1
|
Russo S, Rozeboom HJ, Wijma HJ, Poelarends GJ, Fraaije MW. Biochemical, kinetic, and structural characterization of a Bacillus tequilensis nitroreductase. FEBS J 2024. [PMID: 38946302 DOI: 10.1111/febs.17210] [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: 03/28/2024] [Revised: 05/17/2024] [Accepted: 06/14/2024] [Indexed: 07/02/2024]
Abstract
Nitroreductases (NRs) are NAD(P)H-dependent flavoenzymes that reduce nitro aromatic compounds to their corresponding arylamines via the nitroso and hydroxylamine intermediates. Because of their broad substrate scope and versatility, NRs have found application in multiple fields such as biocatalysis, bioremediation, cell-imaging and prodrug activation. However, only a limited number of members of the broad NR superfamily (> 24 000 sequences) have been experimentally characterized. Within this group of enzymes, only few are capable of amine synthesis, which is a fundamental chemical transformation for the pharmaceutical, agricultural, and textile industries. Herein, we provide a comprehensive description of a recently discovered NR from Bacillus tequilensis, named BtNR. This enzyme has previously been demonstrated to have the capability to fully convert nitro aromatic and heterocyclic compounds to their respective primary amines. In this study, we determined its biochemical, kinetic and structural properties, including its apparent melting temperature (Tm) of 59 °C, broad pH activity range (from pH 3 to 10) and a notably low redox potential (-236 ± 1 mV) in comparison to other well-known NRs. We also determined its steady-state and pre-steady-state kinetic parameters, which are consistent with other NRs. Additionally, we elucidated the crystal structure of BtNR, which resembles the well-characterized Escherichia coli oxygen-insensitive NAD(P)H nitroreductase (NfsB), and investigated the substrate binding in its active site through docking and molecular dynamics studies with four nitro aromatic substrates. Guided by these structural analyses, we probed the functional roles of active site residues by site-directed mutagenesis. Our findings provide valuable insights into the biochemical and structural properties of BtNR, as well as its potential applications in biotechnology.
Collapse
Affiliation(s)
- Sara Russo
- Molecular Enzymology Group, University of Groningen, The Netherlands
- Department of Chemical and Pharmaceutical Biology, University of Groningen, The Netherlands
| | | | - Hein J Wijma
- Molecular Enzymology Group, University of Groningen, The Netherlands
| | - Gerrit J Poelarends
- Department of Chemical and Pharmaceutical Biology, University of Groningen, The Netherlands
| | - Marco W Fraaije
- Molecular Enzymology Group, University of Groningen, The Netherlands
| |
Collapse
|
2
|
Cirqueira ML, Bortot LO, Bolean M, Aleixo MAA, Luccas PH, Costa-Filho AJ, Ramos AP, Ciancaglini P, Nonato MC. Trypanosoma cruzi nitroreductase: Structural features and interaction with biological membranes. Int J Biol Macromol 2022; 221:891-899. [PMID: 36100001 DOI: 10.1016/j.ijbiomac.2022.09.073] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 08/28/2022] [Accepted: 09/08/2022] [Indexed: 11/05/2022]
Abstract
Due to its severe burden and geographic distribution, Chagas disease (CD) has a significant social and economic impact on low-income countries. Benznidazole and nifurtimox are currently the only drugs available for CD. These are prodrugs activated by reducing the nitro group, a reaction catalyzed by nitroreductase type I enzyme from Trypanosoma cruzi (TcNTR), with no homolog in the human host. The three-dimensional structure of TcNTR, and the molecular and chemical bases of the selective activation of nitro drugs, are still unknown. To understand the role of TcNTR in the basic parasite biology, investigate its potential as a drug target, and contribute to the fight against neglected tropical diseases, a combined approach using multiple biophysical and biochemical methods together with in silico studies was employed in the characterization of TcNTR. For the first time, the interaction of TcNTR with membranes was demonstrated, with a preference for those containing cardiolipin, a unique dimeric phospholipid that exists almost exclusively in the inner mitochondrial membrane in eukaryotic cells. Prediction of TcNTR's 3D structure suggests that a 23-residue long insertion (199 to 222), absent in the homologous bacterial protein and identified as conserved in protozoan sequences, mediates enzyme specificity, and is involved in protein-membrane interaction.
Collapse
Affiliation(s)
- Marília L Cirqueira
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (FCFRP-USP), Ribeirão Preto, SP, Brazil
| | - Leandro O Bortot
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (FCFRP-USP), Ribeirão Preto, SP, Brazil; Laboratory of Computational Biology (LBC), Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
| | - Maytê Bolean
- Chemistry Dept., Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, University of São Paulo (FFCLRP-USP), Ribeirão Preto, SP, Brazil
| | - Mariana A A Aleixo
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (FCFRP-USP), Ribeirão Preto, SP, Brazil; Brazilian Nanotechnology National Laboratory (LNNano), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
| | - Pedro H Luccas
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (FCFRP-USP), Ribeirão Preto, SP, Brazil
| | - Antonio J Costa-Filho
- Physics Dept., Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, University of São Paulo (FFCLRP-USP), Ribeirão Preto, SP, Brazil
| | - Ana Paula Ramos
- Chemistry Dept., Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, University of São Paulo (FFCLRP-USP), Ribeirão Preto, SP, Brazil
| | - Pietro Ciancaglini
- Chemistry Dept., Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, University of São Paulo (FFCLRP-USP), Ribeirão Preto, SP, Brazil
| | - M Cristina Nonato
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (FCFRP-USP), Ribeirão Preto, SP, Brazil.
| |
Collapse
|
3
|
Boddu RS, Perumal O, K D. Microbial nitroreductases: A versatile tool for biomedical and environmental applications. Biotechnol Appl Biochem 2020; 68:1518-1530. [PMID: 33156534 DOI: 10.1002/bab.2073] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 11/02/2020] [Indexed: 12/24/2022]
Abstract
Nitroreductases, enzymes found mostly in bacteria and also in few eukaryotes, use nicotinamide adenine dinucleotide (NADH) or nicotinamide adenine dinucleotide phosphate (NADPH) as a cofactor for their activity and metabolize an enormous list of a diverse nitro group-containing compounds. Nitroreductases that are capable of metabolizing nitroaromatic and nitro heterocyclic compounds have drawn great attention in recent years owing to their biotechnological, biomedical, environmental, and human impact. These enzymes attracted medicinal chemists and pharmacologists because of their prodrug selectivity for activation/reduction of nitro compounds that wipe out pathogens/cancer cells, leaving the host/normal cells unharmed. It is applied in diverse fields of study like prodrug activation in treating cancer and leishmaniasis, designing fluorescent probes for hypoxia detection, cell imaging, ablation of specific cell types, biodegradation of nitro-pollutants, and interpretation of mutagenicity of nitro compounds. Keeping in view the immense prospects of these enzymes and a large number of research contributions in this area, the present review encompasses the enzymatic reaction mechanism, their role in antibiotic resistance, hypoxia sensing, cell imaging, cancer therapy, reduction of recalcitrant nitro chemicals, enzyme variants, and their specificity to substrates, reaction products, and their applications.
Collapse
Affiliation(s)
- Ramya Sree Boddu
- Department of Biotechnology, National Institute of Technology, Warangal, India
| | - Onkara Perumal
- Department of Biotechnology, National Institute of Technology, Warangal, India
| | - Divakar K
- Department of Biotechnology, Sri Venkateswara College of Engineering, Sriperumbudur, India
| |
Collapse
|
4
|
Shin GH, Veen M, Stahl U, Lang C. Overexpression of genes of the fatty acid biosynthetic pathway leads to accumulation of sterols in Saccharomyces cerevisiae. Yeast 2012; 29:371-83. [DOI: 10.1002/yea.2916] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Revised: 07/02/2012] [Accepted: 07/11/2012] [Indexed: 11/08/2022] Open
Affiliation(s)
| | | | - Ulf Stahl
- Technische Universität Berlin; Institut für Biotechnologie, FG Mikrobiologie und Genetik; Berlin; Germany
| | | |
Collapse
|
5
|
Bang SY, Kim JH, Lee PY, Bae KH, Lee JS, Kim PS, Lee DH, Myung PK, Park BC, Park SG. Confirmation of Frm2 as a novel nitroreductase in Saccharomyces cerevisiae. Biochem Biophys Res Commun 2012; 423:638-41. [PMID: 22687599 DOI: 10.1016/j.bbrc.2012.05.156] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 05/28/2012] [Indexed: 11/18/2022]
Abstract
Nitroreductases comprise a group of FMN- or FAD-dependent enzymes that reduce nitrosubstituted compounds by using NAD(P)H, and are found in bacterial species and yeast. Although there is little information on the biological functions of nitroreductases, some studies suggest their possible involvement in oxidative stress responses. In the yeast Saccharomyces cerevisiae, a putative nitroreductase protein, Frm2, has been identified based on its sequence similarity with known bacterial nitroreductases. Frm2 has been reported to function in the lipid signaling pathway. To study the functions of Frm2, we measured the nitroreductase activity of purified Frm2 on 4-nitroquinoline-N-oxide (4-NQO) using NADH. LC-MS analysis of the reaction products revealed that Frm2 reduced NQO into 4-aminoquinoline-N-oxide (4-AQO) via 4-hydroxyaminoquinoline (4-HAQO). An Frm2 deletion mutant exhibited growth inhibition in the presence of 4-NQO. Thus, in this study, we demonstrate a novel nitroreductase activity of Frm2 and its involvement in the oxidative stress defense system.
Collapse
Affiliation(s)
- Seo Young Bang
- Medical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | | | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Rossouw D, Du Toit M, Bauer FF. The impact of co-inoculation with Oenococcus oeni on the trancriptome of Saccharomyces cerevisiae and on the flavour-active metabolite profiles during fermentation in synthetic must. Food Microbiol 2011; 29:121-31. [PMID: 22029926 DOI: 10.1016/j.fm.2011.09.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 08/12/2011] [Accepted: 09/10/2011] [Indexed: 11/17/2022]
Abstract
Co-inoculation of commercial yeast strains with a bacterial starter culture at the beginning of fermentation of certain varietal grape juices is rapidly becoming a preferred option in the global wine industry, and frequently replaces the previously dominant sequential inoculation strategy where bacterial strains, responsible for malolactic fermentation, are inoculated after alcoholic fermentation has been completed. However, while several studies have highlighted potential advantages of co-inoculation, such studies have mainly focused on broad fermentation properties of the mixed cultures, and no data exist regarding the impact of this strategy on many oenologically relevant attributes of specific wine yeast strains such as aroma production. Here we investigate the impact of co-inoculation on a commercial yeast strain during alcoholic fermentation by comparing the transcriptome of this strain in yeast-only and in co-inoculated fermentations of synthetic must. The data show that a significant number of genes are differentially expressed in this strain in these two conditions. Some of the differentially expressed genes appear to respond to chemical changes in the fermenting must that are linked to bacterial metabolic activities, whereas others might represent a direct response of the yeast to the presence of a competing organism.
Collapse
Affiliation(s)
- Debra Rossouw
- Institute for Wine Biotechnology, University of Stellenbosch, Stellenbosch, South Africa.
| | | | | |
Collapse
|
7
|
Rodrigues-Pousada C, Menezes RA, Pimentel C. The Yap family and its role in stress response. Yeast 2010; 27:245-58. [DOI: 10.1002/yea.1752] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
|
8
|
de Oliveira IM, Zanotto-Filho A, Moreira JCF, Bonatto D, Henriques JAP. The role of two putative nitroreductases, Frm2p and Hbn1p, in the oxidative stress response in Saccharomyces cerevisiae. Yeast 2010; 27:89-102. [PMID: 19904831 DOI: 10.1002/yea.1734] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The nitroreductase family is comprised of a group of FMN- or FAD-dependent enzymes that are able to metabolize nitrosubstituted compounds using the reducing power of NAD(P)H. These nitroreductases can be found in bacterial species and, to a lesser extent, in eukaryotes. There is little information on the biochemical functions of nitroreductases. Some studies suggest their possible involvement in the oxidative stress response. In the yeast Saccharomyces cerevisiae, two nitroreductase proteins, Frm2p and Hbn1p, have been described. While Frm2p appears to act in the lipid signalling pathway, the function of Hbn1p is completely unknown. In order to elucidate the functions of Frm2p and Hbn1p, we evaluated the sensitivity of yeast strains, proficient and deficient in both oxidative stress proteins, for respiratory competence, antioxidant-enzyme activities, intracellular reactive oxygen species (ROS) production and lipid peroxidation. We found reduced basal activity of superoxide dismutase (SOD), ROS production, lipid peroxidation and petite induction and higher sensitivity to 4-nitroquinoline-oxide (4-NQO) and N-nitrosodiethylamine (NDEA), as well as higher basal activity of catalase (CAT) and glutathione peroxidase (GPx) and reduced glutathione (GSH) content in the single and double mutant strains frm2Delta and frm2Delta hbn1Delta. These strains exhibited less ROS accumulation and lipid peroxidation when exposed to peroxides, H(2)O(2) and t-BOOH. In summary, the Frm1p and Hbn1p nitroreductases influence the response to oxidative stress in S. cerevisae yeast by modulating the GSH contents and antioxidant enzymatic activities, such as SOD, CAT and GPx.
Collapse
Affiliation(s)
- Iuri Marques de Oliveira
- Departamento de Biofísica/Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av Bento Gonçalves 9500, 91507-970 Porto Alegre, RS, Brazil
| | | | | | | | | |
Collapse
|
9
|
Santos PM, Simões T, Sá-Correia I. Insights into yeast adaptive response to the agricultural fungicide mancozeb: A toxicoproteomics approach. Proteomics 2009; 9:657-70. [DOI: 10.1002/pmic.200800452] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
10
|
de Oliveira IM, Henriques JAP, Bonatto D. In silico identification of a new group of specific bacterial and fungal nitroreductases-like proteins. Biochem Biophys Res Commun 2007; 355:919-25. [PMID: 17331467 DOI: 10.1016/j.bbrc.2007.02.049] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2007] [Accepted: 02/09/2007] [Indexed: 11/22/2022]
Abstract
The nitroreductase family comprises a group of FMN- or FAD-dependent and NAD(P)H-dependent enzymes able to metabolize nitrosubstituted compounds. The nitroreductases are found within bacterial and some eukaryotic species. In eukaryotes, there is little information concerning the phylogenetic position and biochemical functions of nitroreductases. The yeast Saccharomyces cerevisiae has two nitroreductase proteins: Frm2p and Hbn1p. While Frm2p acts in lipid signaling pathway, the function of Hbn1p is unknown. In order to elucidate the function of Frm2p/Hbn1p and the presence of homologous sequences in other prokaryotic and eukaryotic species, we performed an in-depth phylogenetic analysis of these proteins. The results showed that bacterial cells have Frm2p/Hbn1p-like sequences (termed NrlAp) forming a distinct clade within the fungal Frm2p/Hbn1p family. Hydrophobic cluster analysis and three-dimensional protein modeling allowed us to compare conserved regions among NrlAp and Frm2/Hbn1p proteins. In addition, the possible functions of bacterial NrlAp and fungal Frm2p/Hbn1p are discussed.
Collapse
Affiliation(s)
- Iuri Marques de Oliveira
- Centro de Biotecnologia/Departamento de Biofísica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | | | | |
Collapse
|
11
|
Azevedo D, Nascimento L, Labarre J, Toledano MB, Rodrigues-Pousada C. The S. cerevisiae Yap1 and Yap2 transcription factors share a common cadmium-sensing domain. FEBS Lett 2007; 581:187-95. [PMID: 17187783 DOI: 10.1016/j.febslet.2006.11.083] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2006] [Revised: 11/17/2006] [Accepted: 11/28/2006] [Indexed: 10/23/2022]
Abstract
Towards elucidating the function of Yap2, which remains unclear, we have taken advantage of the C-terminal homology between Yap1 and Yap2. Swapping domains experiments show that the Yap2 C-terminal domain functionally substitutes for the homologous Yap1 domain in the response to Cd, but not to H2O2. We conclude that specificity determinants of the Cd response are encoded within both Yap1 and Yap2 C-terminus, whereas those required for H2O2 response are only present in the Yap1 C-terminus. Furthermore, our results identify FRM2 as Cd-responsive Yap2 target and indicate a possible role of this protein in regulating a metal stress response.
Collapse
Affiliation(s)
- Dulce Azevedo
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2780-901 Oeiras, Portugal
| | | | | | | | | |
Collapse
|
12
|
Horan S, Bourges I, Meunier B. Transcriptional response to nitrosative stress in Saccharomyces cerevisiae. Yeast 2006; 23:519-35. [PMID: 16710843 DOI: 10.1002/yea.1372] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
Nitric oxide and NO-derived species (RNS) are defence molecules with broad antimicrobial activity. Microorganisms have developed strategies to sense RNS and counteract their damaging effects. We used Saccharomyces cerevisiae, harbouring a deletion of YHB1 that encodes the main NO scavenger enzyme, to study consequences of RNS exposure on whole-genome transcriptional response. The expression of > 700 genes was altered on RNS treatment. No major role for ROS-scavenging enzymes was found, and the respiratory chain, the main site of ROS production, had only minor involvement in the RNS-induced stress. The changes were generally transient and also found after treatment with the respiratory inhibitor myxothiazol. However, 117 genes showed a persistent response that was not observed after myxothiazol treatment. Of these, genes of the glutathione and DNA repair systems, iron homeostasis and transport were found to be upregulated. Severe repression of genes of respiratory chain enzymes was observed. Many of these genes are known to be regulated by the transcription factor Hap1p, suggesting that RNS might interfere with Hap1p activity. We showed also that Msn2/4p and Yap1p, key regulators of the response to general stress and oxidative stress, respectively, played a role in mediating the RNS-induced response.
Collapse
Affiliation(s)
- Susannah Horan
- Wolfson Institute for Biomedical Research, University College London, Gower Street, London WC1E 6BT, UK
| | | | | |
Collapse
|
13
|
Martin CE, Oh CS, Jiang Y. Regulation of long chain unsaturated fatty acid synthesis in yeast. Biochim Biophys Acta Mol Cell Biol Lipids 2006; 1771:271-85. [PMID: 16920014 DOI: 10.1016/j.bbalip.2006.06.010] [Citation(s) in RCA: 163] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2006] [Revised: 06/13/2006] [Accepted: 06/14/2006] [Indexed: 12/20/2022]
Abstract
Saccharomyces cerevisiae forms monounsaturated fatty acids using the ER membrane-bound Delta-9 fatty acid desaturase, Ole1p, an enzyme system that forms a double bond in saturated fatty acyl CoA substrates. Ole1p is a chimeric protein consisting of an amino terminal desaturase domain fused to cytochrome b5. It catalyzes the formation of the double bond through an oxygen-dependent mechanism that requires reducing equivalents from NADH. These are transferred to the enzyme via NADH cytochrome b5 reductase to the Ole1p cytochrome b5 domain and then to the diiron-oxo catalytic center of the enzyme. The control of OLE1 gene expression appears to mediated through the ER membrane proteins Spt23p and Mga2p. N-terminal fragments of these proteins are released by an ubiquitin/proteasome mediated proteolysis system and translocated to the nucleus where they appear to act as transcription coactivators of OLE1. OLE1 is regulated through Spt23p and Mga2p by multiple systems that control its transcription and mRNA stability in response to diverse stimuli that include nutrient fatty acids, carbon source, metal ions and the availability of oxygen.
Collapse
Affiliation(s)
- Charles E Martin
- Rutgers University, Department of Cell Biology and Neuroscience, Nelson Laboratories, 604 Allison Road, Piscataway, NJ 08854-8082, USA.
| | | | | |
Collapse
|
14
|
Tong F, Black PN, Bivins L, Quackenbush S, Ctrnacta V, DiRusso CC. Direct interaction of Saccharomyces cerevisiae Faa1p with the Omi/HtrA protease orthologue Ynm3p alters lipid homeostasis. Mol Genet Genomics 2006; 275:330-43. [PMID: 16470384 DOI: 10.1007/s00438-005-0089-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2005] [Accepted: 12/04/2005] [Indexed: 02/02/2023]
Abstract
In yeast, long chain acyl-CoA synthetase (ACSL) activity is required for fatty acid uptake, metabolism and fatty acid-dependent transcriptional control. The major ACSL contributing these functions is Faa1p. In a yeast two-hybrid screen, the Omi/HtrA serine protease family orthologue Ynm3p (YNL123w) was identified as a specific interactor with Faa1p. Interaction of Ynm3p and Faa1p was confirmed by co-immunoprecipitation. Disruption of the YNM3 gene encoding Ynm3p resulted in increased fatty acid uptake, triglyceride accumulation and reduced expression of the fatty acid-responsive OLE1 gene encoding the essential Delta(9)-acyl-CoA desaturase. These changes were linked with increased Faa1p and Faa4p ACSL activities. We propose that Ynm3p modulates fatty acid metabolism and gene regulation through negative regulation of ACSL activity. Additional strain-specific phenotypes associated with deletion of YNM3 included inability to grow on non-fermentable carbon sources and altered cellular morphology.
Collapse
Affiliation(s)
- Fumin Tong
- Center for Metabolic Disease, Ordway Research Institute, Inc., 150 New Scotland Avenue, Albany, NY 12208-3425, USA
| | | | | | | | | | | |
Collapse
|
15
|
Arous S, Buchrieser C, Folio P, Glaser P, Namane A, Hébraud M, Héchard Y. Global analysis of gene expression in an rpoN mutant of Listeria monocytogenes. MICROBIOLOGY-SGM 2004; 150:1581-1590. [PMID: 15133119 DOI: 10.1099/mic.0.26860-0] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The role of the alternative sigma(54) factor, encoded by the rpoN gene, was investigated in Listeria monocytogenes by comparing the global gene expression of the wild-type EGDe strain and an rpoN mutant. Gene expression, using whole-genome macroarrays, and protein content, using two-dimensional gel electrophoresis, were analysed. Seventy-seven genes and nine proteins, whose expression was modulated in the rpoN mutant as compared to the wild-type strain, were identified. Most of the modifications were related to carbohydrate metabolism and in particular to pyruvate metabolism. However, under the conditions studied, only the mptACD operon was shown to be directly controlled by sigma(54). Therefore, the remaining modifications seem to be due to indirect effects. In parallel, an in silico analysis suggests that sigma(54) may directly control the expression of four different phosphotransferase system (PTS) operons, including mptACD. PTS activity is known to have a direct effect on the pyruvate pool and on catabolite regulation. These results suggest that sigma(54) is mainly involved in the control of carbohydrate metabolism in L. monocytogenes via direct regulation of PTS activity, alteration of the pyruvate pool and modulation of carbon catabolite regulation.
Collapse
Affiliation(s)
- Safia Arous
- Equipe de Microbiologie Fondamentale et Appliquée, Université de Poitiers, 40 avenue du Recteur Pineau, 86022 Poitiers Cedex, France
| | - Carmen Buchrieser
- Laboratoire de Génomique des Micro-organismes Pathogènes, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Patrice Folio
- Station de Recherches sur la Viande, Institut National de la Recherche Agronomique de Theix, 63122 Saint-Genes Champanelle, France
| | - Philippe Glaser
- Laboratoire de Génomique des Micro-organismes Pathogènes, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Abdelkader Namane
- Plateforme de protéomique, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Michel Hébraud
- Station de Recherches sur la Viande, Institut National de la Recherche Agronomique de Theix, 63122 Saint-Genes Champanelle, France
| | - Yann Héchard
- Equipe de Microbiologie Fondamentale et Appliquée, Université de Poitiers, 40 avenue du Recteur Pineau, 86022 Poitiers Cedex, France
| |
Collapse
|
16
|
Black PN, Faergeman NJ, DiRusso CC. Long-chain acyl-CoA-dependent regulation of gene expression in bacteria, yeast and mammals. J Nutr 2000; 130:305S-309S. [PMID: 10721893 DOI: 10.1093/jn/130.2.305s] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Fatty acyl-CoA thioesters are essential intermediates in lipid metabolism. For many years there have been numerous conflicting reports concerning the possibility that these compounds also serve regulatory functions. In this review, we examine the evidence that long-chain acyl-CoA is a regulatory signal that modulates gene expression. In the bacteria Escherichia coli, long-chain fatty acyl-CoA bind directly to the transcription factor FadR. Acyl-CoA binding renders the protein incapable of binding DNA, thus preventing transcription activation and repression of many genes and operons. In the yeast Saccharomyces cerevisiae, genes encoding peroxisomal proteins are activated in response to exogenously supplied fatty acids. In contrast, growth of yeast cells in media containing exogenous fatty acids results in repression of a number of genes, including that encoding the delta9-fatty acid desaturase (OLE1). Both repression and activation are dependent upon the function of either of the acyl-CoA synthetases Faa1p or Faa4p. In mammals, purified hepatocyte nuclear transcription factor 4alpha (HNF-4alpha) like E. coli FadR, binds long chain acyl-CoA directly. Coexpression of HNF-4alpha and acyl-CoA synthetase increases the activation of transcription of a fatty acid-responsive promoter, whereas coexpression with thioesterase decreases the fatty acid-mediated response. Conflicting data exist in support of the notion that fatty acyl-CoA are natural ligands for peroxisomal proliferator-activated receptor alpha (PPARalpha).
Collapse
Affiliation(s)
- P N Black
- Department of Biochemistry and Molecular Biology, The Albany Medical College A-10, NY 12208-3479, USA
| | | | | |
Collapse
|
17
|
Fujiwara D, Kobayashi O, Yoshimoto H, Harashima S, Tamai Y. Molecular mechanism of the multiple regulation of the Saccharomyces cerevisiae ATF1 gene encoding alcohol acetyltransferase. Yeast 1999; 15:1183-97. [PMID: 10487921 DOI: 10.1002/(sici)1097-0061(19990915)15:12<1183::aid-yea444>3.0.co;2-j] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The ATF1 gene encodes an alcohol acetyl transferase (AATase), that catalyses the synthesis of acetate esters from acetyl CoA and several kinds of alcohols. ATF1 transcription is negatively regulated by unsaturated fatty acids and oxygen. A series of analyses of the ATF1 promoter identified an 18 bp element essential for transcriptional activation. Ligation of the 18 bp element into a plasmid carrying the CYC1 promoter deleted UAS-activated transcription and conferred transcriptional repression by unsaturated fatty acids. The 18 bp element contains a binding sequence for Rap1p, which is a transcriptional repressor and activator. In vitro binding studies showed that Rap1p binds to the 18 bp element essential for transcriptional activation. The results of internal deletion studies of the promoter region suggested that there was also a region responsible for ATF1 oxygen regulation. This region contained the consensus binding sequence for the hypoxic repressor Rox1p. In vitro binding studies showed that Rox1p binds to the region responsible for oxygen regulation. To investigate the effect of the hypoxic repressor complex on transcription, ATF1 expression was measured in rox1, tup1 and ssn6 disruptant strains. It was found that rox1, tup1 and ssn6 disruption caused elevated expression of ATF1 under aerobic conditions. Thus, the activation of ATF1 transcription is dependent on Rap1p, and the Rox1p-Tup1p-Ssn6p hypoxic repressor complex is responsible for repression by oxygen. Furthermore, a study of ATF1 expression in a sch9 null mutant suggested that the Sch9p protein kinase is involved in ATF1 trancriptional activation.
Collapse
Affiliation(s)
- D Fujiwara
- Central Laboratories for Key Technology, Kirin Brewery Co Ltd., 1-13-5, Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan.
| | | | | | | | | |
Collapse
|
18
|
DiRusso CC, Black PN, Weimar JD. Molecular inroads into the regulation and metabolism of fatty acids, lessons from bacteria. Prog Lipid Res 1999; 38:129-97. [PMID: 10396600 DOI: 10.1016/s0163-7827(98)00022-8] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- C C DiRusso
- Department of Biochemistry and Molecular Biology, Albany Medical College, New York, USA.
| | | | | |
Collapse
|
19
|
Fujimori K, Anamnart S, Nakagawa Y, Sugioka S, Ohta D, Oshima Y, Yamada Y, Harashima S. Isolation and characterization of mutations affecting expression of the delta9- fatty acid desaturase gene, OLE1, in Saccharomyces cerevisiae. FEBS Lett 1997; 413:226-30. [PMID: 9280286 DOI: 10.1016/s0014-5793(97)00846-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Expression of the delta9- fatty acid desaturase gene, OLE1, of Saccharomyces cerevisiae is negatively regulated transcriptionally and post-transcriptionally by unsaturated fatty acids. In order to isolate mutants exhibiting irregulation of OLE1 expression, we constructed an OLE1p-PHO5 fusion gene as a reporter consisting of the PHO5 gene encoding repressible acid phosphatase (rAPase) under the control of the OLE1 promoter (OLE1p). By EMS mutagenesis, we isolated three classes of mutants, pfo1, pfo2 and pfo3 positive regulatory factor for OLE1) mutants, which show decreased rAPase activity under derepression conditions (absence of oleic acid). Analysis of the transcription of OLE1 in these pfo mutants revealed that pfo1 and pfo3 mutants have a defect in the regulation of OLE1 expression at the transcriptional level while pfo2 mutants were suggested to have a mutation affecting OLE1 expression at a post-transcriptional step. In addition, four other classes of mutants, nfo1, nfo2, nfo3 and nfo4 (negative factor for OLE1) mutants that have mutations causing strong expression of the OLE1p-PHO5 fusion gene under repression conditions (presence of oleic acid), were isolated. Results of Northern analysis of OLE1 as well as OLE1p-PHO5 transcripts in nfo mutants suggested that these mutations occurred in genes encoding global repressors. We also demonstrated that TUP1 and SSN6 gene products are required for full repression of OLE1 gene expression, by showing that either tup1 or ssn6 mutations greatly increase the level of the OLE1 transcript.
Collapse
Affiliation(s)
- K Fujimori
- Takarazuka Research Institute, Novartis Pharma K.K., Japan
| | | | | | | | | | | | | | | |
Collapse
|
20
|
Faergeman NJ, DiRusso CC, Elberger A, Knudsen J, Black PN. Disruption of the Saccharomyces cerevisiae homologue to the murine fatty acid transport protein impairs uptake and growth on long-chain fatty acids. J Biol Chem 1997; 272:8531-8. [PMID: 9079682 DOI: 10.1074/jbc.272.13.8531] [Citation(s) in RCA: 132] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The yeast Saccharomyces cerevisiae is able to utilize exogenous fatty acids for a variety of cellular processes including beta-oxidation, phospholipid biosynthesis, and protein modification. The molecular mechanisms that govern the uptake of these compounds in S. cerevisiae have not been described. We report the characterization of FAT1, a gene that encodes a putative membrane-bound long-chain fatty acid transport protein (Fat1p). Fat1p contains 623 amino acid residues that are 33% identical and 54% with similar chemical properties as compared with the fatty acid transport protein FATP described in 3T3-L1 adipocytes (Schaffer and Lodish (1994) Cell 79, 427-436), suggesting a similar function. Disruption of FAT1 results in 1) an impaired growth in YPD medium containing 25 microM cerulenin and 500 microM fatty acid (myristate (C14:0), palmitate (C16:0), or oleate (C18:1)); 2) a marked decrease in the uptake of the fluorescent long-chain fatty acid analogue boron dipyrromethene difluoride dodecanoic acid (BODIPY-3823); 3) a reduced rate of exogenous oleate incorporation into phospholipids; and 4) a 2-3-fold decrease in the rates of oleate uptake. These data support the hypothesis that Fat1p is involved in long-chain fatty acid uptake and may represent a long-chain fatty acid transport protein.
Collapse
Affiliation(s)
- N J Faergeman
- Department of Biochemistry, University of Tennessee College of Medicine, Memphis, Tennessee 38163, USA
| | | | | | | | | |
Collapse
|