The protein disulfide isomerase 1 of Phytophthora parasitica (PpPDI1) is associated with the haustoria-like structures and contributes to plant infection

The protein disulfide isomerase (PDI) is a ubiquitous and multifunction enzyme belonging to the thioredoxin (TRX) superfamily, which can reduce, oxidize, and catalyze dithiol-disulfide exchange reactions. Except performing housekeeping function in helping to maintain proteins in a more stable conformation, there is some evidence to indicate that PDI is involved in pathogen infection process. In a high-throughput screening for necrosis-inducing factors by Agrobacterium tumefaciens-mediated transient expression assay, a typical PDI gene from Phytophthora parasitica (PpPDI1) was identified and confirmed to induce strong cell death on Nicotiana benthamiana leaves. PpPDI1 is conserved in eukaryotes but predicted a secreted protein. Deletion mutant analyses showed that the first CGHC motif in the active domain of PpPDI1 is essential for inducing cell death. Using P. parasitica transformation method, the silencing efficiency was very low, suggesting that PpPDI1 is essential for the pathogen. Translational fusion to the enhanced green fluorescent protein (EGFP) in stable P. parasitica transformants showed that PpPDI1 is associated with haustoria-like structures during pathogen infection. Furthermore, the PpPDI1-EGFP-expressing transformants increase the number of haustoria-like structures and exhibit enhanced virulence to N. benthamiana. These results indicate that PpPDI1 might be a virulence factor of P. parasitica and contributes to plant infection

Rust Secreted Protein Ps87 Is Conserved in Diverse Fungal Pathogens and Contains a RXLR-like Motif Sufficient for Translocation into Plant Cells

BACKGROUND: Effector proteins of biotrophic plant pathogenic fungi and oomycetes are delivered into host cells and play important roles in both disease development and disease resistance response. How obligate fungal pathogen effectors enter host cells is poorly understood. The Ps87 gene of Puccinia striiformis encodes a protein that is conserved in diverse fungal pathogens. Ps87 homologs from a clade containing rust fungi are predicted to be secreted. The aim of this study is to test whether Ps87 may act as an effector during Puccinia striiformis infection. METHODOLOGY/PRINCIPAL FINDINGS: Yeast signal sequence trap assay showed that the rust protein Ps87 could be secreted from yeast cells, but a homolog from Magnaporthe oryzae that was not predicted to be secreted, could not. Cell re-entry and protein uptake assays showed that a region of Ps87 containing a conserved RXLR-like motif [K/R]RLTG was confirmed to be capable of delivering oomycete effector Avr1b into soybean leaf cells and carrying GFP into soybean root cells. Mutations in the Ps87 motif (KRLTG) abolished the protein translocation ability. CONCLUSIONS/SIGNIFICANCE: The results suggest that Ps87 and its secreted homologs could utilize similar protein translocation machinery as those of oomycete and other fungal pathogens. Ps87 did not show direct suppression activity on plant defense responses. These results suggest Ps87 may represent an "emerging effector" that has recently acquired the ability to enter plant cells but has not yet acquired the ability to alter host physiology

Nucleotide-level prediction of CircRNA-protein binding based on fully convolutional neural network

Introduction: CircRNA-protein binding plays a critical role in complex biological activity and disease. Various deep learning-based algorithms have been proposed to identify CircRNA-protein binding sites. These methods predict whether the CircRNA sequence includes protein binding sites from the sequence level, and primarily concentrate on analysing the sequence specificity of CircRNA-protein binding. For model performance, these methods are unsatisfactory in accurately predicting motif sites that have special functions in gene expression.Methods: In this study, based on the deep learning models that implement pixel-level binary classification prediction in computer vision, we viewed the CircRNA-protein binding sites prediction as a nucleotide-level binary classification task, and use a fully convolutional neural networks to identify CircRNA-protein binding motif sites (CPBFCN).Results: CPBFCN provides a new path to predict CircRNA motifs. Based on the MEME tool, the existing CircRNA-related and protein-related database, we analysed the motif functions discovered by CPBFCN. We also investigated the correlation between CircRNA sponge and motif distribution. Furthermore, by comparing the motif distribution with different input sequence lengths, we found that some motifs in the flanking sequences of CircRNA-protein binding region may contribute to CircRNA-protein binding.Conclusion: This study contributes to identify circRNA-protein binding and provides help in understanding the role of circRNA-protein binding in gene expression regulation

Hyphal editing of the conserved premature stop codon in CHE1 is stimulated by oxidative stress in Fusarium graminearum

Abstract Although genome-wide A-to-I editing mediated by adenosine-deaminase-acting-on-tRNA (ADAT) occurs during sexual reproduction in the presence of stage-specific cofactors, RNA editing is not known to occur during vegetative growth in filamentous fungi. Here we identified 33 A-to-I RNA editing events in vegetative hyphae of Fusarium graminearum and functionally characterized one conserved hyphal-editing site. Similar to ADAT-mediated editing during sexual reproduction, majority of hyphal-editing sites are in coding sequences and nonsynonymous, and have strong preference for U at -1 position and hairpin loops. Editing at TA437G, one of the hyphal-specific editing sites, is a premature stop codon correction (PSC) event that enables CHE1 gene to encode a full-length zinc fingertranscription factor. Manual annotations showed that this PSC site is conserved in CHE1 orthologs from closely-related Fusarium species. Whereas the che1 deletion and CHE1 TAA (G438 to A) mutants had no detectable phenotype, the CHE1 TGG (A437 to G) mutant was defective in hyphal growth, conidiation, sexual reproduction, and plant infection. However, the CHE1 TGG mutant was increased in tolerance against oxidative stress and editing of TA437G in CHE1 was stimulated by H2O2 treatment in F. graminearum. These results indicate that fixation of the premature stop codon in CHE1 has a fitness cost on normal hyphal growth and reproduction but provides a benefit to tolerance against oxidative stress. Taken together, A-to-I editing events, although rare (not genome-wide), occur during vegetative growth and editing in CHE1 plays a role in response to oxidative stress in F. graminearum and likely in other fungal pathogens

PnPMA1, an atypical plasma membrane H+ - ATPase, is required for zoospore development in Phytophthora parasitica

Biflagellate zoospores are the major infective agents that initiate plant infection for most Phytophthora species. Once released from sporangia, zoospores swim and use a number of tactic responses to actively target host tissues. However, the molecular mechanisms controlling zoospore development and behaviour are largely unknown. Previous studies have shown that the PnPMA1 gene is highly expressed in zoospores and germinated cysts of Phytophthora parasitica and encodes an atypical plasma membrane H + -ATPase containing an insertion of ~155 amino acid residues at the C terminus. Using topology determination we now show that the C-terminal insertion loop in the PnPMA1 protein is located in the extracellular space. To elucidate the biological function of PnPMA1, PnPMA1-deficient transformants were generated by homology-dependent gene silencing and were confirmed by quantitative PCR of PnPMA1 transcripts and detection of associated small interfering RNAs (siRNAs). High levels of PnPMA1 silencing in P. parasitica resulted in production of nonflagellate and large aberrant zoospores, rapid transition from zoospores to cysts, and a decreased germination rate of cysts. These results indicate that PnPMA1 plays important roles in zoospore developmentThis research was supported by the National Natural Science Foundation of China (#30771395 and #31125022), the 111 Project from Ministry of Education of China (#B07049) and the China Agriculture Research System (CARS-10)

A TALE/HOX code unlocks WNT signalling response towards paraxial mesoderm

One fundamental yet unresolved question in biology remains how cells interpret the same signalling cues in a context-dependent manner resulting in lineage specification. A key step for decoding signalling cues is the establishment of a permissive chromatin environment at lineage-specific genes triggering transcriptional responses to inductive signals. For instance, bipotent neuromesodermal progenitors (NMPs) are equipped with a WNT-decoding module, which relies on TCFs/LEF activity to sustain both NMP expansion and paraxial mesoderm differentiation. However, how WNT signalling activates lineage specific genes in a temporal manner remains unclear. Here, we demonstrate that paraxial mesoderm induction relies on the TALE/HOX combinatorial activity that simultaneously represses NMP genes and activates the differentiation program. We identify the BRACHYURY-TALE/HOX code that destabilizes the nucleosomes at WNT-responsive regions and establishes the permissive chromatin landscape for de novo recruitment of the WNT-effector LEF1, unlocking the WNT-mediated transcriptional program that drives NMPs towards the paraxial mesodermal fate

The co-enrichment of transcription factor on identified chromatin loops in K562(replicate2) with CTCF ChIA-PET training model.

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