Skip to main content
SpringerLink
Log in

A Medium-Throughput Structural Proteomics Approach Applied to the Genome of E. coli

  • Chapter
Systems Biology and Biotechnology of Escherichia coli

  • 3222 Accesses

Abstract

Structural information of the protein complement of E.coli represents an important component in our quest for a more complete understanding of this organism at the molecular level. Structural proteomics, the application of technologies to enhance the rate of protein structure determination at the genome level, has significantly increased the structural coverage of the E.coli proteome. The Bacterial Structural Genomics Initiative (BSGI) has focused on the structure determination of E.coli proteins of both known and unknown function, using a combination of NMR and X-ray crystallography. This program has resulted in the implementation of several technologies, including robotics platforms, in a coordinated manner in order to streamline the steps involved in protein structure determination. Here, we describe our experimental approaches as well as some examples high-lighting new structural and functional insights of specific targets.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Abergel, C., Coutard, B., Byrne, D., Chenivesse, S., Claude, J.B., Deregnaucourt, C., Fricaux, T., Gianesini-Boutreux, C., Jeudy, S., Lebrun, R., Maza, C., Notredame, C., Poirot, O., Suhre, K., Varagnol, M. and Claverie, J.M. (2003). Structural genomics of highly conserved microbial genes of unknown function in search of new antibacterial targets. J. Struct. Funct. Genomics 4, 141-157.

    Article  PubMed  CAS  Google Scholar 

  • Abeysirigunawardena, S.C. and Chow, C.S. (2008). pH-dependent structural changes of helix 69 from Escherichia coli 23S ribosomal RNA. RNA 14, 782-792.

    Article  PubMed  CAS  Google Scholar 

  • Adams, E. (1995). L-histidinal, a biosynthetic precursor of histidine. J. Biol. Chem. 217, 325-344.

    Google Scholar 

  • Adams, M.A., Suits, M.D., Zheng, J. and Jia, Z. (2007). Piecing together the structure-function puzzle: experiences in structure-based functional annotation of hypothetical proteins. Proteomics 7, 2920-2932.

    Article  PubMed  CAS  Google Scholar 

  • Albeck, S., Burstein, Y., Dym, O., Jacobovitch, Y., Levi, N., Meged, R., Michael, Y., Peleg, Y., Prilusky, J., Schreiber, G., Silman, I., Unger, T. and Sussman, J.L. (2005). Three-dimensional structure determination of proteins related to human health in their functional context at the Israel structural proteomics center (ISPC). Acta Cryst. D61, 1364-1372.

    CAS  Google Scholar 

  • Alifano, P., Fani, R., Lio, P., Lazcano, A., Bazzicalupo, M., Carlomagno, M.S. and Bruni, C.B. (1996). Histidine biosynthetic pathway and genes: structure, regulation and evolution. Microbiol. Rev. 60, 44-69.

    PubMed  CAS  Google Scholar 

  • Allen, K.N. and Dunaway-Mariano, D. (2004). Phosphoryl group transfer: evolution of a catalytic scaffold. Trends Biochem. Sci. 29, 495-503.

    Article  PubMed  CAS  Google Scholar 

  • Anton, I.A. and Coggins, J.R. (1988). Sequencing and overexpression of the Escherichia coli aroE gene encoding shikimate dehydrogenase. Biochem. J. 249, 319-326.

    PubMed  CAS  Google Scholar 

  • Arifuzzaman, M., Maeda, M., Itoh, A., Nishikata, K., Takita, C., Saito, R., Ara, T., Nakahigashi, K., Huang, H.C., Hirai, A., Tsuzuki, K., Nakamura, S., Altaf-Ul-Amin, M., Oshima, T., Baba, T., Yamamoto, N., Kawamura, T., Ioka-Nakamichi, T., Kitagawa, M., Tomita, M., Kanaya, S., Wada, C. and Mori, H. (2006). Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16, 686-691.

    Article  PubMed  CAS  Google Scholar 

  • Baba, T., Huan, H.C., Datsenko, K., Wanner, B.L. and Mori, H. (2007). The applications of systematic in-frame, single-gene knockout mutant collection of Escherichia coli K-12. Methods Mol. Biol. 416, 183-194.

    Article  Google Scholar 

  • Babitzke P, Romeo T. (2007). CsrB sRNA family: sequestration of RNA-binding regulatory proteins. Curr. Opin. Microbiol. 10(2):156-63.

    Google Scholar 

  • Barbosa, J.A., Sivaraman, J., Li, Y., larocque, R., Matte, A., Schrag, J.D. and Cygler, M. (2002). Mechanism of action and NAD+-binding mode revealed by the crystal structure of L-histidinol dehydrogenase. Proc. Natl. Acad. Sci. USA 99, 1859-1864.

    Article  PubMed  CAS  Google Scholar 

  • Bartels, C., Xia, T.-H., Billeter, M., Guntert, P. & Wuthrich, K. (1995). The program XEASY for computer-supported NMR spectral analysis of biological macromolecules. J. Biomol. NMR, 5, 1 – 10.

    Article  Google Scholar 

  • Bax A, Grishaev A. (2005). Weak alignment NMR: a hawk-eyed view of biomolecular structure. Curr. Opin. Struct. Biol. 15(5), 563-70.

    Article  PubMed  CAS  Google Scholar 

  • Benach, J., Lee, I., Edstrom, W., Kuzin, A.P., Chiang, Y., Acton, T.B., Montelione, G.T. and Hunt, J.F. (2003). The 2.3 A crystal structure of the shikimate 5-dehydrogenase orthologue YdiB from Escherichia coli suggests a novel catalytic environment for an NAD-dependent dehydrogenase. J. Biol. Chem. 278, 19176-19182.

    Article  PubMed  CAS  Google Scholar 

  • Bendtsen, J.D., Nielsen, H., von Heijne, G. and Brunak, S. (2004). Improved prediction of signal peptides: SignalP 3.0. J. Mol. Biol. 340, 783-795.

    Article  PubMed  CAS  Google Scholar 

  • Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N. and Bourne, P.E. (2000). The Protein Data Bank. Nucleic Acids Res. 28, 235-242.

    Article  PubMed  CAS  Google Scholar 

  • Blattner, F.R., Plunkett, G. 3rd, Bloch, C.A., Perna, N.T., Burland, V., Riley, M., Collado-Vides, J., Glasner, J.D., Rode, C.K., Mayhew, G.F., Gregor, J., Davis, N.W., Kirkpatrick, H.A., Goeden, M.A., Rose, D.J., Mau, B. and Shao, Y. (1997). The complete genome sequence of Escherichia coli K-12. Science 277, 1453-1474.

    Article  PubMed  CAS  Google Scholar 

  • Bolesch, D.G. and Keasling, J.D. (2000). Polyphosphate binding and chain length recognition by Escherichia coli exopolyphosphatase. J. Biol. Chem. 275, 33814-33819.

    Article  PubMed  CAS  Google Scholar 

  • Brown, E.N. and Ramaswamy, S. (2007). Quality of protein crystal structures. Acta Cryst. D63, 941-950.

    CAS  Google Scholar 

  • Brunger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.S., Kuszewski, J., Nilges, M., Pannu N.S. et al. (1998). Crystallography and NMR system: A new software suite for macromolecular structure determination. Acta Cryst. D54, 905-921.

    CAS  Google Scholar 

  • Butland, G., Peregrin-Alvarez, J.M., Li, J., Yang, W., Yang, X., Canadien, V., Starostine, A., Richards, D., Beattie, B., Krogan, N., Davey, M., Parkinson, J., Greenblatt, J. and Emili, A. (2005). Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433, 531-537.

    Article  PubMed  CAS  Google Scholar 

  • Cabello-Villegas, J. and Nikonowicz, E.P. (2005). Solution structure of psi32-modified anticodon stem-loop of Escherichia coli tRNAPhe. Nucleic Acids Res. 33, 6961-6971.

    Article  PubMed  CAS  Google Scholar 

  • Charette, M. and Gray, M.W. (2000). Pseudouridine in RNA: What, where, how and why. IUBMB Life 49, 341-351.

    Article  PubMed  CAS  Google Scholar 

  • Chen, L., Oughtred, R., Berman, H.M. and Westbrook, J. (2004). targetDB: a target registration database for structural genomics projects. Bioinformatics 20, 2860-2862.

    Article  PubMed  CAS  Google Scholar 

  • Chou, C.P. (2007). Engineering cell physiology to enhance recombinant protein production in Escherichia coli. Appl. Microbiol. Biotechnol. 76, 521-532.

    Article  PubMed  CAS  Google Scholar 

  • Coggins, J.R., Abell, C., Evans, L.B., Frederickson, M., Robinson, D.A., Roszak, A.W. and Lapthorn, A.P. (2003). Experiences with the shikimate-pathway enzymes as targets for rational drug design. Biochem. Soc. Trans. 31, 548-552.

    Article  PubMed  CAS  Google Scholar 

  • Cohen, S.X., Morris, R.J., Fernandez, F.J., Ben Jelloul, M., Kakaris, M., Partasarathy, V., Lamzin, V.S., Kleywegt, G.J. and Perrakis, A. (2004). Towards complete validated models in the next generation of ARP/wARP. Acta Cryst. D60, 2222-2229.

    CAS  Google Scholar 

  • Collins, B., Stevens, R.C. and page, R. (2005). Crystallization optimum solubility screening: using crystallization results to identify the optimal buffer for protein crystal formation. Acta Cryst F61, 1035-1038.

    CAS  Google Scholar 

  • Cornilescu, G., Delaglio, F. and Bax, A. (1999). Protein backbone angle restraints from searching a database for chemical shift and sequence homology. NMR 13, 289-302.

    Article  CAS  Google Scholar 

  • Cowtan, K. and Main, P. (1998). Miscellaneous algorithms for density modification. Acta Cryst. D54, 487-493.

    CAS  Google Scholar 

  • Crooke, E., Akiyama, M., Rao, N.N. and Kornberg, A. (1994). Genetically altered levels of inorganic polyphosphate in Escherichia coli. J. Biol. Chem. 269, 6290-6295.

    PubMed  CAS  Google Scholar 

  • Cygler, M., Hung, M., Wagner, J. and Matte, A. (2008). Bacterial genomics initiative: Overview of methods and technologies applied to the process of structure determination. pp 537-559 In. Methods in Molecular Biology, volume 426, Structural proteomics – High-throughput methods, B. Kobe, M. Guss and T. Huber, eds. Humana Press, Australia.

    Google Scholar 

  • Delaglio, F., Grzesiek, S., Vuister, D.W., Zhu, G., Pfeifer, J. and Bax, A. (1995). NMR-Pipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 6, 277-293.

    Article  PubMed  CAS  Google Scholar 

  • Del Campo, M., Kaya, Y. and Ofengand, J. (2001). Identification and site of action of the remaining four putative pseudouridine synthases in Escherichia coli. RNA 7, 1603-1615.

    PubMed  CAS  Google Scholar 

  • Dominguez, C., Boelens, R., and Bonvin, A. M. (2003). J. Am. Chem. Soc. 125, 1731–1737.

    Article  PubMed  CAS  Google Scholar 

  • Dosset, P., Hus J.C., Marion, D. and Blackledge, M. (2001). J. Biomol. NMR, 20, 223–231.

    Article  PubMed  CAS  Google Scholar 

  • Durfee, T., nelson, R., Baldwin, S., Plunkett, G 3rd, Burland, V., Mau, B., Petrosine, J.F., Qin, X., Muzny, D.M., Ayele, M., Gibbs, R.A., Csorge, B., Posfai, G., Weinstock, G.M. and Blattner, F.R. (2008). The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse. J. Bacteriol. 190, 2597-2606.

    Article  PubMed  CAS  Google Scholar 

  • Ejby, M., Sørensen, M.A. and Pedersen, S. (2007). Pseudouridylation of helix 69 of 23S rRNA is necessary for an effective translation termination. Proc. Natl. Acad. Sci. USA 104, 19410-19415.

    Article  PubMed  CAS  Google Scholar 

  • Emsley, P. and Cowtan, K. (2004). Coot: model-building tools for molecular graphics. Acta Cryst. D60, 2126-2132.

    CAS  Google Scholar 

  • Ericsson, U.B., Hallberg, B.M., Detitta, G.T., Dekker, N. and Nordlund, P. (2006). Thermofluor-based high-throughput stability optimization of proteins for structural studies. Anal. Biochem. 357, 289-298.

    Article  PubMed  CAS  Google Scholar 

  • Ericsson, U.B., Hallberg, B.M., Detitta, G.T., Dekker, N. and Nordlund, P. (2006). Thermofluor-based high-throughput stability optimization of proteins for structural studies. Anal. Biochem. 357, 289-298.

    Article  PubMed  CAS  Google Scholar 

  • Feist, A.M., Henry, C.S., Reed, J.L., Krummenacker, M., Joyce, A.R., Karp, P.D., Broadbelt, L.J., Hatzimanikatis, V. and Palsson, B.ø. (2007). A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol. Syst. Biol. 3, 121.

    Article  PubMed  CAS  Google Scholar 

  • Finn, R.D., Tate, J., Mistry, J., Coggill, P.C., Sammut, S.J., Hotz, H.R., Ceric, G., Forslund, K., Eddy, S.R., Sonnhammer, E.L. and Bateman, A. (2008). The Pfam protein families database. Nucleic Acids Res. 36, D281-288.

    Article  PubMed  CAS  Google Scholar 

  • Fogg. M.J., Alzari, P., Bahar, M., Bertini, I., Betton, J.M., Burmeister, W.P., Cambillau, C., Canard, B., Corrondo, M.A., Coll, M., Daenke, S., Dym, O., Egloff, M.P., Enquita, F.J., Geerlof, A., Haouz, A., Jones, T.A., Ma, Q., Manicka, S.N., Migliardi, M., Nordlund, P., Owens, R.J., Peleg, Y., Schneider, G., Schnell, R., Stuart, D.I., Tarbouriech, N., Unge, T., Wilkinson, A.J., Wilmanns, M., Wilson, K.S., Zimhony, O. and Grimes, J.M. (2006). Application of the use of high-throughput technologies to the determination of protein structures of bacterial and viral pathogens. Acta Cryst. D62, 1196-1207.

    CAS  Google Scholar 

  • Gasteiger, E., Gattiker, A., Hoogland, C., Ivanyi, I., Appel, R.D. and Bairoch, A. (2003). ExPASY: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res. 31, 3784-3788.

    Article  PubMed  CAS  Google Scholar 

  • Ginalski, K. (2006). Comparative modeling for protein structure prediction. Curr. Opin. Struct. Biol. 16, 172-177.

    Article  PubMed  CAS  Google Scholar 

  • Goh, C.S., Lan, N., Echols, N., Douglas, S.M., Milburn, D., Bertone, P., Xiao, R., Ma, L.C., Zheng, D., Wunderlich, Z., Acton, T., Montelione, G.T. and Gerstein, M. (2003). SPINE 2: a system for collaborative structural proteomics within a federated database framework. Nucleic Acids Res. 31, 2833-2838.

    Article  PubMed  CAS  Google Scholar 

  • Gralnick, J. and Downs, D. (2003). The YggX protein of Salmonella enterica is involved in Fe(II) trafficking and minimizes the DNA damage caused by hydroxyl radicals: Residue CYS-7 is essential for YggX function. J. Biol. Chem. 278, 20708-20715.

    Article  PubMed  CAS  Google Scholar 

  • Grubmeyer, C., Skiadopoulos, M. and Senior, A.E. (1989). L-histidinol dehydrogenase, a Zn2+-metalloenzyme. Arch. Biochem. Biophys. 272, 311-317.

    Article  PubMed  CAS  Google Scholar 

  • Gu, X., Liu, Y. and Santi, D.V. (1999). The mechanism of pseudouridine synthase I as deduced from its interaction with 5-fluorouracil-tRNA. Proc. Natl. Acad. Sci. USA 96, 14270-14275.

    Article  PubMed  CAS  Google Scholar 

  • Guntert, P., Mumenthaler, C. and Wuthrich, K. (1997). Torsion angle dynamics for NMR structure calculation with the new program DYANA. J. Mol. Biol. 273, 283-298.

    Article  PubMed  CAS  Google Scholar 

  • Gutièrrez P, Li Y, Osborne MJ, Pomerantseva E, Liu Q, Gehring K. (2005). Solution structure of the carbon storage regulator protein CsrA from Escherichia coli. J. Bacteriol. 187(10), 3496-3501.

    Article  PubMed  CAS  Google Scholar 

  • Gutièrrez P, Kozlov G, Gabrielli L, Elias D, Osborne MJ, Gallouzi IE, Gehring K. (2007). Solution structure of YaeO, a Rho-specific inhibitor of transcription termination. J. Biol. Chem. 282(32), 23348-23353.

    Article  PubMed  CAS  Google Scholar 

  • Hamilton, C.S., Greco, T.M., Vizthum, C.A., Ginter, J.M., Johnston, M.V. and Mueller, E.G. (2006). Mechanistic investigation of the pseudouridine synthase RluA using RNA containing 5-fluorouridine. Biochemistry 45, 12029-12038.

    Article  PubMed  CAS  Google Scholar 

  • Hamilton, C.S., Spedaliere, C.J., Ginter, J.M., Johnston, M.V. and Mueller, E.G. (2005). The roles of the essential Asp-48 and highly conserved His-43 elucidated by the pH dependence of the pseudouridine synthase TruB. Arch. Biochem. Biophys. 433, 322-334.

    Article  PubMed  CAS  Google Scholar 

  • Hayashi, T., Makino, K., Ohnishi, M., Kurokawa, K., Ishii, K., Yokayama, K., Han, C.G., Ohtsubo, E., Nakayama, K., Murata, T., Tanaka, M., Tobe, T., Iida, T., Takami, H., Honda, T., Sasakawa, C., Ogasawara, N., Yasunaga, T., Kuhara, S., Shiba, T., Hattori, M. and Shinagawa, H. (2001). Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12. DNA Res. 8, 11-22.

    Article  PubMed  CAS  Google Scholar 

  • Hendrickson, W.A., Horton, J.R. and LeMaster, D.M. (1990). Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three-dimensional structure. EMBO J. 9, 1665-1672.

    PubMed  CAS  Google Scholar 

  • Herrgard, M.J., Fong, S.S. and Palsson, B.ø. (2006). Identification of genome-scale metabolic network models using experimentally measured flux profiles. PLoS Comput. Biol. 2,e72.

    Article  PubMed  CAS  Google Scholar 

  • Hermann, K.M. and Weaver, L.M. (1999). The shikimate pathway. Annu. Rev. Plant Physiol. Plant Mol. Biol. 50, 473-503.

    Article  Google Scholar 

  • Houston, L.L. and Graham, M.E. (1974). Divalent metal ion effects on a mutant histidinol phosphate phosphatase from Salmonella typhimurium. Arch. Biochem. Biophys. 162, 513-522.

    Article  PubMed  CAS  Google Scholar 

  • Hsu, L.C., Okamoto, M. and Snell, E.E. (1989). L-histidinol phosphate aminotransferase from Salmonella typhimurium: kinetic behavior and sequence at the pyridoxal-P binding site. Biochimie 71, 477-489.

    Article  PubMed  CAS  Google Scholar 

  • Jancarik, J., Pufan, R., Hong, C., Kim, S.H. and Kim, R. (2004). Optimum solubility (OS) screening: an efficient method to optimize buffer conditions for homogeneity and crystallization of proteins. Acta Cryst. D60, 1670-1673.

    CAS  Google Scholar 

  • Kanaori, K., Uodome, N., Nagai, A., Ohta, D., Ogawa, A., Iwasaki, G. and Nosaka, A.Y. (1996). Biochemistry 35, 5949-5954.

    Article  PubMed  CAS  Google Scholar 

  • Kapust, R.B. and Waugh, D.S. (2000). Controlled intracellular processing of fusion proteins by TEV protease. Protein Expr. Purif. 19, 312-318.

    Article  PubMed  CAS  Google Scholar 

  • Kapust, R.B., Tözsèr, J., Fox, J.D., Anderson, D.E., Cherry, S., Copeland, T.D. and Waugh, D.S. (2001). Tobacco etch virus protease: mechanism of autolysis and rational design of stable mutants with wild-type catalytic proficiency. Protein Eng. 14, 993-1000.

    Article  PubMed  CAS  Google Scholar 

  • Karp, P.D., Keseler, I.M., Shearer, A., Latendresse, M., Krummenacker, M., Paley, S.M., Paulsen, I., Collado-Vides, J., Gama-Castro, S., Peralta-Gil, M., Santos-Zavaleta, A., Penaloza-Spinola, M.I., Bonavides-Martinez, C. and Ingraham, J. (2007). Multidimensional annotation of the Escherichia coli K-12 genome. Nucleic Acids Res. 35, 7577-7590.

    Article  PubMed  CAS  Google Scholar 

  • Kaya, Y. and Ofengand, J. (2003). A novel unanticipated type of pseudouridine synthase with homologs in bacteria, archaea and eukarya. RNA 9, 711-721.

    Article  PubMed  CAS  Google Scholar 

  • Kim, S.H., Shin, D.H., Choi, I.G., Schulze-Gahmen, U., Chen, S. and Kim, R. (2003). Structure-based functional inference in structural genomics J. Struct. Funct. Genomics 4, 129-135.

    Article  PubMed  CAS  Google Scholar 

  • Koonin, E.V. (1996). Pseudouridine synthases: four families of enzymes containing a putative uridine-binding motif also conserved in dUTPases and dCTP deaminases. Nucleic Acids Res. 24, 2411-2415.

    Article  PubMed  CAS  Google Scholar 

  • Kozlov, G., Elias, D., Semesi, A., Yee, A., Cygler, M. and Gehring, K. (2004). Structural similarity of YbeD protein from Escherichia coli to allosteric regulatory domains. J. Bacteriol. 186, 8083-8088.

    Article  PubMed  CAS  Google Scholar 

  • Krogh, A., Larsson, B., von Heijne, G. and Sonnhammer, E.L. (2001). Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305, 567-580.

    Article  PubMed  CAS  Google Scholar 

  • Lee, D., Redfern, O. and Orengo, C. (2007). Predicting protein function from sequence and structure. Nat. Rev. Mol. Cell Biol. 8, 995-1005.

    Article  PubMed  CAS  Google Scholar 

  • Lidner, H.A., Nadeau, G., Matte, A., Michel, G., Mènard, R. and Cygler, M. (2005). Site-directed mutagenesis of the active site region in the quinate/shikimate 5-dehydrogenase YdiB of Escherichia coli. J. Biol. Chem. 280, 7162-7169.

    Article  CAS  Google Scholar 

  • Lin, Y. and Kielkopf, C.L. (2008). X-ray structures of U2 snRNA-branchpoint duplexes containing conserved pseudouridines. Biochemistry 47, 5503-5514.

    Article  PubMed  CAS  Google Scholar 

  • Loper, J.C. (1961). Enzyme complementation in mixed extracts of mutants from the Salmonella histidine B locus. Proc. Natl. Acad. Sci. U.S.A. 47, 1440-1450.

    Article  PubMed  CAS  Google Scholar 

  • Macek, B., Gnad, E., Soufi, B., Kumar, C., Olsen, J.V., Mijakovic, I. and Mann, M. (2008). Phosphoproteome analysis of E. coli reveals evolutionary conservation of bacterial Ser/Thr/Tyr phosphorylation. Mol Cell Proteomics 7, 299-307.

    PubMed  CAS  Google Scholar 

  • Maillet, I., Berndt, P., Malo, C., Rodriguez, S., Brunisholz, R.A., Pragai, Z., Arnold, S., Langen, H. and Wyss, M. (2007). From the genome sequence to the proteome and back: Evaluation of E.coli genome annotation with a 2-D gel-based proteomics approach. Proteomics 7, 1097-1106.

    Article  PubMed  CAS  Google Scholar 

  • Manjasetty, B.A., Turnbull, A.P., Panjikar, S., Bussow, K. and Chance, M.R. (2008). Automated technologies and novel techniques to accelerate protein crystallography for structural genomics. Proteomics 8, 612-625.

    Article  PubMed  CAS  Google Scholar 

  • Matte, A., Sivaraman, J., Ekiel, I., Gehring, K., Jia, Z. and Cygler, M. (2003). Contribution of structural genomics to understanding the biology of Escherichia coli. J. Bacteriol. 185, 3994-4002.

    Article  PubMed  CAS  Google Scholar 

  • Matte, A., Louie, G.V., Sivaraman, J., Cygler, M. and Burley, S.K. (2005). Structure of the pseudouridine synthase RsuA from Haemophilus influenzae. Acta Cryst. F61, 350-354.

    CAS  Google Scholar 

  • Matte, A., Jia, Z., Sunita, S., Sivaraman, J. and Cygler, M. (2007). Insights into the biology of Escherichia coli through structural proteomics. J. Struct. Funct. Genomics 8, 44-55.

    Article  CAS  Google Scholar 

  • Matte, A. and Cygler, M. (2007). Using dynamic light scattering to improve protein solution behavior for crystallization. American Biotechnology Laboratory 25, 14-16.

    CAS  Google Scholar 

  • Meroueh, M., Grohar, P.J., Qiu, J., SantaLucia Jr. J., Scaringe, S.A. and Chow, C.S. (2000). Unique structural and stabilizing roles for the individual pseudouridine residues in the 1920 region of Escherichia coli 23S rRNA. Nucleic Acids Res. 28, 2075-2083.

    Article  PubMed  CAS  Google Scholar 

  • Michel, G., Roszak, A.W., Sauvè, V., Maclean, J., Matte, A., Coggins, J.R., Cygler, M. and Lapthorn, A.J. (2003). Structures of shikimate dehydrogenase AroE and its paralog YdiB. A common structural framework for different activities. J. Biol. Chem. 278, 19463-19472.

    CAS  Google Scholar 

  • Minailiuc, O.M., Vavelyuk, O., Gandhi, S., Hung, M-N., Cygler, M. and Ekiel, I. (2007). NMR structure of YcgL, a conserved protein from Escherichia coli representing the DUF709 family, with a novel α/β/α sandwich fold. Proteins 66, 1004-1007.

    Article  PubMed  CAS  Google Scholar 

  • Misra, R.V., Horler, R.S., Reindl, W., Goryanin, I.I. and Thomas, G.H. (2005). EchoBASE: an integrated post-genomic database for Escherichia coli. Nucleic Acids Res. 33, D329-D333.

    Google Scholar 

  • Mulder, N.J. and Apweiler, R. (2008). The InterPro database and tools for protein domain analysis. Curr. Protoc. Bioinformatics, Chapter 2, Unit 2.7

    Google Scholar 

  • Murshudov, G.N., Vagin, A.A., Lebedev, A., Wilson, K.S. and Dodson, E.J. (1999). Efficient anisotropic refinement of macromolecular structures using FFT. Acta Cryst. D55, 247-255.

    CAS  Google Scholar 

  • Nilges M, Macias MJ, O’Donoghue SI, Oschkinat H (1997). Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from beta-spectrin. J. Mol. Biol. 269(3), 408-422.

    Article  PubMed  CAS  Google Scholar 

  • Ofengand, J. (2002). Ribosomal RNA pseudouridines and pseudouridine synthases. FEBS Lett. 514, 17-25.

    Article  PubMed  CAS  Google Scholar 

  • Osborne, M.J., Siddiqui, N., Landgraf, D., Pomposiello, P.J. and Gehring, K. (2005). The solution structure of the oxidative stress-related protein YggX from Escherichia coli. Prot. Sci. 14, 1673-1678.

    Article  CAS  Google Scholar 

  • Otwinowski, Z. and Minor, W. (1997). Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326.

    Article  CAS  Google Scholar 

  • Pape, T. and Schneider, T.R. (2004). HKL2MAP: a graphical user interface for phasing with SHELX programs. J. Appl. Cryst. 37, 843-844.

    Article  CAS  Google Scholar 

  • Perna, N.T., Plunkett, G. 3rd., Burland, V., Mau, B., Glasner, J.D., Rose, D.J., Mayhew, G.F., Evans, P.S., Gregor, J., Kirkpatrick, H.A., Pòsfai, G., Hackett, J., Klink, S., Boutin, A., Shao, Y., Miller, L., Grotbeck, E.J., Davis, N.W., Lim, A., Dimalanta, E.T., Potamousis, K.D., Apodaca, J., Anantharaman, T.S., Lin, J., Yen, G., Schwartz, D.C., Welch, R.A. and Blattner, F.R. (2001). Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409, 529-533.

    Article  PubMed  CAS  Google Scholar 

  • Phannachet, K., Elias, Y. and Huang, R.H. (2005). Dissecting the roles of a strictly conserved tyrosine in substrate revognition and catalysis by pseudouridine 55 synthase. Biochemistry 44, 15488-15494.

    Article  PubMed  CAS  Google Scholar 

  • Pichoff, S., Alibaud, L., Guèdant, A., Castaniè, M.P. and Bouchè, J.P. (1998). An Escherichia coli gene (yaeO) suppresses temperature-sensitive mutations in essential genes by modulating Rho-dependent transcriptional termination. Mol. Microbiol. 29, 859-869.

    Article  PubMed  CAS  Google Scholar 

  • Pons, J.L., Malliavin, T.E. and Delsuc, M.A. (1997). Gifa V.4: a complete package for NMR data set processing. J. Biomol. NMR 8, 445-452.

    Google Scholar 

  • Prilusky, J., Oueillet, E., Ulryck, N., Pajon, A., Bernauer, J., Krimm, I., Quevillon-Cheruel, S., Leulliot, N., Graille, M., Liger, D., Tresaugues, L., Sussman, J.L., Janin, J., van Tilbeurgh, H. and Poupon, A. (2005). HalX: an open-source LIMS (Laboratory Information Management System) for small- to large-scale laboratories. Acta Cryst. D61, 671-678.

    CAS  Google Scholar 

  • Rangarajan, E.S., Proteau, A., Wagner, J., Hung, M-N., Matte, A. and Cygler, M. (2006). Structural snapshots of Escherichia coli histidinol phosphate phosphatase along the reaction pathway. J. Biol. Chem. 281, 37930-37941.

    Article  PubMed  CAS  Google Scholar 

  • Rangarajan, E.S., Nadeau, G., Li, Y., Wagner, J., Hung, M.N., Schrag, J.D., Cygler, M. and Matte, A. (2006). The structure of the exopolyphosphatase (PPX) from Escherichia coli O157:H7 suggests a binding mode for long polyphosphate chains. J. Mol. Biol. 359, 1249-1260.

    Article  PubMed  CAS  Google Scholar 

  • Raymond, S., O’Toole, N. and Cygler, M. (2004). A data management system for structural genomics. Proteome Sci. 2, 4

    Google Scholar 

  • Riley, M., Abe, T., Arnaud, M.B., Berlyn, M.K., Blattner, F.R., Chaudhuri, R.R., Glasner, J.D., Horiuchi, T., Keseler, I.M., Kosuge, T., Mori, H., Perna, N.T., Plunkett, G 3rd, Rudd, K.E., Serres, M.H., Thomas, G.H., Thomson, N.R., Wishart, D. and Wanner, B.L. (2006). Escherichia coli K-12: a cooperatively developed annotation snapshot – 2005. Nucleic Acids Res. 34, 1-9.

    Article  PubMed  CAS  Google Scholar 

  • Sali, A. (1998). 100,000 protein structures for the biologist. Nat. Struct. Biol. 5, 1019-1020.

    Article  CAS  Google Scholar 

  • Schneider, B.L., Kiupakis, A.K. and Reitzer, L.J. (1998). Arginine catabolism and the arginine succinyltransferase pathway in Escherichia coli. J. Bacteriol. 180, 4278-4286.

    PubMed  CAS  Google Scholar 

  • Shapiro, L. and Lima, C.D. (1998). The argonne structural genomics workshop: Lamaze class for the birth of a new science. Structure 6, 265-267.

    Article  PubMed  CAS  Google Scholar 

  • Sheldrick, G.M., (2008). A short history of SHELX. Acta Cryst. A64, 112-122.

    CAS  Google Scholar 

  • Shirai, H. and Mizuguchi, K. (2003). Prediction of the structure and function of AstA and AstB, the first two enzymes of the arginine succinyltransferase pathway of arginine catabolism. FEBS Lett. 555, 505-510.

    Article  PubMed  CAS  Google Scholar 

  • Sivaraman, J., Li, Y., Larocque, R., Schrag, J.D., Cygler, M. and Matte, A. (2001). Crystal structure of histidinol phosphate aminotransferase (HisC) from Escherichia coli and its covalent complex with pyridoxal-5’-phosphate and L-histidinol phosphate. J. Mol. Biol. 311, 761-776.

    Article  PubMed  CAS  Google Scholar 

  • Sivaraman, J., Sauvè, V., Larocque, R., Stura, E.A., Schrag, J.D., Cygler, M. and Matte, A. (2002). Structure of the 16S rRNA pseudouridine synthase RsuA bound to uracil and UMP. Nat. Struct. Biol. 9, 353-358.

    PubMed  CAS  Google Scholar 

  • Sivaraman, J., Iannuzzi, P., Cygler, M. and Matte, A. (2004). Crystal structure of the RluD pseudouridine synthase catalytic module, an enzyme that modifies 23 S rRNA and is essential for normal cell growth of Escherichia coli. J. Mol. Biol. 335, 87-101.

    Article  PubMed  CAS  Google Scholar 

  • Sivaraman, J., Myers, R.S., Boju, L., Sulea, T., Cygler, M., Jo Davisson, V. and Schrag, J.D. (2005). Crystal structure of Methanobacterium thermoautotrophicumphosphoribosyl-AMP cyclohydrolase, HisI. Biochemistry 44, 10071-10080.

    Article  PubMed  CAS  Google Scholar 

  • Slabinski, L., Jaroszewski, L., Rodrigues, A.P., Rychlewski, L., Wilson, I.A., Lesley, S.A. and Godzik, A. (2007a). The challenge of protein structure determination – lessons from structural genomics. Prot. Sci. 16, 2472-2482.

    Article  CAS  Google Scholar 

  • Slabinski, L., Jaroszewski, L., Rychlewski, L., Wilson, I.A., Lesley, S.A. and Godzik, A. (2007b). XtalPred: a web server for prediction of protein crystallizability. Bioinformatics 23, 3403-3405.

    Article  PubMed  CAS  Google Scholar 

  • Smialowski, P., Schmidt, T., Cox, J., Kirschner, A. and Frishman, D. (2006). Will my protein crystallize? A sequence-based predictor. Proteins 62, 343-355.

    Article  PubMed  CAS  Google Scholar 

  • Su, C., Peregrin-Alvarez, J.M., Butland, G., Phandase, S., Fong, V., Emili, A. and Parkinson, J. (2008). Bacteriome.org – an integrated protein interaction database for E.coli. Nucleic Acids Res. D632-D636.

    Google Scholar 

  • Suits, M.D., Pal, G.P., Nakatsu, K., Matte, A., Cygler, M. and Jia, Z. (2005). Identification of an Escherichia coli O157:H7 heme oxygenase with tandem functional repeats. Proc. Natl. Acad. Sci. U.S.A. 102, 16955-16960.

    Article  PubMed  CAS  Google Scholar 

  • Suits, M.D.L., Jaffer, N. and Jia, Z. (2006). Structure of the Escherichia coli O157:H7 heme oxygenase ChuS in complex with heme and enzymatic inactivation by mutation of the heme coordinating residue His-193. J. Biol. Chem. 281, 36776-36782.

    Article  PubMed  CAS  Google Scholar 

  • Sunita, S., Zhenxing, H., Swaathi, J., Cygler, M., Matte, A. and Sivaraman, J. (2006). Domain organization and crystal structure of the catalytic domain of E. coli RluF, a pseudouridine synthase that acts on 23S rRNA. J. Mol. Biol. 359, 998-1009.

    Article  PubMed  CAS  Google Scholar 

  • Teng, H. and Grubmeyer, C. (1999). Biochemistry 38, 7363-7371.

    Article  PubMed  CAS  Google Scholar 

  • Terwilliger, T.C. (2000). Maximum likelihood density modification. Acta Cryst. D56, 965-972.

    CAS  Google Scholar 

  • Terwilliger, T.C. (2003). Automated main-chain model building by template matching and iterative fragment extension. Acta Cryst. D59, 38-44.

    CAS  Google Scholar 

  • Terwilliger, T.C. and Berendzen, J. (1999). Automated MAD and MIR structure solution. Acta Cryst. D55, 849-861.

    CAS  Google Scholar 

  • Thaller, M.C., Schippa, S. and Rossolini, G.M. (1998). Conserved sequence motifs among bacterial, eukaryotic and archaeal phosphatases that define a new phosphohydrolase superfamily. Prot. Sci. 7, 1647-1652.

    Article  CAS  Google Scholar 

  • Tocilj, A., Schrag, J.D., Li, Y., Schneider, B.L., Reitzer, L., Matte, A. and Cygler, M. (2005). Crystal structure of N-succinylarginine dihydrolase AstB, bound to substrate and product, an enzyme from the arginine catabolic pathway of Escherichia coli. J. Biol. Chem. 280, 15800-15808.

    Article  PubMed  CAS  Google Scholar 

  • Trempe, J.F. & Gehring, K. (2003). Observation and interpretation of residual dipolar couplings in biomolecules in NMR of Orientationally Ordered Liquids, (E.E. Burnell, C.A. de Lange, Eds.), Kluwer Academic Publishers B.V.

    Google Scholar 

  • Valente, J.J., Payne, R.W., Manning, M.C., Wilson, W.W. and Henry, C.S. (2005). Colloidal behavior of proteins: effects of the second virial coefficient on solubility, crystallization and aggregation of proteins in aqueous solution. Curr. Pharm. Biotechnol. 6, 427-436.

    Article  PubMed  CAS  Google Scholar 

  • Vedadi, M., Niesen, F.H., Allali-Hassani, A., Fedorov, O.Y., Finerty, P.J. Jr., Wasney, G.A., Yeung, R., Arrowsmith, C., Ball, L.J., Berglund, H., Hui, R., Marsden, B.D., Nordlund, P., Sundstrom, M., Weigelt, J. and Edwards, A.M. (2006). Chemical screening methods to identify ligands that promote protein stability, protein crystallization and structure determination. Proc. Natl. Acad. Sci. USA 103, 15835-15840.

    Article  PubMed  CAS  Google Scholar 

  • Vornhein, C., Blanc, E., Roversi, P. and Bricogne, G. (2007). Automated structure solution with autoSHARP. Methods Mol. Biol. 364, 215-230.

    Google Scholar 

  • Watson, J.D., Sanderson, S., Ezersky, A., Savchenko, A., Edwards, A., Orengo, C., Joachimiak, A., Laskowski, R.A. and Thornton, J.M. (2007). Towards fully automated structure-based function prediction in structural genomics: a case study. J. Mol. Biol. 367, 1511-1522.

    Article  PubMed  CAS  Google Scholar 

  • Welch, R.A., Burland, V., Plunkett, G. 3rd, Redford, P., Roesch, P., Rasko, D., Liou, S.R., Boutin, A., Hackett, J., Stroud, D., Mayhew, G.F., Rose, D.J., Zhou, S., Schwartz, D.C., Perna, N.T., Mobley, H.L., Donnenberg, M.S. and Blattner F.R. (2002). Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc. Natl. Acad. Sci. USA 99, 17020-17024.

    Article  PubMed  CAS  Google Scholar 

  • Yokoyama, S., Hirota, H., Kigawa, T., Yabuki, T., Shirouzu, M., Terada, T., Ito, Y., Matsuo, Y., Kuroda, Y., Nishimura, Y., Kyogoku, Y., Miki, K., Masui, R., Kuramitsu, S. (2000). Structural genomics projects in Japan. Nat. Struct. Biol. Suppl, 943-945.

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Biotechnology Research Institute, National Research Council Canada, 6100 Royalmount Ave, Montreal, Quebec H4P2R2, Canada

    Allan Matte

  2. Department of Chemistry and Biochemistry, Concordia University, Biotechnology Research Institute, National Research Council Canada, 6100 Royalmount Ave, Montreal, QC H4P2R2, Canada

    Irena Ekiel

  3. Department of Biochemistry, Queen’s University, Kingston, ON, Canada

    Zongchao Jia

  4. Department of Biochemistry, McGill University, Montreal, QC, Canada

    Kalle Gehring

  5. Department of Biochemistry McGill University, Biotechnology Research Institute, National Research Council Canada, Montreal, QC H4P2R2, Canada

    Miroslaw Cygler

Authors
  1. Allan Matte
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Irena Ekiel
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Zongchao Jia
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Kalle Gehring
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Miroslaw Cygler
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Miroslaw Cygler .

Editor information

Editors and Affiliations

  1. Dept. of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 335 Gwahangno, Yuseong-gu, Daejeon 305-701, Republic of Korea (South Korea)

    Sang Yup Lee

Rights and permissions

Reprints and permissions

Copyright information

© 2009 Springer Science+Business Media B.V.

About this chapter

Cite this chapter

Matte, A., Ekiel, I., Jia, Z., Gehring, K., Cygler, M. (2009). A Medium-Throughput Structural Proteomics Approach Applied to the Genome of E. coli . In: Lee, S.Y. (eds) Systems Biology and Biotechnology of Escherichia coli . Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-9394-4_4

Download citation

Publish with us

Policies and ethics

Search

Navigation