Comparative analysis of predicted protein sequences encoded by the genomes of Caenorhabditis elegans and Saccharomyces cerevisiae suggests that most of the core biological functions are carried out by orthologous proteins (proteins of different species that can be traced back to a common ancestor) that occur in comparable numbers. The specialized processes of signal transduction and regulatory control that are unique to the multicellular worm appear to use novel proteins, many of which re-use conserved domains. Major expansion of the number of some of these domains seen in the worm may have contributed to the advent of multicellularity. The proteins conserved in yeast and worm are likely to have orthologs throughout eukaryotes; in contrast, the proteins unique to the worm may well define metazoans.

We have investigated mRNA 3-end-processing signals in each of six eukaryotic species (yeast, rice, arabidopsis, fruitfly, mouse, and human) through the analysis of more than 20,000 3-expressed sequence tags. The use and conservation of the canonical AAUAAA element vary widely among the six species and are especially weak in plants and yeast. Even in the animal species, the AAUAAA signal does not appear to be as universal as indicated by previous studies. The abundance of single-base variants of AAUAAA correlates with their measured processing efficiencies. As found previously, the plant polyadenylation signals are more similar to those of yeast than to those of animals, with both common content and arrangement of the signal elements. In all species examined, the complete polyadenylation signal appears to consist of an aggregate of multiple elements. In light of these and previous results, we present a broadened concept of 3-end-processing signals in which no single exact sequence element is universally required for processing. Rather, the total efficiency is a function of all elements and, importantly, an inefficient word in one element can be compensated for by strong words in other elements. These complex patterns indicate that effective tools to identify 3-endprocessing signals will require more than consensus sequence identification. Knowledge of gene sequences and functions comprises only part of the information necessary to understand biological systems at the molecular level. Equally important are identification and characterization of the regulatory elements that govern the temporal and tissue-specific expression of any individual gene. Discovery of nucleic acid control sequences is difficult, because they are short and often degenerate. Sequence databases, however, can provide means for the statistical identification of prospective signals, given a suitable biological hypothesis for the selection of candidate sequences. We have analyzed polyadenylation control signals in six eukaryotic species by examining 20,842 3Ј-expressed sequence tags (ESTs). The results should prove useful in designing future experiments to further elucidate the mechanism of mRNA 3Ј-end-processing.Control sequences have been commonly investigated through mutagenesis of the untranslated regions in the vicinity of coding sequence on vector constructs or by in vitro footprinting of the binding sites for identified regulatory proteins. Although these methods have successfully characterized many control sites, they are limited in both contextual scope and the number of sequences that can be reasonably investigated. Analysis of control sequences in artificial constructs only partially reproduces conditions in genomic sequence, where signal words may be affected by many factors, such as the use of unrelated but overlapping functional elements (1) and the use of multiple signals of varying strength (2).The continually expanding sequence databases provide a method to investigate control sequences in silico. Through statistical investigatio...

Protein kinase CK2 is a ubiquitous serine/threonine kinase involved in many biological processes. It is overexpressed in many malignancies including rodent and human breast cancer, and is up-regulated in Wnt-transfected mammary epithelial cells, where it can be found in a complex with dishevelled and ␤-catenin. ␤-Catenin is a substrate for CK2 and inhibition of CK2 reduces levels of ␤-catenin and dishevelled. Here we report that inhibition of CK2 using pharmacologic agents or expression of kinase inactive subunits reduces ␤-catenindependent transcription and protein levels in a proteasome-dependent fashion. The major region of phosphorylation of ␤-catenin by CK2 is the central armadillo repeat domain, where carrier proteins like axin and the adenomatous polyposis coli gene product APC interact with ␤-catenin. The major CK2 phosphorylation site in this domain is Thr 393 , a solvent-accessible residue in a key hinge region of the molecule. Mutation of this single amino acid reduces ␤-catenin phosphorylation, cotranscriptional activity, and stability. Thus, CK2 is a positive regulator of Wnt signaling through phosphorylation of ␤-catenin at Thr 393 , leading to proteasome resistance and increased protein and co-transcriptional activity.Protein kinase CK2 is ubiquitously expressed in both the cytoplasm and nucleus of eukaryotic cells. It is highly conserved through evolution; mammalian CK2 can substitute for the yeast enzyme (1). CK2 functions as a tetramer assembled by homodimerization of two regulatory ␤ subunits followed by recruitment of two catalytic subunits (␣ or ␣Ј) (2-4). The catalytic subunits are highly homologous to each other but are encoded by different genes (5). Activity is regulated by the ␤ subunit, which confers some of the substrate specificity (6). In S. cerevisiae, deletion of either of the catalytic subunits results in a normal phenotype, but deletion of both leads to growth arrest (7). In mammals, the ␣Ј subunit is required for normal male germ cell development (8).CK2 is not known to be regulated by second messengers, but its activity is enhanced by polyamines and polylysines (9 -11) and inhibited by apigenin (chrysin) (12), 6-dichloro-1-␤-D-ribofuranosylbenzimidazole (13), and emodin (14). Biochemically, CK2 is unusual in that it is one of the few kinases that can efficiently utilize either ATP or GTP as the phosphoryl donor (15), a property that is very useful experimentally to identify its activity.CK2 phosphorylates serine or threonine in acidic domains, with S/TXXD/E being the canonical motif (16 -19). CK2 regulates many fundamental cellular processes. Of particular interest with respect to cancer biology, CK2 phosphorylates many transcription factors, proto-oncoproteins, and tumor suppressor proteins including c-Myc (20), Max (21), p53 (22), Mdm-2 (23), c-Jun (24), SV40 large T antigen (25), and others.CK2 phosphorylation can regulate DNA binding, e.g. for c-Jun (24) or Max (21) or nuclear translocation, e.g. for SV40 large T antigen (25). However, one of the important functions of CK2...