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Plant Physiology 149:103-110 (2009) © 2009 American Society of Plant Biologists For Blighted Waves of Grain: Fusarium graminearum in the Postgenomics EraDepartment of Plant Biology and Department of Plant Pathology, Michigan State University, East Lansing, Michigan 48824–1312
Fungi display astounding diversity in their pathogenicity. We categorize them as biotrophs or necrotrophs and as obligate or facultative pathogens, but these categories do not reflect their polymorphic nature. Our approach to controlling disease would be better served by improving our understanding of the complete life cycle of the fungal pathogen, from infection and colonization to overwintering, using all of the tools at our disposal. A handful of fungal plant pathogens are now being studied at this level, including Fusarium graminearum (sexual stage, Gibberella zeae), the causal agent of head blight of wheat (Triticum aestivum), oat (Avena sativa), and barley (Hordeum vulgare) and ear and stalk rot of maize (Zea mays). Although F. graminearum is arguably one of the best studied fungal plant pathogens, the genetic bases of its life cycle and pathogenicity are poorly defined. This article focuses on the contributions that genomics and postgenomic studies are making to our understanding of the entire life cycle of this important pathogen. The genome of this fungal pathogen cannot be viewed in isolation, just as the fungus does not exist in isolation. Genomics can be used to elucidate F. graminearum's interaction with its hosts, leading to a clearer picture of its ecological niche.
Fusarium head blight is a global problem. F. graminearum is the most prominent causal agent of head blight in the United States, Canada, and Europe (McMullen et al., 1997
F. graminearum produces several mycotoxins, including deoxynivalenol (DON) and derivatives, zearalenone, fusarin C, and aurofusarin. Although head blight causes low grain weight, the primary economic and health consequences of the disease are due to mycotoxin contamination, primarily DON. DON is a potent protein biosynthesis inhibitor affecting the digestive system and major organ function in humans and animals when ingested in sufficient quantities (Council for Agricultural Science and Technology, 2003
The genome sequence was publicly released by the Broad Institute in 2003 (www.broad.mit.edu/annotation/genome/fusarium_group/MultiHome.html). The genome sequence release has greatly stimulated research activity on F. graminearum. An average of 50 articles per year were published between 2004 and 2007, compared with an average of 20 from 1999 through 2002, prior to the genome's release (ISI Web of Science; search criterion: Fusarium graminearum in the title). The genome size (36.1 Mb) is typical for a filamentous fungus. It contains genes encoding 13,937 predicted proteins (mips.gsf.de/genre/proj/FGDB/) distributed over four chromosomes. Of these genes, 2,001 are not similar to those of any other sequenced organism (orphans) and 5,812 have homology to proteins of unknown function. There are fewer repeat sequences and an unusually low number of paralogous genes in comparison with genome sequences of other filamentous ascomycetes (Cuomo et al., 2007
The availability of the F. graminearum genome sequence provides the opportunity to understand how this pathogen has evolved to occupy its niche. The first step in this process was to identify regions of the genome with high sequence variability among strains. Single nucleotide polymorphism (SNP) analysis of the F. graminearum sequence was conducted using the two major U.S. experimental strains (PH-1, nearly complete sequence; GZ3639, 0.4x coverage) and resulted in the identification of regions of high SNP density that correspond with telomeric regions and central chromosomal regions (centromeres have not been identified; Cuomo et al., 2007
One of the most interesting outcomes of genome sequencing is the identification of genes that have limited phylogenetic distribution: the orphan genes. The 2,001 orphan genes identified in the genome sequence of F. graminearum are concentrated in the high SNP regions (Cuomo et al., 2007
A generalized disease cycle of F. graminearum in wheat is illustrated in Figure 1 . In the wheat field, head blight disease is initiated by airborne spores landing on flowering spikelets, germinating, and entering the plant through natural openings such as the base of the lemma and palea or through degenerating anther tissues (for review, see Bushnell et al., 2003
Following infection of wheat florets, the fungus expresses genes for DON biosynthesis almost immediately (Jansen et al., 2005
F. graminearum can readily complete its life cycle in culture or in association with its host. As with the vast majority of fungi, F. graminearum is haploid for most of its life cycle. For this fungus, sexual development begins with the formation of hyphae with binucleate cells. An extended binucleate phase (called the dikaryotic phase when two genetically distinct nuclei remain paired as new cells form) is a hallmark of the phylum Ascomycota (to which F. graminearum belongs). In the Ascomycota, this phase is the initial step in sexual development. F. graminearum is homothallic, meaning that it does not need a sexually distinct partner to develop sexual spores (ascospores), and as a result, the two nuclei of the binucleate cells are genetically identical. Homothallism in F. graminearum is due to the presence of genes associated with both mating types (Mat1-1 and Mat1-2) in the haploid genome (Yun et al., 2000
Sexual development is a critical part of the disease cycle. In infected wheat, perithecium initials develop in association with the plant's stomates and silica cells, and, together with the binucleate hyphae from which they arise, are the overwintering structures (Guenther and Trail, 2005
Copious asexual spores (conidia) are produced on the surface of infected plants or on crop residue during damp periods. Conidia are produced in slimy masses borne on sporodochia (cushion-shaped hyphal structures). The fusiform shape of the conidia and their formation in slimy masses have been associated with rain-splash dispersal (Deacon, 2006
We hypothesize that during vegetative growth within the host, the acquisition of carbon resources is the most important activity. Lipid bodies can be seen in the binucleate hyphae associated with the perithecium initials. These resources would be necessary for overwinter survival and sexual reproduction, and their acquisition appears to occur during the initial colonization of the host's stalk (Guenther and Trail, 2005
The head blight pathogen has been studied for well over a century, beginning with the first report of the disease in England by Smith (1884)
Proteomics is the large-scale study of proteins. Proteomics can be used to enhance the results of expression studies and to differentiate proteins present in specific compartments or cell types. Proteomics analyses have been conducted in F. graminearum to identify proteins regulated by the mating-type gene in a mutant of Mat1-2 (Lee et al., 2008 The term "metabolomics" refers to the large-scale study of metabolites produced by an organism grown under a particular set of conditions or over a period of time. Metabolomic studies of F. graminearum are just being initiated. Understanding the breadth of metabolites produced during the various phases of the life cycle will contribute to our understanding of disease. In addition, knowledge of the chemical diversity, especially of secondary metabolites, will be useful for ecological studies (e.g. what role these metabolites play in the interaction of F. graminearum with its environment) and for pharmaceutical research. Historically, secondary metabolism has been the object of intense studies in mycotoxigenic fungi but has been limited to individual pathways and products (primarily mycotoxins). A comprehensive metabolomics effort focused on understanding the metabolic characteristics associated with DON biosynthesis is ongoing (K. Hammond-Kosack, personal communication). Similar studies of the range of metabolic products produced by F. graminearum will greatly expand our current knowledge of these processes in this fungus.
The genome sequence provides a tableau from which to select individual genes or groups of genes for functional exploration. Techniques for genetic manipulation are well developed for F. graminearum and have greatly enhanced the ability to use the genome for functional analyses. F. graminearum has highly efficient homologous recombination that can be used for targeted gene replacement. Although it is homothallic, F. graminearum can outcross, which makes it possible to perform genetic analyses (Bowden and Leslie, 1999
Since the genome sequence became available, much of the focus of research has been on identifying genes that function in pathogenicity. Several approaches have been taken to identify these genes, including targeting major signal transduction proteins (Hou et al., 2002
A different approach was taken to identify a lipase involved in virulence. The gene (FGSG_05906) was identified from cDNA analysis of a culture grown on wheat germ oil (Voigt et al., 2005
Before the genome sequence was available, the chemical potential of F. graminearum was poorly understood. In fungi, genes for secondary metabolism and some genes for primary metabolism are clustered (Stadler and Keller, 2008
Prior to sequencing of the genome, F. graminearum was known to produce four polyketide mycotoxins: fusarin C, a red pigment (now identified as aurofusarin), fusaric acid, and zearalenone. The sequence revealed an abundance of polyketide synthase (PKS) genes not originally known to exist, and the availability of the genome sequence allowed the entire set of PKS genes to be identified (Kroken et al., 2003
Of the 19 predicted NRPS genes, three have been functionally analyzed (NPS1, NPS2, and NPS6) and determined to be involved in the synthesis of siderophores, which are involved in sexual development and pathogenicity (Oide et al., 2007
The role of the mycotoxins other than DON in the life cycle is not clear. It is possible that the expression of these genes is important for environmental interactions with other organisms. For instance, evidence suggests that zearalenone affects sexual development (Nelson, 1971
Expression array analyses have been performed on five stages of development during the maturation of the perithecia (Hallen et al., 2007
Conidial germination of F. graminearum was followed both microscopically and through gene expression changes using the Affymetrix GeneChip (Seong et al., 2008
In studies of plant disease, the emphasis frequently is on the host, in the belief that understanding the host response will lead to the greatest impact on disease control. This approach has been influenced largely by the traditional approach to breeding for resistance and has, in many cases, been very effective. Another approach to the control of disease has been to use broad-spectrum pesticides, but often with only superficial knowledge of the specific life cycles of the pathogens. The pathogen F. graminearum exemplifies the difficulty of developing effective control by either of these means. Breeding for strong resistance has not been particularly effective in wheat. Moderate resistance has been associated with the Sumai 3 genotype (for review, see Mesterhazy, 2003 The approaches outlined above have begun to identify those genes that can be used to arrest the life cycle. Strikingly, genomic sequencing has revealed that approximately 30% of the predicted genes in filamentous fungi are unique to fungi. This large number of genes provides the greatest potential for identifying controls that uniquely target fungi. These genes need to be examined functionally to determine each of their roles in the life cycle. This knowledge can be used to develop chemical control, modify culture practices, or genetically engineer crops for disease resistance.
The agricultural field is an ecosystem dominated by one plant species and manipulated by chemicals and physical disturbance. However, a microbial community as well as other flora and fauna are parts of this ecosystem. Understanding ecosystem interactions is important for the long-term sustainability of agriculture. The genome sequence of F. graminearum is one tool that can help us elucidate the ecological potential of this species. Genomes of several other Fusarium species (F. verticillioides [sexual stage, Gibberella moniliformis], F. oxysporum [asexual], and F. solani [sexual stage, Nectria haematococca]) have recently also been sequenced. These species illustrate the diversity of lifestyles within this group of phytopathogenic species. To understand what shapes the genomes of the pathogenic fungi, they must also be studied in the context of genomes of the host plants, endophytic and saprobic fungi and bacteria that may also colonize the host tissue, and soil microbes that will be encountered in crop debris. The release of the maize and wheat genome sequences in the future will be a critical step toward this goal. Expression studies of the response of wheat and barley to F. graminearum have already been initiated (Kruger et al., 2002
Genetic changes in one species in an agricultural ecosystem can affect other species in the system. In the future, integration of transcriptome, proteome, metabolome, and functional analyses for fungi of different lifestyles (e.g. saprotrophs, biotrophs, necrotrophs, plant pathogens, and animal pathogens) will affect our understanding of the commonalities and differences among all of these niches (Raes and Bork, 2008
The international community of researchers working on F. graminearum has contributed to interpreting and annotating the genome sequence. Bruce Birren, Christina Cuomo, and colleagues at the Broad Institute performed the genome sequencing and annotation. H. Corby Kistler, Jin-Rong Xu, and Ulrich Güldener are collaborators involved in genome analysis and establishing the Affymetrix GeneChip. The thoughtful comments of an anonymous reviewer are appreciated. Figure 1 was rendered by Marlene Cameron. The sequencing of the genome was supported by the National Research Initiative of the U.S. Department of Agriculture Cooperative State Research, Education, and Extension Service (grant number 2002–35600–12782 to B. Birren, H.C. Kistler, J.-R. Xu, and F.T.). Received September 10, 2008; accepted November 6, 2008; published January 7, 2009.
The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Frances Trail (trail{at}msu.edu). www.plantphysiol.org/cgi/doi/10.1104/pp.108.129684
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