The distribution and evolution of small non-coding RNAs in archaea in light of new archaeal phyla.
Thesis DisciplineBiological Sciences
Degree GrantorUniversity of Canterbury
Degree NameMaster of Science
The archaea are organisms which are currently thought to constitute the third domain of life. Sharing many similarities with the other two domains, bacteria and eukaryotes, the knowledge of the diversity of the archaea has been rapidly expanding as metagenomic technologies continue to be developed. In this study we attempt to expand knowledge about two types of small non-coding RNAs (riboswitches and snoRNAs) within the archaea. Both of these types of RNA are also found in other domains of life making them an interesting point of comparison between the archaea and the bacteria and eukaryotes. We studied the distribution of both riboswitches and snoRNAs across 26 archaeal classes representing 13 archaeal phyla using homology searches based on known models from the Rfam and Pfam databases. Our study finds that riboswitches are distributed throughout relatively few archaeal taxa. Despite this, we identified many new occurrences of the known riboswitch families and identified a potential case of the presence of a riboswitch family not previously known to be found in archaea. We examined the genes found downstream of the riboswitch occurrences within the archaea. We found that while many riboswitches are associated with genes expected from previous studies of these riboswitch families in bacteria, other genes with both known and unknown functions also appear to be associated with these riboswitches in the archaea. The association of the Fluoride riboswitch with ion transporters that are not currently known to transport fluoride ions is one example of this. We also identified at least one case of a likely horizontal gene transfer (HGT) event of a riboswitch-gene pair from the bacteria into the archaeal genus Methanocorpusculum. This result lend weight to the suggestion of a series of HGT thought the evolution of the archaea as an explanation for the current distribution of riboswitches in the archaeal taxa studied. In investigating the distribution of snoRNAs within the archaea, we determined that while most archaeal taxa show evidence of known snoRNA families, these snoRNAs are not necessarily distributed through all species in each taxa. This broad distribution is consistent with a potentially evolutionary ancient origin for the snoRNAs. We identified the need for future work to determine whether the wide distribution of known snoRNPs associated with C/D box snoRNAs suggests as yet unknown RNA families within the archaea and whether a lack of an essential snoRNP for pseudouridylation in the DPANN superphylum indicates the absence of H/ACA box snoRNAs in those phyla.