The Stringent Response-Regulated sRNA Transcriptome of Borrelia burgdorferi.

Dan Drecktrah,D Scott Samuels,Philipp Rescheneder,Meghan Lybecker,Laura S Hall

doi:10.3389/fcimb.2018.00231

Abstract

The Lyme disease spirochete Borrelia (Borreliella) burgdorferi must tolerate nutrient stress to persist in the tick phase of its enzootic life cycle. We previously found that the stringent response mediated by RelBbu globally regulates gene expression to facilitate persistence in the tick vector. Here, we show that RelBbu regulates the expression of a swath of small RNAs (sRNA), affecting 36% of previously identified sRNAs in B. burgdorferi. This is the first sRNA regulatory mechanism identified in any spirochete. Threefold more sRNAs were RelBbu-upregulated than downregulated during nutrient stress and included antisense, intergenic and 5′ untranslated region sRNAs. RelBbu-regulated sRNAs associated with genes known to be important for host infection (bosR and dhhp) as well as persistence in the tick (glpF and hk1) were identified, suggesting potential mechanisms for post-transcriptional regulation of gene expression.

Highlights

Borrelia (Borreliella) burgdorferi, the causative agent of Lyme disease (Burgdorfer et al, 1982; Benach et al, 1983; Steere et al, 1983), exists in nature in an enzootic cycle alternating between Ixodes ticks and vertebrate hosts (Lane et al, 1991; Radolf et al, 2012; Caimano et al, 2016)
We discovered that the RelBbu-mediated stringent response is a major regulator of small RNAs (sRNA) expression in B. burgdorferi, affecting the levels of a third (241 out of 666) of all identified sRNAs. sRNAregulated gene expression may play a larger regulatory role in this bacterium compared to others as many of the proteinmediated transcriptional regulators and signaling pathways are absent in B. burgdorferi (Fraser et al, 1997; Samuels and Radolf, 2009)
We found that RelBbu regulates approximately one third of the 666 sRNAs identified in B. burgdorferi by Popitsch et al (2017), with greater than threefold more sRNAs upregulated than downregulated: 187 sRNAs upregulated (Table S2) and 54 sRNAs downregulated (Table S3) during nutrient stress (Figure 1). sRNAs from each category, IG RNA, Antisense RNAs (asRNAs) and 5′ untranslated region (5′ UTR) sRNA, were RelBburegulated, with asRNAs being the majority of upregulated sRNAs (Figure 2A) and IG RNAs as the largest category of downregulated sRNAs (Figure 3A)

Summary

Introduction

Borrelia (Borreliella) burgdorferi, the causative agent of Lyme disease (Burgdorfer et al, 1982; Benach et al, 1983; Steere et al, 1983), exists in nature in an enzootic cycle alternating between Ixodes ticks and vertebrate hosts (Lane et al, 1991; Radolf et al, 2012; Caimano et al, 2016). In order to survive these disparate environments, B. burgdorferi alters its pattern of gene expression in response to environmental signals, including temperature and nutrients (Radolf et al, 2012; Troxell and Yang, 2013; Iyer and Schwartz, 2016; Samuels and Samuels, 2016; Stevenson and Seshu, 2017) Central to this response is the RpoNRpoS alternative sigma factor cascade that transcriptionally controls expression of numerous genes required for the transmission from the tick and the establishment of infection in the mammal (Hübner et al, 2001; Fisher et al, 2005; Burtnick et al, 2007; Caimano et al, 2007; Dunham-Ems et al, 2012; Ouyang et al, 2012; Grove et al, 2017). The enhancer-binding protein and response regulator Rrp (Yang et al, 2003; Burtnick et al, 2007), the transcriptional regulators BosR (Boylan et al, 2003; Hyde et al, 2009; Ouyang et al, 2009, 2011; Katona, 2015) and BadR

Methods

Results

Conclusion