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Genome-wide translational responses to stress

Department of Biochemistry

Applications accepted all year round Awaiting Funding Decision/Possible External Funding

About the Project

We are interested in gene regulation in responses to stress, using both simple model organisms, human and plant pathogens.

Cells respond to stress conditions by launching complex programs of gene expression, both transcriptional and posttranscriptional, and which are often closely linked with each other. We are particularly interested in the regulation of translation, which is modified in response to stress at multiple levels.

We use the fission yeast Schizosaccharomyces pombe to study these questions, and address them with state-of-the-art genomic methods, classical and molecular genetics, and cell biological approaches.

We have recently demonstrated that certain types of stress cause ribosomes to stall on specific codons (tryptophan), leading to ribosome ’traffic-jams’ on mRNAs. These results suggest the existence of a regulatory programme at the level of translational elongation. A PhD project would involve the study of this phenomenon using a combination of single-gene approaches and genome-wide methods (such as RNA-seq, tRNA-seq and ribosome profiling).

Funding Notes

The Deparment offers competitive fully-funded fellowships. Other competitive studentships may be available. Self-funding students will also be considered.


1. Rubio A, Ghosh S, Muelleder M, Ralser M and Mata J (2020) Ribosome profiling reveals ribosome stalling on tryptophan codons upon oxidative stress in fission yeast. Nucleic Acid Research, in press.

2. Duncan C, Rodriguez-Lopez M, Ruis P, Bahler J and Mata J (2018) General amino acid control in fission yeast is regulated by a nonconserved transcription factor, with functions analogous to Gcn4/Atf4. PNAS doi:10.1073/pnas.1713991115

3. Duncan C and Mata J (2017) Effects of cycloheximide on the interpretation of ribosome profiling experiments in Schizosaccharomyces pombe. Scientific reports 7:10331

4. Duncan C and Mata J (2014) The translational landscape of fission-yeast meiosis and sporulation. Nature Structural and Molecular Biology

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