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

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.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4608-y) contains supplementary material, which is available to authorized users.

Coxiella burnetiismall RNA 12 binds CsrA regulatory protein and transcripts for the CvpD type IV effector, regulates pyrimidine and methionine metabolism, and is necessary for optimal intracellular growth and vacuole formation during infection

“…However, little is known about the roles for IHF and DksA in C. burnetii . The consensus IHF-binding site occurs in a C. burnetii selfish genetic element, suggesting that this binding sequence is maintained in the pathogen [31]. Similarly, a role for DksA in C. burnetii ’s stringent response has been suggested, although no correlations could be drawn [56].…”

“…RNA was folded using mFold [81] and visualized with the Visualization Applet for RNA [82]. Analyses of RNA-Seq data were carried out as previously described [31]. Briefly, raw fastq files were concatenated, quality-filtered with the FASTX toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) and then clipped, aligned, and filtered with Nesoni version 0.128 tools (http://www.vicbioinformatics.com/software.nesoni.shtml).…”

“…Northern blots also showed that CbsR12 was upregulated in SCVs vs. LCVs in ACCM-2, and revealed two distinct sizes of the sRNA, suggesting that either an alternative transcription start site (TSS) or ribonuclease processing of the sRNA was responsible. In a subsequent study, CbsR3 and CbsR13 were found to originate from transcribed loci of a selfish genetic element, termed QMITE1 [31]. However, despite the identification and verification of several CbsRs, none has been functionally characterized, to date.…”

A CsrA-Binding, trans -Acting sRNA of Coxiella burnetii Is Necessary for Optimal Intracellular Growth and Vacuole Formation during Early Infection of Host Cells

“…Northern blots also showed that CbsR12 was upregulated in SCVs versus LCVs in ACCM-2 and revealed two distinct sizes of the sRNA, suggesting that either an alternative transcription start site (TSS) or RNase processing of the sRNA was responsible. In a subsequent study, CbsR3 and CbsR13 were found to originate from transcribed loci of a selfish genetic element, termed QMITE1 (38). However, despite the identification and verification of several CbsRs, none has been functionally characterized to date.…”

“…RNA was folded using Mfold (73) and visualized with Visualization Applet for RNA (74). Analyses of RNA-Seq data were carried out as previously described (38). Briefly, raw fastq files were concatenated, quality filtered with the FASTX toolkit (http://hannonlab.cshl.edu/fastx_toolkit/), and then clipped, aligned, and filtered with Nesoni version 0.128 tools (http://www.vicbioinformatics.com/software.nesoni.shtml).…”