Flammulina velutipes is a fungus with health and medicinal benefits that has been used for consumption and cultivation in East Asia. F. velutipes is also known to degrade lignocellulose and produce ethanol. The overlapping interests of mushroom production and wood bioconversion make F. velutipes an attractive new model for fungal wood related studies. Here, we present the complete sequence of the F. velutipes genome. This is the first sequenced genome for a commercially produced edible mushroom that also degrades wood. The 35.6-Mb genome contained 12,218 predicted protein-encoding genes and 287 tRNA genes assembled into 11 scaffolds corresponding with the 11 chromosomes of strain KACC42780. The 88.4-kb mitochondrial genome contained 35 genes. Well-developed wood degrading machinery with strong potential for lignin degradation (69 auxiliary activities, formerly FOLymes) and carbohydrate degradation (392 CAZymes), along with 58 alcohol dehydrogenase genes were highly expressed in the mycelium, demonstrating the potential application of this organism to bioethanol production. Thus, the newly uncovered wood degrading capacity and sequential nature of this process in F. velutipes, offer interesting possibilities for more detailed studies on either lignin or (hemi-) cellulose degradation in complex wood substrates. The mutual interest in wood degradation by the mushroom industry and (ligno-)cellulose biomass related industries further increase the significance of F. velutipes as a new model.

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Genome sequence analysis of Xanthomonas oryzae pv. oryzae has revealed a cluster of 12 ORFs that are closely related to the gum gene cluster of Xanthomonas campestris pv. campestris. The gum gene cluster of X. oryzae encodes proteins involved in xanthan production; however, there is little experimental evidence supporting this. In this study, biochemical analyses of xanthan produced by a defined set of X. oryzae gum mutant strains allowed us to preliminarily assign functions to most of the gum gene products: biosynthesis of the pentasaccharide repeating unit for GumD, GumM, GumH, GumK, and GumI, xanthan polymerization and transport for GumB, GumC, GumE, and GumJ, and modification of the pentasaccharide repeating unit for GumF, GumG, and GumL. In addition, we found that the exopolysaccharides are essential but not specific for the virulence of X. oryzae.

Genome sequence analysis of Xanthomonas oryzae pv. oryzae KACC10331 provides insight into the X. oryzae gum gene cluster that is composed of 14 open-reading frames (ORFs), designated gumB, -C, -D, -E, -F, -G, -H, -I, -J, -K, -L, -M, XOO3167, and -N. We analyzed the transcriptional linkage of the X. oryzae gum gene cluster by using RT-PCR. Analyses of the gum gene cluster by RT-PCR with the wild-type and mutant strains, which carried a deletion of the promoter-like region upstream of gumB or an insertion of the rrnB transcriptional terminator into the gumF gene, revealed that the ORFs of this gene cluster were transcribed as polycistronic mRNA, from gumB to gumN, and the secondary promoter was located upstream of gumG. Taken together, these results suggest that the genes of this cluster constitute an operon expressed from overlapping transcripts.

The aims of this study wereto investigate the antifungal activity as a bioactive property of dihydrodehydro-diconiferyl alcohol 9'-O-3-D-glucoside (DDDC9G) and the mode of action(s) involved in its effect. Antifungal susceptibility testing showed that DDDC9G possessed potent antifungal activities toward various fungal strains with almost no hemolytic effect. To understand the antifungal mechanism(s) of DDDC9G, we conducted the following experiments in this study using Candida albicans. Fluorescence experiments using the probe 1,6-eiphenyl-1, 3, 5-hexatriene (DPH) and propidium iodide suggested that DDDC9G perturbed the fungal plasma membrane. Consecutively, the analysis of the transmembrane electrical potential (DeltaPsi) with 3, 3'-dipropylthiadicarbocyanine iodide [DiSC3(5)] and bis-(1,3-dibutylbarbituric acid) trimethine oxonol [DiBAC4(3)] indicated that DDDC9G induced membrane-depolarization. Furthermore, model membrane studies were performed wiith rhodamine-labeled giant unilamellar vesicles (GUVs), calcein encapsulating large unilamellar vesicles (ILUVs), and FITC-dextran (FD) loaded LUVs. These results demonstrated that the antifungal effects of DDDC9G upon the fungal plasma membrane were through the formation of pores with the radii between 0.74 nm and 1.4 nm. Finally, in three dimensional (3D) flow cytometric contour plots, a reduced cell size was observed as a result of osmolarity changes from DDDC9G-induced structural and functional membrane damages.Therefore, the present study suggests that DDDC9G exerts its antifungal effect by damaging the membrane through pore formation in the fungal plasma membrane.