Submitted to: Book Chapter
Publication Type: Book / Chapter
Publication Acceptance Date: 7/15/2010
Publication Date: 3/20/2011
Citation: Brown, D.W., Butchko, R.A., Proctor, R. 2011. Identification of genes and gene clusters involved in mycotoxin synthesis. In: De Saeger, S., editor. Determining Mycotoxins and Mycotoxigenic Fungi in Food and Feed. Cambridge, UK: Woodhead Publishing. p. 332-348.
Interpretive Summary: This book chapter describes research methods used to identify groups of genes in fungi that are involved in the synthesis of toxins and how these methods and strategies have changed or evolved over time. Early researchers used a variety of different strategies to identify genes involved in the synthesis of a particular fungal toxin. Technological advances in DNA sequencing now allow entire genomes of an organism to be determined in a relatively short period of time, thereby accelerating the gene discovery process in fungi. The availability of the entire genome sequence of a fungus enabled researchers to identify and study families of genes known to be important for toxin synthesis. At the same time, all neighboring genes could also be examined to see if they may also be involved in toxin synthesis. The development of techniques to study expression of all of the genes at a certain life stage or growth condition has had a similarly advantageous impact on identifying groups of genes involved in a single process. Understanding how genes are organized into groups and how these genes synthesize toxins will allow us to develop novel strategies to limit or control toxin synthesis.
Technical Abstract: Research methods to identify and characterize genes involved in mycotoxin biosynthetic pathways have evolved considerably over the years. Before whole genome sequences were available (e.g. pre-genomics), work focused primarily on chemistry, biosynthetic mutant strains and molecular analysis of single or relatively small numbers of genes. In recent years, reductions in the cost of DNA sequencing technologies have made genomic methods more widely available. The availability of whole genome sequence for multiple mycotoxin-producing fungi has led to important discoveries both within single genomes and between genomes via comparative genomics (post-genomic). The ability to simultaneously analyze the expression of large number of genes through ESTs and microarrays (transcriptomics) has also had a significant impact on gene cluster identification. This chapter discusses the pre-genomic strategies used to identify toxin biosynthetic genes/gene clusters in fungi as well as more recently developed genomic strategies that are used today and that greatly enhance the efficiency of the identification process. Pre-genomic researchers focused on analysis of a small number of genes while post-genomic researchers compare genomes and examine transcription patterns of 1000’s of genes at a time to help define biosynthetically related genes involved in mycotoxin synthesis. An examination of two Fusarium secondary metabolites, the mycotoxins fumonisins and a perithecial pigment, provide models for similar studies with other fungi. The identification of additional mycotoxin gene clusters in other fungi will proceed significantly faster in the future using genomic technologies.