PMCCPMCCPMCC

Search tips
Search criteria 

Advanced

 
Logo of narLink to Publisher's site
 
Nucleic Acids Res. 1994 January 11; 22(1): 32–40.
PMCID: PMC307742

The yeast protein encoded by PUB1 binds T-rich single stranded DNA.

Abstract

We have characterized binding activities in yeast which recognise the T-rich strand of the yeast ARS consensus element and have purified two of these to homogeneity. One (ACBP-60) is detectable in both nuclear and whole cell extracts, while the other (ACBP-67) is apparent only after fractionation of extracts by heparin-sepharose chromatography. The major binding activity detected in nuclear extracts was purified on a sequence-specific DNA affinity column as a single polypeptide with apparent mobility of 60kDa (ACBP-60). This protein co-fractionates with nuclei, is present at several thousand copies per cell and has a Kd for the T-rich single strand of the ARS consensus between 10(-9) and 10(-10) M. Competition studies with simple nucleic acid polymers show that ACBP-60 has marginally higher affinity for poly dT30 than for a 30 nt oligomer containing the T-rich strand of ARS 307, and approximately 10 fold higher affinity for poly rU. Internal sequence information of purified p60 reveals identity with the open reading frames of genes PUB1 and RNP1 which encode polyuridylate binding protein(s). The second binding activity, ACBP-67, also binds specifically to the T-rich single strand of the ARS consensus, but with considerably lower affinity than ACBP-60. Peptide sequence reveals that the 67kDa protein is identical to the major polyA binding protein in yeast, PAB1.

Full text

Full text is available as a scanned copy of the original print version. Get a printable copy (PDF file) of the complete article (2.6M), or click on a page image below to browse page by page. Links to PubMed are also available for Selected References.

Images in this article

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Celniker SE, Sweder K, Srienc F, Bailey JE, Campbell JL. Deletion mutations affecting autonomously replicating sequence ARS1 of Saccharomyces cerevisiae. Mol Cell Biol. 1984 Nov;4(11):2455–2466. [PMC free article] [PubMed]
  • Kearsey S. Structural requirements for the function of a yeast chromosomal replicator. Cell. 1984 May;37(1):299–307. [PubMed]
  • Bouton AH, Smith MM. Fine-structure analysis of the DNA sequence requirements for autonomous replication of Saccharomyces cerevisiae plasmids. Mol Cell Biol. 1986 Jul;6(7):2354–2363. [PMC free article] [PubMed]
  • Palzkill TG, Newlon CS. A yeast replication origin consists of multiple copies of a small conserved sequence. Cell. 1988 May 6;53(3):441–450. [PubMed]
  • Van Houten JV, Newlon CS. Mutational analysis of the consensus sequence of a replication origin from yeast chromosome III. Mol Cell Biol. 1990 Aug;10(8):3917–3925. [PMC free article] [PubMed]
  • Deshpande AM, Newlon CS. The ARS consensus sequence is required for chromosomal origin function in Saccharomyces cerevisiae. Mol Cell Biol. 1992 Oct;12(10):4305–4313. [PMC free article] [PubMed]
  • Bell SP, Stillman B. ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex. Nature. 1992 May 14;357(6374):128–134. [PubMed]
  • Diffley JF, Cocker JH. Protein-DNA interactions at a yeast replication origin. Nature. 1992 May 14;357(6374):169–172. [PubMed]
  • Hofmann JF, Gasser SM. Identification and purification of a protein that binds the yeast ARS consensus sequence. Cell. 1991 Mar 8;64(5):951–960. [PubMed]
  • Schmidt AM, Herterich SU, Krauss G. A single-stranded DNA binding protein from S. cerevisiae specifically recognizes the T-rich strand of the core sequence of ARS elements and discriminates against mutant sequences. EMBO J. 1991 Apr;10(4):981–985. [PubMed]
  • Kuno K, Kuno S, Matsushima K, Murakami S. Evidence for binding of at least two factors, including T-rich strand-binding factor(s) to the single-stranded ARS1 sequence in Saccharomyces cerevisiae. Mol Gen Genet. 1991 Nov;230(1-2):45–48. [PubMed]
  • Kuno K, Murakami S, Kuno S. Single-strand-binding factor(s) which interact with ARS1 of Saccharomyces cerevisiae. Gene. 1990 Oct 30;95(1):73–77. [PubMed]
  • Amati BB, Gasser SM. Chromosomal ARS and CEN elements bind specifically to the yeast nuclear scaffold. Cell. 1988 Sep 23;54(7):967–978. [PubMed]
  • Hofmann JF, Laroche T, Brand AH, Gasser SM. RAP-1 factor is necessary for DNA loop formation in vitro at the silent mating type locus HML. Cell. 1989 Jun 2;57(5):725–737. [PubMed]
  • Hughes GJ, Frutiger S, Paquet N, Jaton JC. The amino acid sequence of rabbit J chain in secretory immunoglobulin A. Biochem J. 1990 Nov 1;271(3):641–647. [PubMed]
  • Laemmli UK. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970 Aug 15;227(5259):680–685. [PubMed]
  • Sachs AB, Bond MW, Kornberg RD. A single gene from yeast for both nuclear and cytoplasmic polyadenylate-binding proteins: domain structure and expression. Cell. 1986 Jun 20;45(6):827–835. [PubMed]
  • Anderson JT, Paddy MR, Swanson MS. PUB1 is a major nuclear and cytoplasmic polyadenylated RNA-binding protein in Saccharomyces cerevisiae. Mol Cell Biol. 1993 Oct;13(10):6102–6113. [PMC free article] [PubMed]
  • Sachs AB, Davis RW. The poly(A) binding protein is required for poly(A) shortening and 60S ribosomal subunit-dependent translation initiation. Cell. 1989 Sep 8;58(5):857–867. [PubMed]
  • Kim C, Snyder RO, Wold MS. Binding properties of replication protein A from human and yeast cells. Mol Cell Biol. 1992 Jul;12(7):3050–3059. [PMC free article] [PubMed]
  • Ripmaster TL, Woolford JL., Jr A protein containing conserved RNA-recognition motifs is associated with ribosomal subunits in Saccharomyces cerevisiae. Nucleic Acids Res. 1993 Jul 11;21(14):3211–3216. [PMC free article] [PubMed]
  • Matunis MJ, Matunis EL, Dreyfuss G. PUB1: a major yeast poly(A)+ RNA-binding protein. Mol Cell Biol. 1993 Oct;13(10):6114–6123. [PMC free article] [PubMed]
  • Chase JW, Williams KR. Single-stranded DNA binding proteins required for DNA replication. Annu Rev Biochem. 1986;55:103–136. [PubMed]
  • Barrijal S, Perros M, Gu Z, Avalosse BL, Belenguer P, Amalric F, Rommelaere J. Nucleolin forms a specific complex with a fragment of the viral (minus) strand of minute virus of mice DNA. Nucleic Acids Res. 1992 Oct 11;20(19):5053–5060. [PMC free article] [PubMed]
  • Jong AY, Clark MW, Gilbert M, Oehm A, Campbell JL. Saccharomyces cerevisiae SSB1 protein and its relationship to nucleolar RNA-binding proteins. Mol Cell Biol. 1987 Aug;7(8):2947–2955. [PMC free article] [PubMed]
  • Gottlieb E, Steitz JA. The RNA binding protein La influences both the accuracy and the efficiency of RNA polymerase III transcription in vitro. EMBO J. 1989 Mar;8(3):841–850. [PubMed]
  • Gottlieb E, Steitz JA. Function of the mammalian La protein: evidence for its action in transcription termination by RNA polymerase III. EMBO J. 1989 Mar;8(3):851–861. [PubMed]
  • Hsu T, King DL, LaBonne C, Kafatos FC. A Drosophila single-strand DNA/RNA-binding factor contains a high-mobility-group box and is enriched in the nucleolus. Proc Natl Acad Sci U S A. 1993 Jul 15;90(14):6488–6492. [PubMed]
  • Haynes SR. The RNP motif protein family. New Biol. 1992 May;4(5):421–429. [PubMed]
  • Kim YJ, Baker BS. Isolation of RRM-type RNA-binding protein genes and the analysis of their relatedness by using a numerical approach. Mol Cell Biol. 1993 Jan;13(1):174–183. [PMC free article] [PubMed]
  • Scherly D, Boelens W, van Venrooij WJ, Dathan NA, Hamm J, Mattaj IW. Identification of the RNA binding segment of human U1 A protein and definition of its binding site on U1 snRNA. EMBO J. 1989 Dec 20;8(13):4163–4170. [PubMed]
  • Sachs AB, Davis RW, Kornberg RD. A single domain of yeast poly(A)-binding protein is necessary and sufficient for RNA binding and cell viability. Mol Cell Biol. 1987 Sep;7(9):3268–3276. [PMC free article] [PubMed]
  • Query CC, Bentley RC, Keene JD. A common RNA recognition motif identified within a defined U1 RNA binding domain of the 70K U1 snRNP protein. Cell. 1989 Apr 7;57(1):89–101. [PubMed]
  • Ishikawa F, Matunis MJ, Dreyfuss G, Cech TR. Nuclear proteins that bind the pre-mRNA 3' splice site sequence r(UUAG/G) and the human telomeric DNA sequence d(TTAGGG)n. Mol Cell Biol. 1993 Jul;13(7):4301–4310. [PMC free article] [PubMed]
  • Santoro IM, Yi TM, Walsh K. Identification of single-stranded-DNA-binding proteins that interact with muscle gene elements. Mol Cell Biol. 1991 Apr;11(4):1944–1953. [PMC free article] [PubMed]
  • Davis TL, Firulli AB, Kinniburgh AJ. Ribonucleoprotein and protein factors bind to an H-DNA-forming c-myc DNA element: possible regulators of the c-myc gene. Proc Natl Acad Sci U S A. 1989 Dec;86(24):9682–9686. [PubMed]
  • Yee HA, Wong AK, van de Sande JH, Rattner JB. Identification of novel single-stranded d(TC)n binding proteins in several mammalian species. Nucleic Acids Res. 1991 Feb 25;19(4):949–953. [PMC free article] [PubMed]
  • Kolluri R, Torrey TA, Kinniburgh AJ. A CT promoter element binding protein: definition of a double-strand and a novel single-strand DNA binding motif. Nucleic Acids Res. 1992 Jan 11;20(1):111–116. [PMC free article] [PubMed]
  • Brunel F, Alzari PM, Ferrara P, Zakin MM. Cloning and sequencing of PYBP, a pyrimidine-rich specific single strand DNA-binding protein. Nucleic Acids Res. 1991 Oct 11;19(19):5237–5245. [PMC free article] [PubMed]
  • Bergemann AD, Ma ZW, Johnson EM. Sequence of cDNA comprising the human pur gene and sequence-specific single-stranded-DNA-binding properties of the encoded protein. Mol Cell Biol. 1992 Dec;12(12):5673–5682. [PMC free article] [PubMed]
  • Tzfati Y, Abeliovich H, Kapeller I, Shlomai J. A single-stranded DNA-binding protein from Crithidia fasciculata recognizes the nucleotide sequence at the origin of replication of kinetoplast DNA minicircles. Proc Natl Acad Sci U S A. 1992 Aug 1;89(15):6891–6895. [PubMed]
  • Carmichael EP, Roome JM, Wahl AF. Binding of a sequence-specific single-stranded DNA-binding factor to the simian virus 40 core origin inverted repeat domain is cell cycle regulated. Mol Cell Biol. 1993 Jan;13(1):408–420. [PMC free article] [PubMed]
  • Bell LR, Maine EM, Schedl P, Cline TW. Sex-lethal, a Drosophila sex determination switch gene, exhibits sex-specific RNA splicing and sequence similarity to RNA binding proteins. Cell. 1988 Dec 23;55(6):1037–1046. [PubMed]
  • Amrein H, Maniatis T, Nöthiger R. Alternatively spliced transcripts of the sex-determining gene tra-2 of Drosophila encode functional proteins of different size. EMBO J. 1990 Nov;9(11):3619–3629. [PubMed]
  • Tazi J, Forne T, Jeanteur P, Cathala G, Brunel C. Mammalian U6 small nuclear RNA undergoes 3' end modifications within the spliceosome. Mol Cell Biol. 1993 Mar;13(3):1641–1650. [PMC free article] [PubMed]
  • Rinke J, Steitz JA. Precursor molecules of both human 5S ribosomal RNA and transfer RNAs are bound by a cellular protein reactive with anti-La lupus antibodies. Cell. 1982 May;29(1):149–159. [PubMed]
  • Shen CK, Maniatis T. The organization, structure, and in vitro transcription of Alu family RNA polymerase III transcription units in the human alpha-like globin gene cluster: precipitation of in vitro transcripts by lupus anti-La antibodies. J Mol Appl Genet. 1982;1(4):343–360. [PubMed]
  • Chambers JC, Kurilla MG, Keene JD. Association between the 7 S RNA and the lupus La protein varies among cell types. J Biol Chem. 1983 Oct 10;258(19):11438–11441. [PubMed]
  • Lerner MR, Andrews NC, Miller G, Steitz JA. Two small RNAs encoded by Epstein-Barr virus and complexed with protein are precipitated by antibodies from patients with systemic lupus erythematosus. Proc Natl Acad Sci U S A. 1981 Feb;78(2):805–809. [PubMed]
  • Terns MP, Lund E, Dahlberg JE. 3'-end-dependent formation of U6 small nuclear ribonucleoprotein particles in Xenopus laevis oocyte nuclei. Mol Cell Biol. 1992 Jul;12(7):3032–3040. [PMC free article] [PubMed]
  • Pollard VW, Harris ME, Hajduk SL. Native mRNA editing complexes from Trypanosoma brucei mitochondria. EMBO J. 1992 Dec;11(12):4429–4438. [PubMed]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press