Modifications of ribosomal RNA: From enzymes to function
Modified nucleosides are present in all kinds of stable RNA molecules, tRNAs being particularly rich in them (Auffinger and Westhof, 1998). Ribosomal RNA (rRNA) from all organisms contains modifications, and there is a correlation between the overall comp
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Petr V. Sergiev, Anna Y. Golovina, Irina V. Prokhorova, Olga V. Sergeeva, Ilya A. Osterman, Mikhail V. Nesterchuk, Dmitry E. Burakovsky, Alexey A. Bogdanov, Olga A. Dontsova
1. Introduction Modified nucleosides are present in all kinds of stable RNA molecules, tRNAs being particularly rich in them (Auffinger and Westhof, 1998). Ribosomal RNA (rRNA) from all organisms contains modifications, and there is a correlation between the overall complexity of an organism and the number of modified nucleosides in its rRNA. The rRNA of the most primitive bacteria, such as some Mycoplasma species, may possess only 14 modified nucleosides (de Crécy-Lagard et al., 2007). In Escherichia coli, there are 36 modified nucleosides in rRNA (Table I). Yeast ribosomes possess about one hundred rRNA modifications, human rRNA over two hundred (Ofengand and Fournier, 1998; Decatur and Fournier, 2002). Eukaryotes and archaea use snoRNA guided rRNA modification mechanism. This mechanism allows archaea and eukarya to use a limited number of modification enzymes, mainly pseudouridine synthase and 2’-Omethyltransferase to introduce the majority of their rRNA modifications (Decatur and Fournier, 2002). By contrast, bacteria have developed specific enzymes for each one of the (fewer) modifications they have. Nevertheless, there are many different rRNA modifications in bacteria. Despite intensive study for several decades, many open questions remain regarding the functional role of modified rRNA nucleosides. In this review we will focus on rRNA modifications in E. coli and discuss their possible functions. Even before high-resolution structures of ribosomal subunits (Ban et al., 2000; Schluenzen et al., 2000; Wimberly et al., 2000) or the entire ribosome (Yusupov et al., 2001; Schuwirth et al., 2005) and its functional complexes (Ogle et al., 2002; Yusupova et al., 2006; Schmeing et al., 2009; Gao et al., 2009) were determined, it was known that modified nucleosides are M. V. Rodnina et al. (eds.), Ribosomes © Springer-Verlag/Wien 2011
concentrated in the functional centers of the ribosome (Brimacombe et al., 1993). Now, the positions of rRNA modifications can be precisely mapped on the threedimensional structure of the ribosome (Figure 1), and it is clearly seen that modified nucleosides are concentrated around the mRNA, the tRNAs in A and P sites, the peptidyl transferase center, the peptide exit tunnel, and on both sides of intersubunit bridges. The concentration of modified nucleosides in the functionally most important regions of the ribosome indicate their important functional role (Brimacombe et al., 1993). Since reconstitution techniques for both subunits of bacterial ribosomes were established, it was possible
Fig. 1 Spatial distribution of modified nucleosides in the bacterial ribosome. The molecular surface of small and large ribosomal subunits are shown in yellow and blue, respectively and signed. Methylated nucleosides are depicted in red, pseudouridines in blue. Other modified bnucleosides are depicted in green. Ribosomal functi
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