Identification of novel MITEs (miniature inverted-repeat transposable elements) in Coxiella burnetii: implications for protein and small RNA evolution

Jenny Wachter,Rahul Raghavan,Shaun Wachter,Michael F Minnick

doi:10.1186/s12864-018-4608-y

Abstract

BackgroundCoxiella burnetii is a Gram-negative gammaproteobacterium and zoonotic agent of Q fever. C. burnetii’s genome contains an abundance of pseudogenes and numerous selfish genetic elements. MITEs (miniature inverted-repeat transposable elements) are non-autonomous transposons that occur in all domains of life and are thought to be insertion sequences (ISs) that have lost their transposase function. Like most transposable elements (TEs), MITEs are thought to play an active role in evolution by altering gene function and expression through insertion and deletion activities. However, information regarding bacterial MITEs is limited.ResultsWe describe two MITE families discovered during research on small non-coding RNAs (sRNAs) of C. burnetii. Two sRNAs, Cbsr3 and Cbsr13, were found to originate from a novel MITE family, termed QMITE1. Another sRNA, CbsR16, was found to originate from a separate and novel MITE family, termed QMITE2. Members of each family occur ~ 50 times within the strains evaluated. QMITE1 is a typical MITE of 300-400 bp with short (2-3 nt) direct repeats (DRs) of variable sequence and is often found overlapping annotated open reading frames (ORFs). Additionally, QMITE1 elements possess sigma-70 promoters and are transcriptionally active at several loci, potentially influencing expression of nearby genes. QMITE2 is smaller (150-190 bps), but has longer (7-11 nt) DRs of variable sequences and is mainly found in the 3′ untranslated region of annotated ORFs and intergenic regions. QMITE2 contains a GTAG repetitive extragenic palindrome (REP) that serves as a target for IS1111 TE insertion. Both QMITE1 and QMITE2 display inter-strain linkage and sequence conservation, suggesting that they are adaptive and existed before divergence of C. burnetii strains.ConclusionsWe have discovered two novel MITE families of C. burnetii. Our finding that MITEs serve as a source for sRNAs is novel. QMITE2 has a unique structure and occurs in large or small versions with unique DRs that display linkage and sequence conservation between strains, allowing for tracking of genomic rearrangements. QMITE1 and QMITE2 copies are hypothesized to influence expression of neighboring genes involved in DNA repair and virulence through transcriptional interference and ribonuclease processing.

Highlights

Coxiella burnetii is a Gram-negative gammaproteobacterium and zoonotic agent of Q fever
We found that CbsR13 RNA produced a stable predicted secondary structure resembling a very long palindromic sequence (Fig. 1b)
This result suggests that the two Small non-coding RNA (sRNA) share a common ancestor, unambiguous Transcripts per million (TPM) values from RNA-Seq show that CbsR13 is expressed at a markedly higher level relative to CbsR3 (Additional file 3)

Summary

Introduction

Coxiella burnetii is a Gram-negative gammaproteobacterium and zoonotic agent of Q fever. Like most transposable elements (TEs), MITEs are thought to play an active role in evolution by altering gene function and expression through insertion and deletion activities. Dot/Icm effectors are translocated to the host cell in a type IV secretion system-dependent manner in order to establish and maintain the vacuole [4]. Lipopolysaccharide is another critical virulence determinant in C. burnetii [5], it has been found to be truncated (rough) in some strains, including the Nine Mile phase II laboratory strain, RSA 439 [6]. It is hypothesized that Dugway either contains a gene(s) that impedes infection in humans, or that the virulent RSA 493 strain has some altered virulence gene(s) rendering it infective [9]

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