Exploiting Gene Regulation As an Approach to Identify, Analyze And
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Study of Actinobacteria and Their Secondary Metabolites from Various Habitats in Indonesia and Deep-Sea of the North Atlantic Ocean
Study of Actinobacteria and their Secondary Metabolites from Various Habitats in Indonesia and Deep-Sea of the North Atlantic Ocean Von der Fakultät für Lebenswissenschaften der Technischen Universität Carolo-Wilhelmina zu Braunschweig zur Erlangung des Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) genehmigte D i s s e r t a t i o n von Chandra Risdian aus Jakarta / Indonesien 1. Referent: Professor Dr. Michael Steinert 2. Referent: Privatdozent Dr. Joachim M. Wink eingereicht am: 18.12.2019 mündliche Prüfung (Disputation) am: 04.03.2020 Druckjahr 2020 ii Vorveröffentlichungen der Dissertation Teilergebnisse aus dieser Arbeit wurden mit Genehmigung der Fakultät für Lebenswissenschaften, vertreten durch den Mentor der Arbeit, in folgenden Beiträgen vorab veröffentlicht: Publikationen Risdian C, Primahana G, Mozef T, Dewi RT, Ratnakomala S, Lisdiyanti P, and Wink J. Screening of antimicrobial producing Actinobacteria from Enggano Island, Indonesia. AIP Conf Proc 2024(1):020039 (2018). Risdian C, Mozef T, and Wink J. Biosynthesis of polyketides in Streptomyces. Microorganisms 7(5):124 (2019) Posterbeiträge Risdian C, Mozef T, Dewi RT, Primahana G, Lisdiyanti P, Ratnakomala S, Sudarman E, Steinert M, and Wink J. Isolation, characterization, and screening of antibiotic producing Streptomyces spp. collected from soil of Enggano Island, Indonesia. The 7th HIPS Symposium, Saarbrücken, Germany (2017). Risdian C, Ratnakomala S, Lisdiyanti P, Mozef T, and Wink J. Multilocus sequence analysis of Streptomyces sp. SHP 1-2 and related species for phylogenetic and taxonomic studies. The HIPS Symposium, Saarbrücken, Germany (2019). iii Acknowledgements Acknowledgements First and foremost I would like to express my deep gratitude to my mentor PD Dr. -
The Degradative Capabilities of New Amycolatopsis Isolates on Polylactic Acid
microorganisms Article The Degradative Capabilities of New Amycolatopsis Isolates on Polylactic Acid Francesca Decorosi 1,2, Maria Luna Exana 1,2, Francesco Pini 1,2, Alessandra Adessi 1 , Anna Messini 1, Luciana Giovannetti 1,2 and Carlo Viti 1,2,* 1 Department of Agriculture, Food, Environment and Forestry (DAGRI)—University of Florence, Piazzale delle Cascine 18, I50144 Florence, Italy; francesca.decorosi@unifi.it (F.D.); [email protected] (M.L.E.); francesco.pini@unifi.it (F.P.); alessandra.adessi@unifi.it (A.A.); anna.messini@unifi.it (A.M.); luciana.giovannetti@unifi.it (L.G.) 2 Genexpress Laboratory, Department of Agriculture, Food, Environment and Forestry (DAGRI)—University of Florence, Via della Lastruccia 14, I50019 Sesto Fiorentino, Italy * Correspondence: carlo.viti@unifi.it; Tel.: +39-05-5457-3224 Received: 15 October 2019; Accepted: 18 November 2019; Published: 20 November 2019 Abstract: Polylactic acid (PLA), a bioplastic synthesized from lactic acid, has a broad range of applications owing to its excellent proprieties such as a high melting point, good mechanical strength, transparency, and ease of fabrication. However, the safe disposal of PLA is an emerging environmental problem: it resists microbial attack in environmental conditions, and the frequency of PLA-degrading microorganisms in soil is very low. To date, a limited number of PLA-degrading bacteria have been isolated, and most are actinomycetes. In this work, a method for the selection of rare actinomycetes with extracellular proteolytic activity was established, and the technique was used to isolate four mesophilic actinomycetes with the ability to degrade emulsified PLA in agar plates. All four strains—designated SO1.1, SO1.2, SNC, and SST—belong to the genus Amycolatopsis. -
Amycolatopsis Kentuckyensis Sp. Nov., Amycolatopsis Lexingtonensis Sp
International Journal of Systematic and Evolutionary Microbiology (2003), 53, 1601–1605 DOI 10.1099/ijs.0.02691-0 Amycolatopsis kentuckyensis sp. nov., Amycolatopsis lexingtonensis sp. nov. and Amycolatopsis pretoriensis sp. nov., isolated from equine placentas D. P. Labeda,1 J. M. Donahue,2 N. M. Williams,2 S. F. Sells2 and M. M. Henton3 Correspondence 1Microbial Genomics and Bioprocessing Research Unit, National Center for Agricultural D. P. Labeda Utilization Research, USDA Agricultural Research Service, 1815 North University Street, [email protected] Peoria, IL 61604, USA 2Livestock Disease Diagnostic Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40511, USA 3Golden Vetlab, PO 1537, Alberton, South Africa Actinomycete strains isolated from lesions on equine placentas from two horses in Kentucky and one in South Africa were subjected to a polyphasic taxonomic study. Chemotaxonomic and morphological characteristics indicated that the isolates are members of the genus Amycolatopsis. On the basis of phylogenetic analysis of 16S rDNA sequences, the isolates are related most closely to Amycolatopsis mediterranei. Physiological characteristics of these strains indicated that they do not belong to A. mediterranei and DNA relatedness determinations confirmed that these strains represent three novel species of the genus Amycolatopsis, for which the names Amycolatopsis kentuckyensis (type strain, NRRL B-24129T=LDDC 9447-99T=DSM 44652T), Amycolatopsis lexingtonensis (type strain, NRRL B-24131T=LDDC 12275-99T=DSM 44653T) and Amycolatopsis pretoriensis (type strain, NRRL B-24133T=ARC OV1 0181T=DSM 44654T) are proposed. INTRODUCTION been associated with nocardioform placentitis. Most of the severe infections were caused by the recently described Over the past decade, actinomycetes have been reported to actinomycete Crossiella equi (Donahue et al., 2002). -
Secondary Metabolites of the Genus Amycolatopsis: Structures, Bioactivities and Biosynthesis
molecules Review Secondary Metabolites of the Genus Amycolatopsis: Structures, Bioactivities and Biosynthesis Zhiqiang Song, Tangchang Xu, Junfei Wang, Yage Hou, Chuansheng Liu, Sisi Liu and Shaohua Wu * Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, China; [email protected] (Z.S.); [email protected] (T.X.); [email protected] (J.W.); [email protected] (Y.H.); [email protected] (C.L.); [email protected] (S.L.) * Correspondence: [email protected] Abstract: Actinomycetes are regarded as important sources for the generation of various bioactive secondary metabolites with rich chemical and bioactive diversities. Amycolatopsis falls under the rare actinomycete genus with the potential to produce antibiotics. In this review, all literatures were searched in the Web of Science, Google Scholar and PubMed up to March 2021. The keywords used in the search strategy were “Amycolatopsis”, “secondary metabolite”, “new or novel compound”, “bioactivity”, “biosynthetic pathway” and “derivatives”. The objective in this review is to sum- marize the chemical structures and biological activities of secondary metabolites from the genus Amycolatopsis. A total of 159 compounds derived from 8 known and 18 unidentified species are summarized in this paper. These secondary metabolites are mainly categorized into polyphenols, linear polyketides, macrolides, macrolactams, thiazolyl peptides, cyclic peptides, glycopeptides, amide and amino derivatives, glycoside derivatives, enediyne derivatives and sesquiterpenes. Meanwhile, they mainly showed unique antimicrobial, anti-cancer, antioxidant, anti-hyperglycemic, and enzyme inhibition activities. In addition, the biosynthetic pathways of several potent bioactive Citation: Song, Z.; Xu, T.; Wang, J.; compounds and derivatives are included and the prospect of the chemical substances obtained from Hou, Y.; Liu, C.; Liu, S.; Wu, S. -
Screening of Antagonistic Marine Actinomycetes: Optimization of Process Parameters for the Production of Novel Antibiotic by Amycolatopsis Alba Var
& Bioch ial em b ic ro a c l i T M e f c Venkata Ratna Ravi Kumar et al., J Microbial Biochem Technol 2011, 3:5 h o Journal of l n o a l n o r DOI: 10.4172/1948-5948.1000058 g u y o J ISSN: 1948-5948 Microbial & Biochemical Technology Research Article Article OpenOpen Access Access Screening of Antagonistic Marine Actinomycetes: Optimization of Process Parameters for the Production of Novel Antibiotic by Amycolatopsis Alba var. nov. DVR D4 Venkata Ratna Ravi Kumar Dasari*, Murali Yugandhar Nikku and Sri Rami Reddy Donthireddy Center for Biotechnology, College of Engineering, Andhra University, Visakhapatnam- 530 003, India Abstract Screening of six marine sediment samples near NTPC of the Visakhapatnam (India) Coast of Bay of Bengal resulted in the isolation of 72 isolates of actinomycetes. Among these, Amycolatopsis alba var. nov. DVR D4 showed broad antibacterial activity spectra against Gram-positive and Gram-negative bacteria; and produced antibacterial metabolite extracellulary under submerged fermentation conditions. The chemical and physical process parameters affecting the production of the antibiotic were optimized. The maximum antibiotic activity was obtained with the optimized production medium containing D-glucose, 2.0 %w/v; malt extract, 4.0 %w/v; yeast extract, 0.4 %w/v; dipotassium hydrogen phosphate, 0.5 %w/v; sodium chloride, 0.25 %w/v; zinc sulphate, 0.004 %w/v; calcium carbonate, 0.04 %w/v; with inoculum volume of 5.0 %v/v at 6.0 pH, 28°C incubation temperature, 220 rpm and for 96 h incubation. Keywords: Screening; Optimization; Submerged fermentation; Apart from the cultural conditions (inoculum age, inoculum Amycolatopsis alba; Antibacterial activity; Minimum inhibitory volume) of the organism, fermentation medium has profound effect concentration on product formation directly or indirectly. -
A Genome Compendium Reveals Diverse Metabolic Adaptations of Antarctic Soil Microorganisms
bioRxiv preprint doi: https://doi.org/10.1101/2020.08.06.239558; this version posted August 6, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. August 3, 2020 A genome compendium reveals diverse metabolic adaptations of Antarctic soil microorganisms Maximiliano Ortiz1 #, Pok Man Leung2 # *, Guy Shelley3, Marc W. Van Goethem1,4, Sean K. Bay2, Karen Jordaan1,5, Surendra Vikram1, Ian D. Hogg1,7,8, Thulani P. Makhalanyane1, Steven L. Chown6, Rhys Grinter2, Don A. Cowan1 *, Chris Greening2,3 * 1 Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, Pretoria 0002, South Africa 2 Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia 3 School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia 4 Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA 5 Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Alameda 340, Santiago 6 Securing Antarctica’s Environmental Future, School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia 7 School of Science, University of Waikato, Hamilton 3240, New Zealand 8 Polar Knowledge Canada, Canadian High Arctic Research Station, Cambridge Bay, NU X0B 0C0, Canada # These authors contributed equally to this work. * Correspondence may be addressed to: A/Prof Chris Greening ([email protected]) Prof Don A. Cowan ([email protected]) Pok Man Leung ([email protected]) bioRxiv preprint doi: https://doi.org/10.1101/2020.08.06.239558; this version posted August 6, 2020. -
Novel Actinomycete Isolated from Bulking Industrial Sludge JOHANNA M
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Dec. 1986, p. 1324-1330 Vol. 52, No. 6 0099-2240/86/121324-07$02.00/0 Copyright © 1986, American Society for Microbiology Novel Actinomycete Isolated from Bulking Industrial Sludge JOHANNA M. WHITE,' DAVID P. LABEDA,2 MARY P. LECHEVALIER,3 JAMES R. OWENS,' DANIEL D. JONES,' AND JOSEPH J. GAUTHIER'* Department of Biology, University ofAlabama at Birmingham, Birmingham, Alabama 352941; U.S. Department of Agriculture, Northern Regional Research Center, Peoria, Illinois 616042; and Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854-07593 Received 14 July 1986/Accepted 5 September 1986 A novel actinomycete was the predominant filamentous microorganism in bulking activated sludge in a bench-scale reactor treating coke plant wastewater. The bacterium was isolated and identified as an actinomycete that is biochemically and morphologically similar to Amycolatopsis orientalis; however, a lack of DNA homology excludes true relatedness. At present, the isolate (NRRL B 16216) cannot be assigned to the recognized taxa of actinomycetes. Successful operation of the activated sludge process de- previously (13). Briefly, they consisted of water-jacketed pends on separation of the microbial biomass from the aeration basins, each with a volume of 12 liters. Overflow treated water in a clarifier. Sludge bulking, which is the was collected in a clarifier from which settled sludge was inability of the biomass to settle properly, represents a major pumped back into the aeration basin. To simulate full-scale problem associated with this treatment method. Although treatment conditions, the reactors were maintained at a some bulking incidents are the result of the formation of temperature of 35°C, an oxygen concentration of 3 mg/liter, pinpoint floc or dispersed growth of the biomass, it is known a pH of 7.2, and a hydraulic retention time of 42 h. -
Amycolatopsis Alba Var. Nov DVR D4, a Bioactive Actinomycete Isolated
J Biochem Tech (2011) 3(2): 251-256 ISSN: 0974-2328 A mycolatopsis alba var. nov DVR D4, a bioactive actinomycete isolated from Indian marine environment Venkata Ratna Ravi Kumar Dasari*, Sri Rami Reddy Donthireddy Received: 09 September 2010 / Received in revised form: 2 November 2011, Accepted: 5 November 2011, Published online: 25 December 2011, © Sevas Educational Society 2008-2011 Abstract The taxonomic position of a bioactive marine isolate, strain DVR Only 10 novel species have been described for this genus until the D4 was established using a polyphasic approach. The organism last decade, But since 2000, many novel species have been merits species status in the genus Amycolatopsis according to the described which were isolated from various terrestrial environments chemical and phenotypic data. Phylogenetic analysis of the strain (Carlson et al. 2007; Groth et al. 2007; Lee et al. 2006; Tan et al. based on its 16S rDNA sequence shows that there was 100% pair- 2006; Saintpierre-Bonaccio et al. 2005; Kim et al. 2002; Huang et wise similarity and identity with no nucleotide gaps with the species al. 2001; Goodfellow et al. 2001) and clinical material (Huang et al. Amycolatopsis alba strain DSM 44262. As the organism was 2004; Labeda et al. 2003). At the time of writing, the genus contains distinguished with substantial differences in some of the phenotypic 48 species (Labeda et al. 2011; Albarracin et al. 2010; Atchareeya et characteristics and other properties, it was proposed as a strain al. 2010; Chen et al. 2010; Duangmal et al. 2010; Tamura et al. variety of Amycolatopsis alba and designated as Amycolatopsis alba 2010; Tang et al. -
Amycolatopsis Rubida Sp. Nov., a New Amycolatopsis Species from Soil
International Journal of Systematic and Evolutionary Microbiology (2001), 51, 1093–1097 Printed in Great Britain Amycolatopsis rubida sp. nov., a new NOTE Amycolatopsis species from soil 1 Institute of Microbiology, Ying Huang,1 Weihong Qi,1 Zhitang Lu,1† Zhiheng Liu1 Chinese Academy of 2 Sciences, Beijing 100080, and Michael Goodfellow People’s Republic of China 2 Department of Author for correspondence: Zhiheng Liu. Tel: j86 10 6255 3628 Fax: j86 10 6256 0912. Agricultural and e-mail: zhliu!sun.im.ac.cn Environmental Science, University of Newcastle, Newcastle upon Tyne T NE1 7RU, UK The taxonomic position of a soil isolate, strain 13.4 , was established using a polyphasic approach. The organism was found to have chemical and morphological properties consistent with its classification in the genus Amycolatopsis. Phylogenetic analysis of the strain based on its 16S rDNA sequence showed that it forms a distinct phyletic line within members of the genus Amycolatopsis. The organism was also readily distinguished from the type strains of all validly described Amycolatopsis species by its phenotypic features. The name Amycolatopsis rubida sp. nov. is proposed for this new species. The type strain is strain 13.4T (l AS 4.1541T l JCM 10871T). Keywords: Amycolatopsis rubida sp. nov., polyphasic taxonomy, 16S rDNA sequencing The genus Amycolatopsis was proposed by Lechevalier passed by the family Pseudonocardiaceae (Embley et al. (1986) to accommodate nocardioform actino- et al., 1988; Warwick et al., 1994). In the present mycetes having type IV cell wall composition, type PII investigation, a soil isolate, strain 13.4T, was subject to phospholipid pattern, and lacking mycolic acid. -
A Systematic Study of the Whole Genome Sequence Of
Synthetic and Systems Biotechnology 1 (2016) 169e186 Contents lists available at ScienceDirect Synthetic and Systems Biotechnology journal homepage: http://www.keaipublishing.com/en/journals/synthetic- and-systems-biotechnology/ A systematic study of the whole genome sequence of Amycolatopsis methanolica strain 239T provides an insight into its physiological and taxonomic properties which correlate with its position in the genus* Biao Tang a, b, Feng Xie c, Wei Zhao b, Jian Wang c, Shengwang Dai c, Huajun Zheng d, Xiaoming Ding a, Xufeng Cen b, Haican Liu e, Yucong Yu a, Haokui Zhou f, Yan Zhou a, d, *** ** * Lixin Zhang c, , Michael Goodfellow g, , Guo-Ping Zhao a, b, d, f, a State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences and Institute of Biomedical Sciences, Fudan University, Shanghai, 200438, China b CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China c CAS-Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing, 100101, China d Shanghai-MOST Key Laboratory of Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, China e State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable -
Chemical Ecology of Streptomyces Albidoflavus Strain A10 Associated
microorganisms Article Chemical Ecology of Streptomyces albidoflavus Strain A10 Associated with Carpenter Ant Camponotus vagus Anna A. Baranova 1,2, Alexey A. Chistov 2,3, Anton P. Tyurin 1,2 , Igor A. Prokhorenko 1,2, Vladimir A. Korshun 1,2 , Mikhail V. Biryukov 1,4 , Vera A. Alferova 1,2,* and Yuliya V. Zakalyukina 5,* 1 Gause Institute of New Antibiotics, B. Pirogovskaya 11, 119021 Moscow, Russia; [email protected] (A.A.B.); [email protected] (A.P.T.); [email protected] (I.A.P.); [email protected] (V.A.K.); [email protected] (M.V.B.) 2 Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; [email protected] 3 Orekhovich Research Institute of Biomedical Chemistry, Pogodinskaya 10, 119121 Moscow, Russia 4 Department of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia 5 Department of Soil Science, Lomonosov Moscow State University, 119991 Moscow, Russia * Correspondence: [email protected] (V.A.A.); [email protected] (Y.V.Z.); Tel.: +7-9266113649 (V.A.A.); +7-9175548004 (Y.V.Z.) Received: 15 November 2020; Accepted: 7 December 2020; Published: 9 December 2020 Abstract: Antibiotics produced by symbiotic microorganisms were previously shown to be of crucial importance for ecological communities, including ants. Previous works on ant–actinobacteria symbiosis are mainly focused on farming ants, which use antifungal microbial secondary metabolites to control pathogens in their fungal gardens. In this work, we studied microorganisms associated with carpenter ant Camponotus vagus. Pronounced antifungal activity of isolated actinobacteria strain A10 was found to be facilitated by biosynthesis of the antimycin A complex, consisting of small hydrophobic depsipeptides with high antimicrobial and cytotoxic activity. -
A Systematic Study of the Whole Genome Sequence
Synthetic and Systems Biotechnology xxx (2016) 1e18 Contents lists available at ScienceDirect Synthetic and Systems Biotechnology journal homepage: http://www.keaipublishing.com/en/journals/synthetic- and-systems-biotechnology/ A systematic study of the whole genome sequence of Amycolatopsis methanolica strain 239T provides an insight into its physiological and taxonomic properties which correlate with its position in the genus* Biao Tang a, b, Feng Xie c, Wei Zhao b, Jian Wang c, Shengwang Dai c, Huajun Zheng d, Xiaoming Ding a, Xufeng Cen b, Haican Liu e, Yucong Yu a, Haokui Zhou f, Yan Zhou a, d, *** ** * Lixin Zhang c, , Michael Goodfellow g, , Guo-Ping Zhao a, b, d, f, a State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences and Institute of Biomedical Sciences, Fudan University, Shanghai, 200438, China b CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China c CAS-Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing, 100101, China d Shanghai-MOST Key Laboratory of Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, China e State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable