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Open Access Research article

Genomewide comparison and novel ncRNAs of Aquificales

Marcus Lechner1, Astrid I Nickel1, Stefanie Wehner2, Konstantin Riege2, Nicolas Wieseke3, Benedikt M Beckmann4, Roland K Hartmann1* and Manja Marz2*

Author Affiliations

1 Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany

2 Faculty of Mathematics and Computer Science, Friedrich-Schiller-University Jena, Leutragraben 1, 07743 Jena, Germany

3 Faculty of Mathematics and Informatics, University of Leipzig, Augustusplatz 10, 04109 Leipzig, Germany

4 IRI for the Life Sciences, Molecular Infection Biology, Humboldt University Berlin, Philippstr. 13, 10115 Berlin, Germany

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BMC Genomics 2014, 15:522  doi:10.1186/1471-2164-15-522

Published: 25 June 2014

Abstract

Background

The 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.

Results

In 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.

Conclusions

We 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.

Keywords:
Aquificales; Thermophiles; ncRNA; Aquificaceae; Desulfurobacteriaceae; Hydrogenothermaceae