Predicting bacterial promoter function and evolution from random sequences

Abstract

Predicting function from sequence is a central problem of biology. Currently, this is possible only locally in a narrow mutational neighborhood around a wildtype sequence rather than globally from any sequence. Using random mutant libraries, we developed a biophysical model that accounts for multiple features of σ70 binding bacterial promoters to predict constitutive gene expression levels from any sequence. We experimentally and theoretically estimated that 10–20% of random sequences lead to expression and ~80% of non-expressing sequences are one mutation away from a functional promoter. The potential for generating expression from random sequences is so pervasive that selection acts against σ70-RNA polymerase binding sites even within inter-genic, promoter-containing regions. This pervasiveness of σ70-binding sites implies that emergence of promoters is not the limiting step in gene regulatory evolution. Ultimately, the inclusion of novel features of promoter function into a mechanistic model enabled not only more accurate predictions of gene expression levels, but also identified that promoters evolve more rapidly than previously thought.

The regulon of Brucella abortus two-component system BvrR/BvrS reveals the coordination of metabolic pathways required for intracellular life

“…These binding sites show different degrees of similarity to the obtained consensus sequence, suggesting that the affinity of BvrR-P for these sites might play a role in controlling virB transcription in coordination with other regulatory molecules previously described [ 75 ]. The detection of more than one significant ChIP-Seq signal close to a gene, including some within the coding region and even at the 3´ end of the coding region, is opening possibilities for further research related to the role of antisense transcription [ 97 ] within the BvrR/BvrS regulon, the presence of gene overlapping [ 98 ] and non-conventional promoter structure [ 99 ] in Brucella . To our knowledge, transcription could be promoted from unusual sites, and multiple binding sites could be needed for optimal binding.…”

The Origins and Functions of De Novo Genes: Against All Odds?

“…On the flip side, although many of these genes may have used this strategy to acquire expression, many others have not, suggesting that expression itself may not be quite so rare in sequence space as we imagine. Indeed, recent work has demonstrated a surprisingly high probability of a basal level of promoter activity) among random sequences: in E. coli , ~ 10%, with 60% one mutational step away) (Yona et al 2018 ; Lagator, et al 2022 ), and in yeast, 83% (Boer et al 2020 ). A violation of the sparsity premise is also likely at play.…”

Gene Birth in a Model of Non-genic Adaptation

“…A majority of studies in genomics and genetics are concerned with the function and evolutionary course of known genes and their regulation. Recent discoveries have attracted focus towards the evolution of non-genic loci; particularly, experimental studies that demonstrate the adaptive potential of random sequences Hayashi et al [2003], Yona et al [2018], Lagator et al [2022]. Furthermore, genomics studies that indicate the frequent occurrence of de novo gene birth demonstrate a need for general, theoretical investigations of the evolution of non-genic loci Tautz and Domazet-Lošo [2011].…”