A cis-acting function for the coronavirus leader in defective interfering RNA replication. (original) (raw)

• Journal List
• J Virol
• v.68(12); 1994 Dec
• PMC237289

J Virol. 1994 Dec; 68(12): 8223–8231.

Department of Microbiology, University of Tennessee, Knoxville 37996-0845.

Abstract

To test the hypothesis that the 65-nucleotide (nt) leader on subgenomic mRNAs suffices as a 5'-terminal cis-acting signal for RNA replication, a corollary to the notion that coronavirus mRNAs behave as replicons, synthetic RNA transcripts of a cloned, reporter-containing N mRNA (mRNA 7) of the bovine coronavirus with a precise 5' terminus and a 3' poly(A) of 68 nt were tested for replication after being transfected into helper virus-infected cells. No replication was observed, but synthetic transcripts of a cloned reporter-containing defective interfering (DI) RNA differing from the N mRNA construct by 433 nt of continuous 5'-proximal genomic sequence between the leader and the N open reading frame did replicate and become packaged, indicating the insufficiency of the leader alone as a 5' signal for replication of transfected RNA molecules. The leader was shown to be a necessary part of the cis-acting signal for DI RNA replication, however, since removal of terminal bases that destroyed a predicted intraleader stem-loop also destroyed replicating ability. Surprisingly, when the same stem-loop was disrupted by base substitutions, replication appeared only minimally impaired and the leader was found to have rapidly reverted to wild type during DI RNA replication, a phenomenon reminiscent of high-frequency leader switching in the mouse hepatitis coronavirus. These results suggest that once a minimal structural requirement for leader is fulfilled for initiation of DI RNA replication, the wild-type leader is strongly preferred for subsequent replication. They also demonstrate that, in contrast to reported natural mouse hepatitis coronavirus DI RNAs, the DI RNA of the bovine coronavirus does not require sequence elements originating from discontinuous downstream regions within the polymerase gene for replication or for packaging.

Full text

Full text is available as a scanned copy of the original print version. Get a printable copy (PDF file) of the complete article (2.2M), or click on a page image below to browse page by page. Links to PubMed are also available for Selected References.

Images in this article

Click on the image to see a larger version.

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

• Abraham S, Kienzle TE, Lapps W, Brian DA. Deduced sequence of the bovine coronavirus spike protein and identification of the internal proteolytic cleavage site. Virology. 1990 May;176(1):296–301. [PMC free article] [PubMed] [Google Scholar]
• Andino R, Rieckhof GE, Achacoso PL, Baltimore D. Poliovirus RNA synthesis utilizes an RNP complex formed around the 5'-end of viral RNA. EMBO J. 1993 Sep;12(9):3587–3598. [PMC free article] [PubMed] [Google Scholar]
• Baker SC, Lai MM. An in vitro system for the leader-primed transcription of coronavirus mRNAs. EMBO J. 1990 Dec;9(12):4173–4179. [PMC free article] [PubMed] [Google Scholar]
• Ball LA, Li Y. cis-acting requirements for the replication of flock house virus RNA 2. J Virol. 1993 Jun;67(6):3544–3551. [PMC free article] [PubMed] [Google Scholar]
• Brian DA, Chang RY, Hofmann MA, Sethna PB. Role of subgenomic minus-strand RNA in coronavirus replication. Arch Virol Suppl. 1994;9:173–180. [PubMed] [Google Scholar]
• Collins PL, Mink MA, Stec DS. Rescue of synthetic analogs of respiratory syncytial virus genomic RNA and effect of truncations and mutations on the expression of a foreign reporter gene. Proc Natl Acad Sci U S A. 1991 Nov 1;88(21):9663–9667. [PMC free article] [PubMed] [Google Scholar]
• de Groot RJ, van der Most RG, Spaan WJ. The fitness of defective interfering murine coronavirus DI-a and its derivatives is decreased by nonsense and frameshift mutations. J Virol. 1992 Oct;66(10):5898–5905. [PMC free article] [PubMed] [Google Scholar]
• Felgner PL, Gadek TR, Holm M, Roman R, Chan HW, Wenz M, Northrop JP, Ringold GM, Danielsen M. Lipofection: a highly efficient, lipid-mediated DNA-transfection procedure. Proc Natl Acad Sci U S A. 1987 Nov;84(21):7413–7417. [PMC free article] [PubMed] [Google Scholar]
• Fosmire JA, Hwang K, Makino S. Identification and characterization of a coronavirus packaging signal. J Virol. 1992 Jun;66(6):3522–3530. [PMC free article] [PubMed] [Google Scholar]
• Hagino-Yamagishi K, Nomoto A. In vitro construction of poliovirus defective interfering particles. J Virol. 1989 Dec;63(12):5386–5392. [PMC free article] [PubMed] [Google Scholar]
• Hofmann MA, Brian DA. A PCR-enhanced method for determining the 5' end sequence of mRNAs. PCR Methods Appl. 1991 Aug;1(1):43–45. [PubMed] [Google Scholar]
• Hofmann MA, Brian DA. Sequencing PCR DNA amplified directly from a bacterial colony. Biotechniques. 1991 Jul;11(1):30–31. [PubMed] [Google Scholar]
• Hofmann MA, Brian DA. The 5' end of coronavirus minus-strand RNAs contains a short poly(U) tract. J Virol. 1991 Nov;65(11):6331–6333. [PMC free article] [PubMed] [Google Scholar]
• Hofmann MA, Sethna PB, Brian DA. Bovine coronavirus mRNA replication continues throughout persistent infection in cell culture. J Virol. 1990 Sep;64(9):4108–4114. [PMC free article] [PubMed] [Google Scholar]
• Horton RM, Cai ZL, Ho SN, Pease LR. Gene splicing by overlap extension: tailor-made genes using the polymerase chain reaction. Biotechniques. 1990 May;8(5):528–535. [PubMed] [Google Scholar]
• Jeong YS, Makino S. Evidence for coronavirus discontinuous transcription. J Virol. 1994 Apr;68(4):2615–2623. [PMC free article] [PubMed] [Google Scholar]
• Kapke PA, Brian DA. Sequence analysis of the porcine transmissible gastroenteritis coronavirus nucleocapsid protein gene. Virology. 1986 May;151(1):41–49. [PMC free article] [PubMed] [Google Scholar]
• Kim YN, Jeong YS, Makino S. Analysis of cis-acting sequences essential for coronavirus defective interfering RNA replication. Virology. 1993 Nov;197(1):53–63. [PMC free article] [PubMed] [Google Scholar]
• Kim YN, Lai MM, Makino S. Generation and selection of coronavirus defective interfering RNA with large open reading frame by RNA recombination and possible editing. Virology. 1993 May;194(1):244–253. [PMC free article] [PubMed] [Google Scholar]
• Kunkel TA. Rapid and efficient site-specific mutagenesis without phenotypic selection. Proc Natl Acad Sci U S A. 1985 Jan;82(2):488–492. [PMC free article] [PubMed] [Google Scholar]
• Lai MM. Coronavirus: organization, replication and expression of genome. Annu Rev Microbiol. 1990;44:303–333. [PubMed] [Google Scholar]
• Lai MM. RNA recombination in animal and plant viruses. Microbiol Rev. 1992 Mar;56(1):61–79. [PMC free article] [PubMed] [Google Scholar]
• Lapps W, Hogue BG, Brian DA. Sequence analysis of the bovine coronavirus nucleocapsid and matrix protein genes. Virology. 1987 Mar;157(1):47–57. [PMC free article] [PubMed] [Google Scholar]
• Lee HJ, Shieh CK, Gorbalenya AE, Koonin EV, La Monica N, Tuler J, Bagdzhadzhyan A, Lai MM. The complete sequence (22 kilobases) of murine coronavirus gene 1 encoding the putative proteases and RNA polymerase. Virology. 1991 Feb;180(2):567–582. [PMC free article] [PubMed] [Google Scholar]
• Levis R, Weiss BG, Tsiang M, Huang H, Schlesinger S. Deletion mapping of Sindbis virus DI RNAs derived from cDNAs defines the sequences essential for replication and packaging. Cell. 1986 Jan 17;44(1):137–145. [PubMed] [Google Scholar]
• Li X, Palese P. Mutational analysis of the promoter required for influenza virus virion RNA synthesis. J Virol. 1992 Jul;66(7):4331–4338. [PMC free article] [PubMed] [Google Scholar]
• Liao CL, Lai MM. RNA recombination in a coronavirus: recombination between viral genomic RNA and transfected RNA fragments. J Virol. 1992 Oct;66(10):6117–6124. [PMC free article] [PubMed] [Google Scholar]
• Lin YJ, Lai MM. Deletion mapping of a mouse hepatitis virus defective interfering RNA reveals the requirement of an internal and discontiguous sequence for replication. J Virol. 1993 Oct;67(10):6110–6118. [PMC free article] [PubMed] [Google Scholar]
• Makino S, Joo M, Makino JK. A system for study of coronavirus mRNA synthesis: a regulated, expressed subgenomic defective interfering RNA results from intergenic site insertion. J Virol. 1991 Nov;65(11):6031–6041. [PMC free article] [PubMed] [Google Scholar]
• Makino S, Lai MM. High-frequency leader sequence switching during coronavirus defective interfering RNA replication. J Virol. 1989 Dec;63(12):5285–5292. [PMC free article] [PubMed] [Google Scholar]
• Makino S, Stohlman SA, Lai MM. Leader sequences of murine coronavirus mRNAs can be freely reassorted: evidence for the role of free leader RNA in transcription. Proc Natl Acad Sci U S A. 1986 Jun;83(12):4204–4208. [PMC free article] [PubMed] [Google Scholar]
• Masters PS, Koetzner CA, Kerr CA, Heo Y. Optimization of targeted RNA recombination and mapping of a novel nucleocapsid gene mutation in the coronavirus mouse hepatitis virus. J Virol. 1994 Jan;68(1):328–337. [PMC free article] [PubMed] [Google Scholar]
• Rice CM, Grakoui A, Galler R, Chambers TJ. Transcription of infectious yellow fever RNA from full-length cDNA templates produced by in vitro ligation. New Biol. 1989 Dec;1(3):285–296. [PubMed] [Google Scholar]
• Sawicki SG, Sawicki DL. Coronavirus transcription: subgenomic mouse hepatitis virus replicative intermediates function in RNA synthesis. J Virol. 1990 Mar;64(3):1050–1056. [PMC free article] [PubMed] [Google Scholar]
• Senanayake SD, Hofmann MA, Maki JL, Brian DA. The nucleocapsid protein gene of bovine coronavirus is bicistronic. J Virol. 1992 Sep;66(9):5277–5283. [PMC free article] [PubMed] [Google Scholar]
• Sethna PB, Hofmann MA, Brian DA. Minus-strand copies of replicating coronavirus mRNAs contain antileaders. J Virol. 1991 Jan;65(1):320–325. [PMC free article] [PubMed] [Google Scholar]
• Sethna PB, Hung SL, Brian DA. Coronavirus subgenomic minus-strand RNAs and the potential for mRNA replicons. Proc Natl Acad Sci U S A. 1989 Jul;86(14):5626–5630. [PMC free article] [PubMed] [Google Scholar]
• Tinoco I, Jr, Borer PN, Dengler B, Levin MD, Uhlenbeck OC, Crothers DM, Bralla J. Improved estimation of secondary structure in ribonucleic acids. Nat New Biol. 1973 Nov 14;246(150):40–41. [PubMed] [Google Scholar]
• van der Most RG, Bredenbeek PJ, Spaan WJ. A domain at the 3' end of the polymerase gene is essential for encapsidation of coronavirus defective interfering RNAs. J Virol. 1991 Jun;65(6):3219–3226. [PMC free article] [PubMed] [Google Scholar]
• Vidal S, Kolakofsky D. Modified model for the switch from Sendai virus transcription to replication. J Virol. 1989 May;63(5):1951–1958. [PMC free article] [PubMed] [Google Scholar]
• Yokomori K, Banner LR, Lai MM. Coronavirus mRNA transcription: UV light transcriptional mapping studies suggest an early requirement for a genomic-length template. J Virol. 1992 Aug;66(8):4671–4678. [PMC free article] [PubMed] [Google Scholar]

Articles from Journal of Virology are provided here courtesy of American Society for Microbiology (ASM)