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Microbiology and Molecular Biology Reviews, March 2004, p. 1-108, Vol. 68, No. 1
1092-2172/04/$08.00+0     DOI: 10.1128/MMBR.68.1.1-108.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

Lessons from the Genome Sequence of Neurospora crassa: Tracing the Path from Genomic Blueprint to Multicellular Organism

Katherine A. Borkovich,1* Lisa A. Alex,2 Oded Yarden,3 Michael Freitag,4 Gloria E. Turner,5 Nick D. Read,6 Stephan Seiler,7 Deborah Bell-Pedersen,8 John Paietta,9 Nora Plesofsky,10 Michael Plamann,11 Marta Goodrich-Tanrikulu,12 Ulrich Schulte,13 Gertrud Mannhaupt,14 Frank E. Nargang,15 Alan Radford,16 Claude Selitrennikoff,17 James E. Galagan,18 Jay C. Dunlap,19 Jennifer J. Loros,20 David Catcheside,21 Hirokazu Inoue,22 Rodolfo Aramayo,8 Michael Polymenis,23 Eric U. Selker,4 Matthew S. Sachs,24 George A. Marzluf,25 Ian Paulsen,26 Rowland Davis,27 Daniel J. Ebbole,28 Alex Zelter,6 Eric R. Kalkman,6 Rebecca O'Rourke,29 Frederick Bowring,21 Jane Yeadon,21 Chizu Ishii,22 Keiichiro Suzuki,22 Wataru Sakai,22 and Robert Pratt8

Department of Plant Pathology, University of California, Riverside, California 92521,1 Department of Chemistry, California State Polytechnic University, Pomona, California 91768,2 Department of Plant Pathology and Microbiology, Faculty of Agricultural, Food and Environmental Quality Sciences, The Hebrew University of Jerusalem, Rehovot 76100, Israel,3 Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403,4 Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095,5 Institute of Cell and Molecular Biology, University of Edinburgh, Edinburgh EH9 3JH,6 Department of Molecular Microbiology & Genetics, Institute of Microbiology & Genetics, Georg-August-University, D-37077 Goettingen,7 Institute of Biochemistry, Heinrich Heine University, 40225 Dusseldorf,13 Department of Biology,8 Department of Biochemistry and Biophysics,23 Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843,28 Department of Biochemistry and Molecular Biology, Wright State University, Dayton, Ohio 45435,9 Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108,10 School of Biological Sciences, University of Missouri—Kansas City, Kansas City, Missouri 64110,11 Bio-Rad Laboratories, Inc., Hercules, California 94547,12 ,14 Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada,15 ,16 Department of Cell and Developmental Biology,17 Department of Cellular and Structural Biology, University of Colorado Health Sciences Center, Denver, Colorado 80262,29 Whitehead Institute Center for Genome Research, Cambridge, Massachusetts 02141,18 Department of Genetics,19 Department of Biochemistry, Dartmouth Medical School, Hanover, New Hampshire 03755,20 School of Biological Sciences, Flinders University, Adelaide 5001, Australia,21 Laboratory of Genetics, Department of Regulation Biology, Saitama University, Saitama City, Saitama 338-8570, Japan,22 Department of Environmental and Biomolecular Systems, School of Science and Engineering, Oregon Health and Science University, Beaverton, Oregon 97006,24 Department of Biochemistry, Ohio State University, Columbus, Ohio 43210,25 The Institute for Genomic Research, Rockville, Maryland 20878,26 Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697,27

We present an analysis of over 1,100 of the ~10,000 predicted proteins encoded by the genome sequence of the filamentous fungus Neurospora crassa. Seven major areas of Neurospora genomics and biology are covered. First, the basic features of the genome, including the automated assembly, gene calls, and global gene analyses are summarized. The second section covers components of the centromere and kinetochore complexes, chromatin assembly and modification, and transcription and translation initiation factors. The third area discusses genome defense mechanisms, including repeat induced point mutation, quelling and meiotic silencing, and DNA repair and recombination. In the fourth section, topics relevant to metabolism and transport include extracellular digestion; membrane transporters; aspects of carbon, sulfur, nitrogen, and lipid metabolism; the mitochondrion and energy metabolism; the proteasome; and protein glycosylation, secretion, and endocytosis. Environmental sensing is the focus of the fifth section with a treatment of two-component systems; GTP-binding proteins; mitogen-activated protein, p21-activated, and germinal center kinases; calcium signaling; protein phosphatases; photobiology; circadian rhythms; and heat shock and stress responses. The sixth area of analysis is growth and development; it encompasses cell wall synthesis, proteins important for hyphal polarity, cytoskeletal components, the cyclin/cyclin-dependent kinase machinery, macroconidiation, meiosis, and the sexual cycle. The seventh section covers topics relevant to animal and plant pathogenesis and human disease. The results demonstrate that a large proportion of Neurospora genes do not have homologues in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe. The group of unshared genes includes potential new targets for antifungals as well as loci implicated in human and plant physiology and disease.

* Corresponding author. Mailing address: Department of Plant Pathology, 2338 Webber Hall, 900 University Ave., University of California, Riverside, CA 92521. Phone: (909) 787-2753. Fax: (909) 787-4294. E-mail: Katherine.Borkovich{at}ucr.edu.

Microbiology and Molecular Biology Reviews, March 2004, p. 1-108, Vol. 68, No. 1
1092-2172/04/$08.00+0     DOI: 10.1128/MMBR.68.1.1-108.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.



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