Phenylalanine Ammonia-Lyase: A Key Gene for Color Discrimination of Edible Mushroom Flammulina velutipes

Abstract

In nature; Flammulina velutipes, also known as winter mushrooms, vary in the color of their fruiting bodies, from black, yellow, pale yellow, or beige to white. The purpose of this study was to compare the genome sequences of different colored strains of F. velutipes and to identify variations in the genes associated with fruiting body color. Comparative genomics of six F. velutipes strains revealed 70 white-strain-specific variations, including single nucleotide polymorphisms (SNPs) and insertions/deletions (indels), in the genome sequences. Among them, 36 variations were located in the open reading frames, and only one variation was identified as a mutation with a disruptive in-frame deletion (ΔGCGCAC) within the annotated gene phenylalanine ammonia-lyase 1 (Fvpal1). This mutation was found to cause a deletion, without a frameshift, of two amino acids at positions 112 and 113 (arginine and threonine, respectively) in the Fvpal1 gene of the white strain. Specific primers to detect this mutation were designed, and amplification refractory mutation system (ARMS) polymerase chain reaction (PCR) was performed to evaluate whether the mutation is color specific for the F. velutipes fruiting body. PCR analysis of a total of 95 F. velutipes strains revealed that this mutation was present only in white strains. In addition, monospores of the heterozygous mutant were isolated, and whether this mutation was related to the color of the fruiting body was evaluated by a mating assay. In the mating analysis of monospores with mutations in Fvpal1, it was found that this mutation plays an important role in determining the color of the fruiting body. Furthermore, the deletion (Δ112RT113) in Fvpal1 is located between motifs that play a key role in the catalytic function of FvPAL1. These results suggest that this mutation can be used as an effective marker for the color-specific breeding of F. velutipes, a representative edible mushroom.

Effects of Light on the Fruiting Body Color and Differentially Expressed Genes in Flammulina velutipes

“…We previously identified a phenylalanine ammonia lyase (Fvpal1) gene with a mutation (∆GCGCAC) specific to white F. velutipes strains [25]. Phenylalanine ammonia-lyase facilitates the deamination of L-phenylalanine into trans-cinnamic acid.…”

“…We previously identified a gene related to the fruiting body color of F. velutipes [25]. Comparative genomic analysis of different F. velutipes strains revealed 70 white strainspecific variations, including single-nucleotide polymorphisms and indels, with one mutation causing a deletion in the phenylalanine ammonia-lyase 1 (Fvpal1; EC 4.3.1.24) gene.…”

“…Therefore, in this study, we performed transcriptome analysis of F. velutipes irradiated using red, green, and blue light-emitting diodes (LEDs) to identify the key genes associated with light response and fruiting body color. Additionally, we conducted protein-protein interaction (PPI) network analysis of a previously identified fruiting body color-related gene, Fvpal1 [25], to identify the hub genes. The light-responsive and fruiting body color-related genes identified in this study provide new insights into the light response mechanisms of fungi and may be used as selective markers for color changes in F. velutipes.…”

Homeodomain 1 Genes of the Different HD Subloci of Flammulina velutipes Can Activate the HD Pathway and Are Involved in Mating, Clamp Cell Formation, and Upregulation of FvClp1

“…The basic model of the PR locus comprises a pheromone receptor gene ( STE3 like ) and pheromone precursor ( Pp ) genes. Single pheromone receptor genes are accompanied by one or several pheromone precursor genes in a sublocus, and multiple of such sets can form the PR locus. − Pheromone receptors and pheromones are not self-compatible and interact only with products of different alleles from corresponding subloci. , A divergently transcribed pair of homeodomain1 ( Hd1 ) and homeodomain2 ( Hd2 ) genes constitutes the basic structure of the HD locus in most basidiomycetes, which is often flanked by the Mitochondrial Intermediate Peptidase ( MIP ) gene and the Beta-flanking ( β-fg ) gene. Multiple pairs of Hd genes within the HD locus typically indicate multiple subloci, although this distinction can become confused in cases where more than two Hd genes (i.e., additional, unpaired genes) are part of the same sublocus. ,, The proteins encoded by Hd1 and Hd2 genes can interact to form a functional transcription factor but only if they are encoded by different alleles from a corresponding sublocus. , …”