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Sánchez KL, Baird JK, Nielsen A, Nurillah A, Agustina F, Komara, Fadilah F, Prameswari W, Nugraha RTP, Saputra S, Nurkanto A, Dharmayanthi AB, Pratama R, Exploitasia I, Greenwood AD. Naturally acquired immunity to Plasmodium pitheci in Bornean orangutans ( Pongo pygmaeus). Parasitology 2024; 151:380-389. [PMID: 38361461 PMCID: PMC11044065 DOI: 10.1017/s0031182024000155] [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: 05/08/2023] [Revised: 01/17/2024] [Accepted: 02/05/2024] [Indexed: 02/17/2024]
Abstract
Naturally acquired immunity to the different types of malaria in humans occurs in areas of endemic transmission and results in asymptomatic infection of peripheral blood. The current study examined the possibility of naturally acquired immunity in Bornean orangutans, Pongo pygmaeus, exposed to endemic Plasmodium pitheci malaria. A total of 2140 peripheral blood samples were collected between January 2017 and December 2022 from a cohort of 135 orangutans housed at a natural forested Rescue and Rehabilitation Centre in West Kalimantan, Indonesia. Each individual was observed for an average of 4.3 years during the study period. Blood samples were examined by microscopy and polymerase chain reaction for the presence of plasmodial parasites. Infection rates and parasitaemia levels were measured among age groups and all 20 documented clinical malaria cases were reviewed to estimate the incidence of illness and risk ratios among age groups. A case group of all 17 individuals that had experienced clinical malaria and a control group of 34 individuals having an event of >2000 parasites μL−1 blood but with no outward or clinical sign of illness were studied. Immature orangutans had higher-grade and more frequent parasitaemia events, but mature individuals were more likely to suffer from clinical malaria than juveniles. The case orangutans having patent clinical malaria were 256 times more likely to have had no parasitaemia event in the prior year relative to asymptomatic control orangutans. The findings are consistent with rapidly acquired immunity to P. pitheci illness among orangutans that wanes without re-exposure to the pathogen.
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Affiliation(s)
- Karmele Llano Sánchez
- IAR Indonesia Foundation, Yayasan Inisiasi Alam Rehabilitasi Indonesia (YIARI), Sinarwangi, Bogor, West Java, Indonesia
- International Animal Rescue, Uckfield, UK
- School of Veterinary Medicine, Freie Universität, Berlin, Germany
| | - John Kevin Baird
- Oxford University Clinical Research Unit-Indonesia, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Aileen Nielsen
- Center for Law and Economics, ETH Zurich, Zurich, Switzerland
| | - Andini Nurillah
- IAR Indonesia Foundation, Yayasan Inisiasi Alam Rehabilitasi Indonesia (YIARI), Sinarwangi, Bogor, West Java, Indonesia
| | - Fitria Agustina
- IAR Indonesia Foundation, Yayasan Inisiasi Alam Rehabilitasi Indonesia (YIARI), Sinarwangi, Bogor, West Java, Indonesia
| | - Komara
- IAR Indonesia Foundation, Yayasan Inisiasi Alam Rehabilitasi Indonesia (YIARI), Sinarwangi, Bogor, West Java, Indonesia
| | - Fina Fadilah
- IAR Indonesia Foundation, Yayasan Inisiasi Alam Rehabilitasi Indonesia (YIARI), Sinarwangi, Bogor, West Java, Indonesia
| | - Wendi Prameswari
- IAR Indonesia Foundation, Yayasan Inisiasi Alam Rehabilitasi Indonesia (YIARI), Sinarwangi, Bogor, West Java, Indonesia
| | | | - Sugiyono Saputra
- Research Center for Applied Zoology, National Research and Innovation Agency (BRIN), Jakarta, Indonesia
| | - Arif Nurkanto
- Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Jakarta, Indonesia
| | - Anik Budhi Dharmayanthi
- Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Jakarta, Indonesia
| | - Rahadian Pratama
- Center for Biomedical Research, Research Organization for Health, National Research and Innovation Agency (BRIN), Jakarta, Indonesia
| | - Indra Exploitasia
- Biodiversity Conservation Directorate of the General Director of Natural Resources and Ecosystem Conservation, Ministry of Environment and Forestry of the Republic of Indonesia, Jakarta, Indonesia
| | - Alex D. Greenwood
- School of Veterinary Medicine, Freie Universität, Berlin, Germany
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
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2
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Kusmiati K, Fanani A, Nurkanto A, Purnaningsih I, Mamangkey J, Ramadhani I, Nurcahyanto DA, Simanjuntak P, Afiati F, Irawan H, Puteri AL, Ewaldo MF, Juanssilfero AB. Profile and in silico analysis of metabolite compounds of the endophytic fungus Alternaria alternata K-10 from Drymoglossum piloselloides as antioxidants and antibacterials. Heliyon 2024; 10:e27978. [PMID: 38524563 PMCID: PMC10958433 DOI: 10.1016/j.heliyon.2024.e27978] [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: 09/07/2023] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 03/26/2024] Open
Abstract
Endophytic fungi are known for producing secondary metabolites with valuable biological activities, including antiviral, anticancer, antibacterial, and antioxidant properties. This study aims to evaluate an endophytic fungus from Dragon Scales leaves (Drymoglossum piloselloides) and analyze its metabolites as antioxidants and antibacterials. In this study, an endophytic fungus was isolated from the leaves of Dragon Scales (D. piloselloides) and identified using molecular analysis of the Internal Transcribed Spacer (ITS) ribosomal RNA locus. The fungus was authenticated as Alternaria alternata strain K-10. Crude extracts were obtained using n-hexane and ethyl acetate and analyzed via GC-MS Shimadzu-QP 2010 Ultra with NIST spectral library. Antibacterial activity was observed against Bacillus subtilis, Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa using the paper disc method, showing inhibition zones of 8.7-9.3 mm and 8.8-9.4 mm for ethyl acetate and n-hexane extracts, respectively. Ethyl acetate and n-hexane extracts exhibited strong antioxidant potential against 2,2-diphenyl-1-picrylhydrazil (DPPH) radical (IC50 values of 50.99 μg mL-1 and 74.44 μg mL-1, respectively). GC-MS analysis revealed 40 compounds in both extracts, some of which, including 2-ethylhexyl ester benzoic acid, benzo-b-dihydropyran-6-hydroxy-4-4-5-7-8-pentamethyl, diethyl phthalate, and octadecanoic acid, were identified through in silico analysis and found to possess antioxidant properties. These findings hold implications for potential applications of the plant and its biological constituent to be developed as lead compounds in the medical sector.
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Affiliation(s)
- Kusmiati Kusmiati
- Research Center for Biosystematics and Evolution- Research Organization for Life Sciences and Environment, The National Research and Innovation Agency (BRIN), Indonesia
| | - Asrul Fanani
- Research and Education Center for Bioinformatics, Indonesia Institute of Bioinformatics, Malang, 65162, Indonesia
| | - Arif Nurkanto
- Research Center for Biosystematics and Evolution- Research Organization for Life Sciences and Environment, The National Research and Innovation Agency (BRIN), Indonesia
| | - Ismu Purnaningsih
- Directorate of Scientific Collection Management, The National Research and Innovation Agency (BRIN)- KST Soekarno, Jl Raya Bogor Km 46, Cibinong Bogor, 16911, Indonesia
| | - Jendri Mamangkey
- Department of Biology Education, Faculty of Education and Teacher Training, Universitas Kristen Indonesia, Jakarta, Indonesia
- Research Center for Genetic Engineering, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), KST Soekarno, Cibinong, Bogor, Indonesia
| | - Indriati Ramadhani
- Research Center for Biosystematics and Evolution- Research Organization for Life Sciences and Environment, The National Research and Innovation Agency (BRIN), Indonesia
| | - Dian Alfian Nurcahyanto
- Research Center for Biosystematics and Evolution- Research Organization for Life Sciences and Environment, The National Research and Innovation Agency (BRIN), Indonesia
| | - Partomuan Simanjuntak
- Research Center for Pharmaceutical Ingredient and Traditional Medicine, National Research and Innovation Agency (BRIN), Indonesia
| | - Fifi Afiati
- Research Center for Applied Microbiology-Research Organization for Life Sciences and Environment, The National Research and Innovation Agency (BRIN), Indonesia
| | - Herman Irawan
- Research Center for Genetic Engineering, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), KST Soekarno, Cibinong, Bogor, Indonesia
| | - Ade Lia Puteri
- Research Center for Biosystematics and Evolution- Research Organization for Life Sciences and Environment, The National Research and Innovation Agency (BRIN), Indonesia
| | - Muhammad Farrel Ewaldo
- Master's Programme in Biomedical Sciences, Faculty of Medicine, Universitas Indonesia Jl. Salemba Raya – Jakarta Pusat, Indonesia
| | - Ario Betha Juanssilfero
- Research Center for Applied Microbiology-Research Organization for Life Sciences and Environment, The National Research and Innovation Agency (BRIN), Indonesia
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3
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Miatmoko A, Marufah NA, Nada Q, Rosita N, Erawati T, Susanto J, Purwantari KE, Nurkanto A, P, Soeratri W. The effect of surfactant type on characteristics, skin penetration and anti-aging effectiveness of transfersomes containing amniotic mesenchymal stem cells metabolite products in UV-aging induced mice. Drug Deliv 2022; 29:3443-3453. [PMID: 36471900 PMCID: PMC9731583 DOI: 10.1080/10717544.2022.2149895] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Transfersome has been developed to enhance dermal delivery of amniotic mesenchymal stem cell metabolite products (AMSC-MP). AMSC-MP contains many growth factors for managing skin aging, thus improving the quality of an adjusted life year. This study aims to determine the effect of surfactant types acting as the edge activator on transfersome-loading AMSC-MP. Transfersome was prepared by thin-layer hydration method and composed of l-α-phosphatidylcholine as a phospholipid and three types of surfactants, namely; cationic (stearylamine), anionic (sodium cholate), and nonionic surfactant (Tween 80) at a weight ratio of 85:15, respectively. Transfersomes were evaluated for physical characteristics, penetration, effectiveness, and safety. The results showed that sodium cholate, an anionic surfactant, produced the smallest transfersome particle size, i.e., 144.2 ± 3.2 nm, among all formulas. Trans-SA containing stearylamine had a positive charge of 41.53 ± 6.03 mV compared to Trans-SC and Trans-TW, whose respective charges were -56.9 ± 0.55 mV and -41.73 ± 0.86 mV. The small particle size and low negative value of zeta potential enabled high dermal penetration by transfersomes containing AMSC-MP, while the positive charge of stearylamine hindered its penetration of deeper skin layers. Trans-SC and Trans-TW produced higher collagen density values at 77.11 ± of 4.15% and 70.05 ± of 6.95%, than that of Trans-SA. All the AMSC-MP transfersomes were relatively safe with 0.5-1.0 macrophage cell numbers invaded the dermis per field of view. In conclusion, sodium cholate, an anionic surfactant, demonstrated considerable capacity as the edge activator of transfersome-loading AMSC-MP for skin anti-aging therapy.
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Affiliation(s)
- Andang Miatmoko
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Universitas Airlangga, Campus C UNAIR Mulyorejo, Surabaya, Indonesia,Stem Cell Research and Development Center, Universitas Airlangga, Campus C UNAIR Mulyorejo, Surabaya, Indonesia,CONTACT Andang Miatmoko Department of Pharmaceutical Science, Faculty of Pharmacy, Universitas Airlangga, Campus C UNAIR Mulyorejo, Surabaya, Indonesia
| | - Nurul Ailda Marufah
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Universitas Airlangga, Campus C UNAIR Mulyorejo, Surabaya, Indonesia
| | - Qothrin Nada
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Universitas Airlangga, Campus C UNAIR Mulyorejo, Surabaya, Indonesia
| | - Noorma Rosita
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Universitas Airlangga, Campus C UNAIR Mulyorejo, Surabaya, Indonesia
| | - Tristiana Erawati
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Universitas Airlangga, Campus C UNAIR Mulyorejo, Surabaya, Indonesia
| | - Joni Susanto
- Department of Anatomy and Histology, Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia
| | - Kusuma Eko Purwantari
- Department of Anatomy and Histology, Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia
| | - Arif Nurkanto
- Research Center for Biology, National Research and Innovation Agency, Kompleks CSC-BG LIPI, Bogor, Indonesia
| | - Purwati
- Stem Cell Research and Development Center, Universitas Airlangga, Campus C UNAIR Mulyorejo, Surabaya, Indonesia
| | - Widji Soeratri
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Universitas Airlangga, Campus C UNAIR Mulyorejo, Surabaya, Indonesia
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4
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Waluyo D, Prabandari EE, Pramisandi A, Hidayati DN, Chrisnayanti E, Puspitasari DJ, Dewi D, Oktaviani AN, Afrianti KR, Nonaka K, Matsumoto A, Tokiwa T, Adipratiwi N, Ariyani T, Hartuti ED, Putri TZ, Rahmawati Y, Inaoka DK, Miyazaki Y, Sakura T, Siska E, Kurnia K, Bernawati P, Mahsunah AH, Nugroho NB, Mori M, Dobashi K, Yamashita M, Nurkanto A, Watanabe A, Shiomi K, Wibowo AE, Nozaki T. Exploring natural microbial resources for the discovery of anti-malarial compounds. Parasitol Int 2021; 85:102432. [PMID: 34363974 DOI: 10.1016/j.parint.2021.102432] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 03/22/2021] [Revised: 06/23/2021] [Accepted: 08/01/2021] [Indexed: 01/21/2023]
Abstract
Microorganisms in nature are highly diverse biological resources, which can be explored for drug discovery. Some countries including Brazil, Columbia, Indonesia, China, and Mexico, which are blessed with geographical uniqueness with diverse climates and display remarkable megabiodiversity, potentially provide microorganismal resources for such exploitation. In this review, as an example of drug discovery campaigns against tropical parasitic diseases utilizing microorganisms from such a megabiodiversity country, we summarize our past and on-going activities toward discovery of new antimalarials. The program was held in a bilateral collaboration between multiple Indonesian and Japanese research groups. In order to develop a new platform of drug discovery utilizing Indonesian bioresources under an international collaborative scheme, we aimed at: 1) establishment of an Indonesian microbial depository, 2) development of robust enzyme-based and cell-based screening systems, and 3) technology transfer necessary for screening, purification, and identification of antimalarial compounds from microbial culture broths. We collected, characterized, and deposited Indonesian microbes. We morphologically and genetically characterized fungi and actinomycetes strains isolated from 5 different locations representing 3 Indonesian geographical areas, and validated genetic diversity of microbes. Enzyme-based screening was developed against two validated mitochondrial enzymes from Plasmodium falciparum, dihydroorotate dehydrogenase and malate:quinone oxidoreductase, while cell-based proliferation assay was developed using the erythrocytic stage parasite of 3D7 strain. More than 17 thousands microbial culture extracts were subjected to the enzyme- and cell-based screening. Representative anti-malarial compounds discovered in this campaign are discussed, including a few isolated compounds that have been identified for the first time as anti-malarial compounds. Our antimalarial discovery campaign validated the Indonesian microbial library as a powerful resource for drug discovery. We also discuss critical needs for selection criteria for hits at each stage of screening and hit deconvolution such as preliminary extraction test for the initial profiling of the active compounds and dereplication techniques to minimize repetitive discovery of known compounds.
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Affiliation(s)
- Danang Waluyo
- Laboratory for Biotechnology (Biotech Center), Agency for the Assessment and Application of Technology (BPPT), Building 630, Puspiptek Area, Setu, South Tangerang 15314, Banten, Indonesia
| | - Erwahyuni Endang Prabandari
- Laboratory for Biotechnology (Biotech Center), Agency for the Assessment and Application of Technology (BPPT), Building 630, Puspiptek Area, Setu, South Tangerang 15314, Banten, Indonesia
| | - Amila Pramisandi
- Laboratory for Biotechnology (Biotech Center), Agency for the Assessment and Application of Technology (BPPT), Building 630, Puspiptek Area, Setu, South Tangerang 15314, Banten, Indonesia
| | - Dyah Noor Hidayati
- Laboratory for Biotechnology (Biotech Center), Agency for the Assessment and Application of Technology (BPPT), Building 630, Puspiptek Area, Setu, South Tangerang 15314, Banten, Indonesia
| | - Evita Chrisnayanti
- Laboratory for Biotechnology (Biotech Center), Agency for the Assessment and Application of Technology (BPPT), Building 630, Puspiptek Area, Setu, South Tangerang 15314, Banten, Indonesia
| | - Dian Japany Puspitasari
- Laboratory for Biotechnology (Biotech Center), Agency for the Assessment and Application of Technology (BPPT), Building 630, Puspiptek Area, Setu, South Tangerang 15314, Banten, Indonesia
| | - Diana Dewi
- Laboratory for Biotechnology (Biotech Center), Agency for the Assessment and Application of Technology (BPPT), Building 630, Puspiptek Area, Setu, South Tangerang 15314, Banten, Indonesia
| | - Avi Nurul Oktaviani
- Laboratory for Biotechnology (Biotech Center), Agency for the Assessment and Application of Technology (BPPT), Building 630, Puspiptek Area, Setu, South Tangerang 15314, Banten, Indonesia
| | - Kiki Rizkia Afrianti
- Laboratory for Biotechnology (Biotech Center), Agency for the Assessment and Application of Technology (BPPT), Building 630, Puspiptek Area, Setu, South Tangerang 15314, Banten, Indonesia
| | - Kenichi Nonaka
- Ōmura Satoshi Memorial Institute, Kitasato University, Tokyo, Japan
| | - Atsuko Matsumoto
- Ōmura Satoshi Memorial Institute, Kitasato University, Tokyo, Japan
| | - Toshiyuki Tokiwa
- Ōmura Satoshi Memorial Institute, Kitasato University, Tokyo, Japan
| | - Nadia Adipratiwi
- Laboratory for Biotechnology (Biotech Center), Agency for the Assessment and Application of Technology (BPPT), Building 630, Puspiptek Area, Setu, South Tangerang 15314, Banten, Indonesia
| | - Titin Ariyani
- Laboratory for Biotechnology (Biotech Center), Agency for the Assessment and Application of Technology (BPPT), Building 630, Puspiptek Area, Setu, South Tangerang 15314, Banten, Indonesia
| | - Endah Dwi Hartuti
- Laboratory for Biotechnology (Biotech Center), Agency for the Assessment and Application of Technology (BPPT), Building 630, Puspiptek Area, Setu, South Tangerang 15314, Banten, Indonesia; School of Tropical Medicine and Global Health, Nagasaki University, 1-12-4, Sakamoto, Nagasaki 852-8523, Japan
| | - Tiara Zovi Putri
- Laboratory for Biotechnology (Biotech Center), Agency for the Assessment and Application of Technology (BPPT), Building 630, Puspiptek Area, Setu, South Tangerang 15314, Banten, Indonesia
| | - Yulia Rahmawati
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Daniel Ken Inaoka
- School of Tropical Medicine and Global Health, Nagasaki University, 1-12-4, Sakamoto, Nagasaki 852-8523, Japan
| | - Yukiko Miyazaki
- School of Tropical Medicine and Global Health, Nagasaki University, 1-12-4, Sakamoto, Nagasaki 852-8523, Japan
| | - Takaya Sakura
- School of Tropical Medicine and Global Health, Nagasaki University, 1-12-4, Sakamoto, Nagasaki 852-8523, Japan
| | - Eka Siska
- Laboratory for Biotechnology (Biotech Center), Agency for the Assessment and Application of Technology (BPPT), Building 630, Puspiptek Area, Setu, South Tangerang 15314, Banten, Indonesia
| | - Kesi Kurnia
- Laboratory for Biotechnology (Biotech Center), Agency for the Assessment and Application of Technology (BPPT), Building 630, Puspiptek Area, Setu, South Tangerang 15314, Banten, Indonesia
| | - Putri Bernawati
- Laboratory for Biotechnology (Biotech Center), Agency for the Assessment and Application of Technology (BPPT), Building 630, Puspiptek Area, Setu, South Tangerang 15314, Banten, Indonesia
| | - Anis Herliyati Mahsunah
- Laboratory for Biotechnology (Biotech Center), Agency for the Assessment and Application of Technology (BPPT), Building 630, Puspiptek Area, Setu, South Tangerang 15314, Banten, Indonesia
| | - Nuki Bambang Nugroho
- Laboratory for Biotechnology (Biotech Center), Agency for the Assessment and Application of Technology (BPPT), Building 630, Puspiptek Area, Setu, South Tangerang 15314, Banten, Indonesia
| | - Mihoko Mori
- Ōmura Satoshi Memorial Institute, Kitasato University, Tokyo, Japan
| | - Kazuyuki Dobashi
- Ōmura Satoshi Memorial Institute, Kitasato University, Tokyo, Japan
| | - Michio Yamashita
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Arif Nurkanto
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan; Research Center for Biology, Indonesia Institute of Science (LIPI), Cibinong, Indonesia
| | | | - Kazuro Shiomi
- Ōmura Satoshi Memorial Institute, Kitasato University, Tokyo, Japan
| | - Agung Eru Wibowo
- Laboratory for Biotechnology (Biotech Center), Agency for the Assessment and Application of Technology (BPPT), Building 630, Puspiptek Area, Setu, South Tangerang 15314, Banten, Indonesia; Center for Pharmaceutical and Medical Technology, Agency for the Assessment and Application of Technology (BPPT), Laptiab, Puspiptek, Setu, South Tangerang 15314, Banten, Indonesia
| | - Tomoyoshi Nozaki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.
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5
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Pramisandi A, Kurnia K, Chrisnayanti E, Bernawati P, Dobashi K, Mori M, Mahsunah AH, Nonaka K, Matsumoto A, Kristiningrum, Hidayati DN, Dewi D, Prabandari EE, Amalia E, Rahmawati Y, Nurkanto A, Inaoka DK, Waluyo D, Kita K, Nozaki T, Ōmura S, Shiomi K. Gentisyl alcohol and homogentisic acid: Plasmodium falciparum dihydroorotate dehydrogenase inhibitors isolated from fungi. J GEN APPL MICROBIOL 2021; 67:114-117. [PMID: 33814517 DOI: 10.2323/jgam.2020.08.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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
Two Indonesian fungi Aspergillus assiutensis BioMCC-f.T.7495 and Penicillium pedernalense BioMCC-f.T.5350 along with a Japanese fungus Hypomyces pseudocorticiicola FKI-9008 have been found to produce gentisyl alcohol (1), which inhibits Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) with an IC50 value of 3.4 μM. Another Indonesian fungus, Penicillium citrinum BioMCC-f.T.6730, produced an analog of 1, homogentisic acid (4), which also inhibits PfDHODH with an IC50 value of 47.6 μM.
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Affiliation(s)
- Amila Pramisandi
- Graduate School of Infection Control Sciences, Kitasato University.,Laboratory for Biotechnology, Agency for the Assessment and Application of Technology (BPPT)
| | - Kesi Kurnia
- Laboratory for Biotechnology, Agency for the Assessment and Application of Technology (BPPT)
| | - Evita Chrisnayanti
- Laboratory for Biotechnology, Agency for the Assessment and Application of Technology (BPPT)
| | - Putri Bernawati
- Laboratory for Biotechnology, Agency for the Assessment and Application of Technology (BPPT)
| | - Kazuyuki Dobashi
- Department of Drug Discovery Sciences, Kitasato Institute for Life Sciences
| | - Mihoko Mori
- Graduate School of Infection Control Sciences, Kitasato University.,Department of Drug Discovery Sciences, Kitasato Institute for Life Sciences
| | - Anis Herliyati Mahsunah
- Laboratory for Biotechnology, Agency for the Assessment and Application of Technology (BPPT)
| | - Kenichi Nonaka
- Graduate School of Infection Control Sciences, Kitasato University.,Department of Drug Discovery Sciences, Kitasato Institute for Life Sciences
| | - Atsuko Matsumoto
- Graduate School of Infection Control Sciences, Kitasato University.,Department of Drug Discovery Sciences, Kitasato Institute for Life Sciences
| | - Kristiningrum
- Laboratory for Biotechnology, Agency for the Assessment and Application of Technology (BPPT)
| | - Dyah Noor Hidayati
- Laboratory for Biotechnology, Agency for the Assessment and Application of Technology (BPPT)
| | - Diana Dewi
- Laboratory for Biotechnology, Agency for the Assessment and Application of Technology (BPPT)
| | | | - Eri Amalia
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo
| | - Yulia Rahmawati
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo
| | - Arif Nurkanto
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo.,Research Center for Biology, Indonesia Institute of Sciences (LIPI)
| | - Daniel Ken Inaoka
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo.,School of Tropical Medicine and Global Health, Nagasaki University.,Department of Molecular Infection Dynamics, Institute of Tropical Medicine (NEKKEN), Nagasaki University
| | - Danang Waluyo
- Laboratory for Biotechnology, Agency for the Assessment and Application of Technology (BPPT)
| | - Kiyoshi Kita
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo.,School of Tropical Medicine and Global Health, Nagasaki University.,Department of Molecular Infection Dynamics, Institute of Tropical Medicine (NEKKEN), Nagasaki University.,Department of Host-Defense Biochemistry, Institute of Tropical Medicine (NEKKEN), Nagasaki University
| | - Tomoyoshi Nozaki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo
| | - Satoshi Ōmura
- Department of Drug Discovery Sciences, Kitasato Institute for Life Sciences
| | - Kazuro Shiomi
- Graduate School of Infection Control Sciences, Kitasato University.,Department of Drug Discovery Sciences, Kitasato Institute for Life Sciences
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6
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Nurkanto A, Jeelani G, Santos HJ, Rahmawati Y, Mori M, Nakamura Y, Goto K, Saikawa Y, Annoura T, Tozawa Y, Sakura T, Inaoka DK, Shiomi K, Nozaki T. Characterization of Plasmodium falciparum Pantothenate Kinase and Identification of Its Inhibitors From Natural Products. Front Cell Infect Microbiol 2021; 11:639065. [PMID: 33768012 PMCID: PMC7985445 DOI: 10.3389/fcimb.2021.639065] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 12/08/2020] [Accepted: 01/29/2021] [Indexed: 12/17/2022] Open
Abstract
Coenzyme A (CoA) is a well-known cofactor that plays an essential role in many metabolic reactions in all organisms. In Plasmodium falciparum, the most deadly among Plasmodium species that cause malaria, CoA and its biosynthetic pathway have been proven to be indispensable. The first and rate-limiting reaction in the CoA biosynthetic pathway is catalyzed by two putative pantothenate kinases (PfPanK1 and 2) in this parasite. Here we produced, purified, and biochemically characterized recombinant PfPanK1 for the first time. PfPanK1 showed activity using pantetheine besides pantothenate, as the primary substrate, indicating that CoA biosynthesis in the blood stage of P. falciparum can bypass pantothenate. We further developed a robust and reliable screening system to identify inhibitors using recombinant PfPanK1 and identified four PfPanK inhibitors from natural compounds.
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Affiliation(s)
- Arif Nurkanto
- Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia.,Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ghulam Jeelani
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Herbert J Santos
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yulia Rahmawati
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mihoko Mori
- Kitasato Institute for Life Sciences, Kitasato University, Tokyo, Japan.,Biological Resource Center, National Institute of Technology and Evaluation (NITE), Chiba, Japan
| | - Yumi Nakamura
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, Yokohama, Japan
| | - Kana Goto
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, Yokohama, Japan
| | - Yoko Saikawa
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, Yokohama, Japan
| | - Takeshi Annoura
- Department of Parasitology, National Institute of Infectious Diseases (NIID), Tokyo, Japan
| | - Yuzuru Tozawa
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Takaya Sakura
- Department of Molecular Infection Dynamics, School of Tropical Medicine and Global Health, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Daniel Ken Inaoka
- Department of Molecular Infection Dynamics, School of Tropical Medicine and Global Health, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Kazuro Shiomi
- Kitasato Institute for Life Sciences, Kitasato University, Tokyo, Japan
| | - Tomoyoshi Nozaki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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7
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Pramisandi A, Dobashi K, Mori M, Nonaka K, Matsumoto A, Tokiwa T, Higo M, Kristiningrum, Amalia E, Nurkanto A, Inaoka DK, Waluyo D, Kita K, Nozaki T, Ōmura S, Shiomi K. Microbial inhibitors active against Plasmodium falciparum dihydroorotate dehydrogenase derived from an Indonesian soil fungus, Talaromyces pinophilus BioMCC-f.T.3979. J GEN APPL MICROBIOL 2020; 66:273-278. [PMID: 32669511 DOI: 10.2323/jgam.2019.11.007] [Citation(s) in RCA: 4] [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: 11/03/2022]
Abstract
An Indonesian soil fungus, Talaromyces pinophilus BioMCC-f.T.3979 was cultured to find novel scaffolds of Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) inhibitors. We obtained altenusin (1), which inhibits PfDHODH, with an IC50 value of 5.9 μM, along with other metabolites: mitorubrinol (2) and mitorubrinic acid (3). Compounds 1 and 2 inhibited PfDHODH but displayed no activity against the human orthologue. They also inhibited P. falciparum 3D7 cell growth in vitro. Compound 3 showed little PfDHODH inhibitory activity or cell growth inhibitory activity.
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Affiliation(s)
- Amila Pramisandi
- Graduate School of Infection Control Sciences, Kitasato University.,Laboratory for Biotechnology, Agency for the Assessment and Application of Technology (BPPT)
| | - Kazuyuki Dobashi
- Department of Drug Discovery Sciences, Kitasato Institute for Life Sciences
| | - Mihoko Mori
- Graduate School of Infection Control Sciences, Kitasato University.,Department of Drug Discovery Sciences, Kitasato Institute for Life Sciences
| | - Kenichi Nonaka
- Graduate School of Infection Control Sciences, Kitasato University.,Department of Drug Discovery Sciences, Kitasato Institute for Life Sciences
| | - Atsuko Matsumoto
- Graduate School of Infection Control Sciences, Kitasato University.,Department of Drug Discovery Sciences, Kitasato Institute for Life Sciences
| | - Toshiyuki Tokiwa
- Department of Drug Discovery Sciences, Kitasato Institute for Life Sciences
| | - Mayuka Higo
- Department of Drug Discovery Sciences, Kitasato Institute for Life Sciences
| | - Kristiningrum
- Laboratory for Biotechnology, Agency for the Assessment and Application of Technology (BPPT)
| | - Eri Amalia
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo
| | - Arif Nurkanto
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo.,Research Center for Biology, Indonesia Institute of Sciences (LIPI)
| | - Daniel Ken Inaoka
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo.,School of Tropical Medicine and Global Health, Nagasaki University.,Department of Molecular Infection Dynamics, Institute of Tropical Medicine (NEKKEN), Nagasaki University
| | - Danang Waluyo
- Laboratory for Biotechnology, Agency for the Assessment and Application of Technology (BPPT)
| | - Kiyoshi Kita
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo.,School of Tropical Medicine and Global Health, Nagasaki University.,Department of Molecular Infection Dynamics, Institute of Tropical Medicine (NEKKEN), Nagasaki University
| | - Tomoyoshi Nozaki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo
| | - Satoshi Ōmura
- Department of Drug Discovery Sciences, Kitasato Institute for Life Sciences
| | - Kazuro Shiomi
- Graduate School of Infection Control Sciences, Kitasato University.,Department of Drug Discovery Sciences, Kitasato Institute for Life Sciences
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8
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Nurkanto A, Jeelani G, Yamamoto T, Hishiki T, Naito Y, Suematsu M, Hashimoto T, Nozaki T. Biochemical, Metabolomic, and Genetic Analyses of Dephospho Coenzyme A Kinase Involved in Coenzyme A Biosynthesis in the Human Enteric Parasite Entamoeba histolytica. Front Microbiol 2018; 9:2902. [PMID: 30555442 PMCID: PMC6284149 DOI: 10.3389/fmicb.2018.02902] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [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: 08/03/2018] [Accepted: 11/13/2018] [Indexed: 11/14/2022] Open
Abstract
Coenzyme A (CoA) is an essential cofactor for numerous cellular reactions in all living organisms. In the protozoan parasite Entamoeba histolytica, CoA is synthesized in a pathway consisting of four enzymes with dephospho-CoA kinase (DPCK) catalyzing the last step. However, the metabolic and physiological roles of E. histolytica DPCK remain elusive. In this study, we took biochemical, reverse genetic, and metabolomic approaches to elucidate role of DPCK in E. histolytica. The E. histolytica genome encodes two DPCK isotypes (EhDPCK1 and EhDPCK2). Epigenetic gene silencing of Ehdpck1 and Ehdpck2 caused significant reduction of DPCK activity, intracellular CoA concentrations, and also led to growth retardation in vitro, suggesting importance of DPCK for CoA synthesis and proliferation. Furthermore, metabolomic analysis showed that suppression of Ehdpck gene expression also caused decrease in the level of acetyl-CoA, and metabolites involved in amino acid, glycogen, hexosamine, nucleic acid metabolisms, chitin, and polyamine biosynthesis. The kinetic properties of E. histolytica and human DPCK showed remarkable differences, e.g., the Km values of E. histolytica and human DPCK were 58-114 and 5.2 μM toward dephospho-CoA and 15-20 and 192 μM for ATP, respectively. Phylogenetic analysis also supported the uniqueness of the amebic enzyme compared to the human counterpart. These biochemical, evolutionary features, and physiological importance of EhDPCKs indicate that EhDPCK represents the rational target for the development of anti-amebic agents.
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Affiliation(s)
- Arif Nurkanto
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
- Research Center for Biology, Indonesia Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Ghulam Jeelani
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takehiro Yamamoto
- Department of Biochemistry, School of Medicine, Keio University, Tokyo, Japan
| | - Takako Hishiki
- Department of Biochemistry, School of Medicine, Keio University, Tokyo, Japan
- Clinical and Translational Research Center, School of Medicine, Keio University, Tokyo, Japan
| | - Yoshiko Naito
- Clinical and Translational Research Center, School of Medicine, Keio University, Tokyo, Japan
| | - Makoto Suematsu
- Department of Biochemistry, School of Medicine, Keio University, Tokyo, Japan
| | - Tetsuo Hashimoto
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Tomoyoshi Nozaki
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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9
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Nurkanto A, Jeelani G, Yamamoto T, Naito Y, Hishiki T, Mori M, Suematsu M, Shiomi K, Hashimoto T, Nozaki T. Characterization and validation of Entamoeba histolytica pantothenate kinase as a novel anti-amebic drug target. Int J Parasitol Drugs Drug Resist 2018; 8:125-136. [PMID: 29518650 PMCID: PMC6114107 DOI: 10.1016/j.ijpddr.2018.02.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 02/19/2018] [Accepted: 02/22/2018] [Indexed: 11/02/2022]
Abstract
The Coenzyme A (CoA), as a cofactor involved in >100 metabolic reactions, is essential to the basic biochemistry of life. Here, we investigated the CoA biosynthetic pathway of Entamoeba histolytica (E. histolytica), an enteric protozoan parasite responsible for human amebiasis. We identified four key enzymes involved in the CoA pathway: pantothenate kinase (PanK, EC 2.7.1.33), bifunctional phosphopantothenate-cysteine ligase/decarboxylase (PPCS-PPCDC), phosphopantetheine adenylyltransferase (PPAT) and dephospho-CoA kinase (DPCK). Cytosolic enzyme PanK, was selected for further biochemical, genetic, and phylogenetic characterization. Since E. histolytica PanK (EhPanK) is physiologically important and sufficiently divergent from its human orthologs, this enzyme represents an attractive target for the development of novel anti-amebic chemotherapies. Epigenetic gene silencing of PanK resulted in a significant reduction of PanK activity, intracellular CoA concentrations, and growth retardation in vitro, reinforcing the importance of this gene in E. histolytica. Furthermore, we screened the Kitasato Natural Products Library for inhibitors of recombinant EhPanK, and identified 14 such compounds. One compound demonstrated moderate inhibition of PanK activity and cell growth at a low concentration, as well as differential toxicity towards E. histolytica and human cells.
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Affiliation(s)
- Arif Nurkanto
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan; Department of Parasitology, National Institute of Infectious Diseases (NIID), Tokyo, Japan; Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Japan; Research Center for Biology, Indonesia Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Ghulam Jeelani
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Japan
| | - Takehiro Yamamoto
- Department of Biochemistry, School of Medicine, Keio University, Tokyo, Japan
| | - Yoshiko Naito
- Clinical and Translational Research Center, Keio University School of Medicine, Japan
| | - Takako Hishiki
- Department of Biochemistry, School of Medicine, Keio University, Tokyo, Japan; Clinical and Translational Research Center, Keio University School of Medicine, Japan
| | - Mihoko Mori
- Kitasato Institute for Life Sciences, Kitasato University, Tokyo, Japan
| | - Makoto Suematsu
- Department of Biochemistry, School of Medicine, Keio University, Tokyo, Japan
| | - Kazuro Shiomi
- Kitasato Institute for Life Sciences, Kitasato University, Tokyo, Japan
| | - Tetsuo Hashimoto
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Tomoyoshi Nozaki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Japan.
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10
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Hamada M, Shibata C, Tamura T, Nurkanto A, Ratnakomala S, Lisdiyanti P, Suzuki KI. Kocuria pelophila sp. nov., an actinobacterium isolated from the rhizosphere of a mangrove. Int J Syst Evol Microbiol 2016; 66:3276-3280. [PMID: 27221097 DOI: 10.1099/ijsem.0.001186] [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: 11/18/2022] Open
Abstract
A novel spherical actinobacterium, designated RS-2-3T, was isolated from the rhizosphere of a mangrove growing on Rambut Island, Indonesia, and its taxonomic position was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparison revealed that strain RS-2-3T was related to the members of the genus Kocuria. The highest 16S rRNA gene sequence similarity value was observed with Kocuria marina KMM 3905T (97.0 %). The peptidoglycan type of strain RS-2-3T was found to be A3α with an interpeptide bridge comprising l-Ala4-5. The predominant menaquinone was MK-7(H2) and the major fatty acids were anteiso-C15 : 0 and iso-C15 : 0. The DNA G+C content was 71.8 mol%. These characteristics were consistent with those of members of the genus Kocuria. Meanwhile, physiological and biochemical characteristics revealed that strain RS-2-3T differed from the species of the genus Kocuria with validly published names. Therefore, strain RS-2-3T represents a novel species of the genus Kocuria, for which the name Kocuria pelophila sp. nov. is proposed. The type strain is RS-2-3T (=NBRC 110990T=InaCC A704T).
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Affiliation(s)
- Moriyuki Hamada
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Chiyo Shibata
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Tomohiko Tamura
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Arif Nurkanto
- Indonesian Institute of Sciences (LIPI), Jl, Raya Jakarta-Bogor Km. 46, Cibinong 16911, Indonesia
| | - Shanti Ratnakomala
- Indonesian Institute of Sciences (LIPI), Jl, Raya Jakarta-Bogor Km. 46, Cibinong 16911, Indonesia
| | - Puspita Lisdiyanti
- Indonesian Institute of Sciences (LIPI), Jl, Raya Jakarta-Bogor Km. 46, Cibinong 16911, Indonesia
| | - Ken-Ichiro Suzuki
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
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11
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Nurkanto A, Lisdiyanti P, Hamada M, Ratnakomala S, Shibata C, Tamura T. Actinoplanes tropicalis sp. nov. and Actinoplanes cibodasensis sp. nov., isolated from leaf litter. Int J Syst Evol Microbiol 2015; 65:3824-3829. [DOI: 10.1099/ijsem.0.000499] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two actinomycete strains, designated LIPI11-2-Ac034T and LIPI11-2-Ac042T, were isolated from leaf litter collected from Cibodas Botanical Garden, West Java, Indonesia. Phylogenetic analysis based on 16S rRNA gene sequences suggested that both isolates belong to the genus Actinoplanes. These isolates were closely related to Actinoplanes ferrugineus and Actinoplanes durhamensis with similarity values of 98.2 % and 97.7 % respectively, for strain LIPI11-2-Ac034T, and 99.0 % and 97.4–97.7 % respectively for strain LIPI11-2-Ac042T. Both isolates grew well on ISP 7 medium with brown soluble pigment production. Spores were motile and sporangia were irregular. The isolates contained meso-diaminopimelic acid in cell-wall hydrolysates, and mannose, glucose and galactose in whole-cell hydrolysates. The predominant menaquinone of strain LIPI11-2-Ac034T was MK-9(H4) while that of strain LIPI11-2-Ac042T was MK-9(H6). The major cellular fatty acids were iso-C16 : 0, iso-C15 : 0 and anteiso-C15 : 0 for strain LIPI11-2-Ac034T, and iso-C16 : 0, anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0 for strain LIPI11-2-Ac042T. Phosphatidylethanolamine was detected as the diagnostic polar lipid. The DNA G+C contents of strains LIPI11-2-Ac034T and LIPI11-2-Ac042T were 71.5 and 70.7 mol%, respectively. Based on the differential phenotypic characteristics and the results of DNA–DNA hybridization and phylogenetic analysis, it is proposed that strains LIPI11-2-Ac034T and LIPI11-2-Ac042T represent two novel species of the genus Actinoplanes, for which the names Actinoplanes tropicalis sp. nov. (type strain LIPI11-2-Ac034T = InaCC A459T = NBRC 110973T) and Actinoplanes cibodasensis sp. nov. (type strain LIPI11-2-Ac042T = InaCC A458T = NBRC 110974T) are proposed.
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Affiliation(s)
- Arif Nurkanto
- Research Center for Biology, Indonesia Institute of Sciences (LIPI), Cibinong Science Center. Jl. Jakarta Bogor KM 46 Bogor, West Java, Indonesia
| | - Puspita Lisdiyanti
- Research Center for Biotechnology, Indonesia Institute of Sciences (LIPI), Cibinong Science Center. Jl. Jakarta Bogor KM 46 Bogor, West Java, Indonesia
| | - Moriyuki Hamada
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Shanti Ratnakomala
- Research Center for Biotechnology, Indonesia Institute of Sciences (LIPI), Cibinong Science Center. Jl. Jakarta Bogor KM 46 Bogor, West Java, Indonesia
| | - Chiyo Shibata
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Tomohiko Tamura
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
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12
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Nurkanto A, Lisdiyanti P, Hamada M, Ratnakomala S, Shibata C, Tamura T. Cryptosporangium cibodasense sp. nov., isolated from leaf litter in Indonesia. Int J Syst Evol Microbiol 2015; 65:4632-4637. [PMID: 26395204 DOI: 10.1099/ijsem.0.000625] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel actinomycete strain, designated LIPI11-2-Ac046T, was isolated from a leaf litter sample obtained from Cibodas Botanical Garden, West Java, Indonesia, using the rehydration and centrifugation method. The taxonomic status of this organism was established using a polyphasic approach. Comparative 16S rRNA gene sequence analysis revealed that strain LIPI11-2-Ac046T had the closest sequence similarities with members of the genus Cryptosporangium (97.99-98.90 %). The strain grew well on ISP 4 and ISP 5 media and formed sporangia. Spores of this strain were motile. The strain grew in the presence of 0-2 % (w/v) NaCl and the temperature range of 15-28 8C. The cell-wall hydrolysate contained meso-diaminopimelic acid as the diagnostic diamino acid and the whole-cell hydrolysate contained mannose, glucose, galactose, ribose and xylose, together with one unidentified O-methyl-pentose. The predominant menaquinones were MK-9(H4), MK-9(H6) and MK-9(H8), and the major polar lipid was phosphatidylethanolamine. The major cellular fatty acids were C18 : 1ω9c, iso-C16 : 0, C16 : 0 andC17 : 1ω9c. These phenotypic characteristics corresponded to those of the genus Cryptosporangium. Meanwhile, the results of DNA-DNA hybridization as well as physiological and biochemical analyses distinguished strain LIPI11-2-Ac046T from known members of the genus Cryptosporangium. On the basis of these data, it is proposed that strain LIPI11-2-Ac046T represents a novel species of the genus Cryptosporangium, with the name Cryptosporangium cibodasense sp. nov. The type strain is LIPI11-2-Ac046T (=InaCC A457T=NBRC 110976T).
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Affiliation(s)
- Arif Nurkanto
- Research Center for Biology, Indonesia Institute of Sciences (LIPI), Cibinong Science Center, . Jl. Jakarta Bogor KM 46 Bogor, West Java, Indonesia
| | - Puspita Lisdiyanti
- Research Center for Biotechnology, Indonesia Institute of Sciences (LIPI), Cibinong Science Center, . Jl. Jakarta Bogor KM 46 Bogor, West Java, Indonesia
| | - Moriyuki Hamada
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Shanti Ratnakomala
- Research Center for Biotechnology, Indonesia Institute of Sciences (LIPI), Cibinong Science Center, . Jl. Jakarta Bogor KM 46 Bogor, West Java, Indonesia
| | - Chiyo Shibata
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Tomohiko Tamura
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
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13
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Nurkanto A, Lisdiyanti P, Hamada M, Ratnakomala S, Shibata C, Tamura T. Actinoplanes bogoriensis sp. nov., a novel actinomycete isolated from leaf litter. J Antibiot (Tokyo) 2015; 69:26-30. [DOI: 10.1038/ja.2015.81] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 06/05/2015] [Accepted: 07/04/2015] [Indexed: 11/09/2022]
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14
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Hamada M, Shibata C, Nurkanto A, Ratnakomala S, Lisdiyanti P, Tamura T, Suzuki KI. Erratum to: Tropicihabitans flavus gen. nov., sp. nov., a new member of the family Cellulomonadaceae. Antonie Van Leeuwenhoek 2015; 108:221. [DOI: 10.1007/s10482-015-0474-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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15
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Hamada M, Shibata C, Nurkanto A, Ratnakomala S, Lisdiyanti P, Tamura T, Suzuki KI. Serinibacter tropicus sp. nov., an actinobacterium isolated from the rhizosphere of a mangrove, and emended description of the genus Serinibacter. Int J Syst Evol Microbiol 2015; 65:1151-1154. [DOI: 10.1099/ijs.0.000068] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-positive actinobacterium, designated PS-14-7T, was isolated from the rhizosphere of a mangrove on Pramuka Island, Indonesia, and its taxonomic position was investigated using a polyphasic approach. The peptidoglycan type of strain PS-14-7T was A4α and lysine was the diagnostic diamino acid of the peptidoglycan. The predominant menaquinone was MK-8(H4) and the major fatty acids were anteiso-C15 : 0, C16 : 0 and iso-C16 : 0. The DNA G+C content was 72.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain PS-14-7T was closely related to
Serinibacter salmoneus
Kis4-28T (99.6 %). However, DNA–DNA hybridization and phenotypic characteristics revealed that strain PS-14-7T differed from
Serinibacter salmoneus
. Therefore, strain PS-14-7T represents a novel species of the genus
Serinibacter
, for which the name Serinibacter
tropicus sp. nov. is proposed. The type strain is PS-14-7T ( = NBRC 110108T = InaCC A 515T). An emended description of the genus
Serinibacter
is also proposed.
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Affiliation(s)
- Moriyuki Hamada
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Chiyo Shibata
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Arif Nurkanto
- Indonesian Institute of Sciences (LIPI), Jl, Raya Jakarta-Bogor Km. 46, Cibinong 16911, Indonesia
| | - Shanti Ratnakomala
- Indonesian Institute of Sciences (LIPI), Jl, Raya Jakarta-Bogor Km. 46, Cibinong 16911, Indonesia
| | - Puspita Lisdiyanti
- Indonesian Institute of Sciences (LIPI), Jl, Raya Jakarta-Bogor Km. 46, Cibinong 16911, Indonesia
| | - Tomohiko Tamura
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Ken-ichiro Suzuki
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
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16
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Hamada M, Shibata C, Nurkanto A, Ratnakomala S, Lisdiyanti P, Tamura T, Suzuki KI. Tropicihabitans flavus gen. nov., sp. nov., a new member of the family Cellulomonadaceae. Antonie Van Leeuwenhoek 2015; 107:1299-306. [PMID: 25761861 DOI: 10.1007/s10482-015-0424-4] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 03/02/2015] [Indexed: 10/23/2022]
Abstract
Two novel Gram-stain positive actinobacteria, designated PS-14-16(T) and RS-7-1, were isolated from the rhizosphere of a mangrove and sea sediment, respectively, and their taxonomic positions were investigated by a polyphasic approach. Both strains were observed to form vegetative hyphae in the early phase of growth but the hyphae eventually fragment into short rods to coccoid cells. The peptidoglycan type of both strains was found to be A4α. Their predominant menaquinone was identified as MK-9(H4) and the major fatty acid as anteiso-C(15:0). The DNA G+C content was determined to be 68.4-68.5 mol%. 16S rRNA gene sequencing revealed that strains PS-14-16(T) and RS-7-1 were related to members of the family Cellulomonadaceae. Their nearest phylogenetic neighbour was found to be Sediminihabitans luteus, which is currently the only species of the genus Sediminihabitans, with a similarity of 97.94%. However, strains PS-14-16(T) and RS-7-1 were distinguishable from the members of the genus Sediminihabitans and the other genera within the family Cellulomonadaceae in terms of chemotaxonomic characteristics and phylogenetic relationship. The results of DNA-DNA hybridization experiments indicated that strains PS-14-16(T) and RS-7-1 belong to the same species. Strains PS-14-16(T) and RS-7-1 are concluded to represent a novel genus and species of the family Cellulomonadaceae, for which the name Tropicihabitans flavus gen. nov., sp. nov. is proposed. The type strain of T. flavus is PS-14-16(T) (=NBRC 110109(T) = IanCC A 516(T)). [corrected].
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Affiliation(s)
- Moriyuki Hamada
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba, 292-0818, Japan,
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Nurkanto A, Julistiono H. Screening and study of antifungal activity of leaf litter actinomycetes isolated from Ternate Island, Indonesia. ASIAN PAC J TROP MED 2014; 7S1:S238-43. [PMID: 25312129 DOI: 10.1016/s1995-7645(14)60239-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [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: 02/20/2014] [Revised: 03/12/2014] [Accepted: 04/26/2014] [Indexed: 10/24/2022] Open
Abstract
OBJECTIVE To characterize abundance of leaf litter actinomycetes from Ternate Island and to assess the antifungal activity of actinomycetes isolates against Candida albicans, Saccharomyces cerevisiae (S. cerevisiae), and Aspergillus niger. METHODS Actinomycetes were isolated from leaf litter of Durio species, Syzygium aromaticum, Piper betle, Myristica fragrans, or Pandanus species and unknown plants. Actinomycetes isolates were cultured in a liquid medium. Bioactive compounds were extracted and tested against fungal using Beury-Kirby method with modification. Minimum inhibitor concentration and cell leakages were conducted. Actinomycetes that produced the highest antifungal activity were indentified using molecular sequence data in 16S rRNA gene. RESULTS Out of 50 selected isolates, two isolates MG-500-1-4 and SR-2-2 has highest activity against S. cerevisiae. Concentration of material containing nucleic acids, proteins, Ca(+) and K(+) ions and morphological observations indicated that extracts of MG-500-1-4 and SR-2-2 caused cell leakage and invagination of S. cerevisiae cells. Based on 16S rRNA gene identification, MG-500-1-4 and SR-2-2 isolates are similar to Streptomyces misakiensis and Streptomyces tricolor respectively. CONCLUSIONS Ternate Island contains interesting biodiversity of actinomycetes that has potential use in agriculture, fisheries, and human health to reduce problem of fungal pathogen.
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Affiliation(s)
- Arif Nurkanto
- Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jl. Jakarta-Bogor KM 46 Cibinong, West Java-16911, Indonesia.
| | - Heddy Julistiono
- Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jl. Jakarta-Bogor KM 46 Cibinong, West Java-16911, Indonesia
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Agusta A, Wulansari D, Praptiwi, Nurkanto A, Fathoni A. Biotransformation of Protoberberine Alkaloids by the Endophytic Fungus Coelomycetes AFKR-3 Isolated from Yellow Moonsheed Plant (Archangelisia Flava (L.) Merr.). ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.proche.2014.12.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Isobe K, Otsuka S, Sudiana I, Nurkanto A, Senoo K. Community composition of soil bacteria nearly a decade after a fire in a tropical rainforest in East Kalimantan, Indonesia. J GEN APPL MICROBIOL 2010; 55:329-37. [PMID: 19940378 DOI: 10.2323/jgam.55.329] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Soil bacterial community compositions in burnt and unburnt areas in a tropical rainforest in East Kalimantan, Indonesia, were investigated 8 and 9 years after a fire by denaturing gradient gel electrophoresis analysis targeting the 16S rRNA gene. Three study sites were set in the forest area devoid of fire damage (control), and in the lightly damaged and heavily damaged forest areas. Succession of aboveground vegetation in the two damaged areas had clearly proceeded after the fire, but the vegetation types still differed from the unburnt area at the time of this study. Community composition of total soil bacteria was similar among the three areas, and so was that of actinobacteria. However, the composition of ammonia oxidizing bacteria clearly differed depending on the presence or absence of past fire damage. These results indicate that even nearly a decade after the forest fire, impacts of the fire remained on the community composition of ammonia oxidizing bacteria, but not apparently on those of dominant bacteria and actinobacteria.
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Affiliation(s)
- Kazuo Isobe
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.
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