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- In Silico Intensive Analysis for the E4 Gene Evolution of Human Adenovirus Species D.
- Chanhee Lee, Anyeseu Park, Jeong Yoon Lee
- J. Microbiol. 2024;62(5):409-418. Published online April 30, 2024
- DOI: https://doi.org/10.1007/s12275-024-00132-1
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Abstract
- Adenovirus (Ad) is a ubiquitous pathogen capable of infecting a wide range of animals and humans. Human Adenovirus (HAdV) can cause severe infection, particularly in individuals with compromised immune systems. To date, over 110 types of HAdV have been classified into seven species from A to G, with the majority belonging to the human adenovirus species D (HAdV-D). In the HAdV-D, the most significant factor for the creation of new adenovirus types is homologous recombination between viral genes involved in determining the virus tropism or evading immune system of host cells. The E4 gene, consisting of seven Open Reading Frames (ORFs), plays a role in both the regulation of host cell metabolism and the replication of viral genes. Despite long-term studies, the function of each ORF remains unclear. Based on our updated information, ORF2, ORF3, and ORF4 have been identified as regions with relatively high mutations compared to other ORFs in the E4 gene, through the use of in silico comparative analysis. Additionally, we managed to visualize high mutation sections, previously undetectable at the DNA level, through a powerful amino acid sequence analysis tool known as proteotyping. Our research has revealed the involvement of the E4 gene in the evolution of human adenovirus, and has established accurate sequence information of the E4 gene, laying the groundwork for further research.
- Metabolomic profiling reveals enrichment of cordycepin in senescence process of Cordyceps militaris fruit bodies
- Junsang Oh , Deok-Hyo Yoon , Bhushan Shrestha , Hyung-Kyoon Choi , Gi-Ho Sung
- J. Microbiol. 2019;57(1):54-63. Published online December 29, 2018
- DOI: https://doi.org/10.1007/s12275-019-8486-z
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Abstract
- Cordyceps militaris is a species of Cordyceps that is classified
in the Cordycipitaceae family and is well known in East Asia
as a traditional medicinal mushroom. Its artificial fruit body
has been widely cultivated for commercial use in cosmetics,
functional food, and medicine. To explore the metabolites
associated with fruit body development, we conducted gas
chromatography mass spectrometry (GC-MS) analyses based
on developmental stage, which was divided into the growth
period (stage 1, stage 2, and stage 3) and aging period (stage
4). We detected 39 biochemical metabolites associated with
nucleotide, carbohydrate, and amino acid metabolism. Cordycepin,
one of the representative bioactive compounds in
C. militaris, was significantly enriched in stage 4 of aging period
and is associated with glucose accumulation. The accumulation
of cordycepin in stage 4 of aging period also seems
to be related to the glutamine and glutamic acid pathway. Our
results
also showed enrichment of other bioactive compounds such as mannitol and xylitol in stage 4 of aging period. Our metabolomic profiling based on the developmental stages of C. militaris is useful for exploring bioactive compounds (e.g., cordycepin, mannitol, GABA, and xylitol) that are enriched in stage 4 of aging period and understanding the biosynthetic mechanisms associated with cordycepin production. Through optimization of fruit body cultivation by selecting stage 4 of aging period as a harvesting time, our findings can be utilized in food and medical applications of C. militaris in future.
- Simultaneous Utilization of Two Different Pathways in Degradation of 2,4,6-Trinitrotoluene by White Rot Fungus Irpex lacteus
- Hyoun-Young Kim , Hong-Gyu Song
- J. Microbiol. 2000;38(4):250-254.
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Abstract
- This study confirmed that white rot fungus Irpex lacteus was able to metabolize 2,4,6-trinitrotoluene (TNT) with two different initial transformations. In one metabolic pathway of TNT a nitro group was removed from the aromatic ring of TNT. Hydride-Meisenheimer complexes of TNT (H^- -TNT), colored dark red, were confirmed as the intermediate in this transformation by comparison with the synthetic compounds. 2,4-Dinitrotoluene as a following metabolic product was detected, and nitrite produced by denitration of H^- -TNT supported this transformation. In the other TNT pathway, nitro groups in TNT were successively reduced to amine groups via hydroxylamines. Hydroxylamino-dinitrotoluenes and amino-dinitrotoluenes were identified as the intermediates. The activity of a membrane-associated aromatic nitroreductase was detected in the cell-free extract of I. lacteus. This enzyme catalyzed the nitro group reduction of TNT with NADPH as a cofactor. Enzyme activity was not observed in the presence of molecular oxygen.
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