Comparisons in conidiation among 38B1, ΔBcPtpA-10, ΔBcPtpB-4, BcPtpA-5 and ΔBcPtpB-C1.

<p>(<b>A</b>) Colony morphology of the wild-type strain 38B1 and the mutants on sterilized cucumber fragments. The photos were taken after 10 days of incubation on sterilized cucumber fragments. (<b>B</b>) Quantification of conidia for each strain. The conidia of 38B1, ΔBcPtpA-10, ΔBcPtpB-4, BcPtpA-5 and ΔBcPtpB-C1 were washed off from each PDA plate after 10 days of incubation, and were counted under a microscope. Bars denote standard errors from three replications. Values on the bars followed by the same letter are not significantly different at <i>P = </i>0.05.</p

Correction: Involvement of Protein Tyrosine Phosphatases BcPtpA and BcPtpB in Regulation of Vegetative Development, Virulence and Multi-Stress Tolerance in <i>Botrytis cinerea</i>

Correction: Involvement of Protein Tyrosine Phosphatases BcPtpA and BcPtpB in Regulation of Vegetative Development, Virulence and Multi-Stress Tolerance in <i>Botrytis cinerea</i

DisoMCS: Accurately Predicting Protein Intrinsically Disordered Regions Using a Multi-Class Conservative Score Approach

<div><p>The precise prediction of protein intrinsically disordered regions, which play a crucial role in biological procedures, is a necessary prerequisite to further the understanding of the principles and mechanisms of protein function. Here, we propose a novel predictor, DisoMCS, which is a more accurate predictor of protein intrinsically disordered regions. The DisoMCS bases on an original multi-class conservative score (MCS) obtained by sequence-order/disorder alignment. Initially, near-disorder regions are defined on fragments located at both the terminus of an ordered region connecting a disordered region. Then the multi-class conservative score is generated by sequence alignment against a known structure database and represented as order, near-disorder and disorder conservative scores. The MCS of each amino acid has three elements: order, near-disorder and disorder profiles. Finally, the MCS is exploited as features to identify disordered regions in sequences. DisoMCS utilizes a non-redundant data set as the training set, MCS and predicted secondary structure as features, and a conditional random field as the classification algorithm. In predicted near-disorder regions a residue is determined as an order or a disorder according to the optimized decision threshold. DisoMCS was evaluated by cross-validation, large-scale prediction, independent tests and CASP (Critical Assessment of Techniques for Protein Structure Prediction) tests. All results confirmed that DisoMCS was very competitive in terms of accuracy of prediction when compared with well-established publicly available disordered region predictors. It also indicated our approach was more accurate when a query has higher homologous with the knowledge database.</p><p>Availability</p><p>The DisoMCS is available at <a href="http://cal.tongji.edu.cn/disorder/" target="_blank">http://cal.tongji.edu.cn/disorder/</a>.</p></div

Involvement of Protein Tyrosine Phosphatases BcPtpA and BcPtpB in Regulation of Vegetative Development, Virulence and Multi-Stress Tolerance in <i>Botrytis cinerea</i>

<div><p>Tyrosine phosphorylation and dephosphorylation have emerged as fundamentally important mechanisms of signal transduction and regulation in eukaryotic cells, governing many processes, but little has been known about their functions in filamentous fungi. In this study, we deleted two putative protein tyrosine phosphatase (PTP) genes (<i>BcPTPA</i> and <i>BcPTPB</i>) in <i>Botrytis cinerea</i>, encoding the orthologs of <i>Saccharomyces cerevisiae</i> Ptp2 and Ptp3, respectively. Although BcPtpA and BcPtpB have opposite functions in conidiation, they are essential for sclerotial formation in <i>B. cinerea</i>. <i>BcPTPA</i> and <i>BcPTPB</i> deletion mutants ΔBcPtpA-10 and ΔBcPtpB-4 showed significantly increased sensitivity to osmotic and oxidative stresses, and to cell wall damaging agents. Inoculation tests showed that both mutants exhibited dramatically decreased virulence on tomato leaves, apples and grapes. In <i>S. cerevisiae</i>, it has been shown that Ptp2 and Ptp3 negatively regulate the high-osmolarity glycerol (HOG) pathway and the cell wall integrity (CWI) pathway. Although both BcPtpA and BcPtpB were able to inactive Hog1 and Mpk1 in <i>S. cerevisiae</i>, in contrast to <i>S. cerevisiae</i>, they positively regulate phosphorylation of BcSak1 (the homologue of Hog1) and BcBmp3 (the homologue of Mpk1) in <i>B. cinerea</i> under stress conditions. These results demonstrated that functions of PTPs in <i>B. cinerea</i> are different from those in <i>S. cerevisiae</i>, and BcPtpA and BcPtpB play important roles in regulation of vegetative development, virulence and in adaptation to oxidative, osmotic and cell-wall damage stresses in <i>B. cinerea</i>.</p> </div

Involvement of <i>BcPTPA</i> and <i>BcPTPB</i> in the regulation of hypal melanization.

<p>(<b>A</b>) Comparisons of mycelial pigmentation among the wild-type strain 38B1, ΔBcPtpA-10, ΔBcPtpB-4, BcPtpA-5 and ΔBcPtpB-C1 after 9 days of incubation on PDA plates amended with or without 50 µg/ml tricyclazole. (<b>B</b>) Relative expression level of <i>THR1</i>, 1,3,8-trihydroxynaphthalene reductase gene, which is involved in melanin biosynthesis. Bars denote standard errors from three replications. Values on the bars followed by the same letter are not significantly different at <i>P = </i>0.05.</p

An example of CASP10.

<p>An example of CASP10.</p

Comparisons in intracellular glycerol concentration among the wild-type strain 38B1, ΔBcPtpA-10, and ΔBcPtpB-4.

<p>Mycelia of each strain were treated with 0.5 M NaCl for 2 hours after grown in potato dextrose broth for 2 days. The cultures without treatment were used as the control (NT). Bars denote standard errors from three repeated experiments. Values on the bars followed by the same letter are not significantly different at <i>P = </i>0.05.</p

Impact of <i>BcPTPA</i> and <i>BcPTPB</i> deletion on sclerotial formation.

<p>The wild-type strain 38B1, ΔBcPtpA-10, ΔBcPtpB-4, BcPtpA-5 and ΔBcPtpB-C1 were incubated on PDA medium at 25°C for 4 weeks in darkness.</p

Adjusting the decision threshold of predicted disorder.

<p>The Sw achieves maximum 76.55% when the decision threshold is 0.03.</p

Phosphorylation levels of BcBmp3 in 38B1, ΔBcPtpA-10, ΔBcPtpB-4.

<p>Mycelia of each strain were treated with 0.3 mg/ml Congo red for 2 hours after being grown in potato dextrose broth for 2 days. The cultures without any treatment were used as the control (NT). BcBmp3 and phosphorylated BcBmp3 proteins were detected using the yeast anti-Mpk1 (yN-19) and phospho-p44/42 MAP kinase antibody (Cell Signaling) antibodies, respectively.</p