RNA turnover in prokaryotes, archaea and organelles:
Gespeichert in:
| Format: | Buch |
|---|---|
| Sprache: | English |
| Veröffentlicht: |
Amsterdam [u.a.]
Elsevier, AP
2008
|
| Schriftenreihe: | Methods in enzymology
447 |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | Auf dem Buchdeckel: RNA turnover in prokaryotes, archae and organelles |
| Beschreibung: | L, 564 S., [3] BL. Ill., graph. Darst. |
| ISBN: | 9780123743770 |
Internformat
MARC
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| 020 | |a 9780123743770 |9 978-0-12-374377-0 | ||
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| 245 | 1 | 0 | |a RNA turnover in prokaryotes, archaea and organelles |c ed. by Lynne E. Maquat ; Cecilia M. Arraiano |
| 246 | 1 | 3 | |a RNA turnover in prokaryotes, archae and organelles |
| 264 | 1 | |a Amsterdam [u.a.] |b Elsevier, AP |c 2008 | |
| 300 | |a L, 564 S., [3] BL. |b Ill., graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 490 | 1 | |a Methods in enzymology |v 447 | |
| 500 | |a Auf dem Buchdeckel: RNA turnover in prokaryotes, archae and organelles | ||
| 650 | 7 | |a Cell organelles |2 blmsh | |
| 650 | 7 | |a Genetic regulation |2 blmsh | |
| 650 | 7 | |a Messenger RNA |2 blmsh | |
| 650 | 7 | |a Prokaryotes |2 blmsh | |
| 650 | 7 | |a RNA-protein interactions |2 blmsh | |
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| 650 | 0 | 7 | |a Prokaryoten |0 (DE-588)4201051-2 |2 gnd |9 rswk-swf |
| 655 | 7 | |0 (DE-588)4143413-4 |a Aufsatzsammlung |2 gnd-content | |
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| 700 | 1 | |a Maquat, Lynne E. |e Sonstige |4 oth | |
| 700 | 1 | |a Arraiano, Cecilia M. |e Sonstige |4 oth | |
| 830 | 0 | |a Methods in enzymology |v 447 |w (DE-604)BV000000938 |9 447 | |
| 856 | 4 | 2 | |m Digitalisierung UB Regensburg |q application/pdf |u http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016738188&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |3 Inhaltsverzeichnis |
| 999 | |a oai:aleph.bib-bvb.de:BVB01-016738188 | ||
Datensatz im Suchindex
| _version_ | 1804138017523236864 |
|---|---|
| adam_text | Contents
Contributors
xv
Preface
xxiii
Volumes in Series
χχν
Section I. Bacteria
1
1.
Analysis of
RNA
Decay, Processing, and Polyadenylation in
Escherichia
coli
and Other Prokaryotes
3
Bijoy K. Mohanty, Hili Giladi, Valerie F. Maples, and Sidney R. Kushner
1.
Introduction
4
2.
General Considerations When Working with
RNA
5
3.
Isolation of Total
RNA
from Exponentially Growing Cells
7
4.
Isolation of Total
RNA
from Stationary Phase Cells
10
5.
Removal of
DNA
Contamination
11
6.
RNA
Yield and Purity Assessment
12
7.
RNA
Integrity Assessment
12
8.
Isolation of Polyadenylated
RNA
13
9.
Northern Analysis
14
10.
Analysis of
RNA
Polyadenylation in
E. coli
20
11.
Reverse Transcription PCR (RT-PCR) to Analyze
З
-ends
of Specific Transcripts
23
12.
Conclusion
28
Acknowledgments
28
References
28
2.
Analyzing the Decay of Stable RNAs in
E. coli
31
Zhongwei Li and Murray P.
Deutscher
1.
Introduction
32
2.
Preparation of Stable
RNA
Substrates for In Vitro
Degradation Assays
35
3.
Detection of Degradation Products In Vitro
37
4.
Examination of Stable
RNA
Decay In Vivo
38
5.
Determination of the
3 -
and S -Termini of Intermediates during the
Processing and Degradation of Stable RNAs
39
vi
Contents
6.
Detection of PolyCA) Tails on Products Generated by Processing or
Degradation of Stable
RNA
43
7.
Concluding Remarks
43
Acknowledgments
44
References
44
3.
Genomic Analysis of
m
RNA
Decay in
£
coli
with
DNA Microarrays 47
Pei-Hsun Lin, Dharam Singh, Jonathan A. Bernstein, and Sue Lin-Chao
1.
Introduction
48
2.
Experimental Strategy for mRNA Half-Life Analysis
49
3.
Methods
51
4.
Data Acquisition and Analysis
58
Acknowledgments
62
References
62
4.
Co-immunopurification of Multiprotein Complexes
Containing RNA-Degrading Enzymes
65
Agamemnon
).
Carpousis, Vanessa Khemici, Soraya
Aït-Bara,
and Leonora
Poljak
1.
Introduction
66
2.
General Considerations
68
3.
Materials
71
4.
Protocols
72
5.
Perspective
76
Acknowledgments
79
References
80
5.
PABLO Analysis of
RNA: ^-Phosphorylation
State and
5 -End Mapping
83
Helena Celesnik,
Afilio
Deana, and Joel G. Belasco
1.
Introduction
84
2.
Concept
84
3.
Detection Method
86
4.
Efficiency of Ligation
87
5.
Determining the S -Phosphorylation State of Long Transcripts
87
6.
Ascertaining Whether the Decay of a Transcript
Begins with
Pyrophosphate
Removal
89
7.
PABLO Protocols
91
8.
Alternative Method for Examining the Phosphorylation State of
RNA
94
9.
The Use of PABLO to Map the 5 -End of
RNA
95
Acknowledgments
97
References
97
Contents
vii
6.
A Proteomic Approach to the Analysis of
RNA Degradosome
Composition in Escherkhia
coli
99
Pierluigi Mauri and Gianni
Dehò
1.
Introduction
100
2.
Experimental Procedures
105
3.
Perspective and Conclusion
113
Acknowledgments
115
References
115
7.
New Approaches to Understanding Double-Stranded
RNA
Processing by Ribonuclease III: Purification and Assays of
Homodimeric and Heterodimeric Forms of RNase III from
Bacterial Extremophiles and Mesophiles
119
Wenzhao
Meng,
Rhonda H. Nicholson, Lilian Nathania,
Alexandre
V. Pertzev, and Allen W. Nicholson
1.
Introduction
120
2.
Heterologous Expression, Affinity Purification, and
Assays of Aquifex aeolicus and Thermotoga
marítima RNases
III
122
3.
Production and Purification of Escherkhia
coli
RNase III Heterodimers
126
References
128
8.
Characterizing Ribonucleases In Vitro: Examples of
Synergies between Biochemical and Structural Analysis
131
Cecília
Maria Arraiano,
Ana Barbas,
and
Monica
Amblar
1.
Introduction
132
2.
RNase
II D209N
Mutant
133
3.
Construction of RNase II Derivatives
134
4.
Overexpression and Purification of RNase II
and Its Derivatives
134
5.
Analysis of Ribonucleolytic Activity
137
6.
Studying the RNA-Binding Abilities
147
7.
Structural Studies of RNase II
156
Acknowledgments
157
References
158
9.
The Role of
RNA Chaperone
Hfq in Poly(A) Metabolism:
Methods to Determine Positions, Abundance, and Lengths of
Short Oligo(A) Tails
161
Philippe Régnier
and Eliane Hajnsdorf
1.
Introduction
162
2.
Global Analysis of Polyadenylated Transcripts
163
v¡¡¡
Contents
3.
RT-PCR-Based Analysis of
З
-RNA
Ends
164
4.
Effect of Hfq on Polyadenylation of the rpsO Transcript
170
5.
A Method to Analyze Polyadenylation of Primary Transcripts
174
6.
Hfq Stimulates PolytA) Synthesis
177
7.
Conclusion
177
Acknowledgment
179
References
179
10.
Assaying DEAD-box
RNA Helicases
and Their Role in
m
RNA
Degradation in
Escherich
ia
coli
183
Agamemnon J. Carpousis, Vanessa Khemici, and Leonora
Poljak
1.
Introduction
184
2.
The RNA-Dependent ATPase Activity of RhIB
185
3.
The ATPase-Dependent
RNA Helicase
Activity of RhIB
187
4.
The RhlB-PNPase mRNA Degradation Pathway
188
5.
Discussion and Perspective
192
6.
Methods
193
Acknowledgments
196
References
196
11.
Preparation of the Escherichia
coli
RNase
E
Protein and
Reconstitution
of the
RNA Degradosome
199
George A. Mackie, Glen A. Cobum, Xin
Miao,
Douglas J.
Briant,
Annie
Prud homme-Généreux,
Leigh M. Stickney, and Janet S. Hankins
1.
introduction
200
2.
Preparation of Crude RNase
E
201
3.
Purification of RNase
E
204
4.
Reconstitution
of the
RNA
Degradosome
207
Acknowledgments
211
References
211
12.
Identifying and Characterizing Substrates of the RNase
E/G Family of Enzymes
215
Louise
Kime,
Stefanie
S.
Jourdan,
and Kenneth J. McDowall
1.
Introduction to
£
coll RNase
E
and its Homologs
216
2.
Identification of Potential In Vivo Substrates of RNase
E
219
3.
Identification of Sites of Endonucleolytic Cleavage
223
4.
Reconstitution
of Cleavages In Vitro
228
5.
Summary
235
Acknowledgments
236
References
236
Contents
¡χ
13.
Construction and Characterization of
E. coli K12
Strains in
Which the Transcription of Selected Genes Is Desynchronized
from Translation
243
Florence Proux and Marc Dreyfus
1.
Introduction
244
2.
Desynchronizing the Transcription and Translation of the
lacZ
Gene in E. co//K1
2
246
3.
Specific Protocols
252
4.
Conclusion
255
Acknowledgments
256
References
256
14.
Analysis of mRNA Decay in Bacillus
subtìlìs
259
David H. Bechhofer,
Irina
A. Oussenko, Gintaras Deikus, Shiyi Yao,
Nathalie Mathy, and
Ciarán
Condon
1.
Introduction
260
2.
Growth Media for Isolation of
RNA
263
3.
Inhibition of
ß.
subtilis Transcription
263
4.
RNA
Isolation Protocol
1 264
5.
RNA
Isolation Protocol
2 265
6.
RNA
Isolation Protocol
3 266
7.
Gel Electrophoresis and Blotting
267
8.
Labeled Size Marker for Small RNAs
267
9.
Northern-Blot Analysis Using Oligonucleotide Probes
268
10.
Northern-Blot Analysis Using Riboprobes
269
11. Quantitäten
of
RNA
by 5S
RNA
Probing
269
12.
Mapping of
5 -
and
З
-Ends
269
13.
Sequencing-Gel Northern Blotting
271
14.
Ribonuclease Mutant Strains
271
References
275
15.
Assay of Bacillus subtilis Ribonudeases In Vitro
277
Ciarán
Condon, Olivier Pellegrini, Nathalie Mathy, Lionel
Benard,
Yulia Redko,
Irina
A. Oussenko, Gintaras Deikus, and David H. Bechhofer
1.
Introduction
278
2.
Purification and Assay of B. subtilis Endoribonucleases
278
3.
Purification and Assay of B. subtilis Exoribonudeases
296
4.
Conclusion
303
Acknowledgments
303
Appendices
303
References
306
Contents
16. Staphylococcus aureus Endoribonuclease
III:
Purification and Properties
309
Clement Chevalier, Eric Huntzinger, Pierre
Fechter,
Sandrine Boisset,
François Vandenesch, Pascale
Romby,
and Thomas
Geissmann
1.
Introduction
310
2.
S.
aureus RNase
1)1
Is Not Essential for Cell Growth but
Regulates Virulence Gene Expression
312
3.
Biochemical Properties and Substrate Specificity of
S. aureus RNase III
314
4.
RNase III Overexpression and Purification
317
5.
RNA
Substrate Preparation
319
6.
End-labeling of
RNA
320
7.
Mapping the RNase III Cleavage Sites In Vitro
320
8.
Denaturing
Agarose Gel
Electrophoresis and Northern Blotting
322
9.
Concluding Remarks
323
Acknowledgments
324
References
324
17.
Studying tmRNA-Mediated Surveillance and
Nonstop
m
RNA
Decay
329
Thomas Sundermeier, Zhiyun Ge, Jamie Richards, Daniel Dulebohn,
and
A. Wali Karzai
1.
Introduction
330
2.
Methodology
334
3.
Activity Assays
341
Acknowledgments
356
References
356
18.
Analyses of mRNA Destabilization and Translational Inhibition
Mediated by Hfq-Binding Small RNAs
359
Teppei Morita, Kimika
Maki, Mieko
Yagi, and Hiroji Aiba
1.
Overview
360
2.
The ptsG mRNA Is Destabilized in Response to
Glucose Phosphate Stress
362
3.
Requirement of
C-Terminal
Scaffold Region of
RNase E, Hfq, and SgrS
З65
4.
Identification of Ribonudeoprotein Complex Containing SgrS,
Hfq, and RNase
E
36g
5.
Translational Repression is the Primary Event for
Silencing of ptsG mRNA by SgrS/Hfq/RNase
Е З68
Contents
x¡
6.
Base-Pairing Near Translation Initiation Region Is
Crucial for SgrS Action
370
7.
Base Pairing between SgrS and ptsG mRNA In Vitro and
Acceleration of Duplex Formation by Hfq
372
8.
Membrane Localization of ptsG mRNA Is
Required for SgrS Action
374
9.
Conclusions
375
Acknowledgments
376
References
376
Section II. Archaea
379
19.
In Vivo and In Vitro Studies of
RNA
Degrading
Activities in Archaea
381
Elena
Evguenieva-Hackenberg, Steffen
Wagner, and
Gabriele Klug
1.
Introduction
383
2.
In Vivo Studies on
RNA
Degrading Activities in Archaea
384
3.
In Vitro Studies on Novel
RNA
Degrading Activities in Archaea
388
4.
Isolation and Characterization of a Protein Complex with Predicted
Ribonuctease Activity from Sulfolobus solfataricus:
The Archaeal Exosome
401
Acknowledgments
413
References
413
20.
Expression,
Reconstitution,
and Structure of an Archaeal
RNA
Degrading Exosome
417
Esben Lorentzen and Elena
Conti
1.
Introduction
418
2.
Cloning, Expression, Purification, and
Reconstitution
of an Archaeal Exosome
420
3.
Archaeal Exosome Structure
425
4.
RNA
Binding Sites in the Archaeal Exosome
428
Acknowledgments
433
References
433
Section III.
Organelies
437
21.
Polyadenylation-Mediated
RNA
Degradation
in Plant Mitochondria
439
Sarah
Holec,
Heike Lange,
André
Dietrich,
and Dominique
Gagliardi
1.
Introduction
440
2.
Identification of Polyadenylated Substrates Destined for
RNA
Degradation
441
xi¡
Contents
3.
Tools to Investigate the Process of Polyadenylation-Mediated
RNA
Degradation
452
Acknowledgments
459
References
459
22.
In Vivo and In Vitro Approaches for Studying the
Yeast Mitochondrial
RNA Degradosome
Complex
463
Michal Malecki,
Robert
Jedrzejczak, Olga Puenta,
Piotr
P.
Stępień,
and
Pawel Golik
1.
Introduction
464
2.
Genetics of the S. cerevisiae Mitochondrial Degradosome
466
3.
RNA
Metabolism in the Mitochondria of
Degradosome-Deficient Strains
469
4.
Expression and Purification of the Yeast Mitochondrial
Degradosome Subunits in
E. coli
472
5.
Assaying the Ribonuclease Activity of the Degradosome and
the Dssl Protein
475
6.
Assaying the ATP Hydrolysis Activity of the Degradosome and the
Suv3 Protein
480
7.
Assaying the
Helicase
Activity of the Degradosome and the
Suv3 Protein
481
8.
Protein-RNA Binding Assay
484
9.
Concluding Remarks
485
Acknowledgments
486
References
486
23.
Measuring mRNA Decay in Human Mitochondria
489
Asuteka Nagao, Narumi Hino-Shigi, and Tsutomu Suzuki
1.
Introduction
490
2.
Quantitative RT-PCR Method for Measuring mRNA Decay
491
3.
Primer Design
491
4.
EtBr Treatment
493
5.
Cell Cultivation and
RNA
Extraction
493
6.
RT-PCR
494
7.
Half-Lives of Mitochondrial mRNAs
494
8.
Polyadenylation Stabilizes Mitochondrial mRNAs
494
9.
Discussion
496
Acknowledgments
498
References
498
Contents xiii
24.
Detection and Characterization of Polyadenylated
RNA
in
Eukarya, Bacteria, Archaea, and
Organelies
501
Shimyn Slomovic, Victoria Portnoy, and
Gadi
Schuster
1.
Introduction
502
2.
OligoCdT) RT-PCR Detection of Polyadenylated
Degradation Intermediates
504
3.
Circularized Reverse Transcription (cRTO-PCR-Sequencing/
Labeling Method for the Characterization of Polyadenylated
RNA
509
4.
cRT-PCR for the Detection of Truncated Polyadenylated
RNA
Degradation Intermediates
516
References
519
25.
RNA
Decay by Messenger
RNA Interferases
521
Mikkel
Christensen-Dalsgaard, Martin Overgaard,
Kristoffer
Skovbo Winther, and
Kenn Gerdes
1.
Introduction
522
2.
In Vitro Analysis of RelE mRNA
interferase
523
3.
In Vivo Analysis of mRNA
interferase
527
References
534
Author Index
537
Subject Index
555
|
| adam_txt |
Contents
Contributors
xv
Preface
xxiii
Volumes in Series
χχν
Section I. Bacteria
1
1.
Analysis of
RNA
Decay, Processing, and Polyadenylation in
Escherichia
coli
and Other Prokaryotes
3
Bijoy K. Mohanty, Hili Giladi, Valerie F. Maples, and Sidney R. Kushner
1.
Introduction
4
2.
General Considerations When Working with
RNA
5
3.
Isolation of Total
RNA
from Exponentially Growing Cells
7
4.
Isolation of Total
RNA
from Stationary Phase Cells
10
5.
Removal of
DNA
Contamination
11
6.
RNA
Yield and Purity Assessment
12
7.
RNA
Integrity Assessment
12
8.
Isolation of Polyadenylated
RNA
13
9.
Northern Analysis
14
10.
Analysis of
RNA
Polyadenylation in
E. coli
20
11.
Reverse Transcription PCR (RT-PCR) to Analyze
З'
-ends
of Specific Transcripts
23
12.
Conclusion
28
Acknowledgments
28
References
28
2.
Analyzing the Decay of Stable RNAs in
E. coli
31
Zhongwei Li and Murray P.
Deutscher
1.
Introduction
32
2.
Preparation of Stable
RNA
Substrates for In Vitro
Degradation Assays
35
3.
Detection of Degradation Products In Vitro
37
4.
Examination of Stable
RNA
Decay In Vivo
38
5.
Determination of the
3'-
and S'-Termini of Intermediates during the
Processing and Degradation of Stable RNAs
39
vi
Contents
6.
Detection of PolyCA) Tails on Products Generated by Processing or
Degradation of Stable
RNA
43
7.
Concluding Remarks
43
Acknowledgments
44
References
44
3.
Genomic Analysis of
m
RNA
Decay in
£
coli
with
DNA Microarrays 47
Pei-Hsun Lin, Dharam Singh, Jonathan A. Bernstein, and Sue Lin-Chao
1.
Introduction
48
2.
Experimental Strategy for mRNA Half-Life Analysis
49
3.
Methods
51
4.
Data Acquisition and Analysis
58
Acknowledgments
62
References
62
4.
Co-immunopurification of Multiprotein Complexes
Containing RNA-Degrading Enzymes
65
Agamemnon
).
Carpousis, Vanessa Khemici, Soraya
Aït-Bara,
and Leonora
Poljak
1.
Introduction
66
2.
General Considerations
68
3.
Materials
71
4.
Protocols
72
5.
Perspective
76
Acknowledgments
79
References
80
5.
PABLO Analysis of
RNA: ^-Phosphorylation
State and
5'-End Mapping
83
Helena Celesnik,
Afilio
Deana, and Joel G. Belasco
1.
Introduction
84
2.
Concept
84
3.
Detection Method
86
4.
Efficiency of Ligation
87
5.
Determining the S'-Phosphorylation State of Long Transcripts
87
6.
Ascertaining Whether the Decay of a Transcript
Begins with
Pyrophosphate
Removal
89
7.
PABLO Protocols
91
8.
Alternative Method for Examining the Phosphorylation State of
RNA
94
9.
The Use of PABLO to Map the 5'-End of
RNA
95
Acknowledgments
97
References
97
Contents
vii
6.
A Proteomic Approach to the Analysis of
RNA Degradosome
Composition in Escherkhia
coli
99
Pierluigi Mauri and Gianni
Dehò
1.
Introduction
100
2.
Experimental Procedures
105
3.
Perspective and Conclusion
113
Acknowledgments
115
References
115
7.
New Approaches to Understanding Double-Stranded
RNA
Processing by Ribonuclease III: Purification and Assays of
Homodimeric and Heterodimeric Forms of RNase III from
Bacterial Extremophiles and Mesophiles
119
Wenzhao
Meng,
Rhonda H. Nicholson, Lilian Nathania,
Alexandre
V. Pertzev, and Allen W. Nicholson
1.
Introduction
120
2.
Heterologous Expression, Affinity Purification, and
Assays of Aquifex aeolicus and Thermotoga
marítima RNases
III
122
3.
Production and Purification of Escherkhia
coli
RNase III Heterodimers
126
References
128
8.
Characterizing Ribonucleases In Vitro: Examples of
Synergies between Biochemical and Structural Analysis
131
Cecília
Maria Arraiano,
Ana Barbas,
and
Monica
Amblar
1.
Introduction
132
2.
RNase
II D209N
Mutant
133
3.
Construction of RNase II Derivatives
134
4.
Overexpression and Purification of RNase II
and Its Derivatives
134
5.
Analysis of Ribonucleolytic Activity
137
6.
Studying the RNA-Binding Abilities
147
7.
Structural Studies of RNase II
156
Acknowledgments
157
References
158
9.
The Role of
RNA Chaperone
Hfq in Poly(A) Metabolism:
Methods to Determine Positions, Abundance, and Lengths of
Short Oligo(A) Tails
161
Philippe Régnier
and Eliane Hajnsdorf
1.
Introduction
162
2.
Global Analysis of Polyadenylated Transcripts
163
v¡¡¡
Contents
3.
RT-PCR-Based Analysis of
З'
-RNA
Ends
164
4.
Effect of Hfq on Polyadenylation of the rpsO Transcript
170
5.
A Method to Analyze Polyadenylation of Primary Transcripts
174
6.
Hfq Stimulates PolytA) Synthesis
177
7.
Conclusion
177
Acknowledgment
179
References
179
10.
Assaying DEAD-box
RNA Helicases
and Their Role in
m
RNA
Degradation in
Escherich
ia
coli
183
Agamemnon J. Carpousis, Vanessa Khemici, and Leonora
Poljak
1.
Introduction
184
2.
The RNA-Dependent ATPase Activity of RhIB
185
3.
The ATPase-Dependent
RNA Helicase
Activity of RhIB
187
4.
The RhlB-PNPase mRNA Degradation Pathway
188
5.
Discussion and Perspective
192
6.
Methods
193
Acknowledgments
196
References
196
11.
Preparation of the Escherichia
coli
RNase
E
Protein and
Reconstitution
of the
RNA Degradosome
199
George A. Mackie, Glen A. Cobum, Xin
Miao,
Douglas J.
Briant,
Annie
Prud'homme-Généreux,
Leigh M. Stickney, and Janet S. Hankins
1.
introduction
200
2.
Preparation of Crude RNase
E
201
3.
Purification of RNase
E
204
4.
Reconstitution
of the
RNA
Degradosome
207
Acknowledgments
211
References
211
12.
Identifying and Characterizing Substrates of the RNase
E/G Family of Enzymes
215
Louise
Kime,
Stefanie
S.
Jourdan,
and Kenneth J. McDowall
1.
Introduction to
£
coll RNase
E
and its Homologs
216
2.
Identification of Potential In Vivo Substrates of RNase
E
219
3.
Identification of Sites of Endonucleolytic Cleavage
223
4.
Reconstitution
of Cleavages In Vitro
228
5.
Summary
235
Acknowledgments
236
References
236
Contents
¡χ
13.
Construction and Characterization of
E. coli K12
Strains in
Which the Transcription of Selected Genes Is Desynchronized
from Translation
243
Florence Proux and Marc Dreyfus
1.
Introduction
244
2.
Desynchronizing the Transcription and Translation of the
lacZ
Gene in E. co//K1
2
246
3.
Specific Protocols
252
4.
Conclusion
255
Acknowledgments
256
References
256
14.
Analysis of mRNA Decay in Bacillus
subtìlìs
259
David H. Bechhofer,
Irina
A. Oussenko, Gintaras Deikus, Shiyi Yao,
Nathalie Mathy, and
Ciarán
Condon
1.
Introduction
260
2.
Growth Media for Isolation of
RNA
263
3.
Inhibition of
ß.
subtilis Transcription
263
4.
RNA
Isolation Protocol
1 264
5.
RNA
Isolation Protocol
2 265
6.
RNA
Isolation Protocol
3 266
7.
Gel Electrophoresis and Blotting
267
8.
Labeled Size Marker for Small RNAs
267
9.
Northern-Blot Analysis Using Oligonucleotide Probes
268
10.
Northern-Blot Analysis Using Riboprobes
269
11. Quantitäten
of
RNA
by 5S
RNA
Probing
269
12.
Mapping of
5'-
and
З'
-Ends
269
13.
Sequencing-Gel Northern Blotting
271
14.
Ribonuclease Mutant Strains
271
References
275
15.
Assay of Bacillus subtilis Ribonudeases In Vitro
277
Ciarán
Condon, Olivier Pellegrini, Nathalie Mathy, Lionel
Benard,
Yulia Redko,
Irina
A. Oussenko, Gintaras Deikus, and David H. Bechhofer
1.
Introduction
278
2.
Purification and Assay of B. subtilis Endoribonucleases
278
3.
Purification and Assay of B. subtilis Exoribonudeases
296
4.
Conclusion
303
Acknowledgments
303
Appendices
303
References
306
Contents
16. Staphylococcus aureus Endoribonuclease
III:
Purification and Properties
309
Clement Chevalier, Eric Huntzinger, Pierre
Fechter,
Sandrine Boisset,
François Vandenesch, Pascale
Romby,
and Thomas
Geissmann
1.
Introduction
310
2.
S.
aureus RNase
1)1
Is Not Essential for Cell Growth but
Regulates Virulence Gene Expression
312
3.
Biochemical Properties and Substrate Specificity of
S. aureus RNase III
314
4.
RNase III Overexpression and Purification
317
5.
RNA
Substrate Preparation
319
6.
End-labeling of
RNA
320
7.
Mapping the RNase III Cleavage Sites In Vitro
320
8.
Denaturing
Agarose Gel
Electrophoresis and Northern Blotting
322
9.
Concluding Remarks
323
Acknowledgments
324
References
324
17.
Studying tmRNA-Mediated Surveillance and
Nonstop
m
RNA
Decay
329
Thomas Sundermeier, Zhiyun Ge, Jamie Richards, Daniel Dulebohn,
and
A. Wali Karzai
1.
Introduction
330
2.
Methodology
334
3.
Activity Assays
341
Acknowledgments
356
References
356
18.
Analyses of mRNA Destabilization and Translational Inhibition
Mediated by Hfq-Binding Small RNAs
359
Teppei Morita, Kimika
Maki, Mieko
Yagi, and Hiroji Aiba
1.
Overview
360
2.
The ptsG mRNA Is Destabilized in Response to
Glucose Phosphate Stress
362
3.
Requirement of
C-Terminal
Scaffold Region of
RNase E, Hfq, and SgrS
З65
4.
Identification of Ribonudeoprotein Complex Containing SgrS,
Hfq, and RNase
E
36g
5.
Translational Repression is the Primary Event for
Silencing of ptsG mRNA by SgrS/Hfq/RNase
Е З68
Contents
x¡
6.
Base-Pairing Near Translation Initiation Region Is
Crucial for SgrS Action
370
7.
Base Pairing between SgrS and ptsG mRNA In Vitro and
Acceleration of Duplex Formation by Hfq
372
8.
Membrane Localization of ptsG mRNA Is
Required for SgrS Action
374
9.
Conclusions
375
Acknowledgments
376
References
376
Section II. Archaea
379
19.
In Vivo and In Vitro Studies of
RNA
Degrading
Activities in Archaea
381
Elena
Evguenieva-Hackenberg, Steffen
Wagner, and
Gabriele Klug
1.
Introduction
383
2.
In Vivo Studies on
RNA
Degrading Activities in Archaea
384
3.
In Vitro Studies on Novel
RNA
Degrading Activities in Archaea
388
4.
Isolation and Characterization of a Protein Complex with Predicted
Ribonuctease Activity from Sulfolobus solfataricus:
The Archaeal Exosome
401
Acknowledgments
413
References
413
20.
Expression,
Reconstitution,
and Structure of an Archaeal
RNA
Degrading Exosome
417
Esben Lorentzen and Elena
Conti
1.
Introduction
418
2.
Cloning, Expression, Purification, and
Reconstitution
of an Archaeal Exosome
420
3.
Archaeal Exosome Structure
425
4.
RNA
Binding Sites in the Archaeal Exosome
428
Acknowledgments
433
References
433
Section III.
Organelies
437
21.
Polyadenylation-Mediated
RNA
Degradation
in Plant Mitochondria
439
Sarah
Holec,
Heike Lange,
André
Dietrich,
and Dominique
Gagliardi
1.
Introduction
440
2.
Identification of Polyadenylated Substrates Destined for
RNA
Degradation
441
xi¡
Contents
3.
Tools to Investigate the Process of Polyadenylation-Mediated
RNA
Degradation
452
Acknowledgments
459
References
459
22.
In Vivo and In Vitro Approaches for Studying the
Yeast Mitochondrial
RNA Degradosome
Complex
463
Michal Malecki,
Robert
Jedrzejczak, Olga Puenta,
Piotr
P.
Stępień,
and
Pawel Golik
1.
Introduction
464
2.
Genetics of the S. cerevisiae Mitochondrial Degradosome
466
3.
RNA
Metabolism in the Mitochondria of
Degradosome-Deficient Strains
469
4.
Expression and Purification of the Yeast Mitochondrial
Degradosome Subunits in
E. coli
472
5.
Assaying the Ribonuclease Activity of the Degradosome and
the Dssl Protein
475
6.
Assaying the ATP Hydrolysis Activity of the Degradosome and the
Suv3 Protein
480
7.
Assaying the
Helicase
Activity of the Degradosome and the
Suv3 Protein
481
8.
Protein-RNA Binding Assay
484
9.
Concluding Remarks
485
Acknowledgments
486
References
486
23.
Measuring mRNA Decay in Human Mitochondria
489
Asuteka Nagao, Narumi Hino-Shigi, and Tsutomu Suzuki
1.
Introduction
490
2.
Quantitative RT-PCR Method for Measuring mRNA Decay
491
3.
Primer Design
491
4.
EtBr Treatment
493
5.
Cell Cultivation and
RNA
Extraction
493
6.
RT-PCR
494
7.
Half-Lives of Mitochondrial mRNAs
494
8.
Polyadenylation Stabilizes Mitochondrial mRNAs
494
9.
Discussion
496
Acknowledgments
498
References
498
Contents xiii
24.
Detection and Characterization of Polyadenylated
RNA
in
Eukarya, Bacteria, Archaea, and
Organelies
501
Shimyn Slomovic, Victoria Portnoy, and
Gadi
Schuster
1.
Introduction
502
2.
OligoCdT) RT-PCR Detection of Polyadenylated
Degradation Intermediates
504
3.
Circularized Reverse Transcription (cRTO-PCR-Sequencing/
Labeling Method for the Characterization of Polyadenylated
RNA
509
4.
cRT-PCR for the Detection of Truncated Polyadenylated
RNA
Degradation Intermediates
516
References
519
25.
RNA
Decay by Messenger
RNA Interferases
521
Mikkel
Christensen-Dalsgaard, Martin Overgaard,
Kristoffer
Skovbo Winther, and
Kenn Gerdes
1.
Introduction
522
2.
In Vitro Analysis of RelE mRNA
interferase
523
3.
In Vivo Analysis of mRNA
interferase
527
References
534
Author Index
537
Subject Index
555 |
| any_adam_object | 1 |
| any_adam_object_boolean | 1 |
| building | Verbundindex |
| bvnumber | BV035069793 |
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| dewey-ones | 572 - Biochemistry |
| dewey-raw | 572.88 |
| dewey-search | 572.88 |
| dewey-sort | 3572.88 |
| dewey-tens | 570 - Biology |
| discipline | Biologie |
| discipline_str_mv | Biologie |
| format | Book |
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| genre_facet | Aufsatzsammlung |
| id | DE-604.BV035069793 |
| illustrated | Illustrated |
| index_date | 2024-07-02T22:03:46Z |
| indexdate | 2024-07-09T21:21:30Z |
| institution | BVB |
| isbn | 9780123743770 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-016738188 |
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| physical | L, 564 S., [3] BL. Ill., graph. Darst. |
| publishDate | 2008 |
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| publisher | Elsevier, AP |
| record_format | marc |
| series | Methods in enzymology |
| series2 | Methods in enzymology |
| spelling | RNA turnover in prokaryotes, archaea and organelles ed. by Lynne E. Maquat ; Cecilia M. Arraiano RNA turnover in prokaryotes, archae and organelles Amsterdam [u.a.] Elsevier, AP 2008 L, 564 S., [3] BL. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Methods in enzymology 447 Auf dem Buchdeckel: RNA turnover in prokaryotes, archae and organelles Cell organelles blmsh Genetic regulation blmsh Messenger RNA blmsh Prokaryotes blmsh RNA-protein interactions blmsh Archaebakterien (DE-588)4002825-2 gnd rswk-swf RNS (DE-588)4076759-0 gnd rswk-swf Katabolismus (DE-588)4234092-5 gnd rswk-swf Prokaryoten (DE-588)4201051-2 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Prokaryoten (DE-588)4201051-2 s RNS (DE-588)4076759-0 s Katabolismus (DE-588)4234092-5 s DE-604 Archaebakterien (DE-588)4002825-2 s b DE-604 Maquat, Lynne E. Sonstige oth Arraiano, Cecilia M. Sonstige oth Methods in enzymology 447 (DE-604)BV000000938 447 Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016738188&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | RNA turnover in prokaryotes, archaea and organelles Methods in enzymology Cell organelles blmsh Genetic regulation blmsh Messenger RNA blmsh Prokaryotes blmsh RNA-protein interactions blmsh Archaebakterien (DE-588)4002825-2 gnd RNS (DE-588)4076759-0 gnd Katabolismus (DE-588)4234092-5 gnd Prokaryoten (DE-588)4201051-2 gnd |
| subject_GND | (DE-588)4002825-2 (DE-588)4076759-0 (DE-588)4234092-5 (DE-588)4201051-2 (DE-588)4143413-4 |
| title | RNA turnover in prokaryotes, archaea and organelles |
| title_alt | RNA turnover in prokaryotes, archae and organelles |
| title_auth | RNA turnover in prokaryotes, archaea and organelles |
| title_exact_search | RNA turnover in prokaryotes, archaea and organelles |
| title_exact_search_txtP | RNA turnover in prokaryotes, archaea and organelles |
| title_full | RNA turnover in prokaryotes, archaea and organelles ed. by Lynne E. Maquat ; Cecilia M. Arraiano |
| title_fullStr | RNA turnover in prokaryotes, archaea and organelles ed. by Lynne E. Maquat ; Cecilia M. Arraiano |
| title_full_unstemmed | RNA turnover in prokaryotes, archaea and organelles ed. by Lynne E. Maquat ; Cecilia M. Arraiano |
| title_short | RNA turnover in prokaryotes, archaea and organelles |
| title_sort | rna turnover in prokaryotes archaea and organelles |
| topic | Cell organelles blmsh Genetic regulation blmsh Messenger RNA blmsh Prokaryotes blmsh RNA-protein interactions blmsh Archaebakterien (DE-588)4002825-2 gnd RNS (DE-588)4076759-0 gnd Katabolismus (DE-588)4234092-5 gnd Prokaryoten (DE-588)4201051-2 gnd |
| topic_facet | Cell organelles Genetic regulation Messenger RNA Prokaryotes RNA-protein interactions Archaebakterien RNS Katabolismus Prokaryoten Aufsatzsammlung |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016738188&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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