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Umar Hussain M, Kainat K, Nawaz H, Irfan Majeed M, Akhtar N, Alshammari A, Albekairi NA, Fatima R, Amber A, Bano A, Shabbir I, Tahira M, Pallares RM. SERS characterization of biochemical changes associated with biodesulfurization of dibenzothiophene using Gordonia sp. HS126-4N. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 320:124534. [PMID: 38878718 DOI: 10.1016/j.saa.2024.124534] [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: 12/14/2023] [Revised: 05/08/2024] [Accepted: 05/24/2024] [Indexed: 07/08/2024]
Abstract
In this study, Gordonia sp. HS126-4N was employed for dibenzothiophene (DBT) biodesulfurization, tracked over 9 days using SERS. During the initial lag phase, no significant spectral changes were observed, but after 48 h, elevated metabolic activity was evident. At 72 h, maximal bacterial population correlated with peak spectrum variance, followed by stable spectral patterns. Despite 2-hydroxybiphenyl (2-HBP) induced enzyme suppression, DBT biodesulfurization persisted. PCA and PLS-DA analysis of the SERS spectra revealed distinctive features linked to both bacteria and DBT, showcasing successful desulfurization and bacterial growth stimulation. PLS-DA achieved a specificity of 95.5 %, sensitivity of 94.3 %, and AUC of 74 %, indicating excellent classification of bacteria exposed to DBT. SERS effectively tracked DBT biodesulfurization and bacterial metabolic changes, offering insights into biodesulfurization mechanisms and bacterial development phases. This study highlights SERS' utility in biodesulfurization research, including its use in promising advancements in the field.
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Affiliation(s)
- Muhammad Umar Hussain
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan
| | - Kiran Kainat
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Haq Nawaz
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan.
| | - Muhammad Irfan Majeed
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan.
| | - Nasrin Akhtar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan.
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, Riyadh 11451, Saudi Arabia
| | - Norah A Albekairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, Riyadh 11451, Saudi Arabia
| | - Rida Fatima
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Arooj Amber
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Aqsa Bano
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Ifra Shabbir
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Maryam Tahira
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Roger M Pallares
- Institute for Experimental Molecular Imaging, RWTH Aachen University Hospital, Aachen 52074, Germany
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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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Pham TD, Poletti C, Tientcheu TMN, Cuccioloni M, Spurio R, Fabbretti A, Milon P, Giuliodori AM. FAST, a method based on split-GFP for the detection in solution of proteins synthesized in cell-free expression systems. Sci Rep 2024; 14:8042. [PMID: 38580785 PMCID: PMC10997616 DOI: 10.1038/s41598-024-58588-5] [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: 12/21/2023] [Accepted: 04/01/2024] [Indexed: 04/07/2024] Open
Abstract
Cell-free protein synthesis (CFPS) systems offer a versatile platform for a wide range of applications. However, the traditional methods for detecting proteins synthesized in CFPS, such as radioactive labeling, fluorescent tagging, or electrophoretic separation, may be impractical, due to environmental hazards, high costs, technical complexity, and time consuming procedures. These limitations underscore the need for new approaches that streamline the detection process, facilitating broader application of CFPS. By harnessing the reassembly capabilities of two GFP fragments-specifically, the GFP1-10 and GFP11 fragments-we have crafted a method that simplifies the detection of in vitro synthesized proteins called FAST (Fluorescent Assembly of Split-GFP for Translation Tests). FAST relies on the fusion of the small tag GFP11 to virtually any gene to be expressed in CFPS. The in vitro synthesized protein:GFP11 can be rapidly detected in solution upon interaction with an enhanced GFP1-10 fused to the Maltose Binding Protein (MBP:GFP1-10). This interaction produces a fluorescent signal detectable with standard fluorescence readers, thereby indicating successful protein synthesis. Furthermore, if required, detection can be coupled with the purification of the fluorescent complex using standardized MBP affinity chromatography. The method's versatility was demonstrated by fusing GFP11 to four distinct E. coli genes and analyzing the resulting protein synthesis in both a homemade and a commercial E. coli CFPS system. Our experiments confirmed that the FAST method offers a direct correlation between the fluorescent signal and the amount of synthesized protein:GFP11 fusion, achieving a sensitivity threshold of 8 ± 2 pmol of polypeptide, with fluorescence plateauing after 4 h. Additionally, FAST enables the investigation of translation inhibition by antibiotics in a dose-dependent manner. In conclusion, FAST is a new method that permits the rapid, efficient, and non-hazardous detection of protein synthesized within CFPS systems and, at the same time, the purification of the target protein.
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Affiliation(s)
- Thuy Duong Pham
- Laboratory of Genetics of Microorganisms and Microbial Biotechnology, School of Biosciences and Veterinary Medicine, University of Camerino, 62032, Camerino, MC, Italy
| | - Chiara Poletti
- Laboratory of Genetics of Microorganisms and Microbial Biotechnology, School of Biosciences and Veterinary Medicine, University of Camerino, 62032, Camerino, MC, Italy
| | - Therese Manuela Nloh Tientcheu
- Laboratory of Genetics of Microorganisms and Microbial Biotechnology, School of Biosciences and Veterinary Medicine, University of Camerino, 62032, Camerino, MC, Italy
| | - Massimiliano Cuccioloni
- Laboratory of Genetics of Microorganisms and Microbial Biotechnology, School of Biosciences and Veterinary Medicine, University of Camerino, 62032, Camerino, MC, Italy
| | - Roberto Spurio
- Laboratory of Genetics of Microorganisms and Microbial Biotechnology, School of Biosciences and Veterinary Medicine, University of Camerino, 62032, Camerino, MC, Italy
| | - Attilio Fabbretti
- Laboratory of Genetics of Microorganisms and Microbial Biotechnology, School of Biosciences and Veterinary Medicine, University of Camerino, 62032, Camerino, MC, Italy
| | - Pohl Milon
- Laboratory of Biomolecules, Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas (UPC), Lima, Peru
| | - Anna Maria Giuliodori
- Laboratory of Genetics of Microorganisms and Microbial Biotechnology, School of Biosciences and Veterinary Medicine, University of Camerino, 62032, Camerino, MC, Italy.
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Kamachi K, Koide K, Otsuka N, Goto M, Kenri T. Strain identity of Bordetella pertussis isolates from household members based on whole-genome sequencing. Microbiol Immunol 2024; 68:111-114. [PMID: 38224024 DOI: 10.1111/1348-0421.13113] [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: 06/21/2023] [Revised: 10/29/2023] [Accepted: 12/23/2023] [Indexed: 01/16/2024]
Abstract
We evaluated the genetic diversity of Bordetella pertussis, the causative agent of pertussis, within households by whole-genome sequencing. In pairwise comparisons of 23 isolates collected from 11 households, single-nucleotide polymorphism (SNP) analysis revealed extremely low SNP diversity (≤1 SNP) between isolate pairs: no SNPs were detected in 10 households and one SNP was obtained in the remaining household. This SNP was uncommon for B. pertussis and resulted in a nonsynonymous substitution (Ala303Thr) in nicotinate phosphoribosyltransferase. We demonstrated that the same strain is transmitted between household members and that B. pertussis is genomically stable during household transmission.
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Affiliation(s)
- Kazunari Kamachi
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kentaro Koide
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Nao Otsuka
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masataka Goto
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tsuyoshi Kenri
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
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Zeng M, Wu H, Han Z, Du Z, Yu X, Luo W. Metabolic Engineering of Escherichia coli for Production of 2,5-Dimethylpyrazine. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:4267-4276. [PMID: 38369722 DOI: 10.1021/acs.jafc.3c08481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
2,5-Dimethylpyrazine (2,5-DMP) is a high-value-added alkylpyrazine compound with important applications in both the food and pharmaceutical fields. In response to the increasing consumer preference for natural products over chemically synthesized ones, efforts have been made to develop efficient microbial cell factories for the production of 2,5-DMP. However, the previously reported recombinant strains have exhibited low yields and relied on expensive antibiotics and inducers. In this study, we employed metabolic engineering strategies to develop an Escherichia coli strain capable of producing 2,5-DMP at high levels without the need for inducers or antibiotics. Initially, the biosynthesis pathway of 2,5-DMP was constructed that realized 2,5-DMP production from glucose. Subsequently, efforts focused on enhancing 2,5-DMP production by improving the availability of the cofactor NAD+ and precursor l-threonine. Additionally, the supply and conversion of l-threonine were balanced by optimizing the copy number of the key gene tdh on the chromosome and by modifying the l-threonine transport system. The final engineering strain D19 produced 3.1 g/L of 2,5-DMP, which is the highest titer for fermentative production of 2,5-DMP using glucose as the carbon source up to date. The strategies used in this study lay a good foundation for the production of 2,5-DMP on a large scale.
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Affiliation(s)
- Mingxi Zeng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Hui Wu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200231, China
| | - Zhenlin Han
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii 96822, United States
| | - Zhiyan Du
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii 96822, United States
| | - Xiaobin Yu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wei Luo
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
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7
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Srivastava Y, Blau ME, Jenkins JL, Wedekind JE. Full-Length NAD +-I Riboswitches Bind a Single Cofactor but Cannot Discriminate against Adenosine Triphosphate. Biochemistry 2023; 62:3396-3410. [PMID: 37947391 PMCID: PMC10702441 DOI: 10.1021/acs.biochem.3c00391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 10/19/2023] [Accepted: 10/19/2023] [Indexed: 11/12/2023]
Abstract
Bacterial riboswitches are structured RNAs that bind small metabolites to control downstream gene expression. Two riboswitch classes have been reported to sense nicotinamide adenine dinucleotide (NAD+), which plays a key redox role in cellular metabolism. The NAD+-I (class I) riboswitch stands out because it comprises two homologous, tandemly arranged domains. However, previous studies examined the isolated domains rather than the full-length riboswitch. Crystallography and ligand binding analyses led to the hypothesis that each domain senses NAD+ but with disparate equilibrium binding constants (KD) of 127 μM (domain I) and 3.4 mM (domain II). Here, we analyzed individual domains and the full-length riboswitch by isothermal titration calorimetry to quantify the cofactor affinity and specificity. Domain I senses NAD+ with a KD of 24.6 ± 8.4 μM but with a reduced ligand-to-receptor stoichiometry, consistent with nonproductive domain self-association observed by gel-filtration chromatography; domain II revealed no detectable binding. By contrast, the full-length riboswitch binds a single NAD+ with a KD of 31.5 ± 1.5 μM; dinucleotides NADH and AP2-ribavirin also bind with one-to-one stoichiometry. Unexpectedly, the full-length riboswitch also binds a single ATP equivalent (KD = 11.0 ± 3.5 μM). The affinity trend of the full-length riboswitch is ADP = ATP > NAD+ = AP2-ribavirin > NADH. Although our results support riboswitch sensing of a single NAD+ at concentrations significantly below the intracellular levels of this cofactor, our findings do not support the level of specificity expected for a riboswitch that exclusively senses NAD+. Gene regulatory implications and future challenges are discussed.
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Affiliation(s)
- Yoshita Srivastava
- Department
of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642, United States
| | - Maya E. Blau
- Department
of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642, United States
| | - Jermaine L. Jenkins
- Department
of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642, United States
| | - Joseph E. Wedekind
- Department
of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642, United States
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Kafle SR, Kushwaha A, Goswami L, Maharjan A, Kim BS. A holistic approach for process intensification of nicotinamide mononucleotide production via high cell density cultivation under exponential feeding strategy. BIORESOURCE TECHNOLOGY 2023; 390:129911. [PMID: 37871744 DOI: 10.1016/j.biortech.2023.129911] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 10/20/2023] [Accepted: 10/20/2023] [Indexed: 10/25/2023]
Abstract
Nicotinamide mononucleotide (NMN) subsists in all living organisms and has drawn tremendous attention as a nutraceutical and pharmaceutical product for several diseases such as Alzheimer's, cancer, aging, and vascular dysfunction. Here, NMN was produced intracellularly in a high cell density bioreactor using an engineered Escherichiacoli strain via exponential feeding of co-substrates. Fed-batch culture via exponential feeding of co-substrate (glucose) and continuous feeding of substrate (nicotinamide) were performed using different cumulative nicotinamide concentrations. The highest concentration of 19.3 g/L NMN with a dry cell weight of 117 g/L was acquired from a cumulative nicotinamide concentration of 7.2 g/L with a conversion of 98 % from nicotinamide in 28 h. Further, liquid chromatography-mass spectrometry analysis validated the NMN production. This approach will be beneficial in achieving simultaneously low cost and ensuring high quality and quantity of NMN production.
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Affiliation(s)
- Saroj Raj Kafle
- Department of Chemical Engineering, Chungbuk National University, Cheongju, Chungbuk 28644, Republic of Korea
| | - Anamika Kushwaha
- Department of Chemical Engineering, Chungbuk National University, Cheongju, Chungbuk 28644, Republic of Korea
| | - Lalit Goswami
- Department of Chemical Engineering, Chungbuk National University, Cheongju, Chungbuk 28644, Republic of Korea
| | - Anoth Maharjan
- Department of Chemical Engineering, Chungbuk National University, Cheongju, Chungbuk 28644, Republic of Korea
| | - Beom Soo Kim
- Department of Chemical Engineering, Chungbuk National University, Cheongju, Chungbuk 28644, Republic of Korea.
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Favate JS, Skalenko KS, Chiles E, Su X, Yadavalli SS, Shah P. Linking genotypic and phenotypic changes in the E. coli long-term evolution experiment using metabolomics. eLife 2023; 12:RP87039. [PMID: 37991493 PMCID: PMC10665018 DOI: 10.7554/elife.87039] [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] [Indexed: 11/23/2023] Open
Abstract
Changes in an organism's environment, genome, or gene expression patterns can lead to changes in its metabolism. The metabolic phenotype can be under selection and contributes to adaptation. However, the networked and convoluted nature of an organism's metabolism makes relating mutations, metabolic changes, and effects on fitness challenging. To overcome this challenge, we use the long-term evolution experiment (LTEE) with E. coli as a model to understand how mutations can eventually affect metabolism and perhaps fitness. We used mass spectrometry to broadly survey the metabolomes of the ancestral strains and all 12 evolved lines. We combined this metabolic data with mutation and expression data to suggest how mutations that alter specific reaction pathways, such as the biosynthesis of nicotinamide adenine dinucleotide, might increase fitness in the system. Our work provides a better understanding of how mutations might affect fitness through the metabolic changes in the LTEE and thus provides a major step in developing a complete genotype-phenotype map for this experimental system.
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Affiliation(s)
- John S Favate
- Department of Genetics, Rutgers UniversityPiscatawayUnited States
- Human Genetics Institute of New JerseyPiscatawayUnited States
| | - Kyle S Skalenko
- Department of Genetics, Rutgers UniversityPiscatawayUnited States
- Waksman Institute, Rutgers UniversityPiscatawayUnited States
| | - Eric Chiles
- Cancer Institute of New JerseyNew BrunswickUnited States
| | - Xiaoyang Su
- Cancer Institute of New JerseyNew BrunswickUnited States
| | - Srujana Samhita Yadavalli
- Department of Genetics, Rutgers UniversityPiscatawayUnited States
- Waksman Institute, Rutgers UniversityPiscatawayUnited States
| | - Premal Shah
- Department of Genetics, Rutgers UniversityPiscatawayUnited States
- Human Genetics Institute of New JerseyPiscatawayUnited States
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10
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Favate JS, Skalenko KS, Chiles E, Su X, Yadavalli SS, Shah P. Linking genotypic and phenotypic changes in the E. coli Long-Term Evolution Experiment using metabolomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.15.528756. [PMID: 36874203 PMCID: PMC9985142 DOI: 10.1101/2023.02.15.528756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Changes in an organism's environment, genome, or gene expression patterns can lead to changes in its metabolism. The metabolic phenotype can be under selection and contributes to adaptation. However, the networked and convoluted nature of an organism's metabolism makes relating mutations, metabolic changes, and effects on fitness challenging. To overcome this challenge, we use the Long-Term Evolution Experiment (LTEE) with E. coli as a model to understand how mutations can eventually affect metabolism and perhaps fitness. We used mass-spectrometry to broadly survey the metabolomes of the ancestral strains and all 12 evolved lines. We combined this metabolic data with mutation and expression data to suggest how mutations that alter specific reaction pathways, such as the biosynthesis of nicotinamide adenine dinucleotide, might increase fitness in the system. Our work provides a better understanding of how mutations might affect fitness through the metabolic changes in the LTEE and thus provides a major step in developing a complete genotype-phenotype map for this experimental system.
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Affiliation(s)
- John S. Favate
- Department of Genetics, Rutgers University, Piscataway, New Jersey, USA
- Human Genetics Institute of New Jersey, Piscataway, New Jersey, USA
| | - Kyle S. Skalenko
- Department of Genetics, Rutgers University, Piscataway, New Jersey, USA
- Waksman Institute, Rutgers University, Piscataway, New Jersey, USA
| | - Eric Chiles
- Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | - Xiaoyang Su
- Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | - Srujana S. Yadavalli
- Department of Genetics, Rutgers University, Piscataway, New Jersey, USA
- Waksman Institute, Rutgers University, Piscataway, New Jersey, USA
| | - Premal Shah
- Department of Genetics, Rutgers University, Piscataway, New Jersey, USA
- Human Genetics Institute of New Jersey, Piscataway, New Jersey, USA
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Moreau PL. Regulation of phosphate starvation-specific responses in Escherichia coli. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 36972330 DOI: 10.1099/mic.0.001312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Toxic agents added into the medium of rapidly growing Escherichia coli induce specific stress responses through the activation of specialized transcription factors. Each transcription factor and downstream regulon (e.g. SoxR) are linked to a unique stress (e.g. superoxide stress). Cells starved of phosphate induce several specific stress regulons during the transition to stationary phase when the growth rate is steadily declining. Whereas the regulatory cascades leading to the expression of specific stress regulons are well known in rapidly growing cells stressed by toxic products, they are poorly understood in cells starved of phosphate. The intent of this review is to both describe the unique mechanisms of activation of specialized transcription factors and discuss signalling cascades leading to the induction of specific stress regulons in phosphate-starved cells. Finally, I discuss unique defence mechanisms that could be induced in cells starved of ammonium and glucose.
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Affiliation(s)
- Patrice L Moreau
- Laboratoire Chimie Bactérienne, LCB-UMR 7283, Institut Microbiologie Méditerranée, CNRS/Université Aix-Marseille, Marseille, France
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12
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Schubert C, Unden G. Fumarate, a central electron acceptor for Enterobacteriaceae beyond fumarate respiration and energy conservation. Adv Microb Physiol 2023; 82:267-299. [PMID: 36948656 DOI: 10.1016/bs.ampbs.2022.10.002] [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: 12/12/2022]
Abstract
C4-dicarboxylates (C4-DCs) such as fumarate, l-malate and l-aspartate are key substrates for Enterobacteria such as Escherichia coli or Salmonella typhimurium during anaerobic growth. In general, C4-DCs are oxidants during biosynthesis, e.g., of pyrimidine or heme, acceptors for redox balancing, a high-quality nitrogen source (l-aspartate) and electron acceptor for fumarate respiration. Fumarate reduction is required for efficient colonization of the murine intestine, even though the colon contains only small amounts of C4-DCs. However, fumarate can be produced endogenously by central metabolism, allowing autonomous production of an electron acceptor for biosynthesis and redox balancing. Bacteria possess a complex set of transporters for the uptake (DctA), antiport (DcuA, DcuB, TtdT) and excretion (DcuC) of C4-DCs. DctA and DcuB exert regulatory functions and link transport to metabolic control through interaction with regulatory proteins. The sensor kinase DcuS of the C4-DC two-component system DcuS-DcuR forms complexes with DctA (aerobic) or DcuB (anaerobic), representing the functional state of the sensor. Moreover, EIIAGlc from the glucose phospho-transferase system binds to DctA and presumably inhibits C4-DC uptake. Overall, the function of fumarate as an oxidant in biosynthesis and redox balancing explains the pivotal role of fumarate reductase for intestinal colonization, while the role of fumarate in energy conservation (fumarate respiration) is of minor importance.
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Affiliation(s)
- Christopher Schubert
- Institute for Molecular Physiology (IMP), Microbiology and Biotechnology; Johannes Gutenberg-University, Mainz, Germany; Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
| | - Gottfried Unden
- Institute for Molecular Physiology (IMP), Microbiology and Biotechnology; Johannes Gutenberg-University, Mainz, Germany.
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Salmonella Central Carbon Metabolism Enhances Bactericidal Killing by Fluoroquinolone Antibiotics. Antimicrob Agents Chemother 2022; 66:e0234421. [PMID: 35658490 DOI: 10.1128/aac.02344-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The efficacy of killing by bactericidal antibiotics has been reported to depend in large part on the ATP levels, with low levels of ATP leading to increased persistence after antibiotic challenge. Here, we show that an atp operon deletion strain of Salmonella enterica serovar Typhimurium lacking the ATP synthase was at least 10-fold more sensitive to killing by the fluoroquinolone antibiotic ciprofloxacin and yet showed either increased survival or no significant difference compared with the wild-type strain when challenged with aminoglycoside or β-lactam antibiotics, respectively. The increased cell killing and reduced bacterial survival (persistence) after fluoroquinolone challenge were found to involve metabolic compensation for the loss of the ATP synthase through central carbon metabolism reactions and increased NAD(P)H levels. We conclude that the intracellular ATP levels per se do not correlate with bactericidal antibiotic persistence to fluoroquinolone killing; rather, the central carbon metabolic pathways active at the time of challenge and the intracellular target of the antibiotic determine the efficacy of treatment.
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14
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Unique C-terminal extension and interactome of Mycobacterium tuberculosis GlmU impacts it's in vivo function and the survival of pathogen. Biochem J 2021; 478:2081-2099. [PMID: 33955473 DOI: 10.1042/bcj20210170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/01/2021] [Accepted: 05/06/2021] [Indexed: 11/17/2022]
Abstract
N-acetyl glucosamine-1-phosphate uridyltransferase (GlmU) is a bifunctional enzyme involved in the biosynthesis of Uridine diphosphate N-acetylglucosamine (UDP-GlcNAc). UDP-GlcNAc is a critical precursor for the synthesis of peptidoglycan and other cell wall components. The absence of a homolog in eukaryotes makes GlmU an attractive target for therapeutic intervention. Mycobacterium tuberculosis GlmU (GlmUMt) has features, such as a C-terminal extension, that are not present in GlmUorthologs from other bacteria. Here, we set out to determine the uniqueness of GlmUMt by performing in vivo complementation experiments using RvΔglmU mutant. We find that any deletion of the carboxy-terminal extension region of GlmUMt abolishes its ability to complement the function of GlmUMt. Results show orthologs of GlmU, including its closest ortholog, from Mycobacterium smegmatis, cannot complement the function of GlmUMt. Furthermore, the co-expression of GlmUMt domain deletion mutants with either acetyl or uridyltransferase activities failed to rescue the function. However, co-expression of GlmUMt point mutants with either acetyl or uridyltransferase activities successfully restored the biological function of GlmUMt, likely due to the formation of heterotrimers. Based on the interactome experiments, we speculate that GlmUMt participates in unique interactions essential for its in vivo function.
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15
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Lee DW, Park YW, Lee MY, Jeong KH, Lee JY. Structural analysis and insight into effector binding of the niacin-responsive repressor NiaR from Bacillus halodurans. Sci Rep 2020; 10:21039. [PMID: 33273654 PMCID: PMC7713382 DOI: 10.1038/s41598-020-78148-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 11/18/2020] [Indexed: 11/30/2022] Open
Abstract
The niacin-responsive repressor, NiaR, is transcriptional repressor of certain nicotinamide adenine dinucleotide (NAD) biosynthetic genes in response to an increase in niacin levels. NAD is a vital molecule involved in various cellular redox reactions as an electron donor or electron acceptor. The NiaR family is conserved broadly in the Bacillus/Clostridium group, as well as in the Fusobacteria and Thermotogales lineages. The NiaR structure consists of two domains: an N-terminal DNA-binding domain, and a C-terminal regulation domain containing a metal-binding site. In this paper, we report the crystal structures of apo and niacin-bound forms of NiaR from Bacillus halodurans (BhNiaR). The analysis of metal-binding and niacin-binding sites through the apo and niacin-bound structures is described. Each N- and C-terminal domain structure of BhNiaR is almost identical with NiaR from Thermotoga maritima, but the overall domain arrangement is quite different. A zinc ion is fully occupied in each subunit with well-conserved residues in the C-terminal domain. Niacin is also located at a hydrophobic pocket near the zinc ion in the C-terminal domain.
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Affiliation(s)
- Dong Won Lee
- Department of Life Science, Dongguk University-Seoul, Ilsandong-gu, Goyang-si, Gyeonggi-do, 10326, Republic of Korea
| | - Young Woo Park
- Department of Life Science, Dongguk University-Seoul, Ilsandong-gu, Goyang-si, Gyeonggi-do, 10326, Republic of Korea.,Structural Biology Lab, B2SBIO, Yeonsu-gu, Incheon, Republic of Korea
| | - Myung Yeon Lee
- Department of Life Science, Dongguk University-Seoul, Ilsandong-gu, Goyang-si, Gyeonggi-do, 10326, Republic of Korea
| | - Kang Hwa Jeong
- Department of Life Science, Dongguk University-Seoul, Ilsandong-gu, Goyang-si, Gyeonggi-do, 10326, Republic of Korea
| | - Jae Young Lee
- Department of Life Science, Dongguk University-Seoul, Ilsandong-gu, Goyang-si, Gyeonggi-do, 10326, Republic of Korea.
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16
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Bitew MA, Wawegama NK, Newton HJ, Sansom FM. Meso-tartrate inhibits intracellular replication of Coxiella burnetii, the causative agent of the zoonotic disease Q fever. Pathog Dis 2020; 77:5679890. [PMID: 31845968 DOI: 10.1093/femspd/ftz066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 12/16/2019] [Indexed: 11/13/2022] Open
Abstract
The zoonotic disease Q fever caused by the intracellular bacterium Coxiella burnetii remains a global health threat due to its high infectivity, environmental stability, the debilitating nature and the long duration of treatment. Designing new and potent drugs that target previously unexplored pathways is essential to shorten treatment time and minimise antibiotic resistance. Nicotinamide adenine dinucleotide (NAD) is an essential and ubiquitous cofactor in all living organisms. NadB, an L-aspartate oxidase catalysing the first step of the prokaryotic-specific NAD de novo biosynthetic pathway, is required for C. burnetii growth and replication inside host cells. In this study, in vitro enzyme assays utilising recombinant glutathione S-transferase tagged NadB (GST-NadB) demonstrated inhibition of the L-aspartate oxidase activity of NadB by meso-tartrate. Furthermore, meso-tartrate inhibits intracellular growth and replication of C. burnetii inside host cells in a dose-dependent manner, and has no effect on the viability of mammalian cells. Unexpectedly, meso-tartrate also inhibited growth of C. burnetii in axenic medium, and further reduces replication of the nadB mutant inside host cells, suggesting it is acting more widely than simple inhibition of NadB. Overall, these results suggest that the antibacterial activity of meso-tartrate warrants further study, including investigation of its additional target(s).
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Affiliation(s)
- Mebratu A Bitew
- Asia-Pacific Centre for Animal Health, Veterinary Preclinical Centre, Melbourne Veterinary School, The University of Melbourne, Parkville 3010, Victoria, Australia
| | - Nadeeka K Wawegama
- Asia-Pacific Centre for Animal Health, Veterinary Preclinical Centre, Melbourne Veterinary School, The University of Melbourne, Parkville 3010, Victoria, Australia
| | - Hayley J Newton
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne 3000, Victoria, Australia
| | - Fiona M Sansom
- Asia-Pacific Centre for Animal Health, Veterinary Preclinical Centre, Melbourne Veterinary School, The University of Melbourne, Parkville 3010, Victoria, Australia
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17
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Rodríguez-Bolaños M, Perez-Montfort R. Medical and Veterinary Importance of the Moonlighting Functions of Triosephosphate Isomerase. Curr Protein Pept Sci 2019; 20:304-315. [DOI: 10.2174/1389203719666181026170751] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 10/16/2018] [Accepted: 10/18/2018] [Indexed: 12/13/2022]
Abstract
Triosephosphate isomerase is the fifth enzyme in glycolysis and its canonical function is the
reversible isomerization of glyceraldehyde-3-phosphate and dihydroxyacetone phosphate. Within the
last decade multiple other functions, that may not necessarily always involve catalysis, have been described.
These include variations in the degree of its expression in many types of cancer and participation
in the regulation of the cell cycle. Triosephosphate isomerase may function as an auto-antigen and
in the evasion of the immune response, as a factor of virulence of some organisms, and also as an important
allergen, mainly in a variety of seafoods. It is an important factor to consider in the cryopreservation
of semen and seems to play a major role in some aspects of the development of Alzheimer's disease. It
also seems to be responsible for neurodegenerative alterations in a few cases of human triosephosphate
isomerase deficiency. Thus, triosephosphate isomerase is an excellent example of a moonlighting protein.
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Affiliation(s)
- Mónica Rodríguez-Bolaños
- Departamento de Bioquimica y Biologia Estructural, Instituto de Fisiologia Celular, Universidad Nacional Autonoma de Mexico, Av. Universidad 3000, Coyoacan, 04510 Mexico DF, Mexico
| | - Ruy Perez-Montfort
- Departamento de Bioquimica y Biologia Estructural, Instituto de Fisiologia Celular, Universidad Nacional Autonoma de Mexico, Av. Universidad 3000, Coyoacan, 04510 Mexico DF, Mexico
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18
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NADP + is an endogenous PARP inhibitor in DNA damage response and tumor suppression. Nat Commun 2019; 10:693. [PMID: 30741937 PMCID: PMC6370829 DOI: 10.1038/s41467-019-08530-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 12/05/2018] [Accepted: 12/30/2018] [Indexed: 11/15/2022] Open
Abstract
ADP-ribosylation is a unique posttranslational modification catalyzed by poly(ADP-ribose) polymerases (PARPs) using NAD+ as ADP-ribose donor. PARPs play an indispensable role in DNA damage repair and small molecule PARP inhibitors have emerged as potent anticancer drugs. However, to date, PARP inhibitor treatment has been restricted to patients with BRCA1/2 mutation-associated breast and ovarian cancer. One of the major challenges to extend the therapeutic potential of PARP inhibitors to other cancer types is the absence of predictive biomarkers. Here, we show that ovarian cancer cells with higher level of NADP+, an NAD+ derivative, are more sensitive to PARP inhibitors. We demonstrate that NADP+ acts as a negative regulator and suppresses ADP-ribosylation both in vitro and in vivo. NADP+ impairs ADP-ribosylation-dependent DNA damage repair and sensitizes tumor cell to chemically synthesized PARP inhibitors. Taken together, our study identifies NADP+ as an endogenous PARP inhibitor that may have implications in cancer treatment. Cancer cells respond differently to inhibitors of Poly (ADP-ribose) polymerase. Here the authors reveal that ovarian cancer cells with higher cellular NADP+ levels are more sensitive to clinically relevant PARP1 inhibitors and show that NADP+ act as an endogenous inhibitor of PARP enzymes.
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19
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Bitew MA, Khoo CA, Neha N, De Souza DP, Tull D, Wawegama NK, Newton HJ, Sansom FM. De novo NAD synthesis is required for intracellular replication of Coxiella burnetii, the causative agent of the neglected zoonotic disease Q fever. J Biol Chem 2018; 293:18636-18645. [PMID: 30315113 PMCID: PMC6290155 DOI: 10.1074/jbc.ra118.005190] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 10/08/2018] [Indexed: 01/22/2023] Open
Abstract
Coxiella burnetii is an intracellular Gram-negative bacterium responsible for the important zoonotic disease Q fever. Improved genetic tools and the ability to grow this bacterium in host cell-free media has advanced the study of C. burnetii pathogenesis, but the mechanisms that allow it to survive inside the hostile phagolysosome remain incompletely understood. Previous screening of a transposon mutant library for replication within HeLa cells has suggested that nadB, encoding a putative l-aspartate oxidase required for de novo NAD synthesis, is needed for intracellular replication. Here, using genetic complementation of two independent nadB mutants and intracellular replication assays, we confirmed this finding. Untargeted metabolite analyses demonstrated key changes in metabolites in the NAD biosynthetic pathway in the nadB mutant compared with the WT, confirming the involvement of NadB in de novo NAD synthesis. Bioinformatic analysis revealed the presence of a functionally conserved arginine residue at position 275. Using site-directed mutagenesis to substitute this residue with leucine, which abolishes the activity of Escherichia coli NadB, and expression of WT and R275L GST-NadB fusion proteins in E. coli JM109, we found that purified recombinant WT GST-NadB has l-aspartate oxidase activity and that the R275L NadB variant is inactive. Complementation of the C. burnetii nadB mutant with a plasmid expressing this inactive R275L NadB failed to restore replication to WT levels, confirming the link between de novo NAD synthesis and intracellular replication of C. burnetii This suggests that targeting this prokaryotic-specific pathway could advance the development of therapeutics to combat C. burnetii infections.
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Affiliation(s)
- Mebratu A Bitew
- From the Asia-Pacific Centre for Animal Health, Melbourne Veterinary School and
| | - Chen Ai Khoo
- the Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne 3000, Australia
| | - Nitika Neha
- From the Asia-Pacific Centre for Animal Health, Melbourne Veterinary School and
- Metabolomics Australia, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville 3010, Australia and
| | - David P De Souza
- Metabolomics Australia, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville 3010, Australia and
| | - Dedreia Tull
- Metabolomics Australia, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville 3010, Australia and
| | - Nadeeka K Wawegama
- From the Asia-Pacific Centre for Animal Health, Melbourne Veterinary School and
| | - Hayley J Newton
- the Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne 3000, Australia
| | - Fiona M Sansom
- From the Asia-Pacific Centre for Animal Health, Melbourne Veterinary School and
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20
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Bouvet O, Bourdelier E, Glodt J, Clermont O, Denamur E. Diversity of the auxotrophic requirements in natural isolates of Escherichia coli. MICROBIOLOGY-SGM 2017; 163:891-899. [PMID: 28651684 DOI: 10.1099/mic.0.000482] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Isolates of Escherichia coli, except Shigella, are generally prototrophic; they do not require any growth factors to grow in mineral medium. However, a nicotinic acid requirement is common among B2 phylogroup STc95 O18 E. coli clone strains. Nicotinic acid is a precursor of nicotinamide adenine dinucleotide (NAD), an essential molecule that plays central role in cellular metabolism. The defect in NAD synthesis of these strains is due to alterations in de novo biosynthesis pathway nadB gene. Here, by studying growth on minimal medium with glycolytic (glucose) or gluconeogenic (pyruvate or succinate) substrates as the carbon supply in a large panel of E. coli natural isolates representative of the species diversity, we identify an absolute nicotinic acid requirement in non-STc95 strains due in one case to a nadA inactivation. The growth on glucose medium of some extraintestinal pathogenic E. coli strains belonging to various non-O18 B2 phylogroup STc95 clones is restored either by aspartate or nicotinate, demonstrating that the nicotinic acid requirement can also be due to an intracellular aspartate depletion. The auxotrophic requirements depend on the carbon source available in the environment. Moreover, some strains prototrophic in glucose medium become auxotrophic in succinate medium, and conversely, some strainsauxotrophic in glucose medium become prototrophic in succinate medium. Finally, a partial depletion of intracellular aspartate can be observed in some prototrophic strains belonging to various phylogroups. The observed more or less significant depletion according to isolates may be due to differences in tricarboxylic acid cycle enzyme activities. These metabolic defects could be involved in the adaptation of E. coli to its various niches.
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Affiliation(s)
- Odile Bouvet
- IAME, UMR 1137, INSERM, Univ Paris Diderot, Sorbonne Paris Cité, F-75018, Paris, France
| | - Emmanuelle Bourdelier
- IAME, UMR 1137, INSERM, Univ Paris Diderot, Sorbonne Paris Cité, F-75018, Paris, France
| | - Jeremy Glodt
- IAME, UMR 1137, INSERM, Univ Paris Diderot, Sorbonne Paris Cité, F-75018, Paris, France
| | - Olivier Clermont
- IAME, UMR 1137, INSERM, Univ Paris Diderot, Sorbonne Paris Cité, F-75018, Paris, France
| | - Erick Denamur
- AP-HP, Laboratoire de Génétique Moléculaire, Hôpital Bichat, F-75018, Paris, France.,IAME, UMR 1137, INSERM, Univ Paris Diderot, Sorbonne Paris Cité, F-75018, Paris, France
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Phosphoribosyl Diphosphate (PRPP): Biosynthesis, Enzymology, Utilization, and Metabolic Significance. Microbiol Mol Biol Rev 2016; 81:81/1/e00040-16. [PMID: 28031352 DOI: 10.1128/mmbr.00040-16] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Phosphoribosyl diphosphate (PRPP) is an important intermediate in cellular metabolism. PRPP is synthesized by PRPP synthase, as follows: ribose 5-phosphate + ATP → PRPP + AMP. PRPP is ubiquitously found in living organisms and is used in substitution reactions with the formation of glycosidic bonds. PRPP is utilized in the biosynthesis of purine and pyrimidine nucleotides, the amino acids histidine and tryptophan, the cofactors NAD and tetrahydromethanopterin, arabinosyl monophosphodecaprenol, and certain aminoglycoside antibiotics. The participation of PRPP in each of these metabolic pathways is reviewed. Central to the metabolism of PRPP is PRPP synthase, which has been studied from all kingdoms of life by classical mechanistic procedures. The results of these analyses are unified with recent progress in molecular enzymology and the elucidation of the three-dimensional structures of PRPP synthases from eubacteria, archaea, and humans. The structures and mechanisms of catalysis of the five diphosphoryltransferases are compared, as are those of selected enzymes of diphosphoryl transfer, phosphoryl transfer, and nucleotidyl transfer reactions. PRPP is used as a substrate by a large number phosphoribosyltransferases. The protein structures and reaction mechanisms of these phosphoribosyltransferases vary and demonstrate the versatility of PRPP as an intermediate in cellular physiology. PRPP synthases appear to have originated from a phosphoribosyltransferase during evolution, as demonstrated by phylogenetic analysis. PRPP, furthermore, is an effector molecule of purine and pyrimidine nucleotide biosynthesis, either by binding to PurR or PyrR regulatory proteins or as an allosteric activator of carbamoylphosphate synthetase. Genetic analyses have disclosed a number of mutants altered in the PRPP synthase-specifying genes in humans as well as bacterial species.
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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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