The obligately anaerobic bacterium Bacteroides fragilis, an opportunistic pathogen and inhabitant of the normal human colonic microbiota, exhibits considerable within-strain phase and antigenic variation of surface components. The complete genome sequence has revealed an unusual breadth (in number and in effect) of DNA inversion events that potentially control expression of many different components, including surface and secreted components, regulatory molecules, and restriction-modification proteins. Invertible promoters of two different types (12 group 1 and 11 group 2) were identified. One group has inversion crossover (fix) sites similar to the hix sites of Salmonella typhimurium. There are also four independent intergenic shufflons that potentially alter the expression and function of varied genes. The composition of the 10 different polysaccharide biosynthesis gene clusters identified (7 with associated invertible promoters) suggests a mechanism of synthesis similar to the O-antigen capsules of Escherichia coli.

Download full-text PDF

Source
http://dx.doi.org/10.1126/science.1107008DOI Listing

Publication Analysis

Top Keywords

invertible promoters
8
extensive dna
4
dna inversions
4
inversions fragilis
4
fragilis genome
4
genome control
4
control variable
4
variable gene
4
gene expression
4
expression obligately
4

Similar Publications

Deep learning revealed the distribution and evolution patterns for invertible promoters across bacterial lineages.

Nucleic Acids Res

November 2024

Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.

Article Synopsis
  • Invertible promoters, or invertons, are key elements in bacteria that enable gene expression changes, especially under stress, but their prevalence and functions were previously unclear.
  • The researchers developed DeepInverton, a deep learning model that can identify invertons across numerous bacterial genomes without sequencing data, uncovering over 200,000 unique invertons, many found in pathogens.
  • The study found that invertons increased after the Cambrian Explosion, regulating various functions like antimicrobial resistance and biofilm formation, which is important for understanding microbial ecology and could have applications in synthetic biology.
View Article and Find Full Text PDF

Optogenetics is a powerful tool for spatiotemporal control of gene expression. Several light-inducible gene regulators have been developed to function in bacteria, and these regulatory circuits have been ported to new host strains. Here, we developed and adapted a red-light-inducible transcription factor for .

View Article and Find Full Text PDF

A new piece of the microbiota pie: Mining 'omics for DNA inversion states.

Cell Host Microbe

March 2024

Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA. Electronic address:

In this issue of Cell Host & Microbe, Carasso et al. survey invertible DNA sites in Bacteroidales from patients with inflammatory bowel disease (IBD) and healthy control individuals. They identify complex functional interactions between Bacteroides fragilis, an invertible promoter, a capsular polysaccharide, a bacteriophage, and the human host.

View Article and Find Full Text PDF

Recent advances in genomic refactoring have been hindered by the ever-present complication of internal or cryptic transcriptional regulation. Typical approaches to these features have been to randomize or perform mass alterations to the gene sequences thought to contain the regulatory motifs; however, this approach can cause problems by altering translational speeds, introducing long distance DNA-DNA interaction effects, and inducing RNA toxicity. Previously, we developed a rational design approach named COdon Restrained Promoter SilEncing (CORPSE) which takes externally identified promoter sequences and uses position-specific scoring matrices as proxy promoter strengths to make minimal changes to promoter sequences to disable their activity.

View Article and Find Full Text PDF

Inflammation and bacteriophages affect DNA inversion states and functionality of the gut microbiota.

Cell Host Microbe

March 2024

Department of Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Rappaport Technion Integrated Cancer Center (RTICC), Haifa 32000, Israel; CIFAR, MaRS Centre, West Tower 661, Suite 505, Toronto, ON M5G 1M1, Canada. Electronic address:

Reversible genomic DNA inversions control the expression of numerous gut bacterial molecules, but how this impacts disease remains uncertain. By analyzing metagenomic samples from inflammatory bowel disease (IBD) cohorts, we identified multiple invertible regions where a particular orientation correlated with disease. These include the promoter of polysaccharide A (PSA) of Bacteroides fragilis, which induces regulatory T cells (Tregs) and ameliorates experimental colitis.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!