Protein Superfamily Evolution

We are interested in using bioinformatics methods to identify very remote homologs of interesting protein families, and a structural phylogenomic approach to predict the domain fusion, shuffling, and gene duplication events that generated the family. We apply these methods to single domains, exploring their evolution in the context of the many folds in which they are found, and also to whole proteins.

Papers from our lab in this area

  • Sjolander, K , "Phylogenetic inference in protein superfamilies: Analysis of SH2 domains," Proceedings of the Conference Intelligent Systems for Molecular Biology 1998 6:165-74. PubMed abstract.
  • Sjolander, K., "Phylogenomic inference of protein molecular function: advances and challenges," Bioinformatics 2004 (20)2:170-179. Oxford University Press access.
  • Mahmut Tör, M., Brown D., Cooper, A., Woods-Tör, A., Sjölander, K., Jones, J.D.G. and Holub, E. "Arabidopsis Downy Mildew Resistance Gene RPP27 Encodes a Receptor-Like Protein Similar to CLAVATA2 and Tomato Cf-9," Plant Physiology, 2004 Jun;135(2):1100-12. PubMed Abstract. PDF version.
  • Kleffmann, T., Russenberger, D., von Zychlinski, A., Christopher, W., Sjölander, K., Gruissem, W., and Baginsky, S. "The Arabidopsis thaliana chloroplast proteome reveals pathway abundance and novel protein functions," Current Biology 2004 Mar 9;14(5):354-62. PDF version.PubMed Abstract.
  • Magnani, E., Sjölander, K. , and Hake S., "From endonucleases to transcription factors: evolution of the AP2 DNA-binding domain in plants", Plant Cell, 2004 Sep;16(9):2265-77.PubMed Abstract.
  • Rowland O, Ludwig AA, Merrick CJ, Baillieul F, Tracy FE, Durrant WE, Fritz-Laylin L, Nekrasov V, Sjolander K, Yoshioka H, Jones JD. Functional Analysis of Avr9/Cf-9 Rapidly Elicited Genes Identifies a Protein Kinase, ACIK1, That Is Essential for Full Cf-9-Dependent Disease Resistance in Tomato, Plant Cell. 2004 PubMed Abstract.
  • Brown D, Krishnamurthy N, Dale J, Christopher W, and Sjolander K, "Subfamily HMMs in Functional Genomics", Proceedings of the Pacific Symposium on Biocomputing, 2005. PSB proceedings.
  • Rebecca Middleton, Kimmen Sjölander, Nandini Krishnamurthy, Jonathan Foley, and Patricia Zambryski, "Predicted hexameric structure of the Agrobacterium VirBB 4 C terminus suggests VirB4 acts as a docking site during type IV secretion", Proceedings of the National Academy of Sciences published January 24, 2005.
  • Stephen T. Chisholm, Douglas Dahlbeck, Nandini Krishnamurthy, Brad Day, Kimmen Sjolander, and Brian J. Staskawicz, "Molecular characterization of proteolytic cleavage sites of the Pseudomonas syringae effector AvrRpt2", Proceedings of the National Academy of Sciences, February 8, 2005, vol. 102, no. 6, 2087-2092.
  • Lillian Fritz-Laylin, Nandini Krishamurthy, Mahmut Tor, Kimmen Sjolander and Jonathan Jones. "Phylogenomic analysis of the receptor-like proteins of rice and Arabidopsis", in press Plant Physiology.
  • Nandini Krishnamurthy and Kimmen Sjolander, "Protein sequence analysis". in press, Current Protocols in Molecular Biology.

    Group Members

  • Nandini Krishnamurthy
  • Duncan Brown
    (bpg group access)