High-resolution transcriptome maps reveal strain-specific regulatory features of multiple Campylobacter jejuni...

Area of Science:

• Microbiology
• Genomics
• Molecular Biology

Background:

• Campylobacter jejuni is a leading cause of bacterial gastroenteritis.
• High genetic and phenotypic diversity exists among C. jejuni strains.
• Transcriptome organization, gene expression, and small RNA (sRNA) repertoires are poorly understood across strains.

Purpose of the Study:

• To perform the first comparative primary transcriptome analysis of C. jejuni isolates.
• To develop and apply a novel method for automated annotation of transcriptional start sites (TSS).
• To investigate strain-specific differences in transcriptome organization, sRNAs, and identify factors contributing to phenotypic variation.

Main Methods:

• Differential RNA-sequencing (dRNA-seq) of four C. jejuni isolates.
• Development of a generic, automated method for TSS annotation.
• Integration of a SuperGenome approach for comparative TSS annotation using whole-genome alignment.
• Analysis of strain-specific sRNA repertoires and CRISPR-systems.

Main Results:

• Genome-wide promoter maps and conserved/strain-specific TSS were identified.
• Single-nucleotide polymorphisms (SNPs) in promoter regions were linked to differential gene expression.
• Strain-specific sRNA repertoires were discovered, potentially regulating differential gene expression.
• A novel, minimal type-II CRISPR-system utilizing RNase III and a trans-encoded sRNA for crRNA maturation was identified.

Conclusions:

• Comparative dRNA-seq provides insights into C. jejuni transcriptome organization and sRNA diversity.
• Identified genetic variations and sRNAs contribute to phenotypic differences among strains.
• The novel automated TSS annotation method is applicable to diverse organisms and conditions.
• The unique CRISPR system in C. jejuni offers a new perspective on microbial adaptive immunity.