Biology subjects

Futagami, T.

Publications and source records attributed to Futagami, T..

4 recordsLinked to original sources

bioRxiv2026

The automated eukaryotic pangenome pipeline EukPan reveals accessory genome differentiation beyond core-gene phylogeny in Aspergillus oryzae

Pangenome analysis reveals recurrent gene-content variation beyond a single reference genome, but its application to eukaryotes is constrained by inconsistent gene annotation. ANNEVO predicts gene models from genome FASTA assemblies without RNA-seq data. We developed EukPan, an automated post-annotation pipeline that standardizes GFF/GTF files, selects representative isoforms, constructs proteomes, infers orthogroups, builds a concatenated single-copy core-protein alignment, and summarizes shared accessory orthogroups while excluding orthogroups detected in only one genome. Applied with ANNEVO to 123 Aspergillus oryzae genomes, EukPan identified 11,245 core and 4,407 shared accessory orthogroups. The core-protein phylogeny broadly recovered the reported A-H classification, whereas accessory-genome analyses clearly separated the 33 group-A strains from the other 90 strains. Directional analysis identified 62 group-A-associated and 158 group-A-depleted orthogroups, with major facilitator superfamily (MFS) transporter and fungal Zn2Cys6 transcription-factor domains prominent in the depleted set. Among 93 orthogroups present in all non-A strains and absent from all group-A strains, 59 mapped to 10 segments of RIB40, the standard A. oryzae reference genome and a non-A (group-F) strain. EukPan therefore enables reproducible, coordinated core- and accessory-pangenome analysis from eukaryotic genome assemblies.

genomics↗

bioRxiv2021

Overexpression of the RNA-binding protein NrdA affects global gene expression and secondary metabolism in Aspergillus species

RNA-binding protein Nrd1 plays a role in RNA polymerase II transcription termination. In this study, we showed that the orthologous NrdA is important in global mRNA expression and secondary metabolism in Aspergillus species. We constructed an nrdA conditional expression strain using the Tet-On system in Aspergillus luchuenesis mut. kawachii. Downregulation of nrdA caused a severe growth defect, indicating that NrdA is essential for the proliferation of A. kawachii. Parallel RNA-sequencing and RNA immunoprecipitation-sequencing analysis identified potential NrdA-interacting transcripts, corresponding to 32% of the predicted protein coding genes of A. kawachii. Subsequent gene ontology analysis suggested that overexpression of NrdA affects the production of secondary metabolites. To clarify this, we constructed NrdA-overexpressing strains of Aspergillus nidulans, Aspergillus fumigatus, and Aspergillus oryzae. Overexpression of NrdA reduced the production of sterigmatocystin and penicillin in A. nidulans, as well as that of helvolic acid and pyripyropene A in A. fumigatus. Moreover, it increased the production of kojic acid and reduced production of penicillin in A. oryzae. These effects were accompanied by almost consistent transcriptional changes in the relevant genes. Collectively, these results suggest that NrdA is the essential RNA-binding protein, which plays a significant role in global gene expression and secondary metabolism in Aspergillus species. IMPORTANCENrd1, a component of the Nrd1-Nab3-Sen1 complex, is an essential RNA-binding protein involved in transcriptional termination in yeast. However, its role in filamentous fungi has not been studied. In this study, we characterized an orthologous NrdA in the Aspergillus species, identified potential NrdA-interacting mRNA, and investigated the effect of overexpression of NrdA on mRNA expression in Aspergillus luchuensis mut. kawachii. The results indicated that NrdA controls global gene expression involved in versatile metabolic pathways, including the secondary metabolic process. We demonstrated that NrdA overexpression significantly affected the production of secondary metabolites in Aspergillus nidulans, Aspergillus oryzae, and Aspergillus fumigatus. Our findings are of importance to the fungal research community because the secondary metabolism is an industrially and clinically important aspect for the Aspergillus species.

microbiology↗

bioRxiv2019

LaeA controls citric acid production through regulation of a citrate exporter encoding cexA in Aspergillus luchuensis mut. kawachii

The putative methyltransferase LaeA is a global regulator of metabolic and development processes in filamentous fungi. We characterized the homologous laeA genes of the white koji fungus Aspergillus luchuensis mut. kawachii (A. kawachii) to determine their role in the hyperproduction of citric acid. The {Delta}laeA strain exhibited a significant reduction in citric acid productivity. Cap-analysis gene expression (CAGE) revealed that laeA is required for the gene expression of a putative citrate exporter encoding cexA, which is critical for citric acid production. The deficit in the productivity of citric acid by the {Delta}laeA strain was rescued by the overexpression of cexA to a level comparable with that of the cexA-overexpressing {Delta}cexA strain. In addition, chromatin immunoprecipitation coupled with quantitative PCR (ChIP-qPCR) analysis indicated that LaeA regulates the expression of cexA via methylation levels of the histones H3K4 and H3K9. These results indicate that LaeA is involved in citric acid production through epigenetic regulation of cexA in A. kawachii.\n\nIMPORTANCEA. kawachii has been traditionally used for production of the distilled spirit shochu in Japan. Citric acid produced by A. kawachii plays an important role in preventing microbial contamination during the shochu fermentation process. This study characterized homologous laeA genes; using CAGE, complementation test, and ChIP-qPCR, it was found that laeA is required for citric acid production though regulation of cexA in A. kawachii. The epigenetic regulation of citrate production elucidated in this study will be useful for controlling the fermentation processes of shochu.

microbiology↗

bioRxiv2018

Mitochondrial citrate transporters CtpA and YhmA are involved in lysine biosynthesis in the white koji fungus, Aspergillus luchuensis mut. kawachii

Aspergillus luchuensis mut. kawachii produces a large amount of citric acid during the process of fermenting shochu, a traditional Japanese distilled spirit. In this study, we characterized A. kawachii CtpA and YhmA, which are homologous to the yeast Saccharomyces cerevisiae mitochondrial citrate transporters Ctp1 and Yhm2, respectively. CtpA and YhmA were purified from A. kawachii and reconstituted into liposomes. The proteoliposomes exhibited only counter-exchange transport activity; CtpA transported citrate using counter substrates especially for cis-aconitate and malate, whereas YhmA transported citrate using a wider variety of counter substrates, including citrate, 2-oxoglutarate, malate, cis-aconitate, and succinate. Disruption of ctpA and yhmA caused deficient hyphal growth and conidia formation with reduced mycelial weight-normalized citrate production. Because we could not obtain a {Delta}ctpA {Delta}yhmA strain, we constructed a ctpA-S conditional expression strain in the {Delta}yhmA background using the Tet-On promoter system. Knockdown of ctpA-S in {Delta}yhmA resulted in a severe growth defect on minimal medium, indicating that double disruption of ctpA and yhmA leads to synthetic lethality; however, we subsequently found that the severe growth defect was relieved by addition of lysine. Our results indicate that CtpA and YhmA are mitochondrial citrate transporters involved in citric acid production and that transport of citrate from mitochondria to the cytosol plays an important role in lysine biogenesis in A. kawachii.\n\nIMPORTANCECitrate transport is believed to play a significant role in citrate production by filamentous fungi; however, details of the process remain unclear. This study characterized two citrate transporters from Aspergillus luchuensis mut. kawachii. Biochemical and gene disruption analyses showed that CtpA and YhmA are mitochondrial citrate transporters required for normal hyphal growth, conidia formation, and citric acid production. In addition, this study provided insights into the links between citrate transport and lysine biosynthesis. The characteristics of fungal citrate transporters elucidated in this study will help expand our understanding of the citrate production mechanism and facilitate the development and optimization of industrial organic acid fermentation processes.

microbiology↗