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Zhao W, Geng H, Dan Z, Zeng Y, Wang M, Xu W, Hu Z, Huang W. The Alpha Subunit of Mitochondrial Processing Peptidase Participated in Fertility Restoration in Honglian-CMS Rice. Int J Mol Sci 2023; 24:ijms24065442. [PMID: 36982518 PMCID: PMC10049570 DOI: 10.3390/ijms24065442] [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: 02/15/2023] [Revised: 03/09/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023] Open
Abstract
The cytoplasmic male sterility (CMS) and nuclear-controlled fertility restoration system is a favorable tool for the utilization of heterosis in plant hybrid breeding. Many restorer-of-fertility (Rf) genes have been characterized in various species over the decades, but more detailed work is needed to investigate the fertility restoration mechanism. Here, we identified an alpha subunit of mitochondrial processing peptidase (MPPA) that is involved in the fertility restoration process in Honglian-CMS rice. MPPA is a mitochondrial localized protein and interacted with the RF6 protein encoded by the Rf6. MPPA indirectly interacted with hexokinase 6, namely another partner of RF6, to form a protein complex with the same molecular weight as the mitochondrial F1F0-ATP synthase in processing the CMS transcript. Loss-of-function of MPPA resulted in a defect in pollen fertility, the mppa+/− heterozygotes showed semi-sterility phenotype and the accumulation of CMS-associated protein ORFH79, showing restrained processing of the CMS-associated atp6-OrfH79 in the mutant plant. Taken together, these results threw new light on the process of fertility restoration by investigating the RF6 fertility restoration complex. They also reveal the connections between signal peptide cleavage and the fertility restoration process in Honglian-CMS rice.
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Affiliation(s)
- Weibo Zhao
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.Z.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Han Geng
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.Z.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zhiwu Dan
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.Z.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yafei Zeng
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.Z.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Mingyue Wang
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.Z.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Wuwu Xu
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.Z.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zhongli Hu
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.Z.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Wenchao Huang
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.Z.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
- Correspondence:
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2
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Jobling RK, Assoum M, Gakh O, Blaser S, Raiman JA, Mignot C, Roze E, Dürr A, Brice A, Lévy N, Prasad C, Paton T, Paterson AD, Roslin NM, Marshall CR, Desvignes JP, Roëckel-Trevisiol N, Scherer SW, Rouleau GA, Mégarbané A, Isaya G, Delague V, Yoon G. PMPCA mutations cause abnormal mitochondrial protein processing in patients with non-progressive cerebellar ataxia. Brain 2015; 138:1505-17. [PMID: 25808372 PMCID: PMC4542620 DOI: 10.1093/brain/awv057] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 12/09/2014] [Accepted: 01/06/2015] [Indexed: 11/13/2022] Open
Abstract
Non-progressive cerebellar ataxias are a rare group of disorders that comprise approximately 10% of static infantile encephalopathies. We report the identification of mutations in PMPCA in 17 patients from four families affected with cerebellar ataxia, including the large Lebanese family previously described with autosomal recessive cerebellar ataxia and short stature of Norman type and localized to chromosome 9q34 (OMIM #213200). All patients present with non-progressive cerebellar ataxia, and the majority have intellectual disability of variable severity. PMPCA encodes α-MPP, the alpha subunit of mitochondrial processing peptidase, the primary enzyme responsible for the maturation of the vast majority of nuclear-encoded mitochondrial proteins, which is necessary for life at the cellular level. Analysis of lymphoblastoid cells and fibroblasts from patients homozygous for the PMPCA p.Ala377Thr mutation and carriers demonstrate that the mutation impacts both the level of the alpha subunit encoded by PMPCA and the function of mitochondrial processing peptidase. In particular, this mutation impacts the maturation process of frataxin, the protein which is depleted in Friedreich ataxia. This study represents the first time that defects in PMPCA and mitochondrial processing peptidase have been described in association with a disease phenotype in humans.
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Affiliation(s)
- Rebekah K Jobling
- 1 Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Mirna Assoum
- 2 Inserm, UMR_S 910, 13385, Marseille, France 3 Aix Marseille Université, GMGF, 13385, Marseille, France
| | - Oleksandr Gakh
- 4 Department of Paediatric and Adolescent Medicine and Mayo Clinic Children's Centre, Mayo Clinic, Rochester, MN, USA
| | - Susan Blaser
- 5 Division of Neuroradiology, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Julian A Raiman
- 1 Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Cyril Mignot
- 6 Département de Génétique, Unité de Génétique Clinique, APHP, Groupe Hospitalier Pitié-Salpêtrière; Centre de Référence Maladies Rares 'Déficiences Intellectuelles de Causes Rares'; Groupe de Recherche Clinique UPMC Univ Paris 06; Paris, France
| | - Emmanuel Roze
- 7 Sorbonne Université, UPMC Univ Paris 06, UM 75, ICM, F-75013 Paris, France 8 Inserm, U 1127, ICM, F-75013 Paris, France 9 Cnrs, UMR 7225, ICM, F-75013 Paris, France 10 ICM, Paris, F-75013 Paris, France 11 AP-HP, Hôpital de la Salpêtrière, Département de Neurologie, F-75013, Paris, France
| | - Alexandra Dürr
- 7 Sorbonne Université, UPMC Univ Paris 06, UM 75, ICM, F-75013 Paris, France 8 Inserm, U 1127, ICM, F-75013 Paris, France 9 Cnrs, UMR 7225, ICM, F-75013 Paris, France 10 ICM, Paris, F-75013 Paris, France 12 AP-HP, Hôpital de la Salpêtrière, Département de Génétique et Cytogénétique, F-75013, Paris, France
| | - Alexis Brice
- 7 Sorbonne Université, UPMC Univ Paris 06, UM 75, ICM, F-75013 Paris, France 8 Inserm, U 1127, ICM, F-75013 Paris, France 9 Cnrs, UMR 7225, ICM, F-75013 Paris, France 10 ICM, Paris, F-75013 Paris, France 12 AP-HP, Hôpital de la Salpêtrière, Département de Génétique et Cytogénétique, F-75013, Paris, France
| | - Nicolas Lévy
- 2 Inserm, UMR_S 910, 13385, Marseille, France 3 Aix Marseille Université, GMGF, 13385, Marseille, France 13 Département de Génétique Médicale, Hôpital d'Enfants de la Timone, AP-HM, Marseille, France
| | - Chitra Prasad
- 14 Medical Genetics Program, Department of Pediatrics, London Health Sciences Centre, London, Ontario, Canada
| | - Tara Paton
- 15 The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Andrew D Paterson
- 15 The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Nicole M Roslin
- 15 The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Christian R Marshall
- 15 The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Jean-Pierre Desvignes
- 2 Inserm, UMR_S 910, 13385, Marseille, France 3 Aix Marseille Université, GMGF, 13385, Marseille, France
| | - Nathalie Roëckel-Trevisiol
- 2 Inserm, UMR_S 910, 13385, Marseille, France 3 Aix Marseille Université, GMGF, 13385, Marseille, France
| | - Stephen W Scherer
- 15 The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada 16 McLaughlin Centre and Department of Molecular Genetics, University of Toronto
| | - Guy A Rouleau
- 17 Montreal Neurological Institute and Hospital and Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
| | - André Mégarbané
- 18 Unité de Génétique Médicale and Laboratoire Associé Inserm UMR S_910, Faculté de Médecine, Université Saint Joseph, Beirut, Lebanon 19 Institut Jérôme Lejeune, Paris, France
| | - Grazia Isaya
- 4 Department of Paediatric and Adolescent Medicine and Mayo Clinic Children's Centre, Mayo Clinic, Rochester, MN, USA
| | - Valérie Delague
- 2 Inserm, UMR_S 910, 13385, Marseille, France 3 Aix Marseille Université, GMGF, 13385, Marseille, France
| | - Grace Yoon
- 1 Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada 20 Division of Neurology, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
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3
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Kučera T, Otyepka M, Matušková A, Samad A, Kutejová E, Janata J. A computational study of the glycine-rich loop of mitochondrial processing peptidase. PLoS One 2013; 8:e74518. [PMID: 24058582 PMCID: PMC3772902 DOI: 10.1371/journal.pone.0074518] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 08/02/2013] [Indexed: 11/21/2022] Open
Abstract
An all atomic, non-restrained molecular dynamics (MD) simulation in explicit water was used to study in detail the structural features of the highly conserved glycine-rich loop (GRL) of the α-subunit of the yeast mitochondrial processing peptidase (MPP) and its importance for the tertiary and quaternary conformation of MPP. Wild-type and GRL-deleted MPP structures were studied using non-restrained MD simulations, both in the presence and the absence of a substrate in the peptidase active site. Targeted MD simulations were employed to study the mechanism of substrate translocation from the GRL to the active site. We demonstrate that the natural conformational flexibility of the GRL is crucial for the substrate translocation process from outside the enzyme towards the MPP active site. We show that the α-helical conformation of the substrate is important not only during its initial interaction with MPP (i.e. substrate recognition), but also later, at least during the first third of the substrate translocation trajectory. Further, we show that the substrate remains in contact with the GRL during the whole first half of the translocation trajectory and that hydrophobic interactions play a major role. Finally, we conclude that the GRL acts as a precisely balanced structural element, holding the MPP subunits in a partially closed conformation regardless the presence or absence of a substrate in the active site.
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Affiliation(s)
- Tomáš Kučera
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Anna Matušková
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Abdul Samad
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Eva Kutejová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jiří Janata
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
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4
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Mach J, Poliak P, Matušková A, Žárský V, Janata J, Lukeš J, Tachezy J. An Advanced System of the Mitochondrial Processing Peptidase and Core Protein Family in Trypanosoma brucei and Multiple Origins of the Core I Subunit in Eukaryotes. Genome Biol Evol 2013; 5:860-75. [PMID: 23563972 PMCID: PMC3673636 DOI: 10.1093/gbe/evt056] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/02/2013] [Indexed: 01/20/2023] Open
Abstract
Mitochondrial processing peptidase (MPP) consists of α and β subunits that catalyze the cleavage of N-terminal mitochondrial-targeting sequences (N-MTSs) and deliver preproteins to the mitochondria. In plants, both MPP subunits are associated with the respiratory complex bc1, which has been proposed to represent an ancestral form. Subsequent duplication of MPP subunits resulted in separate sets of genes encoding soluble MPP in the matrix and core proteins (cp1 and cp2) of the membrane-embedded bc1 complex. As only α-MPP was duplicated in Neurospora, its single β-MPP functions in both MPP and bc1 complexes. Herein, we investigated the MPP/core protein family and N-MTSs in the kinetoplastid Trypanosoma brucei, which is often considered one of the most ancient eukaryotes. Analysis of N-MTSs predicted in 336 mitochondrial proteins showed that trypanosomal N-MTSs were comparable with N-MTSs from other organisms. N-MTS cleavage is mediated by a standard heterodimeric MPP, which is present in the matrix of procyclic and bloodstream trypanosomes, and its expression is essential for the parasite. Distinct Genes encode cp1 and cp2, and in the bloodstream forms the expression of cp1 is downregulated along with the bc1 complex. Phylogenetic analysis revealed that all eukaryotic lineages include members with a Neurospora-type MPP/core protein family, whereas cp1 evolved independently in metazoans, some fungi and kinetoplastids. Evolution of cp1 allowed the independent regulation of respiration and protein import, which is essential for the procyclic and bloodstream forms of T. brucei. These results indicate that T. brucei possesses a highly derived MPP/core protein family that likely evolved in response to its complex life cycle and does not appear to have an ancient character proposed earlier for this eukaryote.
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Affiliation(s)
- Jan Mach
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Pavel Poliak
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Budweis, Czech Republic
| | - Anna Matušková
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Vojtěch Žárský
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jiří Janata
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Budweis, Czech Republic
| | - Jan Tachezy
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
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5
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Amata O, Marino T, Russo N, Toscano M. A Proposal for Mitochondrial Processing Peptidase Catalytic Mechanism. J Am Chem Soc 2011; 133:17824-31. [DOI: 10.1021/ja207065v] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Orazio Amata
- Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite-Centro d'Eccellenza MURST, Universita' della Calabria, I-87030 Arcavacata di Rende (CS), Italy
| | - Tiziana Marino
- Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite-Centro d'Eccellenza MURST, Universita' della Calabria, I-87030 Arcavacata di Rende (CS), Italy
| | - Nino Russo
- Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite-Centro d'Eccellenza MURST, Universita' della Calabria, I-87030 Arcavacata di Rende (CS), Italy
| | - Marirosa Toscano
- Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite-Centro d'Eccellenza MURST, Universita' della Calabria, I-87030 Arcavacata di Rende (CS), Italy
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6
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Dvoráková-Holá K, Matusková A, Kubala M, Otyepka M, Kucera T, Vecer J, Herman P, Parkhomenko N, Kutejova E, Janata J. Glycine-rich loop of mitochondrial processing peptidase alpha-subunit is responsible for substrate recognition by a mechanism analogous to mitochondrial receptor Tom20. J Mol Biol 2010; 396:1197-210. [PMID: 20053354 DOI: 10.1016/j.jmb.2009.12.054] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2009] [Revised: 12/23/2009] [Accepted: 12/28/2009] [Indexed: 02/07/2023]
Abstract
Tryptophan fluorescence measurements were used to characterize the local dynamics of the highly conserved glycine-rich loop (GRL) of the mitochondrial processing peptidase (MPP) alpha-subunit in the presence of the substrate precursor. Reporter tryptophan residue was introduced into the GRL of the yeast alpha-MPP (Y299W) or at a proximal site (Y303W). Time-resolved and steady-state fluorescence spectroscopy demonstrated that for Trp299, the primary contact with the yeast malate dehydrogenase precursor evokes a change of the local GRL mobility. Moreover, time-resolved measurements showed that a functionless alpha-MPP with a single-residue deletion in the loop (Y303W/DeltaG292) is defective particularly in the primary contact with substrate. Thus, the GRL was proved to be part of a contact site of the enzyme specifically recognizing the substrate. Regarding the surface exposure and presence of the hydrophobic patches within the GRL, we proposed a functional analogy between the presequence recognition by the hydrophobic binding groove of the Tom20 mitochondrial import receptor and the GRL of the alpha-MPP. A molecular dynamics (MD) simulation of the MPP-substrate peptide complex model was employed to test this hypothesis. The initial positioning and conformation of the substrate peptide in the model fitting were chosen based on the analogy of its interaction with the Tom20 binding groove. MD simulation confirmed the stability of the proposed interaction and showed also a decrease in GRL flexibility in the presence of substrate, in agreement with fluorescence measurements. Moreover, conserved substrate hydrophobic residues in positions +1 and -4 to the cleavage site remain in close contact with the side chains of the GRL during the entire production part of MD simulation as stabilizing points of the hydrophobic interaction. We conclude that the GRL of the MPP alpha-subunit is the crucial evolutional outcome of the presequence recognition by MPP and represents a functional parallel with Tom20 import receptor.
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Affiliation(s)
- Klára Dvoráková-Holá
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídenská 1083, 142 20 Prague 4, Czech Republic
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7
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Šmíd O, Matušková A, Harris SR, Kučera T, Novotný M, Horváthová L, Hrdý I, Kutějová E, Hirt RP, Embley TM, Janata J, Tachezy J. Reductive evolution of the mitochondrial processing peptidases of the unicellular parasites trichomonas vaginalis and giardia intestinalis. PLoS Pathog 2008; 4:e1000243. [PMID: 19096520 PMCID: PMC2597178 DOI: 10.1371/journal.ppat.1000243] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2008] [Accepted: 11/18/2008] [Indexed: 11/18/2022] Open
Abstract
Mitochondrial processing peptidases are heterodimeric enzymes (alpha/betaMPP) that play an essential role in mitochondrial biogenesis by recognizing and cleaving the targeting presequences of nuclear-encoded mitochondrial proteins. The two subunits are paralogues that probably evolved by duplication of a gene for a monomeric metallopeptidase from the endosymbiotic ancestor of mitochondria. Here, we characterize the MPP-like proteins from two important human parasites that contain highly reduced versions of mitochondria, the mitosomes of Giardia intestinalis and the hydrogenosomes of Trichomonas vaginalis. Our biochemical characterization of recombinant proteins showed that, contrary to a recent report, the Trichomonas processing peptidase functions efficiently as an alpha/beta heterodimer. By contrast, and so far uniquely among eukaryotes, the Giardia processing peptidase functions as a monomer comprising a single betaMPP-like catalytic subunit. The structure and surface charge distribution of the Giardia processing peptidase predicted from a 3-D protein model appear to have co-evolved with the properties of Giardia mitosomal targeting sequences, which, unlike classic mitochondrial targeting signals, are typically short and impoverished in positively charged residues. The majority of hydrogenosomal presequences resemble those of mitosomes, but longer, positively charged mitochondrial-type presequences were also identified, consistent with the retention of the Trichomonas alphaMPP-like subunit. Our computational and experimental/functional analyses reveal that the divergent processing peptidases of Giardia mitosomes and Trichomonas hydrogenosomes evolved from the same ancestral heterodimeric alpha/betaMPP metallopeptidase as did the classic mitochondrial enzyme. The unique monomeric structure of the Giardia enzyme, and the co-evolving properties of the Giardia enzyme and substrate, provide a compelling example of the power of reductive evolution to shape parasite biology.
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Affiliation(s)
- Ondřej Šmíd
- Department of Parasitology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Anna Matušková
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Simon R. Harris
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Tomáš Kučera
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Marián Novotný
- Department of Parasitology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Lenka Horváthová
- Department of Parasitology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Ivan Hrdý
- Department of Parasitology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Eva Kutějová
- Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Robert P. Hirt
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - T. Martin Embley
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jiří Janata
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Jan Tachezy
- Department of Parasitology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
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Ondrovicová G, Liu T, Singh K, Tian B, Li H, Gakh O, Perecko D, Janata J, Granot Z, Orly J, Kutejová E, Suzuki CK. Cleavage site selection within a folded substrate by the ATP-dependent lon protease. J Biol Chem 2005; 280:25103-10. [PMID: 15870080 DOI: 10.1074/jbc.m502796200] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mechanistic studies of ATP-dependent proteolysis demonstrate that substrate unfolding is a prerequisite for processive peptide bond hydrolysis. We show that mitochondrial Lon also degrades folded proteins and initiates substrate cleavage non-processively. Two mitochondrial substrates with known or homology-derived three-dimensional structures were used: the mitochondrial processing peptidase alpha-subunit (MPPalpha) and the steroidogenic acute regulatory protein (StAR). Peptides generated during a time course of Lon-mediated proteolysis were identified and mapped within the primary, secondary, and tertiary structure of the substrate. Initiating cleavages occurred preferentially between hydrophobic amino acids located within highly charged environments at the surface of the folded protein. Subsequent cleavages proceeded sequentially along the primary polypeptide sequence. We propose that Lon recognizes specific surface determinants or folds, initiates proteolysis at solvent-accessible sites, and generates unfolded polypeptides that are then processively degraded.
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Affiliation(s)
- Gabriela Ondrovicová
- Institute of Molecular Biology, Slovak Academy of Sciences, 84551 Bratislava, Slovak Republic
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