Simon J Hubbard

Simon J Hubbard
The University of Manchester · Faculty of Life Sciences

PhD Biochemistry

About

223
Publications
21,708
Reads
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10,802
Citations
Citations since 2016
52 Research Items
2832 Citations
20162017201820192020202120220100200300400
20162017201820192020202120220100200300400
20162017201820192020202120220100200300400
20162017201820192020202120220100200300400
Additional affiliations
January 1998 - December 2012
The University of Manchester
January 1994 - December 1996
January 1991 - December 1994
University College London

Publications

Publications (223)
Article
Full-text available
Mitochondrial i-AAA proteinase Yme1 is a multifunctional protein that plays important roles in maintaining mitochondrial protein homeostasis and regulating biogenesis and function of mitochondrial proteins. However, due to the complex interplay of mitochondria and the multifunctional nature of Yme1, how Yme1 affects mitochondrial function and prote...
Article
Full-text available
Eukaryotic cells have developed a complex circuitry of signalling molecules which monitor changes in their intra- and extracellular environments. One of the most widely studied signalling pathways is the highly conserved cAMP/protein kinase A (PKA) pathway, which is a major glucose sensing circuit in the yeast Saccharomyces cerevisiae. PKA activity...
Article
Full-text available
Regulation of translation is a fundamental facet of the cellular response to rapidly changing external conditions. Specific RNA-binding proteins (RBPs) co-ordinate the translational regulation of distinct mRNA cohorts during stress. To identify RBPs with previously under-appreciated roles in translational control, we used polysome profiling and mas...
Article
Full-text available
When conditions change, unicellular organisms rewire their metabolism to sustain cell maintenance and cellular growth. Such rewiring may be understood as resource re-allocation under cellular constraints. Eukaryal cells contain metabolically active organelles such as mitochondria, competing for cytosolic space and resources, and the nature of the r...
Article
Full-text available
Background: RNA-sequencing of patient biosamples is a promising approach to delineate the impact of genomic variants on splicing, but variable gene expression between tissues complicates selection of appropriate tissues. Relative expression level is often used as a metric to predict RNA-sequencing utility. Here, we describe a gene- and tissue-speci...
Article
Full-text available
Non-membrane-bound compartments such as P-bodies (PBs) and stress granules (SGs) play important roles in the regulation of gene expression following environmental stresses. We have systematically and quantitatively determined the protein and mRNA composition of PBs and SGs formed before and after nutrient stress. We find that high molecular weight...
Preprint
Full-text available
Regulation of translation is a fundamental facet of the cellular response to rapidly changing external conditions. Specific RNA-binding proteins (RBPs) co-ordinate the translational regulation of distinct mRNA cohorts during stress. To identify RBPs with previously under-appreciated roles in translational control, we used polysome profiling and mas...
Preprint
Full-text available
When conditions change, unicellular organisms rewire their metabolism to sustain cell maintenance and cellular growth. Such rewiring may be understood as resource re-allocation under cellular constraints. Eukaryal cells contain metabolically active organelles such as mitochondria, competing for cytosolic space and resources, and the nature of the r...
Preprint
Full-text available
Background: RNA-sequencing of patient biosamples is a promising approach to delineate the impact of genomic variants on splicing, but variable gene expression between tissues complicates selection of appropriate tissues. Relative expression level is often used as a metric to predict RNA-sequencing utility. Here, we describe a gene- and tissue-speci...
Article
Full-text available
Glycolysis is a fundamental metabolic pathway for glucose catabolism across biology, and glycolytic enzymes are amongst the most abundant proteins in cells. Their expression at such levels provides a particular challenge. Here we demonstrate that the glycolytic mRNAs are localized to granules in yeast and human cells. Detailed live cell and smFISH...
Article
Full-text available
When Saccharomyces cerevisiae undergoes heat stress it stimulates several changes that are necessary for its survival, notably in carbon metabolism. Notable changes include increase in trehalose production and glycolytic flux. The increase in glycolytic flux has been postulated to be due to the regulatory effects in upper glycolysis, but this has n...
Preprint
Full-text available
Non-membrane-bound compartments such as P-bodies (PBs) and stress granules (SGs) play important roles in the regulation of gene expression following environmental stresses. We have systematically determined the protein and mRNA composition of PBs and SGs formed in response to a common stress condition imposed by glucose depletion. We find that high...
Article
Full-text available
Integrated regulatory networks can be powerful tools to examine and test properties of cellular systems, such as modelling environmental effects on the molecular bioeconomy, where protein levels are altered in response to changes in growth conditions. Although extensive regulatory pathways and protein interaction data sets exist which represent suc...
Article
Full-text available
The craniofacial disorder Mandibulofacial Dysostosis Guion-Almedia type is caused by haploinsufficiency of the U5 snRNP gene EFTUD2/SNU114. However, it is unclear how reduced expression of this core pre-mRNA splicing factor leads to craniofacial defects. Here we use a CRISPR-Cas9 nickase strategy to generate a human EFTUD2-knockdown cell line, and...
Article
Full-text available
Protein biosynthesis is energetically costly, is tightly regulated and is coupled to stress conditions including glucose deprivation. RNA polymerase III (RNAP III)-driven transcription of tDNA genes for production of tRNAs is a key element in efficient protein biosynthesis. Here we present an analysis of the effects of altered RNAP III activity on...
Article
The regulation of translation is critical in almost every aspect of gene expression. Nonetheless, the ribosome is historically viewed as a passive player in this process. However, evidence is accumulating to suggest that variations in the ribosome can have an important influence on which mRNAs are translated. Scope for variation is provided via mul...
Preprint
Full-text available
Protein biosynthesis is energetically costly, is tightly regulated and is coupled to stress conditions including glucose deprivation. RNA polymerase III (RNAP III) driven transcription of tDNA genes for production of tRNAs is a key element in efficient protein biosynthesis. Here we present an analysis of the effects of altered RNAP III activity on...
Article
Full-text available
The transcriptional responses of yeast cells to diverse stresses typically include gene activation and repression. Specific stress defense, citric acid cycle and oxidative phosphorylation genes are activated, whereas protein synthesis genes are coordinately repressed. This view was achieved from comparative transcriptomic experiments delineating se...
Article
Full-text available
Temperature fluctuation is a common environmental stress that elicits a molecular response in order to maintain intracellular protein levels. Here, for the first time, we report a comprehensive temporal and quantitative study of the proteome during a 240 minute heat stress, using label-free mass spectrometry. We report temporal expression changes o...
Article
Full-text available
Background Translation factors eIF4E and eIF4G form eIF4F, which interacts with the messenger RNA (mRNA) 5′ cap to promote ribosome recruitment and translation initiation. Variations in the association of eIF4F with individual mRNAs likely contribute to differences in translation initiation frequencies between mRNAs. As translation initiation is gl...
Article
Full-text available
Leaves of Arabidopsis thaliana transferred from low to high light increase their capacity for photosynthesis, a process of dynamic acclimation. A mutant, gpt2, lacking a chloroplast glucose-6-phosphate/phosphate translocator, is deficient in its ability to acclimate to increased light. Here, we have used a label-free proteomics approach, to perform...
Data
Figure S1) Extraction of ChapCAT from inclusion bodies. Expressed ChapCAT (shown are ChapCAT001 and ChapCAT003) was isolated from the inclusion bodies of E. coli and subject to further purification. Validation experiments were performed by western blotting with an α‐His antibody. SM: starting material; SF: soluble fraction; IB: inclusion bodies. Ch...
Data
Table S1) Expression Protocol for ChapCATs in minimal medium Following expression testing in LB medium, the optimum expression conditions were determined. For ChapCATs that encountered difficult expression in LB medium, the addition of 10 mM benzyl alcohol was used to attempt higher levels of quantification. This was not successful for the ChapCAT0...
Article
Quantitative mass spectrometry-based proteomics of complex biological samples remains challenging, in part due to the variability and charge competition arising during electrospray ionization (ESI) of peptides and the subsequent transfer and detection of ions. These issues preclude direct quantification from signal intensity alone in the absence of...
Article
Full-text available
Chaperones are fundamental to regulating the heat shock response (HSR), mediating protein recovery from thermal-induced misfolding and aggregation. Using the QconCAT strategy and SRM for absolute protein quantification, we have determined copy per cell (cpc) values for 49 key chaperones in S. cerevisiae under conditions of normal growth and heat sh...
Article
Full-text available
Defining intracellular protein concentration is critical in molecular systems biology. Although strategies for determining relative protein changes are available, defining robust absolute values in copies per cell has proven significantly more challenging. Here we present a reference dataset quantifying over 1800 S. cerevisiae proteins by direct me...
Article
Full-text available
The PUF family of RNA-binding proteins regulate gene expression post-transcriptionally. Saccharomyces cerevisiae Puf3p is characterised as binding nuclear-encoded mRNAs specifying mitochondrial proteins. Extensive studies of its regulation of COX17 demonstrate its role in mRNA decay. Using integrated genome-wide approaches we define an expanded set...
Data
Supplementary File 1 – Methods used in the LC‐MS analysis of dystrophic mice
Data
Supplementary Figure S1. Example of representative peptides from ‘heavy’ yeast samples. Good incorporation efficiency of Arg6 and Lys6 is visible. Two peptides from abundant yeast proteins and with high MS intensity are shown here; AVDDFIISIDGTANK ‐ Enolase 1 peptide and TANDVITIR from Pyruvate kinase 1. RIA = Intensity H/(Intensity H + Intensity L...
Article
Full-text available
The mzQuantML standard has been developed by the Proteomics Standards Initiative for capturing, archiving and exchanging quantitative proteomic data, derived from mass spectrometry. It is a rich XML-based format, capable of representing data about two-dimensional features from LC-MS data, and peptides, proteins or groups of proteins that have been...
Article
Full-text available
Translation initiation factor eIF4E mediates mRNA selection for protein synthesis via the mRNA 5'cap. A family of binding proteins, termed the 4E-BPs, interact with eIF4E to hinder ribosome recruitment. Mechanisms underlying mRNA specificity for 4E-BP control remain poorly understood. Saccharomyces cerevisiae 4E-BPs, Caf20p and Eap1p, each regulate...
Article
Full-text available
The mzQuantML data standard was designed to capture the output of quantitative software in proteomics, to support submissions to public repositories, development of visualisation software and pipeline/modular approaches. The standard is designed around a common core that can be extended to support particular types of technique through the release o...
Article
Full-text available
Molecular chaperones play an important role in protein homeostasis and the cellular response to stress. In particular, the HSP70 chaperones in yeast mediate a large volume of protein folding through transient associations with their substrates. This chaperone interaction network can be disturbed by various perturbations, such as environmental stres...
Article
Full-text available
Analysis of the phosphoproteome by mass spectrometry has become a key technology for the characterisation of dynamic regulatory processes in the cell, since kinase and phosphatase action underlie many major biological functions. However, the addition of a phosphate group to a suitable sidechain often confounds informatic analysis by generating prod...