Genomewide comparison and novel ncRNAs of Aquificales

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 l...

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Bibliographic Details
Published in:BMC genomics 2014-06, Vol.15 (1), p.522-522, Article 522
Main Authors: Lechner, Marcus, Nickel, Astrid I, Wehner, Stefanie, Riege, Konstantin, Wieseke, Nicolas, Beckmann, Benedikt M, Hartmann, Roland K, Marz, Manja
Format: Article
Language:English
Subjects:
Analysis
Aquifex aeolicus
Aquificales
Bacteria
Base Sequence
Clustered Regularly Interspaced Short Palindromic Repeats - genetics
Colleges & universities
Databases, Genetic
Digoxigenin - chemistry
Evolution
Gene expression
Genes
Genetic aspects
Genome, Bacterial
Genomes
Genomics
Gram-Positive Bacteria - classification
Gram-Positive Bacteria - genetics
Nucleic Acid Conformation
Oligonucleotides - chemistry
Oligonucleotides - metabolism
Phylogenetics
Phylogeny
Physiological aspects
Proteins
Ribonuclease P - metabolism
RNA, Bacterial - chemistry
RNA, Bacterial - metabolism
RNA, Ribosomal, 16S - chemistry
RNA, Ribosomal, 16S - genetics
RNA, Transfer - metabolism
RNA, Untranslated - chemistry
RNA, Untranslated - genetics
RNA, Untranslated - metabolism
Sequence Analysis, RNA
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Summary: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. 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. 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.
ISSN:1471-2164
1471-2164
DOI:10.1186/1471-2164-15-522