A 5′-fluorosulfonylbenzoyladenosine-based method to identify physiological substrates of a Drosophila p21-activated kinase

Production and analysis of titin kinase: Exploiting active/inactive kinase homologs in pseudokinase validation

Protein pseudokinases are key regulators of the eukaryotic cell. Understanding their unconventional molecular mechanisms relies on deciphering their putative potential to perform phosphotransfer, their scaffolding properties and the nature of their regulation. Titin pseudokinase (TK) is the defining member of a family of poorly characterized muscle-specific kinases thought to act as sensors and transducers of mechanical signals in the sarcomere. The functional mechanisms of TK remain obscure due to the challenges posed by its production and analysis. Here, we provide guidelines and tailored research approaches for the study of TK, including profiting from its close structure-function relationship to the catalytically active homolog twitchin kinase (TwcK) from C. elegans. We describe a methodological pipeline to produce recombinant TK and TwcK samples; design, prioritize and validate mutated and truncated variants; assess sample stability and perform activity assays. The strategy is exportable to other pseudokinase members of the TK-like kinase family.

K-BILDS: A Kinase Substrate Discovery Tool

Kinases catalyze protein phosphorylation to regulate cell signaling events. However, identifying kinase substrates is challenging due to the often low abundance and dynamic nature of protein phosphorylation. Development of novel techniques to identify kinase substrates is necessary. Here, we report kinase-catalyzed biotinylation with inactivated lysates for discovery of substrates (K-BILDS) as a tool to identify direct substrates of a kinase. As a proof of concept, K-BILDS was applied to cAMP-dependent protein kinase A (PKA) with HeLa cell lysates. Subsequent enrichment and MS/MS analysis identified 279 candidate PKA substrates, including 56 previously known PKA substrates. Of the candidate substrates, nuclear autoantigenic sperm protein (NASP), BCL2-associated athanogene 3 (BAG3), and 14-3-3 protein Tau (YWHAQ) were validated as novel PKA substrates. K-BILDS provides a valuable tool to identify direct substrates of any protein kinase.

Cellular effects of photogenerated oxidants and long-lived, reactive, hydroperoxide photoproducts

Reaction of radicals and singlet oxygen ((1)O(2)) with proteins results in both direct damage and the formation of long-lived reactive hydroperoxides. Elevated levels of protein hydroperoxide-derived products have been detected in multiple human pathologies, suggesting that these secondary oxidants contribute to tissue damage. Previous studies have provided evidence for protein hydroperoxide-mediated inhibition of thiol-dependent enzymes and modulation of signaling processes in isolated systems. In this study (1)O(2) and hydroperoxides have been generated in J774A.1 macrophage-like cells using visible light and the photosensitizer rose bengal, with the consequences of oxidant formation examined both immediately and after subsequent (dark-phase) incubation. Significant losses of GSH (≤50%), total thiols (≤20%), and activity of thiol-dependent proteins (GAPDH, thioredoxin, protein tyrosine phosphatases, creatine kinase, and cathepsins B and L; 10-50% inhibition) were detected after 1 or 2 min photo-oxidation. Non-thiol-dependent enzymes were not affected. In contrast, NADPH levels increased, together with the activity of glutathione reductase, glutathione peroxidase, and thioredoxin reductase; these increases may be components of a rapid global cytoprotective cellular response to stress. Neither oxidized thioredoxin nor radical-mediated protein oxidation products were detected at significant levels. Further decreases in thiol levels and enzyme activity occurred during dark-phase incubation, with this accompanied by decreased cell viability. These secondary events are ascribed to the reactions of long-lived hydroperoxides, generated by (1)O(2)-mediated reactions. Overall, this study provides novel insights into early cellular responses to photo-oxidative damage and indicates that long-lived hydroperoxides can play a significant role in cellular damage.

Pharmacogenetic analysis reveals a post-developmental role for Rac GTPases in Caenorhabditis elegans GABAergic neurotransmission

The nerve-cell cytoskeleton is essential for the regulation of intrinsic neuronal activity. For example, neuronal migration defects are associated with microtubule regulators, such as LIS1 and dynein, as well as with actin regulators, including Rac GTPases and integrins, and have been thought to underlie epileptic seizures in patients with cortical malformations. However, it is plausible that post-developmental functions of specific cytoskeletal regulators contribute to the more transient nature of aberrant neuronal activity and could be masked by developmental anomalies. Accordingly, our previous results have illuminated functional roles, distinct from developmental contributions, for Caenorhabditis elegans orthologs of LIS1 and dynein in GABAergic synaptic vesicle transport. Here, we report that C. elegans with function-altering mutations in canonical Rac GTPase-signaling-pathway members demonstrated a robust behavioral response to a GABA(A) receptor antagonist, pentylenetetrazole. Rac mutants also exhibited hypersensitivity to an acetylcholinesterase inhibitor, aldicarb, uncovering deficiencies in inhibitory neurotransmission. RNA interference targeting Rac hypomorphs revealed synergistic interactions between the dynein motor complex and some, but not all, members of Rac-signaling pathways. These genetic interactions are consistent with putative Rac-dependent regulation of actin and microtubule networks and suggest that some cytoskeletal regulators cooperate to uniquely govern neuronal synchrony through dynein-mediated GABAergic vesicle transport in C. elegans.

The Drosophila p21-activated kinase Mbt modulates DE-cadherin-mediated cell adhesion by phosphorylation of Armadillo

Phosphorylation by tyrosine and serine/threonine kinases regulate the interactions between components of the cadherin-catenin cell-adhesion complex and thus can influence the dynamic modulation of cell adhesion under normal and disease conditions. Previous mutational analysis and localization experiments suggested an involvement of single members of the family of PAKs (p21-activated kinases) in the regulation of cadherin-mediated cell adhesion, but the molecular mechanism remained elusive. In the present study, we address this question using the Drosophila PAK protein Mbt, which is most similar to vertebrate PAK4. Previous phenotypic analysis showed that Mbt has a function to maintain adherens junctions during eye development and indicated a requirement of the protein in regulation of the actin cytoskeleton and the cadherin-catenin complex. Here we show that activation of Mbt leads to destabilization of the interaction of the Drosophila beta-catenin homologue Armadillo with DE-cadherin resulting in a decrease in DE-cadherin-mediated adhesion. Two conserved phosphorylation sites in Armadillo were identified that mediate this effect. The findings of the present study support the previous observation that activation of the human Mbt homologue PAK4 leads to anchorage-independent growth and provide a functional link between a PAK protein and the cadherin-catenin complex.