Functional analysis of a Phytophthora host-translocated effector using the yeast model system

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Functional analysis of a Phytophthora host-translocated effector using the yeast model system https://t.co/sCGKmzsR1d @thePeerJ https://t.co/IRmaLQCs2w
Microbiology

Main article text

 

Introduction

Materials & methods

Expression constructs

Yeast growth inhibition assay

Sample preparation and RNA-sequencing

Bioinformatics analyses

Results

Overexpression of P. sojae RXLR effectors inhibit yeast growth

PsAvh110 represses many PHO4-regulated yeast genes

Discussion

P. sojae RXLR effectors generally target conserved eukaryotic cellular processes

The PsAvh110 effector may disrupt PHO4 regulation

Host-translocated effectors consistently inhibit yeast growth

Future work

Conclusions

Supplemental Information

Yeast Growth Data.

Raw data for Fig. 1 and Article S1. Following induction, the optical density of replicate yeast cultures (Rep1-Rep8) was periodically measured until the OD595 reached 1.0. Experiments 4 and 5 were conducted on different days. Gene indicates the gene inserted in the yeast expression vector; hour indicates the time post-induction.

DOI: 10.7717/peerj.12576/supp-1

Data Analysis of Yeast Growth Inhibition Assay.

This R Notebook presents R code for analyzing the yeast growth inhibition data.

DOI: 10.7717/peerj.12576/supp-2

Computational analysis for matching transcriptome profile.

In this R notebook, we present code to identify publicly available yeast transcriptome profiles similar to that of PsAvh110-expressing yeast cells.

DOI: 10.7717/peerj.12576/supp-3

Additional Information and Declarations

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Avery C. Wilson conceived and designed the experiments, performed the experiments, analyzed the data, authored or reviewed drafts of the paper, and approved the final draft.

William R. Morgan conceived and designed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, and approved the final draft.

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

RNA-seq data are available in the EMBL-EBI ArrayExpress database: E-MTAB-9566.

https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-9566/.

Data Availability

The following information was supplied regarding data availability:

The raw yeast growth data (optical density at 595 nm), the code for its analysis in the R notebook file, and the code for the analysis of matching yeast transcriptome profiles in the R notebook are available in the Supplemental File.

The Galaxy history of the transcriptome data analysis is accessible at

https://usegalaxy.org/u/wmorgan/h/psavh110-rna-seq-analysis.

Funding

This research was funded by the Agriculture and Food Research Initiative competitive grant 2011-68004-30104 of the USDA’s National Institute of Food and Agriculture, as well as The Henry J. Copeland Fund for Independent Study and The Theron L. Peterson and Dorothy R. Peterson Biology Research and Expense Fund at The College of Wooster. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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