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Moon JH, Nam S, Jeung K, Noh MH, Jung GY. Biosensor-Assisted Engineering for Diverse Microbial Cellular Physiologies. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:18321-18334. [PMID: 39107094 DOI: 10.1021/acs.jafc.4c04619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/09/2024]
Abstract
Recent advancements in biosensor technology have revolutionized the field of microbial engineering, enabling efficient and precise optimization of strains for the production of valuable chemicals. This review comprehensively explores the innovative integration of biosensors to enhance microbial cell factories, with a particular emphasis on the crucial role of high-throughput biosensor-assisted screening. Biosensor-assisted approaches have enabled the identification of novel transporters, the elucidation of underlying transport mechanisms, and the fine-tuning of metabolic pathways for enhanced production. Furthermore, this review illustrates the utilization of biosensors for manipulating cellular behaviors, including interactions with environmental factors, and the reduction of nongenetic cell-to-cell variations. This review highlights the indispensable role of biosensors in advancing the field of microbial engineering through the modulation and exploitation of diverse cellular physiological processes.
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Affiliation(s)
- Jo Hyun Moon
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Sunghyun Nam
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Kumyoung Jeung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Myung Hyun Noh
- Research Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), 406-30, Jongga-ro, Jung-gu, Ulsan 44429, Korea
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
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Wang P, Ma Y, Li J, Su J, Chi J, Zhu X, Zhu X, Zhang C, Bi C, Zhang X. Exploring the De Novo NMN Biosynthesis as an Alternative Pathway to Enhance NMN Production. ACS Synth Biol 2024; 13:2425-2435. [PMID: 39023319 DOI: 10.1021/acssynbio.4c00115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Nicotinamide mononucleotide (NMN) serves as a precursor for NAD+ synthesis and has been shown to have positive effects on the human body. Previous research has predominantly focused on the nicotinamide phosphoribosyltransferase-mediated route (NadV-mediated route) for NMN biosynthesis. In this study, we have explored the de novo NMN biosynthesis route as an alternative pathway to enhance NMN production. Initially, we systematically engineered Escherichia coli to enhance its capacity for NMN synthesis and accumulation, resulting in a remarkable over 100-fold increase in NMN yield. Subsequently, we progressively enhanced the de novo NMN biosynthesis route to further augment NMN production. We screened and identified the crucial role of MazG in catalyzing the enzymatic cleavage of NAD+ to NMN. And the de novo NMN biosynthesis route was optimized and integrated with the NadV-mediated NMN biosynthetic pathways, leading to an intracellular concentration of 844.10 ± 17.40 μM NMN. Furthermore, the introduction of two transporters enhanced the uptake of NAM and the excretion of NMN, resulting in NMN production of 1293.73 ± 61.38 μM. Finally, by engineering an E. coli strain with optimized PRPP synthetase, we achieved the highest NMN production, reaching 3067.98 ± 27.25 μM after 24 h of fermentation at the shake flask level. In addition to constructing an efficient E. coli cell factory for NMN production, our findings provide new insights into understanding the NAD+ salvage pathway and its role in energy metabolism within E. coli.
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Affiliation(s)
- Pengju Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yidan Ma
- School of Biological Engineering, Dalian Polytechnic University, Dalian 116034, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Ju Li
- College of Life Science, Tianjin Normal University, Tianjin 300382, China
| | - Junchang Su
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Junxi Chi
- School of Biological Engineering, Dalian Polytechnic University, Dalian 116034, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xingmiao Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xinna Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Chunzhi Zhang
- School of Biological Engineering, Dalian Polytechnic University, Dalian 116034, China
| | - Changhao Bi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
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Tan Z, Yang Y, Wu Y, Yan J, Zhang B, Hou Y, Jia S. Biosynthesis of β-nicotinamide mononucleotide from glucose via a new pathway in Bacillus subtilis. Front Microbiol 2024; 15:1405736. [PMID: 38919503 PMCID: PMC11197623 DOI: 10.3389/fmicb.2024.1405736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Accepted: 05/30/2024] [Indexed: 06/27/2024] Open
Abstract
Introduction β-nicotinamide mononucleotide (β-NMN) is an essential precursor of nicotinamide adenine dinucleotide (NAD+) and plays a key role in supplying NAD+ and maintaining its levels. Existing methods for NMN production have some limitations, including low substrate availability, complex synthetic routes, and low synthetic efficiency, which result in low titers and high costs. Methods We constructed high-titer, genetically engineered strains that produce NMN through a new pathway. Bacillus subtilis WB600 was used as a safe chassis strain. Multiple strains overexpressing NadE, PncB, and PnuC in various combinations were constructed, and NMN titers of different strains were compared via shake-flask culture. Results The results revealed that the strain B. subtilis PncB1-PnuC exhibited the highest total and extracellular NMN titers. Subsequently, the engineered strains were cultured in a 5-L fermenter using batch and fed-batch fermentation. B. subtilis PncB1-PnuC achieved an NMN titer of 3,398 mg/L via fed-batch fermentation and glucose supplementation, which was 30.72% higher than that achieved via batch fermentation. Discussion This study provides a safe and economical approach for producing NMN on an industrial scale.
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Affiliation(s)
- Zhilei Tan
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, China
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Dong CL, Wu T, Dong Y, Qu QW, Chen XY, Li YH. Exogenous methionine contributes to reversing the resistance of Streptococcus suis to macrolides. Microbiol Spectr 2024; 12:e0280323. [PMID: 38230928 PMCID: PMC10923279 DOI: 10.1128/spectrum.02803-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 12/21/2023] [Indexed: 01/18/2024] Open
Abstract
Streptococcus suis (S. suis) has been increasingly recognized as a porcine zoonotic pathogen that threatens the health of both pigs and humans. Multidrug-resistant Streptococcus suis is becoming increasingly prevalent, and novel strategies to treat bacterial infections caused by these organisms are desperately needed. In the present study, an untargeted metabolomics analysis showed that the significant decrease in methionine content and the methionine biosynthetic pathway were significantly affected by the Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis in drug-resistant S. suis. The addition of L-methionine restored the bactericidal activity of macrolides, doxycycline, and ciprofloxacin on S. suis in vivo and in vitro. Further studies showed that the exogenous addition of methionine affects methionine metabolism by reducing S-adenosylmethionine synthetase activity and the contents of S-adenosylmethionine, S-adenosyl homocysteine, and S-ribose homocysteine. Methionine can decrease the total methylation level and methylesterase activity in multidrug resistant S. suis. The drug transport proteins and efflux pump genes were significantly downregulated in S. suis by exogenous L-methionine. Moreover, the exogenous addition of methionine can reduce the survival of S. suis by affecting oxidative stress and metal starvation in bacteria. Thus, L-methionine may influence the development of resistance in S. suis through methyl metabolism and metal starvation. This study provides a new perspective on the mitigation of drug resistance in S. suis.IMPORTANCEBacterial antibiotic resistance has become a severe threat to human and animal health. Increasing the efficacy of existing antibiotics is a promising strategy against antibiotic resistance. Here, we report that L-methionine enhances the efficacy of macrolides, doxycycline, and ciprofloxacin antibiotics in killing Streptococcus suis, including multidrug-resistant pathogens. We investigated the mechanism of action of exogenous methionine supplementation in restoring macrolides in Streptococcus suis and the role of the methionine cycle pathway on methylation levels, efflux pump genes, oxidative stress, and metal starvation in Streptococcus suis. It provides a theoretical basis for the rational use of macrolides in clinical practice and also identifies a possible target for restoring drug resistance in Streptococcus suis.
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Affiliation(s)
- Chun-Liu Dong
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, Heilongjiang, China
| | - Tong Wu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Yue Dong
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Qian-Wei Qu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Xue-Ying Chen
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, Heilongjiang, China
| | - Yan-Hua Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, Heilongjiang, China
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Huang Z, Wang X, Li N, Song F, Zhou J. Systematic engineering of Escherichia coli for efficient production of nicotinamide riboside from nicotinamide and 3-cyanopyridine. BIORESOURCE TECHNOLOGY 2023; 377:128953. [PMID: 36963699 DOI: 10.1016/j.biortech.2023.128953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/17/2023] [Accepted: 03/21/2023] [Indexed: 06/18/2023]
Abstract
Nicotinamide riboside (NR), a key biosynthetic precursor of NAD+, is receiving increasing attention because of its role. In this study, a whole-cell catalysis method to efficiently synthesize NR was established. First, the performance of 5'-nucleotidase (UshA) from Escherichia coli was confirmed to have high catalytic activity to synthesize NR. Then, the endogenous NR degradation pathway was detected, and the genes (rihA, rihB, and rihC) involved in NR degradation were knocked out, which enabled NR biosynthesis. In addition, the important role of the signal peptide of UshA in NR transport had been confirmed. Subsequently, nitrile hydratase was introduced to achieve the conversion of 3-cyanopyridine to NR. Finally, the NR titer reached 25.6 and 29.8 g/L with nicotinamide and 3-cyanopyridine, respectively, as substrates in a 5-L bioreactor, the efficient biosynthesis of NR in E. coli by using nicotinamide and 3-cyanopyridine.
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Affiliation(s)
- Zhongshi Huang
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xinglong Wang
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Ning Li
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Fuqiang Song
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China.
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Peluso AA, Lundgaard AT, Babaei P, Mousovich-Neto F, Rocha AL, Damgaard MV, Bak EG, Gnanasekaran T, Dollerup OL, Trammell SAJ, Nielsen TS, Kern T, Abild CB, Sulek K, Ma T, Gerhart-Hines Z, Gillum MP, Arumugam M, Ørskov C, McCloskey D, Jessen N, Herrgård MJ, Mori MAS, Treebak JT. Oral supplementation of nicotinamide riboside alters intestinal microbial composition in rats and mice, but not humans. NPJ AGING 2023; 9:7. [PMID: 37012386 PMCID: PMC10070358 DOI: 10.1038/s41514-023-00106-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 03/20/2023] [Indexed: 04/05/2023]
Abstract
The gut microbiota impacts systemic levels of multiple metabolites including NAD+ precursors through diverse pathways. Nicotinamide riboside (NR) is an NAD+ precursor capable of regulating mammalian cellular metabolism. Some bacterial families express the NR-specific transporter, PnuC. We hypothesized that dietary NR supplementation would modify the gut microbiota across intestinal sections. We determined the effects of 12 weeks of NR supplementation on the microbiota composition of intestinal segments of high-fat diet-fed (HFD) rats. We also explored the effects of 12 weeks of NR supplementation on the gut microbiota in humans and mice. In rats, NR reduced fat mass and tended to decrease body weight. Interestingly, NR increased fat and energy absorption but only in HFD-fed rats. Moreover, 16S rRNA gene sequencing analysis of intestinal and fecal samples revealed an increased abundance of species within Erysipelotrichaceae and Ruminococcaceae families in response to NR. PnuC-positive bacterial strains within these families showed an increased growth rate when supplemented with NR. The abundance of species within the Lachnospiraceae family decreased in response to HFD irrespective of NR. Alpha and beta diversity and bacterial composition of the human fecal microbiota were unaltered by NR, but in mice, the fecal abundance of species within Lachnospiraceae increased while abundances of Parasutterella and Bacteroides dorei species decreased in response to NR. In conclusion, oral NR altered the gut microbiota in rats and mice, but not in humans. In addition, NR attenuated body fat mass gain in rats, and increased fat and energy absorption in the HFD context.
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Affiliation(s)
- A Augusto Peluso
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Agnete T Lundgaard
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Parizad Babaei
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Felippe Mousovich-Neto
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Andréa L Rocha
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Mads V Damgaard
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Emilie G Bak
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thiyagarajan Gnanasekaran
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ole L Dollerup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Samuel A J Trammell
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas S Nielsen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Timo Kern
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Caroline B Abild
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Karolina Sulek
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Herlev Hospital, Herlev, Denmark
| | - Tao Ma
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Zach Gerhart-Hines
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Matthew P Gillum
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Manimozhiyan Arumugam
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Cathrine Ørskov
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Douglas McCloskey
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Niels Jessen
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Markus J Herrgård
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
- BioInnovation Institute, Copenhagen, Denmark
| | - Marcelo A S Mori
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil
- Obesity and Comorbidities Research Center, University of Campinas, Campinas, SP, Brazil
- Experimental Medicine Research Cluster, University of Campinas, Campinas, SP, Brazil
| | - Jonas T Treebak
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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Kong LH, Liu TY, Yao QS, Zhang XH, Xu WN, Qin JY. Enhancing the biosynthesis of nicotinamide mononucleotide in Lactococcus lactis by heterologous expression of FtnadE. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:450-456. [PMID: 36205212 DOI: 10.1002/jsfa.12253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 10/04/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Nicotinamide mononucleotide (NMN), a key intermediate of nicotinamide adenine dinucleotide, plays an important in anti-aging and disease. Lactococcus lactis, an important probiotic lactic acid bacteria (LAB), has shown great potential for the biosynthesis of NMN, which will significantly affect the probiotic effects of the dairy products. RESULTS We used the CRISPR/nCas9 technique to knockout nadR gene of L. lactis NZ9000 to enhance the accumulation of NMN by 61%. The nadE* gene from Francisella tularensis with codon optimization was heterologous in L. lactis NZ9000ΔnadR and has a positive effect on NMN production. Combined with optimization of the concentration of substrate nicotinamide, a final intracellular NMN titer was 2289 μmol L-1 mg-1 with 10 g L-1 nicotinamide supplement, which was 5.7-fold higher than that of the control. The transcription levels of key genes (pncA, nadD and prs1) involved in NMN biosynthesis were up-regulated by more than two-fold, indicating that the increase of NMN titer was attributed to FtnadE* heterologous expression. CONCLUSION Our study provides a better understanding of the NMN biosynthesis pathway in L. lactis, and can facilitate NMN production in LAB via synthetic biology approaches. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Ling-Hui Kong
- School of Pharmacy, Binzhou Medical University, Yantai, Shandong Province, China
| | - Tai-Yu Liu
- Shanghai BEIONMED Technology Co., Ltd., Shanghai, China
| | - Qing-Shou Yao
- School of Pharmacy, Binzhou Medical University, Yantai, Shandong Province, China
| | - Xiao-Hua Zhang
- School of Pharmacy, Binzhou Medical University, Yantai, Shandong Province, China
| | - Wei-Na Xu
- School of Pharmacy, Binzhou Medical University, Yantai, Shandong Province, China
| | - Jia-Yang Qin
- School of Pharmacy, Binzhou Medical University, Yantai, Shandong Province, China
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8
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Chu X, Hou Y, Meng Q, Croteau DL, Wei Y, De S, Becker KG, Bohr VA. Nicotinamide adenine dinucleotide supplementation drives gut microbiota variation in Alzheimer’s mouse model. Front Aging Neurosci 2022; 14:993615. [PMID: 36185477 PMCID: PMC9520302 DOI: 10.3389/fnagi.2022.993615] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Alzheimer’s disease (AD) is the most common neurodegenerative disease. Growing evidence suggests an important role for gut dysbiosis and gut microbiota-host interactions in aging and neurodegeneration. Our previous works have demonstrated that supplementation with the nicotinamide adenine dinucleotide (NAD+) precursor, nicotinamide riboside (NR), reduced the brain features of AD, including neuroinflammation, deoxyribonucleic acid (DNA) damage, synaptic dysfunction, and cognitive impairment. However, the impact of NR administration on the intestinal microbiota of AD remains unknown. In this study, we investigated the relationship between gut microbiota and NR treatment in APP/PS1 transgenic (AD) mice. Compared with wild type (WT) mice, the gut microbiota diversity in AD mice was lower and the microbiota composition and enterotype were significantly different. Moreover, there were gender differences in gut microbiome between female and male AD mice. After supplementation with NR for 8 weeks, the decreased diversity and perturbated microbial compositions were normalized in AD mice. This included the species Oscillospira, Butyricicoccus, Desulfovibrio, Bifidobacterium, Olsenella, Adlercreutzia, Bacteroides, Akkermansia, and Lactobacillus. Our results indicate an interplay between NR and host-microbiota in APP/PS1 mice, suggesting that the effect of NR on gut dysbiosis may be an important component in its therapeutic functions in AD.
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Affiliation(s)
- Xixia Chu
- DNA Repair Section, National Institute on Aging, Baltimore, MD, United States
| | - Yujun Hou
- DNA Repair Section, National Institute on Aging, Baltimore, MD, United States
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Qiong Meng
- Laboratory of Genetics and Genomics, National Institute on Aging, Baltimore, MD, United States
| | - Deborah L. Croteau
- DNA Repair Section, National Institute on Aging, Baltimore, MD, United States
- Laboratory of Genetics and Genomics, National Institute on Aging, Baltimore, MD, United States
| | - Yong Wei
- DNA Repair Section, National Institute on Aging, Baltimore, MD, United States
| | - Supriyo De
- Laboratory of Genetics and Genomics, National Institute on Aging, Baltimore, MD, United States
| | - Kevin G. Becker
- Laboratory of Genetics and Genomics, National Institute on Aging, Baltimore, MD, United States
| | - Vilhelm A. Bohr
- DNA Repair Section, National Institute on Aging, Baltimore, MD, United States
- *Correspondence: Vilhelm A. Bohr,
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Abstract
With obesity and type 2 diabetes (T2D) at epidemic levels, we need to understand the complex nature of these diseases to design better therapeutics. The underlying causes of both obesity and T2D are complex, but both are thought to develop, in part, based on contributions from the gut microbiota.
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Liu Y, Yasawong M, Yu B. Metabolic engineering of Escherichia coli for biosynthesis of β-nicotinamide mononucleotide from nicotinamide. Microb Biotechnol 2021; 14:2581-2591. [PMID: 34310854 PMCID: PMC8601175 DOI: 10.1111/1751-7915.13901] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/15/2021] [Indexed: 12/31/2022] Open
Abstract
The β-nicotinamide mononucleotide (NMN) is a key intermediate of an essential coenzyme for cellular redox reactions, NAD. Administration of NMN is reported to improve various symptoms, such as diabetes and age-related physiological decline. Thus, NMN is attracting much attention as a promising nutraceutical. Here, we engineered an Escherichia coli strain to produce NMN from cheap substrate nicotinamide (NAM) and glucose. The supply of in vivo precursor phosphoribosyl pyrophosphate (PRPP) and ATP was enhanced by strengthening the metabolic flux from glucose. A nicotinamide phosphoribosyltransferase with high activity was newly screened, which is the key enzyme for converting NAM to NMN with PRPP as cofactor. Notably, the E. coli endogenous protein YgcS, which function is primarily in the uptake of sugars, was firstly proven to be beneficial for NMN production in this study. Fine-tuning regulation of ygcS gene expression in the engineered E. coli strain increased NMN production. Combined with process optimization of whole-cell biocatalysts reaction, a final NMN titre of 496.2 mg l-1 was obtained.
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Affiliation(s)
- Yang Liu
- CAS Key Laboratory of Microbial Physiological and Metabolic EngineeringState Key Laboratory of MycologyInstitute of MicrobiologyChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100049China
| | - Montri Yasawong
- CAS Key Laboratory of Microbial Physiological and Metabolic EngineeringState Key Laboratory of MycologyInstitute of MicrobiologyChinese Academy of SciencesBeijing100101China
- Program on Environmental ToxicologyChulabhorn Graduate InstituteChulabhorn Royal AcademyBangkok10210Thailand
| | - Bo Yu
- CAS Key Laboratory of Microbial Physiological and Metabolic EngineeringState Key Laboratory of MycologyInstitute of MicrobiologyChinese Academy of SciencesBeijing100101China
- China‐Thailand Joint Laboratory on Microbial BiotechnologyBeijingChina
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Brewer KI, Greenlee EB, Higgs G, Yu D, Mirihana Arachchilage G, Chen X, King N, White N, Breaker RR. Comprehensive discovery of novel structured noncoding RNAs in 26 bacterial genomes. RNA Biol 2021; 18:2417-2432. [PMID: 33970790 PMCID: PMC8632094 DOI: 10.1080/15476286.2021.1917891] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/30/2022] Open
Abstract
Comparative sequence analysis methods are highly effective for uncovering novel classes of structured noncoding RNAs (ncRNAs) from bacterial genomic DNA sequence datasets. Previously, we developed a computational pipeline to more comprehensively identify structured ncRNA representatives from individual bacterial genomes. This search process exploits the fact that genomic regions serving as templates for the transcription of structured RNAs tend to be present in longer than average noncoding 'intergenic regions' (IGRs) that are enriched in G and C nucleotides compared to the remainder of the genome. In the present study, we apply this computational pipeline to identify structured ncRNA candidates from 26 diverse bacterial species. Numerous novel structured ncRNA motifs were discovered, including several riboswitch candidates, one whose ligand has been identified and others that have yet to be experimentally validated. Our findings support recent predictions that hundreds of novel ribo-switch classes and other ncRNAs remain undiscovered among the limited number of bacterial species whose genomes have been completely sequenced.
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Affiliation(s)
- Kenneth I Brewer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Etienne B Greenlee
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Gadareth Higgs
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Diane Yu
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | | | - Xi Chen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Nicholas King
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Neil White
- Howard Hughes Medical Institute, Yale University, New Haven, CT, USA
| | - Ronald R Breaker
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.,Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.,Howard Hughes Medical Institute, Yale University, New Haven, CT, USA
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12
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Panchapakesan SSS, Corey L, Malkowski SN, Higgs G, Breaker RR. A second riboswitch class for the enzyme cofactor NAD . RNA (NEW YORK, N.Y.) 2021; 27:99-105. [PMID: 33087526 PMCID: PMC7749635 DOI: 10.1261/rna.077891.120] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 10/19/2020] [Indexed: 06/01/2023]
Abstract
A bacterial noncoding RNA motif almost exclusively associated with pnuC genes was uncovered using comparative sequence analysis. Some PnuC proteins are known to transport nicotinamide riboside (NR), which is a component of the ubiquitous and abundant enzyme cofactor nicotinamide adenine dinucleotide (NAD+). Thus, we speculated that the newly found "pnuC motif" RNAs might function as aptamers for a novel class of NAD+-sensing riboswitches. RNA constructs that encompass the conserved nucleotides and secondary structure features that define the motif indeed selectively bind NAD+, nicotinamide mononucleotide (NMN), and NR. Mutations that disrupt strictly conserved nucleotides of the aptamer also disrupt ligand binding. These bioinformatic and biochemical findings indicate that pnuC motif RNAs are likely members of a second riboswitch class that regulates gene expression in response to NAD+ binding.
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Affiliation(s)
- Shanker S S Panchapakesan
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Lukas Corey
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Sarah N Malkowski
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Gadareth Higgs
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Ronald R Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8103, USA
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8103, USA
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13
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Shoji S, Yamaji T, Makino H, Ishii J, Kondo A. Metabolic design for selective production of nicotinamide mononucleotide from glucose and nicotinamide. Metab Eng 2020; 65:167-177. [PMID: 33220420 DOI: 10.1016/j.ymben.2020.11.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/11/2020] [Accepted: 11/11/2020] [Indexed: 12/30/2022]
Abstract
β-Nicotinamide mononucleotide (NMN) is, one of the nucleotide compounds, a precursor of NAD+ and has recently attracted attention as a nutraceutical. Here, we develop a whole-cell biocatalyst using Escherichia coli, which enabled selective and effective high production of NMN from the inexpensive feedstock substrates glucose and nicotinamide (Nam). Notably, we identify two actively functional transporters (NiaP and PnuC) and a high-activity key enzyme (Nampt), permitting intracellular Nam uptake, efficient conversion of phosphoribosyl pyrophosphate (PRPP; supplied from glucose) and Nam to NMN, and NMN excretion extracellularly. Further, enhancement of the PRPP biosynthetic pathway and optimization of individual gene expression enable drastically higher NMN production than reported thus far. The strain extracellularly produces 6.79 g l-1 of NMN from glucose and Nam, and the reaction selectivity from Nam to NMN is 86%. Our approach will be promising for low-cost, high-quality industrial production of NMN and other nucleotide compounds using microorganisms.
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Affiliation(s)
- Shinichiro Shoji
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.
| | - Taiki Yamaji
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Harumi Makino
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Jun Ishii
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan; Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan; Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan; Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan; RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, 230-0045, Japan
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14
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Black WB, Aspacio D, Bever D, King E, Zhang L, Li H. Metabolic engineering of Escherichia coli for optimized biosynthesis of nicotinamide mononucleotide, a noncanonical redox cofactor. Microb Cell Fact 2020; 19:150. [PMID: 32718347 PMCID: PMC7384224 DOI: 10.1186/s12934-020-01415-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/20/2020] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Noncanonical redox cofactors are emerging as important tools in cell-free biosynthesis to increase the economic viability, to enable exquisite control, and to expand the range of chemistries accessible. However, these noncanonical redox cofactors need to be biologically synthesized to achieve full integration with renewable biomanufacturing processes. RESULTS In this work, we engineered Escherichia coli cells to biosynthesize the noncanonical cofactor nicotinamide mononucleotide (NMN+), which has been efficiently used in cell-free biosynthesis. First, we developed a growth-based screening platform to identify effective NMN+ biosynthetic pathways in E. coli. Second, we explored various pathway combinations and host gene disruption to achieve an intracellular level of ~ 1.5 mM NMN+, a 130-fold increase over the cell's basal level, in the best strain, which features a previously uncharacterized nicotinamide phosphoribosyltransferase (NadV) from Ralstonia solanacearum. Last, we revealed mechanisms through which NMN+ accumulation impacts E. coli cell fitness, which sheds light on future work aiming to improve the production of this noncanonical redox cofactor. CONCLUSION These results further the understanding of effective production and integration of NMN+ into E. coli. This may enable the implementation of NMN+-directed biocatalysis without the need for exogenous cofactor supply.
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Affiliation(s)
- William B Black
- Departments of Chemical and Biomolecular Engineering, University of California, Irvine, CA, United States
| | - Derek Aspacio
- Departments of Chemical and Biomolecular Engineering, University of California, Irvine, CA, United States
| | - Danielle Bever
- Departments of Chemical and Biomolecular Engineering, University of California, Irvine, CA, United States
| | - Edward King
- Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | - Linyue Zhang
- Departments of Chemical and Biomolecular Engineering, University of California, Irvine, CA, United States
| | - Han Li
- Departments of Chemical and Biomolecular Engineering, University of California, Irvine, CA, United States.
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15
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Structural and Functional Characterization of NadR from Lactococcus lactis. Molecules 2020; 25:molecules25081940. [PMID: 32331317 PMCID: PMC7221760 DOI: 10.3390/molecules25081940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/19/2020] [Accepted: 04/21/2020] [Indexed: 12/02/2022] Open
Abstract
NadR is a bifunctional enzyme that converts nicotinamide riboside (NR) into nicotinamide mononucleotide (NMN), which is then converted into nicotinamide adenine dinucleotide (NAD). Although a crystal structure of the enzyme from the Gram-negative bacterium Haemophilus influenzae is known, structural understanding of its catalytic mechanism remains unclear. Here, we purified the NadR enzyme from Lactococcus lactis and established an assay to determine the combined activity of this bifunctional enzyme. The conversion of NR into NAD showed hyperbolic dependence on the NR concentration, but sigmoidal dependence on the ATP concentration. The apparent cooperativity for ATP may be explained because both reactions catalyzed by the bifunctional enzyme (phosphorylation of NR and adenylation of NMN) require ATP. The conversion of NMN into NAD followed simple Michaelis-Menten kinetics for NMN, but again with the sigmoidal dependence on the ATP concentration. In this case, the apparent cooperativity is unexpected since only a single ATP is used in the NMN adenylyltransferase catalyzed reaction. To determine the possible structural determinants of such cooperativity, we solved the crystal structure of NadR from L. lactis (NadRLl). Co-crystallization with NAD, NR, NMN, ATP, and AMP-PNP revealed a ‘sink’ for adenine nucleotides in a location between two domains. This sink could be a regulatory site, or it may facilitate the channeling of substrates between the two domains.
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16
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Characterization and functional analysis of PnuC that is involved in the oxidative stress tolerance and virulence of Streptococcus suis serotype 2. Vet Microbiol 2018. [DOI: 10.1016/j.vetmic.2018.02.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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17
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Afzal M, Kuipers OP, Shafeeq S. Niacin-mediated Gene Expression and Role of NiaR as a Transcriptional Repressor of niaX, nadC, and pnuC in Streptococcus pneumoniae. Front Cell Infect Microbiol 2017; 7:70. [PMID: 28337428 PMCID: PMC5343564 DOI: 10.3389/fcimb.2017.00070] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 02/24/2017] [Indexed: 12/21/2022] Open
Abstract
NAD (Nicotinamide Adenine Dinucleotide) biosynthesis is vital for bacterial physiology and plays an important role in cellular metabolism. A naturally occurring vitamin B complex, niacin (nicotinic acid), is a precursor of coenzymes NAD and NADP. Here, we study the impact of niacin on global gene expression of Streptococcus pneumoniae D39 and elucidate the role of NiaR as a transcriptional regulator of niaX, nadC, and pnuC. Transcriptome comparison of the D39 wild-type grown in chemically defined medium (CDM) with 0 to 10 mM niacin revealed elevated expression of various genes, including niaX, nadC, pnuC, fba, rex, gapN, pncB, gap, adhE, and adhB2 that are putatively involved in the transport and utilization of niacin. Niacin-dependent expression of these genes is confirmed by promoter lacZ-fusion studies. Moreover, the role of transcriptional regulator NiaR in the regulation of these genes is explored by DNA microarray analysis. Our transcriptomic comparison of D39 ΔniaR to D39 wild-type revealed that the transcriptional regulator NiaR acts as a transcriptional repressor of niaX, pnuC, and nadC. NiaR-dependent regulation of niaX, nadC, and pnuC is further confirmed by promoter lacZ-fusion studies. The putative operator site of NiaR (5′-TACWRGTGTMTWKACASYTRWAW-3′) in the promoter regions of niaX, nadC, and pnuC is predicted and further confirmed by promoter mutational experiments.
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Affiliation(s)
- Muhammad Afzal
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenGroningen, Netherlands; Department of Bioinformatics and Biotechnology, Government College UniversityFaisalabad, Pakistan
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen Groningen, Netherlands
| | - Sulman Shafeeq
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet Stockholm, Sweden
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18
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Functional mining of transporters using synthetic selections. Nat Chem Biol 2016; 12:1015-1022. [DOI: 10.1038/nchembio.2189] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 07/28/2016] [Indexed: 12/11/2022]
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19
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Massilamany C, Mohammed A, Loy JD, Purvis T, Krishnan B, Basavalingappa RH, Kelley CM, Guda C, Barletta RG, Moriyama EN, Smith TPL, Reddy J. Whole genomic sequence analysis of Bacillus infantis: defining the genetic blueprint of strain NRRL B-14911, an emerging cardiopathogenic microbe. BMC Genomics 2016; 17 Suppl 7:511. [PMID: 27557119 PMCID: PMC5001198 DOI: 10.1186/s12864-016-2900-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Background We recently reported the identification of Bacillus sp. NRRL B-14911 that induces heart autoimmunity by generating cardiac-reactive T cells through molecular mimicry. This marine bacterium was originally isolated from the Gulf of Mexico, but no associations with human diseases were reported. Therefore, to characterize its biological and medical significance, we sought to determine and analyze the complete genome sequence of Bacillus sp. NRRL B-14911. Results Based on the phylogenetic analysis of 16S ribosomal RNA (rRNA) genes, sequence analysis of the 16S-23S rDNA intergenic transcribed spacers, phenotypic microarray, and matrix-assisted laser desorption ionization time-of-flight mass spectrometry, we propose that this organism belongs to the species Bacillus infantis, previously shown to be associated with sepsis in a newborn child. Analysis of the complete genome of Bacillus sp. NRRL B-14911 revealed several virulence factors including adhesins, invasins, colonization factors, siderophores and transporters. Likewise, the bacterial genome encodes a wide range of methyl transferases, transporters, enzymatic and biochemical pathways, and insertion sequence elements that are distinct from other closely related bacilli. Conclusions The complete genome sequence of Bacillus sp. NRRL B-14911 provided in this study may facilitate genetic manipulations to assess gene functions associated with bacterial survival and virulence. Additionally, this bacterium may serve as a useful tool to establish a disease model that permits systematic analysis of autoimmune events in various susceptible rodent strains. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2900-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chandirasegaran Massilamany
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Akram Mohammed
- University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - John Dustin Loy
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Tanya Purvis
- Kansas State Veterinary Diagnostic Laboratory, Manhattan, KS, 66506, USA
| | - Bharathi Krishnan
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Rakesh H Basavalingappa
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Christy M Kelley
- Genetics, Breeding and Animal Health Unit, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Chittibabu Guda
- University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Raúl G Barletta
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Etsuko N Moriyama
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Timothy P L Smith
- Genetics, Breeding and Animal Health Unit, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Jay Reddy
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA.
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20
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Johnson MDL, Echlin H, Dao TH, Rosch JW. Characterization of NAD salvage pathways and their role in virulence in Streptococcus pneumoniae. MICROBIOLOGY-SGM 2015; 161:2127-36. [PMID: 26311256 DOI: 10.1099/mic.0.000164] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
NAD is a necessary cofactor present in all living cells. Some bacteria cannot de novo synthesize NAD and must use the salvage pathway to import niacin or nicotinamide riboside via substrate importers NiaX and PnuC, respectively. Although homologues of these two importers and their substrates have been identified in other organisms, limited data exist in Streptococcus pneumoniae, specifically, on its effect on overall virulence. Here, we sought to characterize the substrate specificity of NiaX and PnuC in Str. pneumoniae TIGR4 and the contribution of these proteins to virulence of the pathogen. Although binding affinity of each importer for nicotinamide mononucleotide may overlap, we found NiaX to specifically import nicotinamide and nicotinic acid, and PnuC to be primarily responsible for nicotinamide riboside import. Furthermore, a pnuC mutant is completely attenuated during both intranasal and intratracheal infections in mice. Taken together, these findings underscore the importance of substrate salvage in pneumococcal pathogenesis and indicate that PnuC could potentially be a viable small-molecule therapeutic target to alleviate disease progression in the host.
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Affiliation(s)
- Michael D L Johnson
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN 38105-3678, USA
| | - Haley Echlin
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN 38105-3678, USA
| | - Tina H Dao
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN 38105-3678, USA
| | - Jason W Rosch
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN 38105-3678, USA
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21
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Stehr M, Elamin AA, Singh M. Pyrazinamide: the importance of uncovering the mechanisms of action in mycobacteria. Expert Rev Anti Infect Ther 2015; 13:593-603. [PMID: 25746054 DOI: 10.1586/14787210.2015.1021784] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Pyrazinamide (PZA) is still one of the key drugs used in current therapeutic regimens for tuberculosis (TB). Despite its importance for TB therapy, the mode of action of PZA remains unknown. PZA has to be converted to its active form pyrazinoic acid (POA) by the nicotinamidase PncA and is then excreted by an unknown efflux pump. At acidic conditions, POA is protonated to HPOA and is reabsorbed into the cell where it causes cellular damage. For a long time, it has been thought that PZA/POA has no defined target of action, but recent studies have shown that both PZA and POA have several different targets interfering with diverse biochemical pathways, especially in the NAD(+) and energy metabolism. PZA resistance seems to depend not only on a defective pyrazinamidase but is also rather a result of the interplay of many different enzyme targets and transport mechanisms.
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Affiliation(s)
- Matthias Stehr
- LIONEX Diagnostics and Therapeutics GmbH, Salzdahlumer Straße 196, D-38126, Braunschweig, Germany
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22
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Diversity of membrane transport proteins for vitamins in bacteria and archaea. Biochim Biophys Acta Gen Subj 2015; 1850:565-76. [DOI: 10.1016/j.bbagen.2014.05.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 04/30/2014] [Accepted: 05/03/2014] [Indexed: 01/13/2023]
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Jaehme M, Guskov A, Slotboom DJ. Crystal structure of the vitamin B3 transporter PnuC, a full-length SWEET homolog. Nat Struct Mol Biol 2014; 21:1013-5. [PMID: 25291599 DOI: 10.1038/nsmb.2909] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 09/30/2014] [Indexed: 12/31/2022]
Abstract
PnuC transporters catalyze cellular uptake of the NAD+ precursor nicotinamide riboside (NR) and belong to a large superfamily that includes the SWEET sugar transporters. We present a crystal structure of Neisseria mucosa PnuC, which adopts a highly symmetrical fold with 3+1+3 membrane topology not previously observed in any protein. The high symmetry of PnuC with a single NR bound in the center suggests a simple alternating-access translocation mechanism.
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Affiliation(s)
- Michael Jaehme
- University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, Groningen, the Netherlands
| | - Albert Guskov
- University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, Groningen, the Netherlands
| | - Dirk Jan Slotboom
- University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, Groningen, the Netherlands
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24
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Janowicz DM, Zwickl BW, Fortney KR, Katz BP, Bauer ME. Outer membrane protein P4 is not required for virulence in the human challenge model of Haemophilus ducreyi infection. BMC Microbiol 2014; 14:166. [PMID: 24961160 PMCID: PMC4081464 DOI: 10.1186/1471-2180-14-166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 06/04/2014] [Indexed: 01/14/2023] Open
Abstract
Background Bacterial lipoproteins often play important roles in pathogenesis and can stimulate protective immune responses. Such lipoproteins are viable vaccine candidates. Haemophilus ducreyi, which causes the sexually transmitted disease chancroid, expresses a number of lipoproteins during human infection. One such lipoprotein, OmpP4, is homologous to the outer membrane lipoprotein e (P4) of H. influenzae. In H. influenzae, e (P4) stimulates production of bactericidal and protective antibodies and contributes to pathogenesis by facilitating acquisition of the essential nutrients heme and nicotinamide adenine dinucleotide (NAD). Here, we tested the hypothesis that, like its homolog, H. ducreyi OmpP4 contributes to virulence and stimulates production of bactericidal antibodies. Results We determined that OmpP4 is broadly conserved among clinical isolates of H. ducreyi. We next constructed and characterized an isogenic ompP4 mutant, designated 35000HPompP4, in H. ducreyi strain 35000HP. To test whether OmpP4 was necessary for virulence in humans, eight healthy adults were experimentally infected. Each subject was inoculated with a fixed dose of 35000HP on one arm and three doses of 35000HPompP4 on the other arm. The overall parent and mutant pustule formation rates were 52.4% and 47.6%, respectively (P = 0.74). These results indicate that expression of OmpP4 in not necessary for H. ducreyi to initiate disease or progress to pustule formation in humans. Hyperimmune mouse serum raised against purified, recombinant OmpP4 did not promote bactericidal killing of 35000HP or phagocytosis by J774A.1 mouse macrophages in serum bactericidal and phagocytosis assays, respectively. Conclusions Our data suggest that, unlike e (P4), H. ducreyi OmpP4 is not a suitable vaccine candidate. OmpP4 may be dispensable for virulence because of redundant mechanisms in H. ducreyi for heme acquisition and NAD utilization.
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Affiliation(s)
- Diane M Janowicz
- Department of Medicine, Indiana University School of Medicine, 545 Barnhill Drive Room EH-435, Indianapolis, IN 46202, USA.
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Mackie A, Keseler IM, Nolan L, Karp PD, Paulsen IT. Dead end metabolites--defining the known unknowns of the E. coli metabolic network. PLoS One 2013; 8:e75210. [PMID: 24086468 PMCID: PMC3781023 DOI: 10.1371/journal.pone.0075210] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Accepted: 08/12/2013] [Indexed: 12/19/2022] Open
Abstract
The EcoCyc database is an online scientific database which provides an integrated view of the metabolic and regulatory network of the bacterium Escherichia coli K-12 and facilitates computational exploration of this important model organism. We have analysed the occurrence of dead end metabolites within the database – these are metabolites which lack the requisite reactions (either metabolic or transport) that would account for their production or consumption within the metabolic network. 127 dead end metabolites were identified from the 995 compounds that are contained within the EcoCyc metabolic network. Their presence reflects either a deficit in our representation of the network or in our knowledge of E. coli metabolism. Extensive literature searches resulted in the addition of 38 transport reactions and 3 metabolic reactions to the database and led to an improved representation of the pathway for Vitamin B12 salvage. 39 dead end metabolites were identified as components of reactions that are not physiologically relevant to E. coli K-12 – these reactions are properties of purified enzymes in vitro that would not be expected to occur in vivo. Our analysis led to improvements in the software that underpins the database and to the program that finds dead end metabolites within EcoCyc. The remaining dead end metabolites in the EcoCyc database likely represent deficiencies in our knowledge of E. coli metabolism.
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Affiliation(s)
- Amanda Mackie
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales, Australia
| | | | - Laura Nolan
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Peter D. Karp
- SRI International, Menlo Park, California, United States of America
| | - Ian T. Paulsen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales, Australia
- * E-mail:
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Vogl C, Grill S, Schilling O, Stülke J, Mack M, Stolz J. Characterization of riboflavin (vitamin B2) transport proteins from Bacillus subtilis and Corynebacterium glutamicum. J Bacteriol 2007; 189:7367-75. [PMID: 17693491 PMCID: PMC2168442 DOI: 10.1128/jb.00590-07] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2007] [Accepted: 08/03/2007] [Indexed: 01/12/2023] Open
Abstract
Riboflavin (vitamin B(2)) is the direct precursor of the flavin cofactors flavin mononucleotide and flavin adenine dinucleotide, essential components of cellular biochemistry. In this work we investigated the unrelated proteins YpaA from Bacillus subtilis and PnuX from Corynebacterium glutamicum for a role in riboflavin uptake. Based on the regulation of the corresponding genes by a riboswitch mechanism, both proteins have been predicted to be involved in flavin metabolism. Moreover, their primary structures suggested that these proteins integrate into the cytoplasmic membrane. We provide experimental evidence that YpaA is a plasma membrane protein with five transmembrane domains and a cytoplasmic C terminus. In B. subtilis, riboflavin uptake was increased when ypaA was overexpressed and abolished when ypaA was deleted. Riboflavin uptake activity and the abundance of the YpaA protein were also increased when riboflavin auxotrophic mutants were grown in limiting amounts of riboflavin. YpaA-mediated riboflavin uptake was sensitive to protonophors and reduced in the absence of glucose, demonstrating that the protein requires metabolic energy for substrate translocation. In addition, we demonstrate that PnuX from C. glutamicum also is a riboflavin transporter. Transport by PnuX was not energy dependent and had high apparent affinity for riboflavin (K(m) 11 microM). Roseoflavin, a toxic riboflavin analog, appears to be a substrate of PnuX and YpaA. We propose to designate the gene names ribU for ypaA and ribM for pnuX to reflect that the encoded proteins function in riboflavin uptake and that the genes have different phylogenetic origins.
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Affiliation(s)
- Christian Vogl
- Lehrstuhl für Ernährungsphysiologie, Technische Universität München, Am Forum 5, 85350, Freising-Weihenstephan, Germany
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Grill S, Yamaguchi H, Wagner H, Zwahlen L, Kusch U, Mack M. Identification and characterization of two Streptomyces davawensis riboflavin biosynthesis gene clusters. Arch Microbiol 2007; 188:377-87. [PMID: 17541777 DOI: 10.1007/s00203-007-0258-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2006] [Revised: 04/19/2007] [Accepted: 05/04/2007] [Indexed: 10/23/2022]
Abstract
In Streptomyces davawensis roseoflavin is synthesized from GTP and ribulose-5-phosphate through riboflavin. As a first step towards the molecular analysis of flavin metabolism in S. davawensis the genes involved in riboflavin biosynthesis were cloned by hybridization of heterologous probes to a genomic library on a high-density colony-array. The genes ribB (riboflavin synthase, alpha-chain; EC 2.5.1.9), ribM (putative membrane protein), ribA (bifunctional GTP cyclohydrolase II/3,4-dihydroxy-2-butanone-4-phosphate synthase; EC 3.5.4.25) and ribH (lumazine synthase; EC 2.5.1.9) are organized in an operon-like cluster. Northern blot analysis of this cluster revealed two transcripts of 1.7 and 3.1 kb, respectively. The gene ribB was overexpressed in Escherichia coli. The specific riboflavin synthase activity in a cell-free extract of a recombinant strain was 0.246 nmol mg(-1 )min(-1). Overexpression of ribM enhanced the transport of riboflavin in the corresponding recombinant E. coli strain. Furthermore, overexpression of ribM increased roseoflavin sensitivity of E. coli. On another subgenomic fragment a putative S. davawensis ribG gene coding for the missing pyrimidine deaminase/reductase (EC 3.5.4.26 and EC 1.1.1.193) of the riboflavin biosynthetic pathway and ribY coding for a second (monofunctional) GTP cyclohydrolase II were identified.
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Affiliation(s)
- Simon Grill
- Institute for Technical Microbiology, Mannheim University of Applied Sciences, 68163 Mannheim, Germany
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Osterman AL, Begley TP. A subsystems-based approach to the identification of drug targets in bacterial pathogens. PROGRESS IN DRUG RESEARCH. FORTSCHRITTE DER ARZNEIMITTELFORSCHUNG. PROGRES DES RECHERCHES PHARMACEUTIQUES 2007; 64:131, 133-70. [PMID: 17195474 DOI: 10.1007/978-3-7643-7567-6_6] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
This chapter describes a three-stage approach to target identification based upon subsystem analysis. Subsystems analysis focuses on related metabolic pathways as a unit and is a biochemically-informed approach to target selection. The process involves three stages of analysis; the first stage, selection of the target subsystem, is guided by information about its essentiality and on the predicted vulnerability of the targeted pathway or enzyme to inhibition. The second stage involves analysis of the target subsystem by means of comparative genomics, including genome context analysis and metabolic reconstruction. The third stage evaluates the selection of the specific target genes within the subsystem by target prioritization and validation. The whole process allows for a careful consideration of spectrum, drugability, biological rationale and the metabolic role of the specific target within the context of an integrated circuit within a specific metabolic pathway.
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Affiliation(s)
- Andrei L Osterman
- Burnham Institute for Medical Research, Infectious and Inflammatory Disease Center, La Jolla, California, USA.
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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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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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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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