Spatial Chromosome Organization and Adaptation of Escherichia coli under Heat Stress

Abstract

The spatial organization of bacterial chromosomes is crucial for cellular functions. It remains unclear how bacterial chromosomes adapt to high-temperature stress. This study delves into the 3D genome architecture and transcriptomic responses of Escherichia coli under heat-stress conditions to unravel the intricate interplay between the chromosome structure and environmental cues. By examining the role of macrodomains, chromosome interaction domains (CIDs), and nucleoid-associated proteins (NAPs), this work unveils the dynamic changes in chromosome conformation and gene expression patterns induced by high-temperature stress. It was observed that, under heat stress, the short-range interaction frequency of the chromosomes decreased, while the long-range interaction frequency of the Ter macrodomain increased. Furthermore, two metrics, namely, Global Compactness (GC) and Local Compactness (LC), were devised to measure and compare the compactness of the chromosomes based on their 3D structure models. The findings in this work shed light on the molecular mechanisms underlying thermal adaptation and chromosomal organization in bacterial cells, offering valuable insights into the complex inter-relationships between environmental stimuli and genomic responses.

Keywords: 3D genome; Escherichia coli; chromosome conformation; thermal adaptation; transcriptome.

Figure 1

E. coli chromosome interactions under different growth conditions. (A) Interaction frequency of the DNA segments varies with the linear genomic distance. (B) Heat maps for the ratio of the interaction frequency between the high- and normal-temperature growth conditions. Blue indicates a decrease in the interaction frequency under the high-temperature condition, and red indicates an increase. The green dashed lines in the figure indicate 200 kb. (C) Short-range (<100 kb) interaction proportions under different growth conditions. (D) Short-range (<100 kb) interaction frequencies under different growth conditions. The white dashed lines in the subfigures (C,D) indicate 100 kb. The black dotted vertical lines in the subfigures (B–D) indicate the boundaries of the macrodomains.

Figure 2

The relationship between the DNA interaction frequency and transcription level and the CID boundaries under different growth conditions. (A) Correlation between the interaction frequency and transcription level of the DNA segments under different growth conditions. Blue lines represent the Z-score of the DNA interaction frequency, and red lines represent the Z-score of the DNA transcription level. The lower left corner of each subfigure displays the correlation coefficient and corresponding significance level (p-value). (B) CID boundaries under different growth conditions. The horizontal lines represent the genomic coordinates, and the points on each line represent the CID boundaries.

Figure 3

The 3D structural features of the E. coli chromosome under different growth conditions. (A) The 3D structural models of the E. coli chromosome under different growth conditions. In the Norm_Log and Norm_Sta models, green is the Ori macrodomain, red is the Ter macrodomain, purple and blue are the Left and Right macrodomains, respectively, and yellow is the non-structured regions; in the Therm_Log and Therm_Sta models, lighter colors are used correspondingly. (B) Distribution of the distance between points (bins) in these 3D models. (C) Spatial distances between the bins of the macrodomains in the 3D models of the E. coli chromosome under different growth conditions. O: Ori macrodomain; T: Ter macrodomain; L: Left macrodomain; R: Right macrodomain. OT represents the distances between the bins in the Ori macrodomain and the bins in the Ter macrodomain, and so on. (D) Global Compactness of the E. coli chromosome models under different growth conditions.

Figure 4

Comparison of the E. coli nucleoid morphology in different growth conditions. (A) Typical microscopic images of the E. coli nucleoid under various growth conditions. The nucleoids of E. coli were stained blue by DAPI. (B) Statistical results of the E. coli nucleoid width under different growth conditions. (C) Statistical results of the E. coli nucleoid length under different growth conditions. In B and C, significance levels are denoted by the following symbols: ns for p > 0.05 and **** for p ≤ 0.0001.

Figure 5

Local Compactness of the E. coli chromosome and related features. (A) The Local Compactness of the E. coli chromosome 3D structures under different growth conditions and its ratio between high and normal temperatures. The green dashed lines in the bottom two subfigures of figure A indicate the scale of 200 kb. (B) The Local Compactness in the 100 kb range of the E. coli chromosome 3D structures under different growth conditions. (C) The Local Compactness in the 500 kb range of the E. coli chromosome 3D structures under different growth conditions. In subfigures (B,C), the lines of different colors correspond to different growth conditions. The dots on the purple horizontal lines represent the location of MatS, which is the binding site of MatP. The black dashed vertical lines in the subfigures (A–C) represent the boundaries of the macrodomains. (D,E) Transcription levels of MatP and MukBEF in E. coli under different growth conditions, respectively.

Figure 6

Correlation between the Local Compactness and transcription level. (A) The genome-wide correlation between the Local Compactness and transcription level under different growth conditions. (B) The correlation between the transcription levels of four sigma factors and their Local Compactness (where the sigma factor genes reside in the linear genome). Green lines correspond to the Local Compactness; red lines correspond to the transcription level.