Sm-like proteins in Eubacteria: The crystal structure of the Hfq protein from Escherichia coli

Nucleic Acids Research

Volumn 31, Issue 14, 2003, Pages 4091-4098

  Sauter, Claude ^a,b   Basquin, Jérôme ^a   Suck, Dietricht ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b INST DE BIOL MOLEC ET CELLULAIRE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ESCHERICHIA COLI PROTEIN; MONOMER; OLIGOMER; PROTEIN HFQ; PROTEIN SM; RNA; RNA BINDING PROTEIN; UNCLASSIFIED DRUG; AUTOANTIGEN; HFQ PROTEIN, E COLI; HOST FACTOR 1; SM NUCLEAR ANTIGENS; SMALL NUCLEAR RIBONUCLEOPROTEIN;

ARCHAEBACTERIUM; ARTICLE; BIOCHEMISTRY; CONTROLLED STUDY; CRYSTAL STRUCTURE; DATA ANALYSIS; EUBACTERIUM; EUKARYOTE; GENETIC CONSERVATION; METHANOCOCCUS JANNASCHII; NONHUMAN; ORTHOLOGY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FOLDING; RNA BINDING; STAPHYLOCOCCUS AUREUS; STRUCTURE ANALYSIS; AMINO ACID SEQUENCE; BACTERIUM; CHEMISTRY; DIMERIZATION; GENETICS; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; X RAY CRYSTALLOGRAPHY;

ARCHAEA; BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; EUKARYOTA; HOMO; METHANOCALDOCOCCUS JANNASCHII; METHANOCOCCUS; NEGIBACTERIA; STAPHYLOCOCCUS; STAPHYLOCOCCUS AUREUS;

AMINO ACID SEQUENCE; AUTOANTIGENS; BACTERIA; CRYSTALLOGRAPHY, X-RAY; DIMERIZATION; ESCHERICHIA COLI PROTEINS; EVOLUTION, MOLECULAR; HOST FACTOR 1 PROTEIN; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; RIBONUCLEOPROTEINS, SMALL NUCLEAR; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 0242380623     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg480     Document Type: Article

References (44)

1. Franze de Fernandez,M.T., Hayward,W.S. and August,J.T. (1972) Bacterial proteins required for replication of phage Q ribonucleic acid. Purification and properties of host factor I, a ribonucleic acid-binding protein. J. Biol. Chem., 247, 824-831.
2. Tsui,H.C., Leung,H.C. and Winkler,M.E. (1994) Characterization of broadly pleiotropic phenotypes caused by an hfq insertion mutation in Escherichia coli K-12. Mol. Microbiol., 13, 35-49.
3. Brown,L. and Elliott,T. (1996) Efficient translation of the RpoS sigma factor in Salmonella typhimurium requires host factor I, an RNA-binding protein encoded by the hfq gene. J. Bacteriol., 178, 3763-3770.
4. Muffler,A., Fischer,D. and Hengge-Aronis,R. (1996) The RNA-binding protein HF-I, known as a host factor for phage Qbeta RNA replication, is essential for rpoS translation in Escherichia coli. Genes Dev., 10, 1143-1151.
5. Zhang,A., Altuvia,S., Tiwari,A., Argaman,L., Hengge-Aronis,R. and Storz,G. (1998) The OxyS regulatory RNA represses rpoS translation and binds the Hfq (HF-I) protein. EMBO J., 17, 6061-6068.
6. Vytvytska,O., Moll,I., Kaberdin,V.R., von Gabain,A. and Bläsi,U. (2000) Hfq (HF1) stimulates ompA mRNA decay by interfering with ribosome binding. Genes Dev., 14, 1109-1118.
7. Sledjeski,D.D., Whitman,C. and Zhang,A. (2001) Hfq is necessary for regulation by the untranslated RNA DsrA. J. Bacteriol., 183, 1997-2005.
8. Hajnsdorf,E. and Régnier,P. (2000) Host factor Hfq of Escherichia coli stimulates elongation of poly(A) tails by poly(A) polymerase I. Proc. Natl Acad. Sci. USA, 97, 1501-1505.
9. Wassarman,K.M., Repoila,F., Rosenow,C., Storz,G. and Gottesman,S. (2001) Identification of novel small RNAs using comparative genomics and microarrays. Genes Dev., 15, 1637-1651.
10. Senear,A.W. and Steitz,J.A. (1976) Site-specific interaction of Qbeta host factor and ribosomal protein S1 with Qbeta and R17 bacteriophage RNAs. J. Biol. Chem., 251, 1902-1912.
11. Zhang,A., Wassarman,K.M., Ortega,J., Steven,A.C. and Storz,G. (2002) The Sm-like Hfq protein increases OxyS RNA interaction with target mRNAs. Mol. Cell, 9, 11-22.
12. Møller,T., Franch,T., Hojrup,P., Keene,D.R., Bachinger,H.P., Brennan,R.G. and Valentin-Hansen,P. (2002) Hfq: a bacterial Sm-like protein that mediates RNA-RNA interaction. Mol. Cell, 9, 23-30.
13. Brescia,C.C., Mikulecky,P.J., Feig,A.L. and Sledjeski,D.D. (2003) Identification of the Hfq-binding site on DsrA RNA: Hfq binds without altering DsrA secondary structure. RNA, 9, 33-43.
14. Moll,I., Leitsch,D., Steinhauser,T. and Bläsi,U. (2003) RNA chaperone activity of the Sm-like Hfq protein. EMBO Rep., 4, 284-289.
15. Hermann,H., Fabrizio,P., Raker,V.A., Foulaki,K., Hornig,H., Brahms,H. and Lührmann,R. (1995) snRNP Sm proteins share two evolutionarily conserved sequence motifs which are involved in Sm protein-protein interactions. EMBO J., 14, 2076-2088.
16. Séraphin,B. (1995) Sm and Sm-like proteins belong to a large family: identification of proteins of the U6 as well as the U1, U2, U4 and U5 snRNPs. EMBO J., 14, 2089-2098.
17. Salgado-Garrido,J., Bragado-Nilsson,E., Kandels-Lewis,S. and Séraphin,B. (1999) Sm and Sm-like proteins assemble in two related complexes of deep evolutionary origin. EMBO J., 18, 3451-3462.
18. Kambach,C., Walke,S., Young,R., Avis,J.M., de la Fortelle,E., Raker,V.A., Lührmann,R., Li,J. and Nagai,K. (1999) Crystal structures of two Sm protein complexes and their implications for the assembly of the spliceosomal snRNPs. Cell, 96, 375-387.
19. Achsel,T., Brahms,H., Kastner,B., Bachi,A., Wilm,M. and Lührmann,R. (1999) A doughnut-shaped heteromer of human Sm-like proteins binds to the 3′-end of U6 snRNA, thereby facilitating U4/U6 duplex formation in vitro. EMBO J., 18, 5789-5802.
20. Will,C.L. and Lührmann,R. (2001) Spliceosomal UsnRNP biogenesis, structure and function. Curr. Opin. Cell Biol., 13, 290-301.
21. Törö,I., Thore,S., Mayer,C., Basquin,J., Séraphin,B. and Suck,D. (2001) RNA binding in an Sm core domain: X-ray structure and functional analysis of an archaeal Sm protein complex. EMBO J., 20, 2293-2303.
22. Thore,S., Mayer,C., Sauter,C., Weeks,S. and Suck,D. (2003) Crystal structures of the Pyrococcus abyssi Sm core and its complex with RNA. Common features of RNA binding in Archaea and Eukarya. J. Biol. Chem., 278, 1239-1247.
23. Schumacher,M.A., Pearson,R.F., Møller,T., Valentin-Hansen,P. and Brennan,R.G. (2002) Structures of the pleiotropic translational regulator Hfq and an Hfq-RNA complex: a bacterial Sm-like protein. EMBO J., 21, 3546-3556.
24. Arluison,V., Derreumaux,P., Allemand,F., Folichon,M., Hajnsdorf,E. and Régnier,P. (2002) Structural modelling of the Sm-like protein Hfq from Escherichia coli. J. Mol. Biol., 320, 705-712.
25. Sun,X., Zhulin,I. and Wartell,R.M. (2002) Predicted structure and phyletic distribution of the RNA-binding protein Hfq. Nucleic Acids Res., 30, 3662-3671.
26. Otwinowski,Z. and Minor,W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol., 276, 307-326.
27. CCP4 (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D, 50, 760-763.
28. Navaza,J. (1994) AMoRe: an automated package for molecular replacement. Acta Crystallogr. A, 50, 157-163.
29. Brünger,A.T., Adams,P.D., Clore,G.M., DeLano,W.L., Gros,P., Grosse-Kunstleve,R.W., Jiang,J.S., Kuszewski,J., Nilges,M., Pannu,N.S., Read,R.J., Rice,L.M., Simonson,T. and Warren,G.L. (1998) Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D, 54, 905-921.
30. Kleywegt,G.J., Zou,J.Y., Kjeldgaard,M. and Jones,T.A. (2001) Around O. In Rossmann,M.G. and Arnold,E. (eds), International Tables for Crystallography. Volume F. Crystallography of Biological Macromolecules. Kluwer Academic Publishers, Dordrecht, The Netherlands, Vol. F, pp. 353-356, 366-367.
31. Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
32. Galtier,N., Gouy,M. and Gautier,C. (1996) SEA VIEW and PHYLON: two graphic tools for sequence alignment and molecular phylogeny. Comput. Appl. Biosci., 12, 543-548.
33. Cuff,J.A., Clamp,M.E., Siddiqui,A.S., Finlay,M. and Barton,G.J. (1998) JPred: a consensus secondary structure prediction server. Bioinformatics, 14, 892-893.
34. Sonnleitner,E., Moll,I. and Bläsi,U. (2002) Functional replacement of the Escherichia coli hfq gene by the homologue of Pseudomonas aeruginosa. Microbiology, 148, 883-891.
35. Törö,I., Basquin,J., Teo-Dreher,H. and Suck,D. (2002) Archaeal Sm proteins form heptameric and hexameric complexes: crystal structures of the Sm1 and Sm2 proteins from the hyperthermophile Archaeoglobus fulgidus. J. Mol. Biol., 320, 129-142.
36. Raker,V.A., Hartmuth,K., Kastner,B. and Lührmann,R. (1999) Spliceosomal U snRNP core assembly: Sm proteins assemble onto an Sm site RNA nonanucleotide in a specific and thermodynamically stable manner. Mol. Cell. Biol., 19, 6554-6565.
37. Stark,H., Dube,P., Lührmann,R. and Kastner,B. (2001) Arrangement of RNA and proteins in the spliceosomal U1 small nuclear ribonucleoprotein particle. Nature, 409, 539-542.
38. Walke,S., Bragado-Nilsson,E., Séraphin,B. and Nagai,K. (2001) Stoichiometry of the Sm proteins in yeast spliceosomal snRNPs supports the heptamer ring model of the core domain. J. Mol. Biol., 308, 49-58.
39. Jones,S., Daley,D.T., Luscombe,N.M., Berman,H.M. and Thornton,J.M. (2001) Protein-RNA interactions: a structural analysis. Nucleic Acids Res., 29, 943-954.
40. Zhang,D., Abovich,N. and Rosbash,M. (2001) A biochemical function for the Sm complex. Mol. Cell, 7, 319-329.
41. Kajitani,M., Kato,A., Wada,A., Inokuchi,Y. and Ishihama,A. (1994) Regulation of the Escherichia coli hfq gene encoding the host factor for phage Q beta. J. Bacteriol., 176, 531-534.
42. Mura,C., Cascio,D., Sawaya,M.R. and Eisenberg,D.S. (2001) The crystal structure of a heptameric archaeal Sm protein: implications for the eukaryotic snRNP core. Proc. Natl Acad. Sci. USA, 98, 5532-5537.
43. Collins,B.M., Harrop,S.J., Kornfeld,G.D., Dawes,I.W., Curmi,P.M. and Mabbutt,B.C. (2001) Crystal structure of a heptameric Sm-like protein complex from archaea: implications for the structure and evolution of snRNPs. J. Mol. Biol., 309, 915-923.
44. Laskowski,R.A., MacArthur,M.W., Moss,D.S. and Thornton,J.M. (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr., 26, 283-291.