Professor Alison Baker

Profile

1979-1982 BA Cambridge Natural Sciences (Part II Biochemistry)

1982-1985 PhD University of Edinburgh Department of Botany

Nuclear genes encoding the ATP/ADP translocator of maize mitochondria. Supervisor Prof CJ Leaver FRS

1985-1988 Postdoctoral work Biozentrum Univserity of Basel. Protein import into yeast mitochondria. Supervisor Prof G. Schatz. (EMBO Fellowship  1985-1987).

1989-1995 Assistant Lecturer then Lecturer at the Department oif Biochemistry, University of Cambridge

1995-present University of Leeds:

• 1995-1999 Lecturer
• 1999-2004 Senior Lecturer
• 2004-2008 Reader in Plant Cell and Molecular Biology
• 2008- present Professor of  Plant Cell and Molecular Biology

Responsibilities

• MSc Biosciences Programme Leader
• Prosgraduate Resaerch Tutor (Progression; MCB)

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. We have redesigned the major protein import receptor PEX5 and shown that expression of the mutant receptor can swithch peroxisome targeting specificity in vivo [5]   We have identified and characterized a peroxisomal ABC transporter which acts as the primary transport route for fatty acids and pro-hormones into peroxisomes [6-8] and shown that it possesses a novel thioesterase activity that cleaves acyl CoA substrates upon transport [9]. 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 [10]

References

[1] Hu, J.,Baker,  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] Cross LL, Paudyal R, Kamisugi Y, Berry A, Cuming AC, Baker A* and Warriner S.L*. (2017) Towards designer organelles by subverting the peroxisomalnat  import pathway. Nature Communications 8:454 *Joint corresponding authors

[6] 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.

[7] 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 pxa1pxa2Dmutant for metabolism of long chain fatty acids, and exhibits fatty acyl CoA stimulated ATPase activity. Journal of Biological Chemistry 285, 29892-29902.

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

[9] 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

[10] Ceasar S.A., Baker A, Ignacimuthu S (2017) Functional characterizatoion of the PHT1 family transporters of foxtail millet with development of a novel Agrobacterium-mediated transformation procedure. Scientific Reports 7:14064

Biochemical Characterisation of the ABC transporter COMATOSE

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.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. We have developed   purification and reconstitution protocols for this transporter and are working towards structural and further biochemical characetrisation

Collabaorators:

• 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
• Dr Stephen Muench (Leeds)
• Prof Adrian Goldberg (Leeds)

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. We have idenntified and characterized an orthogonal pair of import receptor and tageting sequence and shown that expression of these can efficiently switch targeting specificity in vivo.

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

IMPACT: Improved Millets for Phosphate Acquisition and Transport.

Low P  is a problem afflicting ~50% of agriculltural  land world wide and is a particular problem in sub saharan Africa and east Asia. Therefore crop varieties that show good yield with minimal input of fertiliser iis a desirable goal. We have  established 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. We have characterised expression of the  PHT1 family of membrane transporters  and shown through yeast complementation and RNAi that several members of this family are functional transporters with non redundant roles. Our recently awarded BBSRC India Partnering Award (2018-2022) with the International Crops Research Institute for the Semi Arid Tropics (ICRISAT www.icrisat.org) will be crucial to further development of this work to understand and improve phosphate use efficiency in this important but neglected crop.

Collaborators:

• Dr S.A. Ceasar Loyola college Chennai India

Regulation of polyphosphate metabolism in chlamydomonas and potential for exploitation as a P sink in nutrient recovery systems (BBSRC funded)

Under certain conditions microalgae can take up in phosphate in excess of metabolic need and store it as polyphosphate (poly P). While phosphate uptake and poly P metabolism has been relatively well studied in bacteria and yeast (S. cerevisiae) there is a paucity of information about this process in algae which is a clear research gap that needs to be filled if the ability of algae to grow on nutrient rich wastewaters is to be exploited as a means to recovering and recycling phosphate into fertiliser for sustainable agriculture. The availability of high quality annotated genome sequence, transcriptomic data and molecular tools make chlamydomonas the organism of choice for investigations into mechanisms of phosphate uptake and poly P synthesis and turnover. Some mechanisms may be conserved with yeast but regulation of phosphate deficiency responses is known to be quite distinct. In objective 1 we will investigate the role of the key transcription factor PSR1 and plasma membrane and vacuolar phosphate transporters in poly phosphate accumulation by genetically altering their level of expression in chlamydomonas and testing the consequences for phosphate uptake and poly P levels. In objective 2 we will investigate a candidate for putative poly P phosphatase. A mutant is available which has a phenotype that is consistent with an inability to degrade poly P however the function of the protein is currently unknown. Using degradation of poly P by wild type and mutant cell lysates and measurements of poly P accumulation in mutant and wild type we will test if the corresponding gene encodes a poly P phosphatase. This would be confirmed by enzymatic measurements with the recombinant protein. In objective 3 we will implement genetic screens to identify and characterise poly P hyper accumulating strains. Strains which show increased poly P accumulation will be tested at 2L photobioreactor scale to assess suitability for larger scale process use.

Collaborator:

Dr Miller Alonso Carmargo-Valero (School of Civil Engineering, Leeds)  https://engineering.leeds.ac.uk/staff/361/dr_miller_alonso_camargo_valero

• Do redox modulated PTMs lead to catalase moonlighting?

Qualifications

• BA, MA, Cambridge; PhD 1985, Edinburgh

Student education

I contribute to teaching at all levels of our programmes through lectures, tutorials, seminars and supervsion of  undergraduate and masters project students.

My project teaching is aligned to my research interests as stated above.

Research groups and institutes

• Plant Science