Ward (Archived Page)
The Ward Lab has become part of Synthetic Biology at UCL Biochemical Engineering. You can find an archive of www.ucl.ac.uk/ward below:
The Ward Lab’s core expertise is in microbial molecular biology, which we apply to a wide range of areas. With lab members’ backgrounds –in microbiology, biochemical engineering, geology, biocatalysis, plant biochemistry, biophysics and physics– and long-standing collaborations with biochemical engineers and chemists in particular, we can use molecular and synthetic biology in addressing a wide range of problems. Follow the links below or in the menu on the left to find out more.
Using synthetic biology to construct metabolic pathways in bacterial hosts and to create novel nanoscale devices.
Discovery and engineering of novel biocatalysts for the production of chiral molecules, and improvement of biocatalytic processes.
Achieving plasmid retention without antibiotic selection and large scale production of high-grade supercoiled plasmid.
Investigation of survival of bacteria under Mars-like conditions, and definition of biosignatures which could be used to detect the presence of extraterrestrial life.
What is synthetic biology?
The exact definition of synthetic biology is still debated by some. We work along the lines that whenever synthesised genes or DNA are used in place of more conventional cloning, that is synthetic biology. As the price of gene synthesis has dropped, this has been a natural evolution from more traditional molecular biology approaches. The primary advantage –setting synthetic biology apart from previous methods– is that custom synthesis allows every base to be defined, allowing total design of genetic systems.
We are engineering enzymes in the benzylisoquinoline pathway into Escherichia coli. Each enzyme in the pathway is being characterised individually, using synthetic genes to optimise codon usage for bacterial expression. Native enzymes are being engineered to improve substrate specificity using directed evolution and site-directed mutagenesis. Once candidate enzymes have been developed, they will be incorporated in an integrated pathway for the de novo production of chiral alkaloid variants. This work is funded by the BBSRC and is in conjunction with Helen Hailes and Thomas Pesnot (UCL Chemistry).Engineering benzylisoquinoline alkaloids pathways
Helen Hailes and Thomas Pesnot (Chemistry, UCL)
We are using genetically engineered filamentous bacteriophages and recombinant virus like particles as scaffolds for chemically linking organic molecules and metal ions into regular assemblies. The optical, electronic and spintronic properties of these “molecular wires” are then investigated. The long term aim is to make bio-compatible functional nano-scale devices.Using phage to create novel nanoscale devices
Tim Daffon, Paul Barker, Chris Kay.
Analysing the oral metagenome
PeopleThe importance of the human microbiome (the bacterial communities that colonise the human body) is emerging. The bacterial cells of these communities outnumber human cells tenfold, yet in the main do not cause inflammation or disease. The mouth alone is thought to contain at least 800 bacterial species with recent studies suggesting numbers in the thousands.
Understanding the interactions between commensal bacteria and their host is fundamental to understanding disease; minor changes in the oral community can lead to two of the most common bacterial diseases: dental caries and periodontal disease. Around 50% of oral bacteria cannot be cultured. Therefore, in order to understand the interactions within these communities we have chosen to employ a metagenomic approach: that is, the culture-independent, molecular analysis of the total genomes of oral bacterial communities.
Specifically, we are constructing shot-gun phage display libraries from metagenomic DNA and screening for protein interactions with host cell proteins as well as with whole bacterial cells. Our studies concern the metagenomes of the tongue dorsum, the soft mucosal surfaces of the mouth and dental plaque and have been carried out in collaboration with other members of the Research Department of Structural and Molecular Biology, the UCL Eastman Dental Institute, Kings College London Dental Institute and Wellcome Trust Sanger Centre.
Brian Henderson, Peter Mullany, Philip Warburton, Elaine Allen, David Spratt and Mike Wilson (UCL Eastman Dental Insitute)
Christine Orengo and Corin Yeats (UCL Research Department of Structural and Molecular Biology)
William Wade and Veronica Booth (Kings College London Dental Institute)
Julian Parkhill and Alan Walker (Wellcome Trust Sanger Institute)
We have a long-standing interest in enzymes that can be used to catalyse chemically troublesome reactions. Our main projects in this area have been the identification, cloning and protein engineering of transketolases and transaminases, but we have also carried out projects on oxidases and restriction endonulceases. Our work in this area is all with close collaboration with the departments of biochemical engineering and chemistry here at UCL.
Transketolases and transaminases
Building on our previous identification and engineering of transketolases and transaminases, we currently have a project focussed on intergrating the two types of enzyme in short pathways in vivo. These pathways will allow the production of a wide range of chiral products from simple precursors.
In addition, we are currently cloning a wide range of new transaminases to assess their potential as biocatalysts. Using comprehensive bioinformatic analysis, we have identified a large number of bacterial transaminases that we are now cloning, expressing and biochemically characterising.
Maria Francisca Villegas-Torres
Alternative hosts for whole cell biocatalysis
The aim of our current project in this area is to study the use of Staphylococcus carnosus as an alternative host for whole cell biocatalysis. This is part of ongoing efforts to investigate a range of hosts for biocatalysis and more general protein expression, exploiting the lab's long-standing expertise in micobial molecular biology. Previous projects have included expression and use of cytochrome P450 monoxygenases in Streptomyces lividans.
We chose S. carnosus for the current work as it is an organism used in existing food preparation processes and is tolerant to dessication and high salt conditions.
Doing without antibiotics: the pMB1 origin of replication as a novel selectable marker in enteric bacteria
Plasmids are commonly used for the production of recombinant proteins or DNA for gene therapy and often an antibiotic-resistance gene is used as a selectable marker. There is now a move in the licensing bodies such as the FDA, to eliminate antibiotics from the growth media and resistance genes from plasmids in processes that make therapeutic products. It is important to try to develop novel, effective methods to select for plasmids without using antibiotics. The overall aim of the project is to construct an Escherichia coli host strain that will enable plasmid selection without the use of antibiotics and their resistance genes. This will be done using the antisense RNAs of the pMB1 origin of replication.
Astrobiology is a new field of science, investigating the possibility of life existing beyond the Earth. Astrobiology is a deeply interdisciplinary field, with biochemists, microbiologists, geologists, planetary scientists and astronomers all working together on this search for extraterrestrial life. Here at UCL, the group is focussed on ultra-hardy lifeforms, known as extremophiles, which thrive in some of the most hostile environments on the planet. Scientists in the lab are working on microorganisms we have isolated from inhospitable environments including the Dry Valleys of Antarctica, the volcanic icefields of Iceland, and the very salty and alkaline soda lakes of East Africa. By studying the survival of these organisms we can understand better the broad range of conditions and environments that can support life, and therefore where best to search for life beyond Earth.
An astrobiological study of high latitude Martian-analogue environments
Exploring volcanic environments on Earth can help us understand past or present habitats on Mars. In particular, we are identifying the bacterial and archaeal diversity of environments produced through subglacial volcanism. The eruption of basaltic lava into overlying ice leads to a number of exceptionally varied lithic, hydrothermal and icy habitats, which serve as analogues for past environments on Mars where subglacial volcanism is likely to have been common throughout its history.
We have identified bacterial communities inhabiting basaltic lavas with different physico-chemical properties, showing how lithology may have an important influence on the development of a microbial community within an extreme cold and dry environment. In addition, we have found selected members of these basaltic lava communities remain viable under present-day Martian conditions whilst incorporated into a subglacial volcanic ‘microcosm’. One particular species – a close relation of Rubrobacter radiotolerans – was able to survive full exposure for up to a week.
Astrobiological effects of the cosmic radiation on Mars
One of the locations in the solar system thought most likely to be able to host life, at least in its past, is Mars. The current martian surface is exceedingly cold and dry, however, which would pose a severe restraint on the survival of life. The Dry Valleys region of Antarctica is a good analogue site to the martian surface, and I have isolated hardy bacteria from this environment that can survive very cold and dry conditions. Another major hazard on the martian surface is the constant flood of cosmic radiation, and I perform gamma-ray survival studies on my Antarctic bacteria as well as Deinococcus radiodurans, the most radiation-resistant organism known on Earth. Over long periods of time this cosmic radiation would act to degrade any signs of extinct life on Mars, so I am also investigating how long different 'biosignatures' would persist before we can no longer detect them.
Survivability of microorganisms from alkaline environments under Martian conditions
We have sampled and isolated organisms from a variety of environments, in particular from Lake Magadi, a soda lake in Kenya. The environments sampled have a high pH (>9) and salt content. We are investigating the culturable diversity from samples of water, soil and biomass using media based on sample location chemistry. The cultured organisms we isolate are being used in Martian simulation experiments to look at their survivability under conditions like those found on Mars.
This work is funded by the Natural Environmental Research Council and is in conjunction with the Department of Earth Sciences UCL and the Centre for Planetary Sciences at UCL/Birkbeck. Field work was completed with assistance from Professor E. Odada at the University of Nairobi and The University of Cardiff.
The Mars chamber work is with Dr Manish Patel at the Space Sciences Research Institute at the Open University.
Ward Lab members
Professor John Ward
Postdoctoral Research Associates
- John Hales
- Jack Jeffries
- Pedro Lebre
Past Lab Members
- Sally Hassan
- Stephanie Hunter
- Julio Martinez
- Daniel Gibbons
- Claire Cousins
- Lewis Dartnell
- Markus Gershater
- Oriana Losito
- Maria Torres
- Alex Bour
- Lottie Davis