Loss of Conserved Noncoding RNAs in Genomes of Bacterial Endosymbionts

Genome Biology and Evolution
Dorota MatelskaStanislaw Dunin-Horkawicz

Abstract

The genomes of intracellular symbiotic or pathogenic bacteria, such as of Buchnera, Mycoplasma, and Rickettsia, are typically smaller compared with their free-living counterparts. Here we showed that noncoding RNA (ncRNA) families, which are conserved in free-living bacteria, frequently could not be detected by computational methods in the small genomes. Statistical tests demonstrated that their absence is not an artifact of low GC content or small deletions in these small genomes, and thus it was indicative of an independent loss of ncRNAs in different endosymbiotic lineages. By analyzing the synteny (conservation of gene order) between the reduced and nonreduced genomes, we revealed instances of protein-coding genes that were preserved in the reduced genomes but lost cis-regulatory elements. We found that the loss of cis-regulatory ncRNA sequences, which regulate the expression of cognate protein-coding genes, is characterized by the reduction of secondary structure formation propensity, GC content, and length of the corresponding genomic regions.

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Jun 16, 2016·Wiley Interdisciplinary Reviews. RNA·Michelle M Meyer
Sep 8, 2016·Scientific Reports·Alejandro Manzano-Marín, Amparo Latorre
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Mar 17, 2018·Microbiology Spectrum·Michelle M Meyer
Jul 3, 2021·Molecular Biology and Evolution·Margaret W ThairuAllison K Hansen

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Datasets Mentioned

BETA
SRX529441

Methods Mentioned

BETA
RNA-seq

Software Mentioned

cmfinder
LocaRNA
cmsearch
cmscan
megablast
CombMotif
Basic Local Alignment Search Tool ( BLAST )
Infernal

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