Skip to main content
NCBI home page
The EMBO Journal logoLink to The EMBO Journal
. 1995 May 1;14(9):2076–2088. doi: 10.1002/j.1460-2075.1995.tb07199.x

snRNP Sm proteins share two evolutionarily conserved sequence motifs which are involved in Sm protein-protein interactions.

H Hermann 1, P Fabrizio 1, V A Raker 1, K Foulaki 1, H Hornig 1, H Brahms 1, R Lührmann 1
PMCID: PMC398308  PMID: 7744013

Abstract

The spliceosomal small nuclear ribonucleoproteins (snRNPs) U1, U2, U4/U6 and U5 share eight proteins B', B, D1, D2, D3, E, F and G which form the structural core of the snRNPs. This class of common proteins plays an essential role in the biogenesis of the snRNPs. In addition, these proteins represent the major targets for the so-called anti-Sm auto-antibodies which are diagnostic for systemic lupus erythematosus (SLE). We have characterized the proteins F and G from HeLa cells by cDNA cloning, and, thus, all human Sm protein sequences are now available for comparison. Similar to the D, B/B' and E proteins, the F and G proteins do not possess any of the known RNA binding motifs, suggesting that other types of RNA-protein interactions occur in the snRNP core. Strikingly, the eight human Sm proteins possess mutual homology in two regions, 32 and 14 amino acids long, that we term Sm motifs 1 and 2. The Sm motifs are evolutionarily highly conserved in all of the putative homologues of the human Sm proteins identified in the data base. These results suggest that the Sm proteins may have arisen from a single common ancestor. Several hypothetical proteins, mainly of plant origin, that clearly contain the conserved Sm motifs but exhibit only comparatively low overall homology to one of the human Sm proteins, were identified in the data base. This suggests that the Sm motifs may also be shared by non-spliceosomal proteins. Further, we provide experimental evidence that the Sm motifs are involved, at least in part, in Sm protein-protein interactions. Specifically, we show by co-immunoprecipitation analyses of in vitro translated B' and D3 that the Sm motifs are essential for complex formation between B' and D3. Our finding that the Sm proteins share conserved sequence motifs may help to explain the frequent occurrence in patient sera of anti-Sm antibodies that cross-react with multiple Sm proteins and may ultimately further our understanding of how the snRNPs act as auto-antigens and immunogens in SLE.

Full text

PDF
2076

Images in this article

2079Image
on p.2079
2080Image
on p.2080
2081Image
on p.2081
2083Image
on p.2083
2083Image
on p.2083

Selected References

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

  1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
  2. Bach M., Winkelmann G., Lührmann R. 20S small nuclear ribonucleoprotein U5 shows a surprisingly complex protein composition. Proc Natl Acad Sci U S A. 1989 Aug;86(16):6038–6042. doi: 10.1073/pnas.86.16.6038. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Branlant C., Krol A., Ebel J. P., Lazar E., Haendler B., Jacob M. U2 RNA shares a structural domain with U1, U4, and U5 RNAs. EMBO J. 1982;1(10):1259–1265. doi: 10.1002/j.1460-2075.1982.tb00022.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Brunet C., Quan T., Craft J. Comparison of the Drosophila melanogaster, human and murine Sm B cDNAs: evolutionary conservation. Gene. 1993 Feb 28;124(2):269–273. doi: 10.1016/0378-1119(93)90404-q. [DOI] [PubMed] [Google Scholar]
  5. Burd C. G., Dreyfuss G. Conserved structures and diversity of functions of RNA-binding proteins. Science. 1994 Jul 29;265(5172):615–621. doi: 10.1126/science.8036511. [DOI] [PubMed] [Google Scholar]
  6. Cooper M., Johnston L. H., Beggs J. D. Identification and characterization of Uss1p (Sdb23p): a novel U6 snRNA-associated protein with significant similarity to core proteins of small nuclear ribonucleoproteins. EMBO J. 1995 May 1;14(9):2066–2075. doi: 10.1002/j.1460-2075.1995.tb07198.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Fabrizio P., Esser S., Kastner B., Lührmann R. Isolation of S. cerevisiae snRNPs: comparison of U1 and U4/U6.U5 to their human counterparts. Science. 1994 Apr 8;264(5156):261–265. doi: 10.1126/science.8146658. [DOI] [PubMed] [Google Scholar]
  8. Fautsch M. P., Thompson M. A., Holicky E. L., Schultz P. J., Hallett J. B., Wieben E. D. Conservation of coding and transcriptional control sequences within the snRNP E protein gene. Genomics. 1992 Dec;14(4):883–890. doi: 10.1016/s0888-7543(05)80109-0. [DOI] [PubMed] [Google Scholar]
  9. Fischer U., Sumpter V., Sekine M., Satoh T., Lührmann R. Nucleo-cytoplasmic transport of U snRNPs: definition of a nuclear location signal in the Sm core domain that binds a transport receptor independently of the m3G cap. EMBO J. 1993 Feb;12(2):573–583. doi: 10.1002/j.1460-2075.1993.tb05689.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Fisher D. E., Conner G. E., Reeves W. H., Wisniewolski R., Blobel G. Small nuclear ribonucleoprotein particle assembly in vivo: demonstration of a 6S RNA-free core precursor and posttranslational modification. Cell. 1985 Oct;42(3):751–758. doi: 10.1016/0092-8674(85)90271-5. [DOI] [PubMed] [Google Scholar]
  11. Frohman M. A., Dush M. K., Martin G. R. Rapid production of full-length cDNAs from rare transcripts: amplification using a single gene-specific oligonucleotide primer. Proc Natl Acad Sci U S A. 1988 Dec;85(23):8998–9002. doi: 10.1073/pnas.85.23.8998. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Griffith A. J., Schmauss C., Craft J. The murine gene encoding the highly conserved Sm B protein contains a nonfunctional alternative 3' splice site. Gene. 1992 May 15;114(2):195–201. doi: 10.1016/0378-1119(92)90574-9. [DOI] [PubMed] [Google Scholar]
  13. Guthrie C. Messenger RNA splicing in yeast: clues to why the spliceosome is a ribonucleoprotein. Science. 1991 Jul 12;253(5016):157–163. doi: 10.1126/science.1853200. [DOI] [PubMed] [Google Scholar]
  14. Habets W. J., Berden J. H., Hoch S. O., Van Venrooij W. J. Further characterization and subcellular localization of Sm and U1 ribonucleoprotein antigens. Eur J Immunol. 1985 Oct;15(10):992–997. doi: 10.1002/eji.1830151006. [DOI] [PubMed] [Google Scholar]
  15. Hackl W., Fischer U., Lührmann R. A 69-kD protein that associates reversibly with the Sm core domain of several spliceosomal snRNP species. J Cell Biol. 1994 Feb;124(3):261–272. doi: 10.1083/jcb.124.3.261. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Heinrichs V., Hackl W., Lührmann R. Direct binding of small nuclear ribonucleoprotein G to the Sm site of small nuclear RNA. Ultraviolet light cross-linking of protein G to the AAU stretch within the Sm site (AAUUUGUGG) of U1 small nuclear ribonucleoprotein reconstituted in vitro. J Mol Biol. 1992 Sep 5;227(1):15–28. doi: 10.1016/0022-2836(92)90678-d. [DOI] [PubMed] [Google Scholar]
  17. Higgins D. G., Sharp P. M. CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene. 1988 Dec 15;73(1):237–244. doi: 10.1016/0378-1119(88)90330-7. [DOI] [PubMed] [Google Scholar]
  18. Hirakata M., Craft J., Hardin J. A. Autoantigenic epitopes of the B and D polypeptides of the U1 snRNP. Analysis of domains recognized by the Y12 monoclonal anti-Sm antibody and by patient sera. J Immunol. 1993 Apr 15;150(8 Pt 1):3592–3601. [PubMed] [Google Scholar]
  19. Hirt H., Gartner A., Heberle-Bors E. An alfalfa cDNA encodes a protein with similarity to human snRNP-E. Nucleic Acids Res. 1992 Feb 11;20(3):613–613. doi: 10.1093/nar/20.3.613. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Lehmeier T., Foulaki K., Lührmann R. Evidence for three distinct D proteins, which react differentially with anti-Sm autoantibodies, in the cores of the major snRNPs U1, U2, U4/U6 and U5. Nucleic Acids Res. 1990 Nov 25;18(22):6475–6484. doi: 10.1093/nar/18.22.6475. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Lehmeier T., Raker V., Hermann H., Lührmann R. cDNA cloning of the Sm proteins D2 and D3 from human small nuclear ribonucleoproteins: evidence for a direct D1-D2 interaction. Proc Natl Acad Sci U S A. 1994 Dec 6;91(25):12317–12321. doi: 10.1073/pnas.91.25.12317. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Lerner M. R., Boyle J. A., Hardin J. A., Steitz J. A. Two novel classes of small ribonucleoproteins detected by antibodies associated with lupus erythematosus. Science. 1981 Jan 23;211(4480):400–402. doi: 10.1126/science.6164096. [DOI] [PubMed] [Google Scholar]
  23. Lerner M. R., Steitz J. A. Antibodies to small nuclear RNAs complexed with proteins are produced by patients with systemic lupus erythematosus. Proc Natl Acad Sci U S A. 1979 Nov;76(11):5495–5499. doi: 10.1073/pnas.76.11.5495. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Liautard J. P., Sri-Widada J., Brunel C., Jeanteur P. Structural organization of ribonucleoproteins containing small nuclear RNAs from HeLa cells. Proteins interact closely with a similar structural domain of U1, U2, U4 and U5 small nuclear RNAs. J Mol Biol. 1982 Dec 15;162(3):623–643. doi: 10.1016/0022-2836(82)90392-8. [DOI] [PubMed] [Google Scholar]
  25. Lührmann R., Kastner B., Bach M. Structure of spliceosomal snRNPs and their role in pre-mRNA splicing. Biochim Biophys Acta. 1990 Nov 30;1087(3):265–292. doi: 10.1016/0167-4781(90)90001-i. [DOI] [PubMed] [Google Scholar]
  26. Mattaj I. W. Cap trimethylation of U snRNA is cytoplasmic and dependent on U snRNP protein binding. Cell. 1986 Sep 12;46(6):905–911. doi: 10.1016/0092-8674(86)90072-3. [DOI] [PubMed] [Google Scholar]
  27. Mattaj I. W., De Robertis E. M. Nuclear segregation of U2 snRNA requires binding of specific snRNP proteins. Cell. 1985 Jan;40(1):111–118. doi: 10.1016/0092-8674(85)90314-9. [DOI] [PubMed] [Google Scholar]
  28. McAllister G., Amara S. G., Lerner M. R. Tissue-specific expression and cDNA cloning of small nuclear ribonucleoprotein-associated polypeptide N. Proc Natl Acad Sci U S A. 1988 Jul;85(14):5296–5300. doi: 10.1073/pnas.85.14.5296. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Mitsuda T., Eisenberg R. A., Cohen P. L. The murine Sm-D autoantigen: multiple genes, genetic polymorphism, evolutionary conservation and lack of intervening sequences in the coding region. J Autoimmun. 1992 Jun;5(3):277–287. doi: 10.1016/0896-8411(92)90143-e. [DOI] [PubMed] [Google Scholar]
  30. Mizushima S., Nomura M. Assembly mapping of 30S ribosomal proteins from E. coli. Nature. 1970 Jun 27;226(5252):1214–1214. doi: 10.1038/2261214a0. [DOI] [PubMed] [Google Scholar]
  31. Orlean P., Albright C., Robbins P. W. Cloning and sequencing of the yeast gene for dolichol phosphate mannose synthase, an essential protein. J Biol Chem. 1988 Nov 25;263(33):17499–17507. [PubMed] [Google Scholar]
  32. Pearson W. R., Lipman D. J. Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A. 1988 Apr;85(8):2444–2448. doi: 10.1073/pnas.85.8.2444. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Plessel G., Fischer U., Lührmann R. m3G cap hypermethylation of U1 small nuclear ribonucleoprotein (snRNP) in vitro: evidence that the U1 small nuclear RNA-(guanosine-N2)-methyltransferase is a non-snRNP cytoplasmic protein that requires a binding site on the Sm core domain. Mol Cell Biol. 1994 Jun;14(6):4160–4172. doi: 10.1128/mcb.14.6.4160. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Reuter R., Rothe S., Habets W., Van Venrooij W. J., Lührmann R. Autoantibody production against the U small nuclear ribonucleoprotein particle proteins E, F and G in patients with connective tissue diseases. Eur J Immunol. 1990 Feb;20(2):437–440. doi: 10.1002/eji.1830200231. [DOI] [PubMed] [Google Scholar]
  35. Rokeach L. A., Haselby J. A., Hoch S. O. Molecular cloning of a cDNA encoding the human Sm-D autoantigen. Proc Natl Acad Sci U S A. 1988 Jul;85(13):4832–4836. doi: 10.1073/pnas.85.13.4832. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Rokeach L. A., Hoch S. O. B-cell epitopes of Sm autoantigens. Mol Biol Rep. 1992 Jun;16(3):165–174. doi: 10.1007/BF00464704. [DOI] [PubMed] [Google Scholar]
  37. Rokeach L. A., Jannatipour M., Haselby J. A., Hoch S. O. Primary structure of a human small nuclear ribonucleoprotein polypeptide as deduced by cDNA analysis. J Biol Chem. 1989 Mar 25;264(9):5024–5030. [PubMed] [Google Scholar]
  38. Roy J., Zheng B., Rymond B. C., Woolford J. L., Jr Structurally related but functionally distinct yeast Sm D core small nuclear ribonucleoprotein particle proteins. Mol Cell Biol. 1995 Jan;15(1):445–455. doi: 10.1128/mcb.15.1.445. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Rymond B. C. Convergent transcripts of the yeast PRP38-SMD1 locus encode two essential splicing factors, including the D1 core polypeptide of small nuclear ribonucleoprotein particles. Proc Natl Acad Sci U S A. 1993 Feb 1;90(3):848–852. doi: 10.1073/pnas.90.3.848. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Rymond B. C., Rokeach L. A., Hoch S. O. Human snRNP polypeptide D1 promotes pre-mRNA splicing in yeast and defines nonessential yeast Smd1p sequences. Nucleic Acids Res. 1993 Jul 25;21(15):3501–3505. doi: 10.1093/nar/21.15.3501. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Sauterer R. A., Goyal A., Zieve G. W. Cytoplasmic assembly of small nuclear ribonucleoprotein particles from 6 S and 20 S RNA-free intermediates in L929 mouse fibroblasts. J Biol Chem. 1990 Jan 15;265(2):1048–1058. [PubMed] [Google Scholar]
  42. Schmauss C., Lerner M. R. The closely related small nuclear ribonucleoprotein polypeptides N and B/B' are distinguishable by antibodies as well as by differences in their mRNAs and gene structures. J Biol Chem. 1990 Jun 25;265(18):10733–10739. [PubMed] [Google Scholar]
  43. Smith D. B., Johnson K. S. Single-step purification of polypeptides expressed in Escherichia coli as fusions with glutathione S-transferase. Gene. 1988 Jul 15;67(1):31–40. doi: 10.1016/0378-1119(88)90005-4. [DOI] [PubMed] [Google Scholar]
  44. Stanford D. R., Kehl M., Perry C. A., Holicky E. L., Harvey S. E., Rohleder A. M., Rehder K., Jr, Luhrmann R., Wieben E. D. The complete primary structure of the human snRNP E protein. Nucleic Acids Res. 1988 Nov 25;16(22):10593–10605. doi: 10.1093/nar/16.22.10593. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Strub K., Walter P. Assembly of the Alu domain of the signal recognition particle (SRP): dimerization of the two protein components is required for efficient binding to SRP RNA. Mol Cell Biol. 1990 Feb;10(2):777–784. doi: 10.1128/mcb.10.2.777. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Séraphin B. 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. 1995 May 1;14(9):2089–2098. doi: 10.1002/j.1460-2075.1995.tb07200.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Tan E. M. Antinuclear antibodies: diagnostic markers for autoimmune diseases and probes for cell biology. Adv Immunol. 1989;44:93–151. doi: 10.1016/s0065-2776(08)60641-0. [DOI] [PubMed] [Google Scholar]
  48. Vankan P., McGuigan C., Mattaj I. W. Domains of U4 and U6 snRNAs required for snRNP assembly and splicing complementation in Xenopus oocytes. EMBO J. 1990 Oct;9(10):3397–3404. doi: 10.1002/j.1460-2075.1990.tb07541.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Vincent W. S., 3rd, Goldstein E. S., Allen S. A. Sequence and expression of two regulated transcription units during Drosophila melanogaster development: Deb-A and Deb-B. Biochim Biophys Acta. 1990 May 24;1049(1):59–68. doi: 10.1016/0167-4781(90)90084-f. [DOI] [PubMed] [Google Scholar]
  50. Wilson R., Ainscough R., Anderson K., Baynes C., Berks M., Bonfield J., Burton J., Connell M., Copsey T., Cooper J. 2.2 Mb of contiguous nucleotide sequence from chromosome III of C. elegans. Nature. 1994 Mar 3;368(6466):32–38. doi: 10.1038/368032a0. [DOI] [PubMed] [Google Scholar]
  51. Woppmann A., Patschinsky T., Bringmann P., Godt F., Lührmann R. Characterisation of human and murine snRNP proteins by two-dimensional gel electrophoresis and phosphopeptide analysis of U1-specific 70K protein variants. Nucleic Acids Res. 1990 Aug 11;18(15):4427–4438. doi: 10.1093/nar/18.15.4427. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. van Dam A., Winkel I., Zijlstra-Baalbergen J., Smeenk R., Cuypers H. T. Cloned human snRNP proteins B and B' differ only in their carboxy-terminal part. EMBO J. 1989 Dec 1;8(12):3853–3860. doi: 10.1002/j.1460-2075.1989.tb08563.x. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from The EMBO Journal are provided here courtesy of Nature Publishing Group

RESOURCES