Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2013 May 1;41(10):5494-502.
doi: 10.1093/nar/gkt219. Epub 2013 Apr 10.

A universal RNA structural motif docking the elbow of tRNA in the ribosome, RNAse P and T-box leaders

Jean Lehmann  1 , Fabrice Jossinet, Daniel Gautheret
Affiliations

A universal RNA structural motif docking the elbow of tRNA in the ribosome, RNAse P and T-box leaders

Jean Lehmann et al. Nucleic Acids Res. .

Abstract

The structure and function of conserved motifs constituting the apex of Stem I in T-box mRNA leaders are investigated. We point out that this apex shares striking similarities with the L1 stalk (helices 76-78) of the ribosome. A sequence and structure analysis of both elements shows that, similarly to the head of the L1 stalk, the function of the apex of Stem I lies in the docking of tRNA through a stacking interaction with the conserved G19:C56 base pair platform. The inferred structure in the apex of Stem I consists of a module of two T-loops bound together head to tail, a module that is also present in the head of the L1 stalk, but went unnoticed. Supporting the analysis, we show that a highly conserved structure in RNAse P formerly described as the J11/12-J12/11 module, which is precisely known to bind the elbow of tRNA, constitutes a third instance of this T-loop module. A structural analysis explains why six nucleotides constituting the core of this module are highly invariant among all three types of RNA. Our finding that major RNA partners of tRNA bind the elbow with a same RNA structure suggests an explanation for the origin of the tRNA L-shape.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
Secondary structures of RNA elements displaying a crystallographically established (A and B) or a predicted (D) head-to-tail double T-loop module. T-loops are shown in red (first T-loop along the strand, T-loop 1) and blue (T-loop 2). The two residues preceding a T-loop are shown in orange (T-loop 1) and cyan (T-loop 2). The dotted lines show the (established of predicted) base pairs defining the core of the T-loop module (detailed in Figure 2B) and the functional platform (residues outlined with a circle). (A) B. subtilis L1 stalk (23S rRNA). The established structure and numbering are from the crystal structure of T. thermophilus 23S rRNA (pdb 1VSA) (9). (B) T. maritima RNAse P: region of the head-to-tail double T-loop module (P11–P14) (10,11). The tertiary interactions are from the crystal structure pdb 3Q1Q (12). (C) Sequence conservation encompassing the two T-loops of the structures in A, B and D: 1) L1 stalk (23S rRNA), 2) J11/12–J12/11 module of RNAse P and 3) apex of Stem I in T-box leaders. Sequence logos (highest value = 2 bits) were produced using the Weblogo interface (8) while using the following sequence alignments: 23S rRNA: primary alignments of 592 sequences from three phylogenetic domains, from the Comparative RNA Web site (13); bacterial RNAse P, class A: 340 sequences from the Ribonuclease P database (14); and T-box Stem I: alignment generated from 131 T-box sequences (‘Materials and Methods’ section). (D) B. subtilis tyrS T-box leader: apex of Stem I. Secondary structure (solid lines only) and base numbering according to (2).
Figure 2.
Figure 2.
Core structure of the head-to-tail double T-loop module. (A) Stereo view of the head-to-tail double T-loop module of 23S rRNA L1 stalk [pdb 3U4M (16)] and RNAse P [pdb 3Q1Q (12)]. (B) Core of the head-to-tail double T-loop module, involving the highly conserved AG..A and UG..A residues of the two T-loops (Figure 1C). The two base triple (Leontis/Westhof nomenclature), stacking on each other, are found in both 23S rRNA L1 stalk and RNAse P crystal structures. The structure on the right (pdb 3Q1Q) outlines the oxygen atoms of the hydroxyl groups of both A5′ and U5′ closing residues (shown as van der Waals spheres). The distance between this oxygen atom and A3′ N6 of the corresponding T-loop (dotted lines) is 8.78 Å (L1 stalk) and 9.25 Å (RNAse P) for the A5′–A3′ closing residues, and 6.13 Å (L1 stalk) and 5.46 Å (RNAse P) for the U5′–A3′ closing residues. The color code is identical to that of Figure 1.
Figure 3.
Figure 3.
Platform locations in the sequence pattern and 3D structure of the head-to-tail double T-loop module. (A) Sequence pattern of all known head-to-tail double T-loop module. The two potential (pot.) platforms are constituted by a base pair between the penultimate residue preceding one T-loop and the central residue of the other T-loop. Only one platform is functional in all known structures. (B) Platform–platform interaction between the functional platform of the head-to-tail double T-loop module of T. maritima RNAse P and the G19:C56 platform of the elbow of tRNAPhe [pdb 3Q1Q (12)]. The two T-loop motifs are related by a 2-fold rotation axis (shown at the center). The cyan residue of the shadow platform is included within P12 stem–loop (Figure 1B). The color code is identical to that of Figure 1.
Figure 4.
Figure 4.
Analysis of Stem I structures in T-box leaders. (A) Definition of structural parameters determined in 14 experimentally assessed T-box leaders (Supplementary Table S1). The secondary structure shown is from ProI Stem I, adapted from (22) (Stem Ia = 17, including a non-canonical motif and an E-loop; Stem Ib = 8; N1 = 2; N2 = 0; N3 = 6; N4 = 0). (B) Correlation between (Stem Ib + N4) and (N1 + N2). Note that N4 and N2 almost do not contribute to the correlation (Supplementary Table S1). (C) Apex of B. subtilis ProI Stem I model (‘Materials and Methods’ section), from top. The two curved arrows represent the main axes of the structural contributions of the parameters of the correlation in (B). The dotted double arrow indicates a possible adjustment of the orientation of the platform as a function of the parameters of the correlation in (B). (D) Distribution of the estimated length of Stem Ia. See Supplementary Table S1 for the method of estimation. (E) Improved model of the interaction between a tRNA and a T-box leader, with the head-to-tail double T-loop module constituting a wedge for the elbow of the tRNA. The color code is identical to that of Figure 1.
Figure 5.
Figure 5.
Crystallographically established (A) and model (B) of tRNA–RNA binding in which a stacking interaction between the G19:C56 base pair platform defining the elbow of a tRNA and a platform of a head-to-tail double T-loop module is involved. (A) L1 stalk–tRNA (pdb 1VSA) and RNAse P–pre-tRNA (pdb 3Q1Q) interactions. Only a fragment of RNAse P is shown. (B) Model of B. subtilis ProI Stem I–tRNA interaction (see ‘Materials and Methods’ section and Supplementary Data S2 and S3). The secondary structure of Stem I is shown in Figure 4A. A tRNAPhe (pdb 1EHZ) is shown instead of a tRNAPro (for which no structure is available). A final optimization of the contacts with this non-cognate tRNA was not realized, and Stem I was left in a slightly ‘open’ conformation. The color code is identical to that of Figure 1.
Figure 6.
Figure 6.
Universal contact regions of a canonical tRNA (left) and a mitochondrial tRNA (right). 1 = anticodon (contact through base pairing); 2 = acceptor arm (contact through base pairing); 3 = platform (contact through stacking). Adapted from (27) [see also (28)].
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Grundy FJ, Henkin TM. tRNA as a positive regulator of transcription antitermination in B. subtilis. Cell. 1993;74:475–482. - PubMed
    1. Gutiérrez-Preciado A, Henkin TM, Grundy FJ, Yanofsky C, Merino E. Biochemical features and functional implications of the RNA-based T-box regulatory mechanism. Microbiol. Mol. Biol. Rev. 2009;73:36–61. - PMC - PubMed
    1. Green NJ, Grundy FJ, Henkin TM. The T box mechanism: tRNA as a regulatory molecule. FEBS Lett. 2010;584:318–324. - PMC - PubMed
    1. Grundy FJ, Rollins SM, Henkin TM. Interaction between the acceptor end of tRNA and the T box stimulates antitermination in the Bacillus subtilis tyrS gene: a new role for the discriminator base. J. Bacteriol. 1994;176:4518–4526. - PMC - PubMed
    1. Rollins SM, Grundy FM, Henkin TM. Analysis of cis-acting sequence and structural elements required for antitermination of the Bacillus subtilis tyrS gene. Mol. Microbiol. 1997;25:411–421. - PubMed

Publication types