Shedding Light on Bacterial Chromosome Structure: Exploring the Significance of 3C-Based Approaches

The complex architecture of DNA within living organisms is essential for maintaining the genetic information that dictates their functions and characteristics. Among the many complexities of genetic material organization, the folding and arrangement of DNA into chromosomes play a critical role in regulating gene expression, replication, and other essential cellular processes. Bacteria, despite their apparently simple cellular structure, exhibit a remarkable level of chromosomal organization that influences their adaptability and survival in diverse environments. Understanding the three-dimensional arrangement of bacterial chromosomes has long been a challenge due to technical limitations, but the development of Chromosome Conformation Capture (3C) methods revolutionized our ability to explore the hierarchical structure and the dynamics of bacterial genomes. Here, we review the major advances in the field of bacterial chromosome structure using 3C technology over the past decade.

Enhanced recombinant carbonic anhydrase in T7RNAP-equipped Escherichia coli W3110 for carbon capture storage and utilization (CCSU)

Sulfurihydrogenibium yellowstonense carbonic anhydrase (SyCA) is a well-known thermophilic CA for carbon mineralization. To broaden the applications of SyCA, the activity of SyCA was improved through stepwise engineering and in different cultural conditions, as well as extended to co-expression with other enzymes. The engineered W3110 strains with 4 different T7 RNA polymerase levels were employed for SyCA production. As a result, the best strain WT7L cultured in modified M9 medium with temperature shifted from 37 to 30 °C after induction increased SyCA activity to 9122 U/mL. The SyCA whole-cell biocatalyst was successfully applied for carbon capture and storage (CCS) of CaCO₃. Furthermore, SyCA was applied for low-carbon footprint synthesis of 5-aminolevulinic acid (5-ALA) and cadaverine (DAP) by coupling with ALA synthetase (ALAS) and lysine decarboxylase (CadA), suppressing CO₂ release to -6.1 g-CO₂/g-ALA and -2.53 g-CO₂/g-DAP, respectively. Harnessing a highly active SyCA offers a complete strategy for CCSU in a green process.

Early fate of exogenous promoters in E. coli

Gene gain by horizontal gene transfer is a major pathway of genome innovation in bacteria. The current view posits that acquired genes initially need to be silenced and that a bacterial chromatin protein, H-NS, plays a role in this silencing. However, we lack direct observation of the early fate of a horizontally transferred gene to prove this theory. We combine sequencing, flow cytometry and sorting, followed by microscopy to monitor gene expression and its variability after large-scale random insertions of a reporter gene in a population of Escherichia coli bacteria. We find that inserted promoters have a wide range of gene-expression variability related to their location. We find that high-expression clones carry insertions that are not correlated with H-NS binding. Conversely, binding of H-NS correlates with silencing. Finally, while most promoters show a common level of extrinsic noise, some insertions show higher noise levels. Analysis of these high-noise clones supports a scenario of switching due to transcriptional interference from divergent ribosomal promoters. Altogether, our findings point to evolutionary pathways where newly-acquired genes are not necessarily silenced, but may immediately explore a wide range of expression levels to probe the optimal ones.

Interference of transcription across H-NS binding sites and repression by H-NS

Nucleoid-associated protein H-NS represses transcription by forming extended DNA-H-NS complexes. Repression by H-NS operates mostly at the level of transcription initiation. Less is known about how DNA-H-NS complexes interfere with transcription elongation. In vitro H-NS has been shown to enhance RNA polymerase pausing and to promote Rho-dependent termination, while in vivo inhibition of Rho resulted in a decrease of the genome occupancy by H-NS. Here we show that transcription directed across H-NS binding regions relieves H-NS (and H-NS/StpA) mediated repression of promoters in these regions. Further, we observed a correlation of transcription across the H-NS-bound region and de-repression. The data suggest that the transcribing RNA polymerase is able to remodel the H-NS complex and/or dislodge H-NS from the DNA and thus relieve repression. Such an interference of transcription and H-NS mediated repression may imply that poorly transcribed AT-rich loci are prone to be repressed by H-NS, while efficiently transcribed loci escape repression.

Horizontally acquired AT-rich genes in Escherichia coli cause toxicity by sequestering RNA polymerase

Horizontal gene transfer permits rapid dissemination of genetic elements between individuals in bacterial populations. Transmitted DNA sequences may encode favourable traits. However, if the acquired DNA has an atypical base composition, it can reduce host fitness. Consequently, bacteria have evolved strategies to minimize the harmful effects of foreign genes. Most notably, xenogeneic silencing proteins bind incoming DNA that has a higher AT content than the host genome. An enduring question has been why such sequences are deleterious. Here, we showed that the toxicity of AT-rich DNA in Escherichia coli frequently results from constitutive transcription initiation within the coding regions of genes. Left unchecked, this causes titration of RNA polymerase and a global downshift in host gene expression. Accordingly, a mutation in RNA polymerase that diminished the impact of AT-rich DNA on host fitness reduced transcription from constitutive, but not activator-dependent, promoters.

Comparative Genomics of Interreplichore Translocations in Bacteria: A Measure of Chromosome Topology?

Genomes evolve not only in base sequence but also in terms of their architecture, defined by gene organization and chromosome topology. Whereas genome sequence data inform us about the changes in base sequences for a large variety of organisms, the study of chromosome topology is restricted to a few model organisms studied using microscopy and chromosome conformation capture techniques. Here, we exploit whole genome sequence data to study the link between gene organization and chromosome topology in bacteria. Using comparative genomics across ∼250 pairs of closely related bacteria we show that: (a) many organisms show a high degree of interreplichore translocations throughout the chromosome and not limited to the inversion-prone terminus (ter) or the origin of replication (oriC); (b) translocation maps may reflect chromosome topologies; and (c) symmetric interreplichore translocations do not disrupt the distance of a gene from oriC or affect gene expression states or strand biases in gene densities. In summary, we suggest that translocation maps might be a first line in defining a gross chromosome topology given a pair of closely related genome sequences.

From structure to function of bacterial chromosomes: Evolutionary perspectives and ideas for new experiments

The link between chromosome structure and function is a challenging open question because chromosomes in vivo are highly dynamic and arduous to manipulate. Here, we examine several promising approaches to tackle this question specifically in bacteria, by integrating knowledge from different sources. Toward this end, we first provide a brief overview of experimental tools that have provided insights into the description of the bacterial chromosome, including genetic, biochemical and fluorescence microscopy techniques. We then explore the possibility of using comparative genomics to isolate functionally important features of chromosome organization, exploiting the fact that features shared between phylogenetically distant bacterial species reflect functional significance. Finally, we discuss possible future perspectives from the field of experimental evolution. Specifically, we propose novel experiments in which bacteria could be screened and selected on the basis of the structural properties of their chromosomes.

Gene expression homeostasis and chromosome architecture

In rapidly growing populations of bacterial cells, including those of the model organism Escherichia coli, genes essential for growth--such as those involved in protein synthesis--are expressed at high levels; this is in contrast to many horizontally-acquired genes, which are maintained at low transcriptional levels. (1) This balance in gene expression states between 2 distinct classes of genes is established by a galaxy of transcriptional regulators, including the so-called nucleoid associated proteins (NAP) that contribute to shaping the chromosome. (2) Besides these active players in gene regulation, it is not too far-fetched to anticipate that genome organization in terms of how genes are arranged on the chromosome, (3) which is the result of long-drawn transactions among genome rearrangement processes and selection, and the manner in which it is structured inside the cell, plays a role in establishing this balance. A recent study from our group has contributed to the literature investigating the interplay between global transcriptional regulators and genome organization in establishing gene expression homeostasis. (4) In particular, we address a triangle of functional interactions among genome organization, gene expression homeostasis and horizontal gene transfer.

Gene regulation by H-NS as a function of growth conditions depends on chromosomal position in Escherichia coli

Cellular adaptation to changing environmental conditions requires the coordinated regulation of expression of large sets of genes by global regulatory factors such as nucleoid associated proteins. Although in eukaryotic cells genomic position is known to play an important role in regulation of gene expression, it remains to be established whether in bacterial cells there is an influence of chromosomal position on the efficiency of these global regulators. Here we show for the first time that genome position can affect transcription activity of a promoter regulated by the histone-like nucleoid-structuring protein (H-NS), a global regulator of bacterial transcription and genome organization. We have used as a local reporter of H-NS activity the level of expression of a fluorescent reporter protein under control of an H-NS−regulated promoter (Phns) at different sites along the genome. Our results show that the activity of the Phns promoter depends on whether it is placed within the AT-rich regions of the genome that are known to be bound preferentially by H-NS. This modulation of gene expression moreover depends on the growth phase and the growth rate of the cells, reflecting the changes taking place in the relative abundance of different nucleoid proteins and the inherent heterogeneous organization of the nucleoid. Genomic position can thus play a significant role in the adaptation of the cells to environmental changes, providing a fitness advantage that can explain the selection of a gene’s position during evolution.

The genome-scale interplay amongst xenogene silencing, stress response and chromosome architecture in Escherichia coli

The gene expression state of exponentially growing Escherichia coli cells is manifested by high expression of essential and growth-associated genes and low levels of stress-related and horizontally acquired genes. An important player in maintaining this homeostasis is the H-NS-StpA gene silencing system. A Δhns-stpA deletion mutant results in high expression of otherwise-silent horizontally acquired genes, many located in the terminus-half of the chromosome, and an indirect downregulation of many highly expressed genes. The Δhns-stpA double mutant displays slow growth. Using laboratory evolution we address the evolutionary strategies that E. coli would adopt to redress this gene expression imbalance. We show that two global gene regulatory mutations-(i) point mutations inactivating the stress-responsive sigma factor RpoS or σ38 and (ii) an amplification of ∼40% of the chromosome centred around the origin of replication-converge in partially reversing the global gene expression imbalance caused by Δhns-stpA. Transcriptome data of these mutants further show a three-way link amongst the global gene regulatory networks of H-NS and σ38, as well as chromosome architecture. Increasing gene expression around the terminus of replication results in a decrease in the expression of genes around the origin and vice versa; this appears to be a persistent phenomenon observed as an association across ∼300 publicly-available gene expression data sets for E. coli. These global suppressor effects are transient and rapidly give way to more specific mutations, whose roles in reversing the growth defect of H-NS mutations remain to be understood.

Conserved patterns in bacterial genomes: a conundrum physically tailored by evolutionary tinkering

The proper functioning of bacteria is encoded in their genome at multiple levels or scales, each of which is constrained by specific physical forces. At the smallest spatial scales, interatomic forces dictate the folding and function of proteins and nucleic acids. On longer length scales, stochastic forces emerging from the thermal jiggling of proteins and RNAs impose strong constraints on the organization of genes along chromosomes, more particularly in the context of the building of nucleoprotein complexes and the operational mode of regulatory agents. At the cellular level, transcription, replication and cell division activities generate forces that act on both the internal structure and cellular location of chromosomes. The overall result is a complex multi-scale organization of genomes that reflects the evolutionary tinkering of bacteria. The goal of this review is to highlight avenues for deciphering this complexity by focusing on patterns that are conserved among evolutionarily distant bacteria. To this end, I discuss three different organizational scales: the protein structures, the chromosomal organization of genes and the global structure of chromosomes.

Bacterial nucleoid structure probed by active drag and resistive pulse sensing

We combine steerable optical trap and microcapillary Coulter counter experiments to detect global changes in bacterial nucleoid organization.

Genomic analysis reveals epistatic silencing of "expensive" genes in Escherichia coli K-12

A barrier for horizontal gene transfer is high gene expression, which is metabolically expensive. Silencing of horizontally-acquired genes in the bacterium Escherichia coli is caused by the global transcriptional repressor H-NS. The activity of H-NS is enhanced or diminished by other proteins including its homologue StpA, and Hha and YdgT. The interconnections of H-NS with these regulators and their role in silencing gene expression in E. coli are not well understood on a genomic scale. In this study, we use transcriptome sequencing to show that there is a bi-layered gene silencing system - involving the homologous H-NS and StpA - operating on horizontally-acquired genes among others. We show that H-NS-repressed genes belong to two types, termed "epistatic" and "unilateral". In the absence of H-NS, the expression of "epistatically controlled genes" is repressed by StpA, whereas that of "unilaterally controlled genes" is not. Epistatic genes show a higher tendency to be non-essential and recently acquired, when compared to unilateral genes. Epistatic genes reach much higher expression levels than unilateral genes in the absence of the silencing system. Finally, epistatic genes contain more high affinity H-NS binding motifs than unilateral genes. Therefore, both the DNA binding sites of H-NS as well as the function of StpA as a backup system might be selected for silencing highly transcribable genes.