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Cell Reports Jul 2023Protein phosphorylation modification is crucial for signaling transduction in plant development and environmental adaptation. By precisely phosphorylating crucial... (Review)
Review
Protein phosphorylation modification is crucial for signaling transduction in plant development and environmental adaptation. By precisely phosphorylating crucial components in signaling cascades, plants can switch on and off the specific signaling pathways needed for growth or defense. Here, we have summarized recent findings of key phosphorylation events in typical hormone signaling and stress responses. More interestingly, distinct phosphorylation patterns on proteins result in diverse biological functions of these proteins. Thus, we have also highlighted latest findings that show how the different phosphosites of a protein, also named phosphocodes, determine the specificity of downstream signaling in both plant development and stress responses.
Topics: Phosphorylation; Signal Transduction; Plants; Plant Development; Plant Proteins
PubMed: 37405922
DOI: 10.1016/j.celrep.2023.112729 -
Chemical Society Reviews Jul 2022Protein phosphorylation is a crucial regulator of protein and cellular function, yet, despite identifying an enormous number of phosphorylation sites, the role of most... (Review)
Review
Protein phosphorylation is a crucial regulator of protein and cellular function, yet, despite identifying an enormous number of phosphorylation sites, the role of most is still unclear. Each phosphoform, the particular combination of phosphorylations, of a protein has distinct and diverse biological consequences. Aberrant phosphorylation is implicated in the development of many diseases. To investigate their function, access to defined protein phosphoforms is essential. Materials obtained from cells often are complex mixtures. Recombinant methods can provide access to defined phosphoforms if site-specifically acting kinases are known, but the methods fail to provide homogenous material when several amino acid side chains compete for phosphorylation. Chemical and chemoenzymatic synthesis has provided an invaluable toolbox to enable access to previously unreachable phosphoforms of proteins. In this review, we selected important tools that enable access to homogeneously phosphorylated protein and discuss examples that demonstrate how they can be applied. Firstly, we discuss the synthesis of phosphopeptides and proteins through chemical and enzymatic means and their advantages and limitations. Secondly, we showcase illustrative examples that applied these tools to answer biological questions pertaining to proteins involved in signal transduction, control of transcription, neurodegenerative diseases and aggregation, apoptosis and autophagy, and transmembrane proteins. We discuss the opportunities and challenges in the field.
Topics: Biology; Phosphopeptides; Phosphorylation; Proteins; Signal Transduction
PubMed: 35726784
DOI: 10.1039/d1cs00991e -
The Protein Journal Feb 2017Post translational modifications (PTMs) are involved in variety of cellular activities and phosphorylation is one of the most extensively studied PTM, which regulates a... (Review)
Review
Post translational modifications (PTMs) are involved in variety of cellular activities and phosphorylation is one of the most extensively studied PTM, which regulates a number of cellular functions like cell growth, differentiation, apoptosis and cell signaling in healthy condition. However, alterations in phosphorylation pathways result in serious outcomes in the form of diseases, especially cancer. Many signalling pathways including Tyrosine kinase, MAP kinase, Cadherin-catenin complex, Cyclin-dependent kinase etc. are major players of the cell cycle and deregulation in their phosphorylation-dephosphorylation cascade has been shown to be manifested in the form of various types of cancers. Tyrosine kinase family encompasses the greatest number of oncoproteins. MAPK cascade has an importance role in cancer growth and progression. Bcl-2 family proteins serve either proapoptotic or antiapoptotic function. Cadherin-catenin complex regulates cell adhesion properties and cyclins are the key regulators of cell cycle. Altered phosphorylations in any of the above pathways are strongly associated with cancer, at the same time they serve as the potential tergets for drug development against cancer. Drugs targeting tyrosine kinase are potent anticancer drugs. Inhibitors of MEK, PI3K and ERK signalling pathways are undergoing clinical trials. Thus, drugs targeting phosphorylation pathways represent a promising area for cancer therapy.
Topics: Animals; MAP Kinase Signaling System; Neoplasm Proteins; Neoplasms; Phosphorylation; Protein Kinase Inhibitors
PubMed: 28108801
DOI: 10.1007/s10930-017-9696-z -
Bioorganic & Medicinal Chemistry Aug 2016Protein-protein interaction is one of the key events in the signal transduction pathway. The interaction changes the conformations, activities, localization and... (Review)
Review
Protein-protein interaction is one of the key events in the signal transduction pathway. The interaction changes the conformations, activities, localization and stabilities of the proteins, and transduces the signal to the next step. Frequently, this interaction occurs upon the protein phosphorylation. When upstream signals are stimulated, protein kinase(s) is/are activated and phosphorylate(s) their substrates, and induce the phosphorylation dependent protein-protein interaction. For this interaction, several domains in proteins are known to specifically recognize the phosphorylated residues of target proteins. These specific domains for interaction are important in the progression of the diseases caused by disordered signal transduction such as cancer. Thus small molecules that modulate this interaction are attractive lead compounds for the treatment of such diseases. In this review, we focused on three examples of phosphorylation dependent protein-protein interaction modules (14-3-3, polo box domain of Plk1 and F-box proteins in SCF ubiquitin ligases) and summarize small molecules that modulate their interaction. We also introduce our original screening system to identify such small molecules.
Topics: Animals; Cell Cycle Proteins; Humans; Phosphorylation; Protein Binding; Protein Interaction Maps; Signal Transduction; Small Molecule Libraries
PubMed: 27017542
DOI: 10.1016/j.bmc.2016.03.023 -
Journal of Molecular Microbiology and... 2005The first clearly established example of Ser/Thr/Tyr phosphorylation of a bacterial protein was isocitrate dehydrogenase. In 1979, 25 years after the discovery of... (Review)
Review
The first clearly established example of Ser/Thr/Tyr phosphorylation of a bacterial protein was isocitrate dehydrogenase. In 1979, 25 years after the discovery of protein phosphorylation in eukaryotes, this enzyme was reported to become phosphorylated on a serine residue. In subsequent years, numerous other bacterial proteins phosphorylated on Ser, Thr or Tyr were discovered and the corresponding protein kinases and P-protein phosphatases were identified. These protein modifications regulate all kinds of physiological processes. Ser/Thr/Tyr phosphorylation in bacteria therefore seems to play a similar important role as in eukaryotes. Surprisingly, many bacterial protein kinases do not exhibit any similarity to eukaryotic protein kinases, but rather resemble nucleotide-binding proteins or kinases phosphorylating diverse low-molecular-weight substrates.
Topics: Bacteria; Bacterial Proteins; Phosphoprotein Phosphatases; Phosphorylation; Protein Kinases
PubMed: 16415586
DOI: 10.1159/000089641 -
Molecular Biology Reports Oct 2019Protein phosphorylation is a widespread modification that and plays a significant role in marine bioadhesion. The phosphorylated proteins of the barnacle Amphibalanus...
Protein phosphorylation is a widespread modification that and plays a significant role in marine bioadhesion. The phosphorylated proteins of the barnacle Amphibalanus amphitrite can form strong ionic bonds with mineral surfaces to adapt to marine environments. The adhesion protein PC-3 in the sandcastle worm Phragmatopoma californica contains multipleserine phosphorylations. Interactions between these phosphate groups and the Mg/Ca ions are less soluble at seawater pH, making the cement less fluid and more gel-like. The scallop byssus is characterized by strong wet adhesion performance and substantial byssus secretions. Thus, the excellent underwater adhesion properties of the byssus make it an ideal candidate for studies related to the development of new and versatile composite materials. However, phosphoproteins have not been identified or studied in the scallop Chlamys farreri. Phosphorylated proteins in the C. farreri byssus protein were identified by liquid chromatography-tandem mass spectrometry (LC-MS/MS) and further confirmed by phosphorylation staining and in-gel digestion coupled with mass spectrometric analysis (GeLC-MS/MS). Finally, sequence analyses and potential functional analyses were performed for these newly identified proteins. We have identified previously unreported phosphorylation sites within the C. farreri byssus protein. The results show phosphorylation modifications in all parts of the byssus structure and four foot-specific phosphorylated proteins were verified by two types of mass spectrometry and staining. The annotation of biological functions, based on sequence alignments shows that the protein 40,215.25 is homologous with TIMP-2. Similar to the previously identified TIMP-2-like protein Sbp8-1 in the scallop byssus, it contains an abundance of phosphorylated Cys, which may promote protein polymerization. We speculate that protein 40,215.25 may play an important role in cross-linking and adhesion of the scallop byssus. The phosphorylated protein we have identified in the C. farreri byssus may be related to the formation of protein cross-linkings and adhesion of the scallop foot. Our study lays the groundwork for a better understanding of the adhesion mechanism of the scallop byssus.
Topics: Animals; Chromatography, Liquid; Gene Expression Profiling; Pectinidae; Phosphoproteins; Phosphorylation; Proteins; Sequence Alignment; Tandem Mass Spectrometry
PubMed: 31264161
DOI: 10.1007/s11033-019-04945-x -
BMC Bioinformatics Sep 2020Protein phosphorylation networks play an important role in cell signaling. In these networks, phosphorylation of a protein kinase usually leads to its activation, which...
BACKGROUND
Protein phosphorylation networks play an important role in cell signaling. In these networks, phosphorylation of a protein kinase usually leads to its activation, which in turn will phosphorylate its downstream target proteins. A phosphorylation network is essentially a causal network, which can be learned by causal inference algorithms. Prior efforts have applied such algorithms to data measuring protein phosphorylation levels, assuming that the phosphorylation levels represent protein activity states. However, the phosphorylation status of a kinase does not always reflect its activity state, because interventions such as inhibitors or mutations can directly affect its activity state without changing its phosphorylation status. Thus, when cellular systems are subjected to extensive perturbations, the statistical relationships between phosphorylation states of proteins may be disrupted, making it difficult to reconstruct the true protein phosphorylation network. Here, we describe a novel framework to address this challenge.
RESULTS
We have developed a causal discovery framework that explicitly represents the activity state of each protein kinase as an unmeasured variable and developed a novel algorithm called "InferA" to infer the protein activity states, which allows us to incorporate the protein phosphorylation level, pharmacological interventions and prior knowledge. We applied our framework to simulated datasets and to a real-world dataset. The simulation experiments demonstrated that explicit representation of activity states of protein kinases allows one to effectively represent the impact of interventions and thus enabled our framework to accurately recover the ground-truth causal network. Results from the real-world dataset showed that the explicit representation of protein activity states allowed an effective and data-driven integration of the prior knowledge by InferA, which further leads to the recovery of a phosphorylation network that is more consistent with experiment results.
CONCLUSIONS
Explicit representation of the protein activity states by our novel framework significantly enhances causal discovery of protein phosphorylation networks.
Topics: Algorithms; Gene Regulatory Networks; Humans; Phosphorylation; Proteins
PubMed: 32938361
DOI: 10.1186/s12859-020-03676-2 -
Journal of Cell Science Aug 2021The F-BAR protein Imp2 is an important contributor to cytokinesis in the fission yeast Schizosaccharomyces pombe. Because cell cycle-regulated phosphorylation of the...
The F-BAR protein Imp2 is an important contributor to cytokinesis in the fission yeast Schizosaccharomyces pombe. Because cell cycle-regulated phosphorylation of the central intrinsically disordered region (IDR) of the Imp2 paralog Cdc15 controls Cdc15 oligomerization state, localization and ability to bind protein partners, we investigated whether Imp2 is similarly phosphoregulated. We found that Imp2 is endogenously phosphorylated on 28 sites within its IDR, with the bulk of phosphorylation being constitutive. In vitro, the casein kinase 1 (CK1) isoforms Hhp1 and Hhp2 can phosphorylate 17 sites, and Cdk1 (also known as Cdc2) can phosphorylate the remaining 11 sites. Mutations that prevent Cdk1 phosphorylation result in precocious Imp2 recruitment to the cell division site, and mutations designed to mimic these phosphorylation events delay Imp2 accumulation at the contractile ring (CR). Mutations that eliminate CK1 phosphorylation sites allow CR sliding, and phosphomimetic substitutions at these sites reduce Imp2 protein levels and slow CR constriction. Thus, like Cdc15, the Imp2 IDR is phosphorylated at many sites by multiple kinases. In contrast to Cdc15, for which phosphorylation plays a major cell cycle regulatory role, Imp2 phosphorylation is primarily constitutive, with milder effects on localization and function. This article has an associated First Person interview with the first author of the paper.
Topics: Cell Cycle Proteins; Cytokinesis; Cytoskeletal Proteins; GTP-Binding Proteins; Phosphorylation; Protein Kinases; Schizosaccharomyces; Schizosaccharomyces pombe Proteins
PubMed: 34402513
DOI: 10.1242/jcs.258645 -
Angewandte Chemie (International Ed. in... Oct 2014Proteins interact with each other to fulfill their functions. The importance of weak protein-protein interactions has been increasingly recognized. However, owing to...
Proteins interact with each other to fulfill their functions. The importance of weak protein-protein interactions has been increasingly recognized. However, owing to technical difficulties, ultra-weak interactions remain to be characterized. Phosphorylation can take place via a K(D)≈25 mM interaction between two bacterial enzymes. Using paramagnetic NMR spectroscopy and with the introduction of a novel Gd(III)-based probe, we determined the structure of the resulting complex to atomic resolution. The structure accounts for the mechanism of phosphoryl transfer between the two enzymes and demonstrates the physical basis for their ultra-weak interaction. Further, molecular dynamics (MD) simulations suggest that the complex has a lifetime in the micro- to millisecond regimen. Hence such interaction is termed a fleeting interaction. From mathematical modeling, we propose that an ultra-weak fleeting interaction enables rapid flux of phosphoryl signal, providing a high effective protein concentration.
Topics: Molecular Dynamics Simulation; Nuclear Magnetic Resonance, Biomolecular; Phosphorylation; Proteins; Signal Transduction
PubMed: 25131700
DOI: 10.1002/anie.201405976 -
Molecular Cell Jun 2022Protein phosphorylation is a reversible post-translational modification. Nine of the 20 natural amino acids in proteins can be phosphorylated, but most of what we know... (Review)
Review
Protein phosphorylation is a reversible post-translational modification. Nine of the 20 natural amino acids in proteins can be phosphorylated, but most of what we know about the roles of protein phosphorylation has come from studies of serine, threonine, and tyrosine phosphorylation. Much less is understood about the phosphorylation of histidine, lysine, arginine, cysteine, aspartate, and glutamate, so-called non-canonical phosphorylations. Phosphohistidine (pHis) was discovered 60 years ago as a mitochondrial enzyme intermediate; since then, evidence for the existence of histidine kinases and phosphohistidine phosphatases has emerged, together with examples where protein function is regulated by reversible histidine phosphorylation. pHis is chemically unstable and has thus been challenging to study. However, the recent development of tools for studying pHis has accelerated our understanding of the multifaceted functions of histidine phosphorylation, revealing a large number of proteins that are phosphorylated on histidine and implicating pHis in a wide range of cellular processes.
Topics: Histidine; Phosphorylation; Phosphotyrosine; Proteins
PubMed: 35654043
DOI: 10.1016/j.molcel.2022.05.007