Institute for Cell and Molecular Biosciences

Staff Profile

Professor Tracy Palmer

Professor of Microbiology

Background

Vacancies

We are always open to informal enquiries for PhD or Post-Doctoral positions in this lab, and often find a way to fund good candidates. Please feel free to email me if you are interested tracy.palmer@ncl.ac.uk


Graduate Students

Fatima Ulhuq, BBSRC-EASTBIO funded PhD Student (Media Library)

Postdoctoral Research Fellows

Dr Lisa Bowman, Wellcome Trust Postdoctoral Research Assistant (Media Library)

Dr Guillermina Casabona, Wellcome Trust Postdoctoral Research Assistant (Media Library)

Dr Jon Cherry, BBSRC Postdoctoral Research Assistant (Media Library)

Dr Chriselle Mendonca, Wellcome Trust Postdoctoral Research Assistant (Media Library)


Scientific Officer

Dr Grant Buchanan (Media Library)


Education and Training

2018- Professor of Microbiology, Institute for Cell and Molecular Biosciences, Centre for Bacterial Cell Biology, Newcastle University

2017-2018 Professor of Molecular Microbiology, School of Life Sciences, University of Dundee

2007-2017 - Professor of Molecular Microbiology, Head of the Division of Molecular Microbiology, School of Life Sciences, University of Dundee

2004-2007 - MRC Senior Non Clinical Research Fellow based at John Innes Centre, Norwich

1996-2004 - Royal Society University Research Fellow based at John Innes Centre, Norwich

1993-1996 - University Research Fellow, Department of Biochemistry, University of Dundee

1992-1993 - Postdoctoral Research Assistant, University of Dundee with Prof D.H. Boxer

1988-1991 - Research Associate (RA1B) and PhD student, University of Birmingham with Prof J.B. Jackson

1988-1991 - Postgraduate: Ph.D. Biochemistry, University of Birmingham

1985-1988 - Undergraduate: B.Sc. Biochemistry (First Class Honours), University of Birmingham


Distinctions and Awards

2018 - Elected Fellow of the Royal Society (FRS)

2017- Elected Member of the European Molecular Biology Organisation

2015 - Elected Member of the European Academy of Microbiology

2015 - Elected Fellow of the American Academy of Microbiology

2011-2016 - Royal Society/Wolfson Merit Award Holder

2010 - Elected Fellow of the Society of Biology (FRSB)

2009 - Elected Fellow of the Royal Society of Edinburgh (FRSE)

2004-2009 - Medical Research Council Senior Non Clinical Fellowship

2002 - The Microbiology Society Fleming Medal

1996-2004 - Royal Society University Research Fellowship

Funding

Work in the lab is supported by the BBSRC and the Wellcome Trust






Research

Research Interests

The twin arginine protein transport (Tat) pathway

The Tat protein export system is present in the cytoplasmic membranes of many bacteria and archaea and is also found in the mitochondria and chloroplasts of plants. It has the highly unusual feature of transporting fully folded proteins. Substrates are targeted to the Tat machinery because they are synthesized with N-terminal signal peptides that contain a conserved and essential twin-arginine motif. We are interested in the mechanism of substrate recognition and protein translocation by the Tat pathway in the model organism Escherichia coli. Much of our work on the Tat pathway is undertaken in collaboration with Professors Ben Berks and Susan Lea, and Dr Phillip Stansfeld at the University of Oxford.

The Tat system has a challenging task because it allows the passage of folded substrates of varying sizes while maintaining the impermeability of the membrane to ions. The key components of the E. coli Tat system are three small membrane proteins termed TatA, TatB and TatC. A schematic for the dynamic operation of the Tat pathway is given in Fig 1.

(Fig 1 - Media Library)

We are interested in the organisation of the TatABC receptor complex and the rearrangements that occur upon signal peptide interaction, and take a range of approaches including genetics and in vivo crosslinking analysis to probe these events. Recently we have used disulphide mapping and molecular modelling (with Dr Phillip Stansfeld) to identify the positions of TatA and TatB within the receptor complex in resting state in vivo, and to assess how these change when a substrate is bound. This has allowed us to generate a model for the resting state TatABC complex shown in Fig 2.

(Fig 2 - Media Library)


The Type VII protein secretion pathway

The Type VII secretion system (T7SS) is found primarily in Gram positive bacteria and we study it in the opportunistic human pathogen Staphylococcus aureus. We collaborate with Prof Bill Hunter (School of Life Sciences, University of Dundee) to examine the structure and function of the core components of the secretion machinery (Fig 3) and the mechanism of substrate recognition.

(Fig 3 - Media Library)

We are also interested in T7SS substrate proteins, collaborating with Prof Matthias Trost (Newcastle University) to undertake proteomic identification of secreted effectors. We have identified a secreted nuclease substrate of the T7SS, EsaD, which inhibits the growth of closely related strains (Fig 4). EsaD interacts with two accessory proteins encoded at the T7SS gene cluster, EsaG, a neutralising antitoxin, and EsaE, a putative chaperone that is required for EsaD secretion. Our results have demonstrated that the T7SS has anti-bacterial activity in addition to anti-eukaryotic function.

(Fig 4- Media Library)


Molybdenum Cofactor Mutant Strains


We have the following E. coli strains/plasmids freely available to the molybdenum/ tungsten enzyme community. If you require any of these please send an e-mail either to myself or Dr Grant Buchanan (grant.buchanan@ncl.ac.uk):

TP1000 (As MC4100 ΔmobAB::Kan) published in Palmer et al. (1996) Mol. Microbiol. 20, 875-884. Useful for expressing eukaryotic molybdoenzymes since it does not make the guanine dinucleotide form of the cofactor, instead accumulates MPT. Already used as standard by several groups.

TP1001 (As MC4100 ΔmobA, unmarked mutation). Unpublished. Exactly same strain background as TP1000 but has no antibiotic marker and therefore is useful if you wish to use kanamycin resistant plasmids.

TP1004 (As RK4353 ΔmobAB::Kan). Unpublished. Similar to TP1000 but in a slightly different strain background that may synthesise more moco.

TP1005 (As P4X ΔmobAB::Kan). Unpublished. Strain background, P4X is a methionine auxotroph and therefore is useful for selenomethionine substitution of proteins for crystallographic work. P4X is a much more 'wild type' strain of E. coli and anecdotally has much higher levels of native Mo-enzyme activity than many  'tamer' lab strains.

TP1010 (As BL21(DE3) ΔmobAB::Kan). Unpublished. mob mutant in the BL21 strain. Useful if you wish to express genes under control of the T7 phage promoter. However, be cautious, our experience suggests that BL21 is not a good host strain since its levels of native Mo-enzyme activity are very low.

TP1017 (As JM101 ΔmobAB::Kan). Unpublished. mob mutant in the JM101 background. JM101 has chromosomal lacIq and is therefore a useful strain if you wish to express from any lac-controlled promoter (often present on many standard expression vectors).

Plasmid pTPR1. Unpublished. A medium copy number plasmid (based on pRK415) specifying tetracycline resistance. Carries a 5.9kb fragment of E. coli DNA covering the moa genes. Might be useful to boost MPT synthesis.




Recent Publications (2011-2018)

2018

Jäger F., Kneuper H., Palmer T.

EssC is a specificity determinant for Staphylococcus aureus type VII secretion.

Microbiology 2018 May; 164(5)

[Pubmed]

2017

Casabona M.G., Kneuper H., Alferes de Lima D., Harkins C.P., Zoltner M., Hjerde E., Holden M.T.G., Palmer T.

Haem-iron plays a key role in the regulation of the Ess/type VII secretion system of Staphylococcus aureus RN6390

Microbiology 2017 Dec; 163(12)

[PubMed]


Casabona M.G., Buchanan G., Zoltner M., Harkins C.P., Holden M.T.G., Palmer T.

Functional Analysis of the EsaB component of Staphylococcus aureus Type VII secretion system

Microbiology 2017 Nov

[Pubmed]

 

Habersetzer J., Moore K., Cherry J., Buchanan G., Stansfeld P.J., Palmer T.

Substrate-triggered position switching of TatA and TatB during Tat transport in Escherichia coli

Open Biology 2017 Aug; 7(8)

[Pubmed] 

 

Huang Q., Palmer T.

Signal Peptide Hydrophobicity Modulates Interaction with the Twin-Arginine Translocase

mBio 2017 Jul-Aug; 8(4): e00909-17

[Pubmed]

 

Tooke F.J., Babot M., Chandra G., Buchanan G., Palmer T.

A unifying mechanism for the biogenesis of membrane proteins co-operatively integrated by the Sec and Tat pathways

elife  6:, e26577

[Pubmed]

 

Palmer T.

Structural biology: Mycobacterial ESX secrets revealed

Nature Microbiology 2:, 17074

[Pubmed]

Lamont CM., Kelly C.L., Pinske C., Buchanan G., Palmer T., Sargent F.

Expanding the substrates for a bacterial hydrogenlyase reaction

Microbiology 163:, 649-653

[Pubmed]

 

Huang Q., Alcock F., Kneuper H., Deme J.C., Rollauer S.E., Lea S.M., Berks B.C., Palmer T.

A signal sequence suppressor mutant that stabilizes an assembled state of the twin arginine translocase.

Proc Natl Acad Sci USA 114(10):, E1958 - E1967

[Pubmed]


2016

 

Munnoch J.T., Widdick D.A., Chandra G., Sutcliffe I.C., Palmer T., Hutchings M.I.

Cosmid based mutagenesis causes genetic instability in Streptomyces coelicolor, as shown by targeting of the lipoprotein signal peptidase gene.

Scientific reports 6, 29495

[Pubmed]

 

Cao Z., Casabona M.G., Kneuper, H. Chalmers J.D., Palmer T. 

The type VII secretion system of Staphylococcus aureus secretes a nuclease toxin that targets competitor bacteria

Nature microbiology 2, 16183

[Pubmed]

 

Alcock F., Stansfeld P.J., Basit H., Habersetzer J., Baker M.A., Palmer T., Wallace M.I., Berks, B.C.

Assembling the Tat protein translocase.

eLife, 5

[Pubmed]


Zoltner M., Ng,W.M., Money J.J., Fyfe P.K., Kneuper H., Palmer T., Hunter W.N.

EssC: domain structures inform on the elusive translocation channel in the Type VII secretion system.

The Biochemical Journal 473, 1941-1952

[Pubmed]

 

Parthasarathy S., Parapatla H., Nandavaram A., Palmer T., Siddavattam, D.

Organophosphate Hydrolase Is a Lipoprotein and Interacts with Pi-specific Transport System to Facilitate Growth of Brevundimonas diminuta Using OP Insecticide as Source of Phosphate.

The Journal of Biological Chemistry 291, 7774-7785

[Pubmed]

 

B. Warne, C.P. Harkins, S.R. Harris, A. Vatsiou, N. Stanley-Wall, J. Parkhill, S.J. Peacock, T. Palmer, M. T. G. Holden

The Ess/Type VII secretion system of Staphylococcus aureus shows unexpected genetic diversity

BMC Genomics 17: 222

[Pubmed]

 

F. Jager, M. Zoltner, H. Kneuper, W.N. Hunter, T. Palmer

Membrane interactions and self-association of components of the Ess/Type VII secretion sytem of Staphylococcus aureus

FEBs Letters 590: 349-57

[Pubmed]


2015


C.L. Kelly, C. Pinske, B.J. Murphy, A. Parkin, F. Armstrong, T. Palmer, F. Sargent

Integration of an [FeFe]-hydrogenase into the anaerobic metabolism of Escherichia coli

Biotechnology Reports 8: 94-104

[Pubmed]

 

J.S. McDowall, M.C. Hjersing, T. Palmer, F. Sargent

Dissection and engineering of the  Escherichia coli formate hydrogenlyase complex

FEBS Letters 589:3141-3147

[Pubmed]

 

F. Cleon, J. Habersetzer, F. Alcock, H. Kneuper, P.J. Stansfeld, H. Basit, M.I. Wallace, B.C.Berks, T. Palmer

The TatC component of the twin-arginine protein translocase functions as an obligate oligomer

Molecular Microbiology 98: 111-129

[Pubmed] 

 

D.F. Browning, V.N. Bavro, J.L. Mason, Y.R. Sevastsyanovich, A.E. Rossiter, M. Jeeves, T.J. Wells, T.J. Knowles, A.F. Cunningham, J.W. Donald, T. Palmer, M. Overduin, I.R. Henderson

Cross-species chimeras reveal BamA POTRA and B-barrel domains must be fine-tuned for efficient OMP insertion

Molecular Microbiology 97: 646-659

[Pubmed]


2014


J.J. Hamilton, V.L. Marlow, R.A.Owen, A. Mde. Costa, M. Guo, G. Buchanan, G. Chandra, M. Trost, S.J. Coulthurst, T. Palmer, N.R. Stanley-wall, F. Sargent

A holin and an endopeptidase are essential for chitinolytic protein secretion in Serratia marcescens

Journal of Cell Biology 207:615-626

[Pubmed]

 

J.S McDowall, B.J.Murphy, M. Haumann, T.Palmer, F.A. Armstrong, F. Sargent

Bacterial formate hydrogenlyase complex

Proc Natl Acad Sci USA  111: 3948-3956

[Pubmed]

 

H. Kneuper, Z.P. Cao, K.B. Twomey, M. Zoltner, F. Jager, J.S. Cargill, J. Chalmers, M.M. Van der Kooi-Pol, J.M. van Dijl, R.P. Ryan, W.N. Hunter, T. Palmer

Heterogeneity in ess transcriptional organization and variable contribution of the Ess/Type VII protein secretion system to virulence across closely related Staphylococcus aureus strains

Molecular Microbiology 93:  928-943

[Pubmed]


J. M. Dow, S. Grahl, R. Ward, R. Evans, O. Byron, D. G. Norman, T. Palmer and F. Sargent

Characterization of a periplasmic nitrate reductase in complex with its biosynthetic chaperone

The FEBS Journal 281: 246-260

[Pubmed]



A. P. Hopkins, G. Buchanan and T. Palmer
The role of the twin arginine protein transport pathway in the assembly of the Streptomyces coelicolor A3(2) cytochrome bc1 complex

Journal of Bacteriology 196: 50-59

[Pubmed]


2013


L. Bowman, T. Palmer, and F. Sargent

A regulatory domain controls the transport activity of a twin-arginine signal peptide

FEBS Letters 587: 3365-70

[Pubmed]


F. Sargent, F. A. Davidson, C. L. Kelly, R. Binny, N. Christodoulides, D. Gibson, E. Johansson, K. Kozyrska, L. Licandro Lado, J. MacCallum, R. Montague, B. Ortmann, R. Owen, S. J. Coulthurst, L. Dupuy, A. R. Prescott and T. Palmer

A synthetic system for expression of components of a bacterial microcompartment

Microbiology 159: 2427-2436

[Pubmed]


M. J. James, S. J. Coulthurst, T. Palmer and F. Sargent

Signal peptide etiquette during assembly of a complex respiratory enzyme

Molecular Microbiology 90: 400-414

[Pubmed]


F. Alcock, M. A. B. Baker, N. P. Greene, T. Palmer, M. I. Wallace and B. C. Berks

Live cell imaging shows reversible assembly of the TatA component of the twin-arginine protein transport system

Proceedings of the National Academy of Sciences of the USA 110: E3650-9

[Pubmed]


J. M. Dow, F. Gabel, F. Sargent and T. Palmer

Characterization of a pre-export enzyme-chaperone complex on the twin-arginine transport pathway

Biochemical Journal 452: 57-66

[Pubmed]


M. Zoltner, D. G. Norman, P. K. Fyfe, H. El Mkami, T. Palmer and W. N. Hunter

The architecture of EssB, an integral membrane component of the type VII secretion system

Structure 21: 595-603

[Pubmed]


M. Zoltner, P. K. Fyfe, T. Palmer and W. N. Hunter

Characterization of Staphylococcus aureus EssB, an integral membrane component of the Type VII secretion system: atomic resolution crystal structure of the cytoplasmic segment

Biochemical Journal 449: 469-477

[Pubmed]


J. K. Fyans, D. Bignell, R. Loria, I. Toth and T. Palmer

The ESX/Type VII secretion system modulates development but not virulence of the plant pathogen Streptomyces scabies

Molecular Plant Pathology 14: 119-130

[Pubmed]


2012


S. E. Rollauer, M. J. Tarry, J. E. Graham, M. Jääskeläinen, F. Jäger, S. Johnson, M. Krehenbrink, S.-M. Liu, M. J. Lukey, J. Marcoux, M. A. McDowell, F. Rodriguez, P. Roversi, P. J. Stansfeld, C. V. Robinson, M. S. P. Sansom, T. Palmer, M. Högbom, B. C. Berks and S. M. Lea

Structure of the TatC core of the twin arginine protein transport system

Nature 492: 210-214

[PubMed]


J. Willemse, B. Ruban-Osmialowska, D. Widdick, K. Celler, M. I. Hutchings, G. P. van Wezel and T. Palmer

Dynamic localization of Tat protein transport machinery components in Streptomyces coelicolor

Journal of Bacteriology 194: 6272-6281

[PubMed]


R. Keller, J. de Keyzer, A. J. M. Driessen and T. Palmer

Co-operation between different targeting pathways during integration of a membrane protein

Journal of Cell Biology 199: 303-315

[PubMed]

 

H. Kneuper, B. Maldonado, F. Jäger, M. Krehenbrink, G. Buchanan, R. Keller, M. Müller, B. C. Berks and T. Palmer>

Molecular dissection of TatC defines critical regions essential for protein transport and a TatB-TatC contact site

Molecular Microbiology 85: 945-961

[PubMed]


T. Palmer and B. C. Berks

The twin-arginine translocation (Tat) protein export pathway

Nature Reviews Microbiology 10: 483-496

[PubMed]


M. J. Fritsch, M. Krehenbrink, M. J. Tarry, B. C. Berks and T. Palmer

Processing by rhomboid protease is required for Providentia stuartii TatA to interact with TatC and to form functional homo-oligomeric complexes

Molecular Microbiology 84: 1108-1123

[PubMed]


S. Koch, M. J. Fritsch, G. Buchanan and T. Palmer

The Escherichia coli TatA and TatB proteins have an N-out C-in topology in intact cells

Journal of Biological Chemistry 287: 14420-14431

[PubMed]

 

2011


A. Parkin, L. Bowman, M. M. Roessler, R. A. Davies, T. Palmer, F. A. Armstrong and F. Sargent

How Salmonella oxidises H(2) under aerobic conditions

FEBS Letters 586: 536-544

[PubMed]


J. Bauer, M. J. Fritsch, T. Palmer, G. Unden

Topology and accessibility of the transmembrane helices and the sensory site in the bifunctional transporter DcuB of Escherichia coli

Biochemistry, 50: 5925-5938

[PubMed]


B. Maldonado, H. Kneuper, G. Buchanan, K. Hatzixanthis, F. Sargent, B. C. Berks, T. Palmer

Genetic evidence for a TatC dimer at the core of the Escherichia coli twin arginine (Tat) protein translocase

Journal of Molecular Microbiology and Biotechnology. 20(3): 168-175

[PubMed]


B. Maldonado, G. Buchanan, M. Müller, B. C. Berks, T. Palmer

Characterisation of the membrane-extrinsic domain of the TatB component of the twin arginine protein translocase

FEBS letters. 585: 478-484

[PubMed]


T. Palmer, F. Sargent, B. C. Berks

The Tat protein export pathway.

In Ecosal Plus - Escherichia coli and Salmonella: Cellular and Molecular Biology

[ASMscience] 

 

D. A. Widdick, M. G. Hicks, B. J. Thompson, A. Tschumi, G. Chandra, I. C. Sutcliffe, J. K. Brülle, P. Sander, T. Palmer, M. I. Hutchings

Dissecting the complete lipoprotein biogenesis pathway in Streptomyces scabies

Molecular Microbiology. 80: 1395-1412

[PubMed]