mRNA Stability and Localization

Chapter 22 mRNA Stability and Localization

mRNA Stability and Localization

22.1 Introduction 3′ UTR (3′ untranslated region) – The untranslated sequence downstream from the coding region of an mRNA. 5′ UTR (5′ untranslated region) – The untranslated sequence upstream from the coding region of an mRNA.

mRNA Stability and Localization

FIGURE 01: Features of prokaryotic and eukaryotic mRNAs.

mRNA Stability and Localization

22.1 Introduction stem-loop – A secondary structure that appears in RNAs consisting of a base-paired region (stem) and a terminal loop of single-stranded RNA.– Both are variable in size.

mRNA Stability and Localization

22.2 Messenger RNAs Are Unstable Molecules mRNA instability is due to the action of ribonucleases. Ribonucleases differ in their substrate preference and mode of attack. endoribonuclease – A ribonuclease that cleaves an RNA at an internal site(s). exoribonuclease – A ribonuclease that removes terminal ribonucleotides from RNA.

FIGURE 02: Types of ribonucleases.

mRNA Stability and Localization

22.2 Messenger RNAs Are Unstable Molecules processive (nuclease) – An enzyme that remains associated with the substrate while catalyzing the sequential removal of nucleotides. distributive (nuclease) – An enzyme that catalyzes the removal of only one or a few nucleotides before dissociating from the substrate. mRNAs exhibit a wide range of half-lives.

mRNA Stability and Localization

FIGURE 03: Method for determining mRNA half-lives.

mRNA Stability and Localization

22.2 Messenger RNAs Are Unstable Molecules mRNA decay – mRNA degradation, assuming that the degradation process is stochastic. Differential mRNA stability is an important contributor to mRNA abundance and therefore the spectrum of proteins made in a cell. steady state (molecular concentration) – The concentration of population of molecules when the rates of synthesis and degradation are constant.

mRNA Stability and Localization

22.3 Eukaryotic mRNAs Exist in the Form of mRNPs from Their Birth to Their Death mRNA associates with a changing population of proteins during its nuclear maturation and cytoplasmic life. Some nuclear-acquired mRNP proteins have roles in the cytoplasm. A very large number of RNA-binding proteins (RBPs) exist, most of which remain uncharacterized. Different mRNAs are associated with distinct, but overlapping, sets of regulatory proteins, creating RNA regulons.

mRNA Stability and Localization

FIGURE 04: The concept of an RNA regulon.

mRNA Stability and Localization

22.4 Prokaryotic mRNA Degradation Involves Multiple Enzymes polyribosome (or polysome) – An mRNA that is simultaneously being translated by multiple ribosomes. monocistronic mRNA – mRNA that codes for one polypeptide.

mRNA Stability and Localization

22.4 Prokaryotic mRNA Degradation Involves Multiple Enzymes Degradation of bacterial mRNAs is initiated by removal of a pyrophosphate from the 5′ terminus. Monophosphorylated mRNAs are degraded during translation in a twostep cycle involving endonucleolytic cleavages, followed by 3′ to 5′ digestion of the resulting fragments.FIGURE 05: Degradation of bacterial mRNAs

mRNA Stability and Localization

22.4 Prokaryotic mRNA Degradation Involves Multiple Enzymes 3′ polya

denylation can facilitate the degradation of mRNA fragments containing secondary structure. poly(A) polymerase (PAP) – The enzyme that adds the stretch of polyadenylic acid to the 3′ end of eukaryotic mRNA.– It does not use a template.

mRNA Stability and Localization

22.4 Prokaryotic mRNA Degradation Involves Multiple Enzymes poly(A) – A stretch of adenylic acid that is added to the 3′ end of mRNA following its synthesis. The main degradation enzymes work as a complex called the degradosome.

mRNA Stability and Localization

22.5 Most Eukaryotic mRNA is Degraded via Two Deadenylation-Dependent Pathways The modifications at both ends of mRNA protect it against degradation by exonucleases. poly(A) binding protein (PABP) – The protein that binds to the 3′ stretch of poly(A) on a eukaryotic mRNA.

mRNA Stability and Localization

22.5 Most Eukaryotic mRNA is Degraded via Two Deadenylation-Dependent Pathways The two major mRNA decay pathways are initiated by deadenylation catalyzed by poly(A) nucleases. Deadenylation may be followed either by decapping and 5′ to 3′ exonuclease digestion, or by 3′ to 5′ exonuclease digestion.

FIGURE 06: The major deadenylation-dependent decay pathways in eukaryotes