These supplemental tables and text were submitted with the original Science manuscript, and reflect the state of our annotations at the time of publication.
For the most current Archaeal predictions, annotation, and additional
information, see the main snoRNAdb website.
With the large collection of sRNA genes identified within the Pyrococcus genomes, we were able to assess their locations in the three species relative to protein coding genes and to each other. The sRNA genes are in general dispersed throughout the genome, and in only four cases are two genes located near each other. Three of the pairs are found near each other in all three genomes: sR14/sR22, sR2/sR9, sR12/sR34. All are on opposite strands and oriented away from each other. The distances between pairs ranged from a single nucleotide (Pho sR12/sR34) to 130 nt (Pfu sR2/sR9). The fourth pair, sR50/sR54, found only in P. furiosus, is on the same strand and separated by 34 nucleotides. This is the only possible candidate for a polycistronic sRNA transcript.
Pyrococcus sRNAs may be co-transcribed with mRNAs
Examination of the positions of the 51 P. horikoshii sRNA loci relative to protein coding regions revealed that 17 overlapped partially on the coding strand with annotated open reading frames (ORFs). Of these, eight occur at the 5' ends of protein ORFs. Based on the alignments of the proteins encoded by these ORFs with their homologs from the protein sequence data base, all eight appear to be artifacts resulting from incorrect assignment of translation initiation codons. In the nine cases where the overlap occurs at the 3' end of the protein ORFs, the overlaps extend varying distances into the 5' end of sRNA genes. Almost all sRNAs that do not overlap protein-coding regions were located on the coding strand very near ORF boundaries. It is unclear whether these overlapping and adjacent sRNA are salvaged from the intermediates of mRNA degradation or independently transcribed from their own promoters. A few sRNA genes appear to partially overlap coding regions on the opposite strand, but we found no cases of sRNAs completely within predicted protein ORFs.
We observed only one case where an sRNA was encoded completely within another gene: the Pyrococcus sR40 homologs reside in an intron in the anticodon loop of the gene encoding the tRNA-Trp. This intronic sequence, which exhibits all of the hallmark features of an archaeal sRNA, has been independently identified by Daniels and coworkers (personal communication; see main text).