Changes in Higher-Order Chromosomal Structure of Klebsiella pneumoniae Under Simulated Microgravity

Abstract

Our previous work have shown that certain subpopulations of Klebsiella pneumoniae exhibit significant phenotypic changes under simulated microgravity (SMG), including enhanced biofilm formation and cellulose synthesis, which may be evoked by changes in gene expression patterns. It is well known that prokaryotic cells genomic DNA can be hierarchically organized into different higher-order three-dimensional structures, which can highly influence gene expression. It is remain elusive whether phenotypic changes induced by SMG in the subpopulations of K. pneumoniae are driven by genome higher-order structural changes. Here, we investigated the above-mentioned issue using the wild-type (WT) K. pneumoniae (WT was used as a control strain and continuously cultivated for 2 weeks under standard culture conditions of normal gravity) and two previous identified subpopulations (M1 and M2) obtained after 2 weeks of continuous incubation in a SMG device. By the combination of genome-wide chromosome conformation capture (Hi-C), RNA-seq and whole-genome methylation (WGS) analyses, we found that the along with the global chromosome interactions change, the compacting extent of M1, M2 subpopulations were much looser under SMG and even with an increase in active, open chromosome regions. In addition, transcriptome data showed that most differentially expressed genes (DEGs) were upregulated, whereas a few DEGs were downregulated in M1 and M2. The functions of both types DEGs were mainly associated with membrane fractions. Additionally, WGS analysis revealed that methylation levels were lower in M1 and M2. Using combined analysis of multi-omics data, we discovered that most upregulated DEGs were significantly enriched in the boundary regions of the variable chromosomal interaction domains (CIDs), in which genes regulating biofilm formation were mainly located. These results suggest that K. pneumoniae may regulate gene expression patterns through DNA methylation and changes in genome structure, thus resulting in new phenotypes in response to altered gravity.

High-Resolution 3D Genome Map of Brucella Chromosomes in Exponential and Stationary Phases

“…Unlike eukaryotes, bacteria do not have a nucleus, and most of the bacterial genetic material is concentrated in a specific area of the cell, called the nucleoid. To date, spatial genome structure information has been reported for many bacteria, including Caulobacter crescentus ( 13 – 16 ), Bacillus subtilis ( 17 – 20 ), Vibrio cholerae ( 21 , 22 ), Mycoplasma pneumoniae ( 23 ), Escherichia coli ( 1 , 24 ), Klebsiella pneumoniae ( 25 ), Rhizobium ( 26 – 28 ), Acanthamoeba castellanii ( 29 ), Streptomyces ( 30 ), Pseudomonas aeruginosa ( 31 ), and the Oligo-Mouse-Microbiota community ( 32 ).…”

Moving toward the Inclusion of Epigenomics in Bacterial Genome Evolution: Perspectives and Challenges

“…Furthermore, the difference in global DNA methylation patterns of cyanobacteria between unstressed and nutrient-stressed conditions supports the evidence of partially inheritable DNA methylation pattern changes [28]. Another example of bacteria's ability to adapt to different environments by altering DNA methylation patterns is provided by Klebsiella pneumoniae in altered gravity conditions [29]. Here, the bacteria regulate gene expression patterns through DNA methylation and changes in genome structure, thus resulting in new phenotypes [29].…”

“…Another example of bacteria's ability to adapt to different environments by altering DNA methylation patterns is provided by Klebsiella pneumoniae in altered gravity conditions [29]. Here, the bacteria regulate gene expression patterns through DNA methylation and changes in genome structure, thus resulting in new phenotypes [29]. Moreover, different patterns of DNA methyltransferase activity in lineages of Mycobacterium tuberculosis have been found to be associated with preferences for distinct host environments (characterized by different hypoxia levels) and different disease courses in humans [30].…”

“…Integrating transcriptomic and proteomic analyses into methylation studies provides a holistic view of the functional consequences of DNA methylation. High-throughput sequencing technologies enable the simultaneous profiling of gene expression and methylation patterns, facilitating the identification of direct correlations between epigenetic modifications and changes in the cellular phenotype [29,72], and providing insights into the functional constraints and innovations that shape microbial genomes [29,72]. Finally, comparative epigenomics can offer valuable insights for the functional interpretation of DNA methylation patterns and their relevance to prokaryotic evolution.…”

Spatial reorganization ofEscherichia colichromosome contextualizes triclosan stress-related genetic, epigenetic and transcriptome changes

“…Transcription and higher-order chromosome structures in bacteria are known to be interlinked (11,16,39,40). Previously, it has been shown that under normal growth conditions, increased contact frequency (particularly short-range) strongly correlates with higher transcription levels in E. coli (11).…”