Comparative genomics analysis of the central machinery of life

  • Yang C, Rodionov DA, Li X, Laikova ON, Gelfand MS, Zagnitko OP, Romine MF, Obraztsova AY, Nealson KH, Osterman AL.
    Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensis.
    J Biol Chem. 281:29872-85(2006)
  • Overbeek, R, T Begley, RM Butler, JV Choudhuri, HY Chuang, M Cohoon, V de Crecy-Lagard, …A.Osterman et. al.
    The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes.
    Nucleic Acids Res. 33:5691-702 (2005)
  • Ye, Y., Osterman, A., Overbeek, R., Godzik, A.
    Automatic detection of subsystem/pathway variants in genome analysis.
    BIOINFORMATICS 21,  Suppl. 1, i1–i9 (2005) 
  • Osterman, A. & Overbeek R.
    Missing genes in metabolic pathways: A comparative genomics approach.
    Current Opin. Chem. Biol. 7, 1-14 (2003) 
  • Gerdes, S. Y., M. D. Scholle, J. W. Campbell, G. Balazsi, E. Ravasz, M. D. Daugherty, A. L. Somera, N. C. Kyrpides, I. Anderson, M. S. Gelfand, A. Bhattacharya, V. Kapatral, M. D'Souza, M. V. Baev, Y. Grechkin, F. Mseeh, M. Y. Fonstein, R. Overbeek, A. L. Barabasi, Z. N. Oltvai, and A. L. Osterman. 
    Experimental determination and system level analysis of essential genes in Escherichia coli MG1655. 
    J. Bacteriol. 185:5673-84 (2003)

Applications: examples in individual subsystems 

  • Low, LY, C Yang, M Perego, A Osterman, and RC Liddington 
    Structure and lytic activity of a Bacillus anthracis prophage endolysin. 
    J. Biol. Chem. 280:35433-9 (2005)
  • Golubkov, V. S., S. Boyd, A. Y. Savinov, A. V. Chekanov, A. L. Osterman, A. Remacle, D. V. Rozanov, S. J. Doxsey, and A. Y. Strongin. 
    Membrane type-1 matrix metalloproteinase (MT1-MMP) exhibits an important intracellular cleavage function and causes chromosome instability. 
    J. Biol. Chem., 280(26):25079-86 (2005) 
  • Alonso A, Sasin J, Bottini N, Friedberg I, Friedberg I, Osterman A, Godzik A, Hunter T, Dixon J, Mustelin T. Protein tyrosine phosphatases in the human genome. 
    Cell 117(6):699-711 (2004) 
  • Kurnasov, O., V. Goral, K. Colabroy, S. Gerdes, S. Anantha, A. Osterman, and T. P. Begley.
    NAD biosynthesis: identification of the tryptophan to quinolinate pathway in bacteria. 
    Chem. Biol. 10:1195-204 (2003)  
  • Daugherty, M., Polanuyer, B., Farrell, M., Lykidis, A., de Crécy-Lagard, V. & Osterman, A.
    Human coenzyme A biosynthesis: complete pathway reconstitution via comparative genomics. 
    J. Biol. Chem. 277, 21431-9 (2002) 
  • Kurnasov, O.V., Polanuyer, B.M., Ananta, S., Sloutsky, R., Tam, A., Gerdes, S.Y.& Osterman, A.L. Ribosylnicotinamide kinase domain of NadR protein: Identification and implications in NAD biosynthesis. 
    J. Bacteriology 184, 6906-17 (2002) 
  • Zhang, H., Zhou, T., Kurnasov, O., Cheek, A., Grishin, N.V. & Osterman, A.
    Crystal Structures of E. coli nicotinate mononucleotide adenylyltransferase and its complex with deamido-NAD. 
    Structure 10, 69-79 (2002) 
  • Zhou, T.,  Kurnasov, O., Tomchick, D.R., Binns, D.D., Grishin, N.V.,  Marquez, V.E., Osterman, A. & Zhang, H. 
    Structure of human NMN/NaMN adenylyltransferase: basis for the dual substrate specificity and activation of anticancer drug tiazofurin. 
    J. Biol. Chem. 277, 13148-54 (2002) 
  • Daugherty, M., Vonstein, V., Overbeek, R. & Osterman, A.
    Archaeal shikimate kinase: A New member of the GHMP-kinase family. 
    J. Bacteriol. 183, 292-300 (2001)

Proteolytic events: posttranslational modification

  • Igarashi Y., Eroshkin A., Gramatikova S., Gramatikoff K., Zhang Y., Smith J.W., Osterman A.L., Godzik A.
    CutDB: a proteolytic event database. 
    Nucleic Acids Res. (in press)