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. 2001 Aug 1;357(Pt 3):875–880. doi: 10.1042/0264-6021:3570875

Type-1 ribosome-inactivating protein from iris (Iris hollandica var. Professor Blaauw) binds specific genomic DNA fragments.

Q Hao 1, W J Peumans 1, E J Van Damme 1
PMCID: PMC1222019  PMID: 11463360

Abstract

The capacity of IRIP, a type-1 ribosome-inactivating protein (RIP) isolated from the bulbs of Iris hollandica, to bind specific DNA sequences from a mixture of approx. 200 bp (average length) fragments of total genomic DNA from Iris genome was studied. Fragments that were preferentially bound by IRIP were enriched by several cycles of affinity binding and PCR, and were cloned and sequenced. The selected DNA fragments do not share conserved sequences, indicating that IRIP does not bind DNA fragments in a strictly sequence-specific manner. According to sequence analysis, most IRIP-bound fragments contain one or more possible free energy-stable hairpin structure(s) in their secondary structure, which may be the basis for recognition between IRIP and these DNA fragments. Some, but not all, DNA fragments moderately lower the RNA N-glycosidase activity of IRIP towards rabbit reticulocyte lysate ribosomes. IRIP does not remove adenines from the binding fragments, which implies that it does not act as a polynucleotide:adenosine glycosidase towards these DNA fragments. The selective binding of IRIP to conspecific DNA fragments is also discussed in view of the novel concept that RIPs may act as DNA-binding proteins with a regulatory activity on gene expression.

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Selected References

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

  1. Altschul S. F., Madden T. L., Schäffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997 Sep 1;25(17):3389–3402. doi: 10.1093/nar/25.17.3389. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Barbieri L., Battelli M. G., Stirpe F. Ribosome-inactivating proteins from plants. Biochim Biophys Acta. 1993 Dec 21;1154(3-4):237–282. doi: 10.1016/0304-4157(93)90002-6. [DOI] [PubMed] [Google Scholar]
  3. Barbieri L., Valbonesi P., Bonora E., Gorini P., Bolognesi A., Stirpe F. Polynucleotide:adenosine glycosidase activity of ribosome-inactivating proteins: effect on DNA, RNA and poly(A). Nucleic Acids Res. 1997 Feb 1;25(3):518–522. doi: 10.1093/nar/25.3.518. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Desvoyes B., Poyet J. L., Schlick J. L., Adami P., Jouvenot M., Dulieu P. Identification of a biological inactive complex form of pokeweed antiviral protein. FEBS Lett. 1997 Jun 30;410(2-3):303–308. doi: 10.1016/s0014-5793(97)00648-0. [DOI] [PubMed] [Google Scholar]
  5. Endo Y., Mitsui K., Motizuki M., Tsurugi K. The mechanism of action of ricin and related toxic lectins on eukaryotic ribosomes. The site and the characteristics of the modification in 28 S ribosomal RNA caused by the toxins. J Biol Chem. 1987 Apr 25;262(12):5908–5912. [PubMed] [Google Scholar]
  6. Görschen E., Dunaeva M., Hause B., Reeh I., Wasternack C., Parthier B. Expression of the ribosome-inactivating protein JIP60 from barely in transgenic tobacco leads to an abnormal phenotype and alterations on the level of translation. Planta. 1997;202(4):470–478. doi: 10.1007/s004250050151. [DOI] [PubMed] [Google Scholar]
  7. Habuka N., Miyano M., Kataoka J., Noma M. Escherichia coli ribosome is inactivated by Mirabilis antiviral protein which cleaves the N-glycosidic bond at A2660 of 23 S ribosomal RNA. J Mol Biol. 1991 Oct 5;221(3):737–743. doi: 10.1016/0022-2836(91)80168-t. [DOI] [PubMed] [Google Scholar]
  8. Hao Q., Van Damme E. J., Barre A., Sillen A., Rougé P., Engelborghs Y., Peumans W. J. Microenvironment of cysteine 242 in type-1 ribosome-inactivating protein from iris. Biochem Biophys Res Commun. 2000 Aug 28;275(2):481–487. doi: 10.1006/bbrc.2000.3338. [DOI] [PubMed] [Google Scholar]
  9. Hesselberth J. R., Miller D., Robertus J., Ellington A. D. In vitro selection of RNA molecules that inhibit the activity of ricin A-chain. J Biol Chem. 2000 Feb 18;275(7):4937–4942. doi: 10.1074/jbc.275.7.4937. [DOI] [PubMed] [Google Scholar]
  10. Hirao I., Madin K., Endo Y., Yokoyama S., Ellington A. D. RNA aptamers that bind to and inhibit the ribosome-inactivating protein, pepocin. J Biol Chem. 2000 Feb 18;275(7):4943–4948. doi: 10.1074/jbc.275.7.4943. [DOI] [PubMed] [Google Scholar]
  11. Kinzler K. W., Vogelstein B. Whole genome PCR: application to the identification of sequences bound by gene regulatory proteins. Nucleic Acids Res. 1989 May 25;17(10):3645–3653. doi: 10.1093/nar/17.10.3645. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Lee-Huang S., Kung H. F., Huang P. L., Bourinbaiar A. S., Morell J. L., Brown J. H., Huang P. L., Tsai W. P., Chen A. Y., Huang H. I. Human immunodeficiency virus type 1 (HIV-1) inhibition, DNA-binding, RNA-binding, and ribosome inactivation activities in the N-terminal segments of the plant anti-HIV protein GAP31. Proc Natl Acad Sci U S A. 1994 Dec 6;91(25):12208–12212. doi: 10.1073/pnas.91.25.12208. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Lee-Huang S., Kung H. F., Huang P. L., Huang P. L., Li B. Q., Huang P., Huang H. I., Chen H. C. A new class of anti-HIV agents: GAP31, DAPs 30 and 32. FEBS Lett. 1991 Oct 7;291(1):139–144. doi: 10.1016/0014-5793(91)81122-o. [DOI] [PubMed] [Google Scholar]
  14. Ling J., Li X., Wu X., Liu W. Topological requirements for recognition and cleavage of DNA by ribosome-inactivating proteins. Biol Chem Hoppe Seyler. 1995 Nov;376(11):637–641. doi: 10.1515/bchm3.1995.376.11.637. [DOI] [PubMed] [Google Scholar]
  15. Lord J. M., Roberts L. M., Robertus J. D. Ricin: structure, mode of action, and some current applications. FASEB J. 1994 Feb;8(2):201–208. [PubMed] [Google Scholar]
  16. Madin K., Sawasaki T., Ogasawara T., Endo Y. A highly efficient and robust cell-free protein synthesis system prepared from wheat embryos: plants apparently contain a suicide system directed at ribosomes. Proc Natl Acad Sci U S A. 2000 Jan 18;97(2):559–564. doi: 10.1073/pnas.97.2.559. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Mierendorf R. C., Pfeffer D. Direct sequencing of denatured plasmid DNA. Methods Enzymol. 1987;152:556–562. doi: 10.1016/0076-6879(87)52061-4. [DOI] [PubMed] [Google Scholar]
  18. Nicolas E., Beggs J. M., Haltiwanger B. M., Taraschi T. F. A new class of DNA glycosylase/apurinic/apyrimidinic lyases that act on specific adenines in single-stranded DNA. J Biol Chem. 1998 Jul 3;273(27):17216–17220. doi: 10.1074/jbc.273.27.17216. [DOI] [PubMed] [Google Scholar]
  19. Prestle J., Schönfelder M., Adam G., Mundry K. W. Type 1 ribosome-inactivating proteins depurinate plant 25S rRNA without species specificity. Nucleic Acids Res. 1992 Jun 25;20(12):3179–3182. doi: 10.1093/nar/20.12.3179. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Reinbothe S., Reinbothe C., Lehmann J., Becker W., Apel K., Parthier B. JIP60, a methyl jasmonate-induced ribosome-inactivating protein involved in plant stress reactions. Proc Natl Acad Sci U S A. 1994 Jul 19;91(15):7012–7016. doi: 10.1073/pnas.91.15.7012. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Stirpe F., Barbieri L., Gorini P., Valbonesi P., Bolognesi A., Polito L. Activities associated with the presence of ribosome-inactivating proteins increase in senescent and stressed leaves. FEBS Lett. 1996 Mar 18;382(3):309–312. doi: 10.1016/0014-5793(96)00188-3. [DOI] [PubMed] [Google Scholar]
  23. Taylor S., Massiah A., Lomonossoff G., Roberts L. M., Lord J. M., Hartley M. Correlation between the activities of five ribosome-inactivating proteins in depurination of tobacco ribosomes and inhibition of tobacco mosaic virus infection. Plant J. 1994 Jun;5(6):827–835. doi: 10.1046/j.1365-313x.1994.5060827.x. [DOI] [PubMed] [Google Scholar]
  24. Tumer N. E., Hwang D. J., Bonness M. C-terminal deletion mutant of pokeweed antiviral protein inhibits viral infection but does not depurinate host ribosomes. Proc Natl Acad Sci U S A. 1997 Apr 15;94(8):3866–3871. doi: 10.1073/pnas.94.8.3866. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Van Damme E. J., Barre A., Barbieri L., Valbonesi P., Rouge P., Van Leuven F., Stirpe F., Peumans W. J. Type 1 ribosome-inactivating proteins are the most abundant proteins in iris (Iris hollandica var. Professor Blaauw) bulbs: characterization and molecular cloning. Biochem J. 1997 Jun 15;324(Pt 3):963–970. doi: 10.1042/bj3240963. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Walsh T. A., Morgan A. E., Hey T. D. Characterization and molecular cloning of a proenzyme form of a ribosome-inactivating protein from maize. Novel mechanism of proenzyme activation by proteolytic removal of a 2.8-kilodalton internal peptide segment. J Biol Chem. 1991 Dec 5;266(34):23422–23427. [PubMed] [Google Scholar]
  27. Wang P., Tumer N. E. Pokeweed antiviral protein cleaves double-stranded supercoiled DNA using the same active site required to depurinate rRNA. Nucleic Acids Res. 1999 Apr 15;27(8):1900–1905. doi: 10.1093/nar/27.8.1900. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Wang Y. X., Neamati N., Jacob J., Palmer I., Stahl S. J., Kaufman J. D., Huang P. L., Huang P. L., Winslow H. E., Pommier Y. Solution structure of anti-HIV-1 and anti-tumor protein MAP30: structural insights into its multiple functions. Cell. 1999 Nov 12;99(4):433–442. doi: 10.1016/s0092-8674(00)81529-9. [DOI] [PubMed] [Google Scholar]
  29. Zamboni M., Brigotti M., Rambelli F., Montanaro L., Sperti S. High-pressure-liquid-chromatographic and fluorimetric methods for the determination of adenine released from ribosomes by ricin and gelonin. Biochem J. 1989 May 1;259(3):639–643. doi: 10.1042/bj2590639. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Zarling J. M., Moran P. A., Haffar O., Sias J., Richman D. D., Spina C. A., Myers D. E., Kuebelbeck V., Ledbetter J. A., Uckun F. M. Inhibition of HIV replication by pokeweed antiviral protein targeted to CD4+ cells by monoclonal antibodies. Nature. 1990 Sep 6;347(6288):92–95. doi: 10.1038/347092a0. [DOI] [PubMed] [Google Scholar]

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