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Almeida OAC, de Araujo NO, Dias BHS, de Sant’Anna Freitas C, Coerini LF, Ryu CM, de Castro Oliveira JV. The power of the smallest: The inhibitory activity of microbial volatile organic compounds against phytopathogens. Front Microbiol 2023; 13:951130. [PMID: 36687575 PMCID: PMC9845590 DOI: 10.3389/fmicb.2022.951130] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/20/2022] [Indexed: 01/06/2023] Open
Abstract
Plant diseases caused by phytopathogens result in huge economic losses in agriculture. In addition, the use of chemical products to control such diseases causes many problems to the environment and to human health. However, some bacteria and fungi have a mutualistic relationship with plants in nature, mainly exchanging nutrients and protection. Thus, exploring those beneficial microorganisms has been an interesting and promising alternative for mitigating the use of agrochemicals and, consequently, achieving a more sustainable agriculture. Microorganisms are able to produce and excrete several metabolites, but volatile organic compounds (VOCs) have huge biotechnology potential. Microbial VOCs are small molecules from different chemical classes, such as alkenes, alcohols, ketones, organic acids, terpenes, benzenoids and pyrazines. Interestingly, volatilomes are species-specific and also change according to microbial growth conditions. The interaction of VOCs with other organisms, such as plants, insects, and other bacteria and fungi, can cause a wide range of effects. In this review, we show that a large variety of plant pathogens are inhibited by microbial VOCs with a focus on the in vitro and in vivo inhibition of phytopathogens of greater scientific and economic importance in agriculture, such as Ralstonia solanacearum, Botrytis cinerea, Xanthomonas and Fusarium species. In this scenario, some genera of VOC-producing microorganisms stand out as antagonists, including Bacillus, Pseudomonas, Serratia and Streptomyces. We also highlight the known molecular and physiological mechanisms by which VOCs inhibit the growth of phytopathogens. Microbial VOCs can provoke many changes in these microorganisms, such as vacuolization, fungal hyphal rupture, loss of intracellular components, regulation of metabolism and pathogenicity genes, plus the expression of proteins important in the host response. Furthermore, we demonstrate that there are aspects to investigate by discussing questions that are still not very clear in this research area, especially those that are essential for the future use of such beneficial microorganisms as biocontrol products in field crops. Therefore, we bring to light the great biotechnological potential of VOCs to help make agriculture more sustainable.
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Affiliation(s)
- Octávio Augusto Costa Almeida
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil,Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Natália Oliveira de Araujo
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil,Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Bruno Henrique Silva Dias
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil,Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Carla de Sant’Anna Freitas
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil,Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Luciane Fender Coerini
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil,Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Choong-Min Ryu
- Molecular Phytobacteriology Laboratory, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon, South Korea,Biosystems and Bioengineering Program, University of Science and Technology, Daejeon, South Korea
| | - Juliana Velasco de Castro Oliveira
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil,Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil,*Correspondence: Juliana Velasco de Castro Oliveira,
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Impact of Nuclear De Novo NAD + Synthesis via Histone Dynamics on DNA Repair during Cellular Senescence To Prevent Tumorigenesis. Mol Cell Biol 2022; 42:e0037922. [PMID: 36278823 PMCID: PMC9670974 DOI: 10.1128/mcb.00379-22] [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: 12/25/2022] Open
Abstract
NAD+ synthesis is a fundamental process in living cells. The effects of local metabolite production on chromatin influence the epigenetic status of chromatin in DNA metabolism. We have previously shown that K5 acetylation of H2AX by TIP60 is required for the ADP ribosylation activity of PARP-1, for histone H2AX exchange at DNA damage sites. However, the detailed molecular mechanism has remained unclear. Here, we identified de novo NAD synthetase 1 (NAD syn1) as a novel binding partner to H2AX. The enzymatic activity of NAD syn1 is crucial for the ADP ribosylation activity of PARP-1 for the H2AX dynamics at sites of DNA damage. Inhibition of the NAD synthetase activity in the cell nucleus decreased the overall cellular NAD+ concentration, leading to cellular senescence. Accordingly, the acetylation-dependent H2AX dynamics and homologous recombination repair were suppressed, leading to increased tumorigenesis. Our findings have revealed the importance of de novo NAD+ production in the cell nucleus for protection against the decreased DNA repair capacity caused by cellular senescence and thus against tumorigenesis.
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3
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Yeast as a Tool to Understand the Significance of Human Disease-Associated Gene Variants. Genes (Basel) 2021; 12:genes12091303. [PMID: 34573285 PMCID: PMC8465565 DOI: 10.3390/genes12091303] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 08/23/2021] [Accepted: 08/23/2021] [Indexed: 02/05/2023] Open
Abstract
At present, the great challenge in human genetics is to provide significance to the growing amount of human disease-associated gene variants identified by next generation DNA sequencing technologies. Increasing evidences suggest that model organisms are of pivotal importance to addressing this issue. Due to its genetic tractability, the yeast Saccharomyces cerevisiae represents a valuable model organism for understanding human genetic variability. In the present review, we show how S. cerevisiae has been used to study variants of genes involved in different diseases and in different pathways, highlighting the versatility of this model organism.
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4
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Pinkerton M, Ruetenik A, Bazylianska V, Nyvltova E, Barrientos A. Salvage NAD+ biosynthetic pathway enzymes moonlight as molecular chaperones to protect against proteotoxicity. Hum Mol Genet 2021; 30:672-686. [PMID: 33749726 DOI: 10.1093/hmg/ddab080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/03/2021] [Accepted: 03/15/2021] [Indexed: 11/13/2022] Open
Abstract
Human neurodegenerative proteinopathies are disorders associated with abnormal protein depositions in brain neurons. They include polyglutamine (polyQ) conditions such as Huntington's disease (HD) and α-synucleinopathies such as Parkinson's disease (PD). Overexpression of NMNAT/Nma1, an enzyme in the NAD+ biosynthetic salvage pathway, acts as an efficient suppressor of proteotoxicities in yeast, fly and mouse models. Screens in yeast models of HD and PD allowed us to identify three additional enzymes of the same pathway that achieve similar protection against proteotoxic stress: Npt1, Pnc1 and Qns1. The mechanism by which these proteins maintain proteostasis has not been identified. Here, we report that their ability to maintain proteostasis in yeast models of HD and PD is independent of their catalytic activity and does not require cellular protein quality control systems such as the proteasome or autophagy. Furthermore, we show that, under proteotoxic stress, the four proteins are recruited as molecular chaperones with holdase and foldase activities. The NAD+ salvage proteins act by preventing misfolding and, together with the Hsp90 chaperone, promoting the refolding of extended polyQ domains and α-synuclein (α-Syn). Our results illustrate the existence of an evolutionarily conserved strategy of repurposing or moonlighting housekeeping enzymes under stress conditions to maintain proteostasis. We conclude that the entire salvage NAD+ biosynthetic pathway links NAD+ metabolism and proteostasis and emerges as a target for therapeutics to combat age-associated neurodegenerative proteotoxicities.
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Affiliation(s)
- Meredith Pinkerton
- Department of Neurology and Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Andrea Ruetenik
- Department of Neurology and Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Viktoriia Bazylianska
- Department of Neurology and Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA.,MS in Biochemistry and Molecular Biology, Wayne State University, School of Medicine. Detroit, MI 48201, USA
| | - Eva Nyvltova
- Department of Neurology and Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Antoni Barrientos
- Department of Neurology and Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA.,Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine. Miami, FL 33136, USA
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5
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Orlandi I, Alberghina L, Vai M. Nicotinamide, Nicotinamide Riboside and Nicotinic Acid-Emerging Roles in Replicative and Chronological Aging in Yeast. Biomolecules 2020; 10:E604. [PMID: 32326437 PMCID: PMC7226615 DOI: 10.3390/biom10040604] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/09/2020] [Accepted: 04/13/2020] [Indexed: 02/07/2023] Open
Abstract
Nicotinamide, nicotinic acid and nicotinamide riboside are vitamin B3 precursors of NAD+ in the human diet. NAD+ has a fundamental importance for cellular biology, that derives from its essential role as a cofactor of various metabolic redox reactions, as well as an obligate co-substrate for NAD+-consuming enzymes which are involved in many fundamental cellular processes including aging/longevity. During aging, a systemic decrease in NAD+ levels takes place, exposing the organism to the risk of a progressive inefficiency of those processes in which NAD+ is required and, consequently, contributing to the age-associated physiological/functional decline. In this context, dietary supplementation with NAD+ precursors is considered a promising strategy to prevent NAD+ decrease and attenuate in such a way several metabolic defects common to the aging process. The metabolism of NAD+ precursors and its impact on cell longevity have benefited greatly from studies performed in the yeast Saccharomyces cerevisiae, which is one of the most established model systems used to study the aging processes of both proliferating (replicative aging) and non-proliferating cells (chronological aging). In this review we summarize important aspects of the role played by nicotinamide, nicotinic acid and nicotinamide riboside in NAD+ metabolism and how each of these NAD+ precursors contribute to the different aspects that influence both replicative and chronological aging. Taken as a whole, the findings provided by the studies carried out in S. cerevisiae are informative for the understanding of the complex dynamic flexibility of NAD+ metabolism, which is essential for the maintenance of cellular fitness and for the development of dietary supplements based on NAD+ precursors.
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Affiliation(s)
- Ivan Orlandi
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, 2016 Milan, Italy;
| | | | - Marina Vai
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, 2016 Milan, Italy;
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6
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Chuenchor W, Doukov TI, Chang KT, Resto M, Yun CS, Gerratana B. Different ways to transport ammonia in human and Mycobacterium tuberculosis NAD + synthetases. Nat Commun 2020; 11:16. [PMID: 31911602 PMCID: PMC6946656 DOI: 10.1038/s41467-019-13845-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 12/03/2019] [Indexed: 12/15/2022] Open
Abstract
NAD+ synthetase is an essential enzyme of de novo and recycling pathways of NAD+ biosynthesis in Mycobacterium tuberculosis but not in humans. This bifunctional enzyme couples the NAD+ synthetase and glutaminase activities through an ammonia tunnel but free ammonia is also a substrate. Here we show that the Homo sapiens NAD+ synthetase (hsNadE) lacks substrate specificity for glutamine over ammonia and displays a modest activation of the glutaminase domain compared to tbNadE. We report the crystal structures of hsNadE and NAD+ synthetase from M. tuberculosis (tbNadE) with synthetase intermediate analogues. Based on the observed exclusive arrangements of the domains and of the intra- or inter-subunit tunnels we propose a model for the inter-domain communication mechanism for the regulation of glutamine-dependent activity and NH3 transport. The structural and mechanistic comparison herein reported between hsNadE and tbNadE provides also a starting point for future efforts in the development of anti-TB drugs.
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Affiliation(s)
- Watchalee Chuenchor
- Departments of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Tzanko I Doukov
- Stanford Synchrotron Radiation Lightsource, Menlo Park, CA, 94025, USA
| | - Kai-Ti Chang
- Departments of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Melissa Resto
- Departments of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Chang-Soo Yun
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon, 34114, Korea
| | - Barbara Gerratana
- Departments of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA.
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7
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Bi-allelic Mutations in NADSYN1 Cause Multiple Organ Defects and Expand the Genotypic Spectrum of Congenital NAD Deficiency Disorders. Am J Hum Genet 2020; 106:129-136. [PMID: 31883644 DOI: 10.1016/j.ajhg.2019.12.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 12/05/2019] [Indexed: 12/22/2022] Open
Abstract
Birth defects occur in up to 3% of all live births and are the leading cause of infant death. Here we present five individuals from four unrelated families, individuals who share similar phenotypes with disease-causal bi-allelic variants in NADSYN1, encoding NAD synthetase 1, the final enzyme of the nicotinamide adenine dinucleotide (NAD) de novo synthesis pathway. Defects range from the isolated absence of both kidneys to multiple malformations of the vertebrae, heart, limbs, and kidney, and no affected individual survived for more than three months postnatally. NAD is an essential coenzyme for numerous cellular processes. Bi-allelic loss-of-function mutations in genes required for the de novo synthesis of NAD were previously identified in individuals with multiple congenital abnormalities affecting the heart, kidney, vertebrae, and limbs. Functional assessments of NADSYN1 missense variants, through a combination of yeast complementation and enzymatic assays, show impaired enzymatic activity and severely reduced NAD levels. Thus, NADSYN1 represents an additional gene required for NAD synthesis during embryogenesis, and NADSYN1 has bi-allelic missense variants that cause NAD deficiency-dependent malformations. Our findings expand the genotypic spectrum of congenital NAD deficiency disorders and further implicate mutation of additional genes involved in de novo NAD synthesis as potential causes of complex birth defects.
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8
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Decros G, Beauvoit B, Colombié S, Cabasson C, Bernillon S, Arrivault S, Guenther M, Belouah I, Prigent S, Baldet P, Gibon Y, Pétriacq P. Regulation of Pyridine Nucleotide Metabolism During Tomato Fruit Development Through Transcript and Protein Profiling. FRONTIERS IN PLANT SCIENCE 2019; 10:1201. [PMID: 31681351 PMCID: PMC6798084 DOI: 10.3389/fpls.2019.01201] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 09/02/2019] [Indexed: 05/12/2023]
Abstract
Central metabolism is the engine of plant biomass, supplying fruit growth with building blocks, energy, and biochemical cofactors. Among metabolic cornerstones, nicotinamide adenine dinucleotide (NAD) is particularly pivotal for electron transfer through reduction-oxidation (redox) reactions, thus participating in a myriad of biochemical processes. Besides redox functions, NAD is now assumed to act as an integral regulator of signaling cascades involved in growth and environmental responses. However, the regulation of NAD metabolism and signaling during fruit development remains poorly studied and understood. Here, we benefit from RNAseq and proteomic data obtained from nine growth stages of tomato fruit (var. Moneymaker) to dissect mRNA and protein profiles that link to NAD metabolism, including de novo biosynthesis, recycling, utilization, and putative transport. As expected for a cofactor synthesis pathway, protein profiles failed to detect enzymes involved in NAD synthesis or utilization, except for nicotinic acid phosphoribosyltransferase (NaPT) and nicotinamidase (NIC), which suggested that most NAD metabolic enzymes were poorly represented quantitatively. Further investigations on transcript data unveiled differential expression patterns during fruit development. Interestingly, among specific NAD metabolism-related genes, early de novo biosynthetic genes were transcriptionally induced in very young fruits, in association with NAD kinase, while later stages of fruit growth rather showed an accumulation of transcripts involved in later stages of de novo synthesis and in NAD recycling, which agreed with augmented NAD(P) levels. In addition, a more global overview of 119 mRNA and 78 protein significant markers for NAD(P)-dependent enzymes revealed differential patterns during tomato growth that evidenced clear regulations of primary metabolism, notably with respect to mitochondrial functions. Overall, we propose that NAD metabolism and signaling are very dynamic in the developing tomato fruit and that its differential regulation is certainly critical to fuel central metabolism linking to growth mechanisms.
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Affiliation(s)
| | | | - Sophie Colombié
- UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
| | - Cécile Cabasson
- UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
- MetaboHUB-Bordeaux, MetaboHUB, Phenome-Emphasis, Villenave d’Ornon, France
| | - Stéphane Bernillon
- UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
- MetaboHUB-Bordeaux, MetaboHUB, Phenome-Emphasis, Villenave d’Ornon, France
| | - Stéphanie Arrivault
- Department 2, Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Manuela Guenther
- Department 2, Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Isma Belouah
- UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
| | - Sylvain Prigent
- UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
- MetaboHUB-Bordeaux, MetaboHUB, Phenome-Emphasis, Villenave d’Ornon, France
| | - Pierre Baldet
- UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
| | - Yves Gibon
- UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
- MetaboHUB-Bordeaux, MetaboHUB, Phenome-Emphasis, Villenave d’Ornon, France
| | - Pierre Pétriacq
- UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
- MetaboHUB-Bordeaux, MetaboHUB, Phenome-Emphasis, Villenave d’Ornon, France
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9
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A proteomic investigation of Aspergillus carbonarius exposed to yeast volatilome or to its major component 2-phenylethanol reveals major shifts in fungal metabolism. Int J Food Microbiol 2019; 306:108265. [DOI: 10.1016/j.ijfoodmicro.2019.108265] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/02/2019] [Accepted: 07/09/2019] [Indexed: 12/29/2022]
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10
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Zhao F, Wu W, Wei Q, Shen M, Li B, Jiang Y, Liu K, Liu H. Exogenous adrenocorticotropic hormone affects genome‐wide DNA methylation and transcriptome of corpus luteum in sows. FASEB J 2018; 33:3264-3278. [DOI: 10.1096/fj.201801081rrr] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Fang Zhao
- Laboratory of Animal Genetics and BreedingCollege of Animal Science and TechnologyNanjing Agricultural University Nanjing China
| | - Wangjun Wu
- Laboratory of Animal Genetics and BreedingCollege of Animal Science and TechnologyNanjing Agricultural University Nanjing China
| | - Quanwei Wei
- Laboratory of Animal ReproductionCollege of Animal Science and TechnologyNanjing Agricultural University Nanjing China
| | - Ming Shen
- Laboratory of Animal Genetics and BreedingCollege of Animal Science and TechnologyNanjing Agricultural University Nanjing China
| | - Bojiang Li
- Laboratory of Animal Genetics and BreedingCollege of Animal Science and TechnologyNanjing Agricultural University Nanjing China
| | - Yi Jiang
- Laboratory of Animal Genetics and BreedingCollege of Animal Science and TechnologyNanjing Agricultural University Nanjing China
| | - Kaiqing Liu
- Laboratory of Animal Genetics and BreedingCollege of Animal Science and TechnologyNanjing Agricultural University Nanjing China
| | - Honglin Liu
- Laboratory of Animal Genetics and BreedingCollege of Animal Science and TechnologyNanjing Agricultural University Nanjing China
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11
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Fellner M, Hausinger RP, Hu J. A structural perspective on the PP-loop ATP pyrophosphatase family. Crit Rev Biochem Mol Biol 2018; 53:607-622. [DOI: 10.1080/10409238.2018.1516728] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Matthias Fellner
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Robert P. Hausinger
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Jian Hu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
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12
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Wierman MB, Smith JS. Yeast sirtuins and the regulation of aging. FEMS Yeast Res 2014; 14:73-88. [PMID: 24164855 PMCID: PMC4365911 DOI: 10.1111/1567-1364.12115] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 10/09/2013] [Accepted: 10/13/2013] [Indexed: 11/29/2022] Open
Abstract
The sirtuins are a phylogenetically conserved family of NAD(+) -dependent protein deacetylases that consume one molecule of NAD(+) for every deacetylated lysine side chain. Their requirement for NAD(+) potentially makes them prone to regulation by fluctuations in NAD(+) or biosynthesis intermediates, thus linking them to cellular metabolism. The Sir2 protein from Saccharomyces cerevisiae is the founding sirtuin family member and has been well characterized as a histone deacetylase that functions in transcriptional silencing of heterochromatin domains and as a pro-longevity factor for replicative life span (RLS), defined as the number of times a mother cell divides (buds) before senescing. Deleting SIR2 shortens RLS, while increased gene dosage causes extension. Furthermore, Sir2 has been implicated in mediating the beneficial effects of caloric restriction (CR) on life span, not only in yeast, but also in higher eukaryotes. While this paradigm has had its share of disagreements and debate, it has also helped rapidly drive the aging research field forward. S. cerevisiae has four additional sirtuins, Hst1, Hst2, Hst3, and Hst4. This review discusses the function of Sir2 and the Hst homologs in replicative aging and chronological aging, and also addresses how the sirtuins are regulated in response to environmental stresses such as CR.
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Affiliation(s)
- Margaret B Wierman
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
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13
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Secretion of quinolinic acid, an intermediate in the kynurenine pathway, for utilization in NAD+ biosynthesis in the yeast Saccharomyces cerevisiae. EUKARYOTIC CELL 2013; 12:648-53. [PMID: 23457190 DOI: 10.1128/ec.00339-12] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
NAD(+) is synthesized from tryptophan either via the kynurenine (de novo) pathway or via the salvage pathway by reutilizing intermediates such as nicotinic acid or nicotinamide ribose. Quinolinic acid is an intermediate in the kynurenine pathway. We have discovered that the budding yeast Saccharomyces cerevisiae secretes quinolinic acid into the medium and also utilizes extracellular quinolinic acid as a novel NAD(+) precursor. We provide evidence that extracellular quinolinic acid enters the cell via Tna1, a high-affinity nicotinic acid permease, and thereby helps to increase the intracellular concentration of NAD(+). Transcription of genes involved in the kynurenine pathway and Tna1 was increased, responding to a low intracellular NAD(+) concentration, in cells bearing mutations of these genes; this transcriptional induction was suppressed by supplementation with quinolinic acid or nicotinic acid. Our data thus shed new light on the significance of quinolinic acid, which had previously been recognized only as an intermediate in the kynurenine pathway.
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14
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De Ingeniis J, Kazanov MD, Shatalin K, Gelfand MS, Osterman AL, Sorci L. Glutamine versus ammonia utilization in the NAD synthetase family. PLoS One 2012; 7:e39115. [PMID: 22720044 PMCID: PMC3376133 DOI: 10.1371/journal.pone.0039115] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 05/16/2012] [Indexed: 11/18/2022] Open
Abstract
NAD is a ubiquitous and essential metabolic redox cofactor which also functions as a substrate in certain regulatory pathways. The last step of NAD synthesis is the ATP-dependent amidation of deamido-NAD by NAD synthetase (NADS). Members of the NADS family are present in nearly all species across the three kingdoms of Life. In eukaryotic NADS, the core synthetase domain is fused with a nitrilase-like glutaminase domain supplying ammonia for the reaction. This two-domain NADS arrangement enabling the utilization of glutamine as nitrogen donor is also present in various bacterial lineages. However, many other bacterial members of NADS family do not contain a glutaminase domain, and they can utilize only ammonia (but not glutamine) in vitro. A single-domain NADS is also characteristic for nearly all Archaea, and its dependence on ammonia was demonstrated here for the representative enzyme from Methanocaldococcus jannaschi. However, a question about the actual in vivo nitrogen donor for single-domain members of the NADS family remained open: Is it glutamine hydrolyzed by a committed (but yet unknown) glutaminase subunit, as in most ATP-dependent amidotransferases, or free ammonia as in glutamine synthetase? Here we addressed this dilemma by combining evolutionary analysis of the NADS family with experimental characterization of two representative bacterial systems: a two-subunit NADS from Thermus thermophilus and a single-domain NADS from Salmonella typhimurium providing evidence that ammonia (and not glutamine) is the physiological substrate of a typical single-domain NADS. The latter represents the most likely ancestral form of NADS. The ability to utilize glutamine appears to have evolved via recruitment of a glutaminase subunit followed by domain fusion in an early branch of Bacteria. Further evolution of the NADS family included lineage-specific loss of one of the two alternative forms and horizontal gene transfer events. Lastly, we identified NADS structural elements associated with glutamine-utilizing capabilities.
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Affiliation(s)
- Jessica De Ingeniis
- Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
| | - Marat D. Kazanov
- Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Konstantin Shatalin
- Department of Biochemistry, New York University School of Medicine, New York, United States of America
| | - Mikhail S. Gelfand
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Andrei L. Osterman
- Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
- * E-mail: (LS); (ALO)
| | - Leonardo Sorci
- Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
- Department of Clinical Sciences, Section of Biochemistry, Polytechnic University of Marche, Ancona, Italy
- * E-mail: (LS); (ALO)
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15
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Bogan KL, Evans C, Belenky P, Song P, Burant CF, Kennedy R, Brenner C. Identification of Isn1 and Sdt1 as glucose- and vitamin-regulated nicotinamide mononucleotide and nicotinic acid mononucleotide [corrected] 5'-nucleotidases responsible for production of nicotinamide riboside and nicotinic acid riboside. J Biol Chem 2009; 284:34861-9. [PMID: 19846558 DOI: 10.1074/jbc.m109.056689] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Recently, we discovered that nicotinamide riboside and nicotinic acid riboside are biosynthetic precursors of NAD(+), which are utilized through two pathways consisting of distinct enzymes. In addition, we have shown that exogenously supplied nicotinamide riboside is imported into yeast cells by a dedicated transporter, and it extends replicative lifespan on high glucose medium. Here, we show that nicotinamide riboside and nicotinic acid riboside are authentic intracellular metabolites in yeast. Secreted nicotinamide riboside was detected with a biological assay, and intracellular levels of nicotinamide riboside, nicotinic acid riboside, and other NAD(+) metabolites were determined by a liquid chromatography-mass spectrometry method. A biochemical genomic screen indicated that three yeast enzymes possess nicotinamide mononucleotide 5'-nucleotidase activity in vitro. Metabolic profiling of knock-out mutants established that Isn1 and Sdt1 are responsible for production of nicotinamide riboside and nicotinic acid riboside in cells. Isn1, initially classified as an IMP-specific 5'-nucleotidase, and Sdt1, initially classified as a pyrimidine 5'-nucleotidase, are additionally responsible for dephosphorylation of pyridine mononucleotides. Sdt1 overexpression is growth-inhibitory to cells in a manner that depends on its active site and correlates with reduced cellular NAD(+). Expression of Isn1 protein is positively regulated by the availability of nicotinic acid and glucose. These results reveal unanticipated and highly regulated steps in NAD(+) metabolism.
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Affiliation(s)
- Katrina L Bogan
- Biochemistry Graduate Program, Dartmouth Medical School, Lebanon, New Hampshire 03756, USA
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16
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Avery MA, Sheehan AE, Kerr KS, Wang J, Freeman MR. Wld S requires Nmnat1 enzymatic activity and N16-VCP interactions to suppress Wallerian degeneration. ACTA ACUST UNITED AC 2009; 184:501-13. [PMID: 19237597 PMCID: PMC2654119 DOI: 10.1083/jcb.200808042] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Slow Wallerian degeneration (Wld(S)) encodes a chimeric Ube4b/nicotinamide mononucleotide adenylyl transferase 1 (Nmnat1) fusion protein that potently suppresses Wallerian degeneration, but the mechanistic action of Wld(S) remains controversial. In this study, we characterize Wld(S)-mediated axon protection in vivo using Drosophila melanogaster. We show that Nmnat1 can protect severed axons from autodestruction but at levels significantly lower than Wld(S), and enzyme-dead versions of Nmnat1 and Wld(S) exhibit severely reduced axon-protective function. Interestingly, a 16-amino acid N-terminal domain of Wld(S) (termed N16) accounts for the differences in axon-sparing activity between Wld(S) and Nmnat1, and N16-dependent enhancement of Nmnat1-protective activity in Wld(S) requires the N16-binding protein valosin-containing protein (VCP)/TER94. Thus, Wld(S)-mediated suppression of Wallerian degeneration results from VCP-N16 interactions and Nmnat1 activity converging in vivo. Surprisingly, mouse Nmnat3, a mitochondrial Nmnat enzyme that localizes to the cytoplasm in Drosophila cells, protects severed axons at levels indistinguishable from Wld(S). Thus, nuclear Nmnat activity does not appear to be essential for Wld(S)-like axon protection.
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Affiliation(s)
- Michelle A Avery
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA 01605, USA
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17
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Abstract
The yeast pathogen Candida glabrata is a nicotinamide adenine dinucleotide (NAD(+)) auxotroph and its growth depends on the environmental supply of vitamin precursors of NAD(+). C. glabrata salvage pathways defined in this article allow NAD(+) to be synthesized from three compounds - nicotinic acid (NA), nicotinamide (NAM) and nicotinamide riboside (NR). NA is salvaged through a functional Preiss-Handler pathway. NAM is first converted to NA by nicotinamidase and then salvaged by the Preiss-Handler pathway. Salvage of NR in C. glabrata occurs via two routes. The first, in which NR is phosphorylated by the NR kinase Nrk1, is independent of the Preiss-Handler pathway. The second is a novel pathway in which NR is degraded by the nucleosidases Pnp1 and Urh1, with a minor role for Meu1, and ultimately converted to NAD(+) via the nicotinamidase Pnc1 and the Preiss-Handler pathway. Using C. glabrata mutants whose growth depends exclusively on the external NA or NR supply, we also show that C. glabrata utilizes NR and to a lesser extent NA as NAD(+) sources during disseminated infection.
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Affiliation(s)
- Biao Ma
- Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Hunterian 617, 725 North Wolfe Street, Baltimore, MD 21205-2185, USA
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18
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Palmieri F, Agrimi G, Blanco E, Castegna A, Di Noia MA, Iacobazzi V, Lasorsa FM, Marobbio CMT, Palmieri L, Scarcia P, Todisco S, Vozza A, Walker J. Identification of mitochondrial carriers in Saccharomyces cerevisiae by transport assay of reconstituted recombinant proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2006; 1757:1249-62. [PMID: 16844075 DOI: 10.1016/j.bbabio.2006.05.023] [Citation(s) in RCA: 129] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2006] [Revised: 05/12/2006] [Accepted: 05/16/2006] [Indexed: 10/24/2022]
Abstract
The inner membranes of mitochondria contain a family of carrier proteins that are responsible for the transport in and out of the mitochondrial matrix of substrates, products, co-factors and biosynthetic precursors that are essential for the function and activities of the organelle. This family of proteins is characterized by containing three tandem homologous sequence repeats of approximately 100 amino acids, each folded into two transmembrane alpha-helices linked by an extensive polar loop. Each repeat contains a characteristic conserved sequence. These features have been used to determine the extent of the family in genome sequences. The genome of Saccharomyces cerevisiae contains 34 members of the family. The identity of five of them was known before the determination of the genome sequence, but the functions of the remaining family members were not. This review describes how the functions of 15 of these previously unknown transport proteins have been determined by a strategy that consists of expressing the genes in Escherichia coli or Saccharomyces cerevisiae, reconstituting the gene products into liposomes and establishing their functions by transport assay. Genetic and biochemical evidence as well as phylogenetic considerations have guided the choice of substrates that were tested in the transport assays. The physiological roles of these carriers have been verified by genetic experiments. Various pieces of evidence point to the functions of six additional members of the family, but these proposals await confirmation by transport assay. The sequences of many of the newly identified yeast carriers have been used to characterize orthologs in other species, and in man five diseases are presently known to be caused by defects in specific mitochondrial carrier genes. The roles of eight yeast mitochondrial carriers remain to be established.
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Affiliation(s)
- Ferdinando Palmieri
- Department of Pharmaco-Biology, Laboratory of Biochemistry and Molecular Biology, University of Bari, Via E. Orabona 4, 70125 Bari, Italy.
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Todisco S, Agrimi G, Castegna A, Palmieri F. Identification of the mitochondrial NAD+ transporter in Saccharomyces cerevisiae. J Biol Chem 2005; 281:1524-31. [PMID: 16291748 DOI: 10.1074/jbc.m510425200] [Citation(s) in RCA: 178] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mitochondrial carriers are a family of transport proteins that shuttle metabolites, nucleotides, and cofactors across the inner mitochondrial membrane. In Saccharomyces cerevisiae, NAD+ is synthesized outside the mitochondria and must be imported across the permeability barrier of the inner mitochondrial membrane. However, no protein responsible for this transport activity has ever been isolated or identified. In this report, the identification and functional characterization of the mitochondrial NAD+ carrier protein (Ndt1p) is described. The NDT1 gene was overexpressed in bacteria. The purified protein was reconstituted into liposomes, and its transport properties and kinetic parameters were characterized. It transported NAD+ and, to a lesser extent, (d)AMP and (d)GMP but virtually not alpha-NAD+, NADH, NADP+, or NADPH. Transport was saturable with an apparent Km of 0.38 mM for NAD+. The Ndt1p-GFP was found to be targeted to mitochondria. Consistently with Ndt1p localization and its function as a NAD+ transporter, cells lacking NDT1 had reduced levels of NAD+ and NADH in their mitochondria and reduced activity of mitochondrial NAD+-requiring enzymes. Similar results were also found in the mitochondria of cells lacking NDT2 that encodes a protein (Ndt2p) displaying 70% homology with Ndt1p. The delta ndt1 delta ndt2 double mutant exhibited lower mitochondrial NAD+ and NADH levels than the single deletants and a more pronounced delay in growth on nonfermentable carbon sources. The main role of Ndt1p and Ndt2p is to import NAD+ into mitochondria by unidirectional transport or by exchange with intramitochondrially generated (d)AMP and (d)GMP.
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Affiliation(s)
- Simona Todisco
- Department of Pharmaco-Biology, Laboratory of Biochemistry and Molecular Biology, University of Bari, Via E. Orabona 4, 70125 Bari, Italy
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20
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Current awareness on yeast. Yeast 2003; 20:1309-16. [PMID: 14664230 DOI: 10.1002/yea.951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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