title: Conserved motifs reveal details of ancestry and structure in the small TIM chaperones of the mitochondrial intermembrane space.
abstract: The mitochondrial inner and outer membranes are composed of a variety of integral membrane proteins, assembled into the membranes posttranslationally. The small translocase of the inner mitochondrial membranes (TIMs) are a group of approximately 10 kDa proteins that function as chaperones to ferry the imported proteins across the mitochondrial intermembrane space to the outer and inner membranes. In yeast, there are 5 small TIM proteins: Tim8, Tim9, Tim10, Tim12, and Tim13, with equivalent proteins reported in humans. Using hidden Markov models, we find that many eukaryotes have proteins equivalent to the Tim8 and Tim13 and the Tim9 and Tim10 subunits. Some eukaryotes provide "snapshots" of evolution, with a single protein showing the features of both Tim8 and Tim13, suggesting that a single progenitor gene has given rise to each of the small TIMs through duplication and modification. We show that no "Tim12" family of proteins exist, but rather that variant forms of the cognate small TIMs have been recently duplicated and modified to provide new functions: the yeast Tim12 is a modified form of Tim10, whereas in humans and some protists variant forms of Tim9, Tim8, and Tim13 are found instead. Sequence motif analysis reveals acidic residues conserved in the Tim10 substrate-binding tentacles, whereas more hydrophobic residues are found in the equivalent substrate-binding region of Tim13. The substrate-binding region of Tim10 and Tim13 represent structurally independent domains: when the acidic domain from Tim10 is attached to Tim13, the Tim8-Tim13(10) complex becomes essential and the Tim9-Tim10 complex becomes dispensable. The conserved features in the Tim10 and Tim13 subunits provide distinct binding surfaces to accommodate the broad range of substrate proteins delivered to the mitochondrial inner and outer membranes.
authors.affiliation: Department of Biochemistry & Molecular Biology, University of Melbourne, Parkville, Victoria, Australia.
authors.forename: Ian E
authors.initials: IE
authors.lastname: Gentle
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Perry
authors.forename: Felicity H
authors.initials: FH
authors.lastname: Alcock
authors.forename: Vladimir A
authors.initials: VA
authors.lastname: Likić
authors.forename: Pavel
authors.initials: P
authors.lastname: Dolezal
authors.forename: Ee Ting
authors.initials: ET
authors.lastname: Ng
authors.forename: Anthony W
authors.initials: AW
authors.lastname: Purcell
authors.forename: Malcolm
authors.initials: M
authors.lastname: McConnville
authors.forename: Thomas
authors.initials: T
authors.lastname: Naderer
authors.forename: Anne-Laure
authors.initials: AL
authors.lastname: Chanez
authors.forename: Fabien
authors.initials: F
authors.lastname: Charrière
authors.forename: Caroline
authors.initials: C
authors.lastname: Aschinger
authors.forename: André
authors.initials: A
authors.lastname: Schneider
authors.forename: Kostas
authors.initials: K
authors.lastname: Tokatlidis
authors.forename: Trevor
authors.initials: T
authors.lastname: Lithgow
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000818:Animals; D017124:Conserved Sequence; D019143:Evolution, Molecular; D005656:Fungal Proteins / Q000737:chemistry / Q000235:genetics / Q000502:physiology; D020440:Gene Duplication; D006801:Humans; D008390:Markov Chains; D033681:Mitochondrial Membrane Transport Proteins / Q000737:chemistry / Q000235:genetics / Q000502:physiology*; D051336:Mitochondrial Membranes / Q000737:chemistry / Q000502:physiology*; D008958:Models, Molecular; D018832:Molecular Chaperones / Q000737:chemistry / Q000235:genetics / Q000502:physiology*; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics / Q000502:physiology; D011487:Protein Conformation; D021381:Protein Transport; D015800:Protozoan Proteins / Q000737:chemistry / Q000235:genetics / Q000502:physiology; D014346:Trypanosoma brucei brucei / Q000502:physiology
chemical_list: D005656:Fungal Proteins; D033681:Mitochondrial Membrane Transport Proteins; D018832:Molecular Chaperones; D010940:Plant Proteins; D015800:Protozoan Proteins