SpringerProtocols: Abstract: Studying Vaccinia Virus RNA Processing In Vitro

Studying Vaccinia Virus RNA Processing In Vitro

By: Paul D. Gershon²

Abstract

Full Text

Download PDF (156K)

The study and use of vaccinia virus-derived RNA-modifying proteins has made a significant contribution to molecular biology. Here, the purification and assay of two such proteins, comprising the vaccinia poly(A) polymerase/cap-specific mRNA 2′-O-methyltransferase, is described.

Affiliation(s): (2) Institute of Biosciences and Technology, Center for Genome Research, Texas A&M University Health Science Center, Houston, TX

Book Title: Vaccinia Virus and Poxvirology: Methods and Protocols

Series: Methods in Molecular Biology | Volume: 269 | Pub. Date: Apr-19-2004 | Page Range: 151-167 | DOI: 10.1385/1-59259-789-0:151

Subject: Microbiology

Key Words: Cap - poly(A) - mRNA - protein purification

References

Download References

1.	Wei, C. M. and Moss, B. (1975) Methylated nucleotides block 5′-terminus of vaccinia virus mRNA. Proc. Natl. Acad. Sci. USA 72, 318–322.

2.	Kates, J. and Beeson, J. (1970) Ribonucleic acid synthesis in vaccinia virus II. Synthesis of polyriboadenylic acid. J. Mol. Biol. 50, 19–33.

3.	Martin, S. A., Paoletti, E., and Moss, B. (1975) Purification of mRNA guanylyltransferase and mRNA (guanine-7-)-methyltransferase from vaccinia virions. J. Biol. Chem. 250, 9322–9329.

4.	Moss, B., Rosenblum, E. N., and Gershowitz, A. (1975) Characterization of a polyriboadenylate polymerase from vaccinia virions. J. Biol. Chem. 250, 4722–4729.

5.	Moss, B., Barbosa, E., and Keith, J. M. (1979) Specificity of mRNA methyltransferases, in Transmethylation (Usdin, E., Borchardt, R. T., and Creveling, C. R., eds.), Elsevier, North-Holland, New York, pp. 373–380.

6.	Boone, R. F. and Moss, B. (1977) Methylated 5′ terminal sequences of vaccinia virus mRNA species made in vivo at early and late times after infection. J. Virol. 79, 67–80.

7.	Nevins, J. R. and Joklik, W. K. (1975) Poly(A) sequences of vaccinia virus messenger RNA: Nature, mode of addition and function during translation in vitro and in vivo. Virol. 63, 1–14.

8.	Martin, S. A. and Moss, B. (1975) Modification of RNA by mRNA guanylyltransferase and mRNA (guanine-7-)methyltransferase from vaccinia virions. J. Biol. Chem. 250, 9330–9335.

9.	Shuman, S. (1995) Capping enzyme in eukaryotic mRNA synthesis. Prog. Nucl. Acids Res. Mol. Biol. 50, 101–129.

10.	Gershon, P. D. (1998) mRNA 3′ end formation by vaccinia virus: Mechanism of action of a heterodimeric poly(A) polymerase. Sem. Virol. 8, 343–350.

11.	Barbosa, E. and Moss, B. (1978) mRNA(nucleoside-2′-)-methyltransferase from vaccinia virus: Characteristics and substrate specificity. J. Biol. Chem. 253, 7698–7702.

12.	Barbosa, E. and Moss, B. (1978) mRNA(nucleoside-2′-)-methyltransferase from vaccinia virus: Purification and properties. J. Biol. Chem. 253, 7692–7697.

13.	Schnierle, B. S., Gershon, P. D., and Moss, B. (1992) Cap-specific mRNA (nucleoside-O^2′-)-methyltransferase and poly(A) polymerase stimulatory activities of vaccinia virus are mediated by a single protein. Proc. Natl. Acad. Sci. USA 89, 2897–2901.

14.	Hodel, A. E., Gershon, P. D., and Quiocho, F. A. (1998) Structural basis for sequence non-specific recognition of 5′-capped mRNA by a cap modifying enzyme. Mol. Cell 1, 443–447.

15.	Hodel, A. E., Gershon, P. D., Shi, X., and Quiocho, F. A. (1996) The 1.85Å structure of vaccinia protein VP39: A bifunctional enzyme that participates in the modification of both mRNA ends. Cell 85, 247–256.

16.	Hodel, A. E., Gershon, P. D., Shi, X., Wang, S.-M., and Quiocho, F. A. (1997) Specific protein recognition of an mRNA cap through its alkylated base. Nature Struct. Biol. 4, 350–354.

17.	Hu, G., Oguro, A., Li, C., Gershon, P. D., and Quiocho, F. A. (2002) The “cap-binding slot” of an mRNA cap-binding protein: Quantitative effects of aromatic sidechain choice in the double-stacking sandwich with cap. Biochemistry 41, 7677–7687.

18.	Hu, G., Gershon, P. D., Hodel, A. E., and Quiocho, F. A. (1999) mRNA cap recognition: dominant role of enhanced stacking interactions between methylated bases and protein aromatic sidechains. Proc. Natl. Acad. Sci. USA 96, 7149–7154.

19.	Shi, X., Bernhardt, T. G., Wang, S.-M., and Gershon, P. D. (1997) The surface region of the bifunctional vaccinia RNA modifying protein VP39 that interfaces with poly(A) polymerase is remote from the RNA binding cleft used for its mRNA 5′ cap methylation function. J. Biol. Chem. 272, 23292–23302.

20.	Deng, L., Johnson, L., Neveu, J. M., Hardin, S., Wang, S.-M., Lane, W. S., and Gershon, P. D. (1999) A polyadenylylation-specific RNA-contact site on the surface of the bifunctional vaccinia virus RNA modifying protein VP39 that is distinct from the mRNA 5′ end-binding “cleft”. J. Mol. Biol. 285, 1417–1427.

21.	Oguro, A., Johnson, L., and Gershon, P. D. (2002) Path of an RNA Ligand around the Surface of the Vaccinia VP39 Subunit of Its Cognate VP39-VP55 Protein Heterodimer. Chem. Biol. 9, 679–690.

22.	Hodel, A. E., Quiocho, F. A., and Gershon, P. D. (1999) VP39—an mRNA capspecific 2′-O-methyltransferase, in Structure and Function of AdoMet-Dependent Methyltransferases (Cheng, X., and Blumenthal, R. M., eds.), World Scientific Publishing Co./Imperial College Press, Singapore, pp. 255–282.

23.	Quiocho, F. A., Hu, G., and Gershon, P. D. (2000) Structural basis for mRNA cap recognition by proteins. Curr. Opin. Struct. Biol. 10, 78–86.

24.	Gershon, P. D. and Moss, B. (1996) Expression, purification, and characterization of vaccinia virus-encoded RNA and poly(A) polymerases, in Methods in Enzymology (Kuo, L. C., Olsen, D. B., and Carroll, S. S., eds.), Academic Press, Inc., Orlando, FL, pp. 208–227.

25.	Gershon, P. D. (1997) Poly(A) polymerase/cap-specific 2′-O-methyltransferase from vaccinia virus: Expression, purification, uses and protein-ligand interaction assays, in Analysis of mRNA Formation and Function, Methods in Molecular Genetics (Richter, J., ed.), Academic Press, San Diego, CA, pp. 127–148.

26.	Shi, X., Yau, P., Jose, T., and Gershon, P. D. (1996) Methyltransferase-specific domains within VP39, a bifunctional protein which participates in the modification of both mRNA ends. RNA 2, 88–101.

27.	Lockless, S. W., Cheng, H.-T., Hodel, A. E., Quiocho, F. A., and Gershon, P. D. (1998) Recognition of capped RNA substrates by VP39, the vaccinia virus-encoded mRNA cap-specific 2′-O-methyltransferase. Biochemistry 37, 8564–8574.

28.	Gershon, P. D., Shi, X., and Hodel, A. E. (1998) Evidence that the RNA methylation and poly(A) polymerase stimulatory activities of vaccinia virus protein VP39 do not impinge upon one another. Virology 246, 253–265.

29.	Johnson, L. and Gershon, P. D. (1999) RNA binding characteristics and overall topology of the vaccinia poly(A) polymerase-processivity factor complex. Nucl. Acids Res. 27, 2708–2721.

30.	Johnson, L. and Gershon, P. D. (2002) Direct detection of protein thiol derivatization by PAGE. Biotechniques 33, 1292–1295.

31.	Fuerst, T. R., Niles, E. G., Studier, F. W., and Moss, B. (1986) Eukaryotic transient-expression system based on recombinant vaccinia virus that synthesizes bacteriophage T7 RNA polymerase. Proc. Natl. Acad. Sci. USA 83, 8122–8126.

32.	Moss, B., Elroy-Stein, O., Mizukami, T., Alexander, W. A., and Fuerst, T. R. (1990) New mammalian expression vectors (product review). Nature (London) 348, 91–92.

33.	Gershon, P. D. and Moss, B. (1992) Transition from rapid processive to slow non-processive polyadenylation by vaccinia virus poly(A) polymerase catalytic subunit is regulated by the net length of the poly(A) tail. Genes Dev. 6, 1575–1586.

34.	Gershon, P. D. and Moss, B. (1993) Stimulation of poly(A) tail elongation by the VP39 subunit of the vaccinia virus-encoded poly(A) polymerase. J. Biol. Chem. 268, 2203–2210.

35.	Gershon, P. D., Ahn, B.-Y., Garfield, M., and Moss, B. (1991) Poly(A) polymerase and a dissociable polyadenylation stimulatory factor encoded by vaccinia virus. Cell 66, 1269–1278.

36.	Schnierle, B. S., Gershon, P. D., and Moss, B. (1994) Mutational analysis of a multifunctional protein, with mRNA 5′ cap-specific (nucleoside-2′-O-)-methyltransferase and 3′-adenylyltransferase stimulatory activities, encoded by vaccinia virus. J. Biol. Chem. 269, 20700–20706.

37.	Guan, K. L. and Dixon, J. E. (1991) Eukaryotic proteins expressed in Escherichia coli: An improved thrombin cleavage and purification procedure of fusion proteins with glutathione S-transferase. Anal. Biochem. 192, 262–267.

38.	Earl, P. L. and Moss, B. (1991) Preparation of cell cultures and vaccinia virus stocks, in Current Protocols in Molecular Biology (Ausubel, F. M., et al., eds.), Wiley Interscience, NY, pp. 16.16.1–16.16.7.

39.	Earl, P. E. and Moss, B. (1991) Generation of recombinant vaccinia viruses, in Current Protocols in Molecular Biology (Ausubel, F. M., et al., eds.), Wiley Interscience, NY, pp. 16.17.6–16.17.8.

40.	Shuman, S. and Moss, B. (1990) Purification and use of vaccinia virus messenger RNA capping enzyme. Methods Enzymol. 181, 170–180.

41.	Baroudy, B. M. and Moss, B. (1980) Purification and characterization of a DNAdependent RNA polymerase from vaccinia virions. J. Biol. Chem. 255, 4372–4380.

42.	Shuman, S. and Moss, B. (1988) Vaccinia virus poly(A) polymerase: Specificity for nucleotides and nucleotide analogs. J. Biol. Chem. 263, 8405–8412.

43.	Gershon, P. D. and Moss, B. (1993) Uridylate-containing RNA sequences determine specificity for binding and polyadenylation by the catalytic subunit of vaccinia virus poly(A) polymerase. EMBO J. 12, 4705–4714.

44.	Ausubel, F. M., Brent, R., Kingston, R. E., Moore, D. D., Seidman, J. G., Smith, J. A., and Struhl, K. (1987) Current Protocols in Molecular Biology, Wiley Interscience, NY.

45.	Peng, Z.-H., Sharma, V., Singleton, S., and Gershon, P. D. (2002) Synthesis and application of a chain-terminating dinucleotide mRNA cap analog. Org. Lett. 4, 161–164.

46.	Bouloy, M., Plotch, S. J., and Krug, R. M. (1980) Both the 7-methyl and 2′-Omethyl groups in the cap of mRNA strongly influence its ability to act as a primer for influenza virus RNA transcription. Proc. Natl. Acad. Sci. USA 77, 3952–3956.

47.	Plotch, S. J., Bouloy, M., Ulmanen, I., and Krug, R. M. (1981) A unique cap(m7GpppXm)-dependent influenza virion endonuclease cleaves capped RNAs to generate the primers that initiate viral RNA transcription. Cell 23, 847–858.

48.	Thomson, J. G. and Gershon, P. D. (1995) Use of vaccinia virus poly(A) polymerase for RNA 3′-end labeling with either a chain-terminating nucleotide or a short 3′ homopolymer tract. Biotechniques 19, 416–425.

Comments (Loading...)

Post comment/View all comments