title: Characterization of the mycobacterial acyl-CoA carboxylase holo complexes reveals their functional expansion into amino acid catabolism.
abstract: Biotin-mediated carboxylation of short-chain fatty acid coenzyme A esters is a key step in lipid biosynthesis that is carried out by multienzyme complexes to extend fatty acids by one methylene group. Pathogenic mycobacteria have an unusually high redundancy of carboxyltransferase genes and biotin carboxylase genes, creating multiple combinations of protein/protein complexes of unknown overall composition and functional readout. By combining pull-down assays with mass spectrometry, we identified nine binary protein/protein interactions and four validated holo acyl-coenzyme A carboxylase complexes. We investigated one of these--the AccD1-AccA1 complex from Mycobacterium tuberculosis with hitherto unknown physiological function. Using genetics, metabolomics and biochemistry we found that this complex is involved in branched amino-acid catabolism with methylcrotonyl coenzyme A as the substrate. We then determined its overall architecture by electron microscopy and found it to be a four-layered dodecameric arrangement that matches the overall dimensions of a distantly related methylcrotonyl coenzyme A holo complex. Our data argue in favor of distinct structural requirements for biotin-mediated γ-carboxylation of α-β unsaturated acid esters and will advance the categorization of acyl-coenzyme A carboxylase complexes. Knowledge about the underlying structural/functional relationships will be crucial to make the target category amenable for future biomedical applications.
authors.affiliation: European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany.
authors.forename: Matthias T
authors.initials: MT
authors.lastname: Ehebauer
authors.affiliation: Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
authors.forename: Michael
authors.initials: M
authors.lastname: Zimmermann
authors.affiliation: European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany; European Molecular Biology Laboratory, Structural Biology and Computational Biology Programme, Heidelberg, Germany.
authors.forename: Arjen J
authors.initials: AJ
authors.lastname: Jakobi
authors.affiliation: European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany.
authors.forename: Elke E
authors.initials: EE
authors.lastname: Noens
authors.affiliation: Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland; Department of Genetics & Biotechnology, Warsaw University, Warsaw, Poland.
authors.forename: Daniel
authors.initials: D
authors.lastname: Laubitz
authors.affiliation: Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland; Department of Genetics & Biotechnology, Warsaw University, Warsaw, Poland.
authors.forename: Bogdan
authors.initials: B
authors.lastname: Cichocki
authors.affiliation: Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, Tuberculosis & Infection Biology Department, Toulouse, France; Université Paul Sabatier, Toulouse, France.
authors.forename: Hedia
authors.initials: H
authors.lastname: Marrakchi
authors.affiliation: Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, Tuberculosis & Infection Biology Department, Toulouse, France; Université Paul Sabatier, Toulouse, France.
authors.forename: Marie-Antoinette
authors.initials: MA
authors.lastname: Lanéelle
authors.affiliation: Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, Tuberculosis & Infection Biology Department, Toulouse, France; Université Paul Sabatier, Toulouse, France.
authors.forename: Mamadou
authors.initials: M
authors.lastname: Daffé
authors.affiliation: European Molecular Biology Laboratory, Structural Biology and Computational Biology Programme, Heidelberg, Germany.
authors.forename: Carsten
authors.initials: C
authors.lastname: Sachse
authors.affiliation: Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland; Department of Genetics & Biotechnology, Warsaw University, Warsaw, Poland.
authors.forename: Andrzej
authors.initials: A
authors.lastname: Dziembowski
authors.affiliation: Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
authors.forename: Uwe
authors.initials: U
authors.lastname: Sauer
authors.affiliation: European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany; Center for Structural Systems Biology, Hamburg, Germany.
authors.forename: Matthias
authors.initials: M
authors.lastname: Wilmanns
mesh_terms: D000595:Amino Acid Sequence; D000596:Amino Acids / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism*; D019735:Carbon-Carbon Ligases / Q000737:chemistry / Q000378:metabolism*; D055786:Gene Knockout Techniques; D047468:Immunoprecipitation; D007930:Leucine / Q000378:metabolism*; D013058:Mass Spectrometry; D008660:Metabolism / Q000502:physiology; D008969:Molecular Sequence Data; D009097:Multienzyme Complexes / Q000378:metabolism*; D009169:Mycobacterium tuberculosis / Q000378:metabolism*; D020836:Protein Structure, Quaternary; D012689:Sequence Homology, Nucleic Acid
chemical_list: D000596:Amino Acids; D001426:Bacterial Proteins; D009097:Multienzyme Complexes; D019735:Carbon-Carbon Ligases; C018757:acyl-CoA carboxylase; D007930:Leucine