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Pramanik A, Datta S. Structural and functional insights of itaconyl-CoA hydratase from Pseudomonas aeruginosa highlight a novel N-terminal hotdog fold. FEBS Lett 2024; 598:1387-1401. [PMID: 38575551 DOI: 10.1002/1873-3468.14867] [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] [Received: 07/21/2023] [Revised: 02/29/2024] [Accepted: 03/05/2024] [Indexed: 04/06/2024]
Abstract
Itaconyl-CoA hydratase in Pseudomonas aeruginosa (PaIch) converts itaconyl-CoA to (S)-citramalyl-CoA upon addition of a water molecule, a part of an itaconate catabolic pathway in virulent organisms required for their survival in humans host cells. Crystal structure analysis of PaIch showed that a unique N-terminal hotdog fold containing a 4-residue short helical segment α3-, named as an "eaten sausage", followed by a flexible loop region slipped away from the conserved β-sheet scaffold, whereas the C-terminal hotdog fold is similar to all MaoC. A conserved hydratase motif with catalytic residues provides mechanistic insights into catalysis, and existence of a longer substrate binding tunnel may suggest the binding of longer CoA derivatives.
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Affiliation(s)
- Atanu Pramanik
- Department of Structural Biology and Bio-informatics, CSIR-Indian Institute of Chemical Biology (CSIR-IICB), Kolkata, India
| | - Saumen Datta
- Department of Structural Biology and Bio-informatics, CSIR-Indian Institute of Chemical Biology (CSIR-IICB), Kolkata, India
- Biological Sciences, Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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2
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Schiaffi V, Barras F, Bouveret E. Matching the β-oxidation gene repertoire with the wide diversity of fatty acids. Curr Opin Microbiol 2024; 77:102402. [PMID: 37992547 DOI: 10.1016/j.mib.2023.102402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/23/2023] [Accepted: 10/28/2023] [Indexed: 11/24/2023]
Abstract
Bacteria can use fatty acids (FAs) from their environment as carbon and energy source. This catabolism is performed by the enzymes of the well-known β-oxidation machinery, producing reducing power and releasing acetyl-CoA that can feed the tricarboxylic acid cycle. FAs are extremely diverse: they can be saturated or (poly)unsaturated and are found in different sizes. The need to degrade such a wide variety of compounds may explain why so many seemingly homologous enzymes are found for each step of the β-oxidation cycle. In addition, the degradation of unsaturated fatty acids requires specific auxiliary enzymes for isomerase and reductase reactions. Furthermore, the β-oxidation cycle can be blocked by dead-end products, which are taken care of by acyl-CoA thioesterases. Yet, the functional characterization of the enzymes required for the degradation of the full diversity of FAs remains to be documented in most bacteria.
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Affiliation(s)
- Veronica Schiaffi
- Institut Pasteur, Department of Microbiology, Université Paris-Cité, UMR CNRS 6047, SAMe Unit, France
| | - Frédéric Barras
- Institut Pasteur, Department of Microbiology, Université Paris-Cité, UMR CNRS 6047, SAMe Unit, France
| | - Emmanuelle Bouveret
- Institut Pasteur, Department of Microbiology, Université Paris-Cité, UMR CNRS 6047, SAMe Unit, France.
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3
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Pöschel L, Guevara-Martínez M, Hörnström D, van Maris AJA, Buchhaupt M. Engineering of thioesterase YciA from Haemophilus influenzae for production of carboxylic acids. Appl Microbiol Biotechnol 2023; 107:6219-6236. [PMID: 37572123 PMCID: PMC10560148 DOI: 10.1007/s00253-023-12691-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 07/06/2023] [Accepted: 07/12/2023] [Indexed: 08/14/2023]
Abstract
Acyl-CoA-thioesterases, which hydrolyze acyl-CoA-esters and thereby release the respective acid, have essential functions in cellular metabolism and have also been used to produce valuable compounds in biotechnological processes. Thioesterase YciA originating from Haemophilus influenzae has been previously used to produce specific dicarboxylic acids from CoA-bound intermediates of the ethylmalonyl CoA pathway (EMCP) in Methylorubrum extorquens. In order to identify variants of the YciA enzyme with the capability to hydrolyze so far inaccessible CoA-esters of the EMCP or with improved productivity, we engineered the substrate-binding region of the enzyme. Screening a small semi-rational mutant library directly in M. extorquens yielded the F35L variant which showed a drastic product level increase for mesaconic acid (6.4-fold) and 2-methylsuccinic acid (4.4-fold) compared to the unaltered YciA enzyme. Unexpectedly, in vitro enzyme assays using respective M. extorquens cell extracts or recombinantly produced thioesterases could not deliver congruent data, as the F35L variant showed strongly reduced activity in these experiments. However, applied in an Escherichia coli production strain, the protein variant again outperformed the wild-type enzyme by allowing threefold increased 3-hydroxybutyric acid product titers. Saturation mutagenesis of the codon for position 35 led to the identification of another highly efficient YciA variant and enabled structure-function interpretations. Our work describes an important module for dicarboxylic acid production with M. extorquens and can guide future thioesterase improvement approaches. KEY POINTS: • Substitutions at position F35 of YciAHI changed the productivity of YciA-based release of carboxylic acid products in M. extorquens AM1 and E. coli. • YciAHI F35N and F35L are improved variants for dicarboxylic production of 2-methylsuccinic acid and mesaconic acid with M. extorquens AM1. • In vitro enzyme assays did not reveal superior properties of the optimized protein variants.
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Affiliation(s)
- Laura Pöschel
- DECHEMA-Forschungsinstitut, Microbial Biotechnology, Theodor-Heuss-Allee 25, 60486, Frankfurt Am Main, Germany
- Faculty of Biological Sciences, Goethe University Frankfurt, Max-Von-Laue-Str. 9, 60438, Frankfurt Am Main, Germany
| | - Mónica Guevara-Martínez
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, SE 10691, Stockholm, Sweden
| | - David Hörnström
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, SE 10691, Stockholm, Sweden
| | - Antonius J A van Maris
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, SE 10691, Stockholm, Sweden
| | - Markus Buchhaupt
- DECHEMA-Forschungsinstitut, Microbial Biotechnology, Theodor-Heuss-Allee 25, 60486, Frankfurt Am Main, Germany.
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4
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Klapper M, Hübner A, Ibrahim A, Wasmuth I, Borry M, Haensch VG, Zhang S, Al-Jammal WK, Suma H, Fellows Yates JA, Frangenberg J, Velsko IM, Chowdhury S, Herbst R, Bratovanov EV, Dahse HM, Horch T, Hertweck C, González Morales MR, Straus LG, Vilotijevic I, Warinner C, Stallforth P. Natural products from reconstructed bacterial genomes of the Middle and Upper Paleolithic. Science 2023; 380:619-624. [PMID: 37141315 DOI: 10.1126/science.adf5300] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Major advances over the past decade in the field of ancient DNA are providing access to past paleogenomic diversity, but the diverse functions and biosynthetic capabilities of this growing paleome remain largely elusive. Here, we investigated the dental calculus of 12 Neanderthals and 52 anatomically modern humans spanning 100 kya to the present and reconstructed 459 bacterial metagenome-assembled genomes (MAGs). We identified a biosynthetic gene cluster (BGC) shared by seven Middle and Upper Paleolithic individuals that allows for the heterologous production of a class of previously unknown metabolites we name paleofurans. This paleobiotechnological approach demonstrates that viable biosynthetic machinery can be produced from the preserved genetic material of ancient organisms, allowing access to natural products from the Pleistocene and providing a promising area for natural product exploration.
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Affiliation(s)
- Martin Klapper
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Alexander Hübner
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Anan Ibrahim
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Ina Wasmuth
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Maxime Borry
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Veit G Haensch
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Shuaibing Zhang
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Walid K Al-Jammal
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Harikumar Suma
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - James A Fellows Yates
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Jasmin Frangenberg
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Irina M Velsko
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Somak Chowdhury
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Rosa Herbst
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Evgeni V Bratovanov
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Hans-Martin Dahse
- Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Therese Horch
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
- Faculty of Biological Sciences, Institute of Microbiology, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Manuel Ramon González Morales
- Instituto Internacional de Investigaciones Prehistóricas de Cantabria, Universidad de Cantabria, 39071 Santander, Spain
| | - Lawrence Guy Straus
- Department of Anthropology, University of New Mexico, Albuquerque, NM 87131, USA
- Grupo I+D+i EvoAdapta, Departmento de Ciencias Históricas, Universidad de Cantabria, 39005 Santander, Spain
| | - Ivan Vilotijevic
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
- Faculty of Biological Sciences, Institute of Microbiology, Friedrich Schiller University Jena, 07743 Jena, Germany
- Department of Anthropology, Harvard University, Cambridge, MA 02138, USA
| | - Pierre Stallforth
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany
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5
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Dietl A, Wellach K, Mahadevan P, Mertes N, Winter S, Kutsch T, Walz C, Schlichting I, Fabritz S, Barends TM. Structures of an unusual 3-hydroxyacyl dehydratase (FabZ) from a ladderane-producing organism with an unexpected substrate preference. J Biol Chem 2023; 299:104602. [PMID: 36907440 PMCID: PMC10139942 DOI: 10.1016/j.jbc.2023.104602] [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: 05/23/2022] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/12/2023] Open
Abstract
The genomes of anaerobic ammonium-oxidizing (anammox) bacteria contain a gene cluster comprising genes of unusual fatty acid biosynthesis enzymes that were suggested to be involved in the synthesis of the unique "ladderane" lipids produced by these organisms. This cluster encodes an acyl carrier protein (denoted as "amxACP") and a variant of FabZ, an ACP-3-hydroxyacyl dehydratase. In this study, we characterize this enzyme, which we call anammox-specific FabZ ("amxFabZ"), to investigate the unresolved biosynthetic pathway of ladderane lipids. We find that amxFabZ displays distinct sequence differences to "canonical" FabZ, such as a bulky, apolar residue on the inside of the substrate binding tunnel, where the canonical enzyme has a glycine. Additionally, substrate screens suggest that amxFabZ efficiently converts substrates with acyl chain lengths of up to eight carbons, whereas longer substrates are converted much more slowly under the conditions used. We also present crystal structures of amxFabZs, mutational studies and the structure of a complex between amxFabZ and amxACP, which show that the structures alone cannot explain the apparent differences from canonical FabZ. Moreover, we find that while amxFabZ does dehydrate substrates bound to amxACP, it does not convert substrates bound to canonical ACP of the same anammox organism. We discuss the possible functional relevance of these observations in the light of proposals for the mechanism for ladderane biosynthesis.
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Affiliation(s)
- Andreas Dietl
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany.
| | - Kathrin Wellach
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - Pavithra Mahadevan
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - Nicole Mertes
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - SophieL Winter
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - Tobias Kutsch
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - Carlo Walz
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - Ilme Schlichting
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - Sebastian Fabritz
- Mass Spectrometry Core Facility, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - ThomasR M Barends
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany.
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6
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Kalinger RS, Rowland O. Determinants of substrate specificity in a catalytically diverse family of acyl-ACP thioesterases from plants. BMC PLANT BIOLOGY 2023; 23:1. [PMID: 36588156 PMCID: PMC9806908 DOI: 10.1186/s12870-022-04003-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 12/13/2022] [Indexed: 05/05/2023]
Abstract
BACKGROUND ACYL-LIPID THIOESTERASES (ALTs) are a subclass of plastid-localized, fatty acyl-acyl carrier protein (ACP) thioesterase enzymes from plants. They belong to the single hot dog-fold protein family. ALT enzymes generate medium-chain (C6-C14) and C16 fatty acids, methylketone precursors (β-keto fatty acids), and 3-hydroxy fatty acids when expressed heterologously in E. coli. The diverse substrate chain-length and oxidation state preferences of ALTs set them apart from other plant acyl-ACP thioesterases, and ALTs show promise as metabolic engineering tools to produce high-value medium-chain fatty acids and methylketones in bacterial or plant systems. Here, we used a targeted motif-swapping approach to explore connections between ALT protein sequence and substrate specificity. Guided by comparative motif searches and computational modelling, we exchanged regions of amino acid sequence between ALT-type thioesterases from Arabidopsis thaliana, Medicago truncatula, and Zea mays to create chimeric ALT proteins. RESULTS Comparing the activity profiles of chimeric ALTs in E. coli to their wild-type counterparts led to the identification of interacting regions within the thioesterase domain that shape substrate specificity and enzyme activity. Notably, the presence of a 31-CQH[G/C]RH-36 motif on the central α-helix was shown to shift chain-length specificity towards 12-14 carbon chains, and to be a core determinant of substrate specificity in ALT-type thioesterases with preference for 12-14 carbon 3-hydroxyacyl- and β-ketoacyl-ACP substrates. For an ALT containing this motif to be functional, an additional 108-KXXA-111 motif and compatible sequence spanning aa77-93 of the surrounding β-sheet must also be present, demonstrating that interactions between residues in these regions of the catalytic domain are critical to thioesterase activity. The behaviour of chimeric enzymes in E. coli also indicated that aa77-93 play a significant role in dictating whether an ALT will prefer ≤10-carbon or ≥ 12-carbon acyl chain-lengths, and aa91-96 influence selectivity for substrates of fully or partially reduced oxidation states. Additionally, aa64-67 on the hot dog-fold β-sheet were shown to be important for enabling an ALT to act on 3-hydroxy fatty acyl-ACP substrates. CONCLUSIONS By revealing connections between thioesterase sequence and substrate specificity, this study is an advancement towards engineering recombinant ALTs with product profiles suited for specific applications.
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Affiliation(s)
- Rebecca S Kalinger
- Department of Biology and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, K1S 5B6, Canada
| | - Owen Rowland
- Department of Biology and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, K1S 5B6, Canada.
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7
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Glanville DG, Gazioglu O, Marra M, Tokars VL, Kushnir T, Habtom M, Croucher NJ, Nebenzahl YM, Mondragón A, Yesilkaya H, Ulijasz AT. Pneumococcal capsule expression is controlled through a conserved, distal cis-regulatory element during infection. PLoS Pathog 2023; 19:e1011035. [PMID: 36719895 PMCID: PMC9888711 DOI: 10.1371/journal.ppat.1011035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 11/29/2022] [Indexed: 02/01/2023] Open
Abstract
Streptococcus pneumoniae (the pneumococcus) is the major cause of bacterial pneumonia in the US and worldwide. Studies have shown that the differing chemical make-up between serotypes of its most important virulence factor, the capsule, can dictate disease severity. Here we demonstrate that control of capsule synthesis is also critical for infection and facilitated by two broadly conserved transcription factors, SpxR and CpsR, through a distal cis-regulatory element we name the 37-CE. Strikingly, changing only three nucleotides within this sequence is sufficient to render pneumococcus avirulent. Using in vivo and in vitro approaches, we present a model where SpxR interacts as a unique trimeric quaternary structure with the 37-CE to enable capsule repression in the airways. Considering its dramatic effect on infection, variation of the 37-CE between serotypes suggests this molecular switch could be a critical contributing factor to this pathogen's serotype-specific disease outcomes.
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Affiliation(s)
- David G. Glanville
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Ozcan Gazioglu
- Department of Respiratory Sciences, University of Leicester, University Road, Leicester, United Kingdom
| | - Michela Marra
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Valerie L. Tokars
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Tatyana Kushnir
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of The Negev, Beer-Sheva, Israel
| | - Medhanie Habtom
- Department of Respiratory Sciences, University of Leicester, University Road, Leicester, United Kingdom
| | - Nicholas J. Croucher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Sir Michael Uren Hub, Imperial College London, London, United Kingdom
| | - Yaffa Mizrachi Nebenzahl
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of The Negev, Beer-Sheva, Israel
| | - Alfonso Mondragón
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Hasan Yesilkaya
- Department of Respiratory Sciences, University of Leicester, University Road, Leicester, United Kingdom
| | - Andrew T. Ulijasz
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, United States of America
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8
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Kaur H, Singh V, Kalia M, Mohan B, Taneja N. Identification and functional annotation of hypothetical proteins of uropathogenic Escherichia coli strain CFT073 towards designing antimicrobial drug targets. J Biomol Struct Dyn 2022; 40:14084-14095. [PMID: 34751095 DOI: 10.1080/07391102.2021.2000499] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Urinary tract infections are a serious health concern worldwide, especially in developing countries. Escherichia coli strain CFT073 is a highly virulent pathogenic bacterial strain. CFT073 proteome contains 4897 proteins, out of which 992 have been classified as hypothetical proteins. Identification and characterization of hypothetical proteins can aid in the selection of targets for drug design. In this study, we studied the hypothetical proteins from the UPEC strain CFT073 using various computational tools. By NCBI-CDD, 376 protein sequences showed conserved domains. Based on the functional motifs in their primary sequences, we classified these 376 hypothetical proteins into 7 functional categories. Further KEGG database was used to find the roles of these hypothetical proteins in several pathways. Protein interaction network analysis of hypothetical proteins identified 53 proteins as highly interacting metabolic proteins. Virulence factor analysis of the proteins identified 8 proteins as virulent. We conducted a non-homology search for the identified proteins of UPEC in the available human proteome. We observed that 35 proteins are non-homologous to humans and hence could be selected for drug designing targets. Qualitative characterization of the selected 35 non-homologous hypothetical proteins including essentiality analysis and evaluation of druggability by similarity search against drug bank database was performed. Out of these 35 proteins, three-dimensional structures of six proteins (NP_752562.1, NP_756345.1, NP_754893.1, NP_756600.2, NP_755264.1 and NP_752994.1) could be successfully modelled. These new annotations can help to better understand disease mechanisms at the molecular level, as well as provide new targets for drug development against the UPEC strain CFT073.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Harpreet Kaur
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Vikram Singh
- Center of Computational Biology and Bioinformatics, Central University of Himachal Pradesh, Dharamshala, India
| | - Manmohit Kalia
- Department of Biology, State University of New York, Binghamton, NY, USA
| | - Balvinder Mohan
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Neelam Taneja
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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9
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Zhou Y, Qiao Y, Zhang X, Ma X, Liu H, Wang L. PFOA exposure causes variations of Acot1 among tissues in rats, and Acot1 in serum can be potentially used as a sensitive marker for health monitoring. Toxicol Res (Camb) 2022; 11:872-880. [PMID: 36337235 PMCID: PMC9618101 DOI: 10.1093/toxres/tfac065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 08/26/2022] [Accepted: 09/04/2022] [Indexed: 10/05/2023] Open
Abstract
Perfluorooctanoic acid (PFOA) is a type of 8-carbon perfluoroalkyl substances (PFASs) widely used in industrial and domestic products, which now is a persistent organic pollutant (POP) found in the environment. Its structure is similar to fatty acids, which enables it to induce the expression of ACOT genes. To investigate the expression levels of Acot1 in various tissues and organs after exposure to PFOA for 28 days in rats, and to compare the variations of Acot1 expression in different tissues, we sectioned samples and incubated with Acot1 antibody. The results show that the transcription and protein expression levels of Acot1 in the liver and kidney of rats increased significantly. Meanwhile, the transcription and protein expression of Acot1 gene were also detected in testis, muscle, and adipose. The results of immunohistochemistry were also verified by western blot detection, and we detected the transcription of Acot1 gene in these tissues and found that they all increased in varying degrees. In this study, the expression of Acot1 protein in rat serum was detected for the first time, and the expression of Acot1 in rat serum was found to be significantly increased after PFOA exposure. In addition, the expression level of Acot1 in rat organism was found to be higher than that in the control group after 4 days of depuration for 7 days of acute PFOA exposure, and Acot1 protein expression also showed an increase with increasing exposure time, indicating that Acot1 can be used as a sensitive biomarker for health monitoring of PFOA occupational workers or exposed persons.
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Affiliation(s)
- Yongbing Zhou
- School of Public Health, Bengbu Medical College, Bengbu 233030, PR China
| | - Ying Qiao
- School of Public Health, Bengbu Medical College, Bengbu 233030, PR China
| | - Xuemin Zhang
- Department of Biochemistry and Molecular Biology, School of Laboratory Medicine, Anhui Province Key Laboratory of Immunology in Chronic Diseases, Bengbu Medical College, Bengbu 233030, PR China
| | - Xingzhuang Ma
- School of Public Health, Bengbu Medical College, Bengbu 233030, PR China
| | - Hui Liu
- Department of Biochemistry and Molecular Biology, School of Laboratory Medicine, Anhui Province Key Laboratory of Immunology in Chronic Diseases, Bengbu Medical College, Bengbu 233030, PR China
| | - Li Wang
- School of Public Health, Bengbu Medical College, Bengbu 233030, PR China
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10
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Escherichia coli YigI is a Conserved Gammaproteobacterial Acyl-CoA Thioesterase Permitting Metabolism of Unusual Fatty Acid Substrates. J Bacteriol 2022; 204:e0001422. [PMID: 35876515 PMCID: PMC9380530 DOI: 10.1128/jb.00014-22] [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: 01/27/2023] Open
Abstract
Thioesterases play a critical role in metabolism, membrane biosynthesis, and overall homeostasis for all domains of life. In this present study, we characterize a putative thioesterase from Escherichia coli MG1655 and define its role as a cytosolic enzyme. Building on structure-guided functional predictions, we show that YigI is a medium- to long-chain acyl-CoA thioesterase that is involved in the degradation of conjugated linoleic acid (CLA) in vivo, showing overlapping specificity with two previously defined E. coli thioesterases TesB and FadM. We then bioinformatically identify the regulatory relationships that induce YigI expression, which include: an acidic environment, high oxygen availability, and exposure to aminoglycosides. Our findings define a role for YigI and shed light on why the E. coli genome harbors numerous thioesterases with closely related functions. IMPORTANCE Previous research has shown that long chain acyl-CoA thioesterases are needed for E. coli to grow in the presence of carbon sources such as conjugated linoleic acid, but that E. coli must possess at least one such enzyme that had not previously been characterized. Building off structure-guided function predictions, we showed that the poorly annotated protein YigI is indeed the previously unidentified third acyl CoA thioesterase. We found that the three potentially overlapping acyl-CoA thioesterases appear to be induced by nonoverlapping conditions and use that information as a starting point for identifying the precise reactions catalyzed by each such thioesterase, which is an important prerequisite for their industrial application and for more accurate metabolic modeling of E. coli.
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11
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Vasilev J, Mix AK, Heimerl T, Maier UG, Moog D. Inferred Subcellular Localization of Peroxisomal Matrix Proteins of Guillardia theta Suggests an Important Role of Peroxisomes in Cryptophytes. FRONTIERS IN PLANT SCIENCE 2022; 13:889662. [PMID: 35783940 PMCID: PMC9244630 DOI: 10.3389/fpls.2022.889662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Peroxisomes participate in several important metabolic processes in eukaryotic cells, such as the detoxification of reactive oxygen species (ROS) or the degradation of fatty acids by β-oxidation. Recently, the presence of peroxisomes in the cryptophyte Guillardia theta and other "chromalveolates" was revealed by identifying proteins for peroxisomal biogenesis. Here, we investigated the subcellular localization of candidate proteins of G. theta in the diatom Phaeodactylum tricornutum, either possessing a putative peroxisomal targeting signal type 1 (PTS1) sequence or factors lacking a peroxisomal targeting signal but known to be involved in β-oxidation. Our results indicate important contributions of the peroxisomes of G. theta to the carbohydrate, ether phospholipid, nucleotide, vitamin K, ROS, amino acid, and amine metabolisms. Moreover, our results suggest that in contrast to many other organisms, the peroxisomes of G. theta are not involved in the β-oxidation of fatty acids, which exclusively seems to occur in the cryptophyte's mitochondria.
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Affiliation(s)
- Jana Vasilev
- Laboratory for Cell Biology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Ann-Kathrin Mix
- Laboratory for Cell Biology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Thomas Heimerl
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Uwe G. Maier
- Laboratory for Cell Biology, Department of Biology, Philipps-University Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Daniel Moog
- Laboratory for Cell Biology, Department of Biology, Philipps-University Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
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12
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Li Y, Wang J, Wang F, Wang L, Wang L, Xu Z, Yuan H, Yang X, Li P, Su J, Wang R. Production of 10-Hydroxy-2-decenoic Acid from Decanoic Acid via Whole-Cell Catalysis in Engineered Escherichia coli. CHEMSUSCHEM 2022; 15:e202102152. [PMID: 34796684 DOI: 10.1002/cssc.202102152] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/18/2021] [Indexed: 06/13/2023]
Abstract
10-Hydroxy-2-decenoic acid (10-HDA) is a terminal hydroxylated medium-chain α,β-unsaturated carboxylic acid that performs various unique physiological activities and has a wide market value. Therefore, development of an environmentally friendly, safe, and high-efficiency route to synthesize 10-HDA is required. Here, the β-oxidation pathway of Escherichia coli was modified and a P450 terminal hydroxylase (CYP153A33-CPRBM3 ) was rationally designed to synthesize 10-HDA using decanoic acid as a substrate via two-step whole-cell catalysis. Different homologues of FadDs, FadEs, and YdiIs were analyzed in the first step of the conversion of decanoic acid to trans- -2- decenoic acid. In the second step, CYP153A33 (M228L)-CPRBM3 efficiently catalyzed the conversion of trans- -2- decenoic acid to 10-HDA. Finally, 217 mg L-1 10-HDA was obtained with 500 mg L-1 decanoic acid. This study provides a strategy for biosynthesis of 10-HDA and other α, β-unsaturated carboxylic acid derivatives from specific fatty acids.
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Affiliation(s)
- Yan Li
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
| | - Junqing Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
| | - Fen Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
| | - Li Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
| | - Leilei Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
| | - Ziqi Xu
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
| | - Haibo Yuan
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
| | - Xiaohui Yang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
| | - Piwu Li
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
| | - Jing Su
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
| | - Ruiming Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
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13
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Genomic Insights into Omega-3 Polyunsaturated Fatty Acid Producing Shewanella sp. N2AIL from Fish Gut. BIOLOGY 2022; 11:biology11050632. [PMID: 35625360 PMCID: PMC9138089 DOI: 10.3390/biology11050632] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/09/2022] [Accepted: 04/12/2022] [Indexed: 11/16/2022]
Abstract
The genus Shewanella is widely distributed in niches ranging from an aquatic environment to spoiled fish and is loaded with various ecologically and commercially important metabolites. Bacterial species under this genus find application in bioelectricity generation and bioremediation due to their capability to use pollutants as the terminal electron acceptor and could produce health-beneficial omega-3 fatty acids, particularly eicosapentaenoic acid (EPA). Here, the genome sequence of an EPA-producing bacterium, Shewanella sp. N2AIL, isolated from the gastrointestinal tract of Tilapia fish, is reported. The genome size of the strain was 4.8 Mb with a GC content of 46.3% containing 4385 protein-coding genes. Taxonogenomic analysis assigned this strain to the genus Shewanella on the basis of average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH), phylogenetically most closely related with S. baltica NCTC 10735T. The comparative genome analysis with the type strain of S. baltica revealed 693 unique genes in the strain N2AIL, highlighting the variation at the strain level. The genes associated with stress adaptation, secondary metabolite production, antibiotic resistance, and metal reduction were identified in the genome suggesting the potential of the bacterium to be explored as an industrially important strain. PUFA synthase gene cluster of size ~20.5 kb comprising all the essential domains for EPA biosynthesis arranged in five ORFs was also identified in the strain N2AIL. The study provides genomic insights into the diverse genes of Shewanella sp. N2AIL, which is particularly involved in adaptation strategies and prospecting secondary metabolite potential, specifically the biosynthesis of omega-3 polyunsaturated fatty acids.
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Caswell BT, de Carvalho CC, Nguyen H, Roy M, Nguyen T, Cantu DC. Thioesterase enzyme families: Functions, structures, and mechanisms. Protein Sci 2022; 31:652-676. [PMID: 34921469 PMCID: PMC8862431 DOI: 10.1002/pro.4263] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/11/2021] [Accepted: 12/14/2021] [Indexed: 12/12/2022]
Abstract
Thioesterases are enzymes that hydrolyze thioester bonds in numerous biochemical pathways, for example in fatty acid synthesis. This work reports known functions, structures, and mechanisms of updated thioesterase enzyme families, which are classified into 35 families based on sequence similarity. Each thioesterase family is based on at least one experimentally characterized enzyme, and most families have enzymes that have been crystallized and their tertiary structure resolved. Classifying thioesterases into families allows to predict tertiary structures and infer catalytic residues and mechanisms of all sequences in a family, which is particularly useful because the majority of known protein sequence have no experimental characterization. Phylogenetic analysis of experimentally characterized thioesterases that have structures with the two main structural folds reveal convergent and divergent evolution. Based on tertiary structure superimposition, catalytic residues are predicted.
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Affiliation(s)
- Benjamin T. Caswell
- Department of Chemical and Materials EngineeringUniversity of Nevada, RenoRenoNevadaUSA
| | - Caio C. de Carvalho
- Department of Chemical and Materials EngineeringUniversity of Nevada, RenoRenoNevadaUSA
| | - Hung Nguyen
- Department of Computer Science and EngineeringUniversity of Nevada, RenoRenoNevadaUSA
| | - Monikrishna Roy
- Department of Computer Science and EngineeringUniversity of Nevada, RenoRenoNevadaUSA
| | - Tin Nguyen
- Department of Computer Science and EngineeringUniversity of Nevada, RenoRenoNevadaUSA
| | - David C. Cantu
- Department of Chemical and Materials EngineeringUniversity of Nevada, RenoRenoNevadaUSA
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15
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Biosynthesis of rumbrins and inspiration for discovery of HIV inhibitors. Acta Pharm Sin B 2022; 12:4193-4203. [DOI: 10.1016/j.apsb.2022.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 01/24/2022] [Accepted: 02/04/2022] [Indexed: 11/22/2022] Open
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16
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Lenarčič T, Niemann M, Ramrath DJF, Calderaro S, Flügel T, Saurer M, Leibundgut M, Boehringer D, Prange C, Horn EK, Schneider A, Ban N. Mitoribosomal small subunit maturation involves formation of initiation-like complexes. Proc Natl Acad Sci U S A 2022; 119:e2114710118. [PMID: 35042777 PMCID: PMC8784144 DOI: 10.1073/pnas.2114710118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/29/2021] [Indexed: 01/02/2023] Open
Abstract
Mitochondrial ribosomes (mitoribosomes) play a central role in synthesizing mitochondrial inner membrane proteins responsible for oxidative phosphorylation. Although mitoribosomes from different organisms exhibit considerable structural variations, recent insights into mitoribosome assembly suggest that mitoribosome maturation follows common principles and involves a number of conserved assembly factors. To investigate the steps involved in the assembly of the mitoribosomal small subunit (mt-SSU) we determined the cryoelectron microscopy structures of middle and late assembly intermediates of the Trypanosoma brucei mitochondrial small subunit (mt-SSU) at 3.6- and 3.7-Å resolution, respectively. We identified five additional assembly factors that together with the mitochondrial initiation factor 2 (mt-IF-2) specifically interact with functionally important regions of the rRNA, including the decoding center, thereby preventing premature mRNA or large subunit binding. Structural comparison of assembly intermediates with mature mt-SSU combined with RNAi experiments suggests a noncanonical role of mt-IF-2 and a stepwise assembly process, where modular exchange of ribosomal proteins and assembly factors together with mt-IF-2 ensure proper 9S rRNA folding and protein maturation during the final steps of assembly.
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Affiliation(s)
- Tea Lenarčič
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Moritz Niemann
- Department of Chemistry, Biochemistry, and Pharmaceutical Sciences, University of Bern, CH-3012 Bern, Switzerland
| | - David J F Ramrath
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Salvatore Calderaro
- Department of Chemistry, Biochemistry, and Pharmaceutical Sciences, University of Bern, CH-3012 Bern, Switzerland
| | - Timo Flügel
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Martin Saurer
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Marc Leibundgut
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Daniel Boehringer
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Céline Prange
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Elke K Horn
- Department of Chemistry, Biochemistry, and Pharmaceutical Sciences, University of Bern, CH-3012 Bern, Switzerland
| | - André Schneider
- Department of Chemistry, Biochemistry, and Pharmaceutical Sciences, University of Bern, CH-3012 Bern, Switzerland
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, CH-8093 Zurich, Switzerland;
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17
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Whaley SG, Radka CD, Subramanian C, Frank MW, Rock CO. Malonyl-acyl carrier protein decarboxylase activity promotes fatty acid and cell envelope biosynthesis in Proteobacteria. J Biol Chem 2021; 297:101434. [PMID: 34801557 PMCID: PMC8666670 DOI: 10.1016/j.jbc.2021.101434] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/02/2021] [Accepted: 11/09/2021] [Indexed: 11/20/2022] Open
Abstract
Bacterial fatty acid synthesis in Escherichia coli is initiated by the condensation of an acetyl-CoA with a malonyl-acyl carrier protein (ACP) by the β-ketoacyl-ACP synthase III enzyme, FabH. E. coli ΔfabH knockout strains are viable because of the yiiD gene that allows FabH-independent fatty acid synthesis initiation. However, the molecular function of the yiiD gene product is not known. Here, we show the yiiD gene product is a malonyl-ACP decarboxylase (MadA). MadA has two independently folded domains: an amino-terminal N-acetyl transferase (GNAT) domain (MadAN) and a carboxy-terminal hot dog dimerization domain (MadAC) that encodes the malonyl-ACP decarboxylase function. Members of the proteobacterial Mad protein family are either two domain MadA (GNAT-hot dog) or standalone MadB (hot dog) decarboxylases. Using structure-guided, site-directed mutagenesis of MadB from Shewanella oneidensis, we identified Asn45 on a conserved catalytic loop as critical for decarboxylase activity. We also found that MadA, MadAC, or MadB expression all restored normal cell size and growth rates to an E. coli ΔfabH strain, whereas the expression of MadAN did not. Finally, we verified that GlmU, a bifunctional glucosamine-1-phosphate N-acetyl transferase/N-acetyl-glucosamine-1-phosphate uridylyltransferase that synthesizes the key intermediate UDP-GlcNAc, is an ACP binding protein. Acetyl-ACP is the preferred glucosamine-1-phosphate N-acetyl transferase/N-acetyl-glucosamine-1-phosphate uridylyltransferase substrate, in addition to being the substrate for the elongation-condensing enzymes FabB and FabF. Thus, we conclude that the Mad family of malonyl-ACP decarboxylases supplies acetyl-ACP to support the initiation of fatty acid, lipopolysaccharide, peptidoglycan, and enterobacterial common antigen biosynthesis in Proteobacteria.
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Affiliation(s)
- Sarah G Whaley
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Christopher D Radka
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Chitra Subramanian
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Matthew W Frank
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Charles O Rock
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee, USA.
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18
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Mycolicibacterium cell factory for the production of steroid-based drug intermediates. Biotechnol Adv 2021; 53:107860. [PMID: 34710554 DOI: 10.1016/j.biotechadv.2021.107860] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 10/19/2021] [Accepted: 10/19/2021] [Indexed: 12/30/2022]
Abstract
Steroid-based drugs have been developed as the second largest medical category in pharmaceutics. The well-established route of steroid industry includes two steps: the conversion of natural products with a steroid framework to steroid-based drug intermediates and the synthesis of varied steroid-based drugs from steroid-based drug intermediates. The biosynthesis of steroid-based drug intermediates from phytosterols by Mycolicibacterium cell factories bypasses the potential undersupply of diosgenin in the traditional steroid chemical industry. Moreover, the biosynthesis route shows advantages on multiple steroid-based drug intermediate products, more ecofriendly processes, and consecutive reactions carried out in one operation step and in one pot. Androsta-4-ene-3,17-dione (AD), androsta-1,4-diene-3,17-dione (ADD) and 9-hydroxyandrostra-4-ene-3,17-dione (9-OH-AD) are the representative steroid-based drug intermediates synthesized by mycolicibacteria. Other steroid metabolites of mycolicibacteria, like 4-androstene-17β-ol-3-one (TS), 22-hydroxy-23,24-bisnorchol-4-ene-3-one (4-HBC), 22-hydroxy-23,24-bisnorchol-1,4-diene-3-one (1,4-HBC), 9,22-dihydroxy-23,24-bisnorchol-4-ene-3-one (9-OH-HBC), 3aα-H-4α-(3'-propionic acid)-7aβ-methylhexahydro-1,5-indanedione (HIP) and 3aα-H-4α-(3'-propionic acid)-5α-hydroxy-7aβ-methylhexahydro-1-indanone-δ-lactone (HIL), also show values as steroid-based drug intermediates. To improve the bio-production efficiency of the steroid-based drug intermediates, mycolicibacterial strains and biotransformation processes have been continuously studied in the past decades. Many mycolicibacteria that accumulate steroid drug intermediates have been isolated, and subsequently optimized by conventional mutagenesis and genetic engineering. Especially, with the clarification of the mycolicibacterial steroid metabolic pathway and the developments on gene editing technologies, rational design is becoming an important measure for the construction and optimization of engineered mycolicibacteria strains that produce steroid-based drug intermediates. Hence, by reviewing researches in the past two decades, this article updates the overall process of steroid metabolism in mycolicibacteria and provides comprehensive schemes for the rational construction of mycolicibacterial strains that accumulate steroid-based drug intermediates. In addition, the special strategies for the bioconversion of highly hydrophobic steroid in aqueous media are discussed as well.
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19
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Little RF, Hertweck C. Chain release mechanisms in polyketide and non-ribosomal peptide biosynthesis. Nat Prod Rep 2021; 39:163-205. [PMID: 34622896 DOI: 10.1039/d1np00035g] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Review covering up to mid-2021The structure of polyketide and non-ribosomal peptide natural products is strongly influenced by how they are released from their biosynthetic enzymes. As such, Nature has evolved a diverse range of release mechanisms, leading to the formation of bioactive chemical scaffolds such as lactones, lactams, diketopiperazines, and tetronates. Here, we review the enzymes and mechanisms used for chain release in polyketide and non-ribosomal peptide biosynthesis, how these mechanisms affect natural product structure, and how they could be utilised to introduce structural diversity into the products of engineered biosynthetic pathways.
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Affiliation(s)
- Rory F Little
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Germany.
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Germany.
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20
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Paiva P, Medina FE, Viegas M, Ferreira P, Neves RPP, Sousa JPM, Ramos MJ, Fernandes PA. Animal Fatty Acid Synthase: A Chemical Nanofactory. Chem Rev 2021; 121:9502-9553. [PMID: 34156235 DOI: 10.1021/acs.chemrev.1c00147] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Fatty acids are crucial molecules for most living beings, very well spread and conserved across species. These molecules play a role in energy storage, cell membrane architecture, and cell signaling, the latter through their derivative metabolites. De novo synthesis of fatty acids is a complex chemical process that can be achieved either by a metabolic pathway built by a sequence of individual enzymes, such as in most bacteria, or by a single, large multi-enzyme, which incorporates all the chemical capabilities of the metabolic pathway, such as in animals and fungi, and in some bacteria. Here we focus on the multi-enzymes, specifically in the animal fatty acid synthase (FAS). We start by providing a historical overview of this vast field of research. We follow by describing the extraordinary architecture of animal FAS, a homodimeric multi-enzyme with seven different active sites per dimer, including a carrier protein that carries the intermediates from one active site to the next. We then delve into this multi-enzyme's detailed chemistry and critically discuss the current knowledge on the chemical mechanism of each of the steps necessary to synthesize a single fatty acid molecule with atomic detail. In line with this, we discuss the potential and achieved FAS applications in biotechnology, as biosynthetic machines, and compare them with their homologous polyketide synthases, which are also finding wide applications in the same field. Finally, we discuss some open questions on the architecture of FAS, such as their peculiar substrate-shuttling arm, and describe possible reasons for the emergence of large megasynthases during evolution, questions that have fascinated biochemists from long ago but are still far from answered and understood.
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Affiliation(s)
- Pedro Paiva
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Fabiola E Medina
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Autopista Concepción-Talcahuano, 7100 Talcahuano, Chile
| | - Matilde Viegas
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro Ferreira
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Rui P P Neves
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - João P M Sousa
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria J Ramos
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro A Fernandes
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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21
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Creamer KE, Kudo Y, Moore BS, Jensen PR. Phylogenetic analysis of the salinipostin γ-butyrolactone gene cluster uncovers new potential for bacterial signalling-molecule diversity. Microb Genom 2021; 7:000568. [PMID: 33979276 PMCID: PMC8209734 DOI: 10.1099/mgen.0.000568] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/24/2021] [Indexed: 12/19/2022] Open
Abstract
Bacteria communicate by small-molecule chemicals that facilitate intra- and inter-species interactions. These extracellular signalling molecules mediate diverse processes including virulence, bioluminescence, biofilm formation, motility and specialized metabolism. The signalling molecules produced by members of the phylum Actinobacteria generally comprise γ-butyrolactones, γ-butenolides and furans. The best-known actinomycete γ-butyrolactone is A-factor, which triggers specialized metabolism and morphological differentiation in the genus Streptomyces . Salinipostins A–K are unique γ-butyrolactone molecules with rare phosphotriester moieties that were recently characterized from the marine actinomycete genus Salinispora . The production of these compounds has been linked to the nine-gene biosynthetic gene cluster (BGC) spt . Critical to salinipostin assembly is the γ-butyrolactone synthase encoded by spt9 . Here, we report the surprising distribution of spt9 homologues across 12 bacterial phyla, the majority of which are not known to produce γ-butyrolactones. Further analyses uncovered a large group of spt -like gene clusters outside of the genus Salinispora , suggesting the production of new salinipostin-like diversity. These gene clusters show evidence of horizontal transfer and location-specific recombination among Salinispora strains. The results suggest that γ-butyrolactone production may be more widespread than previously recognized. The identification of new γ-butyrolactone BGCs is the first step towards understanding the regulatory roles of the encoded small molecules in Actinobacteria.
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Affiliation(s)
- Kaitlin E. Creamer
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Yuta Kudo
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Present address: Frontier Research Institute for Interdisciplinary Sciences, Japan Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, Japan
| | - Bradley S. Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Paul R. Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
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22
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Listeria monocytogenes MenI Encodes a DHNA-CoA Thioesterase Necessary for Menaquinone Biosynthesis, Cytosolic Survival, and Virulence. Infect Immun 2021; 89:IAI.00792-20. [PMID: 33619030 DOI: 10.1128/iai.00792-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/13/2021] [Indexed: 12/14/2022] Open
Abstract
Listeria monocytogenes is a Gram-positive, intracellular pathogen that is highly adapted to invade and replicate in the cytosol of eukaryotic cells. Intermediate metabolites in the menaquinone biosynthesis pathway are essential for the cytosolic survival and virulence of L. monocytogenes, independent of the production of menaquinone (MK) and aerobic respiration. Determining which specific intermediate metabolite(s) are essential for cytosolic survival and virulence has been hindered by the lack of an identified 1,4-dihydroxy-2-naphthoyl-coenzyme A (DHNA-CoA) thioesterase essential for converting DHNA-CoA to DHNA in the MK synthesis pathway. Using the recently identified Escherichia coli DHNA-CoA thioesterase as a query, homology sequence analysis revealed a single homolog in L. monocytogenes, LMRG_02730 Genetic deletion of LMRG_02730 resulted in an ablated membrane potential, indicative of a nonfunctional electron transport chain (ETC) and an inability to aerobically respire. Biochemical kinetic analysis of LMRG_02730 revealed strong activity toward DHNA-CoA, similar to its E. coli homolog, further demonstrating that LMRG_02730 is a DHNA-CoA thioesterase. Functional analyses in vitro, ex vivo, and in vivo using mutants directly downstream and upstream of LMRG_02730 revealed that DHNA-CoA is sufficient to facilitate in vitro growth in minimal medium, intracellular replication, and plaque formation in fibroblasts. In contrast, protection against bacteriolysis in the cytosol of macrophages and tissue-specific virulence in vivo requires the production of 1,4-dihydroxy-2-naphthoate (DHNA). Taken together, these data implicate LMRG_02730 (renamed MenI) as a DHNA-CoA thioesterase and suggest that while DHNA, or an unknown downstream product of DHNA, protects the bacteria from killing in the macrophage cytosol, DHNA-CoA is necessary for intracellular bacterial replication.
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23
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Kačar D, Cañedo LM, Rodríguez P, González EG, Galán B, Schleissner C, Leopold-Messer S, Piel J, Cuevas C, de la Calle F, García JL. Identification of trans-AT polyketide clusters in two marine bacteria reveals cryptic similarities between distinct symbiosis factors. Environ Microbiol 2021; 23:2509-2521. [PMID: 33734547 DOI: 10.1111/1462-2920.15470] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/26/2021] [Accepted: 03/16/2021] [Indexed: 12/23/2022]
Abstract
Glutarimide-containing polyketides are known as potent antitumoral and antimetastatic agents. The associated gene clusters have only been identified in a few Streptomyces producers and Burkholderia gladioli symbiont. The new glutarimide-family polyketides, denominated sesbanimides D, E and F along with the previously known sesbanimide A and C, were isolated from two marine alphaproteobacteria Stappia indica PHM037 and Labrenzia aggregata PHM038. Structures of the isolated compounds were elucidated based on 1D and 2D homo and heteronuclear NMR analyses and ESI-MS spectrometry. All compounds exhibited strong antitumor activity in lung, breast and colorectal cancer cell lines. Subsequent whole genome sequencing and genome mining revealed the presence of the trans-AT PKS gene cluster responsible for the sesbanimide biosynthesis, described as sbn cluster. Strikingly, the modular architecture of downstream mixed type PKS/NRPS, SbnQ, revealed high similarity to PedH in pederin and Lab13 in labrenzin gene clusters, although those clusters are responsible for the production of structurally completely different molecules. The unexpected presence of SbnQ homologues in unrelated polyketide gene clusters across phylogenetically distant bacteria, raises intriguing questions about the evolutionary relationship between glutarimide-like and pederin-like pathways, as well as the functionality of their synthetic products.
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Affiliation(s)
- Dina Kačar
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Librada M Cañedo
- Research and Development Department, PharmaMar S.A., Madrid, Spain
| | - Pilar Rodríguez
- Research and Development Department, PharmaMar S.A., Madrid, Spain
| | - Elena G González
- Research and Development Department, PharmaMar S.A., Madrid, Spain
| | - Beatriz Galán
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | | | | | | | - Carmen Cuevas
- Research and Development Department, PharmaMar S.A., Madrid, Spain
| | | | - José L García
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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24
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Bakuła Z, Siedlecki P, Gromadka R, Gawor J, Gromadka A, Pomorski JJ, Panagiotopoulou H, Jagielski T. A first insight into the genome of Prototheca wickerhamii, a major causative agent of human protothecosis. BMC Genomics 2021; 22:168. [PMID: 33750287 PMCID: PMC7941945 DOI: 10.1186/s12864-021-07491-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/26/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Colourless microalgae of the Prototheca genus are the only known plants that have consistently been implicated in a range of clinically relevant opportunistic infections in both animals and humans. The Prototheca algae are emerging pathogens, whose incidence has increased importantly over the past two decades. Prototheca wickerhamii is a major human pathogen, responsible for at least 115 cases worldwide. Although the algae are receiving more attention nowadays, there is still a substantial knowledge gap regarding their biology, and pathogenicity in particular. Here we report, for the first time, the complete nuclear genome, organelle genomes, and transcriptome of the P. wickerhamii type strain ATCC 16529. RESULTS The assembled genome size was of 16.7 Mbp, making it the smallest and most compact genome sequenced so far among the protothecans. Key features of the genome included a high overall GC content (64.5%), a high number (6081) and proportion (45.9%) of protein-coding genes, and a low repetitive sequence content (2.2%). The vast majority (90.6%) of the predicted genes were confirmed with the corresponding transcripts upon RNA-sequencing analysis. Most (93.2%) of the genes had their putative function assigned when searched against the InterProScan database. A fourth (23.3%) of the genes were annotated with an enzymatic activity possibly associated with the adaptation to the human host environment. The P. wickerhamii genome encoded a wide array of possible virulence factors, including those already identified in two model opportunistic fungal pathogens, i.e. Candida albicans and Trichophyton rubrum, and thought to be involved in invasion of the host or elicitation of the adaptive stress response. Approximately 6% of the P. wickerhamii genes matched a Pathogen-Host Interaction Database entry and had a previously experimentally proven role in the disease development. Furthermore, genes coding for proteins (e.g. ATPase, malate dehydrogenase) hitherto considered as potential virulence factors of Prototheca spp. were demonstrated in the P. wickerhamii genome. CONCLUSIONS Overall, this study is the first to describe the genetic make-up of P. wickerhamii and discovers proteins possibly involved in the development of protothecosis.
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Affiliation(s)
- Zofia Bakuła
- Department of Medical Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, I. Miecznikowa 1, 02-096, Warsaw, Poland
| | - Paweł Siedlecki
- Department of Systems Biology, University of Warsaw, I. Miecznikowa 1, 02-096, Warsaw, Poland.,Department of Bioinformatics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, A. Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Robert Gromadka
- DNA Sequencing and Synthesis Facility, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, A. Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Jan Gawor
- DNA Sequencing and Synthesis Facility, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, A. Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Agnieszka Gromadka
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, A. Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Jan J Pomorski
- Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679, Warsaw, Poland
| | - Hanna Panagiotopoulou
- Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679, Warsaw, Poland
| | - Tomasz Jagielski
- Department of Medical Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, I. Miecznikowa 1, 02-096, Warsaw, Poland.
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25
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Liang C, Wang X, Zhang Z, Xiao F, Feng H, Ma Q, Huang J, Qiang G, Zhong D, Liu D. ACOT11 promotes cell proliferation, migration and invasion in lung adenocarcinoma. Transl Lung Cancer Res 2020; 9:1885-1903. [PMID: 33209610 PMCID: PMC7653140 DOI: 10.21037/tlcr-19-509] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Background Lung cancer is one of the most common cancers in the word. However, the underlying mechanism remains largely unknown. ACOT11 encodes enzymes hydrolyzing the fatty acyl-CoA esters into free fatty acids and CoA. Besides from its role in fatty acid metabolism, the other aspects regarding its function in the progression of lung cancer have not been revealed. Methods We first explored the clinical profile of ACOT11 in tumor samples. Next, we combined gene knockdown in vitro and in vivo and microarray gene profiling analysis to decipher the unknown regulatory role of ACOT11 in lung cancer carcinoma. Furthermore, we explored the potential molecular mechanisms of ACOT11 with immunoprecipitation. Results We found high expression of ACOT11 in tumor samples. High expression of ACOT11 showed significantly poor prognosis in lung squamous carcinoma (LUSC) patients. Knocking down of ACOT11 inhibited the cell proliferation, migration as well as invasion in vitro and in vivo. It also promoted the cell apoptosis and cell cycle arrest via multiple signaling pathways. Additionally, ACOT11 could bind with CSE1L, which was proved to be an oncogene in lung cancer and speculated to be a potential target of ACOT11. Conclusions The results revealed that ACOT11 regulates proliferation, migration and invasion of lung cancer carcinoma via multiple signaling pathways, indicating its potential value in molecular therapy.
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Affiliation(s)
- Chaoyang Liang
- Department of Thoracic Surgery, Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China
| | - Xiaowei Wang
- Department of Pathology, China-Japan Friendship Hospital, Beijing, China
| | - Zhenrong Zhang
- Department of Thoracic Surgery, China-Japan Friendship Hospital, Beijing, China
| | - Fei Xiao
- Department of Thoracic Surgery, China-Japan Friendship Hospital, Beijing, China
| | - Hongxiang Feng
- Department of Thoracic Surgery, China-Japan Friendship Hospital, Beijing, China
| | - Qianli Ma
- Department of Thoracic Surgery, China-Japan Friendship Hospital, Beijing, China
| | - Jingjing Huang
- Department of Thoracic Surgery, China-Japan Friendship Hospital, Beijing, China
| | - Guangliang Qiang
- Department of Thoracic Surgery, China-Japan Friendship Hospital, Beijing, China
| | - Dingrong Zhong
- Department of Pathology, China-Japan Friendship Hospital, Beijing, China
| | - Deruo Liu
- Department of Thoracic Surgery, Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China
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26
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Fatty Acid Synthase Beta Dehydratase in the Lipid Biosynthesis Pathway Is Required for Conidiogenesis, Pigmentation and Appressorium Formation in Magnaporthe oryzae S6. Int J Mol Sci 2020; 21:ijms21197224. [PMID: 33007862 PMCID: PMC7582888 DOI: 10.3390/ijms21197224] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/22/2020] [Accepted: 09/23/2020] [Indexed: 01/15/2023] Open
Abstract
Lipid biosynthesis produces glycerol, which is important in fueling turgor pressure necessary for germination and penetration of plant host by fungi. As the relationship between pathogenicity and the lipid biosynthetic pathway is not fully understood, we have elucidated the role of the fatty acid synthase beta subunit dehydratase (FAS1) gene in lipid biosynthesis. The FAS1 gene was silenced through homologous double crossover in Magnaporthe oryzae strain S6 to study the effect on lipid biosynthesis. The vegetative growth of Δfas1 mutants show the highest drop on oleic acid (between 10 and 50%), while the mycelial dry weight of mutants dropped significantly on all media. Conidiation of FAS1 mutants show a ~10- and ~5-fold reduction on oatmeal and Potato Dextrose Agar (PDA), respectively. Mutants formed mycelium that were mildly pigmented, indicating that the deletion of FAS1 may have affected melanin biosynthesis. Biochemical and gene expression studies concluded that the fatty acid degradation pathway might have been interrupted by FAS1 deletion. FAS1 mutants showed no enzyme activity on glucose or olive oil, suggesting that the mutants may lack functional peroxisomes and be defective in β-oxidation of fatty acids, hence explaining the reduced lipid deposits in the spores.
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27
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Xu L, Sun X, Wan X, Li H, Yan F, Han R, Li H, Li Z, Tian Y, Liu X, Kang X, Wang Y. Identification of a Bacillus amyloliquefaciens H6 Thioesterase Involved in Zearalenone Detoxification by Transcriptomic Analysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:10071-10080. [PMID: 32815728 DOI: 10.1021/acs.jafc.0c03954] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Zearalenone (ZEA), a nonsteroidal estrogenic mycotoxin produced by Fusarium graminearum, induces hyperestrogenic responses in mammals and can cause reproductive disorders in farm animals. In this study, a transcriptome analysis of Bacillus amyloliquefaciens H6, which was previously identified as a ZEA-degrading bacterium, was conducted with high-throughput sequencing technology, and the differentially expressed genes were subjected to gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) enrichment analyses. Among the 16 upregulated genes, BAMF_RS30125 was predicted to be the key gene responsible for ZEA degradation. The protein encoded by BAMF_RS30125 was then expressed in Escherichia coli, and this recombinant protein (named ZTE138) significantly reduced the ZEA content, as determined by the enzyme-linked immunosorbent assay (ELISA) and high-performance liquid chromatography (HPLC), and decreased the proliferating activity of ZEA in MCF-7 cells. What is more, the liquid chromatography-tandem mass spectrometry (LC-MS/MS) results showed that the relative molecular mass and the structure of ZEA also changed. Sequence alignment of the ZTE138 protein showed that it is a protease that belongs to the YBGC/FADM family of coenzyme A thioesterases, and thus, the protein can presumably cleave the ZEA lactone bond and break down its macrolide ring.
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Affiliation(s)
- Laipeng Xu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450000, China
| | - Xiangli Sun
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450000, China
| | - Xianhua Wan
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450000, China
| | - Hui Li
- College of Environmental and Resource Sciences, Henan Agricultural University, Zhengzhou 450000, China
| | - Fengbin Yan
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450000, China
- Henan Research Center of Germplasm Resources for Poultry, Zhengzhou 450002, China
| | - Ruili Han
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450000, China
- Henan Research Center of Germplasm Resources for Poultry, Zhengzhou 450002, China
| | - Hong Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450000, China
- Henan Research Center of Germplasm Resources for Poultry, Zhengzhou 450002, China
| | - Zhuanjian Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450000, China
- Henan Research Center of Germplasm Resources for Poultry, Zhengzhou 450002, China
| | - Yadong Tian
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450000, China
- Henan Research Center of Germplasm Resources for Poultry, Zhengzhou 450002, China
| | - Xiaojun Liu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450000, China
- Henan Research Center of Germplasm Resources for Poultry, Zhengzhou 450002, China
| | - Xiangtao Kang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450000, China
- Henan Research Center of Germplasm Resources for Poultry, Zhengzhou 450002, China
| | - Yanbin Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450000, China
- Henan Research Center of Germplasm Resources for Poultry, Zhengzhou 450002, China
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28
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Swarbrick CMD, Nanson JD, Patterson EI, Forwood JK. Structure, function, and regulation of thioesterases. Prog Lipid Res 2020; 79:101036. [PMID: 32416211 DOI: 10.1016/j.plipres.2020.101036] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/30/2020] [Accepted: 05/01/2020] [Indexed: 01/15/2023]
Abstract
Thioesterases are present in all living cells and perform a wide range of important biological functions by catalysing the cleavage of thioester bonds present in a diverse array of cellular substrates. Thioesterases are organised into 25 families based on their sequence conservation, tertiary and quaternary structure, active site configuration, and substrate specificity. Recent structural and functional characterisation of thioesterases has led to significant changes in our understanding of the regulatory mechanisms that govern enzyme activity and their respective cellular roles. The resulting dogma changes in thioesterase regulation include mechanistic insights into ATP and GDP-mediated regulation by oligomerisation, the role of new key regulatory regions, and new insights into a conserved quaternary structure within TE4 family members. Here we provide a current and comparative snapshot of our understanding of thioesterase structure, function, and regulation across the different thioesterase families.
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Affiliation(s)
| | - Jeffrey D Nanson
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience, Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Edward I Patterson
- Centre for Neglected Tropical Diseases, Departments of Vector Biology and Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, New South Wales, Australia.
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29
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Hickman TWP, Baud D, Benhamou L, Hailes HC, Ward JM. Characterisation of four hotdog-fold thioesterases for their implementation in a novel organic acid production system. Appl Microbiol Biotechnol 2020; 104:4397-4406. [PMID: 32193574 PMCID: PMC7190597 DOI: 10.1007/s00253-020-10519-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 02/23/2020] [Accepted: 03/03/2020] [Indexed: 11/24/2022]
Abstract
With increasing interest in the diverse properties of organic acids and their application in synthetic pathways, developing biological tools for producing known and novel organic acids would be very valuable. In such a system, organic acids may be activated as coenzyme A (CoA) esters, then modified by CoA-dependent enzymes, followed by CoA liberation by a broad-acting thioesterase. This study has focused on the identification of suitable thioesterases (TE) for utilisation in such a pathway. Four recombinant hotdog-fold TEs were screened with a range of CoA esters in order to identify a highly active, broad spectrum TE. The TesB-like TE, RpaL, from Rhodopseudomonas palustris was found to be able to use aromatic, alicyclic and both long and short aliphatic CoA esters. Size exclusion chromatography, revealed RpaL to be a monomer of fused hotdog domains, in contrast to the complex quaternary structures found with similar TesB-like TEs. Nonetheless, sequence alignments showed a conserved catalytic triad despite the variation in quaternary arrangement. Kinetic analysis revealed a preference towards short-branched chain CoA esters with the highest specificity towards DL-β-hydroxybutyryl CoA (1.6 × 104 M−1 s−1), which was found to decrease as the acyl chain became longer and more functionalised. Substrate inhibition was observed with the fatty acyl n-heptadecanoyl CoA at concentrations exceeding 0.3 mM; however, this was attributed to its micellar aggregation properties. As a result of the broad activity observed with RpaL, it is a strong candidate for implementation in CoA ester pathways to generate modified or novel organic acids.
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Affiliation(s)
- T W P Hickman
- Department of Biochemical Engineering, University College London, Gower Street, London, WC1E 6BT, UK
| | - D Baud
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - L Benhamou
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - H C Hailes
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - J M Ward
- Department of Biochemical Engineering, University College London, Gower Street, London, WC1E 6BT, UK.
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30
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Kalinger RS, Pulsifer IP, Hepworth SR, Rowland O. Fatty Acyl Synthetases and Thioesterases in Plant Lipid Metabolism: Diverse Functions and Biotechnological Applications. Lipids 2020; 55:435-455. [PMID: 32074392 DOI: 10.1002/lipd.12226] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 01/29/2020] [Accepted: 01/30/2020] [Indexed: 11/09/2022]
Abstract
Plants use fatty acids to synthesize acyl lipids for many different cellular, physiological, and defensive roles. These roles include the synthesis of essential membrane, storage, or surface lipids, as well as the production of various fatty acid-derived metabolites used for signaling or defense. Fatty acids are activated for metabolic processing via a thioester linkage to either coenzyme A or acyl carrier protein. Acyl synthetases metabolically activate fatty acids to their thioester forms, and acyl thioesterases deactivate fatty acyl thioesters to free fatty acids by hydrolysis. These two enzyme classes therefore play critical roles in lipid metabolism. This review highlights the surprisingly complex and varying roles of fatty acyl synthetases in plant lipid metabolism, including roles in the intracellular trafficking of fatty acids. This review also surveys the many specialized fatty acyl thioesterases characterized to date in plants, which produce a great diversity of fatty acid products in a tissue-specific manner. While some acyl thioesterases produce fatty acids that clearly play roles in plant-insect or plant-microbial interactions, most plant acyl thioesterases have yet to be fully characterized both in terms of their substrate specificities and their functions. The biotechnological applications of plant acyl thioesterases and synthetases are also discussed, as there is significant interest in these enzymes as catalysts for the sustainable production of fatty acids and their derivatives for industrial uses.
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Affiliation(s)
- Rebecca S Kalinger
- Department of Biology and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Ian P Pulsifer
- Department of Biology and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Shelley R Hepworth
- Department of Biology and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Owen Rowland
- Department of Biology and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
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31
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Medium-Chain Fatty Acid Synthesis by " Candidatus Weimeria bifida" gen. nov., sp. nov., and " Candidatus Pseudoramibacter fermentans" sp. nov. Appl Environ Microbiol 2020; 86:AEM.02242-19. [PMID: 31704684 PMCID: PMC6974650 DOI: 10.1128/aem.02242-19] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 10/25/2019] [Indexed: 11/20/2022] Open
Abstract
Chain elongation by medium-chain fatty acid (MCFA)-producing microbiomes offers an opportunity to produce valuable chemicals from organic streams that would otherwise be considered waste. However, the physiology and energetics of chain elongation are only beginning to be studied, and many of these organisms remain uncultured. We analyzed MCFA production by two uncultured organisms that were identified as the main MCFA producers in a microbial community enriched from an anaerobic digester; this characterization, which is based on meta-multi-omic analysis, complements the knowledge that has been acquired from pure-culture studies. The analysis revealed previously unreported features of the metabolism of MCFA-producing organisms. Chain elongation is emerging as a bioprocess to produce valuable medium-chain fatty acids (MCFA; 6 to 8 carbons in length) from organic waste streams by harnessing the metabolism of anaerobic microbiomes. Although our understanding of chain elongation physiology is still evolving, the reverse β-oxidation pathway has been identified as a key metabolic function to elongate the intermediate products of fermentation to MCFA. Here, we describe two uncultured chain-elongating microorganisms that were enriched in an anaerobic microbiome transforming the residues from a lignocellulosic biorefining process. Based on a multi-omic analysis, we describe “Candidatus Weimeria bifida” gen. nov., sp. nov., and “Candidatus Pseudoramibacter fermentans” sp. nov., both predicted to produce MCFA but using different substrates. The analysis of a time series metatranscriptomic data set suggests that “Ca. Weimeria bifida” is an effective xylose utilizer since both the pentose phosphate pathway and the bifid shunt are active. Furthermore, the metatranscriptomic data suggest that energy conservation during MCFA production in this organism is essential and occurs via the creation of an ion motive force using both the RNF complex and an energy-conserving hydrogenase. For “Ca. Pseudoramibacter fermentans,” predicted to produce MCFA from lactate, the metatranscriptomic analysis reveals the activity of an electron-confurcating lactate dehydrogenase, energy conservation via the RNF complex, H2 production for redox balance, and glycerol utilization. A thermodynamic analysis also suggests the possibility of glycerol being a substrate for MCFA production by “Ca. Pseudoramibacter fermentans.” In total, this work reveals unknown characteristics of MCFA production in two novel organisms. IMPORTANCE Chain elongation by medium-chain fatty acid (MCFA)-producing microbiomes offers an opportunity to produce valuable chemicals from organic streams that would otherwise be considered waste. However, the physiology and energetics of chain elongation are only beginning to be studied, and many of these organisms remain uncultured. We analyzed MCFA production by two uncultured organisms that were identified as the main MCFA producers in a microbial community enriched from an anaerobic digester; this characterization, which is based on meta-multi-omic analysis, complements the knowledge that has been acquired from pure-culture studies. The analysis revealed previously unreported features of the metabolism of MCFA-producing organisms.
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Chen GY, Kao CY, Smith HB, Rust DP, Powers ZM, Li AY, Sauer JD. Mutation of the Transcriptional Regulator YtoI Rescues Listeria monocytogenes Mutants Deficient in the Essential Shared Metabolite 1,4-Dihydroxy-2-Naphthoate (DHNA). Infect Immun 2019; 88:e00366-19. [PMID: 31685546 PMCID: PMC6921671 DOI: 10.1128/iai.00366-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 10/17/2019] [Indexed: 12/30/2022] Open
Abstract
Listeria monocytogenes, a Gram-positive, facultative intracellular pathogen, survives and replicates in the cytosol of host cells. Synthesis of 1,4-dihydroxy-2-naphthoate (DHNA), an intermediate of menaquinone biosynthesis, is essential for cytosolic survival of L. monocytogenes independent from its role in respiration. Here, we demonstrate that DHNA is essential for virulence in a murine model of listeriosis due to both respiration-dependent and -independent functions. In addition, DHNA can be both secreted and utilized as an extracellular shared metabolite to promote cytosolic survival inside host macrophages. To understand the role(s) of DHNA in L. monocytogenes intracellular survival and virulence, we isolated DHNA-deficient (ΔmenD strain) suppressor mutants that formed plaques in monolayers of fibroblasts. Five ΔmenD suppressor (mds) mutants additionally rescued at least 50% of the cytosolic survival defect of the parent ΔmenD mutant. Whole-genome sequencing revealed that four of the five suppressor mutants had independent missense mutations in a putative transcriptional regulator, ytoI (lmo1576). Clean deletion and complementation in trans confirmed that loss of ytoI could restore plaquing and cytosolic survival of DHNA-deficient L. monocytogenes RNA-seq transcriptome analysis revealed five genes (lmo0944, lmo1575, lmo1577, lmo2005, and lmo2006) expressed at a higher level in the ΔytoI strain than in the wild-type strain, whereas two genes (lmo1917 and lmo2103) demonstrated lower expression in the ΔytoI mutant. Intriguingly, the majority of these genes are involved in controlling pyruvate flux. Metabolic analysis confirmed that acetoin, acetate, and lactate flux were altered in a ΔytoI mutant, suggesting a critical role for regulating these metabolic programs. In conclusion, we have demonstrated that, similar to findings in select other bacteria, DHNA can act as a shared resource, and it is essential for cytosolic survival and virulence of L. monocytogenes Furthermore, we have identified a novel transcriptional regulator in L. monocytogenes and determined that its metabolic regulation is implicated in cytosolic survival of L. monocytogenes.
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Affiliation(s)
- Grischa Y Chen
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison Wisconsin, USA
| | - Cheng-Yen Kao
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison Wisconsin, USA
| | - Hans B Smith
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison Wisconsin, USA
| | - Drew P Rust
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison Wisconsin, USA
| | - Zachary M Powers
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison Wisconsin, USA
| | - Alexandria Y Li
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison Wisconsin, USA
| | - John-Demian Sauer
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison Wisconsin, USA
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Zhao H, Xu Y, Lin S, Spain JC, Zhou NY. The molecular basis for the intramolecular migration (NIH shift) of the carboxyl group duringpara-hydroxybenzoate catabolism. Mol Microbiol 2018; 110:411-424. [PMID: 30070064 DOI: 10.1111/mmi.14094] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Huan Zhao
- State Key Laboratory of Microbial Metabolism; and School of Life Sciences & Biotechnology; Shanghai Jiao Tong University; Shanghai 200240 China
| | - Ying Xu
- State Key Laboratory of Microbial Metabolism; and School of Life Sciences & Biotechnology; Shanghai Jiao Tong University; Shanghai 200240 China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism; and School of Life Sciences & Biotechnology; Shanghai Jiao Tong University; Shanghai 200240 China
| | - Jim C. Spain
- Center for Environmental Diagnostics & Bioremediation; University of West Florida; 11000 University Parkway Pensacola FL 32514-5751 USA
| | - Ning-Yi Zhou
- State Key Laboratory of Microbial Metabolism; and School of Life Sciences & Biotechnology; Shanghai Jiao Tong University; Shanghai 200240 China
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Medina FE, Neves RPP, Ramos MJ, Fernandes PA. QM/MM Study of the Reaction Mechanism of the Dehydratase Domain from Mammalian Fatty Acid Synthase. ACS Catal 2018. [DOI: 10.1021/acscatal.8b02616] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Fabiola E. Medina
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Rui P. P. Neves
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria J. Ramos
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro A. Fernandes
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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Redanz S, Cheng X, Giacaman RA, Pfeifer CS, Merritt J, Kreth J. Live and let die: Hydrogen peroxide production by the commensal flora and its role in maintaining a symbiotic microbiome. Mol Oral Microbiol 2018; 33:337-352. [PMID: 29897662 DOI: 10.1111/omi.12231] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2018] [Indexed: 02/05/2023]
Abstract
The majority of commensal oral streptococci are able to generate hydrogen peroxide (H2 O2 ) during aerobic growth, which can diffuse through the cell membrane and inhibit competing species in close proximity. Competing H2 O2 production is mainly dependent upon the pyruvate oxidase SpxB, and to a lesser extent the lactate oxidase LctO, both of which are important for energy generation in aerobic environments. Several studies point to a broad impact of H2 O2 production in the oral environment, including a potential role in biofilm homeostasis, signaling, and interspecies interactions. Here, we summarize the current research regarding oral streptococcal H2 O2 generation, resistance mechanisms, and the ecological impact of H2 O2 production. We also discuss the potential therapeutic utility of H2 O2 for the prevention/treatment of dysbiotic diseases as well as its potential role as a biomarker of oral health.
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Affiliation(s)
- Sylvio Redanz
- Department of Restorative Dentistry, Oregon Health and Science University, Portland, Oregon
| | - Xingqun Cheng
- The State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.,The Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Rodrigo A Giacaman
- Cariology Unit, Department of Oral Rehabilitation and Interdisciplinary Excellence Research Program on Healthy Aging (PIEI-ES), University of Talca, Talca, Chile
| | - Carmen S Pfeifer
- Department of Restorative Dentistry, Oregon Health and Science University, Portland, Oregon
| | - Justin Merritt
- Department of Restorative Dentistry, Oregon Health and Science University, Portland, Oregon
| | - Jens Kreth
- Department of Restorative Dentistry, Oregon Health and Science University, Portland, Oregon
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Tsai SC(S. The Structural Enzymology of Iterative Aromatic Polyketide Synthases: A Critical Comparison with Fatty Acid Synthases. Annu Rev Biochem 2018; 87:503-531. [DOI: 10.1146/annurev-biochem-063011-164509] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Polyketides are a large family of structurally complex natural products including compounds with important bioactivities. Polyketides are biosynthesized by polyketide synthases (PKSs), multienzyme complexes derived evolutionarily from fatty acid synthases (FASs). The focus of this review is to critically compare the properties of FASs with iterative aromatic PKSs, including type II PKSs and fungal type I nonreducing PKSs whose chemical logic is distinct from that of modular PKSs. This review focuses on structural and enzymological studies that reveal both similarities and striking differences between FASs and aromatic PKSs. The potential application of FAS and aromatic PKS structures for bioengineering future drugs and biofuels is highlighted.
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Affiliation(s)
- Shiou-Chuan (Sheryl) Tsai
- Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, California 92697, USA
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Santín O, Moncalián G. Loading of malonyl-CoA onto tandem acyl carrier protein domains of polyunsaturated fatty acid synthases. J Biol Chem 2018; 293:12491-12501. [PMID: 29921583 DOI: 10.1074/jbc.ra118.002443] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 06/04/2018] [Indexed: 12/13/2022] Open
Abstract
Omega-3 polyunsaturated fatty acids (PUFA) are produced in some unicellular organisms, such as marine gammaproteobacteria, myxobacteria, and thraustochytrids, by large enzyme complexes called PUFA synthases. These enzymatic complexes resemble bacterial antibiotic-producing proteins known as polyketide synthases (PKS). One of the PUFA synthase subunits is a conserved large protein (PfaA in marine proteobacteria) that contains three to nine tandem acyl carrier protein (ACP) domains as well as condensation and modification domains. In this work, a study of the PfaA architecture and its ability to initiate the synthesis by selecting malonyl units has been carried out. As a result, we have observed a self-acylation ability in tandem ACPs whose biochemical mechanism differ from the previously described for type II PKS. The acyltransferase domain of PfaA showed a high selectivity for malonyl-CoA that efficiently loads onto the ACPs domains. These results, together with the structural organization predicted for PfaA, suggest that this protein plays a key role at early stages of the anaerobic pathway of PUFA synthesis.
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Affiliation(s)
- Omar Santín
- From the Departamento de Biología Molecular, Universidad de Cantabria and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), CSIC-Universidad de Cantabria, 39011 Santander, Spain
| | - Gabriel Moncalián
- From the Departamento de Biología Molecular, Universidad de Cantabria and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), CSIC-Universidad de Cantabria, 39011 Santander, Spain
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Kalinger RS, Pulsifer IP, Rowland O. Elucidating the substrate specificities of acyl-lipid thioesterases from diverse plant taxa. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 127:104-118. [PMID: 29571003 DOI: 10.1016/j.plaphy.2018.03.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/09/2018] [Accepted: 03/12/2018] [Indexed: 05/21/2023]
Abstract
Acyl-ACP thioesterase enzymes, which cleave fatty acyl thioester bonds to release free fatty acids, contribute to much of the fatty acid diversity in plants. In Arabidopsis thaliana, a family of four single hot-dog fold domain, plastid-localized acyl-lipid thioesterases (AtALT1-4) generate medium-chain (C6-C14) fatty and β-keto fatty acids as secondary metabolites. These volatile products may serve to attract insect pollinators or deter predatory insects. Homologs of AtALT1-4 are present in all plant taxa, but are nearly all uncharacterized. Despite high sequence identity, AtALT1-4 generate different lipid products, suggesting that ALT homologs in other plants also have highly varied activities. We investigated the catalytic diversity of ALT-like thioesterases by screening the substrate specificities of 15 ALT homologs from monocots, eudicots, a lycophyte, a green microalga, and the ancient gymnosperm Gingko biloba, via expression in Escherichia coli. Overall, these enzymes had highly varied substrate preferences compared to one another and to AtALT1-4, and could be classified into four catalytic groups comprising members from diverse taxa. Group 1 ALTs primarily generated 14:1 β-keto fatty acids, Group 2 ALTs produced 6-10 carbon fatty/β-keto fatty acids, Group 3 ALTs predominantly produced 12-14 carbon fatty acids, and Group 4 ALTs mainly generated 16 carbon fatty acids. Enzymes in each group differed significantly in the quantities of lipids and types of minor products they generated in E. coli. Medium-chain fatty acids are used to manufacture insecticides, pharmaceuticals, and biofuels, and ALT-like proteins are ideal candidates for metabolic engineering to produce specific fatty acids in significant quantities.
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Affiliation(s)
- Rebecca S Kalinger
- Department of Biology and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - Ian P Pulsifer
- Department of Biology and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - Owen Rowland
- Department of Biology and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada.
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Chimeric Fatty Acyl-Acyl Carrier Protein Thioesterases Provide Mechanistic Insight into Enzyme Specificity and Expression. Appl Environ Microbiol 2018; 84:AEM.02868-17. [PMID: 29549102 DOI: 10.1128/aem.02868-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Accepted: 03/12/2018] [Indexed: 12/27/2022] Open
Abstract
Medium-chain fatty acids are commodity chemicals. Increasing and modifying the activity of thioesterases (TEs) on medium-chain fatty acyl-acyl carrier protein (acyl-ACP) esters may enable a high-yield microbial production of these molecules. The plant Cuphea palustris harbors two distinct TEs: C. palustris FatB1 (CpFatB1) (C8 specificity, lower activity) and CpFatB2 (C14 specificity, higher activity) with 78% sequence identity. We combined structural features from these two enzymes to create several chimeric TEs, some of which showed nonnatural fatty acid production as measured by an enzymatic assay and gas chromatography-mass spectrometry (GC-MS). Notably, chimera 4 exhibited an increased C8 fatty acid production in correlation with improved microbial expression. This chimera led us to identify CpFatB2-specific amino acids between positions 219 and 272 that lead to higher protein levels. Chimera 7 produced a broad range of fatty acids and appeared to combine a fatty acid binding pocket with long-chain specificity and an ACP interaction site that may activate fatty acid extrusion. Using homology modeling and in silico docking with ACP, we identified a "positive patch" within amino acids 162 to 218, which may direct the ACP interaction and regulate access to short-chain fatty acids. On the basis of this modeling, we transplanted putative ACP interaction sequences from CpFatB1 into CpFatB2 and created a chimeric thioesterase that produced medium-chain as well as long-chain fatty acids. Thus, the engineering of chimeric enzymes and characterizing their microbial activity and chain-length specificity suggested mechanistic insights into TE functions and also generated thioesterases with potentially useful properties. These observations may inform a rational engineering of TEs to allow alkyl chain length control.IMPORTANCE Medium-chain fatty acids are important commodity chemicals. These molecules are used as plastic precursors and in shampoos and other detergents and could be used as biofuel precursors if production economics were favorable. Hydrocarbon-based liquid fuels must be optimized to have a desired boiling point, low freezing point, low viscosity, and other physical characteristics. Similarly, the solubility and harshness of detergents and the flexibility of plastic polymers can be modulated. The length and distribution of the carbon chains in the hydrophobic tails determine these properties. The biological synthesis of cell membranes and fatty acids produces chains of primarily 16 to 18 carbons, which give rise to current biofuels. The ultimate goal of the work presented here is to engineer metabolic pathways to produce designer molecules with the correct number of carbons in a chain, so that such molecules could be used directly as specialty commodity chemicals or as fuels after minimal processing.
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Hao X, Luo L, Jouhet J, Rébeillé F, Maréchal E, Hu H, Pan Y, Tan X, Chen Z, You L, Chen H, Wei F, Gong Y. Enhanced triacylglycerol production in the diatom Phaeodactylum tricornutum by inactivation of a Hotdog-fold thioesterase gene using TALEN-based targeted mutagenesis. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:312. [PMID: 30455741 PMCID: PMC6231261 DOI: 10.1186/s13068-018-1309-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 10/30/2018] [Indexed: 05/18/2023]
Abstract
BACKGROUND In photosynthetic oleaginous microalgae, acyl-CoA molecules are used as substrates for the biosynthesis of membrane glycerolipids, triacylglycerol (TAG) and other acylated molecules. Acyl-CoA can also be directed to beta-oxidative catabolism. They can be utilized by a number of lipid metabolic enzymes including endogenous thioesterases, which catalyze their hydrolysis to release free fatty acids. Acyl-CoA availability thus plays fundamental roles in determining the quantity and composition of membrane lipids and storage lipids. RESULTS Here, we have engineered the model diatom Phaeodactylum tricornutum to produce significantly increased TAGs by disruption of the gene encoding a Hotdog-fold thioesterase involved in acyl-CoA hydrolysis (ptTES1). This plastidial thioesterase can hydrolyze both medium- and long-chain fatty acyl-CoAs, but has the highest activity toward long-chain saturated and monounsaturated fatty acyl-CoAs. The maximum rate was found with oleoyl-CoA, which is hydrolyzed at 50 nmol/min/mg protein. The stable and targeted interruption of acyl-CoA thioesterase gene was achieved using a genome editing technique, transcription activator-like effector nucleases (TALENs). Disruption of native ptTES1 gene resulted in a 1.7-fold increase in TAG content when algal strains were grown in nitrogen-replete media for 8 days, whereas the content of other lipid classes, including phosphoglycerolipids and galactoglycerolipids, remained almost unchanged. The engineered algal strain also exhibited a marked change in fatty acid profile, including a remarkable increase in 16:0 and 16:1 and a decrease in 20:5. Nitrogen deprivation for 72 h further increased TAG content and titer of the engineered strain, reaching 478 μg/109 cells and 4.8 mg/L, respectively. Quantitative determination of in vivo acyl-CoAs showed that the total acyl-CoA pool size was significantly higher in the engineered algal strain than that in the wild type. CONCLUSIONS This study supports the role of ptTES1 in free fatty acid homeostasis in the plastid of Phaeodactylum and demonstrates the potential of TALEN-based genome editing technique to generate an enhanced lipid-producing algal strain through blocking acyl-CoA catabolism.
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Affiliation(s)
- Xiahui Hao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, No. 2 Xudong Second Road, Wuhan, 430062 People’s Republic of China
- Hubei Key Laboratory of Lipid Chemistry and Nutrition, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Ling Luo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, No. 2 Xudong Second Road, Wuhan, 430062 People’s Republic of China
- Hubei Key Laboratory of Lipid Chemistry and Nutrition, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Juliette Jouhet
- Laboratoire de Physiologie Cellulaire et Végétale, Centre National de la Recherche Scientifique, Commissariat à l’Energie Atomique et aux Energies Alternatives, Institut National de la Recherche Agronomique, Université Grenoble Alpes, UMR 5168, 38041 Grenoble, France
| | - Fabrice Rébeillé
- Laboratoire de Physiologie Cellulaire et Végétale, Centre National de la Recherche Scientifique, Commissariat à l’Energie Atomique et aux Energies Alternatives, Institut National de la Recherche Agronomique, Université Grenoble Alpes, UMR 5168, 38041 Grenoble, France
| | - Eric Maréchal
- Laboratoire de Physiologie Cellulaire et Végétale, Centre National de la Recherche Scientifique, Commissariat à l’Energie Atomique et aux Energies Alternatives, Institut National de la Recherche Agronomique, Université Grenoble Alpes, UMR 5168, 38041 Grenoble, France
| | - Hanhua Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 China
| | - Yufang Pan
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 China
| | - Xiaoming Tan
- Hubei Collaborative Innovation Center for Green Transformation of Bioresources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Zhuo Chen
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Science, Shandong Normal University, Jinan, 250014 China
| | - Lingjie You
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, No. 2 Xudong Second Road, Wuhan, 430062 People’s Republic of China
- Hubei Key Laboratory of Lipid Chemistry and Nutrition, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Hong Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, No. 2 Xudong Second Road, Wuhan, 430062 People’s Republic of China
- Hubei Key Laboratory of Lipid Chemistry and Nutrition, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Fang Wei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, No. 2 Xudong Second Road, Wuhan, 430062 People’s Republic of China
- Hubei Key Laboratory of Lipid Chemistry and Nutrition, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Yangmin Gong
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, No. 2 Xudong Second Road, Wuhan, 430062 People’s Republic of China
- Hubei Key Laboratory of Lipid Chemistry and Nutrition, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
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Van Dolah FM, Kohli GS, Morey JS, Murray SA. Both modular and single-domain Type I polyketide synthases are expressed in the brevetoxin-producing dinoflagellate, Karenia brevis (Dinophyceae). JOURNAL OF PHYCOLOGY 2017; 53:1325-1339. [PMID: 28949419 PMCID: PMC5725682 DOI: 10.1111/jpy.12586] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 09/14/2017] [Indexed: 05/09/2023]
Abstract
Dinoflagellates are prolific producers of polyketide compounds, many of which are potent toxins with adverse impacts on human and marine animal health. To identify polyketide synthase (PKS) genes in the brevetoxin-producing dinoflagellate, Karenia brevis, we assembled a transcriptome from 595 million Illumina reads, sampled under different growth conditions. The assembly included 125,687 transcripts greater than 300 nt in length, with over half having >100× coverage. We found 121 transcripts encoding Type I ketosynthase (KS) domains, of which 99 encoded single KS domains, while 22 contained multiple KS domains arranged in 1-3 protein modules. Phylogenetic analysis placed all single domain and a majority of multidomain KSs within a monophyletic clade of protist PKSs. In contrast with the highly amplified single-domain KSs, only eight single-domain ketoreductase transcripts were found in the assembly, suggesting that they are more evolutionarily conserved. The multidomain PKSs were dominated by trans-acyltransferase architectures, which were recently shown to be prevalent in other algal protists. Karenia brevis also expressed several hybrid nonribosomal peptide synthetase (NRPS)/PKS sequences, including a burA-like sequence previously reported in a wide variety of dinoflagellates. This contrasts with a similarly deep transcriptome of Gambierdiscus polynesiensis, which lacked NRPS/PKS other than the burA-like transcript, and may reflect the presence of amide-containing polyketides in K. brevis and their absence from G. polynesiensis. In concert with other recent transcriptome analyses, this study provides evidence for both single domain and multidomain PKSs in the synthesis of polyketide compounds in dinoflagellates.
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Affiliation(s)
- Frances M. Van Dolah
- College of CharlestonSchool of Sciences and Mathematics66 George St.CharlestonSouth Carolina29424USA
- Hollings Marine Laboratory331 Fort Johnson Rd.CharlestonSouth Carolina29412USA
| | - Gurjeet S. Kohli
- Climate Change ClusterUniversity of Technology Sydney15 Broadway, UltimoSydneyNew South Wales2007Australia
- Singapore Centre for Environmental Life Sciences EngineeringNanyang Technological UniversitySingapore689528
| | - Jeanine S. Morey
- Hollings Marine Laboratory331 Fort Johnson Rd.CharlestonSouth Carolina29412USA
- JHT Incorporated2710 Discovery Dr.OrlandoFlorida32826USA
| | - Shauna A. Murray
- Climate Change ClusterUniversity of Technology Sydney15 Broadway, UltimoSydneyNew South Wales2007Australia
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Khandokar YB, Srivastava P, Cowieson N, Sarker S, Aragao D, Das S, Smith KM, Raidal SR, Forwood JK. Structural insights into GDP-mediated regulation of a bacterial acyl-CoA thioesterase. J Biol Chem 2017; 292:20461-20471. [PMID: 28972175 DOI: 10.1074/jbc.m117.800227] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 09/12/2017] [Indexed: 11/06/2022] Open
Abstract
Thioesterases catalyze the cleavage of thioester bonds within many activated fatty acids and acyl-CoA substrates. They are expressed ubiquitously in both prokaryotes and eukaryotes and are subdivided into 25 thioesterase families according to their catalytic active site, protein oligomerization, and substrate specificity. Although many of these enzyme families are well-characterized in terms of function and substrate specificity, regulation across most thioesterase families is poorly understood. Here, we characterized a TE6 thioesterase from the bacterium Neisseria meningitidis Structural analysis with X-ray crystallographic diffraction data to 2.0-Å revealed that each protein subunit harbors a hot dog-fold and that the TE6 enzyme forms a hexamer with D3 symmetry. An assessment of thioesterase activity against a range of acyl-CoA substrates revealed the greatest activity against acetyl-CoA, and structure-guided mutagenesis of putative active site residues identified Asn24 and Asp39 as being essential for activity. Our structural analysis revealed that six GDP nucleotides bound the enzyme in close proximity to an intersubunit disulfide bond interactions that covalently link thioesterase domains in a double hot dog dimer. Structure-guided mutagenesis of residues within the GDP-binding pocket identified Arg93 as playing a key role in the nucleotide interaction and revealed that GDP is required for activity. All mutations were confirmed to be specific and not to have resulted from structural perturbations by X-ray crystallography. This is the first report of a bacterial GDP-regulated thioesterase and of covalent linkage of thioesterase domains through a disulfide bond, revealing structural similarities with ADP regulation in the human ACOT12 thioesterase.
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Affiliation(s)
| | | | - Nathan Cowieson
- the Life Sciences Division, Diamond Light Source, Didcot OX11 0DE, United Kingdom
| | - Subir Sarker
- the Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Melbourne, Victoria 3086, Australia, and
| | - David Aragao
- the Australian National Synchrotron, Melbourne, Victoria 3168, Australia
| | - Shubagata Das
- School of Animal and Veterinary Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, New South Wales 2678, Australia
| | | | - Shane R Raidal
- School of Animal and Veterinary Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, New South Wales 2678, Australia
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Tillander V, Alexson SEH, Cohen DE. Deactivating Fatty Acids: Acyl-CoA Thioesterase-Mediated Control of Lipid Metabolism. Trends Endocrinol Metab 2017; 28:473-484. [PMID: 28385385 PMCID: PMC5474144 DOI: 10.1016/j.tem.2017.03.001] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 03/01/2017] [Indexed: 12/28/2022]
Abstract
The cellular uptake of free fatty acids (FFA) is followed by esterification to coenzyme A (CoA), generating fatty acyl-CoAs that are substrates for oxidation or incorporation into complex lipids. Acyl-CoA thioesterases (ACOTs) constitute a family of enzymes that hydrolyze fatty acyl-CoAs to form FFA and CoA. Although biochemically and biophysically well characterized, the metabolic functions of these enzymes remain incompletely understood. Existing evidence suggests regulatory roles in controlling rates of peroxisomal and mitochondrial fatty acyl-CoA oxidation, as well as in the subcellular trafficking of fatty acids. Emerging data implicate ACOTs in the pathogenesis of metabolic diseases, suggesting that better understanding their pathobiology could reveal unique targets in the management of obesity, diabetes, and nonalcoholic fatty liver disease.
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Affiliation(s)
- Veronika Tillander
- Division of Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, 14186, Sweden
| | - Stefan E H Alexson
- Division of Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, 14186, Sweden
| | - David E Cohen
- Division of Gastroenterology and Hepatology, Joan & Sanford I. Weill Department of Medicine, Weill Cornell Medical College, New York, NY 10021, USA.
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Abstract
Because of ubiquity of thioesters, thioesterases play a critical role in metabolism, membrane biosynthesis, signal transduction, and gene regulation. In many bacteria, YbgC is such an enzyme, whose coding gene mostly resides in the tol-pal cluster. Although all other proteins encoded in the tol-pal cluster are clearly involved in maintaining cell envelope integrity and cell division, little is known about the physiological role of YbgC. In this study, we identify in Shewanella oneidensis, a γ-proteobacterium used as a research model for environmental microbes, YbgC as a motility regulator. The loss of YbgC results in enhanced motility, which is likely due to the increased rotation rate of the flagellum. The regulatory function of YbgC requires its thioesterase activity but could not be replaced by YbgC homologues of other bacteria. We further show that the regulation of YbgC is mediated by the second message c-di-GMP.
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45
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Sánchez-Reyez A, Batista-García RA, Valdés-García G, Ortiz E, Perezgasga L, Zárate-Romero A, Pastor N, Folch-Mallol JL. A family 13 thioesterase isolated from an activated sludge metagenome: Insights into aromatic compounds metabolism. Proteins 2017; 85:1222-1237. [DOI: 10.1002/prot.25282] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 02/21/2017] [Accepted: 02/27/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Ayixon Sánchez-Reyez
- Centro de Investigación en Dinámica Celular, IICBA, Universidad Autónoma del Estado de Morelos (UAEM), Colonia Chamilpa; CP 62209 Cuernavaca, Morelos Mexico
- Centro de Investigación en Biotecnología UAEM; CP 62209 Cuernavaca Morelos Mexico
| | - Ramón Alberto Batista-García
- Centro de Investigación en Dinámica Celular, IICBA, Universidad Autónoma del Estado de Morelos (UAEM), Colonia Chamilpa; CP 62209 Cuernavaca, Morelos Mexico
| | - Gilberto Valdés-García
- Centro de Investigación en Dinámica Celular, IICBA, Universidad Autónoma del Estado de Morelos (UAEM), Colonia Chamilpa; CP 62209 Cuernavaca, Morelos Mexico
| | - Ernesto Ortiz
- Instituto de Biotecnología. Universidad Nacional Autónoma de México; CP 62210 Cuernavaca Morelos Mexico
| | - Lucía Perezgasga
- Instituto de Biotecnología. Universidad Nacional Autónoma de México; CP 62210 Cuernavaca Morelos Mexico
| | - Andrés Zárate-Romero
- Centro de Investigación en Biotecnología UAEM; CP 62209 Cuernavaca Morelos Mexico
| | - Nina Pastor
- Centro de Investigación en Dinámica Celular, IICBA, Universidad Autónoma del Estado de Morelos (UAEM), Colonia Chamilpa; CP 62209 Cuernavaca, Morelos Mexico
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46
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Taguchi T, Awakawa T, Nishihara Y, Kawamura M, Ohnishi Y, Ichinose K. Bifunctionality of ActIV as a Cyclase-Thioesterase Revealed by in Vitro Reconstitution of Actinorhodin Biosynthesis in Streptomyces coelicolor A3(2). Chembiochem 2017; 18:316-323. [PMID: 27897367 DOI: 10.1002/cbic.201600589] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Indexed: 11/11/2022]
Abstract
Type II polyketide synthases iteratively generate a nascent polyketide thioester of the acyl carrier protein (ACP); this is structurally modified to produce an ACP-free intermediate towards the final metabolite. However, the timing of ACP off-loading is not well defined because of the lack of an apparent thioesterase (TE) among relevant biosynthetic enzymes. Here, ActIV, which had been assigned as a second ring cyclase (CYC) in actinorhodin (ACT) biosynthesis, was shown to possess TE activity in vitro with a model substrate, anthraquinone-2-carboxylic acid-N-acetylcysteamine. In order to investigate its function further, the ACT biosynthetic pathway in Streptomyces coelicolor A3(2) was reconstituted in vitro in a stepwise fashion up to (S)-DNPA, and the product of ActIV reaction was characterized as an ACP-free bicyclic intermediate. These findings indicate that ActIV is a bifunctional CYC-TE and provide clear evidence for the release timing of the intermediate from the ACP anchor.
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Affiliation(s)
- Takaaki Taguchi
- Research Institute of Pharmaceutical Sciences, Musashino University, Shinmachi, Nishitokyo-shi, Tokyo, 202-8585, Japan
| | - Takayoshi Awakawa
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.,Present address: Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yukitaka Nishihara
- Research Institute of Pharmaceutical Sciences, Musashino University, Shinmachi, Nishitokyo-shi, Tokyo, 202-8585, Japan
| | - Michiho Kawamura
- Research Institute of Pharmaceutical Sciences, Musashino University, Shinmachi, Nishitokyo-shi, Tokyo, 202-8585, Japan
| | - Yasuo Ohnishi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Koji Ichinose
- Research Institute of Pharmaceutical Sciences, Musashino University, Shinmachi, Nishitokyo-shi, Tokyo, 202-8585, Japan
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47
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Albanesi D, de Mendoza D. FapR: From Control of Membrane Lipid Homeostasis to a Biotechnological Tool. Front Mol Biosci 2016; 3:64. [PMID: 27766255 PMCID: PMC5052256 DOI: 10.3389/fmolb.2016.00064] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 09/21/2016] [Indexed: 01/22/2023] Open
Abstract
Phospholipids and fatty acids are not only one of the major components of cell membranes but also important metabolic intermediates in bacteria. Since the fatty acid biosynthetic pathway is essential and energetically expensive, organisms have developed a diversity of homeostatic mechanisms to fine-tune the concentration of lipids at particular levels. FapR is the first global regulator of lipid synthesis discovered in bacteria and is largely conserved in Gram-positive organisms including important human pathogens, such as Staphylococcus aureus, Bacillus anthracis, and Listeria monocytogenes. FapR is a transcription factor that negatively controls the expression of several genes of the fatty acid and phospholipid biosynthesis and was first identified in Bacillus subtilis. This review focuses on the genetic, biochemical and structural advances that led to a detailed understanding of lipid homeostasis control by FapR providing unique opportunities to learn how Gram-positive bacteria monitor the status of fatty acid biosynthesis and adjust the lipid synthesis accordingly. Furthermore, we also cover the potential of the FapR system as a target for new drugs against Gram-positive bacteria as well as its recent biotechnological applications in diverse organisms.
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Affiliation(s)
- Daniela Albanesi
- Laboratorio de Fisiología Microbiana, Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Rosario Rosario, Argentina
| | - Diego de Mendoza
- Laboratorio de Fisiología Microbiana, Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Rosario Rosario, Argentina
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Yoshida K, Hashimoto M, Hori R, Adachi T, Okuyama H, Orikasa Y, Nagamine T, Shimizu S, Ueno A, Morita N. Bacterial Long-Chain Polyunsaturated Fatty Acids: Their Biosynthetic Genes, Functions, and Practical Use. Mar Drugs 2016; 14:E94. [PMID: 27187420 PMCID: PMC4882568 DOI: 10.3390/md14050094] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 04/23/2016] [Accepted: 04/29/2016] [Indexed: 02/06/2023] Open
Abstract
The nutritional and pharmaceutical values of long-chain polyunsaturated fatty acids (LC-PUFAs) such as arachidonic, eicosapentaenoic and docosahexaenoic acids have been well recognized. These LC-PUFAs are physiologically important compounds in bacteria and eukaryotes. Although little is known about the biosynthetic mechanisms and functions of LC-PUFAs in bacteria compared to those in higher organisms, a combination of genetic, bioinformatic, and molecular biological approaches to LC-PUFA-producing bacteria and some eukaryotes have revealed the notably diverse organization of the pfa genes encoding a polyunsaturated fatty acid synthase complex (PUFA synthase), the LC-PUFA biosynthetic processes, and tertiary structures of the domains of this enzyme. In bacteria, LC-PUFAs appear to take part in specific functions facilitating individual membrane proteins rather than in the adjustment of the physical fluidity of the whole cell membrane. Very long chain polyunsaturated hydrocarbons (LC-HCs) such as hentriacontanonaene are considered to be closely related to LC-PUFAs in their biosynthesis and function. The possible role of LC-HCs in strictly anaerobic bacteria under aerobic and anaerobic environments and the evolutionary relationships of anaerobic and aerobic bacteria carrying pfa-like genes are also discussed.
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Affiliation(s)
- Kiyohito Yoshida
- Laboratory of Ecological Genetics, Section of Environmental Biology, Faculty of Environmental Earth Science, Hokkaido University, Kita-ku, Sapporo, Hokkaido 060-0810, Japan.
| | - Mikako Hashimoto
- Course in Ecological Genetics, Division of Biosphere Science, Graduate School of Environmental Science, Hokkaido University, Kita-ku, Sapporo, Hokkaido 060-0810, Japan.
| | - Ryuji Hori
- Technical Solution Center First Group, J-OIL MILLS, Inc., Chuo-ku, Tokyo 104-0044, Japan.
| | - Takumi Adachi
- Laboratory of Environmental Microbiology, Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo, Hokkaido 060-8589, Japan.
- Bioproduction Research Institute, Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), Toyohira-ku, Sapporo, Hokkaido 062-8517, Japan.
| | - Hidetoshi Okuyama
- Laboratory of Environmental Molecular Biology, Section of Environmental Biology, Faculty of Environmental Earth Science, Hokkaido University, Kita-ku, Sapporo, Hokkaido 060-0810, Japan.
| | - Yoshitake Orikasa
- Department Food Science, Obihiro University Agriculture Veterinary Medicine, Inada-cho, Obihiro, Hokkaido 080-8555, Japan.
| | - Tadashi Nagamine
- ROM Co. Ltd., Togashi Bld., Chuo-ku, Sapporo, Hokkaido 060-0062, Japan.
| | - Satoru Shimizu
- Horonobe Research Institute for the Subsurface Environment, Northern Advancement Centre for Science and Technology, 5-3, Sakae-machi, Horonobe, Teshio-gun, Hokkaido 098-3221, Japan.
| | - Akio Ueno
- Horonobe Research Institute for the Subsurface Environment, Northern Advancement Centre for Science and Technology, 5-3, Sakae-machi, Horonobe, Teshio-gun, Hokkaido 098-3221, Japan.
| | - Naoki Morita
- Laboratory of Environmental Microbiology, Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo, Hokkaido 060-8589, Japan.
- Bioproduction Research Institute, Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), Toyohira-ku, Sapporo, Hokkaido 062-8517, Japan.
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49
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Microscopic and proteomic analysis of Zea mays roots (P30F53 variety) inoculated with Azospirillum brasilense strain FP2. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/s12892-014-0061-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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50
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Kim HJ, Silva JE, Vu HS, Mockaitis K, Nam JW, Cahoon EB. Toward production of jet fuel functionality in oilseeds: identification of FatB acyl-acyl carrier protein thioesterases and evaluation of combinatorial expression strategies in Camelina seeds. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:4251-65. [PMID: 25969557 PMCID: PMC4493788 DOI: 10.1093/jxb/erv225] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Seeds of members of the genus Cuphea accumulate medium-chain fatty acids (MCFAs; 8:0-14:0). MCFA- and palmitic acid- (16:0) rich vegetable oils have received attention for jet fuel production, given their similarity in chain length to Jet A fuel hydrocarbons. Studies were conducted to test genes, including those from Cuphea, for their ability to confer jet fuel-type fatty acid accumulation in seed oil of the emerging biofuel crop Camelina sativa. Transcriptomes from Cuphea viscosissima and Cuphea pulcherrima developing seeds that accumulate >90% of C8 and C10 fatty acids revealed three FatB cDNAs (CpuFatB3, CvFatB1, and CpuFatB4) expressed predominantly in seeds and structurally divergent from typical FatB thioesterases that release 16:0 from acyl carrier protein (ACP). Expression of CpuFatB3 and CvFatB1 resulted in Camelina oil with capric acid (10:0), and CpuFatB4 expression conferred myristic acid (14:0) production and increased 16:0. Co-expression of combinations of previously characterized Cuphea and California bay FatBs produced Camelina oils with mixtures of C8-C16 fatty acids, but amounts of each fatty acid were less than obtained by expression of individual FatB cDNAs. Increases in lauric acid (12:0) and 14:0, but not 10:0, in Camelina oil and at the sn-2 position of triacylglycerols resulted from inclusion of a coconut lysophosphatidic acid acyltransferase specialized for MCFAs. RNA interference (RNAi) suppression of Camelina β-ketoacyl-ACP synthase II, however, reduced 12:0 in seeds expressing a 12:0-ACP-specific FatB. Camelina lines presented here provide platforms for additional metabolic engineering targeting fatty acid synthase and specialized acyltransferases for achieving oils with high levels of jet fuel-type fatty acids.
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Affiliation(s)
- Hae Jin Kim
- Department of Biochemistry and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Jillian E Silva
- Department of Biochemistry and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Hieu Sy Vu
- Department of Biochemistry and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Keithanne Mockaitis
- Department of Biology, and Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
| | - Jeong-Won Nam
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA
| | - Edgar B Cahoon
- Department of Biochemistry and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
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