In a major collaboration with Professor Craig Cary of the University of Waikato, NZ, IMBM researchers are investigating microbial diversity and function in the cold desert soils of the McMurdo Dry Valleys of Eastern Antarctica. This program is supported by the NRF and Antarctica NZ, who provide the logistics for an annual field expedition to Antarctica.

In a new project linking chemical technologies developed by Leslie Petrik in the Department of Chemistry, UWC and the biological skills of the IMBM laboratory, we aim to engineer new nanocatalysts and nanobiocarriers. These will be based on macroporous zeolite matrices, which will be chemically derivatized such that biomaterials (enzymes, peptides, nucleic acids and antibodies) can be covalently linked to the zeolite surfaces. These nanoparticles will also be impregnated with metals in order to generate magnetic nanobioparticles suitable for recovery using magnetic capture technologies.

The term metagenomics applies to any studies which are based on extraction of total community DNA from an environmental source (i.e., that are not dependent on the isolation and/or culturing of any individual organism).  In collaboration with Professor Steph Burton and others, the IMBM laboratory has been involved in the development of new metagenomic technologies for recovery of novel genes from the environment.

Our approaches have included the use of gene-specific PCR (for identification of thermophilic lipases and esterases), plasmid and fosmid expression libraries, and subtractive hybridisation with magnetic gene capture (for recovering novel multi-copper oxidases). In collaboration with Professor Bill Grant and others, we reported the first construction of metagenomic cDNA libraries for accessing lower eukaryote genomes in the environment. We are currently extending our work in this area to the development of large insert libraries using fosmid vector systems.

In a major collaboration with Professor Craig Cary of the University of Waikato, NZ, IMBM researchers are investigating microbial diversity and function in the cold desert soils of the McMurdo Dry Valleys of Eastern Antarctica. This program is supported by the NRF and Antarctica NZ, who provide the logistics for an annual field expedition to Antarctica.

In an EU-funded collaboration with Professor Bill Grant (U. Leicester, UK), Antonio Ventosa (U. Sevilla, ES), Professor Brian Jones (Genencor International, NE) and Professor Ma Yanhe (IMCAS, Beijing, CH), IMBM researchers have studied the microbial diversity, using both culture-dependent and culture-independent methods, of thermophilic, halophilic and haloalkalophilic habitats in China and neighbouring regions.

Numerous new bacteria and archaea have been identified and isolated. In particular, we have demonstrated that nanoarchaea, a novel group of hyperthermophilic archaeal parasites, are found in high temperature habitats around the world, including S.W. China (Yunnan Province), Chile, and New Zealand. Studies on the isolation and genomics of the nanoarchaea continue in collaboration with Dr Jenny Blamey, Biosciencia, Chile, Professor Hugh Morgan, University of Waikato, NZ and Professor Win Hide, SANBI, UWC.

We have cloned, sequenced and expressed the gene for a thermostable nitrile hydratase from the thermophilic organism Geobacillus pallidus. This gene is co-localized with ORFs encoding an amidase and a P14 protein of unknown function. Specificity studies on the native and recombinant nitrile hydratases show a preference for aliphatic and non-aromatic nitriles, whereas aromatic nitriles act as non-competitive inhibitors.

We have investigated the molecular basis of this specificity using a combination of site-specific mutagenesis and x-ray crystallography. Attempts are also currently underway to modify specificity using enzyme evolution methods.  These studies are undertaken in collaboration with Dr Muhammed Sayed (U. Western Cape), Professor Trevor Sewell (UCT) and Professor Mike Danson (University of Bath, UK) under the auspices of the NRF-Royal Society program. With the recent cloning and expression of a thermostable amidase and nitrilase, we aim to extend our studies of specificity and thermostability using a variety of structural and engineering techniques. We have proposed a novel role for the P14 protein as a pseudo-catalyst in the folding and association pathway of the nitrile hydratases alpha- and beta-subunits.

In collaboration with Professor Yohda (University of Tokyo, JP), we are attempting to generate metastable alpha-subunit/P14 intermediates for structural analysis. In order to evaluate the molecular basis for stability in these enzymes, we are using two strategies – protein evolution of the thermostable nitrile hydratase, and cloning, expression and structural analysis of cold-adapted homologues from psychrotrophic organisms. We are also studying the potential use of these enzymes as industrial catalysts, particularly for the nitrile hydratase catalyzed conversion of 3-cyanopyridine to nicotinamide, and the chiral resolution of amides using the D-specific amidase. These studies are in collaboration with Professor Steph Burton, UCT.

IMBM researchers are involved in several studies aimed at the recovery of valuable chemical and energy products from low value feedstocks.  In collaboration with Professors Steph Burton and Sue Harrison form the Department of Chemical Engineering, UCT, we have identified and characterised a range of filamentous fungal strains which are capable of growing on and depolymerising low rank coal. The long term objectives of this project include the efficient bioconversion of coal-C to valuable energy resources, including protein, CO₂, and organic chemical monomers. IMBM maintains a major collaboration with TMO (UK) Ltd, an exciting biotechnology SMME working in the bioenergy sector. Our role is to assist TMO Ltd to develop new fermentation technology for the thermophilic conversion of pentose feedstocks to biofuel.  IMBM research activities will include basic studies of production strain metabolism and genetic control, together with strain engineering.