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

Microbes produce a wide range of secondary metabolites with diverse medical and industrial
applications. Genes responsible for the synthesis of secondary metabolites are carried on
biosynthetic gene clusters (BGCs), often alongside transcription factors that are involved in the
regulation 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 of
secondary metabolites. Often, the expression of a transferred BGC is sub-optimal or occasionally it
is not expressed at all. This requires modification of existing promoters within the cluster that
must be modified to (i) be recognized by the new host's RNA polymerase; (ii) minimize interactions
between proteins on the BGC and those in the host; (iii) ensure the TF(s) carried on the BGC
maintain their regulatory function. For these reasons, heterologous expression currently involvesan expensive and time-consuming process of refactoring - placing each gene of the BGC under its
own promoter and then individually modifying each promoter in a semi-random manner to
achieve optimal expression levels. An alternative strategy with potential for greater efficiency is to
preserve the structure and regulatory context of the BGC, but to adapt it to regulatory networks of
the new host. This rational approach requires alterations of native BGC promoters in order to
achieve optimal expression in the new host.

The aim of this studentship is to develop a combined experimental and computational
framework for accurate prediction and optimization of expression levels of genes within BGCs
heterologously expressed in E. coli. This will enable optimizing transcriptional expression levels of
each gene in the BGC more rapidly and with less trial-and-error than currently possible.