AUTHOR=Schroeder Casey L. C. , Narra Hema P. , Sahni Abha , Rojas Mark , Khanipov Kamil , Patel Jignesh , Shah Riya , Fofanov Yuriy , Sahni Sanjeev K. 

TITLE=Identification and Characterization of Novel Small RNAs in Rickettsia prowazekii

JOURNAL=Frontiers in Microbiology

VOLUME=7

YEAR=2016

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2016.00859

DOI=10.3389/fmicb.2016.00859

ISSN=1664-302X

ABSTRACT=<p>Emerging evidence implicates a critically important role for bacterial small RNAs (sRNAs) as post-transcriptional regulators of physiology, metabolism, stress/adaptive responses, and virulence, but the roles of sRNAs in pathogenic <italic>Rickettsia</italic> species remain poorly understood. Here, we report on the identification of both novel and well-known bacterial sRNAs in <italic>Rickettsia prowazekii</italic>, known to cause epidemic typhus in humans. RNA sequencing of <underline>h</underline>uman <underline>m</underline>icrovascular <underline>e</underline>ndothelial <underline>c</underline>ells (HMECs), the preferred targets during human rickettsioses, infected with <italic>R. prowazekii</italic> revealed the presence of 35 trans-acting and 23 cis-acting sRNAs, respectively. Of these, expression of two trans-acting (<italic>Rp</italic>_sR17 and <italic>Rp</italic>_sR60) and one cis-acting (<italic>Rp</italic>_sR47) novel sRNAs and four well-characterized bacterial sRNAs (RNaseP_bact_a, α-tmRNA, 4.5S RNA, 6S RNA) was further confirmed by Northern blot or RT-PCR analyses. The transcriptional start sites of five novel rickettsial sRNAs and 6S RNA were next determined using 5′ RLM-RACE yielding evidence for their independent biogenesis in <italic>R. prowazekii</italic>. Finally, computational approaches were employed to determine the secondary structures and potential mRNA targets of novel sRNAs. Together, these results establish the presence and expression of sRNAs in <italic>R. prowazekii</italic> during host cell infection and suggest potential functional roles for these important post-transcriptional regulators in rickettsial biology and pathogenesis.</p>