Faculty of Biological Sciences

Prof Alison Baker

BA, MA, Cambridge; PhD 1985, Edinburgh
Professor in Plant Cell and Molecular Biology
School of Molecular and Cellular Biology

Background: Postdoctoral work at the Biozentrum, Universitat Basel, Switzerland until 1988. Assistant Lecturer, then Lecturer at Department of Biochemistry, University of Cambridge until 1995 when joined University of Leeds as Lecturer. Senior Lecturer from August 1998. Reader from 2004. Professor from 2008.

Contact:  Manton 9.05, +44(0) 113 34 33045, email address for  

You can read more about Prof Baker's interests here:
www.plants.leeds.ac.uk/people/groups_bak.php

Figure 1: (ABa)

Research Interests

Membrane transport processes in plants

My group is interested in membrane transport processes in plants. Much of our work has focused on peroxisomes, essential cellular organelles that are involved in an extraordinarily wide range of processes from primary metabolism, signaling and defence responses [1,2]. We have used a range of biochemical, cell biological, genomic and chemical biology [3,4] approaches to address the mechanism of transport of both proteins and metabolites across the peroxisome membrane. In the latter case we have identified and characterized a peroxisomal ABC transporter which acts as the primary transport route for fatty acids and pro-hormones into peroxisomes [5-7] and shown that it possesses a novel thioesterase activity that cleaves acyl CoA substrates upon transport [8]. We have recently initiated a new area of research studying the families of membrane proteins involved in uptake and transport of phosphate with emphasis on structure-function relationships, to help understand whether these proteins play a role in phosphorus use efficiency.  

References

[1] Hu, J., Baker, A.  Bartel, B. Linka, N.  Mullen, R.T. Reumann, S. and Zolman, B.K. (2012) Plant Peroxisomes, Biogenesis and Function. Plant Cell 24: 2279-2303.

[2] Theodoulou, F.L.,   Bernhardt, K., Linka, N. and Baker A. (2013) Peroxisomal membrane proteins: multiple trafficking routes and multiple functions. Biochemical Journal 451, 345-352.

[3] Brown, LA, O'Leary-Steele, C, Brookes, P, Armitage, L, Kepinski, S, Warriner, SL.,Baker, A (2011) A small molecule with differential effects on the PTS1 and PTS2 peroxisome matrix import pathways Plant Journal 65, 980-990.

[4] Brown LA, Larson T.L., Graham I.A., Hawes, C., Paudyal R., Warriner S.L., and Baker A (2013) An inhibitor of oil body mobilization in Arabidopsis. New Phytologist.200, 641-649.

[5] Dietrich D, Schmuths, H., De Marcos Lousa C., Baldwin JM., Baldwin SA., Baker A., Theodoulou FL and Holdsworth MJ (2009) Mutations in the Arabidopsis Peroxisomal ABC Transporter COMATOSE Allow Differentiation between Multiple Functions In Planta; Insights from an Alleic Series. Molecular Biology of the Cell 20, 530-543.

[6] Nyathi, Y., De Marcos Lousa C., van Roermund C.W.T., Wanders, R.J.A., Johnson, B.,Baldwin, S.A., Theodoulou F. L. and Baker A. (2010) The Arabidopsis Peroxisomal ABC transporter Comatose complements the Saccharomyces cerevisiae pxa1pxa2D mutant for metabolism of long chain fatty acids, and exhibits fatty acyl CoA stimulated ATPase activity.

Journal of Biological Chemistry 285, 29892-29902.

[7] Nyathi, Y., Zhang, X., Baldwin JM, Bernhardt K, Johnson B, Baldwin SA, Theodoulou FLBaker A (2012) Pseudo half molecules of the ABC transporter COMATOSE bind PEX19 and target to peroxisomes independently, but are both required for activity. FEBS LettersFEBS Letters 586, 2280-2286

[8] De Marcos Lousa, C. van Roermund, C.W.T. Postis, V.L.G. Dietrich, D Kerr, I.D. Wanders, R.J.A. Baldwin, S.A. Baker, A* and Theodoulou, F. L. (2013) Intrinsic acyl-CoA thioesterase activity of a peroxisomal ABC transporter is required for transport and metabolism of fatty acids. Proceedings of the National Academy of Sciences (USA) 110 1279-1284. * Corresponding author

 

Current Projects

1.Biochemical Characterisation of the ABC transporter COMATOSE (BBSRC funded)

The import of substrates for peroxisomal β-oxidation, an essential pathway in lipid signalling and metabolism in all organisms, is mediated by members of ATP Binding Cassette (ABC) transporter subfamily D. In our previous BBSRC-funded research we achieved the first purification of such a transporter, the Arabidopsis peroxisomal protein COMATOSE (ABCD1/ CTS), in a form that retained ATPase activity. In a paper recently published in PNAS we demonstrated that insect cell membranes expressing CTS exhibit a novel acyl CoA thioesterase activity which is intrinsic to the transporter. We also showed that CTS is both functionally and physically associated with the peroxisomal Acyl CoA Activating Enzymes (AAEs) LACS6/7, and, together with studies of fatty acid metabolism in yeast, this suggests that thioesterase activity is critical for the transport function not only of CTS but also of many other ABCDs. It is therefore of importance in organisms ranging from fungi and plants to man, where genetic defects in the homologous transporter ALDP result in the serious neurological disorder X-linked adrenoleukodystophy. At present, the molecular mechanisms linking thioesterase activity, AAE binding and fatty acid transport, are unknown, as is the biological function of these linkages. The aim of the proposed research is to understand these mechanisms and their functional roles by addressing the following objectives:

  1. To characterise the relationships between fatty acyl CoA transport, the ATPase and thioesterase activities of CTS, and the binding of Acyl CoA synthetases,
  2. To test the role of ABCD-dependent thioesterase activity in metabolic regulation.

Collaborators:

Prof S.A. Baldwin (Leeds)
http://www.astbury.leeds.ac.uk/people/staff/staffpage.php?StaffID=SAB

Dr Freddie Theodoulou (Rothamsted Research)
http://www.rothamsted.ac.uk/people/theodoul

Prof Ron Wanders and Dr Carlo van Roermund (Amsterdam Medical Centre)
http://www.amc.nl/web/Research/Who-is-Who-in-Research/Metabolic-disorders.htm?p=6

 

2. Synthetic organelles: manipulating peroxisomal protein import to create designer compartments (Leverhulme Trust Funded).

All but the simplest cells have evolved organelles to provide optimal environments for specific aspects of metabolism such as respiration, photosynthesis or the folding and modification of specific sets of proteins. Photosynthetic organisms are the only source of truly renewable resources, as they alone can convert sunlight into biomass. A body of work has looked at using various plant organelles as biofactories. Unfortunately, a drawback of using an organelle as a ‘biofactory’ is that as more of the desired product is accumulated in the organelle the less well the organelle can perform its natural functions, resulting in a decrease in plant fitness. A generic solution is the production of a synthetic organelle that can perform user-defined functions. Such an organelle will physically separate engineered and endogenous pathways yet still benefit from the metabolic and replicative environment of the cell. This has been achieved for ribosomes but there is insufficient knowledge to achieve this for membrane bound organelles. We are using principles of rational design and molecular evolution to test strategies for the development of synthetic and semisynthetic organelles within plant cells.

Collaborators:

Dr Stuart Warriner (Leeds)
http://www.astbury.leeds.ac.uk/people/staff/staffpage.php?StaffID=SLW

Prof Alan Berry (Leeds)
http://www.astbury.leeds.ac.uk/people/staff/staffpage.php?StaffID=ABe

Dr Andrew Cuming (Leeds)
http://www.plants.leeds.ac.uk/people/groups_cum.php

 

3. IMPACT: Improved Millets for Phosphate Acquisition and Transport. (EU Funded)

This project aims to establish foxtail millet as a model system for studying phosphate acquisition and phosphate use efficiency. Millets are highly nutritious and drought resistant members of the poaceae grass family. The PHT1 family of membrane transporters is under investigation. We have identified 12 members of this family and are investigating their expression and function to determine whether they can contribute to increased phosphate acquisition or use efficiency.

4. Investigation of the structure-function relationships of Aluminium activated malate channels.

TaALMT1 (Triticum aestivum aluminium-activated malate transporter 1) is the founding member of a gene family of plant anion channels with vital roles such as stomatal opening, anion homeostasis, and organic anion efflux. TaALMT1 is part of a sub-group of proteins that play a role in aluminium-detoxification in acid soils, which represent over 50% of potentially arable soils worldwide. Members of this family have been physiologically characterised in planta, andby electrophysiological measurements, but they have not been subject to detailed structural studies.

We aim to express, purify, and characterise members of this family from wheat, Arabidopsis and other plants, as well as homologues from bacteria to gain molecular-level insight into their structure and function. Key to this will be X-ray crystallography, in concert with functional assays and biochemical studies.

Collaborators:

 Prof SA Baldwin and Dr S.P.Muench (Leeds)
 http://www.astbury.leeds.ac.uk/people/staff/staffpage.php?StaffID=SAB

 

Faculty Research and Innovation



Studentship information

Undergraduate project topics:

  • Laboratory
  • -Site directed mutagenesis of a peroxisomal ABC transporter.
  • Literature
  • -The potential for Crop Plant Improvement using Acid Soil-Resistance Mechanisms.
  • -Can differences between peroxisomes and glycosomes be exploited for development of novel trypanocidal drugs
  • -Algal biofuels, hype or hope

Postgraduate studentship areas:

  • Mutagenesis and functional analysis of a peroxisomal ABC transporter
  • http://www.findaphd.com/search/ProjectDetails.aspx?PJID=44846&LID=735
  • Expression and function of PHT1 family proteins in foxtail millet

See also:

Modules taught

BIOC1301 - Introductory Integrated Biochemistry: the Molecules and Processes of Life
BIOC2303 - Intermediate Biochemistry: Skills
BIOC3111/12/BIOL3112 A - ATU - How to build organelles
BIOC3160 - Laboratory/Literature/Computing Research Project
BIOL1305 - Integrated Skills in Biosciences 1
BIOL2210/BIOC2301 - Integrated Biochemistry/Biological Membranes
BIOL2301/03 - Skills for Biol Sci & Biosciences
BIOL3306 - Biological Sciences Research Project
BIOL5152M - Topics in Plant Science
BIOL5371M - Research Planning and Scientific Communication
BIOL5373M - Protein Engineering Laboratory Project
BIOW5906X - Theory, computation and bioinformatics
FOBS1135/BIOL1112 - The Basis of Life/The molecules of life
MICR2120/BIOC2301 - Integrated Biochemistry/Medical Bacteriology
SPSC2203 - Exercise Biochemistry

Committees

Member of Graduate School Committee (Postgraduate Research Tutor for Molecular and Cellular Biology)
Member of Masters Taught Student Education Committee (Programme Leader: MSc Bioscience programmes)

Centre membership: The Centre for Plant Sciences

Group Leader Prof Alison Baker  (Professor in Plant Cell and Molecular Biology)

Membrane transport processes in plants 

Dr David Carrier  (Research Fellow)

Dr Heba Ebeed  (Visiting research fellow)

Mr Tony Palmer  (Visiting Research Fellow)


Postgraduates

Jaimie Paterson (Primary supervisor) 50% FTE
Wanjun Qi (Primary supervisor) 50% FTE
James Cooper (Co-supervisor) 10% FTE
Nicola Wood (Co-supervisor) 45% FTE