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Scaltsoyiannes V, Corre N, Waltz F, Giegé P. Types and Functions of Mitoribosome-Specific Ribosomal Proteins across Eukaryotes. Int J Mol Sci 2022; 23:ijms23073474. [PMID: 35408834 PMCID: PMC8998825 DOI: 10.3390/ijms23073474] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/17/2022] [Accepted: 03/21/2022] [Indexed: 02/04/2023] Open
Abstract
Mitochondria are key organelles that combine features inherited from their bacterial endosymbiotic ancestor with traits that arose during eukaryote evolution. These energy producing organelles have retained a genome and fully functional gene expression machineries including specific ribosomes. Recent advances in cryo-electron microscopy have enabled the characterization of a fast-growing number of the low abundant membrane-bound mitochondrial ribosomes. Surprisingly, mitoribosomes were found to be extremely diverse both in terms of structure and composition. Still, all of them drastically increased their number of ribosomal proteins. Interestingly, among the more than 130 novel ribosomal proteins identified to date in mitochondria, most of them are composed of a-helices. Many of them belong to the nuclear encoded super family of helical repeat proteins. Here we review the diversity of functions and the mode of action held by the novel mitoribosome proteins and discuss why these proteins that share similar helical folds were independently recruited by mitoribosomes during evolution in independent eukaryote clades.
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Affiliation(s)
- Vassilis Scaltsoyiannes
- CNRS, Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, 67084 Strasbourg, France; (V.S.); (N.C.)
| | - Nicolas Corre
- CNRS, Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, 67084 Strasbourg, France; (V.S.); (N.C.)
| | - Florent Waltz
- CNRS, Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, 67084 Strasbourg, France; (V.S.); (N.C.)
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Munich, Germany
- Correspondence: (F.W.); (P.G.); Tel.: +33-3-6715-5363 (P.G.); Fax: +33-3-8861-4442 (P.G.)
| | - Philippe Giegé
- CNRS, Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, 67084 Strasbourg, France; (V.S.); (N.C.)
- Correspondence: (F.W.); (P.G.); Tel.: +33-3-6715-5363 (P.G.); Fax: +33-3-8861-4442 (P.G.)
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Wirsing L, Klawonn F, Sassen WA, Lünsdorf H, Probst C, Hust M, Mendel RR, Kruse T, Jänsch L. Linear Discriminant Analysis Identifies Mitochondrially Localized Proteins in Neurospora crassa. J Proteome Res 2015. [PMID: 26215788 DOI: 10.1021/acs.jproteome.5b00329] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Besides their role as powerhouses, mitochondria play a pivotal role in the spatial organization of numerous enzymatic functions. They are connected to the ER, and many pathways are organized through the mitochondrial membranes. Thus, the precise definition of mitochondrial proteomes remains a challenging task. Here, we have established a proteomic strategy to accurately determine the mitochondrial localization of proteins from the fungal model organism Neurospora crassa. This strategy relies on both highly pure mitochondria as well as the quantitative monitoring of mitochondrial components along their consecutive enrichment. Pure intact mitochondria were obtained by a multistep approach combining differential and density Percoll (ultra) centrifugations. When compared with three other intermediate enrichment stages, peptide sequencing and quantitative profiling of pure mitochondrial fractions revealed prototypic regulatory profiles of per se mitochondrial components. These regulatory profiles constitute a distinct cluster defining the mitochondrial compartment and support linear discriminant analyses, which rationalized the annotation process. In total, this approach experimentally validated the mitochondrial localization of 512 proteins including 57 proteins that had not been reported for N. crassa before.
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Affiliation(s)
- Lisette Wirsing
- Cellular Proteomics Research Group, §Central Facility for Microscopy, Helmholtz Centre for Infection Research , 38124 Braunschweig, Germany
| | - Frank Klawonn
- Cellular Proteomics Research Group, §Central Facility for Microscopy, Helmholtz Centre for Infection Research , 38124 Braunschweig, Germany.,Department of Computer Science, Ostfalia University of Applied Sciences , 38302 Wolfenbüttel, Germany
| | | | | | | | | | | | | | - Lothar Jänsch
- Cellular Proteomics Research Group, §Central Facility for Microscopy, Helmholtz Centre for Infection Research , 38124 Braunschweig, Germany
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Smirnov A, Entelis N, Martin RP, Tarassov I. Biological significance of 5S rRNA import into human mitochondria: role of ribosomal protein MRP-L18. Genes Dev 2011; 25:1289-305. [PMID: 21685364 DOI: 10.1101/gad.624711] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
5S rRNA is an essential component of ribosomes of all living organisms, the only known exceptions being mitochondrial ribosomes of fungi, animals, and some protists. An intriguing situation distinguishes mammalian cells: Although the mitochondrial genome contains no 5S rRNA genes, abundant import of the nuclear DNA-encoded 5S rRNA into mitochondria was reported. Neither the detailed mechanism of this pathway nor its rationale was clarified to date. In this study, we describe an elegant molecular conveyor composed of a previously identified human 5S rRNA import factor, rhodanese, and mitochondrial ribosomal protein L18, thanks to which 5S rRNA molecules can be specifically withdrawn from the cytosolic pool and redirected to mitochondria, bypassing the classic nucleolar reimport pathway. Inside mitochondria, the cytosolic 5S rRNA is shown to be associated with mitochondrial ribosomes.
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Affiliation(s)
- Alexandre Smirnov
- "Génétique Moléculaire, Génomique, Microbiologie" (GMGM), Université de Strasbourg-CNRS, France
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Gel-based mass spectrometric and computational approaches to the mitochondrial proteome of Neurospora. Fungal Genet Biol 2011; 48:526-36. [DOI: 10.1016/j.fgb.2010.11.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2010] [Revised: 11/24/2010] [Accepted: 11/24/2010] [Indexed: 11/18/2022]
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Marín I, Hoyas S. Basic networks: definition and applications. J Theor Biol 2009; 258:53-9. [PMID: 19490867 DOI: 10.1016/j.jtbi.2009.01.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2008] [Revised: 01/21/2009] [Accepted: 01/21/2009] [Indexed: 10/21/2022]
Abstract
We define basic networks as the undirected subgraphs with minimal number of units in which the distances (geodesics, minimal path lengths) among a set of selected nodes, which we call seeds, in the original graph are conserved. The additional nodes required to draw the basic network are called connectors. We describe a heuristic strategy to find the basic networks of complex graphs. We also show how the characterization of these networks may help to obtain relevant biological information from highly complex protein-protein interaction data.
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Affiliation(s)
- Ignacio Marín
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), Calle Jaime Roig, 11, Valencia 46010, Spain.
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Qiu J, Noble WS. Predicting co-complexed protein pairs from heterogeneous data. PLoS Comput Biol 2008; 4:e1000054. [PMID: 18421371 PMCID: PMC2275314 DOI: 10.1371/journal.pcbi.1000054] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2007] [Accepted: 03/11/2008] [Indexed: 12/05/2022] Open
Abstract
Proteins do not carry out their functions alone. Instead, they often act by participating in macromolecular complexes and play different functional roles depending on the other members of the complex. It is therefore interesting to identify co-complex relationships. Although protein complexes can be identified in a high-throughput manner by experimental technologies such as affinity purification coupled with mass spectrometry (APMS), these large-scale datasets often suffer from high false positive and false negative rates. Here, we present a computational method that predicts co-complexed protein pair (CCPP) relationships using kernel methods from heterogeneous data sources. We show that a diffusion kernel based on random walks on the full network topology yields good performance in predicting CCPPs from protein interaction networks. In the setting of direct ranking, a diffusion kernel performs much better than the mutual clustering coefficient. In the setting of SVM classifiers, a diffusion kernel performs much better than a linear kernel. We also show that combination of complementary information improves the performance of our CCPP recognizer. A summation of three diffusion kernels based on two-hybrid, APMS, and genetic interaction networks and three sequence kernels achieves better performance than the sequence kernels or diffusion kernels alone. Inclusion of additional features achieves a still better ROC(50) of 0.937. Assuming a negative-to-positive ratio of 600ratio1, the final classifier achieves 89.3% coverage at an estimated false discovery rate of 10%. Finally, we applied our prediction method to two recently described APMS datasets. We find that our predicted positives are highly enriched with CCPPs that are identified by both datasets, suggesting that our method successfully identifies true CCPPs. An SVM classifier trained from heterogeneous data sources provides accurate predictions of CCPPs in yeast. This computational method thereby provides an inexpensive method for identifying protein complexes that extends and complements high-throughput experimental data.
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Affiliation(s)
- Jian Qiu
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - William Stafford Noble
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Department of Computer Science and Engineering, University of Washington, Seattle, Washington, United States of America
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Zíková A, Panigrahi AK, Dalley RA, Acestor N, Anupama A, Ogata Y, Myler PJ, Stuart K. Trypanosoma brucei mitochondrial ribosomes: affinity purification and component identification by mass spectrometry. Mol Cell Proteomics 2008; 7:1286-96. [PMID: 18364347 DOI: 10.1074/mcp.m700490-mcp200] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Although eukaryotic mitochondrial (mt) ribosomes evolved from a putative prokaryotic ancestor their compositions vary considerably among organisms. We determined the protein composition of tandem affinity-purified Trypanosoma brucei mt ribosomes by mass spectrometry and identified 133 proteins of which 77 were associated with the large subunit and 56 were associated with the small subunit. Comparisons with bacterial and mammalian mt ribosomal proteins identified T. brucei mt homologs of L2-4, L7/12, L9, L11, L13-17, L20-24, L27-30, L33, L38, L43, L46, L47, L49, L52, S5, S6, S8, S9, S11, S15-18, S29, and S34, although the degree of conservation varied widely. Sequence characteristics of some of the component proteins indicated apparent functions in rRNA modification and processing, protein assembly, and mitochondrial metabolism implying possible additional roles for these proteins. Nevertheless most of the identified proteins have no homology outside Kinetoplastida implying very low conservation and/or a divergent function in kinetoplastid mitochondria.
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Affiliation(s)
- Alena Zíková
- Seattle Biomedical Research Institute, Seattle, Washington 98109, USA
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Smits P, Smeitink JAM, van den Heuvel LP, Huynen MA, Ettema TJG. Reconstructing the evolution of the mitochondrial ribosomal proteome. Nucleic Acids Res 2007; 35:4686-703. [PMID: 17604309 PMCID: PMC1950548 DOI: 10.1093/nar/gkm441] [Citation(s) in RCA: 140] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
For production of proteins that are encoded by the mitochondrial genome, mitochondria rely on their own mitochondrial translation system, with the mitoribosome as its central component. Using extensive homology searches, we have reconstructed the evolutionary history of the mitoribosomal proteome that is encoded by a diverse subset of eukaryotic genomes, revealing an ancestral ribosome of alpha-proteobacterial descent that more than doubled its protein content in most eukaryotic lineages. We observe large variations in the protein content of mitoribosomes between different eukaryotes, with mammalian mitoribosomes sharing only 74 and 43% of its proteins with yeast and Leishmania mitoribosomes, respectively. We detected many previously unidentified mitochondrial ribosomal proteins (MRPs) and found that several have increased in size compared to their bacterial ancestral counterparts by addition of functional domains. Several new MRPs have originated via duplication of existing MRPs as well as by recruitment from outside of the mitoribosomal proteome. Using sensitive profile-profile homology searches, we found hitherto undetected homology between bacterial and eukaryotic ribosomal proteins, as well as between fungal and mammalian ribosomal proteins, detecting two novel human MRPs. These newly detected MRPs constitute, along with evolutionary conserved MRPs, excellent new screening targets for human patients with unresolved mitochondrial oxidative phosphorylation disorders.
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Affiliation(s)
- Paulien Smits
- Nijmegen Center for Mitochondrial Disorders, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, Geert–Grooteplein-Zuid 10 and Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, Geert-Grooteplein 28, 6525 GA Nijmegen, The Netherlands
| | - Jan A. M. Smeitink
- Nijmegen Center for Mitochondrial Disorders, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, Geert–Grooteplein-Zuid 10 and Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, Geert-Grooteplein 28, 6525 GA Nijmegen, The Netherlands
| | - Lambert P. van den Heuvel
- Nijmegen Center for Mitochondrial Disorders, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, Geert–Grooteplein-Zuid 10 and Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, Geert-Grooteplein 28, 6525 GA Nijmegen, The Netherlands
| | - Martijn A. Huynen
- Nijmegen Center for Mitochondrial Disorders, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, Geert–Grooteplein-Zuid 10 and Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, Geert-Grooteplein 28, 6525 GA Nijmegen, The Netherlands
| | - Thijs J. G. Ettema
- Nijmegen Center for Mitochondrial Disorders, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, Geert–Grooteplein-Zuid 10 and Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, Geert-Grooteplein 28, 6525 GA Nijmegen, The Netherlands
- *To whom correspondence should be addressed.
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Maslov DA, Spremulli LL, Sharma MR, Bhargava K, Grasso D, Falick AM, Agrawal RK, Parker CE, Simpson L. Proteomics and electron microscopic characterization of the unusual mitochondrial ribosome-related 45S complex in Leishmania tarentolae. Mol Biochem Parasitol 2007; 152:203-12. [PMID: 17292489 PMCID: PMC1885204 DOI: 10.1016/j.molbiopara.2007.01.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2006] [Revised: 12/29/2006] [Accepted: 01/12/2007] [Indexed: 11/20/2022]
Abstract
A novel type of ribonucleoprotein (RNP) complex has been described from the kinetoplast-mitochondria of Leishmania tarentolae. The complex, termed the 45S SSU*, contains the 9S small subunit rRNA but does not contain the 12S large subunit rRNA. This complex is the most stable and abundant mitochondrial RNP complex present in Leishmania. As shown by tandem mass spectrometry, the complex contains at least 39 polypeptides with a combined molecular mass of almost 2.1 MDa. These components include several homologs of small subunit ribosomal proteins (S5, S6, S8, S9, S11, S15, S16, S17, S18, MRPS29); however, most of the polypeptides present are unique. Only a few of them show recognizable motifs, such as protein-protein (coiled-coil, Rhodanese) or protein-RNA (pentatricopeptide repeat) interaction domains. A cryo-electron microscopy examination of the 45S SSU* fraction reveals that 27% of particles represent SSU homodimers arranged in a head-to-tail orientation, while the majority of particles are clearly different and show an asymmetric bilobed morphology. Multiple classes of two-dimensional averages were derived for the asymmetrical particles, probably reflecting random orientations of the particles and difficulties in correlating these views with the known projections of ribosomal complexes. One class of the two-dimensional averages shows a SSU moiety attached to a protein mass or masses in a monosome-like appearance. The combined mass spectrometry and electron microscopy data thus indicate that the majority 45S SSU* particles represents a heterodimeric complex in which the SSU of the Leishmania mitochondrial ribosome is associated with an additional protein mass. The biological role of these particles is not known.
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Affiliation(s)
- Dmitri A Maslov
- Department of Biology, University of California, Riverside, CA 92521, USA.
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