Regulatory RNAs in Prokaryotes

Name: Regulatory RNAs in Prokaryotes
Brand: Springer
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Anita Marchfelder Wolfgang Hess(Herausgeber*in)

Springer (Verlag)

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Erschienen am 23. Dezember 2012

XIV, 258 Seiten

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Inhalt

Intro
Title Page
Copyright Page
Editorial Regulatory RNAs in Prokaryotes
References
Table of Contents
Chapter 1 Small RNAs with a Role in the Oxidative Stress Response of Bacteria
1 Introduction
2 OxyS and the Oxidative Stress Response in Enterobacteria
3 The Link Between Iron Levels and Oxidative Stress, and the Role of RyhB
3.1 How Iron Can Cause Oxidative Stress
3.2 Mechanisms of RyhB Regulation
3.3 RyhB Homologues in Other Bacteria
4 Photooxidative Stress-Induced sRNAs in Photosynthetic Alpha-Proteobacteria
5 Other sRNAs Involved in Oxidative Stress Responses
6 Concluding Remarks
References
Chapter 2 Hfq-associated Regulatory Small RNAs
1 Introduction
1.1 Trans-acting sRNAs and the Role for Hfq
2 Regulatory Mechanisms Employed by Hfq-associated sRNAs
2.1 Translational Control Near the SD Sequence and AUG Start Codon
2.2 Primary Role for sRNAs in Translational Silencing
2.3 Non-canonical Repression of Translation Initiation
2.4 Control of Protein Synthesis Through Regulation of mRNA Decay
2.5 Multiple Target Control by sRNAs
2.6 Small RNAs with Multiple Conserved Targeting Regions
2.7 Unusually Complex Mechanisms
2.8 5' Regions as a Conserved Mechanism for Targeting Multiple mRNAs
2.9 Maturation of Small RNAs
2.10 Potential Evolution of New sRNAs from 3' UTRs
3 Perspective
3.1 Overlap of sRNAs and Targets in Regulons
3.2 Titration of Hfq: Regulation or Side-effect?
3.3 Titration of Hfq: Implications for Horizontal Gene Transfer
3.4 Design of Synthetic sRNAs
4 Outlook
References
Chapter 3 A Current Overview of Regulatory RNAs in Staphylococcus Aureus
1 Introduction
2 Cis-acting Regulatory Elements in mRNAs
2.1 RNA Thermosensors
2.2 Riboswitches
2.3 Erythromycin-induced Translation Attenuation
2.4 tRNA-mediated Riboswitches
2.5 Protein-mediated Transcription Termination/Anti-termination
3 Small Non-coding RNAs Targeting mRNAs
3.1 Generalities
3.2 Pathogenicity Island-encoded sRNAs
3.3 sRNA Stress Response and Metabolism
3.4 sRNA and Small Colony Variant
3.5 S. aureus Transcriptome
4 RNAIII, a mRNA and a Regulatory RNA
4.1 Quorum Sensing and Virulence in S. aureus
4.2 RNAIII Encodes a Small Toxin
4.3 RNAIII as the Regulator
4.4 RNAIII and its Regulatory Network
5 CRISPR in Defense Mechanism
6 Perspectives
Acknowledgments
References
Chapter 4 Pseudomonas Aeruginosa Small Regulatory RNAs
1 Introduction
2 Bacterial Regulatory RNAs and their Mode of Action
3 P. aeruginosa Housekeeping RNAs
4 Protein Sequestering RNAs
4.1 RsmY/Z
4.2 CrcZ
5 Verified and Candidate P. Aeruginosa Base-pairing sRNAs
5.1 Prrf 1/2
5.2 RgsA
5.3 PhrS and PhrD
6 CRISPR
7 Uncharacterized P. Aeruginosa sRNAs
8 Conclusion
References
Chapter 5 Natural Antisense Transcripts in Bacteria
1 Defining Features of an Antisense Transcript
2 Antisense RNAs were Discovered in Bacteria
2.1 Known Facts About Antisense RNAs from Bacteriophages, Plasmids and Transposons
3 Antisense Transcripts Come in High Numbers and Occur Throughout the Bacterial Kingdom
4 Bacterial Antisense RNAs are Functionally Important
4.1 How Bacterial Antisense RNAs Exert their Function
5 Outlook
References
Chapter 6 6S RNA: A Regulator of Transcription
1 6S RNA - The Early Years
2 6S RNA Interactions with RNA Polymerase
2.1 6S RNA-RNA Polymerase: In Vivo Analysis
2.2 6S RNA-RNA Polymerase: In Vitro Analysis
2.3 6S RNA: A Mimic of Promoter DNA Near the Active Site
2.4 6S RNA: A Template for RNA Synthesis
2.5 The 6S RNA Upstream Region and s70 Region 4.2 Does Not Mimic Promoter DNA Interactions
3 6S RNA and Regulation of Transcription
3.1 Regulation of Transcription: In Vivo Analysis
3.2 Regulation of Transcription: In Vitro Approaches
3.3 6S RNA and Regulation of Transcription: Mechanism
3.4 6S RNA and sS-Dependent Transcription
4 Physiological Role of 6S RNA
4.1 6S RNA and Stationary Phase Cell Survival
4.2 6S RNA and Stress: Altered Survival at High pH
4.3 6S RNA Integration Into Global Pathways
5 Biogenesis of 6S RNA
6 6S RNAs in Diverse Bacterial Species
6.1 Identification
6.2 6S RNA Function in Other Species
7 Concluding Comments
References
Chapter 7 Archaea Employ Small RNAs as Regulators
1 Introduction
2 The Discovery of a New Type of Non-Coding RNA in Archaea: snoRNAs
3 Expanding the Family of Small Non-Coding RNAs in Archaea
4 Small RNAs in Halophilic Archaea
4.1 Prediction of sRNA Genes
4.2 Experimental Identification of Small RNAs
4.3 Expression of Small RNA Genes
4.4 Functional Analysis
4.5 The Haloferax Lsm Protein
5 Small RNAs in Methanogenic Archaea
5.1 Un-translated Regions of mRNAs
5.2 Small RNAs in M. mazei
6 Conclusion
References
Chapter 8 Structure, Function and RNA Binding Mechanisms of the Prokaryotic Sm-like Protein Hfq
1 Introduction
2 Prevalence of the Sm Fold
3 Biochemical and Genetic Analysis of Hfq
3.1 The RNA-binding Modes of Hfq
3.2 Hfq-mediated sRNA-mRNA Annealing
4 Hfq in RNA decay
5 The Role of the C-terminus of Hfq Proteins
6 Role of Hfq in Low GC Gram-positive Bacteria
6.1 Hfq in Cyanobacteria
6.2 Archaeal Hfq Protein
7 Concluding Remarks
Acknowledgements
References
Chapter 9 CRISPR/Cas and CRISPR/Cmr Immune Systems of Archaea
1 Introduction
2 Archaeal Viruses and Plasmids and Chromosomal Evolution
3 Diversity of Archaeal CRISPR/Cas and CRISPR/Cmr Immune Systems
4 Development and Stability of CRISPR Loci
5 Mobility of CRISPR/Cas and Cmr Modules
6 Targets of the CRISPR/Cas and CRISPR/Cmr Systems
7 Formation of crRNAs and Targeting of Foreign Elements
8 Anti CRISPR/Cas and CRISPR/Cmr Systems
9 Evolutionary Considerations
10 Conclusions
References
Chapter 10 Control of Bacterial Heat Shock and Virulence Genes by RNA Thermometers
1 RNA as Sensory Element
2 RNA Measures Temperature Directly
3 Control of Heat Shock Genes
4 Control of Virulence Genes
5 RNA-based Thermosensors That Do Not Act by Melting
6 Are There More RNA Thermometers?
References
Chapter 11 RNA Sensors of Intracellular Metabolites
1 Introduction. Gene Regulation in Bacteria: From Transcription Initiation to mRNA Degradation
2 Sensing of Metabolites by Cis-Acting Regulatory mRNAs
2.1 Riboswitch RNAs
2.2 Purine Riboswitch Gene Regulation Mechanisms
2.3 Therapeutic Applications Using Purine Riboswitches
3 Indirect Sensing of Metabolites by Cis-Acting Regulatory RNAs
3.1 Sensing of Amino Acids via tRNA Charging Ratios
3.2 Sensing of Amino Acids via tRNA Charging Ratios: Ribosome-Mediated Attenuation
3.3 Sensing of Amino Acids via tRNA Charging Ratios: Direct Sensing of Uncharged tRNAs
3.4 Sensing of Amino Acids via tRNA Charging Ratios: mRNA-Binding tRNA Synthetases
3.5 Sensing of Metabolites by RNA-Binding Proteins: Amino Acids
3.6 Sensing of Metabolites by RNA-Binding Proteins: Carbohydrates and Nucleotides
4 Concluding Remarks
References
Chapter 12 Bioinformatics of Bacterial sRNAs and Their Targets
1 Computational Detection of Bacterial sRNAs
1.1 Definition of RNA Families
1.2 Detection of Homologous Structural RNAs
1.3 ncRNA Gene Finders
2 Computational Target Prediction
2.1 Search for Complementary Regions
2.2 Duplex Evaluation
2.3 Concatenation Approaches
2.4 Accessibility-based Approaches
2.5 Full Joint Structure Prediction
References
Chapter 13 Computational Tools for Predicting sRNA Targets
1 Introduction
1.1 Training and Test Datasets
1.2 RNA Secondary Structure Profile
1.3 Machine-learning Methods
1.4 Construction of Prediction Models for sRNA Targets
2 Program and Usage
2.1 Predicting sRNA Targets Using sRNATarget Webserver
2.2 Predicting sRNA Targets Using Windows System
2.3 Predicting sRNA Targets Under Linux as the Operating System
3 Other Program Tools for Predicting sRNA Targets
3.1 IntaRNA
3.2 TargetRNA
4 An Example, Target Prediction for sRNA Yfr1
5 Future Thinking
Acknowledgements
References
Index

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