Temperature-dependent sRNA transcriptome of the Lyme disease spirochete

Niko Popitsch; Ivana Bilusic; Philipp Rescheneder; Renée Schroeder; Meghan Lybecker

doi:10.1186/s12864-016-3398-3

Temperature-dependent sRNA transcriptome of the Lyme disease spirochete

BMC Genomics. 2017 Jan 5;18(1):28. doi: 10.1186/s12864-016-3398-3.

Authors

Niko Popitsch¹, Ivana Bilusic², Philipp Rescheneder³, Renée Schroeder², Meghan Lybecker⁴

Affiliations

¹ Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
² Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria.
³ Center for Integrative Bioinformatics Vienna, Max F Perutz Laboratories, Medical University of Vienna, University of Vienna, Vienna, Austria.
⁴ Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, USA. meghan.lybecker@uccs.edu.

Abstract

Background: Transmission of Borrelia burgdorferi from its tick vector to a vertebrate host requires extensive reprogramming of gene expression. Small regulatory RNAs (sRNA) have emerged in the last decade as important regulators of bacterial gene expression. Despite the widespread observation of sRNA-mediated gene regulation, only one sRNA has been characterized in the Lyme disease spirochete B. burgdorferi. We employed an sRNA-specific deep-sequencing approach to identify the small RNA transcriptome of B. burgdorferi at both 23 °C and 37 °C, which mimics in vitro the transmission from the tick vector to the mammalian host.

Results: We identified over 1000 sRNAs in B. burgdorferi revealing large amounts of antisense and intragenic sRNAs, as well as characteristic intergenic and 5' UTR-associated sRNAs. A large fraction of the novel sRNAs (43%) are temperature-dependent and differentially expressed at the two temperatures, suggesting a role in gene regulation for adaptation during transmission. In addition, many genes important for maintenance of Borrelia during its enzootic cycle are associated with antisense RNAs or 5' UTR sRNAs. RNA-seq data were validated for twenty-two of the sRNAs via Northern blot analyses.

Conclusions: Our study demonstrates that sRNAs are abundant and differentially expressed by environmental conditions suggesting that gene regulation via sRNAs is a common mechanism utilized in B. burgdorferi. In addition, the identification of antisense and intragenic sRNAs impacts the broadly used loss-of-function genetic approach used to study gene function and increases the coding potential of a small genome. To facilitate access to the analyzed RNA-seq data we have set-up a website at http://www.cibiv.at/~niko/bbdb/ that includes a UCSC browser track hub. By clicking on the respective link, researchers can interactively inspect the data in the UCSC genome browser (Kent et al., Genome Res 12:996-1006, 2002).

Keywords: Antisense RNA (asRNA); Borrelia burgdorferi; Intragenic RNA (intraRNA); Regulatory RNA; Riboswitch; sRNA transcriptome.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Borrelia burgdorferi / genetics*
Computational Biology / methods
Gene Expression Profiling
Gene Expression Regulation, Bacterial*
High-Throughput Nucleotide Sequencing
Humans
Lyme Disease / microbiology
Open Reading Frames
RNA, Bacterial*
RNA, Small Untranslated / genetics*
Repetitive Sequences, Nucleic Acid
Temperature*
Transcriptome*

Substances

RNA, Bacterial
RNA, Small Untranslated