# Decoding the coding and non-coding transcriptomes of Orientia tsutsugamushi in target host cells

> **NIH NIH R21** · UNIVERSITY OF TEXAS MED BR GALVESTON · 2020 · $237,000

## Abstract

PROJECT SUMMARY
Orientia tsutsugamushi (Ot) is a highly virulent, chigger-borne, strictly intracellular Gram-negative bacterium
known to cause scrub typhus in humans, a disease endemic to `Tsutsugamushi triangle' placing more than a
billion people at risk and responsible for more than a million cases every year. Antigenic and genetic variability
among Ot strains is an established phenomenon, yet our appreciation of the regulation of Ot genomes during
host-pathogen interactions remains in its infancy. Bacterial small regulatory RNAs (sRNAs) have only recently
emerged as critical post-transcriptional regulators of gene expression. Among these, trans-acting sRNAs act
by binding to target mRNA(s); cis-acting sRNAs are transcribed antisense to their target RNA; and
riboswitches alter gene expression by interacting with either small ligands or metabolites. Small RNAs regulate
bacterial virulence by initiation/termination of transcription, stabilization/degradation of target mRNAs, and
regulation of translation. Despite their importance as potential therapeutic targets, the identities and functions
of Ot sRNAs have remained a mystery. A major bottleneck precluding the exploration of such regulatory
networks in Ot pertains to the `sticky' genomes punctuated by extensive homologous recombination driven by
transposons, conjugative elements, repetitive sequences, and gene duplication events, but this hurdle can now
be overcome based on the sequencing and annotation of six Ot genomes as closed, circular chromosomes,
including that of prototypical and highly pathogenic Karp strain (OtK). With a long-term goal of defining sRNA-
mRNA interactions in Ot, we have employed this resource for bioinformatic predictions and follow-up validation
to identify sRNAs in OtK. Our intriguing preliminary findings suggest that OtK genome does not encode for
classical bacterial sRNAs 4.5S and 6S, indicating a unique sRNA repertoire which we hypothesize to play an
important role in post-transcriptional gene expression in microvascular endothelium as the preferred, primary
target cell niche in mammalian hosts. Accordingly, the objective of this application is to determine the coding
and non-coding transcriptomes of OtK in correlation with the corresponding proteome during interactions with
the host endothelium. In Aim 1, we will catalogue all expressed sRNAs and coding transcripts and determine
their transcriptional start sites during OtK infection of human/mouse endothelial cells by differential RNA
sequencing. Aim 2 will then identify and validate cognate mRNA targets for all novel trans- and cis-encoded
sRNAs. We will apply a cutting-edge RNA-sequencing platform in conjunction with advanced omics-based
approaches and our previously documented experience with the identification and characterization of sRNAs in
pathogenic Rickettsia species. The outcomes will positively impact the field via first mechanistic understanding
of the contributions of riboregulatory circuitry in Ot to...

## Key facts

- **NIH application ID:** 10058036
- **Project number:** 1R21AI149358-01A1
- **Recipient organization:** UNIVERSITY OF TEXAS MED BR GALVESTON
- **Principal Investigator:** Hema Prasad Narra
- **Activity code:** R21 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $237,000
- **Award type:** 1
- **Project period:** 2020-07-01 → 2022-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10058036

## Citation

> US National Institutes of Health, RePORTER application 10058036, Decoding the coding and non-coding transcriptomes of Orientia tsutsugamushi in target host cells (1R21AI149358-01A1). Retrieved via AI Analytics 2026-05-26 from https://api.ai-analytics.org/grant/nih/10058036. Licensed CC0.

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