Regulating with RNA in Bacteria and Archaea.

Cover -- Half-Title Page -- Title Page -- Copyright Page -- Contents -- Contributors -- Foreword -- Preface -- References -- Acknowledgments -- About the Editors -- I: RNases and Helicases -- 1. RNase E and the High-Fidelity Orchestration of RNA Metabolism -- INTRODUCTION -- A BRIEF EVOLUTIONARY HISTORY OF RNASE E -- DOMAINS, MICRODOMAINS, AND PSEUDODOMAINS OF RNASE E -- THE INTERACTION PARTNERS OF RNASE E -- The Exosome-like PNPase -- RNA Helicase Partners of RNase E and Their Role in Substrate Channeling -- Metabolic Enzymes -- INTERACTION OF RNASE E WITH REGULATORY RNAs AND CHAPERONES -- SUBSTRATE PREFERENCES OF RNASE E -- ENCOUNTERING AND ACTING UPON SUBSTRATES -- CELLULAR LOCALIZATION OF RNASE E AND THE DEGRADOSOME -- SUMMARY AND PERSPECTIVES -- References -- 2. Enzymes Involved in Posttranscriptional RNA Metabolism in Gram-Negative Bacteria -- INTRODUCTION -- GENERAL mRNA DECAY -- Initiation of mRNA Decay by Endonucleases -- The Role of 3´→5´ Exonucleases in mRNA Decay -- ENZYMES INVOLVED IN tRNA PROCESSING -- ENZYMES INVOLVED IN rRNA PROCESSING -- PROCESSING AND DECAY OF sRNAS -- RNA HELICASES -- SPECIALIZED RNASES -- TA Systems -- Bacteriocins Function as RNases -- CRISPR-Cas Systems -- CONTROL OF RNASES -- CONCLUSIONS -- References -- 3. RNases and Helicases in Gram-Positive Bacteria -- INTRODUCTION -- THE MAIN RIBONUCLEASES OF GRAM-POSITIVE BACTERIA -- The Endoribonucleases -- The Exoribonucleases -- HELICASES -- A GRAM-POSITIVE DEGRADOSOME-LIKE NETWORK -- CROSS-REGULATION AND AUTOREGULATION OF RNASE EXPRESSION -- PERSPECTIVES -- References -- II: Cis-Acting RNAs -- 4. RNA Thermometers in Bacterial Pathogens -- INTRODUCTION -- CONTROL OF MASTER REGULATORS OF VIRULENCE -- Listeria monocytogenes-Two Regulatory RNAs Team Up -- Vibrio cholerae-From the Water and Back into the Water -- Yersinia Species-Temperature Sensing at Multiple Levels.

CONTROL OF IMMUNE EVASION AND EXTRACELLULAR FACTORS -- Neisseria meningitidis-Three RNATs To Undermine the Host Immune Response -- Leptospira interrogans-Two Identical RNATs To Colonize the Host -- QUORUM SENSING AND IRON ACQUISITION -- Pseudomonas aeruginosa-RNATs Coordinate Lifestyle Decisions -- Shigella-Host Temperature Facilitates Iron Acquisition -- OTHER VIRULENCE-RELATED FUNCTIONS -- Salmonella-Heat Shock Thermometers Might Contribute to Virulence -- MUCH MORE TO COME? -- References -- 5. Small-Molecule-Binding Riboswitches -- INTRODUCTION -- RIBOSWITCHES-LOCATION, MECHANISM, AND DISTRIBUTION -- THE TPP RIBOSWITCH-AN EXAMPLE ACROSS ALL DOMAINS OF LIFE -- VERSATILITY OF RIBOSWITCHES -- HOW TO FIND NEW RIBOSWITCHES -- GETTING A GLIMPSE OF RIBOSWITCH STRUCTURE -- SYNTHETIC RIBOSWITCHES-NOVEL MEANS FOR THE CONDITIONAL CONTROL OF GENE EXPRESSION -- CONCLUDING REMARKS -- References -- 6. The T-Box Riboswitch: tRNA as an Effector to Modulate Gene Regulation -- INTRODUCTION -- DISCOVERY AND MECHANISM -- CONSERVED ELEMENTS AND STRUCTURAL ORGANIZATION -- PHYLOGENETIC DISTRIBUTION -- T-BOX LEADER RNA-tRNA INTERACTIONS -- Specifier Sequence-tRNA Anticodon Interaction -- Antiterminator-tRNA Acceptor Arm Interaction -- Stem I Platform-tRNA Elbow Interaction -- Stem II and Pseudoknot Interactions with tRNA -- STRUCTURAL ANALYSES OF T-BOX LEADER RNAs -- Antiterminator Domain -- Specifier Loop and K-Turn Motif -- Stem I Platform and Hinge -- Leader RNA-tRNA Complexes -- THE T-BOX REGULATORY SYSTEM AS AN ANTIBIOTIC TARGET -- CONCLUSIONS -- References -- 7. rRNA Mimicry in RNA Regulation of Gene Expression -- THE rRNA AS A SOURCE OF RNA STRUCTURAL MOTIFS -- r-PROTEINS AS AUTOGENOUS REGULATORS -- Discovery of r-Protein Autogenous Regulatory mRNA Structures -- The S8-Interacting mRNA Structure: A Prototype r-Protein cis-Regulatory RNA.

The L10(L12)4-Interacting Regulatory Structure: Homologous Binding Sites, Different Mechanisms of Action -- The L1-Interacting mRNA Structure: Convergence on the Same Binding Determinants -- L20-Interacting mRNA Regulatory Structures: Diverse Scaffolds Support the Same Binding Determinants -- S15-Interacting Regulatory Structures: Diverse Binding Determinants Produce Diverse Structures -- BEYOND AUTOGENOUS REGULATION: L7Ae -- ENGINEERED r-PROTEIN-RESPONSIVE REGULATORY RNA SYSTEMS -- CONCLUDING REMARKS -- References -- 8. Processive Antitermination -- INTRODUCTION -- PROCESSIVE ANTITERMINATION -- Phage Lambda Antitermination -- rRNA Operon Antitermination -- RNA Elements that Promote PA -- SPECIALIZED NusG PARALOGS -- RfaH -- Other NusG Paralogs (ActX, TaA, UpxY, and LoaP) -- Phylogenetic Overview of the NusG Family of Proteins -- OUTLOOK -- References -- 9. Genes within Genes in Bacterial Genomes -- INTRODUCTION -- INITIATION OF TRANSLATION IN BACTERIA -- INTERNAL INITIATION FROM IN-FRAME START CODONS -- The Function of the Alternative Polypeptide Is Closely Related to That of the Primary Protein -- Alternative Protein Facilitates the Function of the Primary Protein -- The Function of the Alternative Protein Differs Significantly from That of the Primary Protein -- Alternative Translation Products with an Unknown Raison d'Être -- INTERNAL INITIATION OF TRANSLATION THAT DIRECTS SYNTHESIS OF A PROTEIN FROM AN ALTERNATIVE READING FRAME -- The Competence Protein ComS Is Encoded within the srfA Gene of B. subtilis -- The Gene of Ribosomal Protein L34 Is Nested within the RNase P Protein Gene of Thermus thermophilus -- A Heat Shock Protein Is Encoded in an Alternative Reading Frame within the gnd Gene of E. coli -- NEW TOOLS FOR IDENTIFYING ALTERNATIVE TRANSLATION START SITES -- CONCLUDING REMARKS -- References.

10. Leaderless mRNAs in the Spotlight: Ancient but Not Outdated! -- WIDESPREAD OCCURRENCE OF lmRNAs -- MAIN PATHWAYS OF TRANSLATION INITIATION -- Translation Initiation on Canonical mRNAs -- Factors and r-Proteins That Affect Translation Initiation on lmRNAs -- Signals Intrinsic to the lmRNA That Affect Translation Initiation -- REGULATION UNDER VARIOUS PHYSIOLOGICAL CONDITIONS -- Continued Translation of lmRNAs during Stress Conditions -- Generation of lmRNAs during Stress -- Differential Expression in Response to Stress -- Further Benefits of 5´-Terminal AUGs -- PERSPECTIVE -- References -- III: Cis-Encoded Base Pairing RNAs -- 11. Type I Toxin-Antitoxin Systems: Regulating Toxin Expression via Shine-Dalgarno Sequence Sequestration and Small RNA Binding -- INTRODUCTION -- EXTENSIVE REGULATION OF TYPE I TA SYSTEMS -- Shine-Dalgarno Sequestration Is Required To Uncouple Transcription and Translation -- Toxin-Encoding mRNAs Require an Activation Step To Be Translated -- Standby RBSs Can Be Required for Translation -- Antisense RNAs Bind to and Repress Activated mRNAs -- Type I TA Systems May Also Be Modulated by RNA Editing -- PERSPECTIVES -- Identifying Type I TA Systems -- Understanding the Functions of Chromosomally Encoded TA Systems -- CONCLUSIONS -- References -- 12. Widespread Antisense Transcription in Prokaryotes -- INTRODUCTION: ANTISENSE RNAs-PERVASIVE TRANSCRIPTION OR FUNCTIONAL IMPORTANCE? -- Some Characteristics of Bacterial asRNAs -- Mapping the Extent of Antisense Transcription in Bacteria -- Are asRNAs and Their Sense Partners Expressed at the Same Time in the Same Cell at Sufficient Levels? -- SPECIFIC MECHANISMS OF asRNA ACTION IN BACTERIA -- Hfq-Associated and trans-Acting, cis-Encoded asRNAs -- Mechanisms That Require RNA-RNA Interaction -- GLOBAL FUNCTIONS THAT HAVE BEEN ASSOCIATED WITH ANTISENSE TRANSCRIPTION IN BACTERIA.

Transcription-Associated Mechanisms -- Transcriptome Reshaping, Repression of General Gene Expression, Cell Fate Decision, and Phenotypic Variation -- asRNAs and Overlapping Transcripts Together with RNase III as a Means for RNA Maturation -- Antisense Transcription and DNA-Repair Processes -- Pervasive (Antisense) Transcription as a Driver of Evolution and Genome Flexibility? -- OUTLOOK AND FURTHER DIRECTIONS -- References -- IV: Trans-Encoded Base Pairing RNAs -- 13. Small Regulatory RNAs in the Enterobacterial Response to Envelope Damage and Oxidative Stress -- INTRODUCTION -- Loss of Hfq-Dependent Regulation Leads to Low Levels of RpoS -- Loss of Hfq-Dependent Regulation Leads to High Levels of RpoE -- Specialized Sigma Factors and Hfq: Changing the Sign of Regulation -- CONSTRUCTING sRNA REGULATORY NETWORKS: GENERAL PRINCIPLES AND EXPECTATIONS -- sRNAs as Guides to a Stress Response -- INVOLVEMENT OF sRNAs IN THE ENVELOPE STRESS RESPONSE -- Cell Envelope Structure and Function in Gram-Negative Bacteria -- sRNAs in the RpoE-Mediated Envelope Stress Response -- sRNAs in the Cpx-Mediated Envelope Stress Response -- Integration of the Cpx and Rcs Envelope Stress Responses via RprA sRNA -- Additional Pathways Mediating Envelope Homeostasis -- Involvement of sRNAs in Modification of LPS -- sRNAs AND THE RESPONSE TO OXIDATIVE STRESS AND DNA DAMAGE -- sRNAs Induced by Oxidative Stress -- RNA-Based Regulation of DNA Mutagenesis -- CONCLUSIONS AND FUTURE DIRECTIONS -- References -- 14. Carbohydrate Utilization in Bacteria: Making the Most Out of Sugars with the Help of Small Regulatory RNAs -- INTRODUCTION -- sRNAs REGULATING UTILIZATION OF PARTICULAR CARBON SOURCES -- Posttranscriptional Regulation of Glucose Uptake -- Regulation of Chitin and Chitosugar Utilization by sRNAs -- Regulation of Mannitol Uptake by a cis-Encoded sRNA in V. cholerae.

Regulation of Polysaccharide Utilization Genes by cis-Encoded sRNAs in Bacteroides.

Revealing the many roles of RNA in regulating gene expressionFor 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.

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Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, 2024. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries.