Dr Phil Mitchell
School of Biosciences
Lecturer
+44 114 222 2821
Full contact details
School of Biosciences
Firth Court
Western Bank
Sheffield
S10 2TN
- Profile
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Career history
- 2004 - present: Lecturer, University of Sheffield
- 1997 - 2004: PDRA (Tollervey lab), Wellcome Trust Centre for Cell Biology, University of Edinburgh
- 1993 - 1996: Research Fellow (Tollervey lab), EMBL, Heidelberg, Germany
- 1993: Visiting Scientist (Zimmerman lab), University of Amherst, USA
- 1991 - 1992: PDRA (Brimacombe lab), Max Planck Institute for Molecular Genetics, Berlin, Germany
- 1988 - 1990: PhD, King’s College, University of London
- Qualifications
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Honours and distinctions
- 2011 - present: Associate Editor, International Journal of Biochemistry and Molecular Biology
- 1993 - 1996: EMBO Research fellowship
- Research interests
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Building on the discovery and characterisation of the exosome ribonuclease complex (Mitchell et al., 1997; Allmang et al., 1999), my lab’s research addresses the molecular mechanisms of RNA quality control in eukaryotic cells.
Counter-intuitively, much of the RNA that a eukaryotic cell produces is rapidly degraded after being transcribed. This widespread turnover reflects highly active RNA quality control systems and the widespread transcription and degradation of unstable noncoding RNAs, as well as the processing of functional RNA from much longer precursors.
Key to many of these processes is the exosome ribonuclease (RNase) complex. Mutations within genes of the exosome directly underlie forms of neurodegenerative disease and autoimmunity and are also associated with multiple myeloma.
We are interested in understanding how RNases recognise their substrates, how the activities of these enzymes are regulated, and how they impact on human health and disease.
We use a range of complementary experimental techniques, including cellular RNA analyses, molecular genetics, protein biochemistry, cell imaging and in vitro RNA degradation assays.
Our current research aims include determining the importance of the different substrate pathways that exist through the exosome complex, understanding the functional redundancy between the exosome and Rex1 RNases, and defining the molecular interactions that are mediated through eukaryotic proteins containing the C1D domain, which is exemplified by the exosome subunit Rrp47.
Addressing the functional significance of distinct paths to catalytic sites within the exosome
The exosome RNase complex contains two associated catalytic subunits, one of which has two distinct catalytic sites (Mitchell, 2014). Substrates can be targeted to these enzymes along a number of multiple pathways.
Which RNA substrates utilise which pathway? Is there an obligatory or stochastic choice of pathway for a given RNA? Is the flux through a given pathway subject to regulation through growth conditions?
Analysis of the exoribonuclease Rex1
Inhibition of one exosome catalytic subunit renders cells dependent upon another RNase called Rex1.
What are the RNA processing or degradation pathways that require either the exosome or Rex1 activity, and which of those are essential for cell growth? What specific features of Rex1 allow it to substitute for the exosome?
Optimisation of gene expression routes for heterologous protein expression in CHO cells
CHO cells are commonly used as a vehicle for the production of heterologous proteins in the biopharmaceutical industry.
We are currently using gene knock down and knock in approaches to increase the expression level of target recombinant proteins for potential use in industrial scale applications.
- Publications
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Show: Featured publications All publications
Featured publications
Journal articles
- The exosome-binding factors Rrp6 and Rrp47 form a composite surface for recruiting the Mtr4 helicase.. EMBO Journal, 33(23), 2829-2846. View this article in WRRO
- Exosome substrate targeting: the long and short of it. Biochemical Society Transactions, 42(4), 1129-1134. View this article in WRRO
- The exosome cofactor Rrp47 is critical for the stability and normal expression of its associated exoribonuclease Rrp6 in Saccharomyces cerevisiae. PLOS One. View this article in WRRO
- Rrp47 functions in RNA surveillance and stable RNA processing when divorced from the exoribonuclease and exosome-binding domains of Rrp6.. RNA, 19(12), 1659-1668.
- Assembly of the yeast exoribonuclease Rrp6 with its associated cofactor Rrp47 occurs in the nucleus and is critical for the controlled expression of Rrp47.. J Biol Chem, 288(22), 15959-15970.
- The C-terminal region of the exosome-associated protein Rrp47 is specifically required for box C/D small nucleolar RNA 3'-maturation.. J Biol Chem, 286(6), 4535-4543.
- Finding the exosome.. Adv Exp Med Biol, 702, 1-8.
- Rrp47 and the function of the Sas10/C1D domain.. Biochem Soc Trans, 38(4), 1088-1092. View this article in WRRO
- Rrp6, Rrp47 and Cofactors of the Nuclear Exosome. Advances in Experimental Medicine and Biology, 702, 91-104.
- The PMC2NT domain of the catalytic exosome subunit Rrp6p provides the interface for binding with its cofactor Rrp47p, a nucleic acid-binding protein.. Nucleic Acids Res, 35(16), 5556-5567. View this article in WRRO
All publications
Journal articles
- Efficient PCR‐based gene targeting in isolates of the nonconventional yeast Debaryomyces hansenii. Yeast.
- Peroxisomal NAD(H) homeostasis in the yeast debaryomyces hansenii depends on two redox shuttles and the NAD+ carrier, Pmp47. Biomolecules, 13(9). View this article in WRRO
- Contribution of domain structure to the function of the yeast DEDD family exoribonuclease and RNase T functional homologue, Rex1. RNA. View this article in WRRO
- The exosome-binding factors Rrp6 and Rrp47 form a composite surface for recruiting the Mtr4 helicase.. EMBO Journal, 33(23), 2829-2846. View this article in WRRO
- Exosome substrate targeting: the long and short of it. Biochemical Society Transactions, 42(4), 1129-1134. View this article in WRRO
- The exosome cofactor Rrp47 is critical for the stability and normal expression of its associated exoribonuclease Rrp6 in Saccharomyces cerevisiae. PLOS One. View this article in WRRO
- Rrp47 functions in RNA surveillance and stable RNA processing when divorced from the exoribonuclease and exosome-binding domains of Rrp6.. RNA, 19(12), 1659-1668.
- Assembly of the yeast exoribonuclease Rrp6 with its associated cofactor Rrp47 occurs in the nucleus and is critical for the controlled expression of Rrp47.. J Biol Chem, 288(22), 15959-15970.
- The C-terminal region of the exosome-associated protein Rrp47 is specifically required for box C/D small nucleolar RNA 3'-maturation.. J Biol Chem, 286(6), 4535-4543.
- Finding the exosome.. Adv Exp Med Biol, 702, 1-8.
- Rrp6, Rrp47 AND COFACTORS OF THE NUCLEAR EXOSOME. ADV EXP MED BIOL, 702, 91-104.
- Rrp47 and the function of the Sas10/C1D domain.. Biochem Soc Trans, 38(4), 1088-1092. View this article in WRRO
- Rrp6, Rrp47 and Cofactors of the Nuclear Exosome. Advances in Experimental Medicine and Biology, 702, 91-104.
- The PMC2NT domain of the catalytic exosome subunit Rrp6p provides the interface for binding with its cofactor Rrp47p, a nucleic acid-binding protein.. Nucleic Acids Res, 35(16), 5556-5567. View this article in WRRO
- Rrp47p is an exosome-associated protein required for the 3' processing of stable RNAs.. Mol Cell Biol, 23(19), 6982-6992.
- An NMD pathway in yeast involving accelerated deadenylation and exosome-mediated 3'-->5' degradation.. Mol Cell, 11(5), 1405-1413.
- mRNA turnover.. Curr Opin Cell Biol, 13(3), 320-325.
- Purification of yeast exosome.. Methods Enzymol, 342, 356-364.
- Musing on the structural organization of the exosome complex.. Nat Struct Biol, 7(10), 843-846.
- Degradation of ribosomal RNA precursors by the exosome.. Nucleic Acids Res, 28(8), 1684-1691.
- mRNA stability in eukaryotes.. Curr Opin Genet Dev, 10(2), 193-198.
- Functions of the exosome in rRNA, snoRNA and snRNA synthesis.. EMBO J, 18(19), 5399-5410.
- The yeast exosome and human PM-Scl are related complexes of 3' --> 5' exonucleases.. Genes Dev, 13(16), 2148-2158.
- The exosome: A conserved eukaryotic RNA processing complex containing multiple 3'->5' exoribonucleases. CELL, 91(4), 457-466.
- The 3' end of yeast 5.8S rRNA is generated by an exonuclease processing mechanism.. Genes Dev, 10(4), 502-513.
- The POP1 gene encodes a protein component common to the RNase MRP and RNase P ribonucleoproteins.. Genes Dev, 8(12), 1423-1433.
- The decoding region of 16S RNA; a cross-linking study of the ribosomal A, P and E sites using tRNA derivatized at position 32 in the anticodon loop.. EMBO J, 13(11), 2677-2685.
- Site-directed cross-linking studies on the E. coli tRNA-ribosome complex: determination of sites labelled with an aromatic azide attached to the variable loop or aminoacyl group of tRNA.. Nucleic Acids Res, 21(4), 887-896.
- Clustering of modified nucleotides at the functional center of bacterial ribosomal RNA.. FASEB J, 7(1), 161-167.
- METHYLATION SITES IN ESCHERICHIA-COLI RIBOSOMAL-RNA - LOCALIZATION AND IDENTIFICATION OF 4 NEW SITES OF METHYLATION IN 23S RIBOSOMAL-RNA. BIOCHEMISTRY-US, 31(44), 10825-10834.
- HOW ARE TRANSFER-RNAS AND MESSENGER-RNA ARRANGED IN THE RIBOSOME - AN ATTEMPT TO CORRELATE THE STEREOCHEMISTRY OF THE TRANSFER-RNA MESSENGER-RNA INTERACTION WITH CONSTRAINTS IMPOSED BY THE RIBOSOMAL TOPOGRAPHY. NUCLEIC ACIDS RES, 20(11), 2627-2637.
- IDENTIFICATION OF INTERMOLECULAR RNA CROSS-LINKS AT THE SUBUNIT INTERFACE OF THE ESCHERICHIA-COLI RIBOSOME. BIOCHEMISTRY-US, 31(11), 3004-3011.
- SELECTIVE ISOLATION AND DETAILED ANALYSIS OF INTRA-RNA CROSS-LINKS INDUCED IN THE LARGE RIBOSOMAL-SUBUNIT OF ESCHERICHIA-COLI - A MODEL FOR THE TERTIARY STRUCTURE OF THE TRANSFER-RNA BINDING DOMAIN IN 23S-RNA. NUCLEIC ACIDS RES, 18(15), 4325-4333.
Chapters
- Rrp6, Rrp47 and Cofactors of the Nuclear Exosome In Jensen TH (Ed.), RNA Exosome (pp. 91-104). Springer
- Finding the Exosome In Jensen TH (Ed.), RNA Exosome (pp. 1-8). Springer
- The role of the exosome and Ski complexes in mRNA turnover In Brakier-Gingras L & Lapointe J (Ed.), Translation Mechanisms (pp. 223-236). Springer
- The organisation of rRNA, tRNA and mRNA in the ribosome In Zimmermann RA & Dahlberg AE (Ed.), Ribosomal RNA: Structure, Evolution, Processing, and Function in Protein Biosynthesis CRC Press Inc
- New techniques for the analysis of intra-RNA and RNA-protein cross-linking data from ribosomes In Spedding G (Ed.), Ribosomes and Protein Synthesis: A Practical Approach (pp. 131-159). Oxford University Press
- Biochemical and immunological characterisation of basement membranes in renal disease In Reid E, Cook GMW & Luzio JP (Ed.), Cells, Membranes, and Disease: Including Renal: Cells, Membranes, and Disease, Including Renal Vol 17 (pp. 465-474). Plenum Press
Conference proceedings papers
- MAPPING THE FUNCTIONAL CENTER OF THE ESCHERICHIA-COLI RIBOSOME. TRANSLATIONAL APPARATUS (pp 433-444)
- THE 3-DIMENSIONAL STRUCTURE AND FUNCTION OF ESCHERICHIA-COLI RIBOSOMAL-RNA, AS STUDIED BY CROSS-LINKING TECHNIQUES. BIOCHIMICA ET BIOPHYSICA ACTA, Vol. 1050(1-3) (pp 8-13)
Website content
- mRNA turnover.
Preprints
- Conserved domains and structural motifs that differentiate closely related Rex1 and Rex3 DEDDh Exoribonuclease families are required for their function in yeast, Cold Spring Harbor Laboratory.
- Efficient PCR-based gene targeting in isolates of the non-conventional yeastDebaryomyces hansenii, Cold Spring Harbor Laboratory.
- The exosome-binding factors Rrp6 and Rrp47 form a composite surface for recruiting the Mtr4 helicase.. EMBO Journal, 33(23), 2829-2846. View this article in WRRO
- Teaching activities
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Level 4 modules
- MBB405 Advanced Research Topics (Module Coordinator)
Level 3 modules
- MBB325 The RNA World
- MBB362 Biochemistry Data Handling
Level 2 modules
- MBB267 Genes, Genomes and Chromosomes (Module Coordinator)
Level 1 modules
- MBB164 Molecular Biology (Module Coordinator)