Dr Mark Collins
Room: E04 Florey building
Brief career history
Cell Signalling and Proteome Dynamics
Our lab is interested in the regulation of signalling pathways by post-translational modifications (PTMs). We use a combination of molecular, cell and mass spectrometry based approaches to study PTMs on a global scale and we are particularly interested in understanding the regulation and activity of enzymes that dynamically regulate PTMs such as protein kinases, palmitoyl-acyltransferases and lysine deacetylases.
The key enabling technology for our research is shotgun proteomics; in which protein samples (whole cell lysates, organelles, protein complexes etc.) are digested with into peptides, separated using nanoflow chromatography and analysed using high-resolution tandem mass spectrometry (biOMICS facility). This approach permits unbiased, quantitative analysis of protein levels and PTMs, with unrivalled accuracy and sensitivity.
Figure 1. Proteome analysis using high-resolution tandem mass spectrometry
Much of our knowledge of the biochemistry of signalling pathways is an aggregate of data from studies of individual PTM sites in single protein experiments. Whilst very useful, this fails to give an integrated and unbiased view of what happens to all relevant proteins for example, when a specific receptor is activated.
The crosstalk of PTMs is emerging as an important mechanism to confer higher order regulation of signalling pathways. We are developing approaches to assay many PTMs from the same sample on a proteome-scale in order to understand how for example, phosphorylation, acetylation and palmitoylation interact to regulate protein function.
We also exploit affinity purification and proximity labelling strategies to purify and characterise multiprotein complexes formed by protein kinases and palmitoyl-acyltransferases to identify their substrates as well as regulatory proteins that determine substrate specificity or target these enzymes to different subcellular compartments or membrane microdomains.
Regulation of membrane protein function by S-acylation (Palmitoylation)
Palmitoylation, the only known reversible lipid modification of proteins, is a critical regulator of protein trafficking, stability and signalling and is important for all cell types, and organisms from yeast to humans.
Proteins can be palmitoylated by a family of 23 protein acyl transferases (PATs) in humans and many of these enzymes have been shown to regulate important aspects of cell biology and in particular in neuronal cells in the brain where palmitoylation of receptors and associated proteins are essential for communication between brain cells and therefore functions such as learning and memory.
Indeed, several PATs have been implicated in the pathophysiology of neurological disorders from Huntington’s disease to intellectual disability and schizophrenia and well as other diseases such as diabetes and cancer.
The identification of determinants of substrate specificity of palmitoyl acyltransferases is an important goal toward understanding how palmitoylation regulates cell function. Development of strategies to enrich, identify and quantify proteins and PTMs is also a major focus of research in our lab.
Figure 2. site-specific-Acyl-Biotin-Exchange (ssABE) for comprehensive identification and quantification of sites of S-acylation
Figure 3. Concurrent identification of palmitoylation and phosphorylation sites by mass spectrometry (click image for enlarged version)
Perturbed signalling pathways in neurodegenerative diseases
Motor Neurone Disease or Amyotrophic lateral sclerosis (ALS) is a disorder that results in fatal paralysis within a few years of symptom onset. Defects in a growing list of genes are associated with the development of ALS/MND.
Many of these gene defects result in the accumulation of aggregates in cells of patients with ALS and these aggregates are believed to cause neurons to die, resulting in the symptoms of the disease.
Recently, a number of large exome sequencing studies of ALS patients have independently identified several loss of function mutations in protein kinases but it is not known how dysregulation of these kinases might contribute to development of disease.
We are using protein biochemistry, immunofluorescence microscopy and phosphoproteomic approaches to understand how human mutations lead to molecular and cellular changes that contribute to to the pathogenesis of ALS.
Figure 4. Monitoring autophagy levels in NSC-34 cells using a tandem mRFP-EGFP-LC3 fluorescent reporter. Autophagosomes are visualised as yellow labelled puncta whilst autolysosomes appear red due to loss of acid sensitive GFP signal.
Campylobacter jejuni is a food-borne pathogen of worldwide importance but little is known about how the pathogenicity of this bacteria is regulated by PTMs. We collaborate with Prof Dave Kelly at the Department of Molecular Biology and Biotechnology, University of Sheffield to develop and apply proteomic approaches to probe the function of acetylation and phosphorylation in C. jejuni though two BBSRC White Rose Mechanistic Biology DTP PhD studentships (2015-2019 & 2017-2021).
Histone deacetylase 1 and 2 (HDAC1/2) containing complexes have important roles in almost all cellular processes, including cell cycle, DNA synthesis, DNA repair and gene expression. In collaboration with Dr Shaun Cowley at the Department of Molecular and Cell Biology, University of Leicester we are developing and apply proteomic approaches (acetylomics and BioID) to probe the function of acetylation in embryonic stem cells (BBSRC-SFI project grant 2017-2020).
Constitutive secretion is required for many biologically important processes such as the secretion of antibodies and the extracellular matrix. In collaboration with Dr Andrew Peden at the Department of Biomedical Science, University of Sheffield, we are investigating the regulation of SNAREs by palmitoylation as well as using quantitative proteomics to characterise novel machinery required for post-Golgi trafficking and antibody secretion.
Peptidoglycan (PG) is an essential component of the bacterial cell envelope, made of glycan strands and peptide stems containing unusual amino acids. In collaboration with Dr Stéphane Mesnage at the Department of Molecular Biology and Biotechnology, University of Sheffield, we are developing an automated, high-resolution analysis pipeline for bacterial peptidoglycan structural analyses though a BBSRC White Rose Mechanistic Biology DTP iCASE PhD studentship (2017-2021).
Undergraduate and postgraduate taught modules
Title: Molecular characterisation of the in vivo targets and mechanism of action of an acetylcholinesterase-derived peptide upregulated in Alzheimer’s disease
Supervisor: Dr Mark Collins
Funding status: Funded by a four-year White Rose DTP studentship from the BBSRC to start in October 2017.
Alzheimer’s disease (AD) is a progressive neurodegenerative disease that is characterised by the deposition and accumulation of amyloid beta plaques and phosphorylated tau filaments in the brain, the latter correlating with the onset of symptoms.
The vast majority of AD cases are sporadic and the basic mechanism driving the continuing process of neurodegeneration in selectively vulnerable cells, has not as yet been identified. However, our industrial partner, NeuroBio has recently determined that an AChE-derived 14-residue peptide (‘T14’) with a conspicuous sequence homology to amyloid beta, is upregulated in Alzheimer’s disease. T14 is present in all vulnerable cell populations irrespective of their neurotransmitter type and it drives the production of both amyloid and hyperphosphorylated tau.
These findings potentially place T14 upstream of amyloid and tau, however, a mechanistic understanding of the role of T14 in health and disease is lacking.
The aim of this project is to understand how T14 is involved in the pathogenesis of AD. We seek enthusiastic students who wish to gain expertise across disciplines including molecular neuroscience, protein biochemistry and mass spectrometry. The student will spend 6 months working in Neuro-Bio Ltd at their site in Abingdon, Oxfordshire.
For further information about projects within the department and how to apply, see our PhD Opportunities page:
- Collins MO, Woodley KT & Choudhary JS (2017) Global, site-specific analysis of neuronal protein S-acylation. Scientific Reports, 7(1). View this article in WRRO
- Bayés À, Collins MO, Reig-Viader R, Gou G, Goulding D, Izquierdo A, Choudhary JS, Emes RD & Grant SG (2017) Evolution of complexity in the zebrafish synapse proteome. Nature Communications, 8, 14613-14613. View this article in WRRO
- Oakes JA, Davies MC & Collins MO (2017) TBK1: a new player in ALS linking autophagy and neuroinflammation.. Mol Brain, 10(1), 5-5. View this article in WRRO
- Bayés À, Collins MO, Galtrey CM, Simonnet C, Roy M, Croning MDR, Gou G, van de Lagemaat LN, Milward D, Whittle IR, Smith C, Choudhary JS & Grant SGN (2014) Human post-mortem synapse proteome integrity screening for proteomic studies of postsynaptic complexes. Molecular Brain, 7. View this article in WRRO
- Collins MO (2014) AMPA Receptor Complex Dynamics in Time and Space. Neuron, 84(1), 1-3.
- Collins MO, Wright JC, Jones M, Rayner JC & Choudhary JS (2014) Confident and sensitive phosphoproteomics using combinations of collision induced dissociation and electron transfer dissociation.. Journal of Proteomics, 103, 1-14. View this article in WRRO
- Brochet M, Collins MO, Smith TK, Thompson E, Sebastian S, Volkmann K, Schwach F, Chappell L, Gomes AR, Berriman M, Rayner JC, Baker DA, Choudhary J & Billker O (2014) Phosphoinositide metabolism links cGMP-dependent protein kinase G to essential Ca²⁺ signals at key decision points in the life cycle of malaria parasites.. PLoS Biol, 12(3). View this article in WRRO
- Jones ML, Collins MO, Goulding D, Choudhary JS & Rayner JC (2012) Analysis of protein palmitoylation reveals a pervasive role in Plasmodium development and pathogenesis.. Cell Host Microbe, 12(2), 246-258. View this article in WRRO
- Wright JC, Collins MO, Yu L, Käll L, Brosch M & Choudhary JS (2012) Enhanced peptide identification by electron transfer dissociation using an improved Mascot Percolator.. Mol Cell Proteomics, 11(8), 478-491. View this article in WRRO
- Pagliuca FW, Collins MO, Lichawska A, Zegerman P, Choudhary JS & Pines J (2011) Quantitative proteomics reveals the basis for the biochemical specificity of the cell-cycle machinery.. Mol Cell, 43(3), 406-417.
- Bayés A, van de Lagemaat LN, Collins MO, Croning MDR, Whittle IR, Choudhary JS & Grant SGN (2011) Characterization of the proteome, diseases and evolution of the human postsynaptic density.. Nat Neurosci, 14(1), 19-21.
- Purcell SM, Moran JL, Fromer M, Ruderfer D, Solovieff N, Roussos P, O'Dushlaine C, Chambert K, Bergen SE, Kähler A, Duncan L, Stahl E, Genovese G, Fernández E, Collins MO, Komiyama NH, Choudhary JS, Magnusson PK, Banks E, Shakir K, Garimella K, Fennell T, Depristo M, Grant SG, Haggarty SJ, Gabriel S, Scolnick EM, Lander ES, Hultman CM, Sullivan PF, McCarroll SA & Sklar P () A polygenic burden of rare disruptive mutations in schizophrenia.. Nature, 506(7487), 185-190. View this article in WRRO