Gene expression shifts during perithecium development in Gibberella zeae (anamorph Fusarium graminearum), with particular emphasis on ion transport proteins.

Gibberella zeae, the causal agent of Fusarium head blight, is a devastating pathogen of small grains worldwide. The sexual cycle is a crucial component of head blight epidemiology, as forcibly discharged ascospores serve as the primary inoculum. The recent development of an Affymetrix GeneChip containing probesets representative of all predicted genes of G. zeae has opened the door to studies of differential gene expression during sexual development. Using GeneChips, a developmental time course was performed in culture, from vegetative hyphae to mature perithecia with multiseptate ascospores. Time-points represent the development of the major cell types comprising the mature perithecium. The majority of the 17,830 G. zeae probesets, 78%, were expressed during at least one of the developmental stages; 12% of these appear to be specific to sexual development. Analysis of the 162 predicted ion transporter genes is reported in detail, due to their association with perithecium function. Expression patterns of the MirA-type siderophores, chloride channels, P-type ATPases and potassium transporters show some specialization in regard to developmental stage. This is the first whole-genome analysis of differential transcript accumulation during sexual development in a filamentous fungus.

[1]  Lynne Yenush,et al.  pH-Responsive, Posttranslational Regulation of the Trk1 Potassium Transporter by the Type 1-Related Ppz1 Phosphatase , 2005, Molecular and Cellular Biology.

[2]  J. Davis.  Bioinformatics and Computational Biology Solutions Using R and Bioconductor , 2007 .

[3]  E. S. Luttrell.  Taxonomy of the Pyrenomycetes , 1951 .

[4]  H. Okayama,et al.  Novel Factor Highly Conserved among Eukaryotes Controls Sexual Development in Fission Yeast , 1998, Molecular and Cellular Biology.

[5]  K. Cunningham,et al.  A Homolog of Voltage-Gated Ca2+Channels Stimulated by Depletion of Secretory Ca2+ in Yeast , 2000, Molecular and Cellular Biology.

[6]  Jean YH Yang,et al.  Bioconductor: open software development for computational biology and bioinformatics , 2004, Genome Biology.

[7]  C. Windels.  Economic and social impacts of fusarium head blight: changing farms and rural communities in the northern great plains. , 2000, Phytopathology.

[8]  J. Fraser,et al.  Isolation and Characterization of Two Ammonium Permease Genes, meaA and mepA, from Aspergillus nidulans , 2002, Eukaryotic Cell.

[9]  Katherine S. Pollard,et al.  Cluster Analysis of Genomic Data , 2005 .

[10]  J. Cairney,et al.  A simple and efficient method for isolating RNA from pine trees , 1993, Plant Molecular Biology Reporter.

[11]  T. Speed,et al.  Summaries of Affymetrix GeneChip probe level data. , 2003, Nucleic acids research.

[12]  R. Metzenberg,et al.  Sexual development genes of Neurospora crassa. , 1992, Genetics.

[13]  W R Taylor,et al.  A model recognition approach to the prediction of all-helical membrane protein structure and topology. , 1994, Biochemistry.

[14]  D. Reynolds.  Ascomycete systematics : the Luttrellian concept , 1982 .

[15]  Rafael A. Irizarry,et al.  Bioinformatics and Computational Biology Solutions using R and Bioconductor , 2005 .

[16]  Gordon K. Smyth,et al.  limma: Linear Models for Microarray Data , 2005 .

[17]  Wen-Hsiung Li,et al.  Transcription Factor Families Have Much Higher Expansion Rates in Plants than in Animals1 , 2005, Plant Physiology.

[18]  J. Leslie,et al.  Sexual Recombination in Gibberella zeae. , 1999, Phytopathology.

[19]  Mark J. van der Laan,et al.  Hybrid Clustering of Gene Expression Data with Visualization and the Bootstrap , 2001 .

[20]  GeneChip® Expression Analysis , 2003 .

[21]  Rafael A Irizarry,et al.  Exploration, normalization, and summaries of high density oligonucleotide array probe level data. , 2003, Biostatistics.

[22]  D. Choi,et al.  Identification of the down-regulated genes in a mat1-2-deleted strain of Gibberella zeae, using cDNA subtraction and microarray analysis. , 2006, Fungal genetics and biology : FG & B.

[23]  Comparative gene expression analysis of fruiting body development in two filamentous fungi. , 2006, FEMS microbiology letters.

[24]  Gordon K Smyth,et al.  Statistical Applications in Genetics and Molecular Biology Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments , 2011 .

[25]  A. Rodríguez-Navarro,et al.  A novel P‐type ATPase from yeast involved in sodium transport , 1991, FEBS letters.

[26]  M. Saier.  A Functional-Phylogenetic Classification System for Transmembrane Solute Transporters , 2000, Microbiology and Molecular Biology Reviews.

[27]  Hans-Werner Mewes,et al.  Development of a Fusarium graminearum Affymetrix GeneChip for profiling fungal gene expression in vitro and in planta. , 2006, Fungal genetics and biology : FG & B.

[28]  M. Saier,et al.  The Transporter Classification (TC) System, 2002 , 2002, Critical reviews in biochemistry and molecular biology.

[29]  B. André,et al.  An overview of membrane transport proteins in Saccharomyces cerevisiae , 1995, Yeast.

[30]  G. Tusnády,et al.  Principles governing amino acid composition of integral membrane proteins: application to topology prediction. , 1998, Journal of molecular biology.

[31]  Sean R. Eddy,et al.  Profile hidden Markov models , 1998, Bioinform..

[32]  H. Arst,et al.  Regulation of Gene Expression by Ambient pH in Filamentous Fungi and Yeasts , 2002, Microbiology and Molecular Biology Reviews.

[33]  T. Iwamoto,et al.  Diversity of Cl− Channels , 2005, Cellular and Molecular Life Sciences.

[34]  J. Leslie,et al.  Nitrate reduction mutants of fusarium moniliforme (gibberella fujikuroi). , 1988, Genetics.

[35]  U. Kück,et al.  Cross-species microarray hybridization to identify developmentally regulated genes in the filamentous fungus Sordaria macrospora , 2005, Molecular Genetics and Genomics.

[36]  F. Trail,et al.  Perithecial development by Gibberella zeae: a light microscopy study , 2000 .

[37]  D. Sanders,et al.  The Saccharomyces cerevisiae CCH1 gene is involved in calcium influx and mating , 1997, FEBS letters.

[38]  M H Saier,et al.  Unified inventory of established and putative transporters encoded within the complete genome of Saccharomyces cerevisiae , 1998, FEBS letters.

[39]  Ian T. Paulsen,et al.  Comparative Analyses of Fundamental Differences in Membrane Transport Capabilities in Prokaryotes and Eukaryotes , 2005, PLoS Comput. Biol..

[40]  Steven Vogel,et al.  Ejection mechanics and trajectory of the ascospores of Gibberella zeae (anamorph Fuarium graminearum). , 2005, Fungal genetics and biology : FG & B.

[41]  B. Dujon,et al.  Phylogenetic classification of transporters and other membrane proteins from Saccharomyces cerevisiae , 2002, Functional & Integrative Genomics.

[42]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[43]  F. Trail,et al.  Microarray analysis of transcript accumulation during perithecium development in the filamentous fungus Gibberella zeae (anamorph Fusarium graminearum) , 2006, Molecular Genetics and Genomics.

[44]  F. Trail,et al.  Physiological and environmental aspects of ascospore discharge in Gibberella zeae (anamorph Fusarium graminearum) , 2002, Mycologia.

[45]  Y. Anraku,et al.  MID1, a novel Saccharomyces cerevisiae gene encoding a plasma membrane protein, is required for Ca2+ influx and mating , 1994, Molecular and cellular biology.

[46]  F. Trail,et al.  The development and differentiation of Gibberella zeae (anamorph: Fusarium graminearum) during colonization of wheat , 2005, Mycologia.