Hee-Kyoung Kim

Evaluation of Potential Reference Genes for Quantitative RT-PCR Analysis in Fusarium graminearum under Different Culture Conditions

Department of Medical Biotehcnology, Soonchunhyang University, Asan 336-745, Korea(Received on October 25, 2011; Accepted on November 2, 2011)The filamentous fungus Fusarium graminearum is animportant cereal pathogen. Although quantitative real-time PCR (qRT-PCR) is commonly used to analyze theexpression of important fungal genes, no detailedvalidation of reference genes for the normalization ofqRT-PCR data has been performed in this fungus.Here, we evaluated 15 candidate genes as references,including those previously described as housekeepinggenes and those selected from the whole transcriptomesequencing data. By a combination of three statisticalalgorithms (BestKeeper, geNorm, and NormFinder),the variation in the expression of these genes wasassessed under different culture conditions that favoredmycelial growth, sexual development, and trichothecenemycotoxin production. When favoring mycelial growth,GzFLO and GzUBH expression were most stable incomplete medium. Both EF1A and GzRPS16 expressionwere relatively stable under all conditions on carrotagar, including mycelial growth and the subsequentperithecial induction stage. These two genes were alsomost stable during trichothecene production. For thecombined data set, GzUBH and EF1A were selected asthe most stable. Thus, these genes are suitable referencegenes for accurate normalization of qRT-PCR data forgene expression analyses of F. graminearum and otherrelated fungi. Keywords : Fusarium graminearum, gene expression,quantitative real-time PCR, reference genesQuantitative real-time PCR (qRT-PCR) is the most sensi-tive and specific method for quantifying mRNA expressionlevels of individual target genes of interest. qRT-PCRexpression analysis has several advantages over otherconventional methods, but requires data normalization withappropriate reference gene(s) whose expression should beunaffected throughout the study conditions (Anderson etal., 2004; Bustin et al., 2004; Gutierrez et al., 2008). Severalhousekeeping genes involved in basic cellular functions,such as ribosomal genes, and those encoding actin, beta-tubulin (BTUB), translation elongation factor (EF1), andglyceraldehyde-3-phosphate dehydrogenase (GAPDH) havebeen used as reference genes for qRT-PCR in humans andother model organisms. However, several studies havedemonstrated that some of these traditional housekeepinggenes are unsuitable references because their expressionlevels vary under certain conditions (Czechowski et al.,2005; Dheda et al., 2004; Lee et al., 2002; Suzuki et al.,2000). Therefore, it is necessary to evaluate candidatereference genes for qRT-PCR expression analysis underspecific experimental conditions in the organism to bestudied. The filamentous fungus Fusarium graminearum (telo-morph: Gibberella zeae) is an important cereal pathogen,and produces mycotoxins that are harmful to humans andanimals (Desjardins and Proctor, 2007; McMullen et al.,1997). Complete genome sequencing of F. graminearum(Cuomo et al., 2007) has allowed for genome-wide expre-ssion profiling using DNA microarrays under variousdevelopmental and physiological conditions, such as my-celial growth (Guldener et al., 2006) sexual development(Hallen et al., 2007), germination (Seong et al., 2008) andpathogenesis (Guldener et al., 2006; Stephens et al., 2008).Although the microarray data in these studies were notvalidated by qRT-PCR, it has become the most commonmethod to obtain specific expression patterns of genesidentified from gene expression profiles (Chen et al., 2011;Liu et al., 2011; Pandolfi et al., 2010) or functional studies(Lee et al., 2009; Lysoe et al., 2009). However, theexpression stabilities of the housekeeping genes used asreferences for qRT-PCR analysis in even these studies havenot been properly validated. The objective of this study was to identify F. gramine-arum reference genes suitable for normalization of qRT-PCR data under different conditions such as mycelialgrowth, sexual development, and mycotoxin production.We selected 15 candidate references, including the commonhousekeeping genes used in previous studies (Chen et al.,2011; Lee et al., 2009; Liu et al., 2011; Lysoe et al., 2009;Pandolfi et al., 2010) and a new set of genes selected from

FgVelB globally regulates sexual reproduction, mycotoxin production and pathogenicity in the cereal pathogen Fusarium graminearum.

The velvet genes are conserved in ascomycetous fungi and function as global regulators of differentiation and secondary metabolism. Here, we characterized one of the velvet genes, designated FgVelB, in the plant-pathogenic fungus Fusarium graminearum, which causes fusarium head blight in cereals and produces mycotoxins within plants. FgVelB-deleted (ΔFgVelB) strains produced fewer aerial mycelia with less pigmentation than those of the wild-type (WT) during vegetative growth. Under sexual development conditions, the ΔFgVelB strains produced no fruiting bodies but retained male fertility, and conidiation was threefold higher compared with the WT strain. Production of trichothecene and zearalenone was dramatically reduced compared with the WT strain. In addition, the ΔFgVelB strains were incapable of colonizing host plant tissues. Transcript analyses revealed that FgVelB was highly expressed during the sexual development stage, and may be regulated by a mitogen-activated protein kinase cascade. Microarray analysis showed that FgVelB affects regulatory pathways mediated by the mating-type loci and a G-protein alpha subunit, as well as primary and secondary metabolism. These results suggest that FgVelB has diverse biological functions, probably by acting as a member of a possible velvet protein complex, although identification of the FgVelB-FgVeA complex and the determination of its roles require further investigation.

A putative pheromone signaling pathway is dispensable for self-fertility in the homothallic ascomycete Gibberella zeae.

Gibberella zeae, a homothallic ascomycetous fungus, does not seek a partner for mating. Here, we focused on the role(s) of putative pheromone and receptor genes during sexual development in G. zeae. Orthologs of two pheromone precursor genes (GzPPG1 and GzPPG2), and their cognate receptor genes (GzPRE2 and GzPRE1) were transcribed during sexual development. The expression of these genes was controlled by the mating-type (MAT) locus and a MAP kinase gene, but not in a MAT-specific manner. Targeted gene deletion and subsequent outcrosses generated G. zeae strains lacking these putative pheromone/receptor genes in various combinations (from single to quadruple deletions). All G. zeae deletion strains were similar to the self-fertile progenitor in both male- and female fertility and other traits. Sometimes, the deletions including DeltaGzPPG1;DeltaGzPRE2 caused increased numbers of immature perithecia. Taken together, it is clear that these putative pheromones/receptors play a non-essential role in the sexual development of G. zeae.

Functional Roles of FgLaeA in Controlling Secondary Metabolism, Sexual Development, and Virulence in Fusarium graminearum

Fusarium graminearum, the causal agent of Fusarium head blight in cereal crops, produces mycotoxins such as trichothecenes and zearalenone in infected plants. Here, we focused on the function of FgLaeA in F. graminearum, a homolog of Aspergillus nidulans LaeA encoding the global regulator for both secondary metabolism and sexual development. Prior to gene analysis, we constructed a novel luciferase reporter system consisting of a transgenic F. graminearum strain expressing a firefly luciferase gene under control of the promoter for either TRI6 or ZEB2 controlling the biosynthesis of these mycotoxins. Targeted deletion of FgLaeA led to a dramatic reduction of luminescence in reporter strains, indicating that FgLaeA controls the expression of these transcription factors in F. graminearum; reduced toxin accumulation was further confirmed by GC-MS analysis. Overexpression of FgLaeA caused the increased production of trichothecenes and additional metabolites. RNA seq-analysis revealed that gene member(s) belonging to ∼70% of total tentative gene clusters, which were previously proposed, were differentially expressed in the ΔFgLaeA strain. In addition, ΔFgLaeA strains exhibited an earlier induction of sexual fruiting body (perithecia) formation and drastically reduced disease symptoms in wheat, indicating that FgLaeA seems to negatively control perithecial induction, but positively control virulence toward the host plant. FgLaeA was constitutively expressed under both mycotoxin production and sexual development conditions. Overexpression of a GFP-FgLaeA fusion construct in the ΔFgLaeA strain restored all phenotypic changes to wild-type levels and led to constitutive expression of GFP in both nuclei and cytoplasm at different developmental stages. A split luciferase assay demonstrated that FgLaeA was able to interact with FgVeA, a homolog of A. nidulans veA. Taken together, these results demonstrate that FgLaeA, a member of putative FgVeA complex, controls secondary metabolism, sexual development, and virulence in F. graminearum, although the specific regulation pattern differs from that of LaeA in A. nidulans.

A Large-Scale Functional Analysis of Putative Target Genes of Mating-Type Loci Provides Insight into the Regulation of Sexual Development of the Cereal Pathogen Fusarium graminearum.

Fusarium graminearum, the causal agent of Fusarium head blight in cereal crops, produces sexual progeny (ascospore) as an important overwintering and dissemination strategy for completing the disease cycle. This homothallic ascomycetous species does not require a partner for sexual mating; instead, it carries two opposite mating-type (MAT) loci in a single nucleus to control sexual development. To gain a comprehensive understanding of the regulation of sexual development in F. graminearum, we used in-depth and high-throughput analyses to examine the target genes controlled transcriptionally by two-linked MAT loci (MAT1-1, MAT1-2). We hybridized a genome-wide microarray with total RNAs from F. graminearum mutants that lacked each MAT locus individually or together, and overexpressed MAT1-2-1, as well as their wild-type progenitor, at an early stage of sexual development. A comparison of the gene expression levels revealed a total of 1,245 differentially expressed genes (DEGs) among all of the mutants examined. Among these, genes involved in metabolism, cell wall organization, cellular response to stimuli, cell adhesion, fertilization, development, chromatin silencing, and signal transduction, were significantly enriched. Protein binding microarray analysis revealed the presence of putative core DNA binding sequences (ATTAAT or ATTGTT) for the HMG (high mobility group)-box motif in the MAT1-2-1 protein. Targeted deletion of 106 DEGs revealed 25 genes that were specifically required for sexual development, most of which were regulated transcriptionally by both the MAT1-1 and MAT1-2 loci. Taken together with the expression patterns of key target genes, we propose a regulatory pathway for MAT-mediated sexual development, in which both MAT loci may be activated by several environmental cues via chromatin remodeling and/or signaling pathways, and then control the expression of at least 1,245 target genes during sexual development via regulatory cascades and/or networks involving several downstream transcription factors and a putative RNA interference pathway.

Functional analyses of individual mating-type transcripts at MAT loci in Fusarium graminearum and Fusarium asiaticum.

Members of the Fusarium graminearum species (Fg) complex, which are homothallic ascomycetous species, carry two opposite mating-type (MAT) loci in a single nucleus for controlling sexual development. We investigated the roles of three (MAT1-1-1, MAT1-1-2, and MAT1-1-3) and two (MAT1-2-1 and MAT1-2-3) transcripts located at both loci in representative Fg complex species (F. graminearum and Fusarium asiaticum). In self-fertile F. graminearum strains, the transcript levels of MAT1-1-1, MAT1-2-1, and MAT1-2-3 peaked 2 days after sexual induction (dai) and then remained high until 12 dai, whereas MAT1-1-2 and MAT1-1-3 transcripts reached peak levels between 4 and 8 dai. In contrast, all of the MAT transcripts in self-sterile F. asiaticum strains accumulated at much lower levels than those in F. graminearum during the entire time. Targeted gene deletions confirmed that MAT1-1-1, MAT1-1-2, MAT1-1-3, and MAT1-2-1 were essential for self-fertility in F. graminearum, but MAT1-2-3 was not. All MAT-deleted strains (except ΔMAT1-2-3) produced recombinant perithecia when outcrossed to a self-fertile strain. These results indicate that developmental up-regulation of the individual MAT genes in both a proper fashion and quantity is critical for sexual development, and that alterations in the gene expression could be attributed to the variation in self-sterility among the Fg complex.

Specific PCR Detection of Four Quarantine Fusarium Species in Korea

Fusarium species, a large group of plant pathogens, potentially pose quarantine concerns worldwide. Here, we focus on the development of a method for detecting four Fusarium species in quarantined plants in Korea: F. solani f. sp. cucurbitae, F. stilboides, F. redolens, and F. semitectum var. majus. Species-specific primers were designed from the nucleotide sequences of either the translation elongation factor-1 alpha (TEF1) gene or RNA polymerase II subunit (RPB2) gene. Two different primer sets derived from TEF1, all specific to F. solani f. sp. cucurbitae, were able to differentiate the two races (1 and 2) of this species. A set of nested primers for each race was designed to confirm the PCR results. Similarly, two primer sets derived from RPB2 successfully amplified specific fragments from five F. stilboides isolates grouped within a single phylogenetic clade. A specific TEF1 primer set amplified a DNA fragment from only four of the 12 F. redolens strains examined, which were grouped within a single phylogenetic clade. All of the F. semitectum var. majus isolates could be specifically detected with a single RPB2 primer set. The specificity of the primer sets developed here was confirmed using a total of 130 Fusarium isolates.

Functional Analysis of a Histidine Auxotrophic Mutation in Gibberella zeae

A plant pathogenic fungus, Gibberella zeae (anamorph: Fusarium graminearum), not only generates economic losses by causing disease on cereal grains, but also leads to severe toxicosis in human and animals through the production of mycotoxins in infected plants. Here, we characterized a histidine auxotrophic mutant of G. zeae, designated Z43R1092, which was generated using a restriction enzyme-mediated integration (REMI) procedure. The mutant exhibited pleiotropic phenotypic changes, including a reduction in mycelial growth and virulence and loss of sexual reproduction. Outcrossing analysis confirmed that the histidine auxotrophy is linked to the insertional vector in Z43R1092. Molecular analysis showed that the histidine requirement of Z43R1092 is caused by a disruption of an open reading frame, designated GzHIS7. The deduced product of GzHIS7 encodes a putative enzyme with an N-terminal glutamine amidotransferase and a C-terminal cyclase domain, similar to the Saccharomyces cerevisiae HIS7 required for histidine biosynthesis. The subsequent gene deletion and complementation analyses confirmed the functions of GzHIS7 in G. zeae. This is the first report of the molecular characterization of histidine auxotrophy in G. zeae, and our results demonstrate that correct histidine biosynthesis is essential for virulence, as well as sexual development, in G. zeae. In addition, our results could provide a G. zeae histidine auxotroph as a recipient strain for genetic transformation using this new selectable marker.

A split luciferase complementation assay for studying in vivo protein–protein interactions in filamentous ascomycetes

Protein–protein interactions play important roles in controlling many cellular events. To date, several techniques have been developed for detection of protein–protein interactions in living cells, among which split luciferase complementation has been applied in animal and plant cells. Here, we examined whether the split luciferase assay could be used in filamentous ascomycetes, such as Gibberella zeae and Cochliobolus heterostrophus. The coding sequences of two strongly interacting proteins (the F-box protein, FBP1, and its partner SKP1) in G. zeae, under the control of the cryparin promoter from Cryphonectria parasitica, were translationally fused to the C- and N-terminal fragments of firefly luciferase (luc), respectively. Each fusion product inserted into a fungal transforming vector carrying the gene for resistance to either geneticin or hygromycin B, was transformed into both fungi. We detected complementation of split luciferase proteins driven by interaction of the two fungal proteins with a high luminescence intensity-to-background ratio only in the fungal transformants expressing both N-luc and C-luc fusion constructs. Using this system, we also confirmed a novel protein interaction between transcription factors, GzMCM1 and FST12 in G. zeae, which could hardly be proven by the yeast two-hybrid method. This is the first study demonstrating that monitoring of split luciferase complementation is a sensitive and efficient method of studying in vivo protein–protein interactions in filamentous ascomycetes.

The white collar complex is involved in sexual development of Fusarium graminearum.

Sexual spores (ascospores) of Fusarium graminearum, a homothallic ascomycetous fungus, are believed to be the primary inocula for epidemics of the diseases caused by this species in cereal crops. Based on the light requirement for the formation of fruiting bodies (perithecia) of F. graminearum under laboratory conditions, we explored whether photoreceptors play an important role in sexual development. Here, we evaluated the roles of three genes encoding putative photoreceptors [a phytochrome gene (FgFph) and two white collar genes (FgWc-1 and FgWc-2)] during sexual development in F. graminearum. For functional analyses, we generated transgenic strains lacking one or two genes from the self-fertile Z3643 strain. Unlike the wild-type (WT) and add-back strains, the single deletion strains (ΔFgWc-1 and ΔFgWc-2) produced fertile perithecia under constant light on complete medium (CM, an unfavorable medium for sexual development) as well as on carrot agar (a perithecial induction condition). The expression of mating-type (MAT) genes increased significantly in the gene deletion strains compared to the WT under both conditions. Deletion of FgFph had no significant effect on sexual development or MAT gene expression. In contrast, all of the deletion strains examined did not show significant changes in other traits such as hyphal growth, mycotoxin production, and virulence. A split luciferase assay confirmed the in vivo protein-protein interactions among three photoreceptors along with FgLaeA, a global regulator of secondary metabolism and fungal development. Introduction of an intact copy of the A. nidulans LreA and LreB genes, which are homologs of FgWc-1 and FgWc-2, into the ΔFgWc-1 and ΔFgWc-2 strains, respectively, failed to repress perithecia formation on CM in the gene deletion strains. Taken together, these results demonstrate that FgWc-1 and FgWc-2, two central components of the blue-light sensing system, negatively regulate sexual development in F. graminearum, which differs from the regulation pattern in A. nidulans.