chemicals due to their inherent ability to utilize carbon dioxide as the sole carbon source. Metabolic pathways can be engineered more readily in cyanobacteria compared to higher photosynthetic organisms. Although significant progress has been made in pathway engineering, intracellular accumulation of the product is a potential bottleneck in large-scale production. Likewise, substrate uptake is known to limit growth and product formation. These limitations can potentially be addressed by targeted and controlled expression of transporter proteins in the metabolically engineered strains. This review focuses on the transporters that have been explored in cyanobacteria. To highlight the progress on characterization and application of cyanobacterial transporters, we applied text analytics to extract relevant information from over 1000 publications. We have categorized the transporters based on their source, their function and the solute they transport. Further, the review provides insights into the potential of transporters in the metabolic engineering of cyanobacteria for improved product titer.
Collapse
Affiliation(s)
- Shinjinee Sengupta
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India; DBT-Pan IIT Center for Bioenergy, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Deepti Sahasrabuddhe
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India; DBT-Pan IIT Center for Bioenergy, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India; Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Pramod P Wangikar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India; DBT-Pan IIT Center for Bioenergy, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India; Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| |
Collapse
|
40
|
Cui J, Sun T, Chen L, Zhang W. Salt-Tolerant Synechococcus elongatus UTEX 2973 Obtained via Engineering of Heterologous Synthesis of Compatible Solute Glucosylglycerol. Front Microbiol 2021; 12:650217. [PMID: 34084156 PMCID: PMC8168540 DOI: 10.3389/fmicb.2021.650217] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/25/2021] [Indexed: 01/08/2023] Open
Abstract
The recently isolated cyanobacterium Synechococcus elongatus UTEX 2973 (Syn2973) is characterized by a faster growth rate and greater tolerance to high temperature and high light, making it a good candidate chassis for autotrophic photosynthetic microbial cell factories. However, Syn2973 is sensitive to salt stress, making it urgently important to improve the salt tolerance of Syn2973 for future biotechnological applications. Glucosylglycerol, a compatible solute, plays an important role in resisting salt stress in moderate and marine halotolerant cyanobacteria. In this study, the salt tolerance of Syn2973 was successfully improved by introducing the glucosylglycerol (GG) biosynthetic pathway (OD750 improved by 24% at 60 h). In addition, the salt tolerance of Syn2973 was further enhanced by overexpressing the rate-limiting step of glycerol-3-phosphate dehydrogenase and downregulating the gene rfbA, which encodes UDP glucose pyrophosphorylase. Taken together, these results indicate that the growth of the end-point strain M-2522-GgpPS-drfbA was improved by 62% compared with the control strain M-pSI-pSII at 60 h under treatment with 0.5 M NaCl. Finally, a comparative metabolomic analysis between strains M-pSI-pSII and M-2522-GgpPS-drfbA was performed to characterize the carbon flux in the engineered M-2522-GgpPS-drfbA strain, and the results showed that more carbon flux was redirected from ADP-GLC to GG synthesis. This study provides important engineering strategies to improve salt tolerance and GG production in Syn2973 in the future.
Collapse
Affiliation(s)
- Jinyu Cui
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Tao Sun
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin, China.,Center for Biosafety Research and Strategy, Tianjin University, Tianjin, China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China.,Center for Biosafety Research and Strategy, Tianjin University, Tianjin, China
| |
Collapse
|
41
|
Yang F, Zhang J, Cai Z, Zhou J, Li Y. Exploring the oxygenase function of Form II Rubisco for production of glycolate from CO 2. AMB Express 2021; 11:65. [PMID: 33963929 PMCID: PMC8106553 DOI: 10.1186/s13568-021-01224-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/26/2021] [Indexed: 12/20/2022] Open
Abstract
The oxygenase activity of Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) converts ribulose-1,5-bisphosphate (RuBP) into 2-phosphoglycolate, which in turn channels into photorespiration, resulting in carbon and energy loss in higher plants. We observed that glycolate can be accumulated extracellularly when two genes encoding the glycolate dehydrogenase of cyanobacteria Synechocystis sp. PCC 6803 were inactivated. This inspired us to explore the oxygenase function of Rubisco for production of glycolate, an important industrial chemical, from CO2 by engineered cyanobacteria. Since the oxygenase activity of Rubisco is generally low in CO2-rich carboxysome of cyanobacteria, we introduced Form II Rubisco, which cannot be assembled in carboxysome, into the cytoplasm of cyanobacteria. Heterologous expression of a Form II Rubisco from endosymbiont of tubeworm Riftia pachyptila (RPE Rubisco) significantly increased glycolate production. We show that the RPE Rubisco is expressed in the cytoplasm. Glycolate production increased upon addition of NaHCO3 but decreased upon supplying CO2. The titer of glycolate reached 2.8 g/L in 18 days, a 14-fold increase compared with the initial strain with glycolate dehydrogenase inactivated. This is also the highest glycolate titer biotechnologically produced from CO2 ever reported. Photosynthetic production of glycolate demonstrated the oxygenase activity of Form II Rubisco can be explored for production of chemicals from CO2.
Collapse
|
42
|
Heo JB, Lee YS, Chung CH. Seagrass-based platform strategies for sustainable hydroxymethylfurfural (HMF) production: toward bio-based chemical products. Crit Rev Biotechnol 2021; 41:902-917. [PMID: 33648387 DOI: 10.1080/07388551.2021.1892580] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Today, sustainable chemistry is a key trend in the chemical manufacturing industry due mainly to concerns over the global environment and resource security. In sustainable chemical manufacture, the choice of a bio-based feedstock plays a pivotal pillar. In terms of feedstock utilization for producing HMF, which is a multivalent platform intermediate easily convertible to valuable chemical products; biopolymers, biofuels, and other important chemicals, seagrass biomasses can be more favorable feedstocks compared with land plant resources due primarily to easy availability and no systematic farming. Moreover, seagrass feedstocks could contribute cost-effectively and sustainably producing HMF by exploiting the beach-cast seagrasses on seagrass-prairies with no feedstock cost, indicating that seagrass biomasses could be a most promising biofeedstock source for sustainable HMF production. We afford a platform bioprocessing technology that has not been attempted before for sustainable HMF production using raw seagrass biomass. This bioprocess can be operated by simple reaction conditions using inorganic Brønsted acids (mainly HCl) and ionic liquid solvents at relatively low temperatures (120-130 °C). In addition, some bioengineering strategies for improving the growth of seagrass biomass and the quantity/quality of nonstructural carbohydrates (starch, sucrose) that can be used as the feeding substrates for HMF production are also discussed. The main aim of this review is to provide some important information about breakthrough bio/technologies conducive to cost-effective and sustainable HMF production.
Collapse
Affiliation(s)
- Jae Bok Heo
- Department of Molecular Genetic Biotechnology, Dong-A University, Busan, South Korea
| | - Yong-Suk Lee
- Division of Applied Life Science (BK21), Gyeongsang National University, Jinju, South Korea
| | - Chung-Han Chung
- Department of Biotechnology, Dong-A University, Busan, South Korea
| |
Collapse
|
43
|
Xie Y, Chen L, Sun T, Zhang W. Deciphering and engineering high-light tolerant cyanobacteria for efficient photosynthetic cell factories. Chin J Chem Eng 2021. [DOI: 10.1016/j.cjche.2020.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
44
|
Stephens S, Mahadevan R, Allen DG. Engineering Photosynthetic Bioprocesses for Sustainable Chemical Production: A Review. Front Bioeng Biotechnol 2021; 8:610723. [PMID: 33490053 PMCID: PMC7820810 DOI: 10.3389/fbioe.2020.610723] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 12/01/2020] [Indexed: 11/13/2022] Open
Abstract
Microbial production of chemicals using renewable feedstocks such as glucose has emerged as a green alternative to conventional chemical production processes that rely primarily on petroleum-based feedstocks. The carbon footprint of such processes can further be reduced by using engineered cells that harness solar energy to consume feedstocks traditionally considered to be wastes as their carbon sources. Photosynthetic bacteria utilize sophisticated photosystems to capture the energy from photons to generate reduction potential with such rapidity and abundance that cells often cannot use it fast enough and much of it is lost as heat and light. Engineering photosynthetic organisms could enable us to take advantage of this energy surplus by redirecting it toward the synthesis of commercially important products such as biofuels, bioplastics, commodity chemicals, and terpenoids. In this work, we review photosynthetic pathways in aerobic and anaerobic bacteria to better understand how these organisms have naturally evolved to harness solar energy. We also discuss more recent attempts at engineering both the photosystems and downstream reactions that transfer reducing power to improve target chemical production. Further, we discuss different methods for the optimization of photosynthetic bioprocess including the immobilization of cells and the optimization of light delivery. We anticipate this review will serve as an important resource for future efforts to engineer and harness photosynthetic bacteria for chemical production.
Collapse
Affiliation(s)
- Sheida Stephens
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada.,Institute of Biomedical Engineering, University of Toronto, Toronto, ON, Canada
| | - D Grant Allen
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| |
Collapse
|
45
|
Lin PC, Zhang F, Pakrasi HB. Enhanced limonene production in a fast-growing cyanobacterium through combinatorial metabolic engineering. Metab Eng Commun 2021; 12:e00164. [PMID: 33659180 PMCID: PMC7890178 DOI: 10.1016/j.mec.2021.e00164] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 01/12/2021] [Accepted: 01/19/2021] [Indexed: 12/14/2022] Open
Abstract
Terpenoids are a large and diverse group of natural products with commercial applications. Microbial production of terpenes is considered as a feasible approach for the stable supply of these complex hydrocarbons. Cyanobacteria, photosynthetic prokaryotes, are attractive hosts for sustainable bioproduction, because these autotrophs require only light and CO2 for growth. Despite cyanobacteria having been engineered to produce a variety of compounds, their productivities of terpenes are generally low. Further research is needed to determine the bottleneck reactions for enhancing terpene production in cyanobacteria. In this study, we engineered the fast-growing cyanobacterium Synechococcus elongatus UTEX 2973 to produce a commercially-used terpenoid, limonene. We identified a beneficial mutation in the gene encoding geranylgeranyl pyrophosphate synthase crtE, leading to a 2.5-fold increase in limonene production. The engineered strain produced 16.4 mg L−1 of limonene at a rate of 8.2 mg L−1 day−1, which is 8-fold higher than limonene productivities previously reported in other cyanobacterial species. Furthermore, we employed a combinatorial metabolic engineering approach to optimize genes involved in the upstream pathway of limonene biosynthesis. By modulating the expression of genes encoding the enzymes in the MEP pathway and the geranyl pyrophosphate synthase, we showed that optimization of the expression level is critical to enhance limonene production in cyanobacteria. Engineering of the fast growing cyanobacterium Synechococcus elongatus UTEX 2973 for limonene production. Identification of a beneficial mutation with 2.5-fold increase in limonene productivity. Pathway optimization for limonene biosynthesis.
Collapse
Affiliation(s)
- Po-Cheng Lin
- Department of Energy, Environmental & Chemical Engineering, Washington University, St. Louis, MO, 63130, USA
| | - Fuzhong Zhang
- Department of Energy, Environmental & Chemical Engineering, Washington University, St. Louis, MO, 63130, USA
| | - Himadri B Pakrasi
- Department of Biology, Washington University, St. Louis, MO, 63130, USA
| |
Collapse
|
46
|
Wang F, Gao Y, Yang G. Recent advances in synthetic biology of cyanobacteria for improved chemicals production. Bioengineered 2020; 11:1208-1220. [PMID: 33124500 PMCID: PMC8291842 DOI: 10.1080/21655979.2020.1837458] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Cyanobacteria are Gram-negative photoautotrophic prokaryotes and have shown great importance to the Earth’s ecology. Based on their capability in oxygenic photosynthesis and genetic merits, they can be engineered as microbial chassis for direct conversion of carbon dioxide to value-added biofuels and chemicals. In the last decades, attempts have given to the application of synthetic biology tools and approaches in the development of cyanobacterial cell factories. Despite the successful proof-of-principle studies, large-scale application is still a technical challenge due to low yields of bioproducts. Therefore, recent efforts are underway to characterize and develop genetic regulatory parts and strategies for the synthetic biology applications in cyanobacteria. In this review, we present the recent advancements and application in cyanobacterial synthetic biology toolboxes. We also discuss the limitations and future perspectives for using such novel tools in cyanobacterial biotechnology.
Collapse
Affiliation(s)
- Fen Wang
- Department of Surgery, College of Medicine, University of Florida , Gainesville, FL, USA
| | - Yuanyuan Gao
- Jining Academy of Agricultural Science , Jining, Shandong, China
| | - Guang Yang
- Department of Aging and Geriatric Research, Institute on Aging, University of Florida , Gainesville, FL, USA
| |
Collapse
|
47
|
Liu D, Liberton M, Hendry JI, Aminian-Dehkordi J, Maranas CD, Pakrasi HB. Engineering biology approaches for food and nutrient production by cyanobacteria. Curr Opin Biotechnol 2020; 67:1-6. [PMID: 33129046 DOI: 10.1016/j.copbio.2020.09.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/13/2020] [Accepted: 09/21/2020] [Indexed: 01/10/2023]
Abstract
As photoautotrophic organisms, cyanobacteria capture and store solar energy in the form of biomass. Cyanobacterial biomass has been an important component of diet and nutrition in several regions for centuries. Synthetic biology strategies are currently being applied to increase the yield and productivity of cyanobacterial biomass by optimizing solar energy utilization and CO2 fixation rates for carbon storage. Likewise, engineering cyanobacteria as cellular factories to synthesize carbohydrates, amino acids, proteins, lipids and fatty acids is providing an attractive way to sustainably produce food and nutrients for human consumption. In this review, we have summarized recent progress in both aspects and prospective trends under development.
Collapse
Affiliation(s)
- Deng Liu
- Department of Biology, Washington University, St. Louis, MO 63130, USA
| | - Michelle Liberton
- Department of Biology, Washington University, St. Louis, MO 63130, USA
| | - John I Hendry
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Javad Aminian-Dehkordi
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Himadri B Pakrasi
- Department of Biology, Washington University, St. Louis, MO 63130, USA.
| |
Collapse
|
48
|
Wang X, Chen L, Liu J, Sun T, Zhang W. Light-Driven Biosynthesis of myo-Inositol Directly From CO 2 in Synechocystis sp. PCC 6803. Front Microbiol 2020; 11:566117. [PMID: 33117313 PMCID: PMC7550737 DOI: 10.3389/fmicb.2020.566117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/11/2020] [Indexed: 11/13/2022] Open
Abstract
myo-inositol (MI) is an essential growth factor, nutritional source, and important precursor for many derivatives like D-chiro-inositol. In this study, attempts were made to achieve the “green biosynthesis” of MI in a model photosynthetic cyanobacterium Synechocystis sp. PCC 6803. First, several genes encoding myo-inositol-1-phosphate synthases and myo-inositol-1-monophosphatase, catalyzing the first or the second step of MI synthesis, were introduced, respectively, into Synechocystis. The results showed that the engineered strain carrying myo-inositol-1-phosphate synthase gene from Saccharomyces cerevisiae was able to produce MI at 0.97 mg L–1. Second, the combined overexpression of genes related to the two catalyzing processes increased the production up to 1.42 mg L–1. Third, to re-direct more cellular carbon flux into MI synthesis, an inducible small RNA regulatory tool, based on MicC-Hfq, was utilized to control the competing pathways of MI biosynthesis, resulting in MI production of ∼7.93 mg L–1. Finally, by optimizing the cultivation condition via supplying bicarbonate to enhance carbon fixation, a final MI production up to 12.72 mg L–1 was achieved, representing a ∼12-fold increase compared with the initial MI-producing strain. This study provides a light-driven green synthetic strategy for MI directly from CO2 in cyanobacterial chassis and represents a renewable alternative that may deserve further optimization in the future.
Collapse
Affiliation(s)
- Xiaoshuai Wang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Jing Liu
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Tao Sun
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, China.,Center for Biosafety Research and Strategy, Tianjin University, Tianjin, China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China.,Center for Biosafety Research and Strategy, Tianjin University, Tianjin, China
| |
Collapse
|
49
|
Sengupta A, Madhu S, Wangikar PP. A Library of Tunable, Portable, and Inducer-Free Promoters Derived from Cyanobacteria. ACS Synth Biol 2020; 9:1790-1801. [PMID: 32551554 DOI: 10.1021/acssynbio.0c00152] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cyanobacteria are emerging as hosts for various biotechnological applications. The ability to engineer these photosynthetic prokaryotes greatly depends on the availability of well-characterized promoters. Inducer-free promoters of a range of activities may be desirable for the eventual large-scale, outdoor cultivations. Further, several native promoters of cyanobacteria are repressed by high carbon dioxide or light, and it would be of interest to alter this property. We started with PrbcL and PcpcB, the well-characterized native promoters of the model cyanobacterium Synechococcus elongatus PCC 7942, found upstream of the two abundantly expressed genes, Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase, and phycocyanin β-1 subunit, respectively. The library of 48 promoters created via error-prone PCR of these 300-bp-long native promoters showed 2 orders of magnitude dynamic range with activities that were both lower and higher than those of the wild-type promoters. A few mutants of the PrbcL showed greater strength than PcpcB, which is widely considered a superstrong promoter. A number of mutant promoters did not show repression by high CO2 or light, typically found for PrbcL and PcpcB, respectively. Further, the wild-type and mutant promoters showed comparable activities in the fast-growing and stress-tolerant strains S. elongatus PCC 11801 and PCC 11802, suggesting that the library can be used in different cyanobacteria. Interestingly, the majority of the promoters showed strong expression in E. coli, thus adding to the repertoire of inducer-free promoters for this heterotrophic workhorse. Our results have implications in the metabolic engineering of cyanobacteria and E. coli.
Collapse
|
50
|
Sengupta S, Jaiswal D, Sengupta A, Shah S, Gadagkar S, Wangikar PP. Metabolic engineering of a fast-growing cyanobacterium Synechococcus elongatus PCC 11801 for photoautotrophic production of succinic acid. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:89. [PMID: 32467730 PMCID: PMC7236211 DOI: 10.1186/s13068-020-01727-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/09/2020] [Indexed: 05/11/2023]
Abstract
BACKGROUND Cyanobacteria, a group of photosynthetic prokaryotes, are being increasingly explored for direct conversion of carbon dioxide to useful chemicals. However, efforts to engineer these photoautotrophs have resulted in low product titers. This may be ascribed to the bottlenecks in metabolic pathways, which need to be identified for rational engineering. We engineered the recently reported, fast-growing and robust cyanobacterium, Synechococcus elongatus PCC 11801 to produce succinate, an important platform chemical. Previously, engineering of the model cyanobacterium S. elongatus PCC 7942 has resulted in succinate titer of 0.43 g l-1 in 8 days. RESULTS Building on the previous report, expression of α-ketoglutarate decarboxylase, succinate semialdehyde dehydrogenase and phosphoenolpyruvate carboxylase yielded a succinate titer of 0.6 g l-1 in 5 days suggesting that PCC 11801 is better suited as host for production. Profiling of the engineered strains for 57 intermediate metabolites, a number of enzymes and qualitative analysis of key transcripts revealed potential flux control points. Based on this, we evaluated the effects of overexpression of sedoheptulose-1,7-bisphosphatase, citrate synthase and succinate transporters and knockout of succinate dehydrogenase and glycogen synthase A. The final construct with seven genes overexpressed and two genes knocked out resulted in photoautotrophic production of 0.93 g l-1 succinate in 5 days. CONCLUSION While the fast-growing strain PCC 11801 yielded a much higher titer than the model strain, the efficient photoautotrophy of this novel isolate needs to be harnessed further for the production of desired chemicals. Engineered strains of S. elongatus PCC 11801 showed dramatic alterations in the levels of several metabolites suggesting far reaching effects of pathway engineering. Attempts to overexpress enzymes deemed to be flux controlling led to the emergence of other potential rate-limiting steps. Thus, this process of debottlenecking of the pathway needs to be repeated several times to obtain a significantly superior succinate titer.
Collapse
Affiliation(s)
- Shinjinee Sengupta
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076 India
- DBT-Pan IIT Center for Bioenergy, Indian Institute of Technology Bombay, Powai, Mumbai, 400076 India
| | - Damini Jaiswal
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076 India
| | - Annesha Sengupta
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076 India
| | - Shikha Shah
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076 India
- DBT-Pan IIT Center for Bioenergy, Indian Institute of Technology Bombay, Powai, Mumbai, 400076 India
| | - Shruti Gadagkar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076 India
| | - Pramod P. Wangikar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076 India
- DBT-Pan IIT Center for Bioenergy, Indian Institute of Technology Bombay, Powai, Mumbai, 400076 India
- Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076 India
| |
Collapse
|