Ribosome origins: The relative age of 23S rRNA Domains

Hury, James; Nagaswamy, Uma; Larios‐Sanz, Maia; Fox, George E.

doi:10.1007/s11084-006-9011-z

Cited by 37 publications

(31 citation statements)

References 24 publications

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“…There is a consensus that some parts of the ribosome are even older than LUCA, predating the protein world. Parts of Domain V of the 23S rRNA are believed to be among the most ancient parts of the ribosome (Woese 2001;Wolf and Koonin 2007;Smith et al 2008;Bokov and Steinberg 2009;Belousoff et al 2010;Fox 2010) while Domain III is thought to be a more recent addition (Hury et al 2006). The data presented here support the hypothesis that Domain III was added as an intact entity to the ancestral ribosome-assuming that the 3D domain is a unit of ribosomal evolution.…”

Section: Evolutionary Implications Of the Domain Structure Of The Domsupporting

confidence: 69%

Domain III of the T. thermophilus 23S rRNA folds independently to a near-native state

Athavale¹,

Gossett²,

Hsiao³

et al. 2012

RNA

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The three-dimensional structure of the ribosomal large subunit (LSU) reveals a single morphological element, although the 23S rRNA is contained in six secondary structure domains. Based upon maps of inter-and intra-domain interactions and proposed evolutionary pathways of development, we hypothesize that Domain III is a truly independent structural domain of the LSU. Domain III is primarily stabilized by intra-domain interactions, negligibly perturbed by inter-domain interactions, and is not penetrated by ribosomal proteins or other rRNA. We have probed the structure of Domain III rRNA alone and when contained within the intact 23S rRNA using SHAPE (selective 29-hydroxyl acylation analyzed by primer extension), in the absence and presence of magnesium. The combined results support the hypothesis that Domain III alone folds to a near-native state with secondary structure, intra-domain tertiary interactions, and inter-domain interactions that are independent of whether or not it is embedded in the intact 23S rRNA or within the LSU. The data presented support previous suggestions that Domain III was added relatively late in ribosomal evolution.

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Section: Evolutionary Implications Of the Domain Structure Of The Domsupporting

confidence: 69%

Domain III of the T. thermophilus 23S rRNA folds independently to a near-native state

Athavale¹,

Gossett²,

Hsiao³

et al. 2012

RNA

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“…The secondary structure of the large rRNA reveals the presence of six domains in the RNA with the PTC being located in Domain V. Hury et al (2006) argue that interconnectivity among distant regions can provide insight to historical timing. The argument is that older regions would have more time to be integrated into the structure and hence would show greater connectivity to other regions than newer additions.…”

Section: Evolution Of the Large Ribosomal Rnamentioning

confidence: 98%

“…The core areas of the structure are again the PTC by assumption, the same portions of Domain II (region 2.1 in red on Fig. 2) and parts of Domain 4 as seen by Hury et al (2006). However, in the context of studies of ribosome evolution, a hierarchical organization is useful in that it offers the potential for organizing diverse data into a single framework.…”

Section: Evolution Of the Large Ribosomal Rnamentioning

confidence: 99%

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Origin and Evolution of the Ribosome

Fox¹

2010

Cold Spring Harbor Perspectives in Biology

212

186

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The modern ribosome was largely formed at the time of the last common ancestor, LUCA. Hence its earliest origins likely lie in the RNA world. Central to its development were RNAs that spawned the modern tRNAs and a symmetrical region deep within the large ribosomal RNA, (rRNA), where the peptidyl transferase reaction occurs. To understand pre-LUCA developments, it is argued that events that are coupled in time are especially useful if one can infer a likely order in which they occurred. Using such timing events, the relative age of various proteins and individual regions within the large rRNA are inferred. An examination of the properties of modern ribosomes strongly suggests that the initial peptides made by the primitive ribosomes were likely enriched for L-amino acids, but did not completely exclude D-amino acids. This has implications for the nature of peptides made by the first ribosomes. From the perspective of ribosome origins, the immediate question regarding coding is when did it arise rather than how did the assignments evolve. The modern ribosome is very dynamic with tRNAs moving in and out and the mRNA moving relative to the ribosome. These movements may have become possible as a result of the addition of a template to hold the tRNAs. That template would subsequently become the mRNA, thereby allowing the evolution of the code and making an RNA genome useful. Finally, a highly speculative timeline of major events in ribosome history is presented and possible future directions discussed.

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“…It is, in fact, the only pore that is found in what are regarded as the most ancient areas of the 23S rRNA, The other 23S rRNA pores are all in regions of the RNA that are relatively recent additions to the structure (Hury et al 2006;Bokov and Steinberg 2009;Hsiao et al 2009;Fox 2010). The unique nature of the PTC pore may reflect a history of being created by hybridization between two or more RNAs in an RNA world rather than simple folding of a single RNA (Davidovich et al 2009;Fox et al 2012).…”

Section: Rna Poresmentioning

confidence: 99%

Nanometer scale pores similar in size to the entrance of the ribosomal exit cavity are a common feature of large RNAs

Rivas

Tran

Fox

2013

RNA

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The highly conserved peptidyl transferase center (PTC) of the ribosome contains an RNA pore that serves as the entrance to the exit tunnel. Analysis of available ribosome crystal structures has revealed the presence of multiple additional well-defined pores of comparable size in the ribosomal (rRNA) RNAs. These typically have dimensions of 1-2 nm, with a total area of ∼100 Å 2 or more, and most are associated with one or more ribosomal proteins. The PTC example and the other rRNA pores result from the packing of helices. However, in the non-PTC cases the nitrogenous bases do not protrude into the pore, thereby limiting the potential for hydrogen bonding within the pore. Instead, it is the RNA backbone that largely defines the pore likely resulting in a negatively charged environment. In many but not all cases, ribosomal proteins are associated with the pores to a greater or lesser extent. With the exception of the PTC case, the large subunit pores are not found in what are thought to be the evolutionarily oldest regions of the 23S rRNA. The unusual nature of the PTC pore may reflect a history of being created by hybridization between two or more RNAs early in evolution rather than simple folding of a single RNA. An initial survey of nonribosomal RNA crystal structures revealed additional pores, thereby showing that they are likely a general feature of RNA tertiary structure.

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Ribosome origins: The relative age of 23S rRNA Domains

Cited by 37 publications

References 24 publications

Domain III of the T. thermophilus 23S rRNA folds independently to a near-native state

Domain III of the T. thermophilus 23S rRNA folds independently to a near-native state

Origin and Evolution of the Ribosome

Nanometer scale pores similar in size to the entrance of the ribosomal exit cavity are a common feature of large RNAs

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