Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptome analysis of Aggregatibacter actinomycetemcomitans serotype b strains of JP2 and non-JP2 genotypes using a pan-genome microarray

ABSTRACT: To characterize the differences in pattern of gene expression between JP2 and non-JP2 genotypes of A. actinomycetemcomitans. Transcriptome analysis of 3 strains of JP2 and 2 strains of non-JP2 genotypes of A. actinomycetemcomitans was performed Transcripome of three strains of JP2 genotype (HK1651, D28S-1 and D41S-1) and two strains of non-JP2 genotype (SCC1398 and ANH9381) were examined where two biological duplicates were carried out for each strain.

ORGANISM(S): Aggregatibacter actinomycetemcomitans

SUBMITTER: Weerayuth Kittichotirat

PROVIDER: E-GEOD-38943 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Campylobacter jejuni is currently the leading cause of bacterial gastroenteritis in humans. Comparison of multiple Campylobacter strains revealed a high genetic and phenotypic diversity. However, little is known about differences in transcriptome organization, gene expression, and small RNA (sRNA) repertoires. Here we present the first comparative primary transcriptome analysis based on the differential RNAM-bM-^@M-^Sseq (dRNAM-bM-^@M-^Sseq) of four C. jejuni isolates. Our approach includes a novel, generic method for the automated annotation of transcriptional start sites (TSS), which allowed us to provide genome-wide promoter maps in the analyzed strains. These global TSS maps are refined through the integration of a SuperGenome approach that allows for a comparative TSS annotation by mapping RNAM-bM-^@M-^Sseq data of multiple strains into a common coordinate system derived from a whole-genome alignment. Considering the steadily increasing amount of RNAM-bM-^@M-^Sseq studies, our automated TSS annotation will not only facilitate transcriptome annotation for a wider range of pro- and eukaryotes but can also be adapted for the analysis among different growth or stress conditions. Our comparative dRNAM-bM-^@M-^Sseq analysis revealed conservation of most TSS, but also single-nucleotide-polymorphisms (SNP) in promoter regions, which lead to strain-specific transcriptional output. Furthermore, we identified strain-specific sRNA repertoires that could contribute to differential gene regulation among strains. In addition, we identified a novel minimal CRISPR-system in Campylobacter of the type-II CRISPR subtype, which relies on the host factor RNase III and a trans-encoded sRNA for maturation of crRNAs. This minimal system of Campylobacter, which seems active in only some strains, employs a unique maturation pathway, since the crRNAs are transcribed from individual promoters in the upstream repeats and thereby minimize the requirements for the maturation machinery. Overall, our study provides new insights into strain-specific transcriptome organization and sRNAs, and reveals genes that could modulate phenotypic variation among strains despite high conservation at the DNA level. Our dRNA-seq study of multiple C. jejuni strains represents the first comparative analysis of the primary transcriptomes of multiple strains and provides new insights into riboregulation in this bacterial pathogen.