Abstract
The Drosophila Nanos protein is a localized repressor of hunchback mRNA translation in the early embryo, and is required for the establishment of the anterior-posterior body axis. Analysis of nanos mutants reveals that a small, evolutionarily conserved, C-terminal region is essential for Nanos function in vivo, while no other single portion of the Nanos protein is absolutely required. Within the C-terminal region are two unusual Cys-Cys-His-Cys (CCHC) motifs that are potential zinc-binding sites. Using absorption spectroscopy and NMR we demonstrate that the CCHC motifs each bind one equivalent of zinc with high affinity. nanos mutations disrupting metal binding at either of these two sites in vitro abolish Nanos translational repression activity in vivo. We show that full-length and C-terminal Nanos proteins bind to RNA in vitro with high affinity, but with little sequence specificity. Mutations affecting the hunchback mRNA target sites for Nanos-dependent translational repression were found to disrupt translational repression in vivo, but had little effect on Nanos RNA binding in vitro. Thus, the Nanos zinc domain does not specifically recognize target hunchback RNA sequences, but might interact with RNA in the context of a larger ribonucleoprotein complex.
Full Text
The Full Text of this article is available as a PDF (503.3 KB).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Barker D. D., Wang C., Moore J., Dickinson L. K., Lehmann R. Pumilio is essential for function but not for distribution of the Drosophila abdominal determinant Nanos. Genes Dev. 1992 Dec;6(12A):2312–2326. doi: 10.1101/gad.6.12a.2312. [DOI] [PubMed] [Google Scholar]
- Barlow P. N., Luisi B., Milner A., Elliott M., Everett R. Structure of the C3HC4 domain by 1H-nuclear magnetic resonance spectroscopy. A new structural class of zinc-finger. J Mol Biol. 1994 Mar 25;237(2):201–211. doi: 10.1006/jmbi.1994.1222. [DOI] [PubMed] [Google Scholar]
- Bartel D. P., Zapp M. L., Green M. R., Szostak J. W. HIV-1 Rev regulation involves recognition of non-Watson-Crick base pairs in viral RNA. Cell. 1991 Nov 1;67(3):529–536. doi: 10.1016/0092-8674(91)90527-6. [DOI] [PubMed] [Google Scholar]
- Berg J. M., Shi Y. The galvanization of biology: a growing appreciation for the roles of zinc. Science. 1996 Feb 23;271(5252):1081–1085. doi: 10.1126/science.271.5252.1081. [DOI] [PubMed] [Google Scholar]
- Berg J. M. Zinc finger domains: hypotheses and current knowledge. Annu Rev Biophys Biophys Chem. 1990;19:405–421. doi: 10.1146/annurev.bb.19.060190.002201. [DOI] [PubMed] [Google Scholar]
- Clemens K. R., Wolf V., McBryant S. J., Zhang P., Liao X., Wright P. E., Gottesfeld J. M. Molecular basis for specific recognition of both RNA and DNA by a zinc finger protein. Science. 1993 Apr 23;260(5107):530–533. doi: 10.1126/science.8475383. [DOI] [PubMed] [Google Scholar]
- Curtis D., Apfeld J., Lehmann R. nanos is an evolutionarily conserved organizer of anterior-posterior polarity. Development. 1995 Jun;121(6):1899–1910. doi: 10.1242/dev.121.6.1899. [DOI] [PubMed] [Google Scholar]
- Curtis D., Lehmann R., Zamore P. D. Translational regulation in development. Cell. 1995 Apr 21;81(2):171–178. doi: 10.1016/0092-8674(95)90325-9. [DOI] [PubMed] [Google Scholar]
- Darlix J. L., Lapadat-Tapolsky M., de Rocquigny H., Roques B. P. First glimpses at structure-function relationships of the nucleocapsid protein of retroviruses. J Mol Biol. 1995 Dec 8;254(4):523–537. doi: 10.1006/jmbi.1995.0635. [DOI] [PubMed] [Google Scholar]
- Feuerstein R., Wang X., Song D., Cooke N. E., Liebhaber S. A. The LIM/double zinc-finger motif functions as a protein dimerization domain. Proc Natl Acad Sci U S A. 1994 Oct 25;91(22):10655–10659. doi: 10.1073/pnas.91.22.10655. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Freyd G., Kim S. K., Horvitz H. R. Novel cysteine-rich motif and homeodomain in the product of the Caenorhabditis elegans cell lineage gene lin-11. Nature. 1990 Apr 26;344(6269):876–879. doi: 10.1038/344876a0. [DOI] [PubMed] [Google Scholar]
- Gavis E. R., Lehmann R. Localization of nanos RNA controls embryonic polarity. Cell. 1992 Oct 16;71(2):301–313. doi: 10.1016/0092-8674(92)90358-j. [DOI] [PubMed] [Google Scholar]
- Gill S. C., von Hippel P. H. Calculation of protein extinction coefficients from amino acid sequence data. Anal Biochem. 1989 Nov 1;182(2):319–326. doi: 10.1016/0003-2697(89)90602-7. [DOI] [PubMed] [Google Scholar]
- Green L. M., Berg J. M. A retroviral Cys-Xaa2-Cys-Xaa4-His-Xaa4-Cys peptide binds metal ions: spectroscopic studies and a proposed three-dimensional structure. Proc Natl Acad Sci U S A. 1989 Jun;86(11):4047–4051. doi: 10.1073/pnas.86.11.4047. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hommel U., Zurini M., Luyten M. Solution structure of a cysteine rich domain of rat protein kinase C. Nat Struct Biol. 1994 Jun;1(6):383–387. doi: 10.1038/nsb0694-383. [DOI] [PubMed] [Google Scholar]
- Hülskamp M., Pfeifle C., Tautz D. A morphogenetic gradient of hunchback protein organizes the expression of the gap genes Krüppel and knirps in the early Drosophila embryo. Nature. 1990 Aug 9;346(6284):577–580. doi: 10.1038/346577a0. [DOI] [PubMed] [Google Scholar]
- Karlsson O., Thor S., Norberg T., Ohlsson H., Edlund T. Insulin gene enhancer binding protein Isl-1 is a member of a novel class of proteins containing both a homeo- and a Cys-His domain. Nature. 1990 Apr 26;344(6269):879–882. doi: 10.1038/344879a0. [DOI] [PubMed] [Google Scholar]
- Klug A., Schwabe J. W. Protein motifs 5. Zinc fingers. FASEB J. 1995 May;9(8):597–604. [PubMed] [Google Scholar]
- Lee M. S., Cavanagh J., Wright P. E. Complete assignment of the 1H NMR spectrum of a synthetic zinc finger from Xfin. Sequential resonance assignments and secondary structure. FEBS Lett. 1989 Aug 28;254(1-2):159–164. doi: 10.1016/0014-5793(89)81030-0. [DOI] [PubMed] [Google Scholar]
- Lim W. A., Sauer R. T., Lander A. D. Analysis of DNA-protein interactions by affinity coelectrophoresis. Methods Enzymol. 1991;208:196–210. doi: 10.1016/0076-6879(91)08014-9. [DOI] [PubMed] [Google Scholar]
- Macdonald P. M. The Drosophila pumilio gene: an unusually long transcription unit and an unusual protein. Development. 1992 Jan;114(1):221–232. doi: 10.1242/dev.114.1.221. [DOI] [PubMed] [Google Scholar]
- Michelsen J. W., Schmeichel K. L., Beckerle M. C., Winge D. R. The LIM motif defines a specific zinc-binding protein domain. Proc Natl Acad Sci U S A. 1993 May 15;90(10):4404–4408. doi: 10.1073/pnas.90.10.4404. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Michelsen J. W., Sewell A. K., Louis H. A., Olsen J. I., Davis D. R., Winge D. R., Beckerle M. C. Mutational analysis of the metal sites in an LIM domain. J Biol Chem. 1994 Apr 15;269(15):11108–11113. [PubMed] [Google Scholar]
- Mosquera L., Forristall C., Zhou Y., King M. L. A mRNA localized to the vegetal cortex of Xenopus oocytes encodes a protein with a nanos-like zinc finger domain. Development. 1993 Jan;117(1):377–386. doi: 10.1242/dev.117.1.377. [DOI] [PubMed] [Google Scholar]
- Murata Y., Wharton R. P. Binding of pumilio to maternal hunchback mRNA is required for posterior patterning in Drosophila embryos. Cell. 1995 Mar 10;80(5):747–756. doi: 10.1016/0092-8674(95)90353-4. [DOI] [PubMed] [Google Scholar]
- Ono Y., Fujii T., Igarashi K., Kuno T., Tanaka C., Kikkawa U., Nishizuka Y. Phorbol ester binding to protein kinase C requires a cysteine-rich zinc-finger-like sequence. Proc Natl Acad Sci U S A. 1989 Jul;86(13):4868–4871. doi: 10.1073/pnas.86.13.4868. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Párraga G., Horvath S. J., Eisen A., Taylor W. E., Hood L., Young E. T., Klevit R. E. Zinc-dependent structure of a single-finger domain of yeast ADR1. Science. 1988 Sep 16;241(4872):1489–1492. doi: 10.1126/science.3047872. [DOI] [PubMed] [Google Scholar]
- Párraga G., Horvath S., Hood L., Young E. T., Klevit R. E. Spectroscopic studies of wild-type and mutant "zinc finger" peptides: determinants of domain folding and structure. Proc Natl Acad Sci U S A. 1990 Jan;87(1):137–141. doi: 10.1073/pnas.87.1.137. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Pérez-Alvarado G. C., Miles C., Michelsen J. W., Louis H. A., Winge D. R., Beckerle M. C., Summers M. F. Structure of the carboxy-terminal LIM domain from the cysteine rich protein CRP. Nat Struct Biol. 1994 Jun;1(6):388–398. doi: 10.1038/nsb0694-388. [DOI] [PubMed] [Google Scholar]
- Quest A. F., Bardes E. S., Bell R. M. A phorbol ester binding domain of protein kinase C gamma. Deletion analysis of the Cys2 domain defines a minimal 43-amino acid peptide. J Biol Chem. 1994 Jan 28;269(4):2961–2970. [PubMed] [Google Scholar]
- Rajavashisth T. B., Taylor A. K., Andalibi A., Svenson K. L., Lusis A. J. Identification of a zinc finger protein that binds to the sterol regulatory element. Science. 1989 Aug 11;245(4918):640–643. doi: 10.1126/science.2562787. [DOI] [PubMed] [Google Scholar]
- Schmeichel K. L., Beckerle M. C. The LIM domain is a modular protein-binding interface. Cell. 1994 Oct 21;79(2):211–219. doi: 10.1016/0092-8674(94)90191-0. [DOI] [PubMed] [Google Scholar]
- Schwabe J. W., Chapman L., Finch J. T., Rhodes D. The crystal structure of the estrogen receptor DNA-binding domain bound to DNA: how receptors discriminate between their response elements. Cell. 1993 Nov 5;75(3):567–578. doi: 10.1016/0092-8674(93)90390-c. [DOI] [PubMed] [Google Scholar]
- Schwabe J. W., Klug A. Zinc mining for protein domains. Nat Struct Biol. 1994 Jun;1(6):345–349. doi: 10.1038/nsb0694-345. [DOI] [PubMed] [Google Scholar]
- Shamoo Y., Webster K. R., Williams K. R., Konigsberg W. H. A retrovirus-like zinc domain is essential for translational repression of bacteriophage T4 gene 32. J Biol Chem. 1991 May 5;266(13):7967–7970. [PubMed] [Google Scholar]
- Shi Y., Beger R. D., Berg J. M. Metal binding properties of single amino acid deletion mutants of zinc finger peptides: studies using cobalt(II) as a spectroscopic probe. Biophys J. 1993 Mar;64(3):749–753. doi: 10.1016/S0006-3495(93)81435-8. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Tautz D., Pfeifle C. A non-radioactive in situ hybridization method for the localization of specific RNAs in Drosophila embryos reveals translational control of the segmentation gene hunchback. Chromosoma. 1989 Aug;98(2):81–85. doi: 10.1007/BF00291041. [DOI] [PubMed] [Google Scholar]
- Theurkauf W. E., Baum H., Bo J., Wensink P. C. Tissue-specific and constitutive alpha-tubulin genes of Drosophila melanogaster code for structurally distinct proteins. Proc Natl Acad Sci U S A. 1986 Nov;83(22):8477–8481. doi: 10.1073/pnas.83.22.8477. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Tzfati Y., Abeliovich H., Avrahami D., Shlomai J. Universal minicircle sequence binding protein, a CCHC-type zinc finger protein that binds the universal minicircle sequence of trypanosomatids. Purification and characterization. J Biol Chem. 1995 Sep 8;270(36):21339–21345. doi: 10.1074/jbc.270.36.21339. [DOI] [PubMed] [Google Scholar]
- Wang C., Dickinson L. K., Lehmann R. Genetics of nanos localization in Drosophila. Dev Dyn. 1994 Feb;199(2):103–115. doi: 10.1002/aja.1001990204. [DOI] [PubMed] [Google Scholar]
- Wharton R. P., Struhl G. RNA regulatory elements mediate control of Drosophila body pattern by the posterior morphogen nanos. Cell. 1991 Nov 29;67(5):955–967. doi: 10.1016/0092-8674(91)90368-9. [DOI] [PubMed] [Google Scholar]