Emergence of Supercoiling-Mediated Regulatory Networks in Bacterial Genomes through Chromosome Rearrangements

Core Concepts

Local variations in DNA supercoiling, due to its coupling with gene transcription, can shape the evolution of genome organization and enable the emergence of complex regulatory networks in bacterial genomes.

Abstract

The content discusses how the transcription-supercoiling coupling, in which the transcription of a gene affects the local supercoiling level and vice versa, can drive the evolution of gene regulation and genome organization in bacteria.
The key insights are:

The model shows that differentiated gene expression patterns adapted to different supercoiling environments can evolve solely through chromosomal rearrangements that leverage the transcription-supercoiling coupling. This includes the emergence of "relaxation-activated" genes, whose expression is increased by a reduction in negative supercoiling.

Analysis of the evolved genome organization reveals enrichment of specific local gene pair and triplet configurations, such as divergent gene pairs forming positive feedback loops, and convergent gene pairs acting as bistable toggle switches.

However, regulating gene expression through local interactions is not sufficient, and the model shows that interactions between larger groups of co-located genes are required to selectively activate or inhibit genes in specific environments.

The evolved genomes display a densely connected genome-wide gene interaction network, in contrast to sparse, disconnected networks in randomly generated genomes. Genes play different regulatory roles in this network depending on their type.

Overall, the results demonstrate that supercoiling-mediated regulation can shape both gene expression patterns and genome organization in bacteria, leading to the emergence of complex regulatory networks.

Stats

"DNA is normally maintained in a negatively supercoiled state, with a typical value of σbasal = −0.06 in Escherichia coli."
"In E. coli, DNA is more negatively supercoiled during exponential growth, and more relaxed in stationary phase."
"In the Long-Term Evolution Experiment, 10 out of the 12 E. coli populations were shown to present a higher level of negative supercoiling relative to their ancestor, with one population in particular presenting an increase of more than 17% in negative supercoiling."

Quotes

"Local variations in DNA supercoiling could therefore help jointly shape both gene regulation and genome organization during evolution."
"Supercoiling-sensitive genes have indeed been shown to group in local up- or down-regulated clusters, found all around the chromosome, in bacteria such as E. coli, S. enterica and S. pneumoniae."
"Synteny segments – clusters of neighboring orthologous genes that show correlated expression patterns – have been shown to be more conserved than expected by chance in a study considering over 1,000 bacterial species, including in particular the distantly related E. coli and Bacillus subtilis, possibly as a consequence of co-regulation of the genes within these segments through supercoiling."

Key Insights Distilled From

Emergence of Supercoiling-Mediated Regulatory Networks through the Evolution of Bacterial Chromosome Organization

by Grohens,T., ... at www.biorxiv.org 09-23-2022

https://www.biorxiv.org/content/10.1101/2022.09.23.509185v4

Deeper Inquiries

How might the transcription-supercoiling coupling interact with other regulatory mechanisms, such as transcription factors, in shaping bacterial genome organization and gene expression

The transcription-supercoiling coupling identified in bacterial genome organization and gene expression could interact with other regulatory mechanisms, such as transcription factors, in a coordinated manner to shape the overall regulatory landscape of the cell. Transcription factors are known to play a crucial role in gene regulation by binding to specific DNA sequences and influencing the recruitment of RNA polymerase to initiate transcription. In the context of supercoiling-mediated regulation, transcription factors could potentially modulate the activity of genes that are sensitive to changes in DNA supercoiling levels.
One possible scenario is that transcription factors could act in conjunction with the transcription-supercoiling coupling to fine-tune gene expression in response to environmental cues. For example, transcription factors could regulate the expression of genes that are involved in supercoiling-mediated interactions, either by directly influencing their transcription or by modulating the activity of the polymerases that generate supercoiling. This coordinated regulation could lead to a more robust and adaptable gene expression program that integrates multiple layers of control.
Furthermore, the interplay between transcription factors and supercoiling-mediated regulation could result in complex regulatory networks where different regulatory elements synergistically or antagonistically influence gene expression. Transcription factors may act as master regulators that coordinate the expression of genes involved in supercoiling-mediated interactions, while supercoiling could provide a feedback mechanism that fine-tunes the activity of transcription factors in response to changes in DNA topology.
Overall, the interaction between the transcription-supercoiling coupling and transcription factors could lead to a sophisticated regulatory network that integrates multiple regulatory inputs to govern gene expression in bacteria. Experimental studies combining genetic perturbations, supercoiling measurements, and transcription factor analyses could provide valuable insights into the crosstalk between these regulatory mechanisms and their impact on bacterial genome organization and gene expression.

What experimental evidence could be used to test the predictions of the model regarding the evolution of specific local gene pair and triplet configurations in bacterial genomes

To test the predictions of the model regarding the evolution of specific local gene pair and triplet configurations in bacterial genomes, experimental evidence from various approaches could be utilized. One possible experimental strategy is to perform comparative genomics analyses across different bacterial species to identify conserved gene pairs and triplets that exhibit coordinated expression patterns. By examining the genomic organization and expression profiles of these gene clusters in diverse bacterial genomes, researchers can assess the evolutionary conservation of specific local gene configurations and their potential role in gene regulation.
Additionally, functional genomics experiments, such as gene knockout studies and transcriptional profiling, could be conducted to validate the regulatory interactions predicted by the model. By systematically perturbing the expression of genes involved in specific pair or triplet configurations and measuring the impact on the expression of neighboring genes, researchers can experimentally confirm the regulatory relationships inferred from the computational model.
Furthermore, chromatin conformation capture techniques, such as Hi-C, could be employed to investigate the spatial organization of genes within the bacterial chromosome and identify physical interactions between genes in close proximity. By mapping the 3D architecture of the genome and analyzing the frequency of interactions between specific gene pairs and triplets, researchers can elucidate the structural basis of supercoiling-mediated gene regulation and validate the model's predictions regarding the evolution of local gene configurations.
Overall, a combination of comparative genomics, functional genomics, and chromatin conformation capture experiments could provide comprehensive experimental evidence to test the predictions of the model regarding the evolution of specific local gene pair and triplet configurations in bacterial genomes.

Could the principles of supercoiling-mediated regulation uncovered in this model apply to other biological systems beyond bacteria, such as eukaryotic gene regulation

The principles of supercoiling-mediated regulation uncovered in this model could potentially apply to other biological systems beyond bacteria, including eukaryotic gene regulation. While the regulatory mechanisms and genomic organization may differ between bacteria and eukaryotes, the fundamental concept of DNA supercoiling as a regulatory parameter that influences gene expression is conserved across different organisms.
In eukaryotic cells, DNA supercoiling is known to play a critical role in chromatin structure and gene regulation. Changes in DNA topology can affect the accessibility of DNA to transcription factors and RNA polymerase, thereby modulating gene expression. Similar to bacteria, the interplay between DNA supercoiling and transcriptional activity in eukaryotic cells could lead to the evolution of regulatory networks that coordinate gene expression in response to environmental stimuli.
Experimental studies in eukaryotic systems have already demonstrated the impact of DNA supercoiling on gene expression and chromatin organization. By investigating the role of supercoiling-sensitive genes, chromatin remodeling complexes, and transcriptional regulators in eukaryotic gene regulation, researchers can uncover parallels with the supercoiling-mediated regulatory networks observed in bacteria.
Furthermore, computational modeling approaches similar to the one described in the context above could be adapted to study the transcription-supercoiling coupling in eukaryotic genomes. By integrating genomic data, chromatin conformation analyses, and gene expression profiles, researchers can explore the evolutionary dynamics of gene regulation mediated by DNA supercoiling in eukaryotic organisms.
Overall, while the specific mechanisms and regulatory elements may differ, the fundamental principles of supercoiling-mediated gene regulation are likely to be conserved across diverse biological systems, highlighting the potential relevance of this mode of regulation in shaping genome organization and gene expression in eukaryotes.