NORMAL GENOMIC

• Russo G et al.
• Ribosomal protein L7a binds RNA through two distinct RNA-binding domains.
• Biochem J. 2005; 385: 289-99
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• The human ribosomal protein L7a is a component of the major ribosomalsubunit. We previously identified three nuclear-localization-competentdomains within L7a, and demonstrated that the domain defined by aa (aminoacids) 52-100 is necessary, although not sufficient, to target the L7aprotein to the nucleoli. We now demonstrate that L7a interacts in vitrowith a presumably G-rich RNA structure, which has yet to be defined. Wealso demonstrate that the L7a protein contains two RNA-binding domains:one encompassing aa 52-100 (RNAB1) and the other encompassing aa 101-161(RNAB2). RNAB1 does not contain any known nucleic-acid-binding motif, andmay thus represent a new class of such motifs. On the other hand, aspecific region of RNAB2 is highly conserved in several other proteincomponents of the ribonucleoprotein complex. We have investigated thetopology of the L7a-RNA complex using a recombinant form of the proteindomain that encompasses residues 101-161 and a 30mer poly(G)oligonucleotide. Limited proteolysis and cross-linking experiments, andmass spectral analyses of the recombinant protein domain and its complexwith poly(G) revealed the RNA-binding region.

• Robert F, Brakier-Gingras L
• Ribosomal protein S7 from Escherichia coli uses the same determinants tobind 16S ribosomal RNA and its messenger RNA.
• Nucleic Acids Res. 2001; 29: 677-82
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• Ribosomal protein S7 from Escherichia coli binds to the lower half of the3' major domain of 16S rRNA and initiates its folding. It also binds toits own mRNA, the str mRNA, and represses its translation. Using filterbinding assays, we show in this study that the same mutations thatinterfere with S7 binding to 16S rRNA also weaken its affinity for itsmRNA. This suggests that the same protein regions are responsible for mRNAand rRNA binding affinities, and that S7 recognizes identical sequenceelements within the two RNA targets, although they have dissimilarsecondary structures. Overexpression of S7 is known to inhibit bacterialgrowth. This phenotypic growth defect was relieved in cells overexpressingS7 mutants that bind poorly the str mRNA, confirming that growthimpairment is controlled by the binding of S7 to its mRNA. Interestingly,a mutant with a short deletion at the C-terminus of S7 was moredetrimental to cell growth than wild-type S7. This suggests that theC-terminal portion of S7 plays an important role in ribosome function,which is perturbed by the deletion.

• Simonsen E, Perez-Urdaniz A
• S4.The borderline concept from an international perspective.
• Eur Psychiatry. 2000; 15: 48-51

• Sapag A, Draper DE
• In vitro evolution used to define a protein recognition site within alarge RNA domain.
• Bioorg Med Chem. 1997; 5: 1097-105
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• A minimum of 460 nucleotides of 16S ribosomal RNA are needed to fold thetarget site for E. coli ribosomal protein S4, although a much smallerregion within this large domain is protected from chemical reagents by theprotein. Starting with a 531-nucleotide tRNA fragment, cycles ofmutagenesis, selection with S4, and amplification ('in vitro evolution')were used to obtain a pool of 30 RNA sequences selected for S4 recognitionbut approximately 30% different from wild type. Numerous compensatory basepair changes have largely preserved the same secondary structure amongthese RNAs as found in wild-type sequences. A 20-base deletion and asingle nucleotide insertion are among several unusual features found inmost of the selected sequences and also prevalent among other prokaryoticrRNAs. Most of the compensatory base changes and selected features arelocated outside of the region protected by S4 from chemical reagents. Itwas unexpected that S4 would select for RNA structures throughout such alarge domain; the selected features are probably contributing indirectlyto S4 recognition by promoting correct tertiary folding of the regionactually contacted by S4. The role of S4 may be to stabilize this domain(nearly one-third of the 16S rRNA) in its proper conformation for ribosomefunction.