Chemical-genetic profile analysis in yeast suggests that a previously uncharacterized open reading frame, YBR261C, affects protein synthesis

BMC Genomics

Volumn 9, Issue , 2008, Pages

  Alamgir, Md ^a   Eroukova, Veronika ^a   Jessulat, Matthew ^a   Xu, Jianhua ^b   Golshani, Ashkan ^a  

^a CARLETON UNIVERSITY   (Canada)

^b JILIN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL DNA; FUNGAL PROTEIN; FUNGAL RNA; PAROMOMYCIN; RIBOSOME PROTEIN; TRANSLATIONAL ASSOCIATED ELEMENT 1 PROTEIN; UNCLASSIFIED DRUG; METHYLTRANSFERASE; SACCHAROMYCES CEREVISIAE PROTEIN; TAE1 PROTEIN, S CEREVISIAE;

ANTIFUNGAL SUSCEPTIBILITY; ARTICLE; CELL METABOLISM; CELL MUTANT; CELL TRANSPORT; CHEMICAL ANALYSIS; CONTROLLED STUDY; DNA METABOLISM; DRUG TARGETING; FUNCTIONAL GENOMICS; FUNGAL GENETICS; FUNGAL STRAIN; GENE DELETION; GENE FUNCTION; GENE INTERACTION; GENE OVEREXPRESSION; GENETIC ANALYSIS; MICROARRAY ANALYSIS; NONHUMAN; OPEN READING FRAME; PROTEIN SYNTHESIS; RNA TRANSLATION; YEAST; BIOSYNTHESIS; GENE EXPRESSION PROFILING; GENETICS; METHODOLOGY; PHYSIOLOGY; SACCHAROMYCES CEREVISIAE; SYSTEMS BIOLOGY;

GENE EXPRESSION PROFILING; METHYLTRANSFERASES; OPEN READING FRAMES; PAROMOMYCIN; PROTEIN BIOSYNTHESIS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SEQUENCE DELETION; SYSTEMS BIOLOGY;

EID: 58149302265     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-9-583     Document Type: Article

References (51)

1. Ito T Chiba T Ozawa R Yoshida M Hattori M Sakaki Y A comprehensive two-hybrid analysis to explore the yeast protein interactome Proc Natl Acad Sci USA 2001, 98(8):4569-4574. 31875 11283351 10.1073/pnas.061034498
2. Gavin AC Bosche M Krause R Grandi P Marzioch M Bauer A Schhultz J Rick JM Michon AM Cruciat CM Functional organization of the yeast proteome by systematic analysis of protein complexes Nature 2002, 415(6868):141-147. 10.1038/415141a 11805826
3. Tong AHY Evangelista M Parsons AB Xu H Bader GD Pagé N Robinson M Raghibizadeh S Hogue CWV Bussey H Andrews B Tyers M Boone C Systematic genetic analysis with ordered arrays of yeast deletion mutants Science 2001, 294:2364-2368. 10.1126/science.1065810 11743205
4. Peña-Castillo L Hughes TR Why are there still over 1000 uncharacterized yeast genes? Genetics 2007, 176(1):7-14. 1893027 17435240 10.1534/genetics.107.074468
5. Parsons AB Lopez A Givoni IE Williams DE Gray CA Porter J Chua G Sopko R Brost RL Ho CH Wang J Ketela T Brenner C Brill JA Fernandez GE Lorenz TC Payne GS Ishihara S Ohya Y Andrews B Hughes TR Frey BJ Graham TR Andersen RJ Boone C Exploring the mode-of-action of bioactive compounds by chemical-genetic profiling in yeast Cell 2006, 126(3):611-625. 10.1016/j.cell.2006.06.040 16901791
6. Lopez A Parsons AB Nislow C Giaever G Boone C Chemical-genetic approaches for exploring the mode of action of natural products Prog Drug Res 2008, 66:237-271. 18416308
7. Parsons AB Brost RL Ding H Li Z Zhang C Sheikh B Brown GW Kane PM Hughes TR Boone C Integration of chemical-genetic and genetic interaction data links bioactive compounds to cellular target pathways Nat Biotechnol 2004, 22(1):62-69. 10.1038/nbt919 14661025
8. Lesage G Sdicu AM Ménard P Shapiro J Hussein S Bussey H Analysis of beta-1,3-glucan assembly in Saccharomyces cerevisiae using a synthetic interaction network and altered sensitivity to caspofungin Genetics 2004, 167(1):35-49. 1470839 15166135 10.1534/genetics.167.1.35
9. Chloupková M LeBard LS Koeller DM MDL1 is a high copy suppressor of ATM1: Evidence for a role in resistance to oxidative stress J Mol Biol 2003, 331(1):155-165. 10.1016/S0022-2836(03)00666-1 12875842
10. Johnstone O Lasko P Translational Regulation and RNA Localization in Drosophila Oocytes and Embryos Annu Rev Genet 2001, 35:365-406. 10.1146/ annurev.genet.35.102401.090756 11700288
11. Kuersten S Goodwin EB The Power of the 3'UTR: Translational Control and Development Nat Rev Genet 2003, 4(8):626-637. 10.1038/nrg1125 12897774
12. Ruggero D Pandolfi PP Does the ribosome translate cancer? Nat Rev Cancer 2003, 3(3):179-192. 10.1038/nrc1015 12612653
13. Holcik M Sonenberg N Translation control in stress and apoptosis Nat Rev Mol Cell Biol 2005, 6(4):318-327. 10.1038/nrm1618 15803138
14. Peng WT Robinson MD Mnaimneh S Krogan NJ Cagney G Morris Q Davierwala AP Grigull J Yang X Zhang W Mitsakakis N Ryan OW Datta N Jojic V Pal C Canadien V Richards D Beattie B Wu LF Altschuler SJ Roweis S Frey BJ Emili A Greenblatt JF Hughes TR A panoramic view of yeast noncoding RNA processing Cell 2003, 113(7):919-933. 10.1016/S0092-8674(03)00466-5 12837249
15. Krogan NJ Peng WT Cagney G Robinson MD Haw R Zhong G Guo X Zhang X Canadien V Richards DP Beattie BK Lalev A Zhang W Davierwala AP Mnaimneh S Starostine A Tikuisis AP Grigull J Datta N Bray JE Hughes TR Emili A Greenblatt JF High-definition macromolecular composition of yeast RNA-processing complexes Mol Cell 2004, 13(2):225-239. 10.1016/ S1097-2765(04)00003-6 14759368
16. Fleischer TC Weaver CM McAfee KJ Jennings JL Link AJ Systematic identification and functional screens of uncharacterized proteins associated with eukaryotic ribosomal complexes Genes Dev 2006, 20(10):1294-1307. 1472904 16702403 10.1101/gad.1422006
17. Fan-Minogue H Bedwell DM Eukaryotic ribosomal RNA determinants of aminoglycoside resistance and their role in translational fidelity RNA 2008, 14:148-157. 2151042 18003936 10.1261/rna.805208
18. Kressler D de la Cruz J Rojo M Linder P Fal1p is an essential DEAD-box protein involved in 40S-ribosomal-subunit biogenesis in Saccharomyces cerevisiae Mol Cell Biol 1997, 17(12):7283-7294. 232585 9372960
19. Frigieri MC João Luiz MVS Apponi LH Zanelli CF Valentini SR Synthetic lethality between eIF5A and Ypt1 reveals a connection between translation and the secretory pathway in yeast Mol Genet Genomics 2008, 280:211-221. 10.1007/s00438-008-0357-y 18568365
20. Memarian N Jessulat M Alirezaie J Mir-Rashed N Xu J Zareie M Smith M Golshani A Colony size measurement of the yeast gene deletion strains for functional genomics BMC Bioinformatics 2007, 8:117. 1854909 17408490 10.1186/1471-2105-8-117
21. Nunes PA Tenreiro S Sá-Correia I Resistance and adaptation to quinidine in Saccharomyces cerevisiae: Role of QDR1 (YIL120w), encoding a plasma membrane transporter of the major facilitator superfamily required for multidrug resistance Antimicrob Agents Chemother 2001, 45(5):1528-1534. 90500 11302822 10.1128/AAC.45.5.1528-1534.2001
22. Hughes TR Marton MJ Jones AR Roberts CJ Stoughton R Armour CD Bennett HA Coffey E Dai H He YD Kidd MJ King AM Meyer MR Slade D Lum PY Stepaniants SB Shoemaker DD Gachotte D Chakraburtty K Simon J Bard M Friend SH Functional discovery via a compendium of expression profiles Cell 2000, 102(1):109-126. 10.1016/S0092-8674(00)00015-5 10929718
23. Katz JE Dlakiæ M Clarke S Automated identification of putative methyltransferases from genomic open reading frames Mol Cell Proteomics 2003, 2(8):525-540. 12872006
24. Zhou W Edelman GM Mauro VP Isolation and identification of short nucleotide sequences that affect translation initiation in Saccharomyces cerevisiae Proc Natl Acad Sci USA 2003, 100(8):4457-4462. 153577 12679518 10.1073/pnas.0437993100
25. Leeds P Wood JM Lee BS Culbertson MR Gene products that promote mRNA turnover in Saccharomyces cerevisiae Mol Cell Biol 1992, 12(5):2165-2177. 364388 1569946
26. Obrig TG Culp WJ McKeehan WL Hardesty B The mechanism by which cycloheximide and related glutarimide antibiotics inhibit peptide synthesis on reticulocyte ribosomes J Biol Chem 1971, 246(1):174-181. 5541758
27. Fingerman I Nagaraj V Norris D Vershon AK Sfp1 plays a key role in yeast ribosome biogenesis Eukaryot Cell 2003, 2(5):1061-1068. 219361 14555489 10.1128/EC.2.5.1061-1068.2003
28. Hillenmeyer ME Fung E Wildenhain J Pierce SE Hoon S Lee W Proctor M St Onge RP Tyers M Koller D Altman RB Davis RW Nislow C Giaever G The chemical genomic portrait of yeast: Uncovering a phenotype for all genes Science 2008, 320(5874):362-365. 10.1126/science.1150021 18420932
29. Deutschbauer AM Jaramillo DF Proctor M Kumm J Hillenmeyer ME Davis RW Nislow C Giaever G Mechanisms of haploinsufficiency revealed by genome-wide profiling in yeast Genetics 2005, 169(4):1915-1925. 1449596 15716499 10.1534/genetics.104.036871
30. Walter F Vicens Q Westhof E Aminoglycoside-RNA interactions Curr Opin Chem Biol 1999, 3(6):694-704. 10.1016/S1367-5931(99)00028-9 10600721
31. Iouk TL Aitchison JD Maguire S Wozniak RW Rrb1p, a yeast nuclear WD-repeat protein involved in the regulation of ribosome biosynthesis Mol Cell Biol 2001, 21(4):1260-1271. 99579 11158312 10.1128/ MCB.21.4.1260-1271.2001
32. Dinman JD Kinzy TG Translational misreading: Mutations in translation elongation factor 1alpha differentially affect programmed ribosomal frameshifting and drug sensitivity RNA 1997, 3(8):870-881. 1369532 9257646
33. Venema J Tollervey D Ribosome synthesis in Saccharomyces cerevisiae Annu Rev Genet 1999, 33:261-311. 10.1146/annurev.genet.33.1.261 10690410
34. Rosado IV Kressler D de la Cruz J Functional analysis of Saccharomyces cerevisiae ribosomal protein Rpl3p in ribosome synthesis Nucleic Acids Res 2007, 35(12):4203-4213. 1919493 17569673 10.1093/nar/gkm388
35. Stansfield I Akhmaloka Tuite MF A mutant allele of the SUP45 (SAL4) gene of Saccharomyces cerevisiae shows temperature-dependent allosuppressor and omnipotent suppressor phenotypes Curr Genet 1995, 27(5):417-426. 10.1007/BF00311210 7586027
36. Ideker T Sharan R Protein networks in disease Genome Res 2008, 18:644-652. 10.1101/gr.071852.107 18381899
37. Boone C Bussey H Andrews BJ Exploring genetic interactions and networks with yeast Nat Rev Genet 2007, 8(6):437-49. 10.1038/nrg2085 17510664
38. Teo SH Jackson SP Telomerase subunit overexpression suppresses telomere-specific checkpoint activation in the yeast yku80 mutant EMBO Rep 2001, 2(3):197-202. 1083835 11266360 10.1093/embo-reports/kve038
39. Vlásek L Phan L Schoenfeld LW Valásková V Hinnebusch AG Related eIF3 subunits TIF32 and HCR1 interact with an RNA recognition motif in PRT1 required for eIF3 integrity and ribosome binding EMBO J 2001, 20:891-904. 145407 11179233 10.1093/emboj/20.4.891
40. Saccharomyces Genome Database http://www.yeastgenome.org/
41. Galván IJ Mir-Rashed N Jessulat M Atanya M Golshani A Durst T Petit P Amiquet VT Boekhout T Summerbell R Cruz I Arnason JT Smith ML Antifungal and antioxidant activities of the phytomedicine pipsissewa, Chimaphila umbellata Phytochemistry 2008, 69(3):738-746. 10.1016/ j.phytochem.2007.09.007 17950387
42. Anderson JB Sirjusingh C Parsons AB Boone C Wickens C Cowen LE Kohn LM Mode of selection and experimental evolution of antifungal drug resistance in Saccharomyces cerevisiae Genetics 2003, 163(4):1287-1298. 1462505 12702675
43. Lucchini G Hinnebusch AG Chen C Fink GR Positive regulatory interactions of the HIS4 gene of Saccharomyces cerevisiae Mol Cell Biol 1984, 4(7):1326-1333. 368915 6095062
44. Shenton D Smirnova JB Selley JN Carroll K Hubbard SJ Pavitt GD Ashe MP Grant CM Global translational responses to oxidative stress impact upon multiple levels of protein synthesis J Biol Chem 2006, 281(39):29011-29021. 10.1074/jbc.M601545200 16849329
45. Krogan NJ Kim M Tong A Golshani A Cagney G Canadien V Richards DP Beattie BK Emili A Boone C Shilatifard A Buratowski S Greenblatt J Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II Mol Cell Biol 2003, 23(12):4207-4218. 427527 12773564 10.1128/MCB.23.12.4207-4218.2003
46. Schwartz DC Parker R Mutations in translation initiation factors lead to increased rates of deadenylation and decapping of mRNAs in Saccharomyces cerevisiae Mol Cell Biol 1999, 19(8):5247-5256. 84368 10409716
47. Yu S Vincent A Opriessnig T Carpenter S Kitikoon P Halbur PG Thacker E Quantification of PCV2 capsid transcript in peripheral blood mononuclear cells (PBMCs) in vitro Vet Microbiol 2007, 123(1-3):34-42. 10.1016/ j.vetmic.2007.02.021 17418508
48. Foiani M Cigan AM Paddon CJ Harashima S Hinnebusch AG GCD2, a translational repressor of the GCN4 gene, has a general function in the initiation of protein synthesis in Saccharomyces cerevisiae Mol Cell Biol 1991, 11(6):3203-3216. 360173 2038326
49. Schuldiner M Collins SR Thompson NJ Denic V Bhamidipati A Punna T Ihmels J Andrews B Boone C Greenblatt JF Weissman JS Krogan NJ Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile Cell 2005, 123(3):507-519. 10.1016/j.cell.2005.08.031 16269340
50. Tong AHY Lesage G Bader GD Ding H Xu H Xin X Young J Berriz GF Brost RL Chang M Global mapping of the yeast genetic interaction network Science 2004, 303:808-813. 10.1126/science.1091317 14764870
51. Sopko R Huang D Preston N Chua G Papp B Kafadar K Snyder M Oliver SG Cyert M Hughes TR Boone C Andrews B Mapping pathways and phenotypes by systematic gene overexpression Mol Cell 2006, 21(3):319-330. 10.1016/ j.molcel.2005.12.011 16455487