Yeast biological networks unfold the interplay of antioxidants, genome and phenotype, and reveal a novel regulator of the oxidative stress response

PLoS ONE

Volumn 5, Issue 10, 2010, Pages

  Otero, Jose M ^a,b   Papadakis, Manos A ^a   Gupta Udatha, D B R K ^b   Nielsen, Jens ^b   Panagiotou, Gianni ^a  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^b CHALMERS UNIVERSITY OF TECHNOLOGY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

BRAIN PROTEIN; FERULIC ACID; FUNGAL PROTEIN; PROTEIN BRP44; PROTEIN FMP43; UNCLASSIFIED DRUG; ANTIOXIDANT;

ADAPTATION; AEROBIC METABOLISM; ANAEROBIC METABOLISM; ARTICLE; BINDING AFFINITY; BINDING SITE; CONTROLLED STUDY; DATA ANALYSIS; FUNGAL GENOME; FUNGAL METABOLISM; FUNGAL STRAIN; FUNGUS GROWTH; FUNGUS MUTANT; GENE EXPRESSION; GENETIC CONSERVATION; GENETIC TRANSCRIPTION; GROWTH RATE; METABOLOMICS; MOLECULAR DOCKING; MOLECULAR INTERACTION; NONHUMAN; OXIDATIVE STRESS; PHENOTYPE; PREDICTION; PROTEIN STRUCTURE; REFERENCE VALUE; SACCHAROMYCES CEREVISIAE; SEQUENCE HOMOLOGY; SYSTEMS BIOLOGY; TRANSCRIPTOMICS; WILD TYPE; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; HUMAN; METABOLISM; METABOLOME;

SACCHAROMYCES CEREVISIAE;

ANTIOXIDANTS; BINDING SITES; FUNGAL PROTEINS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, FUNGAL; GENOME, FUNGAL; HUMANS; METABOLOME; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OXIDATIVE STRESS; PHENOTYPE; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION, GENETIC;

EID: 78149439957     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0013606     Document Type: Article

References (68)

1. Subbiah MTR (2006) Nutrigenetics and nutraceuticals: the next wave riding on personalized medicine. Transl Res 149: 55-61.
2. Hood L, Health JR, Phelps ME, Lin B (2004) Systems biology and new technologies enable predictive and preventative medicine. Science 306: 640-643.
3. Van der Greef J, Martin S, Juhasz P, Adourian A, Plasterer T, et al. (2007) The art and practice of systems biology in medicine: mapping patterns of relationships. J Proteome Res 6: 1540-1559.
4. Fay LB, German JB (2008) Personalizing foods: is genotype necessary? Curr Opin Biotechnol 19: 121-128.
5. Stover PJ (2006) Nutrition and Developmental Biology-Implications for Public Health. Nutr Rev 64: 60-70.
6. Rist MJ, Wenzel U, Daniel H (2006) Nutrition and food science go genomic. Trends Biotechnol 24: 1-7.
7. Ferguson LR (2001) Role of plant polyphenols in genomic stability. Mutat Res 475: 89-111.
8. Middleton EJ, Kandawasami C, Theoharides TC (2000) The effects of plat flavonoids on mammalian cells: implications for inflammation, heart disease, and cancer. Pharmacol Rev 52: 673-751.
9. Jang M, Cai L, Slowing KV, Thomas CF, Beecher CW, et al. (1997) Cancer chemopreventive activity of reservatol, a natural product derived from grapes. Science 275: 218-220.
10. Srinivasan M, Sudheer AR, Menon VP (2007) Ferulic acid: Therapeutic potential through its antioxidant property. J Clin Biochem Nutr 40: 92-100.
11. Ou S, Kwok KC (2004) Ferulic acid: pharmaceutical functions, preparation and applications in foods. J Sc Food Agric 84: 1261-1269.
12. Balasubashini MS, Rukkumani R, Viswanathan P, Menon VP (2004) Ferulic acid alleviates lipid peroxidation in diabetic rats. Phyt Res 18: 310-314.
13. Khanduja KL, Avti PK, Kumar S, Mittal N, Sohi KK, et al. (2006) Antiapoptotic activity of caffeic acid, ellagic acid and ferulic acid in normal human peripheral blood mononuclear cells: a Bcl-2 independent mechanism. Biochim et Bioph Acta 1760: 283-289.
14. Yabe T, Hirahara H, Harada N, Ito N, Nagai T, et al. (2010) Ferulic acid induces neural progenitor cell proliferation in vitro and in vivo. Neuroscience 165: 515-524.
15. Larsson S, Quintana-Sainz A, Reimann A, Nilvebrant NO, Jonsson LJ (2000) Influence of lignocellulose-derived aromatic compounds on oxygen-limited growth and ethanolic fermentation by Saccharomyces cerevisiae. Appl Biochem Biotechn 84-86: 617-632.
16. Huang Z, Dostal L, Rosazza JPN (1993) Microbial transformations of ferulic acid by Saccharomyces cerevisiae and Pseudomonas fluorescens. Appl Environ Microb59: 2244-2250.
17. Verduyn C, Postma E, Scheffers WA, Van Dijken JP (1992) Effect of benzoic acid on metabolic fluxes in yeasts: a continuous-culture study on the regulation of respiration and alcoholic fermentation. Yeast 8: 501-17.
18. Erdeniz N, Mortensen UH, Rothstein R (1997) Cloning-free PCR-based allele replacement methods. Genome Res 7: 1174-1183.
19. Panagiotou G, Olavarria R, Olsson L (2007) Penicillium brasilianum as an enzyme factory: the essential role of feruloyl esterases for the hydrolysis of the cell plant wall. J Biotech 139: 219-228.
20. Panagiotou G, Christakopoulos P, Grotkjær T, Nielsen J, Olsson L (2006) Engineering of the redox imbalance of Fusarium oxysporum enables anaerobic growth on xylose. Met Engin 8: 474-82.
21. Villas-Boas SG, Moxley JF, Åkesson M, Stephanopoulos G, Nielsen J (2005) High-throughput metabolic state analysis: the missing link in integrated functional genomics of yeasts. Biochem J 388: 669-677.
22. Villas-Boas SG, Delicado DG, Akesson M, Nielsen J (2003) Simultaneous analysis of amino and non-amino organic acids as methyl chloroformate derivatives using gas chromatography-mass spectrometry. Anal Biochem 322: 134-138.
23. Schmitt ME, Brown TA, Trumpower BL (1990) A rapid and simple method for preparation of RNA from Saccharomyces cerevisiae. Nucleic Acids Res 18: 3091-3092.
24. Affymetrix (2007) Gene chip expression analysis technical manual P/N 702232 Rev. pp 2.14.
25. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5: R80.
26. Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, et al. (2003) Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 31: e15.
27. Gautier L, Cope L, Bolstad BM, Irizarry RA (2004) affy-analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 20: 307-315.
28. Bolstad BM, Irizarry RA, Astrand M, Speed TP (2003) A comparison of normalization methods for high density oligonucleotide array data based on ariance and bias. Bioinformatics 19: 185-193.
29. Smyth G (2004) Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3: Article 3.
30. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Statist Soc B 57: 289-300.
31. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498-2504.
32. Carmona-Saez P, Chagoyen M, Tirado F, Carazo JM, Pascual-Montano A (2007) GENECODIS: A web-based tool for finding significant concurrent annotations in gene lists. Genome Biol 8: R3.
33. Oliveira AP, Patil KR, Nielsen J (2008) Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks. BMC Systems Biology 2: 17.
34. Ju D, Xie Y (2004) Proteasomal degradation of RPN4 via two distinct mechanisms: ubiquitin- dependent and -independent. J Biol Chem 279: 23851-23854.
35. London M, Keck BI, Ramos PC, Dohmen RJ (2004) Regulatory mechanisms controlling biogenesis of ubiquitin and the proteasome. FEBS Lett 567: 259-264.
36. Wang X, Xu X, Ju D, Xie Y (2008) Disruption of RPN4-induced proteasome expression in Saccharomyces cerevisiae reduces cell viability under stressed conditions. Genetics 180: 1945-1953.
37. Santos PM, Simoes T, Sa-Correia I (2009) Insights into yeast adaptive response to the agricultural fungicide mancozeb: a toxicoproteomics approach. Proteomics 9: 657-670.
38. Domico LM, Cooper KR, Bernard LP, Zeevalk GD (2007) Reactive oxygen species generation by the ethylene-bis-dithiocarbamate (EBDC) fungicide mancozeb and its contribution to neuronal toxicity in mesencephalic cells. Neurotoxicology 28: 1079-1091.
39. Thakur JK, Arthanari H, Yang F, Pan SJ, Fan X, et al. (2008) A nuclear receptor-like pathway regulating multidrug resistance in fungi. Nature 452: 604-609.
40. Kornberg RD (2005) Mediator and the mechanism of transcriptional activation. Trends Biochem Sci 30: 235-239.
41. Tan K, Feizi H, Luo C, Fan SH, Ravasi T, et al. (2007) A systems approach to delineate functions of paralogous transcription factors: role of the Yap family in the DNA damage response. PNAS 105: 2934-2939.
42. Van Slyke C, Grayhack J (2003) The essential transcription factor Reb1p interacts with the CLB2 UAS outside of the G2/M control region. Nucl Acids Res 15: 4597-4607.
43. Niu W, Li Z, Iyer VR, Marcotte EM (2008) Mechanisms of cell cycle control revealed by a systematic and quantitative overexpression screen in S. cerevisiae. PLoS Genetics 4: e1000120.
44. Lin SS, Manchester JK, Gordon JI (2003) Sip2, an N-Myristoylated b-subunit of SNF1 kinase, regulates aging in Saccharomyces cerevisiae by affecting cellular histone kinase activity, recombination at rDNA loci, and silencing. J Biol Chem 278: 13390-13397.
45. Cook M, Tyers M (2007) Size control goes global. Curr Opin Biotechn 18: 341-350.
46. Goranov AI, Cook M, Ricicova M, Ben-Ari G, Gonzalez C, et al. (2009) The rate of cell growth is governed by cell cycle stage. Genes & Development 23: 1408-1422.
47. Katherine EM, Svendsen A, Patkar SA, Wilson KS (2004) Structure of a feruloyl esterase from Aspergillus niger. Acta Cryst D60: 878-887.
48. Prates JAM, Tarbouriech N, Charnock SJ, Fontes CMJA, Ferreira LMA, et al. (2001) The Structure of the Feruloyl Esterase Module of Xylanase 10B from Clostridium thermocellum Provides Insights into Substrate Recognition. Structure 9: 1183-1190.
49. Kann MG (2007) Protein interactions and disease: computational approaches to uncover the etiology of diseases. Brief Bioinform 8: 333-346.
50. Gietz RD, Triggs-Raine B, Robbins A, Graham KC, Woods RA (1997) Identification of proteins that interact with a protein of interest: Applications of the yeast two-hybrid system. Mol Cellul Biochem 172: 67-79.
51. Legrain P, Wojcik J, Gauthier JM (2001) Protein-protein interaction maps: a lead towards cellular functions. Trends Genet 17: 346-352.
52. Valencia A, Pazos F (2002) Computational methods for the prediction of protein interactions. Curr Opin Struct Biol 12: 368-373.
53. Hopkins AL (2008) Network pharmacology: the next paradigm in drug discovery. Nature Chem Biol 4: 683-690.
54. Hillenmeyer ME, Fung E, Wildenhain J, Pierce SE, Hoon S, et al. (2008) The chemical genomic portrait of yeast: uncovering a phenotype for all genes. Science 320: 362-365.
55. Henrich S, Salo-Ahen OM, Huang B, Rippmann FF, Cruciani G, et al. (2010) Computational approaches to identifying and characterizing protein binding ites for ligand design. J Mol Recognit 23: 209-219.
56. Stelzi U, Worm U, Lalowski M, Haenig C, Brembeck FH, et al. (2005) A human protein-protein interaction network: a resource for annotating the proteome. Cell 127: 957-968.
57. Pold M, Zhou J, Chen GL, Hall JM, Vescio RA, et al. (1999) Identification of a new, unorthodox member of the MAGE gene family. Genomics 59: 161-167.
58. Wang H, Bedford FK, Brandon NJ, Moss SJ, Olsen RW (1999) GABA(A)- receptor-associated protein links GABA(A) receptors and the cytoskeleton. Nature 397: 69-72.
59. Morgensen J, Klausen IC, Pedersen AK, Egeblad H, Bross P, et al. (1999) Alpha-cardiac actin is a novel disease gene in familial hypertrophic cardiomyopathy. J Clin Invest 103: 39-43.
60. Martinez-Azorin F, Remacha M, Ballesta JP (2008) Functional characterization of ribosomal P1/P2 proteins in human cells. Biochem J 413: 527-534.
61. Jones G, Willett P (1995) Docking small-molecule ligands into active sites. Curr Opin Biotechnol 6: 652-656.
62. Shoichet BK, McGovern SL, Wei B, Irwin JJ (2002) Lead discovery using molecular docking. Curr Opin Chem Biol 6: 439-446.
63. Oda A, Takahashi O (2009) Validation of ArgusLab Efficiencies for Binding Free Energy Calculations. Chem-Bio Informatics J 9: 52-61.
64. Duverna R, Ablordeppey SY, Lamango NS (2010) Biochemical and Docking Analysis of Substrate Interactions with Polyisoprenylated Methylated Protein Methyl Esterase. Curr Canc Drug Targ 10: 634-648.
65. Almqvist J, Huang Y, Laaksonen A, Wang DN, Hovmöller S (2007) Docking and homology modeling explain inhibition of the human vesicular glutamate transporters. Protein Sci 216: 1819-1829.
66. Hirashima A, Huang H (2008) Homology modeling, agonist binding site identification, and docking in octopamine receptor of Periplaneta Americana. Comput Biol Chem 32: 185-190.
67. McRobb FM, Capuano B, Crosby IT, Chalmers DK, Yuriev E (2010) Homology modeling and docking evaluation of aminergic G protein-coupled receptors. J Chem Inf Model 50: 626-637.
68. Laurie AT, Jackson RM (2006) Methods for the prediction of protein-ligand binding sites for structure-based drug design and virtual ligand screening. Curr Protein Pept Sci 7: 395-406.