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PMID: 18805955 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Distinct roles for Khd1p in the localization and expression of bud-localized mRNAs in yeast.

RNA (New York, N.Y.) ·Vol. 14 ·No. 11 ·2008-11-00 ·Pages 2333-47

Hasegawa Y, Irie K, Gerber AP

Abstract

The RNA-binding protein Khd1p (KH-domain protein 1) is required for efficient localization of ASH1 mRNA to the bud-tip, probably acting as a translational repressor during mRNA transport in yeast. Here, we have systematically examined Khd1p mRNA targets and colocalization with known bud-tip-localized mRNAs in vivo. Affinity purification and DNA microarray analysis of Khd1p-associated mRNAs revealed hundreds of potential mRNAs targets, many of them encoding membrane-associated proteins. The putative targets include the messages for MID2, MTL1, WSC2, SRL1, EGT2, CLB2, ASH1, and Khd1p colocalizes with these mRNAs at the bud-tip. The combination of bioinformatics, RNA localization, and in vitro RNA-binding assays revealed that Khd1p binds to CNN repeats in coding regions of mRNA targets. Among the proteins encoded by previously known bud-tip-localized mRNAs, only Mtl1p levels were decreased in khd1Delta mutant cells, whereas Ash1p and Srl1p were reduced in cells overexpressing KHD1. Hence, Khd1p differentially affects gene expression possibly due to combinatorial arrangement with additional factors reflecting the redundant structure of post-transcriptional regulatory systems.

MeSH Terms
Amino Acid Sequence Calcium-Binding Proteins/genetics DNA-Binding Proteins/genetics Gene Expression Regulation, Fungal Intracellular Signaling Peptides and Proteins Membrane Glycoproteins Membrane Proteins/genetics Molecular Sequence Data Mutation RNA, Fungal/metabolism RNA, Messenger/metabolism RNA-Binding Proteins/genetics,metabolism Repressor Proteins/genetics Ribonucleoproteins Saccharomyces cerevisiae/genetics,metabolism Saccharomyces cerevisiae Proteins/genetics,metabolism Transcription, Genetic
Chemicals
ASH1 protein, S cerevisiae Calcium-Binding Proteins DNA-Binding Proteins HEK2 protein, S cerevisiae Intracellular Signaling Peptides and Proteins MID2 protein, S cerevisiae Membrane Glycoproteins Membrane Proteins RNA, Fungal RNA, Messenger RNA-Binding Proteins Repressor Proteins Ribonucleoproteins Saccharomyces cerevisiae Proteins
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Hasegawa Yuko
Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences, University of Tsukuba, 305-8575 Tsukuba, Japan.
Irie Kenji
Gerber André P
References (70)
70 references, click to expand
  1. Structural elements required for the localization of ASH1 mRNA and of a green fluorescent protein reporter particle in vivo.
    Curr Biol. 1999 Mar 25;9(6):333-6 PMID: 10209102
  2. ASH1 mRNA localization in yeast involves multiple secondary structural elements and Ash1 protein translation.
    Curr Biol. 1999 Mar 25;9(6):337-40 PMID: 10209099
  3. Association of the class V myosin Myo4p with a localised messenger RNA in budding yeast depends on She proteins.
    J Cell Sci. 1999 May;112 ( Pt 10):1511-8 PMID: 10212145
  4. Mid2 is a putative sensor for cell integrity signaling in Saccharomyces cerevisiae.
    Mol Cell Biol. 1999 Jun;19(6):3969-76 PMID: 10330137
  5. Pathways for mRNA localization in the cytoplasm.
    Trends Biochem Sci. 2006 Dec;31(12):687-93 PMID: 17084632
  6. The Stanford Microarray Database: implementation of new analysis tools and open source release of software.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D766-70 PMID: 17182626
  7. hnRNP K: one protein multiple processes.
    Bioessays. 2004 Jun;26(6):629-38 PMID: 15170860
  8. A new yeast PUF family protein, Puf6p, represses ASH1 mRNA translation and is required for its localization.
    Genes Dev. 2004 Jun 15;18(12):1452-65 PMID: 15198983
  9. Determination and augmentation of RNA sequence specificity of the Nova K-homology domains.
    Nucleic Acids Res. 2004;32(16):4852-61 PMID: 15367696
  10. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae.
    Genetics. 1989 May;122(1):19-27 PMID: 2659436
  11. Rapid assessment of S. cerevisiae mating type by PCR.
    Trends Genet. 1990 Aug;6(8):236 PMID: 2238077
  12. A simple and efficient method for direct gene deletion in Saccharomyces cerevisiae.
    Nucleic Acids Res. 1993 Jul 11;21(14):3329-30 PMID: 8341614
  13. Essential role for KH domains in RNA binding: impaired RNA binding by a mutation in the KH domain of FMR1 that causes fragile X syndrome.
    Cell. 1994 Apr 8;77(1):33-9 PMID: 8156595
  14. Identification of MYO4, a second class V myosin gene in yeast.
    J Cell Sci. 1994 Apr;107 ( Pt 4):1055-64 PMID: 8056830
  15. Fitting a mixture model by expectation maximization to discover motifs in biopolymers.
    Proc Int Conf Intell Syst Mol Biol. 1994;2:28-36 PMID: 7584402
  16. Mother cell-specific HO expression in budding yeast depends on the unconventional myosin myo4p and other cytoplasmic proteins.
    Cell. 1996 Mar 8;84(5):687-97 PMID: 8625407
  17. Asymmetric accumulation of Ash1p in postanaphase nuclei depends on a myosin and restricts yeast mating-type switching to mother cells.
    Cell. 1996 Mar 8;84(5):699-709 PMID: 8625408
  18. Identification of asymmetrically localized determinant, Ash1p, required for lineage-specific transcription of the yeast HO gene.
    Cell. 1996 Mar 8;84(5):711-22 PMID: 8625409
  19. pMPY-ZAP: a reusable polymerase chain reaction-directed gene disruption cassette for Saccharomyces cerevisiae.
    Yeast. 1996 Feb;12(2):129-34 PMID: 8686376
  20. A novel fluorescence-activated cell sorter-based screen for yeast endocytosis mutants identifies a yeast homologue of mammalian eps15.
    J Cell Biol. 1996 Dec;135(6 Pt 1):1485-500 PMID: 8978817
  21. Characterization of a beta-actin mRNA zipcode-binding protein.
    Mol Cell Biol. 1997 Apr;17(4):2158-65 PMID: 9121465
  22. Four highly stable eukaryotic mRNAs assemble 3' untranslated region RNA-protein complexes sharing cis and trans components.
    Proc Natl Acad Sci U S A. 1997 Mar 18;94(6):2410-4 PMID: 9122208
  23. Bni1p, a yeast formin linking cdc42p and the actin cytoskeleton during polarized morphogenesis.
    Science. 1997 Apr 4;276(5309):118-22 PMID: 9082982
  24. The neuronal RNA binding protein Nova-1 recognizes specific RNA targets in vitro and in vivo.
    Mol Cell Biol. 1997 Jun;17(6):3194-201 PMID: 9154818
  25. mRNA silencing in erythroid differentiation: hnRNP K and hnRNP E1 regulate 15-lipoxygenase translation from the 3' end.
    Cell. 1997 May 16;89(4):597-606 PMID: 9160751
  26. The splicing factor BBP interacts specifically with the pre-mRNA branchpoint sequence UACUAAC.
    Cell. 1997 May 30;89(5):781-7 PMID: 9182766
  27. Mating type switching in yeast controlled by asymmetric localization of ASH1 mRNA.
    Science. 1997 Jul 18;277(5324):383-7 PMID: 9219698
  28. Actin-dependent localization of an RNA encoding a cell-fate determinant in yeast.
    Nature. 1997 Sep 4;389(6646):90-3 PMID: 9288973
  29. In vitro genetic analysis of the RNA binding site of vigilin, a multi-KH-domain protein.
    Mol Cell Biol. 1998 Jul;18(7):3991-4003 PMID: 9632784
  30. Why cells move messages: the biological functions of mRNA localization.
    Semin Cell Dev Biol. 2007 Apr;18(2):171-7 PMID: 17398125
  31. RNA regulons: coordination of post-transcriptional events.
    Nat Rev Genet. 2007 Jul;8(7):533-43 PMID: 17572691
  32. Local activation of yeast ASH1 mRNA translation through phosphorylation of Khd1p by the casein kinase Yck1p.
    Mol Cell. 2007 Jun 22;26(6):795-809 PMID: 17588515
  33. Post-transcriptional gene regulation: from genome-wide studies to principles.
    Cell Mol Life Sci. 2008 Mar;65(5):798-813 PMID: 18043867
  34. Directional mRNA transport in eukaryotes: lessons from yeast.
    Cell Mol Life Sci. 2007 Jan;64(2):171-80 PMID: 17131056
  35. P bodies and the control of mRNA translation and degradation.
    Mol Cell. 2007 Mar 9;25(5):635-46 PMID: 17349952
  36. A generic protein purification method for protein complex characterization and proteome exploration.
    Nat Biotechnol. 1999 Oct;17(10):1030-2 PMID: 10504710
  37. Genome-wide mRNA surveillance is coupled to mRNA export.
    Genes Dev. 2004 Nov 1;18(21):2652-62 PMID: 15489286
  38. She2p is a novel RNA binding protein with a basic helical hairpin motif.
    Cell. 2004 Nov 12;119(4):491-502 PMID: 15537539
  39. RNA localization in yeast: moving towards a mechanism.
    Biol Cell. 2005 Jan;97(1):75-86 PMID: 15601259
  40. Identification of a conserved RNA motif essential for She2p recognition and mRNA localization to the yeast bud.
    Mol Cell Biol. 2005 Jun;25(11):4752-66 PMID: 15899876
  41. Translation of aberrant mRNAs lacking a termination codon or with a shortened 3'-UTR is repressed after initiation in yeast.
    EMBO J. 2005 Apr 20;24(8):1584-95 PMID: 15933721
  42. Moving messages: the intracellular localization of mRNAs.
    Nat Rev Mol Cell Biol. 2005 May;6(5):363-75 PMID: 15852043
  43. The binding activity of yeast RNAs to yeast Hek2p and mammalian hnRNP K proteins, determined using the three-hybrid system.
    Cell Mol Biol Lett. 2005;10(2):227-35 PMID: 16010288
  44. Unbiased selection of localization elements reveals cis-acting determinants of mRNA bud localization in Saccharomyces cerevisiae.
    Proc Natl Acad Sci U S A. 2005 Dec 13;102(50):18005-10 PMID: 16326802
  45. Genome-wide identification of mRNAs associated with the translational regulator PUMILIO in Drosophila melanogaster.
    Proc Natl Acad Sci U S A. 2006 Mar 21;103(12):4487-92 PMID: 16537387
  46. Coordination of endoplasmic reticulum and mRNA localization to the yeast bud.
    Curr Biol. 2006 Aug 8;16(15):1538-43 PMID: 16890529
  47. Exploring the mode-of-action of bioactive compounds by chemical-genetic profiling in yeast.
    Cell. 2006 Aug 11;126(3):611-25 PMID: 16901791
  48. Visual screening for localized RNAs in yeast revealed novel RNAs at the bud-tip.
    Biochem Biophys Res Commun. 2006 Dec 29;351(4):999-1004 PMID: 17094940
  49. A series of protein phosphatase gene disruptants in Saccharomyces cerevisiae.
    Yeast. 1999 Nov;15(15):1669-79 PMID: 10572263
  50. Large-scale identification of secreted and membrane-associated gene products using DNA microarrays.
    Nat Genet. 2000 May;25(1):58-62 PMID: 10802657
  51. The myosin motor, Myo4p, binds Ash1 mRNA via the adapter protein, She3p.
    Proc Natl Acad Sci U S A. 2000 May 9;97(10):5273-8 PMID: 10792032
  52. Plasma membrane compartmentalization in yeast by messenger RNA transport and a septin diffusion barrier.
    Science. 2000 Oct 13;290(5490):341-4 PMID: 11030653
  53. She2p, a novel RNA-binding protein tethers ASH1 mRNA to the Myo4p myosin motor via She3p.
    EMBO J. 2000 Oct 16;19(20):5514-24 PMID: 11032818
  54. She2p is a novel RNA-binding protein that recruits the Myo4p-She3p complex to ASH1 mRNA.
    EMBO J. 2000 Dec 1;19(23):6592-601 PMID: 11101531
  55. Post-transcriptional regulation through the HO 3'-UTR by Mpt5, a yeast homolog of Pumilio and FBF.
    EMBO J. 2001 Feb 1;20(3):552-61 PMID: 11157761
  56. An exclusively nuclear RNA-binding protein affects asymmetric localization of ASH1 mRNA and Ash1p in yeast.
    J Cell Biol. 2001 Apr 16;153(2):307-18 PMID: 11309412
  57. Significance analysis of microarrays applied to the ionizing radiation response.
    Proc Natl Acad Sci U S A. 2001 Apr 24;98(9):5116-21 PMID: 11309499
  58. Yeast hnRNP K-like genes are involved in regulation of the telomeric position effect and telomere length.
    Mol Cell Biol. 2002 Jan;22(1):286-97 PMID: 11739741
  59. A PUF family portrait: 3'UTR regulation as a way of life.
    Trends Genet. 2002 Mar;18(3):150-7 PMID: 11858839
  60. The Khd1 protein, which has three KH RNA-binding motifs, is required for proper localization of ASH1 mRNA in yeast.
    EMBO J. 2002 Mar 1;21(5):1158-67 PMID: 11867544
  61. Precision and functional specificity in mRNA decay.
    Proc Natl Acad Sci U S A. 2002 Apr 30;99(9):5860-5 PMID: 11972065
  62. The poly(C)-binding proteins: a multiplicity of functions and a search for mechanisms.
    RNA. 2002 Mar;8(3):265-78 PMID: 12003487
  63. Intracellular mRNA localization: motors move messages.
    Trends Genet. 2002 Dec;18(12):636-42 PMID: 12446149
  64. Widespread cytoplasmic mRNA transport in yeast: identification of 22 bud-localized transcripts using DNA microarray analysis.
    Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11429-34 PMID: 13679573
  65. Global analysis of protein expression in yeast.
    Nature. 2003 Oct 16;425(6959):737-41 PMID: 14562106
  66. Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast.
    PLoS Biol. 2004 Mar;2(3):E79 PMID: 15024427
  67. mRNA localization and the cytoskeleton.
    Curr Opin Cell Biol. 2004 Feb;16(1):80-5 PMID: 15037309
  68. Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae.
    Yeast. 1998 Jul;14(10):953-61 PMID: 9717241
  69. Localization of ASH1 mRNA particles in living yeast.
    Mol Cell. 1998 Oct;2(4):437-45 PMID: 9809065
  70. Dissecting the regulatory circuitry of a eukaryotic genome.
    Cell. 1998 Nov 25;95(5):717-28 PMID: 9845373
Article Info
Journal
RNA (New York, N.Y.)
Abbr.
RNA
ISSN
1469-9001
DOI
10.1261/rna.1016508
Published
2008-11-00
Epub
2008-00-19
Pages
2333-47
Language
English
Region
United States
NLM ID
9509184
PMCID
PMC2578860
Subset
IM
External Links
PubMed source DOI: 10.1261/rna.1016508 PMC Full Text View journal details
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