ArticlePloS one2016
Conserved Units of Co-Expression in Bacterial Genomes: An Evolutionary Insight into Transcriptional Regulation.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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38 citing papers in PubMed, 72 citations in OpenAlex.
- Interspecies interactions drive bacterial proteome reorganization and emergent metabolism.Nature ecology & evolution · 2026Article
- Characterizing the ecological niche of insertion sequences within prokaryotic genomes.The ISME journal · 2026Article
- Emergence of supercoiling-mediated regulatory networks through the evolution of bacterial chromosome organization.PLoS computational biology · 2025Article
- Quantitative spatial analysis of bacterial transcriptome and chromosome structural data with GRATIOSA: application to twin-supercoiled domain distribution.Nucleic acids research · 2025Article
- Assessing in vivo the impact of gene context on transcription through DNA supercoiling.Nucleic acids research · 2023Article
- Elucidating the functional roles of prokaryotic proteins using big data and artificial intelligence.FEMS microbiology reviews · 2023Review
- DNA supercoiling in bacteria: state of play and challenges from a viewpoint of physics based modeling.Frontiers in microbiology · 2023Review
- The supragenic organization of glycoside hydrolase encoding genes reveals distinct strategies for carbohydrate utilization in bacteria.Frontiers in microbiology · 2023Article
- Purifying selection enduringly acts on the sequence evolution of highly expressed proteins in Escherichia coli.G3 (Bethesda, Md.) · 2022Article
- Systematic analysis of the underlying genomic architecture for transcriptional-translational coupling in prokaryotes.NAR genomics and bioinformatics · 2022Article
- Polar mutagenesis of polycistronic bacterial transcriptional units using Cas12a.Microbial cell factories · 2022Article
- Mapping the Complex Transcriptional Landscape of the Phytopathogenic Bacterium Dickeya dadantii.mBio · 2022Article
- Relationship between the Chromosome Structural Dynamics and Gene Expression-A Chicken and Egg Dilemma?Microorganisms · 2022Review
- Computational modelling of chromosomally clustering protein domains in bacteria.BMC bioinformatics · 2021Article
- Phylogenetic analysis of the bacterial Pro-Pro-endopeptidase domain reveals a diverse family including secreted and membrane anchored proteins.Current research in microbial sciences · 2021Review
- Article
- Requirements for DNA-Bridging Proteins to Act as Topological Barriers of the Bacterial Genome.Biophysical journal · 2020Article
- Discovery of multi-operon colinear syntenic blocks in microbial genomes.Bioinformatics (Oxford, England) · 2020Article
- A systematic pipeline for classifying bacterial operons reveals the evolutionary landscape of biofilm machineries.PLoS computational biology · 2020Article
- Functional characterization of an inducible bidirectional promoter from Fusarium oxysporum f. sp. cubense.Scientific reports · 2020Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genome-wide measurements of transcriptional activity in bacteria indicate that the transcription of successive genes is strongly correlated beyond the scale of operons. Here, we analyze hundreds of bacterial genomes to identify supra-operonic segments of genes that are proximal in a large number of genomes. We show that these synteny segments correspond to genomic units of strong transcriptional co-expression. Structurally, the segments contain operons with specific relative orientations (co-directional or divergent) and nucleoid-associated proteins are found to bind at their boundaries. Functionally, operons inside a same segment are highly co-expressed even in the apparent absence of regulatory factors at their promoter regions. Remote operons along DNA can also be co-expressed if their corresponding segments share a transcriptional or sigma factor, without requiring these factors to bind directly to the promoters of the operons. As evidence that these results apply across the bacterial kingdom, we demonstrate them both in the Gram-negative bacterium Escherichia coli and in the Gram-positive bacterium Bacillus subtilis. The underlying process that we propose involves only RNA-polymerases and DNA: it implies that the transcription of an operon mechanically enhances the transcription of adjacent operons. In support of a primary role of this regulation by facilitated co-transcription, we show that the transcription en bloc of successive operons as a result of transcriptional read-through is strongly and specifically enhanced in synteny segments. Finally, our analysis indicates that facilitated co-transcription may be evolutionary primitive and may apply beyond bacteria.
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