Archaea: Methods and Protocols

ISBN-13: 9781071624449 / Angielski / Twarda / 2022

Ferreira-Cerca, Sébastien

Opis

This volume provides an overview of well-established methods optimized for diverse archaeal model organisms and is a source of protocols facilitating access to the molecular and cellular biology characterization of these fascinating organisms. Chapters are divided into five parts detailing available genetic tools, molecular and cellular biology methods, strategies to study the ecophysiology of archaea, and classroom protocol. Each main thematic part is also introduced by future-oriented and authoritative primers. 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 reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols.Authoritative and cutting-edge, Archaea: Methods and Protocols aims to be a foundation for future studies and to be a source of inspiration for new investigations in the field.

Spis treści

 

1. Archaea: a goldmine for molecular biologists and evolutionists

Patrick Forterre

 

Part I: Genetic manipulation of Archaea

2. Progress and challenges in archaeal genetic manipulation

Catherine Harrison and Thorsten Allers

 

3. Genetic manipulation of Haloferax species

Ambika Dattani, Catherine Harrison, and Thorsten Allers

 

4. CRISPR interference as a tool to Repress Gene Expression in Haloferax volcanii

Thandi S. Schwarz, Sandra S. Schreiber, and Anita Marchfelder

 

5. Transformation Techniques for the Anaerobic Hyperthermophile Thermococcus kodakarensis

Geraldy L. S. Liman, Meghan E. Stettler and Thomas J. Santangelo

 

6. Genetic Methods and Construction of Chromosomal Mutations in Methanogenic Archaea

Johanna Thomsen, Katrin Weidenbach, William W. Metcalf and Ruth A. Schmitz

 

7. An interdomain conjugation protocol for plasmid-DNA transfer into Methanothermobacter thermautotrophicus ΔH

Christian Fink, Largus T. Angenen, and Bastian Molitor

 

8. Methods for Markerless Gene Deletion and Plasmid-Based Expression in Sulfolobus acidocaldarius

Xing Ye, Alejandra Recalde, Sonja-Verena Albers and Marleen van Wolferen

 

9. A Rapid Targeted Gene Inactivation Approach in Sulfolobus islandicus

Changyi Zhang, Serina M. Taluja, Emily N. Hallett, and Rachel J. Whitaker

 

10. Transposon Insertion Mutagenesis in hyperthermophilic crenarchaeon Sulfolobus islandicus

Changyi Zhang and Rachel J. Whitaker

 

11. Reprogramming CRISPR-mediated RNA interference for silencing of essential genes in Sulfolobales

Erika Wimmer, Isabelle Anna Zink and Christa Schleper

 

Part II: Molecular Biology of Archaea

12. Progress and challenges in archaeal molecular biology

Finn Werner

 

13. ChIP-seq Occupancy Mapping of the Archaeal Transcription Machinery

Fabian Blombach, Kathy L. Smollett, and Finn Werner

 

14. Conversion of ribosome-protected mRNA to DNA and deep sequencing for ribosome profiling in Haloferax volcanii

 Diego Rivera Gelsinger, Emma Dallon, and Jocelyne DiRuggiero

 

15. Small RNA-sequencing library preparation for the halophilic archaeon Haloferax volcanii

Diego Rivera Gelsinger and Jocelyne DiRuggiero

16. Quantitative Mass Spectrometry by SILAC in Haloferax volcanii – Ricardo L. Couto-Rodriguez, Daniel Gal, Lana J. McMillan, Jin Koh, Sixue Chen, and Julie A. Maupin-Furlow

 

17. Proteome turnover analysis in Haloferax volcanii by a heavy isotope multilabelling approach

Roberto A. Paggi, Stefan P. Albaum, Ansgar Poetsch, and Micaela Cerletti

 

18. Proteomic sample preparation and data analysis in line with the Archaeal Proteome

Stefan Schulze and Mechthild Pohlschroder.

 

19. In vivo protein crosslinking and co-immunoprecipitation in Haloferax volcanii

Roberto A. Paggi, Rosana E. De Castro and Micaela Cerletti

 

20. Proteolytic activity assays in haloarchaea

Roberto Alejandro Paggi, María Inés. Giménez, and Rosana Esther De Castro

 

21. Carotenoids from Haloarchaea: Extraction, fractionation and characterization

María Sandra Churio, Micaela Cerletti, and Rosana Esther De Castro

 

22. Metal nanoparticles biosynthesis using the halophilic archaeon Haloferax volcanii Mariana Inés Costa and María Inés Giménez

 

23. Simplified enzymatic synthesis of 2-keto-3-deoxy-D-gluconate from D-gluconate using the gluconate dehydratase from Thermoproteus tenax

Svenja Höfmann, Promise Aku Dziwornu, Thomas Klaus, Thomas Knura, Roland Wohlgemuth, Christopher Bräsen, and Bettina Siebers

 

PART III: Cellular Biology of Archaea

24. Progress and Challenges in Archaeal Cellular Biology Analysis

Marleen van Wolferen and Sonja-Verena Albers

 

25. Methods to Analyze Motility in Eury- And Crenarchaea

Megha Patro, Marleen van Wolferen, Xing Ye, Sonja-Verena Albers, and Tessa E.F. Quax

 

26. Immersed Liquid Biofilm and Honeycomb Pattern Formations in Haloferax volcanii

 Zuha Mutan, Heather Schiller, Stefan Schulze, and Mechthild Pohlschroder

 

27. Cost-effective and Versatile Analysis of Archaeal Surface Adhesion Under Shaking and Standing Conditions

 Stefan Schulze, Heather Schiller, Zuha Mutan, Jordan Solomonic, Orkan Telhan, and Mechthild Pohlschroder

 

28. Cell Adhesion and Biofilm Formation Analysis

Débora Nercessian and Juan Pablo Busalmen

 

29. BrdU incorporation and labelling of nascent DNA to Investigate Archaeal Replication using super-resolution imaging

Roxane Lestini, Yoann Collien, Debora Olivier, Nicolas Olivier, and Hannu Myllykallio

 

30. Isolation, Purification, and Characterization of Membrane Vesicles from Haloarchaea

Joshua Mills and Susanne Erdmann

 

31. Archaeal Viruses: Production of Virus Particles and Vesicle-Like Viruses and Purification Using Asymmetrical Flow Field-Flow Fractionation

 Katri Eskelin and Hanna M. Oksanen

 

Part IV: Environmental Biology

32. Progress and Challenges in Studying the Ecophysiology of Archaea

Panagiotis S. Adam, Till L. V. Bornemann, and Alexander J. Probst

 

33. Reconstruction of Archaeal Genomes Assembly from Short-Read Metagenomes

Till L. V. Bornemann, Panagiotis S. Adam, and Alexander J. Probst

 

Part V: Outreach protocol

34. Outreach: Accessible and Insightful Scientific Learning Experiences Using the Microorganism Haloferax volcanii

 Heather Schiller, Criston Young, Stefan Schulze, and Mechthild Pohlschroder