Regulatory RNAs in prokaryotes:
Gespeichert in:
| Hauptverfasser: | , |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Wien [u.a.]
Springer
2011
|
| Schlagworte: | |
| Online-Zugang: | Inhaltstext Inhaltsverzeichnis |
| Beschreibung: | Literaturangaben |
| Beschreibung: | XIV, 258 S. Ill., graph. Darst. 242 mm x 170 mm |
| ISBN: | 9783709102176 |
Internformat
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Datensatz im Suchindex
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Titel: Regulatory RNAs in prokaryotes
Autor: Hess, Wolfgang René
Jahr: 2011
Contents
RNAs in Prokaryotes . v
References . vii
1 Small RNAs with a Role in the Oxidative
Stress Response of Bacteria. 1
1 Introduction . 1
2 OxyS and the Oxidative Stress Response in Enterobacteria . 3
3 The Link Between Iron Levels and Oxidative Stress, and the Role
of RyhB . 5
3.1 How Iron Can Cause Oxidative Stress . 5
3.2 Mechanisms of RyhB Regulation . 6
3.3 RyhB Homologues in Other Bacteria . 8
4 Photooxidative Stress-Induced sRNAs in Photosynthetic Alpha-
Proteobacteria . 9
5 Other sRNAs Involved in Oxidative Stress Responses . 10
6 Concluding Remarks . 11
References . 12
2 Hfq-associated Regulatory Small RNAs . 15
1 Introduction . 15
1.1 7hms-acting sRNAs and the Role for Hfq . 16
2 Regulatory Mechanisms Employed by Hfq-associated sRNAs . 17
2.1 Translational Control Near the SD Sequence and AUG
Start Codon . 17
2.2 Primary Role for sRNAs in Translational Silencing . 17
2.3 Non-canonical Repression of Translation Initiation . 20
2.4 Control of Protein Synthesis Through Regulation
of mRNA Decay . 21
2.5 Multiple Target Control by sRNAs . 22
2.6 Small RNAs with Multiple Conserved Targeting Regions . 33
2.7 Unusually Complex Mechanisms . 35
2.8 5' Regions as a Conserved Mechanism for Targeting
Multiple mRNAs . 36
2.9 Maturation of Small RNAs . 38
2.10 Potential Evolution of New sRNAs from 3' UTRs . 39
3 Perspective. 39
3.1 Overlap of sRNAs and Targets in Regulons . 39
ix
Contents
3.2 Titration of Hfq: Regulation or Side-effect? . 40
3.3 Titration of Hfq: Implications for Horizontal Gene
Transfer . 41
3.4 Design of Synthetic sRNAs . 42
4 Outlook . 42
References . 43
A Current Overview of Regulatory RNAs in Staphylococcus Aureus . 51
1 Introduction . 51
2 Cis-acting Regulatory Elements in mRNAs . 52
2.1 RNA Thermosensors . 53
2.2 Riboswitches . 53
2.3 Erythromycin-induced Translation Attenuation . 56
2.4 tRNA-mediated Riboswitches . 56
2.5 Protein-mediated Transcription Termination/Anti-
termination. 58
3 Small Non-coding RNAs Targeting mRNAs . 58
3.1 Generalities . 58
3.2 Pathogenicity Island-encoded sRNAs . 60
3.3 sRNA Stress Response and Metabolism . 61
3.4 sRNA and Small Colony Variant. 62
3.5 S. aureus Transcriptome . 63
4 RNAIII, a mRNA and a Regulatory RNA . 63
4.1 Quorum Sensing and Virulence in S. aureus . 63
4.2 RNAIII Encodes a Small Toxin . 64
4.3 RNAIII as the Regulator . 65
4.4 RNAIII and its Regulatory Network . 67
5 CRISPR in Defense Mechanism . 67
6 Perspectives . 69
References . 70
Pseudomonas Aeruginosa Small Regulatory RNAs . 77
1 Introduction . 77
2 Bacterial Regulatory RNAs and their Mode of Action . 79
3 P. aeruginosa Housekeeping RNAs . 81
4 Protein Sequestering RNAs . 82
4.1 RsmY/Z . 82
4.2 CrcZ . 85
5 Verified and Candidate P. Aeruginosa Base-pairing sRNAs . 85
5.1 Prrf 1/2 . 85
5.2 RgsA . 88
5.3 PhrS and PhrD . 88
6 CRISPR . 89
7 Uncharacterized P. Aeruginosa sRNAs . 89
8 Conclusion . 90
References . 90
Contents
Natural Antisense Transcripts in Bacteria. 95
1 Defining Features of an Antisense Transcript . 95
2 Antisense RNAs were Discovered in Bacteria . 97
2.1 Known Facts About Antisense RNAs from
Bacteriophages, Plasmids and Transposons . 97
3 Antisense Transcripts Come in High Numbers
and Occur Throughout the Bacterial Kingdom . 98
4 Bacterial Antisense RNAs are Functionally Important . 100
4.1 How Bacterial Antisense RNAs Exert their Function . 101
5 Outlook . 104
References . 104
6S RNA: A Regulator of Transcription . 109
1 6S RNA- The Early Years . 109
2 6S RNA Interactions with RNA Polymerase. 110
2.1 6S RNA-RNA Polymerase: In Vivo Analysis . 110
2.2 6S RNA-RNA Polymerase: In Vitro Analysis . 110
2.3 6S RNA: A Mimic of Promoter DNA Near the Active Site 112
2.4 6S RNA: A Template for RNA Synthesis . 113
2.5 The 6S RNA Upstream Region and a70 Region 4.2 Does
Not Mimic Promoter DNA Interactions . 114
3 6S RNA and Regulation of Transcription . 116
3.1 Regulation of Transcription: In Vivo Analysis. 116
3.2 Regulation of Transcription: In Vitro Approaches . 117
3.3 6S RNA and Regulation of Transcription: Mechanism . 118
3.4 6S RNA and os-Dependent Transcription . 119
4 Physiological Role of 6S RNA . 120
4.1 6S RNA and Stationary Phase Cell Survival . 120
4.2 6S RNA and Stress: Altered Survival at High pH . 120
4.3 6S RNA Integration Into Global Pathways . 121
5 Biogenesis of 6S RNA. 122
6 6S RNAs in Diverse Bacterial Species . 123
6.1 Identification . 123
6.2 6S RNA Function in Other Species . 124
7 Concluding Comments . 125
References . 126
Archaea Employ Small RNAs as Regulators. 131
1 Introduction . 131
2 The Discovery of a New Type of Non-Coding RNA in Archaea:
snoRNAs . 133
3 Expanding the Family of Small Non-Coding RNAs in Archaea . 134
4 Small RNAs in Halophilic Archaea. 134
4.1 Prediction of sRNA Genes. 136
4.2 Experimental Identification of Small RNAs . 137
4.3 Expression of Small RNA Genes . 137
xii Contents
4.4 Functional Analysis . 138
4.5 The Haloferax Lsm Protein . 138
5 Small RNAs in Methanogenic Archaea . 139
5.1 Un-translated Regions of mRNAs. 140
5.2 Small RNAs in M. mazei . 140
6 Conclusion . 142
References . 143
8 Structure, Function and RNA Binding Mechanisms of the
Prokaryotic Sm-like Protein Hfq . 147
1 Introduction . 147
2 Prevalence of the Sm Fold. 148
3 Biochemical and Genetic Analysis of Hfq . 148
3.1 The RNA-binding Modes of Hfq . 150
3.2 Hfq-mediated sRNA-mRNA Annealing . 150
4 Hfq in RNA decay . 151
5 The Role of the C-terminus of Hfq Proteins . 153
6 Role of Hfq in Low GC Gram-positive Bacteria. 154
6.1 Hfq in Cyanobacteria . 155
6.2 Archaeal Hfq Protein . 156
7 Concluding Remarks . 157
References . 158
9 CRISPR/Cas and CRISPR/Cmr Immune Systems of Archaea . 163
1 Introduction . 163
2 Archaeal Viruses and Plasmids and Chromosomal Evolution . 165
3 Diversity of Archaeal CRISPR/Cas and CRISPR/Cmr Immune
Systems . 167
4 Development and Stability of CRISPR Loci . 170
5 Mobility of CRISPR/Cas and Cmr Modules . 172
6 Targets of the CRISPR/Cas and CRISPR/Cmr Systems . 172
7 Formation of crRNAs and Targeting of Foreign Elements . 174
8 Anti CRISPR/Cas and CRISPR/Cmr Systems . 175
9 Evolutionary Considerations . 177
10 Conclusions . 178
References . 179
10 Control of Bacterial Heat Shock and Virulence Genes by RNA
Thermometers . 183
1 RNAas Sensory Element . 183
2 RNA Measures Temperature Directly . 185
3 Control of Heat Shock Genes . 185
4 Control of Virulence Genes . 189
5 RNA-based Thermosensors That Do Not Act by Melting . 189
6 Are There More RNA Thermometers? . 190
References . 191
Contents xiii
11 RNA Sensors of Intracellular Metabolites . 195
1 Introduction. Gene Regulation in Bacteria: From Transcription
Initiation to mRNA Degradation . 195
2 Sensing of Metabolites by Cis-Acting Regulatory mRNAs . 200
2.1 Riboswitch RNAs . 200
2.2 Purine Riboswitch Gene Regulation Mechanisms . 201
2.3 Therapeutic Applications Using Purine Riboswitches . 203
3 Indirect Sensing of Metabolites by Cis-Acting Regulatory RNAs . 205
3.1 Sensing of Amino Acids via tRNA Charging Ratios . 205
3.2 Sensing of Amino Acids via tRNA Charging Ratios:
Ribosome-Mediated Attenuation . 208
3.3 Sensing of Amino Acids via tRNA Charging Ratios:
Direct Sensing of Uncharged tRNAs. 209
3.4 Sensing of Amino Acids via tRNA Charging Ratios:
mRNA-Binding tRNA Synthetases . 211
3.5 Sensing of Metabolites by RNA-Binding Proteins:
Amino Acids . 212
3.6 Sensing of Metabolites by RNA-Binding Proteins:
Carbohydrates and Nucleotides . 213
4 Concluding Remarks . 214
References . 215
12 Bioinformatics of Bacterial sRNAs and Their Targets . 221
1 Computational Detection of Bacterial sRNAs . 221
1.1 Definition of RNA Families. 221
1.2 Detection of Homologous Structural RNAs . 222
1.3 ncRNA Gene Finders . 226
2 Computational Target Prediction . 227
2.1 Search for Complementary Regions . 227
2.2 Duplex Evaluation . 228
2.3 Concatenation Approaches . 230
2.4 Accessibility-based Approaches . 231
2.5 Full Joint Structure Prediction . 233
References . 235
13 Computational Tools for Predicting sRNA Targets . 241
1 Introduction . 241
1.1 Training and Test Datasets. 242
1.2 RNA Secondary Structure Profile . 242
1.3 Machine-learning Methods . 243
1.4 Construction of Prediction Models for sRN A Targets. 244
2 Program and Usage . 245
2.1 Predicting sRNA Targets Using sRNATarget Webserver . 245
2.2 Predicting sRNA Targets Using Windows System . 246
2.3 Predicting sRNA Targets Under Linux as the Operating
System . 250
xiv Contents
3 Other Program Tools for Predicting sRNA Targets . 250
3.1 IntaRNA. 250
3.2 TargetRNA. 251
4 An Example, Target Prediction for sRNA Yfrl . 251
5 Future Thinking . 252
References . 253
Index. 255 |
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| spelling | Hess, Wolfgang René Verfasser aut Regulatory RNAs in prokaryotes Wolfgang R. Hess, Anita Marchfelder Wien [u.a.] Springer 2011 XIV, 258 S. Ill., graph. Darst. 242 mm x 170 mm txt rdacontent n rdamedia nc rdacarrier Literaturangaben Genregulation (DE-588)4122166-7 gnd rswk-swf Prokaryoten (DE-588)4201051-2 gnd rswk-swf Stoffwechselphysiologie (DE-588)4183413-6 gnd rswk-swf RNS (DE-588)4076759-0 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Prokaryoten (DE-588)4201051-2 s RNS (DE-588)4076759-0 s Genregulation (DE-588)4122166-7 s Stoffwechselphysiologie (DE-588)4183413-6 s b DE-604 Marchfelder, Anita Verfasser aut text/html http://deposit.dnb.de/cgi-bin/dokserv?id=3452677&prov=M&dok_var=1&dok_ext=htm Inhaltstext HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=024420738&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Hess, Wolfgang René Marchfelder, Anita Regulatory RNAs in prokaryotes Genregulation (DE-588)4122166-7 gnd Prokaryoten (DE-588)4201051-2 gnd Stoffwechselphysiologie (DE-588)4183413-6 gnd RNS (DE-588)4076759-0 gnd |
| subject_GND | (DE-588)4122166-7 (DE-588)4201051-2 (DE-588)4183413-6 (DE-588)4076759-0 (DE-588)4143413-4 |
| title | Regulatory RNAs in prokaryotes |
| title_auth | Regulatory RNAs in prokaryotes |
| title_exact_search | Regulatory RNAs in prokaryotes |
| title_full | Regulatory RNAs in prokaryotes Wolfgang R. Hess, Anita Marchfelder |
| title_fullStr | Regulatory RNAs in prokaryotes Wolfgang R. Hess, Anita Marchfelder |
| title_full_unstemmed | Regulatory RNAs in prokaryotes Wolfgang R. Hess, Anita Marchfelder |
| title_short | Regulatory RNAs in prokaryotes |
| title_sort | regulatory rnas in prokaryotes |
| topic | Genregulation (DE-588)4122166-7 gnd Prokaryoten (DE-588)4201051-2 gnd Stoffwechselphysiologie (DE-588)4183413-6 gnd RNS (DE-588)4076759-0 gnd |
| topic_facet | Genregulation Prokaryoten Stoffwechselphysiologie RNS Aufsatzsammlung |
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