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Zou S, Zhang B, Han Y, Liu J, Zhao K, Xue Y, Zheng Y. Design of a cofactor self-sufficient whole-cell biocatalyst for enzymatic asymmetric reduction via engineered metabolic pathways and multi-enzyme cascade. Biotechnol J 2024; 19:e2300744. [PMID: 38509791 DOI: 10.1002/biot.202300744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/22/2024] [Accepted: 03/03/2024] [Indexed: 03/22/2024]
Abstract
NAD(P)H-dependent oxidoreductases are crucial biocatalysts for synthesizing chiral compounds. Yet, the industrial implementation of enzymatic redox reactions is often hampered by an insufficient supply of expensive nicotinamide cofactors. Here, a cofactor self-sufficient whole-cell biocatalyst was developed for the enzymatic asymmetric reduction of 2-oxo-4-[(hydroxy)(-methyl)phosphinyl] butyric acid (PPO) to L-phosphinothricin (L-PPT). The endogenous NADP+ pool was significantly enhanced by regulating Preiss-Handler pathway toward NAD(H) synthesis and, in the meantime, introducing NAD kinase to phosphorylate NAD(H) toward NADP+. The intracellular NADP(H) concentration displayed a 2.97-fold increase with the strategy compared with the wild-type strain. Furthermore, a recombinant multi-enzyme cascade biocatalytic system was constructed based on the Escherichia coli chassis. In order to balance multi-enzyme co-expression levels, the strategy of modulating rate-limiting enzyme PmGluDH by RBS strengths regulation successfully increased the catalytic efficiency of PPO conversion. Finally, the cofactor self-sufficient whole-cell biocatalyst effectively converted 300 mM PPO to L-PPT in 2 h without the need to add exogenous cofactors, resulting in a 2.3-fold increase in PPO conversion (%) from 43% to 100%, with a high space-time yield of 706.2 g L-1 d-1 and 99.9% ee. Overall, this work demonstrates a technological example for constructing a cofactor self-sufficient system for NADPH-dependent redox biocatalysis.
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Affiliation(s)
- Shuping Zou
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Bing Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Yuyue Han
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Jinlong Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Kuo Zhao
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Yaping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Yuguo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
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Guo G, Zhang Y, Wei D, Wang Z, Li Q, Yu Y, Zhang W. Contribution of nadR to the cell growth and virulence of Streptococcus suis serotype 2. Vet Microbiol 2024; 288:109928. [PMID: 38056180 DOI: 10.1016/j.vetmic.2023.109928] [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: 02/08/2022] [Revised: 10/06/2023] [Accepted: 11/20/2023] [Indexed: 12/08/2023]
Abstract
Streptococcus suis serotype 2 (SS2) has been reported to be a highly invasive pathogen in swine and a zoonotic agent for humans. Although many bacterial virulence factors have been identified, our an insightful understanding of SS2 pathogenicity is lacking. The gene nadR, encoding nicotinamide-nucleotide adenylyltransferase, was first reported as a regulator and transporter of the intracellular NAD synthesis pathway in Salmonella typhimurium. In this study, we constructed a mutant strain of nadR (ΔnadR) to test the phenotypic and virulence variations between the deletion mutant and the wild-type strain ZY05719. The phenotypic experimental results showed that ΔnadR obviously inhibited cell growth and exhibited shorter chains than WT. The growth defect of ΔnadR was caused by the loss of the function of nadR for transporting the substrates nicotinamide mononucleotide and nicotinamide riboside in the intracellular NAD synthesis pathway. In the process of interaction with the host, ΔnadR participated in adherence and invasion to the host cells, and it was more easily cleared by RAW264.7 macrophages. More importantly, both zebrafish and BALB/c mice in vivo virulence experimental results showed that ΔnadR dramatically attenuated the virulence of SS2, and the ability of ΔnadR to colonize tissues was notably reduced in comparison with that of WT in the BALB/c mice infection model. To the best of our knowledge, this is the first time to demonstrate that nadR not only plays an important role in bacterial growth, but also in connection with the virulence of SS2 as a global transcriptional regulator.
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Affiliation(s)
- Genglin Guo
- Shandong Institute of Sericulture, Shandong Academy of Agricultural Sciences, Yantai, China
| | - Yuhang Zhang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; OIE Reference Lab for Swine Streptococcosis, Nanjing 210095, China; MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing, China; The Sanya Institute of Nanjing Agricultural University, Sanya, China
| | - Dan Wei
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; OIE Reference Lab for Swine Streptococcosis, Nanjing 210095, China; MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing, China; The Sanya Institute of Nanjing Agricultural University, Sanya, China
| | - Zhuohao Wang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; OIE Reference Lab for Swine Streptococcosis, Nanjing 210095, China; MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing, China; The Sanya Institute of Nanjing Agricultural University, Sanya, China
| | - Quan Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Yanfei Yu
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture and Rural Affairs, Nanjing, China; School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Wei Zhang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; OIE Reference Lab for Swine Streptococcosis, Nanjing 210095, China; MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing, China; The Sanya Institute of Nanjing Agricultural University, Sanya, China.
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Jo MH, Ju JH, Heo SY, Cho J, Jeong KJ, Kim MS, Kim CH, Oh BR. Production of 1,2-propanediol from glycerol in Klebsiella pneumoniae GEM167 with flux enhancement of the oxidative pathway. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:18. [PMID: 36747250 PMCID: PMC9903448 DOI: 10.1186/s13068-023-02269-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 01/27/2023] [Indexed: 02/08/2023]
Abstract
BACKGROUND To support the sustainability of biodiesel production, by-products, such as crude glycerol, should be converted into high-value chemical products. 1,2-propanediol (1,2-PDO) has been widely used as a building block in the chemical and pharmaceutical industries. Recently, the microbial bioconversion of lactic acid into 1,2-PDO is attracting attention to overcome limitations of previous biosynthetic pathways for production of 1,2-PDO. In this study, we examined the effect of genetic engineering, metabolic engineering, and control of bioprocess factors on the production of 1,2-PDO from lactic acid by K. pneumoniae GEM167 with flux enhancement of the oxidative pathway, using glycerol as carbon source. RESULTS We developed K. pneumoniae GEM167ΔadhE/pBR-1,2PDO, a novel bacterial strain that has blockage of ethanol biosynthesis and biosynthesized 1,2-PDO from lactic acid when glycerol is carbon source. Increasing the agitation speed from 200 to 400 rpm not only increased 1,2-PDO production by 2.24-fold to 731.0 ± 24.7 mg/L at 48 h but also increased the amount of a by-product, 2,3-butanediol. We attempted to inhibit 2,3-butanediol biosynthesis using the approaches of pH control and metabolic engineering. Control of pH at 7.0 successfully increased 1,2-PDO production (1016.5 ± 37.3 mg/L at 48 h), but the metabolic engineering approach was not successful. The plasmid in this strain maintained 100% stability for 72 h. CONCLUSIONS This study is the first to report the biosynthesis of 1,2-PDO from lactic acid in K. pneumoniae when glycerol was carbon source. The 1,2-PDO production was enhanced by blocking the synthesis of 2,3-butanediol through pH control. Our results indicate that K. pneumoniae GEM167 has potential for the production of additional valuable chemical products from metabolites produced through oxidative pathways.
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Affiliation(s)
- Min-Ho Jo
- grid.249967.70000 0004 0636 3099Microbial Biotechnology Research Center, Jeonbuk Branch Institute, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Jeonbuk 56212 Republic of Korea
| | - Jung-Hyun Ju
- grid.249967.70000 0004 0636 3099Microbial Biotechnology Research Center, Jeonbuk Branch Institute, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Jeonbuk 56212 Republic of Korea
| | - Sun-Yeon Heo
- grid.249967.70000 0004 0636 3099Microbial Biotechnology Research Center, Jeonbuk Branch Institute, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Jeonbuk 56212 Republic of Korea
| | - Jaehoon Cho
- grid.454135.20000 0000 9353 1134Green and Sustainable Materials R&D Department, Korea Institute of Industrial Technology, Cheonan, Chungcheongnam 31056 Republic of Korea
| | - Ki Jun Jeong
- grid.37172.300000 0001 2292 0500Department of Chemical and Biomolecular Engineering and Institute for the BioCentury, KAIST, Daejeon, 34141 Republic of Korea
| | - Min-Soo Kim
- grid.249967.70000 0004 0636 3099Microbial Biotechnology Research Center, Jeonbuk Branch Institute, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Jeonbuk 56212 Republic of Korea
| | - Chul-Ho Kim
- grid.249967.70000 0004 0636 3099Microbial Biotechnology Research Center, Jeonbuk Branch Institute, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Jeonbuk 56212 Republic of Korea
| | - Baek-Rock Oh
- Microbial Biotechnology Research Center, Jeonbuk Branch Institute, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Jeonbuk, 56212, Republic of Korea.
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Han R, Gao K, Jiang Y, Zhou J, Xu G, Dong J, Schwaneberg U, Ji Y, Ni Y. Self-Sufficient In Vitro Multi-Enzyme Cascade for Efficient Synthesis of Danshensu from l-DOPA. ACS Synth Biol 2023; 12:277-286. [PMID: 36412006 DOI: 10.1021/acssynbio.2c00552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Danshensu (DSS), a traditional Chinese medicine, is widely used for the treatment of cardiovascular and cancer diseases. Here, a one-pot multi-enzyme cascade pathway was designed for DSS synthesis from l-DOPA using tyrosine aminotransferase from Escherichia coli (EcTyrB) and d-isomer-specific 2-hydroxyacid dehydrogenase from Lactobacillus frumenti (LfD2-HDH). Glutamate dehydrogenase from Clostridium difficile (CdgluD) was also introduced for a self-sufficient system of α-ketoglutaric acid and NADH. Under optimal conditions (35 °C, pH 7.0, EcTyrB:LfD2-HDH:CdgluD = 3:2:1, glutamate:NAD+ = 1:1), 98.3% yield (at 20 mM l-DOPA) and space-time yield of 6.61 g L-1 h-1 (at 40 mM l-DOPA) were achieved. Decreased yields of DSS at elevated l-DOPA concentrations (100 mM) could be attributed to an inhibited CdgluD activity caused by NH4+ accumulation. This developed multi-enzyme cascade pathway (including EcTyrB, LfD2-HDH, and CdgluD) provides an efficient and sustainable approach for the production of DSS from l-DOPA.
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Affiliation(s)
- Ruizhi Han
- Key laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi214122, China.,Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, Aachen52074, Germany
| | - Ke Gao
- Key laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi214122, China
| | - Yulin Jiang
- Key laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi214122, China
| | - Jieyu Zhou
- Key laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi214122, China
| | - Guochao Xu
- Key laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi214122, China
| | - Jinjun Dong
- Key laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi214122, China
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, Aachen52074, Germany
| | - Yu Ji
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, Aachen52074, Germany
| | - Ye Ni
- Key laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi214122, China
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Wang JW, Che YC, Sun M, Guo YQ, Liu B, Li XF. Optimal Niacin Requirement of Oriental River Prawn Macrobrachium nipponense as Determined by Growth, Energy Sensing, and Glycolipid Metabolism. AQUACULTURE NUTRITION 2022; 2022:8596427. [PMID: 36860472 PMCID: PMC9973127 DOI: 10.1155/2022/8596427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/23/2022] [Accepted: 08/27/2022] [Indexed: 06/18/2023]
Abstract
Niacin is indispensable for the growth and development of aquatic animals. However, the correlations between dietary niacin supplementations and the intermediary metabolism of crustaceans are still poorly elucidated. This study explored the effects of different dietary niacin levels on the growth, feed utilization, energy sensing, and glycolipid metabolism of oriental river prawn Macrobrachium nipponense. Prawns were fed with different experimental diets containing graded niacin levels (15.75, 37.62, 56.62, 97.78, 176.32, and 339.28 mg/kg, respectively) for 8 weeks. Weight gain, protein efficiency, feed intake, and hepatopancreas niacin contents all maximized in the 176.32 mg/kg group with significance noted with the control group (P <0.05), whereas the opposite was true for feed conversion ratio. Hepatopancreas niacin concentrations increased significantly (P < 0.05) as dietary niacin levels increased, and peaked at the 339.28 mg/kg group. Hemolymph glucose, total cholesterol, and triglyceride concentrations all maximized in the 37.62 mg/kg group, while total protein concentration reached the highest value in the 176.32 mg/kg group. The hepatopancreas mRNA expression of AMP-activated protein kinase α and sirtuin 1 peaked at the 97.78 and 56.62 mg/kg group, respectively, and then both decreased as dietary niacin levels increased furtherly (P < 0.05). Hepatopancreas transcriptions of the genes related to glucose transportation, glycolysis, glycogenesis, and lipogenesis all increased with increasing niacin levels up to 176.32 mg/kg, but decreased significantly (P < 0.05) as dietary niacin levels increased furtherly. However, the transcriptions of the genes related to gluconeogenesis and fatty acid β-oxidation all decreased significantly (P < 0.05) as dietary niacin levels increased. Collectively, the optimum dietary niacin demand of oriental river prawn is 168.01-169.08 mg/kg. In addition, appropriate doses of niacin promoted the energy-sensing capability and glycolipid metabolism of this species.
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Affiliation(s)
- Jing-Wen Wang
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing 210095, China
| | - Yi-Cheng Che
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing 210095, China
| | - Miao Sun
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing 210095, China
| | - Yi-Qing Guo
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing 210095, China
| | - Bo Liu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agricultural and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Xiang-Fei Li
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing 210095, China
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Engineering of Escherichia coli Glyceraldehyde-3-Phosphate Dehydrogenase with Dual NAD+/NADP+ Cofactor Specificity for Improving Amino Acid Production. Microorganisms 2022; 10:microorganisms10050976. [PMID: 35630420 PMCID: PMC9145139 DOI: 10.3390/microorganisms10050976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 12/04/2022] Open
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a key enzyme in the central metabolism of microbial cells. GAPDHs differ in cofactor specificity and use NAD+, NADP+, or both cofactors, reducing them to NADH and NADPH, respectively. Sufficient NADPH supply is one of the critical factors required for synthesis of the amino acids l-lysine, l-threonine, and l-proline in industrially important Escherichia coli-based producer strains. E. coli cells have NAD+-dependent glycolytic GAPDH. One reasonable approach to increase NADPH formation in cells is to change the specificity of the GAPDH from NAD+ to NADP+. In this study, we modified the cofactor specificity of E. coli GAPDH by amino acid substitutions at positions 34, 188 and 189. Several mutant enzymes with dual NAD+/NADP+ cofactor specificity were obtained, and their kinetic parameters were determined. Overexpression of the genes encoding the resulting mutant GAPDHs with dual cofactor specificity in cells of l-lysine-, l-threonine-, and l-proline-producing E. coli strains led to a marked increase in the accumulation of the corresponding amino acid in the culture medium. This effect was more pronounced when cultivating on xylose as a carbon source. Other possible applications of the mutant enzymes are discussed.
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Improving the production of NAD + via multi-strategy metabolic engineering in Escherichia coli. Metab Eng 2021; 64:122-133. [PMID: 33577950 DOI: 10.1016/j.ymben.2021.01.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 01/30/2021] [Accepted: 01/31/2021] [Indexed: 02/07/2023]
Abstract
Nicotinamide adenine dinucleotide (NAD+) is an essential coenzyme involved in numerous physiological processes. As an attractive product in the industrial field, NAD+ also plays an important role in oxidoreductase-catalyzed reactions, drug synthesis, and the treatment of diseases, such as dementia, diabetes, and vascular dysfunction. Currently, although the biotechnology to construct NAD+-overproducing strains has been developed, limited regulation and low productivity still hamper its use on large scales. Here, we describe multi-strategy metabolic engineering to address the NAD+-production bottleneck in E. coli. First, blocking the degradation pathway of NAD(H) increased the accumulation of NAD+ by 39%. Second, key enzymes involved in the Preiss-Handler pathway of NAD+ synthesis were overexpressed and led to a 221% increase in the NAD+ concentration. Third, the PRPP synthesis module and Preiss-Handler pathway were combined to strengthen the precursors supply, which resulted in enhancement of NAD+ content by 520%. Fourth, increasing the ATP content led to an increase in the concentration of NAD+ by 170%. Finally, with the combination of all above strategies, a strain with a high yield of NAD+ was constructed, with the intracellular NAD+ concentration reaching 26.9 μmol/g DCW, which was 834% that of the parent strain. This study presents an efficient design of an NAD+-producing strain through global regulation metabolic engineering.
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Systems Analysis of NADH Dehydrogenase Mutants Reveals Flexibility and Limits of Pseudomonas taiwanensis VLB120's Metabolism. Appl Environ Microbiol 2020; 86:AEM.03038-19. [PMID: 32245760 DOI: 10.1128/aem.03038-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/18/2020] [Indexed: 12/14/2022] Open
Abstract
Obligate aerobic organisms rely on a functional electron transport chain for energy conservation and NADH oxidation. Because of this essential requirement, the genes of this pathway are likely constitutively and highly expressed to avoid a cofactor imbalance and energy shortage under fluctuating environmental conditions. We here investigated the essentiality of the three NADH dehydrogenases of the respiratory chain of the obligate aerobe Pseudomonas taiwanensis VLB120 and the impact of the knockouts of corresponding genes on its physiology and metabolism. While a mutant lacking all three NADH dehydrogenases seemed to be nonviable, the single or double knockout mutant strains displayed no, or only a weak, phenotype. Only the mutant deficient in both type 2 dehydrogenases showed a clear phenotype with biphasic growth behavior and a strongly reduced growth rate in the second phase. In-depth analyses of the metabolism of the generated mutants, including quantitative physiological experiments, transcript analysis, proteomics, and enzyme activity assays revealed distinct responses to type 2 and type 1 dehydrogenase deletions. An overall high metabolic flexibility enables P. taiwanensis to cope with the introduced genetic perturbations and maintain stable phenotypes, likely by rerouting of metabolic fluxes. This metabolic adaptability has implications for biotechnological applications. While the phenotypic robustness is favorable in large-scale applications with inhomogeneous conditions, the possible versatile redirecting of carbon fluxes upon genetic interventions can thwart metabolic engineering efforts.IMPORTANCE While Pseudomonas has the capability for high metabolic activity and the provision of reduced redox cofactors important for biocatalytic applications, exploitation of this characteristic might be hindered by high, constitutive activity of and, consequently, competition with the NADH dehydrogenases of the respiratory chain. The in-depth analysis of NADH dehydrogenase mutants of Pseudomonas taiwanensis VLB120 presented here provides insight into the phenotypic and metabolic response of this strain to these redox metabolism perturbations. This high degree of metabolic flexibility needs to be taken into account for rational engineering of this promising biotechnological workhorse toward a host with a controlled and efficient supply of redox cofactors for product synthesis.
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Effects of NADH Availability on 3-Phenyllactic Acid Production by Lactobacillus plantarum Expressing Formate Dehydrogenase. Curr Microbiol 2019; 76:706-712. [PMID: 30963198 DOI: 10.1007/s00284-019-01681-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 03/27/2019] [Indexed: 10/27/2022]
Abstract
It is well known that cofactors play a key role in the production of different compounds in bioconversion processes, while the high cost of cofactors limits their usage in industrial applications. In the present study, a NADH regeneration system was successfully developed in Lactobacillus plantarum by expressing the fdh gene coding for formate dehydrogenase (FDH) from Candida boidinii. Results indicated that the FDH was expressed with the highest activity of 0.82 U/mg of protein when cells entered early stationary phase. In addition, the expression of FDH increased the intracellular level of NADH and NADH/NAD+ ratio in L. plantarum, and therefore, enhanced the NADH-dependent production of 3-phenyllactic acid (PLA) in repeated and fed-batch bioconversions. In brief, the results demonstrate that the NADH regeneration by expressing FDH is a promising strategy for producing NADH-dependent microbial metabolites in L. plantarum.
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Han Q, Eiteman MA. Enhancement of NAD(H) pool for formation of oxidized biochemicals in Escherichia coli. J Ind Microbiol Biotechnol 2018; 45:939-950. [PMID: 30159648 DOI: 10.1007/s10295-018-2072-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 08/13/2018] [Indexed: 10/28/2022]
Abstract
The NAD+/NADH ratio and the total NAD(H) play important roles for whole-cell biochemical redox transformations. After the carbon source is exhausted, the degradation of NAD(H) could contribute to a decline in the rate of a desired conversion. In this study, methods to slow the native rate of NAD(H) degradation were examined using whole-cell Escherichia coli with two model oxidative NAD+-dependent biotransformations. A high phosphate concentration (50 mM) was observed to slow NAD(H) degradation. We also constructed E. coli strains with deletions in genes coding several enzymes involved in NAD+ degradation. In shake-flask experiments, the total NAD(H) concentration positively correlated with conversion of xylitol to L-xylulose by xylitol 4-dehydrogenase, and the greatest conversion (80%) was observed using MG1655 nadR nudC mazG/pZE12-xdh/pCS27-nox. Controlled 1-L batch processes comparing E. coli nadR nudC mazG with a wild-type background strain demonstrated a 30% increase in final L-xylulose concentration (5.6 vs. 7.9 g/L) and a 25% increase in conversion (0.53 vs. 0.66 g/g). MG1655 nadR nudC mazG was also examined for the conversion of galactitol to L-tagatose by galactitol 2-dehydrogenase. A batch process using 15 g/L glycerol and 10 g/L galactitol generated over 9.4 g/L L-tagatose, corresponding to 90% conversion and a yield of 0.95 g L-tagatose/g galactitol consumed. The results demonstrate the value of minimizing NAD(H) degradation as a means to improve NAD+-dependent biotransformations.
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Affiliation(s)
- Qi Han
- School of Chemical Materials and Biomedical Engineering, University of Georgia, Athens, GA, 30602, USA
| | - Mark A Eiteman
- School of Chemical Materials and Biomedical Engineering, University of Georgia, Athens, GA, 30602, USA.
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Attai H, Boon M, Phillips K, Noben JP, Lavigne R, Brown PJB. Larger Than Life: Isolation and Genomic Characterization of a Jumbo Phage That Infects the Bacterial Plant Pathogen, Agrobacterium tumefaciens. Front Microbiol 2018; 9:1861. [PMID: 30154772 PMCID: PMC6102473 DOI: 10.3389/fmicb.2018.01861] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 07/24/2018] [Indexed: 01/21/2023] Open
Abstract
Agrobacterium tumefaciens is a plant pathogen that causes crown gall disease, leading to the damage of agriculturally-important crops. As part of an effort to discover new phages that can potentially be used as biocontrol agents to prevent crown gall disease, we isolated and characterized phage Atu_ph07 from Sawyer Creek in Springfield, MO, using the virulent Agrobacterium tumefaciens strain C58 as a host. After surveying its host range, we found that Atu_ph07 exclusively infects Agrobacterium tumefaciens. Time-lapse microscopy of A. tumefaciens cells subjected to infection at a multiplicity of infection (MOI) of 10 with Atu_ph07 reveals that lysis occurs within 3 h. Transmission electron microscopy (TEM) of virions shows that Atu_ph07 has a typical Myoviridae morphology with an icosahedral head, long tail, and tail fibers. The sequenced genome of Atu_ph07 is 490 kbp, defining it as a jumbo phage. The Atu_ph07 genome contains 714 open reading frames (ORFs), including 390 ORFs with no discernable homologs in other lineages (ORFans), 214 predicted conserved hypothetical proteins with no assigned function, and 110 predicted proteins with a functional annotation based on similarity to conserved proteins. The proteins with predicted functional annotations share sequence similarity with proteins from bacteriophages and bacteria. The functionally annotated genes are predicted to encode DNA replication proteins, structural proteins, lysis proteins, proteins involved in nucleotide metabolism, and tRNAs. Characterization of the gene products reveals that Atu_ph07 encodes homologs of 16 T4 core proteins and is closely related to Rak2-like phages. Using ESI-MS/MS, the majority of predicted structural proteins could be experimentally confirmed and 112 additional virion-associated proteins were identified. The genomic characterization of Atu_ph07 suggests that this phage is lytic and the dynamics of Atu_ph07 interaction with its host indicate that this phage may be suitable for inclusion in a phage cocktail to be used as a biocontrol agent.
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Affiliation(s)
- Hedieh Attai
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Maarten Boon
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Kenya Phillips
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Jean-Paul Noben
- Biomedical Research Institute and Transnational University Limburg, Hasselt University, Hasselt, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Pamela J B Brown
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
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12
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Zhu Y, Wang Y, Xu J, Chen J, Wang L, Qi B. Enantioselective Biosynthesis of l-Phenyllactic Acid by Whole Cells of Recombinant Escherichia coli. Molecules 2017; 22:E1966. [PMID: 29140277 PMCID: PMC6150373 DOI: 10.3390/molecules22111966] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 11/06/2017] [Accepted: 11/06/2017] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND l-Phenyllactic acid (l-PLA)-a valuable building block in the pharmaceutical and chemical industry-has recently emerged as an important monomer in the composition of the novel degradable biocompatible material of polyphenyllactic acid. However, both normally chemically synthesized and naturally occurring phenyllactic acid are racemic, and the product yields of reported l-PLA synthesis processes remain unsatisfactory. METHODS We developed a novel recombinant Escherichia coli strain, co-expressing l-lactate dehydrogenase (l-LDH) from Lactobacillus plantarum subsp. plantarum and glucose dehydrogenase (GDH) from Bacillus megaterium, to construct a recombinant oxidation/reduction cycle for whole-cell biotransformation of phenylpyruvic acid (PPA) into chiral l-PLA in an enantioselective and continuous manner. RESULTS During fed-batch bioconversion with intermittent PPA feeding, l-PLA yield reached 103.8 mM, with an excellent enantiomeric excess of 99.7%. The productivity of l-PLA was as high as 5.2 mM·h-1 per OD600 (optical density at 600 nm) of whole cells. These results demonstrate the efficient production of l-PLA by the one-pot biotransformation system. Therefore, this stereoselective biocatalytic process might be a promising alternative for l-PLA production.
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Affiliation(s)
- Yibo Zhu
- School of Biotechnology and Food Engineering, Changshu Institute of Technology, Changshu 215500, China.
- Key Laboratory of Food and Biotechnology of Suzhou, Changshu Institute of Technology, Changshu 215500, China.
| | - Ying Wang
- School of Biotechnology and Food Engineering, Changshu Institute of Technology, Changshu 215500, China.
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, China.
| | - Jiayuzi Xu
- School of Biotechnology and Food Engineering, Changshu Institute of Technology, Changshu 215500, China.
| | - Jiahao Chen
- School of Biotechnology and Food Engineering, Changshu Institute of Technology, Changshu 215500, China.
| | - Limei Wang
- School of Biotechnology and Food Engineering, Changshu Institute of Technology, Changshu 215500, China.
- Key Laboratory of Food and Biotechnology of Suzhou, Changshu Institute of Technology, Changshu 215500, China.
| | - Bin Qi
- School of Biotechnology and Food Engineering, Changshu Institute of Technology, Changshu 215500, China.
- Key Laboratory of Food and Biotechnology of Suzhou, Changshu Institute of Technology, Changshu 215500, China.
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13
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Su L, Shen Y, Zhang W, Gao T, Shang Z, Wang M. Cofactor engineering to regulate NAD +/NADH ratio with its application to phytosterols biotransformation. Microb Cell Fact 2017; 16:182. [PMID: 29084539 PMCID: PMC5663084 DOI: 10.1186/s12934-017-0796-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 10/24/2017] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Cofactor engineering is involved in the modification of enzymes related to nicotinamide adenine dinucleotides (NADH and NAD+) metabolism, which results in a significantly altered spectrum of metabolic products. Cofactor engineering plays an important role in metabolic engineering but is rarely reported in the sterols biotransformation process owing to its use of multi-catabolic enzymes, which promote multiple consecutive reactions. Androst-4-ene-3, 17-dione (AD) and androst-1, 4-diene-3, 17-dione (ADD) are important steroid medicine intermediates that are obtained via the nucleus oxidation and the side chain degradation of phytosterols by Mycobacterium. Given that the biotransformation from phytosterols to AD (D) is supposed to be a NAD+-dependent process, this work utilized cofactor engineering in Mycobacterium neoaurum and investigated the effect on cofactor and phytosterols metabolism. RESULTS Through the addition of the coenzyme precursor of nicotinic acid in the phytosterols fermentation system, the intracellular NAD+/NADH ratio and the AD (D) production of M. neoaurum TCCC 11978 (MNR M3) were higher than in the control. Moreover, the NADH: flavin oxidoreductase was identified and was supposed to exert a positive effect on cofactor regulation and phytosterols metabolism pathways via comparative proteomic profiling of MNR cultured with and without phytosterols. In addition, the NADH: flavin oxidoreductase and a water-forming NADH oxidase from Lactobacillus brevis, were successfully overexpressed and heterologously expressed in MNR M3 to improve the intracellular ratio of NAD+/NADH. After 96 h of cultivation, the expression of these two enzymes in MNR M3 resulted in the decrease in intracellular NADH level (by 51 and 67%, respectively) and the increase in NAD+/NADH ratio (by 113 and 192%, respectively). Phytosterols bioconversion revealed that the conversion ratio of engineered stains was ultimately improved by 58 and 147%, respectively. The highest AD (D) conversion ratio by MNR M3N2 was 94% in the conversion system with soybean oil as reaction media to promote the solubility of phytosterols. CONCLUSIONS The ratio of NAD+/NADH is an important factor for the transformation of phytosterols. Expression of NADH: flavin oxidoreductase and water-forming NADH oxidase in MNR improved AD (D) production. Besides the manipulation of key enzyme activities, which included in phytosterols degradation pathways, maintenance the balance of redox also played an important role in promoting steroid biotransformation. The recombinant MNR strain may be useful in industrial production.
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Affiliation(s)
- Liqiu Su
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China
| | - Yanbing Shen
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China.
| | - Wenkai Zhang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China
| | - Tian Gao
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China
| | - Zhihua Shang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China
| | - Min Wang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China.
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14
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Zhao C, Zhao Q, Li Y, Zhang Y. Engineering redox homeostasis to develop efficient alcohol-producing microbial cell factories. Microb Cell Fact 2017; 16:115. [PMID: 28646866 PMCID: PMC5483285 DOI: 10.1186/s12934-017-0728-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 06/16/2017] [Indexed: 12/11/2022] Open
Abstract
The biosynthetic pathways of most alcohols are linked to intracellular redox homeostasis, which is crucial for life. This crucial balance is primarily controlled by the generation of reducing equivalents, as well as the (reduction)-oxidation metabolic cycle and the thiol redox homeostasis system. As a main oxidation pathway of reducing equivalents, the biosynthesis of most alcohols includes redox reactions, which are dependent on cofactors such as NADH or NADPH. Thus, when engineering alcohol-producing strains, the availability of cofactors and redox homeostasis must be considered. In this review, recent advances on the engineering of cellular redox homeostasis systems to accelerate alcohol biosynthesis are summarized. Recent approaches include improving cofactor availability, manipulating the affinity of redox enzymes to specific cofactors, as well as globally controlling redox reactions, indicating the power of these approaches, and opening a path towards improving the production of a number of different industrially-relevant alcohols in the near future.
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Affiliation(s)
- Chunhua Zhao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road Chaoyang District, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Qiuwei Zhao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road Chaoyang District, Beijing, 100101 China
| | - Yin Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road Chaoyang District, Beijing, 100101 China
| | - Yanping Zhang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road Chaoyang District, Beijing, 100101 China
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15
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Lee YD, Park JH. Genomic analysis of WCP30 Phage of Weissella cibaria for Dairy Fermented Foods. Korean J Food Sci Anim Resour 2017; 37:884-888. [PMID: 29725210 PMCID: PMC5932951 DOI: 10.5851/kosfa.2017.37.6.884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Revised: 11/21/2017] [Accepted: 11/21/2017] [Indexed: 11/17/2022] Open
Abstract
In this study, we report the morphogenetic analysis and genome sequence of a new WCP30 phage of Weissella cibaria, isolated from a fermented food. Based on its morphology, as observed by transmission electron microscopy, WCP30 phage belongs to the family Siphoviridae. Genomic analysis of WCP30 phage showed that it had a 33,697-bp double-stranded DNA genome with 41.2% G+C content. Bioinformatics analysis of the genome revealed 35 open reading frames. A BLASTN search showed that WCP30 phage had low sequence similarity compared to other phages infecting lactic acid bacteria. This is the first report of the morphological features and complete genome sequence of WCP30 phage, which may be useful for controlling the fermentation of dairy foods.
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Affiliation(s)
- Young-Duck Lee
- Department of Food Science and Engineering, Seowon University, Cheongju, Korea
| | - Jong-Hyun Park
- Corresponding author Jong-Hyun Park Department of Food Science and Biotechnology, College of Bionano Technology, Gachon University, Sungnam 13120, Korea Tel: +82-31-750-5523 Fax: +82-31-750-5984 E-mail:
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16
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Brickman TJ, Suhadolc RJ, McKelvey PJ, Armstrong SK. Essential role of Bordetella NadC in a quinolinate salvage pathway for NAD biosynthesis. Mol Microbiol 2016; 103:423-438. [PMID: 27783449 DOI: 10.1111/mmi.13566] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2016] [Indexed: 01/03/2023]
Abstract
Nicotinamide adenine dinucleotide (NAD) is produced via de novo biosynthesis pathways and by salvage or recycling routes. The classical Bordetella bacterial species are known to be auxotrophic for nicotinamide or nicotinic acid. This study confirmed that Bordetella bronchiseptica, Bordetella pertussis and Bordetella parapertussis have the recycling/salvage pathway genes pncA and pncB, for use of nicotinamide or nicotinic acid, respectively, for NAD synthesis. Although these Bordetellae lack the nadA and nadB genes needed for de novo NAD biosynthesis, remarkably, they have one de novo pathway gene, nadC, encoding quinolinate phosphoribosyltransferase. Genomic analyses of taxonomically related Bordetella and Achromobacter species also indicated the presence of an 'orphan' nadC and the absence of nadA and nadB. When supplied as the sole NAD precursor, quinolinate promoted B. bronchiseptica growth, and the ability to use it required nadC. Co-expression of Bordetella nadC with the nadB and nadA genes of Paraburkholderia phytofirmans allowed B. bronchiseptica to grow in the absence of supplied pyridines, indicative of de novo NAD synthesis and functional confirmation of Bordetella NadC activity. Expression of nadC in B. bronchiseptica was influenced by nicotinic acid and by a NadQ family transcriptional repressor, indicating that these organisms prioritize their use of pyridines for NAD biosynthesis.
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Affiliation(s)
- Timothy J Brickman
- Department of Microbiology and Immunology, University of Minnesota Medical School, 3-117 Microbiology Research Facility, 689 23rd Ave. S.E, Minneapolis, MN, 55455-1507, USA
| | - Ryan J Suhadolc
- Department of Microbiology and Immunology, University of Minnesota Medical School, 3-117 Microbiology Research Facility, 689 23rd Ave. S.E, Minneapolis, MN, 55455-1507, USA
| | - Pamela J McKelvey
- Department of Microbiology and Immunology, University of Minnesota Medical School, 3-117 Microbiology Research Facility, 689 23rd Ave. S.E, Minneapolis, MN, 55455-1507, USA
| | - Sandra K Armstrong
- Department of Microbiology and Immunology, University of Minnesota Medical School, 3-117 Microbiology Research Facility, 689 23rd Ave. S.E, Minneapolis, MN, 55455-1507, USA
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Buyuktimkin B, Saier MH. Comparative analyses of transport proteins encoded within the genomes of Leptospira species. Microb Pathog 2016; 98:118-31. [PMID: 27296707 DOI: 10.1016/j.micpath.2016.06.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 06/08/2016] [Indexed: 02/02/2023]
Abstract
Select species of the bacterial genus Leptospira are causative agents of leptospirosis, an emerging global zoonosis affecting nearly one million people worldwide annually. We examined two Leptospira pathogens, Leptospira interrogans serovar Lai str. 56601 and Leptospira borgpetersenii serovar Hardjo-bovis str. L550, as well as the free-living leptospiral saprophyte, Leptospira biflexa serovar Patoc str. 'Patoc 1 (Ames)'. The transport proteins of these leptospires were identified and compared using bioinformatics to gain an appreciation for which proteins may be related to pathogenesis and saprophytism. L. biflexa possesses a disproportionately high number of secondary carriers for metabolite uptake and environmental adaptability as well as an increased number of inorganic cation transporters providing ionic homeostasis and effective osmoregulation in a rapidly changing environment. L. interrogans and L. borgpetersenii possess far fewer transporters, but those that they all have are remarkably similar, with near-equivalent representation in most transporter families. These two Leptospira pathogens also possess intact sphingomyelinases, holins, and virulence-related outer membrane porins. These virulence-related factors, in conjunction with decreased transporter substrate versatility, indicate that pathogenicity arose in Leptospira correlating to progressively narrowing ecological niches and the emergence of a limited set of proteins responsible for host invasion. The variability of host tropism and mortality rates by infectious leptospires suggests that small differences in individual sets of proteins play important physiological and pathological roles.
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Affiliation(s)
- Bora Buyuktimkin
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Milton H Saier
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA.
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18
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Zhang L, Xu Y, Gao J, Xu H, Cao C, Xue F, Ding G, Peng Y. Introduction of the exogenous NADH coenzyme regeneration system and its influence on intracellular metabolic flux of Paenibacillus polymyxa. BIORESOURCE TECHNOLOGY 2016; 201:319-328. [PMID: 26687492 DOI: 10.1016/j.biortech.2015.11.067] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 11/22/2015] [Accepted: 11/24/2015] [Indexed: 06/05/2023]
Abstract
The NAD(+)-dependent formate dehydrogenase (FDH) gene from Candida boidinii was introduced into Paenibacillus polymyxa ZJ-9. The effects of this exogenous gene on the growth of the recombinant strain P. polymyxa XG-1, FDH activity, intracellular NADH and NAD(+) level and the synthesis of R,R-2,3-butanediol (R,R-2,3-BD) were determined. Results from the fermentation in the 7.5L bioreactor showed that the exogenous FDH was highly expressed in the recombinant strain. The titers of NADH, lactic acid, ethanol, NADH/NAD(+), and CO2 excretion rate (CER) of the recombinant strain increased considerably, while acetoin and formic acid decreased significantly. The highest titers of R,R-2,3-BD by the recombinant strain in batch and fed-batch fermentation were 36.8g/L and 51.3g/L, increased 10.2% and 8.0% compared with the parent strain, respectively. This study confirmed that coenzyme regeneration system can manipulate substance metabolism in bacteria, and is an efficient way for promoting the synthesis of NADH-dependent products.
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Affiliation(s)
- Li Zhang
- School of Marine and Bioengineering, Yancheng Institute of Technology, Yancheng 224051, PR China
| | - Youyong Xu
- School of Marine and Bioengineering, Yancheng Institute of Technology, Yancheng 224051, PR China; State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing University of Technology, Nanjing 211816, PR China
| | - Jian Gao
- School of Marine and Bioengineering, Yancheng Institute of Technology, Yancheng 224051, PR China.
| | - Hong Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing University of Technology, Nanjing 211816, PR China
| | - Can Cao
- School of Marine and Bioengineering, Yancheng Institute of Technology, Yancheng 224051, PR China; State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing University of Technology, Nanjing 211816, PR China
| | - Feng Xue
- School of Marine and Bioengineering, Yancheng Institute of Technology, Yancheng 224051, PR China
| | - Ge Ding
- School of Marine and Bioengineering, Yancheng Institute of Technology, Yancheng 224051, PR China
| | - Yingyun Peng
- School of Marine and Bioengineering, Yancheng Institute of Technology, Yancheng 224051, PR China
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19
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Buyuktimkin B, Saier MH. Comparative genomic analyses of transport proteins encoded within the genomes of Leptospira species. Microb Pathog 2015; 88:52-64. [PMID: 26247102 DOI: 10.1016/j.micpath.2015.07.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 07/21/2015] [Accepted: 07/23/2015] [Indexed: 11/17/2022]
Abstract
Select species of the bacterial genus Leptospira are causative agents of leptospirosis, an emerging global zoonosis affecting nearly one million people worldwide annually. We examined two Leptospira pathogens, Leptospira interrogans serovar Lai str. 56601 and Leptospira borgpetersenii serovar Hardjo-bovis str. L550, as well as the free-living leptospiral saprophyte, Leptospira biflexa serovar Patoc str. 'Patoc 1 (Ames)'. The transport proteins of these leptospires were identified and compared using bioinformatics to gain an appreciation for which proteins may be related to pathogenesis and saprophytism. L. biflexa possesses a disproportionately high number of secondary carriers for metabolite uptake and environmental adaptability as well as an increased number of inorganic cation transporters providing ionic homeostasis and effective osmoregulation in a rapidly changing environment. L. interrogans and L. borgpetersenii possess far fewer transporters, but those that they have are remarkably similar, with near-equivalent representation in most transporter families. These two Leptospira pathogens also possess intact sphingomyelinases, holins, and virulence-related outer membrane porins. These virulence-related factors, in conjunction with decreased transporter substrate versatility, indicate that pathogenicity was accompanied by progressively narrowing ecological niches and the emergence of a limited set of proteins responsible for host invasion. The variability of host tropism and mortality rates by infectious leptospires suggests that small differences in individual sets of proteins play important physiological and pathological roles.
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Affiliation(s)
- Bora Buyuktimkin
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Milton H Saier
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA.
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20
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Zhuge X, Li J, Shin HD, Liu L, Du G, Chen J. Improved propionic acid production with metabolically engineered Propionibacterium jensenii by an oxidoreduction potential-shift control strategy. BIORESOURCE TECHNOLOGY 2015; 175:606-612. [PMID: 25453933 DOI: 10.1016/j.biortech.2014.10.038] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 10/08/2014] [Accepted: 10/09/2014] [Indexed: 06/04/2023]
Abstract
In this study, a three-stage oxidoreduction potential (ORP) control strategy was developed to improve propionic acid (PA) production using engineered Propionibacterium jensenii ATCC 4868 (pZGX04-gldA) in a 3-L bioreactor. Specifically, ORP was controlled at -200mV from 0 to 36h, -300mV from 36 to 156h, and -400mV after 156h. The PA titer increased from 21.38 to 27.31g/L. The effects of ORP regulation on key intracellular metabolites were studied, demonstrating that ORP can both regulate NADH/NAD(+) ratio and the activities of some enzymes involved in electron transport and redistribute metabolic flux. We integrated the ORP control strategy with a fed-batch culture method and increased PA production to 39.53g/L. This new ORP control strategy may be useful in the optimization of other anaerobic processes.
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Affiliation(s)
- Xin Zhuge
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Synergetic Innovation Center of Food Safety and Nutrition, Wuxi 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Synergetic Innovation Center of Food Safety and Nutrition, Wuxi 214122, China
| | - Hyun-Dong Shin
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta 30332, USA
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Synergetic Innovation Center of Food Safety and Nutrition, Wuxi 214122, China.
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Synergetic Innovation Center of Food Safety and Nutrition, Wuxi 214122, China.
| | - Jian Chen
- Synergetic Innovation Center of Food Safety and Nutrition, Wuxi 214122, China; National Engineering of Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China
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Enhancement of ascomycin production in Streptomyces hygroscopicus var. ascomyceticus by combining resin HP20 addition and metabolic profiling analysis. ACTA ACUST UNITED AC 2014; 41:1365-74. [DOI: 10.1007/s10295-014-1473-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 06/09/2014] [Indexed: 10/25/2022]
Abstract
Abstract
Combinatorial approach of adsorbent resin HP20 addition and metabolic profiling analysis were carried out to enhance ascomycin production. Under the optimal condition of 5 % m/v HP20 added at 24 h, ascomycin production was increased to 380 from 300 mg/L. To further rationally guide the improvement of ascomycin production, metabolic profiling analysis was employed to investigate the intracellular metabolite changes of Streptomyces hygroscopicus var. ascomyceticus FS35 in response to HP20 addition. A correlation between the metabolic profiles and ascomycin accumulation was revealed by partial least-squares to latent structures discriminant analysis, and 11 key metabolites that most contributed to metabolism differences and ascomycin biosynthesis were identified. Based on the analysis of metabolite changes together with their pathways, the potential key factors associated with ascomycin overproduction were determined. Finally, rationally designed fermentation strategies based on HP20 addition were performed as follows: 2 % v/v n-hexadecane was added at 24 h; 1.0 g/L valine was supplemented at 48 h; 1.0 g/L lysine was added at 72 h. The ascomycin production was ultimately improved to 460 mg/L, a 53.3 % enhancement compared with that obtained in initial condition. These results demonstrated that the combination of HP20 addition and metabolic profiling analysis could be successfully applied to the rational guidance of production improvement of ascomycin, as well as other clinically important compounds.
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Kim H, Shibayama K, Rimbara E, Mori S. Biochemical characterization of quinolinic acid phosphoribosyltransferase from Mycobacterium tuberculosis H37Rv and inhibition of its activity by pyrazinamide. PLoS One 2014; 9:e100062. [PMID: 24949952 PMCID: PMC4065032 DOI: 10.1371/journal.pone.0100062] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 05/22/2014] [Indexed: 11/19/2022] Open
Abstract
Quinolinic acid phosphoribosyltransferase (QAPRTase, EC 2.4.2.19) is a key enzyme in the de novo pathway of nicotinamide adenine dinucleotide (NAD) biosynthesis and a target for the development of new anti-tuberculosis drugs. QAPRTase catalyzes the synthesis of nicotinic acid mononucleotide from quinolinic acid (QA) and 5-phosphoribosyl-1-pyrophosphate (PRPP) through a phosphoribosyl transfer reaction followed by decarboxylation. The crystal structure of QAPRTase from Mycobacterium tuberculosis H37Rv (MtQAPRTase) has been determined; however, a detailed functional analysis of MtQAPRTase has not been published. Here, we analyzed the enzymatic activities of MtQAPRTase and determined the effect on catalysis of the anti-tuberculosis drug pyrazinamide (PZA). The optimum temperature and pH for MtQAPRTase activity were 60°C and pH 9.2. MtQAPRTase required bivalent metal ions and its activity was highest in the presence of Mg2+. Kinetic analyses revealed that the Km values for QA and PRPP were 0.08 and 0.39 mM, respectively, and the kcat values for QA and PRPP were 0.12 and 0.14 [s-1], respectively. When the amino acid residues of MtQAPRTase, which may interact with QA, were substituted with alanine residues, catalytic activity was undetectable. Further, PZA, which is an anti-tuberculosis drug and a structural analog of QA, markedly inhibited the catalytic activity of MtQAPRTase. The structure of PZA may provide the basis for the design of new inhibitors of MtQAPRTase. These findings provide new insights into the catalytic properties of MtQAPRTase.
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Affiliation(s)
- Hyun Kim
- Department of Bacteriology II, National Institute of Infectious Diseases, Musashi-Murayama, Tokyo, Japan
| | - Keigo Shibayama
- Department of Bacteriology II, National Institute of Infectious Diseases, Musashi-Murayama, Tokyo, Japan
| | - Emiko Rimbara
- Department of Bacteriology II, National Institute of Infectious Diseases, Musashi-Murayama, Tokyo, Japan
| | - Shigetarou Mori
- Department of Bacteriology II, National Institute of Infectious Diseases, Musashi-Murayama, Tokyo, Japan
- * E-mail:
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Yee DC, Shlykov MA, Västermark A, Reddy VS, Arora S, Sun EI, Saier MH. The transporter-opsin-G protein-coupled receptor (TOG) superfamily. FEBS J 2013; 280:5780-800. [PMID: 23981446 DOI: 10.1111/febs.12499] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Revised: 08/06/2013] [Accepted: 08/06/2013] [Indexed: 01/27/2023]
Abstract
Visual rhodopsins are recognized members of the large and diverse family of G protein-coupled receptors (GPCRs), but their evolutionary origin and relationships to other proteins are not known. In a previous paper [Shlykov MA, Zheng WH, Chen JS & Saier MH Jr (2012) Biochim Biophys Acta 1818, 703-717], we characterized the 4-toluene sulfonate uptake permease (TSUP) family of transmembrane proteins, and showed that these 7-transmembrane segment (TMS) or 8-TMS proteins arose by intragenic duplication of a gene encoding a 4-TMS protein, sometimes followed by loss of a terminal TMS. In this study, we show that the TSUP, GPCR and microbial rhodopsin families are related to each other and to six other currently recognized transport protein families. We designate this superfamily the transporter/opsin/G protein-coupled receptor (TOG) superfamily. Despite their 8-TMS origins, the members of most constituent families exhibit 7-TMS topologies that are well conserved, and these arose by loss of either the N-terminal TMS (more frequent) or the C-terminal TMS (less frequent), depending on the family. Phylogenetic analyses revealed familial relationships within the superfamily and protein relationships within each of the nine families. The results of the statistical analyses leading to the conclusion of homology were confirmed using hidden Markov models, Pfam and 3D superimpositions. Proteins functioning by dissimilar mechanisms (channels, primary active transporters, secondary active transporters, group translocators and receptors) are interspersed on a phylogenetic tree of the TOG superfamily, suggesting that changes in the transport and energy-coupling mechanisms occurred multiple times during evolution of this superfamily.
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Affiliation(s)
- Daniel C Yee
- Division of Biological Sciences, University of California at San Diego, La Jolla, CA, USA
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Centeno-Leija S, Utrilla J, Flores N, Rodriguez A, Gosset G, Martinez A. Metabolic and transcriptional response of Escherichia coli with a NADP(+)-dependent glyceraldehyde 3-phosphate dehydrogenase from Streptococcus mutans. Antonie van Leeuwenhoek 2013; 104:913-24. [PMID: 23989925 DOI: 10.1007/s10482-013-0010-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 08/17/2013] [Indexed: 11/26/2022]
Abstract
The NAD(+)-dependent glyceraldehyde-3-phosphate-dehydrogenase (NAD(+)-GAPDH) is a key enzyme to sustain the glycolytic function in Escherichia coli and to generate NADH. In the absence of NAD(+)-GAPDH activity, the glycolytic function can be restored through NADP(+)-dependent GAPDH heterologous expression. Here, some metabolic and transcriptional effects are described when the NAD(+)-GAPDH gene from E. coli (gapA) is replaced with the NADP(+)-GAPDH gene from Streptococcus mutans (gapN). Expression of gapN was controlled by the native gapA promoter (E. coliΔgapA::gapN) or by the constitutive trc promoter in a multicopy plasmid (E. coliΔgapA::gapN/pTrcgapN). The specific NADP(+)-GAPDH activity was 4.7 times higher in E. coliΔgapA::gapN/pTrcgapN than E. coliΔgapA::gapN. Growth, glucose consumption and acetic acid production rates increased in agreement with the NADP(+)-GAPDH activity level. Analysis of E. coliΔgapA::gapN/pTrcgapN showed that although gapN expression complemented NAD(+)-GAPDH activity, the resulting low NADH levels decreased the expression of the respiratory chain and oxidative phosphorylation genes (ndh, cydA, cyoB and atpA). In comparison with the wild type strain, E. coliΔgapA::gapN/pTrcgapN decreased the percentage of mole of oxygen consumed per mole of glucose metabolized by 40 % with a concomitant reduction of 54 % in the ATP/ADP ratio. The cellular response to avoid NADPH excess led to the overexpression of the transhydrogenase coded by udhA and the down-regulation of the pentose-phosphate and Krebs cycle genes, which reduced the CO2 production and increased the acetic acid synthesis. The E. coli strains obtained in this work can be useful for future metabolic engineering efforts aiming for the production of metabolites which biosynthesis depends on NADPH.
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Affiliation(s)
- Sara Centeno-Leija
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apartado postal 510-3, 62210, Cuernavaca, MOR, Mexico
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25
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Ji XJ, Xia ZF, Fu NH, Nie ZK, Shen MQ, Tian QQ, Huang H. Cofactor engineering through heterologous expression of an NADH oxidase and its impact on metabolic flux redistribution in Klebsiella pneumoniae. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:7. [PMID: 23351660 PMCID: PMC3563507 DOI: 10.1186/1754-6834-6-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 01/23/2013] [Indexed: 05/10/2023]
Abstract
BACKGROUND Acetoin is an important bio-based platform chemical. However, it is usually existed as a minor byproduct of 2,3-butanediol fermentation in bacteria. RESULTS The present study reports introducing an exogenous NAD+ regeneration sysytem into a 2,3-butanediol producing strain Klebsiella pneumoniae to increse the accumulation of acetoin. Batch fermentation suggested that heterologous expression of the NADH oxidase in K. pneumoniae resulted in large decreases in the intracellular NADH concentration (1.4 fold) and NADH/NAD+ ratio (2.0 fold). Metabolic flux analysis revealed that fluxes to acetoin and acetic acid were enhanced, whereas, production of lactic acid and ethanol were decreased, with the accumualation of 2,3-butanediol nearly unaltered. By fed-batch culture of the recombinant, the highest reported acetoin production level (25.9 g/L) by Klebsiella species was obtained. CONCLUSIONS The present study indicates that microbial production of acetoin could be improved by decreasing the intracellular NADH/NAD+ ratio in K. pneumoniae. It demonstrated that the cofactor engineering method, which is by manipulating the level of intracellular cofactors to redirect cellular metabolism, could be employed to achieve a high efficiency of producing the NAD+-dependent microbial metabolite.
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Affiliation(s)
- Xiao-Jun Ji
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, No. 5 Xinmofan Road, Nanjing, 210009, People’s Republic of China
| | - Zhi-Fang Xia
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, No. 5 Xinmofan Road, Nanjing, 210009, People’s Republic of China
| | - Ning-Hua Fu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, No. 5 Xinmofan Road, Nanjing, 210009, People’s Republic of China
| | - Zhi-Kui Nie
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, No. 5 Xinmofan Road, Nanjing, 210009, People’s Republic of China
| | - Meng-Qiu Shen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, No. 5 Xinmofan Road, Nanjing, 210009, People’s Republic of China
| | - Qian-Qian Tian
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, No. 5 Xinmofan Road, Nanjing, 210009, People’s Republic of China
| | - He Huang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, No. 5 Xinmofan Road, Nanjing, 210009, People’s Republic of China
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Kang A, Tan MH, Ling H, Chang MW. Systems-level characterization and engineering of oxidative stress tolerance in Escherichia coli under anaerobic conditions. MOLECULAR BIOSYSTEMS 2012; 9:285-95. [PMID: 23224080 DOI: 10.1039/c2mb25259g] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Despite many prior studies on microbial response to oxidative stress, our understanding of microbial tolerance against oxidative stress is currently limited to aerobic conditions, and few engineering strategies have been devised to resolve toxicity issues of oxidative stress under anaerobic conditions. Since biological processes, such as anaerobic fermentation, are frequently hampered by toxicity arising from oxidative stress, increased microbial tolerance against oxidative stress improves the overall productivity and yield of biological processes. Here, we show a systems-level analysis of oxidative stress response of Escherichia coli under anaerobic conditions, and present an engineering strategy to improve oxidative stress tolerance. First, we identified essential cellular mechanisms and regulatory factors underlying oxidative stress response under anaerobic conditions using a transcriptome analysis. In particular, we showed that nitrogen metabolisms and respiratory pathways were differentially regulated in response to oxidative stress under anaerobic and aerobic conditions. Further, we demonstrated that among transcription factors with oxidative stress-derived perturbed activity, the deletion of arcA and arcB significantly improved oxidative stress tolerance under aerobic and anaerobic conditions, respectively, whereas fnr was identified as an essential transcription factor for oxidative stress tolerance under anaerobic conditions. Moreover, we showed that oxidative stress increased the intracellular NADH : NAD(+) ratio under aerobic and anaerobic conditions, which indicates a regulatory role of NADH in oxidative stress tolerance. Based on this finding, we demonstrated that increased NADH availability through fdh1 overexpression significantly improved oxidative stress tolerance under aerobic conditions. Our results here provide novel insight into better understanding of cellular mechanisms underlying oxidative stress tolerance under anaerobic conditions, and into developing strain engineering strategies to enhance microbial tolerance against oxidative stress towards improved biological processes.
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Affiliation(s)
- Aram Kang
- Division of Chemical and Biomolecular Engineering, School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore 637459, Singapore
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Determining the extremes of the cellular NAD(H) level by using an Escherichia coli NAD(+)-auxotrophic mutant. Appl Environ Microbiol 2011; 77:6133-40. [PMID: 21742902 DOI: 10.1128/aem.00630-11] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
NAD (NAD(+)) and its reduced form (NADH) are omnipresent cofactors in biological systems. However, it is difficult to determine the extremes of the cellular NAD(H) level in live cells because the NAD(+) level is tightly controlled by a biosynthesis regulation mechanism. Here, we developed a strategy to determine the extreme NAD(H) levels in Escherichia coli cells that were genetically engineered to be NAD(+) auxotrophic. First, we expressed the ntt4 gene encoding the NAD(H) transporter in the E. coli mutant YJE001, which had a deletion of the nadC gene responsible for NAD(+) de novo biosynthesis, and we showed NTT4 conferred on the mutant strain better growth in the presence of exogenous NAD(+). We then constructed the NAD(+)-auxotrophic mutant YJE003 by disrupting the essential gene nadE, which is responsible for the last step of NAD(+) biosynthesis in cells harboring the ntt4 gene. The minimal NAD(+) level was determined in M9 medium in proliferating YJE003 cells that were preloaded with NAD(+), while the maximal NAD(H) level was determined by exposing the cells to high concentrations of exogenous NAD(H). Compared with supplementation of NADH, cells grew faster and had a higher intracellular NAD(H) level when NAD(+) was fed. The intracellular NAD(H) level increased with the increase of exogenous NAD(+) concentration, until it reached a plateau. Thus, a minimal NAD(H) level of 0.039 mM and a maximum of 8.49 mM were determined, which were 0.044× and 9.6× those of wild-type cells, respectively. Finally, the potential application of this strategy in biotechnology is briefly discussed.
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28
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Lin Y, Zhu N, Yu P, Su L, Mao L. Physiologically relevant online electrochemical method for continuous and simultaneous monitoring of striatum glucose and lactate following global cerebral ischemia/reperfusion. Anal Chem 2010; 81:2067-74. [PMID: 19281258 DOI: 10.1021/ac801946s] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This study demonstrates a new electroanalytical method with a high physiological relevance for simultaneous online monitoring of glucose and lactate in the striatum of the rat brain following global cerebral ischemia/reperfusion. The online analytical method is based on the efficient integration of in vivo microdialysis sampling with an online selective electrochemical detection with the electrochemical biosensors with dehydrogenases, i.e., glucose and lactate dehydrogenases, as recognition elements. The dehydrogenase-based electrochemical biosensors are developed onto the dual split-disk plastic carbon film (SPCF) electrodes with methylene green (MG) adsorbed onto single-walled carbon nanotubes (SWNTs) as the electrocatalyst for the oxidation of dihydronicotiamide adenine dinucleotide (NADH) at a low potential of 0.0 V (vs Ag/AgCl). Artificial cerebrospinal fluid (aCSF) containing NAD(+) is externally perfused from a second pump and online mixed with the brain microdialysates to minimize the variation of pH that occurred following the cerebral ischemia/reperfusion and to supply NAD(+) cofactor and O(2) for the enzymatic reactions of dehydrogenases and ascorbate oxidase, respectively. As a result, the developed online electroanalytical method exhibits a high selectivity against the electrochemically active species endogenously existing in the cerebral systems and a high tolerance against the variation of pH and O(2) following cerebral ischemia/reperfusion. This property, along with the good linearity and a high stability toward glucose and lactate as well as little cross-talk between two biosensors, substantially makes this method possible for the continuous, simultaneous, and online monitoring of glucose and lactate in the rat brain following global cerebral ischemia/reperfusion. This study establishes a new and effective platform for the investigation of the energy metabolism in physiological and pathological processes.
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Affiliation(s)
- Yuqing Lin
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, The Chinese Academy of Sciences, Beijing 100190, China
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Regulation of the expression of genes involved in NAD de novo biosynthesis in Corynebacterium glutamicum. Appl Environ Microbiol 2010; 76:5488-95. [PMID: 20601509 DOI: 10.1128/aem.00906-10] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Three genes, nadA, nadB, and nadC, involved in NAD de novo biosynthesis are broadly conserved in the genomes of numerous bacterial species. In the genome of Corynebacterium glutamicum, nadA and nadC but not nadB are annotated. The nadA and nadC genes are located in a gene cluster containing two other genes, designated ndnR and nadS herein. ndnR encodes a member of the Nudix-related transcriptional regulator (NrtR) family. nadS encodes a homologue of cysteine desulfurase involved in Fe-S cluster assembly. The gene cluster ndnR-nadA-nadC-nadS is genetically characterized herein. Mutant strains deficient in nadA, nadC, or nadS required exogenous nicotinate for growth, and the nicotinate auxotrophy was complemented by introduction of the corresponding gene in trans, indicating that each of these genes is essential for growth in the absence of an exogenous source of NAD biosynthesis. The results of reverse transcriptase PCR analyses and ndnR promoter-lacZ expression analyses revealed that the expression of ndnR, nadA, nadC, and nadS genes was markedly and coordinately repressed by nicotinate. The expression of these genes was enhanced by the disruption of ndnR, resulting in the loss of the nicotinate-responsive regulation of gene expression. These results suggest that NdnR acts as a transcriptional repressor of NAD de novo biosynthesis genes and plays an essential role in the regulation of the response to nicotinate.
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Liu H, Gao J, Xue M, Zhu N, Zhang M, Cao T. Processing of graphene for electrochemical application: noncovalently functionalize graphene sheets with water-soluble electroactive methylene green. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:12006-10. [PMID: 19764798 DOI: 10.1021/la9029613] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
To explore graphene applications in various fields, the processability of graphene becomes one of the important key issues, particularly with the increasing availability of synthetic graphene approaches, because the direct dispersion of hydrophobic graphene in water is prone to forming agglomerates irreversibly. Here, a facile method is proposed to increase the dispersity of graphene through noncovalent functionalization graphene with a water-soluble aromatic electroactive dye, methylene green (MG), during chemical reduction of graphene oxide (GO) with hydrazine. Atomic force microscopic and UV-vis spectrophotometric results demonstrate that chemically reduced graphene (CRG) functionalized with MG (CRG-MG) is well-dispersed into water through the coulomb repulsion between MG-adsorbed CRG sheets. The electrochemical properties of the formed CRG-MG are investigated, and the results demonstrate that CRG-MG confined onto a glassy carbon (GC) electrode has lower charge-transfer resistance and better electrocatalytic activity toward the oxidation of NADH, in relation to pristine CRG (i.e., without MG functionalization). This method not only offers a facile approach to dispersing graphene in water but also is envisaged to be useful for investigations on graphene-based electrochemistry.
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Affiliation(s)
- Huan Liu
- Department of Chemistry, Renmin University of China, Beijing 100872, PR China
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Zhai RG, Rizzi M, Garavaglia S. Nicotinamide/nicotinic acid mononucleotide adenylyltransferase, new insights into an ancient enzyme. Cell Mol Life Sci 2009; 66:2805-18. [PMID: 19448972 PMCID: PMC11115848 DOI: 10.1007/s00018-009-0047-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2009] [Revised: 04/16/2009] [Accepted: 04/28/2009] [Indexed: 12/14/2022]
Abstract
Nicotinamide/nicotinic acid mononucleotide adenylyltransferase (NMNAT) has long been known as the master enzyme in NAD biosynthesis in living organisms. A burst of investigations on NMNAT, going beyond enzymology, have paralleled increasing discoveries of key roles played by NAD homeostasis in a number or patho-physiological conditions. The availability of in-depth kinetics and structural enzymology analyses carried out on NMNATs from different organisms offer a powerful tool for uncovering fascinating evolutionary relationships. On the other hand, additional functions featuring NMNAT have emerged from investigations aimed at unraveling the molecular mechanisms responsible for complex biological phenomena such as neurodegeneration. NMNAT appears to be a multifunctional protein that sits both at the core of central metabolism and at a crossroads of multiple cellular processes. The resultant wealth of biochemical data has built a robust framework upon which design of NMNAT activators, inhibitors or enzyme variants of potential medical interest can be based.
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Affiliation(s)
- Rong Grace Zhai
- Department of Molecular and Cellular Pharmacology, Neuroscience Center, Miller School of Medicine, University of Miami, Miami, FL 33136 USA
| | - Menico Rizzi
- DiSCAFF, University of Piemonte Orientale “A. Avogadro”, Via Bovio, 6, 28100 Novara, Italy
| | - Silvia Garavaglia
- DiSCAFF, University of Piemonte Orientale “A. Avogadro”, Via Bovio, 6, 28100 Novara, Italy
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Hashimoto T, Horikawa M, Nomura T, Sakamoto K. Nicotinamide adenine dinucleotide extends the lifespan of Caenorhabditis elegans mediated by sir-2.1 and daf-16. Biogerontology 2009; 11:31-43. [PMID: 19370397 DOI: 10.1007/s10522-009-9225-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2009] [Accepted: 04/02/2009] [Indexed: 10/20/2022]
Abstract
It is well understood that sir2 (sirtuin), an NAD-dependent deacetylase, is essential for the extension of lifespan under caloric restriction. However, the mechanism underlying activation of sir2 is unclear. Life extension through caloric restriction requires the sir2 ortholog sir-2.1 in nematodes but occurs independently of the forkhead-type transcription factor DAF-16. We aimed here to elucidate the correlation between life extension in nematodes and NAD-dependent activation of sirtuin by analyzing the relationship between NAD and DAF-16. Lifespan was extended when Caenorhabditis elegans were bred using medium containing NAD. An RNA interference experiment revealed that life extension by NAD was sir-2.1 dependent. However, life extension by NAD did not occur in daf-16-RNAi nematodes, suggesting that NAD-dependent longevity requires daf-16. This result suggested that different signaling pathways are involved in life extension resulting from caloric restriction and from NAD addition. Expression of sod-3, a target gene of daf-16, and increased oxidative-stress resistance and adiposity were observed in response to NAD addition, indicating that NAD activated daf-16 in each phenotype. These results suggest that NAD affected lifespan through the activation of SIR-2.1 and DAF-16 along a signaling pathway, namely insulin-like signalling pathway (at least parts of it), different from that associated with caloric restriction.
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Affiliation(s)
- Teppei Hashimoto
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki, Japan
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Zhang Y, Huang Z, Du C, Li Y, Cao Z. Introduction of an NADH regeneration system into Klebsiella oxytoca leads to an enhanced oxidative and reductive metabolism of glycerol. Metab Eng 2008; 11:101-6. [PMID: 19100856 DOI: 10.1016/j.ymben.2008.11.001] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2008] [Revised: 09/09/2008] [Accepted: 11/03/2008] [Indexed: 10/21/2022]
Abstract
Redox cofactors play crucial roles in the metabolic and regulatory network of living organisms. We reported here the effect of introducing a heterogeneous NADH regeneration system into Klebsiella oxytoca on cell growth and glycerol metabolism. Expression of fdh gene from Candida boidinii in K. oxytoca resulted in higher intracellular concentrations of both NADH and NAD(+) during the fermentation metaphase, with the ratio of NADH to NAD(+) unaltered and cell growth unaffected, interestingly different from that in engineered Escherichia coli, Lactococcus lactis, and others. Metabolic flux analysis revealed that fluxes to 1,3-propanediol, ethanol, and lactate were all increased, suggesting both the oxidative and reductive metabolisms of glycerol were enhanced. It demonstrates that in certain microbial system NADH availability can be increased with NADH to NAD(+) ratio unaltered, providing a new strategy to improve the metabolic flux in those microorganisms where glycolysis is not the only central metabolic pathways.
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Affiliation(s)
- Yanping Zhang
- Department of Chemical Engineering, Tsinghua University, Beijing, China
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35
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Huang N, Sorci L, Zhang X, Brautigam CA, Li X, Raffaelli N, Magni G, Grishin NV, Osterman AL, Zhang H. Bifunctional NMN adenylyltransferase/ADP-ribose pyrophosphatase: structure and function in bacterial NAD metabolism. Structure 2008; 16:196-209. [PMID: 18275811 DOI: 10.1016/j.str.2007.11.017] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2007] [Revised: 10/30/2007] [Accepted: 11/18/2007] [Indexed: 11/28/2022]
Abstract
Bacterial NadM-Nudix is a bifunctional enzyme containing a nicotinamide mononucleotide (NMN) adenylyltransferase and an ADP-ribose (ADPR) pyrophosphatase domain. While most members of this enzyme family, such as that from a model cyanobacterium Synechocystis sp., are involved primarily in nicotinamide adenine dinucleotide (NAD) salvage/recycling pathways, its close homolog in a category-A biodefense pathogen, Francisella tularensis, likely plays a central role in a recently discovered novel pathway of NAD de novo synthesis. The crystal structures of NadM-Nudix from both species, including their complexes with various ligands and catalytic metal ions, revealed detailed configurations of the substrate binding and catalytic sites in both domains. The structure of the N-terminal NadM domain may be exploited for designing new antitularemia therapeutics. The ADPR binding site in the C-terminal Nudix domain is substantially different from that of Escherichia coli ADPR pyrophosphatase, and is more similar to human NUDT9. The latter observation provided new insights into the ligand binding mode of ADPR-gated Ca2+ channel TRPM2.
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Affiliation(s)
- Nian Huang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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Yang H, Yang T, Baur JA, Perez E, Matsui T, Carmona JJ, Lamming DW, Souza-Pinto NC, Bohr VA, Rosenzweig A, de Cabo R, Sauve AA, Sinclair DA. Nutrient-sensitive mitochondrial NAD+ levels dictate cell survival. Cell 2007; 130:1095-107. [PMID: 17889652 PMCID: PMC3366687 DOI: 10.1016/j.cell.2007.07.035] [Citation(s) in RCA: 770] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2006] [Revised: 02/06/2007] [Accepted: 07/20/2007] [Indexed: 12/17/2022]
Abstract
A major cause of cell death caused by genotoxic stress is thought to be due to the depletion of NAD(+) from the nucleus and the cytoplasm. Here we show that NAD(+) levels in mitochondria remain at physiological levels following genotoxic stress and can maintain cell viability even when nuclear and cytoplasmic pools of NAD(+) are depleted. Rodents fasted for 48 hr show increased levels of the NAD(+) biosynthetic enzyme Nampt and a concomitant increase in mitochondrial NAD(+). Increased Nampt provides protection against cell death and requires an intact mitochondrial NAD(+) salvage pathway as well as the mitochondrial NAD(+)-dependent deacetylases SIRT3 and SIRT4. We discuss the relevance of these findings to understanding how nutrition modulates physiology and to the evolution of apoptosis.
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Affiliation(s)
- Hongying Yang
- Department of Pathology, Paul F. Glenn Laboratories, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Tianle Yang
- Department of Pharmacology, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10021, USA
| | - Joseph A. Baur
- Department of Pathology, Paul F. Glenn Laboratories, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Evelyn Perez
- Laboratory of Experimental Gerontology, National Institute on Aging, Institutes of Health, 5600 Nathan Shock Drive, Baltimore, MD, 21224, USA
| | - Takashi Matsui
- Cardiovascular Division, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA
| | - Juan J. Carmona
- Department of Pathology, Paul F. Glenn Laboratories, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Dudley W. Lamming
- Department of Pathology, Paul F. Glenn Laboratories, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Nadja C. Souza-Pinto
- Laboratory of Molecular Gerontology, National Institute on Aging, Institutes of Health, 5600 Nathan Shock Drive, Baltimore, MD, 21224, USA
| | - Vilhelm A. Bohr
- Laboratory of Molecular Gerontology, National Institute on Aging, Institutes of Health, 5600 Nathan Shock Drive, Baltimore, MD, 21224, USA
| | - Anthony Rosenzweig
- Cardiovascular Division, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA
| | - Rafael de Cabo
- Laboratory of Experimental Gerontology, National Institute on Aging, Institutes of Health, 5600 Nathan Shock Drive, Baltimore, MD, 21224, USA
| | - Anthony A. Sauve
- Department of Pharmacology, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10021, USA
| | - David A. Sinclair
- Department of Pathology, Paul F. Glenn Laboratories, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
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37
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Abstract
A major cause of cell death caused by genotoxic stress is thought to be due to the depletion of NAD(+) from the nucleus and the cytoplasm. Here we show that NAD(+) levels in mitochondria remain at physiological levels following genotoxic stress and can maintain cell viability even when nuclear and cytoplasmic pools of NAD(+) are depleted. Rodents fasted for 48 hr show increased levels of the NAD(+) biosynthetic enzyme Nampt and a concomitant increase in mitochondrial NAD(+). Increased Nampt provides protection against cell death and requires an intact mitochondrial NAD(+) salvage pathway as well as the mitochondrial NAD(+)-dependent deacetylases SIRT3 and SIRT4. We discuss the relevance of these findings to understanding how nutrition modulates physiology and to the evolution of apoptosis.
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Heuser F, Schroer K, Lütz S, Bringer-Meyer S, Sahm H. Enhancement of the NAD(P)(H) Pool inEscherichia coli for Biotransformation. Eng Life Sci 2007. [DOI: 10.1002/elsc.200720203] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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39
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Gerlach G, Reidl J. NAD+ utilization in Pasteurellaceae: simplification of a complex pathway. J Bacteriol 2006; 188:6719-27. [PMID: 16980474 PMCID: PMC1595515 DOI: 10.1128/jb.00432-06] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- Gabriele Gerlach
- Institut für Hygiene und Mikrobiologie, Universität Würzburg, Josef Schneider Str. 2, E1, 97080 Würzburg, Germany
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40
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Liu L, Li Y, Shi Z, Du G, Chen J. Enhancement of pyruvate productivity in Torulopsis glabrata: Increase of NAD+ availability. J Biotechnol 2006; 126:173-85. [PMID: 16713000 DOI: 10.1016/j.jbiotec.2006.04.014] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2006] [Revised: 03/06/2006] [Accepted: 04/05/2006] [Indexed: 10/24/2022]
Abstract
This study aimed at increasing the pyruvate productivity from a multi-vitamin auxotrophic yeast Torulopsis glabrata, by increasing the availability of NAD+. We examined two strategies for increasing availability of NAD+. To supplement nicotinic acid (NA), the precursor of NAD+; and to increase the activity of alcohol dehydrogenase integrating with addition acetaldehyde as exterior electron acceptor. The addition of 8 mg l(-1) NA to the fermentation medium resulted in a significant increase in the glucose consumption rate (48.4%) and the pyruvate concentration (29%). An ethanol-utilizing mutant WSH-13 was screened and selected after nitrosoguanidine mutagenesis of the parent strain T. glabrata CCTCC M202019. Compared with the parent strain, the alcohol dehydrogenase activity of the mutant WSH-13 increased about 110% and the mutant could utilize ethanol as the sole carbon source for growth (1.8 g l(-1) dry cell weight). When growing with glucose, the addition of 4 mg l(-1) acetaldehyde to the mutant WSH-13 culture broth led to a significant increase in the glucose consumption rate (26.3%) and pyruvate production (22.5%), but the ratio of NADH/NAD+ decreased to 0.22. Acetaldehyde did not affect the glucose and energy metabolism at high dissolved oxygen (DO) concentration. However, at lower DO concentration (20%), maintaining the acetaldehyde concentration in the mutant culture broth at 4 mg l(-1) caused an increased NAD+ concentration but a decreased NADH concentration. As a consequence, the pyruvate production rate, the pyruvate yield on glucose and the pyruvate concentration were 68, 44 and 45% higher, respectively, than the corresponding values of the control (without acetaldehyde). The strategy for increasing the glycolytic flux and the pyruvate productivity in T. glabrata by increasing the availability of NAD+ may provide an alternative approach to enhance the metabolites productivity in yeast.
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Affiliation(s)
- Liming Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Southern Yangtze University, 170 Huihe Road, Wuxi 214036, PR China
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41
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Wang H, Wang J, Xu J, Cai RX. Study on the influence of potassium iodate on the metabolism of Escherichia coli by intrinsic fluorescence. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2006; 64:316-20. [PMID: 16384739 DOI: 10.1016/j.saa.2005.07.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2005] [Revised: 07/07/2005] [Accepted: 07/11/2005] [Indexed: 05/05/2023]
Abstract
Intrinsic fluorescence, in particular, has the advantage over the extrinsic fluorescence of an unperturbed environment during investigation, especially in complex systems such as biological cells and tissues. Potassium iodate may restrain bacteria growth as well as it acts as an additive in the salt. The influence of potassium iodate (KIO3) on the metabolism of Escherichia coli (E. coli) is investigated for the first time with the intrinsic fluorescence of tryptophan (Trp) and reduced nicotinamide adenine dinucleotide (NADH). We found that potassium iodate may restrain the growth of E. coli as a bacteriostatic agent. When the potassium iodate concentration was below 1.32 mmol/L, the intensity of tryptophan fluorescence decreased linearly whereas the NADH fluorescence did not change. When the KIO3 concentration was over 1.32 mmol/L, the fluorescence of tryptophan and NADH increased a little and their fluorescence intensity decreased when KIO3 was over 6.67 mmol/L. And the bacteria could not continue growing if the KIO3 was over 6.67 mmol/L.We could conclude that potassium iodate has great inhibiting effects on the growth of E. coli through the pathway of protein synthesis and respiratory chain.
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Affiliation(s)
- Hongmei Wang
- Department of Chemistry, Wuhan University, Wuhan 430072, China
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42
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Flores S, Flores N, de Anda R, González A, Escalante A, Sigala JC, Gosset G, Bolívar F. Nutrient-scavenging stress response in an Escherichia coli strain lacking the phosphoenolpyruvate: carbohydrate phosphotransferase system, as explored by gene expression profile analysis. J Mol Microbiol Biotechnol 2006; 10:51-63. [PMID: 16491026 DOI: 10.1159/000090348] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The physiological role of the phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) has been studied in Escherichia coli. It has been shown that it directly or indirectly regulates the activity of most catabolic genes involved in carbohydrate transport. Accordingly, strains lacking PTS have pleiotropic phenotypes and are impaired in their capacity to grow on glucose and other PTS sugars. We have previously reported the characterization of a mutant harboring a pts operon deletion (PB11) which, as expected, showed a severe reduction of its growth capacity when incubated on glucose as carbon source, as compared to that of the isogenic wild-type strain. These observations corroborate that PTS is the main determinant of the capacity to grow on glucose and confirm the existence of other systems that allow glucose utilization although at a reduced level. To explore the physiological state and the metabolic pathways involved in glucose utilization in a pts(-) background, we analyzed the global transcriptional response of the PB11 mutant when growing in minimal medium with glucose as carbon source. Genome-wide transcriptional analysis using microarrays revealed that, under this condition, expression of several genes related to carbon transport and metabolism was upregulated, as well as that of genes encoding transporters for certain nucleotides, nitrogen, phosphorus and sulfur sources. In addition, upregulation of rpoS and several genes transcribed by this sigma subunit was detected. These results indicate that the reduced capacity of glucose utilization present in the PB11 strain induces a general nutrient-scavenging response and this behavior is not dependent on a functional PTS. This condition is responsible of the utilization of secondary carbon sources in the presence of glucose.
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Affiliation(s)
- Salvador Flores
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
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43
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Gerasimova AV, Gelfand MS. Evolution of the NadR regulon in Enterobacteriaceae. J Bioinform Comput Biol 2005; 3:1007-19. [PMID: 16078372 DOI: 10.1142/s0219720005001387] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2005] [Revised: 02/18/2005] [Accepted: 02/24/2005] [Indexed: 12/23/2022]
Abstract
The NAD biosynthetic pathway and NAD transformations in E. coli and S. typhi are well characterized. Using comparative genomics methods we describe the NadR regulon in other Enterobacteriaceae, identity new candidate regulon members and demonstrate that even a very simple regulon covering an essential methabolic pathway could be different in closely related genomes.
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Affiliation(s)
- Anna V Gerasimova
- Laboratory of Bioinformatics, State Scientific Center GOSNIIGenetika, 1-iy Dorozhny proezd 1, Moscow, 113545, Russia.
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44
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Merdanovic M, Sauer E, Reidl J. Coupling of NAD+ biosynthesis and nicotinamide ribosyl transport: characterization of NadR ribonucleotide kinase mutants of Haemophilus influenzae. J Bacteriol 2005; 187:4410-20. [PMID: 15968050 PMCID: PMC1151767 DOI: 10.1128/jb.187.13.4410-4420.2005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Previously, we characterized a pathway necessary for the processing of NAD+ and for uptake of nicotinamide riboside (NR) in Haemophilus influenzae. Here we report on the role of NadR, which is essential for NAD+ utilization in this organism. Different NadR variants with a deleted ribonucleotide kinase domain or with a single amino acid change were characterized in vitro and in vivo with respect to cell viability, ribonucleotide kinase activity, and NR transport. The ribonucleotide kinase mutants were viable only in a nadV+ (nicotinamide phosphoribosyltransferase) background, indicating that the ribonucleotide kinase domain is essential for cell viability in H. influenzae. Mutations located in the Walker A and B motifs and the LID region resulted in deficiencies in both NR phosphorylation and NR uptake. The ribonucleotide kinase function of NadR was found to be feedback controlled by NAD+ under in vitro conditions and by NAD+ utilization in vivo. Taken together, our data demonstrate that the NR phosphorylation step is essential for both NR uptake across the inner membrane and NAD+ synthesis and is also involved in controlling the NAD+ biosynthesis rate.
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Affiliation(s)
- Melisa Merdanovic
- Institut für Hygiene und Mikrobiologie, Universität Würzburg, Josef Schneider Str. 2, E1, 97080 Würzburg, Germany
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45
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Grose JH, Bergthorsson U, Xu Y, Sterneckert J, Khodaverdian B, Roth JR. Assimilation of nicotinamide mononucleotide requires periplasmic AphA phosphatase in Salmonella enterica. J Bacteriol 2005; 187:4521-30. [PMID: 15968063 PMCID: PMC1151756 DOI: 10.1128/jb.187.13.4521-4530.2005] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Salmonella enterica can obtain pyridine from exogenous nicotinamide mononucleotide (NMN) by three routes. In route 1, nicotinamide is removed from NMN in the periplasm and enters the cell as the free base. In route 2, described here, phosphate is removed from NMN in the periplasm by acid phosphatase (AphA), and the produced nicotinamide ribonucleoside (NmR) enters the cell via the PnuC transporter. Internal NmR is then converted back to NMN by the NmR kinase activity of NadR. Route 3 is seen only in pnuC* transporter mutants, which import NMN intact and can therefore grow on lower levels of NMN. Internal NMN produced by either route 2 or route 3 is deamidated to nicotinic acid mononucleotide and converted to NAD by the biosynthetic enzymes NadD and NadE.
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Affiliation(s)
- Julianne H Grose
- Department of Biology, University of Utah, Salt Lake City, Utah 84112, USA
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46
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Marek-Kozaczuk M, Rogalski J, Skorupska A. The nadA gene of Pseudomonas fluorescens PGPR strain 267.1. Curr Microbiol 2005; 51:122-6. [PMID: 16049659 DOI: 10.1007/s00284-005-4553-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2005] [Accepted: 03/13/2005] [Indexed: 10/25/2022]
Abstract
An insertion mutant of Pseudomonas fluorescens PGPR strain 267.1 was found to be auxotrophic for niacin (nicotinic acid) and could not synthesize quinolinic acid. The Tn5 interrupted gene was cloned and sequenced. The cloned fragment contained an open reading frame, nadA, capable of encoding a 359-amino-acid protein (39.0 kDa) with substantial identity to various bacterial quinolinate synthetases. The nadA gene complemented quinolinic acid synthesis deficiency and niacin auxotrophy of the P. fluorescens 106 P nadA mutant.
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Affiliation(s)
- Monika Marek-Kozaczuk
- Department of General Microbiology, University of Maria Curie-Skłodowska, Akademicka 19 st, Lublin 20-033, Poland
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47
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Bergthorsson U, Roth JR. Natural isolates of Salmonella enterica serovar Dublin carry a single nadA missense mutation. J Bacteriol 2005; 187:400-3. [PMID: 15601727 PMCID: PMC538839 DOI: 10.1128/jb.187.1.400-403.2005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nicotinic acid is required by most isolates of Salmonella enterica (serovar Dublin), a pathogen of cattle. A single nadA missense mutation causes the nutritional requirement of all serovar Dublin isolates tested. Models for persistence of this allele are tested and discussed.
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48
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Bitterman KJ, Medvedik O, Sinclair DA. Longevity regulation in Saccharomyces cerevisiae: linking metabolism, genome stability, and heterochromatin. Microbiol Mol Biol Rev 2003; 67:376-99, table of contents. [PMID: 12966141 PMCID: PMC193872 DOI: 10.1128/mmbr.67.3.376-399.2003] [Citation(s) in RCA: 165] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
When it was first proposed that the budding yeast Saccharomyces cerevisiae might serve as a model for human aging in 1959, the suggestion was met with considerable skepticism. Although yeast had proved a valuable model for understanding basic cellular processes in humans, it was difficult to accept that such a simple unicellular organism could provide information about human aging, one of the most complex of biological phenomena. While it is true that causes of aging are likely to be multifarious, there is a growing realization that all eukaryotes possess surprisingly conserved longevity pathways that govern the pace of aging. This realization has come, in part, from studies of S. cerevisiae, which has emerged as a highly informative and respected model for the study of life span regulation. Genomic instability has been identified as a major cause of aging, and over a dozen longevity genes have now been identified that suppress it. Here we present the key discoveries in the yeast-aging field, regarding both the replicative and chronological measures of life span in this organism. We discuss the implications of these findings not only for mammalian longevity but also for other key aspects of cell biology, including cell survival, the relationship between chromatin structure and genome stability, and the effect of internal and external environments on cellular defense pathways. We focus on the regulation of replicative life span, since recent findings have shed considerable light on the mechanisms controlling this process. We also present the specific methods used to study aging and longevity regulation in S. cerevisiae.
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Affiliation(s)
- Kevin J Bitterman
- Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
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49
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Kurnasov OV, Polanuyer BM, Ananta S, Sloutsky R, Tam A, Gerdes SY, Osterman AL. Ribosylnicotinamide kinase domain of NadR protein: identification and implications in NAD biosynthesis. J Bacteriol 2002; 184:6906-17. [PMID: 12446641 PMCID: PMC135457 DOI: 10.1128/jb.184.24.6906-6917.2002] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
NAD is an indispensable redox cofactor in all organisms. Most of the genes required for NAD biosynthesis in various species are known. Ribosylnicotinamide kinase (RNK) was among the few unknown (missing) genes involved with NAD salvage and recycling pathways. Using a comparative genome analysis involving reconstruction of NAD metabolism from genomic data, we predicted and experimentally verified that bacterial RNK is encoded within the 3' region of the nadR gene. Based on these results and previous data, the full-size multifunctional NadR protein (as in Escherichia coli) is composed of (i) an N-terminal DNA-binding domain involved in the transcriptional regulation of NAD biosynthesis, (ii) a central nicotinamide mononucleotide adenylyltransferase (NMNAT) domain, and (iii) a C-terminal RNK domain. The RNK and NMNAT enzymatic activities of recombinant NadR proteins from Salmonella enterica serovar Typhimurium and Haemophilus influenzae were quantitatively characterized. We propose a model for the complete salvage pathway from exogenous N-ribosylnicotinamide to NAD which involves the concerted action of the PnuC transporter and NRK, followed by the NMNAT activity of the NadR protein. Both the pnuC and nadR genes were proven to be essential for the growth and survival of H. influenzae, thus implicating them as potential narrow-spectrum drug targets.
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50
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Bitterman KJ, Anderson RM, Cohen HY, Latorre-Esteves M, Sinclair DA. Inhibition of silencing and accelerated aging by nicotinamide, a putative negative regulator of yeast sir2 and human SIRT1. J Biol Chem 2002; 277:45099-107. [PMID: 12297502 DOI: 10.1074/jbc.m205670200] [Citation(s) in RCA: 762] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Saccharomyces cerevisiae Sir2 protein is an NAD(+)-dependent histone deacetylase that plays a critical role in transcriptional silencing, genome stability, and longevity. A human homologue of Sir2, SIRT1, regulates the activity of the p53 tumor suppressor and inhibits apoptosis. The Sir2 deacetylation reaction generates two products: O-acetyl-ADP-ribose and nicotinamide, a precursor of nicotinic acid and a form of niacin/vitamin B(3). We show here that nicotinamide strongly inhibits yeast silencing, increases rDNA recombination, and shortens replicative life span to that of a sir2 mutant. Nicotinamide abolishes silencing and leads to an eventual delocalization of Sir2 even in G(1)-arrested cells, demonstrating that silent heterochromatin requires continual Sir2 activity. We show that physiological concentrations of nicotinamide noncompetitively inhibit both Sir2 and SIRT1 in vitro. The degree of inhibition by nicotinamide (IC(50) < 50 microm) is equal to or better than the most effective known synthetic inhibitors of this class of proteins. We propose a model whereby nicotinamide inhibits deacetylation by binding to a conserved pocket adjacent to NAD(+), thereby blocking NAD(+) hydrolysis. We discuss the possibility that nicotinamide is a physiologically relevant regulator of Sir2 enzymes.
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Affiliation(s)
- Kevin J Bitterman
- Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
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