PETER J. LAMMERS, Ph.D.
B.S. The University of Idaho
Ph.D.
Portland State University, 1982
Postdoctoral,
The University of Chicago
plammers@nmsu.edu
(505)-646-3918
Arbuscular mycorrhizal (AM) fungi form obligate symbioses with most plants species. Plants benefit from the association via improved mineral uptake and water relations while the fungus receives fixed carbon from the plant. In collaboration with Dr. Yair Shachar-Hill, we are utilizing functional genomics to broaden our knowledge of metabolic pathways operating in Glomus intraradices. Specific goals are to identify biochemical pathways functioning in both carbon and nitrogen transfer between the fungal symbiont and host plant roots.
Identifying functions for new genes remains a bottleneck in genome studies. At least some "orphan" genes are likely to assume a known structure despite lacking recognizable sequence similarity. We have proposed that predicted protein secondary structures can be used as the basis for identifying structural homologs in the Protein Data Bank (PDB). We employ hidden Markov Model (HMM) based only on the predicted sequence of helix, sheet or coil elements within each protein sequence. In a validation study 45 of 50 HMMs (90%) correctly identified structural homologs in the PDB. The method is now being systematically applied to all groups of orphan proteins.