UNcleProt (Universal Nuclear Protein database of barley): The first nuclear protein database that distinguishes proteins from different phases of the cell cycle

Blavet, Nicolas; Uřinovská, Jana; Jeřábková, Hana; Chamrád, Ivo; Vrána, Jan; Lenobel, René; Beinhauer, Jana; Šebela, Marek; Doležel, Jaroslav; Petrovská, Beáta

doi:10.1080/19491034.2016.1255391

Cited by 8 publications

(9 citation statements)

References 55 publications

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“…A total of 3,401 and 209 proteins accounting for 70% of both NPs and NPPs were predicted to be nuclear localized by, at least, one of the five prediction tools used (Table S4). Additionally, we compared these proteins with those listed according to the stages of cell cycle (G1, S, G2) available at UNcleProt (Blavet et al, ; Table S5). The complete lists of the proteins identified were subjected to Blast2GO analyses and classified on the basis of their GO.…”

Section: Resultsmentioning

confidence: 99%

Dehydration‐responsive nuclear proteome landscape of chickpea (Cicer arietinum L.) reveals phosphorylation‐mediated regulation of stress response

Barua

Lande

Subba

et al. 2018

Plant Cell & Environment

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Nonavailability of water or dehydration remains recurring climatic disorder affecting yield of major food crops, legumes in particular. Nuclear proteins (NPs) and phosphoproteins (NPPs) execute crucial cellular functions that form the regulatory hub for coordinated stress response. Phosphoproteins hold enormous influence over cellular signalling. Four-week-old seedlings of a grain legume, chickpea, were subjected to gradual dehydration, and NPs were extracted from unstressed control and from 72- and 144-hr stressed tissues. We identified 4,832 NPs and 478 phosphosites, corresponding to 299 unique NPPs involved in multivariate cellular processes including protein modification and gene expression regulation, among others. The identified proteins included several novel kinases, phosphatases, and transcription factors, besides 660 uncharacterized proteins. Spliceosome complex and splicing related proteins were dominant among differentially regulated NPPs, indicating their dehydration modulated regulation. Phospho-motif analysis revealed stress-induced enrichment of proline-directed serine phosphorylation. Association mapping of NPPs revealed predominance of differential phosphorylation of spliceosome and splicing associated proteins. Also, regulatory proteins of key processes viz., protein degradation, regulation of flowering time, and circadian clock were observed to undergo dehydration-induced dephosphorylation. The characterization of novel regulatory proteins would provide new insights into stress adaptation and enable directed genetic manipulations for developing climate-resilient crops.

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Section: Resultsmentioning

confidence: 99%

Dehydration‐responsive nuclear proteome landscape of chickpea (Cicer arietinum L.) reveals phosphorylation‐mediated regulation of stress response

Barua

Lande

Subba

et al. 2018

Plant Cell & Environment

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“…Recently, Blavet et al created a barley (Hordeum vulgare L., cv. Morex) nuclear protein database [40]. This database contains large numbers of proteins identified from nuclei at the G1, S, and G2 cell cycle phases, and follows on from their previous study reporting 803 proteins [72].…”

Section: Localization Analyses Of Proteins With Coiled-coil or Transmmentioning

confidence: 99%

“…http://barley.gambrinus.ueb.cas.cz/) [40]. Subsequently, more than 800 proteins was identified in rice [41,42] and Arabidopsis [37].…”

Section: Introductionmentioning

confidence: 99%

Comprehensive nuclear proteome of Arabidopsis obtained by sequential extraction

Goto

Hashizume

Fukao

et al. 2019

Nucleus

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In eukaryotes, the nucleus plays key roles in fundamental cellular processes, including DNA replication, chromatin maintenance, transcription, and translation. To better understand the functional diversity of nuclei, we developed a method for the comprehensive extraction of the nuclear proteome from Arabidopsis. We used a buffer with a high sucrose concentration to purify nuclei and then conducted solubility-based fractionation to increase proteome coverage. We identified 1539 proteins and two novel nuclear envelope (NE) proteins in the nuclear fraction of Arabidopsis cultured cells. The localization of 25 proteins was determined by GFP fusion analyses; 23 of these proteins were localized either in the nucleus or the NE-associated endoplasmic reticulum. This result was indicative of the high quality of the proteome. These findings will be useful for clarifying novel nuclear functions in plants. ARTICLE HISTORY

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“…The higher number of Arg-ending over Lys-ending peptides in the MALDI-TOF/TOF MS/MS results (but not in the ESI-based results; not shown) probably reflected the fact that Arg-peptides provide more intense signals in MALDI-TOF MS [ 50 ], and thus they are preferably selected for the subsequent data-dependent fragmentation. Database searches allowed identifying novel proteins which had not previously been recognized based on standard tryptic peptides and deposited in the database UNcleProt [ 51 ]. They accounted for around 10 % of all identifications.…”

Section: The Use Of Pseudotrypsin For Protein Identification In Prmentioning

confidence: 99%

Pseudotrypsin: A Little-Known Trypsin Proteoform

Perutka

Šebela

2018

Molecules

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Trypsin is the protease of choice for protein sample digestion in proteomics. The most typical active forms are the single-chain β-trypsin and the two-chain α-trypsin, which is produced by a limited autolysis of β-trypsin. An additional intra-chain split leads to pseudotrypsin (ψ-trypsin) with three chains interconnected by disulfide bonds, which can be isolated from the autolyzate by ion-exchange chromatography. Based on experimental data with artificial substrates, peptides, and protein standards, ψ-trypsin shows altered kinetic properties, thermodynamic stability and cleavage site preference (and partly also cleavage specificity) compared to the above-mentioned proteoforms. In our laboratory, we have analyzed the performance of bovine ψ-trypsin in the digestion of protein samples with a different complexity. It cleaves predominantly at the characteristic trypsin cleavage sites. However, in a comparison with common tryptic digestion, non-specific cleavages occur more frequently (mostly after the aromatic residues of Tyr and Phe) and more missed cleavages are generated. Because of the preferential cleavages after the basic residues and more developed side specificity, which is not expected to occur for the major trypsin forms (but may appear anyway because of their autolysis), ψ-trypsin produces valuable information, which is complementary in part to data based on a strictly specific trypsin digestion and thus can be unnoticed following common proteomics protocols.

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UNcleProt (Universal Nuclear Protein database of barley): The first nuclear protein database that distinguishes proteins from different phases of the cell cycle

Cited by 8 publications

References 55 publications

Dehydration‐responsive nuclear proteome landscape of chickpea (Cicer arietinum L.) reveals phosphorylation‐mediated regulation of stress response

Dehydration‐responsive nuclear proteome landscape of chickpea (Cicer arietinum L.) reveals phosphorylation‐mediated regulation of stress response

Comprehensive nuclear proteome of Arabidopsis obtained by sequential extraction

Pseudotrypsin: A Little-Known Trypsin Proteoform

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