Identification and characterization of novel small RNAs in Rickettsia prowazekii

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

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

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 Rickettsia species remain poorly understood. Here, we report on the identification of both novel and well-known bacterial sRNAs in Rickettsia prowazekii, known to cause epidemic typhus in humans. RNA sequencing of human microvascular endothelial cells (HMECs), the preferred targets during human rickettsioses, infected with R. prowazekii revealed the presence of 35 trans-acting and 23 cis-acting sRNAs, respectively. Of these, expression of two trans-acting (Rp_sR17 and Rp_sR60) and one cis-acting (Rp_sR47) novel sRNAs and four well-characterized bacterial sRNAs (RNaseP_bact_a, a-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 R. prowazekii. 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 R. prowazekii during host cell infection and suggest potential functional roles for these important post-transcriptional regulators in rickettsial biology and pathogenesis.

Original languageEnglish (US)
Article number859
JournalFrontiers in Microbiology
Volume7
Issue numberJUN
DOIs
StatePublished - 2016

Fingerprint

Rickettsia prowazekii
Bacterial RNA
RNA
Epidemic Louse-Borne Typhus
RNA Sequence Analysis
Rickettsia
Northern Blotting
Virulence
Endothelial Cells
Polymerase Chain Reaction
Messenger RNA
Infection

Keywords

  • Epidemic typhus
  • Rickettsia prowazekii
  • RNA sequencing
  • Small RNAs
  • Vascular endothelium

ASJC Scopus subject areas

  • Microbiology
  • Microbiology (medical)

Cite this

Identification and characterization of novel small RNAs in Rickettsia prowazekii. / Schroeder, Casey L C; Narra, Hema P.; Sahni, Abha; Rojas, Mark; Khanipov, Kamil; Patel, Jignesh; Shah, Riya; Fofanov, Yuriy; Sahni, Sanjeev.

In: Frontiers in Microbiology, Vol. 7, No. JUN, 859, 2016.

Research output: Contribution to journalArticle

Schroeder, Casey L C ; Narra, Hema P. ; Sahni, Abha ; Rojas, Mark ; Khanipov, Kamil ; Patel, Jignesh ; Shah, Riya ; Fofanov, Yuriy ; Sahni, Sanjeev. / Identification and characterization of novel small RNAs in Rickettsia prowazekii. In: Frontiers in Microbiology. 2016 ; Vol. 7, No. JUN.
@article{38de14de019d47c6a6a83d6a9ae48c0b,
title = "Identification and characterization of novel small RNAs in Rickettsia prowazekii",
abstract = "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 Rickettsia species remain poorly understood. Here, we report on the identification of both novel and well-known bacterial sRNAs in Rickettsia prowazekii, known to cause epidemic typhus in humans. RNA sequencing of human microvascular endothelial cells (HMECs), the preferred targets during human rickettsioses, infected with R. prowazekii revealed the presence of 35 trans-acting and 23 cis-acting sRNAs, respectively. Of these, expression of two trans-acting (Rp_sR17 and Rp_sR60) and one cis-acting (Rp_sR47) novel sRNAs and four well-characterized bacterial sRNAs (RNaseP_bact_a, a-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 R. prowazekii. 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 R. prowazekii during host cell infection and suggest potential functional roles for these important post-transcriptional regulators in rickettsial biology and pathogenesis.",
keywords = "Epidemic typhus, Rickettsia prowazekii, RNA sequencing, Small RNAs, Vascular endothelium",
author = "Schroeder, {Casey L C} and Narra, {Hema P.} and Abha Sahni and Mark Rojas and Kamil Khanipov and Jignesh Patel and Riya Shah and Yuriy Fofanov and Sanjeev Sahni",
year = "2016",
doi = "10.3389/fmicb.2016.00859",
language = "English (US)",
volume = "7",
journal = "Frontiers in Microbiology",
issn = "1664-302X",
publisher = "Frontiers Media S. A.",
number = "JUN",

}

TY - JOUR

T1 - Identification and characterization of novel small RNAs in Rickettsia prowazekii

AU - Schroeder, Casey L C

AU - Narra, Hema P.

AU - Sahni, Abha

AU - Rojas, Mark

AU - Khanipov, Kamil

AU - Patel, Jignesh

AU - Shah, Riya

AU - Fofanov, Yuriy

AU - Sahni, Sanjeev

PY - 2016

Y1 - 2016

N2 - 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 Rickettsia species remain poorly understood. Here, we report on the identification of both novel and well-known bacterial sRNAs in Rickettsia prowazekii, known to cause epidemic typhus in humans. RNA sequencing of human microvascular endothelial cells (HMECs), the preferred targets during human rickettsioses, infected with R. prowazekii revealed the presence of 35 trans-acting and 23 cis-acting sRNAs, respectively. Of these, expression of two trans-acting (Rp_sR17 and Rp_sR60) and one cis-acting (Rp_sR47) novel sRNAs and four well-characterized bacterial sRNAs (RNaseP_bact_a, a-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 R. prowazekii. 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 R. prowazekii during host cell infection and suggest potential functional roles for these important post-transcriptional regulators in rickettsial biology and pathogenesis.

AB - 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 Rickettsia species remain poorly understood. Here, we report on the identification of both novel and well-known bacterial sRNAs in Rickettsia prowazekii, known to cause epidemic typhus in humans. RNA sequencing of human microvascular endothelial cells (HMECs), the preferred targets during human rickettsioses, infected with R. prowazekii revealed the presence of 35 trans-acting and 23 cis-acting sRNAs, respectively. Of these, expression of two trans-acting (Rp_sR17 and Rp_sR60) and one cis-acting (Rp_sR47) novel sRNAs and four well-characterized bacterial sRNAs (RNaseP_bact_a, a-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 R. prowazekii. 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 R. prowazekii during host cell infection and suggest potential functional roles for these important post-transcriptional regulators in rickettsial biology and pathogenesis.

KW - Epidemic typhus

KW - Rickettsia prowazekii

KW - RNA sequencing

KW - Small RNAs

KW - Vascular endothelium

UR - http://www.scopus.com/inward/record.url?scp=84979971922&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84979971922&partnerID=8YFLogxK

U2 - 10.3389/fmicb.2016.00859

DO - 10.3389/fmicb.2016.00859

M3 - Article

AN - SCOPUS:84979971922

VL - 7

JO - Frontiers in Microbiology

JF - Frontiers in Microbiology

SN - 1664-302X

IS - JUN

M1 - 859

ER -