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Katsuki N, Masuo S, Nukui N, Minakawa H, Takaya N. Gallic acid fermentation by metabolically engineered Escherichia coli producing p-hydroxybenzoate hydroxylase from Hylemonella gracilis NS1. J GEN APPL MICROBIOL 2024; 69:301-308. [PMID: 37648467 DOI: 10.2323/jgam.2023.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Plant-derived phenolic gallic acid (GA) is an important raw material for antioxidants and food additives. Efforts to ferment GA using microbial processes have aimed at minimizing production costs and environmental load using enzymes that hydroxylate p-hydroxybenzoate and protocatechuate (PCA). Here, we found a p-hydroxybenzoate hydroxylase (PobA) in the bacterium Hylemonella gracilis NS1 (HgPobA) with 1.5-fold more hydroxylation activity than that from Pseudomonas aeruginosa PAO1 and thus converted PCA to GA more efficiently. The PCA hydroxylation activity of HgPobA was improved by introducing the amino acid substitutions L207V/Y393F or T302A/Y393F. These mutants had 2.9- and 3.7-fold lower Kmapp for PCA than wild-type HgPobA. An Escherichia coli strain that reinforces shikimate pathway metabolism and produces HgPobA when cultured for 60 h generated 0.27 g L-1 of GA. This is the first report of fermenting glucose to generate GA using a natural enzyme from the PobA family. The E. coli strain harboring the HgPobA L207V/Y393F mutant increased GA production to 0.56 g L-1. During the early stages of culture, GA was fermented at a 10-fold higher rate by a strain producing either HgPobA L207V/Y393F or T302A/Y393F compared with wild-type HgPobA, which agreed with the high kcatapp/Kmapp PCA values of this mutant. We enhanced a PobA isozyme and its PCA hydroxylating function to efficiently and cost-effectively ferment GA.
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Affiliation(s)
- Nozomi Katsuki
- Faculty of Life and Environmental Sciences, Microbiology Research Center for Sustainability, University of Tsukuba
| | - Shunsuke Masuo
- Faculty of Life and Environmental Sciences, Microbiology Research Center for Sustainability, University of Tsukuba
| | - Noriyuki Nukui
- Faculty of Life and Environmental Sciences, Microbiology Research Center for Sustainability, University of Tsukuba
| | - Hajime Minakawa
- Faculty of Life and Environmental Sciences, Microbiology Research Center for Sustainability, University of Tsukuba
| | - Naoki Takaya
- Faculty of Life and Environmental Sciences, Microbiology Research Center for Sustainability, University of Tsukuba
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Morigasaki S, Matsui M, Ohtsu I, Doi Y, Kawano Y, Nakai R, Iwasaki W, Hayashi H, Takaya N. Temporal and fertilizer-dependent dynamics of soil bacterial communities in buckwheat fields under long-term management. Sci Rep 2024; 14:9896. [PMID: 38688974 PMCID: PMC11061196 DOI: 10.1038/s41598-024-60655-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 04/25/2024] [Indexed: 05/02/2024] Open
Abstract
This study integrated bacterial community and soil chemicals to characterize the soil ecosystem in an open upland field managed by six controlled fertilizer programs using the minimum amount of pesticides. Amplicon sequencing the 16S rRNA gene revealed that inorganic nitrogen fertilizer and compost altered the diversity and structure of the soil bacterial community throughout buckwheat (Fagopyrum esculentum Moench 'Hitachiakisoba') cultivation. The bacterial community comprised three clusters that contained bacteria that are prevalent in soils fertilized with nitrogen (cluster 1, 340 taxa), without nitrogen and compost (cluster 2, 234 taxa), and with compost-fertilized (cluster 3, 296 taxa). Cluster 2 contained more taxa in Actinobacteriota and less in Acidobacteriota, and cluster 3 contained more taxa in Gemmatimonadota compared with the other clusters. The most frequent taxa in cluster 1 were within the Chloroflexi phylum. The bacterial community structure correlated with soil chemical properties including pH, total organic carbon, SO42-, soluble Ca2+. A co-occurrence network of bacterial taxa and chemicals identified key bacterial groups comprising the center of a community network that determined topology and dynamics of the network. Temporal dynamics of the bacterial community structure indicated that Burkholderiales were associated with buckwheat ripening, indicating plant-bacteria interaction in the ecosystem.
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Affiliation(s)
- Susumu Morigasaki
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Motomu Matsui
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan
| | - Iwao Ohtsu
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
- Microbiology Research Center for Sustainability, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Yuki Doi
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
- Microbiology Research Center for Sustainability, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Yusuke Kawano
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
- Microbiology Research Center for Sustainability, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Ryosuke Nakai
- Microbial Ecology and Technology Research Group, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 2-17-2-1 Tsukisamu-Higashi, Toyohiraku, Sapporo, Hokkaido, 062-8517, Japan
| | - Wataru Iwasaki
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan
| | - Hisayoshi Hayashi
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
- Tsukuba-Plant Innovation Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Naoki Takaya
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan.
- Microbiology Research Center for Sustainability, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan.
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Amahisa M, Tsukagoshi M, Kadooka C, Masuo S, Takeshita N, Doi Y, Takagi H, Takaya N. The Metabolic Regulation of Amino Acid Synthesis Counteracts Reactive Nitrogen Stress via Aspergillus nidulans Cross-Pathway Control. J Fungi (Basel) 2024; 10:58. [PMID: 38248967 PMCID: PMC10817288 DOI: 10.3390/jof10010058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 01/23/2024] Open
Abstract
Nitric oxide (NO) is a natural reactive nitrogen species (RNS) that alters proteins, DNA, and lipids and damages biological activities. Although microorganisms respond to and detoxify NO, the regulation of the cellular metabolic mechanisms that cause cells to tolerate RNS toxicity is not completely understood. We found that the proline and arginine auxotrophic proA5 and argB2 mutants of the fungus Aspergillus nidulans require more arginine and proline for normal growth under RNS stress that starves cells by accumulating fewer amino acids. Fungal transcriptomes indicated that RNS stress upregulates the expression of the biosynthetic genes required for global amino acids, including proline and arginine. A mutant of the gene disruptant, cpcA, which encodes the transcriptional regulation of the cross-pathway control of general amino acid synthesis, did not induce these genes, and cells accumulated fewer amino acids under RNS stress. These results indicated a novel function of CpcA in the cellular response to RNS stress, which is mediated through amino acid starvation and induces the transcription of genes for general amino acid synthesis. Since CpcA also controls organic acid biosynthesis, impaired intermediates of such biosynthesis might starve cells of amino acids. These findings revealed the importance of the mechanism regulating amino acid homeostasis for fungal responses to and survival under RNS stress.
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Affiliation(s)
- Madoka Amahisa
- Microbiology Research Center for Sustainability, Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8572, Japan; (M.A.); (C.K.); (S.M.); (N.T.); (Y.D.)
| | - Madoka Tsukagoshi
- Microbiology Research Center for Sustainability, Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8572, Japan; (M.A.); (C.K.); (S.M.); (N.T.); (Y.D.)
| | - Chihiro Kadooka
- Microbiology Research Center for Sustainability, Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8572, Japan; (M.A.); (C.K.); (S.M.); (N.T.); (Y.D.)
| | - Shunsuke Masuo
- Microbiology Research Center for Sustainability, Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8572, Japan; (M.A.); (C.K.); (S.M.); (N.T.); (Y.D.)
| | - Norio Takeshita
- Microbiology Research Center for Sustainability, Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8572, Japan; (M.A.); (C.K.); (S.M.); (N.T.); (Y.D.)
| | - Yuki Doi
- Microbiology Research Center for Sustainability, Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8572, Japan; (M.A.); (C.K.); (S.M.); (N.T.); (Y.D.)
| | - Hiroshi Takagi
- Institute for Research Initiatives, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma 630-0192, Japan;
| | - Naoki Takaya
- Microbiology Research Center for Sustainability, Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8572, Japan; (M.A.); (C.K.); (S.M.); (N.T.); (Y.D.)
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Katsuki N, Fukushima R, Doi Y, Masuo S, Arakawa T, Yamada C, Fushinobu S, Takaya N. Protocatechuate hydroxylase is a novel group A flavoprotein monooxygenase with a unique substrate recognition mechanism. J Biol Chem 2024; 300:105508. [PMID: 38029967 PMCID: PMC10770758 DOI: 10.1016/j.jbc.2023.105508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/01/2023] Open
Abstract
Para-hydroxybenzoate hydroxylase (PHBH) is a group A flavoprotein monooxygenase that hydroxylates p-hydroxybenzoate to protocatechuate (PCA). Despite intensive studies of Pseudomonas aeruginosa p-hydroxybenzoate hydroxylase (PaPobA), the catalytic reactions of extremely diverse putative PHBH isozymes remain unresolved. We analyzed the phylogenetic relationships of known and predicted PHBHs and identified eight divergent clades. Clade F contains a protein that lacks the critical amino acid residues required for PaPobA to generate PHBH activity. Among proteins in this clade, Xylophilus ampelinus PobA (XaPobA) preferred PCA as a substrate and is the first known natural PCA 5-hydroxylase (PCAH). Crystal structures and kinetic properties revealed similar mechanisms of substrate carboxy group recognition between XaPobA and PaPobA. The unique Ile75, Met72, Val199, Trp201, and Phe385 residues of XaPobA form the bottom of a hydrophobic cavity with a shape that complements the 3-and 4-hydroxy groups of PCA and its binding site configuration. An interaction between the δ-sulfur atom of Met210 and the aromatic ring of PCA is likely to stabilize XaPobA-PCA complexes. The 4-hydroxy group of PCA forms a hydrogen bond with the main chain carbonyl of Thr294. These modes of binding constitute a novel substrate recognition mechanism that PaPobA lacks. This mechanism characterizes XaPobA and sheds light on the diversity of catalytic mechanisms of PobA-type PHBHs and group A flavoprotein monooxygenases.
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Affiliation(s)
- Nozomi Katsuki
- Faculty of Life and Environmental Sciences, Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Riku Fukushima
- Department of Biotechnology, The University of Tokyo, Tokyo, Japan
| | - Yuki Doi
- Faculty of Life and Environmental Sciences, Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Shunsuke Masuo
- Faculty of Life and Environmental Sciences, Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Takatoshi Arakawa
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Chiba, Japan
| | - Chihaya Yamada
- School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
| | - Shinya Fushinobu
- Department of Biotechnology, The University of Tokyo, Tokyo, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan.
| | - Naoki Takaya
- Faculty of Life and Environmental Sciences, Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Ibaraki, Japan.
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Yoshikawa Y, Nasuno R, Takaya N, Takagi H. Metallothionein Cup1 attenuates nitrosative stress in the yeast Saccharomyces cerevisiae. Microb Cell 2023; 10:170-177. [PMID: 37545644 PMCID: PMC10399457 DOI: 10.15698/mic2023.08.802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 08/08/2023]
Abstract
Metallothionein (MT), which is a small metal-binding protein with cysteine-rich motifs, functions in the detoxification of heavy metals in a variety of organisms. Even though previous studies suggest that MT is involved in the tolerance mechanisms against nitrosative stress induced by toxic levels of nitric oxide (NO) in mammalian cells, the physiological functions of MT in relation to NO have not been fully understood. In this study, we analyzed the functions of MT in nitrosative stress tolerance in the yeast Saccharomyces cerevisiae. Our phenotypic analyses showed that deletion or overexpression of the MT-encoding gene, CUP1, led to higher sensitivity or tolerance to nitrosative stress in S. cerevisiae cells, respectively. We further examined whether the yeast MT Cup1 in the cell-free lysate scavenges NO. These results showed that the cell-free lysate containing a higher level of Cup1 degraded NO more efficiently. On the other hand, the transcription level of CUP1 was not affected by nitrosative stress treatment. Our findings suggest that the yeast MT Cup1 contributes to nitrosative stress tolerance, possibly as a constitutive rather than an inducible defense mechanism.
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Affiliation(s)
- Yuki Yoshikawa
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
- Present address: Department of Biotechnology, Faculty of Bioresource Science, Akita Prefectural University, 241-438 Kaidoubata-Nishi, Shimoshinjo-Nakano, Akita, Akita 010-0195, Japan
| | - Ryo Nasuno
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
- Present address: Engineering Biology Research Center, Kobe University, 7-1-48, Minatojima Minami-machi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
| | - Naoki Takaya
- Faculty of Life and Environmental Sciences, Microbiology Research Center for Sustainability, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Hiroshi Takagi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
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Yan Y, Huang X, Zhou Y, Li J, Liu F, Li X, Hu X, Wang J, Guo L, Liu R, Takaya N, Zhou S. Cytosol Peroxiredoxin and Cell Surface Catalase Differentially Respond to H 2O 2 Stress in Aspergillus nidulans. Antioxidants (Basel) 2023; 12:1333. [PMID: 37507873 PMCID: PMC10376852 DOI: 10.3390/antiox12071333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/18/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
Both catalase and peroxiredoxin show high activities of H2O2 decomposition and coexist in the same organism; however, their division of labor in defense against H2O2 is unclear. We focused on the major peroxiredoxin (PrxA) and catalase (CatB) in Aspergillus nidulans at different growth stages to discriminate their antioxidant roles. The dormant conidia lacking PrxA showed sensitivity to high concentrations of H2O2 (>100 mM), revealing that PrxA is one of the important antioxidants in dormant conidia. Once the conidia began to swell and germinate, or further develop to young hyphae (9 h to old age), PrxA-deficient cells (ΔprxA) did not survive on plates containing H2O2 concentrations higher than 1 mM, indicating that PrxA is an indispensable antioxidant in the early growth stage. During these early growth stages, absence of CatB did not affect fungal resistance to either high (>1 mM) or low (<1 mM) concentrations of H2O2. In the mature hyphae stage (24 h to old age), however, CatB fulfills the major antioxidant function, especially against high doses of H2O2. PrxA is constitutively expressed throughout the lifespan, whereas CatB levels are low in the early growth stage of the cells developing from swelling conidia to early growth hyphae, providing a molecular basis for their different contributions to H2O2 resistance in different growth stages. Further enzyme activity and cellular localization analysis indicated that CatB needs to be secreted to be functionalized, and this process is confined to the growth stage of mature hyphae. Our results revealed differences in effectiveness and timelines of two primary anti-H2O2 enzymes in fungus.
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Affiliation(s)
- Yunfeng Yan
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Xiaofei Huang
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Yao Zhou
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Jingyi Li
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Feiyun Liu
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Xueying Li
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Xiaotao Hu
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Jing Wang
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Lingyan Guo
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Renning Liu
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Naoki Takaya
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan
| | - Shengmin Zhou
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
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Itani A, Masuo S, Yamamoto R, Serizawa T, Fukasawa Y, Takaya N, Toyota M, Betsuyaku S, Takeshita N. Local calcium signal transmission in mycelial network exhibits decentralized stress responses. PNAS Nexus 2023; 2:pgad012. [PMID: 36896124 PMCID: PMC9991499 DOI: 10.1093/pnasnexus/pgad012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 01/03/2023] [Accepted: 01/18/2023] [Indexed: 03/09/2023]
Abstract
Many fungi live as mycelia, which are networks of hyphae. Mycelial networks are suited for the widespread distribution of nutrients and water. The logistical capabilities are critical for the extension of fungal survival areas, nutrient cycling in ecosystems, mycorrhizal symbioses, and virulence. In addition, signal transduction in mycelial networks is predicted to be vital for mycelial function and robustness. A lot of cell biological studies have elucidated protein and membrane trafficking and signal transduction in fungal hyphae; however, there are no reports visualizing signal transduction in mycelia. This paper, by using the fluorescent Ca2+ biosensor, visualized for the first time how calcium signaling is conducted inside the mycelial network in response to localized stimuli in the model fungus Aspergillus nidulans. The wavy propagation of the calcium signal inside the mycelium or the signal blinking in the hyphae varies depending on the type of stress and proximity to the stress. The signals, however, only extended around 1,500 μm, suggesting that the mycelium has a localized response. The mycelium showed growth delay only in the stressed areas. Local stress caused arrest and resumption of mycelial growth through reorganization of the actin cytoskeleton and membrane trafficking. To elucidate the downstream of calcium signaling, calmodulin, and calmodulin-dependent protein kinases, the principal intracellular Ca2+ receptors were immunoprecipitated and their downstream targets were identified by mass spectrometry analyses. Our data provide evidence that the mycelial network, which lacks a brain or nervous system, exhibits decentralized response through locally activated calcium signaling in response to local stress.
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Affiliation(s)
- Ayaka Itani
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, 305-8572, Japan
| | - Shunsuke Masuo
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, 305-8572, Japan
| | - Riho Yamamoto
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, 305-8572, Japan
| | - Tomoko Serizawa
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, 305-8572, Japan
| | - Yu Fukasawa
- Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko, Osaki, Miyagi, 989-6711, Japan
| | - Naoki Takaya
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, 305-8572, Japan
| | - Masatsugu Toyota
- Department of Biochemistry and Molecular Biology, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan.,Suntory Rising Stars Encouragement Program in Life Sciences (SunRiSE), Kyoto, Japan.,Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA
| | - Shigeyuki Betsuyaku
- Department of Plant Life Science, Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga, 520-2194Japan
| | - Norio Takeshita
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, 305-8572, Japan
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Aida H, Uchida K, Nagai M, Hashizume T, Masuo S, Takaya N, Ying BW. Machine learning-assisted medium optimization revealed the discriminated strategies for improved production of the foreign and native metabolites. Comput Struct Biotechnol J 2023; 21:2654-2663. [PMID: 37138901 PMCID: PMC10149329 DOI: 10.1016/j.csbj.2023.04.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 05/05/2023] Open
Abstract
The composition of medium components is crucial for achieving the best performance of synthetic construction in genetically engineered cells. Which and how medium components determine the performance, e.g., productivity, remain poorly investigated. To address the questions, a comparative survey with two genetically engineered Escherichia coli strains was performed. As a case study, the strains carried the synthetic pathways for producing the aromatic compounds of 4-aminophenylalanine (4APhe) or tyrosine (Tyr), common in the upstream but differentiated in the downstream metabolism. Bacterial growth and compound production were examined in hundreds of medium combinations that comprised 48 pure chemicals. The resultant data sets linking the medium composition to bacterial growth and production were subjected to machine learning for improved production. Intriguingly, the primary medium components determining the production of 4PheA and Tyr were differentiated, which were the initial resource (glucose) of the synthetic pathway and the inducer (IPTG) of the synthetic construction, respectively. Fine-tuning of the primary component significantly increased the yields of 4APhe and Tyr, indicating that a single component could be crucial for the performance of synthetic construction. Transcriptome analysis observed the local and global changes in gene expression for improved production of 4APhe and Tyr, respectively, revealing divergent metabolic strategies for producing the foreign and native metabolites. The study demonstrated that ML-assisted medium optimization could provide a novel point of view on how to make the synthetic construction meet the designed working principle and achieve the expected biological function.
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Affiliation(s)
- Honoka Aida
- School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8572 Ibaraki, Japan
| | - Keisuke Uchida
- School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8572 Ibaraki, Japan
| | - Motoki Nagai
- School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8572 Ibaraki, Japan
| | - Takamasa Hashizume
- School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8572 Ibaraki, Japan
| | - Shunsuke Masuo
- School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8572 Ibaraki, Japan
- Microbiology Research Center for Sustainability, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8572 Ibaraki, Japan
| | - Naoki Takaya
- School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8572 Ibaraki, Japan
- Microbiology Research Center for Sustainability, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8572 Ibaraki, Japan
- Corresponding author at: School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8572 Ibaraki, Japan.
| | - Bei-Wen Ying
- School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8572 Ibaraki, Japan
- Corresponding author.
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Gupta A, Badam R, Takamori N, Minakawa H, Masuo S, Takaya N, Matsumi N. Microbial pyrazine diamine is a novel electrolyte additive that shields high-voltage LiNi 1/3Co 1/3Mn 1/3O 2 cathodes. Sci Rep 2022; 12:19888. [PMID: 36434117 PMCID: PMC9700740 DOI: 10.1038/s41598-022-22018-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 10/07/2022] [Indexed: 11/27/2022] Open
Abstract
The uncontrolled oxidative decomposition of electrolyte while operating at high potential (> 4.2 V vs Li/Li+) severely affects the performance of high-energy density transition metal oxide-based materials as cathodes in Li-ion batteries. To restrict this degradative response of electrolyte species, the need for functional molecules as electrolyte additives that can restrict the electrolytic decomposition is imminent. In this regard, bio-derived molecules are cost-effective, environment friendly, and non-toxic alternatives to their synthetic counter parts. Here, we report the application of microbially synthesized 2,5-dimethyl-3,6-bis(4-aminobenzyl)pyrazine (DMBAP) as an electrolyte additive that stabilizes high-voltage (4.5 V vs Li/Li+) LiNi1/3Mn1/3Co1/3O2 cathodes. The high-lying highest occupied molecular orbital of bio-additive (DMBAP) inspires its sacrificial in situ oxidative decomposition to form an organic passivation layer on the cathode surface. This restricts the excessive electrolyte decomposition to form a tailored cathode electrolyte interface to administer cyclic stability and enhance the capacity retention of the cathode.
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Affiliation(s)
- Agman Gupta
- grid.444515.50000 0004 1762 2236Graduate School of Advanced Science and Technology, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa 923-1292 Japan
| | - Rajashekar Badam
- grid.444515.50000 0004 1762 2236Graduate School of Advanced Science and Technology, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa 923-1292 Japan
| | - Noriyuki Takamori
- grid.444515.50000 0004 1762 2236Graduate School of Advanced Science and Technology, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa 923-1292 Japan
| | - Hajime Minakawa
- grid.20515.330000 0001 2369 4728Faculty of Life and Environmental Sciences, Microbiology Research Center for Sustainability, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572 Japan
| | - Shunsuke Masuo
- grid.20515.330000 0001 2369 4728Faculty of Life and Environmental Sciences, Microbiology Research Center for Sustainability, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572 Japan
| | - Naoki Takaya
- grid.20515.330000 0001 2369 4728Faculty of Life and Environmental Sciences, Microbiology Research Center for Sustainability, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572 Japan
| | - Noriyoshi Matsumi
- grid.444515.50000 0004 1762 2236Graduate School of Advanced Science and Technology, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa 923-1292 Japan
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10
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You Y, Doi Y, Maeda N, Masuo S, Takeshita N, Takaya N. Carboxypeptidase G and pterin deaminase metabolic pathways degrade folic acid in Variovorax sp. F1. BMC Microbiol 2022; 22:225. [PMID: 36167524 PMCID: PMC9513972 DOI: 10.1186/s12866-022-02643-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 09/15/2022] [Indexed: 12/05/2022] Open
Abstract
Background Folic acid (FA) is a synthetic vitamin (B9) and the oxidized form of a metabolic cofactor that is essential for life. Although the biosynthetic mechanisms of FA are established, its environmental degradation mechanism has not been fully elucidated. The present study aimed to identify bacteria in soil that degrade FA and the mechanisms involved. Results We isolated the soil bacterium Variovorax sp. F1 from sampled weed rhizospheres in a grassland and investigated its FA degradation mechanism. Cultured Variovorax sp. F1 rapidly degraded FA to pteroic acid (PA), indicating that FA hydrolysis to PA and glutamate. We cloned the carboxypeptidase G (CPG) gene and found widely distributed paralogs within the Variovorax genus. Recombinant CPG preferred FA and deaminofolic acid as substrates, indicating its involvement in FA degradation by Variovorax. Prolonged culture of Variovorax sp. F1 resulted in decreased rates of deaminofolic acid (DFA) and deaminopteroic acid (DPA) accumulation. This indicated that the deamination reaction also comprised a route of FA degradation. We also identified an F1 gene that was orthologous to the pterin deaminase gene (Arad3529) of Agrobacterium radiobacter. The encoded protein deaminated FA and PA to DFA and DPA, which was consistent with the deamination activity of FA and PA in bacterial cell-free extracts. Conclusion We discovered that the two enzymes required for FA degradation pathways in isolates of Variovorax sp. F1 comprise CPG and pterin deaminase, and that DFA and PA are intermediates in the generation of DPA. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02643-6.
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Affiliation(s)
- Yungmi You
- Faculty of Life and Environmental Sciences, Microbiology Research Center for Sustainability, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Yuki Doi
- Faculty of Life and Environmental Sciences, Microbiology Research Center for Sustainability, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Norifumi Maeda
- Faculty of Life and Environmental Sciences, Microbiology Research Center for Sustainability, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Shunsuke Masuo
- Faculty of Life and Environmental Sciences, Microbiology Research Center for Sustainability, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Norio Takeshita
- Faculty of Life and Environmental Sciences, Microbiology Research Center for Sustainability, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Naoki Takaya
- Faculty of Life and Environmental Sciences, Microbiology Research Center for Sustainability, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan.
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11
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Minakawa H, Masuo S, Takada K, Kumakura T, Katsuki N, Kaneko T, Takaya N. Fermentative production of 2-(4-aminophenyl)ethylamine to synthesize a novel heat-resistant biopolyurea. Biosci Biotechnol Biochem 2022; 86:1114-1121. [PMID: 35612977 DOI: 10.1093/bbb/zbac077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 05/15/2022] [Indexed: 11/14/2022]
Abstract
The aromatic diamine 2-(4-aminophenyl)ethylamine (4APEA) is a potential monomer for polymers and advanced materials. Here, 4APEA was produced by fermentation with using genetically engineered Escherichia coli [Masuo et al., Sci Rep, 2016]. Optimizing fed-batch cultures of this strain produced the highest reported yield to date of 4APEA (7.2%; 3.5 g/L vs. glucose) within 72 h. Appropriate aeration was important to maximize production and avoid unfavorable 4APEA degradation. Fermented 4APEA was purified from culture medium and polymerized with methylene diphenyldiisocyanate and hexamethylene diisocyanate to produce polyureas PU-1 and PU-2, respectively. The decomposition temperatures for 10% weight loss (Td10) of PU-1 and PU-2 were 276°C and 302°C, respectively, and were comparable with that of other thermostable aromatic polyureas. This study is the first to synthesize polyureas from the microbial aromatic diamine. Their excellent thermostability will be useful for the industrial production of heat-resistant polymer materials.
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Affiliation(s)
- Hajime Minakawa
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, Japan
| | - Shunsuke Masuo
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, Japan
| | - Kenji Takada
- Graduate School of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa, Japan
| | - Takuya Kumakura
- Graduate School of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa, Japan
| | - Nozomi Katsuki
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, Japan
| | - Tatsuo Kaneko
- Graduate School of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa, Japan
| | - Naoki Takaya
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, Japan
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12
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Masuo S, Saga C, Usui K, Sasakura Y, Kawasaki Y, Takaya N. Glucose-Derived Raspberry Ketone Produced via Engineered Escherichia coli Metabolism. Front Bioeng Biotechnol 2022; 10:843843. [PMID: 35237585 PMCID: PMC8883332 DOI: 10.3389/fbioe.2022.843843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 01/18/2022] [Indexed: 11/13/2022] Open
Abstract
The demand for raspberry ketone (RK) as a plant-based natural flavoring agent is high, but natural RK is one of the most expensive flavor compounds due to its limited content in plants. Here, we produced RK de novo from simple carbon sources in Escherichia coli. We genetically engineered E. coli metabolism to overproduce the metabolic precursors tyrosine and p-coumaric acid and increase RK production. The engineered E. coli produced 19.3- and 1.9 g/L of tyrosine and p-coumaric acid from glucose, respectively. The p-coumaric acid CoA ligase from Agrobacterium tumefaciens and amino acid substituted benzalacetone synthase of Rhemu palmatum (Chinese rhubarb) were overexpressed in E. coli overproducing p-coumaric acid. The overexpression of fabF, encoding β-ketoacyl-acyl carrier protein synthetase II increased intracellular malonyl-CoA, the precursor of benzalacetone synthase for RK biosynthesis, and improved RK production. Fed-batch cultures given glucose as a carbon source produced 62 mg/L of RK under optimized conditions. Our production system is inexpensive and does not rely on plant extraction; thus, it should significantly contribute to the flavor and fragrance industries.
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13
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Abeysinghe G, Kuchira M, Kudo G, Masuo S, Ninomiya A, Takahashi K, Utada AS, Hagiwara D, Nomura N, Takaya N, Obana N, Takeshita N. Fungal mycelia and bacterial thiamine establish a mutualistic growth mechanism. Life Sci Alliance 2020; 3:3/12/e202000878. [PMID: 32962971 PMCID: PMC7574024 DOI: 10.26508/lsa.202000878] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 09/07/2020] [Accepted: 09/14/2020] [Indexed: 12/22/2022] Open
Abstract
Bacterial cells travel along fungal highway and pay thiamine as a toll to the fungus. Simultaneous spatial and metabolic interactions in communicating bacterial and fungal species establish a mutualism that facilitates them to obtain an environmental niche and nutrient. Exclusivity in physical spaces and nutrients is a prerequisite for survival of organisms, but a few species have been able to develop mutually beneficial strategies that allow them to co-habit. Here, we discovered a mutualistic mechanism between filamentous fungus, Aspergillus nidulans, and bacterium, Bacillus subtilis. The bacterial cells co-cultured with the fungus traveled along mycelia using their flagella and dispersed farther with the expansion of fungal colony, indicating that the fungal mycelia supply space for bacteria to migrate, disperse, and proliferate. Transcriptomic, genetic, molecular mass, and imaging analyses demonstrated that the bacteria reached the mycelial edge and supplied thiamine to the growing hyphae, which led to a promotion of hyphal growth. The thiamine transfer from bacteria to the thiamine non-auxotrophic fungus was directly demonstrated by stable isotope labeling. The simultaneous spatial and metabolic interactions demonstrated in this study reveal a mutualism that facilitates the communicating fungal and bacterial species to obtain an environmental niche and nutrient, respectively.
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Affiliation(s)
- Gayan Abeysinghe
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Momoka Kuchira
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Gamon Kudo
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Shunsuke Masuo
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Akihiro Ninomiya
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Kohei Takahashi
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Andrew S Utada
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Daisuke Hagiwara
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Nobuhiko Nomura
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Naoki Takaya
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Nozomu Obana
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Norio Takeshita
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
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Yasui M, Oda K, Masuo S, Hosoda S, Katayama T, Maruyama JI, Takaya N, Takeshita N. Invasive growth of Aspergillus oryzae in rice koji and increase of nuclear number. Fungal Biol Biotechnol 2020; 7:8. [PMID: 32518660 PMCID: PMC7275602 DOI: 10.1186/s40694-020-00099-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 05/23/2020] [Indexed: 01/02/2023] Open
Abstract
Background 'Rice koji' is a solid culture of Aspergillus oryzae on steamed rice grains. Multiple parallel fermentation, wherein saccharification of rice by A. oryzae and alcohol fermentation by the budding yeast occur simultaneously, leads to the formation of a variety of ingredients of Japanese sake. In sake brewing, the degree of mycelial invasive growth into the steamed rice, called 'haze-komi', highly correlates with the digestibility and quality of rice koji, since the hyphae growing into the rice secrete amylases and digest starch. Results In this study, we investigated mycelial distribution of GFP-tagged A. oryzae in rice koji made with different types of rice, such as sake rice and eating rice, with 50 or 90% polishing rate to remove abundant proteins and lipids near the surface. In addition, we compared transcriptomes of A. oryzae in the different types of rice koji. Finally, we found that A. oryzae increases the nuclear number and hyphal width in the course of 1-3 days cultivation. Conclusions Our imaging analyses indicate that A. oryzae hyphae grew more deeply into 50% polished rice than 90% polished rice. The increases of nuclear number may be a selectively acquired characteristic for the high secretory capacity during the long history of cultivation of this species.
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Affiliation(s)
- Mizuki Yasui
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Ken Oda
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi-hiroshima, Hiroshima, 739-0046 Japan
| | - Shunsuke Masuo
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Shuji Hosoda
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Takuya Katayama
- Department of Biotechnology, Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Jun-Ichi Maruyama
- Department of Biotechnology, Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Naoki Takaya
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Norio Takeshita
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
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15
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Abstract
Unlike its biosynthetic mechanisms and physiological function, current understanding of riboflavin degradation in soil is limited to a few bacteria that decompose it to lumichrome. Here, we isolated six Microbacterium and three Nocardioides strains. These strains utilized riboflavin and lumichrome, respectively, as carbon sources. Among these strains, we identified Microbacterium paraoxydans R16 (R16) and Nocardioides nitrophenolicus L16 (L16), which were isolated form the same enrichment culture. Co-cultured R16 and L16 reconstituted a riboflavin-degrading interspecies consortium, in which the R16 strain degraded riboflavin to lumichrome and ᴅ-ribose. The L16 strain utilized the lumichrome as a carbon source, indicating that R16 is required for L16 to grow in the consortium. Notably, rates of riboflavin degradation and growth were increased in co-cultured, compared with monocultured R16 cells. These results indicated that a beneficial symbiotic interaction between M. paraoxydans R16 and N. nitrophenolicus L16 results in the ability to degrade riboflavin.
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Affiliation(s)
- Hiroshi Kanazawa
- Faculty of Life and Environmental Sciences, Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Japan
| | - Sayoko Ozaki
- Faculty of Life and Environmental Sciences, Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Japan
| | - Yuki Doi
- Faculty of Life and Environmental Sciences, Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Japan
| | - Shunsuke Masuo
- Faculty of Life and Environmental Sciences, Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Japan
| | - Naoki Takaya
- Faculty of Life and Environmental Sciences, Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Japan
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16
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Masuo S, Tsuda Y, Namai T, Minakawa H, Shigemoto R, Takaya N. Enzymatic Cascade in Pseudomonas that Produces Pyrazine from α-Amino Acids. Chembiochem 2019; 21:353-359. [PMID: 31322801 DOI: 10.1002/cbic.201900448] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Indexed: 12/31/2022]
Abstract
Pyrazines are widespread chemical compounds that include pheromones and odors. Herein, a novel mechanism used by Pseudomonas fluorescens SBW25 to biosynthesize monocyclic pyrazines is reported. Heterologous expression of the papABC genes that synthesize the natural α-amino acid 4-aminophenylalanine (4APhe), together with three adjacent papDEF genes of unknown function, in Escherichia coli resulted in the production of 2,5-dimethyl-3,6-bis(4-aminobenzyl)pyrazine (DMBAP), which comprised two symmetrical aminobenzyl moieties derived from 4APhe. It is found that PapD is a novel amino acid C-acetyltransferase, which decarboxylates and transfers acetyl residues to 4APhe, to generate an α-aminoketone, which spontaneously dehydrates and condenses to give dihydro DMBAP. PapF is a novel oxidase in the amine oxidase superfamily that oxidizes dihydro DMBAP to yield the pyrazine ring of DMBAP. These two enzymes constitute a unique mechanism for synthesizing monocyclic pyrazines and might serve as a novel strategy for the enzymatic synthesis of pyrazine derivatives from natural α-amino acids.
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Affiliation(s)
- Shunsuke Masuo
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Yusuke Tsuda
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Tomohito Namai
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Hajime Minakawa
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Ryosuke Shigemoto
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Naoki Takaya
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
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Kawaguchi H, Miyagawa H, Nakamura-Tsuruta S, Takaya N, Ogino C, Kondo A. Enhanced Phenyllactic Acid Production in Escherichia coli Via Oxygen Limitation and Shikimate Pathway Gene Expression. Biotechnol J 2019; 14:e1800478. [PMID: 30810277 DOI: 10.1002/biot.201800478] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/27/2019] [Indexed: 11/11/2022]
Abstract
3-Phenyllactic acid (PhLA) is useful as a start-up material in the pharmaceutical and biorefinery industries. To enhance the production of PhLA from glucose using recombinant Escherichia coli, the effects of glucose concentration and oxygen limitation on PhLA production are assessed in a fed-batch system using dissolved oxygen (DO)-stat method. The highest titer of PhLA (7.3 g L-1 ) is observed with a high concentration of glucose and under oxygen-limited conditions (DO = 0 ppm). Under oxygen limitation, cell growth and the formation of acetate and l-phenylalanine (Phe) by-products after 72 h of cultivation are reduced by 30%, 70%, and 81%, respectively, as compared to that under high DO conditions (DO = 5 ppm). Gene expression levels are compared between low and high DO conditions by quantitative polymerase chain reaction (qPCR) analysis. Several genes in the glycolysis (gapA and pykA), pentose phosphate (tktA), and early shikimate pathways for PhLA biosynthesis (aroF, aroG, and aroH) are upregulated under oxygen limitation. The results suggest that oxygen limitation affects metabolism in the shikimate pathway at both metabolic and transcriptional levels and that controlling the DO level is critical for enhanced production of a variety of aromatic compounds through the shikimate pathway.
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Affiliation(s)
- Hideo Kawaguchi
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Hiroki Miyagawa
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Sachiko Nakamura-Tsuruta
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan.,Department of Human and Living Sciences, Minatogawa College, 1430 Yotsutsuji, Sanda, Hyogo, 669-1342, Japan
| | - Naoki Takaya
- Faculty of Life and Environmental Science, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Chiaki Ogino
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan.,Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.,Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan.,Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.,Center for Sustainable Resource, RIKEN, 1-7-22 Suehiro, Turumi, Yokohama, Kanagawa, 230-0045, Japan
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18
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Oinuma KI, Yamaguchi I, Shindo D, Fujimoto M, Nishiyama T, Takano H, Takaya N, Ueda K. Extracytoplasmic diaphorase activity of Streptomyces coelicolor A3(2). Biochem Biophys Res Commun 2018; 503:1581-1586. [PMID: 30054046 DOI: 10.1016/j.bbrc.2018.07.083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 07/17/2018] [Indexed: 11/18/2022]
Abstract
Metabolism and utilization of plant-derived aromatic substances are fundamental to the saprophytic growth of Streptomyces. Here, we studied an enzyme activity reducing 2,6-dichlorophenolindophenol and nitroblue tetrazolium in the culture supernatant of Streptomyces coelicolor A3(2). N-terminal amino acid sequencing of a nitroblue tetrazolium-reducing enzyme revealed that the enzyme corresponds to the SCO2180 product. The protein exhibited a marked similarity with dihydrolipoamide dehydrogenase, the E3 subunit of 2-oxo-acid dehydrogenase complex. A recombinant SCO2180 protein formed a homodimer and exhibited a diaphorase activity catalyzing NADH-dependent reduction of various quinonic substrates. Similar nitroblue tetrazolium-reducing activities were observed for other Streptomyces strains isolated from soil, implying that the diaphorase-catalyzed reduction of quinonic substances widely occurs in the extracytoplasmic space of Streptomyces.
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Affiliation(s)
- Ken-Ichi Oinuma
- Life Science Research Center, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan.
| | - Itaru Yamaguchi
- Life Science Research Center, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Daiki Shindo
- Life Science Research Center, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Masahiro Fujimoto
- Life Science Research Center, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Tatsuya Nishiyama
- Life Science Research Center, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Hideaki Takano
- Life Science Research Center, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Naoki Takaya
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Kenji Ueda
- Life Science Research Center, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan.
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Xia Y, Yu H, Zhou Z, Takaya N, Zhou S, Wang P. Peroxiredoxin System of Aspergillus nidulans Resists Inactivation by High Concentration of Hydrogen Peroxide-Mediated Oxidative Stress. J Microbiol Biotechnol 2018; 28:145-156. [PMID: 29361208 DOI: 10.4014/jmb.1707.07024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Most eukaryotic peroxiredoxins (Prxs) are readily inactivated by a high concentration of hydrogen peroxide (H₂O₂) during catalysis owing to their "GGLG" and "YF" motifs. However, such oxidative stress sensitive motifs were not found in the previously identified filamentous fungal Prxs. Additionally, the information on filamentous fungal Prxs is limited and fragmentary. Herein, we cloned and gained insight into Aspergillus nidulans Prx (An.PrxA) in the aspects of protein properties, catalysis characteristics, and especially H₂O₂ tolerability. Our results indicated that An.PrxA belongs to the newly defined family of typical 2-Cys Prxs with a marked characteristic that the "resolving" cysteine (CR) is invertedly located preceding the "peroxidatic" cysteine (CP) in amino acid sequences. The inverted arrangement of CR and CP can only be found among some yeast, bacterial, and filamentous fungal deduced Prxs. The most surprising characteristic of An.PrxA is its extraordinary ability to resist inactivation by extremely high concentrations of H₂O₂, even that approaching 600 mM. By screening the H₂O₂-inactivation effects on the components of Prx systems, including Trx, Trx reductase (TrxR), and Prx, we ultimately determined that it is the robust filamentous fungal TrxR rather than Trx and Prx that is responsible for the extreme H₂O₂ tolerence of the An.PrxA system. This is the first investigation on the effect of the electron donor partner in the H₂O₂ tolerability of the Prx system.
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Affiliation(s)
- Yang Xia
- State Key Laboratory of Bioreactor Engineering, Biomedical Nanotechnology Center, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, P.R. China
| | - Haijun Yu
- State Key Laboratory of Bioreactor Engineering, Biomedical Nanotechnology Center, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, P.R. China
| | - Zhemin Zhou
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
| | - Naoki Takaya
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-0006, Japan
| | - Shengmin Zhou
- State Key Laboratory of Bioreactor Engineering, Biomedical Nanotechnology Center, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, P.R. China
| | - Ping Wang
- State Key Laboratory of Bioreactor Engineering, Biomedical Nanotechnology Center, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, P.R. China
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Shigemoto R, Matsumoto T, Masuo S, Takaya N. 5-Methylmellein is a novel inhibitor of fungal sirtuin and modulates fungal secondary metabolite production. J GEN APPL MICROBIOL 2018; 64:240-247. [PMID: 29794367 DOI: 10.2323/jgam.2018.01.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Sirtuin is an NAD+-dependent histone deacetylase that is highly conserved among prokaryotes and eukaryotes. Sirtuin deacetylates histones and non-histone proteins, and it is involved in fungal growth and secondary metabolite production. Here, we screened 579 fungal culture extracts that inhibited the histone deacetylase activity of Sirtuin A (SirA), produced by the fungus Aspergillus nidulans. Eight fungal strains containing three Ascomycota, two Basidiomycota and three Deuteromycetes produced SirA inhibitors. We purified the SirA inhibitor from the culture broth of Didymobotryum rigidum JCM 8837, and identified it as 5-methylmellein-a known polyketide. This polyketide and its structurally-related compound, mellein, inhibited SirA activity with IC50 of 120 and 160 μM, respectively. Adding 5-methylmellein to A. nidulans cultures increased secondary metabolite production in the medium. The metabolite profiles were different from those obtained by adding other sirtuin inhibitors nicotinamide and sirtinol to the culture. These results indicated that 5-methylmellein modulates fungal secondary metabolism, and is a potential tool for screening novel compounds derived from fungi.
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Affiliation(s)
| | - Takara Matsumoto
- Faculty of Life and Environmental Sciences, University of Tsukuba
| | - Shunsuke Masuo
- Faculty of Life and Environmental Sciences, University of Tsukuba
| | - Naoki Takaya
- Faculty of Life and Environmental Sciences, University of Tsukuba
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21
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Masuo S, Komatsuzaki A, Takeshita N, Itoh E, Takaaki O, Zhou S, Takaya N. Spatial heterogeneity of glycogen and its metabolizing enzymes in Aspergillus nidulans hyphal tip cells. Fungal Genet Biol 2017; 110:48-55. [PMID: 29175367 DOI: 10.1016/j.fgb.2017.11.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 11/18/2017] [Accepted: 11/22/2017] [Indexed: 01/13/2023]
Abstract
Glycogen is a homopolymer of glucose and a ubiquitous cellular-storage carbon. This study investigated which Aspergillus nidulans genes are involved in glycogen metabolism. Gene disruptants of predicted glycogen synthase (gsyA) and glycogenin (glgA) genes accumulated less cellular glycogen than the wild type strain, indicating that GsyA and GlgA synthesize glycogen similarly to other eukaryotes. Meanwhile, gene disruption of gphA encoding glycogen phosphorylase increased the amount of glycogen to a higher degree than wild type during the stationary phase that accompanies carbon-source limitation. GFP-tagged GsyA and GphA were distributed in the cytosol and formed punctate and filamentous structures, respectively. Carbon starvation resulted in elongated GphA-GFP filaments and increased numbers of filaments. These structures were more frequently located in the basal regions of tip cells and adjacent cells than in the apical regions of tip cells. Cellular glycogen visualized by incorporation of a fluorescent glucose analog accumulated in cytoplasmic puncta that were more prevalent in the basal regions, a pattern similar to that seen for GsyA. The colocalization of glycogen and GsyA at punctate structures in tip and sub-apical cells likely represents the cellular machinery for synthesizing glycogen. More frequent colocalization in the basal, rather than tip cell apical regions indicated that tip cells have differentiated subcellular regions for glycogen synthesis. Our findings regarding glycogen, GsyA and GphA distribution evoke the spatial heterogeneity of glycogen metabolism in fungal hyphae.
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Affiliation(s)
- Shunsuke Masuo
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Airi Komatsuzaki
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Norio Takeshita
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Eriko Itoh
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Okazoe Takaaki
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Shengmin Zhou
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Naoki Takaya
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan.
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Kawasaki Y, Aniruddha N, Minakawa H, Masuo S, Kaneko T, Takaya N. Novel polycondensed biopolyamide generated from biomass-derived 4-aminohydrocinnamic acid. Appl Microbiol Biotechnol 2017; 102:631-639. [PMID: 29150705 DOI: 10.1007/s00253-017-8617-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 10/26/2017] [Accepted: 10/30/2017] [Indexed: 01/09/2023]
Abstract
Biomass plastics are expected to contribute to the establishment of a carbon-neutral society by replacing conventional plastics derived from petroleum. The biomass-derived aromatic amine 4-aminocinnamic acid (4ACA) produced by recombinant bacteria is applied to the synthesis of high-performance biopolymers such as polyamides and polyimides. Here, we developed a microbial catalyst that hydrogenates the α,β-unsaturated carboxylic acid of 4ACA to generate 4-aminohydrocinnamic acid (4AHCA). The ability of 10 microbial genes for enoate and xenobiotic reductases expressed in Escherichia coli to convert 4ACA to 4AHCA was assessed. A strain producing 2-enoate reductase from Clostridium acetobutylicum (ca2ENR) reduced 4ACA to 4AHCA with a yield of > 95% mol mol-1 and reaction rates of 3.4 ± 0.4 and 4.4 ± 0.6 mM h-1 OD600-1 at the optimum pH of 7.0 under aerobic and anaerobic conditions, respectively. This recombinant strain reduced caffeic, cinnamic, coumaric, and 4-nitrocinnamic acids to their corresponding propanoic acid derivatives. We polycondensed 4AHCA generated from biomass-derived 4ACA by dehydration under a catalyst to form high-molecular-weight poly(4AHCA) with a molecular weight of M n = 1.94 MDa. This polyamide had high thermal properties as indicated by a 10% reduction in weight at a temperature of T d10 = 394 °C and a glass transition temperature of T g = 240 °C. Poly(4AHCA) derived from biomass is stable at high temperatures and could be applicable to the production of high-performance engineering plastics.
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Affiliation(s)
- Yukie Kawasaki
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Nag Aniruddha
- Graduate School of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa, 923-1292, Japan
| | - Hajime Minakawa
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Shunsuke Masuo
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Tatsuo Kaneko
- Graduate School of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa, 923-1292, Japan.
| | - Naoki Takaya
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan.
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Itoh E, Shigemoto R, Oinuma KI, Shimizu M, Masuo S, Takaya N. Sirtuin A regulates secondary metabolite production by Aspergillus nidulans. J GEN APPL MICROBIOL 2017; 63:228-235. [PMID: 28674377 DOI: 10.2323/jgam.2016.11.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Late-stage cultures of filamentous fungi under nutrient starvation produce valuable secondary metabolites such as pharmaceuticals and pigments, as well as deleterious mycotoxins, all of which have remarkable structural diversity and wide-spectrum bioactivity. The fungal mechanisms regulating the synthesis of many of these compounds are not fully understood, but sirtuin A (SirA) is a key factor that initiates production of the secondary metabolites, sterigmatocystin and penicillin G, by Aspergillus nidulans. Sirtuin is a ubiquitous NAD+-dependent histone deacetylase that converts euchromatin to heterochromatin and silences gene expression. In this study, we have investigated the transcriptome of a sirA gene disruptant (SirAΔ), and found that SirA concomitantly repressed the expression of gene clusters for synthesizing secondary metabolites and activated that of others. Extracts of SirAΔ cultures grown on solid agar and analyzed by HPLC indicated that SirA represses the production of austinol, dehydroaustinol and sterigmatocystin. These results indicated that SirA is a transcriptional regulator of fungal secondary metabolism.
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Affiliation(s)
- Eriko Itoh
- Faculty of Life and Environmental Sciences, University of Tsukuba
| | | | - Ken-Ichi Oinuma
- Faculty of Life and Environmental Sciences, University of Tsukuba
| | - Motoyuki Shimizu
- Faculty of Life and Environmental Sciences, University of Tsukuba
| | - Shunsuke Masuo
- Faculty of Life and Environmental Sciences, University of Tsukuba
| | - Naoki Takaya
- Faculty of Life and Environmental Sciences, University of Tsukuba
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Itoh E, Odakura R, Oinuma KI, Shimizu M, Masuo S, Takaya N. Sirtuin E is a fungal global transcriptional regulator that determines the transition from the primary growth to the stationary phase. J Biol Chem 2017; 292:11043-11054. [PMID: 28465348 DOI: 10.1074/jbc.m116.753772] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Revised: 04/20/2017] [Indexed: 11/06/2022] Open
Abstract
In response to limited nutrients, fungal cells exit the primary growth phase, enter the stationary phase, and cease proliferation. Although fundamental to microbial physiology in many environments, the regulation of this transition is poorly understood but likely involves many transcriptional regulators. These may include the sirtuins, which deacetylate acetyllysine residues of histones and epigenetically regulate global transcription. Therefore, we investigated the role of a nuclear sirtuin, sirtuin E (SirE), from the ascomycete fungus Aspergillus nidulans An A. nidulans strain with a disrupted sirE gene (SirEΔ) accumulated more acetylated histone H3 during the stationary growth phase when sirE was expressed at increased levels in the wild type. SirEΔ exhibited decreased mycelial autolysis, conidiophore development, sterigmatocystin biosynthesis, and production of extracellular hydrolases. Moreover, the transcription of the genes involved in these processes was also decreased, indicating that SirE is a histone deacetylase that up-regulates these activities in the stationary growth phase. Transcriptome analyses indicated that SirE repressed primary carbon and nitrogen metabolism and cell-wall synthesis. Chromatin immunoprecipitation demonstrated that SirE deacetylates acetylated Lys-9 residues in histone H3 at the gene promoters of α-1,3-glucan synthase (agsB), glycolytic phosphofructokinase (pfkA), and glyceraldehyde 3-phosphate (gpdA), indicating that SirE represses the expression of these primary metabolic genes. In summary, these results indicate that SirE facilitates the metabolic transition from the primary growth phase to the stationary phase. Because the observed gene expression profiles in stationary phase matched those resulting from carbon starvation, SirE appears to control this metabolic transition via a mechanism associated with the starvation response.
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Affiliation(s)
- Eriko Itoh
- From the Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Rika Odakura
- From the Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Ken-Ichi Oinuma
- From the Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Motoyuki Shimizu
- From the Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Shunsuke Masuo
- From the Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Naoki Takaya
- From the Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
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26
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Miyamoto M, Hori K, Goshima T, Takaya N, Oumi Y, Uemiya S. An Organoselective Zirconium-Based Metal-Organic-Framework UiO-66 Membrane for Pervaporation. Eur J Inorg Chem 2017. [DOI: 10.1002/ejic.201700010] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Manabu Miyamoto
- Department of Chemistry and Biomolecular Science; Gifu University; 1-1 Yanagido 501-1193 Gifu Japan
| | - Keisuke Hori
- Department of Materials Science and Technology; Gifu University; 1-1 Yanagido 501-1193 Gifu Japan
| | - Tatsumasa Goshima
- Department of Materials Science and Technology; Gifu University; 1-1 Yanagido 501-1193 Gifu Japan
| | - Naoki Takaya
- Department of Materials Science and Technology; Gifu University; 1-1 Yanagido 501-1193 Gifu Japan
| | - Yasunori Oumi
- Division of Instrument Analysis; Life Science Research Center; Gifu University; 1-1 Yanagido 501-1193 Gifu Japan
| | - Shigeyuki Uemiya
- Department of Chemistry and Biomolecular Science; Gifu University; 1-1 Yanagido 501-1193 Gifu Japan
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Akiyama T, Yamada Y, Takaya N, Ito S, Sasaki Y, Yajima S. Crystal structure of an IclR homologue from Microbacterium sp. strain HM58-2. Acta Crystallogr F Struct Biol Commun 2017; 73:16-23. [PMID: 28045389 PMCID: PMC5287369 DOI: 10.1107/s2053230x16019208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 12/02/2016] [Indexed: 11/10/2022] Open
Abstract
The bacterial transcription factor IclR (isocitrate lyase regulator) is a member of a one-component signal transduction system, which shares the common motif of a helix-turn-helix (HTH)-type DNA-binding domain (DBD) connected to a substrate-binding domain (SBD). Here, the crystal structure of an IclR homologue (Mi-IclR) from Microbacterium sp. strain HM58-2, which catabolizes acylhydrazide as the sole carbon source, is reported. Mi-IclR is expected to regulate an operon responsible for acylhydrazide degradation as an initial step. Native single-wavelength anomalous diffraction (SAD) experiments were performed in combination with molecular replacement. CRANK2 from the CCP4 suite successfully phased and modelled the complete structure of a homotetramer composed of 1000 residues in an asymmetric unit, and the model was refined to 2.1 Å resolution. The overall structure of Mi-IclR shared the same domain combination as other known IclR structures, but the relative geometry between the DBD and SBD differs. Accordingly, the geometry of the Mi-IclR tetramer was unique: the putative substrate-binding site in each subunit is accessible from the outside of the tetramer, as opposed to buried inside as in the previously known IclR structures. These differences in the domain geometry may contribute to the transcriptional regulation of IclRs.
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Affiliation(s)
- Tomonori Akiyama
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan
| | - Yusuke Yamada
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba 305-0801, Japan
| | - Naoki Takaya
- Department of Environmental and Life Sciences, Tsukuba University, Tennodai, Tsukuba, Japan
| | - Shinsaku Ito
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan
| | - Yasuyuki Sasaki
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan
| | - Shunsuke Yajima
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan
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Akiyama T, Ishii M, Takuwa A, Oinuma KI, Sasaki Y, Takaya N, Yajima S. Structural basis of the substrate recognition of hydrazidase isolated from Microbacterium sp. strain HM58-2, which catalyzes acylhydrazide compounds as its sole carbon source. Biochem Biophys Res Commun 2016; 482:1007-1012. [PMID: 27908731 DOI: 10.1016/j.bbrc.2016.11.148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Accepted: 11/27/2016] [Indexed: 11/26/2022]
Abstract
Hydrazidase was an enzyme that remained unidentified for a half century. However, recently, it was purified, and its encoding gene was cloned. Microbacterium sp. strain HM58-2 grows with acylhydrazides as its sole carbon source; it produces hydrazidase and degrades acylhydrazides to acetate and hydrazides. The bacterial hydrazidase belongs to the amidase signature enzyme family and contains a Ser-cisSer-Lys catalytic motif. The condensation of hydrazine and carbonic acid produces various hydrazides, some of which are raw materials for synthesizing pharmaceuticals and other useful chemicals. Although natural hydrazide compounds have been identified, the metabolic systems for hydrazides are not fully understood. Here, we report the crystal structure of hydrazidase from Microbacterium sp. strain HM58-2. The active site was revealed to consist of a Ser-cisSer-Lys catalytic triad, in which Ser179 forms a covalent bond with a carbonyl carbon of the substrate. 4-Hydroxybenzoic acid hydrazide bound to the S179A mutant, showing an oxyanion hole composed of the three backbone amide groups. Furthermore, H336 in the non-conserved region in the amidase family may define the substrate specificity, which was confirmed by mutation analysis. A wild-type apoenzyme structure revealed an unidentified molecule covalently bound to S179, representing a tetrahedral intermediate.
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Affiliation(s)
- Tomonori Akiyama
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan
| | - Misaki Ishii
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan
| | - Atsushi Takuwa
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai, Tsukuba 305-8572, Japan
| | - Ken-Ichi Oinuma
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai, Tsukuba 305-8572, Japan
| | - Yasuyuki Sasaki
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan
| | - Naoki Takaya
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai, Tsukuba 305-8572, Japan
| | - Shunsuke Yajima
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan.
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Shimizu M, Masuo S, Itoh E, Zhou S, Kato M, Takaya N. Thiamine synthesis regulates the fermentation mechanisms in the fungus Aspergillus nidulans. Biosci Biotechnol Biochem 2016; 80:1768-75. [DOI: 10.1080/09168451.2016.1158631] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Abstract
Thiamine pyrophosphate (TPP) is a critical cofactor and its biosynthesis is under the control of TPP availability. Here we disrupted a predicted thiA gene of the fungus Aspergillus nidulans and demonstrated that it is essential for synthesizing cellular thiamine. The thiamine riboswitch is a post-transcriptional mechanism for TPP to repress gene expression and it is located on A. nidulans thiA pre-messenger RNA. The thiA riboswitch was not fully derepressed under thiamine-limited conditions, and fully derepressed under environmental stressors. Upon exposure to hypoxic stress, the fungus accumulated more ThiA and NmtA proteins, and more thiamine than under aerobic conditions. The thiA gene was required for the fungus to upregulate hypoxic branched-chain amino acids and ethanol fermentation that involve enzymes containing TPP. These findings indicate that hypoxia modulates thiA expression through the thiamine riboswitch, and alters cellular fermentation mechanisms by regulating the activity of the TPP enzymes.
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Affiliation(s)
- Motoyuki Shimizu
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Faculty of Agriculture, Department of Applied Biological Chemistry, Meijo University, Nagoya, Japan
| | - Shunsuke Masuo
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Eriko Itoh
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Shengmin Zhou
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Masashi Kato
- Faculty of Agriculture, Department of Applied Biological Chemistry, Meijo University, Nagoya, Japan
| | - Naoki Takaya
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
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Kumar A, Tateyama S, Yasaki K, Ali MA, Takaya N, Singh R, Kaneko T. (1)H NMR and FT-IR dataset based structural investigation of poly(amic acid)s and polyimides from 4,4'-diaminostilbene. Data Brief 2016; 7:123-8. [PMID: 26933669 PMCID: PMC4764896 DOI: 10.1016/j.dib.2016.02.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 01/20/2016] [Accepted: 02/02/2016] [Indexed: 12/05/2022] Open
Abstract
Structural investigation of polymers by various available analytical methods is important in order to correlate the structure with polymer properties for which understanding of polymer structure is very important factor. The data presented here in this article shows the (1)H NMR spectra used for the characterization of prepared poly(amic acid)s (PAAs). It is often difficult to assigns the peak in NMR of polymers due to its complexity. Data presented here helps in assigning the proton peak in complex NMR of PAAs prepared from aromatic diamines. Further functionality in polymer chains can be confirmed by FT-IR spectra. Change in functionality during some reaction or process can be monitored by disappearance or appearance of peaks in FT-IR. The complete imidization of PAAs to Polyimides (PIs) is difficult to analyze because of the chemical stability i.e. insolubility of PIs in most of the solvent therefore the completion of imidization process was confirmed using FTIR.
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Affiliation(s)
- Amit Kumar
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi-shi, Ishikawa 923-1292, Japan
- Material/Organometallics Laboratory, Department of Chemistry, ARSD College, University of Delhi, Delhi 110021, India
| | - Seiji Tateyama
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi-shi, Ishikawa 923-1292, Japan
- JST, ALCA, Japan
| | - Katsuaki Yasaki
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi-shi, Ishikawa 923-1292, Japan
| | - Mohammad Asif Ali
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi-shi, Ishikawa 923-1292, Japan
| | - Naoki Takaya
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki 305-8572, Japan
- JST, ALCA, Japan
| | - Rajeev Singh
- Material/Organometallics Laboratory, Department of Chemistry, ARSD College, University of Delhi, Delhi 110021, India
| | - Tatsuo Kaneko
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi-shi, Ishikawa 923-1292, Japan
- JST, ALCA, Japan
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31
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Masuo S, Zhou S, Kaneko T, Takaya N. Bacterial fermentation platform for producing artificial aromatic amines. Sci Rep 2016; 6:25764. [PMID: 27167511 PMCID: PMC4863162 DOI: 10.1038/srep25764] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 04/21/2016] [Indexed: 12/03/2022] Open
Abstract
Aromatic amines containing an aminobenzene or an aniline moiety comprise versatile natural and artificial compounds including bioactive molecules and resources for advanced materials. However, a bio-production platform has not been implemented. Here we constructed a bacterial platform for para-substituted aminobenzene relatives of aromatic amines via enzymes in an alternate shikimate pathway predicted in a Pseudomonad bacterium. Optimization of the metabolic pathway in Escherichia coli cells converted biomass glucose to 4-aminophenylalanine with high efficiency (4.4 g L−1 in fed-batch cultivation). We designed and produced artificial pathways that mimicked the fungal Ehrlich pathway in E. coli and converted 4-aminophenylalanine into 4-aminophenylethanol and 4-aminophenylacetate at 90% molar yields. Combining these conversion systems or fungal phenylalanine decarboxylases, the 4-aminophenylalanine-producing platform fermented glucose to 4-aminophenylethanol, 4-aminophenylacetate, and 4-phenylethylamine. This original bacterial platform for producing artificial aromatic amines highlights their potential as heteroatoms containing bio-based materials that can replace those derived from petroleum.
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Affiliation(s)
- Shunsuke Masuo
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Shengmin Zhou
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Tatsuo Kaneko
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa, 923-1292 Japan
| | - Naoki Takaya
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
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Tateyama S, Masuo S, Suvannasara P, Oka Y, Miyazato A, Yasaki K, Teerawatananond T, Muangsin N, Zhou S, Kawasaki Y, Zhu L, Zhou Z, Takaya N, Kaneko T. Ultrastrong, Transparent Polytruxillamides Derived from Microbial Photodimers. Macromolecules 2016. [DOI: 10.1021/acs.macromol.6b00220] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Seiji Tateyama
- School
of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292 Japan
| | - Shunsuke Masuo
- Faculty
of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Ten-nodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Phruetchika Suvannasara
- School
of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292 Japan
- Bioorganic
Chemistry and Biomaterials Research Group, Department of Chemistry,
Faculty of Science, Chulalongkorn University, 254 Pathumwan, Bangkok 10330, Thailand
| | - Yuuki Oka
- School
of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292 Japan
| | - Akio Miyazato
- School
of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292 Japan
| | - Katsuaki Yasaki
- School
of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292 Japan
| | - Thapong Teerawatananond
- Bioorganic
Chemistry and Biomaterials Research Group, Department of Chemistry,
Faculty of Science, Chulalongkorn University, 254 Pathumwan, Bangkok 10330, Thailand
| | - Nongnuj Muangsin
- Bioorganic
Chemistry and Biomaterials Research Group, Department of Chemistry,
Faculty of Science, Chulalongkorn University, 254 Pathumwan, Bangkok 10330, Thailand
| | - Shengmin Zhou
- Faculty
of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Ten-nodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Yukie Kawasaki
- Faculty
of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Ten-nodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Longbao Zhu
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, School
of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zhemin Zhou
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, School
of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Naoki Takaya
- Faculty
of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Ten-nodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Tatsuo Kaneko
- School
of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292 Japan
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Kaneko T, Tateyam S, Okajima M, Hojoon S, Takaya N. Ultrahigh Heat-resistant, Transparent Bioplastics from Exotic Amino Acid. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.matpr.2016.01.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Shimizu M, Kaneko Y, Ishihara S, Mochizuki M, Sakai K, Yamada M, Murata S, Itoh E, Yamamoto T, Sugimura Y, Hirano T, Takaya N, Kobayashi T, Kato M. Novel β-1,4-Mannanase Belonging to a New Glycoside Hydrolase Family in Aspergillus nidulans. J Biol Chem 2015; 290:27914-27. [PMID: 26385921 PMCID: PMC4646033 DOI: 10.1074/jbc.m115.661645] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Indexed: 11/10/2022] Open
Abstract
Many filamentous fungi produce β-mannan-degrading β-1,4-mannanases that belong to the glycoside hydrolase 5 (GH5) and GH26 families. Here we identified a novel β-1,4-mannanase (Man134A) that belongs to a new glycoside hydrolase (GH) family (GH134) in Aspergillus nidulans. Blast analysis of the amino acid sequence using the NCBI protein database revealed that this enzyme had no similarity to any sequences and no putative conserved domains. Protein homologs of the enzyme were distributed to limited fungal and bacterial species. Man134A released mannobiose (M2), mannotriose (M3), and mannotetraose (M4) but not mannopentaose (M5) or higher manno-oligosaccharides when galactose-free β-mannan was the substrate from the initial stage of the reaction, suggesting that Man134A preferentially reacts with β-mannan via a unique catalytic mode. Man134A had high catalytic efficiency (kcat/Km) toward mannohexaose (M6) compared with the endo-β-1,4-mannanase Man5C and notably converted M6 to M2, M3, and M4, with M3 being the predominant reaction product. The action of Man5C toward β-mannans was synergistic. The growth phenotype of a Man134A disruptant was poor when β-mannans were the sole carbon source, indicating that Man134A is involved in β-mannan degradation in vivo. These findings indicate a hitherto undiscovered mechanism of β-mannan degradation that is enhanced by the novel β-1,4-mannanase, Man134A, when combined with other mannanolytic enzymes including various endo-β-1,4-mannanases.
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Affiliation(s)
- Motoyuki Shimizu
- From the Faculty of Agriculture, Meijo University, Nagoya, Aichi 468-8502, Japan,
| | - Yuhei Kaneko
- From the Faculty of Agriculture, Meijo University, Nagoya, Aichi 468-8502, Japan
| | - Saaya Ishihara
- From the Faculty of Agriculture, Meijo University, Nagoya, Aichi 468-8502, Japan
| | - Mai Mochizuki
- From the Faculty of Agriculture, Meijo University, Nagoya, Aichi 468-8502, Japan
| | - Kiyota Sakai
- From the Faculty of Agriculture, Meijo University, Nagoya, Aichi 468-8502, Japan
| | - Miyuki Yamada
- From the Faculty of Agriculture, Meijo University, Nagoya, Aichi 468-8502, Japan
| | - Shunsuke Murata
- From the Faculty of Agriculture, Meijo University, Nagoya, Aichi 468-8502, Japan
| | - Eriko Itoh
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan, and
| | - Tatsuya Yamamoto
- From the Faculty of Agriculture, Meijo University, Nagoya, Aichi 468-8502, Japan
| | - Yu Sugimura
- From the Faculty of Agriculture, Meijo University, Nagoya, Aichi 468-8502, Japan
| | - Tatsuya Hirano
- From the Faculty of Agriculture, Meijo University, Nagoya, Aichi 468-8502, Japan
| | - Naoki Takaya
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan, and
| | - Tetsuo Kobayashi
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Masashi Kato
- From the Faculty of Agriculture, Meijo University, Nagoya, Aichi 468-8502, Japan
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Kawaguchi H, Teramura H, Uematsu K, Hara KY, Hasunuma T, Hirano K, Sazuka T, Kitano H, Tsuge Y, Kahar P, Niimi-Nakamura S, Oinuma KI, Takaya N, Kasuga S, Ogino C, Kondo A. Phenyllactic acid production by simultaneous saccharification and fermentation of pretreated sorghum bagasse. Bioresour Technol 2015; 182:169-178. [PMID: 25689311 DOI: 10.1016/j.biortech.2015.01.097] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 01/22/2015] [Accepted: 01/23/2015] [Indexed: 06/04/2023]
Abstract
Dilute acid-pretreated sorghum bagasse, which was predominantly composed of glucan (59%) and xylose (7.2%), was used as a lignocellulosic feedstock for d-phenyllactic acid (PhLA) production by a recombinant Escherichia coli strain expressing phenylpyruvate reductase from Wickerhamia fluorescens. During fermentation with enzymatic hydrolysate of sorghum bagasse as a carbon source, the PhLA yield was reduced by 35% compared to filter paper hydrolysate, and metabolomics analysis revealed that NAD(P)H regeneration and intracellular levels of erythrose-4-phosphate and phosphoenolpyruvate for PhLA biosynthesis markedly reduced. Compared to separate hydrolysis and fermentation (SHF) with sorghum bagasse hydrolysate, simultaneous saccharification and fermentation (SSF) of sorghum bagasse under glucose limitation conditions yielded 4.8-fold more PhLA with less accumulation of eluted components, including p-coumaric acid and aldehydes, which inhibited PhLA fermentation. These results suggest that gradual enzymatic hydrolysis during SSF enhances PhLA production under glucose limitation and reduces the accumulation of fermentation inhibitors, collectively leading to increased PhLA yield.
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Affiliation(s)
- Hideo Kawaguchi
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe 657-8501, Japan
| | - Hiroshi Teramura
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe 657-8501, Japan
| | - Kouji Uematsu
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe 657-8501, Japan
| | - Kiyotaka Y Hara
- Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Tomohisa Hasunuma
- Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Ko Hirano
- Bioscience and Biotechnology Center, Nagoya University, Furo, Chikusa, Nagoya 464-8601, Japan
| | - Takashi Sazuka
- Bioscience and Biotechnology Center, Nagoya University, Furo, Chikusa, Nagoya 464-8601, Japan
| | - Hidemi Kitano
- Bioscience and Biotechnology Center, Nagoya University, Furo, Chikusa, Nagoya 464-8601, Japan
| | - Yota Tsuge
- Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Prihardi Kahar
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe 657-8501, Japan
| | - Satoko Niimi-Nakamura
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe 657-8501, Japan
| | - Ken-Ichi Oinuma
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Naoki Takaya
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Shigemitsu Kasuga
- Education and Research Center of Alpine Field Science, Faculty of Agriculture, Shinshu University, Minamiminowa, Nagano 399-4598, Japan
| | - Chiaki Ogino
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe 657-8501, Japan
| | - Akihiko Kondo
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe 657-8501, Japan; RIKEN Center for Sustainable Resource Science, 1-7-22 Suehirocho, Turumi-ku, Yokohama, Kanagawa 230-0045, Japan.
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Graminho ER, Takaya N, Nakamura A, Hoshino T. Purification, biochemical characterization, and genetic cloning of the phytase produced by Burkholderia sp. strain a13. J GEN APPL MICROBIOL 2015; 61:15-23. [DOI: 10.2323/jgam.61.15] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
| | - Naoki Takaya
- Faculty of Life and Environmental Sciences, University of Tsukuba
| | - Akira Nakamura
- Faculty of Life and Environmental Sciences, University of Tsukuba
| | - Takayuki Hoshino
- Faculty of Life and Environmental Sciences, University of Tsukuba
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Abstract
Achromobacter denitrificans YD35 is an NO2 (-)-tolerant bacterium that expresses the aconitase genes acnA3, acnA4, and acnB, of which acnA3 is essential for growth tolerance against 100 mm NO2 (-). Atmospheric oxygen inactivated AcnA3 at a rate of 1.6 × 10(-3) min(-1), which was 2.7- and 37-fold lower compared with AcnA4 and AcnB, respectively. Stoichiometric titration showed that the [4Fe-4S](2+) cluster of AcnA3 was more stable against oxidative inactivation by ferricyanide than that of AcnA4. Aconitase activity of AcnA3 persisted against high NO2 (-) levels that generate reactive nitrogen species with an inactivation rate constant of k = 7.8 × 10(-3) min(-1), which was 1.6- and 7.8-fold lower than those for AcnA4 and AcnB, respectively. When exposed to NO2 (-), the acnA3 mutant (AcnA3Tn) accumulated higher levels of cellular citrate compared with the other aconitase mutants, indicating that AcnA3 is a major producer of cellular aconitase activity. The extreme resistance of AcnA3 against oxidation and reactive nitrogen species apparently contributes to bacterial NO2 (-) tolerance. AcnA3Tn accumulated less cellular NADH and ATP compared with YD35 under our culture conditions. The accumulation of more NO by AcnA3Tn suggested that NADH-dependent enzymes detoxify NO for survival in a high NO2 (-) milieu. This novel aconitase is distributed in Alcaligenaceae bacteria, including pathogens and denitrifiers, and it appears to contribute to a novel NO2 (-) tolerance mechanism in this strain.
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Affiliation(s)
- Yuki Doi
- From the Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Naoki Takaya
- From the Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
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Sasaki Y, Takaya N, Morita A, Nakamura A, Shoun H. Nitrite formation from organic nitrogen by Streptomyces antibioticus supporting bacterial cell growth and possible involvement of nitric oxide as an intermediate. Biosci Biotechnol Biochem 2014; 78:1603-10. [PMID: 25209510 DOI: 10.1080/09168451.2014.932665] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The actinomycete Streptomyces antibioticus was shown to produce nitrite (NO-(2)) and ammonium (NH+(4)]) when aerobically incubated in an organic nitrogen-rich medium. The production of NO-(2) was synchronized with rapid cell growth, whereas most NH+(4)] was produced after cell proliferation had ceased. Intracellular formation of nitric oxide (NO) was also observed during the incubation. The production of these inorganic nitrogen compounds along with cell growth was prevented by several enzyme inhibitors (of nitric oxide synthase or nitrate reductase) or glucose. Distinct, membrane-bound nitrate reductase was induced in the NO-(2)-producing cells. Tungstate (a potent inhibitor of this enzyme) prevented the NO-(2) production and cell growth, whereas it did not prevent the NO formation. These results revealed the occurrence of novel nitrogen metabolic pathway in S. antibioticus forming NO-(2) from organic nitrogen by which rapid cell growth is possible. NO synthase, NO dioxygenase (flavohemoglobin), and dissimilatory nitrate reductase are possible enzymes responsible for the NO-(2) formation.
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Affiliation(s)
- Yasuyuki Sasaki
- a Faculty of Applied Bioscience, Department of Bioscience , Tokyo University of Agriculture , Tokyo , Japan
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Kawaguchi H, Uematsu K, Ogino C, Teramura H, Niimi-Nakamura S, Tsuge Y, Hasunuma T, Oinuma KI, Takaya N, Kondo A. Simultaneous saccharification and fermentation of kraft pulp by recombinant Escherichia coli for phenyllactic acid production. Biochem Eng J 2014. [DOI: 10.1016/j.bej.2014.04.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Sasaki Y, Takaya N, Nakamura A, Shoun H. Isolation of Flavohemoglobin from the ActinomyceteStreptomyces antibioticusGrown without External Nitric Oxide Stress. Biosci Biotechnol Biochem 2014; 68:1106-12. [PMID: 15170116 DOI: 10.1271/bbb.68.1106] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A flavocytochrome protein was isolated from the actinomycete Streptomyces antibioticus. The purified protein contained protoheme and FAD, and its M(r) was estimated to be 52000. The absorption spectra in its resting oxidized, dithionite-reduced, carbon monoxide-bound, and oxygenated (O(2)-bound) forms were characteristic of those of flavohemoglobin (Fhb). The N-terminal amino acid sequence showed high identities to those of other Fhb's. Furthermore, the actinomycete flavocytochrome scavenged nitric oxide in the presence of NADH. These results demonstrated that the flavocytochrome is the first Fhb purified from actinomycetes. The actinomycete Fhb was produced in S. antibioticus cells in large amounts without any external nitric oxide (NO) stress, which is indicative of a physiological function of Fhb other than detoxification of NO.
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Affiliation(s)
- Yasuyuki Sasaki
- Institute of Applied Biochemistry, University of Tsukuba, Ibaraki, Japan
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Takasaki K, Shoun H, Nakamura A, Hoshino T, Takaya N. Unusual Transcription Regulation of theniaDGene under Anaerobic Conditions Supporting Fungal Ammonia Fermentation. Biosci Biotechnol Biochem 2014; 68:978-80. [PMID: 15118339 DOI: 10.1271/bbb.68.978] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The niaD gene of the fungus Aspergillus nidulans encodes an assimilatory nitrate reductase and exogenous ammonium represses its expression. Under anoxic conditions, however, A. nidulans expressed niaD even in the presence of ammonium and used the gene product for dissimilatory nitrate reduction (ammonia fermentation). This transcription regulation mechanism under anaerobiosis is critical for the fungus to ferment ammonium.
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Affiliation(s)
- Kazuto Takasaki
- Institute of Applied Biochemistry, University of Tsukuba, Ibaraki, Japan
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Suvannasara P, Tateyama S, Miyasato A, Matsumura K, Shimoda T, Ito T, Yamagata Y, Fujita T, Takaya N, Kaneko T. Biobased Polyimides from 4-Aminocinnamic Acid Photodimer. Macromolecules 2014. [DOI: 10.1021/ma402499m] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Phruetchika Suvannasara
- School
of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
- Program
of Petrochemistry and Polymer Science, Faculty of Science, Chulalongkorn University, Patumwan, Bangkok, 10330 Thailand
| | - Seiji Tateyama
- School
of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Akio Miyasato
- School
of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Kazuaki Matsumura
- School
of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Tatsuya Shimoda
- School
of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Takashi Ito
- Graduate
School of Life and Environmental Sciences, University of Tsukuba, Tsukuba,
Ibaraki 305-8572, Japan
| | - Yukiho Yamagata
- Graduate
School of Life and Environmental Sciences, University of Tsukuba, Tsukuba,
Ibaraki 305-8572, Japan
| | - Tomoya Fujita
- Graduate
School of Life and Environmental Sciences, University of Tsukuba, Tsukuba,
Ibaraki 305-8572, Japan
| | - Naoki Takaya
- Graduate
School of Life and Environmental Sciences, University of Tsukuba, Tsukuba,
Ibaraki 305-8572, Japan
| | - Tatsuo Kaneko
- School
of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
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Toyofuku M, Zhou S, Sawada I, Takaya N, Uchiyama H, Nomura N. Membrane vesicle formation is associated with pyocin production under denitrifying conditions inPseudomonas aeruginosa PAO1. Environ Microbiol 2013; 16:2927-38. [DOI: 10.1111/1462-2920.12260] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 08/16/2013] [Accepted: 08/21/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Masanori Toyofuku
- Graduate School of Life and Environmental Sciences; University of Tsukuba; Tsukuba Ibaraki 305-8572 Japan
| | - Shengmin Zhou
- Graduate School of Life and Environmental Sciences; University of Tsukuba; Tsukuba Ibaraki 305-8572 Japan
| | - Isao Sawada
- Department of Material and Environmental Chemistry; Graduate School of Engineering; Utsunomiya University; Utsunomiya Tochigi Japan
| | - Naoki Takaya
- Graduate School of Life and Environmental Sciences; University of Tsukuba; Tsukuba Ibaraki 305-8572 Japan
| | - Hiroo Uchiyama
- Graduate School of Life and Environmental Sciences; University of Tsukuba; Tsukuba Ibaraki 305-8572 Japan
| | - Nobuhiko Nomura
- Graduate School of Life and Environmental Sciences; University of Tsukuba; Tsukuba Ibaraki 305-8572 Japan
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Abstract
Nucleoside diphosphates linked to moiety X (Nudix) hydrolase functions were investigated in hypoxic Aspergillus nidulans cells. Among three nudix hydrolase isozymes, NdxA transcription was up-regulated under oxygen (O2)-limited conditions. A gene disruptant of the NdxA-encoding gene (NdxAΔ) accumulated more NADH and ADP-ribose than the wild type (WT) under the same conditions. These results indicate that NdxA hydrolyzes these nucleotides in hypoxic fungal cells, which accords with the thesis that NdxA hydrolyzes NADH and ADP-ribose. Under O2-limited conditions, NdxAΔ decreased glucose consumption, the production of ethanol and lactate, cellular ATP levels, and growth as compared with WT. WT cultured under hypoxia converted exogenously added fructose 1,6-bisphophate, a glycolytic intermediate, to glyceraldehyde 3-phosphate (GAP). The hypoxic NdxAΔ cells accumulated 3.0- to 4.2-fold more GAP than WT under the same conditions, indicating that NdxA increased GAP oxidation by a glycolytic mechanism. Steady-state kinetics indicated that NADH and ADP-ribose competitively inhibited fungal GAP dehydrogenase (GAPDH) with Ki values of 34- and 55-µM, respectively. These results indicate that NdxA hydrolyzes cellular NADH- and ADP-ribose, derepresses GAPDH activity, and hence up-regulates glycolysis in hypoxic A. nidulans cells. That NdxAΔ consumed less pyruvate and tricarboxylate cycle intermediates than WT suggests that NdxA-dependent hydrolysis of nucleotides controls the catabolism of these carbon sources under O2-limited conditions.
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Affiliation(s)
- Motoyuki Shimizu
- Graduate School of Life and Environmental Sciences, University of Tsukuba
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Zhou S, Narukami T, Masuo S, Shimizu M, Fujita T, Doi Y, Kamimura Y, Takaya N. NO-inducible nitrosothionein mediates NO removal in tandem with thioredoxin. Nat Chem Biol 2013; 9:657-63. [DOI: 10.1038/nchembio.1316] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 07/08/2013] [Indexed: 11/09/2022]
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Fujita T, Nguyen HD, Ito T, Zhou S, Osada L, Tateyama S, Kaneko T, Takaya N. Microbial monomers custom-synthesized to build true bio-derived aromatic polymers. Appl Microbiol Biotechnol 2013; 97:8887-94. [PMID: 23949992 DOI: 10.1007/s00253-013-5078-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 06/19/2013] [Accepted: 06/19/2013] [Indexed: 12/01/2022]
Abstract
Aromatic polymers include novel and extant functional materials although none has been produced from biotic building blocks derived from primary biomass glucose. Here we screened microbial aromatic metabolites, engineered bacterial metabolism and fermented the aromatic lactic acid derivative β-phenyllactic acid (PhLA). We expressed the Wickerhamia fluorescens gene (pprA) encoding a phenylpyruvate reductase in Escherichia coli strains producing high levels of phenylalanine, and fermented optically pure (>99.9 %) D-PhLA. Replacing pprA with bacterial ldhA encoding lactate dehydrogenase generated L-PhLA, indicating that the produced enzymes converted phenylpyruvate, which is an intermediate of phenylalanine synthesis, to these chiral PhLAs. Glucose was converted under optimized fermentation conditions to yield 29 g/l D-PhLA, which was purified from fermentation broth. The product satisfied the laboratory-scale chemical synthesis of poly(D-PhLA) with M w 28,000 and allowed initial physiochemical characterization. Poly(D-PhLA) absorbed near ultraviolet light, and has the same potential as all other biomass-derived aromatic bioplastics of phenylated derivatives of poly(lactic acid). This approach to screening and fermenting aromatic monomers from glucose exploits a new era of bio-based aromatic polymer design and will contribute to petroleum conservation and carbon dioxide fixation.
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Affiliation(s)
- Tomoya Fujita
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
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Abstract
BACKGROUND L-Glucose, the enantiomer of D-glucose, was believed not to be utilized by any organisms. RESULTS An L-glucose-utilizing bacterium was isolated, and its L-glucose catabolic pathway was identified genetically and enzymatically. CONCLUSION L-Glucose was utilized via a novel pathway to pyruvate and D-glyceraldehyde 3-phosphate. SIGNIFICANCE This might lead to an understanding of homochirality in sugar metabolism. An L-glucose-utilizing bacterium, Paracoccus sp. 43P, was isolated from soil by enrichment cultivation in a minimal medium containing L-glucose as the sole carbon source. In cell-free extracts from this bacterium, NAD(+)-dependent L-glucose dehydrogenase was detected as having sole activity toward L-glucose. This enzyme, LgdA, was purified, and the lgdA gene was found to be located in a cluster of putative inositol catabolic genes. LgdA showed similar dehydrogenase activity toward scyllo- and myo-inositols. L-Gluconate dehydrogenase activity was also detected in cell-free extracts, which represents the reaction product of LgdA activity toward L-glucose. Enzyme purification and gene cloning revealed that the corresponding gene resides in a nine-gene cluster, the lgn cluster, which may participate in aldonate incorporation and assimilation. Kinetic and reaction product analysis of each gene product in the cluster indicated that they sequentially metabolize L-gluconate to glycolytic intermediates, D-glyceraldehyde-3-phosphate, and pyruvate through reactions of C-5 epimerization by dehydrogenase/reductase, dehydration, phosphorylation, and aldolase reaction, using a pathway similar to L-galactonate catabolism in Escherichia coli. Gene disruption studies indicated that the identified genes are responsible for L-glucose catabolism.
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Affiliation(s)
- Tetsu Shimizu
- From the Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Naoki Takaya
- From the Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Akira Nakamura
- From the Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
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Shimizu M, Masuo S, Fujita T, Doi Y, Kamimura Y, Takaya N. Hydrolase controls cellular NAD, sirtuin, and secondary metabolites. Mol Cell Biol 2012; 32:3743-55. [PMID: 22801369 PMCID: PMC3430197 DOI: 10.1128/mcb.00032-12] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Accepted: 07/09/2012] [Indexed: 12/21/2022] Open
Abstract
Cellular levels of NAD(+) and NADH are thought to be controlled by de novo and salvage mechanisms, although evidence has not yet indicated that they are regulated by NAD(+) degradation. Here we show that the conserved nudix hydrolase isozyme NdxA hydrolyzes and decreases cellular NAD(+) and NADH in Aspergillus nidulans. The NdxA-deficient fungus accumulated more NAD(+) during the stationary growth phase, indicating that NdxA maintains cellular NAD(+)/NADH homeostasis. The deficient strain also generated less of the secondary metabolites sterigmatocystin and penicillin G and of their gene transcripts than did the wild type. These defects were associated with a reduction in acetylated histone H4 on the gene promoters of aflR and ipnA that are involved in synthesizing secondary metabolites. Thus, NdxA increases acetylation levels of histone H4. We discovered that the novel fungal sirtuin isozyme SirA uses NAD(+) as a cosubstrate to deacetylate the lysine 16 residue of histone H4 on the gene promoter and represses gene expression. The impaired acetylation of histone and secondary metabolite synthesis in the NdxA-deficient strain were restored by eliminating functional SirA, indicating that SirA mediates NdxA-dependent regulation. These results indicated that NdxA controls total levels of NAD(+)/NADH and negatively regulates sirtuin function and chromatin structure.
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Affiliation(s)
- Motoyuki Shimizu
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
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Terabayashi Y, Shimizu M, Kitazume T, Masuo S, Fujii T, Takaya N. Conserved and specific responses to hypoxia in Aspergillus oryzae and Aspergillus nidulans determined by comparative transcriptomics. Appl Microbiol Biotechnol 2011; 93:305-17. [PMID: 22170104 DOI: 10.1007/s00253-011-3767-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 11/13/2011] [Accepted: 11/16/2011] [Indexed: 01/27/2023]
Abstract
Hypoxia imposes stress on filamentous fungi that require oxygen to proliferate. Global transcription analysis of Aspergillus oryzae grown under hypoxic conditions found that the expression of about 50% of 4,244 affected genes was either induced or repressed more than 2-fold. A comparison of these genes with the hypoxically regulated genes of Aspergillus nidulans based on their predicted amino acid sequences classified them as bi-directional best hit (BBH), one-way best hit (extra homolog, EH), and no-hit (non-syntenic genes, NSG) genes. Clustering analysis of the BBH genes indicated that A. oryzae and A. nidulans down-regulated global translation and transcription under hypoxic conditions, respectively. Under hypoxic conditions, both fungi up-regulated genes for alcohol fermentation and the γ-aminobutyrate shunt of the tricarboxylate cycle, whereas A. oryzae up-regulated the glyoxylate pathway, indicating that both fungi eliminate NADH accumulation under hypoxic conditions. The A. oryzae NS genes included specific genes for secondary and nitric oxide metabolism under hypoxic conditions. This comparative transcriptomic analysis discovered common and strain-specific responses to hypoxia in hypoxic Aspergillus species.
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Affiliation(s)
- Yasunobu Terabayashi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
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