Understanding regulation of biosynthetic gene clusters to facilitate production of secondary metabolites

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Microbes produce a wide range of secondary metabolites with diverse medical and industrialapplications. Genes responsible for the synthesis of secondary metabolites are carried onbiosynthetic gene clusters (BGCs), often alongside transcription factors that are involved in theregulation of the BGC. The exploitation of BGCs is sometimes impossible in their native host,necessitating heterologous expression in another host, such as E. coli, to obtain good yields ofsecondary metabolites. Often, the expression of a transferred BGC is sub-optimal or occasionally itis not expressed at all. This requires modification of existing promoters within the cluster thatmust be modified to (i) be recognized by the new host's RNA polymerase; (ii) minimize interactionsbetween proteins on the BGC and those in the host; (iii) ensure the TF(s) carried on the BGCmaintain their regulatory function. For these reasons, heterologous expression currently involvesan expensive and time-consuming process of refactoring - placing each gene of the BGC under itsown promoter and then individually modifying each promoter in a semi-random manner toachieve optimal expression levels. An alternative strategy with potential for greater efficiency is topreserve the structure and regulatory context of the BGC, but to adapt it to regulatory networks ofthe new host. This rational approach requires alterations of native BGC promoters in order toachieve optimal expression in the new host.The aim of this studentship is to develop a combined experimental and computationalframework for accurate prediction and optimization of expression levels of genes within BGCsheterologously expressed in E. coli. This will enable optimizing transcriptional expression levels ofeach gene in the BGC more rapidly and with less trial-and-error than currently possible.