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Dr Jane Usher

Dr Jane Usher

Research fellow

 Not Known

 Geoffrey Pope 

 

Geoffrey Pope Building, University of Exeter , Stocker Road, Exeter, EX4 4QD, UK

Qualifications

2007 PhD Eukaryotic Gene Regulation, Trinity College Dublin, Ireland.
2003 MSc Molecular Medicine, Trinity College Dublin Ireland.
2002 BSc (Hons) Biology & Statistics, NUI Maynooth, Ireland.

Career

May 2011 – present: Research Fellow in University of Exeter.
2009 – 2011: Post-doctoral fellow. Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ontario, Canada.
2009: Guest lecturer in Carleton University, Ottawa, Ontario, Canada.
2007 - 2009: Postdoctoral Researcher. Department of Microbiology, Trinity Collge Dublin. Ireland.

Research

Research projects

I joined the Haynes Group in the summer of 2011 as part of the Combinatorial Response in Stress Pathways (CRISP) project. This is a collaboration between Abderdeen, Exeter and Imperial seeking to analyse the responses of fungal pathogens C. albicans and C. glabrata to combinations of stress similar to those encountered in vivo.

Through this funding my main areas of research are:

1: To elucidate a role for mating gene orthologs in C. glabrata.

Candida glabrata is a pathogenic yeast of increasing medical concern and has been regarded as asexual since its initial description. However phylogenetic analysis and genome studies have revealed that it is more closely related to sexual yeasts such as the model organism S. cerevisiae. In a study by Wong et al.,(Genome Biology, 2003) the C. glabrata genome was shown to contain genes involved in mating and meiosis. Orthologs of at least 31 genes that in S. cerevisiae have no known functions other than that of mating or meiosis, including FUS3, IME1 and SMK1 were identified.

Is it possible that C. glabrata has an undiscovered sexual stage in its life cycle? Why would all 31 genes have been preserved in its genome, do they have undiscovered roles in non-sexual processes?

In order to determine if there is a novel function for these genes in C. glabrata, we have generated a series of deletion and overexpression clones to conduct phenotypic screens and utilising SGA techniques to identify genetic interactions.

2: Mapping of the transcription factor binding sites in fungal pathogens.

Eukaryotic gene regulation is mediated by binding of transcription factors near or within their target genes. Transcription factor binding sites are often identified globally through the use of ChIP in which specific protein-DNA interactions are isolated using an antibody against the factor of interest. The coupling of ChIP with high-throughput DNA sequencing allows for the identification of TFBS in a direct and unbiased fashion. The understanding of gene regulation in C. glabrata requires more than knowledge of the genome sequence, it is necessary to identify the array of TF present. As the sequence of many TFs is conserved through the course of evolution thus allowing for their discovery by comparison to homologous TS from closely related organisms, namely S. cerevisiae in this work. It is also crucial to establish a list of regulated genes for each TF. As the presence of a consensus binding motif is not always directly linked to transcription factor binding, as many perfect motifs are not bound by a TF whereas some imperfect motifs are bound under the same environmental conditions. TFs can also regulate genes subjugated to multiple cellular environment and stresses.

To date little is known about the binding motifs in C. glabrata, we have compiled a  comprehensive list of TFs to investigate, containing TFs which have known homologues in S. cerevisiae and the remainder that are C. glabrata specific.

3: To develop a model of cooperative binding of transcription factors and transcriptional activation under stress conditions.

Synopsis of Research from Ottawa:
Though highly efficient at fermenting hexose sugars, S. cerevisiae has limited ability to ferment five-carbon sugars. As a significant portion of sugars found in cellulosic biomass is the five-carbon sugar xylose, S. cerevisiae must be engineered to metabolize pentose sugars, commonly by the addition of exogenous genes from xylose fermenting fungi. However, these recombinant strains grow poorly on xylose and require further improvement through rational engineering or evolutionary adaptation. To identify unknown genes that contribute to improved xylose fermentation in these recombinant S. cerevisiae, we performed genome-wide synthetic interaction screens to identify deletion mutants that impact xylose utilization of strains expressing the xylose isomerase gene XYLA from Piromyces sp. E2 alone or with an additional copy of the endogenous xylulokinase gene XKS1. We also screened the deletion mutant array to identify mutants whose growth is affected by xylose. Our genetic network reveals that more than 80 nonessential genes from a diverse range of cellular processes impact xylose utilization. Surprisingly, we identified four genes, ALP1, ISC1, RPL20B, and BUD21, that when individually deleted improved xylose utilization of both S. cerevisiae S288C and CEN.PK strains. We further characterized BUD21 deletion mutant cells in batch fermentations and found that they produce ethanol even the absence of exogenous XYLA. We have demonstrated that the ability of laboratory strains of S. cerevisiae to utilize xylose as a sole carbon source is suppressed, which implies that S. cerevisiae may not require the addition of exogenous genes for efficient xylose fermentation.

Synopsis of Research from TCD:
A long-term goal of the brewing industry is to identify yeast strains with increased tolerance to the stresses experienced during the brewing process. We characterised the genomes of a number of stress-tolerant mutants, derived from the lager yeast strain CMBS-33, that were selected for tolerance to high temperatures and to growth in high specific gravity wort. Our results indicate that the heat-tolerant strains have undergone a number of gross chromosomal rearrangements when compared to the parental strain. To determine if such rearrangements can spontaneously arise in response to exposure to stress conditions experienced during the brewing process, we examined the chromosome integrity of both the stress-tolerant strains and their parent during a single round of fermentation under a variety of environmental stresses. The results show that the lager yeast genome shows tremendous plasticity during fermentation, especially when fermentations are carried out in high specific gravity wort and at higher than normal temperatures. Many localised regions of gene amplification were observed especially at the telomeres and at the rRNA gene locus on chromosome XII, and general chromosomal instability was evident. However, gross chromosomal rearrangements were not detected, indicating that continued selection in the stress conditions are required to obtain clonal isolates with stable rearrangements. Taken together, the data suggest that lager yeasts display a high degree of genomic plasticity and undergo genomic changes in response to environmental stress.

Key publications | Publications by category | Publications by year

Publications by category


Journal articles

Usher J, Thomas G, Haynes K (2015). Utilising established SDL-screening methods as a tool for the functional genomic characterisation of model and non-model organisms. FEMS Yeast Res, 15(8). Abstract.  Author URL.
Usher J, Berthelet S, Shulist K, Hamza A, Maltez N, Johnston A, Fong Y, Baetz K (2012). Functional Genomics Analysis of the Saccharomyces cerevisiae Iron Responsive Transcription Factor Aft1 Reveals Iron-independent Functions. , 185(3), 11111-11128.
Usher J, Balderas-Hernandez V, Quon P, Gold ND, Martin V, Mahadevan R, Baetz K (2011). Chemical and Synthetic Genetic Array Analysis Identifies Genes that Suppress Xylose Utilization and Fermentation in Saccharomyces cerevisiae. G3: Genes, Genomes and Genetics, 1(4), 247-258.
Usher J, Bond U (2009). Recombination between homoeologous chromosomes of lager yeasts leads to loss of function of the hybrid GPH1 gene. Appl Environ Microbiol, 75(13), 4573-4579.
Usher J, James TC, Campbell S, Bond U (2008). Lager yeasts possess dynamic genomes that undergo rearrangements and gene amplification in response to stress. Current Genetics, 53(3), 139-152.

Publications by year


2015

Usher J, Thomas G, Haynes K (2015). Utilising established SDL-screening methods as a tool for the functional genomic characterisation of model and non-model organisms. FEMS Yeast Res, 15(8). Abstract.  Author URL.

2012

Usher J, Berthelet S, Shulist K, Hamza A, Maltez N, Johnston A, Fong Y, Baetz K (2012). Functional Genomics Analysis of the Saccharomyces cerevisiae Iron Responsive Transcription Factor Aft1 Reveals Iron-independent Functions. , 185(3), 11111-11128.

2011

Usher J, Balderas-Hernandez V, Quon P, Gold ND, Martin V, Mahadevan R, Baetz K (2011). Chemical and Synthetic Genetic Array Analysis Identifies Genes that Suppress Xylose Utilization and Fermentation in Saccharomyces cerevisiae. G3: Genes, Genomes and Genetics, 1(4), 247-258.

2009

Usher J, Bond U (2009). Recombination between homoeologous chromosomes of lager yeasts leads to loss of function of the hybrid GPH1 gene. Appl Environ Microbiol, 75(13), 4573-4579.

2008

Usher J, James TC, Campbell S, Bond U (2008). Lager yeasts possess dynamic genomes that undergo rearrangements and gene amplification in response to stress. Current Genetics, 53(3), 139-152.

Jane_Usher Details from cache as at 2018-04-20 02:02:18

Refresh publications

Workshops/Conferences organised

Hosting and Scientific Committee member for British Yeast Group meeting 2014.

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