Mead PS. Epidemiology of Lyme disease. Infect Dis Clin N Am. 2015;29(2):187–210.
Article
Google Scholar
Lane RS, Piesman J, Burgdorfer W. Lyme borreliosis: relation of its causative agent to its vectors and hosts in North America and Europe. Annu Rev Entomol. 1991;36:587–609.
Article
CAS
PubMed
Google Scholar
Piesman J, Schwan T. Ecology of borreliae and their arthropod vectors. In: Samuels DS, Radolf JD, editors. Borrelia: molecular biology, host interaction and pathogenesis. Norfolk UK: Caister Academic Press; 2010.
Google Scholar
Radolf JD, Caimano MJ, Stevenson B, Hu LT. Of ticks, mice and men: understanding the dual-host lifestyle of Lyme disease spirochaetes. Nat Rev Microbiol. 2012;10(2):87–99.
CAS
PubMed
PubMed Central
Google Scholar
Samuels DS. Gene regulation in Borrelia burgdorferi. Annu Rev Microbiol. 2011;65:479–99.
Article
CAS
PubMed
Google Scholar
Schwan TG, Piesman J, Golde WT, Dolan MC, Rosa PA. Induction of an outer surface protein on Borrelia burgdorferi during tick feeding. Proc Natl Acad Sci U S A. 1995;92(7):2909–13.
Article
CAS
PubMed
PubMed Central
Google Scholar
Alverson J, Bundle SF, Sohaskey CD, Lybecker MC, Samuels DS. Transcriptional regulation of the ospAB and ospC promoters from Borrelia burgdorferi. Mol Microbiol. 2003;48(6):1665–77.
Article
CAS
PubMed
Google Scholar
Yang X, Goldberg MS, Popova TG, Schoeler GB, Wikel SK, Hagman KE, Norgard MV. Interdependence of environmental factors influencing reciprocal patterns of gene expression in virulent Borrelia burgdorferi. Mol Microbiol. 2000;37(6):1470–9.
Article
CAS
PubMed
Google Scholar
Iyer R, Caimano MJ, Luthra A, Axline Jr D, Corona A, Iacobas DA, Radolf JD, Schwartz I. Stage-specific global alterations in the transcriptomes of Lyme disease spirochetes during tick feeding and following mammalian host adaptation. Mol Microbiol. 2015;95(3):509–38.
Article
CAS
PubMed
Google Scholar
Kazmierczak MJ, Wiedmann M, Boor KJ. Alternative sigma factors and their roles in bacterial virulence. Microbiology and molecular biology reviews : MMBR. 2005;69(4):527–43.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hubner A, Yang X, Nolen DM, Popova TG, Cabello FC, Norgard MV. Expression of Borrelia burgdorferi OspC and DbpA is controlled by a RpoN-RpoS regulatory pathway. Proc Natl Acad Sci U S A. 2001;98(22):12724–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Groshong AM, Blevins JS. Insights into the biology of Borrelia burgdorferi gained through the application of molecular genetics. Adv Appl Microbiol. 2014;86:41–143.
Article
CAS
PubMed
Google Scholar
Caimano MJ, Drecktrah D, Kung F, Samuels DS. Interaction of the Lyme disease spirochete with its tick vector. Cell Microbiol. 2016;18(7):919–27.
Article
CAS
PubMed
PubMed Central
Google Scholar
Samuels DS, Radolf JD. Who is the BosR around here anyway? Mol Microbiol. 2009;74(6):1295–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Beisel CL, Storz G. Base pairing small RNAs and their roles in global regulatory networks. FEMS Microbiol Rev. 2010;34(5):866–82.
Article
CAS
PubMed
PubMed Central
Google Scholar
Waters LS, Storz G. Regulatory RNAs in bacteria. Cell. 2009;136(4):615–28.
Article
CAS
PubMed
PubMed Central
Google Scholar
Storz G, Vogel J, Wassarman KM. Regulation by small RNAs in bacteria: expanding frontiers. Mol Cell. 2011;43(6):880–91.
Article
CAS
PubMed
PubMed Central
Google Scholar
Caldelari I, Chao Y, Romby P, Vogel J. RNA-mediated regulation in pathogenic bacteria. Cold Spring Harb Perspect Med. 2013;3(9):a010298.
Article
PubMed
PubMed Central
Google Scholar
Vogel J, Luisi BF. Hfq and its constellation of RNA. Nat Rev Microbiol. 2011;9(8):578–89.
Article
CAS
PubMed
PubMed Central
Google Scholar
Georg J, Hess WR. cis-antisense RNA, another level of gene regulation in bacteria. Microbiol Mol Biol Rev. 2011;75(2):286–300.
Article
CAS
PubMed
PubMed Central
Google Scholar
Thomason MK, Storz G. Bacterial antisense RNAs: how many are there, and what are they doing? Annu Rev Genet. 2010;44:167–88.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lybecker M, Zimmermann B, Bilusic I, Tukhtubaeva N, Schroeder R. The double-stranded transcriptome of Escherichia coli. Proc Natl Acad Sci U S A. 2014;111(8):3134–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Heidrich N, Brantl S. Antisense RNA-mediated transcriptional attenuation in plasmid pIP501: the simultaneous interaction between two complementary loop pairs is required for efficient inhibition by the antisense RNA. Microbiology. 2007;153(Pt 2):420–7.
Article
CAS
PubMed
Google Scholar
Wagner EG, Simons RW. Antisense RNA control in bacteria, phages, and plasmids. Annu Rev Microbiol. 1994;48:713–42.
Article
CAS
PubMed
Google Scholar
Brantl S, Wagner EG. Antisense RNA-mediated transcriptional attenuation occurs faster than stable antisense/target RNA pairing: an in vitro study of plasmid pIP501. EMBO J. 1994;13(15):3599–607.
CAS
PubMed
PubMed Central
Google Scholar
Breaker RR. Riboswitches: from ancient gene-control systems to modern drug targets. Future Microbiol. 2009;4(7):771–3.
Article
PubMed
Google Scholar
Narberhaus F. Translational control of bacterial heat shock and virulence genes by temperature-sensing mRNAs. RNA Biol. 2010;7(1):84–9.
Article
CAS
PubMed
Google Scholar
Ramesh A, Winkler WC. Magnesium-sensing riboswitches in bacteria. RNA Biol. 2010;7(1):77–83.
Article
CAS
PubMed
Google Scholar
Marzi S, Romby P. RNA mimicry, a decoy for regulatory proteins. Mol Microbiol. 2012;83(1):1–6.
Article
CAS
PubMed
Google Scholar
Romeo T, Vakulskas CA, Babitzke P. Post-transcriptional regulation on a global scale: form and function of Csr/Rsm systems. Environ Microbiol. 2013;15(2):313–24.
Article
CAS
PubMed
Google Scholar
Bilusic I, Popitsch N, Rescheneder P, Schroeder R, Lybecker M. Revisiting the coding potential of the E. coli genome through Hfq co-immunoprecipitation. RNA Biol. 2014;11(5):641–54.
Article
CAS
PubMed
PubMed Central
Google Scholar
Novick RP. Autoinduction and signal transduction in the regulation of staphylococcal virulence. Mol Microbiol. 2003;48(6):1429–49.
Article
CAS
PubMed
Google Scholar
Novick RP, Geisinger E. Quorum sensing in staphylococci. Annu Rev Genet. 2008;42:541–64.
Article
CAS
PubMed
Google Scholar
Gripenland J, Netterling S, Loh E, Tiensuu T, Toledo-Arana A, Johansson J. RNAs: regulators of bacterial virulence. Nat Rev Microbiol. 2010;8(12):857–66.
Article
CAS
PubMed
Google Scholar
Papenfort K, Vogel J. Regulatory RNA in bacterial pathogens. Cell Host Microbe. 2010;8(1):116–27.
Article
CAS
PubMed
Google Scholar
Lebreton A, Cossart P. RNA- and protein-mediated control of Listeria monocytogenes virulence gene expression. RNA Biol. 2016:1–11. Epub ahead of print.
Lybecker MC, Samuels DS. Temperature-induced regulation of RpoS by a small RNA in Borrelia burgdorferi. Mol Microbiol. 2007;64(4):1075–89.
Article
CAS
PubMed
Google Scholar
Ouyang Z, Zhou J, Norgard MV. CsrA (BB0184) is not involved in activation of the RpoN-RpoS regulatory pathway in Borrelia burgdorferi. Infect Immun. 2014;82(4):1511–22.
Article
PubMed
PubMed Central
Google Scholar
Lybecker MC, Abel CA, Feig AL, Samuels DS. Identification and function of the RNA chaperone Hfq in the Lyme disease spirochete Borrelia burgdorferi. Mol Microbiol. 2010;78(3):622–35.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sanjuan E, Esteve-Gassent MD, Maruskova M, Seshu J. Overexpression of CsrA (BB0184) alters the morphology and antigen profiles of Borrelia burgdorferi. Infect Immun. 2009;77(11):5149–62.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sze CW, Li C. Inactivation of bb0184, which encodes carbon storage regulator A, represses the infectivity of Borrelia burgdorferi. Infect Immun. 2011;79(3):1270–9.
Article
CAS
PubMed
Google Scholar
Thorvaldsdottir H, Robinson JT, Mesirov JP. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 2013;14(2):178–92.
Article
CAS
PubMed
Google Scholar
Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res. 2002;12(6):996–1006.
Article
CAS
PubMed
PubMed Central
Google Scholar
Patton TG, Brandt KS, Nolder C, Clifton DR, Carroll JA, Gilmore RD. Borrelia burgdorferi bba66 gene inactivation results in attenuated mouse infection by tick transmission. Infect Immun. 2013;81(7):2488–98.
Article
CAS
PubMed
PubMed Central
Google Scholar
Caimano MJ, Kenedy MR, Kairu T, Desrosiers DC, Harman M, Dunham-Ems S, Akins DR, Pal U, Radolf JD. The hybrid histidine kinase Hk1 is part of a two-component system that is essential for survival of Borrelia burgdorferi in feeding Ixodes scapularis ticks. Infect Immun. 2011;79(8):3117–30.
Article
CAS
PubMed
PubMed Central
Google Scholar
He M, Ouyang Z, Troxell B, Xu H, Moh A, Piesman J, Norgard MV, Gomelsky M, Yang XF. Cyclic di-GMP is essential for the survival of the lyme disease spirochete in ticks. PLoS Pathog. 2011;7(6):e1002133.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kostick JL, Szkotnicki LT, Rogers EA, Bocci P, Raffaelli N, Marconi RT. The diguanylate cyclase, Rrp1, regulates critical steps in the enzootic cycle of the Lyme disease spirochetes. Mol Microbiol. 2011;81(1):219–31.
Article
CAS
PubMed
PubMed Central
Google Scholar
Salman-Dilgimen A, Hardy PO, Dresser AR, Chaconas G. HrpA, a DEAH-box RNA helicase, is involved in global gene regulation in the Lyme disease spirochete. PLoS One. 2011;6(7):e22168.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chaconas G, Stewart PE, Tilly K, Bono JL, Rosa P. Telomere resolution in the Lyme disease spirochete. EMBO J. 2001;20(12):3229–37.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jewett MW, Lawrence KA, Bestor A, Byram R, Gherardini F, Rosa PA. GuaA and GuaB are essential for Borrelia burgdorferi survival in the tick-mouse infection cycle. J Bacteriol. 2009;191(20):6231–41.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kobryn K, Chaconas G. ResT, a telomere resolvase encoded by the Lyme disease spirochete. Mol Cell. 2002;9(1):195–201.
Article
CAS
PubMed
Google Scholar
Revel AT, Talaat AM, Norgard MV. DNA microarray analysis of differential gene expression in Borrelia burgdorferi, the Lyme disease spirochete. Proc Natl Acad Sci U S A. 2002;99(3):1562–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chao Y, Papenfort K, Reinhardt R, Sharma CM, Vogel J. An atlas of Hfq-bound transcripts reveals 3′ UTRs as a genomic reservoir of regulatory small RNAs. EMBO J. 2012;31(20):4005–19.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chao Y, Vogel J. A 3′ UTR-Derived Small RNA Provides the Regulatory Noncoding Arm of the Inner Membrane Stress Response. Mol Cell. 2016;61(3):352–63.
Article
CAS
PubMed
Google Scholar
Lybecker M, Bilusic I, Raghavan R. Pervasive transcription: detecting functional RNAs in bacteria. Transcription. 2014;5(4):e944039.
Article
PubMed
PubMed Central
Google Scholar
Gossringer M, Hartmann RK. 3′-UTRs as a source of regulatory RNAs in bacteria. EMBO J. 2012;31(20):3958–60.
Article
PubMed
PubMed Central
Google Scholar
Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H, Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, et al. The Listeria transcriptional landscape from saprophytism to virulence. Nature. 2009;459(7249):950–6.
Article
CAS
PubMed
Google Scholar
Beaume M, Hernandez D, Francois P, Schrenzel J. New approaches for functional genomic studies in staphylococci. Int J Med Microbiol. 2010;300(2–3):88–97.
Article
CAS
PubMed
Google Scholar
Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiss S, Sittka A, Chabas S, Reiche K, Hackermuller J, Reinhardt R, et al. The primary transcriptome of the major human pathogen Helicobacter pylori. Nature. 2010;464(7286):250–5.
Article
CAS
PubMed
Google Scholar
Kortmann J, Narberhaus F. Bacterial RNA thermometers: molecular zippers and switches. Nat Rev Microbiol. 2012;10(4):255–65.
Article
CAS
PubMed
Google Scholar
Narberhaus F, Waldminghaus T, Chowdhury S. RNA thermometers. FEMS Microbiol Rev. 2006;30(1):3–16.
Article
CAS
PubMed
Google Scholar
Thomason MK, Bischler T, Eisenbart SK, Forstner KU, Zhang A, Herbig A, Nieselt K, Sharma CM, Storz G. Global transcriptional start site mapping using differential RNA sequencing reveals novel antisense RNAs in Escherichia coli. J Bacteriol. 2015;197(1):18–28.
Article
PubMed
Google Scholar
Lluch-Senar M, Delgado J, Chen WH, Llorens-Rico V, O’Reilly FJ, Wodke JA, Unal EB, Yus E, Martinez S, Nichols RJ, et al. Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome-reduced bacterium. Mol Syst Biol. 2015;11(1):780.
Article
PubMed
PubMed Central
Google Scholar
Mackowiak SD, Zauber H, Bielow C, Thiel D, Kutz K, Calviello L, Mastrobuoni G, Rajewsky N, Kempa S, Selbach M, et al. Extensive identification and analysis of conserved small ORFs in animals. Genome Biol. 2015;16:179.
Article
PubMed
PubMed Central
Google Scholar
Drecktrah D, Lybecker M, Popitsch N, Rescheneder P, Hall LS, Samuels DS. The borrelia burgdorferi RelA/SpoT homolog and stringent response regulate survival in the tick vector and global gene expression during starvation. PLoS Pathog. 2015;11(9):e1005160.
Article
PubMed
PubMed Central
Google Scholar
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnetjournal. 2011;17(1):10–2.
Google Scholar
Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26(6):841–2.
Article
CAS
PubMed
PubMed Central
Google Scholar
Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26(1):139–40.
Article
CAS
PubMed
Google Scholar
Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010;11(10):R106.
Article
CAS
PubMed
PubMed Central
Google Scholar
Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP. Integrative genomics viewer. Nat Biotechnol. 2011;29(1):24–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Casjens S. Borrelia genomes in the year 2000. J Mol Microbiol Biotechnol. 2000;2(4):401–10.
CAS
PubMed
Google Scholar
Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics. 2010;26(17):2204–7.
Article
CAS
PubMed
PubMed Central
Google Scholar