Focus Issue: The Kinome--Techniques and Methods for Analysis

A Review in this week's issue of Science represents a landmark for the field of signal transduction. Manning et al . provide analysis of the complete set of human protein kinases--and the coining of the inevitable terminology, "the human kinome." Science , STKE, and sponsors Cell Signaling Technology, Inc., and Sugen, Inc., also mark the occasion with a pull-out poster displaying a phylogenetic tree with all 518 enzymes. Related new and archived material is also provided at STKE. One cannot be certain at this stage that each and every kinase has been uncovered, but for most intents and purposes, the full extent of this critical set of signaling regulators is now evident. This allows comparison with the related complements of enzymes from other organisms for which (relatively) complete genomic sequences are known. The authors turn up over 60 enzymes not previously described. The implications of the work are dramatic, both in terms of basic science and the application of that science to development of new therapeutics. For example, four families of functionally uncharacterized kinases are evident in the human genome, and these have orthologs in flies and worm. This presumably indicates that the proteins are conserved to serve an important function, but no biological role has yet been described. The value of detailed understanding of the protein kinases and their inhibitors could hardly be more apparent than after the phenomenal success recently achieved with the tyrosine kinase inhibitor STI571 [Gleevec(TM); imatinib mesylate] in treatment of chronic myelogenous leukemia and recent approval of the drug for use against gastrointestinal stromal tumors. Many tyrosine kinases are implicated in cancer, but scores of other disease states also reflect inappropriate regulation of these key enzymes. In the 50 years since regulation of protein activity by covalent phosphorylation was discovered, intense research efforts have been applied to characterize a broad range of kinases. Nevertheless, identification of the relevant biological substrates for any particular kinase in a particular biological role has proven to be very difficult. In a Perspective in this issue of Science's STKE , Manning and Cantley take a critical look at the techniques currently available to aid investigators in the search for the targets of their favorite kinase. These range from improvements to traditional in vitro assays to proteomic screens and a new method to create engineered kinases that specifically use modified adenosine triphosphate (ATP) analogs to label their substrates. STKE Protocols contain several of these conventional and newer methodologies for studying protein kinases and phosphorylation-dependent protein interactions (see Wooten; Steen et al .; and Shaywitz et al .). In this issue, in a Protocol by Eyckerman et al ., the Janus kinases are put to use in a modification of the yeast two-hybrid method that uses modified cytokine receptor molecules to allow detection of protein interactions in mammalian cells. In the postgenomic age, bioinformatics tools to identify new members of protein families and to search for interaction targets are powerful aids that help reveal protein functions and refine our understanding of signaling networks. Manning and Cantley discuss some of the advantages and disadvantages to these "dry" experiments. Many tools that are available on the World Wide Web are listed in at the STKE in the "ST on the Web" section, which has brief descriptions and links providing access to these resources (see Bioinformatics Resources and Protein Databases). A Perspective by Pelech and Zhang represents a new type of article for STKE, but one that may become more common as investigators present data sets from high-throughput screens. Pelech and colleagues at Kinexus Bioinformatics Corporation have assembled a panel of commercial antibodies that recognize more than 70 kinases. They agreed to share recently obtained data in which the panel of antibodies was used to examine expression of the enzymes in cell lines and various tissues from rat and monkey. The primary data are available as supplementary material to the Perspective in which the authors describe the screen and the unexpected variation they observe in abundance of the kinases in various tissues. The editors note that this contribution represents a less formal communication than an original research paper, in particular because the data provided have not been peer reviewed. STKE also features three new Connections Maps from Johnson and Lapadat describing mitogen-activated protein kinase (MAPK) signaling. The MAPKs participate in regulation of a broad range of biological activities and are among the most widely expressed enzymes in the screen described by Pelech and Zhang. Each of the three major subfamilies of MAPKs is represented with a separate Connections Map. The ERK Pathway describes regulation of the extracellular signal-regulated kinases (ERKs), which have critical roles in control of cell division. The JNK Pathway describes the c-Jun NH2-terminal kinases, an intricate web of signaling proteins that are key regulators of transcription. A third map depicts the p38 MAPK Pathway, with roles in stress responses and cytokine signaling. In a Science Viewpoint, Johnson and Lapadat describe the basic characteristics and physiological roles of these pathways. These kinase cascades provide a sense of the elaborate complexity of kinase-mediated signaling in cells as hundreds of enzymes monitor and respond to signals from the environment and the cell's interior to control decisions to grow, divide, or die. Other STKE Connections Maps contain many signaling pathways with central roles for protein and lipid kinases. Featured in This Focus Issue Related Resources at STKE