Whi3, an S. cerevisiae RNA-binding protein, is a component of stress granules that regulates levels of its target mRNAS

PLoS ONE

Volumn 8, Issue 12, 2013, Pages

  Holmes, Kristen J ^a   Klass, Daniel M ^b   Guiney, Evan L ^a   Cyert, Martha S ^a  

^a STANFORD UNIVERSITY   (United States)

^b STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID MOTIFS; CHLORIDES; CYTOSOL; GLUCOSE; GLUTAMINE; HEAT-SHOCK RESPONSE; PROTEIN STRUCTURE, TERTIARY; PROTEIN TRANSPORT; RNA, MESSENGER; RNA-BINDING PROTEINS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; STRESS, PHYSIOLOGICAL; ZINC COMPOUNDS;

EID: 84893601051     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0084060     Document Type: Article

References (49)

1. Hilgers V, Teixeira D, Parker R (2006) Translation-independent inhibition of mRNA deadenylation during stress in Saccharomyces cerevisiae. Rna 12: 1835-1845. (Pubitemid 44484257)
2. Sheth U, Parker R (2003) Decapping and decay of messenger RNA occur in cytoplasmic processing bodies. Science 300: 805-808. (Pubitemid 36532117)
3. Balagopal V, Parker R (2009) Polysomes, P bodies and stress granules: states and fates of eukaryotic mRNAs. Curr Opin Cell Biol 21: 403-408.
4. Teixeira D, Sheth U, Valencia-Sanchez MA, Brengues M, Parker R (2005) Processing bodies require RNA for assembly and contain nontranslating mRNAs. Rna 11: 371-382. (Pubitemid 40397171)
5. Buchan JR, Muhlrad D, Parker R (2008) P bodies promote stress granule assembly in Saccharomyces cerevisiae. J Cell Biol 183: 441-455.
6. Anderson P, Kedersha N (2008) Stress granules: the Tao of RNA triage. Trends Biochem Sci 33: 141-150.
7. Erickson SL, Lykke-Andersen J (2011) Cytoplasmic mRNP granules at a glance. J Cell Sci 124: 293-297.
8. Aldea M, Gari E, Colomina N (2007) Control of cell cycle and cell growth by molecular chaperones. Cell Cycle 6: 2599-2603. (Pubitemid 350224040)
9. Nash RS, Volpe T, Futcher B (2001) Isolation and characterization of WHI3, a size-control gene of Saccharomyces cerevisiae. Genetics 157: 1469-1480. (Pubitemid 32298817)
10. Wang H, Gari E, Verges E, Gallego C, Aldea M (2004) Recruitment of Cdc28 by Whi3 restricts nuclear accumulation of the G1 cyclin-Cdk complex to late G1. Embo J 23: 180-190. (Pubitemid 38165758)
11. Colomina N, Ferrezuelo F, Wang H, Aldea M, Gari E (2008) Whi3, a developmental regulator of budding yeast, binds a large set of mRNAs functionally related to the endoplasmic reticulum. J Biol Chem 283: 28670-28679.
12. Verges E, Colomina N, Gari E, Gallego C, Aldea M (2007) Cyclin Cln3 is retained at the ER and released by the J chaperone Ydj1 in late G1 to trigger cell cycle entry. Mol Cell 26: 649-662. (Pubitemid 46856242)
13. Riordan DP, Herschlag D, Brown PO (2011) Identification of RNA recognition elements in the Saccharomyces cerevisiae transcriptome. Nucleic Acids Res 39: 1501-1509.
14. Gari E, Volpe T, Wang H, Gallego C, Futcher B, et al. (2001) Whi3 binds the mRNA of the G1 cyclin CLN3 to modulate cell fate in budding yeast. Genes & Dev 15: 2803-2808. (Pubitemid 33042051)
15. Sudbery P (2002) Cell biology. When wee meets whi. Science 297: 351-352.
16. Gallego C, Gari E, Colomina N, Herrero E, Aldea M (1997) The Cln3 cyclin is down-regulated by translational repression and degradation during the G1 arrest caused by nitrogen deprivation in budding yeast. Embo J 16: 7196-7206. (Pubitemid 27520817)
17. Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, et al. (2012) Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res 40: D700-705.
18. Tarassov K, Messier V, Landry CR, Radinovic S, Serna Molina MM, et al. (2008) An in vivo map of the yeast protein interactome. Science 320: 1465-1470. (Pubitemid 351929421)
19. Ghaemmaghami S, Huh WK, Bower K, Howson RW, Belle A, et al. (2003) Global analysis of protein expression in yeast. Nature 425: 737-741. (Pubitemid 37314318)
20. Brengues M, Parker R (2007) Accumulation of polyadenylated mRNA, Pab1p, eIF4E, and eIF4G with P-bodies in Saccharomyces cerevisiae. Mol Biol Cell 18: 2592-2602. (Pubitemid 47025724)
21. Buchan JR, Yoon JH, Parker R (2011) Stress-specific composition, assembly and kinetics of stress granules in Saccharomyces cerevisiae. J Cell Sci 124: 228-239.
22. Swisher KD, Parker R (2009) Related mechanisms for mRNA and rRNA quality control. Mol Cell 34: 401-402.
23. Yoon JH, Choi EJ, Parker R (2010) Dcp2 phosphorylation by Ste20 modulates stress granule assembly and mRNA decay in Saccharomyces cerevisiae. J Cell Biol 189: 813-827.
24. Hoyle NP, Castelli LM, Campbell SG, Holmes LE, Ashe MP (2007) Stress-dependent relocalization of translationally primed mRNPs to cytoplasmic granules that are kinetically and spatially distinct from P-bodies. J Cell Biol 179: 65-74. (Pubitemid 47606684)
25. Eisinger-Mathason TS, Andrade J, Groehler AL, Clark DE, Muratore-Schroeder TL, et al. (2008) Codependent functions of RSK2 and the apoptosis-promoting factor TIA-1 in stress granule assembly and cell survival. Mol Cell 31: 722-736.
26. Grousl T, Ivanov P, Frydlova I, Vasicova P, Janda F, et al. (2009) Robust heat shock induces eIF2alpha-phosphorylation-independent assembly of stress granules containing eIF3 and 40S ribosomal subunits in budding yeast, Saccharomyces cerevisiae. J Cell Sci 122: 2078-2088.
27. Buchan JR, Parker R (2009) Eukaryotic stress granules: the ins and outs of translation. Mol Cell 36: 932-941.
28. Gilks N, Kedersha N, Ayodele M, Shen L, Stoecklin G, et al. (2004) Stress granule assembly is mediated by prion-like aggregation of TIA-1. Mol Biol Cell 15: 5383-5398. (Pubitemid 39564732)
29. Tsvetanova NG, Klass DM, Salzman J, Brown PO (2010) Proteome-wide search reveals unexpected RNA-binding proteins in Saccharomyces cerevisiae. PLoS One 5.
30. Tusher VG, Tibshirani R, Chu G (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A 98: 5116-5121. (Pubitemid 32397092)
31. Falcon S, Gentleman R (2007) Using GOstats to test gene lists for GO term association. Bioinformatics 23: 257-258. (Pubitemid 46189622)
32. Hendrickson DG, Hogan DJ, McCullough HL, Myers JW, Herschlag D, et al. (2009) Concordant regulation of translation and mRNA abundance for hundreds of targets of a human microRNA. PLoS Biol 7: e1000238.
33. Bird AJ, Blankman E, Stillman DJ, Eide DJ, Winge DR (2004) The Zap1 transcriptional activator also acts as a repressor by binding downstream of the TATA box in ZRT2. EMBO J 23: 1123-1132. (Pubitemid 38436876)
34. Frey AG, Bird AJ, Evans-Galea MV, Blankman E, Winge DR, et al. (2011) Zinc-regulated DNA binding of the yeast Zap1 zinc-responsive activator. PloS One 6: e22535.
35. Zhao H, Eide DJ (1997) Zap1p, a metalloregulatory protein involved in zinc-responsive transcriptional regulation in Saccharomyces cerevisiae. Mol Cell Biol 17: 5044-5052. (Pubitemid 27357603)
36. Lee C, Zhang H, Baker AE, Occhipinti P, Borsuk ME, et al. (2013) Protein aggregation behavior regulates cyclin transcript localization and cell-cycle control. Dev Cell 25: 572-584.
37. Kedersha N, Stoecklin G, Ayodele M, Yacono P, Lykke-Andersen J, et al. (2005) Stress granules and processing bodies are dynamically linked sites of mRNP remodeling. J Cell Biol 169: 871-884. (Pubitemid 41002864)
38. Nash R, Tokiwa G, Anand S, Erickson K, Futcher AB (1988) The WHI1+ gene of Saccharomyces cerevisiae tethers cell division to cell size and is a cyclin homolog. EMBO J 7: 4335-4346.
39. Di Talia S, Wang H, Skotheim JM, Rosebrock AP, Futcher B, et al. (2009) Daughter-specific transcription factors regulate cell size control in budding yeast. PLoS Biol 7: e1000221.
40. Ragni E, Piberger H, Neupert C, Garcia-Cantalejo J, Popolo L, et al. (2011) The genetic interaction network of CCW12, a Saccharomyces cerevisiae gene required for cell wall integrity during budding and formation of mating projections. BMC genomics 12: 107.
41. Cai Y, Futcher B (2013) Effects of the yeast RNA-binding protein Whi3 on the half-life and abundance of CLN3 mRNA and other targets. PLoS One (in press).
42. Longtine MS, McKenzie A III, Demarini DJ, Shah NG, Wach A, et al. (1998) Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast 14: 953-961. (Pubitemid 28328001)
43. Snaith HA, Samejima I, Sawin KE (2005) Multistep and multimode cortical anchoring of tea1p at cell tips in fission yeast. Embo J 24: 3690-3699. (Pubitemid 41581686)
44. Buttery SM, Yoshida S, Pellman D (2007) Yeast formins Bni1 and Bnr1 utilize different modes of cortical interaction during the assembly of actin cables. Mol Biol Cell 18: 1826-1838. (Pubitemid 46717563)
45. Sikorski RS, Hieter P (1989) A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122: 19-27.
46. Buchan JR, Nissan T, Parker R (2010) Analyzing P-bodies and stress granules in Saccharomyces cerevisiae. Methods Enzymol 470: 619-640.
47. Nissan T, Parker R (2008) Analyzing P-bodies in Saccharomyces cerevisiae. Methods Enzymol 448: 507-520.
48. Iyer VR, Eisen MB, Ross DT, Schuler G, Moore T, et al. (1999) The transcriptional program in the response of human fibroblasts to serum. Science 283: 83-87. (Pubitemid 29044852)
49. Schneider CA, Rasband WS, Eliceiri KW (2012) NIH Image to ImageJ: 25 years of image analysis. Nature Meth 9: 671-675.