NMR-Based Characterization of the Interaction Between Yeast Oxa1-CTD and Ribosomes

Overview

Journal Int J Mol Sci

Publisher MDPI

Specialties Biochemistry
Chemistry
Molecular Biology

Date 2023 Oct 14

PMID 37834108

Authors

Yong Liu

Jing Yang

Maosen Ruan

Huiqin Zhang

Junfeng Wang

Yunyan Li

Affiliations

Soon will be listed here.

Abstract

In mitochondria, the major subunits of oxidative phosphorylation complexes are translated by the mitochondrial ribosome (mito-ribosome). The correct insertion and assembly of these subunits into the inner mitochondrial membrane (IMM) are facilitated by mitochondrial oxidase assembly protein 1 (Oxa1) during the translation process. This co-translational insertion process involves an association between the mito-ribosome and the C-terminus of Oxa1 (Oxa1-CTD) Nuclear magnetic resonance (NMR) methods were mainly used to investigate the structural characterization of yeast Oxa1-CTD and its mode of interaction with the 70S ribosome. Oxa1-CTD forms a transient α-helical structure within the residues P342-Q385, which were reported to form an α-helix when combining with the ribosome. Two conserved contact sites that could interact with the ribosome were further identified. The first site was located on the very end of the N-terminus (V321-I327), and the second one encompassed a stretch of amino acid residues I348-Q370. Based on our discoveries and previous reports, a model has been proposed in which Oxa1-CTD interacts with ribosomes, accompanied by transient-to-stable transitions at the second contact site. These observations may enhance our understanding of the potential role of Oxa1-CTD in facilitating the assembly of oxidative phosphorylation complexes and provide insight into the structural characteristics of Oxa1-CTD.

References

Lupas A, Van Dyke M, Stock J . Predicting coiled coils from protein sequences. Science. 1991; 252(5009):1162-4. DOI: 10.1126/science.252.5009.1162. View

Zimmermann L, Stephens A, Nam S, Rau D, Kubler J, Lozajic M . A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core. J Mol Biol. 2017; 430(15):2237-2243. DOI: 10.1016/j.jmb.2017.12.007. View

Funes S, Hasona A, Bauerschmitt H, Grubbauer C, Kauff F, Collins R . Independent gene duplications of the YidC/Oxa/Alb3 family enabled a specialized cotranslational function. Proc Natl Acad Sci U S A. 2009; 106(16):6656-61. PMC: 2672490. DOI: 10.1073/pnas.0809951106. View

Keil M, Bareth B, Woellhaf M, Peleh V, Prestele M, Rehling P . Oxa1-ribosome complexes coordinate the assembly of cytochrome C oxidase in mitochondria. J Biol Chem. 2012; 287(41):34484-93. PMC: 3464553. DOI: 10.1074/jbc.M112.382630. View

Mirdita M, Schutze K, Moriwaki Y, Heo L, Ovchinnikov S, Steinegger M . ColabFold: making protein folding accessible to all. Nat Methods. 2022; 19(6):679-682. PMC: 9184281. DOI: 10.1038/s41592-022-01488-1. View

Jia L, Dienhart M, Schramp M, McCauley M, Hell K, Stuart R . Yeast Oxa1 interacts with mitochondrial ribosomes: the importance of the C-terminal region of Oxa1. EMBO J. 2003; 22(24):6438-47. PMC: 291819. DOI: 10.1093/emboj/cdg624. View

Kelly S, Price N . The use of circular dichroism in the investigation of protein structure and function. Curr Protein Pept Sci. 2002; 1(4):349-84. DOI: 10.2174/1389203003381315. View

Kruger V, Deckers M, Hildenbeutel M, van der Laan M, Hellmers M, Dreker C . The mitochondrial oxidase assembly protein1 (Oxa1) insertase forms a membrane pore in lipid bilayers. J Biol Chem. 2012; 287(40):33314-26. PMC: 3460435. DOI: 10.1074/jbc.M112.387563. View

Wang P, Dalbey R . Inserting membrane proteins: the YidC/Oxa1/Alb3 machinery in bacteria, mitochondria, and chloroplasts. Biochim Biophys Acta. 2010; 1808(3):866-75. DOI: 10.1016/j.bbamem.2010.08.014. View

10.

Baker J, Hudson R, Kanelis V, Choy W, Thibodeau P, Thomas P . CFTR regulatory region interacts with NBD1 predominantly via multiple transient helices. Nat Struct Mol Biol. 2007; 14(8):738-45. PMC: 3943242. DOI: 10.1038/nsmb1278. View

11.

Dahal S, Lewellen J, Chaudhary B, Mohanty S . H, C, and N resonance assignment and secondary structure of the pheromone-binding protein2 from the agricultural pest Ostrinia furnacalis (OfurPBP2). Biomol NMR Assign. 2020; 14(1):115-118. DOI: 10.1007/s12104-020-09930-1. View

12.

Eaglesfield R, Tokatlidis K . Targeting and Insertion of Membrane Proteins in Mitochondria. Front Cell Dev Biol. 2022; 9:803205. PMC: 8740019. DOI: 10.3389/fcell.2021.803205. View

13.

Bonnefoy N, Fiumera H, Dujardin G, Fox T . Roles of Oxa1-related inner-membrane translocases in assembly of respiratory chain complexes. Biochim Biophys Acta. 2008; 1793(1):60-70. PMC: 2658530. DOI: 10.1016/j.bbamcr.2008.05.004. View

14.

Maris C, Jayne S, Damberger F, Beusch I, Dorn G, Ravindranathan S . A transient α-helix in the N-terminal RNA recognition motif of polypyrimidine tract binding protein senses RNA secondary structure. Nucleic Acids Res. 2020; 48(8):4521-4537. PMC: 7192611. DOI: 10.1093/nar/gkaa155. View

15.

Wang L, Markley J . Empirical correlation between protein backbone 15N and 13C secondary chemical shifts and its application to nitrogen chemical shift re-referencing. J Biomol NMR. 2009; 44(2):95-9. PMC: 2782637. DOI: 10.1007/s10858-009-9324-0. View

16.

Sulo P, Szaboova D, Bielik P, Polakova S, Soltys K, Jatzova K . The evolutionary history of Saccharomyces species inferred from completed mitochondrial genomes and revision in the 'yeast mitochondrial genetic code'. DNA Res. 2017; 24(6):571-583. PMC: 5726470. DOI: 10.1093/dnares/dsx026. View

17.

Haque M, Spremulli L, Fecko C . Identification of protein-protein and protein-ribosome interacting regions of the C-terminal tail of human mitochondrial inner membrane protein Oxa1L. J Biol Chem. 2010; 285(45):34991-8. PMC: 2966113. DOI: 10.1074/jbc.M110.163808. View

18.

Itoh Y, Andrell J, Choi A, Richter U, Maiti P, Best R . Mechanism of membrane-tethered mitochondrial protein synthesis. Science. 2021; 371(6531):846-849. PMC: 7610362. DOI: 10.1126/science.abe0763. View

19.

Wishart D, Case D . Use of chemical shifts in macromolecular structure determination. Methods Enzymol. 2001; 338:3-34. DOI: 10.1016/s0076-6879(02)38214-4. View

20.

Kohler R, Boehringer D, Greber B, Bingel-Erlenmeyer R, Collinson I, Schaffitzel C . YidC and Oxa1 form dimeric insertion pores on the translating ribosome. Mol Cell. 2009; 34(3):344-53. DOI: 10.1016/j.molcel.2009.04.019. View