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4. Comprehensive genomic and transcriptomic analysis of polycyclic aromatic hydrocarbon degradation by a mycoremediation fungus, Dentipellis sp. KUC8613

Author

Park, Hongjae, Min, Byoungnam, Jang, Yeongseon, Kim, Jungyeon, Lipzen, Anna, Sharma, Aditi, Andreopoulos, Bill, Johnson, Jenifer, Riley, Robert, Spatafora, Joseph W, Henrissat, Bernard, Kim, Kyoung Heon, Grigoriev, Igor V, Kim, Jae-Jin, and Choi, In-Geol

Subjects
Microbiology, Biological Sciences, Environmental Sciences, Pollution and Contamination, Human Genome, Genetics, Basidiomycota, Biotransformation, Gene Expression Profiling, Genomics, Metabolic Networks and Pathways, Polycyclic Aromatic Hydrocarbons, PAH, Mycoremediation, Dentipellis sp, KUC8613, White rot fungus, Transcriptomics, Dentipellis sp. KUC8613, Biotechnology
Abstract

The environmental accumulation of polycyclic aromatic hydrocarbons (PAHs) is of great concern due to potential carcinogenic and mutagenic risks, as well as their resistance to remediation. While many fungi have been reported to break down PAHs in environments, the details of gene-based metabolic pathways are not yet comprehensively understood. Specifically, the genome-scale transcriptional responses of fungal PAH degradation have rarely been reported. In this study, we report the genomic and transcriptomic basis of PAH bioremediation by a potent fungal degrader, Dentipellis sp. KUC8613. The genome size of this fungus was 36.71 Mbp long encoding 14,320 putative protein-coding genes. The strain efficiently removed more than 90% of 100 mg/l concentration of PAHs within 10 days. The genomic and transcriptomic analysis of this white rot fungus highlights that the strain primarily utilized non-ligninolytic enzymes to remove various PAHs, rather than typical ligninolytic enzymes known for playing important roles in PAH degradation. PAH removal by non-ligninolytic enzymes was initiated by both different PAH-specific and common upregulation of P450s, followed by downstream PAH-transforming enzymes such as epoxide hydrolases, dehydrogenases, FAD-dependent monooxygenases, dioxygenases, and glycosyl- or glutathione transferases. Among the various PAHs, phenanthrene induced a more dynamic transcriptomic response possibly due to its greater cytotoxicity, leading to highly upregulated genes involved in the translocation of PAHs, a defense system against reactive oxygen species, and ATP synthesis. Our genomic and transcriptomic data provide a foundation of understanding regarding the mycoremediation of PAHs and the application of this strain for polluted environments.

Published
2019

8. Detection of RNA Mycoviruses in Wild Strains of Lentinula edodes in Korea

Author

Kim Eunjin, Park Mi-Jeong, Jang Yeongseon, Ryoo Rhim, and Kang-Hyeon Ka

Subjects
lentinula edodes, multiple infection, mushroom, mycovirus, rt-pcr (reverse transcription-polymerase chain reaction), Biology (General), QH301-705.5
Abstract

In general, mycoviruses remain latent and rarely cause visible symptoms in fungal hosts; however, some viral infections have demonstrated abnormal mycelial growth and fruiting body development in commercial macrofungi, including Lentinula edodes. Compared to other cultivated mushrooms, L. edodes is more vulnerable to viral infections as it is still widely cultivated under near-natural conditions. In this study, we investigated whether Korean wild strains of L. edodes were infected by RNA mycoviruses that have previously been reported in other parts of the world (LeSV, LePV1, LeV-HKB, LeNSRV1, and LeNSRV2). Using specific primer sets that target the RNA-dependent RNA polymerase genes of each of the RNA mycovirus, reverse transcription-polymerase chain reaction (RT-PCR) was used to detect viral infection. Viral infection was detected in about 90% of the 112 wild strains that were collected in Korea between 1983 and 2020. Moreover, multiple infections with RNA mycoviruses were detected in strains that had normal fruiting bodies. This work contributes to our understanding of the distribution of RNA mycoviruses in Korea and the impact of multiple viral infections in a single strain of L. edodes.

Published
2021
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19. The genus Wrightoporia in Korea

Author

Jang, Yeongseon, Lee, Sung Wook, Lim, Young Woon, Lee, Jin Sung, Hattori, Tsutomu, Kim, Jae-Jin, and BioStor

Published
2013

24. Novel SarcoscyphaSpecies from National Parks in Korea: Sarcoscypha humidasp. nov.

Author

Cho, Minseo, Heo, Young Mok, Jang, Yeongseon, Kim, Changmu, Kwon, Sun Lul, and Kim, Jae-Jin

Abstract

AbstractSarcoscypha(Sarcoscyphaceae, Pezizales) is a saprobic fungus characterized by the cup or disc-shaped blight red apothecium and oblong to ellipsoid ascospores. The 18 species of Sarcoscyphawere known to occur in Europe, North America, and tropical Asia. However, up to date, only two Sarcoscyphaspecies have been reported in Korea. In this study, novel Sarcoscyphaspecimens were collected from Juwangsan, Odaesan, and Taebaeksan National Parks from September to October in Korea. This species is well distinguished from other Sarcoscyphaspecies according to the molecular and phylogenetic analysis based on internal transcribed spacer (ITS) region. Here, we provided detailed descriptions with illustrations and a phylogenetic tree to report our specimens as novel Sarcoscyphaspecies.

Published
2024
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25. Cloning and Expression Analysis of Bioluminescence Genes in Omphalotus guepiniiformisReveal Stress-Dependent Regulation of Bioluminescence

Author

Park, Mi-Jeong, Kim, Eunjin, Kim, Min-Jun, Jang, Yeongseon, Ryoo, Rhim, and Ka, Kang-Hyeon

Abstract

AbstractBioluminescence is a type of chemiluminescence that arises from a luciferase-catalyzed oxidation reaction of luciferin. Molecular biology and comparative genomics have recently elucidated the genes involved in fungal bioluminescence and the evolutionary history of their clusters. However, most studies on fungal bioluminescence have been limited to observing the changes in light intensity under various conditions. To understand the molecular basis of bioluminescent responses in Omphalotus guepiniiformisunder different environmental conditions, we cloned and sequenced the genes of hispidin synthase, hispidin-3-hydroxylase, and luciferase enzymes, which are pivotal in the fungal bioluminescence pathway. Each gene showed high sequence similarity to that of other luminous fungal species. Furthermore, we investigated their transcriptional changes in response to abiotic stresses. Wound stress enhanced the bioluminescence intensity by increasing the expression of bioluminescence pathway genes, while temperature stress suppressed the bioluminescence intensity viathe non-transcriptional pathway. Our data suggested that O. guepiniiformisregulates bioluminescence to respond differentially to specific environmental stresses. To our knowledge, this is the first study on fungal bioluminescence at the gene expression level. Further studies are required to address the biological and ecological meaning of different bioluminescence responses in changing environments, and O. quepiniiformiscould be a potential model species.

Published
2024
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26. Rational design and engineering of polypeptide/protein vesicles for advanced biological applications.

Author

Shin, Jooyong and Jang, Yeongseon

Abstract

Synthetic vesicles have gained considerable popularity in recent years for numerous biological and medical applications. Among the various types of synthetic vesicles, the utilization of polypeptides and/or proteins as fundamental constituents has garnered significant interest for vesicle construction owing to the unique bio-functionalities inherent in rationally designed amino acid sequences. Especially the incorporation of functional proteins onto the vesicle surface facilitates a wide range of advanced biological applications that are not easily attainable with traditional building blocks, such as lipids and polymers. The main goal of this review is to provide a comprehensive overview of the latest advancements in polypeptide/protein vesicles. Moreover, this review encompasses the rational design and engineering strategies employed in the creation of polypeptide/protein vesicles, including the synthesis of building blocks, the modulation of their self-assembly, as well as their diverse applications. Furthermore, this work includes an in-depth discussion of the key challenges and opportunities associated with polypeptide/protein vesicles, providing valuable insights for future research. By offering an up-to-date review of this burgeoning field of polypeptide/protein vesicle research, this review will shed light on the potential applications of these biomaterials. [ABSTRACT FROM AUTHOR]

Published
2023
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33. Determination and Analysis of Hyper-Variable AMating Types in Wild Strains of Lentinula edodesin Korea

Author

Park, Mi-Jeong, Kim, Eunjin, Jeong, Yeun Sug, Son, Mi-Young, Jang, Yeongseon, and Ka, Kang-Hyeon

Abstract

AbstractThe diversity of Amating type in wild strains of Lentinula edodeswas extensively analyzed to characterize and utilize them for developing new cultivars. One hundred twenty-three Amating type alleles, including 67 newly discovered alleles, were identified from 106 wild strains collected for the past four decades in Korea. Based on previous studies and current findings, a total of 130 Amating type alleles have been found, 124 of which were discovered from wild strains, indicating the hyper-variability of Amating type alleles of L. edodes. About half of the Amating type alleles in wild strains were found in more than two strains, whereas the other half of the alleles were found in only one strain. About 90% of Amating type combinations in dikaryotic wild strains showed a single occurrence. Geographically, diverse Amating type alleles were intensively located in the central region of the Korean peninsula, whereas only allele A17was observed throughout Korea. We also found the conservation of the TCCCAC motif in addition to the previously reported motifs, including ATTGT, ACAAT, and GCGGAG, in the intergenic regions of Amating loci. Sequence comparison among some alleles indicated that accumulated mutation and recombination would contribute to the diversification of Amating type alleles in L. edodes. Our data support the rapid evolution of Amating locus in L. edodes, and would help to understand the characteristics of Amating loci of wild strains in Korea and help to utilize them for developing new cultivars.

Published
2023
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47. Ergothioneine Contents of Shiitake (Lentinula edodes) Fruiting Bodies on Sawdust Media with Different Nitrogen Sources

Author

Park Jiheon, Ryoo Rhim, Park Youngae, Jang Yeongseon, and Ka Kang-Hyeon

Subjects
0301 basic medicine, Ecology, biology, chemistry.chemical_element, Plant Science, biology.organism_classification, High-performance liquid chromatography, Nitrogen, Edible mushroom, 03 medical and health sciences, chemistry.chemical_compound, 030104 developmental biology, Lentinula, chemistry, Ergothioneine, visual_art, visual_art.visual_art_medium, Food science, Sawdust, Ecology, Evolution, Behavior and Systematics
Published
2016

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