A vestige of a prebiotic bonding machine is functioning within the contemporary ribosome

Krupkin, Miri; Matzov, Donna; Tang, Hua; Metz, Markus; Kalaora, Rinat; Belousoff, Matthew J.; Zimmerman, Ella; Bashan, Anat; Yonath, Ada

doi:10.1098/rstb.2011.0146

Cited by 56 publications

(49 citation statements)

References 32 publications

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“…We identified a region around the peptide bond formation site that contains a geometrical twofold rotational symmetry. This small universal region (3-4% of the prokaryotic and eukaryotic ribosomes, respectively), in an otherwise gigantic, completely unsymmetrical molecular machine, has been suggested to be a protoribosome precursor (1)(2)(3). We assume necessary (although not sufficient) conditions that a true protoribosome must be minimally capable of include (i) energetic structural stability and (ii) energetic stable attachment to substrates that can ultimately lead to formation of peptide bonds needed for production of proteins.…”

Section: Discussionmentioning

confidence: 99%

“…which may have evolved and emerged from an RNA world before a subsequent evolution into the modern protein/nucleic acid world, has been reported (1)(2)(3). In contemporary cells the ribosomes translate the genetic information (stored in the DNA) into proteins.…”

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confidence: 99%

“…Aptly referred to as the protein factory of all living cells, the ribosome is essential to the contemporary life, and its activity may have been crucial to the formation of life itself. Structural analysis identified an internal RNA region that exists in all known structures (1)(2)(3)(4)(5) and has universally conserved sequence (1), which contains the site of peptide bond formation, and thus may well be that of a remaining RNA world entity. Consistent with the findings that the main ribosomal functions-namely, the decoding of the genetic code, the formation of peptide bonds, and the creation of elongating proteins-are performed by ribosomal RNA and with the universality of this region among all kingdoms of life, we proposed that this region is a remnant of a prebiotic chemical entity with catalytic capabilities, and called it the "protoribosome."…”

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confidence: 99%

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Protoribosome by quantum kernel energy method

Huang

Krupkin

Bashan

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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Experimental evidence suggests the existence of an RNA molecular prebiotic entity, called by us the "protoribosome," which may have evolved in the RNA world before evolution of the genetic code and proteins. This vestige of the RNA world, which possesses all of the capabilities required for peptide bond formation, seems to be still functioning in the heart of all of the contemporary ribosome. Within the modern ribosome this remnant includes the peptidyl transferase center. Its highly conserved nucleotide sequence is suggestive of its robustness under diverse environmental conditions, and hence on its prebiotic origin. Its twofold pseudosymmetry suggests that this entity could have been a dimer of self-folding RNA units that formed a pocket within which two activated amino acids might be accommodated, similar to the binding mode of modern tRNA molecules that carry amino acids or peptidyl moieties. Using quantum mechanics and crystal coordinates, this work studies the question of whether the putative protoribosome has properties necessary to function as an evolutionary precursor to the modern ribosome. The quantum model used in the calculations is density functional theory-B3LYP/3-21G*, implemented using the kernel energy method to make the computations practical and efficient. It occurs that the necessary conditions that would characterize a practicable protoribosome-namely (i) energetic structural stability and (ii) energetically stable attachment to substrates-are both well satisfied.bonding apparatus | puromycin | interaction energy | self-assembly | chemical model

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Section: Discussionmentioning

confidence: 99%

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confidence: 99%

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Protoribosome by quantum kernel energy method

Huang

Krupkin

Bashan

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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“…Our proposal is an alternative to nowadays largely consensual RNA world hypothesis (Gilbert, 1986, Lilley, 2011, Krupkin et al, 2011. It is a metabolism first hypothesis (Kurland, 2010, Zaia andZaia, 2008), related to de Duve's thiolester world (De Duve, 2003), and somehow linked to Sutherland's cyanosulfidic protometabolism (Patel et al, 2015), also to Carter's urzyme theory (Li et al, 2013).…”

Section: Biological Considerationsmentioning

confidence: 99%

At the very beginning of life on Earth: the thiol-rich peptide (TRP) world hypothesis

Vallée¹,

Shalayel²,

Ly³

et al. 2017

Int. J. Dev. Biol.

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Life developed on Earth probably about 3.8 billion years ago, on a planet that was already largely covered by oceans and where the atmosphere was very humid. The reactions, which may have led to the formation of the first polymers, particularly to the first peptides and nucleic acids, must have been compatible with these conditions. This is the case of the reaction of nitriles with aminothiols, such as cysteine and homocysteine. Since aminonitriles are the probable precursors of amino acids, this condensation reaction has been able to rapidly yield dipeptides, tripeptides, oligomers and even true polymers, each containing thiol functions. These thiol-rich peptides (TRP's) would then have assumed the various catalytic roles that the peptides containing cysteine residues play today. They allowed a rapid bloom of life in the primitive ocean. In this scenario, RNA's are not the first polymers, but have been synthesized, like DNA's, thanks to the catalytic properties of thiols in a mostly TRP world. In this world, due to its ability to form a thiolactone, homocysteine may have played the leading role in enabling the previously formed oligomers to be stappled together, thus accelerating the formation of long peptide chains.

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“…The roles during evolution of these two nucleic acids are not clear, but what is definite is that double-stranded DNA, which is much less susceptible to mutation and chemical change than RNA, took over as the carrier of genetic information. Whether stress at an early time of evolution led to the multiple roles of RNA cannot be said, but the variety of RNA structures and the possibility of a primitive ribosome (Krupkin et al 2011) and catalytic RNAs are an indication that RNA led the charge to more modern biochemistry and, recognizable to us, new organisms. …”

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confidence: 99%

The RNA–Protein World

Altman

2013

RNA

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Following the naming of the RNA World for the hypothetical biochemical world during very early life forms, the current world was named the Protein World. However, the astonishing high level of transcripts from virtually all chromosomes in an organism now found in eucaryotes, as well as their extensive roles in regulating gene expression, suggests that today's world should be labeled as the RNA-Protein World.

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A vestige of a prebiotic bonding machine is functioning within the contemporary ribosome

Cited by 56 publications

References 32 publications

Protoribosome by quantum kernel energy method

Protoribosome by quantum kernel energy method

At the very beginning of life on Earth: the thiol-rich peptide (TRP) world hypothesis

The RNA–Protein World

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