We have noted an interesting correlation between optimal growth temperature of an archaeal species and the number of highly probable sRNAs that were identified by our search program. At one end of the spectrum is M. thermoautotrophicum (65C growth temperature) where no highly probable sRNAs were identified, and at the other end are the Pyrococcal species (100C growth temperature) where 50 or more sRNAs were identified. The remaining species with growth temperatures between these extremes produced intermediate numbers of candidate sRNAs. There are at least two explanations for this apparent correlation. First, higher growth temperatures may require a larger number of methylation modifications in order to efficiently fold, process, assemble or stabilize rRNA within ribosomal particles. The observation by Noon and colleagues [Noon et al., 1998] that the amount of rRNA methylation in S. solfataricus increases with increasing growth temperatures is consistent with this possibility. Second, it is possible that we systematically identified only a specific subset of highly uniform sRNAs that contain the characteristic features found in the cDNA clones isolated from S. acidocaldarius and used to define the parameters of our search program. If this is correct it may mean that the sRNA sequence/structure is more rigidly defined at higher growth temperatures; at lower growth temperatures where the sequence/structure requirements might be less stringent, our program would become less efficient in identifying sRNAs.
Do mesophilic and moderately thermophilic Archaeal species contain C/D box sRNAs? The answer is probably yes. The gene encoding the sRNA associated protein aFIB was first identified in two mesophilic Archaeal species, Methanococcus voltae and Methanococcus vannielii [Amiri, 1994], and both the aFIB and aNOP56 genes are present in the genome of the moderate thermophile, M. thermoautotrophicum. Indeed, our search of the M. jannaschii genome revealed other less probable candidate sRNAs; it seems likely that some of these candidates are legitimate sRNAs but independent conformation is required.