@misc{oh_donofrio_pan_coughlan_brown_meng_mitchell_dean_2008, title={Transcriptome analysis reveals new insight into appressorium formation and function in the rice blast fungus Magnaporthe oryzae}, volume={9}, ISSN={["1474-760X"]}, DOI={10.1186/gb-2008-9-5-r85}, abstractNote={Rice blast disease is caused by the filamentous Ascomycetous fungus Magnaporthe oryzae and results in significant annual rice yield losses worldwide. Infection by this and many other fungal plant pathogens requires the development of a specialized infection cell called an appressorium. The molecular processes regulating appressorium formation are incompletely understood.We analyzed genome-wide gene expression changes during spore germination and appressorium formation on a hydrophobic surface compared to induction by cAMP. During spore germination, 2,154 (approximately 21%) genes showed differential expression, with the majority being up-regulated. During appressorium formation, 357 genes were differentially expressed in response to both stimuli. These genes, which we refer to as appressorium consensus genes, were functionally grouped into Gene Ontology categories. Overall, we found a significant decrease in expression of genes involved in protein synthesis. Conversely, expression of genes associated with protein and amino acid degradation, lipid metabolism, secondary metabolism and cellular transportation exhibited a dramatic increase. We functionally characterized several differentially regulated genes, including a subtilisin protease (SPM1) and a NAD specific glutamate dehydrogenase (Mgd1), by targeted gene disruption. These studies revealed hitherto unknown findings that protein degradation and amino acid metabolism are essential for appressorium formation and subsequent infection.We present the first comprehensive genome-wide transcript profile study and functional analysis of infection structure formation by a fungal plant pathogen. Our data provide novel insight into the underlying molecular mechanisms that will directly benefit efforts to identify fungal pathogenicity factors and aid the development of new disease management strategies.}, number={5}, journal={GENOME BIOLOGY}, author={Oh, Yeonyee and Donofrio, Nicole and Pan, Huaqin and Coughlan, Sean and Brown, Douglas E. and Meng, Shaowu and Mitchell, Thomas and Dean, Ralph A.}, year={2008} }
 @article{donofrio_oh_lundy_pan_brown_jeong_coughlan_mitchell_dean_2006, title={Global gene expression during nitrogen starvation in the rice blast fungus, Magnaporthe grisea}, volume={43}, ISSN={["1087-1845"]}, DOI={10.1016/j.fgb.2006.03.005}, abstractNote={Efficient regulation of nitrogen metabolism likely plays a role in the ability of fungi to exploit ecological niches. To learn about regulation of nitrogen metabolism in the rice blast pathogen Magnaporthe grisea, we undertook a genome-wide analysis of gene expression under nitrogen-limiting conditions. Five hundred and twenty genes showed increased transcript levels at 12 and 48 h after shifting the fungus to media lacking nitrate as a nitrogen source. Thirty-nine of these genes have putative functions in amino acid metabolism and uptake, and include the global nitrogen regulator in M. grisea, NUT1. Evaluation of seven nitrogen starvation-induced genes revealed that all were expressed during rice infection. Targeted gene replacement on one such gene, the vacuolar serine protease, SPM1, resulted in decreased sporulation and appressorial development as well as a greatly attenuated ability to cause disease. Data are discussed in the context of nitrogen metabolism under starvation conditions, as well as conditions potentially encountered during invasive growth in planta.}, number={9}, journal={FUNGAL GENETICS AND BIOLOGY}, author={Donofrio, N. M. and Oh, Y. and Lundy, R. and Pan, H. and Brown, D. E. and Jeong, J. S. and Coughlan, S. and Mitchell, T. K. and Dean, R. A.}, year={2006}, month={Sep}, pages={605–617} }
 @article{thon_pan_diener_papalas_taro_mitchell_dean_2006, title={The  role of transposable element clusters in genome evolution and loss of synteny in the rice blast fungus Magnaporthe oryzae}, volume={7}, number={2}, journal={Genome Biology}, author={Thon, M. R. and Pan, H. Q. and Diener, S. and Papalas, J. and Taro, A. and Mitchell, T. K. and Dean, R. A.}, year={2006} }
 @article{kulkarni_thon_pan_dean_2005, title={Novel G-protein-coupled receptor-like proteins in the plant pathogenic fungus Magnaporthe grisea}, volume={6}, number={3}, journal={Genome Biology}, author={Kulkarni, R. D. and Thon, M. R. and Pan, H. Q. and Dean, R. A.}, year={2005} }
 @article{kudo_bao_a d'souza_ying_pan_roe_canfield_2005, title={The alpha- and beta-subunits of the human UDP-N-acetylglucosamine : lysosomal enzyme phosphotransferase are encoded by a single cDNA}, volume={280}, ISSN={["1083-351X"]}, DOI={10.1074/jbc.m509008200}, abstractNote={Lysosomal enzymes are targeted to the lysosome through binding to mannose 6-phosphate receptors because their glycans are modified with mannose 6-phosphate. This modification is catalyzed by UDP-N-acetylglucosamine:lysosomal enzyme N-acetylglucosamine-1-phosphotransferase (GlcNAc-phosphotransferase). Bovine GlcNAc-phosphotransferase was isolated using monoclonal antibody affinity chromatography, and an α2β2γ2-subunit structure was proposed. Although cDNA encoding the γ-subunit has been described, cDNAs for the α- and β-subunits have not. Using partial amino acid sequences from the bovine α- and β-subunits, we have isolated a human cDNA that encodes both the α- and β-subunits. Both subunits contain a single predicted membrane-spanning domain. The α- and β-subunits appear to be generated by a proteolytic cleavage at the Lys928-Asp929 bond. Transfection of 293T cells with the α/β-subunits-precursor cDNA with or without the γ-subunit cDNA results in a 3.6- or 17-fold increase in GlcNAc-phosphotransferase activity in cell lysates, suggesting that the precursor cDNA contains the catalytic domain. The sequence lacks significant similarity with any described vertebrate enzyme except for two Notch-like repeats in the α-subunit. However, a 112-amino acid sequence is highly similar to a group of bacterial capsular polymerases (46% identity). A BAC clone containing the gene that spanned 85.3 kb and was composed of 21 exons was sequenced and localized to chromosome 12q23. We now report the cloning of both the cDNA and genomic DNA of the precursor of Glc-NAc-phosphotransferase. The completion of cloning all three subunits of GlcNAc-phosphotransferase allows expression of recombinant enzyme and dissection of lysosomal targeting disorders.}, number={43}, journal={JOURNAL OF BIOLOGICAL CHEMISTRY}, author={Kudo, M and Bao, M and A D'Souza and Ying, F and Pan, HQ and Roe, BA and Canfield, WM}, year={2005}, month={Oct}, pages={36141–36149} }
 @article{dean_talbot_ebbole_farman_mitchell_orbach_thon_kulkarni_xu_pan_et al._2005, title={The genome sequence of the rice blast fungus Magnaporthe grisea}, volume={434}, ISSN={["1476-4687"]}, DOI={10.1038/nature03449}, abstractNote={Magnaporthe grisea is the most destructive pathogen of rice worldwide and the principal model organism for elucidating the molecular basis of fungal disease of plants. Here, we report the draft sequence of the M. grisea genome. Analysis of the gene set provides an insight into the adaptations required by a fungus to cause disease. The genome encodes a large and diverse set of secreted proteins, including those defined by unusual carbohydrate-binding domains. This fungus also possesses an expanded family of G-protein-coupled receptors, several new virulence-associated genes and large suites of enzymes involved in secondary metabolism. Consistent with a role in fungal pathogenesis, the expression of several of these genes is upregulated during the early stages of infection-related development. The M. grisea genome has been subject to invasion and proliferation of active transposable elements, reflecting the clonal nature of this fungus imposed by widespread rice cultivation.}, number={7036}, journal={NATURE}, author={Dean, RA and Talbot, NJ and Ebbole, DJ and Farman, ML and Mitchell, TK and Orbach, MJ and Thon, M and Kulkarni, R and Xu, JR and Pan, HQ and et al.}, year={2005}, month={Apr}, pages={980–986} }
 @article{ebbole_jin_thon_pan_bhattarai_thomas_dean_2004, title={Gene discovery and gene expression in the rice blast fungus, Magnaporthe grisea: Analysis of expressed sequence tags}, volume={17}, ISSN={["0894-0282"]}, DOI={10.1094/MPMI.2004.17.12.1337}, abstractNote={ Over 28,000 expressed sequence tags (ESTs) were produced from cDNA libraries representing a variety of growth conditions and cell types. Several Magnaporthe grisea strains were used to produce the libraries, including a nonpathogenic strain bearing a mutation in the PMK1 mitogen-activated protein kinase. Approximately 23,000 of the ESTs could be clustered into 3,050 contigs, leaving 5,127 singleton sequences. The estimate of 8,177 unique sequences indicates that over half of the genes of the fungus are represented in the ESTs. Analysis of EST frequency reveals growth and cell type-specific patterns of gene expression. This analysis establishes criteria for identification of fungal genes involved in pathogenesis. A large fraction of the genes represented by ESTs have no known function or described homologs. Manual annotation of the most abundant cDNAs with no known homologs allowed us to identify a family of metallothionein proteins present in M. grisea, Neurospora crassa, and Fusarium graminearum. In addition, multiply represented ESTs permitted the identification of alternatively spliced mRNA species. Alternative splicing was rare, and in most cases, the alternate mRNA forms were unspliced, although alternative 5′ splice sites were also observed. }, number={12}, journal={MOLECULAR PLANT-MICROBE INTERACTIONS}, author={Ebbole, DJ and Jin, Y and Thon, M and Pan, HQ and Bhattarai, E and Thomas, T and Dean, R}, year={2004}, month={Dec}, pages={1337–1347} }