Michael McArthur
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Our primary interest is in understanding how bacterial genes are regulated in vivo with the ambition of producing tools to control their expression. Streptomyces coelicolor is an excellent model as its relatively large genome (8.9Mb) is tightly compacted by proteins and RNA into the nucleoid but still manages to sponsor a complex programme of gene expression. The nucleoid associated proteins and modifying enzymes to some extent resemble eukaryotic histone proteins and enzymes, in particular the histone deacetylases. The central hypothesis of the laboratory is that a simulacrum of eukaryotic chromatin exists in S. coelicolor and rapid progress can be made in understanding this novel regulatory mechanism by adapting techniques developed for study of eukaryotes. Potentially the ‘cryptic’ secondary metabolic pathways are controlled by nucleoid structure. These are the genes that are silent under normal laboratory conditions but are predicted to encode new natural products with pharmaceutical potential. Presumably the products have a biological role when the bacterium is in its ecological niche. By dissecting the mechanism of developmental regulation we hope to gain insights into the functions of these molecules and the signals that trigger their activity. Hence, we have three main questions:
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We previously demonstrated that nucleoid structure, as measured by sensitivity of a panel of genes to in vivo DNaseI digestion, changes with transcriptional activity: a panel of expressed genes are more accessible than the non-expressed genes. This is consistent with nucleoid structure being predictive of transcriptional activity and, as in eukaryotic chromatin, playing a role in establishing the pattern of gene regulation. How does this happen? We are using proteomics, transcriptomics, genetic and biochemical approaches to identify the proteins involved in establishing nucleoid structure and to understand the nature of the biophysical interactions. By adapting techniques to map human chromatin structure, such as ChIP-seq and high-throughput DNaseI-sensitivity assays, we aim to gain a global understanding of how the nucleoid structure changes, which proteins are implicated and with what effect on expression.
In eukaryotes the ‘histone code’ refers to the post-translational modification of the basic, lysine-rich histone tails to create variants that seem to affect the expression of the underlying genes. How it does so is being actively investigated, and the effect of biophysical effects, recruitment of remodelling complexes and triggering movement to compartments of the nucleus are all being considered. In S. coelicolor the nucleoid associated proteins also have basic tails that are targeted by modifying enzymes. Further, changes in modification trigger remodelling of nucleoid structure, including over the cryptic pathways, with concomitant relief of transcriptional silencing. Is the prokaryotic ‘nucleoid code’ playing a key role in regulating secondary metabolism?
As genetical and chemical methods can be used to manipulate nucleoid structure and expression of the cryptic pathways in S. coelicolor, can such approaches be developed to relieve repression in other Actinomycetes? This family of bacteria have traditionally supplied the ‘feedstock of the pharmaceutical industry’ accounting for over two-thirds of the currently prescribed antibiotics and a host of other important therapeutics. As cryptic pathways seem widely distributed throughout the Actinomycetes and are predicted to contain novel structures with diverse biological activities developing techniques to access this chemical diversity would be potentially very valuable.
