1
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Wang Z, Wen H. A review of the recombination events, mechanisms and consequences of Coxsackievirus A6. INFECTIOUS MEDICINE 2024; 3:100115. [PMID: 38974347 PMCID: PMC11225671 DOI: 10.1016/j.imj.2024.100115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/25/2024] [Accepted: 04/22/2024] [Indexed: 07/09/2024]
Abstract
Hand, foot, and mouth disease (HFMD) is one of the most common class C infectious diseases, posing a serious threat to public health worldwide. Enterovirus A71 (EV-A71) and coxsackievirus A16 (CV-A16) have been regarded as the major pathogenic agents of HFMD; however, since an outbreak caused by coxsackievirus A6 (CV-A6) in France in 2008, CV-A6 has gradually become the predominant pathogen in many regions. CV-A6 infects not only children but also adults, and causes atypical clinical symptoms such as a more generalized rash, eczema herpeticum, high fever, and onychomadesis, which are different from the symptoms associated with EV-A71 and CV-A16. Importantly, the rate of genetic recombination of CV-A6 is high, which can lead to changes in virulence and the rapid evolution of other characteristics, thus posing a serious threat to public health. To date, no specific vaccines or therapeutics have been approved for CV-A6 prevention or treatment, hence it is essential to fully understand the relationship between recombination and evolution of this virus. Here, we systematically review the genetic recombination events of CV-A6 that have occurred worldwide and explore how these events have promoted virus evolution, thus providing important information regarding future HFMD surveillance and prevention.
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Affiliation(s)
- Zequn Wang
- Department of Microbiological Laboratory Technology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Key Laboratory of Prevention and Control of Emerging Infectious Diseases, Biosafety in Universities of Shandong, Jinan 250012, China
| | - Hongling Wen
- Department of Microbiological Laboratory Technology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Key Laboratory of Prevention and Control of Emerging Infectious Diseases, Biosafety in Universities of Shandong, Jinan 250012, China
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2
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Nguyen HM, Watanabe S, Sharmin S, Kawaguchi T, Tan XE, Wannigama DL, Cui L. RNA and Single-Stranded DNA Phages: Unveiling the Promise from the Underexplored World of Viruses. Int J Mol Sci 2023; 24:17029. [PMID: 38069353 PMCID: PMC10707117 DOI: 10.3390/ijms242317029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/26/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
RNA and single-stranded DNA (ssDNA) phages make up an understudied subset of bacteriophages that have been rapidly expanding in the last decade thanks to advancements in metaviromics. Since their discovery, applications of genetic engineering to ssDNA and RNA phages have revealed their immense potential for diverse applications in healthcare and biotechnology. In this review, we explore the past and present applications of this underexplored group of phages, particularly their current usage as therapeutic agents against multidrug-resistant bacteria. We also discuss engineering techniques such as recombinant expression, CRISPR/Cas-based genome editing, and synthetic rebooting of phage-like particles for their role in tailoring phages for disease treatment, imaging, biomaterial development, and delivery systems. Recent breakthroughs in RNA phage engineering techniques are especially highlighted. We conclude with a perspective on challenges and future prospects, emphasizing the untapped diversity of ssDNA and RNA phages and their potential to revolutionize biotechnology and medicine.
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Affiliation(s)
- Huong Minh Nguyen
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan; (H.M.N.); (S.W.); (S.S.); (T.K.); (X.-E.T.)
| | - Shinya Watanabe
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan; (H.M.N.); (S.W.); (S.S.); (T.K.); (X.-E.T.)
| | - Sultana Sharmin
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan; (H.M.N.); (S.W.); (S.S.); (T.K.); (X.-E.T.)
| | - Tomofumi Kawaguchi
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan; (H.M.N.); (S.W.); (S.S.); (T.K.); (X.-E.T.)
| | - Xin-Ee Tan
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan; (H.M.N.); (S.W.); (S.S.); (T.K.); (X.-E.T.)
| | - Dhammika Leshan Wannigama
- Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata 990-2292, Yamagata, Japan;
| | - Longzhu Cui
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan; (H.M.N.); (S.W.); (S.S.); (T.K.); (X.-E.T.)
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3
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Ueda K, Mizuuchi R, Ichihashi N. Emergence of linkage between cooperative RNA replicators encoding replication and metabolic enzymes through experimental evolution. PLoS Genet 2023; 19:e1010471. [PMID: 37540715 PMCID: PMC10431678 DOI: 10.1371/journal.pgen.1010471] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 08/16/2023] [Accepted: 07/18/2023] [Indexed: 08/06/2023] Open
Abstract
The integration of individually replicating genes into a primitive chromosome is a key evolutionary transition in the development of life, allowing the simultaneous inheritance of genes. However, how this transition occurred is unclear because the extended size of primitive chromosomes replicate slower than unlinked genes. Theoretical studies have suggested that a primitive chromosome can evolve in the presence of cell-like compartments, as the physical linkage prevents the stochastic loss of essential genes upon division, but experimental support for this is lacking. Here, we demonstrate the evolution of a chromosome-like RNA from two cooperative RNA replicators encoding replication and metabolic enzymes. Through their long-term replication in cell-like compartments, linked RNAs emerged with the two cooperative RNAs connected end-to-end. The linked RNAs had different mutation patterns than the two unlinked RNAs, suggesting that they were maintained as partially distinct lineages in the population. Our results provide experimental evidence supporting the plausibility of the evolution of a primitive chromosome from unlinked gene fragments, an important step in the emergence of complex biological systems.
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Affiliation(s)
- Kensuke Ueda
- Department of Life Science, Graduate School of Arts and Science, the University of Tokyo, Meguro, Tokyo, Japan
| | - Ryo Mizuuchi
- Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, Shinjuku, Tokyo, Japan
- JST, FOREST, Kawaguchi, Saitama, Japan
| | - Norikazu Ichihashi
- Department of Life Science, Graduate School of Arts and Science, the University of Tokyo, Meguro, Tokyo, Japan
- Komaba Institute for Science, the University of Tokyo, Meguro, Tokyo, Japan
- Universal Biology Institute, the University of Tokyo, Meguro, Tokyo, Japan
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4
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Lobodin KV, Chetverina HV, Chetverin AB. Slippage at the initiation of RNA synthesis by Qβ replicase results in a periodic polyG pattern. FEBS Lett 2023; 597:458-471. [PMID: 36477752 DOI: 10.1002/1873-3468.14556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 10/16/2022] [Accepted: 11/25/2022] [Indexed: 12/13/2022]
Abstract
The repetitive copying of template nucleotides due to transcriptional slippage has not been reported for RNA-directed RNA polymerases of positive-strand RNA phages. We unexpectedly observed that, with GTP as the only substrate, Qβ replicase, the RNA-directed RNA polymerase of bacteriophage Qβ, synthesizes by transcriptional slippage polyG strands, which on denaturing electrophoresis produce a ladder with at least three clusters of bolder bands. The ≈ 15-nt-long G15 , the major product of the shortest cluster, is tightly bound by the enzyme but can be released by the ribosomal protein S1, which, as a Qβ replicase subunit, normally promotes the release of a completed transcript. 7-deaza-GTP suppresses the polyG synthesis and abolishes the periodic pattern, suggesting that the N7 atom is needed for the initiation of RNA synthesis and the formation of the structure recognized by protein S1. The results provide new insights into the mechanism of RNA synthesis by the RNA-directed RNA polymerase of a single-stranded RNA phage.
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Affiliation(s)
- Kirill V Lobodin
- Institute of Protein Research of the Russian Academy of Sciences, Pushchino, Russia
| | - Helena V Chetverina
- Institute of Protein Research of the Russian Academy of Sciences, Pushchino, Russia
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5
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Kim H, Aponte-Diaz D, Sotoudegan MS, Shengjuler D, Arnold JJ, Cameron CE. The enterovirus genome can be translated in an IRES-independent manner that requires the initiation factors eIF2A/eIF2D. PLoS Biol 2023; 21:e3001693. [PMID: 36689548 PMCID: PMC9894558 DOI: 10.1371/journal.pbio.3001693] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 02/02/2023] [Accepted: 01/04/2023] [Indexed: 01/24/2023] Open
Abstract
RNA recombination in positive-strand RNA viruses is a molecular-genetic process, which permits the greatest evolution of the genome and may be essential to stabilizing the genome from the deleterious consequences of accumulated mutations. Enteroviruses represent a useful system to elucidate the details of this process. On the biochemical level, it is known that RNA recombination is catalyzed by the viral RNA-dependent RNA polymerase using a template-switching mechanism. For this mechanism to function in cells, the recombining genomes must be located in the same subcellular compartment. How a viral genome is trafficked to the site of genome replication and recombination, which is membrane associated and isolated from the cytoplasm, is not known. We hypothesized that genome translation was essential for colocalization of genomes for recombination. We show that complete inactivation of internal ribosome entry site (IRES)-mediated translation of a donor enteroviral genome enhanced recombination instead of impairing it. Recombination did not occur by a nonreplicative mechanism. Rather, sufficient translation of the nonstructural region of the genome occurred to support subsequent steps required for recombination. The noncanonical translation initiation factors, eIF2A and eIF2D, were required for IRES-independent translation. Our results support an eIF2A/eIF2D-dependent mechanism under conditions in which the eIF2-dependent mechanism is inactive. Detection of an IRES-independent mechanism for translation of the enterovirus genome provides an explanation for a variety of debated observations, including nonreplicative recombination and persistence of enteroviral RNA lacking an IRES. The existence of an eIF2A/eIF2D-dependent mechanism in enteroviruses predicts the existence of similar mechanisms in other viruses.
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Affiliation(s)
- Hyejeong Kim
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - David Aponte-Diaz
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Mohamad S. Sotoudegan
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | | | - Jamie J. Arnold
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Craig E. Cameron
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
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6
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Multiple Levels of Triggered Factors and the Obligated Requirement of Cell-to-Cell Movement in the Mutation Repair of Cucumber Mosaic Virus with Defects in the tRNA-like Structure. BIOLOGY 2022; 11:biology11071051. [PMID: 36101429 PMCID: PMC9312275 DOI: 10.3390/biology11071051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/07/2022] [Accepted: 07/12/2022] [Indexed: 11/17/2022]
Abstract
Simple Summary Based on analysis of the tRNA-like structure (TLS) mutation in cucumber mosaic virus (CMV), mutation repair is correlated with several levels of triggered factors, including the dose of inoculation of virus mutants, the quantity effect on corresponding viral RNA, and the quality effect on corresponding viral RNA. All types of TLS mutation in different RNAs of CMV can be repaired at a low dose around the dilution end-point. At a high dose of inoculation, TLS mutations in RNA2 and RNA3, but not RNA1, can be repaired, which correlates with the relative quantity defect of RNA2 or the genome size defect of RNA3. In addition, all the above types of mutation repair necessarily require cell-to-cell movement, which presents the obligated effect of cell-to-cell movement on mutation repair. Abstract Some debilitating mutations in RNA viruses are repairable; however, the triggering factors of mutation repair remain largely unknown. In this study, multiple triggering factors of mutation repair are identified based on genetic damage to the TLS in CMV. TLS mutations in different RNAs distinctively impact viral pathogenicity and present different types of mutation repair. RNA2 relative reduction level or RNA3 sequence change resulting from TLS mutation is correlated with a high rate of mutation repair, and the TLS mutation of RNA1 fails to be repaired at the high inoculum dose. However, the TLS mutation of RNA1 can be repaired at a low dose of inoculation, particularly around the dilution end-point or in the mixed inoculation with RNA2 having a pre-termination mutation of the 2b gene, an RNAi suppressor. Taken together, TLS mutations resulting in quality or quantity defects of the viral genome or TLS mutations at low doses around the dilution end-point are likely to be repaired. Different levels of TLS mutation repair necessarily require cell-to-cell movement, therefore implying its obligated effect on the evolution of low-fitness viruses and providing a new insight into Muller’s ratchet. This study provides important information on virus evolution and the application of mild viral vaccines.
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7
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Chetverin AB. Alexander Spirin on Molecular Machines and Origin of Life. BIOCHEMISTRY (MOSCOW) 2021; 86:913-925. [PMID: 34488569 DOI: 10.1134/s0006297921080034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Once it was believed that ribosomal RNA encodes proteins, and GTP hydrolysis supplies the energy for protein synthesis. Everything has changed, when Alexander Spirin joined the science. It turned out that proteins are encoded by a completely different RNA, and GTP hydrolysis only accelerates the process already provided with energy. It was Spirin who first put forward the idea of a Brownian ratchet and explained how and why molecular machines could arise in the RNA world.
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Affiliation(s)
- Alexander B Chetverin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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8
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Cárdenas M, Galleguillos C, Acevedo K, Ananias C, Alarcón J, Michelson S, Toledo J, Montoya M, Meneses C, Castro-Nallar E, Vásquez-Martínez Y, Cortez-San Martin M. Rapid sequence modification in the highly polymorphic region (HPR) of the hemagglutinin gene of the infectious salmon anaemia virus (ISAV) suggests intra-segmental template switching recombination. JOURNAL OF FISH DISEASES 2020; 43:1483-1496. [PMID: 32955147 DOI: 10.1111/jfd.13242] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 07/11/2020] [Accepted: 07/13/2020] [Indexed: 06/11/2023]
Abstract
The ISAV has a genome composed of eight segments of (-)ssRNA, segment 6 codes for the hemagglutinin-esterase protein, and has the most variable region of the genome, the highly polymorphic region (HPR), which is unique among orthomyxoviruses. The HPR has been associated with virulence, infectivity and pathogenicity. The full length of the HPR is called HPR0 and the strain with this HPR is avirulent, in contrast to strains with deleted HPR that are virulent to varying degrees. The molecular mechanism that gives rise to the different HPRs remains unclear. Here, we studied in vitro the evolution of reassortant recombinant ISAV (rISAV) in Atlantic salmon head kidney (ASK) cells. To this end, we rescued and cultivated a set of rISAV with different segment 6-HPR genotypes using a reverse genetics system and then sequencing HPR regions of the viruses. Our results show rapid multiple recombination events in ISAV, with sequence insertions and deletions in the HPR, indicating a dynamic process. Inserted sequences can be found in four segments of the ISAV genome (segments 1, 5, 6, and 8). The results suggest intra-segmental heterologous recombination, probably by class I and class II template switching, similar to the proposed segment 5 recombination mechanism.
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Affiliation(s)
- Matías Cárdenas
- Molecular Virology and Pathogen Control Laboratory, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Claudia Galleguillos
- Molecular Virology and Pathogen Control Laboratory, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Karina Acevedo
- Molecular Virology and Pathogen Control Laboratory, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Catarina Ananias
- Molecular Virology and Pathogen Control Laboratory, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Javiera Alarcón
- Molecular Virology and Pathogen Control Laboratory, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Sofía Michelson
- Molecular Virology and Pathogen Control Laboratory, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Jorge Toledo
- Biotechnology and Biopharmaceutical Laboratory, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Margarita Montoya
- Cell Biochemistry Laboratory, Department of Biology, Faculty of Chemistry and Biology, University of Santiago, Santiago, Chile
| | - Claudio Meneses
- Plant Biotechnology Center, Andres Bello University, Santiago, Chile
| | - Eduardo Castro-Nallar
- Center of Bioinformatics and Integrative Biology, Faculty of Life Sciences, University Andrés Bello, Santiago, Chile
| | - Yesseny Vásquez-Martínez
- Molecular Virology and Pathogen Control Laboratory, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago, Chile
- Programa Centro de Investigaciones Biomédicas Aplicadas, Facultad de Ciencias Médicas, University of Santiago de Chile, Santiago, Chile
| | - Marcelo Cortez-San Martin
- Molecular Virology and Pathogen Control Laboratory, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago, Chile
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9
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Zhang W, Wu Q. Applications of phage-derived RNA-based technologies in synthetic biology. Synth Syst Biotechnol 2020; 5:343-360. [PMID: 33083579 PMCID: PMC7564126 DOI: 10.1016/j.synbio.2020.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 09/22/2020] [Accepted: 09/27/2020] [Indexed: 12/20/2022] Open
Abstract
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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Affiliation(s)
- Wenhui Zhang
- MOE Key Lab. Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Qiong Wu
- MOE Key Lab. Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
- Corresponding author. MOE Key Lab. Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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10
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Furubayashi T, Ueda K, Bansho Y, Motooka D, Nakamura S, Mizuuchi R, Ichihashi N. Emergence and diversification of a host-parasite RNA ecosystem through Darwinian evolution. eLife 2020; 9:e56038. [PMID: 32690137 PMCID: PMC7378860 DOI: 10.7554/elife.56038] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 07/01/2020] [Indexed: 12/11/2022] Open
Abstract
In prebiotic evolution, molecular self-replicators are considered to develop into diverse, complex living organisms. The appearance of parasitic replicators is believed inevitable in this process. However, the role of parasitic replicators in prebiotic evolution remains elusive. Here, we demonstrated experimental coevolution of RNA self-replicators (host RNAs) and emerging parasitic replicators (parasitic RNAs) using an RNA-protein replication system we developed. During a long-term replication experiment, a clonal population of the host RNA turned into an evolving host-parasite ecosystem through the continuous emergence of new types of host and parasitic RNAs produced by replication errors. The host and parasitic RNAs diversified into at least two and three different lineages, respectively, and they exhibited evolutionary arms-race dynamics. The parasitic RNA accumulated unique mutations, thus adding a new genetic variation to the whole replicator ensemble. These results provide the first experimental evidence that the coevolutionary interplay between host-parasite molecules plays a key role in generating diversity and complexity in prebiotic molecular evolution.
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Affiliation(s)
- Taro Furubayashi
- Laboratoire Gulliver, CNRS, ESPCI Paris,
PSL Research UniversityParisFrance
| | - Kensuke Ueda
- Department of Life Science, Graduate
School of Arts and Science, The University of
TokyoTokyoJapan
| | - Yohsuke Bansho
- Graduate School of Frontier Biosciences,
Osaka UniversityOsakaJapan
| | - Daisuke Motooka
- Research Institute for Microbial
Diseases, Osaka UniversityOsakaJapan
| | - Shota Nakamura
- Research Institute for Microbial
Diseases, Osaka UniversityOsakaJapan
| | - Ryo Mizuuchi
- Komaba Institute for Science, The
University of TokyoTokyoJapan
- JST,
PRESTOKawaguchiJapan
| | - Norikazu Ichihashi
- Department of Life Science, Graduate
School of Arts and Science, The University of
TokyoTokyoJapan
- Graduate School of Frontier Biosciences,
Osaka UniversityOsakaJapan
- Komaba Institute for Science, The
University of TokyoTokyoJapan
- Universal Biology Institute, The
University of TokyoTokyoJapan
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11
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Mizuuchi R, Usui K, Ichihashi N. Structural transition of replicable RNAs during in vitro evolution with Qβ replicase. RNA (NEW YORK, N.Y.) 2020; 26:83-90. [PMID: 31690585 PMCID: PMC6913131 DOI: 10.1261/rna.073106.119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 10/26/2019] [Indexed: 06/10/2023]
Abstract
Single-stranded RNAs (ssRNAs) are utilized as genomes in some viruses and also in experimental models of ancient life-forms, owing to their simplicity. One of the largest problems for ssRNA replication is the formation of double-stranded RNA (dsRNA), a dead-end product for ssRNA replication. A possible strategy to avoid dsRNA formation is to create strong intramolecular secondary structures of ssRNA. To design ssRNAs that efficiently replicate by Qβ replicase with minimum dsRNA formation, we previously proposed the "fewer unpaired GC rule." According to this rule, ssRNAs that have fewer unpaired G and C bases in the secondary structure should efficiently replicate with less dsRNA formation. However, the validity of this rule still needs to be examined, especially for longer ssRNAs. Here, we analyze nine long ssRNAs that successively appeared during an in vitro evolution of replicable ssRNA by Qβ replicase and examine whether this rule can explain the structural transitions of the RNAs. We found that these ssRNAs improved their template abilities step-by-step with decreasing dsRNA formation as mutations accumulated. We then examine the secondary structures of all the RNAs by a chemical modification method. The analysis of the structures revealed that the probabilities of unpaired G and C bases tended to decrease gradually in the course of evolution. The decreases were caused by the local structural changes around the mutation sites in most of the cases. These results support the validity of the "fewer unpaired GC rule" to efficiently design replicable ssRNAs by Qβ replicase, useful for more complex ssRNA replication systems.
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Affiliation(s)
- Ryo Mizuuchi
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo 153-8902, Japan
- JST, PRESTO, Kawaguchi, Saitama 332-0012, Japan
| | - Kimihito Usui
- Japan Science and Technology Agency, Suita, Osaka, 565-0871, Japan
| | - Norikazu Ichihashi
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo 153-8902, Japan
- Department of Life Science, Graduate School of Arts and Science, The University of Tokyo, Meguro-ku, Tokyo, 153-8902, Japan
- Universal Biology Institute, The University of Tokyo, Meguro-ku, Tokyo, 153-8902, Japan
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12
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13
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Muslin C, Mac Kain A, Bessaud M, Blondel B, Delpeyroux F. Recombination in Enteroviruses, a Multi-Step Modular Evolutionary Process. Viruses 2019; 11:E859. [PMID: 31540135 PMCID: PMC6784155 DOI: 10.3390/v11090859] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 09/05/2019] [Accepted: 09/06/2019] [Indexed: 01/15/2023] Open
Abstract
RNA recombination is a major driving force in the evolution and genetic architecture shaping of enteroviruses. In particular, intertypic recombination is implicated in the emergence of most pathogenic circulating vaccine-derived polioviruses, which have caused numerous outbreaks of paralytic poliomyelitis worldwide. Recent experimental studies that relied on recombination cellular systems mimicking natural genetic exchanges between enteroviruses provided new insights into the molecular mechanisms of enterovirus recombination and enabled to define a new model of genetic plasticity for enteroviruses. Homologous intertypic recombinant enteroviruses that were observed in nature would be the final products of a multi-step process, during which precursor nonhomologous recombinant genomes are generated through an initial inter-genomic RNA recombination event and can then evolve into a diversity of fitter homologous recombinant genomes over subsequent intra-genomic rearrangements. Moreover, these experimental studies demonstrated that the enterovirus genome could be defined as a combination of genomic modules that can be preferentially exchanged through recombination, and enabled defining the boundaries of these recombination modules. These results provided the first experimental evidence supporting the theoretical model of enterovirus modular evolution previously elaborated from phylogenetic studies of circulating enterovirus strains. This review summarizes our current knowledge regarding the mechanisms of recombination in enteroviruses and presents a new evolutionary process that may apply to other RNA viruses.
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Affiliation(s)
- Claire Muslin
- One Health Research Group, Faculty of Health Sciences, Universidad de las Américas, Quito EC170125, Pichincha, Ecuador.
| | - Alice Mac Kain
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, 75015 Paris, France.
| | - Maël Bessaud
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, 75015 Paris, France.
| | - Bruno Blondel
- Institut Pasteur, Biology of Enteric Viruses Unit, 75015 Paris, France.
- INSERM U994, Institut National de la Santé et de la Recherche Médicale, 75015 Paris, France.
| | - Francis Delpeyroux
- Institut Pasteur, Biology of Enteric Viruses Unit, 75015 Paris, France.
- INSERM U994, Institut National de la Santé et de la Recherche Médicale, 75015 Paris, France.
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14
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Smail BA, Clifton BE, Mizuuchi R, Lehman N. Spontaneous advent of genetic diversity in RNA populations through multiple recombination mechanisms. RNA (NEW YORK, N.Y.) 2019; 25:453-464. [PMID: 30670484 PMCID: PMC6426292 DOI: 10.1261/rna.068908.118] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 01/14/2019] [Indexed: 06/09/2023]
Abstract
There are several plausible abiotic synthetic routes from prebiotic chemical materials to ribonucleotides and even short RNA oligomers. However, for refinement of the RNA World hypothesis to help explain the origins of life on the Earth, there needs to be a manner by which such oligomers can increase their length and expand their sequence diversity. Oligomers longer than at least 10-20 nucleotides would be needed for raw material for subsequent natural selection. Here, we explore spontaneous RNA-RNA recombination as a facile means by which such length and diversity enhancement could have been realized. Motivated by the discovery that RNA oligomers stored for long periods of time in the freezer expand their lengths, we systematically investigated RNA-RNA recombination processes. In addition to one known mechanism, we discovered at least three new mechanisms. In these, one RNA oligomer acts as a splint to catalyze the hybridization of two other oligomers and facilitates the attack of a 5'-OH, a 3'-OH, or a 2'-OH nucleophile of one oligomer onto a target atom of another. This leads to the displacement of one RNA fragment and the production of new recombinant oligomers. We show that this process can explain the spontaneous emergence of sequence complexity, both in vitro and in silico.
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Affiliation(s)
- Benedict A Smail
- Department of Chemistry, Portland State University, Portland, Oregon 97207, USA
| | - Bryce E Clifton
- Department of Chemistry, Portland State University, Portland, Oregon 97207, USA
| | - Ryo Mizuuchi
- Department of Chemistry, Portland State University, Portland, Oregon 97207, USA
| | - Niles Lehman
- Department of Chemistry, Portland State University, Portland, Oregon 97207, USA
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15
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Mutschler H, Taylor AI, Porebski BT, Lightowlers A, Houlihan G, Abramov M, Herdewijn P, Holliger P. Random-sequence genetic oligomer pools display an innate potential for ligation and recombination. eLife 2018; 7:43022. [PMID: 30461419 PMCID: PMC6289569 DOI: 10.7554/elife.43022] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 11/16/2018] [Indexed: 02/06/2023] Open
Abstract
Recombination, the exchange of information between different genetic polymer strands, is of fundamental importance in biology for genome maintenance and genetic diversification and is mediated by dedicated recombinase enzymes. Here, we describe an innate capacity for non-enzymatic recombination (and ligation) in random-sequence genetic oligomer pools. Specifically, we examine random and semi-random eicosamer (N20) pools of RNA, DNA and the unnatural genetic polymers ANA (arabino-), HNA (hexitol-) and AtNA (altritol-nucleic acids). While DNA, ANA and HNA pools proved inert, RNA (and to a lesser extent AtNA) pools displayed diverse modes of spontaneous intermolecular recombination, connecting recombination mechanistically to the vicinal ring cis-diol configuration shared by RNA and AtNA. Thus, the chemical constitution that renders both susceptible to hydrolysis emerges as the fundamental determinant of an innate capacity for recombination, which is shown to promote a concomitant increase in compositional, informational and structural pool complexity and hence evolutionary potential.
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Affiliation(s)
| | | | | | | | | | - Mikhail Abramov
- REGA Institute, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Piet Herdewijn
- REGA Institute, Katholieke Universiteit Leuven, Leuven, Belgium
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16
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Bentley K, Evans DJ. Mechanisms and consequences of positive-strand RNA virus recombination. J Gen Virol 2018; 99:1345-1356. [PMID: 30156526 DOI: 10.1099/jgv.0.001142] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Genetic recombination in positive-strand RNA viruses is a significant evolutionary mechanism that drives the creation of viral diversity by the formation of novel chimaeric genomes. The process and its consequences, for example the generation of viruses with novel phenotypes, has historically been studied by analysis of the end products. More recently, with an appreciation that there are both replicative and non-replicative mechanisms at work, and with new approaches and techniques to analyse intermediate products, the viral and cellular factors that influence the process are becoming understood. The major influence on replicative recombination is the fidelity of viral polymerase, although RNA structures and sequences may also have an impact. In replicative recombination the viral polymerase is necessary and sufficient, although roles for other viral or cellular proteins may exist. In contrast, non-replicative recombination appears to be mediated solely by cellular components. Despite these insights, the relative importance of replicative and non-replicative mechanisms is not clear. Using single-stranded positive-sense RNA viruses as exemplars, we review the current state of understanding of the processes and consequences of recombination.
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Affiliation(s)
- Kirsten Bentley
- Biomedical Sciences Research Complex and School of Biology, University of St Andrews, St Andrews, UK
| | - David J Evans
- Biomedical Sciences Research Complex and School of Biology, University of St Andrews, St Andrews, UK
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17
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Yoshiyama T, Ichii T, Yomo T, Ichihashi N. Automated in vitro evolution of a translation-coupled RNA replication system in a droplet flow reactor. Sci Rep 2018; 8:11867. [PMID: 30089835 PMCID: PMC6082869 DOI: 10.1038/s41598-018-30374-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 07/27/2018] [Indexed: 01/23/2023] Open
Abstract
Automation is a useful strategy to make laborious evolutionary experiments faster and easier. To date, several types of continuous flow reactors have been developed for the automated evolutionary experiments of viruses and bacteria. However, the development of a flow reactor applicable to compartmentalized in vitro self-replication systems is still a challenge. In this study, we demonstrate automated in vitro evolution of a translation-coupled RNA system in a droplet flow reactor for the first time. This reactor contains approximately 1010 micro-scale droplets (average diameter is approximately 0.8 μm), which continuously fuse and divide among each other at a controllable rate. In the droplets, an RNA (artificial genomic RNA) replicate through the translation of self-encoded RNA replicase with spontaneously appearing parasitic RNA. We performed two automated replication experiments for more than 400 hours with different mixing intensities. We found that several mutations displayed increased frequencies in the genomic RNA populations and the dominant RNA mutants acquired the ability to replicate faster or acquired resistance to the parasitic RNA, demonstrating that Darwinian evolution occurred during the long-term replication. The droplet flow reactor we developed can be a useful tool to perform in vitro evolutionary experiments of translation-coupled systems.
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Affiliation(s)
- Tomoaki Yoshiyama
- Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Tetsuo Ichii
- Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Tokyo, Japan
| | - Tetsuya Yomo
- Institute of Biology and Information Science, East China Normal University, 3663 Zhongshan North Rd., Shanghai, 200062, P.R. China
| | - Norikazu Ichihashi
- Graduate School of Information Science and Technology, Osaka University, Osaka, Japan.
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.
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18
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Chetverin AB. Thirty Years of Studies of Qβ Replicase: What Have We Learned and What Is Yet to Be Learned? BIOCHEMISTRY (MOSCOW) 2018; 83:S19-S32. [DOI: 10.1134/s0006297918140031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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19
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Pesce D, Lehman N, de Visser JAGM. Sex in a test tube: testing the benefits of in vitro recombination. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0529. [PMID: 27619693 DOI: 10.1098/rstb.2015.0529] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2016] [Indexed: 01/06/2023] Open
Abstract
The origin and evolution of sex, and the associated role of recombination, present a major problem in biology. Sex typically involves recombination of closely related DNA or RNA sequences, which is fundamentally a random process that creates but also breaks up beneficial allele combinations. Directed evolution experiments, which combine in vitro mutation and recombination protocols with in vitro or in vivo selection, have proved to be an effective approach for improving functionality of nucleic acids and enzymes. As this approach allows extreme control over evolutionary conditions and parameters, it also facilitates the detection of small or position-specific recombination benefits and benefits associated with recombination between highly divergent genotypes. Yet, in vitro approaches have been largely exploratory and motivated by obtaining improved end products rather than testing hypotheses of recombination benefits. Here, we review the various experimental systems and approaches used by in vitro studies of recombination, discuss what they say about the evolutionary role of recombination, and sketch their potential for addressing extant questions about the evolutionary role of sex and recombination, in particular on complex fitness landscapes. We also review recent insights into the role of 'extracellular recombination' during the origin of life.This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'.
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Affiliation(s)
- Diego Pesce
- Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands
| | - Niles Lehman
- Department of Chemistry, Portland State University, Portland, OR 97207, USA
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20
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Staroseletz Y, Nechaev S, Bichenkova E, Bryce RA, Watson C, Vlassov V, Zenkova M. Non-enzymatic recombination of RNA: Ligation in loops. Biochim Biophys Acta Gen Subj 2017; 1862:705-725. [PMID: 29097301 DOI: 10.1016/j.bbagen.2017.10.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 10/10/2017] [Accepted: 10/26/2017] [Indexed: 12/23/2022]
Abstract
BACKGROUND While the RNA world hypothesis is widely accepted, it is still far from complete: the existence of self-replicating ribozyme, consisting of potentially hundreds of nucleotides, is a core assumption for the majority of RNA world models. The appearance of such long RNA molecules under prebiotic conditions is not self-evident. Recombination seems to be a plausible way of creating RNA diversity, resulting in the appearance of functional RNAs, capable of self-replicating. METHODS We report here on the study of recombination process modelled with two 96 nts RNA fragments. Detection of recombination products was performed with RT-PCR followed by TA-cloning and Sanger sequencing. RESULTS A wide range of recombinant products was detected. We found that (i) the most efficient ligation was observed for RNA species forming bulges or internal loops, with ligation partners located within the loop; (ii) a strong preference was observed for formation of a few types of major products with a large variety of minor products; (iii) ligation could occur with participation of either 2',3'-cyclophosphate or 5'-ppp; (iv) the presence of key reaction components, i.e. 5'ppp-RNAs, enabled the formation of additional types of product; (v) molecular dynamics simulations of one of the most abundant products suggests that the ligation results in a preferable formation of 2'-5'- rather than 3'-5'-linkages. CONCLUSIONS The study demonstrates regularities of new RNA molecules formation with non-enzymatic recombination process. GENERAL SIGNIFICANCE Our findings provide new data supporting the RNA World hypothesis and show the way of new RNA sequences emergence under prebiotic conditions.
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Affiliation(s)
- Yaroslav Staroseletz
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Sergey Nechaev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Elena Bichenkova
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Richard A Bryce
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Catherine Watson
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Valentin Vlassov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Marina Zenkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia.
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21
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Kleine Büning M, Meyer D, Austermann-Busch S, Roman-Sosa G, Rümenapf T, Becher P. Nonreplicative RNA Recombination of an Animal Plus-Strand RNA Virus in the Absence of Efficient Translation of Viral Proteins. Genome Biol Evol 2017; 9:817-829. [PMID: 28338950 PMCID: PMC5381556 DOI: 10.1093/gbe/evx046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2017] [Indexed: 12/27/2022] Open
Abstract
RNA recombination is a major driving force for the evolution of RNA viruses and is significantly implicated in the adaptation of viruses to new hosts, changes of virulence, as well as in the emergence of new viruses including drug-resistant and escape mutants. However, the molecular details of recombination in animal RNA viruses are only poorly understood. In order to determine whether viral RNA recombination depends on translation of viral proteins, a nonreplicative recombination system was established which is based on cotransfection of cells with synthetic bovine viral diarrhea virus (family Flaviviridae) RNA genome fragments either lacking the internal ribosome entry site required for cap-independent translation or lacking almost the complete polyprotein coding region. The emergence of a number of recombinant viruses demonstrated that IRES-mediated translation of viral proteins is dispensable for efficient recombination and suggests that RNA recombination can occur in the absence of viral proteins. Analyses of 58 independently emerged viruses led to the detection of recombinant genomes with duplications, deletions and insertions in the 5′ terminal region of the open reading frame, leading to enlarged core fusion proteins detectable by Western blot analysis. This demonstrates a remarkable flexibility of the pestivirus core protein. Further experiments with capped and uncapped genome fragments containing a luciferase gene for monitoring the level of protein translation revealed that even a ∼1,000-fold enhancement of translation of viral proteins did not increase the frequency of RNA recombination. Taken together, this study highlights that nonreplicative RNA recombination does not require translation of viral proteins.
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Affiliation(s)
- Maximiliane Kleine Büning
- Department of Infectious Diseases, Institute of Virology, University of Veterinary Medicine Hannover, Germany
| | - Denise Meyer
- Department of Infectious Diseases, Institute of Virology, University of Veterinary Medicine Hannover, Germany
| | - Sophia Austermann-Busch
- Department of Infectious Diseases, Institute of Virology, University of Veterinary Medicine Hannover, Germany
| | | | - Tillmann Rümenapf
- Department of Pathobiology, Institute of Virology, University of Veterinary Medicine Vienna, Austria
| | - Paul Becher
- Department of Infectious Diseases, Institute of Virology, University of Veterinary Medicine Hannover, Germany
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22
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Ichihashi N, Yomo T. Constructive Approaches for Understanding the Origin of Self-Replication and Evolution. Life (Basel) 2016; 6:life6030026. [PMID: 27420098 PMCID: PMC5041002 DOI: 10.3390/life6030026] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 07/07/2016] [Accepted: 07/07/2016] [Indexed: 11/16/2022] Open
Abstract
The mystery of the origin of life can be divided into two parts. The first part is the origin of biomolecules: under what physicochemical conditions did biomolecules such as amino acids, nucleotides, and their polymers arise? The second part of the mystery is the origin of life-specific functions such as the replication of genetic information, the reproduction of cellular structures, metabolism, and evolution. These functions require the coordination of many different kinds of biological molecules. A direct strategy to approach the second part of the mystery is the constructive approach, in which life-specific functions are recreated in a test tube from specific biological molecules. Using this approach, we are able to employ design principles to reproduce life-specific functions, and the knowledge gained through the reproduction process provides clues as to their origins. In this mini-review, we introduce recent insights gained using this approach, and propose important future directions for advancing our understanding of the origins of life.
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Affiliation(s)
- Norikazu Ichihashi
- Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Tetsuya Yomo
- Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
- Graduate School of Frontier Biosciences, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
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23
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Bansho Y, Furubayashi T, Ichihashi N, Yomo T. Host-parasite oscillation dynamics and evolution in a compartmentalized RNA replication system. Proc Natl Acad Sci U S A 2016; 113:4045-50. [PMID: 27035976 PMCID: PMC4839452 DOI: 10.1073/pnas.1524404113] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
To date, various cellular functions have been reconstituted in vitro such as self-replication systems using DNA, RNA, and proteins. The next important challenges include the reconstitution of the interactive networks of self-replicating species and investigating how such interactions generate complex ecological behaviors observed in nature. Here, we synthesized a simple replication system composed of two self-replicating host and parasitic RNA species. We found that the parasitic RNA eradicates the host RNA under bulk conditions; however, when the system is compartmentalized, a continuous oscillation pattern in the population dynamics of the two RNAs emerges. The oscillation pattern changed as replication proceeded mainly owing to the evolution of the host RNA. These results demonstrate that a cell-like compartment plays an important role in host-parasite ecological dynamics and suggest that the origin of the host-parasite coevolution might date back to the very early stages of the evolution of life.
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Affiliation(s)
- Yohsuke Bansho
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan; Japan Society for the Promotion of Science, Chiyoda-ku, Tokyo 102-0083, Japan
| | - Taro Furubayashi
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Norikazu Ichihashi
- Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Kawaguchi-shi, Saitama 332-0012, Japan; Graduate School of Information Science and Technology, Osaka University, Suita, Osaka 565-0871, Japan
| | - Tetsuya Yomo
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan; Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Kawaguchi-shi, Saitama 332-0012, Japan; Graduate School of Information Science and Technology, Osaka University, Suita, Osaka 565-0871, Japan
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24
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Abstract
Despite having very limited coding capacity, RNA viruses are able to withstand challenge of antiviral drugs, cause epidemics in previously exposed human populations, and, in some cases, infect multiple host species. They are able to achieve this by virtue of their ability to multiply very rapidly, coupled with their extraordinary degree of genetic heterogeneity. RNA viruses exist not as single genotypes, but as a swarm of related variants, and this genomic diversity is an essential feature of their biology. RNA viruses have a variety of mechanisms that act in combination to determine their genetic heterogeneity. These include polymerase fidelity, error-mitigation mechanisms, genomic recombination, and different modes of genome replication. RNA viruses can vary in their ability to tolerate mutations, or “genetic robustness,” and several factors contribute to this. Finally, there is evidence that some RNA viruses exist close to a threshold where polymerase error rate has evolved to maximize the possible sequence space available, while avoiding the accumulation of a lethal load of deleterious mutations. We speculate that different viruses have evolved different error rates to complement the different “life-styles” they possess.
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Affiliation(s)
- J.N. Barr
- University of Leeds, Leeds, United Kingdom
| | - R. Fearns
- Boston University School of Medicine, Boston, MA, United States
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25
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Sustainable proliferation of liposomes compatible with inner RNA replication. Proc Natl Acad Sci U S A 2015; 113:590-5. [PMID: 26711996 DOI: 10.1073/pnas.1516893113] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although challenging, the construction of a life-like compartment via a bottom-up approach can increase our understanding of life and protocells. The sustainable replication of genome information and the proliferation of phospholipid vesicles are requisites for reconstituting cell growth. However, although the replication of DNA or RNA has been developed in phospholipid vesicles, the sustainable proliferation of phospholipid vesicles has remained difficult to achieve. Here, we demonstrate the sustainable proliferation of liposomes that replicate RNA within them. Nutrients for RNA replication and membranes for liposome proliferation were combined by using a modified freeze-thaw technique. These liposomes showed fusion and fission compatible with RNA replication and distribution to daughter liposomes. The RNAs in daughter liposomes were repeatedly used as templates in the next RNA replication and were distributed to granddaughter liposomes. Liposome proliferation was achieved by 10 cycles of iterative culture operation. Therefore, we propose the use of culturable liposomes as an advanced protocell model with the implication that the concurrent supplement of both the membrane material and the nutrients of inner reactions might have enabled protocells to grow sustainably.
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26
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Ichihashi N, Aita T, Motooka D, Nakamura S, Yomo T. Periodic Pattern of Genetic and Fitness Diversity during Evolution of an Artificial Cell-Like System. Mol Biol Evol 2015; 32:3205-14. [PMID: 26342111 DOI: 10.1093/molbev/msv189] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Genetic and phenotypic diversity are the basis of evolution. Despite their importance, however, little is known about how they change over the course of evolution. In this study, we analyzed the dynamics of the adaptive evolution of a simple evolvable artificial cell-like system using single-molecule real-time sequencing technology that reads an entire single artificial genome. We found that the genomic RNA population increases in fitness intermittently, correlating with a periodic pattern of genetic and fitness diversity produced by repeated diversification and domination. In the diversification phase, a genomic RNA population spreads within a genetic space by accumulating mutations until mutants with higher fitness are generated, resulting in an increase in fitness diversity. In the domination phase, the mutants with higher fitness dominate, decreasing both the fitness and genetic diversity. This study reveals the dynamic nature of genetic and fitness diversity during adaptive evolution and demonstrates the utility of a simplified artificial cell-like system to study evolution at an unprecedented resolution.
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Affiliation(s)
- Norikazu Ichihashi
- Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Osaka, Japan
| | - Takuyo Aita
- Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Osaka, Japan
| | - Daisuke Motooka
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Shota Nakamura
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Tetsuya Yomo
- Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Osaka, Japan Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
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27
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Chetverina HV, Chetverin AB. Identifying RNA recombination events and non-covalent RNA-RNA interactions with the molecular colony technique. Methods Mol Biol 2015; 1240:1-25. [PMID: 25352133 DOI: 10.1007/978-1-4939-1896-6_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Molecular colonies (also known under names nanocolonies, polonies, RNA or DNA colonies, PCR colonies) form when nucleic acids are amplified in a porous solid or semi-solid medium, such as a gel, which contains a system for the exponential multiplication of RNA or DNA. As an individual colony comprises many copies of a single molecule (a molecular clone), the method can be used for the detection, enumeration, and analysis of individual DNA or RNA molecules, including the products of such rare events as RNA recombinations. Here we describe protocols for the detection of RNA molecules by growing colonies of RNA (in a gel containing Qβ replicase, the RNA-dependent RNA polymerase of phage Qβ) or cDNA (in a gel containing the components of PCR), and visualizing them by hybridization with fluorescent probes directly in the gel, including in real time, or by hybridization with fluorescent or radioactive probes followed by transfer to a nylon membrane.
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Affiliation(s)
- Helena V Chetverina
- Institute of Protein Research of the Russian Academy of Sciences, Institutskaya st., 4, Pushchino, Moscow Region, 142290, Russia
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28
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Lopes AM, Dalton KP, Magalhães MJ, Parra F, Esteves PJ, Holmes EC, Abrantes J. Full genomic analysis of new variant rabbit hemorrhagic disease virus revealed multiple recombination events. J Gen Virol 2015; 96:1309-1319. [PMID: 25626685 DOI: 10.1099/vir.0.000070] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 01/22/2015] [Indexed: 12/22/2022] Open
Abstract
Rabbit hemorrhagic disease virus (RHDV), a Lagovirus of the family Caliciviridae, causes rabbit hemorrhagic disease (RHD) in the European rabbit (Oryctolagus cuniculus). The disease was first documented in 1984 in China and rapidly spread worldwide. In 2010, a new RHDV variant emerged, tentatively classified as 'RHDVb'. RHDVb is characterized by affecting vaccinated rabbits and those <2 months old, and is genetically distinct (~20 %) from older strains. To determine the evolution of RHDV, including the new variant, we generated 28 full-genome sequences from samples collected between 1994 and 2014. Phylogenetic analysis of the gene encoding the major capsid protein, VP60, indicated that all viruses sampled from 2012 to 2014 were RHDVb. Multiple recombination events were detected in the more recent RHDVb genomes, with a single major breakpoint located in the 5' region of VP60. This breakpoint divides the genome into two regions: one that encodes the non-structural proteins and another that encodes the major and minor structural proteins, VP60 and VP10, respectively. Additional phylogenetic analysis of each region revealed two types of recombinants with distinct genomic backgrounds. Recombinants always include the structural proteins of RHDVb, with non-structural proteins from non-pathogenic lagoviruses or from pathogenic genogroup 1 strains. Our results show that in contrast to the evolutionary history of older RHDV strains, recombination plays an important role in generating diversity in the newly emerged RHDVb.
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Affiliation(s)
- Ana M Lopes
- INSERM, UMR892, Université de Nantes, Nantes, France.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal.,CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal
| | - Kevin P Dalton
- Instituto Universitario de Biotecnología de Asturias, Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, Oviedo, Spain
| | - Maria J Magalhães
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal
| | - Francisco Parra
- Instituto Universitario de Biotecnología de Asturias, Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, Oviedo, Spain
| | - Pedro J Esteves
- CITS, Centro de Investigação em Tecnologias da Saúde, IPSN, CESPU, Gandra, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal.,CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Joana Abrantes
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal
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Nghe P, Hordijk W, Kauffman SA, Walker SI, Schmidt FJ, Kemble H, Yeates JAM, Lehman N. Prebiotic network evolution: six key parameters. MOLECULAR BIOSYSTEMS 2015; 11:3206-17. [DOI: 10.1039/c5mb00593k] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Akin to biological networks, prebiotic chemical networks can evolve and we have identified six key parameters that govern their evolution.
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Affiliation(s)
- Philippe Nghe
- Laboratoire de Biochimie
- CNRS – ESPCI ParisTech
- France
| | | | | | - Sara I. Walker
- School of Earth and Space Exploration and Beyond Center for Fundamental Concepts in Science
- Arizona State University
- Tempe
- USA
| | | | - Harry Kemble
- Laboratoire de Biochimie
- CNRS – ESPCI ParisTech
- France
| | | | - Niles Lehman
- Department of Chemistry
- Portland State University
- Portland
- USA
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30
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Ribozyme Activity of RNA Nonenzymatically Polymerized from 3′,5′-Cyclic GMP. ENTROPY 2013. [DOI: 10.3390/e15125362] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Usui K, Ichihashi N, Kazuta Y, Matsuura T, Yomo T. Effects of ribosomes on the kinetics of Qβ replication. FEBS Lett 2013; 588:117-23. [PMID: 24269228 DOI: 10.1016/j.febslet.2013.11.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 11/05/2013] [Accepted: 11/12/2013] [Indexed: 10/26/2022]
Abstract
Bacteriophage Qβ utilizes some host cell translation factors during replication. Previously, we constructed a kinetic model that explains replication of long RNA molecules by Qβ replicase. Here, we expanded the previous kinetic model to include the effects of ribosome concentration on RNA replication. The expanded model quantitatively explained single- and double-strand formation kinetics during replication with various ribosome concentrations for two artificial long RNAs. This expanded model and the knowledge obtained in this study provide useful frameworks to understand the precise replication mechanism of Qβ replicase with ribosomes and to design amplifiable RNA genomes in translation-coupling systems.
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Affiliation(s)
- Kimihito Usui
- Japan Science and Technology Agency (JST), ERATO, Yomo Dynamical Micro-scale Reaction Environment Project, Yamadaoka 1-5, Suita, Osaka, Japan
| | - Norikazu Ichihashi
- Japan Science and Technology Agency (JST), ERATO, Yomo Dynamical Micro-scale Reaction Environment Project, Yamadaoka 1-5, Suita, Osaka, Japan; Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka 1-5, Suita, Osaka, Japan
| | - Yasuaki Kazuta
- Japan Science and Technology Agency (JST), ERATO, Yomo Dynamical Micro-scale Reaction Environment Project, Yamadaoka 1-5, Suita, Osaka, Japan
| | - Tomoaki Matsuura
- Japan Science and Technology Agency (JST), ERATO, Yomo Dynamical Micro-scale Reaction Environment Project, Yamadaoka 1-5, Suita, Osaka, Japan; Graduate School of Engineering, Osaka University, Yamadaoka 1-5, Suita, Osaka, Japan
| | - Tetsuya Yomo
- Japan Science and Technology Agency (JST), ERATO, Yomo Dynamical Micro-scale Reaction Environment Project, Yamadaoka 1-5, Suita, Osaka, Japan; Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka 1-5, Suita, Osaka, Japan; Graduate School of Frontier Biosciences, Osaka University, Yamadaoka 1-5, Suita, Osaka, Japan.
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32
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Usui K, Ichihashi N, Kazuta Y, Matsuura T, Yomo T. Kinetic model of double-stranded RNA formation during long RNA replication by Qβ replicase. FEBS Lett 2013; 587:2565-71. [DOI: 10.1016/j.febslet.2013.06.033] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 05/29/2013] [Accepted: 06/25/2013] [Indexed: 11/28/2022]
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33
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Cabanillas L, Arribas M, Lázaro E. Evolution at increased error rate leads to the coexistence of multiple adaptive pathways in an RNA virus. BMC Evol Biol 2013; 13:11. [PMID: 23323937 PMCID: PMC3556134 DOI: 10.1186/1471-2148-13-11] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 01/11/2013] [Indexed: 11/30/2022] Open
Abstract
Background When beneficial mutations present in different genomes spread simultaneously in an asexual population, their fixation can be delayed due to competition among them. This interference among mutations is mainly determined by the rate of beneficial mutations, which in turn depends on the population size, the total error rate, and the degree of adaptation of the population. RNA viruses, with their large population sizes and high error rates, are good candidates to present a great extent of interference. To test this hypothesis, in the current study we have investigated whether competition among beneficial mutations was responsible for the prolonged presence of polymorphisms in the mutant spectrum of an RNA virus, the bacteriophage Qβ, evolved during a large number of generations in the presence of the mutagenic nucleoside analogue 5-azacytidine. Results The analysis of the mutant spectra of bacteriophage Qβ populations evolved at artificially increased error rate shows a large number of polymorphic mutations, some of them with demonstrated selective value. Polymorphisms distributed into several evolutionary lines that can compete among them, making it difficult the emergence of a defined consensus sequence. The presence of accompanying deleterious mutations, the high degree of recurrence of the polymorphic mutations, and the occurrence of epistatic interactions generate a highly complex interference dynamics. Conclusions Interference among beneficial mutations in bacteriophage Qβ evolved at increased error rate permits the coexistence of multiple adaptive pathways that can provide selective advantages by different molecular mechanisms. In this way, interference can be seen as a positive factor that allows the exploration of the different local maxima that exist in rugged fitness landscapes.
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Affiliation(s)
- Laura Cabanillas
- Centro de Astrobiología (CSIC-INTA) Ctra de Ajalvir Km 4, Torrejón de Ardoz, Madrid, 28850, Spain
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34
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Bujarski JJ. Genetic recombination in plant-infecting messenger-sense RNA viruses: overview and research perspectives. FRONTIERS IN PLANT SCIENCE 2013; 4:68. [PMID: 23533000 PMCID: PMC3607795 DOI: 10.3389/fpls.2013.00068] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 03/11/2013] [Indexed: 05/09/2023]
Abstract
RNA recombination is one of the driving forces of genetic variability in (+)-strand RNA viruses. Various types of RNA-RNA crossovers were described including crosses between the same or different viral RNAs or between viral and cellular RNAs. Likewise, a variety of molecular mechanisms are known to support RNA recombination, such as replicative events (based on internal or end-to-end replicase switchings) along with non-replicative joining among RNA fragments of viral and/or cellular origin. Such mechanisms as RNA decay or RNA interference are responsible for RNA fragmentation and trans-esterification reactions which are likely accountable for ligation of RNA fragments. Numerous host factors were found to affect the profiles of viral RNA recombinants and significant differences in recombination frequency were observed among various RNA viruses. Comparative analyses of viral sequences allowed for the development of evolutionary models in order to explain adaptive phenotypic changes and co-evolving sites. Many questions remain to be answered by forthcoming RNA recombination research. (1) How various factors modulate the ability of viral replicase to switch templates, (2) What is the intracellular location of RNA-RNA template switchings, (3) Mechanisms and factors responsible for non-replicative RNA recombination, (4) Mechanisms of integration of RNA viral sequences with cellular genomic DNA, and (5) What is the role of RNA splicing and ribozyme activity. From an evolutionary stand point, it is not known how RNA viruses parasitize new host species via recombination, nor is it obvious what the contribution of RNA recombination is among other RNA modification pathways. We do not understand why the frequency of RNA recombination varies so much among RNA viruses and the status of RNA recombination as a form of sex is not well documented.
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Affiliation(s)
- Jozef J. Bujarski
- Plant Molecular Biology Center and the Department of Biological Sciences, Northern Illinois UniversityDeKalb, IL, USA
- Laboratory of Molecular and Systems Biology, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
- *Correspondence: Jozef J. Bujarski, Plant Molecular Biology Center and the Department of Biological Sciences, Northern Illinois University, Montgomery Hall, DeKalb, IL 60115, USA. e-mail:
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35
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Routh A, Ordoukhanian P, Johnson JE. Nucleotide-resolution profiling of RNA recombination in the encapsidated genome of a eukaryotic RNA virus by next-generation sequencing. J Mol Biol 2012; 424:257-69. [PMID: 23069247 PMCID: PMC3502730 DOI: 10.1016/j.jmb.2012.10.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 10/09/2012] [Indexed: 11/25/2022]
Abstract
Next-generation sequencing has been used in numerous investigations to characterize and quantify the genetic diversity of a virus sample through the mapping of polymorphisms and measurement of mutation frequencies. Next-generation sequencing has also been employed to identify recombination events occurring within the genomes of higher organisms, for example, detecting alternative RNA splicing events and oncogenic chromosomal rearrangements. Here, we combine these two approaches to profile RNA recombination within the encapsidated genome of a eukaryotic RNA virus, flock house virus. We detect hundreds of thousands of recombination events, with single-nucleotide resolution, which result in diversity in the encapsidated genome rivaling that due to mismatch mutation. We detect previously identified defective RNAs as well as many other abundant and novel defective RNAs. Our approach is exceptionally sensitive and unbiased and requires no prior knowledge beyond the virus genome sequence. RNA recombination is a powerful driving force behind the evolution and adaptation of RNA viruses. The strategy implemented here is widely applicable and provides a highly detailed description of the complex mutational landscape of the transmissible viral genome.
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Affiliation(s)
- Andrew Routh
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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36
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Importance of parasite RNA species repression for prolonged translation-coupled RNA self-replication. ACTA ACUST UNITED AC 2012; 19:478-87. [PMID: 22520754 DOI: 10.1016/j.chembiol.2012.01.019] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2011] [Revised: 01/18/2012] [Accepted: 01/19/2012] [Indexed: 01/03/2023]
Abstract
Increasingly complex reactions are being constructed by bottom-up approaches with the aim of developing an artificial cell. We have been engaged in the construction of a translation-coupled replication system of genetic information from RNA and a reconstituted translation system. Here a mathematical model was established to gain a quantitative understanding of the complex reaction network. The sensitivity analysis predicted that the limiting factor for the present replication reaction was the appearance of parasitic replicators. We then confirmed experimentally that repression of such parasitic replicators by compartmentalization of the reaction in water-in-oil emulsions improved the duration of self-replication. We also found that the main source of the parasite was genomic RNA, probably by nonhomologous recombination. This result provided experimental evidence for the importance of parasite repression for the development of long-lasting genome replication systems.
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37
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Abstract
When RNA is replicated in cell-free systems, a ubiquitous problem is the hijacking of the system by short parasitic RNA sequences. In this issue of Chemistry & Biology, Bansho et al. show that compartmentalization into water-in-oil droplets can ameliorate this problem, but only if the droplets are small. This result helps to both recapitulate abiogenesis and optimize synthetic biology.
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38
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Saladino R, Botta G, Pino S, Costanzo G, Di Mauro E. Genetics first or metabolism first? The formamide clue. Chem Soc Rev 2012; 41:5526-65. [PMID: 22684046 DOI: 10.1039/c2cs35066a] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Life is made of the intimate interaction of metabolism and genetics, both built around the chemistry of the most common elements of the Universe (hydrogen, oxygen, nitrogen, and carbon). The transmissible interaction of metabolic and genetic cycles results in the hypercycles of organization and de-organization of chemical information, of living and non-living. The origin-of-life quest has long been split into several attitudes exemplified by the aphorisms "genetics-first" or "metabolism-first". Recently, the opposition between these approaches has been solved by more unitary theoretical and experimental frames taking into account energetic, evolutionary, proto-metabolic and environmental aspects. Nevertheless, a unitary and simple chemical frame is still needed that could afford both the precursors of the synthetic pathways eventually leading to RNA and to the key components of the central metabolic cycles, possibly connected with the synthesis of fatty acids. In order to approach the problem of the origin of life it is therefore reasonable to start from the assumption that both metabolism and genetics had a common origin, shared a common chemical frame, and were embedded under physical-chemical conditions favourable for the onset of both. The singleness of such a prebiotically productive chemical process would partake of Darwinian advantages over more complex fragmentary chemical systems. The prebiotic chemistry of formamide affords in a single and simple physical-chemical frame nucleic bases, acyclonucleosides, nucleotides, biogenic carboxylic acids, sugars, amino sugars, amino acids and condensing agents. Thus, we suggest the possibility that formamide could have jointly provided the main components for the onset of both (pre)genetic and (pre)metabolic processes. As a note of caution, we discuss the fact that these observations only indicate possible solutions at the level of organic substrates, not at the systemic chemical level.
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Affiliation(s)
- Raffaele Saladino
- Dipartimento di Agrobiologia ed Agrochimica, Università della Tuscia, Via San Camillo De Lellis, 01100 Viterbo, Italy.
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Kwon SJ, Rao ALN. Emergence of distinct brome mosaic virus recombinants is determined by the polarity of the inoculum RNA. J Virol 2012; 86:5204-20. [PMID: 22357282 PMCID: PMC3347362 DOI: 10.1128/jvi.00351-12] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Accepted: 02/14/2012] [Indexed: 12/22/2022] Open
Abstract
Despite overwhelming interest in the impact exerted by recombination during evolution of RNA viruses, the relative contribution of the polarity of inoculum templates remains poorly understood. Here, by agroinfiltrating Nicotiana benthamiana leaves, we show that brome mosaic virus (BMV) replicase is competent to initiate positive-strand [(+)-strand] synthesis on an ectopically expressed RNA3 negative strand [(-) strand] and faithfully complete the replication cycle. Consequently, we sought to examine the role of RNA polarity in BMV recombination by expressing a series of replication-defective mutants of BMV RNA3 in (+) or (-) polarity. Temporal analysis of progeny sequences revealed that the genetic makeup of the primary recombinant pool is determined by the polarity of the inoculum template. When the polarity of the inoculum template was (+), the recombinant pool that accumulated during early phases of replication was a mixture of nonhomologous recombinants. These are longer than the inoculum template length, and a nascent 3' untranslated region (UTR) of wild-type (WT) RNA1 or RNA2 was added to the input mutant RNA3 3' UTR due to end-to-end template switching by BMV replicase during (-)-strand synthesis. In contrast, when the polarity of the inoculum was (-), the progeny contained a pool of native-length homologous recombinants generated by template switching of BMV replicase with a nascent UTR from WT RNA1 or RNA2 during (+)-strand synthesis. Repair of a point mutation caused by polymerase error occurred only when the polarity of the inoculum template was (+). These results contribute to the explanation of the functional role of RNA polarity in recombination mediated by copy choice mechanisms.
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Affiliation(s)
- Sun-Jung Kwon
- Department of Plant Pathology & Microbiology, University of California, Riverside, California, USA
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40
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RNA structural elements determine frequency and sites of nonhomologous recombination in an animal plus-strand RNA virus. J Virol 2012; 86:7393-402. [PMID: 22532677 DOI: 10.1128/jvi.00864-12] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
For highly variable RNA viruses, RNA recombination significantly contributes to genetic variations which may lead to changes of virulence, adaptation to new hosts, escape from the host immune response, and emergence of new infectious agents. Using a system based on transfection of cells with synthetic nonreplicable subgenomic transcripts derived from bovine viral diarrhea virus (family Flaviviridae), the existence of a replication-independent mechanism of RNA recombination, in addition to the commonly accepted replicative copy-choice recombination, has been previously proven (A. Gallei et al., J. Virol. 78:6271-6281, 2004). To identify RNA signals involved in efficient joining of RNA molecules, RNA recombination in living cells was targeted to the 3' nontranslated region. Molecular characterization of 40 independently emerged recombinant viruses revealed that the majority of recombination sites are located in single-stranded regions of the RNA molecules. Furthermore, the results of this study showed that the frequency of RNA recombination directly correlated with the RNA amounts of both recombination partners. The frequency can be strongly increased by modification of the 5' triphosphates and 3' hydroxyls of the recombining RNA molecules to 5' hydroxyl and 3' monophosphoryl ends, respectively. Analysis of recombinants that emerged after transfection with such modified RNA molecules revealed a complete integration and efficient end-to-end joining of the recombination partner(s) in at least 80% of recombinants, while unmodified RNA molecules recombined exclusively at internal positions. These results are in line with the hypothesis that endoribonucleolytic cleavage and a subsequent ligation reaction can cause RNA recombination.
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41
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Screening of feral and wood pigeons for viruses harbouring a conserved mobile viral element: characterization of novel Astroviruses and Picornaviruses. PLoS One 2011; 6:e25964. [PMID: 22043297 PMCID: PMC3197151 DOI: 10.1371/journal.pone.0025964] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 09/13/2011] [Indexed: 01/23/2023] Open
Abstract
A highly conserved RNA-motif of yet unknown function, called stem-loop-2-like motif (s2m), has been identified in the 3′ end of the genomes of viruses belonging to different RNA virus families which infect a broad range of mammal and bird species, including Astroviridae, Picornaviridae, Coronaviridae and Caliciviridae. Since s2m is such an extremely conserved motif, it is an ideal target for screening for viruses harbouring it. In this study, we have detected and characterized novel viruses harbouring this motif in pigeons by using a s2m-specific amplification. 84% and 67% of the samples from feral pigeons and wood pigeons, respectively, were found to contain a virus harbouring s2m. Four novel viruses were identified and characterized. Two of the new viruses belong to the genus Avastrovirus in the Astroviridae family. We propose two novel species to be included in this genus, Feral pigeon astrovirus and Wood pigeon astrovirus. Two other novel viruses, Pigeon picornavirus A and Pigeon picornavirus B, belong to the Picornaviridae family, presumably to the genus Sapelovirus. Both of the novel picornaviruses harboured two adjacent s2m, called (s2m)2, suggesting a possible increased functional effect of s2m when present in two copies.
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Abstract
Recombination occurs in many RNA viruses and can be of major evolutionary significance. However, rates of recombination vary dramatically among RNA viruses, which can range from clonal to highly recombinogenic. Here, we review the factors that might explain this variation in recombination frequency and show that there is little evidence that recombination is favoured by natural selection to create advantageous genotypes or purge deleterious mutations, as predicted if recombination functions as a form of sexual reproduction. Rather, recombination rates seemingly reflect larger-scale patterns of viral genome organization, such that recombination may be a mechanistic by-product of the evolutionary pressures acting on other aspects of virus biology.
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Affiliation(s)
- Etienne Simon-Loriere
- Center for Infectious Disease Dynamics, Department of Biology, Mueller Laboratory, The Pennsylvania State University, University Park, USA.
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43
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Morel V, Fournier C, François C, Brochot E, Helle F, Duverlie G, Castelain S. Genetic recombination of the hepatitis C virus: clinical implications. J Viral Hepat 2011; 18:77-83. [PMID: 21235686 DOI: 10.1111/j.1365-2893.2010.01367.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Genetic recombination is a well-known feature of RNA viruses that plays a significant role in their evolution. Although recombination is well documented for Flaviviridae family viruses, the first natural recombinant strain of hepatitis C virus (HCV) was identified as recently as 2002. Since then, a few other natural inter-genotypic, intra-genotypic and intra-subtype recombinant HCV strains have been described. However, the frequency of recombination may have been underestimated because not all known HCV recombinants are screened for in routine practice. Furthermore, the choice of treatment regimen and its predictive outcome remain problematic as the therapeutic strategy for HCV infection is genotype dependent. HCV recombination also raises many questions concerning its mechanisms and effects on the epidemiological and physiopathological features of the virus. This review provides an update on recombinant HCV strains, the process that gives rise to recombinants and clinical implications of recombination.
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Affiliation(s)
- V Morel
- Virology Department, Amiens University Hospital Center, South Hospital, Amiens, France
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44
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Chetverina EV, Chetverin AB. Nanocolonies and diagnostics of oncological diseases associated with chromosomal translocations. BIOCHEMISTRY (MOSCOW) 2011; 75:1667-91. [DOI: 10.1134/s0006297910130109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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45
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Sztuba-Solińska J, Urbanowicz A, Figlerowicz M, Bujarski JJ. RNA-RNA recombination in plant virus replication and evolution. ANNUAL REVIEW OF PHYTOPATHOLOGY 2011; 49:415-43. [PMID: 21529157 DOI: 10.1146/annurev-phyto-072910-095351] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
RNA-RNA recombination is one of the strongest forces shaping the genomes of plant RNA viruses. The detection of recombination is a challenging task that prompted the development of both in vitro and in vivo experimental systems. In the divided genome of Brome mosaic virus system, both inter- and intrasegmental crossovers are described. Other systems utilize satellite or defective interfering RNAs (DI-RNAs) of Turnip crinkle virus, Tomato bushy stunt virus, Cucumber necrosis virus, and Potato virus X. These assays identified the mechanistic details of the recombination process, revealing the role of RNA structure and proteins in the replicase-mediated copy-choice mechanism. In copy choice, the polymerase and the nascent RNA chain from which it is synthesized switch from one RNA template to another. RNA recombination was found to mediate the rearrangement of viral genes, the repair of deleterious mutations, and the acquisition of nonself sequences influencing the phylogenetics of viral taxa. The evidence for recombination, not only between related viruses but also among distantly related viruses, and even with host RNAs, suggests that plant viruses unabashedly test recombination with any genetic material at hand.
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Affiliation(s)
- Joanna Sztuba-Solińska
- Plant Molecular Biology Center, Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois 60115, USA
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46
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47
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Ichihashi N, Matsuura T, Hosoda K, Yomo T. Identification of two forms of Q{beta} replicase with different thermal stabilities but identical RNA replication activity. J Biol Chem 2010; 285:37210-7. [PMID: 20858892 DOI: 10.1074/jbc.m110.117846] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The enzyme Qβ replicase is an RNA-dependent RNA polymerase, which plays a central role in infection by the simple single-stranded RNA virus bacteriophage Qβ. This enzyme has been used in a number of applications because of its unique activity in amplifying RNA from an RNA template. Determination of the thermal stability of Qβ replicase is important to gain an understanding of its function and potential applications, but data reported to date have been contradictory. Here, we provide evidence that these previous inconsistencies were due to the heterogeneous forms of the replicase with different stabilities. We purified two forms of replicase expressed in Escherichia coli, which differed in their thermal stability but showed identical RNA replication activity. Furthermore, we found that the replicase undergoes conversion between these forms due to oxidation, and the Cys-533 residue in the catalytic β subunit and Cys-82 residue in the EF-Tu subunit of the replicase are essential prerequisites for this conversion to occur. These results strongly suggest that the thermal stable replicase contains the intersubunit disulfide bond between these cysteines. The established strategies for isolating and purifying a thermally stable replicase should increase the usefulness of Qβ replicase in various applications, and the data regarding thermal stability obtained in this study may yield insight into the precise mechanism of infection by bacteriophage Qβ.
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Affiliation(s)
- Norikazu Ichihashi
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka 1-5, Suita, Osaka 565-0871, Japan
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48
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Zhang C, Xing D. Single-Molecule DNA Amplification and Analysis Using Microfluidics. Chem Rev 2010; 110:4910-47. [DOI: 10.1021/cr900081z] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Chunsun Zhang
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Da Xing
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China
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49
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Urabe H, Ichihashi N, Matsuura T, Hosoda K, Kazuta Y, Kita H, Yomo T. Compartmentalization in a Water-in-Oil Emulsion Repressed the Spontaneous Amplification of RNA by Qβ Replicase. Biochemistry 2010; 49:1809-13. [PMID: 20108973 DOI: 10.1021/bi901805u] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hiroya Urabe
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University
| | - Norikazu Ichihashi
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University
| | - Tomoaki Matsuura
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University
| | - Kazufumi Hosoda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University
| | - Yasuaki Kazuta
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University
| | - Hiroshi Kita
- Exploratory Research for Advanced Technology (ERATO), Japan Science and Technology Agency (JST)
| | - Tetsuya Yomo
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University
- Exploratory Research for Advanced Technology (ERATO), Japan Science and Technology Agency (JST)
- Graduate School of Frontier Biosciences, Osaka University
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Draghici HK, Varrelmann M. Evidence for similarity-assisted recombination and predicted stem-loop structure determinant in potato virus X RNA recombination. J Gen Virol 2010; 91:552-62. [PMID: 19864501 DOI: 10.1099/vir.0.014712-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Virus RNA recombination, one of the main factors for genetic variability and evolution, is thought to be based on different mechanisms. Here, the recently described in vivo potato virus X (PVX) recombination assay [Draghici, H.-K. & Varrelmann, M. (2009). J Virol 83, 7761-7769] was applied to characterize structural parameters of recombination. The assay uses an Agrobacterium-mediated expression system incorporating a PVX green fluorescent protein (GFP)-labelled full-length clone. The clone contains a partial coat protein (CP) deletion that causes defectiveness in cell-to-cell movement, together with a functional CP+3' non-translated region (ntr) transcript, in Nicotiana benthamiana leaf tissue. The structural parameters assessed were the length of sequence overlap, the distance between mutations and the degree of sequence similarity. The effects on the observed frequency of reconstitution and the composition of the recombination products were characterized. Application of four different type X intact PVX CP genes with variable composition allowed the estimation of the junction sites of precise homologous recombination. Although one template switch would have been sufficient for functional reconstitution, between one and seven template switches were observed. Use of PVX-GFP mutants with CP deletions of variable length resulted in a linear decrease of the reconstitution frequency. The critical length observed for homologous recombination was 20-50 nt. Reduction of the reconstitution frequency was obtained when a phylogenetically distant PVX type Bi CP gene was used. Finally, the prediction of CP and 3'-ntr RNA secondary structure demonstrated that recombination-junction sites were located mainly in regions of stem-loop structures, allowing the recombination observed to be categorized as similarity-assisted.
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Affiliation(s)
- Heidrun-Katharina Draghici
- Department of Crop Sciences, Section Plant Virology, University of Göttingen, Grisebachstrasse 6, D-37077 Göttingen, Germany
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