Abstract
BackgroundThe minimal genome of the tiny, hyperthermophilic archaeon Nanoarchaeum equitans contains several fragmented genes and revealed unusual RNA processing pathways. These include the maturation of tRNA molecules via the trans-splicing of tRNA halves and genomic rearrangements to compensate for the absence of RNase P.ResultsHere, the RNA processing events in the N. equitans cell are analyzed using RNA-Seq deep sequencing methodology. All tRNA half precursor and tRNA termini were determined and support the tRNA trans-splicing model. The processing of CRISPR RNAs from two CRISPR clusters was verified. Twenty-seven C/D box small RNAs (sRNAs) and a H/ACA box sRNA were identified. The C/D box sRNAs were found to flank split genes, to form dicistronic tRNA-sRNA precursors and to be encoded within the tRNAMet intron.ConclusionsThe presented data provide an overview of the production and usage of small RNAs in a cell that has to survive with a highly reduced genome. N. equitans lost many essential metabolic pathways but maintains highly active CRISPR/Cas and rRNA modification systems that appear to play an important role in genome fragmentation.
Highlights
The minimal genome of the tiny, hyperthermophilic archaeon Nanoarchaeum equitans contains several fragmented genes and revealed unusual RNA processing pathways
Analysis of the abundance of different RNA species verified that all expected different types of RNA species were detected in the RNA-Seq data, including rRNAs, tRNAs, tRNA half molecules, small RNAs and CRISPR RNA (crRNA)
The analysis of the abundant small RNA population identified a considerable fraction of crRNAs as well as C/D box and H/ACA box sRNAs
Summary
The minimal genome of the tiny, hyperthermophilic archaeon Nanoarchaeum equitans contains several fragmented genes and revealed unusual RNA processing pathways. These include the maturation of tRNA molecules via the trans-splicing of tRNA halves and genomic rearrangements to compensate for the absence of RNase P. The genome sequence of N. equitans Kin4-M revealed a minimal, compact genome of only 490 kilobases and an extremely high gene density with little noncoding DNA or pseudogenes [3]. This highly reduced genome lacks almost all known genes for the synthesis of amino acids, nucleotides, cofactors, and lipids. Examples of such splits are the two open reading frames encoding domains of the alanyl-tRNA
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