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Evolution of protein phosphorylation across 18 fungal species

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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An Augmented Multiple-Protease-Based Human Phosphopeptide Atlas
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Weak functional constraints on phosphoproteomes
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Value of Using Multiple Proteases for Large-Scale Mass Spectrometry-Based Proteomics
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Molecular evidence for an ancient duplication of the entire yeast genome
inferredcites →https://doi.org/10.1038/nbt.1566openalex-snapshot
Sensitive multiplexed analysis of kinase activities and activity-based kinase identification
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The SCX/IMAC enrichment approach for global phosphorylation analysis by mass spectrometry
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Evolution of transcription factor binding in metazoans — mechanisms and functional implications
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A comprehensive library of histone mutants identifies nucleosomal residues required for H3K4 methylation
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Characterization of yeast pyruvate kinase 1 as a protein kinase A substrate, and specificity of the phosphorylation site sequence in the whole protein
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Regulatory evolution in proteins by turnover and lineage-specific changes of cyclin-dependent kinase consensus sites
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GPS 2.0, a Tool to Predict Kinase-specific Phosphorylation Sites in Hierarchy
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APE: Analyses of Phylogenetics and Evolution in R language
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Jalview Version 2—a multiple sequence alignment editor and analysis workbench
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Biopython: freely available Python tools for computational molecular biology and bioinformatics
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The Newick utilities: high-throughput phylogenetic tree processing in the U nix shell
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featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
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The PhosphoGRID Saccharomyces cerevisiae protein phosphorylation site database: version 2.0 update
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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
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A High-Definition View of Functional Genetic Variation from Natural Yeast Genomes
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Tree of Life Reveals Clock-Like Speciation and Diversification
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The FoldX web server: an online force field
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Saccharomyces Genome Database: the genomics resource of budding yeast
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EvolView, an online tool for visualizing, annotating and managing phylogenetic trees
inferredcites →https://doi.org/10.1093/nar/gkt1158openalex-snapshot
Saccharomycesgenome database provides new regulation data
inferredcites →https://doi.org/10.1093/nar/gku1158openalex-snapshot
The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026334openalex-snapshot
Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis
inferredcites →https://doi.org/10.1101/gad.1362105openalex-snapshot
Biochemical and genetic analysis of the yeast proteome with a movable ORF collection
inferredcites →https://doi.org/10.1126/science.1090005openalex-snapshot
Evolution at Two Levels in Humans and Chimpanzees
inferredcites →https://doi.org/10.1126/science.1172867openalex-snapshot
Global Analysis of Cdk1 Substrate Phosphorylation Sites Provides Insights into Evolution
inferredcites →https://doi.org/10.1126/science.1180189openalex-snapshot
Phosphorylation of H2A by Bub1 Prevents Chromosomal Instability Through Localizing Shugoshin
inferredcites →https://doi.org/10.1126/science.1198851openalex-snapshot
Transient Activation of the HOG MAPK Pathway Regulates Bimodal Gene Expression
inferredcites →https://doi.org/10.1186/gb-2013-14-4-r36openalex-snapshot
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
inferredcites →https://doi.org/10.1186/s13059-014-0550-8openalex-snapshot
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
inferredcites →https://doi.org/10.1371/journal.pbio.0060038openalex-snapshot
The Evolution of Combinatorial Gene Regulation in Fungi
inferredcites →https://doi.org/10.1371/journal.pbio.1000134openalex-snapshot
Evolution of Phosphoregulation: Comparison of Phosphorylation Patterns across Yeast Species
inferredcites →https://doi.org/10.1371/journal.pgen.1004062openalex-snapshot
Functional Divergence and Evolutionary Turnover in Mammalian Phosphoproteomes
inferredcites →https://doi.org/10.1371/journal.pone.0003273openalex-snapshot
Unphosphorylated SR-Like Protein Npl3 Stimulates RNA Polymerase II Elongation
inferredcites →https://doi.org/10.1371/journal.pone.0021169openalex-snapshot
Predicting Protein Kinase Specificity: Predikin Update and Performance in the DREAM4 Challenge
inferredcites →https://doi.org/10.7554/elife.00603openalex-snapshot
Evolutionary principles of modular gene regulation in yeasts

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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A Tyrosine Phosphorylation Cycle of a Plant Receptor Ser/Thr Kinase Controls the on and Off of Chitin Signaling
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Importance of protein Ser/Thr/Tyr phosphorylation for bacterial pathogenesis
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Finding the ΔΔG spot: Are predictors of binding affinity changes upon mutations in protein–protein interactions ready for it?
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Recent advances in MOF–phosphate interaction-based bioanalysis: from enrichment to sensing
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Bioinformatics Approaches for Fungal Biotechnology
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Relationship between perturbation specificity and functional dispensability in yeast phosphoproteome
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The phosphorylation landscape of infection-related development by the rice blast fungus
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Phosphoproteomic Analysis across the Yeast Life Cycle Reveals Control of Fatty Acyl Chain Length by Phosphorylation of the Fatty Acid Synthase Complex
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Sequence and Structure-Based Analysis of Specificity Determinants in Eukaryotic Protein Kinases
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ADP-ribosylome analysis reveals homogeneous DNA-damage-induced serine ADP-ribosylation across wild-type and BRCA-mutant breast cancer cell lines
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Conservation of metabolic regulation by phosphorylation and non-covalent small-molecule interactions
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The substrate quality of CK2 target sites has a determinant role on their function and evolution
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A Tyrosine Phosphorylation Cycle Regulates Fungal Activation of a Plant Receptor Ser/Thr Kinase
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PTMoreR-enabled cross-species PTM mapping and comparative phosphoproteomics across mammals
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Insights regarding fungal phosphoproteomic analysis
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The evolution of post-translational modifications
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Evolution of short linear motifs and disordered proteins Topic: yeast as model system to study evolution
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Analysis of eIF4E-family members in fungi contributes to their classification in eukaryotes
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Diazonium-based derivatization for enhanced detection of phosphorylated metabolites by LC-MS in cells
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The mechanism of iron-compensation for manganese deficiency of Streptococcus pneumoniae
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Decoding Post-Translational Modification Crosstalk With Proteomics
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Mitochondrial protein phosphorylation in yeast revisited
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Evolution, dynamics and dysregulation of kinase signalling
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Homing in: Mechanisms of Substrate Targeting by Protein Kinases
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The expanding landscape of canonical and non-canonical protein phosphorylation
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Mass spectrometry-based phosphoproteomics in clinical applications
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Systematic Identification of Protein Phosphorylation-Mediated Interactions
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ProteoSushi: A Software Tool to Biologically Annotate and Quantify Modification-Specific, Peptide-Centric Proteomics Data Sets
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Profiling the Human Phosphoproteome to Estimate the True Extent of Protein Phosphorylation
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Profiling of Yeast Saccharomyces cerevisiae Mitochondrial AMPylome Reveals a Regulation of OXPHOS Coupling through ATP Synthase Subunit Delta
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Phosphate Group-Derivated Bipyridine–Ruthenium Complex and Titanium Dioxide Nanoparticles for Electrochemical Sensing of Protein Kinase Activity
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Hydrogen bond based smart polymer for highly selective and tunable capture of multiply phosphorylated peptides
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A phosphorylation switch turns a positive regulator of phototropism into an inhibitor of the process
inferred← citeshttps://doi.org/10.1038/s41467-019-09695-9openalex-snapshot
Metabolic profiling of cancer cells reveals genome-wide crosstalk between transcriptional regulators and metabolism
inferred← citeshttps://doi.org/10.1038/s41467-019-09952-xopenalex-snapshot
Conserved phosphorylation hotspots in eukaryotic protein domain families
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Estimating dispensable content in the human interactome
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Mapping protein states and interactions across the tree of life with co-fractionation mass spectrometry
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Distinct functional constraints driving conservation of the cofilin N-terminal regulatory tail
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Global comparative structural analysis of responses to protein phosphorylation
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Evolutionary tuning of the molecular charge state of UBP24 shapes responses to high temperature
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The functional landscape of the human phosphoproteome
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High-throughput functional characterization of protein phosphorylation sites in yeast
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The regulatory landscape of the yeast phosphoproteome
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The fitness cost of spurious phosphorylation
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Reconstructing phosphorylation signalling networks from quantitative phosphoproteomic data
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Evolution of resilience in protein interactomes across the tree of life
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The evolutionary scaling of cellular traits imposed by the drift barrier
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Nuclear receptor phosphorylation in xenobiotic signal transduction
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Computational prediction and analysis of species-specific fungi phosphorylation via feature optimization strategy
inferred← citeshttps://doi.org/10.1093/bib/bbz169openalex-snapshot
EPSD: a well-annotated data resource of protein phosphorylation sites in eukaryotes
inferred← citeshttps://doi.org/10.1093/bioinformatics/btab284openalex-snapshot
DIAmeter: matching peptides to data-independent acquisition mass spectrometry data
inferred← citeshttps://doi.org/10.1093/genetics/iyad087openalex-snapshot
y-mtPTM: Yeast mitochondrial posttranslational modification database
inferred← citeshttps://doi.org/10.1093/molbev/msx320openalex-snapshot
Most m6A RNA Modifications in Protein-Coding Regions Are Evolutionarily Unconserved and Likely Nonfunctional
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A genetic analysis reveals novel histone residues required for transcriptional reprogramming upon stress
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Data-driven identification of inherent features of eukaryotic stress-responsive genes
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Protein Management
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Global analysis of specificity determinants in eukaryotic protein kinases
inferred← citeshttps://doi.org/10.1101/2020.10.26.355438openalex-snapshot
Evolutionary dynamics of neutral phenotypes under DNA substitution models
inferred← citeshttps://doi.org/10.1101/2021.12.15.472747openalex-snapshot
Non-random organization of flux control mechanisms in yeast central metabolic pathways
inferred← citeshttps://doi.org/10.1101/2023.12.15.571635openalex-snapshot
A Site-Specific Analysis of the ADP-Ribosylome Unveils Homogeneous DNA Damage-Induced Serine ADP-Ribosylation Across Wild-Type and BRCA-Mutant Breast Cancer Cell Lines
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Profiling of yeast Saccharomyces cerevisiae mitochondrial AMPylome reveals a regulation of ATP synthase coupling trough subunit δ
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Deep Learning-coupled Proximity Proteomics to Deconvolve Kinase Signaling In Vivo
inferred← citeshttps://doi.org/10.1101/872770openalex-snapshot
Towards a systematic map of the functional role of protein phosphorylation
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The Functional Role of Fungi and Bacteria in Sulfur Cycling During Kelp ( Ecklonia Radiata ) Degradation: Unconventional Use of PiCrust2
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What is the main mechanism of the origin of phosphorylation sites? Still an open question
inferred← citeshttps://doi.org/10.1126/science.aai8833openalex-snapshot
Young phosphorylation is functionally silent
inferred← citeshttps://doi.org/10.1128/jvi.00200-26openalex-snapshot
Evolution-guided prioritization identifies a tissue-specific phosphorylation switch on herpes simplex virus 1 UL7 regulating viral replication and pathogenicity
inferred← citeshttps://doi.org/10.1128/jvi.01055-20openalex-snapshot
Phosphoregulation of a Conserved Herpesvirus Tegument Protein by a Virally Encoded Protein Kinase in Viral Pathogenicity and Potential Linkage between Its Evolution and Viral Phylogeny
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Ancient Regulatory Role of Lysine Acetylation in Central Metabolism
inferred← citeshttps://doi.org/10.1128/spectrum.00127-22openalex-snapshot
Coordinated Regulation of Membrane Homeostasis and Drug Accumulation by Novel Kinase STK-17 in Response to Antifungal Azole Treatment
inferred← citeshttps://doi.org/10.1186/s12862-022-02088-5openalex-snapshot
Positive selection-driven fixation of a hominin-specific amino acid mutation related to dephosphorylation in IRF9
inferred← citeshttps://doi.org/10.1186/s12864-018-4661-6openalex-snapshot
Evaluation of functionality for serine and threonine phosphorylation with different evolutionary ages in human and mouse
inferred← citeshttps://doi.org/10.1186/s42483-024-00270-9openalex-snapshot
Unraveling the phosphorylation landscape: a leap forward in understanding the rice blast fungus pathogenicity
inferred← citeshttps://doi.org/10.1371/journal.pbio.3000341openalex-snapshot
Evolution of protein kinase substrate recognition at the active site
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1006349openalex-snapshot
Discerning evolutionary trends in post-translational modification and the effect of intrinsic disorder: Analysis of methylation, acetylation and ubiquitination sites in human proteins
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1010013openalex-snapshot
Are transient protein-protein interactions more dispensable?
inferred← citeshttps://doi.org/10.1371/journal.pgen.1007092openalex-snapshot
Flip/flop mating-type switching in the methylotrophic yeast Ogataea polymorpha is regulated by an Efg1-Rme1-Ste12 pathway
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A functionally divergent intrinsically disordered region underlying the conservation of stochastic signaling
inferred← citeshttps://doi.org/10.15252/embr.202051121openalex-snapshot
In-depth and 3-dimensional exploration of the budding yeast phosphoproteome
inferred← citeshttps://doi.org/10.1534/g3.116.037218openalex-snapshot
The Pivotal Role of Protein Phosphorylation in the Control of Yeast Central Metabolism
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iProteinDB: An Integrative Database of Drosophila Post-translational Modifications
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Gly-LysPred: Identification of Lysine Glycation Sites in Protein Using Position Relative Features and Statistical Moments Via Chou’s 5 Step Rule
inferred← citeshttps://doi.org/10.3389/fbinf.2021.690769openalex-snapshot
Mutation Edgotype Drives Fitness Effect in Human
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Phospho-Regulation of Meiotic Prophase
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Post-translational Modification Crosstalk and Hotspots in Sirtuin Interactors Implicated in Cardiovascular Diseases
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The Anti-Fungal Activity of Nitropropenyl Benzodioxole (NPBD), a Redox-Thiol Oxidant and Tyrosine Phosphatase Inhibitor
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eIF4E and Interactors from Unicellular Eukaryotes
inferred← citeshttps://doi.org/10.5772/intechopen.1015651openalex-snapshot
Phosphorylation and Its Influence on Fungal Nutrient Sensing
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Plk1 mitotic phosphorylation in the N-terminal region of the BRCA2 protein : identification, characterization and role in protein interactions
inferred← citeshttps://doi.org/10.70675/defa0693z9da4z4615z8ce2z63f207c08391openalex-snapshot
Décryptage des cascades de signalisation liées au stress par phosphoprotéomique et génétique fonctionnelle chez Botrytis cinerea
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Peer Review #1 of "Phospho-islands and the evolution of phosphorylated amino acids in mammals (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.10436v0.1/reviews/2openalex-snapshot
Peer Review #2 of "Phospho-islands and the evolution of phosphorylated amino acids in mammals (v0.1)"
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Understanding evolutionary dynamics of phosphorylation with fungal species as model system
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Phospho-islands and the evolution of phosphorylated amino acids in mammals
Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.