Diverse Mechanisms of RNA Recombination

Overview

Journal Mol Biol

Specialties Biochemistry
Biology

Date 2020 Mar 28

PMID 32214466

Citations 7

Authors

A P Gmyl

V I Agol

Affiliations

Soon will be listed here.

Abstract

Recombination is widespread among RNA viruses, but many molecular mechanisms of this phenomenon are still poorly understood. It was believed until recently that the only possible mechanism of RNA recombination is replicative template switching, with synthesis of a complementary strand starting on one viral RNA molecule and being completed on another. The newly synthesized RNA is a primary recombinant molecule in this case. Recent studies have revealed other mechanisms of replicative RNA recombination. In addition, recombination between the genomes of RNA viruses can be nonreplicative, resulting from a joining of preexisting parental molecules. Recombination is a potent tool providing for both the variation and conservation of the genome in RNA viruses. Replicative and nonreplicative mechanisms may contribute differently to each of these evolutionary processes. In the form of splicing, nonreplicative recombination of cell RNAs plays an important role in at least some organisms. It is conceivable that RNA recombination continues to contribute to the evolution of DNA genomes.

Citing Articles

Design of Novel Synthetic RNA Replicons Based on .

Wagner A, Mutschler H ACS Synth Biol. 2024; 13(6):1773-1780.

PMID: 38806167 PMC: 11197098. DOI: 10.1021/acssynbio.4c00097.

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.

Liu S, Mu J, Yu C, Geng G, Su C, Yuan X Biology (Basel). 2022; 11(7).

PMID: 36101429 PMC: 9312275. DOI: 10.3390/biology11071051.

From RNA World to SARS-CoV-2: The Edited Story of RNA Viral Evolution.

Kockler Z, Gordenin D Cells. 2021; 10(6).

PMID: 34202997 PMC: 8234929. DOI: 10.3390/cells10061557.

Recombination in Enteroviruses, a Multi-Step Modular Evolutionary Process.

Muslin C, Mac Kain A, Bessaud M, Blondel B, Delpeyroux F Viruses. 2019; 11(9).

PMID: 31540135 PMC: 6784155. DOI: 10.3390/v11090859.

Emergency Services of Viral RNAs: Repair and Remodeling.

Agol V, Gmyl A Microbiol Mol Biol Rev. 2018; 82(2).

PMID: 29540453 PMC: 5968460. DOI: 10.1128/MMBR.00067-17.

References

Reid C, Lazinski D . A host-specific function is required for ligation of a wide variety of ribozyme-processed RNAs. Proc Natl Acad Sci U S A. 2000; 97(1):424-9. PMC: 26679. DOI: 10.1073/pnas.97.1.424. View

Duggal R, Wimmer E . Genetic recombination of poliovirus in vitro and in vivo: temperature-dependent alteration of crossover sites. Virology. 1999; 258(1):30-41. DOI: 10.1006/viro.1999.9703. View

Figlerowicz M . Role of RNA structure in non-homologous recombination between genomic molecules of brome mosaic virus. Nucleic Acids Res. 2000; 28(8):1714-23. PMC: 102819. DOI: 10.1093/nar/28.8.1714. View

Furione M, Guillot S, Otelea D, Balanant J, Candrea A, Crainic R . Polioviruses with natural recombinant genomes isolated from vaccine-associated paralytic poliomyelitis. Virology. 1993; 196(1):199-208. DOI: 10.1006/viro.1993.1468. View

King A, McCahon D, SLADE W, Newman J . Recombination in RNA. Cell. 1982; 29(3):921-8. PMC: 7133258. DOI: 10.1016/0092-8674(82)90454-8. View

Mindich L, Qiao X, Onodera S, Gottlieb P, Strassman J . Heterologous recombination in the double-stranded RNA bacteriophage phi 6. J Virol. 1992; 66(5):2605-10. PMC: 241013. DOI: 10.1128/JVI.66.5.2605-2610.1992. View

Tang J, Breaker R . Structural diversity of self-cleaving ribozymes. Proc Natl Acad Sci U S A. 2000; 97(11):5784-9. PMC: 18511. DOI: 10.1073/pnas.97.11.5784. View

Wierzchoslawski R, Dzianott A, Kunimalayan S, Bujarski J . A transcriptionally active subgenomic promoter supports homologous crossovers in a plus-strand RNA virus. J Virol. 2003; 77(12):6769-76. PMC: 156210. DOI: 10.1128/jvi.77.12.6769-6776.2003. View

Lukashev A, Lashkevich V, Koroleva G, Ilonen J, Hinkkanen A . Recombination in uveitis-causing enterovirus strains. J Gen Virol. 2004; 85(Pt 2):463-470. DOI: 10.1099/vir.0.19469-0. View

10.

Nagy P, Zhang C, Simon A . Dissecting RNA recombination in vitro: role of RNA sequences and the viral replicase. EMBO J. 1998; 17(8):2392-403. PMC: 1170582. DOI: 10.1093/emboj/17.8.2392. View

11.

Nagy P, Bujarski J . Targeting the site of RNA-RNA recombination in brome mosaic virus with antisense sequences. Proc Natl Acad Sci U S A. 1993; 90(14):6390-4. PMC: 46937. DOI: 10.1073/pnas.90.14.6390. View

12.

Kassavetis G, Geiduschek E . RNA polymerase marching backward. Science. 1993; 259(5097):944-5. DOI: 10.1126/science.7679800. View

13.

Bujarski J, Kaesberg P . Genetic recombination between RNA components of a multipartite plant virus. Nature. 1986; 321(6069):528-31. PMC: 7095370. DOI: 10.1038/321528a0. View

14.

Baroth M, Orlich M, Thiel H, Becher P . Insertion of cellular NEDD8 coding sequences in a pestivirus. Virology. 2000; 278(2):456-66. DOI: 10.1006/viro.2000.0644. View

15.

Morl M, Schmelzer C . Integration of group II intron bI1 into a foreign RNA by reversal of the self-splicing reaction in vitro. Cell. 1990; 60(4):629-36. DOI: 10.1016/0092-8674(90)90666-3. View

16.

Lukashev A, Lashkevich V, Ivanova O, Koroleva G, Hinkkanen A, Ilonen J . Recombination in circulating enteroviruses. J Virol. 2003; 77(19):10423-31. PMC: 228507. DOI: 10.1128/jvi.77.19.10423-10431.2003. View

17.

Charini W, Todd S, Gutman G, Semler B . Transduction of a human RNA sequence by poliovirus. J Virol. 1994; 68(10):6547-52. PMC: 237075. DOI: 10.1128/JVI.68.10.6547-6552.1994. View

18.

Monroe S, Schlesinger S . RNAs from two independently isolated defective interfering particles of Sindbis virus contain a cellular tRNA sequence at their 5' ends. Proc Natl Acad Sci U S A. 1983; 80(11):3279-83. PMC: 394024. DOI: 10.1073/pnas.80.11.3279. View

19.

Pilipenko E, Gmyl A, MASLOVA S, Svitkin Y, Sinyakov A, Agol V . Prokaryotic-like cis elements in the cap-independent internal initiation of translation on picornavirus RNA. Cell. 1992; 68(1):119-31. DOI: 10.1016/0092-8674(92)90211-t. View

20.

Qi F, Ridpath J, Berry E . Insertion of a bovine SMT3B gene in NS4B and duplication of NS3 in a bovine viral diarrhea virus genome correlate with the cytopathogenicity of the virus. Virus Res. 1998; 57(1):1-9. DOI: 10.1016/s0168-1702(98)00073-2. View