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Liu X, Wang X, Shao Z, Dang J, Wang W, Liu C, Wang J, Yuan H, Zhao G. The global nitrogen regulator GlnR is a direct transcriptional repressor of the key gluconeogenic gene pckA in actinomycetes. J Bacteriol 2024:e0000324. [PMID: 38606980 DOI: 10.1128/jb.00003-24] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/04/2024] [Indexed: 04/13/2024] Open
Abstract
In most actinomycetes, GlnR governs both nitrogen and non-nitrogen metabolisms (e.g., carbon, phosphate, and secondary metabolisms). Although GlnR has been recognized as a global regulator, its regulatory role in central carbon metabolism [e.g., glycolysis, gluconeogenesis, and the tricarboxylic acid (TCA) cycle] is largely unknown. In this study, we characterized GlnR as a direct transcriptional repressor of the pckA gene that encodes phosphoenolpyruvate carboxykinase, catalyzing the conversion of the TCA cycle intermediate oxaloacetate to phosphoenolpyruvate, a key step in gluconeogenesis. Through the transcriptomic and quantitative real-time PCR analyses, we first showed that the pckA transcription was upregulated in the glnR null mutant of Amycolatopsis mediterranei. Next, we proved that the pckA gene was essential for A. mediterranei gluconeogenesis when the TCA cycle intermediate was used as a sole carbon source. Furthermore, with the employment of the electrophoretic mobility shift assay and DNase I footprinting assay, we revealed that GlnR was able to specifically bind to the pckA promoter region from both A. mediterranei and two other representative actinomycetes (Streptomyces coelicolor and Mycobacterium smegmatis). Therefore, our data suggest that GlnR may repress pckA transcription in actinomycetes, which highlights the global regulatory role of GlnR in both nitrogen and central carbon metabolisms in response to environmental nutrient stresses. IMPORTANCE The GlnR regulator of actinomycetes controls nitrogen metabolism genes and many other genes involved in carbon, phosphate, and secondary metabolisms. Currently, the known GlnR-regulated genes in carbon metabolism are involved in the transport of carbon sources, the assimilation of short-chain fatty acid, and the 2-methylcitrate cycle, although little is known about the relationship between GlnR and the TCA cycle and gluconeogenesis. Here, based on the biochemical and genetic results, we identified GlnR as a direct transcriptional repressor of pckA, the gene that encodes phosphoenolpyruvate carboxykinase, a key enzyme for gluconeogenesis, thus highlighting that GlnR plays a central and complex role for dynamic orchestration of cellular carbon, nitrogen, and phosphate fluxes and bioactive secondary metabolites in actinomycetes to adapt to changing surroundings.
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Affiliation(s)
- Xinqiang Liu
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
- CAS Key Laboratory of Synthetic Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xinyun Wang
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Zhihui Shao
- CAS Key Laboratory of Synthetic Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jun Dang
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Wei Wang
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Chaoyue Liu
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Jin Wang
- Tolo Biotechnology Company Limited, Shanghai, China
| | - Hua Yuan
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Guoping Zhao
- CAS Key Laboratory of Synthetic Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
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Saito S, Arai MA. Methodology for awakening the potential secondary metabolic capacity in actinomycetes. Beilstein J Org Chem 2024; 20:753-766. [PMID: 38633912 PMCID: PMC11022428 DOI: 10.3762/bjoc.20.69] [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: 12/15/2023] [Accepted: 03/27/2024] [Indexed: 04/19/2024] Open
Abstract
Secondary metabolites produced by actinomycete strains undoubtedly have great potential for use in applied research areas such as drug discovery. However, it is becoming difficult to obtain novel compounds because of repeated isolation around the world. Therefore, a new strategy for discovering novel secondary metabolites is needed. Many researchers believe that actinomycetes have as yet unanalyzed secondary metabolic activities, and the associated undiscovered secondary metabolite biosynthesis genes are called "silent" genes. This review outlines several approaches to further activate the metabolic potential of actinomycetes.
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Affiliation(s)
- Shun Saito
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Midori A Arai
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
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Girão M, Freitas S, Martins TP, Urbatzka R, Carvalho MF, Leão PN. Decylprodigiosin: a new member of the prodigiosin family isolated from a seaweed-associated Streptomyces. Front Pharmacol 2024; 15:1347485. [PMID: 38576493 PMCID: PMC10991731 DOI: 10.3389/fphar.2024.1347485] [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: 11/30/2023] [Accepted: 03/11/2024] [Indexed: 04/06/2024] Open
Abstract
Bioprospecting actinobacterial secondary metabolism from untapped marine sources may lead to the discovery of biotechnologically-relevant compounds. While studying the diversity and bioactive potential of Actinomycetota associated with Codium tomentosum, a green seaweed collected in the northern Portuguese cost, strain CT-F61, identified as Streptomyces violaceoruber, was isolated. Its extracts displayed a strong anticancer activity on breast carcinoma T-47D and colorectal carcinoma HCT116 cells, being effective as well against a panel of human and fish pathogenic bacteria. Following a bioactivity-guided isolation pipeline, a new analogue of the red-pigmented family of the antibiotics prodigiosins, decylprodigiosin (1), was identified and chemically characterized. Despite this family of natural products being well-known for a long time, we report a new analogue and the first evidence for prodigiosins being produced by a seaweed-associated actinomycete.
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Affiliation(s)
- Mariana Girão
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal
- School of Medicine and Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Sara Freitas
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal
| | - Teresa P. Martins
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal
| | - Ralph Urbatzka
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal
| | - Maria F. Carvalho
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal
- School of Medicine and Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Pedro N. Leão
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal
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Li X, Yao Y, Xia Z, Luo X, Zhang L. Myceligenerans pegani sp. nov., an endophytic actinomycete isolated from Peganum harmala L. in Xinjiang, PR China. Int J Syst Evol Microbiol 2024; 74. [PMID: 38315520 DOI: 10.1099/ijsem.0.006179] [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: 02/07/2024] Open
Abstract
An endophytic actinomycete designated TRM65318T, was isolated from the root of Peganum harmala L. Its taxonomic status was determined using a polyphasic approach. Comparative 16S rRNA gene sequence analysis indicated that strain TRM65318T is phylogenetically most closely related to Myceligenerans salitolerans XHU 5031T (98.15 %) and Myceligenerans xiligouense DSM 15700T (97.78 %). The peptidoglycan belonged to type A4α. The polar lipids were phosphatidylinositol, phosphatidylglycerol, diphosphatidylglycerol, two unknown lipids and three glycolipids. The predominant menaquinones were MK-9(H4) and MK-9(H6) and the whole-cell sugars contained glucose, mannose and galactose. Major fatty acids were anteiso-C15 : 0, iso-C15 : 0 and C16 : 0. Strain TRM65318T had a genome size of 5881012 bp with a genome G+C content of 71.79 mol%. The average nucleotide identity and DNA-DNA hybridization values between strain TRM65318T and the most closely related species were much lower than the thresholds commonly used to define species. At the same time, differences in phenotypic and genotypic data showed that strain TRM65318T could be clearly distinguished from M. salitolerans XHU 5031T. Therefore, it is concluded that strain TRM65318T represents a novel species of the genus of Myceligenerans. The proposed name for this organism is Myceligenerans pegani sp. nov., with type strain TRM65318T (=CCTCC AA 2019057T=LMG 31679T).
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Affiliation(s)
- Xin Li
- Key Laboratory of Conservation and Utilisation of Biological Resources in the Tarim Basin of the Xinjiang Production and Construction Corps/College of Life Sciences and Technology, Tarim University, Alar 843300, PR China
| | - YuXiang Yao
- Key Laboratory of Conservation and Utilisation of Biological Resources in the Tarim Basin of the Xinjiang Production and Construction Corps/College of Life Sciences and Technology, Tarim University, Alar 843300, PR China
| | - Zhanfeng Xia
- Key Laboratory of Conservation and Utilisation of Biological Resources in the Tarim Basin of the Xinjiang Production and Construction Corps/College of Life Sciences and Technology, Tarim University, Alar 843300, PR China
| | - XiaoXia Luo
- Key Laboratory of Conservation and Utilisation of Biological Resources in the Tarim Basin of the Xinjiang Production and Construction Corps/College of Life Sciences and Technology, Tarim University, Alar 843300, PR China
| | - LiLi Zhang
- Key Laboratory of Conservation and Utilisation of Biological Resources in the Tarim Basin of the Xinjiang Production and Construction Corps/College of Life Sciences and Technology, Tarim University, Alar 843300, PR China
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Abraham E, Lawther HA, Wang Y, Zarins-Tutt JS, Rivera GS, Wu C, Connolly JA, Florence G, Agbo M, Gao H, Goss RJM. The Identification and Heterologous Expression of the Biosynthetic Gene Cluster Encoding the Antibiotic and Anticancer Agent Marinomycin. Biomolecules 2024; 14:117. [PMID: 38254717 PMCID: PMC10813093 DOI: 10.3390/biom14010117] [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: 12/19/2023] [Revised: 12/31/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
With the rise in antimicrobial resistance, there is an urgent need for new classes of antibiotic with which to treat infectious disease. Marinomycin, a polyene antibiotic from a marine microbe, has been shown capable of killing methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus faecium (VREF), as well as having promising activity against melanoma. An attractive solution to the photoprotection of this antibiotic has been demonstrated. Here, we report the identification and analysis of the marinomycin biosynthetic gene cluster (BGC), and the biosynthetic assembly of the macrolide. The marinomycin BGC presents a challenge in heterologous expression due to its large size and high GC content, rendering the cluster prone to rearrangement. We demonstrate the transformation of Streptomyces lividans using a construct containing the cluster, and the heterologous expression of the encoded biosynthetic machinery and production of marinomycin B.
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Affiliation(s)
- Emily Abraham
- Department of Chemistry & BSRC, University of St. Andrews, St. Andrews KY16 9ST, UK; (E.A.); (J.A.C.)
| | - Hannah A. Lawther
- Department of Chemistry & BSRC, University of St. Andrews, St. Andrews KY16 9ST, UK; (E.A.); (J.A.C.)
| | - Yunpeng Wang
- Department of Chemistry & BSRC, University of St. Andrews, St. Andrews KY16 9ST, UK; (E.A.); (J.A.C.)
| | - Joseph S. Zarins-Tutt
- Department of Chemistry & BSRC, University of St. Andrews, St. Andrews KY16 9ST, UK; (E.A.); (J.A.C.)
| | | | - Chengcang Wu
- Intact Genomics, St. Louis, MO 63132, USA (C.W.)
| | - Jack A. Connolly
- Department of Chemistry & BSRC, University of St. Andrews, St. Andrews KY16 9ST, UK; (E.A.); (J.A.C.)
| | - Gordon Florence
- Department of Chemistry & BSRC, University of St. Andrews, St. Andrews KY16 9ST, UK; (E.A.); (J.A.C.)
| | - Matthias Agbo
- Department of Chemistry & BSRC, University of St. Andrews, St. Andrews KY16 9ST, UK; (E.A.); (J.A.C.)
| | - Hong Gao
- Department of Chemistry & BSRC, University of St. Andrews, St. Andrews KY16 9ST, UK; (E.A.); (J.A.C.)
| | - Rebecca J. M. Goss
- Department of Chemistry & BSRC, University of St. Andrews, St. Andrews KY16 9ST, UK; (E.A.); (J.A.C.)
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Ishibashi M. [Learning from Natural Products: Study on Actinomycetes of the Genus Nocardia]. YAKUGAKU ZASSHI 2024; 144:33-37. [PMID: 38171791 DOI: 10.1248/yakushi.23-00161-3] [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: 01/05/2024]
Abstract
The genus Nocardia comprises gram-positive bacteria, most of which are pathogenic and cause opportunistic infections of the lungs, skin, and brain in humans. Based on a collaboration study with the Medical Mycology Research Center, Chiba University, we focused on Nocardia actinomycetes as a new natural-product resource. First, by culturing (monoculture) Nocardia in various media, we isolated a new aminocyclitol nabscessin A from Nocardia abscessus IFM10029T and a new γ-lactone inohanalactone from Nocardia inohanaensis IFM0092T. On the other hand, by imitating the state in which the genus Nocardia actinomycete infects animal cells and culturing the genus in the presence of animal cells (coculture), this genus was expected to produce new compounds through interactions with the animal cells. Using mouse macrophage-like cells (J774.1) as animal cells, a new pantothenic acid amide derivative and a cyclic peptide, nocarjamide, with Wnt signal activation activity were isolated from Nocardia tenerifensis IFM10554T strain.
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Affiliation(s)
- Masami Ishibashi
- School of Pharmacy at Fukuoka, International University of Health and Welfare
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Triningsih DW, Harunari E, Hamada M, Enomoto N, Tamura T, Komaki H, Igarashi Y. Phytohabitans aurantiacus sp. nov., an actinomycete isolated from soil. Int J Syst Evol Microbiol 2023; 73. [PMID: 38113095 DOI: 10.1099/ijsem.0.006106] [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: 12/21/2023] Open
Abstract
A novel actinomycete, designated RD004123T, was isolated from a soil sample collected in Hokkaido, Japan, and its taxonomic position was investigated by a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain RD004123T fell within the cluster of the family Micromonosporaceae but did not form a reliable cluster with any member of the family. The similarity values between strain RD004123T and the type species of 29 genera in the family Micromonosporaceae were 91.7-97.7 %. Meanwhile, phylogenomic analyses indicated that strain RD004123T was closely related to members of the genus Phytohabitans. Strain RD004123T contained both meso-diaminopimelic acid and l-lysine as the diagnostic diamino acids of the peptidoglycan. The predominant isoprenoid quinones were MK-10(H8) and MK-10(H6), and the major fatty acids were anteiso-C17 : 0, iso-C16 : 0, iso-C15 : 0 and C17 : 0. The detected polar lipids were phosphatidylinositol mannosides, phosphatidylinositol, phosphatidylethanolamine and diphosphatidylglycerol. These chemotaxonomic features corresponded to those of the genus Phytohabitans. Meanwhile, the results of genome comparison analyses and phenotypic characterizations distinguished strain RD004123T from the other members of the genus Phytohabitans. Therefore, strain RD004123T should be assigned as representing a novel species of the genus Phytohabitans, for which the name Phytohabitans aurantiacus sp. nov. is proposed. The type strain is RD004123T (=NBRC 114997T=DSM 114330T).
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Affiliation(s)
- Desy Wulan Triningsih
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, Japan
| | - Enjuro Harunari
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, Japan
| | - Moriyuki Hamada
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba, Japan
| | - Narumi Enomoto
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba, Japan
| | - Tomohiko Tamura
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba, Japan
| | - Hisayuki Komaki
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba, Japan
| | - Yasuhiro Igarashi
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, Japan
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Chantavorakit T, Muangham S, Aaron TWF, Duangmal K, Hong K. Actinoallomurus soli sp. nov. and Actinoallomurus rhizosphaericola sp. nov., two novel actinobacteria isolated from rhizosphere soil of Oryza rufipogon Griff. Int J Syst Evol Microbiol 2023; 73. [PMID: 37994910 DOI: 10.1099/ijsem.0.006177] [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: 11/24/2023] Open
Abstract
The taxonomic position of two novel Actinoallomurus strains isolated from rhizosphere soil of wild rice (Oryza rufipogon Griff.) was established using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains WRP6H-15T and WRP9H-5T were closely related to Actinoallomurus spadix JCM 3146T and Actinoallomurus purpureus TTN02-30T. Chemotaxonomic and morphological characteristics of both strains were consistent with members of the genus Actinoallomurus, while phenotypic properties, genome-based comparisons and phylogenomic analyses distinguished strains WRP6H-15T and WRP9H-5T from their closest phylogenetic relatives. The two strains showed nearly identical 16S rRNA gene sequences (99.9 %). Strain WRP6H-15T showed 68.7 % digital DNA-DNA hybridization, 95.9 % average nucleotide identity (ANI) based on blast and 96.4 % ANI based on MUMmer to strain WRP9H-5T. A phylogenomic tree based on draft genome sequences of the strains and representative of the genus Actinoallomurus confirmed the phylogenetic relationships. The genomes sizes of strains WRP6H-15T and WRP9H-5T were 9.42 Mb and 9.68 Mb, with DNA G+C contents of 71.5 and 71.3 mol%, respectively. In silico analysis predicted that the strains contain biosynthetic gene clusters encoding for specialized metabolites. Characterization based on chemotaxonomic, phylogenetic, phenotypic and genomic evidence demonstrated that strains WRP6H-15T and WRP9H-5T represent two novel species of the genus Actinoallomurus, for which the names Actinoallomurus soli sp. nov. (type strain WRP6H-15T=TBRC 15726T=NBRC 115556T) and Actinoallomurus rhizosphaericola sp. nov. (type strain WRP9H-5T=TBRC 15727T=NBRC 115557T) are proposed.
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Affiliation(s)
- Tanatorn Chantavorakit
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, Chatuchak 10900, Thailand
| | - Supattra Muangham
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, Chatuchak 10900, Thailand
- National Biobank of Thailand (NBT), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathumthani 12120, Thailand
| | - Teo Wee Fei Aaron
- Center for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Kannika Duangmal
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, Chatuchak 10900, Thailand
- Biodiversity Center Kasetsart University (BDCKU), Bangkok 10900, Thailand
| | - Kui Hong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, PR China
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Bautista-Crescencio C, Casimiro-Ramos A, Fragoso-Vázquez MJ, Correa-Basurto J, Olano C, Hernández-Rodríguez C, Villa-Tanaca L. Streptomyces albidoflavus Q antifungal metabolites inhibit the ergosterol biosynthesis pathway and yeast growth in fluconazole-resistant Candida glabrata: phylogenomic and metabolomic analyses. Microbiol Spectr 2023; 11:e0127123. [PMID: 37754674 PMCID: PMC10581079 DOI: 10.1128/spectrum.01271-23] [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: 03/23/2023] [Accepted: 08/08/2023] [Indexed: 09/28/2023] Open
Abstract
There is an urgent need to develop new antifungals due to the increasing prevalence of multidrug-resistant fungal infections and the recent emergence of COVID-19-associated candidiasis. A good study model for evaluating new antifungal compounds is Candida glabrata, an opportunistic fungal pathogen with intrinsic resistance to azoles (the most common clinical drugs for treating fungal infections). The aim of the current contribution was to conduct in vitro tests of antifungal metabolites produced by the bacteria Streptomyces albidoflavus Q, identify their molecular structures, and utilize several techniques to provide evidence of their therapeutic target. S. albidoflavus was isolated from maize rhizospheric soil in Mexico and identified by phylogenomic analysis using a 92-gene core. Of the 66 metabolites identified in S. albidoflavus Q by a liquid chromatography-high resolution mass spectrometry (LC-HRMS) metabolomic analysis of the lyophilized supernatant, six were selected by the Way2drug server based on their in silico binding to the likely target, 3-hydroxy-3-methyl-glutaryl-CoA reductase (HMGR, the key enzyme in the ergosterol biosynthesis pathway). Molecular modeling studies show a relatively high binding affinity for the CgHMGR enzyme by two secondary metabolites: isogingerenone B (diaryl heptanoid) and notoginsenoside J (polycyclic triterpene). These secondary metabolites were able to inhibit ergosterol synthesis and affect yeast viability in vitro. They also caused alterations in the ultrastructure of the yeast cytoplasmic membrane, as evidenced by transmission electron microscopy. The putative target of isogingerenone B and notoginsenoside J is distinct from that of azole drugs (the most common clinical antifungals). The target for the latter is the lanosterol 14 alpha-demethylase enzyme (Erg11). IMPORTANCE Multidrug resistance has emerged among yeasts of the genus Candida, posing a severe threat to global health. The problem has been exacerbated by the pandemic associated with COVID-19, during which resistant strains of Candida auris and Candida glabrata have been isolated from patients infected with the SARS-CoV-2 virus. To confront this challenge, the World Health Organization has invoked scientists to search for new antifungals with alternative molecular targets. This study identified 66 metabolites produced by the bacteria Streptomyces albidoflavus Q, 6 of which had promising properties for potential antifungal activity. The metabolites were tested in vitro as inhibitors of ergosterol synthesis and C. glabrata growth, with positive results. They were also found to damage the cytoplasmic membrane of the fungus. The corresponding molecular structures and their probable therapeutic target were established. The target is apparently distinct from that of azole drugs.
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Affiliation(s)
- Celia Bautista-Crescencio
- Departamento de Microbiología, Laboratorio de Biología Molecular de Bacterias y Levaduras, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional. Prolongación de Carpio y Plan de Ayala, Casco de Santo Tomás, Ciudad de México, Ciudad de México, México
| | - Arturo Casimiro-Ramos
- Departamento de Microbiología, Laboratorio de Biología Molecular de Bacterias y Levaduras, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional. Prolongación de Carpio y Plan de Ayala, Casco de Santo Tomás, Ciudad de México, Ciudad de México, México
| | - M. Jonathan Fragoso-Vázquez
- Departamento de Química Orgánica, Escuela Nacional de Ciencias, Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala, Col. Casco de Santo Tomás, Ciudad de México, México
| | - José Correa-Basurto
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), SEPI-Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón, Casco de Santo Tomás, Ciudad de México, México
| | - Carlos Olano
- Departamento de Biología Funcional, Universidad de Oviedo, Oviedo, Spain
| | - César Hernández-Rodríguez
- Departamento de Microbiología, Laboratorio de Biología Molecular de Bacterias y Levaduras, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional. Prolongación de Carpio y Plan de Ayala, Casco de Santo Tomás, Ciudad de México, Ciudad de México, México
| | - Lourdes Villa-Tanaca
- Departamento de Microbiología, Laboratorio de Biología Molecular de Bacterias y Levaduras, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional. Prolongación de Carpio y Plan de Ayala, Casco de Santo Tomás, Ciudad de México, Ciudad de México, México
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Ding L, Zhou H, Liang HD, Tan L, Zhao H, Chen XJ, Ren ZH. Efficacy of Streptomyces melanosporofaciens strain X216 at controlling clubroot disease on oilseed rape. Front Microbiol 2023; 14:1249813. [PMID: 37795295 PMCID: PMC10546314 DOI: 10.3389/fmicb.2023.1249813] [Citation(s) in RCA: 1] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 08/30/2023] [Indexed: 10/06/2023] Open
Abstract
Oilseed rape (Brassica napus L.) is highly susceptible to infection from the soilborne pathogen Plasmodiophora brassicae Woronin that causes clubroot disease and deleteriously affects production throughout the world. In this study, biological control resources were explored by isolating 237 strains of bacteria from fields of oilseed rape using the gradient dilution coating method. A strain with strong antagonistic ability was screened using a plate confrontation test and designated X216. It was identified as Streptomyces melanosporofaciens owing to its morphological characteristics and 16S rRNA gene sequence. This study also examined the lethality of strain X216 to the resting spores of P. brassicae, its influence on infection in root hairs, and its ability to control clubroot on oilseed rape. The corrected lethality rate on resting spores after strain X216 had been used for 14 days was 56.59% ± 1.97%, which was significantly higher than the use of 75% of the fungicides chlorothalonil WP and 20% Fluazinam SC. Significantly fewer root hairs were infected after this treatment. A pot test showed that X216 was 62.14% effective at controlling the disease, which was not significantly different from that of the fungicide 100 g L-1 cyazofamid SC diluted 1,000-fold but significantly higher than those of 75% chlorothalonil and 50% carbendazim WP. Strain X216 controlled 43.16% of the incidence of clubroot in the field, which could significantly reduce the disease index of oilseed rape clubroot. Therefore, strain X216 is promising to study for the biological control of oilseed rape clubroot.
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Affiliation(s)
- Lin Ding
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Hu Zhou
- College of Plant Protection, Hunan Agricultural University, Changsha, China
- Yueyang Inspection and Testing Center, Yueyang, China
| | - Hai-di Liang
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Lin Tan
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Hui Zhao
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Xiao-jun Chen
- College of Agricultural, Hunan Agricultural University, Changsha, China
| | - Zuo-hua Ren
- College of Plant Protection, Hunan Agricultural University, Changsha, China
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11
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Klaysubun C, Butdee W, Suriyachadkun C, Igarashi Y, Duangmal K. Streptomyces silvisoli sp. nov., a polyene producer, and Streptomyces tropicalis sp. nov., two novel actinobacterial species from peat swamp forests in Thailand. Int J Syst Evol Microbiol 2023; 73. [PMID: 37768174 DOI: 10.1099/ijsem.0.006063] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2023] Open
Abstract
Two novel actinobacterial strains, designated RB6PN23T and K1PA1T, were isolated from peat swamp soil samples in Thailand and characterized using a polyphasic taxonomic approach. The strains were filamentous Gram-stain-positive bacteria containing ll-diaminopimelic acid in their whole-cell hydrolysates. Phylogenetic analysis of their 16S rRNA gene sequences revealed that strain RB6PN23T was most closely related to Streptomyces rubrisoli (99.1 % sequence similarity) and Streptomyces ferralitis (98.5%), while strain K1PA1T showed 98.8 and 98.7% sequence similarities to Streptomyces coacervatus and Streptomyces griseoruber, respectively. However, the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values were below the species-level thresholds (95-96 % ANI and 70 % dDDH). The genomes of strains RB6PN23T and K1PA1T were estimated to be 7.88 Mbp and 7.39 Mbp in size, respectively, with DNA G+C contents of 70.2 and 73.2 mol%. Moreover, strains RB6PN23T and K1PA1T encode 37 and 24 putative biosynthetic gene clusters, respectively, and in silico analysis revealed that these new species have a high potential to produce unique natural products. Genotypic and phenotypic characteristics confirmed that strains RB6PN23T and K1PA1T represented two novel species in the genus Streptomyces. The names proposed for these strains are Streptomyces silvisoli sp. nov. (type strain RB6PN23T=TBRC 17040T=NBRC 116113T) and Streptomyces tropicalis sp. nov. (type strain K1PA1T=TBRC 17041T=NBRC 116114T). Additionally, a giant linear polyene compound, neotetrafibricin A, exhibiting antifungal activity in strain RB6PN23T, was identified through HPLC and quadrupole time-of-flight MS analysis. The crude extract from the culture broth of strain RB6PN23T exhibited strong antifungal activity against Fusarium verticillioides, Fusarium fujikuroi and Bipolaris zeicola. This finding suggests that strain RB6PN23T could be a promising candidate for biological control of fungal diseases.
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Affiliation(s)
- Chollachai Klaysubun
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Waranya Butdee
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Chanwit Suriyachadkun
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani 12120, Thailand
| | - Yasuhiro Igarashi
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Kannika Duangmal
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
- Biodiversity Center Kasetsart University (BDCKU), Bangkok 10900, Thailand
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12
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Pansomsuay R, Duangupama T, Pittayakhajonwut P, Intaraudom C, Suriyachadkun C, He YW, Tanasupawat S, Thawai C. Gordonia aquimaris sp. nov., a novel marine actinobacterium isolated from seawater in the upper gulf of Thailand. Int J Syst Evol Microbiol 2023; 73. [PMID: 36961870 DOI: 10.1099/ijsem.0.005804] [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: 03/25/2023] Open
Abstract
An actinobacterium strain, SW21T, was isolated from seawater collected in the upper Gulf of Thailand. Cells were Gram-stain-positive, aerobic and rod-shaped. Growth was observed from 15 to 37 °C and at pH 6-8. Maximum NaCl for growth was 14 % (w/v). meso-Diaminopimelic acid, arabinose, galactose, glucose, rhamnose and ribose were detected in the whole-cell hydrolysate. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside were detected as the phospholipids in the cells. The major menaquinones were MK-9(H2) and MK-7(H2). The major cellular fatty acids were C16 : 0, C18 : 1 ω9c, C18 : 0 and C18 : 010-methyl (TBSA). The 16S rRNA gene sequence data supported the assignment of strain SW21T to the genus Gordonia and showed that Gordonia mangrovi KCTC 49383T (98.7 %) was the closest relative. Moreover, the average nucleotide identity-blast (85.5 %) and digital DNA-DNA hybridization (30.7 %) values between strain SW21T and its closest neighbour were below the threshold values for delineation of a novel species. The combination of genotypic and phenotypic data indicated that strain SW21T is representative of novel species of the genus Gordonia. The name Gordonia aquimaris sp. nov. is proposed for strain SW21T. The type strain is SW21T (=TBRC 15691T=NBRC 115558T).
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Affiliation(s)
- Rawirat Pansomsuay
- Department of Biology, School of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok, 10520, Thailand
| | - Thitikorn Duangupama
- Department of Biology, School of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok, 10520, Thailand
| | - Pattama Pittayakhajonwut
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phaholyothin Road, Klong Luang, Pathum Thani 12120, Thailand
| | - Chakapong Intaraudom
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phaholyothin Road, Klong Luang, Pathum Thani 12120, Thailand
| | - Chanwit Suriyachadkun
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phaholyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Ya-Wen He
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Chitti Thawai
- Department of Biology, School of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok, 10520, Thailand
- Actinobacterial Research Unit, School of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok, 10520, Thailand
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13
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Miyanishi M, Hamada M, Taniguchi T, Enomoto N, Oota T, Teramoto M. Lolliginicoccus levis gen. nov., sp. nov., a novel bacterium isolated from the brain of the Chiroteuthis picteti squid, and reclassification of two Hoyosella species as Lolliginicoccus suaedae comb. nov. and Lolliginicoccus lacisalsi comb. nov. Int J Syst Evol Microbiol 2023; 73. [PMID: 37000174 DOI: 10.1099/ijsem.0.005788] [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: 04/01/2023] Open
Abstract
A Gram-stain-positive, non-motile, mesophilic, aerobic, coccus-shaped bacterium, designated strain Y7R2T, was isolated from the brain of a Chiroteuthis picteti squid living in mesopelagic water near Muroto, Kochi, Japan. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain was most closely related to the genus Hoyosella (96.1 % similarity to the type strain of the type species Hoyosella altamirensis) and formed a separate distinct cluster in a stable, deep-branching lineage with the type strains of Hoyosella suaedae and Hoyosella lacisalsi (98.7-99.5% similarities). The major fatty acids (>10 %) of strain Y7R2T were C17 : 1 ω8c, C15 : 0, C16 : 1 ω6c/C16 : 1 ω7c and C16 : 0, and the isoprenoid quinones were menaquinone-7 (57.8 %) and menaquinone-8 (42.2 %). The principal polar lipids were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylinositol, and the DNA G+C content was 68.0 %. These chemotaxonomic features, with the exception of the fatty acid composition, were similar to those of the phylogenetically clustered species (H. suaedae and H. lacisalsi) but different from those of core Hoyosella species (including H. altamirensis). These results suggested that Y7R2T, H. suaedae and H. lacisalsi strains should be assigned to a novel genus. Furthermore, strain Y7R2T showed low average nucleotide identity values (88.0-88.2 %) and low digital DNA-DNA hybridization values (34.3-34.7 %) to the type strains of H. suaedae and H. lacisalsi. These data indicated that strain Y7R2T should be assigned to a novel genus and species, for which the name Lolliginicoccus levis gen. nov., sp. nov. is proposed. The type strain is Y7R2T (=NBRC 114883T=KCTC 49749T). Accordingly, reclassification of H. suaedae and H. lacisalsi as Lolliginicoccus suaedae comb. nov. (type species) and Lolliginicoccus lacisalsi comb. nov. is also proposed.
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Affiliation(s)
- Makoto Miyanishi
- Department of Marine Resource Science, Kochi University, Otsu 200, Monobe, Nankoku, Kochi 783-8502, Japan
| | - Moriyuki Hamada
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Tomomi Taniguchi
- Department of Marine Resource Science, Kochi University, Otsu 200, Monobe, Nankoku, Kochi 783-8502, Japan
| | - Narumi Enomoto
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Takamasa Oota
- Department of Marine Resource Science, Kochi University, Otsu 200, Monobe, Nankoku, Kochi 783-8502, Japan
| | - Maki Teramoto
- Department of Marine Resource Science, Kochi University, Otsu 200, Monobe, Nankoku, Kochi 783-8502, Japan
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14
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Beroigui O, El Ghadraoui L, Errachidi F. Production, purification, and characterization of inulinase from Streptomyces anulatus. J Basic Microbiol 2023; 63:427-438. [PMID: 36707409 DOI: 10.1002/jobm.202200491] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 12/24/2022] [Accepted: 01/14/2023] [Indexed: 01/29/2023]
Abstract
Inulinase is an enzyme that catalyzes inulin to d-fructose. This enzyme can be extracted from plants, but it is difficult to obtain it in large quantities, so its production cost is high. Therefore, microbial inulinase has great potential for industrial needs. In the last decade, there have been very few reports on actinobacterial inulinases, especially on purification and characterization of inulinase process extraction. This study aims to select actinomycetes that possess high inulinase activity from the soil. To screen inulinase-producing bacteria, modified Czapex-Dox agar supplemented with 1% inulin powder was used. The most effective isolate was Streptomyces sp. EFBO8, morphological and genotypic identification methods, confirmed that the strain is Streptomyces anulatus and that its nucleotide sequence has been deposited in GenBank under accession number OQ073700. To optimize inulinase production, kinetics were performed by using S. anulatus strain, which proved to be most productive with a value of 24,024 EU/mL. The enzyme was purified from the culture filtrate by precipitation with ammonium sulfate (NH4 )2 SO4 , followed by column chromatography Sephadex (G-50) separation. Purified protein has a molecular mass of 3331.83 Da.
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Affiliation(s)
- Oumaima Beroigui
- Department of Biology, Functional Ecology and Environmental Engineering Laboratory, University Sidi Mohammed Ben Abdellah, Fez, Morocco
| | - Lahsen El Ghadraoui
- Department of Biology, Functional Ecology and Environmental Engineering Laboratory, University Sidi Mohammed Ben Abdellah, Fez, Morocco
| | - Faouzi Errachidi
- Department of Biology, Functional Ecology and Environmental Engineering Laboratory, University Sidi Mohammed Ben Abdellah, Fez, Morocco
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15
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Butdee W, Muangham S, Chonudomkul D, Duangmal K. Streptomyces rhizoryzae sp. nov., isolated from paddy rhizosphere soil and formal proposal to reclassify Streptomyces albulus as a later heterotypic synonym of Streptomyces noursei. Int J Syst Evol Microbiol 2023; 73. [PMID: 36748589 DOI: 10.1099/ijsem.0.005639] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The taxonomic position of a novel actinomycete, designated strain RS10V-4T, was determined using a polyphasic approach. Strain RS10V-4T was isolated from paddy rhizosphere soil of rice plant (Oryzae sativa L.). The morphological, physiological and chemotaxonomic properties were consistent with its classification in the genus Streptomyces. On the basis of 16S rRNA gene sequence analysis, strain RS10V-4T belongs to the genus Streptomyces and had the highest sequence similarity to Streptomyces noursei NBRC 15452T (98.3 %). The G+C content of the genomic DNA was 73.8 %. Digital DNA-DNA hybridization and average nucleotide identity values between the genome sequences of strain RS10V-4T and S.noursei ATCC 11455T were lower than the recommendation threshold values for the recognition of species within the same genus. The whole-cell hydrolysates of strain RS10V-4 T contained ll -diaminopimelic acid as the diagnostic diamino acid and the whole-cell sugars were glucose and ribose. The predominant menaquinones were MK-9(H6) and MK-9(H8). The predominant cellular fatty acids (>10 %) were iso-C16 : 0, anteiso-C15 : 0, iso-C14 : 0 and iso-C15 : 0. The polar lipids of strain RS10V-4T contained diphosphatidylglycerol, hydroxyphosphatidylethanolamine, phosphatidylethanolamine, phosphatidylinositol, an unidentified aminolipid, two unidentified lipids and an unidentified phospholipid. On the basis of these phenotypic and genotypic characteristics, it is supported that strain RS10V-4T represents a novel species of the genus Streptomyces, for which the name Streptomyces rhizoryzae sp. nov. is proposed. The type strain is RS10V-4T (=TBRC 15167T=NBRC 115345T). In addition, the comparison of the whole genome sequences and phenotypic features suggested that S. noursei and S. albulus belong to the same species. Therefore, it is proposed that S. albulus is reclassified as a later heterotypic synonym of S. noursei.
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Affiliation(s)
- Waranya Butdee
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Supattra Muangham
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Duenrut Chonudomkul
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand.,Biodiversity Center Kasetsart University (BDCKU), Bangkok 10900, Thailand
| | - Kannika Duangmal
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand.,Biodiversity Center Kasetsart University (BDCKU), Bangkok 10900, Thailand
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16
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Moaddabi A, Cernera M, Armogida NG, Soltani P, Spagnuolo G. Actinomycotic Sinomaxillary Infection in a COVID-19 Patient: A Case Report and Review of the Literature. J Investig Med High Impact Case Rep 2023; 11:23247096231217823. [PMID: 38102073 PMCID: PMC10725094 DOI: 10.1177/23247096231217823] [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: 08/30/2023] [Revised: 11/05/2023] [Accepted: 11/12/2023] [Indexed: 12/17/2023] Open
Abstract
Individuals with COVID-19 are prone to a variety of infections due to immune dysregulation. The present report presents a case of actinomycotic infection in the maxillary bone and sinus region in a patient with a history of COVID-19. This case report highlights the importance of considering bacterial infections including actinomycosis when encountering destructive lesions resembling more prevalent fungal infections due to different therapeutic medication protocols. In addition, a literature review of the existing reports of similar post-COVID-19 actinomycotic infection is presented.
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Affiliation(s)
- Amirhossein Moaddabi
- Department of Oral and Maxillofacial Surgery, Dental Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mariangela Cernera
- Department of Neurosciences, Reproductive and Odontostomatological Sciences, University of Naples “Federico II”, Naples, Italy
| | - Niccolò Giuseppe Armogida
- Department of Neurosciences, Reproductive and Odontostomatological Sciences, University of Naples “Federico II”, Naples, Italy
| | - Parisa Soltani
- Department of Neurosciences, Reproductive and Odontostomatological Sciences, University of Naples “Federico II”, Naples, Italy
- Department of Oral and Maxillofacial Radiology, Dental Implants Research Center, Dental Research Institute, School of Dentistry, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Gianrico Spagnuolo
- Department of Neurosciences, Reproductive and Odontostomatological Sciences, University of Naples “Federico II”, Naples, Italy
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17
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Honma S, Ito S, Yajima S, Sasaki Y. Nitric Oxide Signaling for Aerial Mycelium Formation in Streptomyces coelicolor A3(2) M145. Appl Environ Microbiol 2022; 88:e0122222. [PMID: 36354316 DOI: 10.1128/aem.01222-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Nitric oxide (NO) is a well-known signaling molecule in various organisms. Streptomyces undergoes complex morphological differentiation, similar to that of fungi. A recent study revealed a nitrogen oxide metabolic cycle that forms NO in Streptomyces coelicolor A3(2) M145. Further, endogenously produced NO serves as a signaling molecule. Here, we report that endogenously produced NO regulates cyclic 3',5'-diguanylate (c-di-GMP) levels and controls aerial mycelium formation through the c-di-GMP-binding transcriptional regulator BldD in S. coelicolor A3(2) M145. These observations provide important insights into the mechanisms regulating morphological differentiation. This is the first study to demonstrate a link between NO and c-di-GMP in S. coelicolor A3(2) M145. Morphological differentiation is closely linked to the initiation of secondary metabolism in actinomycetes. Thus, the NO signaling-based regulation of aerial mycelium formation has potential applications in the fermentation industry employing useful actinomycetes. IMPORTANCE Eukaryotic and prokaryotic cells utilize nitric oxide (NO) to regulate physiological functions. Besides its role as a producer of different bioactive substances, Streptomyces is suggested to be involved in mycelial development regulated by endogenously produced NO. However, the regulatory mechanisms are unclear. In this study, we proposed that NO signaling is involved in aerial mycelium formation in S. coelicolor A3(2) M145. NO serves as a signaling molecule for the regulation of intracellular cyclic 3',5'-diguanylate (c-di-GMP) levels, resulting in aerial mycelium formation controlled by a c-di-GMP receptor, BldD. As the abundant production of valuable secondary metabolites is closely related to the initiation of morphological differentiation in Streptomyces, NO may provide value for application in industrial fermentation by serving as a tool for regulating secondary metabolism.
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Sakdapetsiri C, Ngaemthao W, Suriyachadkun C, Pinyakong O. Paeniglutamicibacter quisquiliarum sp. nov., isolated from midden soil waste. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748475 DOI: 10.1099/ijsem.0.005651] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
A Gram-stain-positive, irregular short-rod and non-motile bacterium, designated strain ABSL32-1T, was isolated from a soil sample collected from the Suphan Buri municipal solid waste disposal area. According to the results of a polyphasic taxonomic study, a novel species belonging to the genus Paeniglutamicibacter was described. Strain ABSL32-1T grew optimally at 20-25 °C and at pH 6.0-8.0 in the presence of 1 % (w/v) NaCl. The whole-cell sugars were ribose, mannose and glucose. The peptidoglycan structure contained A4α peptidoglycan (Lys-Glu; A11.54). The polar lipids contained digalactosyldiacylglycerol, diphosphatidylglycerol, phosphatidylglycerol, unidentified phospholipids and two unidentified lipids. The major menaquinones were MK-9 and MK-10. The major cellular fatty acid was anteiso-C15 : 0 (70.1 %). Based on 16S rRNA gene sequence analysis, strain ABSL32-1T showed the highest similarity to Paeniglutamicibacter sulfureus DSM 20167T (99.5 %), followed by Paeniglutamicibacter antarcticus SPC26T (99.0 %) and Paeniglutamicibacter psychrophenolicus AG31T (98.8 %). The genome of strain ABSL32-1T is 4.4 Mbp with a DNA G+C content of 66.0 mol%. The average nucleotide identity values between strain ABSL32-1T and the type strains P. sulfureus DSM20167T, P. antarcticus SPC26T and P. psychrophenolicus AG31T were 86.6, 74.7 and 83.6 %, respectively. On the basis of phenotypic, chemotaxonomic and genotypic properties, strain ABSL32-1T is proposed to represent a novel species to be named Paeniglutamicibacter quisquiliarum sp. nov. The type strain is ABSL32-1T (=TBRC 14976T=NBRC 115252T).
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Affiliation(s)
- Chatsuda Sakdapetsiri
- Center of Excellence in Microbial Technology for Marine Pollution Treatment (MiTMaPT), Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.,Department of Plant Pathology, Faculty of Agriculture at Kamphaengsaen, Kasetsart University Kamphaengsaen Campus, Nakhon Pathom 73140, Thailand
| | - Wipaporn Ngaemthao
- Microbial Diversity and Utilization Research Team, Thailand Bioresource Research Center, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani 12120, Thailand
| | - Chanwit Suriyachadkun
- Microbial Diversity and Utilization Research Team, Thailand Bioresource Research Center, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani 12120, Thailand
| | - Onruthai Pinyakong
- Center of Excellence in Microbial Technology for Marine Pollution Treatment (MiTMaPT), Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.,Research Program on Remediation Technologies for Petroleum Contamination, Center of Excellence on Hazardous Substance Management (HSM), Chulalongkorn University, Bangkok 10330, Thailand
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19
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Nammali A, Duangupama T, Pittayakhajonwut P, Intaraudom C, Suriyachadkun C, He YW, Tanasupawat S, Thawai C. Streptomyces acidipaludis sp. nov., an actinobacterium isolated from peat swamp forest soil. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748585 DOI: 10.1099/ijsem.0.005626] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
An actinobacterium strain PLK6-54T was isolated from Lankwai peat swamp forest soil collected from Yala province, Thailand. Strain PLK6-54T exhibited morphological and chemotaxonomic properties described for the genus Streptomyces. It formed a spiral spore chain directly on aerial mycelium. Growth was observed between 20 and 40 °C and at pH 5-8. The maximum NaCl for growth was 2 % (w/v). ll-Diaminopimelic acid, arabinose and ribose were detected in the whole-cell hydrolysate. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositolmannoside were detected as the phospholipids. The major menaquinones were MK-10(H2) and MK-9(H6). The major cellular fatty acids were iso-C16 : 0, anteiso-C15 : 0 and iso-C14 : 0. 16S rRNA gene sequence data supported the assignment of strain PLK6-54T to the genus Streptomyces and showed that Streptomyces rubidus NBRC 102073T (99.0 %) was the closest relative. Moreover, the average nucleotide identity-blast (85.5 %) and digital DNA-DNA hybridization (30.7 %) values reported between strain PLK6-54T and its closest neighbour were below the threshold values for delineation of a novel species. Strain PLK6-54T could be distinguished from related validly described Streptomyces species by several phenotypic properties. The combination of genotypic and phenotypic data indicated that strain PLK6-54T is representative of a novel species of the genus Streptomyces. The name Streptomyces acidipaludis sp. nov. is proposed for strain PLK6-54T. The type strain is PLK6-54T (=TBRC 11250T=NBRC 114297T).
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Affiliation(s)
- Achararak Nammali
- Department of Biology, School of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok 10520, Thailand
| | - Thitikorn Duangupama
- Department of Biology, School of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok 10520, Thailand
| | - Pattama Pittayakhajonwut
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phaholyothin Road, Klong Luang, Pathum Thani 12120, Thailand
| | - Chakapong Intaraudom
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phaholyothin Road, Klong Luang, Pathum Thani 12120, Thailand
| | - Chanwit Suriyachadkun
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phaholyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Ya-Wen He
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Chitti Thawai
- Department of Biology, School of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok 10520, Thailand.,Actinobacterial Research Unit, School of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok 10520, Thailand
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20
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Klaysubun C, Srisuk N, Duangmal K. Streptomyces humicola sp. nov., a novel actinobacterium isolated from peat swamp forest soil in Thailand. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748553 DOI: 10.1099/ijsem.0.005665] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
A polyphasic approach was used to describe strain RB6PN25T, an actinobacterium isolated from peat swamp forest soil in Rayong Province, Thailand. The strain was a Gram-stain-positive and filamentous bacterium that contained ll-diaminopimelic acid, mannose and ribose in whole-cell hydrolysates. MK-9(H8) was the major menaquinone. The major fatty acids were iso-C16 : 0, anteiso-C15 : 0 and iso-C15 : 0. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, two unidentified glycophospholipids, two unidentified aminolipids and an unidentified phospholipid. The 16S rRNA gene sequences analysis indicated that it was most closely related to Streptomyces rubrisoli DSM 42083T (97.6 %) and Streptomyces palmae TBRC 1999T (97.4 %). Strain RB6PN25T exhibited low average nucleotide identity and digital DNA-DNA hybridization values with S. rubrisoli DSM 42083T (78.6 %, 23.2 %) and S. palmae TBRC 1999T (76.0 %, 22.6 %). The DNA G+C content of strain RB6PN25T was 69.9%. The results of phenotypic, chemotaxonomic, genotypic and phylogenetic analyses reveal that strain RB6PN25T represents a novel species of the genus Streptomyces, for which the name Streptomyces humicola sp. nov. is proposed. The type strain is RB6PN25T (=TBRC 14819T=NBRC 115204T).
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Affiliation(s)
- Chollachai Klaysubun
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Nantana Srisuk
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand.,Biodiversity Center Kasetsart University (BDCKU), Bangkok 10900, Thailand
| | - Kannika Duangmal
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand.,Biodiversity Center Kasetsart University (BDCKU), Bangkok 10900, Thailand
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21
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Ran Y, Zhang Y, Wang X, Li G. Nematicidal Metabolites from the Actinomycete Micromonospora sp. WH06. Microorganisms 2022; 10:microorganisms10112274. [PMID: 36422344 PMCID: PMC9693860 DOI: 10.3390/microorganisms10112274] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/11/2022] [Accepted: 11/11/2022] [Indexed: 11/18/2022] Open
Abstract
A nematicidal actinomycete strain WH06 was isolated from soil samples and was identified using 16S rRNA as Micromonospora sp. Through medium screening and fermentation, 10 metabolites were isolated from the ethyl acetate extract of its fermentation broth using Sephadex LH-20 and silica gel column chromatography. These compounds were identified as N-acetyltyramine (1), N-acetyltryptamine (2), 1-methylhydantoin (3), benzenepropanoic acid (4), cyclo-(L-Pro-L-Tyr) (5), cyclo(L-Phe-Gly) (6), catechol (7), methyl (4-hydroxyphenyl)acetate (8), 3-hydroxybenzoic acid (9), and 4-hydroxybenzoic acid (10). In an in vitro assay against Meloidogyne incognita, a root-knot nematode, compounds 1, 4, 9, and 10 show nematicidal activity. Among them, benzenepropanoic acid (4) causes 99.02% mortality of nematode at 200 μg mL−1 after 72 h. Moreover, compound 4 also displays activity in inhibiting egg hatching of M. incognita. This suggests that Micromonospora sp. WH06 is a promising candidate for biocontrol of M. incognita.
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22
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Chen C, Yang H, Liu J, Luo H, Zou W. Systematic Review of Actinomycetes in the Baijiu Fermentation Microbiome. Foods 2022; 11. [PMID: 36429142 DOI: 10.3390/foods11223551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 10/28/2022] [Accepted: 11/04/2022] [Indexed: 11/10/2022] Open
Abstract
Actinomycetes (a group of filamentous bacteria) are the dominant microbial order in the Daqu (DQ) fermentation starter and in the pit mud (PM) of the Baijiu fermentation microbiome. Actinomycetes produce many of the key enzymes and flavor components, and supply important precursors, which have a major influence on its characteristic aroma components, to other microorganisms during fermentation. This paper reviews the current progress on actinomycete research related to Baijiu fermentation, including the isolation and identification, distribution, interspecies interactions, systems biology, and main metabolites. The main metabolites and applications of the actinomycetes during Baijiu fermentation are also discussed.
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23
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Tezuka T, Nitta S, Ohnishi Y. Involvement of BldC in the Formation of Physiologically Mature Sporangium in Actinoplanes missouriensis. J Bacteriol 2022; 204:e0018922. [PMID: 36005811 DOI: 10.1128/jb.00189-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
AmBldD is a global transcriptional regulator that represses the transcription of several genes required for sporangium formation in Actinoplanes missouriensis. Here, we characterized one of the AmBldD regulons: AMIS_1980, encoding an ortholog of BldC, which is a transcriptional regulator involved in the morphological development of Streptomyces. We determined the transcriptional start point of the bldC ortholog by high-resolution S1 nuclease mapping and found an AmBldD box in its 5'-untranslated region. Reverse transcription-quantitative PCR analysis revealed that the transcription of bldC is activated during sporangium formation. A bldC null mutant (ΔbldC) strain formed normally shaped sporangia, but they exhibited defective sporangium dehiscence; under a dehiscence-inducing condition, the number of spores released from the sporangia of the ΔbldC strain was 2 orders of magnitude lower than that from the sporangia of the wild-type strain. RNA sequencing analysis indicated that BldC functions as a transcriptional activator of several developmental genes, including tcrA, which encodes a key transcriptional activator that regulates sporangium formation, sporangium dehiscence, and spore dormancy. Using electrophoretic mobility shift assay (EMSA), we showed that a recombinant BldC protein directly binds to upstream regions of at least 18 genes, the transcription of which is downregulated in the ΔbldC strain. Furthermore, using DNase I footprinting and EMSA, we demonstrated that BldC binds to the direct repeat sequences containing an AT-rich motif. Thus, BldC is a global regulator that activates the transcription of several genes, some of which are likely to be required for sporangium dehiscence. IMPORTANCE BldC is a global transcriptional regulator that acts as a "brake" in the morphological differentiation of Streptomyces. BldC-like proteins are widely distributed throughout eubacteria, but their orthologs have not been studied outside streptomycetes. Here, we revealed that the BldC ortholog in Actinoplanes missouriensis is essential for sporangium dehiscence and that its regulon is different from the BldC regulon in Streptomyces venezuelae, suggesting that BldC has evolved to play different roles in morphological differentiation between the two genera of filamentous actinomycetes.
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Deng MR, Li Y, Luo X, Zheng XL, Chen Y, Zhang YL, Zhang W, Zhou H, Zhu H. Discovery of Mycothiogranaticins from Streptomyces vietnamensis GIMV4.0001 and the Regulatory Effect of Mycothiol on the Granaticin Biosynthesis. Front Chem 2021; 9:802279. [PMID: 35004619 PMCID: PMC8733708 DOI: 10.3389/fchem.2021.802279] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/06/2021] [Indexed: 11/24/2022] Open
Abstract
Granaticins are benzoisochromanequinone polyketides with remarkable antibacterial and anticancer activities. Three sulfur-containing granaticin congeners, mycothiogranaticins A (1), B (2) and granaticin MA (3) were discovered from a granaticin-producing strain of Streptomyces vietnamensis GIMV4.0001. Two of them were structurally determined with mycothiol or N-acetylcysteine moieties and found to be bio-actively reluctant. Disruption of the mshA gene (SVTN_RS20640) that encodes the D-inositol-3-phosphate glycosyltransferase crucial for mycothiol biosynthesis, fully abolished the production of mycothiogranaticins. The result substantiated that the newly discovered mycothiogranaticins are consequences of the combination of the granaticin and mycothiol biosynthetic pathways. The overall granaticin production of the ΔmshA mutant strain was unexpectedly decreased by at least more than 50%, while similar production level of granaticins to that of the wild type strain was observed in an mycothiol-S transferase gene (SVTN_RS22215) disruptant Δmst. These results indicated that the mycothiol deficiency was responsible for the decreased production of granaticins. Mycothiol may positively regulate the biosynthesis of granaticin possibly by maintaining the cellular redox balance. To the best of our knowledge, this is the first report that mycothiol can not only be a direct building block of polyketides but also play a regulatory role in the polyketide biosynthesis.
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Affiliation(s)
- Ming-Rong Deng
- Key Laboratory of Agricultural Microbiomics and Precision Application — Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yan Li
- Key Laboratory of Agricultural Microbiomics and Precision Application — Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xiao Luo
- Key Laboratory of Agricultural Microbiomics and Precision Application — Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xiang-Ling Zheng
- Key Laboratory of Agricultural Microbiomics and Precision Application — Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | | | - Yu-Lian Zhang
- Key Laboratory of Agricultural Microbiomics and Precision Application — Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | | | - Hao Zhou
- Key Laboratory of Functional Molecules Analysis and Biotransformation of Universities in Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, China
| | - Honghui Zhu
- Key Laboratory of Agricultural Microbiomics and Precision Application — Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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Abstract
A novel actinobacterium, designated strain DW4-2T, was isolated from duckweed (Spirodela sp.) collected from an agricultural pond in Kasetsart University, Bangkok, Thailand. The morphological, chemotaxonomic and phylogenetic characteristics were consistent with its classification in the genus Streptomyces. Strain DW4-2T showed the highest 16S rRNA gene sequence similarity values to Streptomyces qinglanensis DSM 42035T (98.5 %), Streptomyces smyrnaeus DSM 42105T (98.4 %) and Streptomyces oryzae S16-07T (98.4 %). Digital DNA-DNA hydridization and average nucleotide identity values between the genome sequences of strain DW4-2T with S. qinglanensis DSM 42035T (29.8 and 87.8 %), S. smyrnaeus DSM 42105T (33.1 and 89.0 %) and S. oryzae S16-07T (33.0 and 88.9 %) were below the thresholds of 70 and 95-96 % for prokaryotic conspecific assignation. Chemotaxonomic data revealed that strain DW4-2T possessed MK-9(H6) and MK-9(H8) as the predominant menaquinones. It contained ll -diaminopimelic acid as the diagnostic diamino acid and glucose, ribose and trace amount of madurose in whole-cell sugars. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, an unidentified aminolipid, an unidentified lipid and an unidentified phospholipid. The predominant cellular fatty acids were anteiso-C17 : 0, anteiso-C15 : 0 and iso-C16 : 0. The genomic DNA size of the strain DW4-2T was 7 310 765 bp with DNA G+C content 71.0 mol%. Genomic analysis of the genome indicated that the strain DW4-2T had the potential to produce bioactive compounds. On the basis of these genotypic and phenotypic data, it is supported that strain DW4-2T represents a novel species of the genus Streptomyces, for which the name Streptomyces spirodelae sp. nov. is proposed. The type strain is strain DW4-2T (=TBRC 13095T=NBRC 114803T).
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Affiliation(s)
- Yuparat Saimee
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Kannika Duangmal
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand.,Biodiversity Center Kasetsart University (BDCKU), Bangkok 10900, Thailand
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Wang H, Wang J, Ge C, Yao H. Fungi Dominated the Incorporation of 13C-CO 2 into Microbial Biomass in Tomato Rhizosphere Soil under Different CO 2 Concentrations. Microorganisms 2021; 9:2121. [PMID: 34683442 DOI: 10.3390/microorganisms9102121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/25/2021] [Accepted: 10/05/2021] [Indexed: 11/24/2022] Open
Abstract
An elevated CO2 (eCO2) fumigation experiment was carried out to study the influence of various CO2 concentrations on microorganisms involved in the incorporation of root-derived C in greenhouse soil systems. In this study, 400 and 800 µmol·mol−1 CO2 fumigation treatments were conducted during tomato planting. Phospholipid fatty acid (PLFA) profiling based on the stable isotope probing (SIP) technique was applied to trace active microorganisms. The absolute total abundance of 13C-PLFAs was much higher under eCO2 treatment. Most of the 13C-CO2 was incorporated into the 13C-PLFAs 18:2ω6,9 (fungi), 16:0 (general PLFA), 18:1ω9c (Gram-negative bacteria, G−) and i17:0 (Gram-positive bacteria, G+) via rhizodeposition from tomato under ambient CO2 (aCO2) and eCO2 treatments, suggesting similar responses of active microorganisms to different CO2 treatments. However, the fungi (characterized by the 13C-PLFA 18:2ω6,9) played a much more dominant role in the incorporation of root-derived C under eCO2. Actinomycetes, marked by the 13C-PLFA 10-Me-18:0, occurred only on labeling day 15 under the eCO2 treatment, indicating that the actinomycetes fed on both soil organic carbon and fresh rhizodeposition. It was indicated that eCO2 significantly affected microbial biomass and microbial community structures involved in the incorporation of 13C-CO2 via tomato root secretions, as supported by Adonis analysis and the Mantel test.
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27
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Li K, Su Z, Gao Y, Lin X, Pang X, Yang B, Tao H, Luo X, Liu Y, Zhou X. Cytotoxic Minor Piericidin Derivatives from the Actinomycete Strain Streptomyces psammoticus SCSIO NS126. Mar Drugs 2021; 19:md19080428. [PMID: 34436267 PMCID: PMC8398042 DOI: 10.3390/md19080428] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 07/07/2021] [Revised: 07/21/2021] [Accepted: 07/26/2021] [Indexed: 12/18/2022] Open
Abstract
The mangrove-sediment-derived actinomycete strain Streptomyces psammoticus SCSIO NS126 was found to have productive piericidin metabolites featuring anti-renal cell carcinoma activities. In this study, in order to explore more diverse piericidin derivatives, and therefore to discover superior anti-tumor lead compounds, the NS126 strain was further fermented at a 300-L scale under optimized fermentation conditions. As a result, eight new minor piericidin derivatives (piericidins L-R (1-7) and 11-demethyl-glucopiericidin A (8)) were obtained, along with glucopiericidin B (9). The new structures including absolute configurations were determined by spectroscopic methods coupled with experimental and calculated electronic circular dichroism. We also proposed plausible biosynthetic pathways for these unusual post-modified piericidins. Compounds 1 and 6 showed selective cytotoxic activities against OS-RC-2 cells, and 2-5 exhibited potent cytotoxicity against HL-60 cells, with IC50 values lower than 0.1 μM. The new piericidin glycoside 8 was cytotoxic against ACHN, HL-60 and K562, with IC50 values of 2.3, 1.3 and 5.5 μM, respectively. The ability to arrest the cell cycle and cell apoptosis effects induced by 1 and 6 in OS-RC-2 cells, 2 in HL-60 cells, and 8 in ACHN cells were then further investigated. This study enriched the structural diversity of piericidin derivatives and confirmed that piericidins deserve further investigations as promising anti-tumor agents.
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Affiliation(s)
- Kunlong Li
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (K.L.); (X.L.); (X.P.); (B.Y.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China;
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ziqi Su
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China; (Z.S.); (H.T.)
| | - Yongli Gao
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China;
- Institutional Center for Shared Technologies and Facilities, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Xiuping Lin
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (K.L.); (X.L.); (X.P.); (B.Y.)
| | - Xiaoyan Pang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (K.L.); (X.L.); (X.P.); (B.Y.)
| | - Bin Yang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (K.L.); (X.L.); (X.P.); (B.Y.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China;
| | - Huaming Tao
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China; (Z.S.); (H.T.)
| | - Xiaowei Luo
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning 530200, China
- Correspondence: (X.L.); (Y.L.); (X.Z.); Tel.: +86-020-89023174 (X.Z.)
| | - Yonghong Liu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (K.L.); (X.L.); (X.P.); (B.Y.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China;
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning 530200, China
- Correspondence: (X.L.); (Y.L.); (X.Z.); Tel.: +86-020-89023174 (X.Z.)
| | - Xuefeng Zhou
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (K.L.); (X.L.); (X.P.); (B.Y.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China;
- Correspondence: (X.L.); (Y.L.); (X.Z.); Tel.: +86-020-89023174 (X.Z.)
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28
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Breitling R, Avbelj M, Bilyk O, Carratore F, Filisetti A, Hanko EKR, Iorio M, Redondo RP, Reyes F, Rudden M, Severi E, Slemc L, Schmidt K, Whittall DR, Donadio S, García AR, Genilloud O, Kosec G, De Lucrezia D, Petković H, Thomas G, Takano E. Synthetic biology approaches to actinomycete strain improvement. FEMS Microbiol Lett 2021; 368:6289918. [PMID: 34057181 PMCID: PMC8195692 DOI: 10.1093/femsle/fnab060] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/28/2021] [Indexed: 12/17/2022] Open
Abstract
Their biochemical versatility and biotechnological importance make actinomycete bacteria attractive targets for ambitious genetic engineering using the toolkit of synthetic biology. But their complex biology also poses unique challenges. This mini review discusses some of the recent advances in synthetic biology approaches from an actinomycete perspective and presents examples of their application to the rational improvement of industrially relevant strains.
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Affiliation(s)
- Rainer Breitling
- Department of Chemistry, Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYNBIOCHEM, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Martina Avbelj
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Oksana Bilyk
- Department of Chemistry, Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYNBIOCHEM, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Francesco Del Carratore
- Department of Chemistry, Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYNBIOCHEM, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | | | - Erik K R Hanko
- Department of Chemistry, Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYNBIOCHEM, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | | | | | - Fernando Reyes
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnologico de Ciencias de la Salud, 18016 Armilla, Granada, Spain
| | - Michelle Rudden
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | | | - Lucija Slemc
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Kamila Schmidt
- Department of Chemistry, Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYNBIOCHEM, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Dominic R Whittall
- Department of Chemistry, Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYNBIOCHEM, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | | | | | - Olga Genilloud
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnologico de Ciencias de la Salud, 18016 Armilla, Granada, Spain
| | - Gregor Kosec
- Acies Bio d.o.o., Tehnološki Park 21, 1000, Ljubljana, Slovenia
| | - Davide De Lucrezia
- Explora Biotech Srl, Doulix business unit, Via Torino 107, 30133 Venice, Italy
| | - Hrvoje Petković
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Gavin Thomas
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Eriko Takano
- Corresponding author: Department of Chemistry, Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYNBIOCHEM, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK. E-mail:
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29
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Ueoka R, Hashimoto J, Kozone I, Hashimoto T, Kudo K, Kagaya N, Suenaga H, Ikeda H, Shin-Ya K. A novel methymycin analog, 12-ketomethymycin N-oxide, produced by the heterologous expression of the large pikromycin/methymycin biosynthetic gene cluster of Streptomyces sp. AM4900. Biosci Biotechnol Biochem 2021; 85:890-894. [PMID: 33590846 DOI: 10.1093/bbb/zbaa111] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 12/11/2020] [Indexed: 11/13/2022]
Abstract
A novel methymycin analog, 12-ketomethymycin N-oxide, was produced by the heterologous expression of the pikromycin/methymycin biosynthetic gene cluster of Streptomyces sp. AM4900 together with 12-ketomethymycin, which was only isolated by the biotransformation of the synthetic intermediate before. Their structures were determined by the spectroscopic data and the chemical derivatization. 12-Ketomethymycin showed a weak cytotoxicity against SKOV-3 and Jurkat cells, although its N-oxide analog did not show any activity. Both showed no antibacterial activities against Escherichia coli and Micrococcus luteus.
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Affiliation(s)
- Reiko Ueoka
- National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Junko Hashimoto
- Japan Biological Informatics Consortium (JBIC), Tokyo, Japan
| | - Ikuko Kozone
- Japan Biological Informatics Consortium (JBIC), Tokyo, Japan
| | - Takuya Hashimoto
- National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Kei Kudo
- National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Noritaka Kagaya
- National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Hikaru Suenaga
- National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Haruo Ikeda
- Kitasato Institute for Life Sciences, Kitasato University, Kanagawa, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.,Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
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30
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Abstract
A novel actinomycete, strain SMC 257T, was isolated from a soil sample collected from mountain forest, Nan Province, Thailand. Strain SMC 257T formed tightly closed spiral spore chains on aerial mycelia. A polyphasic approach was used for the taxonomic study of this strain. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SMC 257T belonged to the genus Nonomuraea, and the closest phylogenetically related species were Nonomuraea roseoviolacea subsp. carminata JCM 9946T (98.9 % 16S rRNA gene sequence similarity), Nonomuraea rhodomycinica TBRC 6557T (98.4 %), and Nonomuraea roseoviolacea subsp. roseoviolacea JCM 3145T (98.3 %). Genome sequencing revealed a genome size of 9.76 Mbp and a G+C content of 72.3 mol%. The genome average nucleotide identity (ANI) and the digital DNA-DNA hybridization (dDDH) values that distinguished this novel strain from its closest related species were species boundary of 95-96 % and 70 %, respectively. The cell wall peptidoglycan contained meso-diaminopimelic acid. The whole-cell sugars were glucose, ribose, madurose and mannose. The major menaquinone was MK-9(H4). The polar lipid profile consisted of phosphatidylethanolamine, hydroxyphosphatidylethanolamine, lysophosphatidylethanolamine, diphosphatidylglycerol, N-phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. The predominant cellular fatty acids were C17 : 0 10-methyl and iso-C16 : 0. Based on comparative analysis of phenotypic, chemotaxonomic and genotypic data, strain SMC 257T is considered to represent a novel species of the genus Nonomuraea, for which the name Nonomuraea montanisoli is proposed. The type strain is SMC 257T (=TBRC 13065T=NBRC 114772T).
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Affiliation(s)
- Suchart Chanama
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Chanwit Suriyachadkun
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Manee Chanama
- Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok 10400, Thailand
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Sakdapetsiri C, Kuntaveesuk A, Ngaemthao W, Suriyachadkun C, Muangchinda C, Chavanich S, Viyakarn V, Chen B, Pinyakong O. Paeniglutamicibacter terrestris sp. nov., isolated from phenanthrene-degrading consortium enriched from Antarctic soil. Int J Syst Evol Microbiol 2021; 71. [PMID: 33555249 DOI: 10.1099/ijsem.0.004689] [Citation(s) in RCA: 3] [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: 11/18/2022] Open
Abstract
A novel bacterium, designated strain ANT13_2T, was isolated from a phenanthrene-degrading consortium enriched from a soil sample collected near the Great Wall Station located in the southwestern area of King George Island, Antarctica. Following a polyphasic taxonomic study, a novel species belonging to the genus Paeniglutamicibacter was described. The strain was a Gram-stain-positive bacterium that exhibited a rod-coccus growth cycle. Strain ANT13_2T grew aerobically at an optimum temperature of 20-25 °C and at pH 7.0-8.0. Ribose, arabinose and glucose were detected as whole-cell sugars. The predominant menaquinone was MK-9. The diagnostic phospholipids were diphosphatidylglycerol, phosphatidylglycerol and an unidentified phospholipid. The predominant cellular fatty acids were anteiso-C15 : 0 (67.7 %) and anteiso-C17 : 0 (11.2 %). The DNA G+C content of the genomic DNA was 60.6 mol%. Based on 16S rRNA gene sequence analysis, strain ANT13_2T showed the highest similarities to Paeniglutamicibacter antarcticus SPC26T (98.9 %) followed by Paeniglutamicibacter gangotriensis Lz1yT (98.4 %), Paeniglutamicibacter sulfureus DSM 20167T (98.3%) and Paeniglutamicibacter kerguelensis KGN15T (97.9 %). The average nucleotide identity values between strain ANT13_2T and the type strains of P. antarcticus SPC26T and P. gangotriensis Lz1yT were 73.8 and 77.5 %, respectively, which are well below the 95-96 % species circumscription threshold. On the basis of this polyphasic taxonomic study, strain ANT13_2T is proposed to represent a novel species to be named Paeniglutamicibacter terrestris sp. nov. The type strain is ANT13_2T (=TBRC 11756T=NBRC 114615T).
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Affiliation(s)
- Chatsuda Sakdapetsiri
- Microbial Technology for Marine Pollution Treatment Research Unit, Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Aunchisa Kuntaveesuk
- Microbial Technology for Marine Pollution Treatment Research Unit, Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Wipaporn Ngaemthao
- Microbial Diversity and Utilization Research Team, Thailand Bioresource Research Center, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phaholyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Chanwit Suriyachadkun
- Microbial Diversity and Utilization Research Team, Thailand Bioresource Research Center, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phaholyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Chanokporn Muangchinda
- Microbial Technology for Marine Pollution Treatment Research Unit, Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Suchana Chavanich
- Reef Biology Research Group, Department of Marine Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Voranop Viyakarn
- Reef Biology Research Group, Department of Marine Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Bo Chen
- Key Laboratory of Polar Science, MNR, Polar Research Institute of China, Shanghai, 200136, PR China
| | - Onruthai Pinyakong
- Microbial Technology for Marine Pollution Treatment Research Unit, Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.,Research Program on Remediation Technologies for Petroleum Contamination, Center of Excellence on Hazardous Substance Management (HSM), Chulalongkorn University, Bangkok 10330, Thailand
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32
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Zhao HW, Li JQ, Ding WJ. Chemical constituents from salt lake-derived Streptomyces sp. QHA10. J Asian Nat Prod Res 2021; 23:26-32. [PMID: 31847583 DOI: 10.1080/10286020.2019.1700230] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 11/29/2019] [Indexed: 06/10/2023]
Abstract
Two new alkaloids (1,2) and one new enoic acid (3), together with three known piericidins (4-6), were isolated from the liquid fermentation of the salt lake derived Streptomyces sp. QHA10. The structures of 1-3 were elucidated based on extensive spectroscopic data (NMR, HRESIMS) as well as single-crystal X-ray diffraction. Compound 3 showed potential anti-inflammatory activity by inhibiting the production of nitric oxide (NO) in lipopolysaccharide (LPS)-induced RAW 264.7 mouse macrophages with the IC50 value of 24.5 μM.
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Affiliation(s)
- Hao-Wen Zhao
- Ocean College, Zhejiang University, Zhoushan 316021, China
| | - Jia-Qi Li
- Ocean College, Zhejiang University, Zhoushan 316021, China
| | - Wan-Jing Ding
- Ocean College, Zhejiang University, Zhoushan 316021, China
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Komaki H, Tamura T. Polyketide Synthase and Nonribosomal Peptide Synthetase Gene Clusters in Type Strains of the Genus Phytohabitans. Life (Basel) 2020; 10:life10110257. [PMID: 33120960 PMCID: PMC7692728 DOI: 10.3390/life10110257] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/06/2020] [Accepted: 10/22/2020] [Indexed: 12/22/2022]
Abstract
(1) Background: Phytohabitans is a recently established genus belonging to rare actinomycetes. It has been unclear if its members have the capacity to synthesize diverse secondary metabolites. Polyketide and nonribosomal peptide compounds are major secondary metabolites in actinomycetes and expected as a potential source for novel pharmaceuticals. (2) Methods: Whole genomes of Phytohabitans flavus NBRC 107702T, Phytohabitans rumicis NBRC 108638T, Phytohabitans houttuyneae NBRC 108639T, and Phytohabitans suffuscus NBRC 105367T were sequenced by PacBio. Polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) gene clusters were bioinformatically analyzed in the genome sequences. (3) Results: These four strains harbored 10, 14, 18 and 14 PKS and NRPS gene clusters, respectively. Most of the gene clusters were annotated to synthesis unknown chemistries. (4) Conclusions: Members of the genus Phytohabitans are a possible source for novel and diverse polyketides and nonribosomal peptides.
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34
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Klaysubun C, Lipun K, Duangmal K. Pseudonocardia acidicola sp. nov., a novel actinomycete isolated from peat swamp forest soil. Int J Syst Evol Microbiol 2020; 70:5648-5653. [PMID: 32931406 DOI: 10.1099/ijsem.0.004459] [Citation(s) in RCA: 8] [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: 11/18/2022] Open
Abstract
A novel actinobacterium, designated strain K10HN5T, was isolated from a peat soil sample collected from Kantulee peat swamp forest, Surat Thani Province, Thailand and its taxonomic position was determined using a polyphasic approach. Strain K10HN5T contained meso-diaminopimelic acid, arabinose, galactose, glucose and ribose in its whole-cell hydrolysates. The predominant menaquinone was MK-8(H4). The major fatty acids were iso-C16 : 0, iso-C15 : 0 and iso-C16 : 1H. Mycolic acids were not present. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylmethylethanolamine, hydroxyphosphatidylethanolamine, hydroxyphosphatidylmethylethanolamine and phosphatidylinositol. The 16S rRNA gene sequence analysis indicated that it was closely related to Pseudonocardia bannensis DSM 45300T (97.9 %) and Pseudonocardia xinjiangensis JCM 11839T (97.9 %). Strain K10HN5T exhibited low average nucleotide identity and digital DNA-DNA hybridization values with P. bannensis DSM 45300T (82.6, 28.7 %) and P. xinjiangensis JCM11839T (76.3, 22.2 %). The DNA G+C content of strain K10HN5T was 72.4 mol%. Based on polyphasic data, strain K10HN5T represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia acidicola sp. nov. is proposed. The type strain is K10HN5T (=TBRC 10048T=NBRC 113897T).
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Affiliation(s)
- Chollachai Klaysubun
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Kenika Lipun
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Kannika Duangmal
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
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35
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Liu WX, Ma LR, Xia ZF, Zeng H, Luo XX, Zhang LL, Wan CX. Streptomyces apocyni sp. nov., an endogenous actinomycete isolated from Apocynum venetum. Int J Syst Evol Microbiol 2020; 70:4883-4889. [PMID: 32790603 DOI: 10.1099/ijsem.0.004357] [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: 11/18/2022] Open
Abstract
A novel actinomycete, designated strain TRM 66233T, was isolated from Apocynum venetum L. collected from the Xinjiang Uygur Autonomous Region of China and characterized using a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA gene sequences affiliated strain TRM 66233T with the genus Streptomyces. Strain TRM 66233T showed a high similarity value to Streptomyces bikiniensis NRRL B-1049T (98.07 %) based on the 16S rRNA gene phylogenetic tree. The whole-cell sugar pattern of TRM 66233T consisted of glucose, galactose, mannose and ribose. The predominant menaquinones were MK-9(H2), MK-9(H6), MK-9(H8) and MK-9(H10). The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and four unidentified lipids. The major fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0, C16 : 0 and iso-C17 : 0. The G+C content of the DNA was 70.35 mol%. The DNA-DNA relatedness and average nucleotide identity values as well as evolutionary distances based on multilocus (atpD, gyrB, recA, rpoB and trpB) sequences between strain TRM 66233T and closely related type strains were significantly lower than the recommended threshold values. The whole-genome average nucleotide identity and digital DNA-DNA hybridization values between strain TRM 66233T and S. bikiniensis NRRL B-1049T were 78.86 and 23.2 %, respectively. On the basis of evidence from this polyphasic study, strain TRM 66233T should represent a novel species of the genus Streptomyces, for which the name Streptomyces apocyni sp. nov. is proposed. The type strain is TRM 66233T (=CCTCC AA 2019056T=LMG 31559T).
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Affiliation(s)
- Wen-Xiang Liu
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps/College of Life Science, Tarim University, Alar 843300, PR China
| | - Li-Ran Ma
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps/College of Life Science, Tarim University, Alar 843300, PR China
| | - Zhan-Feng Xia
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps/College of Life Science, Tarim University, Alar 843300, PR China
| | - Hong Zeng
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps/College of Life Science, Tarim University, Alar 843300, PR China
| | - Xiao-Xia Luo
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps/College of Life Science, Tarim University, Alar 843300, PR China
| | - Li-Li Zhang
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps/College of Life Science, Tarim University, Alar 843300, PR China
| | - Chuan-Xing Wan
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps/College of Life Science, Tarim University, Alar 843300, PR China
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36
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Komaki H, Oguchi A, Tamura T, Hamada M, Ichikawa N. Diversity of nonribosomal peptide synthetase and polyketide synthase gene clusters in the genus Acrocarpospora. J GEN APPL MICROBIOL 2020; 66:315-322. [PMID: 32801283 DOI: 10.2323/jgam.2020.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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
Acrocarpospora is a rare, recently established actinomycete genus of the family Streptosporangiaceae. In the present study, we sequenced whole genomes of the type strains of Acrocarpospora corrugate, Acrocarpospora macrocephala, and Acrocarpospora pleiomorpha to assess their potency as secondary metabolite producers; we then surveyed their nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) gene clusters. The genome sizes of A. corrugate NBRC 13972T, A. macrocephala NBRC 16266T, and A. pleiomorpha NBRC 16267T were 9.3 Mb, 12.1 Mb, and 11.8 Mb, respectively. Each genome contained 12-17 modular NRPS and PKS gene clusters. Among the 23 kinds of NRPS and PKS gene clusters identified from the three strains, eight clusters were conserved in all the strains, six were shared between A. macrocephala and A. pleiomorpha, and the remaining nine were strain-specific. We predicted the chemical structures of the products synthesized by these gene clusters based on bioinformatic analyses. Since the chemical structures are diverse, Acrocarpospora strains are considered an attractive source of diverse nonribosomal peptide and polyketide compounds.
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Affiliation(s)
- Hisayuki Komaki
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC)
| | | | - Tomohiko Tamura
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC)
| | - Moriyuki Hamada
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC)
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Abstract
A Gram-stain-positive actinobacterial strain, designated ANK073T, was isolated from rhizosphere soil sampled at a spinach farming field in Shinan, Republic of Korea. Cells of strain ANK073T were found to be aerobic, non-motile, non-spore-forming rods which could grow at 20-40 °C (optimum, 30 °C), at pH 6.0-10.0 (optimum, pH 6.5-7.5) and at salinities of 0-4 % (w/v) NaCl (optimum, 0 % NaCl). The 16S rRNA gene sequence analysis showed that strain ANK073T belongs to the genus Agromyces with high sequence similarities to Agromyces humatus CD5T (98.8 %), Agromyces tardus SJ-23T (98.5 %) and Agromyces iriomotensis IY07-20T (98.4 %). The phylogenetic analysis indicated that strain ANK073T formed a distinct phyletic line in the genus Agromyces and the results of DNA-DNA relatedness and phylogenomic analysis based on whole genome sequences demonstrated that strain ANK073T could be separated from its closest relatives in the genus Agromyces. The strain contained 2,4-diaminobutylic acid, glycine, d-glutamic acid and d-alanine in the peptidoglycan. The predominant menaquinones were identified as MK-12 and MK-11, and the major fatty acids were anteiso-C17 : 0, anteiso-C15 : 0 and iso-C15:0. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The G+C content of the genome was determined to be 70.2 mol%. On the basis of its phenotypic and chemotaxonomic properties and the results of phylogenetic and phylogenomic analyses, strain ANK073T is considered to represent a novel species in the genus Agromyces, for which the name Agromyces humi sp. nov. is proposed. The type strain is ANK073T (=KACC 18683T=NBRC 111825T).
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Affiliation(s)
- Jae-Chan Lee
- Department of Microbiology & Resources, College of Science & Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 35349, Republic of Korea.,Institute of Microbial Ecology and Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 35349, Republic of Korea
| | - Kyung-Sook Whang
- Institute of Microbial Ecology and Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 35349, Republic of Korea.,Department of Microbiology & Resources, College of Science & Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 35349, Republic of Korea
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38
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Tamura T, Saito S, Hamada M, Kang Y, Hoshino Y, Gonoi T, Mikami Y, Yaguchi T. Gordonia crocea sp. nov. and Gordonia spumicola sp. nov. isolated from sludge of a wastewater treatment plant. Int J Syst Evol Microbiol 2020; 70:3718-3723. [PMID: 32427091 DOI: 10.1099/ijsem.0.004225] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Two novel actinobacteria, designated NBRC 107696T and NBRC 107697T, were isolated from sludge samples from a wastewater treatment plant and their taxonomic positions were investigated by a polyphasic approach. The cells of the strains were aerobic, rod-shaped, non-motile and non-endospore-forming. The strains contained glutamic acid, alanine and meso-diaminopimelic acid in the peptidoglycan. Galactose and arabinose were detected as cell-wall sugars. The predominant menaquinone was identified as MK-9(H2) and the major fatty acids were C16 : 0, C18 : 1ω9c and C16 : 1ω7c. The DNA G+C contents of NBRC 107696T and NBRC 107697T were 68.07 and 68.99 mol%, respectively. Phylogenetic analyses based on 16S rRNA gene sequence comparisons revealed that NBRC 107696T and NBRC 107697T were a clade with members of the genus Gordonia. The highest 16S rRNA gene sequence similarity values were obtained with Gordonia araii IFM 10211T (98.9 %) for NBRC 107697T, and Gordonia malaquae IMMIB WWCC-22T, Gordonia neofelifaecis AD-6T and Gordonia humi CC-12301T (98.1 %) for NBRC 107696T, respectively. The digital DNA-DNA relatedness data coupled with the combination of genotypic and phenotypic data indicated that the two strains are representatives of two novel separate species. The names proposed to accommodate these two strains are Gordonia spumicola sp. nov. and Gordonia crocea sp. nov., and the type strains are NBRC 107696T (=IFM 10067T=TBRC 11239T) and NBRC 107697T (=IFM 10881T=TBRC 11240T), respectively.
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Affiliation(s)
- Tomohiko Tamura
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Satomi Saito
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Moriyuki Hamada
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | | | - Yasutaka Hoshino
- National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku, Tokyo, 162-8640, Japan
| | - Tohru Gonoi
- Medical Mycology Research Center (MMRC), Chiba University, 1-8-1, Inohana, Chuo-ku, Chiba, Chiba 260-8673, Japan
| | - Yuzuru Mikami
- Medical Mycology Research Center (MMRC), Chiba University, 1-8-1, Inohana, Chuo-ku, Chiba, Chiba 260-8673, Japan
| | - Takashi Yaguchi
- Medical Mycology Research Center (MMRC), Chiba University, 1-8-1, Inohana, Chuo-ku, Chiba, Chiba 260-8673, Japan
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Abstract
A novel actinobacterial strain, designated K81G1T, was isolated from a soil sample collected in Kantulee peat swamp forest, Surat Thani Province, Thailand, and its taxonomic position was determined using a polyphasic approach. Optimal growth of strain K81G1T occurred at 28-30 °C, at pH 5.0-6.0 and without NaCl. Strain K81G1T had cell-wall chemotype IV (meso-diaminopimelic acid as the diagnostic diamino acid, and arabinose and galactose as diagnostic sugars) and phospholipid pattern type II, characteristic of the genus Amycolatopsis. It contained MK-9(H4) as the predominant menaquinone, iso-C16 : 0, C17 : 0 cyclo and C16 : 0 as the major cellular fatty acids, and phospholipids consisting of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylinositol and two unidentified phospholipids. Based on 16S rRNA gene sequence similarity and phylogenetic analyses, strain K81G1T was most closely related to Amycolatopsis rhizosphaerae TBRC 6029T (97.8 % similarity), Amycolatopsis acidiphila JCM 30562T (97.8 %) and Amycolatopsis bartoniae DSM 45807T (97.6 %). Strain K81G1T exhibited low average nucleotide identity and digital DNA-DNA hybridization values with A. rhizosphaerae TBRC 6029T (76.4 %, 23.0 %), A. acidiphila JCM 30562T (77.9 %, 24.6 %) and A. bartoniae DSM 45807T (77.8 %, 24.3 %). The DNA G+C content of strain K81G1T was 69.7 mol%. Based on data from this polyphasic study, strain K81G1T represents a novel species of the genus Amycolatopsis, for which the name Amycolatopsis acidicola sp. nov. is proposed. The type strain is K81G1T (=TBRC 10047T=NBRC 113896T).
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Affiliation(s)
- Wee Fei Aaron Teo
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Nantana Srisuk
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Kannika Duangmal
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
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Kittisrisopit S, Bunbamrung N, Thawai C, Tadtong S, Niemhom N, Komwijit S, Rachtawee P, Pittayakhajonwut P. Neuroprotective potential of new chromones isolated from the soil actinomycete Microbispora sp. TBRC6027. Nat Prod Res 2019; 35:2881-2886. [PMID: 31631706 DOI: 10.1080/14786419.2019.1679135] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Nine new chromone analogs (1-9) were isolated from the soil actinomycete Microbispora sp. TBRC6027. The chemical structures were determined based upon NMR spectroscopic methods. These compounds were evaluated in vitro by using P19-derived neurons for neuroprotective activity against oxidative stress induced by serum deprivation and showed % viability of neurons at the concentration of 1 ng/mL varied from 43.51% to 52.99% without significant neurotoxicity for P19-derived neurons at the same concentration. Moreover, all tested compounds were inactive for antibacterial activity against both Gram-positive and Gram-negative bacteria and for cytotoxicity against MCF-7 (human breast cancer) and Vero cells at maximum tested concentration 50 μg/mL. However, compounds 4, 6, and 7 displayed weak cytotoxicity against NCI-H187 (human small-cell lung cancer) cells with IC50 in a range of 87.99-91.57 μM.
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Affiliation(s)
- Suchada Kittisrisopit
- Department of Biology, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand
| | - Nantiya Bunbamrung
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chitti Thawai
- Department of Biology, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand.,Antinobacterial Research Unit, Faculty of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand.,Center of Excellence in Applied Biosciences, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand
| | - Sarin Tadtong
- Faculty of Pharmacy, Srinakharinwiroj University, Ongkharak, Nakhon-Nayok, Thailand
| | - Nantawan Niemhom
- Scientific Instruments Centre, Faculty of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand
| | - Somjit Komwijit
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Pranee Rachtawee
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Pattama Pittayakhajonwut
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
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Carey J, Nguyen T, Korchak J, Beecher C, de Jong F, Lane AL. An Isotopic Ratio Outlier Analysis Approach for Global Metabolomics of Biosynthetically Talented Actinomycetes. Metabolites 2019; 9:E181. [PMID: 31510039 DOI: 10.3390/metabo9090181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 09/04/2019] [Indexed: 01/01/2023] Open
Abstract
Actinomycetes are powerhouses of natural product biosynthesis. Full realization of this biosynthetic potential requires approaches for recognizing novel metabolites and determining mediators of metabolite production. Herein, we develop an isotopic ratio outlier analysis (IROA) ultra-high performance liquid chromatography-mass spectrometry (UHPLC/MS) global metabolomics strategy for actinomycetes that facilitates recognition of novel metabolites and evaluation of production mediators. We demonstrate this approach by determining impacts of the iron chelator 2,2′-bipyridyl on the Nocardiopsis dassonvillei metabolome. Experimental and control cultures produced metabolites with isotopic carbon signatures that were distinct from corresponding “standard” culture metabolites, which were used as internal standards for LC/MS. This provided an isotopic MS peak pair for each metabolite, which revealed the number of carbon atoms and relative concentrations of metabolites and distinguished biosynthetic products from artifacts. Principal component analysis (PCA) and random forest (RF) differentiated bipyridyl-treated samples from controls. RF mean decrease accuracy (MDA) values supported perturbation of metabolites from multiple amino acid pathways and novel natural products. Evaluation of bipyridyl impacts on the nocazine/XR334 diketopiperazine (DKP) pathway revealed upregulation of amino acid precursors and downregulation of late stage intermediates and products. These results establish IROA as a tool in the actinomycete natural product chemistry arsenal and support broad metabolic consequences of bipyridyl.
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Cao DD, Trinh TTV, Mai HDT, Vu VN, Le HM, Thi QV, Nguyen MA, Duong TT, Tran DT, Chau VM, Ma R, Shetye G, Cho S, Murphy BT, Pham VC. Antimicrobial Lavandulylated Flavonoids from a Sponge-Derived Streptomyces sp. G248 in East Vietnam Sea. Mar Drugs 2019; 17:E529. [PMID: 31510079 DOI: 10.3390/md17090529] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 08/30/2019] [Accepted: 09/06/2019] [Indexed: 11/18/2022] Open
Abstract
Three new lavandulylated flavonoids, (2S,2″S)-6-lavandulyl-7,4′-dimethoxy-5,2′-dihydroxylflavanone (1), (2S,2″S)-6-lavandulyl-5,7,2′,4′-tetrahydroxylflavanone (2), and (2″S)-5′-lavandulyl-2′-methoxy-2,4,4′,6′-tetrahydroxylchalcone (3), along with seven known compounds 4–10 were isolated from culture broth of Streptomyces sp. G248. Their structures were established by spectroscopic data analysis, including 1D and 2D nuclear magnetic resonance (NMR), and high-resolution electrospray ionization mass spectrometry (HR-ESI-MS). The absolute configurations of 1–3 were resolved by comparison of their experimental and calculated electronic circular dichroism spectra. Compounds 1–3 exhibited remarkable antimicrobial activity. Whereas, two known compounds 4 and 5 exhibited inhibitory activity against Mycobacterium tuberculosis H37Rv with minimum inhibitory concentration (MIC) values of 6.0 µg/mL and 11.1 µg/mL, respectively.
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Tesche S, Rösemeier-Scheumann R, Lohr J, Hanke R, Büchs J, Krull R. Salt-enhanced cultivation as a morphology engineering tool for filamentous actinomycetes: Increased production of labyrinthopeptin A1 in Actinomadura namibiensis. Eng Life Sci 2019; 19:781-794. [PMID: 32624971 DOI: 10.1002/elsc.201900036] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 02/26/2019] [Revised: 08/03/2019] [Accepted: 08/23/2019] [Indexed: 12/11/2022] Open
Abstract
Salt-enhanced cultivation as a morphology engineering tool for the filamentous actinomycete Actinomadura namibiensis was evaluated in 500-mL shaking flasks (working volume 100 mL) with the aim of increasing the concentration of the pharmaceutically interesting peptide labyrinthopeptin A1. Among the inorganic salts added to a complex production medium, the addition of (NH4)2SO4 led to the highest amount of labyrinthopeptin A1 production. By using 50 mM (NH4)2SO4, the labyrinthopeptin A1 concentration increased up to sevenfold compared to the non-supplemented control, resulting in 325 mg L-1 labyrinthopeptin A1 after 10 days of cultivation. The performance of other ammonium- and sulfate-containing salts (e.g., NH4Cl, K2SO4) was much lower than the performance of (NH4)2SO4. A positive correlation between the uptake of glycerol as one of the main carbon sources and nongrowth-associated labyrinthopeptin productivity was found. The change in the cell morphology of A. namibiensis in conjunction with increased osmolality by the addition of 50 mM (NH4)2SO4, was quantified by image analysis. A. namibiensis always developed a heterogeneous morphology with pellets and loose mycelia present simultaneously. In contrast to the non-supplemented control, the morphology of (NH4)2SO4-supplemented cultures was characterized by smaller and circular pellets that were more stable against disintegration in the stationary production phase.
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Affiliation(s)
- Sebastian Tesche
- Institute of Biochemical Engineering Technische Universität Braunschweig Braunschweig Germany.,Center of Pharmaceutical Engineering (PVZ) Technische Universität Braunschweig Braunschweig Germany
| | - René Rösemeier-Scheumann
- Institute of Biochemical Engineering Technische Universität Braunschweig Braunschweig Germany.,Center of Pharmaceutical Engineering (PVZ) Technische Universität Braunschweig Braunschweig Germany
| | - Jonas Lohr
- Institute of Biochemical Engineering Technische Universität Braunschweig Braunschweig Germany.,Center of Pharmaceutical Engineering (PVZ) Technische Universität Braunschweig Braunschweig Germany
| | - René Hanke
- AVT - Chair of Biochemical Engineering RWTH Aachen University Aachen Germany
| | - Jochen Büchs
- AVT - Chair of Biochemical Engineering RWTH Aachen University Aachen Germany
| | - Rainer Krull
- Institute of Biochemical Engineering Technische Universität Braunschweig Braunschweig Germany.,Center of Pharmaceutical Engineering (PVZ) Technische Universität Braunschweig Braunschweig Germany
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44
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Yu M, Li Y, Banakar SP, Liu L, Shao C, Li Z, Wang C. New Metabolites From the Co-culture of Marine-Derived Actinomycete Streptomyces rochei MB037 and Fungus Rhinocladiella similis 35. Front Microbiol 2019; 10:915. [PMID: 31134000 PMCID: PMC6514141 DOI: 10.3389/fmicb.2019.00915] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [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: 11/15/2018] [Accepted: 04/10/2019] [Indexed: 12/24/2022] Open
Abstract
Co-culture of different microbes simulating the natural state of microbial community may produce potentially new compounds because of nutrition or space competition. To mine its metabolic potential in depth, co-culture of Streptomyces rochei MB037 with a gorgonian-derived fungus Rhinocladiella similis 35 was carried out to stimulate the production of new metabolites in this study, using pure cultivation as control. Five metabolites were isolated successfully from co-culture broth, including two new fatty acids with rare nitrile group, borrelidins J and K (1 and 2), one chromone derivative as a new natural product, 7-methoxy-2,3-dimethylchromone-4-one (3), together with two known 18-membered macrolides, borrelidin (4) and borrelidin F (5). The structures of 1–3 were elucidated by using a combination of NMR and MS spectroscopy, ester hydrolysis, and optical rotation methods. Interestingly, 1 and 2 were obtained only in co-culture. Though 3 was gained from either co-culture or single culture, its production was increased significantly by co-culture. Compound 1 exhibited significant antibacterial activity against methicillin-resistant Staphylococcus aureus with a MIC value of 0.195 μg/mL.
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Affiliation(s)
- Meilin Yu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yingxin Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shivakumar P Banakar
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Lu Liu
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Changlun Shao
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhiyong Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Changyun Wang
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
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45
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Choi ME, Jung CJ, Won CH, Chang SE, Lee MW, Choi JH, Lee WJ. Case report of cutaneous nodule caused by Gordonia bronchialis in an immunocompetent patient after receiving acupuncture. J Dermatol 2019; 46:343-346. [PMID: 30710379 DOI: 10.1111/1346-8138.14785] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 12/24/2018] [Indexed: 12/14/2022]
Abstract
Gordonia species were recently found to cause human infection. Most Gordonia bronchialis infections are associated with sternal wounds and foreign bodies. Here, we present a case of a firm cutaneous nodule caused by G. bronchialis on an immunocompetent patient's lower extremity after receiving acupuncture. Our present case indicates that spontaneous cutaneous infection of G. bronchialis can develop even in a healthy patient. With the popularity of complementary and alternative medicine, physicians should be aware that G. bronchialis infection can be associated with Oriental medicine similar to mycobacterial infection. Recognizing the diverse clinical features of newly emerging Gordonia species will facilitate appropriate diagnosis and management of future patients.
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Affiliation(s)
- Myoung Eun Choi
- Department of Dermatology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Chang Jin Jung
- Department of Dermatology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Chong Hyun Won
- Department of Dermatology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Sung Eun Chang
- Department of Dermatology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Mi Woo Lee
- Department of Dermatology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jee Ho Choi
- Department of Dermatology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Woo Jin Lee
- Department of Dermatology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
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46
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Hara S, Hara Y, Arai MA, Kusuya Y, Takahashi H, Yaguchi T, Ishibashi M. Isolation of Nabscessin C from Nocardia abscessus IFM 10029 T and a Study on Biosynthetic Pathway for Nabscessins. Chem Pharm Bull (Tokyo) 2018; 66:976-982. [PMID: 30270243 DOI: 10.1248/cpb.c18-00430] [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: 11/22/2022]
Abstract
A new aminocyclitol derivative, designated nabscessin C (1), was isolated from Nocardia abscessus IFM 10029T. Nabcessin C is an isomer of nabscessins A (2) and B (3) with different positioning of the acyl group. Absolute configuration of nabscessin A was determined by conversion into the 2-deoxy-scyllo-inosamine pentaacetyl derivative (4) by hydrolysis and acetylation of 2. The biosynthetic pathway of nabscessins is proposed based on gene expression analysis.
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Affiliation(s)
- Shoko Hara
- Graduate School of Pharmaceutical Sciences, Chiba University
| | - Yasumasa Hara
- Graduate School of Pharmaceutical Sciences, Chiba University
| | - Midori A Arai
- Graduate School of Pharmaceutical Sciences, Chiba University
| | - Yoko Kusuya
- Medical Mycology Research Center, Chiba University
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Pishchany G, Mevers E, Ndousse-Fetter S, Horvath DJ Jr, Paludo CR, Silva-Junior EA, Koren S, Skaar EP, Clardy J, Kolter R. Amycomicin is a potent and specific antibiotic discovered with a targeted interaction screen. Proc Natl Acad Sci U S A 2018; 115:10124-9. [PMID: 30228116 DOI: 10.1073/pnas.1807613115] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The rapid emergence of antibiotic-resistant pathogenic bacteria has accelerated the search for new antibiotics. Many clinically used antibacterials were discovered through culturing a single microbial species under nutrient-rich conditions, but in the environment, bacteria constantly encounter poor nutrient conditions and interact with neighboring microbial species. In an effort to recapitulate this environment, we generated a nine-strain actinomycete community and used 16S rDNA sequencing to deconvolute the stochastic production of antimicrobial activity that was not observed from any of the axenic cultures. We subsequently simplified the community to just two strains and identified Amycolatopsis sp. AA4 as the producing strain and Streptomyces coelicolor M145 as an inducing strain. Bioassay-guided isolation identified amycomicin (AMY), a highly modified fatty acid containing an epoxide isonitrile warhead as a potent and specific inhibitor of Staphylococcus aureus Amycomicin targets an essential enzyme (FabH) in fatty acid biosynthesis and reduces S. aureus infection in a mouse skin-infection model. The discovery of AMY demonstrates the utility of screening complex communities against specific targets to discover small-molecule antibiotics.
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Abstract
A novel Gram-stain-positive, aerobic actinomycete, designated strain SMC 195T, was isolated from soil collected from a mangrove forest in Thailand. The strain produced extensively branched substrate and aerial mycelia. The substrate mycelium was fragmented into rod-shaped elements, and spore chains consisting of smooth and rod-shaped spores were formed on the aerial mycelium. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that SMC 195T represented a member of the genus Pseudonocardia, and the most closely phylogenetically related species were Pseudonocardia yuanmonensisJCM 18055T (99.2 % 16S rRNA gene sequence similarity), Pseudonocardia halophobicaNRRL B-16514T (98.9 %) and Pseudonocardia kujensisNRRL B-24890T (98.7 %). However, the DNA-DNA relatedness values between SMC 195Tand the closest phylogenetically related species were significantly below 70 %. The G+C content of the genomic DNA was 74±0.8 mol%. The cell wall peptidoglycan contained meso-diaminopimelic acid. The whole-cell sugars consisted of arabinose, galactose, glucose, rhamnose and ribose. The menaquinone was MK-8(H4) only. The major cellular fatty acid was the branched fatty acid iso-C16 : 0 (33.6 %). The polar lipids detected were phosphatidylethanolamine, phosphatidylmethylethanolamine, hydroxyphosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol and unidentified glycolipids. On the basis of the results from phenotypic, chemotaxonomic and genotypic studies, it is concluded that SMC 195T represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia mangrovi sp. nov. is proposed. The type strain is SMC 195T (=TBRC 7778T=NBRC 113150T).
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Affiliation(s)
- Suchart Chanama
- 1Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Suphansa Janphen
- 2Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok 10400, Thailand
| | - Chanwit Suriyachadkun
- 3BIOTEC Culture Collection, Bioresources Technology Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Thanon Phahonyothin, Tambon Khlong Nueng, Amphoe Khlong Luang, Pathum Thani 12120, Thailand
| | - Manee Chanama
- 2Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok 10400, Thailand
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Wang Y, Luo XX, Xia ZF, Wan CX, Alim A, Zhang LL. Glycomyces xiaoerkulensis sp. nov., isolated from Xiaoerkule lake in Xinjiang, China. Int J Syst Evol Microbiol 2018; 68:2722-2726. [PMID: 29985122 DOI: 10.1099/ijsem.0.002842] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel actinomycete, strain TRM 41368T, was isolated from a silt sample from Xiaoerkule lake in Xinjiang province, China, and was examined using a polyphasic approach. Strain TRM 41368T was aerobic, Gram-stain-positive, with an optimum NaCl concentration for growth of 5 % (w/v), and an optimum temperature for growth of 35-37 °C. On the basis of 16S rRNA gene sequence analysis, strain TRM 41368T was most closely related to Glycomycesfuscus TRM 49117T (98.46 % similarity). However, it had a relatively low DNA-DNA relatedness value with G. fuscus TRM 49117T (ANI=70.59 %). The organism had chemical and morphological features typical of the genus Glycomyces. The cell wall of TRM 41368T contained meso-diaminopimelic acid; xylose, ribose and glucose were the major whole-cell sugars. The diagnostic polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol and phosphatidylinositolmannosides. The predominant menaquinone was MK-9(H6). The major fatty acids were C18 : 1ω9c, C16 : 0, iso-C16 : 0, anteiso-C17 : 0 and anteiso-C15 : 0. The G+C content of the DNA was 69.9 mol%. On the basis of the polyphasic evidence, strain TRM 41368T should be designated as a novel species of the genus Glycomyces, for which the name Glycomyces xiaoerkulensis sp. nov. is proposed. The type strain is TRM 41368T (=CCTCC AA 2017005T=KCTC 39932T).
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Affiliation(s)
- Yang Wang
- College of Life Science/Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production and Construction Corps, Tarim University, Alar 843300, PR China
| | - Xiao-Xia Luo
- College of Life Science/Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production and Construction Corps, Tarim University, Alar 843300, PR China
| | - Zhan-Feng Xia
- College of Life Science/Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production and Construction Corps, Tarim University, Alar 843300, PR China
| | - Chuan-Xing Wan
- College of Life Science/Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production and Construction Corps, Tarim University, Alar 843300, PR China
| | - Almira Alim
- College of Life Science/Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production and Construction Corps, Tarim University, Alar 843300, PR China
| | - Li-Li Zhang
- College of Life Science/Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production and Construction Corps, Tarim University, Alar 843300, PR China
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50
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Kwon Y, Byun WS, Kim BY, Song MC, Bae M, Yoon YJ, Shin J, Lee SK, Oh DC. Depsidomycins B and C: New Cyclic Peptides from a Ginseng Farm Soil-Derived Actinomycete. Molecules 2018; 23:molecules23061266. [PMID: 29799492 PMCID: PMC6099933 DOI: 10.3390/molecules23061266] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 05/19/2018] [Accepted: 05/24/2018] [Indexed: 12/13/2022] Open
Abstract
LC/MS-based chemical profiling of a ginseng farm soil-derived actinomycete strain, Streptomyces sp. BYK1371, enabled the discovery of two new cyclic heptapeptides, depsidomycins B and C (1 and 2), each containing two piperazic acid units and a formyl group at their N-terminus. The structures of 1 and 2 were elucidated by a combination of spectroscopic and chemical analyses. These new compounds were determined to possess d-leucine, d-threonine, d-valine, and S-piperazic acid based on the advanced Marfey's method and a GITC (2,3,4,6-tetra-O-acetyl-β-d-glucopyranosyl isothiocyanate) derivatization of their hydrolysates, followed by LC/MS analysis. Depsidomycins B and C displayed significant antimetastatic activities against metastatic breast cancer cells (MDA-MB-231).
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Affiliation(s)
- Yun Kwon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.
| | - Woong Sub Byun
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.
| | - Byung-Yong Kim
- ChunLab, Inc., JW TOWER, Seocho-gu, Seoul 06725, Republic of Korea.
| | - Myoung Chong Song
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea.
| | - Munhyung Bae
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.
| | - Yeo Joon Yoon
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea.
| | - Jongheon Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.
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