N‐terminal domain, residues 1–91, of ribosomal protein TL5 from <i>Thermus thermophilus</i> binds specifically and strongly to the region of 5S rRNA containing loop E

Gongadze, G.M.; Meshcheryakov, V. A.; Serganov, Alexander; Fomenkova, N.P.; Mudrik, Elena S.; Jonsson, Bengt‐Harald; Liljas, Anders; Nikonov, S.V.; Garber, Maria

doi:10.1016/s0014-5793(99)00538-4

Cited by 18 publications

(17 citation statements)

References 31 publications

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“…The structural analysis of YbbR domains from Desulfitobacterium hafniense (35) revealed a striking similarity to the ribosomal protein L25. Because L25 proteins bind the 5 S ribosomal RNA (48,49), it is tempting to speculate that CdaR might also bind RNA and that this binding might in turn control the interaction with and activation of CdaA.…”

Section: Discussionmentioning

confidence: 99%

Cyclic Di-AMP Homeostasis in Bacillus subtilis

Mehne

Gunka

Eilers

et al. 2013

Journal of Biological Chemistry

186

171

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Section: Discussionmentioning

confidence: 99%

Cyclic Di-AMP Homeostasis in Bacillus subtilis

Mehne

Gunka

Eilers

et al. 2013

Journal of Biological Chemistry

186

171

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“…Loop E is present in a wide range of RNAs (Branch et al, 1985;Wimberly et al, 1993;Szewczak and Moore, 1995;Leontis and Westhof, 1998a) and functions as an important motif in RNA-RNA and RNA-protein interactions (Correll et al, 1997;Westhof, 1998a, 1998b;Gongadze et al, 1999;Hampel and Burke, 2001). This loop may contain submotifs (Leontis and Westhof, 1998c).…”

Section: A Viroid Motif Can Have Multiple Functionsmentioning

confidence: 99%

Inhibition of Cell Growth and Shoot Development by a Specific Nucleotide Sequence in a Noncoding Viroid RNA

Qi¹,

Ding²

2003

Plant Cell

129

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Viroids are small noncoding and infectious RNAs that replicate autonomously and move systemically throughout an infected plant. The RNAs of the family Pospiviroidae contain a central conserved region (CCR) that has long been thought to be involved in replication. Here, we report that the CCR of Potato spindle tuber viroid (PSTVd) also plays a role in pathogenicity. A U257A change in the CCR converted the intermediate strain PSTVd Int to a lethal strain that caused severe growth stunting and premature death of infected plants. PSTVd with nucleotide U257 changed to C or G did not cause such symptoms. The pathogenic effect of the U257A substitution was abolished by a C259U substitution in the same RNA. Analyses of the pathogenic effects of the U257A substitution in three other PSTVd variants established A257 as a new pathogenicity determinant that functions independently and synergistically with the classic pathogenicity domain. The U257A substitution did not alter PSTVd secondary structure, replication levels, or tissue tropism. The stunted growth of PSTVd Int U257A-infected tomato plants resulted from restricted cell expansion but not cell division or differentiation. This was correlated positively with the downregulated expression of an expansin gene, LeExp2 . Our results demonstrate that specific nucleotides in a noncoding, pathogenic RNA have a profound effect in altering distinct cellular responses, which then lead to well-defined alterations in plant growth and developmental patterns. The feasibility of correlating viroid RNA sequence/structure with the altered expression of specific host genes, cellular processes, and developmental patterns makes viroid infection a valuable system in which to investigate host factors for symptom expression and perhaps also to characterize the mechanisms of RNA regulation of gene expression in plants.

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“…Its RNA-binding N-terminal domain is homologous to E. coli L25. The isolated N-terminal fragment of TL5 (NfrTL5) 1 possesses the same 5 S rRNA binding ability as the full-size protein (14). The crystal structures of E. coli L25 and T. thermophilus TL5 complexed with virtually the same fragment of E. coli 5 S rRNA ( Fig.…”

mentioning

confidence: 99%

“…Beside L25, two other proteins of the CTC family were found in bacterial ribosomes, TL5 of T. thermophilus (12) and CTC of Deinococcus radiodurans (10). E. coli L25, T. thermophilus TL5, and D. radiodurans CTC specifically bind 5 S rRNA at the same site, the so-called loop E region (10,13,14). The stress protein CTC of B. subtilis was also shown to bind to the same site on 5 S rRNA (15).…”

mentioning

confidence: 99%

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The Crucial Role of Conserved Intermolecular H-bonds Inaccessible to the Solvent in Formation and Stabilization of the TL5·5 SrRNA Complex

Gongadze

Korepanov

Stolboushkina

et al. 2005

Journal of Biological Chemistry

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Analysis of the structures of two complexes of 5 S rRNA with homologous ribosomal proteins, Escherichia coli L25 and Thermus thermophilus TL5, revealed that amino acid residues interacting with RNA can be divided into two different groups. The first group consists of non-conserved residues, which form intermolecular hydrogen bonds accessible to solvent. The second group, comprised of strongly conserved residues, form intermolecular hydrogen bonds that are shielded from solvent. Site-directed mutagenesis was used to introduce mutations into the RNA-binding site of protein TL5. We found that replacement of residues of the first group does not influence the stability of the TL5⅐5 S rRNA complex, whereas replacement of residues of the second group leads to destabilization or disruption of the complex. Stereochemical analysis shows that the replacements of residues of the second group always create complexes with uncompensated losses of intermolecular hydrogen bonds. We suggest that these shielded intermolecular hydrogen bonds are responsible for the recognition between the protein and RNA.Abundant structural information on RNA⅐protein complexes has appeared during last five years (see for review Refs. 1-4). Thorough analysis of this information should contribute fundamentally toward understanding the principles of RNA⅐ protein recognition. In the present work the structures of two complexes of 5 S rRNA with homologous ribosomal proteins, Escherichia coli L25 (5) (PDB code 1DFU) and Thermus thermophilus TL5 (6) (PDB code 1FEU), have been analyzed. L25 and TL5 belong to the so-called CTC family of bacterial proteins. The first protein described under the CTC abbreviation was a general stress protein of Bacillus subtilis (7). Later the genes for homologous proteins were found in most of the sequenced bacterial genomes (8, 9). Among these proteins there are one-domain, two-domain, and even three-domain representatives (5, 6, 10, 11); all of them have a domain homologous to E. coli 5 S rRNA-binding ribosomal protein L25, which consists of only one domain (11). Beside L25, two other proteins of the CTC family were found in bacterial ribosomes, TL5 of T. thermophilus (12) and CTC of Deinococcus radiodurans (10). E. coli L25, T. thermophilus TL5, and D. radiodurans CTC specifically bind 5 S rRNA at the same site, the so-called loop E region (10,13,14). The stress protein CTC of B. subtilis was also shown to bind to the same site on 5 S rRNA (15). It was suggested that all CTC proteins could bind 5 S rRNA through a domain homologous to E. coli L25 (6).T. thermophilus ribosomal protein TL5 was discovered and investigated thoroughly by our group (12,14,16). It is a twodomain protein. Its RNA-binding N-terminal domain is homologous to E. coli L25. The isolated N-terminal fragment of TL5 (NfrTL5) 1 possesses the same 5 S rRNA binding ability as the full-size protein (14). The crystal structures of E. coli L25 and T. thermophilus TL5 complexed with virtually the same fragment of E. coli 5 S rRNA (Fig. 1) have been determined at a...

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N‐terminal domain, residues 1–91, of ribosomal protein TL5 from Thermus thermophilus binds specifically and strongly to the region of 5S rRNA containing loop E

Cited by 18 publications

References 31 publications

Cyclic Di-AMP Homeostasis in Bacillus subtilis

Cyclic Di-AMP Homeostasis in Bacillus subtilis

Inhibition of Cell Growth and Shoot Development by a Specific Nucleotide Sequence in a Noncoding Viroid RNA

The Crucial Role of Conserved Intermolecular H-bonds Inaccessible to the Solvent in Formation and Stabilization of the TL5·5 SrRNA Complex

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