Given that ribosomes are one of the most important cellular macromolecular machines, it is not surprising that there is intensive research in ribosome biogenesis. Ribosome biogenesis is a complex process. The maturation of ribosomal RNAs (rRNAs) requires not only the precise cleaving and folding of the pre-rRNA but also extensive nucleotide modifications. At the heart of the processing and modifications of pre-rRNAs in Archaea and Eukarya are ribonucleoprotein (RNP) machines. They are called small RNPs (sRNPs), in Archaea, and small nucleolar RNPs (snoRNPs), in Eukarya. Studies on ribosome biogenesis originally focused on eukaryotic systems. However, recent studies on archaeal sRNPs have provided important insights into the functions of these RNPs. This paper will introduce archaeal rRNA gene organization and pre-rRNA processing, with a particular focus on the discovery of the archaeal sRNP components, their functions in nucleotide modification, and their structures. 1. Introduction Without ribosomes, cells cannot grow and divide. Thus, it is not surprising that ribosomes have been selectively conserved through millennia and are one of the few macromolecular machines present in all three domains of life. Having been under such tight selective pressure, ribosomes have been and continue to be used in establishing phylogenetic relationships through one specific component, the 16S rRNA in Bactria and Archaea and the 18S rRNA in Eukarya [1–3]. This led scientists to uncover that instead of only “prokaryotes” and “eukaryotes,” there is an additional third domain that would become the Archaea [4, 5]. Ribosome biogenesis and processing begins with ribosomal gene organization. This paper will cover both the genome organization of various rRNA operons in Archaea as well as the small ribonucleoproteins (sRNPs) responsible for chemical modification of nucleotides on the rRNA. In particular, the two most abundant types of chemical modifications are mediated by box C/D and box H/ACA sRNPs. It is not yet well understood why these nucleotides are chemically modified. In considering these modifications of rRNA, it is first important to understand why ribosomes are essential, how Archaea are unique, and how their ribosomal RNA loci are organized in the genome. 2. Ribosomes and rRNA Ribosomes are essential for the translation of mRNA into a polypeptide chain that is then folded into a functional protein [6]. These cellular machines are not only comprised of rRNA (transcribed from ribosomal DNA, rDNA), but also a number of ribosomal proteins that are required for the
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