The Arabidopsis thaliana 2-D gel mitochondrial proteome: Refining the value of reference maps for assessing protein abundance, contaminants and post-translational modifications

PROTEOMICS ◽  
2011 ◽  
Vol 11 (9) ◽  
pp. 1720-1733 ◽  
Author(s):  
Nicolas L. Taylor ◽  
Joshua L. Heazlewood ◽  
A. Harvey Millar
Keyword(s):  
Arabidopsis Thaliana ◽  
Protein Abundance ◽  
Post Translational Modifications ◽  
Mitochondrial Proteome

scholarly journals Integration and Visualization of Regulatory Elements and Variations of the EPAS1 Gene in Human

Genes ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1793
Author(s):  
Aleša Kristan ◽  
Nataša Debeljak ◽  
Tanja Kunej
Keyword(s):  
Target Genes ◽  
Regulatory Elements ◽  
Future Research ◽  
Protein Abundance ◽  
Interacting Proteins ◽  
Pas Domain ◽  
Expression Stability ◽  
Post Translational Modifications ◽  
Oxygen Homeostasis ◽  
Cancer Types

Endothelial PAS domain-containing protein 1 (EPAS1), also HIF2α, is an alpha subunit of hypoxia-inducible transcription factor (HIF), which mediates cellular and systemic response to hypoxia. EPAS1 has an important role in the transcription of many hypoxia-responsive genes, however, it has been less researched than HIF1α. The aim of this study was to integrate an increasing number of data on EPAS1 into a map of diverse OMICs elements. Publications, databases, and bioinformatics tools were examined, including Ensembl, MethPrimer, STRING, miRTarBase, COSMIC, and LOVD. The EPAS1 expression, stability, and activity are tightly regulated on several OMICs levels to maintain complex oxygen homeostasis. In the integrative EPAS1 map we included: 31 promoter-binding proteins, 13 interacting miRNAs and one lncRNA, and 16 post-translational modifications regulating EPAS1 protein abundance. EPAS1 has been associated with various cancer types and other diseases. The development of neuroendocrine tumors and erythrocytosis was shown to be associated with 11 somatic and 20 germline variants. The integrative map also includes 12 EPAS1 target genes and 27 interacting proteins. The study introduced the first integrative map of diverse genomics, transcriptomics, proteomics, regulomics, and interactomics data associated with EPAS1, to enable a better understanding of EPAS1 activity and regulation and support future research.

scholarly journals Post-Translational Modifications of the Endogenous and Transgenic FLC Protein in Arabidopsis thaliana

2008 ◽  
Vol 49 (12) ◽  
pp. 1859-1866 ◽  
Author(s):  
Masumi Robertson ◽  
Chris A. Helliwell ◽  
Elizabeth S. Dennis
Keyword(s):  
Arabidopsis Thaliana ◽  
Post Translational Modifications

scholarly journals Quantitative Proteome and PTMome Analysis of Arabidopsis Thaliana Root Responses to Persistent Osmotic and Salinity Stress.

2021 ◽  
Author(s):  
M C Rodriguez ◽  
D Mehta ◽  
M Tan ◽  
R G Uhrig
Keyword(s):  
Arabidopsis Thaliana ◽  
Salt Stress ◽  
Stress Responses ◽  
Protein Level ◽  
Economic Losses ◽  
Plant Responses ◽  
Protein Abundance ◽  
Lysine Acetylation ◽  
Label Free ◽  
Proteome Level

ABSTRACT Abiotic stresses such as drought result in large annual economic losses around the world. As sessile organisms, plants cannot escape the environmental stresses they encounter, but instead must adapt to survive. Studies investigating plant responses to osmotic and/or salt stress have largely focused on short-term systemic responses, leaving our understanding of intermediate to longer-term adaptation (24 h - days) lacking. In addition to protein abundance and phosphorylation changes, evidence suggests reversible lysine acetylation may also be important for abiotic stress responses. Therefore, to characterize the protein-level effects of osmotic and salt stress, we undertook a label-free proteomic analysis of Arabidopsis thaliana roots exposed to 300 mM Mannitol and 150 mM NaCl for 24 h. We assessed protein phosphorylation, lysine acetylation and changes in protein abundance, detecting significant changes in 245, 35 and 107 total proteins, respectively. Comparison with available transcriptome data indicates that transcriptome- and proteome-level changes occur in parallel, while PTMs do not. Further, we find significant changes in PTMs and protein abundance involve different proteins from the same networks, indicating a multifaceted regulatory approach to prolonged osmotic and salt stress. In particular, we find extensive protein-level changes involving sulphur metabolism under both osmotic and salt conditions as well as changes in protein kinases and transcription factors that may represent new targets for drought stress signaling. Collectively, we find that protein-level changes continue to occur in plant roots 24 h from the onset of osmotic and salt stress and that these changes differ across multiple proteome levels.

Phosphoproteomic studies in Arabidopsis and tobacco male gametophytes

2014 ◽  
Vol 42 (2) ◽  
pp. 383-387 ◽  
Author(s):  
Jan Fíla ◽  
Věra Čapková ◽  
David Honys
Keyword(s):  
Amino Acids ◽  
Arabidopsis Thaliana ◽  
Cell Wall ◽  
Nicotiana Tabacum ◽  
Pollen Tube ◽  
Protein Phosphorylation ◽  
Pollen Tube Growth ◽  
Mature Pollen ◽  
Phosphorylation Sites ◽  
Post Translational Modifications

Mature pollen represents an extremely resistant quiescent structure surrounded by a tough cell wall. After its hydration on stigma papillary cells, pollen tube growth starts rapidly. Massive metabolic changes are likely to be accompanied by changes in protein phosphorylation. Protein phosphorylation belongs among the most rapid post-translational modifications. To date, only Arabidopsis thaliana and tobacco (Nicotiana tabacum) mature pollen have been subjected to phosphoproteomic studies in order to identify the phosphoproteins present. In the present mini-review, Arabidopsis and tobacco datasets were compared with each other. The representation of the O-phosphorylated amino acids was compared between these two datasets, and the putative pollen-specific or pollen-abundant phosphopeptides were highlighted. Finally, the phosphorylation sites common for both Arabidopsis and tobacco phosphoproteins are listed as well as the phosphorylation motifs identified.

scholarly journals Proteomic analysis of cell cycle progression in asynchronous cultures, including mitotic subphases, using PRIMMUS

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Tony Ly ◽  
Arlene Whigham ◽  
Rosemary Clarke ◽  
Alejandro J Brenes-Murillo ◽  
Brett Estes ◽  
...  
Keyword(s):  
Gene Expression ◽  
Mass Spectrometry ◽  
Proteomic Analysis ◽  
Cell Cycle Progression ◽  
Protein Abundance ◽  
Phosphorylation Sites ◽  
Mitotic Progression ◽  
Cycle Progression ◽  
Post Translational Modifications ◽  
Temporal Regulation

The temporal regulation of protein abundance and post-translational modifications is a key feature of cell division. Recently, we analysed gene expression and protein abundance changes during interphase under minimally perturbed conditions (Ly et al., 2014, 2015). Here, we show that by using specific intracellular immunolabelling protocols, FACS separation of interphase and mitotic cells, including mitotic subphases, can be combined with proteomic analysis by mass spectrometry. Using this PRIMMUS (PRoteomic analysis of Intracellular iMMUnolabelled cell Subsets) approach, we now compare protein abundance and phosphorylation changes in interphase and mitotic fractions from asynchronously growing human cells. We identify a set of 115 phosphorylation sites increased during G2, termed ‘early risers’. This set includes phosphorylation of S738 on TPX2, which we show is important for TPX2 function and mitotic progression. Further, we use PRIMMUS to provide the first a proteome-wide analysis of protein abundance remodeling between prophase, prometaphase and anaphase.

scholarly journals Importance of Post-Translational Modifications for Functionality of a Chloroplast-Localized Carbonic Anhydrase (CAH1) in Arabidopsis thaliana

PLoS ONE ◽  
2011 ◽  
Vol 6 (6) ◽  
pp. e21021 ◽  
Author(s):  
Stefan Burén ◽  
Cristina Ortega-Villasante ◽  
Amaya Blanco-Rivero ◽  
Andrea Martínez-Bernardini ◽  
Tatiana Shutova ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Carbonic Anhydrase ◽  
Post Translational Modifications

scholarly journals Characterization of the Free and Membrane-Associated Fractions of the Thylakoid Lumen Proteome in Arabidopsis thaliana

2021 ◽  
Vol 22 (15) ◽  
pp. 8126
Author(s):  
Peter J. Gollan ◽  
Andrea Trotta ◽  
Azfar A. Bajwa ◽  
Ilaria Mancini ◽  
Eva-Mari Aro
Keyword(s):  
Arabidopsis Thaliana ◽  
Photosynthetic Electron Transport ◽  
Oxygen Evolving Complex ◽  
Ps Ii ◽  
Post Translational Modifications ◽  
Thylakoid Lumen ◽  
Novel Proteins ◽  
The Difference ◽  
Oxygen Evolving

The thylakoid lumen houses proteins that are vital for photosynthetic electron transport, including water-splitting at photosystem (PS) II and shuttling of electrons from cytochrome b6f to PSI. Other lumen proteins maintain photosynthetic activity through biogenesis and turnover of PSII complexes. Although all lumen proteins are soluble, these known details have highlighted interactions of some lumen proteins with thylakoid membranes or thylakoid-intrinsic proteins. Meanwhile, the functional details of most lumen proteins, as well as their distribution between the soluble and membrane-associated lumen fractions, remain unknown. The current study isolated the soluble free lumen (FL) and membrane-associated lumen (MAL) fractions from Arabidopsis thaliana, and used gel- and mass spectrometry-based proteomics methods to analyze the contents of each proteome. These results identified 60 lumenal proteins, and clearly distinguished the difference between the FL and MAL proteomes. The most abundant proteins in the FL fraction were involved in PSII assembly and repair, while the MAL proteome was enriched in proteins that support the oxygen-evolving complex (OEC). Novel proteins, including a new PsbP domain-containing isoform, as well as several novel post-translational modifications and N-termini, are reported, and bi-dimensional separation of the lumen proteome identified several protein oligomers in the thylakoid lumen.

scholarly journals The biogenesis of CLEL peptides involves several processing events in consecutive compartments of the secretory pathway

2018 ◽  
Author(s):  
Nils Stührwohldt ◽  
Stefan Scholl ◽  
Lisa Lang ◽  
Julia Katzenberger ◽  
Karin Schumacher ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Growth And Development ◽  
Secretory Pathway ◽  
Plant Growth And Development ◽  
Tyrosine Sulfation ◽  
Post Translational Modifications ◽  
Stringent Control ◽  
Peptide Precursors ◽  
Modified Peptides ◽  
Proline Hydroxylation

AbstractPost-translationally modified peptides are involved in many aspects of plant growth and development. The maturation of these peptides from their larger precursors is still poorly understood. We show here that the biogenesis of CLEL6 and CLEL9 peptides in Arabidopsis thaliana requires a series of processing events in consecutive compartments of the secretory pathway. Following cleavage of the signal peptide upon entry into the endoplasmic reticulum (ER), the peptide precursors are processed in the cis-Golgi by the subtilase SBT6.1. SBT6.1-mediated cleavage within the variable domain allows for continued passage of the partially processed precursors through the secretory pathway, and is a prerequisite for subsequent post-translational modifications including tyrosine sulfation and proline hydroxylation within, and proteolytic maturation after exit from the Golgi. Activation by subtilase SBT3.8 in post-Golgi compartments depends on the N-terminal aspartate of the mature peptides. Our work highlights the complexity of post-translational precursor maturation allowing for stringent control of peptide biogenesis.

scholarly journals Proteomic analysis of cell cycle progression in asynchronous cultures, including mitotic subphases, using PRIMMUS

2017 ◽  
Author(s):  
Tony Ly ◽  
Arlene Whigham ◽  
Rosemary Clarke ◽  
Alejandro Brenes-Murillo ◽  
Brett Estes ◽  
...  
Keyword(s):  
Gene Expression ◽  
Mass Spectrometry ◽  
Proteomic Analysis ◽  
Cell Cycle Progression ◽  
Protein Abundance ◽  
Phosphorylation Sites ◽  
Mitotic Progression ◽  
Cycle Progression ◽  
Post Translational Modifications ◽  
Temporal Regulation

AbstractThe temporal regulation of protein abundance and post-translational modifications is a key feature of cell division. Recently, we analysed gene expression and protein abundance changes during interphase under minimally perturbed conditions (Ly et al. 2014; Ly et al. 2015). Here we show that by using specific intracellular immunolabeling protocols, FACS separation of interphase and mitotic cells, including mitotic subphases, can be combined with proteomic analysis by mass spectrometry. Using this PRIMMUS (PRoteomic analysis of Intracellular iMMUnolabeled cell Subsets) approach, we now compare protein abundance and phosphorylation changes in interphase and mitotic fractions from asynchronously growing human cells. We identify a set of 115 phosphorylation sites increased during G2, which we term ‘early risers’. This set includes phosphorylation of S738 on TPX2, which we show is important for TPX2 function and mitotic progression. Further, we use PRIMMUS to provide a proteome-wide analysis of protein abundance remodeling between prophase, prometaphase and anaphase.

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