• Title/Summary/Keyword: Protein dynamics

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Isotopic palaeodiet studies of human bone from Gyeongju Donggung Palace and Wolji pond site (pond No.3), Goryeo period (경주 동궁과 월지 3호 우물 출토 옛사람 뼈의 동위원소에 기록된 고려시대 식생활 양상)

  • Choe, Hyeon Goo;Shin, Ji Young
    • Analytical Science and Technology
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    • v.32 no.6
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    • pp.262-270
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    • 2019
  • The stable isotopic composition of bone collagen plays an important role in reconstructing palaeodiet, nutrition, palaeoenvironment and their lifestyle. This is the first case in extracting palaeodietary information and breastfeeding pattern of Goryeo people using stable isotope analysis due to the lack of human remains in this period. We analyzed human bone collagen excavated from Gyeongju Donggung palace and Wolji pond No.3. The average values of δ13C and δ15N are as follows: (δ13C(‰) = -19.5 ± 0.9‰, δ15N(‰) = 11.1 ± 1.1 ‰, (n = 4). Stable carbon isotope values shows a mainly C3 based diet such as rice and barley. Stable nitrogen isotope results implies the protein sources attributed to terrestrial animals. There are various age groups in this study, which are adult, child and infant. Two individuals within early childhood age ranges (< 3 years) shows more elevated δ15N values than that of adult and this result implies the continuation of breastfeeding in this group until the age of 3. The results provide new insight into the breastfeeding pattern of Goryeo people, where breastfeeding and weaning practices have important implication for fertility, population dynamics, migration pattern and disease.

Supplementing Maize or Soybean Hulls to Cattle Fed Rice Straw:Intake, Apparent Digestion, In situ Disappearance and Ruminal Dynamics

  • Von, Nguyen Tien;St. Louis, David G.;Orr, Adam I.;Rude, Brian J.
    • Asian-Australasian Journal of Animal Sciences
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    • v.21 no.6
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    • pp.807-817
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    • 2008
  • Steers with ad libitum access to rice straw were assigned to four diets to evaluate the effects of maize or soybean hull supplementation on intake, in vivo digestibility, ruminal pH, VFA, ammonia-nitrogen ($NH_3-N$) and in situ ruminal disappearance of feed nutrients by cattle consuming rice straw. Supplement treatments were: no supplement (RS); soybean meal at 0.127% BW (SBM); cracked maize at 0.415% BW plus 0.044% BW soybean meal (MAIZE); or soybean hulls at 0.415% BW plus 0.044% BW soybean meal (HULLS). The MAIZE and HULLS diets were formulated to provide approximately 4 MJ of $NE_m$ per kg of diet. Rice straw DMI was not affected (p = 0.34) by supplement. Apparent dry matter (DM) digestibility was greater (p<0.001) for MAIZE and HULLS (56.6 and 60.0%, respectively) than for steers consuming SBM or RS (51.8 and 44.4%, respectively). Apparent NDF digestibility was greater (p<0.0004) for HULLS than MAIZE (61.7 vs. 58.0%, respectively) and apparent ADF digestibility was greater (p<0.0008) for HULLS than MAIZE (61.1 vs. 49.2%, respectively). There was no difference in apparent hemicellulose digestibility (p = 0.43). Analysis of ruminal fluid collected 0, 2, 4, 6, and 8 h post-feeding revealed ammonia-nitrogen was greatest (p<0.05) for steers on SBM and HULLS diets at 2 h (24.08 and 22.57 mg/dl, respectively) and total volatile fatty acids was greatest (p<0.05) for HULLS at 4 h (230 mM/L). In situ disappearance, measured at 0, 2, 4, 6, 8, 16 and 24 h, indicated that SBM, MAIZE and HULLS tended to enhance the digestibility of DM and fiber components of rice straw. In situ disappearance of rice straw DM was greatest for SBM and/or HULLS from 4 to 24 h (p = 0.03). Rice straw NDF and ADF disappearance was enhanced by supplementation from 16 to 24 h (p<0.02). Rice straw DM, NDF and ADF disappearances at 24 h were similar for MAIZE and HULLS treatments. When feeding cattle rice straw diets, energy and protein-based supplements are essential. This study showed that fiber-based supplements are just as, if not more, effective as starch-based supplements in rice straw utilization. This study shows that soybean hulls, in spite of their high fiber content, are as efficient as maize for supplementing rice straw primarily because fiber in soybean hulls is highly digestible as shown by in vivo digestibility and in situ disappearance.

Evidence for the Drp1-dependent Mitochondrial Fission in the Axon of the Rat Cerebral Cortex Neurons (흰쥐 대뇌 피질 신경세포의 축삭에서 Drp1 의존적 미토콘드리아의 분열)

  • Cho, Bong-Ki;Lee, Seung-Bok;Sun, Woong;Kim, Young-Hwa
    • Applied Microscopy
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    • v.41 no.4
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    • pp.249-255
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    • 2011
  • Neurons utilize a large quantity of energy for their survival and function, and thereby require active mitochondrial function. Mitochondrial morphology shows dynamic changes, depending on the cellular condition, and mitochondrial dynamics are required for neuronal development and function. In this study, we found that the length of mitochondria in the distal axon is significantly shorter than that of mitochondria in dendrites or proximal axons of cerebral cortical neurons, and the reason for this difference is the local fission within the axon. We also found that suppression of Drp1, a key regulator of mitochondrial fission, resulted in significant elongation of mitochondria in axons. Collectively, these results suggest that local mitochondrial fission within the axon contributes to region-dependent mitochondrial length differences in the axons of cortical neurons.

Bioinformatic Analysis of NLS (Nuclear Localization Signals)-containing Proteins from Mollusks (생물정보학을 이용한 연체동물의 NLS (Nuclear Localization Signals) 포함 단백질의 분석)

  • Lee, Yong-Seok;Kang, Se-Won;Jo, Yong-Hun;Gwak, Heui-Chul;Chae, Sung-Hwa;Choi, Sang-Haeng;Ahn, In-Young;Park, Hong-Seog;Han, Yeon-Soo;Kho, Weon-Gyu
    • The Korean Journal of Malacology
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    • v.22 no.2
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    • pp.109-113
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    • 2006
  • Subcellular localization of a protein containing nuclear localization signals (NLS) has been well studied in many organisms ranging from invertebrates to vertebrates. However, no systematic analysis of NLS-containing proteins available from Mollusks has been reported. Here, we describe in silico screening of NLS-containing proteins using the mollusks database that contains 22,138 amino acids. To screen putative proteins with NLS-motif, we used both predict NLS and perl script. As a result, we have found 266 proteins containing NLS sequences which are about 1.2% out of the entire proteins. On the basis of KOG (The eukaryotic orthologous groups) analysis, we can't predict the precise functions of the NLS-containing proteins. However, we found out that these proteins belong to several types of proteins such as chromatin structure and dynamics, translation, ribosomal structure, biogenesis, and signal transduction mechanism. In addition, we have analysed these sequences based on the classes of mollusks. We could not find many from the species that are the main subjects of phylogenetic studies. In contrast, we noticed that cephalopods has the highest number of NLS-containing proteins. Thus, we have constructed mollusks NLS database and added these information and data to the mollusks database by constructing web interface. Taken together, these information will be very useful for those who are or will be studying NLS-containing proteins from mollusks.

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Small molecule natural compound agonist of SIRT3 as a therapeutic target for the treatment of intervertebral disc degeneration

  • Wang, Jianle;Nisar, Majid;Huang, Chongan;Pan, Xiangxiang;Lin, Dongdong;Zheng, Gang;Jin, Haiming;Chen, Deheng;Tian, Naifeng;Huang, Qianyu;Duan, Yue;Yan, Yingzhao;Wang, Ke;Wu, Congcong;Hu, Jianing;Zhang, Xiaolei;Wang, Xiangyang
    • Experimental and Molecular Medicine
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    • v.50 no.11
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    • pp.5.1-5.14
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    • 2018
  • Oxidative stress-induced mitochondrial dysfunction is implicated in the pathogenesis of intervertebral disc degeneration (IVDD). Sirtuin 3 (SIRT3), a sirtuin family protein located in mitochondria, is essential for mitochondrial homeostasis; however, the role of SIRT3 in the process of IVDD has remained elusive. Here, we explored the expression of SIRT3 in IVDD in vivo and in vitro; we also explored the role of SIRT3 in senescence, apoptosis, and mitochondrial homeostasis under oxidative stress. We subsequently activated SIRT3 using honokiol to evaluate its therapeutic potential for IVDD. We assessed SIRT3 expression in degenerative nucleus pulposus (NP) tissues and oxidative stress-induced nucleus pulposus cells (NPCs). SIRT3 was knocked down by lentivirus and activated by honokiol to determine its role in oxidative stress-induced NPCs. The mechanism by which honokiol affected SIRT3 regulation was investigated in vitro, and the therapeutic potential of honokiol was assessed in vitro and in vivo. We found that the expression of SIRT3 decreased with IVDD, and SIRT3 knockdown reduced the tolerance of NPCs to oxidative stress. Honokiol ($10{\mu}M$) improved the viability of NPCs under oxidative stress and promoted their properties of anti-oxidation, mitochondrial dynamics and mitophagy in a SIRT3-dependent manner. Furthermore, honokiol activated SIRT3 through the AMPK-PGC-$1{\alpha}$ signaling pathway. Moreover, honokiol treatment ameliorated IVDD in rats. Our study indicated that SIRT3 is involved in IVDD and showed the potential of the SIRT3 agonist honokiol for the treatment of IVDD.

Ginsenoside Ro, an oleanolic saponin of Panax ginseng, exerts anti-inflammatory effect by direct inhibiting toll like receptor 4 signaling pathway

  • Xu, Hong-Lin;Chen, Guang-Hong;Wu, Yu-Ting;Xie, Ling-Peng;Tan, Zhang-Bin;Liu, Bin;Fan, Hui-Jie;Chen, Hong-Mei;Huang, Gui-Qiong;Liu, Min;Zhou, Ying-Chun
    • Journal of Ginseng Research
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    • v.46 no.1
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    • pp.156-166
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    • 2022
  • Background: Panax ginseng Meyer (P. ginseng), a herb distributed in Korea, China and Japan, exerts benefits on diverse inflammatory conditions. However, the underlying mechanism and active ingredients remains largely unclear. Herein, we aimed to explore the active ingredients of P. ginseng against inflammation and elucidate underlying mechanisms. Methods: Inflammation model was constructed by lipopolysaccharide (LPS) in C57BL/6 mice and RAW264.7 macrophages. Molecular docking, molecular dynamics, surface plasmon resonance imaging (SPRi) and immunofluorescence were utilized to predict active component. Results: P. ginseng significantly inhibited LPS-induced lung injury and the expression of proinflammatory factors, including TNF-α, IL-6 and IL-1β. Additionally, P. ginseng blocked fluorescencelabeled LPS (LPS488) binding to the membranes of RAW264.7 macrophages, the phosphorylation of nuclear factor-κB (NF-κB) and mitogen-activated protein kinases (MAPKs). Furthermore, molecular docking demonstrated that ginsenoside Ro (GRo) docked into the LPS binding site of toll like receptor 4 (TLR4)/myeloid differentiation factor 2 (MD2) complex. Molecular dynamic simulations showed that the MD2-GRo binding conformation was stable. SPRi demonstrated an excellent interaction between TLR4/ MD2 complex and GRo (KD value of 1.16 × 10-9 M). GRo significantly inhibited LPS488 binding to cell membranes. Further studies showed that GRo markedly suppressed LPS-triggered lung injury, the transcription and secretion levels of TNF-α, IL-6 and IL-1β. Moreover, the phosphorylation of NF-κB and MAPKs as well as the p65 subunit nuclear translocation were inhibited by GRo dose-dependently. Conclusion: Our results suggest that GRo exerts anti-inflammation actions by direct inhibition of TLR4 signaling pathway.

Development and Biogenesis of Peroxisome in Oil-seed Plants (지방 저장 식물의 퍼옥시좀 생성과 발달)

  • Dae-Jae Kim
    • Journal of Life Science
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    • v.33 no.8
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    • pp.651-662
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    • 2023
  • Peroxisomes, known as microbodies, are a class of morphologically similar subcellular organelles commonly found in most eukaryotic cells. They are 0.2~1.8 ㎛ in diameter and are bound by a single membrane. The matrix is usually finely granular, but occasionally crystalline or fibrillary inclusions are observed. They characteristically contain hydrogen peroxide (H2O2) generating oxidases and contain the enzyme catalase, thus confining the metabolism of the poisonous H2O2 within these organelles. Therefore, the eukaryotic organelles are greatly dynamic both in morphology and metabolism. Plant peroxisomes, in particular, are associated with numerous metabolic processes, including β-oxidation, the glyoxylate cycle and photorespiration. Furthermore, plant peroxisomes are involved in development, along with responses to stresses such as the synthesis of important phytohormones of auxins, salicylic acid and jasmonic acids. In the past few decades substantial progress has been made in the study of peroxisome biogenesis in eukaryotic organisms, mainly in animals and yeasts. Advancement of sophisticated techniques in molecular biology and widening of the range of genomic applications have led to the identification of most peroxisomal genes and proteins (peroxins, PEXs). Furthermore, recent applications of proteome study have produced fundamental information on biogenesis in plant peroxisomes, together with improving our understanding of peroxisomal protein targeting, regulation, and degradation. Nonetheless, despite this progress in peroxisome development, much remains to be explained about how peroxisomes originate from the endoplasmic reticulum (ER), then assemble and divide. Peroxisomes perform dynamic roles in many phases of plant development, and in this review, we focus on the latest progress in furthering our understanding of plant peroxisome functions, biogenesis, and dynamics.

The Effect of Methanol on the Structural Parameters of Neuronal Membrane Lipid Bilayers

  • Joo, Hyung-Jin;Ahn, Shin-Ho;Lee, Hang-Rae;Jung, Sung-Woo;Choi, Chang-Won;Kim, Min-Seok;Bae, Moon-Kyoung;Chung, In-Kyo;Bae, Soo-Kyoung;Jang, Hye-Ock;Yun, Il
    • The Korean Journal of Physiology and Pharmacology
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    • v.16 no.4
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    • pp.255-264
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    • 2012
  • The structures of the intact synaptosomal plasma membrane vesicles (SPMVs) isolated from bovine cerebral cortexs, and the outer and the inner monolayer separately, were evaluated with 1,6-diphenyl-1,3,5-hexatriene (DPH) and 1,3-di(1-pyrenyl)propane (Py-3-Py) as fluorescent reporters and trinitrophenyl groups as quenching agents. The methanol increased bulk rotational and lateral mobilities of SPMVs lipid bilayers. The methanol increased the rotational and lateral mobilities of the outer monolayers more than of the inner monolayers. n-(9-Anthroyloxy)stearic acid (n-AS) were used to evaluate the effect of the methanol on the rotational mobility at the 16, 12, 9, 6, and 2 position of aliphatic chains present in phospholipids of the SPMVs outer monolayers. The methanol decreased the anisotropy of the 16-(9-anthroyloxy)palmitic acid (16-AP), 12-(9-anthroyloxy)stearic acid (12-AS), 9-(9-anthroyloxy)stearic acid (9-AS), and 6-(9-anthroyloxy)stearic acid (6-AS) in the SPMVs outer monolayer but it increased the anisotropy of 2-(9-anthroyloxy)stearic acid (2-AS) in the monolayers. The magnitude of the increased rotational mobility by the methanol was in the order at the position of 16, 12, 9, and 6 of aliphatic chains in phospholipids of the outer monolayers. Furthermore, the methanol increased annular lipid fluidity and also caused membrane proteins to cluster. The important finding is that was far greater increase by methanol in annular lipid fluidity than increase in lateral and rotational mobilities by the methanol. Methanol alters the stereo or dynamics of the proteins in the lipid bilayers by combining with lipids, especially with the annular lipids. In conclusion, the present data suggest that methanol, in additions to its direct interaction with proteins, concurrently interacts with membrane lipids, fluidizing the membrane, and thus inducing conformational changes of proteins known to be intimately associated with membranes lipids.

Sesquiterpenoids Bioconversion Analysis by Wood Rot Fungi

  • Lee, Su-Yeon;Ryu, Sun-Hwa;Choi, In-Gyu;Kim, Myungkil
    • 한국균학회소식:학술대회논문집
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    • 2016.05a
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    • pp.19-20
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    • 2016
  • Sesquiterpenoids are defined as $C_{15}$ compounds derived from farnesyl pyrophosphate (FPP), and their complex structures are found in the tissue of many diverse plants (Degenhardt et al. 2009). FPP's long chain length and additional double bond enables its conversion to a huge range of mono-, di-, and tri-cyclic structures. A number of cyclic sesquiterpenes with alcohol, aldehyde, and ketone derivatives have key biological and medicinal properties (Fraga 1999). Fungi, such as the wood-rotting Polyporus brumalis, are excellent sources of pharmaceutically interesting natural products such as sesquiterpenoids. In this study, we investigated the biosynthesis of P. brumalis sesquiterpenoids on modified medium. Fungal suspensions of 11 white rot species were inoculated in modified medium containing $C_6H_{12}O_6$, $C_4H_{12}N_2O_6$, $KH_2PO_4$, $MgSO_4$, and $CaCl_2$ for 20 days. Cultivation was stopped by solvent extraction via separation of the mycelium. The metabolites were identified as follows: propionic acid (1), mevalonic acid lactone (2), ${\beta}$-eudesmane (3), and ${\beta}$-eudesmol (4), respectively (Figure 1). The main peaks of ${\beta}$-eudesmane and ${\beta}$-eudesmol, which were indicative of sesquiterpene structures, were consistently detected for 5, 7, 12, and 15 days These results demonstrated the existence of terpene metabolism in the mycelium of P. brumalis. Polyporus spp. are known to generate flavor components such as methyl 2,4-dihydroxy-3,6-dimethyl benzoate; 2-hydroxy-4-methoxy-6-methyl benzoic acid; 3-hydroxy-5-methyl phenol; and 3-methoxy-2,5-dimethyl phenol in submerged cultures (Hoffmann and Esser 1978). Drimanes of sesquiterpenes were reported as metabolites from P. arcularius and shown to exhibit antimicrobial activity against Gram-positive bacteria such as Staphylococcus aureus (Fleck et al. 1996). The main metabolites of P. brumalis, ${\beta}$-Eudesmol and ${\beta}$-eudesmane, were categorized as eudesmane-type sesquiterpene structures. The eudesmane skeleton could be biosynthesized from FPP-derived IPP, and approximately 1,000 structures have been identified in plants as essential oils. The biosynthesis of eudesmol from P. brumalis may thus be an important tool for the production of useful natural compounds as presumed from its identified potent bioactivity in plants. Essential oils comprising eudesmane-type sesquiterpenoids have been previously and extensively researched (Wu et al. 2006). ${\beta}$-Eudesmol is a well-known and important eudesmane alcohol with an anticholinergic effect in the vascular endothelium (Tsuneki et al. 2005). Additionally, recent studies demonstrated that ${\beta}$-eudesmol acts as a channel blocker for nicotinic acetylcholine receptors at the neuromuscular junction, and it can inhibit angiogenesis in vitro and in vivo by blocking the mitogen-activated protein kinase (MAPK) signaling pathway (Seo et al. 2011). Variation of nutrients was conducted to determine an optimum condition for the biosynthesis of sesquiterpenes by P. brumalis. Genes encoding terpene synthases, which are crucial to the terpene synthesis pathway, generally respond to environmental factors such as pH, temperature, and available nutrients (Hoffmeister and Keller 2007, Yu and Keller 2005). Calvo et al. described the effect of major nutrients, carbon and nitrogen, on the synthesis of secondary metabolites (Calvo et al. 2002). P. brumalis did not prefer to synthesize sesquiterpenes under all growth conditions. Results of differences in metabolites observed in P. brumalis grown in PDB and modified medium highlighted the potential effect inorganic sources such as $C_4H_{12}N_2O_6$, $KH_2PO_4$, $MgSO_4$, and $CaCl_2$ on sesquiterpene synthesis. ${\beta}$-eudesmol was apparent during cultivation except for when P. brumalis was grown on $MgSO_4$-free medium. These results demonstrated that $MgSO_4$ can specifically control the biosynthesis of ${\beta}$-eudesmol. Magnesium has been reported as a cofactor that binds to sesquiterpene synthase (Agger et al. 2008). Specifically, the $Mg^{2+}$ ions bind to two conserved metal-binding motifs. These metal ions complex to the substrate pyrophosphate, thereby promoting the ionization of the leaving groups of FPP and resulting in the generation of a highly reactive allylic cation. Effect of magnesium source on the sesquiterpene biosynthesis was also identified via analysis of the concentration of total carbohydrates. Our current study offered further insight that fungal sesquiterpene biosynthesis can be controlled by nutrients. To profile the metabolites of P. brumalis, the cultures were extracted based on the growth curve. Despite metabolites produced during mycelia growth, there was difficulty in detecting significant changes in metabolite production, especially those at low concentrations. These compounds may be of interest in understanding their synthetic mechanisms in P. brumalis. The synthesis of terpene compounds began during the growth phase at day 9. Sesquiterpene synthesis occurred after growth was complete. At day 9, drimenol, farnesol, and mevalonic lactone (or mevalonic acid lactone) were identified. Mevalonic acid lactone is the precursor of the mevalonic pathway, and particularly, it is a precursor for a number of biologically important lipids, including cholesterol hormones (Buckley et al. 2002). Farnesol is the precursor of sesquiterpenoids. Drimenol compounds, bi-cyclic-sesquiterpene alcohols, can be synthesized from trans-trans farnesol via cyclization and rearrangement (Polovinka et al. 1994). They have also been identified in the basidiomycota Lentinus lepideus as secondary metabolites. After 12 days in the growth phase, ${\beta}$-elemene caryophyllene, ${\delta}$-cadiene, and eudesmane were detected with ${\beta}$-eudesmol. The data showed the synthesis of sesquiterpene hydrocarbons with bi-cyclic structures. These compounds can be synthesized from FPP by cyclization. Cyclic terpenoids are synthesized through the formation of a carbon skeleton from linear precursors by terpene cyclase, which is followed by chemical modification by oxidation, reduction, methylation, etc. Sesquiterpene cyclase is a key branch-point enzyme that catalyzes the complex intermolecular cyclization of the linear prenyl diphosphate into cyclic hydrocarbons (Toyomasu et al. 2007). After 20 days in stationary phase, the oxygenated structures eudesmol, elemol, and caryophyllene oxide were detected. Thus, after growth, sesquiterpenes were identified. Per these results, we showed that terpene metabolism in wood-rotting fungi occurs in the stationary phase. We also showed that such metabolism can be controlled by magnesium supplementation in the growth medium. In conclusion, we identified P. brumalis as a wood-rotting fungus that can produce sesquiterpenes. To mechanistically understand eudesmane-type sesquiterpene biosynthesis in P. brumalis, further research into the genes regulating the dynamics of such biosynthesis is warranted.

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