Structure of genes for virus-associated RNAI and RNAII of adenovirus type 2 (original) (raw)

Abstract

A DNA sequence, 552 base pairs in length, encoding the two "virus-associated" (VA) RNAs of adenovirus type 2 is presented. Comparison of the oligonucleotide maps of VA RNAI and VA RNII with the established sequence permits identification of the genes for these RNAs. VA RNAI is 157-160 nucleotides long and VA RNAII 158-163 nucleotides long, depending on the exact length of their heterogeneous 3' end. The genes are separated by a spacer of about 98 nucleotides. The RNAs exhibit scattered regions of primary sequence homology and can adopt secondary structures which resemble each other closely in their configuration and stability. VA RNAII is also capable of assuming a different configuration that is energetically more favorable. The data suggest that the two RNA genes may have arisen by duplication of an ancestral gene and that the folding of the RNA chain may be of importance for the function of VA RNAs. Hypothetical RNA polymerase III recognition sequences and the coding potential of the region are discussed.

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Selected References

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  1. Akusjärvi G., Pettersson U. Sequence analysis of adenovirus DNA: complete nucleotide sequence of the spliced 5' noncoding region of adenovirus 2 hexon messenger RNA. Cell. 1979 Apr;16(4):841–850. doi: 10.1016/0092-8674(79)90099-0. [DOI] [PubMed] [Google Scholar]
  2. Aleström P., Akusjärvi G., Perricaudet M., Mathews M. B., Klessig D. F., Pettersson U. The gene for polypeptide IX of adenovirus type 2 and its unspliced messenger RNA. Cell. 1980 Mar;19(3):671–681. doi: 10.1016/s0092-8674(80)80044-4. [DOI] [PubMed] [Google Scholar]
  3. Bogenhagen D. F., Sakonju S., Brown D. D. A control region in the center of the 5S RNA gene directs specific initiation of transcription: II. The 3' border of the region. Cell. 1980 Jan;19(1):27–35. doi: 10.1016/0092-8674(80)90385-2. [DOI] [PubMed] [Google Scholar]
  4. Celma M. L., Pan J., Weissman S. M. Studies of low molecular weight RNA from cells infected with adenovirus 2. I. The sequences at the 3' end of VA-RNA I. J Biol Chem. 1977 Dec 25;252(24):9032–9042. [PubMed] [Google Scholar]
  5. Celma M. L., Pan J., Weissman S. M. Studies of low molecular weight RNA from cells infected with adenovirus 2. II. Heterogeneity at the 5' end of VA-RNA I. J Biol Chem. 1977 Dec 25;252(24):9043–9046. [PubMed] [Google Scholar]
  6. Chow L. T., Broker T. R. The spliced structures of adenovirus 2 fiber message and the other late mRNAs. Cell. 1978 Oct;15(2):497–510. doi: 10.1016/0092-8674(78)90019-3. [DOI] [PubMed] [Google Scholar]
  7. Korn L. J., Brown D. D. Nucleotide sequence of Xenopus borealis oocyte 5S DNA: comparison of sequences that flank several related eucaryotic genes. Cell. 1978 Dec;15(4):1145–1156. doi: 10.1016/0092-8674(78)90042-9. [DOI] [PubMed] [Google Scholar]
  8. Kozak M. How do eucaryotic ribosomes select initiation regions in messenger RNA? Cell. 1978 Dec;15(4):1109–1123. doi: 10.1016/0092-8674(78)90039-9. [DOI] [PubMed] [Google Scholar]
  9. Kressmann A., Hofstetter H., Di Capua E., Grosschedl R., Birnstiel M. L. A tRNA gene of Xenopus laevis contains at least two sites promoting transcription. Nucleic Acids Res. 1979 Dec 11;7(7):1749–1763. doi: 10.1093/nar/7.7.1749. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Mathews M. B. Genes for VA-RNA in adenovirus 2. Cell. 1975 Oct;6(2):223–229. doi: 10.1016/0092-8674(75)90013-6. [DOI] [PubMed] [Google Scholar]
  11. Mathews M. B., Pettersson U. The low molecular weight of RNAs of adenovirus 2-infected cells. J Mol Biol. 1978 Feb 25;119(2):293–328. doi: 10.1016/0022-2836(78)90439-4. [DOI] [PubMed] [Google Scholar]
  12. Maxam A. M., Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci U S A. 1977 Feb;74(2):560–564. doi: 10.1073/pnas.74.2.560. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Nevins J. R., Darnell J. E., Jr Steps in the processing of Ad2 mRNA: poly(A)+ nuclear sequences are conserved and poly(A) addition precedes splicing. Cell. 1978 Dec;15(4):1477–1493. doi: 10.1016/0092-8674(78)90071-5. [DOI] [PubMed] [Google Scholar]
  14. Ohe K., Weissman S. M. The nucleotide sequence of a low molecular weight ribonucleic acid from cells infected with adenovirus 2. J Biol Chem. 1971 Nov 25;246(22):6991–7009. [PubMed] [Google Scholar]
  15. Pan J., Celma M. L., Weissman S. M. Studies of low molecular weight RNA from cells infected with adenovirus 2. III. The sequence of the promoter for VA-RNA I. J Biol Chem. 1977 Dec 25;252(24):9047–9054. [PubMed] [Google Scholar]
  16. Pettersson U., Philipson L. Location of sequences on the adenovirus genome coding for the 5.5S RNA. Cell. 1975 Sep;6(1):1–4. doi: 10.1016/0092-8674(75)90066-5. [DOI] [PubMed] [Google Scholar]
  17. Price R., Penman S. Transcription of the adenovirus genome by an -amanitine-sensitive ribonucleic acid polymerase in HeLa cells. J Virol. 1972 Apr;9(4):621–626. doi: 10.1128/jvi.9.4.621-626.1972. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Reich P. R., Baum S. G., Rose J. A., Rowe W. P., Weissman S. M. Nucleic acid homology studies of adenovirus type 7-SV40 interactions. Proc Natl Acad Sci U S A. 1966 Feb;55(2):336–341. doi: 10.1073/pnas.55.2.336. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Sakonju S., Bogenhagen D. F., Brown D. D. A control region in the center of the 5S RNA gene directs specific initiation of transcription: I. The 5' border of the region. Cell. 1980 Jan;19(1):13–25. doi: 10.1016/0092-8674(80)90384-0. [DOI] [PubMed] [Google Scholar]
  20. Seif I., Khoury G., Dhar R. BKV splice sequences based on analysis of preferred donor and acceptor sites. Nucleic Acids Res. 1979 Jul 25;6(10):3387–3398. doi: 10.1093/nar/6.10.3387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Söderlund H., Pettersson U., Vennström B., Philipson L., Mathews M. B. A new species of virus-coded low molecular weight RNA from cells infected with adenovirus type 2. Cell. 1976 Apr;7(4):585–593. doi: 10.1016/0092-8674(76)90209-9. [DOI] [PubMed] [Google Scholar]
  22. Telford J. L., Kressmann A., Koski R. A., Grosschedl R., Müller F., Clarkson S. G., Birnstiel M. L. Delimitation of a promoter for RNA polymerase III by means of a functional test. Proc Natl Acad Sci U S A. 1979 Jun;76(6):2590–2594. doi: 10.1073/pnas.76.6.2590. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Thimmappaya B., Jones N., Shenk T. A mutation which alters initiation of transcription by RNA polymerase III on the Ad5 chromosome. Cell. 1979 Dec;18(4):947–954. doi: 10.1016/0092-8674(79)90207-1. [DOI] [PubMed] [Google Scholar]
  24. Tinoco I., Jr, Borer P. N., Dengler B., Levin M. D., Uhlenbeck O. C., Crothers D. M., Bralla J. Improved estimation of secondary structure in ribonucleic acids. Nat New Biol. 1973 Nov 14;246(150):40–41. doi: 10.1038/newbio246040a0. [DOI] [PubMed] [Google Scholar]
  25. Vennström B., Pettersson U., Philipson L. Initiation of transcription in nuclei isolated from adenovirus infected cells. Nucleic Acids Res. 1978 Jan;5(1):205–219. doi: 10.1093/nar/5.1.205. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Vennström B., Pettersson U., Philipson L. Two initiation sites for adenovirus 5.5S RNA. Nucleic Acids Res. 1978 Jan;5(1):195–204. doi: 10.1093/nar/5.1.195. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Volckaert G., Jou W. M., Fiers W. Analysis of 32P-labeled bacteriophage MS2 RNA by a mini-fingerprinting procedure. Anal Biochem. 1976 May 7;72:433–446. doi: 10.1016/0003-2697(76)90551-0. [DOI] [PubMed] [Google Scholar]
  28. Wallace R. D., Kates J. State of adenovirus 2 deoxyribonucleic acid in the nucleus and its mode of transcription: studies with isolated viral deoxyribonucleic acid-protein complexes and isolated nuclei. J Virol. 1972 Apr;9(4):627–635. doi: 10.1128/jvi.9.4.627-635.1972. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Weil P. A., Segall J., Harris B., Ng S. Y., Roeder R. G. Faithful transcription of eukaryotic genes by RNA polymerase III in systems reconstituted with purified DNA templates. J Biol Chem. 1979 Jul 10;254(13):6163–6173. [PubMed] [Google Scholar]
  30. Weinmann R., Brendler T. G., Raskas H. J., Roeder R. G. Low molecular weight viral RNAs transcribed by RNA polymerase III during adenovirus 2 infection. Cell. 1976 Apr;7(4):557–566. doi: 10.1016/0092-8674(76)90206-3. [DOI] [PubMed] [Google Scholar]
  31. Zain S., Gingeras T. R., Bullock P., Wong G., Gelinas R. E. Determination and analysis of adenovirus-2 DNA sequences which may include signals for late messenger RNA processing. J Mol Biol. 1979 Dec 5;135(2):413–433. doi: 10.1016/0022-2836(79)90444-3. [DOI] [PubMed] [Google Scholar]
  32. Zain S., Sambrook J., Roberts R. J., Keller W., Fried M., Dunn A. R. Nucleotide sequence analysis of the leader segments in a cloned copy of adenovirus 2 fiber mRNA. Cell. 1979 Apr;16(4):851–861. doi: 10.1016/0092-8674(79)90100-4. [DOI] [PubMed] [Google Scholar]
  33. Ziff E. B., Evans R. M. Coincidence of the promoter and capped 5' terminus of RNA from the adenovirus 2 major late transcription unit. Cell. 1978 Dec;15(4):1463–1475. doi: 10.1016/0092-8674(78)90070-3. [DOI] [PubMed] [Google Scholar]