Abstract
Signal recognition particles (SRPs) are universal ribonucleoprotein complexes found in all three domains of life that direct the cellular traffic and secretion of proteins. These complexes consist of SRP proteins and a single, highly structured SRP RNA. Canonical SRP RNA genes have not been identified for some Thermoproteus species even though they contain SRP19 and SRP54 proteins. Here, we show that genome rearrangement events in Thermoproteus tenax created a permuted SRP RNA gene. The 5'- and 3'-termini of this SRP RNA are located close to a functionally important loop present in all known SRP RNAs. RNA-Seq analyses revealed that these termini are ligated together to generate circular SRP RNA molecules that can bind to SRP19 and SRP54. The circularization site is processed by the tRNA splicing endonuclease. This moonlighting activity of the tRNA splicing machinery permits the permutation of the SRP RNA and creates highly stable and functional circular RNA molecules.
Highlights
We identified a similar permuted SRP RNA gene in T. uzoniensis and noticed that nucleic acid sequence variations do not occur in conserved regions of the SRP RNA and in most cases do not disrupt the structure of the SRP RNA (i.e. G-C base pairs are replaced by G-U or A-U basepairs) (Figure 1—figure supplement 1)
The presence of a bulge helix bulge (BHB) motif suggests that RtcB could be responsible for SRP RNA circularization, if the T. tenax splicing endonuclease recognized the identified BHB motif
We produced recombinant T. tenax splicing endonuclease (TTX_1594, catalytic subunit and TTX_1893 structural subunit, Figure 3—figure supplement 1) and could verify specific cleavage of the proposed BHB motif (Figure 4B). This suggests that the transfer RNAs (tRNAs) splicing machinery has a moonlighting activity and processes and circularizes permuted SRP RNA molecules
Summary
Biochemistry Genomics and evolutionary biology eLife digest Cells make many proteins that are eventually released outside the cell or inserted into the cell’s membrane. The presence of a BHB motif suggests that RtcB could be responsible for SRP RNA circularization, if the T. tenax splicing endonuclease recognized the identified BHB motif It should be noted, that T. tenax contains a record number of 48 introns in 46 tRNAs (Chan and Lowe, 2009). We produced recombinant T. tenax splicing endonuclease (TTX_1594, catalytic subunit and TTX_1893 structural subunit, Figure 3—figure supplement 1) and could verify specific cleavage of the proposed BHB motif (Figure 4B) This suggests that the tRNA splicing machinery (i.e. tRNA splicing endonuclease & tRNA ligase RtcB) has a moonlighting activity and processes and circularizes permuted SRP RNA molecules. One example is the observed occurrence of permuted and circularized SRP RNA molecules whose increased stability should provide a selective advantage
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