Transcriptomic Insights on the Virulence-Controlling CsrA, BadR, RpoN, and RpoS Regulatory Networks in the Lyme Disease Spirochete

Authors

William K. Arnold, Addgene
Christina R. Savage, University of KentuckyFollow
Kathryn G. Lethbridge, University of KentuckyFollow
Trever C. Smith, Tufts University
Catherine A. Brisette, University of North Dakota
Janakiram Seshu, University of Texas at San Antonio
Brian Stevenson, University of KentuckyFollow

Abstract

Borrelia burgdorferi, the causative agent of Lyme disease, survives in nature through a cycle that alternates between ticks and vertebrates. To facilitate this defined lifestyle, B. burgdorferi has evolved a gene regulatory network that ensures transmission between those hosts, along with specific adaptations to niches within each host. Several regulatory proteins are known to be essential for the bacterium to complete these critical tasks, but interactions between regulators had not previously been investigated in detail, due to experimental uses of different strain backgrounds and growth conditions. To address that deficit in knowledge, the transcriptomic impacts of four critical regulatory proteins were examined in a uniform strain background. Pairs of mutants and their wild-type parent were grown simultaneously under a single, specific culture condition, permitting direct comparisons between the mutant strains. Transcriptomic analyses were strand-specific, and assayed both coding and noncoding RNAs. Intersection analyses identified regulatory overlaps between regulons, including transcripts involved in carbohydrate and polyamine metabolism. In addition, it was found that transcriptional units such as ospC and dbpBA, which were previously observed to be affected by alternative sigma factors, are transcribed by RNA polymerase using the housekeeping sigma factor, RpoD.

Document Type

Article

Publication Date

8-30-2018

Notes/Citation Information

Published in PLOS ONE, v. 13, no. 8, e0203286, p. 1-39.

© 2018 Arnold et al.

This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Digital Object Identifier (DOI)

https://doi.org/10.1371/journal.pone.0203286

Funding Information

This work was supported by the National Institutes of Health, R03 AI113648 (BS).

Related Content

The full set of Unix commands, the R scripts formatted as an R Markdown document, and the custom transcriptome multi-fasta are available at https://doi.org/10.6084/m9.figshare.5502175. Raw sequence read files have been deposited to the NCBI SRA database under BioProject PRJNA408156.

S1 Fig. Principal component analysis of RNA-Seq samples. https://doi.org/10.1371/journal.pone.0203286.s001 (PDF)

S1 Table. Primers used in these studies. https://doi.org/10.1371/journal.pone.0203286.s002 (DOCX)

S2 Table. Differentially expressed transcripts when comparing the csrAmutant to wild-type, listed in order of fold change. https://doi.org/10.1371/journal.pone.0203286.s003 (DOCX)

S3 Table. Differentially expressed transcripts when comparing the badRmutant to wild-type, listed in order of fold change. https://doi.org/10.1371/journal.pone.0203286.s004 (DOCX)

S4 Table. Intersection table of all transcripts that differentially expressed across all mutants. https://doi.org/10.1371/journal.pone.0203286.s005 (XLSX)

S5 Table. Total differential expression testing table for the csrAmutant. https://doi.org/10.1371/journal.pone.0203286.s006 (XLSX)

S6 Table. Total differential expression testing table for the badRmutant. https://doi.org/10.1371/journal.pone.0203286.s007 (XLSX)

S7 Table. Total differential expression testing table for the rpoSmutant. https://doi.org/10.1371/journal.pone.0203286.s008 (XLSX)

S8 Table. Total differential expression testing table for the rpoNmutant. https://doi.org/10.1371/journal.pone.0203286.s009 (XLSX)

Repository Citation

Arnold, William K.; Savage, Christina R.; Lethbridge, Kathryn G.; Smith, Trever C.; Brisette, Catherine A.; Seshu, Janakiram; and Stevenson, Brian, "Transcriptomic Insights on the Virulence-Controlling CsrA, BadR, RpoN, and RpoS Regulatory Networks in the Lyme Disease Spirochete" (2018). Microbiology, Immunology, and Molecular Genetics Faculty Publications. 134.
https://uknowledge.uky.edu/microbio_facpub/134