The Mitoribosome: Methods and Protocols

ISBN-13: 9781071631706 / Angielski / Twarda / 2023 / 305 str.

Antonio Barrientos; Flavia Fontanesi

Opis

This volume provides classic and new methods to study the structure, assembly pathway, and protein synthesis ability of mitoribosomes across species.  Following an introduction of fundamental concepts on the topic, method chapters present detailed protocols based on cryo-electron tomography, cryo-EM approaches, mitoribosome purification techniques, mitochondrial translation assays, and methods to study mitochondrial mRNAs that are translated on mitoribosomes. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and methods, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, The Mitoribosome: Methods and Protocols, aims to be a comprehensive guide for researchers in the field.

Spis treści

 

PART I GENERAL CONCEPTS

 

1. Discovery of Mitochondrial Ribosomes

Thomas W. O’Brien

2.  Evolution: Mitochondrial Ribosomes across Species

Rajendra K. Agrawal  and Soneya Majumdar

3. Mitoribosome Biogenesis

J. Conor Moran, Samuel Del’Olio, Austin Choi, Hui Zhong and Antoni Barrientos

4. Translation in Mitochondrial Ribosomes

Zofia M Chrzanowska-Lightowlers and Robert N Lightowlers

 

PART II METHODS TO STUDY MITORIBOSOME STRUCTURE, FUNCTION AND BIOGENESIS

 

5. Sample Preparation of Isolated Mitochondria for Cryoelectron Tomography and in situ Studies of Translation

Lena Thärichen, Robert Englmeier and Friedrich Förster

6. Cryo-EM for Structure Determination of Mitochondrial Ribosome Samples

Hauke S. Hillen

7. Sucrose Gradient Analysis of Human Mitochondrial Ribosomes and RNA

Kah Ying Ng and Brendan J. Battersby

8. Yeast Mitoribosome Purification and Analyses by Sucrose Density Centrifugation and Immunoprecipitation

Andreas Aufschnaiter, Andreas Carlström and Martin Ott

9. Rapid Cryo-Purification of the Yeast Mitochondrial Ribosome

Hong Weng Pang and Antoni Barrientos

10. Methods to Study the Biogenesis of Mitoribosomal Proteins in Yeast

Lea Bertgen, Tamara Flohr and Johannes M. Herrmann

11. Systematic Analysis of Assembly Intermediates in Yeast to Decipher the Mitoribosome Assembly Pathway

Samuel Del’Olio and Antoni Barrientos

12. Metabolic Labelling of Mitochondrial Translation Products in Whole Cells and Isolated Organelles

Priyanka Maiti and Flavia Fontanesi

13. Assembly of the Mitochondrial Translation Initiation Complex

Cristina Remes, Minh Duc Nguyen, Henrik Spahr, Martin Ng, Clark Fritsch_, Arpan Bhattacharya, Hong Li, Barry Cooperman, Joanna Rorbach

14. Reconstitution of Mammalian Mitochondrial Translation System Capable of Long Polypeptide Synthesis

Muhoon Lee and Nono Takeuchi-Tomita

15. Human Mitoribosome Profiling: a Re-engineered Approach Tailored to Study Mitochondrial Translation

Iliana Soto, Mary Couvillion and L. Stirling Churchman

16. The ARG8^m Reporter for the Study of Yeast Mitochondrial Translation

Daniel Flores-Mireles, Yolanda Camacho-Villasana and Xochitl Pérez-Martínez

17. Four Colour Super-Resolution RNA Fluorescent In Situ Hybridization and Immunocytochemistry to Visualise Mitochondrial mRNAs in Context with Mitochondrial Ribosomes

Christin A Albus, Rolando Berlinguer-Palmini, Zofia M Chrzanowska-Lightowlers and Robert N Lightowlers

18. Digital RNase Footprinting of RNA-protein Complexes and Ribosomes in Mitochondria

Danielle L. Rudler, Stefan J. Siira, Oliver Rackham and Aleksandra Filipovska

19. Dead-seq: Discovering Synthetic Lethal Interactions from Dead Cells Genomics

Joan Blanco-Fernández and Alexis A. Jourdain