Unknown,Transcriptomics,Genomics,Proteomics

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RNA-seq analysis of the fungal mycelium of the plant pathogen Pyricularia oryzae treated with and antimicrobial peptide analog of a Trichoderma peptaibol

ABSTRACT: We aimed at investigating the mode of action of an antimicrobial peptide analog of a Trichoderma peptaibol. Conidia of P. oryzae (IT10 strain) were cultured in Complete Medium at a final concentration of 2x105 conidia per mL for 3 days at 30 °C under shaking at 150 rpm. After three days, 50 µM of the Peptide 4rink were added to samples containing actively growing mycelium. Untreated samples were used as control. Three h after peptide treatment, fungal mycelia were collected, filtered with 100 µm Cell Strainer (Corning®), rinsed with sterile water and stored at -80 °C for RNA extraction. Total RNA was extracted with the RNeasy Plant Mini kit (Qiagen) following the manufacturer’s instructions, performing the DNase digestion directly on the column. The integrity and concentration of the RNA samples were checked with Qubit fluorimeter and Bioanalyzer. RNA samples with RIN values < 7 were discarded. Four biological replicates of each treatment were submitted to RNA sequencing and analysis at CRIBI Biotechnology Center (University of Padova). Two µg of total RNA were subjected to PolyA tail capture and rRNA depletion for selection of mRNA. Directional (stranded) RNA libraries were prepared, quantified and subjected to quality control. Sequencing was performed on Illumina Nova Seq 6000 platform. Twenty million reads were produced for each sample and checked for quality control. Based on our RNA-seq data, the molecular mechanisms of the fungicidal activity of these peptide analogs appear to be related to their ability to cause cell wall and membrane damages and to induce autophagic cell death in fungal cells. This is the first transcriptomic analysis on a fungus treated with peptaibol analogs.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Pyricularia oryzae 70-15

SUBMITTER: Luca Sella

PROVIDER: E-MTAB-10927 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:INTRODUCTION Ischemia and reperfusion injury (IRI)-elicited tissue injury contributes to morbidity and mortality in a wide range of pathologies, including myocardial infarction, ischemic stroke, acute kidney injury, trauma, circulatory arrest 1. Ischemia-reperfusion injury is also a major challenge during organ transplantation and cardiothoracic, vascular and general surgery 1. IRI, one of the biggest challenges for organ transplantation, continues to be a vital source of morbidity among recipients, especially in liver transplantation 2. With the enlarging shortage of available donor livers, the increased use of extended criteria donor grafts further increases IRI, adversely affecting both short-term and long-term outcomes of graft and patient survival 3. Numerous studies have investigated the benefits of pharmacological, heat shock, and ischemic preconditioning interventions aimed at decreasing liver IRI 4. However, the benefit was limited. Our center has been making great effort in conquering IRI and have developed a novel surgical technique called ischemia-free liver transplantation 5. It is an ultimate method to overcome IRI in liver transplantation, but there is still a long way to popularize it. As a result, it is still of great significance to study IRI and identify the core genes in the process and the underlying mechanism. Comprehensive bioinformatics analysis has been increasingly important as a method to study various pathological and physiological condition 6. By enrolling multiple omics or combining different types of omics, comprehensive bioinformatics analysis was able to recognize key factors that could have potentially pathogenic impact such as gene expression, protein function, and downstream pathways. With the rapid development of high-throughput sequencing technologies, several transcriptomic datasets on IRI of liver transplantation have become available in the Gene Expression Omnibus (GEO) database. Herein, we recruited 3 GEO datasets to conduct comprehensive analysis with the GEO dataset from our center. Moreover, we performed the first proteome of liver tissues to study liver IRI. Then the transcriptome and proteome were used for combined analysis to reveal key factors in liver IRI.

Dataset Information

RNA-seq analysis of the fungal mycelium of the plant pathogen Pyricularia oryzae treated with and antimicrobial peptide analog of a Trichoderma peptaibol

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