Fng1 is specifically associated with the NuA4 complex and involved in H4 acetylation

In the genome sequence of F. graminearum strain PH-1 (RR1), the predicted gene FGRAMPH1_01G03341 encodes a protein with the N-terminal ING (PF12998) and C-terminal PHD (PF00628) domains based on Pfam database (http://pfam.xfam.org/) (S1 Fig) [22]. It was named FNG1 for F. graminearum ING1 ortholog 1 in this study. Fng1 is orthologous to yeast YNG2. In S. cerevisiae, Yng1 and Yng2, are paralogous subunits of the NuA3 and NuA4 HAT complexes. To determine whether Fng1 functions as Yng1 and/or Yng2, FgSas3 (FGRAMPH1_01G10071) and FgEsa1 (FGRAMPH1_01G14849) were identified as the orthologs of yeast Sas3 and Esa1, the histone acetyltransferases in the NuA3 and NuA4 complexes[5, 6], by homologous alignment. FNG1-GFP and FgESA1-FLAG constructs were individually transformed and co-transformed into the wild-type strain PH-1 to generate PH-1/FNG1-GFP (FG1), PH-1/FgESA1-3×FLAG (EF1), and PH-1/FNG1-GFP FgESA1-3×FLAG (FGEF1) transformants. In total proteins isolated from vegetative hyphae of the FNG1-GFP FgESA1-FLAG transformant (FGEF1) (Table 1) and proteins co-purified with anti-GFP affinity beads, the 61-kD FgEsa1-FLAG band was detected with an anti-FLAG antibody (Fig 1A), indicating the association of Fng1 with FgEsa1 in vivo. We also generated the FgSAS3-FLAG construct and co-transformed it with FNG1-GFP into PH-1. In the resulting FNG1-GFP FgSAS3-FLAG transformant (FGSF1) (Table 1), the 125-kD FgSas3-FLAG band was detected in total proteins but not in proteins co-purified with anti-GFP affinity beads (Fig 1B). Therefore, Fng1 may not interact with FgSas3 or their interaction may be too weak to be detected by co-immunoprecipitation (co-IP) assays.

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Fig 1. Fng1 is associated with FgEsa1 and required for H4 acetylation.

(A). Co-immunoprecipitation (co-IP) assays for the interaction between Fng1 and FgEsa1. Western blots of total protein isolated from transformants expressing the FNG1-GFP and/or FgESA1-3×FLAG (input) and proteins eluted from anti-GFP affinity beads (GFP IP) were detected with anti-FLAG and anti-GFP antibodies. (B). Co-IP assays for the interaction between Fng1 and FgSas3. Western blots of total protein isolated from transformants expressing the FNG1-GFP and/or FgSAS3-3×FLAG (input) and proteins eluted from anti-GFP affinity beads (GFP IP) were detected with anti-FLAG and anti-GFP antibodies. (C). Western blots of total proteins isolated from the wild type (PH-1) and fng1 mutant (FN3) were detected with the anti-H4ac, anti-H3ac, and H2AK5ac antibodies. Detection with the anti-H4, anti-H3, or anti-H2A antibodies was used as loading control. (D). Western blots of total proteins isolated from PH-1 and the fng1 mutant were detected with the antibodies specific for H4K5ac, H4K8ac, H4K12ac, and H4K16ac.

https://doi.org/10.1371/journal.pgen.1009185.g001

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Table 1. The wild type and transformants of Fusarium graminearum used in this study.

https://doi.org/10.1371/journal.pgen.1009185.t001

To characterize the role of Fng1 in histone acetylation, we generated the fng1 deletion mutant (Table 1) in the wild-type strain PH-1 (S2 Fig). When assayed for histone acetylation with the anti-H4ac antibody, the fng1 deletion mutant was significantly reduced in H4 acetylation (Fig 1C) in comparison with the wild type. However, H3 and H2AK5 acetylation were not affected in the fng1 mutant (Fig 1C). We then assayed the acetylation of H4 with the antibodies specific for H4K5ac, H4K8ac, H4K12ac, and H4K16ac. In comparison with the wild type, the fng1 mutant was significantly reduced in the acetylation of H4K5, H4K8, and H4K12 (Fig 1D). The acetylation of H4K16 also was reduced in the mutant, but the wild type also had a relatively low level of H4K16ac (Fig 1D). These results indicate that Fng1 is associated with the NuA4 complex and it is important for H4 acetylation but deletion of FNG1 had no obvious effect on H3 or H2AK5 acetylation.

FNG1 plays a critical role in vegetative growth, conidiation, and sexual reproduction.

In comparison with the wild type, the fng1 deletion mutant was significantly reduced in growth (Table 2) and rarely produced aerial hyphae on PDA plates (Fig 2A). The fng1 mutant also was defective in asexual and sexual reproduction. In CMC cultures, it failed to produce any conidia (Table 2). In mating cultures on carrot agar plates, the fng1 mutant failed to form perithecia at 8 days post-fertilization (dpf) or longer (Fig 2B).

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Fig 2. Assays for the function of Fng1 in growth, reproduction, and pathogenesis.

(A). Three-day-old PDA cultures of the wild type (PH-1), fng1 mutant (FN3), and fng1/FNG1 transformant (FC1). (B). Perithecia from mating cultures of the same set of strains were examined at 8 dpf. Ascospore cirrhi are marked with arrows. Bar, 1 mm. (C). Wheat heads inoculated with the indicated strains were examined for head blight symptoms at 14 days post-inoculation (dpi). Black dots mark the inoculated spikelets. (D). Infection cushions formed by PH-1 and fng1 mutant FN3 on wheat lemma were examined by SEM under ×2,000 amplification at 2 dpi. Bar, 20 μm. (E). Wheat coleoptiles infected with PH-1 and FN3 were examined for invasive hyphae at 3 dpi after staining with Alexa Fluor 488. Bar, 20 μm.

https://doi.org/10.1371/journal.pgen.1009185.g002

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Table 2. Growth, conidiation, and virulence of the fng1 mutant and fng1/FNG1^ΔPHD transformant.

https://doi.org/10.1371/journal.pgen.1009185.t002

For complementation assays, we generated the FNG1-GFP construct and transformed it into the fng1 mutant. The resulting fng1/FNG1-GFP transformants were normal in vegetative growth, conidiation and perithecium formation (Fig 2), indicating that the expression of FNG1-GFP fully complemented the fng1 mutant. Therefore, Fng1 is important for vegetative growth, sexual and asexual reproduction.

FNG1 is important for infection cushion formation and infectious growth

In infection assays with wheat heads, the fng1 deletion mutant failed to cause symptoms on the inoculated kernels (Fig 2C). The fng1 mutant was defective in DON production (S3 Fig) and the expression of the TRI4, TRI5, TRI6, and TRI10 genes important for DON biosynthesis [24] (S4 Fig). It also failed to cause discoloration or necrosis on corn silks (S5 Fig). The fng1/FNG1 complemented transformant was normal in virulence. These results indicate that the fng1 mutant is non-pathogenic and FNG1 is essential for plant infection.

To further characterize the defects of fng1 mutant in plant infection, we examined the formation of infection cushions in infected wheat heads by scanning electron microscopy (SEM). Although the wild-type strain PH-1 developed infection cushions on wheat lemma at 2 days post-inoculation which enable it to penetrate into the plant cell, typical infection cushions were not detected in fng1 mutant-infected samples (Fig 2D), indicating that Fng1 plays a crucial role in infection cushion formation. In infection assays with wheat seedlings [25], the fng1 mutant was only able to infect through wounds in a few samples and had limited infectious growth inside coleoptile cells adjacent to the wound sites (Fig 2E). While abundant invasive hyphae were produced by the wild type inside plant cells at 3 dpi, extensive spreading of invasive hyphae was not observed in wheat coleoptiles inoculated the fng1 mutant (Fig 2E). These results indicated Fng1 may be also important for penetration and infectious growth inside plant tissues.

Fng1 mainly localizes to euchromatin

To determine the localization of Fng1, we transformed the FNG1-GFP fusion construct into the fng1 mutant. In the resulting fng1/FNG1-GFP transformants (Table 1), GFP signals were observed in the nucleus in conidia and vegetative hyphae (Fig 3A), which is consistent with its function as a component of the NuA4 HAT complex in F. graminearum. However, because GFP signals were unevenly distributed in the nucleus (Fig 3A), we generated and transformed the FgNOP1-RFP construct into the fng1/FNG1-GFP transformant FC1. Nop1 is a marker for the nucleolus [26]. When the FNG1-GFP FgNOP1-RFP transformant (FCNR1) (Table 1) was stained with DAPI and examined by epifluorescence microscopy, Fng1-GFP signals were consistently observed adjacent to the FgNop1-RFP signals in the nucleus but they did not overlap (Fig 3B). Fluorescent signals of DAPI-stained DNA also rarely overlapped with Fng1-GFP and FgNop1-RFP signals (Fig 3B). Because the regions stained strongly with DAPI correspond to centromeric heterochromatins [27], our data suggested that Fng1 and its associated NuA4 complex are likely enriched in euchromatin.

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Fig 3. Subcellular localization of Fng1-GFP and chromosomal regions enriched for Fng1-dependent H4ac.

(A). Conidia and germlings of the FNG1-GFP transformant were stained with DAPI and examined by DIC and epifluorescence microscopy. Bar, 5 μm. (B). Germlings of the FNG1-GFP FgNOP1-RFP transformant (FCNR1) were stained with DAPI and examined by DIC and epifluorescence microscopy. Bar, 5 μm. The lower panels are close-up view of the indicated nuclei. (C). The distribution of DNA sequences co-immunoprecipitated with the anti-H4ac antibody in the wild-type strain PH-1 and fng1 mutant (chromosomes 1–4) was compared with chromosomal regions enriched for H3K27me3 and H3K4me2 in the genome of F. graminearum.

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A previous study has reported that H3K4me2 and H3K27me3 are associated with euchromatin and heterochromatin, respectively, in F. graminearum [28]. To verify the association between Fng1 and euchromatin, ChIP-seq data were generated with the anti-H4ac antibody for the wild type and fng1 mutant. Genome-wide comparison showed that H4ac enrichment was significantly reduced or almost lost in the fng1 mutant compared to PH-1 (Fig 3C). Chromosomal regions enriched for Fng1-dependent H4ac had a similar distribution pattern with that of H3K4me2, which is mutually exclusive of H3K27me3 (Fig 3C). These results suggested that Fng1-mediated H4 acetylation is associated with euchromatin.

The PHD finger domain is important but not essential for the function of Fng1

The PHD finger domain present in many chromatin-associated proteins is known to bind with trimethylated lysines on histone tails [16]. To determine the function of the C-terminal PHD domain in FNG1, we generated the FNG1^ΔPHD construct deleted of residues 386–433 (Fig 4A, S6 Fig) and transformed it into the fng1 mutant. The resulting fng1/FNG1^ΔPHD transformant FCPD1 (Table 1) grew slower than the wild-type strain PH-1 on PDA (Fig 4B) and was reduced in conidiation (Table 2). It produced fewer perithecia with normal asci and ascospores on mating plates than the wild type and formed fewer ascospore cirrhi (Fig 4C). Deletion of the PHD domain in FNG1 also affected forcible discharge of ascospores (Fig 4C). In infection assays with flowering wheat heads, the fng1/FNG1^ΔPHD transformant caused typical scab symptoms in the inoculated wheat kernels and was able to spread to nearby spikelets (Fig 4D). Nevertheless, its virulence was reduced by 70% compared with PH-1 (Table 2). These results indicate that the PHD finger domain is important but not essential for the function of Fng1.

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Fig 4. The effects of PHD domain deletion on FNG1 functions.

(A). Schematic drawing of the Fng1 protein with the ING and PHD domains indicated by red arrow. (B). Three-day-old PDA cultures of PH-1 and fng1/FNG1^ΔPHD transformant (FCPD1). (C). Mating cultures were examined for perithecium formation (left), ascospore discharge (middle), and asci with ascospores (right) at 8 dpf. Ascospore cirrhi are indicated by arrows. White bar, 1 mm; Black bar, 20 μm. (D). Wheat heads inoculated with the indicated strains were examined for head blight symptoms at 14 dpi. Black dots mark the inoculated spikelets. (E). Corn silks inoculated with culture blocks were photographed at 5 dpi.

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Spontaneous suppressors of the fng1 mutant

The fng1 mutant was unstable and often formed fast-growing sectors on the edge of colonies that had limited growth on PDA plates after incubation for two weeks (Fig 5A). A total of 34 fast-growing sectors were isolated as spontaneous suppressor mutants and categorized into three groups based on average radial growth per day (S1 Table). While eight type I suppressor strains had the fastest growth (>50% of the wild type) and wild-type colony morphology, growth of 15 type II suppressor strains recovered to 35–50% of that of the wild type. The remaining 11 Type III suppressor strains had the slowest growth rate but still grew faster than the fng1 mutant (Fig 5B, S1 Table).

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Fig 5. Spontaneous suppressors of the fng1 mutant.

(A). PDA cultures of the fng1 mutant strains after incubation for more than two weeks. Suppressor strains are indicated by the red arrows. (B). Four-day-old PDA cultures of the wild type (PH-1) and representative suppressor mutants which were divided into three types based on growth rate. (C). Mating cultures of PH-1 and indicated suppressor strains were examined at 8 dpf. Bar, 1 mm. Perithecia are indicated by arrows. (D). Flowering wheat heads were inoculated with PH-1 and indicated suppressor strains, and photographed at 14 dpi. Black dots mark the inoculated spikelets.

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Besides changes in growth rate and colony morphology, all the suppressor mutants were assayed for phenotypes in conidiation, sexual reproduction, plant infection and DON production (Fig 5C and 5D, S1 Table). Most of the suppressor strains, except S22 and S32, produced conidia, but conidiation was reduced in comparison with the wild type (S1 Table). While most of the suppressor mutants were still blocked in perithecium formation, three suppressor mutants (S4, S12 and S29) formed smaller perithecia that lacked asci or ascospores (Fig 5C, S1 Table). In infection assays with wheat heads, similar to the original fng1 mutant, most suppressor strains were non-pathogenic. However, suppressor strains S4, S12, S23, S24, S26, S31, S34, S47, S49 and S52 caused discoloration on the inoculated kernel but failed to spread to neighboring spikelets (Fig 5D, S1 Table). While majority of these suppressor strains still failed to produce DON in LTB (liquid trichothecene biosynthesis) cultures, eight of them (S24, S25, S26, S31, S33, S36, S38, and S46) were partially recovered in DON biosynthesis (S1 Table). These results suggested that those suppressor mutations resulting in faster growth rate often partially rescued conidiation defects of the fng1 mutant. However, none of them resulted in ascospore or ascus development and spreading in infected wheat heads although some of them also rescued the defects of the fng1 mutant in early stage of sexual reproduction and initial plant infection.

Identification of suppressor mutations in components of the RPD3L HDAC complex

The original fng1 mutant and four suppressor strains (S18, S19, S32 and S38) were selected for genome sequencing. Suppressor mutations were identified in FgRPD3 (FGRAMPH1_01G01959), FgSIN3 (FGRAMPH1_01G27415), FgSDS3 (FGRAMPH1_01G02071) and FGRAMPH1_01G22839 (S2 Table). We then amplified and sequenced these four genes in the remaining 30 suppressor strains, and found that another 12, 9, 8, and 1 of them had mutations in the FgRPD3, FgSIN3, FgSDS3, and FGRAMPH1_01G22839 genes, respectively (Table 3). Interestingly, FgRpd3, FgSin3, and FgSds3 are the key subunits of the Rpd3 histone deacetylase (HDAC) complexes (Fig 6A). In S. cerevisiae, the histone deacetylase Rpd3 resides in the Rpd3L (large) and Rpd3S (small) HDAC complexes that differ in functions [29]. Rpd3 and Sin3 belong to both Rpd3L and Rpd3S complexes, but Sds3 is a Rpd3L-specific subunit [30]. Because multiple suppressor strains had mutations in FgSDS3 and they were similar to suppressor strains with mutations in FgRPD3 and FgSIN3 in colony morphology or growth rate, it is likely that mutations in the FgRpd3L HDAC complex were suppressive to the fng1 mutant. Therefore, it is possible that only the RPD3L HDAC complex is associated with the function of Fng1 and NuA4 HAT complex in F. graminearum.

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Fig 6. Suppressors identified in the RPD3 HDAC complex.

(A). Schematic diagrams showing components of the yeast Rpd3L and Rpd3S complexes with orthologs in F. graminearum. (B). Spontaneous suppressor mutations identified in FgRpd3. The histone deacetylase (HD) domain and transcription initiation factor IIF-alpha (TFα) domain are shaded in blue and red. Sequence alignments of the marked region of FgRpd3 with its orthologs from F. oxysporum (Fo), F. verticillioides (Fv), M. oryzae (Mo), N. crassa (Nc), A. nidulans (An), S. cerevisiae (Sc), and S. pombe (Sp). (C). Schematic drawing of FgSin3 and spontaneous suppressor mutations. Sequence alignments of the marked region of FgSin3 with its orthologs from Fo, Fv, Mo, Nc, An, Sc, and Sp. HID, histone deacetylase interacting domain; CD, C-terminal domain. (D). Schematic drawing of FgSds3 and spontaneous suppressor mutations. SLD, Sds3-like domain.

https://doi.org/10.1371/journal.pgen.1009185.g006

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Table 3. Mutations identified in suppressor strains.

https://doi.org/10.1371/journal.pgen.1009185.t003

In total, 32 suppressor strains had suppressor mutations in FgRPD3, FgSIN3, and FgSDS3 genes, including 16 frame-shift, 7 nonsense, and 8 missense mutations (Fig 6B, 6C and 6D). Four of the frame-shift mutations in suppressor strains S1, S29, S37, and S49 had intron splicing defects caused by nucleotide sequence changes at the splicing sites. Suppressor S29 had an A-to-C mutation at the predicted branch point of intron 3 of FgRPD3. RT-PCR analysis indicated an intron retention in this suppressor strain S29, suggesting that the splicing efficiency was significantly reduced (S7 Fig). Suppressor S49 had the AG⁴⁶⁸ to AA mutation that affected the splicing of the first intron of FgSDS3, resulting in the 60-bp intron retention (S8 Fig). Only two suppressor mutations were not in genes that may be related to the Rpd3L HDAC complex. Suppressor strains S22 and S32 had frameshift and nonsense mutations in FGRAMPH1_01G22839 (Table 3) that lacks homologs in the budding or fission yeast and has no known homolog in GenBank.

Twenty-five suppressor strains with >30% growth rate of the wild-type were selected for correlation analysis between their phenotypes and suppressor mutations. In general, suppressor strains with mutations in FgRPD3 and FgSIN3 grew faster than the ones with mutations in FgSDS3 (S1 Table, S9 Fig). However, there were significant variations among suppressor strains with mutations in the same gene (S1 Table, S9 Fig). For examples, among the five suppressor strains with missense mutations in FgRPD3, S47, S4, S12, and S11 had similar growth rate but strain S19 grew much slower (S1 Table). Strain S5 had a slower growth rate than other suppressor strains with frame shift mutations in FgRPD3 (S1 Table,). Although most of the suppressor mutations in FgSIN3 were frame-shift mutations, the two suppressor strains with missense mutation in FgSIN3, S42 and S43, differed significantly in growth rates and colony morphology (S10 Fig). Interestingly, all the suppressor strains that were partially recovered in DON biosynthesis had mutations in FgSDS3.

The growth defect of fng1 mutant is partially rescued by the Y248C mutation and C-terminal truncation of FgRpd3

Among the mutations in the FgRPD3 HDAC gene, all six missense mutations are in the histone deacetylase (HD) domain(PF00850), including the Y248C mutation identified in suppressor S12 (Fig 6B). We also identified six frame-shift mutations resulting in the truncation of the TFα domain (PF05793) at the C-terminus of FgRpd3, including the P480fs mutation identified in suppressor S5. The Y248C and P480fs mutations were selected for verification because sequence alignment revealed that Y248 is well conserved in Rpd3 orthologs and frame-shift mutation at P480 likely affects the function of FgRpd3 by disrupting the TFα domain (Fig 6B).

To determine the effect of Y248C mutation, the FgRPD3^Y248C mutant allele was generated and used to replace the FgRPD3 allele. The resulting transformant RP12 (Table 1) grew slower than the wild type (Fig 7A), indicating mutations occurred at Y248 affected the function of FgRpd3 in growth. We then used the gene replacement approach to delete FNG1 in the FgRPD3^Y248C transformant RP12. Similar to the suppressor strain S12, the fng1 FgRPD3^Y248C transformant (Table 1) grew faster than the fng1 mutant (Fig 7A) and had normal H4 acetylation levels (Fig 7B).

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Fig 7. Mutations in FgRPD3 suppressive to the growth defects of the fng1 mutant.

(A). Three-day-old PDA cultures of wild type (PH-1), fng1 mutant (FN3), FgRPD3^Y248C (RP12), fng1 FgRPD3^Y248C (FRP12), and S12. (B). Western blots of total proteins isolated from the indicated strains were detected with the anti-H4ac antibody. Detection with the anti-H4 antibody was used as a loading control. (C). Three-day-old PDA cultures of PH-1, FN3, FgRPD3^Δ480–649 (RF5), fng1 FgRPD3^Δ480–649 (FRF5), and S5. (D). Western blots of total proteins isolated from the indicated strains were detected with the anti-H4ac antibody. Detection with the anti-H4 antibody was used as a loading control.

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To verify the suppressive effects of these frameshift mutations, we replaced the original FgRPD3 allele with FgRPD3^Δ480–649 to disrupt the TFα domain. The resulting FgRPD3^Δ480–649 transformant RF5 (Table 1) was only slightly reduced in growth rate (Fig 7C). We also generated the fng1 FgRPD3^Δ480–649 mutant (Table 1) by targeted deletion of FNG1 in the FgRPD3^Δ480–649 transformant. The fng1 FgRPD3^Δ480–649 mutant had a growth rate (Fig 7C) and H4 acetylation level (Fig 7D) similar to suppressor strain S5. These results indicate that frameshift mutations in FgRpd3 resulting in truncations of the TFα domain had little effect on vegetative growth but partially rescued the growth defects of the fng1 mutant.

FgRpd3 co-localizes with Fng1 and negatively impacts H4 acetylation

To further determine the relationship between Fng1 and FgRpd3, we first generated the FgRPD3-RFP fusion construct and transformed it into the fng1/FNG1-GFP strain FC1 (Table 1). In the resulting transformant fng1/FNG1-GFP FgRPD3-RFP (FCRR1) (Table 1), both FgRpd3-RFP and Fng1-GFP proteins accumulated in the nucleus (Fig 8A). Close examination of germ tubes in transformant FCRR1 showed that the FgRpd3-RFP and Fng1-GFP signals overlapped in the nucleus, probably in euchromatin (Fig 8A), indicating a high degree of co-localization.

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Fig 8. Localization of FgRpd3 and phenotypes of the Fgrpd3 deletion mutant.

(A). Germlings of the FNG1-GFP FgRPD3-RFP transformant (FCRR1) were examined by DIC and epifluorescence microscopy. The lower panels are close-up view of the indicated nuclei. Bar, 5 μm. (B). Three-day-old PDA cultures of PH-1, fng1 mutant (FN3), and Fgrpd3 mutant (RP2). (C). 8 days post-fertilization (dpf) mating cultures of the indicated strains. Bar, 1 mm. (D). Flowering wheat heads inoculated with PH-1, FN3, and RP2 were photographed at 14 dpi. Black dots mark the inoculated spikelets. (E). Western blots of total proteins isolated from PH-1, FN3, and RP2 were detected with an anti-H4ac antibody. Detection with the anti-H4 antibody was used as a loading control.

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We then generated the Fgrpd3 deletion mutant by gene replacement (Table 1, S2 Fig). The Fgrpd3 mutant had severe growth defects (Fig 8B) and failed to form perithecia on mating plates (Fig 8C) and was non-pathogenic in infection assays with wheat heads (Fig 8D). However, the H4 acetylation level was significantly increased in the Fgrpd3 mutant (Fig 8E), indicating that FgRPD3 negatively regulates the acetylation of H4.

Mutations in FgSin3 also suppress the growth defects of the fng1 mutant

FgSin3 and FgSds3 are two other main subunits of the FgRPD3L histone deacetylase complex. Ten mutations identified in FgSIN3 include eight non-sense or frameshift mutations and two missense mutations (Fig 6C). Because four nonsense mutations occured in the N-terminal region of FgSIN3 (Fig 6C), we attempted multiple times to generate the Fgsin3 deletion mutant. Unfortunately, no Fgsin3 mutant was identified after screening transformants from repeated transformations, suggesting that FgSIN3 is an essential gene in F. graminearum. Based on published RNA-seq data [25, 31], we found that FgSIN3 has two transcripts with alternative transcript initiation sites (Fig 9A). The nonsense mutations in the N-terminal region of FgSIN3 affected the translation of the longer transcript but had no effect on the translation of the shorter transcript. The FgSin3 protein translated from the shorter transcript has the intact histone deacetylase interacting (HID) domain (PF08295) and C-terminal (CD) domain (PF16879) (Fig 9A).

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Fig 9. Mutations in FgSIN3 suppress the growth defect of the fng1 mutant.

(A). Schematic drawing of different alleles of FgSIN3 and its transcripts. The longer (T1) and shorter (T2) transcripts were generated with alternative transcript initiation sites (P1 and P2) but the same termination site (T). While suppressor strain S18 had the non-sense mutation at W1326, the FgSIN3^ΔCT mutant had the C-terminal 180 amino acid residues replaced with the hygromycin phosphotransferase (hph) cassette. HID, histone deacetylase-interacting domain; CD, C-terminal domain. (B). Three-day-old PDA cultures of wild type (PH-1), fng1 mutant (FN3), FgSIN3^ΔCT (SIS18), fng1 FgSIN3^ΔCT (FSIS18), and suppressor strain S18. (C). Western blots of total proteins isolated from the indicated strains were detected with an anti-H4ac antibody. Detection with the anti-H4 antibody was used as a loading control.

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The FgSIN3 gene also had three nonsense mutations that resulted in the truncation of the CD domain (Fig 6C). To verify the suppressive effect of mutations, we used the gene replacement approach to delete the C-terminal 180 amino acid residues (CT, 1326–1505 aa) of FgSIN3 (Fig 9A) to mimic the nonsense mutation at W1326 in suppressor S18. The resulting FgSIN3^ΔCT transformant SIS18 (Table 1) was defective in vegetative growth, suggesting the importance of the C-terminus for FgSin3 function (Fig 9B). We then deleted the FNG1 gene in the FgSIN3^ΔCT transformant SIS18. The resulting fng1 FgSIN3^ΔCT mutant (Table 1) was partially rescued in the growth defect of fng1 (Fig 9B) and increased in the H4 acetylation level (Fig 9C), confirming the suppressive effect of truncation of the C-terminal 180 aa of FgSIN3 on the fng1 mutant.

Null mutation in Rpd3L-specific subunit FgSds3 is suppressive to the fng1 mutant

Among the nine suppressor strains with mutations in FgSDS3, six (S24, S26, S31, S33, S36 and S46) had frame shift mutations and one (S38) had a C³¹⁰GA to TGA nonsense mutation at residue R104 (Fig 6D) that disrupted the Sds3-like domain (SLD) (PF08598). To investigate the relationship between Fng1 and FgSds3, we first used the gene replacement approach to generate the FgSDS3^N103 transformant SD38 (Table 1) in which all but the N-terminal 104 amino acid residues were deleted (Fig 10A) to mimic the nonsense mutation in suppressor strain S38. The FgSDS3^N103 mutant (Table 1) was reduced in growth in comparison with the wild type and had abnormal colony morphology (Fig 10B). We then deleted the FNG1 gene in the FgSDS3^N103 mutant SD38. The resulting fng1 FgSDS3^N103 mutant FSD38 (Table 1) had similar growth defects (Fig 10B) and H4 acetylation level with suppressor strain S38 (Fig 10C), suggesting that the nonsense mutation at R104 of FgSDS3 partially rescued the defects of the fng1 deletion mutant.

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Fig 10. Null mutations in FgSDS3 suppress the growth defect of the fng1 mutant.

(A). Schematic drawing of different alleles of FgSDS3. In suppressor strain S38, the nonsense mutation at R104 resulted in the truncation of part of the SLD (sds3-like domain) and the rest of FgSds3 protein. While the entire FgSDS3 gene was deleted in the Fgsds3 deletion, only the region after R104 was replaced with the hph cassette in the FgSDS3^N103 mutant. (B). Three-day-old PDA cultures of PH-1, FN3, FgSDS3^N103 (SD38), fng1 FgSDS3^N103 (FSD38), and suppressor strain S38. (C). Western blots of total proteins isolated from the indicated strains were detected with an anti-H4ac antibody. Detection with the anti-H4 antibody was used as a loading control. (D). Three-day-old PDA cultures of the wild type (PH-1), Fgsds3 mutant (SD2), and Fgsds3/FgSDS3 transformant (SC1). (E). Germlings of the FgSDS3-GFP FgRPD3-RFP transformant (SCRR1) were examined by DIC and epifluorescence microscopy. The lower panels are close-up view of the indicated nuclei. Bar, 5 μm.

https://doi.org/10.1371/journal.pgen.1009185.g010

Because the FgSDS3^N103 allele has only the N-terminal 103 residues (Fig 10A), we also generated the gene replacement mutants deleted of the entire FgSDS3 gene (Table 1, S2 Fig). The Fgsds3 deletion mutant had similar phenotypes with the FgSDS3^N103 mutant but the Fgsds3/FgSDS3-GFP complemented transformants were normal in vegetative growth (Fig 10D). Therefore, it is likely that the null mutations in FgSDS3 are suppressive to the fng1 mutant. In fact, all the mutations identified in FgSDS3 in this study were nonsense or frameshift mutations. We also transformed the FgRPD3-RFP fusion construct into the Fgsds3/FgSDS3-GFP strain SC1 (Table 1). In the resulting transformant Fgsds3/FgSDS3-GFP FgRPD3-RFP (SCRR1), both FgRpd3-RFP and FgSds3-GFP signals were observed in the nucleus (Fig 10E). The overlapping distribution of FgRpd3-RFP and FgSds3-GFP signals indicated that FgSds3 likely colocalizes with FgRpd3 to the FgRpd3 HDAC complex in F. graminearum.

Deletion of FNG1 affects H4Ac in euchromatin and the expression of over 3,000 genes

Because histone acetylation is associated with gene expression, we used the RNA-seq approach to identify genes affected by deletion of FNG1. RNA samples were isolated from hyphae of the wild type and fng1 mutant harvested from YEPD cultures at 24 h. In comparison with the wild type, 2039 differentially expressed genes (DEGs) were down-regulated over 2-fold in the fng1 mutant (Fig 11A). The expression of 1507 DEGs, including two histone methyltransferase genes, KMT6 [28] and FgSET1 (FGRAMPH1_01G24837), were significantly increased in the fng1 mutant (Fig 11A, S3 Table), indicating that Fng1 may negatively regulate their transcription. Increased transcription levels of KMT6 and FgSET1 likely resulted in higher H3K27 and H3K4 methylation. Interestingly, a number of genes including FGRAMPH1_01G02359, FGRAMPH1_01G02645, FGRAMPH1_01G04153, FGRAMPH1_01G11343, FGRAMPH1_01G17415, FGRAMPH1_01G18549, FGRAMPH1_01G19861, FGRAMPH1_01G26281, and FGRAMPH1_01G07387 that were specifically or highly expressed during sexual reproduction in the wild type based published RNA-seq data [31] were expressed in the hyphae of the fng1 mutant. FGRAMPH1_01G07387 is orthologous to Neurospora crassa SAD-3 that encodes a helicase required for ascospore development, RNAi-induced heterochromatin assembly, and meiotic silencing by unpaired DNA (MSUD) [32]. FGRAMPH1_01G02645 is the Puk1 protein kinase that plays a specific role during ascosporogenesis in filamentous ascomycetes but lacks a distinct ortholog in the budding and fission yeast [31]. The improper expression of SAD3, PUK1, and other genes that function specifically during sexual reproduction in vegetative hyphae may cause defects in hyphal growth.

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Fig 11. RNA-seq analysis of fng1 mutant and suppressor strains S12 and S38.

(A). Venn diagram showing the numbers of genes down-regulated (left panel) and up-regulated (right panel) in the fng1 mutant, suppressor strain S12 and suppressor strain S38. (B). GO enrichment analysis of the down-regulated (DR12-38, left panel) and up-regulated (UR12-38, right panel) genes in fng1 mutant and recovered in both suppressor strains S12 and S38. BP, MF, and CC stand for biological process, molecular function, and cellular component, respectively. (C). Pie chart showing the proportion of genes (DR12-38 and UR12-38) with and without orthologs in budding yeast.

https://doi.org/10.1371/journal.pgen.1009185.g011

To determine the relationship between genes with altered expression levels in the Fng1 mutant and Fng1-dependent H4Ac, we compared their distribution on four chromosomes. For the 2039 down-regulated DEGs in the mutant, only 14.2% of them are in chromosomal regions enriched for Fng1-dependent H4Ac but 55.9% of them are in chromosomal regions enriched for H3K27me3 (S11 Fig). Among the DEGs up-regulated in the fng1 mutant, 22.7% of them are in chromosomal regions deprived of Fng1-dependent H4Ac but 41.8% are in regions enriched for H3K4me2 (S11 Fig). These results suggested that many genes with altered expression in the fng1 mutant were not directly regulated by Fng1-dependent H4Ac in F. graminearum. Defects in histone acetylation are known to indirectly regulate gene expression by affecting histone methylation or other epigenetic factors [33]. In the fng1 mutant the upregulation of genes like KMT6 (2.37-fold) and FgSET1 (1.93-fold) that are important for the methylation of H3K27 and H3K4 [28] may indirectly affect gene expression in the F. graminearum.

Mutations in suppressor strains S12 and S38 rescue the expression of many DEGS in the fng1 mutant

To determine changes in expression profiles in spontaneous suppressors of the fng1 mutant, RNA samples were isolated from suppressor strains S12 and S38 for RNA-seq analysis. While suppressor strain S12 had the Y248C missense mutation at a well conserved residue inside the HD domain of FgRpd3, S38 had a nonsense mutation at R104* of FgSds3. Among the genes with over 2-fold reduction in the fng1 mutant, 781 of them had their expression increased to the wild-type levels in both suppressor strains S12 and S38 (Fig 11A). GO enrichment analysis showed that those 781 genes were enriched for genes involved in metabolic process, RNA biosynthetic process, transcription, and regulation of gene expression (Fig 11B). A number of them, such as small GTPase RAB7 [34], isocitrate lyase GzICL1 [35], and two cytochrome P450 monooxygenase genes (FGRAMPH1_01G04233 and FGRAMPH1_01G08139) [36], are known to be important for vegetative growth in F. graminearum. Down-regulation of these genes may directly affect hyphal growth in the fng1 mutant.

Among the 1507 genes that were up-regulated over 2-fold in the fng1 mutant, 590 of them had normal expression levels in suppressor strains S12 and S38 (Fig 11A). Those 590 genes are enriched for genes involved in preribosome, nucleolus, ncRNA metabolic process, RNA processing, intracellular organelle lumen, and membrane-enclosed lumen (Fig 11B). The recovery to their normal expression levels for genes with detrimental effects due to overexpression in suppressor strains S12 and S38 may also contribute to the partial rescue of growth. For examples, FGRAMPH1_01G11303 and FGRAMPH1_01G09871 orthologous to yeast ERG6 and SRS2, respectively, had the wild-type expression level but upregulated over 2-fold in the fng1 mutant. In S. cerevisiae, overexpression of SRS2 [37] or ERG6 [38] is detrimental to cell growth. Interestingly, 88.6% of the genes that were down-regulated in the fng1 mutant but recovered to normal expression in both S12 and S38 have no homologs in the budding yeast (Fig 11C). Even for the genes up-regulated in the fng1 mutant, 64.9% of them with normal expression in S12 and S38 have no homologs in S. cerevisiae. Therefore, the majority of those genes co-regulated by Fng1 and the Rpd3 HDAC complex with opposing functions appear to be unique to F. graminearum and other filamentous fungi.

Furthermore, in comparison with the wild type, 593 genes were down-regulated in both S12 and S38 but their expression was not affected in the fng1 mutant. We also found 795 genes that were up-regulated in both S12 and S38 but not affected in the fng1 mutant. These results suggested that the Rpd3 HDAC complex may play an important role in regulating the expression of those 1388 genes. However, Fng1 and H4 acetylation are not involved in their transcriptional regulation. On the other hand, we also found that suppressor mutations in S12 and S38 had no effects on the expression of 1290 genes with altered expression levels (over two-fold) in the fng1 mutant (Fig 11A). These results indicate that although Fng1 and the Rpd3 HDAC complex have opposing regulatory effects on H4 acetylation and the expression of 1371 genes, they have distinct functions on regulating other subsets of genes.

Identification of FNG1, FgSAS3, FgESA1, FgRPD3, FgSIN3, and FgSDS3 in F. graminearum

The protein sequences of yeast Yng1 (YOR064C), Yng2 (YHR090C), Sas3 (YBL052C), and Esa1 (YOR244W) were obtained from the Saccharomyces genome database (www.yeastgenome.org) and used to search against the genome database of Fusarium graminearum strain PH-1 (RR1) at EnsemblFungi (fungi.ensembl.org/index.html) by BlastP. The protein sequences of F. graminearum homologs were then used as queries to search against the Saccharomyces genome database for verification. Protein domains were analyzed with Pfam (www.pfam.xfam.org).

Strains and culture conditions

The wild-type F. graminearum strain PH-1 [23] and mutant strains generated in this study were routinely cultured on potato dextrose agar (PDA). PDA cultures grown at 25°C for 3 days were used to assay the average growth per day and colony morphology. Conidiation was determined with conidia harvested from carboxymethyl cellulose (CMC) cultures as described [57]. For sexual reproduction, aerial hyphae on carrot agar cultures were pressed down with 0.1% Tween 20 for self-fertilization and cultured at 25°C under black light (330-400nm). Perithecium formation was examined at 8 days post-fertilization (dpf) [58]. DON production in 7-day-old LTB (liquid trichothecene biosynthesis) cultures was measured using the Beacon DON Plate Kit (Beacon Analytical Systems, USA) [59].

Targeted gene deletion

To generate the gene replacement construct for FNG1 by the split marker approach, the 576-bp upstream and 608-bp downstream flanking sequences of the target genes were amplified with the primer pairs FNG1/1F - FNG1/2R and FNG1/3F - FNG1/4R (S4 Table) by polymerase chain reaction (PCR) from genomic DNA of PH-1. The resulting PCR products were ligated to the hygromycin phosphotransferase (hph) gene cassette under the control of A. nidulans trpC promoter by overlapping PCR and transformed into protoplasts of PH-1 as described [57]. Protoplast preparation and PEG-mediated transformation were performed as described [57]. Hygromycin B (CalBiochem, La Jolla, CA, USA) was added to the final concentration of 300 μg ml^–1 for selection of transformants. Similar approaches were used to generate the Fgrpd3 and Fgsds3 deletion mutants with primers listed in S4 Table.

Plasmid generation

For complementation assays, the full-length FNG1 gene including the 1.2-kb promotor region was amplified with primer pair FNG1 N/F—FNG1 G/R (S4 Table) and co-transformed with XhoI-digested pFL2 (geneticin resistance) into yeast strain XK1-25 as described [60]. The resulting FNG1-GFP construct was verified by sequence analysis and integrated ectopically into the genome of fng1 mutant. Transformants resistant to both hygromycin and geneticin were screened by PCR and examined for GFP signals with an Olympus BX-53 epifluorescence microscopy. The same yeast gap repair approach was used to generate the FNG1^ΔPHD, FgRPD3-RFP, and FgNOP1-RFP constructs with primer pairs FNG1 N/F—FNG1^ΔPHD/R and FNG1^ΔPHD/F—FNG1 UTR/R, FgRPD3 N/F—FgRPD3 R/R, and FgNOP1 N/F—FgNOP1 R/R (S4 Table). The FNG1^ΔPHD construct was transformed into the fng1 mutant to generate the complemented transformants. The FgRPD3-RFP, and FgNOP1-RFP constructs were respectively transformed into the fng1/FNG1-GFP transformant. Transformants resistant to hygromycin, geneticin, and zeocin were verified by PCR and examined for GFP and RFP signals with an Olympus BX-53 epifluorescence microscopy.

Plant infection

Intact flowering wheat heads of cultivar Xiaoyan 22 were inoculated with PDA culture blocks. Infected wheat heads were examined for diseased spikelets at 14 days post-inoculation (dpi) to estimate the disease index. Wheat kernels at the inoculation site were collected and assayed for DON production as described [61]. To assay infection cushion formation, infected lemmas were sampled at 2 dpi, fixed with 4% (vol/vol) glutaraldehyde, and coated with gold-palladium before examination by scanning electron microscopy (SEM) as described [25]. Coleoptiles of 3-day-old seedlings of the wheat cultivar Norm were used for infection assays as described [62]. Briefly, the top 1–2 mm portion of wheat coleoptiles was excised and inoculated over the wound sites with 2 μl of freshly prepared hyphal suspensions. The seedlings were then grown at 25°C with a 12 h light/12 h dark photoperiod. Necrotic lesions on leaf sheaths were stained with Alexa Fluor 488 at 3 dpi and examined with an Olympus BX-53 epifluorescence microscopy.

Analysis of histone acetylation levels

Hyphae were harvested from 24 h YEPD (Yeast extract peptone dextrose) cultures by filtration through two layers of Miracloth (Sigma, USA) and washed with sterile distilled water. Proteins were isolated from vegetative hyphae as described [63]. For Western blot analyses, total proteins were separated on 12.5% SDS-PAGE gels and transferred to nitrocellulose membranes. Acetylation of histone H3 and H4 was detected with the anti-Histone H3ac (K9+K14+K18+K23+K27) (ab47915), anti-Histone H4ac (K5+K8+K12+K16) (ab177790), anti-Histone H4K5ac (ab51997), anti-Histone H4K8ac (ab15823), anti-Histone H4K12ac (ab46983), anti-Histone H4K16ac (ab194352), and anti-Histone H2AK5ac (ab45152) antibodies from Abcam (Cambridge, UK). Detection with the anti-Histone H3 (ab209023, Abcam), anti-Histone H4 (ab10158, Abcam), and anti-Histone H2A (ab188312, Abcam) antibodies was used as the loading controls.

Co-immunoprecipitation assays

To generate the FgSAS3-FLAG fusion construct, a FgSAS3 fragment containing its entire open reading frame (ORF) and native promoter was amplified with primers FgSAS3 N/F and FgSAS3 FLAG/R (S4 Table) and cloned in pFL7 (geneticin resistance) by the yeast gap repair approach [60]. The FgSAS3-FLAG fusion construct recovered from yeast transformants was verified by sequence analysis and transformed individually or co-transformed with FNG1-GFP into the wild-type strain PH-1 to generate the FgSAS3-FLAG and FgSAS3-FLAG FNG1-GFP transformants. Similar approaches were used to generate the FgESA1-FLAG construct that was transformed alone or together with FNG1-GFP into PH-1 to generate the FgESA1-FLAG and FgESA1-FLAG FNG1-GFP transformants. Total proteins were isolated from the resulting transformants as described [63] and the expression of transforming constructs was verified by western blot analysis with the anti-GFP (11814460001, Roche, USA) and anti-FLAG (F9291, Sigma, USA) antibodies. For co-IP assays, total proteins were incubated with anti-GFP affinity beads (SA070001, Smart-lifesciences, China) for 4 h at 4°C. After washing twice, proteins bound to anti-GFP affinity beads were eluted as described [63]. Western blots of total proteins and proteins eluted from anti-GFP affinity beads were detected with the anti-GFP (11814460001, Roche) and anti-FLAG (F9291, Sigma) antibodies. Detection with an anti-Tub2 β-tubulin antibody [64] was used as the loading control.

Spontaneous suppressor strains of the fng1 mutant and whole genome re-sequencing analysis

Fast-growing sectors of the fng1 mutant were transferred with sterile toothpicks to fresh PDA plates. After single spore isolation, each sub-culture of spontaneous suppressors were assayed for defects in growth, conidiation, sexual reproduction and plant infection [46]. To identify mutations in selected suppressor strains, DNA isolated from 24 h hyphae were sequenced by Illumina HiSeq-PE150 at Novogene Bioinformatics Institute (Beijing, China) to 50x coverage with pair-end libraries. The sequence reads were mapped onto the reference genome of strain PH-1 by Bowtie 2.23 [65, 66], and variants were called by SAMtools with the default parameters [67]. Annotation of the mutation sites was performed with Variant Effect Predictor (VEP) [68].

Chromatin immunoprecipitation-sequencing (ChIP-seq) assays

ChIP assays were performed by Wuhan IGENEBOOK Biotechnology (www.igenebook.com) with hyphae harvested from 24 h YEPD cultures of PH-1 and fng1 mutant. In brief, 1 g of hyphae were washed twice in cold 0.01 M PBS buffer (pH 7.4), cross-linked with 1% formaldehyde for 10 min at room temperature, and then quenched by the addition of glycine to the final concentration 125 mmol/L [28]. The resulting samples were resuspended in lysis buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0 and 150 mM NaCl) and sonicated as described [28] to obtain soluble sheared chromatin (average DNA length of 200–500 bp). After immunoprecipitation with an anti-H4ac antibody (Cat# 39026, active motif, USA), DNA was extracted and used to construct sequencing libraries with the INEXTFLEX ChIP-Seq Library Prep Kit (NOVA-514120, Bioo Scientific, USA), and sequenced on Illumina Xten. After filtering out low-quality reads with Fastp [69], clean reads were mapped to the F. graminearum genome by Bowtie 2 [65]. The Picard toolkit was used to remove potential PCR duplicates (broadinstitute.github.io/picard/). The deepTools was used to turn BAM files of aligned reads into bigWig files which could be displayed in Integrative Genomics Viewer (IGV) [70, 71].

Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) assays

RNA samples of the wild type and fng1 mutant were isolated from hyphae of 3-day-old LTB cultures with the Eastep Super Total RNA Extraction Kit (Promega, USA). The FastKing RT Kit (TIANGEN, China) was used to synthesize cDNA and qRT-PCR assays were performed with the CFX96 Real-Time System (Bio-RAD, USA) [72]. Relative expression levels of TRI genes were assayed by qRT-PCR with primers listed in S4 Table using the F. graminearum actin gene FGRAMPH1_01G24551 as the internal control [73].

RNA-seq analysis

Hyphae of PH-1, the fng1 mutant, and two suppressor strains S12 and S38 were harvested from YEPD cultures at 24 h and used for RNA extraction with TRIzol (Invitrogen, USA). RNA-seq libraries were prepared with the NEBNext Ultra Directional RNA Library Prep Kit (NEB, USA) following the manufacturer’s instructions and sequenced with Illumina HiSeq 2500 with the paired-end 2 × 150 bp model at the Novogene Bioinformatics Institute (Beijing, China). For each sample, at least 24 Mb of paired-end reads were obtained. The resulting RNA-seq reads were mapped onto the reference genome of F. graminearum strain PH-1 [23, 66] by HISAT2 [74]. The number of reads (count) mapped to each gene were calculated by featureCounts [75]. Differential expression analysis of genes was performed using the edgeRun package [76] with the exactTest function. Genes with log₂FC (log₂ fold change) greater than 1 and FDR less than 0.05 were regarded as differentially expressed genes. GO enrichment analysis was performed with Blast2GO [77]. The P-values were adjusted with the Benjamini-Hochberg procedure [78] by controlling false discovery rate (FDR) to 0.05. All the Perl, R, and Shell scripts used in this study for sequencing and other analysis were available on GitHub as described [79].