A study of intragenic promoters in E.coli

Warman, Emily ORCID: 0000-0002-7967-9700 (2020). A study of intragenic promoters in E.coli. University of Birmingham. Ph.D.

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Abstract

RNA polymerases initiate transcription at DNA sequences called promoters. In bacteria, the best conserved promoter feature is the AT-rich -10 element; a sequence essential for DNA unwinding. Sequences that resemble the -10 element occur frequently in AT-rich DNA. As a result, horizontally-acquired genes are predisposed to spurious transcription. However, it is not clear how RNA polymerase initially recognises such sequences.

This work explores the properties of promoters located inside AT-rich genes. Intragenic promoter sequences frequently contain a short AT-tract which resides upstream of sub-optimal -10 elements. The AT-tract stimulates transcription by altering DNA conformation and enhancing contacts between the DNA backbone and RNA polymerase.

Intragenic promoter regions are also frequently divergent; able to drive transcription in both directions. We show that this is an inherent property of all promoters. Hence, whilst promoters are traditionally believed to drive transcription in a single direction, they are often bidirectional. Mechanistically, this occurs because -10 elements have inherent symmetry and often coincide on opposite DNA strands.

Finally, this work shows that RNAP-associated proteins σ38, Rho and NusA are recruited to AT-rich DNA. The alternative σ factor σ38 frequently recognises intragenic promoters and plays a role in initiating spurious transcription. Rho and NusA are involved in termination of non-coding transcripts and so are also recruited to sites of spurious transcription. Titration of these proteins away from sites of normal function is expected to be toxic to the cell.

Type of Work:

Thesis (Doctorates > Ph.D.)

Award Type:

Doctorates > Ph.D.

Supervisor(s):