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The CCA-end of P-tRNA Contacts Both the Human RPL36AL and the A-site Bound Translation Termination Factor eRF1 at the Peptidyl Transferase Center of the Human 80S Ribosome.

Hountondji C, Bulygin K, Créchet JB, Woisard A, Tuffery P, Nakayama J, Frolova L, Nierhaus KH, Karpova G, Baouz S - Open Biochem J (2014)

Bottom Line: Surprisingly, we observed a crosslinked ternary complex containing the tRNA, eRF1 and RPL36AL crosslinked both to the aldehyde groups of tRNAox at the 2'- and 3'-positions of the ultimate A.We also demonstrated that, upon binding to the ribosomal A-site, eRF1 induces an alternative conformation of the ribosome and/or the tRNA, leading to a novel crosslink of tRNAox to another large-subunit ribosomal protein (namely L37) rather than to RPL36AL, both ribosomal proteins being labeled in a mutually exclusive fashion.Since the human 80S ribosome in complex with P-site bound tRNAox and A-site bound eRF1 corresponds to the post-termination state of the ribosome, the results represent the first biochemical evidence for the positioning of the CCA-arm of the P-tRNA in close proximity to both RPL36AL and eRF1 at the end of the translation process.

View Article: PubMed Central - PubMed

Affiliation: Sorbonne Universités UPMC Univ Paris 06, Unité de Recherche UPMC UR6 "Enzymologie de l'ARN", 2, Place Jussieu, F-75252 Paris Cedex 05, France.

ABSTRACT
We have demonstrated previously that the E-site specific protein RPL36AL present in human ribosomes can be crosslinked with the CCA-end of a P-tRNA in situ. Here we report the following: (i) We modeled RPL36AL into the structure of the archaeal ortholog RPL44E extracted from the known X-ray structure of the 50S subunit of Haloarcula marismortui. Superimposing the obtained RPL36AL structure with that of P/E tRNA observed in eukaryotic 80S ribosomes suggested that RPL36AL might in addition to its CCA neighbourhood interact with the inner site of the tRNA elbow similar to an interaction pattern known from tRNA•synthetase pairs. (ii) Accordingly, we detected that the isolated recombinant protein RPL36AL can form a tight binary complex with deacylated tRNA, and even tRNA fragments truncated at their CCA end showed a high affinity in the nanomolar range supporting a strong interaction outside the CCA end. (iii) We constructed programmed 80S complexes containing the termination factor eRF1 (stop codon UAA at the A-site) and a 2',3'-dialdehyde tRNA (tRNAox) analog at the P-site. Surprisingly, we observed a crosslinked ternary complex containing the tRNA, eRF1 and RPL36AL crosslinked both to the aldehyde groups of tRNAox at the 2'- and 3'-positions of the ultimate A. We also demonstrated that, upon binding to the ribosomal A-site, eRF1 induces an alternative conformation of the ribosome and/or the tRNA, leading to a novel crosslink of tRNAox to another large-subunit ribosomal protein (namely L37) rather than to RPL36AL, both ribosomal proteins being labeled in a mutually exclusive fashion. Since the human 80S ribosome in complex with P-site bound tRNAox and A-site bound eRF1 corresponds to the post-termination state of the ribosome, the results represent the first biochemical evidence for the positioning of the CCA-arm of the P-tRNA in close proximity to both RPL36AL and eRF1 at the end of the translation process.

No MeSH data available.


Reaction scheme of the Schiff base formation and its in situ reduction with sodium borohydride (NaBH4) or sodium cyanoborohydride (NaBH3CN). With both reducing agents, the overall crosslinking reaction is rate-limited by the formation of the imminium moiety, not by its in situ reduction.
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Figure 8: Reaction scheme of the Schiff base formation and its in situ reduction with sodium borohydride (NaBH4) or sodium cyanoborohydride (NaBH3CN). With both reducing agents, the overall crosslinking reaction is rate-limited by the formation of the imminium moiety, not by its in situ reduction.

Mentions: The strong increase of the crosslinking yields at pH 8.0 (Fig. 5B) prompted us to follow the crosslinking reaction between RPL36AL and [5’-32P]tRNAAsp75ox as a function of the pH of the incubation mixture. This truncated tRNAox species was previously found to crosslink to Lys-53 of RPL36AL through the formation of a reversible Schiff base between the ε-amino group of Lys-53 and the 2’, 3’ aldehyde groups of tRNAox [7]. Fig. (8) shows the formation of the reversible Schiff base and its irreversible reduction with sodium borohydride (NaBH4) or with sodium cyanoborohydride (NaBH3CN) [16]. The equilibrium of the Schiff base is frozen by reduction with sodium borohydride (NaBH4) which simultaneously reduces the Schiff base and the unreacted tRNA dialdehyde, while NaBH3CN is capable of continuously displacing this equilibrium by specifically reducing the imminium group and leaving intact the reacting 2’, 3’ aldehyde groups of tRNAox [16]. In the experiment of Fig. (5B), the strong reducing agent NaBH4 was preferred to the latter mild one, in order to trap the fraction of unprotonated reactive ε-amino group that is only responsible for the rate-limiting nucleophilic addition to the aldehyde to form the Schiff base (Fig. 8). Therefore, the crosslinking yield at a given pH in the presence of NaBH4 reflects the fraction of unprotonated reactive ε-amino groups.


The CCA-end of P-tRNA Contacts Both the Human RPL36AL and the A-site Bound Translation Termination Factor eRF1 at the Peptidyl Transferase Center of the Human 80S Ribosome.

Hountondji C, Bulygin K, Créchet JB, Woisard A, Tuffery P, Nakayama J, Frolova L, Nierhaus KH, Karpova G, Baouz S - Open Biochem J (2014)

Reaction scheme of the Schiff base formation and its in situ reduction with sodium borohydride (NaBH4) or sodium cyanoborohydride (NaBH3CN). With both reducing agents, the overall crosslinking reaction is rate-limited by the formation of the imminium moiety, not by its in situ reduction.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4150381&req=5

Figure 8: Reaction scheme of the Schiff base formation and its in situ reduction with sodium borohydride (NaBH4) or sodium cyanoborohydride (NaBH3CN). With both reducing agents, the overall crosslinking reaction is rate-limited by the formation of the imminium moiety, not by its in situ reduction.
Mentions: The strong increase of the crosslinking yields at pH 8.0 (Fig. 5B) prompted us to follow the crosslinking reaction between RPL36AL and [5’-32P]tRNAAsp75ox as a function of the pH of the incubation mixture. This truncated tRNAox species was previously found to crosslink to Lys-53 of RPL36AL through the formation of a reversible Schiff base between the ε-amino group of Lys-53 and the 2’, 3’ aldehyde groups of tRNAox [7]. Fig. (8) shows the formation of the reversible Schiff base and its irreversible reduction with sodium borohydride (NaBH4) or with sodium cyanoborohydride (NaBH3CN) [16]. The equilibrium of the Schiff base is frozen by reduction with sodium borohydride (NaBH4) which simultaneously reduces the Schiff base and the unreacted tRNA dialdehyde, while NaBH3CN is capable of continuously displacing this equilibrium by specifically reducing the imminium group and leaving intact the reacting 2’, 3’ aldehyde groups of tRNAox [16]. In the experiment of Fig. (5B), the strong reducing agent NaBH4 was preferred to the latter mild one, in order to trap the fraction of unprotonated reactive ε-amino group that is only responsible for the rate-limiting nucleophilic addition to the aldehyde to form the Schiff base (Fig. 8). Therefore, the crosslinking yield at a given pH in the presence of NaBH4 reflects the fraction of unprotonated reactive ε-amino groups.

Bottom Line: Surprisingly, we observed a crosslinked ternary complex containing the tRNA, eRF1 and RPL36AL crosslinked both to the aldehyde groups of tRNAox at the 2'- and 3'-positions of the ultimate A.We also demonstrated that, upon binding to the ribosomal A-site, eRF1 induces an alternative conformation of the ribosome and/or the tRNA, leading to a novel crosslink of tRNAox to another large-subunit ribosomal protein (namely L37) rather than to RPL36AL, both ribosomal proteins being labeled in a mutually exclusive fashion.Since the human 80S ribosome in complex with P-site bound tRNAox and A-site bound eRF1 corresponds to the post-termination state of the ribosome, the results represent the first biochemical evidence for the positioning of the CCA-arm of the P-tRNA in close proximity to both RPL36AL and eRF1 at the end of the translation process.

View Article: PubMed Central - PubMed

Affiliation: Sorbonne Universités UPMC Univ Paris 06, Unité de Recherche UPMC UR6 "Enzymologie de l'ARN", 2, Place Jussieu, F-75252 Paris Cedex 05, France.

ABSTRACT
We have demonstrated previously that the E-site specific protein RPL36AL present in human ribosomes can be crosslinked with the CCA-end of a P-tRNA in situ. Here we report the following: (i) We modeled RPL36AL into the structure of the archaeal ortholog RPL44E extracted from the known X-ray structure of the 50S subunit of Haloarcula marismortui. Superimposing the obtained RPL36AL structure with that of P/E tRNA observed in eukaryotic 80S ribosomes suggested that RPL36AL might in addition to its CCA neighbourhood interact with the inner site of the tRNA elbow similar to an interaction pattern known from tRNA•synthetase pairs. (ii) Accordingly, we detected that the isolated recombinant protein RPL36AL can form a tight binary complex with deacylated tRNA, and even tRNA fragments truncated at their CCA end showed a high affinity in the nanomolar range supporting a strong interaction outside the CCA end. (iii) We constructed programmed 80S complexes containing the termination factor eRF1 (stop codon UAA at the A-site) and a 2',3'-dialdehyde tRNA (tRNAox) analog at the P-site. Surprisingly, we observed a crosslinked ternary complex containing the tRNA, eRF1 and RPL36AL crosslinked both to the aldehyde groups of tRNAox at the 2'- and 3'-positions of the ultimate A. We also demonstrated that, upon binding to the ribosomal A-site, eRF1 induces an alternative conformation of the ribosome and/or the tRNA, leading to a novel crosslink of tRNAox to another large-subunit ribosomal protein (namely L37) rather than to RPL36AL, both ribosomal proteins being labeled in a mutually exclusive fashion. Since the human 80S ribosome in complex with P-site bound tRNAox and A-site bound eRF1 corresponds to the post-termination state of the ribosome, the results represent the first biochemical evidence for the positioning of the CCA-arm of the P-tRNA in close proximity to both RPL36AL and eRF1 at the end of the translation process.

No MeSH data available.