Fip1--an essential component of the Saccharomyces cerevisiae polyadenylation machinery is phosophorylated by protein kinase CK2

Fateful Decisions of Where to Cut the Line: Pathology Associated with Aberrant 3' End Processing and Transcription Termination

Aberrant gene expression lies at the heart of many pathologies. This review will point out how 3' end processing, the final mRNA-maturation step in the transcription cycle, is surprisingly prone to regulated as well as stochastic variations with a wide range of consequences. Whereas smaller variations contribute to the plasticity of gene expression, larger alternations to 3' end processing and coupled transcription termination can lead to pathological consequences. These can be caused by the local mutation of one gene or affect larger numbers of genes systematically, if aspects of the mechanisms of 3' end processing and transcription termination are altered.

Yeast Protein Asf1 Possesses Modulating Activity towards Protein Kinase CK2

Protein kinase CK2 plays an important role in cell survival and protects regulatory proteins from caspase-mediated degradation during apoptosis. The consensus sequence of proteins phosphorylated by CK2 contains a cluster of acidic amino acids around the phosphorylation site. The poly-acidic sequence in yeast protein Asf1 is similar to the acidic loop in CK2β, which possesses a regulatory function. We observed that the overexpression of Asf1 in yeast cells influences cell growth. Experiments performed in vitro and in vivo indicate that yeast protein Asf1 inhibits protein kinase CK2. Our data suggest that each CK2 isoform might be regulated in a different way. Deletion of the amino or carboxyl end of Asf1 reveals that the acidic cluster close to the C-terminus is responsible for the activation or inhibition of CK2 activity.

Interactions between subunits of protein kinase CK2 and their protein substrates influences its sensitivity to specific inhibitors

Five isoforms of CK2 may exist simultaneously in yeast cells: free catalytic subunits CK2α', CK2α and three holoenzymatic structures composed of αα'ββ', α(2)ββ' and α'(2)ββ'. Each isolated and purified form exhibits properties typical for CK2, but they differ in substrate specificity as well as in sensitivity to specific modulators. All five isoforms of protein kinase CK2 from Saccharomyces cerevisiae were examined for their binding capacity with ATP/GTP and two commonly used ATP-competitive inhibitors TBB and TBI. Enzymes were tested with protein substrates differently interacting with CK2 subunits: Elf1, Fip1, Svf1, P2B and synthetic peptide. Obtained results show that K(m) for ATP varies from 2.4-53 μM for Elf1/CK2α' and Svf1/CK2α, respectively. Similar differences can be seen in case when GTP was used as phosphate donor. The inhibitory effect depends on composition of CK2/substrate complexes. Highest sensitivity to TBB shows all complexes containing αα'ββ' isoform with K (i) values between 0.2 and 1.1 μM. The prospect that TBB and TBI could be utilized to discriminate between different molecular forms of CK2 in yeast cells was examined. Both inhibitors, TBB as well as TBI, decreases cell growth to extents devoting interactions with different CK2 isoforms present in the cell but the presence of β/β'-dimer has a high importance towards sensitivity. Conceivably, a given inhibitor concentration can inhibit only selected CK2-mediated processes in the cell.

Unphosphorylated SR-like protein Npl3 stimulates RNA polymerase II elongation

The production of a functional mRNA is regulated at every step of transcription. An area not well-understood is the transition of RNA polymerase II from elongation to termination. The S. cerevisiae SR-like protein Npl3 functions to negatively regulate transcription termination by antagonizing the binding of polyA/termination proteins to the mRNA. In this study, Npl3 is shown to interact with the CTD and have a direct stimulatory effect on the elongation activity of the polymerase. The interaction is inhibited by phosphorylation of Npl3. In addition, Casein Kinase 2 was found to be required for the phosphorylation of Npl3 and affect its ability to compete against Rna15 (Cleavage Factor I) for binding to polyA signals. Our results suggest that phosphorylation of Npl3 promotes its dissociation from the mRNA/RNAP II, and contributes to the association of the polyA/termination factor Rna15. This work defines a novel role for Npl3 in elongation and its regulation by phosphorylation.

Finishing touches: post-translational modification of protein factors involved in mammalian pre-mRNA 3' end formation

In eukaryotes, a pre-messenger RNA (pre-mRNA) must undergo several processing reactions before it is exported to the cytoplasm for translation. One of these reactions, endonucleolytic 3' cleavage at the polyadenylation site, prepares the pre-mRNA for addition of the poly(A) tail and defines the 3' untranslated region (UTR), which typically contains important gene expression regulatory sequences. While the protein factors responsible for the endonucleolytic cleavage have been largely identified, the means by which their action is limited to the 3' end of the transcription unit and coordinated with other co-transcriptional events remains unclear. In this review, we summarize and review recent findings revealing that the mammalian 3' cleavage factors undergo extensive post-translational modification. These modifications include: arginine methylation, lysine sumoylation, lysine acetylation, and the phosphorylation of serine, threonine and tyrosine residues. Every cleavage factor, though not every subunit, is affected. Human Fip1 and the 59 kDa subunit of cleavage factor I emerge as the most frequently modified core cleavage factor subunits. We outline and compare the various proteomic methods that have uncovered these modifications, and review emerging hypotheses concerning their function. The roles of these covalent but reversible modifications in other systems suggest that 3' end formation in mammals relies upon post-translational modification for proper function and regulation.

Yeast holoenzyme of protein kinase CK2 requires both beta and beta' regulatory subunits for its activity

Protein kinase CK2 is a highly conserved Ser/Thr protein kinase that is ubiquitous among eucaryotic organisms and appears to play an important role in many cellular functions. This enzyme in yeast has a tetrameric structure composed of two catalytic (alpha and/or alpha') subunits and two regulatory beta and beta' subunits. Previously, we have reported isolation from yeast cells four active forms of CK2, composed of alphaalpha'betabeta', alpha2betabeta', alpha'2betabeta' and a free alpha'-catalytic subunit. Now, we report that in Saccharomyces cerevisiae CK2 holoenzyme regulatory beta subunit cannot substitute other beta' subunit and only both of them can form fully active enzymatic unit. We have examined the subunit composition of tetrameric complexes of yeast CK2 by transformation of yeast strains containing single deletion of the beta or beta' regulatory subunits with vectors carrying lacking CKB1 or CKB2 genes. CK2 holoenzyme activity was restored only in cases when both of them were present in the cell. Additional, co-immunoprecypitation experiments show that polyadenylation factor Fip1 interacts with catalytic alpha subunits of CK2 and interaction with beta subunits in the holoenzyme decreases CK2 activity towards this protein substrate. These data may help to elucidate the role of yeast protein kinase CK2beta/beta' subunits in the regulation of holoenzyme assembly and phosphotransferase activity.