Mechanisms and control of mRNA turnover in the yeast saccharomyces cerevisiae.

-----------------------------------------------------------------------------------------XIII SUMÁRIO---------------------------------------------------------------------------------------------XV RÉSUMÉ ----------------------------------------------------------------------------------------------XIX ORGANIZATION OF THE THESIS-------------------------------------------------------------XXIII ABBREVIATIONS ----------------------------------------------------------------------------------XXV CHAPTER I. GENERAL INTRODUCTION -----------------------------------------------------1 I.1 Transcription to degradationthe life cycle of mRNA -----------------------------------3 I.2 Biological significance of mRNA turnover--------------------------------------------------4 I.3 Pathways of eukaryotic mRNA turnover----------------------------------------------------6 I.3.1 Deadenylation-dependent mRNA decay-------------------------------------------------6 I.3.1.1 The enzymes involved in the deadenylation-dependent decay------------------8 I.3.1.1.1 The mRNA deadenylases --------------------------------------------------------------8 I.3.1.1.1.1 Ccr4p/Pop2p/Not complex-----------------------------------------------------------8 I.3.1.1.1.2 PAN: Pan2p/Pan3p Complex ------------------------------------------------------10 I.3.1.1.2 The mRNA decapping enzymes ------------------------------------------------------11 I.3.1.1.2.1 Dcp1p/Dcp2p decapping enzyme--------------------------------------------------11 I.3.1.1.2.2 Scavenger decapping enzyme -----------------------------------------------------14 I.3.1.1. 3 The 5’ to 3’ exonuclease: Xrn1p ------------------------------------------------------15 I.3.1.1. 4 The exosome------------------------------------------------------------------------------15 I.3.1.2 The deadenylation-dependent decay is a conserved turnover mechanism--18 I.3.2 Endonucleolytic cleavage as a mechanism for mRNA turnover ------------------20 I.3.3 mRNA quality control mechanisms ------------------------------------------------------21 I.3.3.1 Nonsense-mediated mRNA decay -----------------------------------------------------22 I.3.3.2 Nonstop-mediated mRNA decay--------------------------------------------------------25 I.3.3.3 No-Go mRNA decay ----------------------------------------------------------------------25 I.4 Mechanisms of control of mRNA turnover -------------------------------------------------26 I.4. 1 Structural features that affect mRNA turnover -----------------------------------------26 I.4. 1.1 Modulation of mRNA turnover rates by specific cis-acting elements ----------27 I.4. 1.2 Coupling mRNA turnover and translation ---------------------------------------------28 I.4. 2 mRNA deadenylation and control ---------------------------------------------------------30 I.4. 2.1 Regulation of deadenylation by poly(A) shortening nucleases------------------31 I.4. 2.2 Pab1p and regulation of deadenylation------------------------------------------------32 I.4. 2.3 Specific regulators of deadenylation --------------------------------------------------34 I.4. 3 mRNA decapping and control -------------------------------------------------------------35 I.4. 3.1 Poly(A) tails as an inhibitor of decapping ---------------------------------------------35 I.4. 3.1.1 Pab1p as a decapping blocker --------------------------------------------------------36 I.4. 3.2 Decapping requires a transition to a non-translation competent mRNP ------38 I.4. 3.3 Factors involved in decapping ----------------------------------------------------------39 I.4. 3.4 Assembly of decapping complexes-----------------------------------------------------42 I.4. 3.5 Processing bodies-sites of mRNA decapping and decay ------------------------43 CHAPTER II. P-BODIES REQUIRE RNA FOR ASSEMBLY AND CONTAIN NONTRANSLATING mRNAS ---------------------------------------------------------------------47 II. Abstract -------------------------------------------------------------------------------------------49 II.