Open Access Research article

Gene expression and proteomic analysis of the formation of Phakopsora pachyrhizi appressoria

Christine L Stone1, Michael B McMahon1, Laurie L Fortis24, Alberto Nuñez2, Gary W Smythers3, Douglas G Luster1 and Reid D Frederick1*

Author affiliations

1 USDA-Agricultural Research Service, Foreign Disease-Weed Science Research Unit, 1301 Ditto Avenue, Fort Detrick, MD, 21702, USA

2 USDA-Agricultural Research Service, Eastern Regional Research Center, 600 East Mermaid Lane, Wyndmoor, PA, 19038, USA

3 National Cancer Institute, Advanced Biomedical Computing Center, Building 430, Fort Detrick, MD, 21702, USA

4 Present address: USDA-National Institute of Food and Agriculture, Institute of Bioenergy, Climate, and Environment, 3245 Waterfront Centre, 800 9th Street, Southwest, Washington, District of Columbia, 20024, USA

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Citation and License

BMC Genomics 2012, 13:269  doi:10.1186/1471-2164-13-269

Published: 22 June 2012



Phakopsora pachyrhizi is an obligate fungal pathogen causing Asian soybean rust (ASR). A dual approach was taken to examine the molecular and biochemical processes occurring during the development of appressoria, specialized infection structures by which P. pachyrhizi invades a host plant. Suppression subtractive hybridization (SSH) was utilized to generate a cDNA library enriched for transcripts expressed during appressoria formation. Two-dimensional gel electrophoresis and mass spectroscopy analysis were used to generate a partial proteome of proteins present during appressoria formation.


Sequence analysis of 1133 expressed sequence tags (ESTs) revealed 238 non-redundant ESTs, of which 53% had putative identities assigned. Twenty-nine of the non-redundant ESTs were found to be specific to the appressoria-enriched cDNA library, and did not occur in a previously constructed germinated urediniospore cDNA library. Analysis of proteins against a custom database of the appressoria-enriched ESTs plus Basidiomycota EST sequences available from NCBI revealed 256 proteins. Fifty-nine of these proteins were not previously identified in a partial proteome of P. pachyrhizi germinated urediniospores. Genes and proteins identified fell into functional categories of metabolism, cell cycle and DNA processing, protein fate, cellular transport, cellular communication and signal transduction, and cell rescue. However, 38% of ESTs and 24% of proteins matched only to hypothetical proteins of unknown function, or showed no similarity to sequences in the current NCBI database. Three novel Phakopsora genes were identified from the cDNA library along with six potentially rust-specific genes. Protein analysis revealed eight proteins of unknown function, which possessed classic secretion signals. Two of the extracellular proteins are reported as potential effector proteins.


Several genes and proteins were identified that are expressed in P. pachyrhizi during appressoria formation. Understanding the role that these genes and proteins play in the molecular and biochemical processes in the infection process may provide insight for developing targeted control measures and novel methods of disease management.