Regulating With Rna in Bacteria and Archaea

Revealing the many roles of RNA in regulating gene expression

For decades after the discoveries of messenger RNA, transfer RNA, and ribosomal RNA, it was largely assumed that the role of RNA in the cell was limited to shuttling the genomic message, chaperoning amino acids, and toiling in the ribosomes.

Eventually, hints that RNA molecules might have regulatory roles began to appear. With the advent of genomics and bioinformatics, it became evident that numerous other RNA forms exist and have specific functions, including small RNAs (sRNA), RNA thermometers, and riboswitches to regulate core metabolic pathways, bacterial pathogenesis, iron homeostasis, quorum sensing, and biofilm formation.

All of these functions, and more, are presented in Regulating with RNA in Bacteria and Archaea, written by RNA biologists from around the globe. Divided into eight sections-RNases and Helicases, Cis-Acting RNAs, Cis Encoded Base Pairing RNAs, Trans-Encoded Base Pairing RNAs, Protein Titration and Scaffolding, General Considerations, Emerging Topics, and Resources-this book serves as an excellent resource for established RNA biologists and for the many scientists who are studying regulated cellular systems.

It is no longer a fair assumption that gene expression regulation is the provenance of proteins only or that control is exerted primarily at the level of transcription. This book makes clear that regulatory RNAs are key partners along with proteins in controlling the complex interactions and pathways found within prokaryotes.

Gisela Storz is an NIH Distinguished Investigator in the Eunice Kennedy Shriver National Institute of Child Health and Human Development in Bethesda, Maryland. She carried out graduate work with Dr. Bruce Ames at the University of California, Berkeley and postdoctoral work with Dr. Sankar Adhya at the National Cancer Institute and Dr. Fred Ausubel at Harvard Medical School. As a result of the serendipitous discovery of the peroxide-induced OxyS RNA in E. coli, one of the first small, regulatory RNAs to be found, much of the work in her lab has focused on the genome-wide identification of small RNAs and their characterization.

Kai Papenfort is a Professor of Microbiology at the Ludwig Maximilians University of Munich, Germany. He received a diploma in biology from the University of Marburg and carried out graduate work with Dr. Jörg Vogel at the Max Planck Institute for Infection Biology and the Humboldt University of Berlin. In his postdoctoral work at the University of Würzburg and Princeton University, Dr. Papenfort studied the regulatory functions of small RNA in bacterial pathogens and their involvement in bacterial communication processes such as quorum sensing. His laboratory focuses on the molecular mechanisms underlying the regulation by small RNAs in the major human pathogen, Vibrio cholerae.

Contributors

Foreword

Preface

Acknowledgments

About the Editors

Section I: RNases and Helicases

1. RNase E and the High-Fidelity Orchestration of RNA Metabolism
Katarzyna J. Bandyra and Ben F. Luisi

2. Enzymes Involved in Posttranscriptional RNA Metabolism in Gram-Negative Bacteria
Bijoy K. Mohanty and Sidney R. Kushner

3. RNases and Helicases in Gram-Positive Bacteria
Sylvain Durand and Ciarán Condon

Section II: Cis-acting RNAs

4. RNA Thermometers in Bacterial Pathogens
Edmund Loh, Francesco Righetti, Hannes Eichner, Christian Twittenhoff, Franz Narberhaus

5. Small Molecule-Binding Riboswitches
Thea S. Lotz and Beatrix Suess

6. The T-Box Riboswitch: tRNA as an Effector to Modulate Gene Regulation
Kiel D. Kreuzer and Tina M. Henkin

7. rRNA Mimicry in RNA Regulation of Gene Expression
Michelle M. Meyer

8. Processive Antitermination
Jonathan R. Goodson and Wade C. Winkler

9. Genes within genes in bacterial genomes
Sezen Meydan, Nora Vázquez-Laslop, and Alexander S. Mankin

10. Leaderless mRNAs in the Spotlight: Ancient but Not Outdated!
Heather J. Beck and Isabella Moll

Section III: Cis-encoded base pairing RNAs

11. Type I Toxin-Antitoxin Systems: Regulating Toxin Expression via Shine-Dalgarno Sequence Sequestration and Small RNA Binding
Sara Masachis and Fabien Darfeuille

12. Widespread Antisense Transcription in Prokaryotes
Jens Georg and Wolfgang R. Hess

Section IV: Trans-encoded base pairing RNAs

13. Small Regulatory RNAs in the Enterobacterial Response to Envelope Damage and Oxidative Stress
Kathrin S. Fröhlich and Susan Gottesman

14. Carbohydrate Utilization in Bacteria: Making the Most Out of Sugars with the Help of Small Regulatory RNAs
Svetlana Durica-Mitic, Yvonne Göpel, Boris Görke

15. Small RNAs Involved in Regulation of Nitrogen Metabolism
Daniela Prasse and Ruth A. Schmitz

16. Bacterial Iron Homeostasis Regulation by sRNAs
Sylvia Chareyre and Pierre Mandin

17. Small-RNA-Based Regulation of Bacterial Quorum Sensing and Biofilm Formation
Sine Lo Svenningsen

18. Regulatory RNAs in Virulence and Host-Microbe Interactions
Alexander J. Westermann

Section V: Protein titration and scaffolding

19. Global Regulation by CsrA and Its sRNA Antagonists
Tony Romeo and Paul Babitzke

20. 6S RNA, a Global Regulator of Transcription
Karen M. Wassarman

21. Bacterial Y RNAs: Gates, Tethers, and tRNA Mimics
Soyeong Sim and Sandra L. Wolin

Section VI: General considerations

22. Proteins That Chaperone RNA Regulation
Sarah A. Woodson, Subrata Panja, and Andrew Santiago-Frangos

23. Epitranscriptomics: RNA Modifications in Bacteria and Archaea
Katharina Höfer and Andres Jäschke

24. RNA Localization in Bacteria
Jingyi Fei and Cynthia M. Sharma

25. Sponges and Predators in the Small RNA World
Nara Figueroa‐Bossi and Lionello Bossi

26. Bacterial Small RNAs in Mixed Regulatory Networks
Anaïs Brosse and Maude Guillier

27. Dual-Function RNAs
Medha Raina, Alisa King, Colleen Bianco, and Carin K. Vanderpool

28. Origin, Evolution, and Loss of Bacterial Small RNAs
H. Auguste Dutcher and Rahul Raghavan

Section VII: Emerging topics

29. Cross-regulation between bacteria and phages at a posttranscriptional Level
Shoshy Altuvia, Gisela Storz, Kai Papenfort

30. Large Noncoding RNAs in Bacteria
Kimberly A. Harris and Ronald R. Breaker

31. Synthetic Biology of Small RNAs and Riboswitches
Jordan K. Villa, Yichi Su, Lydia M. Contreras, Ming C. Hammond

Section VIII: Resources

32. Functional Transcriptomics for Bacterial Gene Detectives
Blanca Perez-Sepulveda and Jay C.D. Hinton

33. Structure and Interaction Prediction in Prokaryotic RNA Biology
Patrick R. Wright, Martin Mann, Rolf Backofen

Index

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