ABSTRACT
Nutrient-dependent variations in transcript levels of the filamentous fungus Neurospora crassa were studied on a microarray containing some 4700 cDNAs. Cells were grown in minimal and acetate medium. The isolated RNA was analyzed in comparison to the results obtained upon the hybridization of samples prepared from the RNA of cells grown in full medium. Altogether, 160 cDNA clones exhibited significant variations, falling into five distinct subgroups of very similar transcription profiles. This is indicative of the occurrence of a high degree of co-regulation of genes in N. crassa. Especially the regulation of the expression of proteins involved in metabolic pathways was found to be strongly regulated at the RNA level.
Subject(s)
Gene Expression Regulation, Fungal/genetics , Genetic Variation/genetics , Neurospora crassa/genetics , Transcription, Genetic/genetics , Culture Media , Fungal Proteins/genetics , Neurospora crassa/growth & development , Nucleic Acid Hybridization , RNA, Fungal/genetics , RNA, Fungal/isolation & purificationABSTRACT
The German Neurospora Genome Project has assembled sequences from ordered cosmid and BAC clones of linkage groups II and V of the genome of Neurospora crassa in 13 and 12 contigs, respectively. Including additional sequences located on other linkage groups a total of 12 Mb were subjected to a manual gene extraction and annotation process. The genome comprises a small number of repetitive elements, a low degree of segmental duplications and very few paralogous genes. The analysis of the 3218 identified open reading frames provides a first overview of the protein equipment of a filamentous fungus. Significantly, N.crassa possesses a large variety of metabolic enzymes including a substantial number of enzymes involved in the degradation of complex substrates as well as secondary metabolism. While several of these enzymes are specific for filamentous fungi many are shared exclusively with prokaryotes.
Subject(s)
Genome, Fungal , Neurospora crassa/genetics , Chromosome Mapping , Chromosomes, Fungal/genetics , DNA, Fungal/chemistry , DNA, Fungal/genetics , Databases, Nucleic Acid , Internet , Open Reading Frames/genetics , Phylogeny , Sequence Analysis, DNAABSTRACT
While the deciphering of basic sequence information on a genomic scale is yielding complete genomic sequences in ever-shorter intervals, experimental procedures for elucidating the cellular effects and consequences of the DNA-encoded information become critical for further analyses. In recent years, DNA microarray technology has emerged as a prime candidate for the performance of many such functional assays. Technically, array technology has come a long way since its conception some 15 years ago, initially designed as a means for large-scale mapping and sequencing.The basic arrangement, however, could be adapted readily to serve eventually as an analytical tool in a large variety of applications. On their own or in combination with other methods, microarrays open up many new avenues of functional analysis.
