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EASTBIO: Dehalogenases from the brown algal genome model Ectocarpus siliculosus

  • Full or part time
    Prof F Kuepper
    Dr H Deng
    Prof M Jaspars
  • Application Deadline
    Sunday, January 05, 2020
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

Supervisors:

Professor Frithjof Kuepper (University of Aberdeen)
http://www.abdn.ac.uk/oceanlab/research/frithjof-kuepper.php

Dr Hai Deng (University of Aberdeen)
http://www.abdn.ac.uk/ncs/profiles/h.deng/

Professor Marcel Jaspars (University of Aberdeen)
http://www.abdn.ac.uk/ncs/profiles/m.jaspars/

The cosmopolitan, filamentous brown alga Ectocarpus siliculosus is the first fully-sequenced multicellular alga (Cock et al. 2010) and widely established biological model with a plethora of information about its biochemistry, developmental biology, genetics (including mutants), and pathologies (including fungi, oomycetes and viruses). It is also an important fouling organism on many natural and man-made surfaces in the sea. It can easily be cultured in small volumes of seawater-derived or synthetic media and its full life cycle can be completed in culture within a matter of weeks. As such, it has potential for industrial biotechnology which is nevertheless untapped to date.
Interestingly, its genome annotation has revealed the presence of several putative haloalkane dehalogenases – the first cases found in algal systems. We hypothesize that these haloalkane dehalogenases

(1) facilitate detoxification of chemical defence metabolites produced by other marine organisms on which Ectocarpus commonly lives as an epiphyte;
(2) have biotechnological potential for the degradation of anthropogenic, halogenated pollutants.

Within the framework of this PhD project, we aim to further elucidate the structure and function of brown algal dehalogenases. Specifically, we aim to

(1) elucidate the naturally occurring halometabolites of Ectocarpus and the role of dehalogenases in the degradation (or synthesis);
(2) generate mutants, in which the identified genes are inactivated, and compare the detoxification process among the wild type Ectocarpus and the mutants monitored by LC-MS and GC-MS;
(3) clone and heterologously express these enzymes in Escherichia coli;
(4) study the substrate specificity, kinetics and potential inhibitors of these inhibitors;
(5) explore their biotechnological potential as biocatalysts for the degradation of halogenated pollutants.

We will collaborate with the group of James Naismith (St. Andrews) for the further X-ray structure elucidation of dehalogenases from Ectocarpus, and with the Aberdeen Marine Biodiscovery Centre for the potential commercial development of metabolites and enzymes of biotechnological interest.

Our group has a long-standing track record with Ectocarpus. Significant for this project, we have expertise in its unialgal and axenic culturing, genome annotation (Cock et al. 2010), transcriptomics, elucidation of speciation of its in vivo halogen storage by X-ray absorption spectroscopy and, most recently, its halogen and oxidative metabolism in the context of defense against the oomycete pathogen Eurychasma. We are currently preparing publication of a substantial dataset about the cellular localization of halogens and volatile emissions of halocarbons and molecular iodine (I2). We have also discovered the antioxidant role of iodide in the related kelp Laminaria, impacting atmospheric chemistry, and contributed to the field of algal halogen biochemistry in general (reviewed by Küpper et al. 2011). Dr Deng has 15 years research experience of identification of new halogenated metabolites, elucidation of the functions of halogenases and application of halogenases as biocatalysts (O’Hagan and Deng 2015)

Application Procedure:
http://www.eastscotbiodtp.ac.uk/how-apply-0

Please send your completed EASTBIO application form, along with academic transcripts and CV to Alison McLeod at . Two references should be provided by the deadline using the EASTBIO reference form. Please advise your referees to return the reference form to .

Funding Notes

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership. This opportunity is only open to UK nationals (or EU students who have been resident in the UK for 3+ years immediately prior to the programme start date) due to restrictions imposed by the funding body. Queries on eligibility? Email Alison McLeod ().

Candidates should have (or expect to achieve) a minimum of a First Class Honours degree in a relevant subject. Applicants with a minimum of a 2:1 Honours degree may be considered provided they have a Distinction at Masters level.

References

Cock JM et al. (2010) The Ectocarpus genome and the independent evolution of multicellularity in the brown algae. Nature 465:617-621

Küpper FC et al. (2011) Commemorating two centuries of iodine research: An interdisciplinary overview of current research. Angewandte Chemie - International Edition 50:11598 – 11620

O'Hagan D, Deng H (2015) Enzymatic fluorination and biotechnological developments of the fluorinase. Chemical Reviews 115:634-649 doi:10.1021/cr500209t



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