Promoter Motifs Influence the Emergence and Evolution of Gene Expression in Prokaryotes

Core Concepts

Promoter motifs for RNA polymerase binding can both facilitate and impede the emergence and evolution of gene expression, depending on their specific locations and interactions.

Abstract

The study investigates how promoter motifs, specifically the -10 and -35 box sequences, influence the emergence and evolution of gene expression in prokaryotes. The key findings are:

Sequences enriched with -10 and -35 box motifs but lacking promoter activity show a wide range (over 200-fold) in the probability that mutations can create new active promoters (Pnew). This probability is not correlated with the number of existing motifs, but rather with the number of "hotspots" - regions where mutations significantly impact expression.

The majority (∼67%) of new promoters emerge from mutations that create additional -10 and -35 box motifs, often adjacent to preexisting motifs (a process called "Shiko emergence"). However, the presence of a motif does not guarantee that a promoter will emerge there.

In active promoters, gaining additional -10 or -35 box motifs can either increase or decrease expression, depending on whether the new motifs are created in tandem, shift the spacing between existing motifs, or overlap with the original promoter binding sites.

Destroying -10 or -35 box motifs does not increase promoter activity, contrary to a previous report. Instead, the data suggests that mutations primarily modulate promoter strength by creating, shifting, or overlapping motifs rather than removing them.

In summary, the study demonstrates the complex interplay between promoter motifs and their influence on the emergence and evolution of gene expression in prokaryotes. The findings have implications for understanding regulatory evolution, de-novo gene emergence, and predicting promoter activity.

Stats

The probability that mutations create an active promoter from an inactive parent sequence varies more than 200-fold, from 0.002 to 0.41.
Approximately 67% of new promoters emerge from mutations that create additional -10 and -35 box motifs.
Gaining additional -10 or -35 box motifs can either increase or decrease promoter activity, depending on the specific location and arrangement of the new motifs.

Quotes

"The probability that mutations create an active promoter from an inactive parent sequence varies dramatically among parents, with the lowest Pnew being 0.002 and the highest 0.41, a 205-fold difference."
"The majority (∼67%) of new promoters emerge from mutations that create additional -10 and -35 box motifs, often adjacent to preexisting motifs (a process called "Shiko emergence")."
"Gaining additional -10 or -35 box motifs can either increase or decrease promoter activity, depending on whether the new motifs are created in tandem, shift the spacing between existing motifs, or overlap with the original promoter binding sites."

Key Insights Distilled From

The emergence and evolution of gene expression in genome regions replete with regulatory motifs

by Fuqua,T., Su... at www.biorxiv.org 02-26-2024

https://www.biorxiv.org/content/10.1101/2024.02.26.581924v2

Deeper Inquiries

How do the findings of this study apply to eukaryotic gene regulation, where promoter architecture and transcription factor binding are more complex

The findings of this study on prokaryotic gene regulation can be extrapolated to eukaryotic gene regulation, where the complexity of promoter architecture and transcription factor binding is significantly higher. In eukaryotes, gene regulation involves a wide array of regulatory elements, including enhancers, silencers, insulators, and various transcription factor binding sites. These elements interact in a highly coordinated manner to regulate gene expression in a cell- and tissue-specific manner.
While the study focused on the role of -10 and -35 box motifs in prokaryotic promoters, eukaryotic promoters are characterized by a diverse set of regulatory motifs that interact with a larger repertoire of transcription factors. The principles of promoter emergence and evolution elucidated in the study can be applied to understand how new regulatory elements may emerge in eukaryotic gene regulation. The interplay between different regulatory motifs, the spatial organization of enhancers and promoters, and the complex regulatory networks in eukaryotic gene expression can be further explored using similar methodologies to uncover the mechanisms underlying gene regulation in higher organisms.

What other factors, beyond promoter motifs, might influence the probability of de-novo promoter emergence from non-regulatory DNA sequences

Beyond promoter motifs, several other factors may influence the probability of de-novo promoter emergence from non-regulatory DNA sequences. Some of these factors include:

Epigenetic Modifications: DNA methylation, histone modifications, and chromatin remodeling play crucial roles in regulating gene expression. Changes in the epigenetic landscape can impact the accessibility of DNA sequences for transcription factors, influencing the emergence of new promoters.

Cis-Regulatory Elements: Enhancers, silencers, and insulators located in the vicinity of non-regulatory DNA sequences can interact with the DNA to modulate gene expression. The presence of these elements can either facilitate or impede the emergence of de-novo promoters.

Transcription Factor Availability: The availability and activity of transcription factors in the cellular environment can determine the likelihood of de-novo promoter emergence. Changes in transcription factor expression levels or post-translational modifications can alter the regulatory landscape of the genome.

Chromatin Structure: The three-dimensional organization of chromatin, including the formation of chromatin loops and topologically associating domains (TADs), can influence the accessibility of DNA sequences for transcriptional machinery. Alterations in chromatin structure can impact the emergence of new promoters.

Non-Coding RNAs: Regulatory non-coding RNAs can interact with DNA sequences and transcription factors to modulate gene expression. The presence of non-coding RNAs in the vicinity of non-regulatory DNA sequences can affect the probability of de-novo promoter emergence.

Considering these additional factors alongside promoter motifs can provide a more comprehensive understanding of the mechanisms underlying de-novo promoter emergence in gene regulation.

Could the principles of Shiko emergence and modulation of promoter activity through motif rearrangement be leveraged for synthetic biology applications, such as the design of novel gene circuits

The principles of Shiko emergence and the modulation of promoter activity through motif rearrangement uncovered in this study hold significant potential for synthetic biology applications, particularly in the design of novel gene circuits. By leveraging these principles, synthetic biologists can engineer synthetic gene regulatory networks with enhanced functionality and controllability.

Design of Synthetic Promoters: The concept of Shiko emergence, where mutations create new promoter motifs to drive gene expression, can be harnessed to design synthetic promoters with specific activity levels. By strategically introducing or modifying promoter motifs, synthetic biologists can tailor the strength and specificity of gene expression in engineered systems.

Modulation of Gene Expression: Understanding how motif rearrangement can modulate promoter activity offers a powerful tool for fine-tuning gene expression levels in synthetic gene circuits. By manipulating the arrangement and composition of regulatory motifs, researchers can dynamically regulate gene expression in response to different environmental cues or inputs.

Construction of Complex Gene Networks: The ability to manipulate promoter motifs and their interactions can facilitate the construction of complex gene regulatory networks in synthetic biology. By applying the principles of motif rearrangement and promoter modulation, researchers can design sophisticated genetic circuits with precise control over gene expression dynamics and regulatory behavior.

Overall, the insights gained from this study provide a foundation for the development of advanced synthetic biology tools and platforms that can be applied in a wide range of biotechnological and biomedical applications.