Coherent Domains of Transcription Coordinate Gene Expression During Bacterial Growth and Adaptation.
Georgi MuskhelishviliRaphaël ForquetSylvie ReverchonSam MeyerWilliam NasserPublished in: Microorganisms (2019)
Recent studies strongly suggest that in bacteria, both the genomic pattern of DNA thermodynamic stability and the order of genes along the chromosomal origin-to-terminus axis are highly conserved and that this spatial organization plays a crucial role in coordinating genomic transcription. In this article, we explore the relationship between genomic sequence organization and transcription in the commensal bacterium Escherichia coli and the plant pathogen Dickeya. We argue that, while in E. coli the gradient of DNA thermodynamic stability and gene order along the origin-to-terminus axis represent major organizational features orchestrating temporal gene expression, the genomic sequence organization of Dickeya is more complex, demonstrating extended chromosomal domains of thermodynamically distinct DNA sequences eliciting specific transcriptional responses to various kinds of stress encountered during pathogenic growth. This feature of the Dickeya genome is likely an adaptation to the pathogenic lifestyle utilizing differences in genomic sequence organization for the selective expression of virulence traits. We propose that the coupling of DNA thermodynamic stability and genetic function provides a common organizational principle for the coordinated expression of genes during both normal and pathogenic bacterial growth.
Keyphrases
- copy number
- genome wide
- gene expression
- dna methylation
- escherichia coli
- circulating tumor
- transcription factor
- cell free
- single molecule
- poor prognosis
- machine learning
- nucleic acid
- staphylococcus aureus
- physical activity
- metabolic syndrome
- deep learning
- biofilm formation
- type diabetes
- pseudomonas aeruginosa
- circulating tumor cells
- amino acid
- room temperature
- antimicrobial resistance
- weight loss
- heat shock
- case control