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Yu J, Youngson NA, Laybutt DR, Morris MJ, Leigh SJ. Complementary yet divergent effects of exercise and an exercise mimetic on microbiome in high-fat diet-induced obesity. Physiol Genomics 2024; 56:136-144. [PMID: 38009223 DOI: 10.1152/physiolgenomics.00066.2023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/21/2023] [Accepted: 11/17/2023] [Indexed: 11/28/2023] Open
Abstract
Exercise is beneficial for obesity, partially through increased mitochondrial activity and raised nicotinamide adenine dinucleotide (NAD), a coenzyme critical for mitochondrial function and metabolism. Recent work has shown that increasing the availability of NAD through pharmacological means improves metabolic health in rodent models of diet-induced obesity and that the effect of these supplements when administered orally may be modulated by the gut microbiome. The gut microbiome is altered by both diet and exercise and is thought to contribute to some aspects of high-fat diet-induced metabolic dysfunction. We examined the independent and combined effects of treadmill exercise and nicotinamide mononucleotide (NMN) supplementation on the gut microbiome of female C57Bl6/J mice chronically fed a high-fat diet. We showed that 8 wk of treadmill exercise, oral-administered NMN, or combined therapy exert unique effects on gut microbiome composition without changing bacterial species richness. Exercise and NMN exerted additive effects on microbiota composition, and NMN partially or fully restored predicted microbial functions, specifically carbohydrate and lipid metabolism, to control levels. Further research is warranted to better understand the mechanisms underpinning the interactions between exercise and oral NAD+ precursor supplementation on gut microbiome.NEW & NOTEWORTHY Exercise and NAD+ precursor supplementation exerted additive and independent effects on gut microbiota composition and inferred function in female mice with diet-induced obesity. Notably, combining exercise and oral nicotinamide mononucleotide supplementation restored inferred microbial functions to control levels, indicating that this combination may improve high-fat diet-induced alterations to microbial metabolism.
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Affiliation(s)
- Josephine Yu
- School of Biomedical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Neil A Youngson
- School of Biomedical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - D Ross Laybutt
- Garvan Institute of Medical Research, St Vincent's Clinical School, UNSW Sydney, Sydney, New South Wales, Australia
| | - Margaret J Morris
- School of Biomedical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Sarah-Jane Leigh
- School of Biomedical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
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2
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Li Y, Mao K, Zang Y, Lu G, Qiu Q, Ouyang K, Zhao X, Song X, Xu L, Liang H, Qu M. Revealing the developmental characterization of rumen microbiome and its host in newly received cattle during receiving period contributes to formulating precise nutritional strategies. MICROBIOME 2023; 11:238. [PMID: 37924150 PMCID: PMC10623857 DOI: 10.1186/s40168-023-01682-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 09/27/2023] [Indexed: 11/06/2023]
Abstract
BACKGROUND Minimizing mortality losses due to multiple stress and obtaining maximum performance are the production goals for newly received cattle. In recent years, vaccination and metaphylaxis treatment significantly decreased the mortality rate of newly received cattle, while the growth block induced by treatment is still obvious. Assessment of blood metabolites and behavior monitoring offer potential for early identification of morbid animals. Moreover, the ruminal microorganisms' homeostasis is a guarantee of beef steers' growth and health. The most critical period for newly received cattle is the first-month post-transport. Therefore, analyzing rumen metagenomics, rumen metabolomics, host metabolomics, and their interaction during receiving period (1 day before transport and at days 1/4, 16, and 30 after transport) is key to revealing the mechanism of growth retardation, and then to formulating management and nutritional practices for newly received cattle. RESULTS The levels of serum hormones (COR and ACTH), and pro-inflammatory factors (IL-1β, TNF-α, and IL-6) were highest at day 16, and lowest at day 30 after arrival. Meanwhile, the antioxidant capacity (SOD, GSH-Px, and T-AOC) was significantly decreased at day 16 and increased at day 30 after arrival. Metagenomics analysis revealed that rumen microbes, bacteria, archaea, and eukaryota had different trends among the four different time points. At day 16 post-transport, cattle had a higher abundance of ruminal bacteria and archaea than those before transport, but the eukaryote abundance was highest at day 30 post-transport. Before transport, most bacteria were mainly involved in polysaccharides digestion. At day 4 post-transport, the most significantly enriched KEGG pathways were nucleotide metabolism (pyrimidine metabolism and purine metabolism). At day 16 post-transport, the energy metabolism (glycolysis/gluconeogenesis, pyruvate metabolism) and ruminal contents of MCP and VFAs were significantly increased, but at the same time, energy loss induced by methane yields (Methanobrevibacter) together with pathogenic bacteria (Saccharopolyspora rectivirgula) were also significantly increased. At this time, the most upregulated ruminal L-ornithine produces more catabolite polyamines, which cause oxidative stress to rumen microbes and their host; the most downregulated ruminal 2',3'-cAMP provided favorable growth conditions for pathogenic bacteria, and the downregulated ruminal vitamin B6 metabolism and serum PC/LysoPC disrupt immune function and inflammation reaction. At day 30 post-transport, the ruminal L-ornithine and its catabolites (mainly spermidine and 1,3-propanediamine) were decreased, and the serum PC/LysoPC and 2',3'-cNMPs pools were increased. This is also consistent with the changes in redox, inflammation, and immune status of the host. CONCLUSIONS This study provides new ideas for regulating the health and performance of newly received cattle during the receiving period. The key point is to manage the newly received cattle about day 16 post-transport, specifically to inhibit the production of methane and polyamines, and the reproduction of harmful bacteria in the rumen, therefore improving the immunity and performance of newly received cattle. Video Abstract.
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Affiliation(s)
- Yanjiao Li
- Jiangxi Province Key Laboratory of Animal Nutrition/Animal Nutrition and Feed Safety Innovation Team, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China.
| | - Kang Mao
- Jiangxi Province Key Laboratory of Animal Nutrition/Animal Nutrition and Feed Safety Innovation Team, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Yitian Zang
- Jiangxi Province Key Laboratory of Animal Nutrition/Animal Nutrition and Feed Safety Innovation Team, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Guwei Lu
- Jiangxi Province Key Laboratory of Animal Nutrition/Animal Nutrition and Feed Safety Innovation Team, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Qinghua Qiu
- Jiangxi Province Key Laboratory of Animal Nutrition/Animal Nutrition and Feed Safety Innovation Team, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Kehui Ouyang
- Jiangxi Province Key Laboratory of Animal Nutrition/Animal Nutrition and Feed Safety Innovation Team, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Xianghui Zhao
- Jiangxi Province Key Laboratory of Animal Nutrition/Animal Nutrition and Feed Safety Innovation Team, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Xiaozhen Song
- Jiangxi Province Key Laboratory of Animal Nutrition/Animal Nutrition and Feed Safety Innovation Team, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Lanjiao Xu
- Jiangxi Province Key Laboratory of Animal Nutrition/Animal Nutrition and Feed Safety Innovation Team, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Huan Liang
- Jiangxi Province Key Laboratory of Animal Nutrition/Animal Nutrition and Feed Safety Innovation Team, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Mingren Qu
- Jiangxi Province Key Laboratory of Animal Nutrition/Animal Nutrition and Feed Safety Innovation Team, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China.
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Tao X, Morgan JS, Liu J, Kempher ML, Xu T, Zhou J. Target integration of an exogenous β-glucosidase enhances cellulose degradation and ethanol production in Clostridium cellulolyticum. BIORESOURCE TECHNOLOGY 2023; 376:128849. [PMID: 36898565 DOI: 10.1016/j.biortech.2023.128849] [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: 02/06/2023] [Revised: 03/03/2023] [Accepted: 03/05/2023] [Indexed: 06/18/2023]
Abstract
The bacteria Clostridium cellulolyticum is a promising candidate for consolidated bioprocessing (CBP). However, genetic engineering is necessary to improve this organism's cellulose degradation and bioconversion efficiencies to meet standard industrial requirements. In this study, CRISPR-Cas9n was used to integrate an efficient β-glucosidase into the genome of C. cellulolyticum, disrupting lactate dehydrogenase (ldh) expression and reducing lactate production. The engineered strain showed a 7.4-fold increase in β-glucosidase activity, a 70% decrease in ldh expression, a 12% increase in cellulose degradation, and a 32% increase in ethanol production compared to wild type. Additionally, ldh was identified as a potential site for heterologous expression. These results demonstrate that simultaneous β-glucosidase integration and lactate dehydrogenase disruption is an effective strategy for increasing cellulose to ethanol bioconversion rates in C. cellulolyticum.
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Affiliation(s)
- Xuanyu Tao
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA
| | - Josiah S Morgan
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA
| | - Jiantao Liu
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA
| | - Megan L Kempher
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA
| | - Tao Xu
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA; Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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Minazzato G, Gasparrini M, Heroux A, Sernova NV, Rodionov DA, Cianci M, Sorci L, Raffaelli N. Bacterial NadQ (COG4111) is a Nudix-like, ATP-responsive regulator of NAD biosynthesis. J Struct Biol 2022; 214:107917. [PMID: 36332744 DOI: 10.1016/j.jsb.2022.107917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 10/13/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022]
Abstract
Nicotinamide-adenine dinucleotide (NAD) is centrally important to metabolic reactions that involve redox chemistry. In bacteria, NAD biosynthesis is controlled by different transcription factors, depending on the species. Among the four regulators identified so far, the protein NadQ is reported to act as a repressor of the de novo NAD biosynthetic pathway in proteobacteria. Using comparative genomics, a systematic reconstruction of NadQ regulons in thousands of fully sequenced bacterial genomes has been performed, confirming that NadQ is present in α-proteobacteria and some β- and γ-proteobacteria, including pathogens like Bordetella pertussis and Neisseria meningitidis, where it likely controls de novo NAD biosynthesis. Through mobility shift assay and mutagenesis, the DNA binding activity of NadQ from Agrobacterium tumefaciens was experimentally validated and determined to be suppressed by ATP. The crystal structures of NadQ in native form and in complex with ATP were determined, indicating that NadQ is a dimer, with each monomer composed of an N-terminal Nudix domain hosting the effector binding site and a C-terminal winged helix-turn-helix domain that binds DNA. Within the dimer, we found one ATP molecule bound, at saturating concentration of the ligand, in keeping with an intrinsic asymmetry of the quaternary structure. Overall, this study provided the basis for depicting a working model of NadQ regulation mechanism.
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Affiliation(s)
- Gabriele Minazzato
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Massimiliano Gasparrini
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Annie Heroux
- Elettra - Sincrotrone Trieste S.C.P.A., Basovizza, Italy
| | - Natalia V Sernova
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry A Rodionov
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia; Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Michele Cianci
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Leonardo Sorci
- Department of Materials, Environmental Sciences and Urban Planning, Division of Bioinformatics and Biochemistry, Polytechnic University of Marche, Ancona, Italy.
| | - Nadia Raffaelli
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy.
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5
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Minazzato G, Gasparrini M, Amici A, Cianci M, Mazzola F, Orsomando G, Sorci L, Raffaelli N. Functional Characterization of COG1713 (YqeK) as a Novel Diadenosine Tetraphosphate Hydrolase Family. J Bacteriol 2020; 202:e00053-20. [PMID: 32152217 PMCID: PMC7186459 DOI: 10.1128/jb.00053-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 03/03/2020] [Indexed: 12/29/2022] Open
Abstract
Diadenosine tetraphosphate (Ap4A) is a dinucleotide found in both prokaryotes and eukaryotes. In bacteria, its cellular levels increase following exposure to various stress signals and stimuli, and its accumulation is generally correlated with increased sensitivity to a stressor(s), decreased pathogenicity, and enhanced antibiotic susceptibility. Ap4A is produced as a by-product of tRNA aminoacylation, and is cleaved to ADP molecules by hydrolases of the ApaH and Nudix families and/or by specific phosphorylases. Here, considering evidence that the recombinant protein YqeK from Staphylococcus aureus copurified with ADP, and aided by thermal shift and kinetic analyses, we identified the YqeK family of proteins (COG1713) as an unprecedented class of symmetrically cleaving Ap4A hydrolases. We validated the functional assignment by confirming the ability of YqeK to affect in vivo levels of Ap4A in B. subtilis YqeK shows a catalytic efficiency toward Ap4A similar to that of the symmetrically cleaving Ap4A hydrolases of the known ApaH family, although it displays a distinct fold that is typical of proteins of the HD domain superfamily harboring a diiron cluster. Analysis of the available 3D structures of three members of the YqeK family provided hints to the mode of substrate binding. Phylogenetic analysis revealed the occurrence of YqeK proteins in a consistent group of Gram-positive bacteria that lack ApaH enzymes. Comparative genomics highlighted that yqeK and apaH genes share a similar genomic context, where they are frequently found in operons involved in integrated responses to stress signals.IMPORTANCE Elevation of Ap4A level in bacteria is associated with increased sensitivity to heat and oxidative stress, reduced antibiotic tolerance, and decreased pathogenicity. ApaH is the major Ap4A hydrolase in gamma- and betaproteobacteria and has been recently proposed as a novel target to weaken the bacterial resistance to antibiotics. Here, we identified the orphan YqeK protein family (COG1713) as a highly efficient Ap4A hydrolase family, with members distributed in a consistent group of bacterial species that lack the ApaH enzyme. Among them are the pathogens Staphylococcus aureus, Streptococcus pneumoniae, and Mycoplasma pneumoniae By identifying the player contributing to Ap4A homeostasis in these bacteria, we disclose a novel target to develop innovative antibacterial strategies.
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Affiliation(s)
- Gabriele Minazzato
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Massimiliano Gasparrini
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Adolfo Amici
- Department of Clinical Sciences DISCO, Section of Biochemistry, Polytechnic University of Marche, Ancona, Italy
| | - Michele Cianci
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Francesca Mazzola
- Department of Clinical Sciences DISCO, Section of Biochemistry, Polytechnic University of Marche, Ancona, Italy
| | - Giuseppe Orsomando
- Department of Clinical Sciences DISCO, Section of Biochemistry, Polytechnic University of Marche, Ancona, Italy
| | - Leonardo Sorci
- Department of Materials, Environmental Sciences and Urban Planning, Division of Bioinformatics and Biochemistry, Polytechnic University of Marche, Ancona, Italy
| | - Nadia Raffaelli
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
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Santos ARS, Gerhardt ECM, Parize E, Pedrosa FO, Steffens MBR, Chubatsu LS, Souza EM, Passaglia LMP, Sant'Anna FH, de Souza GA, Huergo LF, Forchhammer K. NAD + biosynthesis in bacteria is controlled by global carbon/nitrogen levels via PII signaling. J Biol Chem 2020; 295:6165-6176. [PMID: 32179648 PMCID: PMC7196632 DOI: 10.1074/jbc.ra120.012793] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 03/10/2020] [Indexed: 01/01/2023] Open
Abstract
NAD+ is a central metabolite participating in core metabolic redox reactions. The prokaryotic NAD synthetase enzyme NadE catalyzes the last step of NAD+ biosynthesis, converting nicotinic acid adenine dinucleotide (NaAD) to NAD+. Some members of the NadE family use l-glutamine as a nitrogen donor and are named NadEGln. Previous gene neighborhood analysis has indicated that the bacterial nadE gene is frequently clustered with the gene encoding the regulatory signal transduction protein PII, suggesting a functional relationship between these proteins in response to the nutritional status and the carbon/nitrogen ratio of the bacterial cell. Here, using affinity chromatography, bioinformatics analyses, NAD synthetase activity, and biolayer interferometry assays, we show that PII and NadEGln physically interact in vitro, that this complex relieves NadEGln negative feedback inhibition by NAD+. This mechanism is conserved in distantly related bacteria. Of note, the PII protein allosteric effector and cellular nitrogen level indicator 2-oxoglutarate (2-OG) inhibited the formation of the PII-NadEGln complex within a physiological range. These results indicate an interplay between the levels of ATP, ADP, 2-OG, PII-sensed glutamine, and NAD+, representing a metabolic hub that may balance the levels of core nitrogen and carbon metabolites. Our findings support the notion that PII proteins act as a dissociable regulatory subunit of NadEGln, thereby enabling the control of NAD+ biosynthesis according to the nutritional status of the bacterial cell.
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Affiliation(s)
- Adrian Richard Schenberger Santos
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná (UFPR), Curitiba, Paraná, CEP: 81531-980 Brazil; Interfakultäres Institut für Mikrobiologie und Infektionsmedizin der Eberhard-Karls Universität Tübingen, Auf der Morgenstelle 28, Tübingen 72076, Germany
| | | | - Erick Parize
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná (UFPR), Curitiba, Paraná, CEP: 81531-980 Brazil
| | - Fabio Oliveira Pedrosa
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná (UFPR), Curitiba, Paraná, CEP: 81531-980 Brazil
| | - Maria Berenice Reynaud Steffens
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná (UFPR), Curitiba, Paraná, CEP: 81531-980 Brazil
| | - Leda Satie Chubatsu
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná (UFPR), Curitiba, Paraná, CEP: 81531-980 Brazil
| | - Emanuel Maltempi Souza
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná (UFPR), Curitiba, Paraná, CEP: 81531-980 Brazil
| | - Luciane Maria Pereira Passaglia
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, CEP:91501-970 CP 15053 Brazil
| | - Fernando Hayashi Sant'Anna
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, CEP:91501-970 CP 15053 Brazil
| | - Gustavo Antônio de Souza
- Departamento de Bioquímica, Universidade Federal do Rio Grande do Norte, Natal/RN, CEP: 59072-970 Brazil
| | - Luciano Fernandes Huergo
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná (UFPR), Curitiba, Paraná, CEP: 81531-980 Brazil; Interfakultäres Institut für Mikrobiologie und Infektionsmedizin der Eberhard-Karls Universität Tübingen, Auf der Morgenstelle 28, Tübingen 72076, Germany; Setor Litoral, UFPR, Matinhos, Paraná, CEP: 83260-000 Brazil.
| | - Karl Forchhammer
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin der Eberhard-Karls Universität Tübingen, Auf der Morgenstelle 28, Tübingen 72076, Germany.
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7
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Bhat SA, Iqbal IK, Kumar A. Quantification of the Metabolic Heterogeneity in Mycobacterial Cells Through the Measurement of the NADH/NAD+ Ratio Using a Genetically Encoded Sensor. Methods Mol Biol 2019; 1745:261-275. [PMID: 29476473 DOI: 10.1007/978-1-4939-7680-5_14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
NADH/NAD+ levels are an indicator of the bacterial metabolic state. NAD(H) levels are maintained through coordination of pathways involved in NAD(H) synthesis and its catabolic utilization. Conventional methods of estimating NADH/NAD+ require cell disruption and suffer from low specificity and sensitivity and are inadequate in providing spatiotemporal resolution. Recently, genetically encoded biosensors of the NADH/NAD+ ratio have been developed. One of these sensors, Peredox-mCherry, was adapted for the measurement of cellular levels of NADH/NAD+ in the slow-growing Mycobacterium tuberculosis (Mtb) and the fast-growing Mycobacterium smegmatis. Importantly, the use of the engineered reporter strains of Mtb demonstrated a significantly higher heterogeneity among the bacteria residing in macrophages compared to the bacteria grown in synthetic media. Previous estimations of NADH/NAD+ levels have missed this important aspect of the biology of Mtb, which may contribute to the variable response of intracellular Mtb to different antimycobacterial agents. In this chapter, we describe the details of a method used in the generation of reporter strains for the measurement of the NADH/NAD+ ratio in mycobacteria. Importantly, once the reporter strains are created, they can be exploited with fluorescence spectroscopy, FACS, and confocal microscopy to access the dynamic changes in the NADH/NAD+ levels in intact individual bacterial cells. Although we have only described the method for the creation of reporter strains capable of measuring NADH/NAD+ in mycobacteria in this chapter, a similar method can be used for generating reporter strains for other bacterial species, as well. We believe that such reporter stains can be used in novel screens for small molecules that could alter the metabolism of bacterial cells and thus aid in the development of new class of therapeutic agents.
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Affiliation(s)
- Shabir Ahmad Bhat
- Council of Scientific and Industrial Research, Institute of Microbial Technology, Chandigarh, India
| | - Iram Khan Iqbal
- Council of Scientific and Industrial Research, Institute of Microbial Technology, Chandigarh, India
| | - Ashwani Kumar
- Council of Scientific and Industrial Research, Institute of Microbial Technology, Chandigarh, India.
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8
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Smith CA, Mont S, Traver G, Sekhar KR, Crooks PA, Freeman ML. Targeting Enox1 in tumor stroma increases the efficacy of fractionated radiotherapy. Oncotarget 2018; 7:77926-77936. [PMID: 27788492 PMCID: PMC5363632 DOI: 10.18632/oncotarget.12845] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 10/14/2016] [Indexed: 02/07/2023] Open
Abstract
The goal of this investigation was to clarify the question of whether targeting Enox1 in tumor stroma would synergistically enhance the survival of tumor-bearing mice treated with fractionated radiotherapy. Enox1, a NADH oxidase, is expressed in tumor vasculature and stroma. However, it is not expressed in many tumor types, including HT-29 colorectal carcinoma cells. Pharmacological inhibition of Enox1 in endothelial cells inhibited repair of DNA double strand breaks, as measured by γH2AX and 53BP1 foci formation, as well as neutral comet assays. For 4 consecutive days athymic mice bearing HT-29 hindlimb xenografts were injected with a small molecule inhibitor of Enox1 or solvent control. Tumors were then administered 2 Gy of x-rays. On day 5 tumors were administered a single ‘top-up’ fraction of 30 Gy, the purpose of which was to amplify intrinsic differences in the radiation fractionation regimen produced by Enox1 targeting. Pharmacological targeting of Enox1 resulted in 80% of the tumor-bearing mice surviving at 90 days compared to only 40% of tumor-bearing mice treated with solvent control. The increase in survival was not a consequence of reoxygenation, as measured by pimonidazole immunostaining. These results are interpreted to indicate that targeting of Enox1 in tumor stroma significantly enhances the effectiveness of 2 Gy fractionated radiotherapy and identifies Enox1 as a potential therapeutic target.
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Affiliation(s)
- Clayton A Smith
- Department of Radiation Oncology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Current Address: Department of Radiation Oncology, Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA
| | - Stacey Mont
- Department of Radiation Oncology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Geri Traver
- Department of Radiation Oncology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Konjeti R Sekhar
- Department of Radiation Oncology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Peter A Crooks
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Michael L Freeman
- Department of Radiation Oncology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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9
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Longevity of major coenzymes allows minimal de novo synthesis in microorganisms. Nat Microbiol 2017; 2:17073. [PMID: 28504670 DOI: 10.1038/nmicrobiol.2017.73] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 04/05/2017] [Indexed: 02/04/2023]
Abstract
Coenzymes are vital for cellular metabolism and act on the full spectrum of enzymatic reactions. Intrinsic chemical reactivity, enzyme promiscuity and high flux through their catalytic cycles make coenzymes prone to damage. To counteract such compromising factors and ensure stable levels of functional coenzymes, cells use a complex interplay between de novo synthesis, salvage, repair and degradation. However, the relative contribution of these factors is currently unknown, as is the overall stability of coenzymes in the cell. Here, we use dynamic 13C-labelling experiments to determine the half-life of major coenzymes of Escherichia coli. We find that coenzymes such as pyridoxal 5-phosphate, flavins, nicotinamide adenine dinucleotide (phosphate) and coenzyme A are remarkably stable in vivo and allow biosynthesis close to the minimal necessary rate. In consequence, they are essentially produced to compensate for dilution by growth and passed on over generations of cells. Exceptions are antioxidants, which are short-lived, suggesting an inherent requirement for increased renewal. Although the growth-driven turnover of stable coenzymes is apparently subject to highly efficient end-product homeostasis, we exemplify that coenzyme pools are propagated in excess in relation to actual growth requirements. Additional testing of Bacillus subtilis and Saccharomyces cerevisiae suggests that coenzyme longevity is a conserved feature in biology.
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Martínez-Moñino AB, Zapata-Pérez R, García-Saura AG, Gil-Ortiz F, Pérez-Gilabert M, Sánchez-Ferrer Á. Characterization and mutational analysis of a nicotinamide mononucleotide deamidase from Agrobacterium tumefaciens showing high thermal stability and catalytic efficiency. PLoS One 2017; 12:e0174759. [PMID: 28388636 PMCID: PMC5384747 DOI: 10.1371/journal.pone.0174759] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 03/15/2017] [Indexed: 01/07/2023] Open
Abstract
NAD+ has emerged as a crucial element in both bioenergetic and signaling pathways since it acts as a key regulator of cellular and organismal homeostasis. Among the enzymes involved in its recycling, nicotinamide mononucleotide (NMN) deamidase is one of the key players in the bacterial pyridine nucleotide cycle, where it catalyzes the conversion of NMN into nicotinic acid mononucleotide (NaMN), which is later converted to NAD+ in the Preiss-Handler pathway. The biochemical characteristics of bacterial NMN deamidases have been poorly studied, although they have been investigated in some firmicutes, gamma-proteobacteria and actinobacteria. In this study, we present the first characterization of an NMN deamidase from an alphaproteobacterium, Agrobacterium tumefaciens (AtCinA). The enzyme was active over a broad pH range, with an optimum at pH 7.5. Moreover, the enzyme was quite stable at neutral pH, maintaining 55% of its activity after 14 days. Surprisingly, AtCinA showed the highest optimal (80°C) and melting (85°C) temperatures described for an NMN deamidase. The above described characteristics, together with its high catalytic efficiency, make AtCinA a promising biocatalyst for the production of pure NaMN. In addition, six mutants (C32A, S48A, Y58F, Y58A, T105A and R145A) were designed to study their involvement in substrate binding, and two (S31A and K63A) to determine their contribution to the catalysis. However, only four mutants (C32A, S48A Y58F and T105A) showed activity, although with reduced catalytic efficiency. These results, combined with a thermal and structural analysis, reinforce the Ser/Lys catalytic dyad mechanism as the most plausible among those proposed.
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Affiliation(s)
- Ana Belén Martínez-Moñino
- Department of Biochemistry and Molecular Biology-A, Faculty of Biology, Regional Campus of International Excellence “Campus Mare Nostrum”, University of Murcia, Campus Espinardo, E-30100 MURCIA, Spain
- Murcia Biomedical Research Institute (IMIB), Murcia, Spain
| | - Rubén Zapata-Pérez
- Department of Biochemistry and Molecular Biology-A, Faculty of Biology, Regional Campus of International Excellence “Campus Mare Nostrum”, University of Murcia, Campus Espinardo, E-30100 MURCIA, Spain
- Murcia Biomedical Research Institute (IMIB), Murcia, Spain
| | - Antonio Ginés García-Saura
- Department of Biochemistry and Molecular Biology-A, Faculty of Biology, Regional Campus of International Excellence “Campus Mare Nostrum”, University of Murcia, Campus Espinardo, E-30100 MURCIA, Spain
- Murcia Biomedical Research Institute (IMIB), Murcia, Spain
| | | | - Manuela Pérez-Gilabert
- Department of Biochemistry and Molecular Biology-A, Faculty of Biology, Regional Campus of International Excellence “Campus Mare Nostrum”, University of Murcia, Campus Espinardo, E-30100 MURCIA, Spain
- Murcia Biomedical Research Institute (IMIB), Murcia, Spain
| | - Álvaro Sánchez-Ferrer
- Department of Biochemistry and Molecular Biology-A, Faculty of Biology, Regional Campus of International Excellence “Campus Mare Nostrum”, University of Murcia, Campus Espinardo, E-30100 MURCIA, Spain
- Murcia Biomedical Research Institute (IMIB), Murcia, Spain
- * E-mail:
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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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