Archaeal RNA ligase from thermoccocus kodakarensis for template dependent ligation

Zhang, Lei; Tripathi, Anubhav

doi:10.1080/15476286.2016.1239688

“…Some of the aspects of this hypothesis could be tested experimentally. For example, is any of the in vitro generated RNA ligase ribozymes [25] able to generate random ligation products similar to protein-based ligases [61,62]? This could be tested by providing the RNA ligase with a pool of random RNA oligomers, or longer ribozymes, followed by deep sequencing of the reaction.…”

Section: Discussionmentioning

confidence: 99%

“…Regarding the first point, template-independent ligation of single-stranded DNA and RNA molecules has been demonstrated to be catalyzed by T4 DNA ligase and an RNA ligase from the archaeon Thermococcus kodakarensis, respectively (both are protein enzymes) [61,62]. RNA ligase ribozymes, especially short ones, have been shown experimentally to be able to accept a broad range of substrates [63], yet, to the best of my knowledge, non-templated ribozyme-catalyzed RNA ligation has not been demonstrated experimentally to date.…”

Section: Figurementioning

confidence: 99%

Genome Evolution from Random Ligation of RNAs of Autocatalytic Sets

Bröcker¹

2021

Preprint

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The evolutionary origin of the genome remains elusive. Here, I hypothesize that its first iteration, the protogenome, was a multi-ribozyme RNA. It evolved, likely within liposomes (the protocells) forming in dry-wet cycling environments, through the random fusion of ribozymes by a ligase and was amplified by a polymerase. The protogenome thereby linked, in one molecule, the information required to seed the protometabolism (a combination of RNA-based autocatalytic sets) in newly forming protocells. If this combination of autocatalytic sets was evolutionarily advantageous, the protogenome would have amplified in a population of multiplying protocells. It likely was a quasispecies with redundant information, e.g., multiple copies of one ribozyme. As such, new functionalities could evolve, including a genetic code. Once one or more components of the protometabolism were templated by the protogenome (e.g., when a ribozyme was replaced by a protein enzyme), and/or addiction modules evolved, the protometabolism became dependent on the protogenome. Along with increasing fidelity of the RNA polymerase, the protogenome could grow, e.g., by incorporating additional ribozyme domains. Finally, the protogenome could have evolved into a DNA genome with increased stability and storage capacity. I will provide suggestions for experiments to test some aspects of this hypothesis.

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“…Regarding the first point, template-independent ligation of single-stranded DNA and RNA molecules has been demonstrated to be catalyzed by T4 DNA ligase and an RNA ligase from the archaeon Thermococcus kodakarensis, respectively (both are protein enzymes) [73,74]. RNA ligase ribozymes, especially short ones, have been shown experimentally to be able to accept a broad range of substrates [75], yet, to the best of my knowledge, non-templated ribozyme-catalyzed RNA ligation has not been demonstrated experimentally to date.…”

Section: Protogenome Evolution Within the Dry-wet Cycle Scenariomentioning

confidence: 99%

Genome Evolution from Random Ligation of RNAs of Autocatalytic Sets

Broecker

¹

2021

IJMS

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The evolutionary origin of the genome remains elusive. Here, I hypothesize that its first iteration, the protogenome, was a multi-ribozyme RNA. It evolved, likely within liposomes (the protocells) forming in dry-wet cycling environments, through the random fusion of ribozymes by a ligase and was amplified by a polymerase. The protogenome thereby linked, in one molecule, the information required to seed the protometabolism (a combination of RNA-based autocatalytic sets) in newly forming protocells. If this combination of autocatalytic sets was evolutionarily advantageous, the protogenome would have amplified in a population of multiplying protocells. It likely was a quasispecies with redundant information, e.g., multiple copies of one ribozyme. As such, new functionalities could evolve, including a genetic code. Once one or more components of the protometabolism were templated by the protogenome (e.g., when a ribozyme was replaced by a protein enzyme), and/or addiction modules evolved, the protometabolism became dependent on the protogenome. Along with increasing fidelity of the RNA polymerase, the protogenome could grow, e.g., by incorporating additional ribozyme domains. Finally, the protogenome could have evolved into a DNA genome with increased stability and storage capacity. I will provide suggestions for experiments to test some aspects of this hypothesis, such as evaluating the ability of ribozyme RNA polymerases to generate random ligation products and testing the catalytic activity of linked ribozyme domains.

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“…The thermal stability and high-temperature catalytic activity of thermostable RNA ligases makes them suitable for RNA ligase-mediated rapid amplification of cDNA ends (RLM-RACE) and other RNA or DNA ligation reactions. Based on current research on T4 RNA ligase, more specific and effective RNA ligases were designed, further expanding their function of modifying RNA molecules [ 66 ].…”

Section: Rna-based Synthetic Biology Parts From Phage Componentsmentioning

confidence: 99%

Applications of phage-derived RNA-based technologies in synthetic biology

Zhang

¹

,

Wu

²

2020

Synthetic and Systems Biotechnology

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As the most abundant biological entities with incredible diversity, bacteriophages (also known as phages) have been recognized as an important source of molecular machines for the development of genetic-engineering tools. At the same time, phages are crucial for establishing and improving basic theories of molecular biology. Studies on phages provide rich sources of essential elements for synthetic circuit design as well as powerful support for the improvement of directed evolution platforms. Therefore, phages play a vital role in the development of new technologies and central scientific concepts. After the RNA world hypothesis was proposed and developed, novel biological functions of RNA continue to be discovered. RNA and its related elements are widely used in many fields such as metabolic engineering and medical diagnosis, and their versatility led to a major role of RNA in synthetic biology. Further development of RNA-based technologies will advance synthetic biological tools as well as provide verification of the RNA world hypothesis. Most synthetic biology efforts are based on reconstructing existing biological systems, understanding fundamental biological processes, and developing new technologies. RNA-based technologies derived from phages will offer abundant sources for synthetic biological components. Moreover, phages as well as RNA have high impact on biological evolution, which is pivotal for understanding the origin of life, building artificial life-forms, and precisely reprogramming biological systems. This review discusses phage-derived RNA-based technologies terms of phage components, the phage lifecycle, and interactions between phages and bacteria. The significance of RNA-based technology derived from phages for synthetic biology and for understanding the earliest stages of biological evolution will be highlighted.

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Archaeal RNA ligase from thermoccocus kodakarensis for template dependent ligation

Cited by 8 publications

References 40 publications

Genome Evolution from Random Ligation of RNAs of Autocatalytic Sets

Genome Evolution from Random Ligation of RNAs of Autocatalytic Sets

Genome Evolution from Random Ligation of RNAs of Autocatalytic Sets

Applications of phage-derived RNA-based technologies in synthetic biology

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