The Arabidopsis thaliana PeptideAtlas; harnessing world-wide proteomics data for a comprehensive community proteomics resource

We developed a new resource, the Arabidopsis PeptideAtlas (www.peptideatlas.org/builds/arabidopsis/), to solve central questions about the Arabidopsis proteome, such as the significance of protein splice forms, post-translational modifications (PTMs), or simply obtain reliable information about specific proteins. PeptideAtlas is based on published mass spectrometry (MS) analyses collected through ProteomeXchange and reanalyzed through a uniform processing and metadata annotation pipeline. All matched MS-derived peptide data are linked to spectral, technical and biological metadata. Nearly 40 million out of ~143 million MSMS spectra were matched to the reference genome Araport11, identifying ~0.5 million unique peptides and 17858 uniquely identified proteins (only isoform per gene) at the highest confidence level (FDR 0.0004; 2 non-nested peptides ≥ 9 aa each), assigned canonical proteins, and 3543 lower confidence proteins. Physicochemical protein properties were evaluated for targeted identification of unobserved proteins. Additional proteins and isoforms currently not in Araport11 were identified, generated from pseudogenes, alternative start, stops and/or splice variants and sORFs; these features should be considered for updates to the Arabidopsis genome. Phosphorylation can be inspected through a sophisticated PTM viewer. This new PeptideAtlas is integrated with community resources including TAIR, tracks in JBrowse, PPDB and UniProtKB. Subsequent PeptideAtlas builds will incorporate millions more MS data.

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Proteomic Analysis of Capacitated and Non-Capacitated Spermatozoa of Yanbian Yellow Cattle

10.21203/rs.3.rs-125470/v1 ◽

2020 ◽

Author(s):

Xuan Chen ◽

Zuochen Li ◽

Yanqiu Lv ◽

Yichao Xu ◽

Mimi Cheng ◽

...

Keyword(s):

Protein Transport ◽

Expression Level ◽

Molecular Processes ◽

Proteomics Data ◽

Pathway Enrichment ◽

Protein Protein Interaction ◽

Go Enrichment ◽

Yellow Cattle ◽

Specific Proteins ◽

The Difference

Abstract Background: Sperm capacitation is a process which occurs prior to fertilization, and is essential for producing high-quality living embryos. The main purpose of this study was to explore the difference of proteomics between capacitated and non-capacitated sperm of Yanbian yellow cattle. Bioinformatic analyses of LC-MS/MS data included GO enrichment, KEGG pathway enrichment, and protein-protein interaction (PPI) analysis. Results: The results revealed 23 specific proteins in the capacitated group and 345 in the non-capacitated group. Compared with non-capacitated sperm, capacitated sperm exhibited 89 upregulated proteins and 509 downregulated proteins. Western blotting was used to confirm our proteomics data. The expression level of PSMD1 in the capacitated sperm group was significantly lower than that in the non-capacitated sperm group, and the expression level of HSPA5 was significantly higher than in the non-capacitated sperm group. Conclusions: Our results revealed that many proteins were differentially expressed between capacitated and non-capacitated sperm, particularly those involved in the proteasome signaling and protein transport signaling pathways. This work enhances our understanding of molecular processes involved in sperm viability in Yanbian yellow cattle, and provides a framework for future studies.

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Molecular dynamics shows complex interplay and long-range effects of post-translational modifications in yeast protein interactions

PLoS Computational Biology ◽

10.1371/journal.pcbi.1008988 ◽

2021 ◽

Vol 17 (5) ◽

pp. e1008988

Author(s):

Nikolina ŠoŠtarić ◽

Vera van Noort

Keyword(s):

Molecular Dynamics ◽

Conformational Changes ◽

Protein Interactions ◽

Protein Structures ◽

Cellular Protein ◽

Free Energy Calculations ◽

Protein Protein Interactions ◽

Post Translational Modifications ◽

Protein Properties ◽

Dynamics Simulations

Post-translational modifications (PTMs) play a vital, yet often overlooked role in the living cells through modulation of protein properties, such as localization and affinity towards their interactors, thereby enabling quick adaptation to changing environmental conditions. We have previously benchmarked a computational framework for the prediction of PTMs’ effects on the stability of protein-protein interactions, which has molecular dynamics simulations followed by free energy calculations at its core. In the present work, we apply this framework to publicly available data on Saccharomyces cerevisiae protein structures and PTM sites, identified in both normal and stress conditions. We predict proteome-wide effects of acetylations and phosphorylations on protein-protein interactions and find that acetylations more frequently have locally stabilizing roles in protein interactions, while the opposite is true for phosphorylations. However, the overall impact of PTMs on protein-protein interactions is more complex than a simple sum of local changes caused by the introduction of PTMs and adds to our understanding of PTM cross-talk. We further use the obtained data to calculate the conformational changes brought about by PTMs. Finally, conservation of the analyzed PTM residues in orthologues shows that some predictions for yeast proteins will be mirrored to other organisms, including human. This work, therefore, contributes to our overall understanding of the modulation of the cellular protein interaction networks in yeast and beyond.

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The olfactory secretome varies according to season in female sheep and goat

10.21203/rs.2.12918/v4 ◽

2019 ◽

Author(s):

Paul CANN ◽

Malika CHABI ◽

Aliénor DELSART ◽

Chrystelle LE DANVIC ◽

Jean-Michel SALIOU ◽

...

Keyword(s):

Sexual Activity ◽

Hormonal Control ◽

Physiological Status ◽

Sexually Active ◽

Hormonal Changes ◽

Seasonal Breeding ◽

Proteomics Data ◽

Specific Expression ◽

Two Dimensional Gel Electrophoresis ◽

Post Translational Modifications

Abstract Abstract: Background : Small ungulates (sheep and goat) display a seasonal breeding, characterised by two successive periods, sexual activity (SA) and sexual rest (SR). Odours emitted by a sexually active male can reactivate the ovulation of anoestrus females. The plasticity of the olfactory system under these hormonal changes has never been explored at the peripheral level of odours reception. As it was shown in pig that the olfactory secretome (proteins secreted in the nasal mucus) could be modified under hormonal control, we monitored its composition in females of both species through several reproductive seasons, thanks to a non-invasive sampling of olfactory mucus. For this purpose, two-dimensional gel electrophoresis (2D-E), western-blot with specific antibodies, MALDI-TOF and high-resolution (nano-LC-MS/MS) mass spectrometry, RACE-PCR and molecular modelling were used. Results : In both species the olfactory secretome is composed of isoforms of OBP-like proteins, generated by post-translational modifications, as phosphorylation, N-glycosylation and O -GlcNAcylation. Important changes were observed in the olfactory secretome between the sexual rest and the sexual activity periods, characterised in ewe by the specific expression of SAL-like proteins and the emergence of OBPs O- GlcNAcylation. In goat, the differences between SA and SR did not come from new proteins expression, but from different post-translational modifications, the main difference between the SA and SR secretome being the number of isoforms of each protein. Proteomics data are available via ProteomeXchange with identifier PXD014833. Conclusion : Despite common behaviour, seasonal breeding, and genetic resources, the two species seem to adapt their sensory equipment in SA by different modalities: the variation of olfactory secretome in ewe could correspond to a specialization to detect male odours only in SA, whereas in goat the stability of the olfactory secretome could indicate a constant capacity of odours detection suggesting that the hallmark of SA in goat might be the emission of specific odours by the sexually active male. In both species, the olfactory secretome is a phenotype reflecting the physiological status of females, and could be used by breeders to monitor their receptivity to the male effect.

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Distribution and oligomeric association of splice forms of Na+-K+-ATPase regulatory γ-subunit in rat kidney

AJP Renal Physiology ◽

10.1152/ajprenal.00146.2001 ◽

2002 ◽

Vol 282 (3) ◽

pp. F393-F407 ◽

Cited By ~ 55

Author(s):

Elena Arystarkhova ◽

Randall K. Wetzel ◽

Kathleen J. Sweadner

Keyword(s):

Splice Variants ◽

Rat Kidney ◽

Thick Ascending Limb ◽

Outer Medulla ◽

Α Subunit ◽

Proximal Tubule Cells ◽

Γ Subunit ◽

Outer Stripe ◽

A Minor ◽

Splice Forms

Renal Na+-K+-ATPase is associated with the γ-subunit (FXYD2), a single-span membrane protein that modifies ATPase properties. There are two splice variants with different amino termini, γa and γb. Both were found in the inner stripe of the outer medulla in the thick ascending limb. Coimmunoprecipitation with each other and the α-subunit indicated that they were associated in macromolecular complexes. Association was controlled by ligands that affect Na+-K+-ATPase conformation. In the cortex, the proportion of the γb-subunit was markedly lower, and the γa-subunit predominated in isolated proximal tubule cells. By immunofluorescence, the γb-subunit was detected in the superficial cortex only in the distal convoluted tubule and connecting tubule, which are rich in Na+-K+-ATPase but comprise a minor fraction of cortex mass. In the outer stripe of the outer medulla and for a short distance in the deep cortex, the thick ascending limb predominantly expressed the γb-subunit. Because different mechanisms maintain and regulate Na+ homeostasis in different nephron segments, the splice forms of the γ-subunit may have evolved to control the renal Na+ pump through pump properties, gene expression, or both.

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Post-Translational Modifications of Proteins: Novel Insights in the Autoimmune Response in Rheumatoid Arthritis

Cells ◽

10.3390/cells8070657 ◽

2019 ◽

Vol 8 (7) ◽

pp. 657 ◽

Cited By ~ 10

Author(s):

Francesco Carubbi ◽

Alessia Alunno ◽

Roberto Gerli ◽

Roberto Giacomelli

Keyword(s):

Rheumatoid Arthritis ◽

Wide Spectrum ◽

Clinical Manifestations ◽

Autoimmune Response ◽

Response To Treatment ◽

Post Translational Modifications ◽

Wide Range ◽

Specific Proteins ◽

Modified Proteins ◽

Immunogenic Properties

Post-translational modifications (PTM) are chemical changes mostly catalyzed by enzymes that recognize specific target sequences in specific proteins. These modifications play a key role in regulating the folding of proteins, their targeting to specific subcellular compartments, their interaction with ligands or other proteins, and eventually their immunogenic properties. Citrullination is the best characterized PTM in the field of rheumatology, with antibodies anticyclic citrullinated peptides being the gold standard for the diagnosis of rheumatoid arthritis (RA). In recent years, growing evidence supports not only that a wide range of proteins are subject to citrullination and can trigger an autoimmune response in RA, but also that several other PTMs such as carbamylation and acetylation occur in patients with this disease. This induces a wide spectrum of autoantibodies, as biomarkers, with different sensitivity and specificity for diagnosis, which may be linked to peculiar clinical manifestations and/or response to treatment. The purpose of this review article is to critically summarize the available literature on antibodies against post-translationally modified proteins, in particular antibodies against citrullinated proteins (ACPA) and antibodies against modified proteins (AMPA), and outline their diagnostic and prognostic role to be implemented in clinical practice for RA patients.

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Identification of embryo specific human isoforms using a database of predicted alternative splice forms

Journal of Integrative Bioinformatics ◽

10.1515/jib-2006-17 ◽

2006 ◽

Vol 3 (1) ◽

pp. 1-10

Author(s):

Heike Pospisil

Keyword(s):

Alternative Splice ◽

Splice Site ◽

Splice Variants ◽

Main Idea ◽

Protein Isoforms ◽

Unequal Distribution ◽

Interesting Candidate ◽

Alternatively Spliced ◽

Specific Alternative ◽

Splice Forms

Abstract Alternative splicing is one of the most important mechanisms to generate a large number of mRNA and protein isoforms from a small number of genes. Its study became one of the hot topics in computational genome analysis. The repository EASED (Extended Alternatively Spliced EST Database, http://eased.bioinf.mdc-berlin.de/) stores a large collection of splice variants predicted from comparing the human genome against EST databases. It enables finding new unpublished splice forms that could be interesting candidate genes for stage specific, diseases specific or tissue specific splicing. The main idea behind selecting specific splice forms is to compare the number and the origin of ESTs confirming one isoform with the number and the origin of ESTs confirming the opposite isoform. A measure asDcs is introduced to take into account the unequal distribution of ESTs per splice site on one hand, and the possible uncertainties due to the relatively low quality of EST data on the other hand. First, the number of ESTs per splice site is scaled with a modified Hill function. The measure asDcs computes in the second step the distance of each pair of ESTs from equipartition. Equipartition exists if for every number of adult ESTs the same number of embryonic ESTs. The effect of several input parameters for the scaling of true EST values is analysed and can be reproduced on http://cardigan.zbh.uni-hamburg.de/asDcs. Some of the obtained best scoring hits for selected parameters (transcription factor P65, drebrin, and fetuin) have been already described in literature as been involved in embryonic development. This result shows the plausibility of this approach and looks promising for the identification of unplublished embryo specific alternative splice sites in human.

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Parasites, proteomes and systems: has Descartes’ clock run out of time?

Parasitology ◽

10.1017/s0031182012000716 ◽

2012 ◽

Vol 139 (9) ◽

pp. 1103-1118 ◽

Cited By ~ 18

Author(s):

J. M. WASTLING ◽

S. D. ARMSTRONG ◽

R. KRISHNA ◽

D. XIA

Keyword(s):

Systems Biology ◽

Protein Interactions ◽

Biological Data ◽

Protein Protein Interactions ◽

Proteomics Data ◽

Data Types ◽

Quality Of Data ◽

Post Translational Modifications ◽

Systems Modelling ◽

New Generation

SUMMARYSystems biology aims to integrate multiple biological data types such as genomics, transcriptomics and proteomics across different levels of structure and scale; it represents an emerging paradigm in the scientific process which challenges the reductionism that has dominated biomedical research for hundreds of years. Systems biology will nevertheless only be successful if the technologies on which it is based are able to deliver the required type and quality of data. In this review we discuss how well positioned is proteomics to deliver the data necessary to support meaningful systems modelling in parasite biology. We summarise the current state of identification proteomics in parasites, but argue that a new generation of quantitative proteomics data is now needed to underpin effective systems modelling. We discuss the challenges faced to acquire more complete knowledge of protein post-translational modifications, protein turnover and protein-protein interactions in parasites. Finally we highlight the central role of proteome-informatics in ensuring that proteomics data is readily accessible to the user-community and can be translated and integrated with other relevant data types.

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High-Density Lipoproteins-Associated Proteins and Subspecies Related to Arterial Stiffness in Young Adults with Type 2 Diabetes Mellitus

Complexity ◽

10.1155/2018/7514709 ◽

2018 ◽

Vol 2018 ◽

pp. 1-14

Author(s):

Xiaoting Zhu ◽

Amy S. Shah ◽

Debi K. Swertfeger ◽

Hailong Li ◽

Sheng Ren ◽

...

Keyword(s):

Type 2 Diabetes ◽

Arterial Stiffness ◽

High Density ◽

High Density Lipoproteins ◽

Proteomics Data ◽

Association Analyses ◽

Associated Proteins ◽

Specific Proteins ◽

Related Proteins

Lower plasma levels of high-density lipoproteins (HDL) in adolescents with type 2 diabetes (T2D) have been associated with a higher pulse wave velocity (PWV), a marker of arterial stiffness. Evidence suggests that HDL proteins or particle subspecies are altered in T2D and these may drive these relationships. In this work, we set out to reveal any specific proteins and subspecies that are related to arterial stiffness in youth with T2D from proteomics data. Plasma and PWV measurements were previously acquired from lean and T2D adolescents. Each plasma sample was separated into 18 fractions and evaluated by mass spectrometry. Then, we applied a validated network-based computational approach to reveal HDL subspecies associated with PWV. Among 68 detected phospholipid-associated proteins, we found that seven were negatively correlated with PWV, indicating that they may be atheroprotective. Conversely, nine proteins show positive correlation with PWV, suggesting that they may be related to arterial stiffness. Intriguingly, our results demonstrate that apoA-I and histidine-rich glycoprotein may reverse their protective roles and become antagonistic in the setting of T2D. Furthermore, we revealed two arterial stiffness-associated HDL subspecies, each of which contains multiple PWV-related proteins. Correlation and disease association analyses suggest that these HDL subspecies might link T2D to its cardiovascular-related complications.

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Four novel splice variants of sulfonylurea receptor 1

AJP Cell Physiology ◽

10.1152/ajpcell.00083.2002 ◽

2002 ◽

Vol 283 (2) ◽

pp. C587-C598 ◽

Cited By ~ 18

Author(s):

Annette Hambrock ◽

Regina Preisig-Müller ◽

Ulrich Russ ◽

Anke Piehl ◽

Peter J. Hanley ◽

...

Keyword(s):

Fluorescent Protein ◽

Splice Variants ◽

Functional Characterization ◽

Pcr Analysis ◽

Sulfonylurea Receptor ◽

Transmembrane Segments ◽

Sulfonylurea Receptor 1 ◽

Green Fluorescent ◽

Splice Forms

ATP-sensitive K+ (KATP) channels are composed of pore-forming Kir6.x subunits and regulatory sulfonylurea receptor (SUR) subunits. SURs are ATP-binding cassette proteins with two nucleotide-binding folds (NBFs) and binding sites for sulfonylureas, like glibenclamide, and for channel openers. Here we report the identification and functional characterization of four novel splice forms of guinea pig SUR1. Three splice forms originate from alternative splicing of the region coding for NBF1 and lack exons 17 (SUR1Δ17), 19 (SUR1Δ19), or both (SUR1Δ17Δ19). The fourth (SUR1C) is a COOH-terminal SUR1-fragment formed by exons 31–39 containing the last two transmembrane segments and the COOH terminus of SUR1. RT-PCR analysis showed that these splice forms are expressed in several tissues with strong expression of SUR1C in cardiomyocytes. Confocal microscopy using enhanced green fluorescent protein-tagged SUR or Kir6.x did not provide any evidence for involvement of these splice forms in the mitochondrial KATP channel. Only SUR1 and SUR1Δ17 showed high-affinity binding of glibenclamide ( K d≈ 2 nM in the presence of 1 mM ATP) and formed functional KATPchannels upon coexpression with Kir6.2.

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