Molecular Biology of RNA

Preface

I RNA as an Enzyme


1 Cleavage of RNA by RNAse P from Escherichia coli

I. Introduction

II. Aspects of the RNase P Reaction

III. Studies of Enzyme-Substrate Interactions

IV. Structure-Function Relationships in Ml RNA

V. Studies of the Protein Subunit of RNase P

VI. Hybrid Enzymes

VII. Conclusion

References


2 Bacillus Subtilis RNase

I. The RNase P Components

II. Mechanism of RNase P Cleavage

III. Toward the Higher-Order Structure of RNase P RNA

IV. Structure-Function Relationships in the RNase P RNA

V. Why Is the Catalytic Element of RNase P Composed of RNA?

References


3 Multiple Enzymatic Activities of an Intervening Sequence RNA from Tetrahymena

I. Introduction

II. Self-Splicing RNA

III. The IVS RNA Enzyme

References


4 Processing and Genetic Characterization of Self-Splicing RNAs of Bacteriophage

I. Introduction

II. Group I Splicing Mechanism for T4 td RN

III. Nondirected Mutagenesis and Delineation of Two Functional Domains for Splicing in the td Intron

IV. Multiple Self-Splicing Introns in T4

V. Conclusions

References

II RNA Splicing


5 The Mammalian Pre-Messenger RNA Splicing Apparatus: A Ribosome in Pieces?

I. Introduction

II. The Discovery of snRNPs

III. The snRNPs-and-Splicing Hypothesis

IV. snRNP Components and Structure

V. Is Eukaryotic RNase P an Sm snRNP?

VI. U1 snRNPs Bind 5' Splice Sites

VII. U2, U5, and U4/U6 snRNPs Also Participate in Splicing

VIII. The Spliceosome-Ribosome Analogy

References


6 Exon Sequences and Splice Site Proximity Play a Role in Splice Site Selection

I. Introduction

II. Exon Sequences and Splice Site Proximity Play a Role in Splice Site Selection

III. The Pattern of Splice Site Selection Is Altered in Different Extract Preparations and in Diluted Extracts

IV. Splice Site Selection Can Be Altered by Competition in Trans

V. Discussion

References


7 Factors That Influence Alternative Splice Site Selection in Vitro

I. Introduction

II. Materials and Methods

III. Results

IV. Discussion

References


8 Messenger RNA Splicing in Yeast

I. An Overview of Nuclear mRNA Splicing

II. Preliminary in Vitro and in Vivo Characterization of Yeast mRNA Splicing

III. Characterization of Mutations in the Splicing Process

IV. The RNA Gene Products and the Spliceosome

V. Speculations

References


9 Architecture of Fungal Introns: Implications for Spliceosome Assembly

I. Introduction

II. Branch Site-3' Splice Junction Relationship

III. Branch Site-5' Splice Junction Relationship

IV. Perspectives

References


10 RNA Joining and Trypanosome Gene Expression

I. Introduction

II. Materials and Methods

III. Results

IV. Discussion

V. Summary

References

III RNA Viruses


11 The Polio virus Genome: A Unique RNA in Structure, Gene Organization, and Replication

I. Introduction

II. Translation and Processing of the Polyprotein

III. RNA Replication

IV. Conclusions

References


12 Permanent Expression of Influenza Virus Genes Coding for Transcriptase Complexes: Complementation of Viral Mutants

I. Establishment of a Functional Expression System

II. Addition of Nuclear Protein to the Transcription Complex

III. Conclusions and Outlook

References


13 Molecular Mechanisms of Pathogenesis

Text

References

IV RNA in DNA Replication


14 Changes in RNA Secondary Structure May Mediate the Regulation of IncFII Plasmid Gene Expression and DNA Replication

I. Introduction

II. RNA Secondary Structure Predictions

III. Discussion

References


15 Regulation of Co IE 1 DNA Replication by Antisense RNA

I. Introduction

II. RNA Primer Formation

III. Regulation of Primer Formation

IV. Binding of RNA I to RNA II

V. Importance of the Rate of Binding of RNA I to RNA II

VI. Secondary Structure of RNA II and Its Alteration by Binding of RNA I

VII. Conclusions

References


16 A Transfer RNA Implicated in DNA Replication

I. Introduction

II. Expression of the DNA Y Gene

III. Implication in DNA Replication

IV. Summary and Models for Replication Role

References

V RNA: Structure, Function, and Isolation


17 Stable Branched RNA Covalently Linked to the 5' End of a Single-Stranded DNA of Myxobacteria

I. Introduction

II. DNA Structure of Stigmatella aurantiaca msDNA

III. RNA Sequence of RNA-Linked msDNA

IV. Determination of the Linkage between RNA and msDNA

V. Gene Arrangement of the Coding Regions for msDNA (msd) and msdRNA (msr) on the Chromosome

VI. Biosynthesis of Branched RNA-Linked msDNA

VII. How Is Branched RNA-Linked msDNA Synthesized?

References


18 Recognition of RNA by Proteins

I. A Simple RNA-Protein Interaction

II. A Complex RNA-Protein Interaction

References


19 A New Role for Transfer RNA: A Chloroplast Transfer RNA Is a Cofactor in the Conversion of Glutamate to Delta-Aminolevulinic Acid

I. Introduction

II. RNA DALA Is a Unique Glutamine-Accepting tRNA

III. RNA as a Cofactor: Possible Reaction Mechanism

IV. Outlook

References


20 Natural Suppressor Transfer RNA in Eukaryotes: Its Implication in the Evolution of the Genetic Code and Expression of Specific Genes

I. Introduction

II. Isolation from Tetrahymena of the tRNA Gene and tRNA Corresponding to the Termination Codon UAA

III. Deviation of the Genetic Code of Tetrahymena from the Universal Genetic Code

IV. Evolution of Glutamine tRNAs Recognizing UAA and UAG Termination Codons in Tetrahymena

V. Isolation of a Natural UAG Suppressor Glutamine tRNA from Mouse Cells

VI. A Large Increase of tRNAg[;UG in Mouse Cells Infected with Mo-MuLV

VII. Concluding Remarks

References


21 The Purification of Small RNAs by High-Performance Liquid Chromatography

I. Introduction

II. Materials and Methods

III. Results

IV. Discussion

References


22 Comparative Studies on the Secondary Structure of the RNAs of Related RNA Coliphages

I. Introduction

II. Results

III. Discussion

References

VI RNA in Regulation and Repression


23 Autogenous Regulation of Transcription of the crp Operon by a Divergent RNA Transcript

I. Introduction

II. Activation of a Divergent Promoter by Cyclic AMP-CRP is Required for crp Autoregulation

III. Autoregulation of crp Is Mediated by Divergent RNA

IV. A Model for crp Autoregulation

V. Conclusion

References


24 The Role of Translational Regulation in Growth Rate-Dependent and Stringent Control of the Synthesis of Ribosomal Proteins in Escherichia Coli

I. Secondary Structure of the LI Target Site on L11 mRNA

II. Growth Rate-Dependent Control of Ribosomal Protein Synthesis

III. Stringent Control of Ribosomal Protein Synthesis

IV. Concluding Remarks

References


25 Sequence and Structural Elements Associated with the Degradation of Apolipoprotein II Messenger RNA

I. Introduction

II. Effect of 5' Noncoding Sequences on apo II mRNA Stability

III. Use of Enzymatic Probes and Reverse Transcriptase to Analyze apo II mRNA Secondary Structure

IV. Analysis of apo II mRNA in Polysomes

V. Summary and Perspective

References


26 A New Immune System against Viral Infection Using Antisense RNA: micRNA-Immune System

I. Introduction

II. micRNA Mutagenesis

III. micRNA-Immune System

IV. Conclusion

References


27 Regulation of IS10 Transposase Expression by RNA/RNA Pairing

I. Introduction

II. Biological Role of Multicopy Inhibition

III. Molecular Mechanism of Multicopy Inhibition

IV. Mechanism of Pairing between RNA-IN and RNA-OUT In Vitro

V. In Vivo Phenotypes of Mutations in RNA-OUT

References


28 Characterization and Functional Analysis of the Factors Required for Transcription of the Adenovirus Major Late Promoter

I. Introduction

II. Fractionation and Functional Analysis of the Factors Required for Transcription of the Adenovirus Major Late Promoter

III. Concluding Remarks

References

Index