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.

Selected Publications

Govindarajulu, M., P.E. Pfeffer, H. Jin, J. Abubaker, D.D. Douds, J.W. Allen, H. Bücking, P.J. Lammers, and Y. Shachar-Hill. 2005. Nitrogen transfer in the arbuscular mycorrhizal symbiosis. Nature In Press.

Torres, S., C.R. Fjetland, and P.J. Lammers. 2005. Alkane-induced expression, substrate binding profile, and immunolocalization of a cytochrome P450 encoded on the nifD excision element of Anabaena 7120 BMC Microbiology 5, 16-28.

Lammers, P, J., Abubaker, M. Govindarajulu, J. Jun, O. Krijgsman, and M. de Jong. 2004. Quantitative analysis of gene expression in the arbuscular mycorrhizal symbiosis. In: Basic Research and Applications of Mycorrhizae. Eds. Podila, G.K. and Varma, A. I.K. International, New Delhi.

Spalding, J. B. and P.J. Lammers. 2004. BLAST Filter and GraphAlign: rule-based formation and analysis of sets of related DNA and protein sequences. Nucleic Acids Research. 32: W26-W32.

Martin, F., G.A. Tuskan, S.P. DiFazio, P. Lammers, G. Newcombe and G.K. Podila. 2004. In the Wake of the Poplar Genome Sequence - Whole Genome Sequencing of the Endomycorrhizal Glomus Intraradices and the Ectomycorrhizal Laccaria Bicolor for 2004. New Phytologist. 161: 330-335.

Lammers, P.J. 2004. Symbiotic signaling: new roles for familiar proteins. New Phytologist. 161: 321-324.

Mori, S., A. Castoreno, M.E. Mulligan and P.J. Lammers. 2003. Nitrogen status modulates the expression of RNA-binding proteins in cyanobacteria. FEMS Microbiology Letters. 227, 203-210.

Bago, B., P.E Pfeffer, J. Abubaker, J. Jun, J.W. Allen, J. Brouillette, D.D. Douds, P.J. Lammers and Y. Shachar-Hill. 2003. Carbon export from arbuscular mycorrhizal roots involves the translocation of carbohydrate as well as lipid. Plant Physiol. 131: 1496-1507.

Bago, B., P.E. Pfeffer, W. Zipfel, P.J. Lammers and Y. Shachar-Hill. 2002. Tracking metabolism and imaging transport in arbuscular mycorrhizal fungi. Metabolism and transport in AM fungi. Plant & Soil. 244, 189-197.

Jeongwon, J., J. Abubaker, C. Rehrer, P.E. Pfeffer, Y. Shachar-Hill and P.J. Lammers. 2002. Expression in an arbuscular mycorrhizal fungus of genes involved in metabolism, transport, the cytoskeleton and the cell cycle. Plant & Soil. 244, 141-148.

Mori, S., A. Castoreno and P.J. Lammers. 2002. Transcript levels of rbcR1, ntcA, and rbcL/S genes in the cyanobacterium Anabaena sp. PCC 7120 are downregulated in response to cold and osmotic stress. FEMS Microbiol. Lett. FEMS Microbiol. Lett. 213, 167-173.

Bago, B., P.E. Pfeffer, J. Abubaker, J. Jun, J.W. Allen, J. Brouillette, D.D. Douds, P.J. Lammers and Y. Shachar-Hill. 2002. Carbon export from arbuscular mycorrhizal roots involves the translocation of carbohydrate as well as lipid. Plant Physiol.

Bago, B., W. Zipfel, R. Williams, J. Jun, R. Arreola, P. Lammers, P.E. Pfeffer and Y. Schachar-Hill. 2002. Translocation and utilization of fungalstorage lipid in the arbuscular mycorrhizal symbiosis. Plant Physiology 128, 108-124.

Lammers, P.J., J. Jun, J. Abubaker, R. Arreola, A. Gopalan, B. Bago, C. Hernandez-Sebastia, J.W. Allen, D.D. Douds, P.E. Pfeffer and Y. Shachar-Hill. 2001. The glyoxylate cycle in an arbuscular mycorrhizal fungus: gene expression and carbon flow. Plant Physiology, 127, 1287-1298.

Lammers, P.J. 2001. Consensus Builder. Science 292, 519.

Lammers, P.J., J.B. Spalding, S.P. Duran and N.B. Garcia. 1998. Orphan protein identification through comparisons of predicted versus experimental secondary structures. Microbiol. & Comparative Genomics 3, C76-77.

Torres, S., C.R. Fjetland and P.J. Lammers. 1997. Expression of cyp110 and immuno-localization of a cyanobacterial cytochrome P450 in Anabaena sp. Strain PCC 7120. FASEB J. 11, A813.

Fjetland, C.R., S. Torres, S. McLaughlin and P.J. Lammers. 1997. Characterization of CYP110 from Anabaena 7120. FASEB J. 11, A814.

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