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Li Y, Zhang Q, Liu Z, Jiang H, Jia Q. Genome mining discovery of hydrogen production pathway of Klebsiella sp. WL1316 fermenting cotton stalk hydrolysate. Int Microbiol 2022; 25:503-513. [PMID: 35147786 DOI: 10.1007/s10123-022-00241-0] [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: 08/16/2021] [Revised: 01/18/2022] [Accepted: 02/07/2022] [Indexed: 11/26/2022]
Abstract
Genome sequencing was used to identify key genes for the generation of hydrogen gas through cotton stalk hydrolysate fermentation by Klebsiella sp. WL1316. Genome annotation indicated that the genome size was 5.2 Mb with GC content 57.6%. Xylose was metabolized in the pentose phosphate pathway via the conversion of xylose to xylulose in Klebsiella sp. WL1316. This strain contained diverse formate-hydrogen lyases and hydrogenases with gene numbers higher than closely related species. A metabolic network involving glucose, xylose utilisation, and fermentative hydrogen production was reconstructed. Metabolic analysis of key node metabolites showed that glucose and xylose metabolism influenced biomass synthesis and biohydrogen production. Formic acid accumulated during fermentation at 24-48 h but decreased sharply after 48 h, illustrating the splitting of formic acid to hydrogen gas during early-to-mid fermentation. The Kreb's cycle was the main competitive metabolic branch of biohydrogen synthesis at 24 h of fermentation. Lactic and acetic acid fermentation and late ethanol accumulation competed the carbon skeleton of biohydrogen synthesis after 72 h of fermentation, indicating that these competitive pathways are regulated in middle-to-late fermentation (48-96 h). This study is the first to elucidate the metabolic mechanisms of mixed sugar utilisation and biohydrogen synthesis based on genomic information.
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Affiliation(s)
- Yanbin Li
- College of Biological and Food Engineering, Anhui Polytechnic University, Wuhu, 241000, Anhui, China
| | - Qin Zhang
- College of Biological and Food Engineering, Anhui Polytechnic University, Wuhu, 241000, Anhui, China.
| | - Zhanwen Liu
- College of Life Science, Tarim University, Alaer, 843300, Xinjiang, China
| | - Hui Jiang
- College of Life Science, Tarim University, Alaer, 843300, Xinjiang, China
| | - Qinghua Jia
- College of Life Science, Tarim University, Alaer, 843300, Xinjiang, China
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Wu Y, Chu W, Yang J, Xu Y, Shen Q, Yang H, Xu F, Liu Y, Lu P, Jiang K, Zhao H. Metabolic Engineering of Enterobacter aerogenes for Improved 2,3-Butanediol Production by Manipulating NADH Levels and Overexpressing the Small RNA RyhB. Front Microbiol 2021; 12:754306. [PMID: 34691005 PMCID: PMC8531500 DOI: 10.3389/fmicb.2021.754306] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/16/2021] [Indexed: 11/29/2022] Open
Abstract
Biotechnological production of 2,3-butanediol (2,3-BD), a versatile platform bio-chemical and a potential biofuel, is limited due to by-product toxicity. In this study, we aimed to redirect the metabolic flux toward 2,3-BD in Enterobacter aerogenes (E. aerogenes) by increasing the intracellular NADH pool. Increasing the NADH/NAD+ ratio by knocking out the NADH dehydrogenase genes (nuoC/nuoD) enhanced 2,3-BD production by up to 67% compared with wild-type E. aerogenes. When lactate dehydrogenase (ldh) was knocked out, the yield of 2,3-BD was increased by 71.2% compared to the wild type. Metabolic flux analysis revealed that upregulated expression of the sRNA RyhB led to a noteworthy shift in metabolism. The 2,3-BD titer of the best mutant Ea-2 was almost seven times higher than that of the parent strain in a 5-L fermenter. In this study, an effective metabolic engineering strategy for improved 2,3-BD production was implemented by increasing the NADH/NAD+ ratio and blocking competing pathways.
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Affiliation(s)
- Yan Wu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
- Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Wanying Chu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Jiayao Yang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Yudong Xu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Qi Shen
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Haoning Yang
- Department of Bioengineering, Liaoning Technical University, Fuxin, China
| | - Fangxu Xu
- Experimental Teaching Center, College of Life Science, Shenyang Normal University, Shenyang, China
| | - Yefei Liu
- Experimental Teaching Center, College of Life Science, Shenyang Normal University, Shenyang, China
| | - Ping Lu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Ke Jiang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Hongxin Zhao
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
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Rao R, Basak N. Development of novel strategies for higher fermentative biohydrogen recovery along with novel metabolites from organic wastes: The present state of the art. Biotechnol Appl Biochem 2020; 68:421-444. [PMID: 32474946 DOI: 10.1002/bab.1964] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 05/30/2020] [Indexed: 01/15/2023]
Abstract
Depletion of fossil fuels and environmental concern has compelled us to search for alternative fuel. Hydrogen is considered as a dream fuel as it has high energy content (142 kJ g-1 ) and is not chemically bound to carbon. At present, fossil fuel-based methods for producing hydrogen require high-energy input, which makes the processes expensive. The major processes for biohydrogen production are biophotolysis, microbial electrolysis, dark fermentation, and photofermentation. Fermentative hydrogen production has the additional advantages of potentially using various waste streams from different industries as feedstock. Novel strategies to enhance the productivity of fermentative hydrogen production include optimization in pretreatment methods, integrated fermentation systems (sequential and combined fermentation), use of nanoparticles as additives, metabolic engineering of microorganisms, improving the light utilization efficiency, developing more efficient photobioreactors, etc. More focus has been given to produce biohydrogen in a biorefinery approach in which, along with hydrogen gas, other metabolites (ethanol, butyric acid, 1,3-propanediol, etc.) are also produced, which have direct/indirect industrial applications. In present review, various emerging technologies that highlight biohydrogen production methods as effective and sustainable methods on a large scale have been critically reviewed. The possible future developments are also outlined.
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Affiliation(s)
- Raman Rao
- Department of Biotechnology, Dr. B. R Ambedkar National Institute of Technology, Jalandhar, 144 011, India
| | - Nitai Basak
- Department of Biotechnology, Dr. B. R Ambedkar National Institute of Technology, Jalandhar, 144 011, India
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Zhang Q, You S, Li Y, Qu X, Jiang H. Enhanced biohydrogen production from cotton stalk hydrolysate of Enterobacter cloacae WL1318 by overexpression of the formate hydrogen lyase activator gene. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:94. [PMID: 32489423 PMCID: PMC7245044 DOI: 10.1186/s13068-020-01733-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 05/16/2020] [Indexed: 05/29/2023]
Abstract
BACKGROUND Biohydrogen production from lignocellulose has become an important hydrogen production method due to its diversity, renewability, and cheapness. Overexpression of the formate hydrogen lyase activator (fhlA) gene is a promising tactic for enhancement of hydrogen production in facultative anaerobic Enterobacter. As a species of Enterobacter, Enterobacter cloacae was reported as a highly efficient hydrogen-producing bacterium. However, little work has been reported in terms of cloning and expressing the fhlA gene in E. cloacae for lignocellulose-based hydrogen production. RESULTS In this study, the formate hydrogen lyase activator (fhlA) gene was cloned and overexpressed in Enterobacter cloacae WL1318. We found that the recombinant strain significantly enhanced cumulative hydrogen production by 188% following fermentation of cotton stalk hydrolysate for 24 h, and maintained improved production above 30% throughout the fermentation process compared to the wild strain. Accordingly, overexpression of the fhlA gene resulted in an enhanced hydrogen production potential (P) and maximum hydrogen production rate (R m), as well as a shortened lag phase time (λ) for the recombinant strain. Additionally, the recombinant strain also displayed improved glucose (12%) and xylose (3.4%) consumption and hydrogen yield Y(H2/S) (37.0%) compared to the wild strain. Moreover, the metabolites and specific enzyme profiles demonstrated that reduced flux in the competitive branch, including succinic, acetic, and lactic acids, and ethanol generation, coupled with increased flux in the pyruvate node and formate splitting branch, benefited hydrogen synthesis. CONCLUSIONS The results conclusively prove that overexpression of fhlA gene in E. cloacae WL1318 can effectively enhance the hydrogen production from cotton stalk hydrolysate, and reduce the metabolic flux in the competitive branch. It is the first attempt to engineer the fhlA gene in the hydrogen-producing bacterium E. cloacae. This work provides a highly efficient engineered bacterium for biohydrogen production from fermentation of lignocellulosic hydrolysate in the future.
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Affiliation(s)
- Qin Zhang
- College of Biological and Chemical Engineering, Anhui Polytechnic University, Wuhu, 241000 Anhui China
| | - Shaolin You
- College of Biological and Chemical Engineering, Anhui Polytechnic University, Wuhu, 241000 Anhui China
| | - Yanbin Li
- College of Biological and Chemical Engineering, Anhui Polytechnic University, Wuhu, 241000 Anhui China
| | - Xiaowei Qu
- College of Life Science, Tarim University, Alaer, 843300 Xinjiang China
| | - Hui Jiang
- College of Life Science, Tarim University, Alaer, 843300 Xinjiang China
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Li Y, Hu J, Qu C, Chen L, Guo X, Fu H, Wang J. Engineered Thermoanaerobacterium aotearoense with nfnAB knockout for improved hydrogen production from lignocellulose hydrolysates. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:214. [PMID: 31528202 PMCID: PMC6737674 DOI: 10.1186/s13068-019-1559-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 08/31/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND As a renewable and clean energy carrier, the production of biohydrogen from low-value feedstock such as lignocellulose has increasingly garnered interest. The NADH-dependent reduced ferredoxin:NADP+ oxidoreductase (NfnAB) complex catalyzes electron transfer between reduced ferredoxin and NAD(P)+, which is critical for production of NAD(P)H-dependent products such as hydrogen and ethanol. In this study, the effects on end-product formation of deletion of nfnAB from Thermoanaerobacterium aotearoense SCUT27 were investigated. RESULTS Compared with the parental strain, the NADH/NAD+ ratio in the ∆nfnAB mutant was increased. The concentration of hydrogen and ethanol produced increased by (41.1 ± 2.37)% (p < 0.01) and (13.24 ± 1.12)% (p < 0.01), respectively, while the lactic acid concentration decreased by (11.88 ± 0.96)% (p < 0.01) when the ∆nfnAB mutant used glucose as sole carbon source. No obvious inhibition effect was observed for either SCUT27 or SCUT27/∆nfnAB when six types of lignocellulose hydrolysate pretreated with dilute acid were used for hydrogen production. Notably, the SCUT27/∆nfnAB mutant produced 190.63-209.31 mmol/L hydrogen, with a yield of 1.66-1.77 mol/mol and productivity of 12.71-13.95 mmol/L h from nonsterilized rice straw and corn cob hydrolysates pretreated with dilute acid. CONCLUSIONS The T. aotearoense SCUT27/∆nfnAB mutant showed higher hydrogen yield and productivity compared with those of the parental strain. Hence, we demonstrate that deletion of nfnAB from T. aotearoense SCUT27 is an effective approach to improve hydrogen production by redirecting the electron flux, and SCUT27/∆nfnAB is a promising candidate strain for efficient biohydrogen production from lignocellulosic hydrolysates.
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Affiliation(s)
- Yang Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 China
| | - Jialei Hu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 China
| | - Chunyun Qu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 China
| | - Lili Chen
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 China
| | - Xiaolong Guo
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 China
| | - Hongxin Fu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 China
| | - Jufang Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 China
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou, 510640 China
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Bioprocess engineering for biohythane production from low-grade waste biomass: technical challenges towards scale up. Curr Opin Biotechnol 2018; 50:25-31. [DOI: 10.1016/j.copbio.2017.08.014] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 08/21/2017] [Accepted: 08/22/2017] [Indexed: 01/05/2023]
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Perturbation of formate pathway and NADH pathway acting on the biohydrogen production. Sci Rep 2017; 7:9587. [PMID: 28852065 PMCID: PMC5575262 DOI: 10.1038/s41598-017-10191-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 08/03/2017] [Indexed: 11/21/2022] Open
Abstract
The formate pathway and NADH pathway as two common hydrogen-producing metabolic pathways have been well characterized to understand and improve biohydrogen production. These two pathways have been thought to be separate and have been independently investigated. However, in this study, perturbation of genes (hycA, fdhF, fhlA, ldhA, nuoB, hybO, fdh1, narP, and ppk) in Enterobacter aerogenes related to the formate pathway or NADH pathway revealed that these two pathways affected each other. Further metabolic analysis suggested that a linear relationship existed between the relative change of hydrogen yield in the formate pathway or NADH pathway and the relative change of NADH yield or ATP yield. Thus, this finding provides new insight into the role of cellular reducing power and energy level in the hydrogen metabolism. It also establishes a rationale for improving hydrogen production from a global perspective.
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Lu Y. Cell-free synthetic biology: Engineering in an open world. Synth Syst Biotechnol 2017; 2:23-27. [PMID: 29062958 PMCID: PMC5625795 DOI: 10.1016/j.synbio.2017.02.003] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 02/06/2017] [Indexed: 10/26/2022] Open
Abstract
Cell-free synthetic biology emerges as a powerful and flexible enabling technology that can engineer biological parts and systems for life science applications without using living cells. It provides simpler and faster engineering solutions with an unprecedented freedom of design in an open environment than cell system. This review focuses on recent developments of cell-free synthetic biology on biological engineering fields at molecular and cellular levels, including protein engineering, metabolic engineering, and artificial cell engineering. In cell-free protein engineering, the direct control of reaction conditions in cell-free system allows for easy synthesis of complex proteins, toxic proteins, membrane proteins, and novel proteins with unnatural amino acids. Cell-free systems offer the ability to design metabolic pathways towards the production of desired products. Buildup of artificial cells based on cell-free systems will improve our understanding of life and use them for environmental and biomedical applications.
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Affiliation(s)
- Yuan Lu
- Key Lab of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China.,Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
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Boboescu IZ, Gherman VD, Lakatos G, Pap B, Bíró T, Maróti G. Surpassing the current limitations of biohydrogen production systems: The case for a novel hybrid approach. BIORESOURCE TECHNOLOGY 2016; 204:192-201. [PMID: 26790867 DOI: 10.1016/j.biortech.2015.12.083] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 12/22/2015] [Accepted: 12/28/2015] [Indexed: 06/05/2023]
Abstract
The steadily increase of global energy requirements has brought about a general agreement on the need for novel renewable and environmentally friendly energy sources and carriers. Among the alternatives to a fossil fuel-based economy, hydrogen gas is considered a game-changer. Certain methods of hydrogen production can utilize various low-priced industrial and agricultural wastes as substrate, thus coupling organic waste treatment with renewable energy generation. Among these approaches, different biological strategies have been investigated and successfully implemented in laboratory-scale systems. Although promising, several key aspects need further investigation in order to push these technologies towards large-scale industrial implementation. Some of the major scientific and technical bottlenecks will be discussed, along with possible solutions, including a thorough exploration of novel research combining microbial dark fermentation and algal photoheterotrophic degradation systems, integrated with wastewater treatment and metabolic by-products usage.
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Affiliation(s)
- Iulian Zoltan Boboescu
- Polytechnic University of Timisoara, Victoriei Square, nr. 2, 300006 Timisoara, Romania; Hungarian Academy of Sciences, Biological Research Centre Szeged, Temesvari krt. 62, 6726 Szeged, Hungary
| | - Vasile Daniel Gherman
- Polytechnic University of Timisoara, Victoriei Square, nr. 2, 300006 Timisoara, Romania
| | - Gergely Lakatos
- Hungarian Academy of Sciences, Biological Research Centre Szeged, Temesvari krt. 62, 6726 Szeged, Hungary
| | - Bernadett Pap
- Seqomics Biotechnology Ltd., Vállalkozók útja 7, 6782 Mórahalom, Hungary
| | - Tibor Bíró
- Szent István University, Faculty of Economics, Agricultural and Health Studies, Szarvas, Hungary
| | - Gergely Maróti
- Polytechnic University of Timisoara, Victoriei Square, nr. 2, 300006 Timisoara, Romania; Hungarian Academy of Sciences, Biological Research Centre Szeged, Temesvari krt. 62, 6726 Szeged, Hungary.
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Microbial communities from 20 different hydrogen-producing reactors studied by 454 pyrosequencing. Appl Microbiol Biotechnol 2016; 100:3371-84. [PMID: 26825820 DOI: 10.1007/s00253-016-7325-y] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 01/12/2016] [Accepted: 01/14/2016] [Indexed: 01/10/2023]
Abstract
To provide new insight into the dark fermentation process, a multi-lateral study was performed to study the microbiology of 20 different lab-scale bioreactors operated in four different countries (Brazil, Chile, Mexico, and Uruguay). Samples (29) were collected from bioreactors with different configurations, operation conditions, and performances. The microbial communities were analyzed using 16S rRNA genes 454 pyrosequencing. The results showed notably uneven communities with a high predominance of a particular genus. The phylum Firmicutes predominated in most of the samples, but the phyla Thermotogae or Proteobacteria dominated in a few samples. Genera from three physiological groups were detected: high-yield hydrogen producers (Clostridium, Kosmotoga, Enterobacter), fermenters with low-hydrogen yield (mostly from Veillonelaceae), and competitors (Lactobacillus). Inocula, reactor configurations, and substrates influence the microbial communities. This is the first joint effort that evaluates hydrogen-producing reactors and operational conditions from different countries and contributes to understand the dark fermentation process.
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