Homologs of Small Nucleolar RNAs in Archaea

Abstract

In eukaryotes, dozens of posttranscriptional modifications are directed to specific nucleotides in ribosomal RNAs (rRNAs) by small nucleolar RNAs (snoRNAs). We identified homologs of snoRNA genes in both branches of the Archaea. Eighteen small sno-like RNAs (sRNAs) were cloned from the archaeon Sulfolobus acidocaldarius by coimmunoprecipitation with archaeal fibrillarin and NOP56, the homologs of eukaryotic snoRNA-associated proteins. We trained a probabilistic model on these sRNAs to search for more sRNAs in archaeal genomic sequences. Over 200 additional sRNAs were identified in seven archaeal genomes representing both the Crenarchaeota and the Euryarchaeota. snoRNA-based rRNA processing was therefore probably present in the last common ancestor of Archaea and Eukarya, predating the evolution of a morphologically distinct nucleolus.

Kink turn sRNA folding upon L7Ae binding using molecular dynamics simulations

“…[11][12][13][14] L7Ae protein binds directly to box C/D elements, 8,14 Nop5p binds to L7Ae, and fibrillarin serves as the core catalytic component. [15][16][17] This conserved structure is homologous to the box C/D snoRNP in eukaryotes, 16 which contains a K-turn snoRNA and four protein components. 18,19 Both sRNA and protein components are required in the methylation process.…”

On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells

“…The evolutionary basis for the fundamental differences that distinguish eubacteria and archaebacteria, but which more or less uniformly unite the respective groups, could be sought in the age of biochemical discovery during the persistence of proto-eubacterial and protoarchaebacterial lineages living within the confines of their energy-laden mineral incubator. Such differences would include their use of many fundamentally different cofactors such as pterin derivatives versus tetrahydrofolate, coenzyme B, methanofuran, coenzyme F420, coenzyme M and cobamids in many archaebacteria (see DiMarco et al 1990;Thauer 1998;White 2001), their use of different pathways for the same metabolic intermediates such as IPP (Lange et al 2000) or their differences in purine biosynthesis (White 1997), their use (archaebacteria) or disuse (eubacteria) of small nucleolar RNAs for the modification of ribosomes (Omer et al 2000), the differences between their DNA maintenance and repair machineries (Tye 2000), the differences between their transcriptional regulatory apparatus (Thomm 1996;Bell et al 2001) and RNA polymerases (Langer et al 1995;Bell & Jackson 1998), their quinones (Schü tz et al 2000;Berry 2002), or, and what is probably the most important point for this paper, the differences between their membrane lipid biosynthetic pathways and cell-wall constituents (Kandler 1982). Many other such differences could be listed.…”

Circular box C/D RNAs in Pyrococcus furiosus

“…In other cases, linear box C͞D RNAs are processed from mono-or polycistronic transcripts synthesized from independent promoters. Box C͞D RNAs were found only recently in archaea (12,13). The pathway by which archaeal box C͞D RNAs are made is unknown.…”

“…The pathway by which archaeal box C͞D RNAs are made is unknown. The archaeal box C͞D RNAs are located primarily in intergenic regions of the genome, sometimes overlapping the 3Ј or 5Ј end of flanking ORFs (1,4,12,13). Independent promoters have not been identified.…”