Interplay Between CMGC Kinases Targeting SR Proteins and Viral Replication: Splicing and Beyond

Abstract

Protein phosphorylation constitutes a major post-translational modification that critically regulates the half-life, intra-cellular distribution, and activity of proteins. Among the large number of kinases that compose the human kinome tree, those targeting RNA-binding proteins, in particular serine/arginine-rich (SR) proteins, play a major role in the regulation of gene expression by controlling constitutive and alternative splicing. In humans, these kinases belong to the CMGC [Cyclin-dependent kinases (CDKs), Mitogen-activated protein kinases (MAPKs), Glycogen synthase kinases (GSKs), and Cdc2-like kinases (CLKs)] group and several studies indicate that they also control viral replication via direct or indirect mechanisms. The aim of this review is to describe known and emerging activities of CMGC kinases that share the common property to phosphorylate SR proteins, as well as their interplay with different families of viruses, in order to advance toward a comprehensive knowledge of their pro- or anti-viral phenotype and better assess possible translational opportunities.

Keywords: CMGC kinases; RS domain; serine/arginine-rich proteins; splicing; viral replication.

Figure 1

Functions of serine/arginine-rich (SR) proteins in mRNA metabolism. SR proteins (red circles) regulate transcription by activating the RNA polymerase II (in green). They also regulate constitutive and alternative splicing of pre-mRNAs by the spliceosome (in yellow). After splicing, SR proteins remain linked to mRNAs and some of them are involved in their nucleocytoplasmic export. In the cytoplasm, SR proteins can be redirected to the nucleus or regulate mRNA translation and/or stability: indeed, splicing regulation by SR proteins can induce the inclusion of a premature stop codon, which favors the recruitment of cellular proteins involved in RNA degradation by the non-sense mediated decay (NMD) pathway. Finally, some SR proteins can be involved in the nuclear import of Cdc2-like kinase 1 (CLK1). All these functions are tightly regulated by multi-site phosphorylation of SR proteins that also modulates their subcellular localization in the cytoplasm and the nucleus.

Figure 2

Structure of the SR-proteins family. The human family of SR proteins is composed by 12 proteins that share a similar modular organization with one or two RNA recognition motifs (RRM) in their N-terminal part, followed by a length-variable serine/arginine-rich (RS) domain in their C-terminal part. SRSF7 contains an additional zinc finger (Zn) domain. Numbers below the sequence refer to the amino acid position. The total number of amino acids is indicated between parentheses close to the protein name.

Figure 3

The group of human CMGC kinases. Of the 518 human protein kinases, 61 belong to the CMGC group and can be clustered into eight families and several sub-families of increasing sequence similarity and biochemical function. The unrooted kinase dendrogram shows the sequence similarity between the catalytic domains of the CMGC kinases: the distance along the branches between two kinases is proportional to the divergence between their sequences. Arrows indicate the kinases in SR proteins phosphorylation. NCBI accession number are indicated in gray. Illustration reproduced courtesy of Cell Signaling Technology, Inc. (www.cellsignal.com).

Figure 4

Phosphorylation cycle of SR proteins by serine-arginine protein kinase 1 (SRPK1) and CLK1. The sequence of events leading to the phosphorylation of SR proteins by SRPK1 and CLK1 has been well-documented for SRSF1, the prototype of the SR protein family, schematically represented here with two RRM domains followed by one RS domain. A first wave of SRSF1 phosphorylation takes place in the cytoplasm via SRPK1 that targets serine residues in its RS domain. This initial event triggers SRSF1 translocation to the nucleus through the nuclear pore complex (NPC) via association with the SR-specific transportin-2 (TRN-SR2) protein. Within the nucleus, SRSF1 accumulates in nuclear speckles (in yellow) together with other RNA-binding proteins. There, CLK1 further hyper-phosphorylates SRSF1 at serine residues in the RS domain. This second event drives the egress of SRSF1 from the speckles toward the nucleoplasm where it binds to pre-mRNA and to several other splicing factors to support co-transcriptional splicing. Dephosphorylation events by phosphatases are then required to complete the splicing reaction and for nuclear egress of SRSF1 together with spliced mRNA.

Figure 5

Summary of the major known effects resulting from the interplay between kinases that target SR proteins and viruses. When identified, the viral target of the kinase is indicated between brackets. The red asterisk indicates if the protein contains an arginine/serine-rich domain. NA, nucleic acid.