Why Neurospora?

The orange bread mold Neurospora has served as a beautiful and simple model organism for genetic and biochemical studies since Beadle and Tatum used it to establish the one gene-one enzyme model in 1941.  The many ways that Neurospora has provided insights into biological processes  have been enumerated briefly (Horowitz, 1991; Perkins, 1992) and in exceptional detail (Davis, 2000).  Neurospora is the best-characterized of the filamentous fungi, a group of organisms critically important to agriculture, medicine, and the environment.  Neurospora is widespread in nature and thus, like the fly Drosophila, it is exceptionally suited as a subject for population studies.  While, like Saccharomyces cerevisiae, it is an ascomycete and thus shares the advantage of this group of organisms in yielding complete tetrads for genetic analyses in the laboratory, it is more similar to animals than yeasts in many important ways.  For example, unlike yeast but like mammals, it contains complex I in its respiratory chain,  it has a clearly discernable circadian rhythm, and it methylates DNA to control gene expression.

The six decades of intensive studies on the genetics, biochemistry and cell biology of Neurospora establish this organism as a gold mine of biological knowledge.  The sequence of the genome will provide the key to deeper exploration of this rich and well mapped mine.  The N. crassa genome has been extensively characterized by classical genetic and physical means.

  • It is estimated to contain 43 Mb of DNA of 54% G/C content, which is organized in seven linkage groups (Table 1, Perkins et al., 2001)
  • It has little repeated DNA other than the ~150 copies of rDNA genes (Krumlauf and Marzluf, 1979, 1980).
  • Other repeated DNA is dispersed and tends to be short and/or diverged, presumably because of the phenomenon of "RIP" (repeat-induced point mutation).
  • RIP searches the genome for duplicated (repeated) sequences in haploid nuclei of special premeiotic cells, efficiently finds them and then litters them with numerous GC to AT mutations (Selker, 1990). Apparently RIP serves as a genome defense system for Neurospora, inactivating transposons and resisting genome expansion (Kinsey et al., 1994).
  • More than 1000 distinct genetic markers have been mapped to these linkage groups (Table 1, Perkins et al., 2001). 248 of these mapped markers represent genes that have been both cloned and sequenced; these well-characterized genes are distributed uniformly throughout the genome on each linkage group and will be used for verification of the genome sequence. It has been estimated that Neurospora has more than twice as many genes as S. cerevisiae (Nelson et al., 1997).
  • A recent analysis has shown that over 50% of the expressed Neurospora genes lack identifiable homologues in any organism, and only about 33% have homologues in S. cerevisiae (Braun et al., 2000).
Linkage Group Size (Mb) Genetic markers Chromosome Band (PFGE)
I 10.3 267 1
II  4.6  119 
III  5.1  111 
IV  5.7  155 
9.2  180 
VI  4.0  87  6* 
VII  4.0  95  6* 
*Resolved with use of insertional translocation strains.

Table 1. The N. crassa genome.  Linkage groups, their estimated sizes in megabases (Mb) estimated from pulsed field gel electrophoresis, and the number of mapped genetic markers on each linkage group. Linkage group numbering, assigned from genetic data, is not correlated to physical chromosome size. Physical sizes are listed for each chromosome as determined by pulse field gel electrophoresis (Orbach et al., 1988). Genetic markers are from (Perkins et al., 2001).

Other projects to analyze the Neurospora genome are underway.  Links to these resources can be found at the Fungal Genetics Stock Center.  A German consortium led by Ulrich Schulte is engaged in the large-scale sequencing of BAC and cosmid clones of DNA from linkage groups II and V . Complete or partial sequences for many other genes are available . Nearly 24,000 EST reads have been deposited in databases by investigators at the University of New Mexico, and by a joint effort between Dartmouth Medical School and the University of Oklahoma. Many of these unique sequences have as yet no homolog in Saccharomyces or in other organisms; clearly the Neurospora genome contains a large complement of novel genes. A group led by Jonathan Arnold at the University of Georgia has constructed cosmid libraries of N. crassa DNA in fungal transformation vectors, has sorted these cosmids based on their hybridization to chromosome-specific probes, and is tiling these cosmids onto linkage groups.

References

Braun, E. L., Halpern, A. L., Nelson, M. A., and Natvig, D. O. (2000). Large-scale comparison of fungal sequence information: mechanisms of innovation in Neurospora crassa and gene loss in Saccharomyces cerevisiae. Genome Res. 10, 416-430. 

Davis, R. H. (2000). Neurospora: Contributions of a Model Organism (Oxford, Great Britain: Oxford University Press).

Horowitz, N. H. (1991). Fifty years ago: the Neurospora revolution. Genetics 127, 631-636.

Kinsey, J. A., Garrett-Engele, P. W., Cambareri, E. B., and Selker, E. U. (1994). The Neurospora transposon Tad is sensitive to repeat- induced point mutation (RIP). Genetics 138, 657-664.

Krumlauf, R., and Marzluf, G. A. (1979). Characterization of the sequence complexity and organization of the Neurospora crassa genome. Biochemistry 18, 3705-3713.

Krumlauf, R., and Marzluf, G. A. (1980). Genome organization and characterization of the repetitive and inverted repeat DNA sequences in Neurospora crassa. J. Biol. Chem. 255, 1138-1145.

Nelson, M. A., Kang, S., Braun, E. L., Crawford, M. E., Dolan, P. L., Leonard, P. M., Mitchell, J., Armijo, A. M., Bean, L., Blueyes, E., Cushing, T., Errett, A., Fleharty, M., Gorman, M., Judson, K., Miller, R., Ortega, J., Pavlova, I., Perea, J., Todisco, S., Trujillo, R., Valentine, J., Wells, A., Werner-Washburne, M., and Natvig, D. O. (1997). Expressed sequences from conidial, mycelial, and sexual stages of Neurospora crassa. Fungal Genet. Biol. 21, 348-363.

Orbach, M. J., Vollrath, D., Davis, R. W., and Yanofsky, C. (1988). An electrophoretic karyotype of Neurospora crassa. Mol. Cell. Biol. 8, 1469-1473.

Perkins, D. D. (1992). Neurospora: the organism behind the molecular revolution. Genetics 130, 687-701.

Perkins, D. D., Radford, A., and Sachs, M. S. (2001). The Neurospora Compendium: Chromosomal loci (San Diego, CA: Academic Press).

Selker, E. U. (1990). Premeiotic instability of repeated sequences in Neurospora crassa. Ann. Rev. Genet. 24, 579-613.