title: In vivo expression technology and 5' end mapping of the Borrelia burgdorferi transcriptome identify novel RNAs expressed during mammalian infection.
abstract: Borrelia burgdorferi, the bacterial pathogen responsible for Lyme disease, modulates its gene expression profile in response to the environments encountered throughout its tick-mammal infectious cycle. To begin to characterize the B. burgdorferi transcriptome during murine infection, we previously employed an in vivo expression technology-based approach (BbIVET). This identified 233 putative promoters, many of which mapped to un-annotated regions of the complex, segmented genome. Herein, we globally identify the 5' end transcriptome of B. burgdorferi grown in culture as a means to validate non-ORF associated promoters discovered through BbIVET. We demonstrate that 119 BbIVET promoters are associated with transcription start sites (TSSs) and validate novel RNA transcripts using Northern blots and luciferase promoter fusions. Strikingly, 49% of BbIVET promoters were not found to associate with TSSs. This finding suggests that these sequences may be primarily active in the mammalian host. Furthermore, characterization of the 6042 B. burgdorferi TSSs reveals a variety of RNAs including numerous antisense and intragenic transcripts, leaderless RNAs, long untranslated regions and a unique nucleotide frequency for initiating intragenic transcription. Collectively, this is the first comprehensive map of TSSs in B. burgdorferi and characterization of previously un-annotated RNA transcripts expressed by the spirochete during murine infection.
authors.affiliation: Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, Orlando, FL 32827, USA.
authors.forename: Philip P
authors.initials: PP
authors.lastname: Adams
authors.affiliation: Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, Orlando, FL 32827, USA.
authors.forename: Carlos
authors.initials: C
authors.lastname: Flores Avile
authors.affiliation: Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
authors.forename: Niko
authors.initials: N
authors.lastname: Popitsch
authors.affiliation: Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Vienna 1030, Austria.
authors.forename: Ivana
authors.initials: I
authors.lastname: Bilusic
authors.affiliation: Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Vienna 1030, Austria.
authors.forename: Renée
authors.initials: R
authors.lastname: Schroeder
authors.affiliation: Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA.
authors.forename: Meghan
authors.initials: M
authors.lastname: Lybecker
authors.affiliation: Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, Orlando, FL 32827, USA Mollie.Jewett@ucf.edu.
authors.forename: Mollie W
authors.identifier: 0000-0003-3130-3795
authors.initials: MW
authors.lastname: Jewett
mesh_terms: D000818:Animals; D025065:Borrelia burgdorferi / Q000235:genetics*; D015870:Gene Expression; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D017930:Genes, Reporter; D016680:Genome, Bacterial; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008193:Lyme Disease / Q000382:microbiology*; D051379:Mice; D011401:Promoter Regions, Genetic; D015203:Reproducibility of Results; D024363:Transcription Initiation Site; D059467:Transcriptome; D020506:Untranslated Regions
chemical_list: D020506:Untranslated Regions