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Autophagy Jun 2021Macroautophagy/autophagy is the cellular process responsible for the elimination and recycling of aggregated proteins and damaged organelles. Whereas autophagy is...
Macroautophagy/autophagy is the cellular process responsible for the elimination and recycling of aggregated proteins and damaged organelles. Whereas autophagy is strictly regulated by several signaling cascades, the link between this process and the subcellular distribution of its regulatory pathways remains to be established. Our recent work suggests that the compartmentalization of PRKA/PKA (protein kinase cAMP-activated) determines its effects on autophagy. We found that increased cAMP levels generate dramatically different PRKA activity "signatures" mainly dependent on the actions of phosphatases and the distribution of the PRKA holoenzymes containing type II regulatory subunits (PRKAR2A and PRKAR2B; RII). In this punctum we discuss how compartmentalized PRKA signaling events are generated and affect the autophagic flux in specific cell types.
Topics: Autophagy; Phosphoric Monoester Hydrolases; Protein Kinases; Proteins; Signal Transduction
PubMed: 33971785
DOI: 10.1080/15548627.2021.1924501 -
Plant Physiology Oct 2021Protein kinase dynamics play key roles in regulation of cell differentiation, growth, development and in diverse cell signaling networks. Protein kinase sensors enable... (Review)
Review
Protein kinase dynamics play key roles in regulation of cell differentiation, growth, development and in diverse cell signaling networks. Protein kinase sensors enable visualization of protein kinase activity in living cells and tissues in time and space. These sensors have therefore become important and powerful molecular tools for investigation of diverse kinase activities and can resolve long-standing and challenging biological questions. In the present Update, we review new advanced approaches for genetically encoded protein kinase biosensor designs developed in animal systems together with the basis of each biosensor's working principle and components. In addition, we review recent first examples of real time plant protein kinase activity biosensor development and application. We discuss how these sensors have helped to resolve how stomatal signal transduction in response to elevated CO2 merges with abscisic acid signaling downstream of a resolved basal SnRK2 kinase activity in guard cells. Furthermore, recent advances, combined with the new strategies described in this Update, can help deepen the understanding of how signaling networks regulate unique functions and responses in distinct plant cell types and tissues and how different stimuli and signaling pathways can interact.
Topics: Biosensing Techniques; Plant Cells; Protein Kinases; Single-Cell Analysis
PubMed: 35142856
DOI: 10.1093/plphys/kiab277 -
Plant Communications Jan 2022Reproduction is a crucial process in the life span of flowering plants, and directly affects human basic requirements in agriculture, such as grain yield and quality.... (Review)
Review
Reproduction is a crucial process in the life span of flowering plants, and directly affects human basic requirements in agriculture, such as grain yield and quality. Typical receptor-like protein kinases (RLKs) are a large family of membrane proteins sensing extracellular signals to regulate plant growth, development, and stress responses. In and other plant species, RLK-mediated signaling pathways play essential roles in regulating the reproductive process by sensing different ligand signals. Molecular understanding of the reproductive process is vital from the perspective of controlling male and female fertility. Here, we summarize the roles of RLKs during plant reproduction at the genetic and molecular levels, including RLK-mediated floral organ development, ovule and anther development, and embryogenesis. In addition, the possible molecular regulatory patterns of those RLKs with unrevealed mechanisms during reproductive development are discussed. We also point out the thought-provoking questions raised by the research on these plant RLKs during reproduction for future investigation.
Topics: Arabidopsis; Ovule; Plants; Protein Kinases; Reproduction
PubMed: 35059634
DOI: 10.1016/j.xplc.2021.100273 -
Molecular Biology of the Cell Aug 2021With No Lysine (K) WNK kinases regulate electro-neutral cotransporters that are controlled by osmotic stress and chloride. We showed previously that autophosphorylation...
With No Lysine (K) WNK kinases regulate electro-neutral cotransporters that are controlled by osmotic stress and chloride. We showed previously that autophosphorylation of WNK1 is inhibited by chloride, raising the possibility that WNKs are activated by osmotic stress. Here we demonstrate that unphosphorylated WNK isoforms 3 and 1 autophosphorylate in response to osmotic pressure in vitro, applied with the crowding agent polyethylene glycol (PEG)400 or osmolyte ethylene glycol (EG), and that this activation is opposed by chloride. Small angle x-ray scattering of WNK3 in the presence and absence of PEG400, static light scattering in EG, and crystallography of WNK1 were used to understand the mechanism. Osmosensing in WNK3 and WNK1 appears to occur through a conformational equilibrium between an inactive, unphosphorylated, chloride-binding dimer and an autophosphorylation-competent monomer. An improved structure of the inactive kinase domain of WNK1, and a comparison with the structure of a monophosphorylated form of WNK1, suggests that large cavities, greater hydration, and specific bound water may participate in the osmosensing mechanism. Our prior work showed that osmolytes have effects on the structure of phosphorylated WNK1, suggestive of multiple stages of osmotic regulation in WNKs.
Topics: Autoradiography; Chromatography, Gel; Ethylene Glycol; Osmotic Pressure; Phosphorylation; Polyethylene Glycols; Protein Conformation; Protein Kinases; Protein Multimerization; Scattering, Small Angle; WNK Lysine-Deficient Protein Kinase 1; Water; X-Ray Diffraction
PubMed: 33689398
DOI: 10.1091/mbc.E20-01-0089 -
Pharmacological Reviews Oct 2021Mitogen-activated protein kinase (MAPK) cascades are evolutionarily conserved signaling pathways that play essential roles in transducing extracellular environmental... (Review)
Review
Mitogen-activated protein kinase (MAPK) cascades are evolutionarily conserved signaling pathways that play essential roles in transducing extracellular environmental signals into diverse cellular responses to maintain homeostasis. These pathways are classically organized into an architecture of three sequentially acting protein kinases: a MAPK kinase kinase that phosphorylates and activates a MAPK kinase, which in turn phosphorylates and activates the effector MAPK. The activity of MAPKs is tightly regulated by phosphorylation of their activation loop, which can be modulated by positive and negative feedback mechanisms to control the amplitude and duration of the signal. The signaling outcomes of MAPK pathways are further regulated by interactions of MAPKs with scaffolding and regulatory proteins. Accumulating evidence indicates that, in addition to these mechanisms, MAPK signaling is commonly regulated by ubiquitin-proteasome system (UPS)-mediated control of the stability and abundance of MAPK pathway components. Notably, the biologic activity of some MAPKs appears to be regulated mainly at the level of protein turnover. Recent studies have started to explore the potential of targeted protein degradation as a powerful strategy to investigate the biologic functions of individual MAPK pathway components and as a new therapeutic approach to overcome resistance to current small-molecule kinase inhibitors. Here, we comprehensively review the mechanisms, physiologic importance, and pharmacological potential of UPS-mediated protein degradation in the control of MAPK signaling. SIGNIFICANCE STATEMENT: Accumulating evidence highlights the importance of targeted protein degradation by the ubiquitin-proteasome system in regulating and fine-tuning the signaling output of mitogen-activated protein kinase (MAPK) pathways. Manipulating protein levels of MAPK cascade components may provide a novel approach for the development of selective pharmacological tools and therapeutics.
Topics: Humans; Mitogen-Activated Protein Kinase Kinases; Mitogen-Activated Protein Kinases; Phosphorylation; Proteasome Endopeptidase Complex; Signal Transduction; Ubiquitin
PubMed: 34732541
DOI: 10.1124/pharmrev.120.000170 -
Journal of Medicinal Chemistry Jan 2023The death-associated protein kinase (DAPK) family is a member of the calcium/calmodulin-regulated serine/threonine protein kinase family, and studies have shown that its... (Review)
Review
The death-associated protein kinase (DAPK) family is a member of the calcium/calmodulin-regulated serine/threonine protein kinase family, and studies have shown that its role, as its name suggests, is mainly to regulate cell death. The DAPK family comprises five members, including DAPK1, DAPK2, DAPK3, DRAK1 and DRAK2, which show high homology in the common N-terminal kinase domain but differ in the extra-catalytic domain. Notably, previous research has suggested that the DAPK family plays an essential role in both the development and regulation of human diseases. However, only a few small-molecule inhibitors have been reported. In this Perspective, we mainly discuss the structure, biological function, and role of DAPKs in diseases and the currently discovered small-molecule inhibitors, providing valuable information for the development of the DAPK field.
Topics: Humans; Death-Associated Protein Kinases; Protein Serine-Threonine Kinases; Catalytic Domain; Calcium-Calmodulin-Dependent Protein Kinases
PubMed: 36645394
DOI: 10.1021/acs.jmedchem.2c01606 -
Pharmacological Reviews Oct 2022The number of cancer drugs is increasing as new chemical entities are developed to target molecules, often protein kinases, driving cancer progression. In 2009, Fedorov... (Review)
Review
The number of cancer drugs is increasing as new chemical entities are developed to target molecules, often protein kinases, driving cancer progression. In 2009, Fedorov et al. identified that of the protein kinases in the human kinome, most of the focus has been on a small subset. They highlighted that many poorly investigated protein kinases were cancer drivers, but there was no relationship between publications and involvement in cancer development or progression. Since 2009, there has been a doubling in the number of publications, patents, and drugs targeting the kinome. To determine whether this was an expansion in knowledge of well-studied targets-searching in the light under the lamppost-or an explosion of investigations into previously poorly investigated targets, we searched the literature for publications on each kinase, updating Federov et al.'s assessment of the druggable kinome. The proportion of papers focusing on the 50 most-studied kinases had not changed, and the makeup of those 50 had barely changed. The majority of new drugs (80%) were against the same group of 50 kinases identified as targets 10 years ago, and the proportion of studies investigating previously poorly investigated kinases (1%) was unchanged. With three exceptions [p38 mitogenactivated protein kinase (p38a), AMP-activated protein kinase catalytic -subunit 1,2, and B-Raf proto-oncogene (BRAF) serine/threonine kinase], 95% of publications addressing kinases still focused on a relatively small proportion (50%) of the human kinome independently of their involvement as cancer drivers. There is, therefore, still extensive scope for discovery of therapeutics targeting different protein kinases in cancer and still a bias toward well-characterized targets over the innovative searchlight into the unknown. SIGNIFICANCE STATEMENT: This study presents evidence that drug discovery efforts in cancer are still to some extent focused on a narrow group of well-studied kinases 10 years after the identification of multiple novel cancer targets in the human kinome. This suggests that there is still room for researchers in academia, industry, and the not-for-profit sector to develop new and diverse therapies targeting kinases for cancer.
Topics: AMP-Activated Protein Kinases; Antineoplastic Agents; Humans; Neoplasms; Protein Kinase Inhibitors; Protein Serine-Threonine Kinases; Proto-Oncogene Proteins B-raf; Serine
PubMed: 36180110
DOI: 10.1124/pharmrev.121.000410 -
Advances in Protein Chemistry and... 2021Diabetes mellitus has emerged as a severe burden on the medical health system across the globe. Presently, around 422 million people are suffering from diabetes which is... (Review)
Review
Diabetes mellitus has emerged as a severe burden on the medical health system across the globe. Presently, around 422 million people are suffering from diabetes which is speculated to be expanded to about 600 million by 2035. Patients with type 2 diabetes are at increased risk of developing detrimental metabolic and cardiovascular complications. The scientific understanding of this chronic disease and its underlying root cause is not yet fully unraveled. Protein kinases are well known to regulate almost every cellular process through phosphorylation of target protein in diverse signaling pathways. The important role of several protein kinases including AMP-activated protein kinase, IκB kinase and protein kinase C have been well demonstrated in various animal models. They modulate glucose tolerance, inflammation and insulin resistance in the cells via acting on diverse downstream targets and signaling pathways. Thus, modulating the activity of potential human kinases which are significantly involved in diabetes by targeting with small molecule inhibitors could be an attractive therapeutic strategy to tackle diabetes. In this chapter, we have discussed the potential role of protein kinases in glucose metabolism and insulin sensitivity, and in the pathogenesis of diabetes mellitus. Furthermore, the small molecules reported in the literature that can be potentially used for the treatment of diabetes have been discussed in detail.
Topics: Animals; Diabetes Mellitus, Type 2; Glucose; Glucose Intolerance; Humans; Insulin Resistance; Protein Kinase Inhibitors; Protein Kinases; Signal Transduction
PubMed: 33632470
DOI: 10.1016/bs.apcsb.2020.11.001 -
The Journal of Biological Chemistry 2021The mitogen-activated protein kinase (MAPK) cascade is a fundamental signaling pathway that regulates cell fate decisions in response to external stimuli. Several...
The mitogen-activated protein kinase (MAPK) cascade is a fundamental signaling pathway that regulates cell fate decisions in response to external stimuli. Several scaffold proteins bind directly to kinase components of this pathway and regulate their activation by growth factors. One of the best studied MAPK scaffolds is kinase suppressor of Ras1 (KSR1), which is induced by epidermal growth factor (EGF) to translocate to the plasma membrane where it activates extracellular signal-regulated kinase (ERK). While Ca has been shown to modulate MAPK signaling, the molecular mechanisms by which this occurs are incompletely understood. Here we tested the hypothesis that Ca alters MAPK activity at least in part via KSR1. Using several approaches, including fusion proteins, immunoprecipitation, confocal microscopy, and a cell-permeable chemical inhibitor, we investigated the functional interaction between KSR1 and calmodulin. In vitro analysis with pure proteins reveals that calmodulin binds directly to KSR1. Moreover, endogenous calmodulin and KSR1 co-immunoprecipitate from mammalian cell lysates. Importantly, Ca is required for the association between calmodulin and KSR1, both in vitro and in cells. The cell-permeable calmodulin antagonist CGS9343B significantly reduced activation of ERK by EGF in mouse embryo fibroblasts that overexpress KSR1, but not in control cells. Moreover, CGS9343B impaired the ability of EGF to induce KSR1 translocation to the plasma membrane and to stimulate formation of KSR1-ERK and KSR1-pERK (phosphorylated ERK) complexes in cells. Collectively, our data identify a previously unrecognized mechanism by which the scaffold protein KSR1 couples Ca and calmodulin signaling to the MAPK cascade.
Topics: Animals; Calmodulin; MAP Kinase Signaling System; Mice; Mitogen-Activated Protein Kinases; Protein Binding; Protein Kinases
PubMed: 33766558
DOI: 10.1016/j.jbc.2021.100577 -
Pharmacological Research May 2023Because genetic alterations including mutations, overexpression, translocations, and dysregulation of protein kinases are involved in the pathogenesis of many illnesses,... (Review)
Review
Because genetic alterations including mutations, overexpression, translocations, and dysregulation of protein kinases are involved in the pathogenesis of many illnesses, this enzyme family is the target of many drug discovery programs in the pharmaceutical industry. Overall, the US FDA has approved 74 small molecule protein kinase inhibitors, nearly all of which are orally effective. Of the 74 approved drugs, thirty-nine block receptor protein-tyrosine kinases, nineteen target nonreceptor protein-tyrosine kinases, twelve are directed against protein-serine/threonine protein kinases, and four target dual specificity protein kinases. The data indicate that 65 of these medicinals are approved for the management of neoplasms (51 against solid tumors such as breast, colon, and lung cancers, eight against nonsolid tumors such as leukemia, and six against both types of tumors). Nine of the FDA-approved kinase inhibitors form covalent bonds with their target enzymes and they are accordingly classified as TCIs (targeted covalent inhibitors). Medicinal chemists have examined the physicochemical properties of drugs that are orally effective. Lipinski's rule of five (Ro5) is a computational procedure that is used to estimate solubility, membrane permeability, and pharmacological effectiveness in the drug-discovery setting. It relies on four parameters including molecular weight, number of hydrogen bond donors and acceptors, and the Log of the partition coefficient. Other important descriptors include the lipophilic efficiency, the polar surface area, and the number of rotatable bonds and aromatic rings. We tabulated these and other properties of the FDA-approved kinase inhibitors. Of the 74 approved drugs, 30 fail to comply with the rule of five.
Topics: Humans; Protein Kinase Inhibitors; Protein Serine-Threonine Kinases; Lung Neoplasms; Protein Kinases; Leukemia
PubMed: 37075870
DOI: 10.1016/j.phrs.2023.106774