Signaling pathways that control mRNA turnover

Abstract

Cells regulate their genomes mainly at the level of transcription and at the level of mRNA decay. While regulation at the level of transcription is clearly important, the regulation of mRNA turnover by signaling networks is essential for a rapid response to external stimuli. Signaling pathways result in posttranslational modification of RNA binding proteins by phosphorylation, ubiquitination, methylation, acetylation etc. These modifications are important for rapid remodeling of dynamic ribonucleoprotein complexes and triggering mRNA decay. Understanding how these posttranslational modifications alter gene expression is therefore a fundamental question in biology. In this review we highlight recent findings on how signaling pathways and cell cycle checkpoints involving phosphorylation, ubiquitination, and arginine methylation affect mRNA turnover.

Figure 1. Commonly found cis-elements in the 3′ UTRs of mRNAs that influence the rate of mRNA decay are shown

The trans-acting factors that bind these elements are depicted. (A) The poly (A) tail is present in most eukaryotic mRNA transcripts and binds poly (A) binding protein, PABP. (B) AU-rich elements are present in a number of cytokine, chemokine, and proto-oncogene mRNAs such as c-Myc, c-Jun, and GM-CSF mRNA. Several ARE-BPs such as AUF1, TTP, KSRP are known to exist. (C) The 16 nt stem-loop in the 3′ UTRs of histone mRNAs is a regulator of mRNA stability and binds SLBP (D) A stem-loop sequence specific for the iron response element binding protein (IRE-BP) is found in the transferrin receptor mRNA. (E) Several mRNAs are regulated by microRNAs that bind in the 3′ UTR of the mRNA target and recruit the RISC complex.

Figure 2. Regulation of TTP mRNA targets by the p38 MAPK pathway

The p38 MAPK is activated by environmental stress and inflammatory cytokines. p38 MAPK activates MK2 which in turn phosphorylates the ARE-binding and mRNA-destabilizing protein tristetraprolin (TTP) at serines 52 and 178 (Mouse TTP numbering). Phosphorylation of TTP by MK2 reduces binding affinity of TTP for the TNF-α, GM-CSF, and IL-2 ARE sequence, and promotes its interaction with 14-3-3 proteins thereby altering its subcellular distribution and inhibiting its mRNA decay activity.

Figure 3. Regulation of the proinflammatory cytokine GM-CSF mRNA stability by the MAPK pathway

When eosinophils are activated by hyaluronic acid, it triggers ERK phosphorylation by the Ras/Raf/MEK pathway. Activated ERK phosphorylates the AU-rich binding protein AUF-1 at Ser⁸³-Pro⁸⁴, a binding site for the prolyl isomerase Pin1. Pin1 regulates cytokine decay by interacting with and modulating the mRNA-binding activity of AUF1.

Figure 4. Regulation of the myogenin mRNA stability by the PI3K-AKT signaling pathway and the ARE-BP KSRP

PI3K/AKT activation in myoblasts C2C12 regulates myomiR maturation via the ARE-BP KSRP. Phosphorylation of KSRP by AKT inhibits its ability to promote the decay of myogenin mRNA by dissociating KSRP from myogenin mRNA in the cytoplasm. The released KSRP binds 14-3-3, translocates to the nucleus where it promotes the maturation of myogenic miRNAs.

Figure 5. A schematic illustration of activation of the replication checkpoint in response to inhibition of DNA synthesis

When DNA replication stalls due to DNA damage or cessation of DNA synthesis, a checkpoint response is activated. Three members of the phosphoinositide 3-kinase (PI3 kinase)-related kinase (PIKK) family, namely ATR, DNA-PK, and SMG-1 have been implicated in histone mRNA decay. Pin1 is also activated in response to the replication checkpoint. Activation of these kinases and Pin1 triggers histone mRNA decay via the RNA binding protein SLBP and the helicase Upf1 by an unknown mechanism.

Figure 6. Steps in histone mRNA degradation in response to cell-cycle regulated phosphorylation events

A schematic of the various steps involved in bidirectional decay of histone mRNA and the factors involved is shown.

Figure 7. Upf1 phosphorylation and dephosphorylation cycles that regulate NMD

Upf1 is phosphorylated by the SMG-1 complex on several S/Q motifs in vivo. SMG-1 activity is regulated by SMG8 and SMG9. Phosphorylation of Upf1 also requires Upf2 and Upf3 and association with the exon junction complex (EJC), triggering NMD. Upf1 is dephosphorylated by PP2A associated with SMG5, SMG6, and SMG7.

Figure 8

Domain organization of E3 Ubiquitin Ligases that have RNA binding domains.

Figure 9. Arginine methylation reactions regulate assembly of small RNA containing granules

(A) The different types of arginine methylation reactions characterized by specific arginine methyltransferases (PRMTs) are shown. Types I, II and III PRMTs generate monomethylarginine (MMA) on one of the terminal (ω) guanidino nitrogen atoms. Type I enzymes can act on MMA substrates to yield asymmetric dimethylarginine (aDMA) whereas Type II enzymes generate the symmetric dimethylarginine product (sDMA). (B) Arginine and MMA can be converted to citrulline by Arginine Deiminases whereas all three modifications can be demethylated back to arginine by Amine Oxidases. (C) PIWI proteins are modified to generate dDMA products by the PRMT5/WDR77 complex. The sDMA is specifically recognized by Tudor domain containing proteins in nuage like granules in animal gonads.