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.2021 Dec 15;85(4):e0010421.
doi: 10.1128/MMBR.00104-21. Epub 2021 Nov 10.

The Peptidyl Transferase Center: a Window to the Past

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The Peptidyl Transferase Center: a Window to the Past

Madhan R Tirumalai et al. Microbiol Mol Biol Rev..

Abstract

In his 2001 article, "Translation: in retrospect and prospect," the late Carl Woese made a prescient observation that there was a need for the then-current view of translation to be "reformulated to become an all-embracing perspective about which 21st century Biology can develop" (RNA 7:1055-1067, 2001, https://doi.org/10.1017/s1355838201010615). The quest to decipher the origins of life and the road to the genetic code are both inextricably linked with the history of the ribosome. After over 60 years of research, significant progress in our understanding of how ribosomes work has been made. Particularly attractive is a model in which the ribosome may facilitate an ∼180° rotation of the CCA end of the tRNA from the A-site to the P-site while the acceptor stem of the tRNA would then undergo a translation from the A-site to the P-site. However, the central question of how the ribosome originated remains unresolved. Along the path from a primitive RNA world or an RNA-peptide world to a proto-ribosome world, the advent of the peptidyl transferase activity would have been a seminal event. This functionality is now housed within a local region of the large-subunit (LSU) rRNA, namely, the peptidyl transferase center (PTC). The PTC is responsible for peptide bond formation during protein synthesis and is usually considered to be the oldest part of the modern ribosome. What is frequently overlooked is that by examining the origins of the PTC itself, one is likely going back even further in time. In this regard, it has been proposed that the modern PTC originated from the association of two smaller RNAs that were once independent and now comprise a pseudosymmetric region in the modern PTC. Could such an association have survived? Recent studies have shown that the extant PTC is largely depleted of ribosomal protein interactions. It is other elements like metallic ion coordination and nonstandard base/base interactions that would have had to stabilize the association of RNAs. Here, we present a detailed review of the literature focused on the nature of the extant PTC and its proposed ancestor, the proto-ribosome.

Keywords: PTC; accretion model; evolutionary history; peptidyl transferase center; protein synthesis; ribosomes; translation.

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Figures

FIG 1
FIG 1
Fragment from the complete secondary structure of the LSU of Thermus thermophilus derived from crystallographic data (19), which contains the nucleotides within and around the PTC. Modified bases described in the text are marked with a red symbol in front of the corresponding base, “Ψ” for pseudouridine, “μ” for methylation, and “s” for 2-thiocytidine. Helix numbers are in large blue font, while position numbers are in smaller red font. (A) PTC residues mentioned throughout the text with a previously described functional role are highlighted within red circles. Details on functional role and/or implication for the ribosome activity are summarized in Table 1. As can be seen, PTC functional residues are not represented by a single contiguous chain of residues; instead, the PTC is formed from a diverse collection of distant residues that, when the RNA is folded into their tridimensional shape, act together as a catalytic unit, the PTC. (B) Conservation of the nucleobases within this fragment according to crystallographic data and corresponding alignments from Bernier et al. (275). This fragment comprises 282 nucleotides (nt). Red circles highlight those with 100% conservation (78 nt). Orange circles highlight those with 90 to 99.9% conservation (68 nt). Yellow and green circles highlight those with 70 to 89.9% and 50 to 69.9% conservation, respectively (52 and 49 nt). Thirty-five nucleotides from this fragment have shown less than 50% conservation.
FIG 2
FIG 2
Closeup view of PTC with P-site and A-site tRNAs associated. View of some of the nucleotides that coordinate the CCA end and the amino acid residue that is carried by the P-site and A-site tRNAs. P-site rRNA chain and residues are colored green, and A-site rRNA chain and residues are colored blue. P-site tRNA is colored orange, while A-site tRNA is colored yellow. The CCA end of P-site tRNA is mainly coordinated by the Watson and Crick (WC) base pairs of G2252:C74 and G2251:C75, while an A-minor interaction of A76 with A2450 from the P-site tRNA is established. Both P-site residues A2450 and A2451 are considered important to the transpeptidation reaction. The CCA end of A-site tRNA is mainly stabilized by WC base pair G2553:C75, while U2554 establishes a hydrogen bond with C74. A2583 creates an A-minor interaction with A76 from the A-site tRNA. The “rotatory motion” mechanism implies that the 3′ end of the tRNA passage moves in a helical motion of almost 180° coupled with peptide bond formation. The tRNA transitions from the A- to the P-site along a rotation axis and around U2585 and A2602. This figure was created from the crystal structure NCBI ID4WPO, using the PyMOL Molecular Graphics System, version 2.0 (Schrödinger, LLC).
FIG 3
FIG 3
Three-dimensional representation of the pseudosymmetrical region (SymR; Agmon et al. [250]) extracted from the Thermus thermophilus crystallographic structure (NCBI ID4WPO) using PyMOL (The PyMOL Molecular Graphics System, version 2.0; Schrödinger, LLC). The residues from the P-site and the A-site are colored green and blue, respectively. Residues delineating the entrance to the PTC pore are colored orange (P-site) and purple (A-site), as defined by Fox et al. (22). Sixteen conserved magnesium ions that are around the contact area of the SymR residues are shown as yellow spheres, as described by Rivas and Fox (68). Regions where the addition of fragments is required for the ligation of smaller fragments are highlighted by red numbers within red circles at the end of each helix, three at the P-site and one at the A-site. Also, the last residues of each ligation point are colored red. A secondary structure depiction of these elements is presented in Fig. 4.
FIG 4
FIG 4
Secondary structure of the pseudosymmetrical region (SymR; Agmon et al. [250]), derived from the LSU secondary structure of Thermus thermophilus (Petrov et al. [19]). A black dotted line indicates the boundary between the P-site and the A-site. Bases from the P-site are highlighted by green circles, and bases from the A-site are highlighted by blue circles. The orange (P-site) and purple (A-site) colored circles highlight residues that delineate the entrance to the exit pore of the PTC, as defined by Fox et al. (22). In order to dissect SymR from the extant ribosomal structure, one must artificially cut and anneal the four sites highlighted by red numbers within red circles, three at the P-site (H75, H80, and H89) and one at the A-site (H91). Also, the last residues of each ligation point are highlighted by red circles. Bases involved in the “rotatory motion” mechanism from the front and rear walls and the P- and A-loops are marked by a black plus symbol in front of each base according to Agmon et al. (251) and Bashan et al. (74, 256).
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References

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