Chemical inhibition of the Pho85 cyclin-dependent kinase reveals a role in the environmental stress response

In addition to its well-established role in responding to phosphate starvation, the cyclin-dependent kinase Pho85 has been implicated in a number of other physiological responses of the budding yeast Saccharomyces cerevisiae, including synthesis of glycogen. To comprehensively characterize the range of Pho85-dependent gene expression, we used a chemical genetic approach that enabled us to control Pho85 kinase activity with a cell-permeable inhibitor and whole genome transcript profiling. We found significant phenotypic differences between the rapid loss of activity caused by inhibition and the deletion of the genomic copy of PHO85. We demonstrate that Pho85 controls the expression of not only previously identified glycogen synthetic genes, but also a significant regulon of genes involved in the cellular response to environmental stress. In addition, we show that the effects of this inhibitor are both rapid and reversible, making it well suited to the study of the behavior of dynamic signaling pathways.

Magic bullets for protein kinases

A chemical-genetic method for the generation of target-specific protein kinase inhibitors has been developed recently. This strategy utilizes a functionally silent active-site mutation to sensitize a target kinase to inhibition by a small molecule that does not inhibit wild-type kinases. Tyrosine and serine/threonine kinases are equally amenable to the drug-sensitization approach, which has been used to generate selective inhibitors of mutant Src-family kinases, Abl-family kinases, cyclin-dependent kinases, mitogen-activated kinases, p21-activated kinases and Ca(2+)/calmodulin-dependent kinases. The designed inhibitors are specific for the sensitized kinase in a cellular background where the wild-type kinase has been inactivated. By these means, kinase-sensitization has been used systematically to generate and analyze conditional alleles of several yeast protein kinases in vivo.

Src-Abl tyrosine kinase chimeras: replacement of the adenine binding pocket of c-Abl with v-Src to swap nucleotide and inhibitor specificities

Engineered protein kinases with unnatural nucleotide specificity and inhibitor sensitivity have been developed to trace kinase substrate targets. We first engineered unnatural nucleotide specificity into v-Src by mutating one residue, isoleucine 338, to alanine. This position is highly conserved among all kinases in the sense that it is always occupied by either a large hydrophobic residue or threonine. Because of the conservation of this residue and the highly conserved fold of the kinase family, we have attempted to generalize the engineering of all kinases on the basis of our success with v-Src. Although many kinases can be similarly engineered using v-Src as a blueprint, we encountered one kinase, c-Abl, which when mutated, does not display the ability to accept unnatural ATP analogues. To overcome this failure of the engineered c-Abl (T315A) to accept unnatural nucleotides, we developed a new strategy for introducing unnatural nucleotide specificity into kinases. We generated a chimeric kinase in which regions of the kinase domain of c-Abl were swapped with the corresponding regions of v-Src (I338A). Specifically, we engineered two chimeras in which the N-terminal lobe of the SH1 domain of c-Abl was swapped with that of v-Src. These kinase chimeras were found to have the same unnatural nucleotide specificity as that of v-Src (I338A), while retaining the peptide specificity of c-Abl. Thus, these chimeric kinases are suitable for identifying the direct substrates of c-Abl. These engineered chimeric enzymes provide a new strategy for constructing kinases with tailor-made ligand binding properties.

Chemical genetic analysis of the budding-yeast p21-activated kinase Cla4p

The p21-activated kinases (PAKs) are effectors for the Rho-family GTPase Cdc42p. Here we define the in vivo function of the kinase activity of the budding yeast PAK Cla4p, using cla4 alleles that are specifically inhibited by a cell-permeable compound that does not inhibit the wild-type kinase. CLA4 kinase inhibition in cells lacking the partially redundant PAK Ste20p causes reversible SWE1-dependent cell-cycle arrest and gives rise to narrow, highly elongated buds in which both actin and septin are tightly polarized to bud tips. Inhibition of Cla4p does not prevent polarization of F-actin, and cytokinesis is blocked only in cells that have not formed a bud before inhibitor treatment; cell polarization and bud emergence are not affected by Cla4p inhibition. Although localization of septin to bud necks is restored in swe1Delta cells, cytokinesis remains defective. Inhibition of Cla4p activity in swe1Delta cells causes a delay of bud emergence after cell polarization, indicating that this checkpoint may mediate an adaptive response that is capable of promoting budding when Cla4p function is reduced. Our data indicate that CLA4 PAK activity is required at an early stage of budding, after actin polarization and coincident with formation of the septin ring, for early bud morphogenesis and assembly of a cytokinesis site.

A chemical switch for inhibitor-sensitive alleles of any protein kinase

Protein kinases have proved to be largely resistant to the design of highly specific inhibitors, even with the aid of combinatorial chemistry. The lack of these reagents has complicated efforts to assign specific signalling roles to individual kinases. Here we describe a chemical genetic strategy for sensitizing protein kinases to cell-permeable molecules that do not inhibit wild-type kinases. From two inhibitor scaffolds, we have identified potent and selective inhibitors for sensitized kinases from five distinct subfamilies. Tyrosine and serine/threonine kinases are equally amenable to this approach. We have analysed a budding yeast strain carrying an inhibitor-sensitive form of the cyclin-dependent kinase Cdc28 (CDK1) in place of the wild-type protein. Specific inhibition of Cdc28 in vivo caused a pre-mitotic cell-cycle arrest that is distinct from the G1 arrest typically observed in temperature-sensitive cdc28 mutants. The mutation that confers inhibitor-sensitivity is easily identifiable from primary sequence alignments. Thus, this approach can be used to systematically generate conditional alleles of protein kinases, allowing for rapid functional characterization of members of this important gene family.

Acquisition of inhibitor-sensitive protein kinases through protein design

Protein phosphorylation is the major post-translational modification used by eukaryotic cells to control cellular signaling. Protein kinases have emerged as attractive drug targets because heightened protein kinase activity has been associated with several proliferative diseases, most notably cancer and restenosis. Until now, it has been very difficult to confirm the utility of protein kinases as inhibitor targets because very few small molecules that selectively inhibit one particular kinase are known. Discovery of highly specific kinase inhibitors has been slow because the protein family contains approximately 2000 members, all of which share a conserved active site fold. Recent work in several laboratories has sought to circumvent the problem of kinase structural degeneracy by engineering drug sensitivity into Src family tyrosine kinases and mitogen-activated protein kinases through site-directed mutagenesis. By introducing a unique non-naturally occurring amino acid into a conserved region of the enzyme's binding site, a target protein kinase can be rapidly sensitized to a small molecule. Introduction of the engineered kinase into a cell line or animal model should greatly expedite the investigation of protein kinase inhibition as a viable drug treatment. The purpose of this review is to summarize these recent advances in protein kinase drug sensitization.

Design of allele-specific inhibitors to probe protein kinase signaling

BACKGROUND

Deconvoluting protein kinase signaling pathways using conventional genetic and biochemical approaches has been difficult because of the overwhelming number of closely related kinases. If cell-permeable inhibitors of individual kinases could be designed, the role of each kinase could be systematically assessed.

RESULTS

We have devised an approach combining chemistry and genetics to develop the first highly specific cell-permeable inhibitor of the oncogenic tyrosine kinase v-Src. A functionally silent active-site mutation was made in v-Src to distinguish it from all other cellular kinases. A tight-binding cell-permeable inhibitor of this mutant kinase that does not inhibit wild-type kinases was designed and synthesized. In vitro and whole-cell assays established the unique specificity of the mutant v-Src-inhibitor pair. The inhibitor reversed cell transformation by the engineered but not the 'wild type' v-Src, establishing that changes in cellular signaling can be attributed to specific inhibition of the engineered kinase. The generality of the method was tested by engineering another tyrosine kinase, Fyn, to contain the corresponding active-site mutation to the one in v-Src. The same compound that inhibited mutant v-Src could also potently inhibit the engineered Fyn kinase.

CONCLUSIONS

Allele-specific cell-permeable inhibitors of individual Src family kinases can be rapidly developed in an approach that should be applicable to all kinases. This approach will be useful for the deconvolution of kinase-mediated cellular pathways and for validating novel kinases as good targets for drug discovery both in vitro and in vivo.

Field studies of cadmium in potatoes (Solanum tuberosum L.) I. Effects of lime and phosphorus on cv. Russet Burbank

Field experiments were conducted at three sites on basaltic krasnozems to examine cadmium (Cd) responses of Russet Burbank potatoes to different rates of broadcast lime and banded phosphorus (P). Double superphosphate (DSP, containing 15 and 90 mg Cd kg-1) and triple superphosphate (TSP, 12 mg Cd kg-1)) were the sources of P. In a fourth experiment, lime was banded with the basal fertilizer. Despite producing a range of topsoil pH (1:5 H20) of 5.2 to 7.1, broadcast lime had no effect on tuber Cd concentrations. Lime had no effect when banded with the basal fertilizer, and the practice did not adversely affect yields. With broadcast lime, Cd availability from the fertilizer band may have been unaffected. However, there were also no lime x P interactions at any site, suggesting that lime also had no effect on the availability of Cd in the soil. It is possible that Tasmanian krasnozems, with their high organic matter and iron oxide content, restrict the availability of Cd in the soil such that pH change exerts little net influence on Cd availability. Increasing amounts of Cd applied in P fertilizer increased tuber Cd concentrations significantly, but the increases were less per unit of P than those found previously when TSP with 151 mg Cd kg-1) was used.

Field studies of cadmium in potatoes (Solanum tuberosum L.). Response of cvv. Russet Burbank and Kennebec to two double superphosphates of different cadmium concentration

Separate field experiments were conducted with Russet Burbank and Kennebec potatoes on a basaltic krasnozem where tuber cadmium (Cd) responses were examined over three rates of banded phosphorus (P), supplied as double superphosphate (DSP) containing either 15 or 90 mg Cd kg-1. In both cultivars, tuber Cd concentrations increased with rate of DSP. This response was due more to the amount of P supplied in the DSP than the amount of Cd supplied in the DSP and may be a result of banded P encouraging root proliferation in the fertilizer band. Even with DSP at 15 mg Cd kg-1, Cd additions at rates of DSP needed for high yields were 6-20 times higher than corresponding rates of Cd removal in tubers. Examination of data from all studies of Cd in Russet Burbank on Tasmanian krasnozems showed a significant relationship between petiole and tuber Cd concentrations, but the estimation of a petiole concentration associated with the critical tuber Cd concentration in Australia was subject to unacceptable uncertainty due to variation between sites.

Empirical approach to psychopharmacology for institutionalized individuals with severe or profound mental retardation

There is at this time no conceptual model of psychopharmacology for individuals with severe or profound mental retardation who exhibit behavior disorders that unifies this area of psychopharmacology with general psychiatry practice while addressing the unique aspects of this population. The following article presents a 6-step program of diagnostic inquiry and treatment strategy that allows alternate etiological hypotheses to be tested in a clinical practice framework. This format unifies psychopharmacy practice in mental retardation with psychopharmacy practice in general psychiatry.

Monitoring quality of nursing care

The first phase of a cooperative project to develop and pilot-test an improved system for monitoring the quality of nursing care is described. Evaluation criteria from existing methodologies were grouped in a comprehensive framework of nursing objectives and subobjectives, and both the framework and the criteria developed were tested statistically. The master criteria list was placed in a computer file, from which criteria subsets are systematically selected for actual quality monitoring. The methodology has been used in two pilot hospitals; in the second phase of the project, now under way, the system is being implemented in a wider sample of hospitals to further test the validity of the conceptual framework and the reliability of individual criteria.