Role of Aspergillus fumigatus gene clusters in mammalian niche-adaptation

A small number of fungi are able to cause infection in humans. Among them, the soil-dwelling fungus Aspergillus fumigatus is a serious threat to human health. Aspergillus fumigatus spores are extremely small and remain airborne for long periods of time. If inhaled by humans with defective or deficient immunity they can germinate and grow within the lung, causing invasive infection which is often fatal. It is currently unknown why Aspergillus fumigatus is able to cause human disease whereas closely related fungal species are not. The Aspergillus fumigatus genome has been sequenced and comparisons to genomes of non-pathogenic relatives identify the greatest differences, at the level of DNA sequence, at the ends of chromosomes, which are known as telomeres. We previously used a technique called microarray analysis to record gene activity, simultaneously from every Aspergillus fumigatus gene, in an attempt to identify genes involved in establishing mammalian infection. There were two surprising features of the resulting dataset. Firstly, the vast majority of active genes were located at the telomeres of genes. Secondly we identified many clusters of neighbouring genes which seem to be co-regulated. Recently, gene clusters have been identified in other disease-causing fungi, such as those infecting plants, and have been implicated in infection. We therefore wish to investigate the function of the Aspergillus gene clusters to determine whether, and how, they are involved in establshing disease. Aspergillus fumigatus may have developed the ability to colonise the human lung as a result of evolving to withstand stresses in the soil environment. We therefore plan to investigate the process of adaptation to the mammalian lung environment to identify factors important for establishing infection. The process of adapting to the stresses of varying habitats is known as niche-adaptation.

In our recent gene expression screens for niche-adapting gene functions in the major mould pathogen of humans, Aspergillus fumigatus, we discovered multiple clusters of physically-linked co-ordinately regulated genes preferentially expressed during germinative growth in the murine lung relative to laboratory culture. The likely physiological significance of this discovery is heightened by the presence of known virulence loci among those we identified, including that encoding biosynthesis of the immunotoxin gliotoxin, and a siderophore biosynthetic gene cluster containing genes essential for virulence. Similar experimentation in the biotrophic fungal phytopathogen, Ustilago maydis, recently identified a similar phenomenon, linking gene function to virulence for a number of loci. We hypothesise that co-regulation of genes located within the A. fumigatus 'infection clusters' indicates concerted function during initiation of mammalian infection and we now wish to determine the role of such 'infection' clusters (ICs) in A. fumigatus niche-adaptation, host damage and virulence. In order to do this we plan to expand our microarray anlayses, assessing time series gene expression profiles during initiation of infection in two murine models. We will also optimise a recombineering protocol suitable for high throughput aspergillus fumigatus gene deletion cassette construction . This will enable us to delete genes within, and surrounding, important ICs. Using this approach we will make full deletions of up to 96 ICs. IC mutants will be characterised for defects in growth, development, proteinase secretion, cytotoxicty, virulence and adhesion. We will further interrogate the transcriptional regulation of five important ICs using RT-PCR analysis. Epigenetic regulation will also be assessed using A. fumigatus mutants defective in histone deacetylase activity and methyltransferase activity.