Quantitative Modeling of Transcription Initiation in Bacteria (BioSysBio 2009)

M Djordjevic
Arkansas State University and Arkansas Biosciences Institute

Starts witha nice introduction into RNA polymerase (RNAP). There are a number of stages of transcription by RNA polymerase. The first step in transcription initiation, which he is interested in, is the formation of the open complex. How is the open complex formed? Even after 20 years of research, this question still hasn’t been completely answered. Using their biophysical model, they want to identify some of the quantities related to transcription initiation that are optimized by the design of RNAP and genomic sequence.

Recent findings may help us understand what happens: firstly, a bioinformatics study shoes that the region of ~15bps immediately upstram of transcription start site is prone to to melting; secondly, single molecule experiments show that the promoter region is melted in at least one step. Why is the entire ~15bp region prone to melting? It could be an artifical consequence of the fact that only the upstream -10 region is prone to melting, while the rest of the bubble is not prone to melting – has the same melting energy as random DNA elements. Therefore in the first step, only the -10 region would be melted through thermal fluctuations facilitated by RNAP-ssDNA interactions. This first step has to be rate limiting (from the single-molecule experiment). The second step is where the bubble extends towards the transcription start site. There is very good agreement with experimental data. This is the first quantitative model of open complex formation. The results strongly support the qualitative hypothesis. The model allows the efficient analysis of kinetic properites of DNA sequences on a whole-genome scale.

Is RNAP kinetically trapped at many locations in the genome? That is, does it bind with high affinity but with a low rate of transcription initiation? Such promoters are called cryptic promoters. If not, how is the RNAP and the genomic sequence designed to prevent this? The existence of cryptic promoters has been mentioned as a major cause for false positives in both experimental and computational studies. There is no a priori reason for why binding affinity and the rate of transcription initiation should be related to each other.

The did an experiment with E.coli, which found that as they go to higher binding affinities, most (or all) of these strong binders correspond to functional promoters.  Good correlation between the binding affinity and the rate of transcription initiation is entirely dependent upon the level of RNAP protein domains. The good correlation is not due to the genome sequence. However, is this good correlation due to some generic properties of DNA binding domains? Subsitute specific binding domains with those of different DNA binding proteins. They find that interaction domains of RNAP are hardwired so as to ensure the evasion of crypic promoters.

Is RNAP and/or genomic sequences designed to maximize the rate of transcription from strong promoters? The calculated the difference between maximal transcription activity and average transcription activity for intergeneic sequences. This led to the conclusion that the maximization of rates of transcription for strong promoters is entirely at the level of protein-DNA binding domains, and not at the level of the DNA sequence.

They developed a quantitative model of open complex formation of RNAP, and used it to infer some of the design principles behind transcription initiation by bacterial RNAP.

Monday Session 1

Please note that this post is merely my notes on the presentation. They are not guaranteed to be correct, and unless explicitly stated are not my opinions. They do not reflect the opinions of my employers. Any errors you can happily assume to be mine and no-one else’s. I’m happy to correct any errors you may spot – just let me know!

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