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Proteins at the Polypeptide Tunnel Exit of the Yeast Mitochondrial Ribosome
Technische Universität Kaiserslautern, Germany.
Technische Universität Kaiserslautern, Germany.
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2010 (English)In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 285, no 25, 19022-19028 p.Article in journal (Refereed) Published
Abstract [en]

Oxidative phosphorylation in mitochondria requires the synthesis of proteins encoded in the mitochondrial DNA. The mitochondrial translation machinery differs significantly from that of the bacterial ancestor of the organelle. This is especially evident from many mitochondria-specific ribosomal proteins. An important site of the ribosome is the polypeptide tunnel exit. Here, nascent chains are exposed to an aqueous environment for the first time. Many biogenesis factors interact with the tunnel exit of pro- and eukaryotic ribosomes to help the newly synthesized proteins to mature. To date, nothing is known about the organization of the tunnel exit of mitochondrial ribosomes. We therefore undertook a comprehensive approach to determine the composition of the yeast mitochondrial ribosomal tunnel exit. Mitochondria contain homologues of the ribosomal proteins located at this site in bacterial ribosomes. Here, we identified proteins located in their proximity by chemical cross-linking and mass spectrometry. Our analysis revealed a complex network of interacting proteins including proteins and protein domains specific to mitochondrial ribosomes. This network includes Mba1, the membrane-bound ribosome receptor of the inner membrane, as well as Mrpl3, Mrpl13, and Mrpl27, which constitute ribosomal proteins exclusively found in mitochondria. This unique architecture of the tunnel exit is presumably an adaptation of the translation system to the specific requirements of the organelle.

Place, publisher, year, edition, pages
2010. Vol. 285, no 25, 19022-19028 p.
National Category
Biochemistry and Molecular Biology
Research subject
Biochemistry
Identifiers
URN: urn:nbn:se:su:diva-81044DOI: 10.1074/jbc.M110.113837ISI: 000278727800010OAI: oai:DiVA.org:su-81044DiVA: diva2:559172
Available from: 2012-10-08 Created: 2012-10-08 Last updated: 2017-12-07Bibliographically approved
In thesis
1. Early steps in the biogenesis of the bc1 complex in yeast mitochondria: The role of the Cbp3-Cbp6 complex in cytochrome b synthesis and assembly
Open this publication in new window or tab >>Early steps in the biogenesis of the bc1 complex in yeast mitochondria: The role of the Cbp3-Cbp6 complex in cytochrome b synthesis and assembly
2012 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The inner membrane of mitochondria harbors the complexes of the respiratory chain and the ATP synthase, which perform the key metabolic process oxidative phosphorylation. These complexes are composed of subunits from two different genetic origins: the majority of constituents is synthesized on cytosolic ribosomes and imported into mitochondria, but a handful of proteins, which represent core catalytic subunits, are encoded in the organellar DNA and translated on mitochondrial ribosomes. Using yeast as a model organism, I investigated the mitochondrial ribosomal tunnel exit, the region of the ribosome where the nascent chain emerges and that in cytosolic ribosomes serves as a platform to bind biogenesis factors that help the newly synthesized protein to mature. This study provided insights into the structural composition of this important site of mitochondrial ribosomes and revealed the positioning of Cbp3 at the tunnel exit region, a chaperone required specifically for the assembly of the bc1 complex. In my further work I found that Cbp3 structurally and functionally forms a tight complex with Cbp6 and that this complex exhibits fundamental roles in the biogenesis of cytochrome b, the mitochondrially encoded subunit of the bc1 complex. Bound to the ribosome, Cbp3-Cbp6 stimulates translation of the cytochrome b mRNA (COB mRNA). Cbp3-Cbp6 then binds the fully synthesized cytochrome b, thereby stabilizing and guiding it further through bc1 complex assembly. The next steps involve the recruitment of the assembly factor Cbp4 to the Cbp3-Cbp6/cytochrome b complex and presumably acquisition of two redox active heme b cofactors. During further assembly Cbp3-Cbp6 is released from cytochrome b, can again bind to the ribosome and activate further rounds of COB mRNA translation. The dual role of Cbp3-Cbp6 in both translation and assembly allows the complex to act as a regulatory switch to modulate the level of cytochrome b synthesis in response to the bc1 complex assembly process.

Place, publisher, year, edition, pages
Stockholm: Department of Biochemistry and Biophysics, Stockholm University, 2012. 54 p.
Keyword
mitochondria, respiratory chain assembly, bc1 complex, mitochondrial gene expression, translational regulation, hemylation
National Category
Biochemistry and Molecular Biology
Research subject
Biochemistry
Identifiers
urn:nbn:se:su:diva-81033 (URN)978-91-7447-534-0 (ISBN)
Public defence
2012-12-07, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, 10:00 (English)
Opponent
Supervisors
Note

At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Manuscript.

Available from: 2012-11-15 Created: 2012-10-08 Last updated: 2012-11-07Bibliographically approved
2. Mitochondrial Energy Metabolism: Kgd4 is a novel subunit of the α-ketoglutarate dehydrogenase complex
Open this publication in new window or tab >>Mitochondrial Energy Metabolism: Kgd4 is a novel subunit of the α-ketoglutarate dehydrogenase complex
2014 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Mitochondria are essential organelles of eukaryotic cells and are responsible for their energy metabolism. The citric acid cycle, a chain of redox reactions in the mitochondrial matrix, is a central metabolic hub. The energy of these redox reactions is preserved in reducing equivalents, which are fed into the electron transport chain of the inner mitochondrial membrane. This process ultimately produces ATP.

Mitochondrial ribosomes are responsible for the synthesis of the hydrophobic core components of the respiratory chain complexes. Using the baker’s yeast Saccharomyces cerevisiae as a eukaryotic model organism, the composition of the polypeptide tunnel exit of mitochondrial ribosomes was defined. We identified novel mitochondria-specific ribosomal proteins and generated insights into how they contribute to the specialization of mitochondrial ribosomes.

In a second approach, Kgd4 was identified as a novel structural component of the a-ketoglutarate dehydrogenase complex (KGDH), which is part of the citric acid cycle. We demonstrate that this protein is responsible for recruiting one essential subunit to the catalytic core of the complex. By ensuring the structural integrity, Kgd4 indirectly maintains the catalytic function of the enzyme complex. Kgd4 also represents a rare exception from the standard protein synthesis process. There are two isofroms of the protein, which differ in the length of the amino acid sequence. Both Kgd4 forms contribute to KGDH stability and activity. Translation of the long isoform starts from a non-canonical UUG codon upstream of the commonly used start-codon AUG. This provides insights into the flexibility of translation initiation in yeast. Finally, we purified the fully intact and functional KGDH complex from isolated yeast mitochondria for future structural studies. These experiments also revealed details about the interaction of the complex with the inner mitochondrial membrane.

Place, publisher, year, edition, pages
Stockholm: Department of Biochemistry and Biophysics, Stockholm University, 2014. 60 p.
Keyword
Mitochondria, α-ketoglutarate dehydrogenase, Kgd4, Krebs cycle
National Category
Biochemistry and Molecular Biology
Research subject
Biochemistry
Identifiers
urn:nbn:se:su:diva-106696 (URN)978-91-7447-958-4 (ISBN)
Public defence
2014-09-30, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, 10:00 (English)
Opponent
Supervisors
Note

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 3: Manuscript. Paper 4: Manuscript.

Available from: 2014-09-08 Created: 2014-08-15 Last updated: 2014-09-15Bibliographically approved

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