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Mazzoli R, Pescarolo S, Gilli G, Gilardi G, Valetti F. Hydrogen production pathways in Clostridia and their improvement by metabolic engineering. Biotechnol Adv 2024; 73:108379. [PMID: 38754796 DOI: 10.1016/j.biotechadv.2024.108379] [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: 12/04/2023] [Revised: 05/13/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024]
Abstract
Biological production of hydrogen has a tremendous potential as an environmentally sustainable technology to generate a clean fuel. Among the different available methods to produce biohydrogen, dark fermentation features the highest productivity and can be used as a means to dispose of organic waste biomass. Within this approach, Clostridia have the highest theoretical H2 production yield. Nonetheless, most strains show actual yields far lower than the theoretical maximum: improving their efficiency becomes necessary for achieving cost-effective fermentation processes. This review aims at providing a survey of the metabolic network involved in H2 generation in Clostridia and strategies used to improve it through metabolic engineering. Together with current achievements, a number of future perspectives to implement these results will be illustrated.
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Affiliation(s)
- Roberto Mazzoli
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123 Torino, Italy.
| | - Simone Pescarolo
- Biology applied to the environment, Laboratories of microbiology and ecotoxicology, Ecobioqual, Environment Park. Via Livorno 60, 10144 Torino, Italy
| | - Giorgio Gilli
- Department of Sciences of Public Health and Pediatrics, School of Medicine, University of Torino, Via Santena 5 bis, 10126 Torino, Italy
| | - Gianfranco Gilardi
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123 Torino, Italy
| | - Francesca Valetti
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123 Torino, Italy.
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2
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Liu S, Lu SY, Patel M, Qureshi N, Dunlap C, Hoecker E, Skory CD. Production of a Bacteriocin Like Protein PEG 446 from Clostridium tyrobutyricum NRRL B-67062. Probiotics Antimicrob Proteins 2024:10.1007/s12602-023-10211-1. [PMID: 38252201 DOI: 10.1007/s12602-023-10211-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/29/2023] [Indexed: 01/23/2024]
Abstract
Clostridium tyrobutyricum strain NRRL B-67062 was previously isolated from an ethanol production facility and shown to produce high yields of butyric acid. In addition, the cell-free supernatant of the fermentation broth from NRRL B-67062 contained antibacterial activity against certain Gram-positive bacteria. To determine the source of this antibacterial activity, we report the genome and genome mining of this strain. The complete genome of NRRL B-67062 showed one circular chromosome of 3,242,608 nucleotides, 3114 predicted coding sequences, 79 RNA genes, and a G+C content of 31.0%. Analyses of the genome data for genes potentially associated with antimicrobial features were sought after by using BAGEL-4 and anti-SMASH databases. Among the leads, a polypeptide of 66 amino acids (PEG 446) contains the DUF4177 domain, which is an uncharacterized highly conserved domain (pfam13783). The cloning and expression of the peg446 gene in Escherichia coli and Bacillus subtilis confirmed the antibacterial property against Lactococcus lactis LM 0230, Limosilactobacillus fermentum 0315-25, and Listeria innocua NRRL B-33088 by gel overlay and well diffusion assays. Molecular modeling suggested that PEG 446 contains one alpha-helix and three anti-parallel short beta-sheets. These results will aid further functional studies and facilitate simultaneously fermentative production of both butyric acid and a putative bacteriocin from agricultural waste and lignocellulosic biomass materials.
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Affiliation(s)
- Siqing Liu
- U.S. Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Renewable Product Technology Research Unit, Peoria, IL, 61604, USA.
| | - Shao-Yeh Lu
- U.S. Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Renewable Product Technology Research Unit, Peoria, IL, 61604, USA
| | - Maulik Patel
- Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN, 37830, USA
| | - Nasib Qureshi
- U.S. Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Bioenergy Research Unit, Peoria, IL, 61604, USA
| | - Christopher Dunlap
- U.S. Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Crop Bioprotection Research Unit, Peoria, IL, 61604, USA
| | - Eric Hoecker
- U.S. Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Renewable Product Technology Research Unit, Peoria, IL, 61604, USA
| | - Christopher D Skory
- U.S. Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Renewable Product Technology Research Unit, Peoria, IL, 61604, USA
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3
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Kim S, Kim KJ. Crystal Structure and Molecular Mechanism of Phosphotransbutyrylase from Clostridium acetobutylicum. J Microbiol Biotechnol 2021; 31:1393-1400. [PMID: 34584034 PMCID: PMC9706017 DOI: 10.4014/jmb.2109.09036] [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: 09/16/2021] [Revised: 09/17/2021] [Accepted: 09/23/2021] [Indexed: 12/15/2022]
Abstract
Acetone-butanol-ethanol (ABE) fermentation by the anaerobic bacterium Clostridium acetobutylicum has been considered a promising process of industrial biofuel production. Phosphotransbutyrylase (phosphate butyryltransferase, PTB) plays a crucial role in butyrate metabolism by catalyzing the reversible conversion of butyryl-CoA into butyryl phosphate. Here, we report the crystal structure of PTB from the Clostridial host for ABE fermentation, C. acetobutylicum, (CaPTB) at a 2.9 Å resolution. The overall structure of the CaPTB monomer is quite similar to those of other acyltransferases, with some regional structural differences. The monomeric structure of CaPTB consists of two distinct domains, the N- and C-terminal domains. The active site cleft was formed at the interface between the two domains. Interestingly, the crystal structure of CaPTB contained eight molecules per asymmetric unit, forming an octamer, and the size-exclusion chromatography experiment also suggested that the enzyme exists as an octamer in solution. The structural analysis of CaPTB identifies the substrate binding mode of the enzyme and comparisons with other acyltransferase structures lead us to speculate that the enzyme undergoes a conformational change upon binding of its substrate.
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Affiliation(s)
- Sangwoo Kim
- School of Life Sciences, BK21 FOUR KNU Creative BioSesearch Group, Kyungpook National University, Daegu 41566, Republic of Korea,KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences, BK21 FOUR KNU Creative BioSesearch Group, Kyungpook National University, Daegu 41566, Republic of Korea,KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea,Corresponding author Phone: +82-53-950-5377 Fax: +82-53-955-5522 E-mail:
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4
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Liu T, Zhu L, Zhu Z, Jiang L. Genome Sequence Analysis of Clostridium tyrobutyricum, a Promising Microbial Host for Human Health and Industrial Applications. Curr Microbiol 2020; 77:3685-3694. [DOI: 10.1007/s00284-020-02175-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 08/21/2020] [Indexed: 11/30/2022]
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5
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Jiang L, Fu H, Yang HK, Xu W, Wang J, Yang ST. Butyric acid: Applications and recent advances in its bioproduction. Biotechnol Adv 2018; 36:2101-2117. [PMID: 30266343 DOI: 10.1016/j.biotechadv.2018.09.005] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 09/24/2018] [Accepted: 09/24/2018] [Indexed: 12/20/2022]
Abstract
Butyric acid is an important C4 organic acid with broad applications. It is currently produced by chemosynthesis from petroleum-based feedstocks. However, the fermentative production of butyric acid from renewable feedstocks has received growing attention because of consumer demand for green products and natural ingredients in foods, pharmaceuticals, animal feed supplements, and cosmetics. In this review, strategies for improving microbial butyric acid production, including strain engineering and novel fermentation process development are discussed and compared regarding product yield, titer, purity and productivity. Future perspectives on strain and process improvements for butyric acid production are also discussed.
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Affiliation(s)
- Ling Jiang
- School of Biology & Biological Engineering, South China University of Technology, Guangzhou 510006, China; College of Food Science and Light Industry, Nanjing Tech University, No. 5 Xinmofan Road, Nanjing 210009, China
| | - Hongxin Fu
- School of Biology & Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Hopen K Yang
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Wei Xu
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA; School of Chemical and Biological Engineering, Yancheng Institute of Technology, Yancheng 224051, China
| | - Jufang Wang
- School of Biology & Biological Engineering, South China University of Technology, Guangzhou 510006, China; Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA.
| | - Shang-Tian Yang
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA.
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6
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Huang J, Tang W, Zhu S, Du M. Biosynthesis of butyric acid by Clostridium tyrobutyricum. Prep Biochem Biotechnol 2018; 48:427-434. [PMID: 29561227 DOI: 10.1080/10826068.2018.1452257] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Butyric acid (C3H7COOH) is an important chemical that is widely used in foodstuffs along with in the chemical and pharmaceutical industries. The bioproduction of butyric acid through large-scale fermentation has the potential to be more economical and efficient than petrochemical synthesis. In this paper, the metabolic pathways involved in the production of butyric acid from Clostridium tyrobutyricum using hexose and pentose as substrates are investigated, and approaches to enhance butyric acid production through genetic modification are discussed. Finally, bioreactor modifications (including fibrous bed bioreactor, inner disk-shaped matrix bioreactor, fibrous matrix packed in porous levitated sphere carriers), low-cost feedstocks, and special treatments (including continuous fermentation with cell recycling, extractive fermentation with solvent, using different artificial electron carriers) intended to improve the feasibility of commercial butyric acid bioproduction are summarized.
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Affiliation(s)
- Jin Huang
- a College of Pharmaceutical Science , Zhejiang University of Technology , Hangzhou , China
| | - Wan Tang
- a College of Pharmaceutical Science , Zhejiang University of Technology , Hangzhou , China
| | - Shengquan Zhu
- a College of Pharmaceutical Science , Zhejiang University of Technology , Hangzhou , China
| | - Meini Du
- a College of Pharmaceutical Science , Zhejiang University of Technology , Hangzhou , China
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7
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Suo Y, Ren M, Yang X, Liao Z, Fu H, Wang J. Metabolic engineering of Clostridium tyrobutyricum for enhanced butyric acid production with high butyrate/acetate ratio. Appl Microbiol Biotechnol 2018; 102:4511-4522. [DOI: 10.1007/s00253-018-8954-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 03/15/2018] [Accepted: 03/18/2018] [Indexed: 11/30/2022]
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8
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Luo H, Yang R, Zhao Y, Wang Z, Liu Z, Huang M, Zeng Q. Recent advances and strategies in process and strain engineering for the production of butyric acid by microbial fermentation. BIORESOURCE TECHNOLOGY 2018; 253:343-354. [PMID: 29329775 DOI: 10.1016/j.biortech.2018.01.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 12/28/2017] [Accepted: 01/01/2018] [Indexed: 06/07/2023]
Abstract
Butyric acid is an important platform chemical, which is widely used in the fields of food, pharmaceutical, energy, etc. Microbial fermentation as an alternative approach for butyric acid production is attracting great attention as it is an environmentally friendly bioprocessing. However, traditional fermentative butyric acid production is still not economically competitive compared to chemical synthesis route, due to the low titer, low productivity, and high production cost. Therefore, reduction of butyric acid production cost by utilization of alternative inexpensive feedstock, and improvement of butyric acid production and productivity has become an important target. Recently, several advanced strategies have been developed for enhanced butyric acid production, including bioprocess techniques and metabolic engineering methods. This review provides an overview of advances and strategies in process and strain engineering for butyric acid production by microbial fermentation. Additionally, future perspectives on improvement of butyric acid production are also proposed.
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Affiliation(s)
- Hongzhen Luo
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China.
| | - Rongling Yang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Yuping Zhao
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Zhaoyu Wang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Zheng Liu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Mengyu Huang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Qingwei Zeng
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
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Enhanced butyric acid production in Clostridium tyrobutyricum by overexpression of rate-limiting enzymes in the Embden-Meyerhof-Parnas pathway. J Biotechnol 2018; 272-273:14-21. [PMID: 29501473 DOI: 10.1016/j.jbiotec.2018.02.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Revised: 02/23/2018] [Accepted: 02/27/2018] [Indexed: 11/22/2022]
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Wu Q, Zhu L, Xu Q, Huang H, Jiang L, Yang ST. Tailoring the Oxidative Stress Tolerance of Clostridium tyrobutyricum CCTCC W428 by Introducing Trehalose Biosynthetic Capability. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:8892-8901. [PMID: 28925260 DOI: 10.1021/acs.jafc.7b03172] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Fermentations employing anaerobes always suffer from the restriction of stringent anaerobic conditions during the production of bulk and fine chemicals. This work aims to improve the oxidative stress tolerance of C. tyrobutyricum CCTCC W428, an ideal butyric-acid-producing anaerobe, via the introduction of trehalose biosynthesis capability. Compared with the wild type, the engineered strain showed a wider substrate spectrum, an improved metabolic profile, and a significantly increased specific growth rate upon aeration and acid challenge. Molecular simulation experiments indicated that CoA transferase maintained its native folded state when protected by the trehalose system. Furthermore, qRT-PCR was combined assays for acid-related enzyme activities under various conditions to verify the effects of trehalose. These results demonstrate that introducing a trehalose biosynthetic pathway, which is redundant for the metabolism of C. tyrobutyricum, can increase the robustness of the host to achieve a better oxidative resistance.
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Affiliation(s)
| | | | | | | | | | - Shang-Tian Yang
- Department of Chemical Engineering, The Ohio State University , Columbus, Ohio 43210, United States
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Fermentative hydrogen production from Jerusalem artichoke by Clostridium tyrobutyricum expressing exo-inulinase gene. Sci Rep 2017; 7:7940. [PMID: 28801602 PMCID: PMC5554141 DOI: 10.1038/s41598-017-07207-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 06/23/2017] [Indexed: 12/01/2022] Open
Abstract
Clostridium tyrobutyricum ATCC25755 has been reported as being able to produce significant quantities of hydrogen. In this study, the exo-inulinase encoding gene cloned from Paenibacillus polymyxa SC-2 was into the expression plasmid pSY6 and expressed in the cells of C. tyrobutyricum. The engineered C. tyrobutyricum strain efficiently fermented the inulin-type carbohydrates from Jerusalem artichoke, without any pretreatment being necessary for the production of hydrogen. A comparatively high hydrogen yield (3.7 mol/mol inulin-type sugar) was achieved after 96 h in a batch process with simultaneous saccharification and fermentation (SSF), with an overall volumetric productivity rate of 620 ± 60 mL/h/L when the initial total sugar concentration of the inulin extract was increased to 100 g/L. Synthesis of inulinase in the batch SSF culture was closely associated with strain growth until the end of the exponential phase, reaching a maximum activity of 28.4 ± 0.26 U/mL. The overall results show that the highly productive and abundant biomass crop Jerusalem artichoke can be a good substrate for hydrogen production, and that the application of batch SSF for its conversion has the potential to become a cost-effective process in the near future.
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Suo Y, Luo S, Zhang Y, Liao Z, Wang J. Enhanced butyric acid tolerance and production by Class I heat shock protein-overproducing Clostridium tyrobutyricum ATCC 25755. ACTA ACUST UNITED AC 2017; 44:1145-1156. [DOI: 10.1007/s10295-017-1939-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 03/17/2017] [Indexed: 01/16/2023]
Abstract
Abstract
The response of Clostridium tyrobutyricum to butyric acid stress involves various stress-related genes, and therefore overexpression of stress-related genes can improve butyric acid tolerance and yield. Class I heat shock proteins (HSPs) play an important role in the process of protecting bacteria from sudden changes of extracellular stress by assisting protein folding correctly. The results of quantitative real-time PCR indicated that the Class I HSGs grpE, dnaK, dnaJ, groEL, groES, and htpG were significantly upregulated under butyric acid stress, especially the dnaK and groE operons. Overexpression of groESL and htpG could significantly improve the tolerance of C. tyrobutyricum to butyric acid, while overexpression of dnaK and dnaJ showed negative effects on butyric acid tolerance. Acid production was also significantly promoted by increased GroESL expression levels; the final butyric acid and acetic acid concentrations were 28.2 and 38% higher for C. tyrobutyricum ATCC 25755/groESL than for the wild-type strain. In addition, when fed-batch fermentation was carried out using cell immobilization in a fibrous-bed bioreactor, the butyric acid yield produced by C. tyrobutyricum ATCC 25755/groESL reached 52.2 g/L, much higher than that for the control. The improved butyric acid yield is probably attributable to the high GroES and GroEL levels, which can stabilize the biosynthetic machinery of C. tyrobutyricum under extracellular butyric acid stress.
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Affiliation(s)
- Yukai Suo
- 0000 0004 1764 3838 grid.79703.3a School of Bioscience & Bioengineering South China University of Technology 510006 Guangzhou China
| | - Sheng Luo
- 0000 0004 1764 3838 grid.79703.3a School of Bioscience & Bioengineering South China University of Technology 510006 Guangzhou China
| | - Yanan Zhang
- 0000 0004 1764 3838 grid.79703.3a School of Bioscience & Bioengineering South China University of Technology 510006 Guangzhou China
| | - Zhengping Liao
- 0000 0004 1764 3838 grid.79703.3a School of Bioscience & Bioengineering South China University of Technology 510006 Guangzhou China
| | - Jufang Wang
- 0000 0004 1764 3838 grid.79703.3a School of Bioscience & Bioengineering South China University of Technology 510006 Guangzhou China
- 0000 0004 1764 3838 grid.79703.3a State Key Laboratory of Pulp and Paper Engineering South China University of Technology 510640 Guangzhou China
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Wu Q, Liu T, Zhu L, Huang H, Jiang L. Insights from the complete genome sequence of Clostridium tyrobutyricum provide a platform for biotechnological and industrial applications. J Ind Microbiol Biotechnol 2017; 44:1245-1260. [PMID: 28536840 DOI: 10.1007/s10295-017-1956-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 05/18/2017] [Indexed: 11/26/2022]
Abstract
Genetic research enables the evolution of novel biochemical reactions for the production of valuable chemicals from environmentally-friendly raw materials. However, the choice of appropriate microorganisms to support these reactions, which must have strong robustness and be capable of a significant product output, is a major difficulty. In the present study, the complete genome of the Clostridium tyrobutyricum strain CCTCC W428, a hydrogen- and butyric acid-producing bacterium with increased oxidative tolerance was analyzed. A total length of 3,011,209 bp of the C. tyrobutyricum genome with a GC content of 31.04% was assembled, and 3038 genes were discovered. Furthermore, a comparative clustering of proteins from C. tyrobutyricum CCTCC W428, C. acetobutylicum ATCC 824, and C. butyricum KNU-L09 was conducted. The results of genomic analysis indicate that butyric acid is produced by CCTCC W428 from butyryl-CoA through acetate reassimilation via CoA transferase, instead of the well-established phosphotransbutyrylase-butyrate kinase pathway. In addition, we identified ten proteins putatively involved in hydrogen production and 21 proteins associated with CRISPR systems, together with 358 ORFs related to ABC transporters and transcriptional regulators. Enzymes, such as oxidoreductases, HNH endonucleases, and catalase, were also found in this species. The genome sequence illustrates that C. tyrobutyricum has several desirable traits, and is expected to be suitable as a platform for the high-level production of bulk chemicals as well as bioenergy.
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Affiliation(s)
- Qian Wu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 210019, People's Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing, 210019, People's Republic of China
| | - Tingting Liu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 210019, People's Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing, 210019, People's Republic of China
| | - Liying Zhu
- College of Chemical and Molecular Engineering, Nanjing Tech University, Nanjing, 210019, People's Republic of China
| | - He Huang
- College of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 210009, People's Republic of China
| | - Ling Jiang
- Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing, 210019, People's Republic of China.
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 210009, People's Republic of China.
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Wang Y, Shou JW, Li XY, Zhao ZX, Fu J, He CY, Feng R, Ma C, Wen BY, Guo F, Yang XY, Han YX, Wang LL, Tong Q, You XF, Lin Y, Kong WJ, Si SY, Jiang JD. Berberine-induced bioactive metabolites of the gut microbiota improve energy metabolism. Metabolism 2017; 70:72-84. [PMID: 28403947 DOI: 10.1016/j.metabol.2017.02.003] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 02/02/2017] [Accepted: 02/03/2017] [Indexed: 12/30/2022]
Abstract
OBJECTIVE Berberine (BBR) clinically lowers blood lipid and glucose levels via multi-target mechanisms. One of the possible mechanisms is related to its effect on the short chain fatty acids (SCFAs) of the gut microbiota. The goal of this study is to investigate the therapeutic effect and mode of action of BBR working through SCFAs of the gut microbiota (especially, butyrate). METHODS Gas chromatography (GC) was used to detect butyrate and other SCFAs chemically. The effect of BBR on butyrate production was investigated in vitro as well as in several animal systems. Microarrays were used to analyze the composition change in the intestinal bacteria community after treatment with BBR. BBR-induced change in the energy production and gene regulation of intestinal bacteria was examined in order to elucidate the underlying molecular mechanisms. RESULTS We show that oral administration of BBR in animals promoted the gut microbiota to produce butyrate, which then enters the blood and reduces blood lipid and glucose levels. Incubating gut bacterial strains in vitro with BBR increased butyrate production. Orally treating animals directly with butyrate reduced blood lipid and glucose levels through a mechanism different from that of BBR. Intraperitoneal BBR administration did not increase butyrate but reduced blood lipid and glucose levels, suggesting that BBR has two modes of action: the direct effect of the circulated BBR and the indirect effect working through butyrate of the gut microbiota. Pre-treating animals orally with antibiotics abolished the effect of BBR on butyrate. A mechanism study showed that BBR (given orally) modified mice intestinal bacterial composition by increasing the abundance of butyrate-producing bacteria. Furthermore, BBR suppressed bacterial ATP production and NADH levels, resulting in increased butyryl-CoA and, eventually, butyrate production via upregulating phosphotransbutyrylase/butyrate kinase and butyryl-CoA:acetate-CoA transferase in bacteria. CONCLUSION Promotion of butyrate (etc) production in gut microbiota might be one of the important mechanisms of BBR in regulating energy metabolism.
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Affiliation(s)
- Yan Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences / Peking Union Medical College, Beijing, 100050, China.
| | - Jia-Wen Shou
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences / Peking Union Medical College, Beijing, 100050, China
| | - Xiao-Yang Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences / Peking Union Medical College, Beijing, 100050, China
| | - Zhen-Xiong Zhao
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences / Peking Union Medical College, Beijing, 100050, China
| | - Jie Fu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences / Peking Union Medical College, Beijing, 100050, China
| | - Chi-Yu He
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences / Peking Union Medical College, Beijing, 100050, China
| | - Ru Feng
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences / Peking Union Medical College, Beijing, 100050, China
| | - Chao Ma
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences / Peking Union Medical College, Beijing, 100050, China
| | - Bao-Ying Wen
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences / Peking Union Medical College, Beijing, 100050, China
| | - Fang Guo
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences / Peking Union Medical College, Beijing, 100050, China
| | - Xin-Yi Yang
- Insitute of Medicinal Biotechnology, Chinese Academy of Medical Sciences / Peking Union Medical College, Beijing, 100050, China
| | - Yan-Xing Han
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences / Peking Union Medical College, Beijing, 100050, China
| | - Lu-Lu Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences / Peking Union Medical College, Beijing, 100050, China
| | - Qian Tong
- The First Hospital of Jilin University, Changchun, 130021, China
| | - Xue-Fu You
- Insitute of Medicinal Biotechnology, Chinese Academy of Medical Sciences / Peking Union Medical College, Beijing, 100050, China
| | - Yuan Lin
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences / Peking Union Medical College, Beijing, 100050, China
| | - Wei-Jia Kong
- Insitute of Medicinal Biotechnology, Chinese Academy of Medical Sciences / Peking Union Medical College, Beijing, 100050, China
| | - Shu-Yi Si
- Insitute of Medicinal Biotechnology, Chinese Academy of Medical Sciences / Peking Union Medical College, Beijing, 100050, China
| | - Jian-Dong Jiang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences / Peking Union Medical College, Beijing, 100050, China; Insitute of Medicinal Biotechnology, Chinese Academy of Medical Sciences / Peking Union Medical College, Beijing, 100050, China.
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15
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Soggiu A, Piras C, Mortera SL, Alloggio I, Urbani A, Bonizzi L, Roncada P. Unravelling the effect of clostridia spores and lysozyme on microbiota dynamics in Grana Padano cheese: A metaproteomics approach. J Proteomics 2016; 147:21-27. [DOI: 10.1016/j.jprot.2016.03.035] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 02/21/2016] [Accepted: 03/21/2016] [Indexed: 01/14/2023]
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16
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Lee SH, Yun EJ, Kim J, Lee SJ, Um Y, Kim KH. Biomass, strain engineering, and fermentation processes for butanol production by solventogenic clostridia. Appl Microbiol Biotechnol 2016; 100:8255-71. [PMID: 27531513 DOI: 10.1007/s00253-016-7760-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 07/26/2016] [Accepted: 07/28/2016] [Indexed: 12/14/2022]
Abstract
Butanol is considered an attractive biofuel and a commercially important bulk chemical. However, economical production of butanol by solventogenic clostridia, e.g., via fermentative production of acetone-butanol-ethanol (ABE), is hampered by low fermentation performance, mainly as a result of toxicity of butanol to microorganisms and high substrate costs. Recently, sugars from marine macroalgae and syngas were recognized as potent carbon sources in biomass feedstocks that are abundant and do not compete for arable land with edible crops. With the aid of systems metabolic engineering, many researchers have developed clostridial strains with improved performance on fermentation of these substrates. Alternatively, fermentation strategies integrated with butanol recovery processes such as adsorption, gas stripping, liquid-liquid extraction, and pervaporation have been designed to increase the overall titer of butanol and volumetric productivity. Nevertheless, for economically feasible production of butanol, innovative strategies based on recent research should be implemented. This review describes and discusses recent advances in the development of biomass feedstocks, microbial strains, and fermentation processes for butanol production.
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Affiliation(s)
- Sang-Hyun Lee
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841, South Korea
| | - Eun Ju Yun
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841, South Korea
| | - Jungyeon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841, South Korea
| | - Sang Jun Lee
- Biosystems and Bioengineering Program, University of Science and Technology and Microbiomics and Immunity Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, South Korea
| | - Youngsoon Um
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul, 02792, South Korea
| | - Kyoung Heon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841, South Korea.
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Deciphering Clostridium tyrobutyricum Metabolism Based on the Whole-Genome Sequence and Proteome Analyses. mBio 2016; 7:mBio.00743-16. [PMID: 27302759 PMCID: PMC4916380 DOI: 10.1128/mbio.00743-16] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Clostridium tyrobutyricum is a Gram-positive anaerobic bacterium that efficiently produces butyric acid and is considered a promising host for anaerobic production of bulk chemicals. Due to limited knowledge on the genetic and metabolic characteristics of this strain, however, little progress has been made in metabolic engineering of this strain. Here we report the complete genome sequence of C. tyrobutyricum KCTC 5387 (ATCC 25755), which consists of a 3.07-Mbp chromosome and a 63-kbp plasmid. The results of genomic analyses suggested that C. tyrobutyricum produces butyrate from butyryl-coenzyme A (butyryl-CoA) through acetate reassimilation by CoA transferase, differently from Clostridium acetobutylicum, which uses the phosphotransbutyrylase-butyrate kinase pathway; this was validated by reverse transcription-PCR (RT-PCR) of related genes, protein expression levels, in vitro CoA transferase assay, and fed-batch fermentation. In addition, the changes in protein expression levels during the course of batch fermentations on glucose were examined by shotgun proteomics. Unlike C. acetobutylicum, the expression levels of proteins involved in glycolytic and fermentative pathways in C. tyrobutyricum did not decrease even at the stationary phase. Proteins related to energy conservation mechanisms, including Rnf complex, NfnAB, and pyruvate-phosphate dikinase that are absent in C. acetobutylicum, were identified. Such features explain why this organism can produce butyric acid to a much higher titer and better tolerate toxic metabolites. This study presenting the complete genome sequence, global protein expression profiles, and genome-based metabolic characteristics during the batch fermentation of C. tyrobutyricum will be valuable in designing strategies for metabolic engineering of this strain. IMPORTANCE Bio-based production of chemicals from renewable biomass has become increasingly important due to our concerns on climate change and other environmental problems. C. tyrobutyricum has been used for efficient butyric acid production. In order to further increase the performance and expand the capabilities of this strain toward production of other chemicals, metabolic engineering needs to be performed. For this, better understanding on the metabolic and physiological characteristics of this bacterium at the genome level is needed. This work reporting the results of complete genomic and proteomic analyses together with new insights on butyric acid biosynthetic pathway and energy conservation will allow development of strategies for metabolic engineering of C. tyrobutyricum for the bio-based production of various chemicals in addition to butyric acid.
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18
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Deng Y, Mao Y, Zhang X. Driving carbon flux through exogenous butyryl-CoA: Acetate CoA-transferase to produce butyric acid at high titer in Thermobifida fusca. J Biotechnol 2015; 216:151-7. [PMID: 26535965 DOI: 10.1016/j.jbiotec.2015.10.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 10/07/2015] [Accepted: 10/29/2015] [Indexed: 12/31/2022]
Abstract
Butyric acid, a 4-carbon short chain fatty acid, is widely used in chemical, food, and pharmaceutical industries. The low activity of butyryl-CoA: acetate CoA-transferase in Thermobifida fusca muS, a thermophilic actinobacterium whose optimal temperature was 55°C, was found to hinder the accumulation of high yield of butyric acid. In order to solve this problem, an exogenous butyryl-CoA: acetate CoA-transferase gene (actA) from Thermoanaerobacterium thermosaccharolyticum DSM571 was integrated into the chromosome of T. fusca muS by replacing celR gene, forming T. fusca muS-1. We demonstrated that on 5g/L cellulose, the yield of butyric acid by the engineered muS-1 strain was increased by 42.9 % compared to the muS strain. On 100g/L of cellulose, the muS-1 strain could consume 90.5% of total cellulose in 144h, with 33.2g/L butyric acid produced. Furthermore, on the mix substrates including the major components of biomass: cellulose, xylose, mannose and galactose, 70.4g/L butyric acid was produced in 168h by fed-batch fermentation. To validate the ability of fermenting biomass, the muS-1 strain was grown on the milled corn stover ranging from 200 to 250μm. The muS-1 strain had the highest butyrate titer 17.1g/L on 90g/L corn stover.
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Affiliation(s)
- Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
| | - Yin Mao
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Xiaojuan Zhang
- School of Pharmaceutical Science, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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19
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Ou J, Ma C, Xu N, Du Y, Liu X. High butanol production by regulating carbon, redox and energy in Clostridia. Front Chem Sci Eng 2015. [DOI: 10.1007/s11705-015-1522-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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20
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Yu L, Zhao J, Xu M, Dong J, Varghese S, Yu M, Tang IC, Yang ST. Metabolic engineering of Clostridium tyrobutyricum for n-butanol production: effects of CoA transferase. Appl Microbiol Biotechnol 2015; 99:4917-30. [DOI: 10.1007/s00253-015-6566-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 03/18/2015] [Accepted: 03/20/2015] [Indexed: 01/31/2023]
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21
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I-SceI-mediated scarless gene modification via allelic exchange in Clostridium. J Microbiol Methods 2015; 108:49-60. [DOI: 10.1016/j.mimet.2014.11.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 10/21/2014] [Accepted: 11/07/2014] [Indexed: 02/06/2023]
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22
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Thakker C, Martínez I, Li W, San KY, Bennett GN. Metabolic engineering of carbon and redox flow in the production of small organic acids. J Ind Microbiol Biotechnol 2014; 42:403-22. [PMID: 25502283 DOI: 10.1007/s10295-014-1560-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 11/24/2014] [Indexed: 11/26/2022]
Abstract
The review describes efforts toward metabolic engineering of production of organic acids. One aspect of the strategy involves the generation of an appropriate amount and type of reduced cofactor needed for the designed pathway. The ability to capture reducing power in the proper form, NADH or NADPH for the biosynthetic reactions leading to the organic acid, requires specific attention in designing the host and also depends on the feedstock used and cell energetic requirements for efficient metabolism during production. Recent work on the formation and commercial uses of a number of small mono- and diacids is discussed with redox differences, major biosynthetic precursors and engineering strategies outlined. Specific attention is given to those acids that are used in balancing cell redox or providing reduction equivalents for the cell, such as formate, which can be used in conjunction with metabolic engineering of other products to improve yields. Since a number of widely studied acids derived from oxaloacetate as an important precursor, several of these acids are covered with the general strategies and particular components summarized, including succinate, fumarate and malate. Since malate and fumarate are less reduced than succinate, the availability of reduction equivalents and level of aerobiosis are important parameters in optimizing production of these compounds in various hosts. Several other more oxidized acids are also discussed as in some cases, they may be desired products or their formation is minimized to afford higher yields of more reduced products. The placement and connections among acids in the typical central metabolic network are presented along with the use of a number of specific non-native enzymes to enhance routes to high production, where available alternative pathways and strategies are discussed. While many organic acids are derived from a few precursors within central metabolism, each organic acid has its own special requirements for high production and best compatibility with host physiology.
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Affiliation(s)
- Chandresh Thakker
- Department of Biochemistry and Cell Biology, Rice University, Houston, TX, USA
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23
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Wang J, Yang X, Chen CC, Yang ST. Engineering clostridia for butanol production from biorenewable resources: from cells to process integration. Curr Opin Chem Eng 2014. [DOI: 10.1016/j.coche.2014.09.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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24
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Morshedi D, Aliakbari F, Nouri HR, Lotfinia M, Fallahi J. Using small molecules as a new challenge to redirect metabolic pathway. 3 Biotech 2014; 4:513-522. [PMID: 28324386 PMCID: PMC4162896 DOI: 10.1007/s13205-013-0185-6] [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: 08/22/2013] [Accepted: 11/09/2013] [Indexed: 11/26/2022] Open
Abstract
The presence of acetate in the bacterial medium leads to a reduction in the growth rate of cells and recombinant protein production. In this study, three compounds including propionic acid, lithium chloride and butyric acid were added to the medium which decreased acetate levels and enhanced recombinant protein production (alpha-synuclein). In fact, propionic acid and lithium chloride are both known as acetate kinase inhibitors. The results obtained in the case of butyric acid were similar to those of the two other compounds indicating that butyric acid may act through a mechanism similar to propionic acid and lithium chloride. Consequently, it was shown that the presence of each of these supplements (5–200 μM) increased recombinant alpha-synuclein production and cell density by approximately 10–15 %. HPLC analysis showed that the levels of acetate in the media containing the supplements were considerably less than those of the control. Furthermore, pH values remained almost constant in the supplemented cultures. Growing the bacteria at lower temperatures (25 °C) indicated that the positive effects of these supplements were not as effective as at higher temperatures (37 °C), presumably due to the adequate balance between oxygen and carbon consumption. This study can confirm the viewpoint regarding the harmful effects of acetate on the recombinant protein production and cell density. Besides, such methods represent easy and complementary ways to increase target recombinant protein production without negatively affecting host cell density, and requiring complex genetic manipulation.
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Affiliation(s)
- Dina Morshedi
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Shahrak-e Pajoohesh, km 15, Tehran-Karaj Highway, P. O. Box: 14965/161, Tehran, Iran.
| | - Farhang Aliakbari
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Shahrak-e Pajoohesh, km 15, Tehran-Karaj Highway, P. O. Box: 14965/161, Tehran, Iran
- Department of Biotechnology, Semnan University of Medical Sciences, Semnan, Iran
| | - Hamid Reza Nouri
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Shahrak-e Pajoohesh, km 15, Tehran-Karaj Highway, P. O. Box: 14965/161, Tehran, Iran
| | - Majid Lotfinia
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Biochemistry, Pasteur Institute of Iran, Tehran, Iran
| | - Jafar Fallahi
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Shahrak-e Pajoohesh, km 15, Tehran-Karaj Highway, P. O. Box: 14965/161, Tehran, Iran
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25
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Metabolic engineering of Clostridium acetobutylicum for enhanced production of butyric acid. Appl Microbiol Biotechnol 2013; 97:9355-63. [DOI: 10.1007/s00253-013-5161-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 07/29/2013] [Accepted: 07/30/2013] [Indexed: 10/26/2022]
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26
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Baek JM, Mazumdar S, Lee SW, Jung MY, Lim JH, Seo SW, Jung GY, Oh MK. Butyrate production in engineered Escherichia coli with synthetic scaffolds. Biotechnol Bioeng 2013; 110:2790-4. [PMID: 23568786 DOI: 10.1002/bit.24925] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 03/20/2013] [Accepted: 03/25/2013] [Indexed: 02/04/2023]
Abstract
Butyrate pathway was constructed in recombinant Escherichia coli using the genes from Clostridium acetobutylicum and Treponema denticola. However, the pathway constructed from exogenous enzymes did not efficiently convert carbon flux to butyrate. Three steps of the productivity enhancement were attempted in this study. First, pathway engineering to delete metabolic pathways to by-products successfully improved the butyrate production. Second, synthetic scaffold protein that spatially co-localizes enzymes was introduced to improve the efficiency of the heterologous pathway enzymes, resulting in threefold improvement in butyrate production. Finally, further optimizations of inducer concentrations and pH adjustment were tried. The final titer of butyrate was 4.3 and 7.2 g/L under batch and fed-batch cultivation, respectively. This study demonstrated the importance of synthetic scaffold protein as a useful tool for optimization of heterologous butyrate pathway in E. coli.
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Affiliation(s)
- Jang-Mi Baek
- Department of Chemical and Biological Engineering, Korea University, Sungbuk-Gu, Seoul 136-713, South Korea
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27
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Bhandiwad A, Guseva A, Lynd L. Metabolic Engineering of <i>Thermoanaerobacterium thermosaccharolyticum</i> for Increased n-Butanol Production. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/aim.2013.31007] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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28
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Cooksley CM, Zhang Y, Wang H, Redl S, Winzer K, Minton NP. Targeted mutagenesis of the Clostridium acetobutylicum acetone-butanol-ethanol fermentation pathway. Metab Eng 2012; 14:630-41. [PMID: 22982601 DOI: 10.1016/j.ymben.2012.09.001] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 08/30/2012] [Accepted: 09/06/2012] [Indexed: 01/29/2023]
Abstract
The production of the chemical solvents acetone and butanol by the bacterium Clostridium acetobutylicum was one of the first large-scale industrial processes to be developed, and in the first part of the last century ranked second in importance only to ethanol production. After a steep decline in its industrial use, there has been a recent resurgence of interest in the acetone-butanol-ethanol (ABE) fermentation process, with a particular emphasis on butanol production. In order to generate strains suitable for efficient use on an industrial scale, metabolic engineering is required to alter the AB ratio in favour of butanol, and eradicate the production of unwanted products of fermentation. Using ClosTron technology, a large-scale targeted mutagenesis in C. acetobutylicum ATCC 824 was carried out, generating a set of 10 mutants, defective in alcohol/aldehyde dehydrogenases 1 and 2 (adhE1, adhE2), butanol dehydrogenases A and B (bdhA, bdhB), phosphotransbutyrylase (ptb), acetate kinase (ack), acetoacetate decarboxylase (adc), CoA transferase (ctfA/ctfB), and a previously uncharacterised putative alcohol dehydrogenase (CAP0059). However, inactivation of the main hydrogenase (hydA) and thiolase (thl) could not be achieved. Constructing such a series of mutants is paramount for the acquisition of information on the mechanism of solvent production in this organism, and the subsequent development of industrial solvent producing strains. Unexpectedly, bdhA and bdhB mutants did not affect solvent production, whereas inactivation of the previously uncharacterised gene CAP0059 resulted in increased acetone, butanol, and ethanol formation. Other mutants showed predicted phenotypes, including a lack of acetone formation (adc, ctfA, and ctfB mutants), an inability to take up acids (ctfA and ctfB mutants), and a much reduced acetate formation (ack mutant). The adhE1 mutant in particular produced very little solvents, demonstrating that this gene was indeed the main contributor to ethanol and butanol formation under the standard batch culture conditions employed in this study. All phenotypic changes observed could be reversed by genetic complementation, with exception of those seen for the ptb mutant. This mutant produced around 100 mM ethanol, no acetone and very little (7 mM) butanol. The genome of the ptb mutant was therefore re-sequenced, together with its parent strain (ATCC 824 wild type), and shown to possess a frameshift mutation in the thl gene, which perfectly explained the observed phenotype. This finding reinforces the need for mutant complementation and Southern Blot analysis (to confirm single ClosTron insertions), which should be obligatory in all further ClosTron applications.
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Affiliation(s)
- Clare M Cooksley
- Clostridia Research Group, BBSRC Sustainable Bioenergy Centre, School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK
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29
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Novel system for efficient isolation of Clostridium double-crossover allelic exchange mutants enabling markerless chromosomal gene deletions and DNA integration. Appl Environ Microbiol 2012; 78:8112-21. [PMID: 22983967 DOI: 10.1128/aem.02214-12] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Isolation of Clostridium mutants based on gene replacement via allelic exchange remains a major limitation for this important genus. Use of a heterologous counterselection marker can facilitate the identification of the generally rare allelic exchange events. We report on the development of an inducible counterselection marker and describe its utility and broad potential in quickly and efficiently generating markerless DNA deletions and integrations at any genomic locus without the need for auxotrophic mutants or the use of the mobile group II introns. This system is based on a codon-optimized mazF toxin gene from Escherichia coli under the control of a lactose-inducible promoter from Clostridium perfringens. This system is potentially applicable to almost all members of the genus Clostridium due to their similarly low genomic GC content and comparable codon usage. We isolated all allelic-exchange-based gene deletions (ca_p0167, sigF, and sigK) or disruptions (ca_p0157 and sigF) we attempted and integrated a 3.6-kb heterologous DNA sequence (made up of a Clostridium ljungdahlii 2.1-kb formate dehydrogenase [fdh] gene plus a FLP recombination target [FRT]-flanked thiamphenicol resistance marker) into the Clostridium acetobutylicum chromosome. Furthermore, we report on the development of a plasmid system with inducible segregational instability, thus enabling efficient deployment of the FLP-FRT system to generate markerless deletion or integration mutants. This enabled expeditious deletion of the thiamphenicol resistance marker from the fdh integrant strain as well as the sigK deletion strain. More generally, our system can potentially be applied to other organisms with underdeveloped genetic tools.
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30
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Kubiak P, Leja K, Myszka K, Celińska E, Spychała M, Szymanowska-Powałowska D, Czaczyk K, Grajek W. Physiological predisposition of various Clostridium species to synthetize 1,3-propanediol from glycerol. Process Biochem 2012. [DOI: 10.1016/j.procbio.2012.05.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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31
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Lehmann D, Radomski N, Lütke-Eversloh T. New insights into the butyric acid metabolism of Clostridium acetobutylicum. Appl Microbiol Biotechnol 2012; 96:1325-39. [PMID: 22576943 DOI: 10.1007/s00253-012-4109-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Revised: 04/13/2012] [Accepted: 04/16/2012] [Indexed: 01/17/2023]
Abstract
Biosynthesis of acetone and n-butanol is naturally restricted to the group of solventogenic clostridia with Clostridium acetobutylicum being the model organism for acetone-butanol-ethanol (ABE) fermentation. According to limited genetic tools, only a few rational metabolic engineering approaches were conducted in the past to improve the production of butanol, an advanced biofuel. In this study, a phosphotransbutyrylase-(Ptb) negative mutant, C. acetobutylicum ptb::int(87), was generated using the ClosTron methodology for targeted gene knock-out and resulted in a distinct butyrate-negative phenotype. The major end products of fermentation experiments without pH control were acetate (3.2 g/l), lactate (4.0 g/l), and butanol (3.4 g/l). The product pattern of the ptb mutant was altered to high ethanol (12.1 g/l) and butanol (8.0 g/l) titers in pH ≥ 5.0-regulated fermentations. Glucose fed-batch cultivation elevated the ethanol concentration to 32.4 g/l, yielding a more than fourfold increased alcohol to acetone ratio as compared to the wildtype. Although butyrate was never detected in cultures of C. acetobutylicum ptb::int(87), the mutant was still capable to take up butyrate when externally added during the late exponential growth phase. These findings suggest that alternative pathways of butyrate re-assimilation exist in C. acetobutylicum, supposably mediated by acetoacetyl-CoA:acyl-CoA transferase and acetoacetate decarboxylase, as well as reverse reactions of butyrate kinase and Ptb with respect to previous studies.
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Affiliation(s)
- Dörte Lehmann
- Abteilung Mikrobiologie, Institut für Biowissenschaften, Universität Rostock, Albert-Einstein-Str. 3, 18059, Rostock, Germany
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