Genomewide comparison and novel ncRNAs of Aquificales

BMC Genomics

Research Article

Manja Marz¹  Stefanie Wehner¹  Konstantin Riege¹  Nicolas Wieseke²  Benedikt M Beckmann³  Astrid I Nickel⁴  Marcus Lechner⁴  Roland K Hartmann⁴ 

[1] Faculty of Mathematics and Computer Science, Friedrich-Schiller-University Jena, Leutragraben 1, 07743, Jena, Germany;Faculty of Mathematics and Informatics, University of Leipzig, Augustusplatz 10, 04109, Leipzig, Germany;IRI for the Life Sciences, Molecular Infection Biology, Humboldt University Berlin, Philippstr. 13, 10115, Berlin, Germany;Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany;

关键词: Aquificales;    Thermophiles;    ncRNA;    Aquificaceae;    Desulfurobacteriaceae;    Hydrogenothermaceae;   

DOI  :  10.1186/1471-2164-15-522

 received in 2013-11-29, accepted in 2014-05-08,  发布年份 2014

来源: Springer

【 摘 要 】

BackgroundThe Aquificales are a diverse group of thermophilic bacteria that thrive in terrestrial and marine hydrothermal environments. They can be divided into the families Aquificaceae, Desulfurobacteriaceae and Hydrogenothermaceae. Although eleven fully sequenced and assembled genomes are available, only little is known about this taxonomic order in terms of RNA metabolism.ResultsIn this work, we compare the available genomes, extend their protein annotation, identify regulatory sequences, annotate non-coding RNAs (ncRNAs) of known function, predict novel ncRNA candidates, show idiosyncrasies of the genetic decoding machinery, present two different types of transfer-messenger RNAs and variations of the CRISPR systems. Furthermore, we performed a phylogenetic analysis of the Aquificales based on entire genome sequences, and extended this by a classification among all bacteria using 16S rRNA sequences and a set of orthologous proteins.Combining several in silico features (e.g. conserved and stable secondary structures, GC-content, comparison based on multiple genome alignments) with an in vivo dRNA-seq transcriptome analysis of Aquifex aeolicus, we predict roughly 100 novel ncRNA candidates in this bacterium.ConclusionsWe have here re-analyzed the Aquificales, a group of bacteria thriving in extreme environments, sharing the feature of a small, compact genome with a reduced number of protein and ncRNA genes. We present several classical ncRNAs and riboswitch candidates. By combining in silico analysis with dRNA-seq data of A. aeolicus we predict nearly 100 novel ncRNA candidates.

【 授权许可】

Unknown   
© Lechner et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.