title: Loss of Conserved Noncoding RNAs in Genomes of Bacterial Endosymbionts.
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.
authors.affiliation: Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland.
authors.forename: Dorota
authors.initials: D
authors.lastname: Matelska
authors.affiliation: Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland.
authors.forename: Malgorzata
authors.initials: M
authors.lastname: Kurkowska
authors.affiliation: Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland.
authors.forename: Elzbieta
authors.initials: E
authors.lastname: Purta
authors.affiliation: Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland Laboratory of Structural Bioinformatics, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland sdh@genesilico.pl iamb@genesilico.pl.
authors.forename: Janusz M
authors.initials: JM
authors.lastname: Bujnicki
authors.affiliation: Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland sdh@genesilico.pl iamb@genesilico.pl.
authors.forename: Stanislaw
authors.initials: S
authors.lastname: Dunin-Horkawicz
mesh_terms: D001482:Base Composition; D020635:Buchnera / Q000235:genetics*; D017124:Conserved Sequence; D016680:Genome, Bacterial; D009174:Mycoplasma / Q000235:genetics*; D016366:Open Reading Frames; D062085:RNA, Long Noncoding / Q000235:genetics*; D012281:Rickettsia / Q000235:genetics*; D017384:Sequence Deletion; D013559:Symbiosis
chemical_list: D062085:RNA, Long Noncoding
keywords: Rfam; covariance models; endosymbionts; noncoding RNA loss