1
|
Spirov A. Evolution of the RNA world: From signals to codes. Biosystems 2023; 234:105043. [PMID: 37852409 DOI: 10.1016/j.biosystems.2023.105043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 09/25/2023] [Accepted: 09/25/2023] [Indexed: 10/20/2023]
Abstract
The accumulated material in evolutionary biology, greatly enhanced by the achievements of modern synthetic biology, allows us to envision certain key hypothetical stages of prebiotic (chemical) evolution. This is often understood as the further evolution in the RNA World towards the RNA-protein World. It is a path towards the emergence of translation and the genetic code (I), signaling pathways with signaling molecules (II), and the appearance of RNA-based components of future gene regulatory networks (III). We believe that these evolutionary paths can be constructively viewed from the perspective of the concept of biological codes (Barbieri, 2003). Crucial evolutionary events in these directions would involve the emergence of RNA-based adaptors. Such adaptors connect two families of functionally and chemically distinct molecules into one functional entity. The emergence of primitive translation processes is undoubtedly the major milestone in the evolutionary path towards modern life. The key aspect here is the appearance of adaptors between amino acids and their cognate triplet codons. The initial steps are believed to involve the emergence of proto-transfer RNAs capable of self-aminoacylation. The second significant evolutionary breakthrough is the development of biochemical regulatory networks based on signaling molecules of the RNA World (ribonucleotides and their derivatives), as well as receptors and effectors (riboswitches) for these messengers. Some authors refer to this as the "lost language of the RNA World." The third evolutionary step is the emergence of signal sequences for ribozymes on the molecules of their RNA targets. This level of regulation in the RNA World is comparable to the gene regulatory networks of modern organisms. We believe that the signal sequences on target molecules have been rediscovered and developed by evolution into the gene regulatory networks of modern cells. In conclusion, the immense diversity of modern biological codes, in some of its key characteristics, can be traced back to the achievements of prebiotic evolution.
Collapse
Affiliation(s)
- Alexander Spirov
- The Institute of Scientific Information for Social Sciences RAS, Moscow, Russia.
| |
Collapse
|
2
|
Dagenais P, Legault P. In Vitro Selection of Varkud Satellite Ribozyme Variants that Cleave a Modified Stem-Loop Substrate. Methods Mol Biol 2021; 2167:61-77. [PMID: 32712915 DOI: 10.1007/978-1-0716-0716-9_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In vitro selection is an established approach to create artificial ribozymes with defined activities or to modify the properties of naturally occurring ribozymes. For the Varkud satellite ribozyme of Neurospora, an in vitro selection protocol based on its phosphodiester bond cleavage activity has not been previously reported. Here, we describe a simple protocol for cleavage-based in vitro selection that we recently used to identify variants of the Varkud satellite ribozyme able to target and cleave a non-natural stem-loop substrate derived from the HIV-1 TAR RNA. It allows quick selection of active ribozyme variants from the transcription reaction based on the size of the self-cleavage product without the need for RNA labeling. This results in a streamlined procedure that is easily adaptable to engineer ribozymes with new activities.
Collapse
Affiliation(s)
- Pierre Dagenais
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, QC, Canada
| | - Pascale Legault
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, QC, Canada.
| |
Collapse
|
3
|
Abdullah HP, Morse DP. Changing the Ligand Specificity of a Guanine Riboswitch by
In Vitro
Selection. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.625.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
4
|
Ke W, Hong E, Saito RF, Rangel MC, Wang J, Viard M, Richardson M, Khisamutdinov EF, Panigaj M, Dokholyan NV, Chammas R, Dobrovolskaia MA, Afonin KA. RNA-DNA fibers and polygons with controlled immunorecognition activate RNAi, FRET and transcriptional regulation of NF-κB in human cells. Nucleic Acids Res 2019; 47:1350-1361. [PMID: 30517685 PMCID: PMC6379676 DOI: 10.1093/nar/gky1215] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 11/19/2018] [Accepted: 11/22/2018] [Indexed: 12/17/2022] Open
Abstract
Nucleic acid-based assemblies that interact with each other and further communicate with the cellular machinery in a controlled manner represent a new class of reconfigurable materials that can overcome limitations of traditional biochemical approaches and improve the potential therapeutic utility of nucleic acids. This notion enables the development of novel biocompatible 'smart' devices and biosensors with precisely controlled physicochemical and biological properties. We extend this novel concept by designing RNA-DNA fibers and polygons that are able to cooperate in different human cell lines and that have defined immunostimulatory properties confirmed by ex vivo experiments. The mutual intracellular interaction of constructs results in the release of a large number of different siRNAs while giving a fluorescent response and activating NF-κB decoy DNA oligonucleotides. This work expands the possibilities of nucleic acid technologies by (i) introducing very simple design principles and assembly protocols; (ii) potentially allowing for a simultaneous release of various siRNAs together with functional DNA sequences and (iii) providing controlled rates of reassociation, stabilities in human blood serum, and immunorecognition.
Collapse
Affiliation(s)
- Weina Ke
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Enping Hong
- Nanotechnology Characterization Lab., Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21702, USA
| | - Renata F Saito
- Centro de Investigação Translacional em Oncologia (LIM24), Departamento de Radiologia e Oncologia, Faculdade de Medicina da Universidade de São Paulo and Instituto do Câncer do Estado de São Paulo, São Paulo, SP, Brazil
| | - Maria Cristina Rangel
- Centro de Investigação Translacional em Oncologia (LIM24), Departamento de Radiologia e Oncologia, Faculdade de Medicina da Universidade de São Paulo and Instituto do Câncer do Estado de São Paulo, São Paulo, SP, Brazil
| | - Jian Wang
- Department of Pharmacology, Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Mathias Viard
- Basic Science Program, Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Melina Richardson
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | | | - Martin Panigaj
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Safarik University in Kosice, Kosice, Slovak Republic
| | - Nikolay V Dokholyan
- Department of Pharmacology, Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Roger Chammas
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
- Centro de Investigação Translacional em Oncologia (LIM24), Departamento de Radiologia e Oncologia, Faculdade de Medicina da Universidade de São Paulo and Instituto do Câncer do Estado de São Paulo, São Paulo, SP, Brazil
| | - Marina A Dobrovolskaia
- Nanotechnology Characterization Lab., Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21702, USA
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
- The Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| |
Collapse
|