https://www.cell.com/cell/pdf/S0092-8674(03)00432-X.pdf

Mechanisms of TGF-β Signaling from Cell Membrane to the Nucleus

Mitogen-activated protein (MAP) kinases comprise a family of ubiquitous proline-directed, protein-serine/threonine kinases, which participate in signal transduction pathways that control intracellular events including acute responses to hormones and major developmental changes in organisms. MAP kinases lie in protein kinase cascades. This review discusses the regulation and functions of mammalian MAP kinases. Nonenzymatic mechanisms that impact MAP kinase functions and findings from gene disruption studies are highlighted. Particular emphasis is on ERK1/2.

/pdf/mitogen-activated-protein-map-kinase-pathways-regulation-and-3nsauvepr2.pdf

Mitogen-activated protein (MAP) kinase pathways: regulation and physiological functions.

Protein-tyrosine kinases (PTKs) are important regulators of intracellular signal-transduction pathways mediating development and multicellular communication in metazoans Their activity is normally tightly controlled and regulated Perturbation of PTK signalling by mutations and other genetic alterations results in deregulated kinase activity and malignant transformation The lipid kinase phosphoinositide 3-OH kinase (PI(3)K) and some of its downstream targets, such as the protein-serine/threonine kinases Akt and p70 S6 kinase (p70S6K), are crucial effectors in oncogenic PTK signalling This review emphasizes how oncogenic conversion of protein kinases results from perturbation of the normal autoinhibitory constraints on kinase activity and provides an update on our knowledge about the role of deregulated PI(3)K/Akt and mammalian target of rapamycin/p70S6K signalling in human malignancies

Oncogenic kinase signalling

Activating mutation in the tyrosine kinase JAK2 in polycythemia vera, essential thrombocythemia, and myeloid metaplasia with myelofibrosis.

AACR Centennial Conference: Translational Cancer Medicine-- Nov 4-8, 2007; Singapore

PL02-05 

All cancers are due to abnormalities in DNA. The availability of the human genome sequence has led to the proposal that resequencing of cancer genomes will reveal the full complement of somatic mutations and hence all the cancer genes. To explore the nature of the information that will be derived from cancer genome sequencing we have sequenced the coding exons of the family of 518 protein kinases, ~1.3Mb DNA per cancer sample, in 210 cancers of diverse histological types. Despite the screen being directed toward the coding regions of a gene family that has previously been strongly implicated in oncogenesis, the results indicate that the majority of somatic mutations detected are “passengers”. There is considerable variation in the number and pattern of these mutations between individual cancers, indicating substantial diversity of processes of molecular evolution between cancers. The imprints of exogenous mutagenic exposures, mutagenic treatment regimes and DNA repair defects can all be seen in the distinctive mutational signatures of individual cancers. This systematic mutation screen and others have previously yielded a number of cancer genes that are frequently mutated in one or more cancer types and which are now anticancer drug targets (for example BRAF , PIK3CA , and EGFR ). However, detailed analyses of the data from our screen additionally suggest that there exist a large number of additional “driver” mutations which are distributed across a substantial number of genes. It therefore appears that cells may be able to utilise mutations in a large repertoire of potential cancer genes to acquire the neoplastic phenotype. However, many of these genes are employed only infrequently. These findings may have implications for future anticancer drug development.

Patterns of Somatic Mutation in Human Cancer Genomes

We have catalogued the protein kinase complement of the human genome (the "kinome") using public and proprietary genomic, complementary DNA, and expressed sequence tag (EST) sequences. This provides a starting point for comprehensive analysis of protein phosphorylation in normal and disease states, as well as a detailed view of the current state of human genome analysis through a focus on one large gene family. We identify 518 putative protein kinase genes, of which 71 have not previously been reported or described as kinases, and we extend or correct the protein sequences of 56 more kinases. New genes include members of well-studied families as well as previously unidentified families, some of which are conserved in model organisms. Classification and comparison with model organism kinomes identified orthologous groups and highlighted expansions specific to human and other lineages. We also identified 106 protein kinase pseudogenes. Chromosomal mapping revealed several small clusters of kinase genes and revealed that 244 kinases map to disease loci or cancer amplicons.

http://science.sciencemag.org/content/sci/298/5600/1912.full.pdf

The Protein Kinase Complement of the Human Genome

Caenorhabditis elegans should soon be the first multicellular organism whose complete genomic sequence has been determined. This achievement provides a unique opportunity for a comprehensive assessment of the signal transduction molecules required for the existence of a multicellular animal. Although the worm C. elegans may not much resemble humans, the molecules that regulate signal transduction in these two organisms prove to be quite similar. We focus here on the content and diversity of protein kinases present in worms, together with an assessment of other classes of proteins that regulate protein phosphorylation. By systematic analysis of the 19,099 predicted C. elegans proteins, and thorough analysis of the finished and unfinished genomic sequences, we have identified 411 full length protein kinases and 21 partial kinase fragments. We also describe 82 additional proteins that are predicted to be structurally similar to conventional protein kinases even though they share minimal primary sequence identity. Finally, the richness of phosphorylation-dependent signaling pathways in worms is further supported with the identification of 185 protein phosphatases and 128 phosphoprotein-binding domains (SH2, PTB, STYX, SBF, 14-3-3, FHA, and WW) in the worm genome.

https://www.pnas.org/content/pnas/96/24/13603.full.pdf

The protein kinases of Caenorhabditis elegans: A model for signal transduction in multicellular organisms

http://www.jbc.org/content/277/1/550.full.pdf

Requirement for PAK4 in the anchorage-independent growth of human cancer cell lines.

The mammalian STE20/mitogen-activated protein kinase kinase kinase kinase (MAP4K) family consists of 28 serine/threonine kinases related in their catalytic domains (reviewed in reference 14). By analogy with the prototype STE20 kinase in Saccharomyces cerevisiae, mammalian MAP4K kinases are likely to regulate changes in transcription, cytoskeletal organization, and cell cycle progression in response to extracellular signals (17). Comparison of the overall domain structure places these kinases into two structural classes, the p21-activated protein kinases (PAKs) (1) and germinal center kinases (GCKs) (28). The GCK kinases lack the regulatory Cdc42/Rac-interacting domain found in the PAKs, having instead an N-terminal kinase domain and a C-terminal extension of variable length. Unlike PAKs, several GCKs appear to be activated in the absence of stimuli when overexpressed (3, 10, 38), suggesting that these kinases are regulated either by oligomerization or by binding of negative regulatory factors.

GCK kinases show little sequence homology outside of the kinase domain and are further broken down into nine subfamilies (14, 31a). HGK (hepatocyte progenitor kinase-like/GCK-like kinase) is one of four members of the GCK group IV (recently renamed the MSN subfamily) that also includes TNIK, MINK, and NRK/NESK (13, 22, 27, 35, 51). HGK, TNIK, and MINK are highly homologous in their kinase and C-terminal domains (about 92 and 87% amino acid identity, respectively), with variability in the intervening region that is less conserved (53% between HGK and TNIK). NRK/NESK is more divergent, with only 59% homology in the kinase domain and 37% homology in the C-terminal domain. The C-terminal domain is a citron homology (CNH) domain, named for citron rho-interacting kinase (CRIK), where it was first described (16, 31). CNH domains are found not only in the GCK group IV/MSN kinases but also in group I GCKs (KHS subfamily) (14, 31a), as well as in proteins other than kinases, including human Vam6p homologs, involved in membrane vesicle docking and fusion, and the S. cerevisiae Rho GDP-exchange factor Rom1p (9). The CNH domain has been shown to be important for protein-protein interactions. In CRIK itself, this domain mediates association with rho family GTPases (30, 31). In Vam6p, it mediates association with lysosomes (9). In GCK (a group I/KHS kinase), this domain is important for homodimerization, leading to the activation of mitogen-activated protein kinase/extracellular signal-regulated kinase MEKK1 (10). In mouse HGK, the CNH domain has been shown to interact with MEKK1 and also recently shown to mediate interaction of this kinase with the cytoplasmic domain of β1-integrin receptors (37, 43).

Orthologs of the HGK group are known in both Drosophila melanogaster and Caenorhabditis elegans, called misshapen (msn) and mig-15, respectively (46, 53). msn and mig-15 show striking sequence conservation with HGK in both the kinase and CNH domains, with more than 80% amino acid identity in both domains.

msn functions in multiple signaling pathways, including those downstream of frizzled (Wnt receptor) in determining epithelial polarity, in the regulation of dorsal closure, and in neuronal targeting. In the Wnt pathway, msn bifurcates from the β-catenin/cadherin signaling pathway at the upstream signaling protein coded by disheveled, signaling to a separate pathway leading to the activation of both JNK and p38 (36). In dorsal closure, msn also signals through a JNK module that mediates the spreading of epithelial sheets to close the embryo through induction of transforming growth factor β (44, 46). In photoreceptor neuronal targeting, msn functions downstream of dock, the Drosophila homolog of the Nck adapter protein, to guide axons to their target (40, 44). In nematodes, mig-15 functions in the processes of muscle arm targeting, where muscle cells extend cytoplasmic protrusions to synapse with motor neurons during development, as well as in neuroblast migration (53). The common factor to both model systems is the involvement of an HGK homolog in processes requiring cell migration or cell shape change.

The mouse ortholog of HGK, Nck-interacting kinase (NIK), was cloned in an interaction screen with the SH3 domain of the Nck adapter protein (43). NIK has been shown to be activated by stimulation of the ephrin receptor family (3). Ephrins are cell surface ligands shown to be involved in cell migration and tissue remodeling (52) and have been proposed to be involved in inside-out integrin regulation (15, 33). Consistent with a positive function for NIK in cell migration and morphogenesis, NIK−/− knockout mice showed an early embryonic-lethal phenotype, with defects in mesoderm differentiation and migration (50). This embryonic lethality indicates a lack of functional redundancy between the GCK group IV family members during development.

Human HGK was previously cloned from a macrophage cDNA library (51). Yao et al. demonstrated that HGK activated JNK in transient transfections and further suggested that this activation occurred through the mitogen-activated protein kinase kinase kinase transforming growth factor β-activated kinase (TAK1) rather than MEKK1.

We present the characterization of an alternatively spliced form of HGK identified from a human glioblastoma library and provide an analysis of a complex family of alternatively spliced HGK isoforms. We found HGK mRNA to be broadly overexpressed in tumor cell lines relative to normal adult tissue. Ectopic expression of various mutants of the tumor-derived HGK isoform suggested an active role for this protein in cell transformation and invasion as well as in reducing the adhesive properties of tissue culture cells. HGK appeared to function in these processes through modulation of growth factor and integrin receptor signaling.

The STE20 kinase HGK is broadly expressed in human tumor cells and can modulate cellular transformation, invasion, and adhesion

The present invention relates to kinase polypeptides, nucleotide sequences encoding the kinase polypeptides, as well as various products and methods useful for the diagnosis and treatment of various kinase-related diseases and conditions. Through the use of a bioinformatics strategy, mammalian members of the PTK's and STK's have been identified and their protein structure predicted.

David Whyte

Papers

The Protein Kinase Complement of the Human Genome

The protein kinases of Caenorhabditis elegans: A model for signal transduction in multicellular organisms

Requirement for PAK4 in the anchorage-independent growth of human cancer cell lines.

The STE20 kinase HGK is broadly expressed in human tumor cells and can modulate cellular transformation, invasion, and adhesion

Novel human protein kinases and protein kinase-like enzymes