tRNA-like elements in Haloferax volcanii

Abstract

All functional RNAs are generated from precursor molecules by a plethora of processing steps. The generation of mature RNA molecules by processing is an important layer of gene expression regulation catalysed by ribonucleases. Here, we analysed 5S rRNA processing in the halophilic Archaeon Haloferax volcanii. Earlier experiments showed that the 5S rRNA is cleaved at its 5' end by the endonuclease tRNase Z. Interestingly, a tRNA-like structure was identified upstream of the 5S rRNA that might be used as a processing signal. Here, we show that this tRNA-like element is indeed recognised as a processing signal by tRNase Z. Substrates containing mutations in the tRNA-like sequence are no longer processed, whereas a substrate containing a deletion in the 5S rRNA sequence is still cleaved. Therefore, an intact 5S rRNA structure is not required for processing. Further, we used bioinformatics analyses to identify additional sequences in Haloferax containing tRNA-like structures. This search resulted in the identification of all tRNAs, the tRNA-like structure upstream of the 5S RNA and 47 new tRNA-like structural elements. However, the in vitro processing of selected examples showed no cleavage of these newly identified elements. Thus, tRNA-like elements are not a general processing signal in Haloferax.

An Active Immune Defense with a Minimal CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) RNA and without the Cas6 Protein

“…The crRNA is derived from the Haloferax CRISPR locus C and contains spacer 1 of this locus. The t-element is a tRNA-like structure that has been previously detected directly upstream of the 5 S rRNA in H. volcanii , and it is processed by tRNase Z to generate the 5 S rRNA 5′ end ( 36 , 37 ). Generally t-elements are substrates for both tRNA-processing enzymes, the 5′-processing enzyme RNase P, and the 3′-processing enzyme tRNase Z ( 36 , 38 ).…”

Splicing Endonuclease Is an Important Player in rRNA and tRNA Maturation in Archaea

“…Furthermore, the ribonucleases which catalyze many key processing steps in cellular reactions remain unknown. It has been suggested that the few currently known archaeal ribonucleases may have a broader substrate spectrum and catalyze more processing steps than their bacterial and eukaryal homologs (Hölzle et al, 2012). For instance the H. volcanii tRNase Z -an endonuclease known for catalyzing tRNA 3 processing (Schiffer et al, 2002;Späth et al, 2008)has been shown to have an additional function besides tRNA processing; it is also involved in maturation of 5S ribosomal RNA (Hölzle et al, 2008).…”