Ribozyme Engineering and Early Evolution

Landweber, Laura F.; Simon, Peter J.; Wagner, Thor A.

doi:10.2307/1313134

Cited by 32 publications

(17 citation statements)

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“…Szathmáry 32,33 has proposed a way to evolve novel aptamers in vitro, which was realized many times over the next decade. The success of the SELEX technique 34 to obtain ribozymes for many important reactions convincingly demonstrates that RNA can have a rich catalytic repertoire [35][36][37][38][39] . All types of reactions necessary for nucleotide and peptide syntheses can be catalyzed by such ribozymes 36 .…”

Section: Hypercyclesmentioning

confidence: 99%

The dynamics of the RNA world: insights and challenges

Kun

Szilágyi

Könnyű

et al. 2015

Annals of the New York Academy of Sciences

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The problem of the origin of life is not only one of structure but also that of dynamics. Ever since the seminal result of Manfred Eigen in 1971 showing that early template replication suffers from an error threshold, research has tackled the issue of how early genomes could have been dynamically stable without highly evolved mechanisms such as accurate replication and chromosomes. We review the theory of the origin, maintenance and enhancement of the RNA world as an evolving population of dynamical systems. Investigation of sequence space has revealed how structures are allocated in sequence space and how this affects the nature of the error threshold that sets the selectively maintainable genome length. New applications of old dynamical theory are still possible: the application of Gause's principle of competitive exclusion, based on resource utilisation, to RNA replication predicts that at most four pairs (plus and minus strands) can stably be maintained on four nucleotides. Other mechanisms of early template coexistence should be regarded as additional means to raise the number of coexisting species above the number set by the competitive exclusion principle. One such example is the hypercycle in which templates were postulated to help replication of the next member in a cycle superimposed on individual replication cycles. Although the hypercycle is ecologically unstable it is evolutionarily unstable because it cannot efficiently compete against emerging parasites. Population structure can modify this conclusion but not without further qualification. The simplest form of population structure is limited diffusion on a surface. This simple mechanism can ensure the coexistence of competing ribozymes contributing to surface metabolism as well as the spread of efficient replicases despite the parasite problem. Hypercyclescan only be saved by active compartmentalization when replicators are enclosed in reproducing protocells. Once there are protocells there is no need for internal hypercyclic organization, however. Finally we review two crucial adaptations that enhanced the RNA world: chromosomes and enzymatic metabolism. Interestingly, it was shown that these two have been presumably coevolutionarily linked because protocells harbouring unlinked, competing ribozymes are better off if the ribozymes remain inefficient but generalists. The appearance of chromosomes alleviates intragenomic conflict and is enabling constraint for the emergence of specific and efficient enzymes.The possibility of an RNA world, a period in the origin of life on Earth, when RNA molecules acted both as enzymes and as genetic material, was suggested well before the name was coined by Gilbert in 1986 1 . The history of the research on the origin of life 2 tells us that the potential prebiotic importance of RNA was suggested as early as in the late 50's. When it became established that living cells harbour much more RNA than DNA some biologist have proposed that RNA preceded DNA during evolution 3,4 . The discovery of the details of protein ...

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Section: Hypercyclesmentioning

confidence: 99%

The dynamics of the RNA world: insights and challenges

Kun

Szilágyi

Könnyű

et al. 2015

Annals of the New York Academy of Sciences

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“…The ability of directed evolution and ribozyme engineering to evoke secondary activities of group I variants such as cleavage of aminoacyl ester or amide bonds (5-7; reviewed in ref. 8) suggests that RNA has an intrinsic capacity to adapt to novel contexts or substrates, although in these cases the acquisition of new catalytic activity was aided by careful design of the substrate to mimic the natural phosphodiester bond.…”

mentioning

confidence: 99%

Emergence of a dual-catalytic RNA with metal-specific cleavage and ligase activities: The spandrels of RNA evolution

Landweber

Pokrovskaya

1999

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

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In vitro selection, or directed molecular evolution, allows the isolation and amplification of rare sequences that satisfy a functional-selection criterion. This technique can be used to isolate novel ribozymes (RNA enzymes) from large pools of random sequences. We used in vitro evolution to select a ribozyme that catalyzes a novel template-directed RNA ligation that requires surprisingly few nucleotides for catalytic activity. With the exception of two nucleotides, most of the ribozyme contributes to a template, suggesting that it is a general prebiotic ligase. More surprisingly, the catalytic core built from randomized sequences actually contains a 7-nt manganese-dependent self-cleavage motif originally discovered in the Tetrahymena group I intron. Further experiments revealed that we have selected a dual-catalytic RNA from random sequences: the RNA promotes both cleavage at one site and ligation at another site, suggesting two conformations surrounding at least one divalent metal ion-binding site. Together, these results imply that similar catalytic RNA motifs can arise under fairly simple conditions and that multiple catalytic structures, including bifunctional ligases, can evolve from very small preexisting parts. By breaking apart and joining different RNA strands, such ribozymes could have led to the production of longer and more complex RNA polymers in prebiotic evolution.The in vitro selection of functional RNA molecules from random sequence pools has successfully isolated far more classes of ribozymes than have yet been found in nature. The classic experiment (1) revealed an abundance of RNA ligase ribozymes in a random sampling of 10 15 unique sequences. The first experiments to probe in vitro evolution of ribozymes searched for improved or altered versions of the naturally occurring Tetrahymena group I ribozyme. For example, Green et al. (2) used in vitro evolution to restore and to improve activity of a pool of molecules based on the Tetrahymena group I intron, whereas Joyce and colleagues subsequently isolated variants of the group I ribozyme that performed subtly different tasks, such as cleavage of a DNA substrate (3) or acquisition of a novel dependency on a specific divalent metal cation (4). The ability of directed evolution and ribozyme engineering to evoke secondary activities of group I variants such as cleavage of aminoacyl ester or amide bonds (5-7; reviewed in ref. 8) suggests that RNA has an intrinsic capacity to adapt to novel contexts or substrates, although in these cases the acquisition of new catalytic activity was aided by careful design of the substrate to mimic the natural phosphodiester bond.In this paper we report the in vitro selection and evolution of a very small ribozyme that catalyzes the ligation of two substrate RNAs but also possesses the unexpected ability to undergo a separate self-cleavage reaction. Substitution of a divalent metal ion in the absence of further sequence evolution triggers the switch from selected ligase to unselected selfcleaving RNA. The fa...

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“…This complex system was likely preceded by a stage in which RNA played a central role both in information storage and as the only genetically-encoded catalyst (Figure 1) [1,2]. The early prominence of RNA is substantiated by its ability to store genetic information, as in mRNA, and to impart catalysis, as demonstrated by the abundance of catalytic RNAs present in nature and produced in laboratories [3]. The primacy of functional RNAs in the process of protein translation (transfer and ribosomal RNAs and other functional RNAs that modify them), coupled to the ubiquity of those RNAs across all extant life, suggests that the translation system emerged from an RNA-catalyzed metabolism [4].…”

Section: Early Genome Evolutionmentioning

confidence: 99%

“…In contrast to ribozyme polymerases, several ribozyme ligases are present in modern organisms [3] and more have been synthesized by directed evolution [31,32]. Polymerases are in fact a specialized kind of ligase in which one of the ligated partners is a single nucleotide [31].…”

Section: Oxytricha and Early Genome Replicationmentioning

confidence: 99%

Oxytricha as a modern analog of ancient genome evolution

Goldman¹,

Landweber²

2012

Trends in Genetics

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Several independent lines of evidence suggest that the modern genetic system was preceded by the ‘RNA world’ in which RNA genes encoded RNA catalysts. Current gaps in our conceptual framework of early genetic systems make it difficult to imagine how a stable RNA genome may have functioned and how the transition to a DNA genome could have taken place. Here we use the single-celled ciliate, Oxytricha, as an analog to some of the genetic and genomic traits that may have been present in organisms before and during the establishment of a DNA genome. Oxytricha and its close relatives have a unique genome architecture involving two differentiated nuclei, one of which encodes the genome on small, linear nanochromosomes. While its unique genomic characteristics are relatively modern, some physiological processes related to the genomes and nuclei of Oxytricha may exemplify primitive states of the developing genetic system.

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Ribozyme Engineering and Early Evolution

Cited by 32 publications

References 64 publications

The dynamics of the RNA world: insights and challenges

The dynamics of the RNA world: insights and challenges

Emergence of a dual-catalytic RNA with metal-specific cleavage and ligase activities: The spandrels of RNA evolution

Oxytricha as a modern analog of ancient genome evolution

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