The next frontier of systems biology: Higher-order and interspecies interactions

Genome Biology

Volumn 11, Issue 5, 2010, Pages

  Fischbach, Michael A ^a   Krogan, Nevan J ^b  

^a San Francisco   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; GROWTH FACTOR; GUANOSINE TRIPHOSPHATASE;

BIOCHEMISTRY; DNA REPLICATION; DNA SEQUENCE; DROSOPHILA MELANOGASTER; GENE EXPRESSION PROFILING; GENE INTERACTION; GENETIC ANALYSIS; HOST PATHOGEN INTERACTION; HUMAN; MOLECULAR BIOLOGY; MOLECULAR GENETICS; MUTAGENESIS; NONHUMAN; PROTEIN PROTEIN INTERACTION; REVIEW; SCHIZOSACCHAROMYCES POMBE; SIGNAL TRANSDUCTION; TRANSPOSON; ANIMAL; ARTICLE; SPECIES DIFFERENCE; SYSTEMS BIOLOGY; TIME;

ANIMALS; HUMANS; SPECIES SPECIFICITY; SYSTEMS BIOLOGY; TIME FACTORS;

EID: 77957283851     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2010-11-5-208     Document Type: Review

References (35)

1. Alberts B. The cell as a collection of protein machines: preparing the next generation of molecular biologists. Cell 1998, 92:291-294. 10.1016/S0092-8674(00)80922-8, 9476889.
2. Hartwell LH, Hopfield JJ, Leibler S, Murray AW. From molecular to modular cell biology. Nature 1999, 402:C47-C52. 10.1038/35011540, 10591225.
3. Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, Marzioch M, Rau C, Jensen LJ, Bastuck S, Dümpelfeld B, Edelmann A, Heurtier MA, Hoffman V, Hoefert C, Klein K, Hudak M, Michon AM, Schelder M, Schirle M, Remor M, Rudi T, Hooper S, Bauer A, Bouwmeester T, Casari G, Drewes G, Neubauer G, Rick JM, Kuster B, Bork P, et al. Proteome survey reveals modularity of the yeast cell machinery. Nature 2006, 440:631-636. 10.1038/nature04532, 16429126.
4. Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, Punna T, Peregrín-Alvarez JM, Shales M, Zhang X, Davey M, Robinson MD, Paccanaro A, Bray JE, Sheung A, Beattie B, Richards DP, Canadien V, Lalev A, Mena F, Wong P, Starostine A, Canete MM, Vlasblom J, Wu S, Orsi C, et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 2006, 440:637-643. 10.1038/nature04670, 16554755.
5. Butland G, Peregrín-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A. Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 2005, 433:531-537. 10.1038/nature03239, 15690043.
6. Hu P, Janga SC, Babu M, Díaz-Mejía JJ, Butland G, Yang W, Pogoutse O, Guo X, Phanse S, Wong P, Chandran S, Christopoulos C, Nazarians-Armavil A, Nasseri NK, Musso G, Ali M, Nazemof N, Eroukova V, Golshani A, Paccanaro A, Greenblatt JF, Moreno-Hagelsieb G, Emili A, et al. Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol 2009, 7:e96. 10.1371/journal.pbio.1000096, 2672614, 19402753.
7. Kühner S, van Noort V, Betts MJ, Leo-Macias A, Batisse C, Rode M, Yamada T, Maier T, Bader S, Beltran-Alvarez P, Castaño-Diez D, Chen WH, Devos D, Güell M, Norambuena T, Racke I, Rybin V, Schmidt A, Yus E, Aebersold R, Herrmann R, Böttcher B, Frangakis AS, Russell RB, Serrano L, Bork P, Gavin AC. Proteome organization in a genome-reduced bacterium. Science 2009, 326:1235-1240. 10.1126/science.1176343, 19965468.
8. Hutchins JR, Toyoda Y, Hegemann B, Poser I, Hériché JK, Sykora MM, Augsburg M, Hudecz O, Buschhorn BA, Bulkescher J, Conrad C, Comartin D, Schleiffer A, Sarov M, Pozniakovsky A, Slabicki MM, Schloissnig S, Steinmacher I, Leuschner M, Ssykor A, Lawo S, Pelletier L, Stark H, Nasmyth K, Ellenberg J, Durbin R, Buchholz F, Mechtler K, Hyman AA, Peters JM. Systematic analysis of human protein complexes identifies chromosome segregation proteins. Science 2010, DOI:10.1126/science.1181348..
9. Ewing RM, Chu P, Elisma F, Li H, Taylor P, Climie S, McBroom-Cerajewski L, Robinson MD, O'Connor L, Li M, Taylor R, Dharsee M, Ho Y, Heilbut A, Moore L, Zhang S, Ornatsky O, Bukhman YV, Ethier M, Sheng Y, Vasilescu J, Abu-Farha M, Lambert JP, Duewel HS, Stewart II, Kuehl B, Hogue K, Colwill K, Gladwish K, Muskat B, Kinach R, Adams SL, Moran MF, Morin GB, Topaloglou T, Figeys D. Large-scale mapping of human protein-protein interactions by mass spectrometry. Mol Syst Biol 2007, 3:89. 10.1038/msb4100134, 1847948, 17353931.
10. Lehman IR, Bessman MJ, Simms ES, Kornberg A. Enzymatic synthesis of deoxyribonucleic acid. I. Preparation of substrates and partial purification of an enzyme from Escherichia coli. J Biol Chem 1958, 233:163-170.
11. Bessman MJ, Lehman IR, Simms ES, Kornberg A. Enzymatic synthesis of deoxyribonucleic acid. II. General properties of the reaction. J Biol Chem 1958, 233:171-177.
12. Güell M, van Noort V, Yus E, Chen WH, Leigh-Bell J, Michalodimitrakis K, Yamada T, Arumugam M, Doerks T, Kühner S, Rode M, Suyama M, Schmidt S, Gavin AC, Bork P, Serrano L. Transcriptome complexity in a genome-reduced bacterium. Science 2009, 326:1268-1271. 10.1126/science.1176951, 19965477.
13. Yus E, Maier T, Michalodimitrakis K, van Noort V, Yamada T, Chen WH, Wodke JA, Güell M, Martínez S, Bourgeois R, Kühner S, Raineri E, Letunic I, Kalinina OV, Rode M, Herrmann R, Gutiérrez-Gallego R, Russell RB, Gavin AC, Bork P, Serrano L. Impact of genome reduction on bacterial metabolism and its regulation. Science 2009, 326:1263-1268. 10.1126/science.1177263, 19965476.
14. Winzeler EA, Shoemaker DD, Astromoff A, Liang H, Anderson K, Andre B, Bangham R, Benito R, Boeke JD, Bussey H, Chu AM, Connelly C, Davis K, Dietrich F, Dow SW, El Bakkoury M, Foury F, Friend SH, Gentalen E, Giaever G, Hegemann JH, Jones T, Laub M, Liao H, Liebundguth N, Lockhart DJ, Lucau-Danila A, Lussier M, M'Rabet N, Menard P, et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 1999, 285:901-906. 10.1126/science.285.5429.901, 10436161.
15. 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, 102:109-126. 10.1016/S0092-8674(00)00015-5, 10929718.
16. Giaever G, Chu AM, Ni L, Connelly C, Riles L, Véronneau S, Dow S, Lucau-Danila A, Anderson K, André B, Arkin AP, Astromoff A, El-Bakkoury M, Bangham R, Benito R, Brachat S, Campanaro S, Curtiss M, Davis K, Deutschbauer A, Entian KD, Flaherty P, Foury F, Garfinkel DJ, Gerstein M, Gotte D, Güldener U, Hegemann JH, Hempel S, Herman Z, et al. Functional profiling of the Saccharomyces cerevisiae genome. Nature 2002, 418:387-391. 10.1038/nature00935, 12140549.
17. 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, 320:362-365. 10.1126/science.1150021, 2794835, 18420932.
18. Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2006, 2:2006.0008. 10.1038/msb4100050, 1681482, 16738554.
19. Bioneer Schizosaccharomyces pombe. , http://pombe.bioneer.co.kr
20. Morgan TH. The origin of five mutations in eye color in Drosophila and their modes of inheritance. Science 1911, 33:534-537. 10.1126/science.33.849.534-a, 17817675.
21. Morgan TH. The origin of nine wing mutations in Drosophila. Science 1911, 33:496-499. 10.1126/science.33.848.496, 17774436.
22. Sturtevant AH. The linear arrangement of six sex-linked factors in Drosophila, as shown by their mode of association. J Exp Zool 1913, 14:43-59.
23. Snyder M, Elledge S, Davis RW. Rapid mapping of antigenic coding regions and constructing insertion mutations in yeast genes by mini-Tn10 "transplason" mutagenesis. Proc Natl Acad Sci USA 1986, 83:730-734. 10.1073/pnas.83.3.730, 322938, 3003747.
24. Tong AH, Evangelista M, Parsons AB, Xu H, Bader GD, Pagé N, Robinson M, Raghibizadeh S, Hogue CW, 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.
25. Roguev A, Wiren M, Weissman JS, Krogan NJ. High-throughput genetic interaction mapping in the fission yeast Schizosaccharomyces pombe. Nat Methods 2007, 4:861-866. 10.1038/nmeth1098, 17893680.
26. Butland G, Babu M, Díaz-Mejía JJ, Bohdana F, Phanse S, Gold B, Yang W, Li J, Gagarinova AG, Pogoutse O, Mori H, Wanner BL, Lo H, Wasniewski J, Christopolous C, Ali M, Venn P, Safavi-Naini A, Sourour N, Caron S, Choi JY, Laigle L, Nazarians-Armavil A, Deshpande A, Joe S, Datsenko KA, Yamamoto N, Andrews BJ, Boone C, Ding H, et al. eSGA: E. coli synthetic genetic array analysis. Nat Methods 2008, 5:789-795. 10.1038/nmeth.1239, 18677321.
27. Typas A, Nichols RJ, Siegele DA, Shales M, Collins SR, Lim B, Braberg H, Yamamoto N, Takeuchi R, Wanner BL, Mori H, Weissman JS, Krogan NJ, Gross CA. High-throughput, quantitative analyses of genetic interactions in E. coli. Nat Methods 2008, 5:781-787. 10.1038/nmeth.1240, 2700713, 19160513.
28. Nagai S, Dubrana K, Tsai-Pflugfelder M, Davidson MB, Roberts TM, Brown GW, Varela E, Hediger F, Gasser SM, Krogan NJ. Functional targeting of DNA damage to a nuclear pore-associated SUMO-dependent ubiquitin ligase. Science 2008, 322:597-602. 10.1126/science.1162790, 18948542.
29. Stremlau M, Owens CM, Perron MJ, Kiessling M, Autissier P, Sodroski J. The cytoplasmic body component TRIM5alpha restricts HIV-1 infection in Old World monkeys. Nature 2004, 427:848-853. 10.1038/nature02343, 14985764.
30. Aktories K, Schmidt G, Just I. Rho GTPases as targets of bacterial protein toxins. Biol Chem 2000, 381:421-426. 10.1515/BC.2000.054, 10937872.
31. Kumar D, Nath L, Kamal MA, Varshney A, Jain A, Singh S, Rao KV. Genome-wide analysis of the host intracellular network that regulates survival of Mycobacterium tuberculosis. Cell 2010, 140:731-743. 10.1016/j.cell.2010.02.012, 20211141.
32. Brass AL, Dykxhoorn DM, Benita Y, Yan N, Engelman A, Xavier RJ, Lieberman J, Elledge SJ. Identification of host proteins required for HIV infection through a functional genomic screen. Science 2008, 319:921-926. 10.1126/science.1152725, 18187620.
33. König R, Zhou Y, Elleder D, Diamond TL, Bonamy GM, Irelan JT, Chiang CY, Tu BP, De Jesus PD, Lilley CE, Seidel S, Opaluch AM, Caldwell JS, Weitzman MD, Kuhen KL, Bandyopadhyay S, Ideker T, Orth AP, Miraglia LJ, Bushman FD, Young JA, Chanda SK. Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. Cell 2008, 135:49-60. 10.1016/j.cell.2008.07.032, 2628946, 18854154.
34. Zhou H, Xu M, Huang Q, Gates AT, Zhang XD, Castle JC, Stec E, Ferrer M, Strulovici B, Hazuda DJ, Espeseth AS. Genome-scale RNAi screen for host factors required for HIV replication. Cell Host Microbe 2008, 4:495-504. 10.1016/j.chom.2008.10.004, 18976975.
35. Xu J, Bjursell MK, Himrod J, Deng S, Carmichael LK, Chiang HC, Hooper LV, Gordon JI. A genomic view of the human-Bacteroides thetaiotaomicron symbiosis. Science 2003, 299:2074-2076. 10.1126/science.1080029, 12663928.