Quantitative Genome-Wide Genetic Interaction Screens Reveal Global Epistatic Relationships of Protein Complexes in


Large-scale proteomic analyses in Escherichia coli have documented the composition and physical relationships of multiprotein complexes, but not their functional organization into biological pathways and processes. Conversely, genetic interaction (GI) screens can provide insights into the biological role(s) of individual gene and higher order associations. Combining the information from both approaches should elucidate how complexes and pathways intersect functionally at a systems level. However, such integrative analysis has been hindered due to the lack of relevant GI data. Here we present a systematic, unbiased, and quantitative synthetic genetic array screen in E. coli describing the genetic dependencies and functional cross-talk among over 600,000 digenic mutant combinations. Combining this epistasis information with putative functional modules derived from previous proteomic data and genomic context-based methods revealed unexpected associations, including new components required for the biogenesis of iron-sulphur and ribosome integrity, and the interplay between molecular chaperones and proteases. We find that functionally-linked genes co-conserved among γ-proteobacteria are far more likely to have correlated GI profiles than genes with divergent patterns of evolution. Overall, examining bacterial GIs in the context of protein complexes provides avenues for a deeper mechanistic understanding of core microbial systems.


Vyšlo v časopise: Quantitative Genome-Wide Genetic Interaction Screens Reveal Global Epistatic Relationships of Protein Complexes in. PLoS Genet 10(2): e32767. doi:10.1371/journal.pgen.1004120
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1004120

Souhrn

Large-scale proteomic analyses in Escherichia coli have documented the composition and physical relationships of multiprotein complexes, but not their functional organization into biological pathways and processes. Conversely, genetic interaction (GI) screens can provide insights into the biological role(s) of individual gene and higher order associations. Combining the information from both approaches should elucidate how complexes and pathways intersect functionally at a systems level. However, such integrative analysis has been hindered due to the lack of relevant GI data. Here we present a systematic, unbiased, and quantitative synthetic genetic array screen in E. coli describing the genetic dependencies and functional cross-talk among over 600,000 digenic mutant combinations. Combining this epistasis information with putative functional modules derived from previous proteomic data and genomic context-based methods revealed unexpected associations, including new components required for the biogenesis of iron-sulphur and ribosome integrity, and the interplay between molecular chaperones and proteases. We find that functionally-linked genes co-conserved among γ-proteobacteria are far more likely to have correlated GI profiles than genes with divergent patterns of evolution. Overall, examining bacterial GIs in the context of protein complexes provides avenues for a deeper mechanistic understanding of core microbial systems.


Zdroje

1. BabuM, MussoG, Diaz-MejiaJJ, ButlandG, GreenblattJF, et al. (2009) Systems-level approaches for identifying and analyzing genetic interaction networks in Escherichia coli and extensions to other prokaryotes. Mol Biosyst 12: 1439–1455.

2. HuP, JangaSC, BabuM, Diaz-MejiaJJ, ButlandG (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol 7: e1000096.

3. Peregrin-AlvarezJM, XiongX, SuC, ParkinsonJ (2009) The Modular Organization of Protein Interactions in Escherichia coli. PLoS Comput Biol 5: e1000523.

4. Moreno-HagelsiebG, Collado-VidesJ (2002) A powerful non-homology method for the prediction of operons in prokaryotes. Bioinformatics 18 Suppl 1: S329–336.

5. SalgadoH, Moreno-HagelsiebG, SmithTF, Collado-VidesJ (2000) Operons in Escherichia coli: genomic analyses and predictions. Proc Natl Acad Sci U S A 97: 6652–6657.

6. GagarinovaA, EmiliA (2012) Genome-scale genetic manipulation methods for exploring bacterial molecular biology. Mol Biosyst 8: 1626–1638.

7. BabuM, VlasblomJ, PuS, GuoX, GrahamC, et al. (2012) Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae. Nature 489: 585–589.

8. GavinAC, AloyP, GrandiP, KrauseR, BoescheM, et al. (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature 631–636.

9. KroganNJ, CagneyG, YuH, ZhongG, GuoX, et al. (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440: 637–643.

10. ButlandG, Peregrín-AlvarezJM, LiJ, YangW, YangX, et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433: 531–537.

11. ArifuzzamanM, MaedaM, ItohA, NishikataK, TakitaC, et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res 16: 686–691.

12. Díaz-MejíaJJ, BabuM, EmiliA (2009) Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome. FEMS Microbiol Rev 33: 66–97.

13. ButlandG, BabuM, Díaz-MejíaJJ, BohdanaF, PhanseS, et al. (2008) eSGA: E. coli synthetic genetic array analysis. Nat Methods 5: 789–795.

14. TypasA, NicholsRJ, SiegeleDA, ShalesM, CollinsSR, et al. (2008) High-throughput, quantitative analyses of genetic interactions in E. coli. Nat Methods 5: 781–787.

15. van OpijnenT, BodiKL, CamilliA (2009) Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms. Nat Methods 6: 767–772.

16. BabuM, Díaz-MejíaJJ, VlasblomJ, GagarinovaA, PhanseS, et al. (2011) Genetic interaction maps in Escherichia coli reveal functional crosstalk among cell envelope biogenesis pathways. PLoS Genet 7: e1002377.

17. BarabasiAL, OltvaiZN (2004) Network biology: understanding the cell's functional organization. Nat Rev Genet 5: 101–113.

18. RileyM, AbeT, ArnaudMB, BerlynMK, BlattnerFR, et al. (2006) Escherichia coli K-12: a cooperatively developed annotation snapshot–2005. Nucleic Acids Res 34: 1–9.

19. BabaT, AraT, HasegawaM, TakaiY, OkumuraY, et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2: 2006.0008.

20. BandyopadhyayS, KelleyR, KroganNJ, IdekerT (2008) Functional maps of protein complexes from quantitative genetic interaction data. PLoS Comput Biol 4: e1000065.

21. BeltraoP, CagneyG, KroganNJ (2010) Quantitative genetic interactions reveal biological modularity. Cell 141: 739–745.

22. BooneC, BusseyH, AndrewsBJ (2007) Exploring genetic interactions and networks with yeast. Nat Rev Genet 8: 437–449.

23. UlitskyI, ShlomiT, KupiecM, ShamirR (2008) From E-MAPs to module maps: dissecting quantitative genetic interactions using physical interactions. Mol Syst Biol 4: 209.

24. CostanzoM, BaryshnikovaA, BellayJ, KimY, SpearED, et al. (2010) The genetic landscape of a cell. Science 327: 425–431.

25. CollinsSR, SchuldinerM, KroganNJ, WeissmanJS (2006) A strategy for extracting and analyzing large-scale quantitative epistatic interaction data. Genome Biol 7: R63.

26. BaryshnikovaA, CostanzoM, KimY, DingH, KohJ, et al. (2010) Quantitative analysis of fitness and genetic interactions in yeast on a genome scale. Nat Methods 7: 1017–1024.

27. SchuldinerM, CollinsSR, ThompsonNJ, DenicV, BhamidipatiA, et al. (2005) Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile. Cell 123: 507–519.

28. ManiR, St OngeRP, HartmanJLt, GiaeverG, RothFP (2008) Defining genetic interaction. Proc Natl Acad Sci U S A 105: 3461–3466.

29. DixonSJ, CostanzoM, BaryshnikovaA, AndrewsB, BooneC (2009) Systematic mapping of genetic interaction networks. Annu Rev Genet 43: 601–625.

30. CostanzoM, BaryshnikovaA, MyersCL, AndrewsB, BooneC (2011) Charting the genetic interaction map of a cell. Curr Opin Biotechnol 22: 66–74.

31. BellayJ, AtluriG, SingTL, ToufighiK, CostanzoM, et al. (2011) Putting genetic interactions in context through a global modular decomposition. Genome Res 21: 1375–1387.

32. CollinsSR, MillerKM, MaasNL, RoguevA, FillinghamJ, et al. (2007) Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature 446: 806–810.

33. DavierwalaAP, HaynesJ, LiZ, BrostRL, RobinsonMD, et al. (2005) The synthetic genetic interaction spectrum of essential genes. Nat Genet 37: 1147–1152.

34. WilmesGM, BergkesselM, BandyopadhyayS, ShalesM, BrabergH, et al. (2008) A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing. Mol Cell 32: 735–746.

35. UeguchiC, ShiozawaT, KakedaM, YamadaH, MizunoT (1995) A study of the double mutation of dnaJ and cbpA, whose gene products function as molecular chaperones in Escherichia coli. J Bacteriol 177: 3894–3896.

36. CourcelleJ, Carswell-CrumptonC, HanawaltPC (1997) recF and recR are required for the resumption of replication at DNA replication forks in Escherichia coli. Proc Natl Acad Sci U S A 94: 3714–3719.

37. ChenaultSS, EarhartCF (1991) Organization of genes encoding membrane proteins of the Escherichia coli ferrienterobactin permease. Mol Microbiol 5: 1405–1413.

38. SheaCM, McIntoshMA (1991) Nucleotide sequence and genetic organization of the ferric enterobactin transport system: homology to other periplasmic binding protein-dependent systems in Escherichia coli. Mol Microbiol 5: 1415–1428.

39. OrchardSS, RostronJE, SegallAM (2012) Escherichia coli enterobactin synthesis and uptake mutants are hypersensitive to an antimicrobial peptide that limits the availability of iron in addition to blocking Holliday junction resolution. Microbiology 158: 547–559.

40. FaithJJ, DriscollME, FusaroVA, CosgroveEJ, HayeteB, et al. (2008) Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata. Nucleic Acids Res 36: D866–870.

41. NicholsRJ, SenS, ChooYJ, BeltraoP, ZietekM, et al. (2011) Phenotypic landscape of a bacterial cell. Cell 144: 143–156.

42. PriceMN, ArkinAP, AlmEJ (2006) The life-cycle of operons. PLoS Genet 2: e96.

43. IkeuchiY, ShigiN, KatoJ, NishimuraA, SuzukiT (2006) Mechanistic insights into sulfur relay by multiple sulfur mediators involved in thiouridine biosynthesis at tRNA wobble positions. Mol Cell 21: 97–108.

44. SegrèD, DelunaA, ChurchGM, KishonyR (2005) Modular epistasis in yeast metabolism. Nat Genet 37: 77–83.

45. MichautM, BaryshnikovaA, CostanzoM, MyersCL, AndrewsBJ, et al. (2011) Protein complexes are central in the yeast genetic landscape. PLoS Comput Biol 7: e1001092.

46. SilhavyTJ, KahneD, WalkerS (2010) The bacterial cell envelope. Cold Spring Harb Perspect Biol 2: a000414.

47. DelmasS, MaticI (2006) Interplay between replication and recombination in Escherichia coli: impact of the alternative DNA polymerases. Proc Natl Acad Sci U S A 103: 4564–4569.

48. DahlJU, UrbanA, BolteA, SriyabhayaP, DonahueJL, et al. (2011) The identification of a novel protein involved in molybdenum cofactor biosynthesis in Escherichia coli. J Biol Chem 286: 35801–35812.

49. SniderJ, HouryWA (2006) MoxR AAA+ ATPases: a novel family of molecular chaperones? J Struct Biol 156: 200–209.

50. BrillasE, SiresI, OturanMA (2009) Electro-Fenton process and related electrochemical technologies based on Fenton's reaction chemistry. Chem Rev 109: 6570–6631.

51. DjamanO, OuttenFW, ImlayJA (2004) Repair of oxidized iron-sulfur clusters in Escherichia coli. J Biol Chem 279: 44590–44599.

52. KohanskiMA, DwyerDJ, HayeteB, LawrenceCA, CollinsJJ (2007) A common mechanism of cellular death induced by bactericidal antibiotics. Cell 130: 797–810.

53. SchwartzCJ, DjamanO, ImlayJA, KileyPJ (2000) The cysteine desulfurase, IscS, has a major role in in vivo Fe-S cluster formation in Escherichia coli. Proc Natl Acad Sci U S A 97: 9009–9014.

54. EzratyB, VergnesA, BanzhafM, DuvergerY, HuguenotA, et al. (2013) Fe-S cluster biosynthesis controls uptake of aminoglycosides in a ROS-less death pathway. Science 340: 1583–1587.

55. TakahashiY, NakamuraM (1999) Functional assignment of the ORF2-iscS-iscU-iscA-hscB-hscA-fdx-ORF3 gene cluster involved in the assembly of Fe-S clusters in Escherichia coli. J Biochem 126: 917–926.

56. WooffE, MichellSL, GordonSV, ChambersMA, BardarovS, et al. (2002) Functional genomics reveals the sole sulphate transporter of the Mycobacterium tuberculosis complex and its relevance to the acquisition of sulphur in vivo. Mol Microbiol 43: 653–663.

57. LithgowJK, HayhurstEJ, CohenG, AharonowitzY, FosterSJ (2004) Role of a cysteine synthase in Staphylococcus aureus. J Bacteriol 186: 1579–1590.

58. BykowskiT, van der PloegJR, Iwanicka-NowickaR, HryniewiczMM (2002) The switch from inorganic to organic sulphur assimilation in Escherichia coli: adenosine 5′-phosphosulphate (APS) as a signalling molecule for sulphate excess. Mol Microbiol 43: 1347–1358.

59. EichhornE, van der PloegJR, LeisingerT (2000) Deletion analysis of the Escherichia coli taurine and alkanesulfonate transport systems. J Bacteriol 182: 2687–2695.

60. WadaA, MikkolaR, KurlandCG, IshihamaA (2000) Growth phase-coupled changes of the ribosome profile in natural isolates and laboratory strains of Escherichia coli. J Bacteriol 182: 2893–2899.

61. O'ConnorM, GoringerHU, DahlbergAE (1992) A ribosomal ambiguity mutation in the 530 loop of E. coli 16S rRNA. Nucleic Acids Res 20: 4221–4227.

62. JomaaA, StewartG, Martin-BenitoJ, ZielkeR, CampbellTL, et al. (2011) Understanding ribosome assembly: the structure of in vivo assembled immature 30S subunits revealed by cryo-electron microscopy. RNA 17: 697–709.

63. LeongV, KentM, JomaaA, OrtegaJ (2013) Escherichia coli rimM and yjeQ null strains accumulate immature 30S subunits of similar structure and protein complement. RNA 19: 789–802.

64. HartlFU, Hayer-HartlM (2009) Converging concepts of protein folding in vitro and in vivo. Nat Struct Mol Biol 16: 574–581.

65. WongP, HouryWA (2004) Chaperone networks in bacteria: analysis of protein homeostasis in minimal cells. J Struct Biol 146: 79–89.

66. GongY, KakiharaY, KroganN, GreenblattJ, EmiliA, et al. (2009) An atlas of chaperone-protein interactions in Saccharomyces cerevisiae: implications to protein folding pathways in the cell. Mol Syst Biol 5: 275.

67. KumarM, SourjikV (2012) Physical map and dynamics of the chaperone network in Escherichia coli. Mol Microbiol 84: 736–747.

68. BakerTA, SauerRT (2012) ClpXP, an ATP-powered unfolding and protein-degradation machine. Biochim Biophys Acta 1823: 15–28.

69. SauerRT, BakerTA (2011) AAA+ proteases: ATP-fueled machines of protein destruction. Annu Rev Biochem 80: 587–612.

70. ReidBG, FentonWA, HorwichAL, Weber-BanEU (2001) ClpA mediates directional translocation of substrate proteins into the ClpP protease. Proc Natl Acad Sci U S A 98: 3768–3772.

71. RatajczakE, ZietkiewiczS, LiberekK (2009) Distinct activities of Escherichia coli small heat shock proteins IbpA and IbpB promote efficient protein disaggregation. J Mol Biol 386: 178–189.

72. StrozeckaJ, ChruscielE, GornaE, SzymanskaA, ZietkiewiczS, et al. (2012) Importance of N- and C-terminal regions of IbpA, Escherichia coli small heat shock protein, for chaperone function and oligomerization. J Biol Chem 287: 2843–2853.

73. SinghSK, RozyckiJ, OrtegaJ, IshikawaT, LoJ, et al. (2001) Functional domains of the ClpA and ClpX molecular chaperones identified by limited proteolysis and deletion analysis. J Biol Chem 276: 29420–29429.

74. ThomasJG, BaneyxF (1998) Roles of the Escherichia coli small heat shock proteins IbpA and IbpB in thermal stress management: comparison with ClpA, ClpB, and HtpG In vivo. J Bacteriol 180: 5165–5172.

75. KirsteinJ, MoliereN, DouganDA, TurgayK (2009) Adapting the machine: adaptor proteins for Hsp100/Clp and AAA+ proteases. Nat Rev Microbiol 7: 589–599.

76. SaibilH (2000) Molecular chaperones: containers and surfaces for folding, stabilising or unfolding proteins. Curr Opin Struct Biol 10: 251–258.

77. GenestO, HoskinsJR, CambergJL, DoyleSM, WicknerS (2011) Heat shock protein 90 from Escherichia coli collaborates with the DnaK chaperone system in client protein remodeling. Proc Natl Acad Sci U S A 108: 8206–8211.

78. UlitskyI, ShamirR (2007) Identification of functional modules using network topology and high-throughput data. BMC Syst Biol 1: 8.

79. ArenasFA, DiazWA, LealCA, Perez-DonosoJM, ImlayJA, et al. (2010) The Escherichia coli btuE gene, encodes a glutathione peroxidase that is induced under oxidative stress conditions. Biochem Biophys Res Commun 398: 690–694.

80. Ayala-CastroC, SainiA, OuttenFW (2008) Fe-S cluster assembly pathways in bacteria. Microbiol Mol Biol Rev 72: 110–125.

81. PyB, MoreauPL, BarrasF (2011) Fe-S clusters, fragile sentinels of the cell. Curr Opin Microbiol 14: 218–223.

82. KitaokaS, WadaK, HasegawaY, MinamiY, FukuyamaK, et al. (2006) Crystal structure of Escherichia coli SufC, an ABC-type ATPase component of the SUF iron-sulfur cluster assembly machinery. FEBS Lett 580: 137–143.

83. HarmsC, DomotoY, CelikC, RaheE, StumpeS, et al. (2001) Identification of the ABC protein SapD as the subunit that confers ATP dependence to the K+-uptake systems Trk(H) and Trk(G) from Escherichia coli K-12. Microbiology 147: 2991–3003.

84. JolyN, EnglC, JovanovicG, HuvetM, ToniT, et al. (2010) Managing membrane stress: the phage shock protein (Psp) response, from molecular mechanisms to physiology. FEMS Microbiol Rev 34: 797–827.

85. SamantS, LeeH, GhassemiM, ChenJ, CookJL, et al. (2008) Nucleotide biosynthesis is critical for growth of bacteria in human blood. PLoS Pathog 4: e37.

86. BerteroMG, RotheryRA, PalakM, HouC, LimD, et al. (2003) Insights into the respiratory electron transfer pathway from the structure of nitrate reductase A. Nat Struct Biol 10: 681–687.

87. MessaoudiN, GautierV, KthiriF, LelandaisG, MihoubM, et al. (2013) Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism. J Bacteriol 195: 1167–1178.

88. WangJ, HartlingJA, FlanaganJM (1998) Crystal structure determination of Escherichia coli ClpP starting from an EM-derived mask. J Struct Biol 124: 151–163.

89. PowellS, SzklarczykD, TrachanaK, RothA, KuhnM, et al. (2012) eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Res 40: D284–289.

90. ClarkRL, NeidhardtFC (1990) Roles of the two lysyl-tRNA synthetases of Escherichia coli: analysis of nucleotide sequences and mutant behavior. J Bacteriol 172: 3237–3243.

91. OnestiS, MillerAD, BrickP (1995) The crystal structure of the lysyl-tRNA synthetase (LysU) from Escherichia coli. Structure 3: 163–176.

92. ChilcottGS, HughesKT (2000) Coupling of flagellar gene expression to flagellar assembly in Salmonella enterica serovar typhimurium and Escherichia coli. Microbiol Mol Biol Rev 64: 694–708.

93. RoguevA, BandyopadhyayS, ZofallM, ZhangK, FischerT, et al. (2008) Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast. Science 322: 405–410.

94. DixonSJ, FedyshynY, KohJL, PrasadTS, ChahwanC, et al. (2008) Significant conservation of synthetic lethal genetic interaction networks between distantly related eukaryotes. Proc Natl Acad Sci U S A 105: 16653–16658.

95. FischbachMA, LinH, LiuDR, WalshCT (2006) How pathogenic bacteria evade mammalian sabotage in the battle for iron. Nat Chem Biol 2: 132–138.

96. MiethkeM, MarahielMA (2007) Siderophore-based iron acquisition and pathogen control. Microbiol Mol Biol Rev 71: 413–451.

97. DuQ, WangH, XieJ (2011) Thiamin (vitamin B1) biosynthesis and regulation: a rich source of antimicrobial drug targets? Int J Biol Sci 7: 41–52.

98. JurgensonCT, BegleyTP, EalickSE (2009) The structural and biochemical foundations of thiamin biosynthesis. Annu Rev Biochem 78: 569–603.

99. CampillosM, von MeringC, JensenLJ, BorkP (2006) Identification and analysis of evolutionarily cohesive functional modules in protein networks. Genome Res 16: 374–382.

100. BalchWE, MorimotoRI, DillinA, KellyJW (2008) Adapting proteostasis for disease intervention. Science 319: 916–919.

101. CalloniG, ChenT, SchermannSM, ChangHC, GenevauxP, et al. (2012) DnaK functions as a central hub in the E. coli chaperone network. Cell Rep 1: 251–264.

102. TongAH, EvangelistaM, ParsonsAB, XuH, BaderGD, et al. (2001) Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 294: 2364–2368.

103. MichautM, BaderGD (2012) Multiple genetic interaction experiments provide complementary information useful for gene function prediction. PLoS Comput Biol 8: e1002559.

104. BorensteinE (2012) Computational systems biology and in silico modeling of the human microbiome. Brief Bioinform 13: 769–780.

105. GarciaEC, BrumbaughAR, MobleyHL (2011) Redundancy and specificity of Escherichia coli iron acquisition systems during urinary tract infection. Infect Immun 79: 1225–1235.

106. PappasCJ, IyerR, PetzkeMM, CaimanoMJ, RadolfJD, et al. (2011) Borrelia burgdorferi requires glycerol for maximum fitness during the tick phase of the enzootic cycle. PLoS Pathog 7: e1002102.

107. LiZ, PanditS, DeutscherMP (1999) RNase G (CafA protein) and RNase E are both required for the 5′ maturation of 16S ribosomal RNA. EMBO J 18: 2878–2885.

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