Abstract
BackgroundGene reshuffling, point mutations and horizontal gene transfer contribute to bacterial genome variation, but require the genome to rewire its transcriptional circuitry to ensure that inserted, mutated or reshuffled genes are transcribed at appropriate levels. The genomes of Epsilonproteobacteria display very low synteny, due to high levels of reshuffling and reorganisation of gene order, but still share a significant number of gene orthologs allowing comparison. Here we present the primary transcriptome of the pathogenic Epsilonproteobacterium Campylobacter jejuni, and have used this for comparative and predictive transcriptomics in the Epsilonproteobacteria.ResultsDifferential RNA-sequencing using 454 sequencing technology was used to determine the primary transcriptome of C. jejuni NCTC 11168, which consists of 992 transcription start sites (TSS), which included 29 putative non-coding and stable RNAs, 266 intragenic (internal) TSS, and 206 antisense TSS. Several previously unknown features were identified in the C. jejuni transcriptional landscape, like leaderless mRNAs and potential leader peptides upstream of amino acid biosynthesis genes. A cross-species comparison of the primary transcriptomes of C. jejuni and the related Epsilonproteobacterium Helicobacter pylori highlighted a lack of conservation of operon organisation, position of intragenic and antisense promoters or leaderless mRNAs. Predictive comparisons using 40 other Epsilonproteobacterial genomes suggests that this lack of conservation of transcriptional features is common to all Epsilonproteobacterial genomes, and is associated with the absence of genome synteny in this subdivision of the Proteobacteria.ConclusionsBoth the genomes and transcriptomes of Epsilonproteobacteria are highly variable, both at the genome level by combining and division of multicistronic operons, but also on the gene level by generation or deletion of promoter sequences and 5′ untranslated regions. Regulatory features may have evolved after these species split from a common ancestor, with transcriptome rewiring compensating for changes introduced by genomic reshuffling and horizontal gene transfer.
Highlights
Gene reshuffling, point mutations and horizontal gene transfer contribute to bacterial genome variation, but require the genome to rewire its transcriptional circuitry to ensure that inserted, mutated or reshuffled genes are transcribed at appropriate levels
To assess whether the dRNA-seq Copy DNA (cDNA) libraries are a good representation of transcribed sequences of C. jejuni, we compared the Reads per kilobase per million mapped reads (RPKM)-values obtained for the coding sequences (CDS) from the non-enriched (−Terminator Exonuclease (TEX)) 454 cDNA sequencing with the previously published Illumina-based RNA-seq data for C. jejuni NCTC 11168 [21] and the signal intensity on a PCR-product based C. jejuni microarray [23,24] normalised to a genomic DNA reference [25]
Genome-wide identification of C. jejuni transcription start sites and promoters The dRNA-seq data were subsequently used for the identification of transcription start sites (TSS) of primary RNAs, which are protected from digestion by Terminator Exonuclease (TEX) through their 5′-triphosphate modification [10,26]
Summary
Point mutations and horizontal gene transfer contribute to bacterial genome variation, but require the genome to rewire its transcriptional circuitry to ensure that inserted, mutated or reshuffled genes are transcribed at appropriate levels. Diversity at the level of gene order and genome content can be introduced via the reorganisation of the genome, through combinations of gene inversion, recombination, gene duplication, deletion and horizontal gene transfer [3,4]. Such movement, deletion or introduction of genes or operons can create a problem for the cell, as the reorganisation of the genome may result in disruption of transcriptional circuitry controlling the expression levels of such genes. The level of RNA in a cell is usually controlled at the transcriptional and post-transcriptional levels. The high level of phylogenetic diversity within the bacterial kingdom has so far limited the possibilities for interspecies transcriptome comparison, since the species for which high resolution transcriptome maps are available are either too closely related (e.g. the Enterobacteriaceae) or too distantly related to allow meaningful comparisons at the evolutionary level
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