4.3 Article

Plant Phosphoproteomics: Known Knowns, Known Unknowns, and Unknown Unknowns of an Emerging Systems Science Frontier

Related references

Note: Only part of the references are listed.
Review Biochemical Research Methods

EPSD: a well-annotated data resource of protein phosphorylation sites in eukaryotes

Shaofeng Lin et al.

Summary: Protein phosphorylation is crucial in regulating biological processes in eukaryotes, with a growing number of phosphorylation sites being identified through mass spectrometry-based phosphoproteomics. The development of the eukaryotic phosphorylation site database (EPSD) has provided a comprehensive collection and annotation of phosphorylation sites in eukaryotic proteins, serving as a valuable resource for further analysis in this field.

BRIEFINGS IN BIOINFORMATICS (2021)

Article Multidisciplinary Sciences

The membrane-localized protein kinase MAP4K4/TOT3 regulates thermomorphogenesis

Lam Dai Vu et al.

Summary: Through a phosphoproteomics approach, this study identifies MITOGEN-ACTIVATED PROTEIN KINASE TOT3 as a regulator of thermomorphogenesis in both wheat and Arabidopsis, affecting brassinosteroid signaling in Arabidopsis. This expands our understanding of thermal regulation in plants and can contribute to food security under changing climate conditions.

NATURE COMMUNICATIONS (2021)

Article Multidisciplinary Sciences

Mapping proteome-wide targets of protein kinases in plant stress responses

Pengcheng Wang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Multidisciplinary Sciences

Mass-spectrometry-based draft of the Arabidopsis proteome

Julia Mergner et al.

NATURE (2020)

Article Multidisciplinary Sciences

Proteomic and transcriptomic profiling of aerial organ development in Arabidopsis

Julia Mergner et al.

SCIENTIFIC DATA (2020)

Review Plant Sciences

Updates on BES1/BZR1 Regulatory Networks Coordinating Plant Growth and Stress Responses

Alfredo Kono et al.

FRONTIERS IN PLANT SCIENCE (2020)

Article Plant Sciences

The Plant PTM Viewer, a central resource for exploring plant protein modifications

Patrick Willems et al.

PLANT JOURNAL (2019)

Article Biochemistry & Molecular Biology

Strong anion exchange-mediated phosphoproteomics reveals extensive human non-canonical phosphorylation

Gemma Hardman et al.

EMBO JOURNAL (2019)

Article Multidisciplinary Sciences

Phosphoproteomics of Arabidopsis Highly ABA-Induced1 identifies AT-Hook-Like10 phosphorylation required for stress growth regulation

Min May Wong et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Review Biotechnology & Applied Microbiology

Plant Proteome Databases and Bioinformatic Tools: An Expert Review and Comparative Insights

Pratigya Subba et al.

OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY (2019)

Article Plant Sciences

Early mannitol-triggered changes in the Arabidopsis leaf (phospho) proteome reveal growth regulators

Natalia Nikonorova et al.

JOURNAL OF EXPERIMENTAL BOTANY (2018)

Article Biochemical Research Methods

Universal Plant Phosphoproteomics Workflow and Its Application to Tomato Signaling in Response to Cold Stress

Chuan-Chih Hsu et al.

MOLECULAR & CELLULAR PROTEOMICS (2018)

Article Biochemistry & Molecular Biology

Reciprocal Regulation of the TOR Kinase and ABA Receptor Balances Plant Growth and Stress Response

Pengcheng Wang et al.

MOLECULAR CELL (2018)

Review Plant Sciences

Nuclear Signaling of Plant MAPKs

Jean Bigeard et al.

FRONTIERS IN PLANT SCIENCE (2018)

Article Multidisciplinary Sciences

An extracellular network of Arabidopsis leucine-rich repeat receptor kinases

Elwira Smakowska-Luzan et al.

NATURE (2018)

Article Plant Sciences

Protein sumoylation and phosphorylation intersect in Arabidopsis signaling

Ella Nukarinen et al.

PLANT JOURNAL (2017)

Article Plant Sciences

Abundant protein phosphorylation potentially regulates Arabidopsis anther development

Juanying Ye et al.

JOURNAL OF EXPERIMENTAL BOTANY (2016)

Letter Biochemistry & Molecular Biology

A Quantitative Phosphoproteome Analysis of cGMP-Dependent Cellular Responses in Arabidopsis thaliana

Claudius Marondedze et al.

MOLECULAR PLANT (2016)

Article Biotechnology & Applied Microbiology

A proteomic atlas of the legume Medicago truncatula and its nitrogen-fixing endosymbiont Sinorhizobium meliloti

Harald Marx et al.

NATURE BIOTECHNOLOGY (2016)

Article Multidisciplinary Sciences

PP2A-3 interacts with ACR4 and regulates formative cell division in the Arabidopsis root

Kun Yue et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

Review Biochemical Research Methods

Advances in targeted proteomics and applications to biomedical research

Tujin Shi et al.

PROTEOMICS (2016)

Article Plant Sciences

A phylogenetic approach to study the origin and evolution of the CRINKLY4 family

Natalia Nikonorova et al.

FRONTIERS IN PLANT SCIENCE (2015)

Article Biotechnology & Applied Microbiology

The Arabidopsis Kinome: phylogeny and evolutionary insights into functional diversification

Monika Zulawski et al.

BMC GENOMICS (2014)

Article Biochemical Research Methods

A Kinase-Phosphatase Signaling Module with BSK8 and BSL2 Involved in Regulation of Sucrose-Phosphate Synthase

XuNa Wu et al.

JOURNAL OF PROTEOME RESEARCH (2014)

Article Biochemistry & Molecular Biology

EKPD: a hierarchical database of eukaryotic protein kinases and protein phosphatases

Yongbo Wang et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Biochemistry & Molecular Biology

P3DB 3.0: From plant phosphorylation sites to protein networks

Qiuming Yao et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Plant Sciences

Phosphoproteomic Analyses Reveal Early Signaling Events in the Osmotic Stress Response

Kelly E. Stecker et al.

PLANT PHYSIOLOGY (2014)

Article Multidisciplinary Sciences

A Peptide Hormone and Its Receptor Protein Kinase Regulate Plant Cell Expansion

Miyoshi Haruta et al.

SCIENCE (2014)

Article Biochemistry & Molecular Biology

TOR and S6K1 promote translation reinitiation of uORF-containing mRNAs via phosphorylation of eIF3h

Mikhail Schepetilnikov et al.

EMBO JOURNAL (2013)

Article Biochemical Research Methods

Identification of Novel in vivo MAP Kinase Substrates in Arabidopsis thaliana Through Use of Tandem Metal Oxide Affinity Chromatography

Wolfgang Hoehenwarter et al.

MOLECULAR & CELLULAR PROTEOMICS (2013)

Article Biochemical Research Methods

Sucrose-induced Receptor Kinase SIRK1 Regulates a Plasma Membrane Aquaporin in Arabidopsis

Xu Na Wu et al.

MOLECULAR & CELLULAR PROTEOMICS (2013)

Article Multidisciplinary Sciences

Glucose-TOR signalling reprograms the transcriptome and activates meristems

Yan Xiong et al.

NATURE (2013)

Article Biochemistry & Molecular Biology

PhosPhAt goes kinases-searchable protein kinase target information in the plant phosphorylation site database PhosPhAt

Monika Zulawski et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Multidisciplinary Sciences

Quantitative phosphoproteomics identifies SnRK2 protein kinase substrates and reveals the effectors of abscisic acid action

Pengcheng Wang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Biochemical Research Methods

Targeted Quantitative Phosphoproteomics Approach for the Detection of Phospho-tyrosine Signaling in Plants

Sharon C. Mithoe et al.

JOURNAL OF PROTEOME RESEARCH (2012)

Article Plant Sciences

Characterization of the phosphoproteome of mature Arabidopsis pollen

Pururawa Mayank et al.

PLANT JOURNAL (2012)

Article Plant Sciences

Quantitative Phosphoproteome Profiling of Iron-Deficient Arabidopsis Roots

Ping Lan et al.

PLANT PHYSIOLOGY (2012)

Article Plant Sciences

Phosphoproteomic Analysis of Seed Maturation in Arabidopsis, Rapeseed, and Soybean

Louis J. Meyer et al.

PLANT PHYSIOLOGY (2012)

Article Multidisciplinary Sciences

Sensitive kinase assay linked with phosphoproteomics for identifying direct kinase substrates

Liang Xue et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Biochemical Research Methods

Evaluation of HCD- and CID-type Fragmentation Within Their Respective Detection Platforms For Murine Phosphoproteomics

Mark P. Jedrychowski et al.

MOLECULAR & CELLULAR PROTEOMICS (2011)

Review Biotechnology & Applied Microbiology

SnRK2 Protein Kinases-Key Regulators of Plant Response to Abiotic Stresses

Anna Kulik et al.

OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY (2011)

Article Multidisciplinary Sciences

Arabidopsis decuple mutant reveals the importance of SnRK2 kinases in osmotic stress responses in vivo

Hiroaki Fujii et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Multidisciplinary Sciences

Comparative phosphoproteome profiling reveals a function of the STN8 kinase in fine-tuning of cyclic electron flow (CEF)

Sonja Reiland et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Biochemical Research Methods

Systematic evaluation of alternating CID and ETD fragmentation for phosphorylated peptides

Min-Sik Kim et al.

PROTEOMICS (2011)

Article Biochemistry & Molecular Biology

Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana

Jelle Van Leene et al.

MOLECULAR SYSTEMS BIOLOGY (2010)

Article Multidisciplinary Sciences

In planta changes in protein phosphorylation induced by the plant hormone abscisic acid

Kelli G. Kline et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Biochemical Research Methods

Phosphoproteomic analysis of nuclei-enriched fractions from Arabidopsis thaliana

Alexandra M. E. Jones et al.

JOURNAL OF PROTEOMICS (2009)

Article Biochemical Research Methods

A simple and effective method for detecting phosphopeptides for phosphoproteomic analysis

Zenglan Wang et al.

JOURNAL OF PROTEOMICS (2009)

Article Multidisciplinary Sciences

Type 2C protein phosphatases directly regulate abscisic acid-activated protein kinases in Arabidopsis

Taishi Umezawa et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Article Biochemical Research Methods

A survey of the Arabidopsis thaliana mitochondrial phosphoproteome

Jun Ito et al.

PROTEOMICS (2009)

Review Plant Sciences

Protein tyrosine phosphorylation in plants: more abundant than expected?

Sergio de la Fuente van Bentem et al.

TRENDS IN PLANT SCIENCE (2009)

Article Biochemical Research Methods

Site-specific phosphorylation profiling of Arabidopsis proteins by mass spectrometry and peptide chip analysis

Sergio de la Fuente van Bentem et al.

JOURNAL OF PROTEOME RESEARCH (2008)

Article Biochemical Research Methods

Proteomics studies of brassinosteroid signal transduction using prefractionation and two-dimensional DIGE

Wenqiang Tang et al.

MOLECULAR & CELLULAR PROTEOMICS (2008)

Article Biochemistry & Molecular Biology

Large-scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis

Naoyuki Sugiyama et al.

MOLECULAR SYSTEMS BIOLOGY (2008)

Article Biochemical Research Methods

Temporal analysis of sucrose-induced phosphorylation changes in plasma membrane proteins of Arabidopsis

Totte Niittylae et al.

MOLECULAR & CELLULAR PROTEOMICS (2007)

Article Biochemical Research Methods

A tandem affinity purification-based technology platform to study the cell cycle interactome in Arabidopsis thaliana

Jelle Van Leene et al.

MOLECULAR & CELLULAR PROTEOMICS (2007)

Article Biochemical Research Methods

Quantitative phosphoproteomics of early elicitor signaling in Arabidopsis

Joris J. Benschop et al.

MOLECULAR & CELLULAR PROTEOMICS (2007)

Article Biochemical Research Methods

Proteome and phosphoproteome dynamic change during cell dedifferentiation in Arabidopsis

Brahmananda Reddy Chitteti et al.

PROTEOMICS (2007)

Article Multidisciplinary Sciences

Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry

Henrik Molina et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Biochemical Research Methods

Analysis of the defence phosphoproteome of Arabidopsis thaliana using differential mass tagging

Alexandra M. E. Jones et al.

PROTEOMICS (2006)

Article Biochemistry & Molecular Biology

Phosphoproteomics reveals extensive in vivo phosphorylation of Arabidopsis proteins involved in RNA metabolism

Sergio de la Fuente van Bentem et al.

NUCLEIC ACIDS RESEARCH (2006)

Article Biochemistry & Molecular Biology

Genome-wide analysis and experimentation of plant serine/threonine/tyrosine-specific protein kinases

P Rudrabhatla et al.

PLANT MOLECULAR BIOLOGY (2006)

Article Biochemistry & Molecular Biology

Phosphoproteomics of the arabidopsis plasma membrane and a new phosphorylation site database

TS Nühse et al.

PLANT CELL (2004)

Article Chemistry, Multidisciplinary

A mechanism-based cross-linker for the identification of kinase-substrate pairs

DJ Maly et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2004)

Article Multidisciplinary Sciences

The protein kinase complement of the human genome

G Manning et al.

SCIENCE (2002)

Article Multidisciplinary Sciences

Expression and disruption of the Arabidopsis TOR (target of rapamycin) gene

B Menand et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)

Article Plant Sciences

Plant two-component signaling systems and the role of response regulators

J Lohrmann et al.

PLANT PHYSIOLOGY (2002)