Project Description
Due to the relatively recent discovery of the Domain Archaea and the extremophilic nature of many of its members, they have historically been considered as part of a fringe discipline within microbiology, and are therefore hugely understudied. Several recent findings have changed our perception of archaea by showing that not only are they ubiquitous, they play vital roles in environmental processes such as nutrient cycling, participate in interspecies and interdomain interactions, and have great biotechnological potential. Their remarkable stress tolerance has provided insights into the theoretical limits for life on Earth and elsewhere, with some extreme environments dominated by archaea having similar conditions to those on Mars, making archaea excellent models for studies of extraterrestrial habitability. As their importance becomes increasingly clear, it is vital that we improve our understanding of archaeal behaviour, and how it is impacted by external influences such as climate change, environmental fluctuations, and interactions with other microbial species.
This project aims to identify global response systems in archaea, primarily using proteomic analysis, to determine how they respond or adapt to environmental changes. Studies will mainly be conducted using the model archaeon Haloferax volcanii, and will evaluate its responses to diverse environmental conditions. This species has good utility as a model system, with a fully characterised proteome, well-developed molecular tools, and an existing transposon insertion mutant library, making it an excellent option for foundational studies. Other species will also be included where possible.
Proteomics is a powerful collection of analytical techniques. It serves as a rapid and robust method that enables us to answer questions relating to microbial behaviour and responses to environmental changes by profiling the proteome (the entire complement of proteins being produced at a given point in time). Techniques including BONCAT, iTRAQ, and others, will be used to evaluate changes in protein expression following exposure to diverse environmental conditions. This will involve: (1) identification of test conditions e.g. environmentally relevant stressors, fluctuating environments, or the presence of other species. (2) Exposure of test organisms to these conditions and assessment of their phenotypic responses. (3) Extraction of proteins and analysis by mass spectrometry. (4) Identification and quantification of individual proteins compared to control samples.
The other arm of the project involves the use of a H. volcanii transposon insertion mutant library to elucidate the underlying genetic basis of some key archaeal behaviours and will involve: (1) Identification of relevant test conditions (as above). (2) Exposure of wild-type H. volcanii to those conditions, to determine its normal phenotypic responses. (3) Screening the H. volcanii transposon library to identify mutants with altered responses. (4) Identification of transposon insertion sites using sequencing/bioinformatics. (5) Analysing the effects of gene mutations on the proteome.
The student will work with research groups with expertise in archaeal biology and proteomics, and will receive training in all necessary techniques: archaeal culture, phenotypic/stress tolerance assays, protein tagging, protein extraction, mass spectrometry, protein identification and quantification, the use of bioinformatic tools, culture and screening of transposon insertion mutants, and identification of genomic insertion sites.
CANDIDATE BACKGROUND
Essential skills: Candidates should have, or expect to achieve, a minimum of a 2.1 Honours degree (or equivalent) in a relevant subject. Applicants with a minimum of a 2.2 Honours degree may be considered providing they have a Distinction at Master’s level. Relevant work experience will also be considered.
Desirable skills: Applications from candidates with a working knowledge or experience of some of the microbiological and analytical techniques outlined in the project description are particularly welcomed.
Photo credit: Julianne Megaw, QUB
Supervisors
Julianne MegawPrimary Supervisor: | Profile: Julianne Megaw Email: j.megaw@qub.ac.uk Institution: Queen's University, Belfast Department/School: School of Biological Sciences |
Cécile Gubry-RanginSecondary Supervisor: | Profile: Cécile Gubry-Rangin Email: c.rangin@abdn.ac.uk Institution: University of Aberdeen Department/School: School of Biological Sciences |
Bobby GrahamAdditional Supervisor: | Profile: Bobby Graham Email: r.graham@qub.ac.uk Institution: Queen's University, Belfast Department/School: School of Biological Sciences |
QUADRAT Themes
- biodiversity
