Percentage of predicted candidate proteins for <i>S</i>-nitrosylation in signaling subclasses.

<p>Functional classification of the predicted candidates has been done using the MapMan Ontology software (<a href="http://mapman.gabipd.org/web/guest/mapman" target="_blank">http://mapman.gabipd.org/web/guest/mapman</a>).</p><p>Percentage of predicted candidate proteins for <i>S</i>-nitrosylation in signaling subclasses.</p

Functional distribution of predicted candidate proteins for <i>S</i>-nitrosylation has been determined using the MapMan Ontology tool (http://mapman.gabipd.org/).

<p>Others; include all functional classes which have less than 5% of predicted candidates.</p

Computational Prediction of Candidate Proteins for S-Nitrosylation in <i>Arabidopsis thaliana</i>

<div><p>Nitric oxide (NO) is an important signaling molecule that regulates many physiological processes in plants. One of the most important regulatory mechanisms of NO is S-nitrosylation—the covalent attachment of NO to cysteine residues. Although the involvement of cysteine S-nitrosylation in the regulation of protein functions is well established, its substrate specificity remains unknown. Identification of candidates for S-nitrosylation and their target cysteine residues is fundamental for studying the molecular mechanisms and regulatory roles of S-nitrosylation in plants. Several experimental methods that are based on the biotin switch have been developed to identify target proteins for S-nitrosylation. However, these methods have their limits. Thus, computational methods are attracting considerable attention for the identification of modification sites in proteins. Using GPS-SNO version 1.0, a recently developed S-nitrosylation site-prediction program, a set of 16,610 candidate proteins for S-nitrosylation containing 31,900 S-nitrosylation sites was isolated from the entire <i>Arabidopsis</i> proteome using the medium threshold. In the compartments “chloroplast,” “CUL4-RING ubiquitin ligase complex,” and “membrane” more than 70% of the proteins were identified as candidates for S-nitrosylation. The high number of identified candidates in the proteome reflects the importance of redox signaling in these compartments. An analysis of the functional distribution of the predicted candidates showed that proteins involved in signaling processes exhibited the highest prediction rate. In a set of 46 proteins, where 53 putative S-nitrosylation sites were already experimentally determined, the GPS-SNO program predicted 60 S-nitrosylation sites, but only 11 overlap with the results of the experimental approach. In general, a computer-assisted method for the prediction of targets for S-nitrosylation is a very good tool; however, further development, such as including the three dimensional structure of proteins in such analyses, would improve the identification of S-nitrosylation sites.</p></div

Percentage of candidate proteins for <i>S</i>-nitrosylation in different functional categories.

<p>Functional assignment has been done using the MapMan Ontology tool (<a href="http://mapman.gabipd.org/web/guest/mapman" target="_blank">http://mapman.gabipd.org/web/guest/mapman</a>).</p

Subcellular compartment classification of <i>Arabidopsis</i> proteins.

<p>Total number of proteins, number of predicted candidates for <i>S</i>-nitrosylation, and the number of candidates with the highest 10% prediction confidence were assigned to their subcellular localization according to gene ontology cellular component classification. The prediction confidence was calculated by dividing the raw score value by the cutoff value of a particular cluster.</p><p>Subcellular compartment classification of <i>Arabidopsis</i> proteins.</p

Computational prediction of <i>S</i>-nitrosylation sites from experimentally identified <i>S</i>-nitrosylated proteins in plants using GPS-SNO 1.0, iSNO-PseAAC, iSNO-AAPair, and SNOSite software.

<p>Amino acid sequences were downloaded from the most recent version of the <i>Arabidopsis</i> information resource TAIR (TAIR10, <a href="http://www.arabidopsis.org" target="_blank">www.arabidopsis.org</a>) and subjected to the different programs for prediction of S-nitrosylation sites. NPR1, non-expresser of pathogenesis related genes 1; GAPDH, glyceraldehyde 3-phosphate dehydrogenase; SABP3, salicylic acid binding protein 3; TGA1, TGACG motif binding factor; cALD2, cytosolic fructose 1,6-bisphosphate aldolase; TIR1, transport inhibitor response 1; CDC48, cell division cycle 48; AtMYB30, <i>Arabidopsis thaliana</i> MYB transcription factor.</p><p>C in bold, matched cysteine residues, "_" not predicted</p><p>Computational prediction of <i>S</i>-nitrosylation sites from experimentally identified <i>S</i>-nitrosylated proteins in plants using GPS-SNO 1.0, iSNO-PseAAC, iSNO-AAPair, and SNOSite software.</p

Computational analysis of proteins, which <i>S</i>-nitrosylation sites were identified by BS-ICAT technology [28].

<p>Computational analysis of proteins, which <i>S</i>-nitrosylation sites were identified by BS-ICAT technology <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0110232#pone.0110232-Fares1" target="_blank">[28]</a>.</p

Prediction of <i>Arabidopsis</i> candidate proteins for S-nitrosylation using the GPS-SNO 1.0 software.

<p><i>Arabidopsis</i> amino acid sequences were extracted from TAIR 10 database (<a href="http://www.arabidopsis.org" target="_blank">www.arabidopsis.org</a>) and analysed by GPS-SNO 1.0 software using medium threshold condition. The 10% of predicted sites with the highest prediction confidence were determined by ranking the prediction results according to the raw score divided by the threshold (Cutoff) for a particular cluster.</p><p>Prediction of <i>Arabidopsis</i> candidate proteins for S-nitrosylation using the GPS-SNO 1.0 software.</p

Anchoring of the QTL target intervals to the Genome Zipper of chromosome 6H.

<p>Comparison of chromosome 6HL genetic map developed earlier <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067336#pone.0067336-Silvar4" target="_blank">[20]</a> to the 7H Genome Zipper described by Mayer et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067336#pone.0067336-Mayer2" target="_blank">[24]</a>. For the sake of clarity, only the telomeric part of chromosome 6H is represented.</p

Genetic linkage maps after saturation with new contig-based markers.

<p>(A) chromosome 7HS, (B) 7HL and (C) 6HL. New markers are represented <i>in bold</i>. Scratched bars indicate the position of potential chromosomal regions conferring resistance to <i>B. graminis</i> in 7HS and 7HL. A diagram of the DH lines of the SBCC145×Beatrix population showing recombination on the regions harboring the QTL is presented for the chromosome 6HL. The disease score (ranging from 0 to 4) of each DH line is indicate for each isolate (211, 224).</p