Redefining the rules - widespread bidirectional transcription from prokaryotic promoters

All lifeforms embody the information encoded by their DNA. Like any set of instructions, the DNA code is divided into specific sections. Each section provides information about a given process and must be read before the information can be used. Inside cells, reading of the DNA is a carefully controlled. For instance, cells do not open their DNA "instruction manual" at random. Instead, cells identify the start of each section before reading of the DNA code commences. This is possible because the DNA code contains "signposts" to direct DNA reading events. These signposts were discovered in the 1960s and have always been assumed to direct reading of the DNA in one direction; it would seem illogical to read backwards. Our recent work has shown that the signposts are often symmetrical in nature. As such, when the cell recognises the signpost, the direction in which to read is ambiguous. Whilst counterintuitive, we have found that this occurs in many different lifeforms. In this proposal, we wish to understand the phenomenon and its impact. Our preliminary work suggests cells can turn this "bidirectional" reading of the DNA to their advantage. Our experimental aims are as follows:

1. Understand how symmetrical DNA signposts work.
2. Understand the consequences of bidirectional reading of DNA in cells.
3. Understand symmetrical DNA signposts in distantly related lifeforms.

Given the high profile of DNA in science, society, and popular culture, our work has substantial potential for socio-economic impact. Of particular benefit to the UK economy is the potential to develop technologies that allow more precise control of DNA reading events. To this end, we will collaborate with Robin Dickinson, CEO Aruru Molecular LTD, a biotechnology company, to identify opportunities to exploit the results of our research commercially. The wider societal benefits of our work will be realised by engaging the next generation of scientists, and the public in general. Our socio-economic impact aims are as follows:

1. Work with Aruru Molecular LTD to identify opportunities for commercialisation.
2. Offer laboratory experience to young people interested in science to help them take the next step.
3. Use the media to engage the wider public to raise awareness of our research and science in general.

Understanding how cells utilise their genetic material is fundamental to all aspects of biology. The first step is reading of the DNA to generate RNA molecules. This process, mediated by the enzyme RNA polymerase, is called transcription. The initiation of transcription occurs at DNA sequences called promoters. In prokaryotic organisms, promoters are widely considered to have strict directionality. That is, the promoter acts to drive transcription of a specific DNA strand in the 5' to 3' direction. Our recent work, currently available as a preprint (Warman et al. bioRxiv 2020.01.31.928960) and accepted for publication in Nature Microbiology, shows that promoters in prokaryotes are frequently "bidirectional". Such promoters are widespread throughout the prokaryotic domain of life and stimulate transcription of both DNA strands in the 5' to 3' direction. The phenomenon occurs because the key promoter sequences for RNA polymerase binding have inherent sequence symmetry. Our hypothesis is that bidrectional promoters, hidden in plain sight for decades, pervade the control of prokaryotic gene expression. We have three experimental questions to address:

Hypothesis: bidirectional promoters pervade the control of prokaryotic gene expression

Aim 1. Understand how bidirectional promoters work
Aim 2. Understand the role of antisense transcription from bidirectional promoters
Aim 3. Understand the implications for eukaryotic systems

Prokaryotic promoters are used widely in biotechnology and synthetic biology. Hence, bidirectional promoters have the potential to be exploited commercially. We will also use our project to enthuse the next generation of researchers and engage the general public. Our socio-economic impact aims are as follows:

Aim 1. Work with Aruru Molecular LTD to identify opportunities for commercialisation.
Aim 2. Offer laboratory experience to young people interested in science.
Aim 3. Use the media to engage the wider public.