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Watanabe T, Kimura Y, Umeno D. Systematic promoter design for plasmid-encoded S-adenosylmethionine sensing systems. J GEN APPL MICROBIOL 2024; 70:n/a. [PMID: 38281753 DOI: 10.2323/jgam.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
S-adenosylmethionine (SAM) is an important biomolecule that mainly acts as a methyl donor and plays many roles in a variety of biological functions. SAM is also required for the biosynthesis of valuable methylated compounds, but its supply is a bottleneck for these biosynthetic pathways. To overcome this bottleneck and to reconfigure SAM homeostasis, a high-throughput sensing system for changes in intracellular SAM availability is required. We constructed a plasmid that can detect the factors that can alter SAM availability using minimal components. It does so by placing a fluorescent protein under a promoter controlled by endogenous MetJ, a transcription factor that represses its own regulons upon binding with SAM. Next, to validate SAM-responsive behavior, we systematically reconstructed 10 synthetic promoters with different positions and with different number of metbox sites. We found that a position between the -35 box and the -10 box was the most effective for repression and that this setup was suitable for detecting the genetic or environmental factors that can deplete and recover the intracellular SAM availability. Overall, the response patterns of the synthetic MetJ-regulated promoters characterized in this study may be useful for the development of better SAM biosensing systems.
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Affiliation(s)
- Taro Watanabe
- Department of Applied Chemistry, Faculty of Science, and Engineering, Waseda University
- Kirin Central Research Institute, Kirin Holdings Company, Limited
| | - Yuki Kimura
- Department of Applied Chemistry, Faculty of Science, and Engineering, Waseda University
| | - Daisuke Umeno
- Department of Applied Chemistry, Faculty of Science, and Engineering, Waseda University
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2
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Boutchouang RP, Fliniaux O, Eyamo JVE, Djabou ASM, Fontaine JX, Molinié R, Mesnard F, Niemenak N. Metabolome profiling of cacao (Theobroma cacao L.) callus under drought stress conditions induced by polyethylene glycol (PEG) as osmoticant. PHYTOCHEMICAL ANALYSIS : PCA 2024; 35:708-722. [PMID: 38246169 DOI: 10.1002/pca.3323] [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: 07/07/2023] [Revised: 11/21/2023] [Accepted: 12/16/2023] [Indexed: 01/23/2024]
Abstract
INTRODUCTION The cacao tree (Theobroma cacao), a perennial crop that serves as a source of cacao beans, can suffer from drastic climate changes such as irregular rainfall and shorter rainy seasons. The search for hybrids which are capable of producing specific metabolites favoring adaptation in new climatic conditions is a challenge in cacao farming. OBJECTIVES We aimed to (1) analyze the metabolic changes in calli of three cacao genotypes during water deficit induced by incubation with polyethylene glycol and (2) assess their response to water deficit stress with regard to somatic embryo differentiation. METHODS Metabolic profiling was carried out using 1H-NMR spectroscopy and multivariate data analysis was applied to crude extracts of calli grown in non-stress or water deficit stress conditions. RESULTS Water deficit stress influences the capacity of calli to produce embryos. The SCA12 genotype exhibited the best conversion capacity under severe conditions and was considered as tolerant to drought, followed by the SCA6 genotype (mid-tolerant) and the MA12 genotype (sensitive). Fifty-four metabolites were identified in the three cacao genotypes and discriminant metabolites were identified. Metabolites involved in water stress tolerance such as fructose, trans-aconitic acid, leucine, and hydroxybenzene derivatives were observed in SCA12, the tolerant genotype. CONCLUSION These results demonstrate the utility of 1H-NMR metabolomics as an essential tool for the analysis of the drought tolerance characteristics of T. cacao.
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Affiliation(s)
- Rodrigue Pouengue Boutchouang
- Department of Biochemistry, Faculty of Sciences, University of Yaoundé I, Yaoundé, Cameroon
- Laboratory of Biochemistry and Plant Physiology, Department of Biological Science, Higher Teachers' Training College, University of Yaoundé I, Yaoundé, Cameroon
| | - Ophélie Fliniaux
- BIOPI-BioEcoAgro UMRT 1158 INRAE Université de Picardie Jules Verne, Amiens, France
| | - Jos Victor Evina Eyamo
- Laboratory of Biochemistry and Plant Physiology, Department of Biological Science, Higher Teachers' Training College, University of Yaoundé I, Yaoundé, Cameroon
- Department of Agriculture and Agropastoral, Higher Technical Teacher Training College, University of Ebolowa, Ebolowa, Cameroon
| | - Astride Stephanie Mouafi Djabou
- Laboratory of Biochemistry and Plant Physiology, Department of Biological Science, Higher Teachers' Training College, University of Yaoundé I, Yaoundé, Cameroon
- Faculty of Agronomy and Agricultural Science, University of Dschang, Dschang, Cameroon
| | - Jean-Xavier Fontaine
- BIOPI-BioEcoAgro UMRT 1158 INRAE Université de Picardie Jules Verne, Amiens, France
| | - Roland Molinié
- BIOPI-BioEcoAgro UMRT 1158 INRAE Université de Picardie Jules Verne, Amiens, France
| | - François Mesnard
- BIOPI-BioEcoAgro UMRT 1158 INRAE Université de Picardie Jules Verne, Amiens, France
| | - Nicolas Niemenak
- Laboratory of Biochemistry and Plant Physiology, Department of Biological Science, Higher Teachers' Training College, University of Yaoundé I, Yaoundé, Cameroon
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3
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Abstract
Biotin plays an essential role in growth of mycobacteria. Synthesis of the cofactor is essential for Mycobacterium tuberculosis to establish and maintain chronic infections in a murine model of tuberculosis. Although the late steps of mycobacterial biotin synthesis, assembly of the heterocyclic rings, are thought to follow the canonical pathway, the mechanism of synthesis of the pimelic acid moiety that contributes most of the biotin carbon atoms is unknown. We report that the Mycobacterium smegmatis gene annotated as encoding Tam, an O-methyltransferase that monomethylates and detoxifies trans-aconitate, instead encodes a protein having the activity of BioC, an O-methyltransferase that methylates the free carboxyl of malonyl-ACP. The M. smegmatis Tam functionally replaced Escherichia coli BioC both in vivo and in vitro. Moreover, deletion of the M. smegmatis tam gene resulted in biotin auxotrophy, and addition of biotin to M. smegmatis cultures repressed tam gene transcription. Although its pathogenicity precluded in vivo studies, the M. tuberculosis Tam also replaced E. coli BioC both in vivo and in vitro and complemented biotin-independent growth of the M. smegmatis tam deletion mutant strain. Based on these data, we propose that the highly conserved mycobacterial tam genes be renamed bioCM. tuberculosis BioC presents a target for antituberculosis drugs which thus far have been directed at late reactions in the pathway with some success.
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Affiliation(s)
- Zhe Hu
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - John E Cronan
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801;
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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Niehaus TD, Hillmann KB. Enzyme promiscuity, metabolite damage, and metabolite damage control systems of the tricarboxylic acid cycle. FEBS J 2020; 287:1343-1358. [DOI: 10.1111/febs.15284] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/26/2020] [Accepted: 03/05/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Thomas D. Niehaus
- Department of Plant and Microbial Biology University of Minnesota Twin Cities Saint Paul MN USA
| | - Katie B. Hillmann
- Department of Plant and Microbial Biology University of Minnesota Twin Cities Saint Paul MN USA
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5
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Polese V, de Paula Soares C, da Silva PRA, Simões-Araújo JL, Baldani JI, Vidal MS. Selection and validation of reference genes for RT-qPCR indicates that juice of sugarcane varieties modulate the expression of C metabolism genes in the endophytic diazotrophic Herbaspirillum rubrisubalbicans strain HCC103. Antonie Van Leeuwenhoek 2017; 110:1555-1568. [DOI: 10.1007/s10482-017-0906-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 06/28/2017] [Indexed: 12/24/2022]
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6
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Sun J, Jeffryes JG, Henry CS, Bruner SD, Hanson AD. Metabolite damage and repair in metabolic engineering design. Metab Eng 2017; 44:150-159. [PMID: 29030275 DOI: 10.1016/j.ymben.2017.10.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 09/21/2017] [Accepted: 10/09/2017] [Indexed: 01/05/2023]
Abstract
The necessarily sharp focus of metabolic engineering and metabolic synthetic biology on pathways and their fluxes has tended to divert attention from the damaging enzymatic and chemical side-reactions that pathway metabolites can undergo. Although historically overlooked and underappreciated, such metabolite damage reactions are now known to occur throughout metabolism and to generate (formerly enigmatic) peaks detected in metabolomics datasets. It is also now known that metabolite damage is often countered by dedicated repair enzymes that undo or prevent it. Metabolite damage and repair are highly relevant to engineered pathway design: metabolite damage reactions can reduce flux rates and product yields, and repair enzymes can provide robust, host-independent solutions. Herein, after introducing the core principles of metabolite damage and repair, we use case histories to document how damage and repair processes affect efficient operation of engineered pathways - particularly those that are heterologous, non-natural, or cell-free. We then review how metabolite damage reactions can be predicted, how repair reactions can be prospected, and how metabolite damage and repair can be built into genome-scale metabolic models. Lastly, we propose a versatile 'plug and play' set of well-characterized metabolite repair enzymes to solve metabolite damage problems known or likely to occur in metabolic engineering and synthetic biology projects.
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Affiliation(s)
- Jiayi Sun
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA
| | - James G Jeffryes
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA
| | - Christopher S Henry
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA; Computation Institute, The University of Chicago, Chicago, IL, USA
| | - Steven D Bruner
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA.
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Du C, Cao S, Shi X, Nie X, Zheng J, Deng Y, Ruan L, Peng D, Sun M. Genetic and Biochemical Characterization of a Gene Operon for trans-Aconitic Acid, a Novel Nematicide from Bacillus thuringiensis. J Biol Chem 2017; 292:3517-3530. [PMID: 28087696 DOI: 10.1074/jbc.m116.762666] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 12/31/2016] [Indexed: 12/31/2022] Open
Abstract
trans-Aconitic acid (TAA) is an isomer of cis-aconitic acid (CAA), an intermediate of the tricarboxylic acid cycle that is synthesized by aconitase. Although TAA production has been detected in bacteria and plants for many years and is known to be a potent inhibitor of aconitase, its biosynthetic origins and the physiological relevance of its activity have remained unclear. We have serendipitously uncovered key information relevant to both of these questions. Specifically, in a search for novel nematicidal factors from Bacillus thuringiensis, a significant nematode pathogen harboring many protein virulence factors, we discovered a high yielding component that showed activity against the plant-parasitic nematode Meloidogyne incognita and surprisingly identified it as TAA. Comparison with CAA, which displayed a much weaker nematicidal effect, suggested that TAA is specifically synthesized by B. thuringiensis as a virulence factor. Analysis of mutants deficient in plasmids that were anticipated to encode virulence factors allowed us to isolate a TAA biosynthesis-related (tbr) operon consisting of two genes, tbrA and tbrB We expressed the corresponding proteins, TbrA and TbrB, and characterized them as an aconitate isomerase and TAA transporter, respectively. Bioinformatics analysis of the TAA biosynthetic gene cluster revealed the association of the TAA genes with transposable elements relevant for horizontal gene transfer as well as a distribution across B. cereus bacteria and other B. thuringiensis strains, suggesting a general role for TAA in the interactions of B. cereus group bacteria with nematode hosts in the soil environment. This study reveals new bioactivity for TAA and the TAA biosynthetic pathway, improving our understanding of virulence factors employed by B. thuringiensis pathogenesis and providing potential implications for nematode management applications.
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Affiliation(s)
- Cuiying Du
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shiyun Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiangyu Shi
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiangtao Nie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinshui Zheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yun Deng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lifang Ruan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Donghai Peng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ming Sun
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
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Kramer A, Beck HC, Kumar A, Kristensen LP, Imhoff JF, Labes A. Proteomic Analysis of Anti-Cancerous Scopularide Production by a Marine Microascus brevicaulis Strain and Its UV Mutant. PLoS One 2015; 10:e0140047. [PMID: 26460745 PMCID: PMC4603891 DOI: 10.1371/journal.pone.0140047] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 09/21/2015] [Indexed: 11/19/2022] Open
Abstract
The marine fungus Microascus brevicaulis strain LF580 is a non-model secondary metabolite producer with high yields of the two secondary metabolites scopularides A and B, which exhibit distinct activities against tumour cell lines. A mutant strain was obtained using UV mutagenesis, showing faster growth and differences in pellet formation besides higher production levels. Here, we show the first proteome study of a marine fungus. Comparative proteomics were applied to gain deeper understanding of the regulation of production and of the physiology of the wild type strain and its mutant. For this purpose, an optimised protein extraction protocol was established. In total, 4759 proteins were identified. The central metabolic pathway of strain LF580 was mapped using the KEGG pathway analysis and GO annotation. Employing iTRAQ labelling, 318 proteins were shown to be significantly regulated in the mutant strain: 189 were down- and 129 upregulated. Proteomics are a powerful tool for the understanding of regulatory aspects: The differences on proteome level could be attributed to limited nutrient availability in the wild type strain due to a strong pellet formation. This information can be applied for optimisation on strain and process level. The linkage between nutrient limitation and pellet formation in the non-model fungus M. brevicaulis is in consensus with the knowledge on model organisms like Aspergillus niger and Penicillium chrysogenum.
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Affiliation(s)
- Annemarie Kramer
- Research Unit Marine Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Hans Christian Beck
- Centre for Clinical Proteomics, Department for Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark
| | - Abhishek Kumar
- Department for Botany and Molecular Biology, Institute of Botany, Christian-Albrechts University of Kiel, Kiel, Germany
| | - Lars Peter Kristensen
- Centre for Clinical Proteomics, Department for Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark
| | - Johannes F. Imhoff
- Research Unit Marine Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Antje Labes
- Research Unit Marine Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
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9
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Abstract
This review focuses on the steps unique to methionine biosynthesis, namely the conversion of homoserine to methionine. The past decade has provided a wealth of information concerning the details of methionine metabolism and the review focuses on providing a comprehensive overview of the field, emphasizing more recent findings. Details of methionine biosynthesis are addressed along with key cellular aspects, including regulation, uptake, utilization, AdoMet, the methyl cycle, and growing evidence that inhibition of methionine biosynthesis occurs under stressful cellular conditions. The first unique step in methionine biosynthesis is catalyzed by the metA gene product, homoserine transsuccinylase (HTS, or homoserine O-succinyltransferase). Recent experiments suggest that transcription of these genes is indeed regulated by MetJ, although the repressor-binding sites have not yet been verified. Methionine also serves as the precursor of S-adenosylmethionine, which is an essential molecule employed in numerous biological processes. S-adenosylhomocysteine is produced as a consequence of the numerous AdoMet-dependent methyl transfer reactions that occur within the cell. In E. coli and Salmonella, this molecule is recycled in two discrete steps to complete the methyl cycle. Cultures challenged by oxidative stress appear to experience a growth limitation that depends on methionine levels. E. coli that are deficient for the manganese and iron superoxide dismutases (the sodA and sodB gene products, respectively) require the addition of methionine or cysteine for aerobic growth. Modulation of methionine levels in response to stressful conditions further increases the complexity of its regulation.
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10
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Abstract
Trans-aconitate methyltransferase regulator (TamR) is a member of the ligand-responsive multiple antibiotic resistance regulator (MarR) family of transcription factors. In Streptomyces coelicolor, TamR regulates transcription of tamR (encoding TamR), tam (encoding trans-aconitate methyltransferase) and sacA (encoding aconitase); up-regulation of these genes promotes metabolic flux through the citric acid cycle. DNA binding by TamR is attenuated and transcriptional derepression is achieved on binding of ligands such as citrate and trans-aconitate to TamR. In the present study, we show that three additional genes are regulated by S. coelicolor TamR. Genes encoding malate synthase (aceB1; SCO6243), malate dehydrogenase (mdh; SCO4827) and isocitrate dehydrogenase (idh; SCO7000) are up-regulated in vivo when citrate and trans-aconitate accumulate, and TamR binds the corresponding gene promoters in vitro, a DNA binding that is attenuated by cognate ligands. Mutations to the TamR binding site attenuate DNA binding in vitro and result in constitutive promoter activity in vivo. The predicted TamR binding sites are highly conserved in the promoters of these genes in Streptomyces species that encode divergent tam-tamR gene pairs, suggesting evolutionary conservation. Like aconitase and trans-aconitate methyltransferase, malate dehydrogenase, isocitrate dehydrogenase and malate synthase are closely related to the citric acid cycle, either catalysing individual reaction steps or, in the case of malate synthase, participating in the glyoxylate cycle to produce malate that enters the citric acid cycle to replenish the intermediate pool. Taken together, our data suggest that TamR plays an important and conserved role in promoting metabolic flux through the citric acid cycle.
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11
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Breitenbach M, Rinnerthaler M, Hartl J, Stincone A, Vowinckel J, Breitenbach-Koller H, Ralser M. Mitochondria in ageing: there is metabolism beyond the ROS. FEMS Yeast Res 2014; 14:198-212. [PMID: 24373480 DOI: 10.1111/1567-1364.12134] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 12/19/2013] [Accepted: 12/21/2013] [Indexed: 12/22/2022] Open
Abstract
Mitochondria are responsible for a series of metabolic functions. Superoxide leakage from the respiratory chain and the resulting cascade of reactive oxygen species-induced damage, as well as mitochondrial metabolism in programmed cell death, have been intensively studied during ageing in single-cellular and higher organisms. Changes in mitochondrial physiology and metabolism resulting in ROS are thus considered to be hallmarks of ageing. In this review, we address 'other' metabolic activities of mitochondria, carbon metabolism (the TCA cycle and related underground metabolism), the synthesis of Fe/S clusters and the metabolic consequences of mitophagy. These important mitochondrial activities are hitherto less well-studied in the context of cellular and organismic ageing. In budding yeast, they strongly influence replicative, chronological and hibernating lifespan, connecting the diverse ageing phenotypes studied in this single-cellular model organism. Moreover, there is evidence that similar processes equally contribute to ageing of higher organisms as well. In this scenario, increasing loss of metabolic integrity would be one driving force that contributes to the ageing process. Understanding mitochondrial metabolism may thus be required for achieving a unifying theory of eukaryotic ageing.
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12
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Mackie A, Keseler IM, Nolan L, Karp PD, Paulsen IT. Dead end metabolites--defining the known unknowns of the E. coli metabolic network. PLoS One 2013; 8:e75210. [PMID: 24086468 PMCID: PMC3781023 DOI: 10.1371/journal.pone.0075210] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Accepted: 08/12/2013] [Indexed: 12/19/2022] Open
Abstract
The EcoCyc database is an online scientific database which provides an integrated view of the metabolic and regulatory network of the bacterium Escherichia coli K-12 and facilitates computational exploration of this important model organism. We have analysed the occurrence of dead end metabolites within the database – these are metabolites which lack the requisite reactions (either metabolic or transport) that would account for their production or consumption within the metabolic network. 127 dead end metabolites were identified from the 995 compounds that are contained within the EcoCyc metabolic network. Their presence reflects either a deficit in our representation of the network or in our knowledge of E. coli metabolism. Extensive literature searches resulted in the addition of 38 transport reactions and 3 metabolic reactions to the database and led to an improved representation of the pathway for Vitamin B12 salvage. 39 dead end metabolites were identified as components of reactions that are not physiologically relevant to E. coli K-12 – these reactions are properties of purified enzymes in vitro that would not be expected to occur in vivo. Our analysis led to improvements in the software that underpins the database and to the program that finds dead end metabolites within EcoCyc. The remaining dead end metabolites in the EcoCyc database likely represent deficiencies in our knowledge of E. coli metabolism.
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Affiliation(s)
- Amanda Mackie
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales, Australia
| | | | - Laura Nolan
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Peter D. Karp
- SRI International, Menlo Park, California, United States of America
| | - Ian T. Paulsen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales, Australia
- * E-mail:
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13
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Metabolite damage and its repair or pre-emption. Nat Chem Biol 2013; 9:72-80. [PMID: 23334546 DOI: 10.1038/nchembio.1141] [Citation(s) in RCA: 218] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Accepted: 11/13/2012] [Indexed: 01/25/2023]
Abstract
It is increasingly evident that metabolites suffer various kinds of damage, that such damage happens in all organisms and that cells have dedicated systems for damage repair and containment. First, chemical biology is demonstrating that diverse metabolites are damaged by side reactions of 'promiscuous' enzymes or by spontaneous chemical reactions, that the products are useless or toxic and that the unchecked buildup of these products can be devastating. Second, genetic and genomic evidence from prokaryotes and eukaryotes is implicating a network of new, conserved enzymes that repair damaged metabolites or somehow pre-empt damage. Metabolite (that is, small-molecule) repair is analogous to macromolecule (DNA and protein) repair and seems from comparative genomic evidence to be equally widespread. Comparative genomics also implies that metabolite repair could be the function of many conserved protein families lacking known activities. How--and how well--cells deal with metabolite damage affects fields ranging from medical genetics to metabolic engineering.
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Huang H, Grove A. The transcriptional regulator TamR from Streptomyces coelicolor controls a key step in central metabolism during oxidative stress. Mol Microbiol 2013; 87:1151-66. [PMID: 23320788 DOI: 10.1111/mmi.12156] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2013] [Indexed: 01/04/2023]
Abstract
Multiple antibiotic resistance regulator (MarR) family transcriptional regulators usually regulate gene activity by responding to specific ligands. Here we show that TamR (trans-aconitate methyltransferase regulator), a MarR homologue from Streptomyces coelicolor, functions in oxidative stress responses to regulate a key step in central metabolism. The gene encoding TamR is oriented divergently from the tam gene, which encodes trans-aconitate methyltransferase. Trans-aconitate methyltransferase methylates trans-aconitate, which is formed when cis-aconitate is released during aconitase-mediated isomerization of citrate to isocitrate; trans-aconitate, but not its methyl ester, is a potent inhibitor of aconitase. We show that TamR binds with high affinity to the intergenic region between the tamR and tam genes. Notably, trans-aconitate attenuates DNA-binding by TamR, as do citrate, cis-aconitate and isocitrate, which are the substrate, intermediate and product of aconitase respectively. In vivo, hydrogen peroxide and citrate induce significant upregulation of the tam (SCO3132), tamR (SCO3133) and aconitase (SCO5999) genes. Since oxidative stress leads to disassembly of the [4Fe-4S] cluster that is essential for aconitase activity, resulting in accumulation of citrate and release of cis-aconitate and its subsequent conversion to trans-aconitate, we propose that TamR mediates a novel regulatory function in which the inhibitory effects of trans-aconitate and accumulated citrate are alleviated.
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Affiliation(s)
- Hao Huang
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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15
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Regulation and evolution of malonate and propionate catabolism in proteobacteria. J Bacteriol 2012; 194:3234-40. [PMID: 22505679 DOI: 10.1128/jb.00163-12] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteria catabolize malonate via two pathways, encoded by the mdc and mat genes. In various bacteria, transcription of these genes is controlled by the GntR family transcription factors (TFs) MatR/MdcY and/or the LysR family transcription factor MdcR. Propionate is metabolized via the methylcitrate pathway, comprising enzymes encoded by the prp and acn genes. PrpR, the Fis family sigma 54-dependent transcription factor, is known to be a transcriptional activator of the prp genes. Here, we report a detailed comparative genomic analysis of malonate and propionate metabolism and its regulation in proteobacteria. We characterize genomic loci and gene regulation and identify binding motifs for four new TFs and also new regulon members, in particular, tripartite ATP-independent periplasmic (TRAP) transporters. We describe restructuring of the genomic loci and regulatory interactions during the evolution of proteobacteria.
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16
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Maciag A, Peano C, Pietrelli A, Egli T, De Bellis G, Landini P. In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements. Nucleic Acids Res 2011; 39:5338-55. [PMID: 21398637 PMCID: PMC3141248 DOI: 10.1093/nar/gkr129] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Specific promoter recognition by bacterial RNA polymerase is mediated by σ subunits, which assemble with RNA polymerase core enzyme (E) during transcription initiation. However, σ70 (the housekeeping σ subunit) and σS (an alternative σ subunit mostly active during slow growth) recognize almost identical promoter sequences, thus raising the question of how promoter selectivity is achieved in the bacterial cell. To identify novel sequence determinants for selective promoter recognition, we performed run-off/microarray (ROMA) experiments with RNA polymerase saturated either with σ70 (Eσ70) or with σS (EσS) using the whole Escherichia coli genome as DNA template. We found that Eσ70, in the absence of any additional transcription factor, preferentially transcribes genes associated with fast growth (e.g. ribosomal operons). In contrast, EσS efficiently transcribes genes involved in stress responses, secondary metabolism as well as RNAs from intergenic regions with yet-unknown function. Promoter sequence comparison suggests that, in addition to different conservation of the −35 sequence and of the UP element, selective promoter recognition by either form of RNA polymerase can be affected by the A/T content in the −10/+1 region. Indeed, site-directed mutagenesis experiments confirmed that an A/T bias in the −10/+1 region could improve promoter recognition by EσS.
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Affiliation(s)
- Anna Maciag
- Department of Biomolecular Sciences and Biotechnology, Università degli Studi di Milano, Milan, Italy
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Lin S, Hanson RE, Cronan JE. Biotin synthesis begins by hijacking the fatty acid synthetic pathway. Nat Chem Biol 2010; 6:682-8. [PMID: 20693992 PMCID: PMC2925990 DOI: 10.1038/nchembio.420] [Citation(s) in RCA: 143] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2010] [Accepted: 07/09/2010] [Indexed: 11/20/2022]
Abstract
Although biotin is an essential enzyme cofactor found in all three domains of life, our knowledge of its biosynthesis remains fragmentary. Most of the carbon atoms of biotin are derived from pimelic acid, a seven-carbon dicarboxylic acid, but the mechanism whereby this intermediate is assembled remains unknown. Genetic analysis in Escherichia coli identified only two genes of unknown function required for pimelate synthesis, bioC and bioH. We report in vivo and in vitro evidence that the pimeloyl moiety is synthesized by a modified fatty acid synthetic pathway in which the omega-carboxyl group of a malonyl-thioester is methylated by BioC, which allows recognition of this atypical substrate by the fatty acid synthetic enzymes. The malonyl-thioester methyl ester enters fatty acid synthesis as the primer and undergoes two reiterations of the fatty acid elongation cycle to give pimeloyl-acyl carrier protein (ACP) methyl ester, which is hydrolyzed to pimeloyl-ACP and methanol by BioH.
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Affiliation(s)
- Steven Lin
- Department of Microbiology, University of Illinois, Urbana, Illinois 61801
| | - Ryan E. Hanson
- Department of Microbiology, University of Illinois, Urbana, Illinois 61801
| | - John E. Cronan
- Department of Microbiology, University of Illinois, Urbana, Illinois 61801
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801
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Dalhoff C, Hüben M, Lenz T, Poot P, Nordhoff E, Köster H, Weinhold E. Synthesis of S-Adenosyl-L-homocysteine Capture Compounds for Selective Photoinduced Isolation of Methyltransferases. Chembiochem 2010; 11:256-65. [DOI: 10.1002/cbic.200900349] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Rémus-Borel W, Menzies JG, Bélanger RR. Aconitate and methyl aconitate are modulated by silicon in powdery mildew-infected wheat plants. JOURNAL OF PLANT PHYSIOLOGY 2009; 166:1413-22. [PMID: 19345440 DOI: 10.1016/j.jplph.2009.02.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Revised: 02/27/2009] [Accepted: 02/27/2009] [Indexed: 05/24/2023]
Abstract
The accumulation of 5,6-O-methyl trans-aconitate in wheat was previously found to be linked with the presence of powdery mildew (Blumeria graminis) and silicon (Si) feeding. In this work, we sought to determine if trans-aconitate (TA) could act as a precursor of methylated forms of TA in wheat and if a relationship existed between Si treatment, disease development, TA and methyl TA concentration within wheat leaves. In absence of infection, TA concentration increased over time regardless of Si feeding. By contrast, TA concentration remained fairly constant over time in both Si(-) and Si(+)-infected plants but Si(+) plants had a significantly lower level than Si(-) plants. Conversely, methyl TA concentration increased in wheat leaves in response to infection and was linked to wheat's increased resistance induced by Si. The effect of Si feeding was only noticeable on methyl TA concentration in presence of the fungus. This suggests that Si does not act directly on TA concentration in leaves but somehow accentuate the production of methyl TA in stressed plants. Based on the concurrent increase in methyl TA and leveling off of TA concentration, it appears that the latter, instead of accumulating, is used by diseased plants to produce antifungal methylated forms of TA that would act as phytoalexins to limit disease development, a phenomenon more pronounced in plants treated with Si.
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Optimization based automated curation of metabolic reconstructions. BMC Bioinformatics 2007; 8:212. [PMID: 17584497 PMCID: PMC1933441 DOI: 10.1186/1471-2105-8-212] [Citation(s) in RCA: 216] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2006] [Accepted: 06/20/2007] [Indexed: 11/17/2022] Open
Abstract
Background Currently, there exists tens of different microbial and eukaryotic metabolic reconstructions (e.g., Escherichia coli, Saccharomyces cerevisiae, Bacillus subtilis) with many more under development. All of these reconstructions are inherently incomplete with some functionalities missing due to the lack of experimental and/or homology information. A key challenge in the automated generation of genome-scale reconstructions is the elucidation of these gaps and the subsequent generation of hypotheses to bridge them. Results In this work, an optimization based procedure is proposed to identify and eliminate network gaps in these reconstructions. First we identify the metabolites in the metabolic network reconstruction which cannot be produced under any uptake conditions and subsequently we identify the reactions from a customized multi-organism database that restores the connectivity of these metabolites to the parent network using four mechanisms. This connectivity restoration is hypothesized to take place through four mechanisms: a) reversing the directionality of one or more reactions in the existing model, b) adding reaction from another organism to provide functionality absent in the existing model, c) adding external transport mechanisms to allow for importation of metabolites in the existing model and d) restore flow by adding intracellular transport reactions in multi-compartment models. We demonstrate this procedure for the genome- scale reconstruction of Escherichia coli and also Saccharomyces cerevisiae wherein compartmentalization of intra-cellular reactions results in a more complex topology of the metabolic network. We determine that about 10% of metabolites in E. coli and 30% of metabolites in S. cerevisiae cannot carry any flux. Interestingly, the dominant flow restoration mechanism is directionality reversals of existing reactions in the respective models. Conclusion We have proposed systematic methods to identify and fill gaps in genome-scale metabolic reconstructions. The identified gaps can be filled both by making modifications in the existing model and by adding missing reactions by reconciling multi-organism databases of reactions with existing genome-scale models. Computational results provide a list of hypotheses to be queried further and tested experimentally.
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Wang L, Li J, March JC, Valdes JJ, Bentley WE. luxS-dependent gene regulation in Escherichia coli K-12 revealed by genomic expression profiling. J Bacteriol 2006; 187:8350-60. [PMID: 16321939 PMCID: PMC1316998 DOI: 10.1128/jb.187.24.8350-8360.2005] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The bacterial quorum-sensing autoinducer 2 (AI-2) has received intense interest because the gene for its synthase, luxS, is common among a large number of bacterial species. We have identified luxS-controlled genes in Escherichia coli under two different growth conditions using DNA microarrays. Twenty-three genes were affected by luxS deletion in the presence of glucose, and 63 genes were influenced by luxS deletion in the absence of glucose. Minimal overlap among these gene sets suggests the role of luxS is condition dependent. Under the latter condition, the metE gene, the lsrACDBFG operon, and the flanking genes of the lsr operon (lsrR, lsrK, tam, and yneE) were among the most significantly induced genes by luxS. The E. coli lsr operon includes an additional gene, tam, encoding an S-adenosyl-l-methionine-dependent methyltransferase. Also, lsrR and lsrK belong to the same operon, lsrRK, which is positively regulated by the cyclic AMP receptor protein and negatively regulated by LsrR. lsrK is additionally transcribed by a promoter between lsrR and lsrK. Deletion of luxS was also shown to affect genes involved in methionine biosynthesis, methyl transfer reactions, iron uptake, and utilization of carbon. It was surprising, however, that so few genes were affected by luxS deletion in this E. coli K-12 strain under these conditions. Most of the highly induced genes are related to AI-2 production and transport. These data are consistent with the function of LuxS as an important metabolic enzyme but appear not to support the role of AI-2 as a true signal molecule for E. coli W3110 under the investigated conditions.
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Affiliation(s)
- Liang Wang
- Center for Biosystems Research, University of Maryland Biotechnology Institute, College Park, MD 20742, USA
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Katz JE, Dumlao DS, Clarke S, Hau J. A new technique (COMSPARI) to facilitate the identification of minor compounds in complex mixtures by GC/MS and LC/MS: tools for the visualization of matched datasets. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2004; 15:580-584. [PMID: 15047062 DOI: 10.1016/j.jasms.2003.12.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2003] [Revised: 12/18/2003] [Accepted: 12/18/2003] [Indexed: 05/24/2023]
Abstract
In the rapidly growing field of metabolomics, it is common to analyze complex biological samples by chromatography coupled to mass spectrometry. While several techniques are available for the detection of significant peaks in individual samples, it is still difficult to determine small differences between similar samples. Using conventional software, visual inspections of individual chromatograms or individual mass spectra are often of little use because the differences in the composition of small molecules are too small to be recognizable. Thus, we developed a new approach to visualizing mass spectral datasets using a tool that allows one to easily detect these small differences between mass spectra and chromatograms derived from matched samples. Using these tools on extracts from wild-type and methyltransferase knockout strains of the yeast Saccharomyces cerevisiae, we were able to readily identify those mass spectra in our data sets that were different between the wild-type and the knockout extracts and to identify the molecules involved. The software was also successfully applied to a set of LC/MS data from peptide digests that were performed with identical substrates but different enzymes. We have named this visualization tool COMSPARI (COMparision of SPectrAl Retention Information) and are making the software publicly available via Internet at.
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Affiliation(s)
- Jonathan E Katz
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, Los Angeles, California 90095-1570, USA
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Abstract
We present a summary of recent progress in understanding Escherichia coli K-12 gene and protein functions. New information has come both from classical biological experimentation and from using the analytical tools of functional genomics. The content of the E. coli genome can clearly be seen to contain elements acquired by horizontal transfer. Nevertheless, there is probably a large, stable core of >3500 genes that are shared among all E. coli strains. The gene-enzyme relationship is examined, and, in many cases, it exhibits complexity beyond a simple one-to-one relationship. Also, the E. coli genome can now be seen to contain many multiple enzymes that carry out the same or closely similar reactions. Some are similar in sequence and may share common ancestry; some are not. We discuss the concept of a minimal genome as being variable among organisms and obligatorily linked to their life styles and defined environmental conditions. We also address classification of functions of gene products and avenues of insight into the history of protein evolution.
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Affiliation(s)
- M Riley
- The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts 02543, USA. ,
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Abstract
The promoter recognition specificity of Escherichia coli RNA polymerase is modulated by replacement of the sigma subunit in the first step and by interaction with transcription factors in the second step. The overall differentiated state of approximately 2000 molecules of the RNA polymerase in a single cell can be estimated after measurement of both the intracellular concentrations and the RNA polymerase-binding affinities for all seven species of the sigma subunit and 100-150 transcription factors. The anticipated impact from this line of systematic approach is that the prediction of the expression hierarchy of approximately 4000 genes on the E. coli genome can be estimated.
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Affiliation(s)
- A Ishihama
- National Institute of Genetics, Department of Molecular Genetics, Mishima, Shizuoka 411-8540, Japan.
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