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Gandham P, Vadla N, Saji A, Srinivas V, Ruperao P, Selvanayagam S, Saxena RK, Rathore A, Gopalakrishnan S, Thakur V. Genome assembly, comparative genomics, and identification of genes/pathways underlying plant growth-promoting traits of an actinobacterial strain, Amycolatopsis sp. (BCA-696). Sci Rep 2024; 14:15934. [PMID: 38987320 PMCID: PMC11237095 DOI: 10.1038/s41598-024-66835-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 07/04/2024] [Indexed: 07/12/2024] Open
Abstract
The draft genome sequence of an agriculturally important actinobacterial species Amycolatopsis sp. BCA-696 was developed and characterized in this study. Amycolatopsis BCA-696 is known for its biocontrol properties against charcoal rot and also for plant growth-promotion (PGP) in several crop species. The next-generation sequencing (NGS)-based draft genome of Amycolatopsis sp. BCA-696 comprised of ~ 9.05 Mb linear chromosome with 68.75% GC content. In total, 8716 protein-coding sequences and 61 RNA-coding sequences were predicted in the genome. This newly developed genome sequence has been also characterized for biosynthetic gene clusters (BGCs) and biosynthetic pathways. Furthermore, we have also reported that the Amycolatopsis sp. BCA-696 produces the glycopeptide antibiotic vancomycin that inhibits the growth of pathogenic gram-positive bacteria. A comparative analysis of the BCA-696 genome with publicly available closely related genomes of 14 strains of Amycolatopsis has also been conducted. The comparative analysis has identified a total of 4733 core and 466 unique orthologous genes present in the BCA-696 genome The unique genes present in BCA-696 was enriched with antibiotic biosynthesis and resistance functions. Genome assembly of the BCA-696 has also provided genes involved in key pathways related to PGP and biocontrol traits such as siderophores, chitinase, and cellulase production.
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Affiliation(s)
- Prasad Gandham
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, USA
| | - Nandini Vadla
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Angeo Saji
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Vadlamudi Srinivas
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Pradeep Ruperao
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Rachit K Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Gujarat Biotechnology University, Gandhinagar, Gujarat, India
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
- Excellence in Breeding, International Maize and Wheat Improvement Center (CIMMYT), Hyderabad, India.
| | - Subramaniam Gopalakrishnan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
- International Institute of Tropical Agriculture (IITA), Dar es Salaam, Tanzania.
| | - Vivek Thakur
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India.
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Chang S, Luo Y, Wang M, He N, Chen M, Huang X, Wang J, Yuan L, Xie Y. Pairing comparative genomics with tandem mass-based molecular networking allows to highly efficient discovery of nonribosomal peptides from Nocardia spp. J Chromatogr A 2023; 1708:464343. [PMID: 37717450 DOI: 10.1016/j.chroma.2023.464343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 08/25/2023] [Accepted: 08/29/2023] [Indexed: 09/19/2023]
Abstract
Microbial natural products, particularly nonribosomal peptides (NRPs), have attracted significant attention due to their structural diversity and therapeutic potential. Nocardia, a genus of Actinomyces, is an important reservoir for natural products, especially NRPs. However, rediscovery is a significant challenge for mining new specialized metabolites from Nocardia, as well as from other sources. To overcome this challenge, we developed a strategy that combines comparative genomics with tandem mass-based molecular networking, which allows to efficiently discover new NRPs from Nocardia spp.. As a proof of concept, all genomes of Norcardia in NCBI database, including three strains from our lab, were compared with each other to prioritize unique biosynthetic gene clusters (BGCs) in the three in-house Nocardia strains, particularly those containing nonribosomal peptide synthases (NRPSs). Subsequently, the metabolomics data of those three in-house strains were analyzed employing tandem mass-based molecular networking. This led to the identification of a known lipopeptide, nocarjamide (1), and five new congeners (2-6) of nocarjamide, as well as a new decalipopeptide, nocarlipoamide (7), along with nocardimicin, a known compound found in Nocardia. The structure of the new decalipopeptide 7 was further extensively characterized using NMR, MS/MS, Marfey's analysis, and X-ray. In addition, the biosynthesis pathways for 1-7 were proposed through bioinformatics analysis, and thus the gene clusters responsible for biosynthesizing them were confirmed. Our results indicate that this strategy enables prompt dereplication of known compounds, rapid linkage of identified compounds with their biosynthesis gene cluster, and efficient discovery of new compounds.
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Affiliation(s)
- Shanshan Chang
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Tiantan xili No.1, Beijing, 100050, China
| | - Yajun Luo
- Hebei Key Laboratory for Chronic Diseases, Tangshan Key Laboratory for Preclinical and Basic Research on Chronic Diseases, School of Basic Medical Sciences, North China University of Science and Technology, Tangshan, Hebei, 063210, P.R. China
| | - Mengyuan Wang
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Tiantan xili No.1, Beijing, 100050, China
| | - Ning He
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Tiantan xili No.1, Beijing, 100050, China
| | - Mingxu Chen
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Tiantan xili No.1, Beijing, 100050, China
| | - Xinyue Huang
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Tiantan xili No.1, Beijing, 100050, China
| | - Jiahan Wang
- Hebei Key Laboratory for Chronic Diseases, Tangshan Key Laboratory for Preclinical and Basic Research on Chronic Diseases, School of Basic Medical Sciences, North China University of Science and Technology, Tangshan, Hebei, 063210, P.R. China
| | - Lijie Yuan
- Hebei Key Laboratory for Chronic Diseases, Tangshan Key Laboratory for Preclinical and Basic Research on Chronic Diseases, School of Basic Medical Sciences, North China University of Science and Technology, Tangshan, Hebei, 063210, P.R. China.
| | - Yunying Xie
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Tiantan xili No.1, Beijing, 100050, China.
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Kalra R, Conlan XA, Goel M. Recent advances in research for potential utilization of unexplored lichen metabolites. Biotechnol Adv 2023; 62:108072. [PMID: 36464145 DOI: 10.1016/j.biotechadv.2022.108072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/28/2022] [Accepted: 11/26/2022] [Indexed: 12/03/2022]
Abstract
Several research studies have shown that lichens are productive organisms for the synthesis of a broad range of secondary metabolites. Lichens are a self-sustainable stable microbial ecosystem comprising an exhabitant fungal partner (mycobiont) and at least one or more photosynthetic partners (photobiont). The successful symbiosis is responsible for their persistence throughout time and allows all the partners (holobionts) to thrive in many extreme habitats, where without the synergistic relationship they would be rare or non-existent. The ability to survive in harsh conditions can be directly correlated with the production of some unique metabolites. Despite the potential applications, these unique metabolites have been underutilised by pharmaceutical and agrochemical industries due to their slow growth, low biomass availability and technical challenges involved in their artificial cultivation. However, recent development of biotechnological tools such as molecular phylogenetics, modern tissue culture techniques, metabolomics and molecular engineering are opening up a new opportunity to exploit these compounds within the lichen holobiome for industrial applications. This review also highlights the recent advances in culturing the symbionts and the computational and molecular genetics approaches of lichen gene regulation recognized for the enhanced production of target metabolites. The recent development of multi-omics novel biodiscovery strategies aided by synthetic biology in order to study the heterologous expressed lichen-derived biosynthetic gene clusters in a cultivatable host offers a promising means for a sustainable supply of specialized metabolites.
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Affiliation(s)
- Rishu Kalra
- Sustainable Agriculture Program, The Energy and Resources Institute, Gurugram, Haryana, India
| | - Xavier A Conlan
- Deakin University, School of Life and Environmental Sciences, Geelong, Victoria, Australia
| | - Mayurika Goel
- Sustainable Agriculture Program, The Energy and Resources Institute, Gurugram, Haryana, India.
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He Z, Naganuma T. Chronicle of Research into Lichen-Associated Bacteria. Microorganisms 2022; 10:2111. [PMID: 36363703 PMCID: PMC9698887 DOI: 10.3390/microorganisms10112111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/30/2022] [Accepted: 10/21/2022] [Indexed: 02/12/2024] Open
Abstract
Lichens are mutually symbiotic systems consisting of fungal and algal symbionts. While diverse lichen-forming fungal species are known, limited species of algae form lichens. Plasticity in the combination of fungal and algal species with different eco-physiological properties may contribute to the worldwide distribution of lichens, even in extreme habitats. Lichens have been studied systematically for more than 200 years; however, plasticity in fungal-algal/cyanobacterial symbiotic combinations is still unclear. In addition, the association between non-cyanobacterial bacteria and lichens has attracted attention in recent years. The types, diversity, and functions of lichen-associated bacteria have been studied using both culture-based and culture-independent methods. This review summarizes the history of systematic research on lichens and lichen-associated bacteria and provides insights into the current status of research in this field.
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Affiliation(s)
| | - Takeshi Naganuma
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima 739-8528, Japan
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Zakalyukina YV, Osterman IA, Wolf J, Neumann-Schaal M, Nouioui I, Biryukov MV. Amycolatopsis camponoti sp. nov., new tetracenomycin-producing actinomycete isolated from carpenter ant Camponotus vagus. Antonie Van Leeuwenhoek 2022; 115:533-544. [PMID: 35218449 PMCID: PMC8930869 DOI: 10.1007/s10482-022-01716-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/30/2022] [Indexed: 01/15/2023]
Abstract
An actinobacterial strain A23T, isolated from adult ant Camponotus vagus collected in Ryazan region (Russia) and established as tetracenomycin X producer, was subjected to a polyphasic taxonomic study. Morphological characteristics of this strain included well-branched substrate mycelium and aerial hyphae fragmented into rod-shaped elements. Phylogenetic analyses based on 16S rRNA gene and genome sequences showed that strain A23T was most closely related to Amycolatopsis pretoriensis DSM 44654T. Average nucleotide identity and digital DNA-DNA hybridization values between the genome sequences of isolate A23T and its closest relative, Amycolatopsis pretoriensis DSM 44654T, were 39.5% and 88.6%, which were below the 70% and 95-96% cut-off point recommended for bacterial species demarcation, respectively. The genome size of the isolate A23T was 10,560,374 bp with a DNA G + C content of 71.2%. The whole-cell hydrolysate contained meso-diaminopimelic acid and arabinose and galactose as main diagnostic sugars as well as ribose and rhamnose. It contained MK-9(H4) as the predominant menaquinone and iso-C16:0, iso-C15:0, anteiso-C17:0 and C16:0 as the major cellular fatty acids. Diphosphatidylglycerol and phosphatidylethanolamine prevailed among phospholipids. Mycolic acids were not detected. Based on the phenotypic, genomic and phylogenetic data, isolate A23T represents a novel species of the genus Amycolatopsis, for which the name Amycolatopsis camponoti sp. nov. is proposed, and the type strain is A23T (= DSM 111725T = VKM 2882T).
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Affiliation(s)
- Yuliya V Zakalyukina
- Scientific Center of Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Russia, 354340.
- Department of Soil Science, Lomonosov Moscow State University, Moscow, Russia, 119991.
| | - Ilya A Osterman
- Scientific Center of Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Russia, 354340
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region, Russia, 143025
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Jacqueline Wolf
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124, Braunschweig, Germany
| | - Meina Neumann-Schaal
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124, Braunschweig, Germany
| | - Imen Nouioui
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124, Braunschweig, Germany
| | - Mikhail V Biryukov
- Scientific Center of Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Russia, 354340
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia, 119991
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Looking Back to Amycolatopsis: History of the Antibiotic Discovery and Future Prospects. Antibiotics (Basel) 2021; 10:antibiotics10101254. [PMID: 34680834 PMCID: PMC8532670 DOI: 10.3390/antibiotics10101254] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 10/07/2021] [Accepted: 10/12/2021] [Indexed: 11/17/2022] Open
Abstract
The emergence of antibiotic-resistant pathogenic bacteria in recent decades leads us to an urgent need for the development of new antibacterial agents. The species of the genus Amycolatopsis are known as producers of secondary metabolites that are used in medicine and agriculture. The complete genome sequences of the Amycolatopsis demonstrate a wide variety of biosynthetic gene clusters, which highlights the potential ability of actinomycetes of this genus to produce new antibiotics. In this review, we summarize information about antibiotics produced by Amycolatopsis species. This knowledge demonstrates the prospects for further study of this genus as an enormous source of antibiotics.
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Świecimska M, Golińska P, Wypij M, Goodfellow M. Genomic-based classification of Catenulispora pinisilvae sp. nov., novel actinobacteria isolated from a pine forest soil in Poland and emended description of Catenulispora rubra. Syst Appl Microbiol 2020; 44:126164. [PMID: 33360072 DOI: 10.1016/j.syapm.2020.126164] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 11/07/2020] [Accepted: 11/12/2020] [Indexed: 12/14/2022]
Abstract
Two actinobacteria, strains NF3 and NH11T, isolated from a pine forest soil, near Torun, Poland were examined for diverse chemotaxonomic and morphological properties that placed them in the genus Catenulispora. They produced an extensively branched stable mycelium, contained LL-diaminopimelic acid as the diamino acid of the peptidoglycan, arabinose as the diagnostic whole-organism sugar, tetra-, hexa- and octa-hydrogenated menaquinones with nine isoprenoid units as the predominant isoprenologues, iso-C16:0 and anteiso-C17:0 as major fatty acids, and formed a well supported clade within the Catenulispora 16S rRNA gene tree together with Catenulispora acidiphila DSM 44928T and Catenulispora rubra DSM 44948T sharing sequence similarities with the latter of 98.8 and 99.0%, respectively. The sizes of whole genome sequences generated for the isolates and the C. rubra strain ranged from 11.20 to 12.80 Mbp with corresponding in silico DNA G+C values of 69.9-70.0%. The isolates and the C. acidiphila and C. rubra strains formed a well supported branch in the actinobacterial phylogenomic tree. Isolates NF3 and NH11T belong to the same species as they have identical 16S rRNA gene sequences, share many chemotaxonomic, cultural and phenotypic features and show very high average nucleotide identity (ANI) and digital DNA:DNA relatedness (dDDH) similarities. They can be distinguished from their closest phylogenomic neighbours by using a combination of chemotaxonomic and phenotypic properties and by ANI and dDDH values well below the thresholds of these metrics used to assign closely related strains to different species. Consequently, we propose that the isolates be classified as a new Catenulispora species, Catenulispora pinisilvae sp. nov., the type strain is NH11T (=DSM 111109T =PCM 3046T). An emended description is given for C. rubra based on data acquired in the present study. Analyses of the draft genomes of the isolates and the C. acidiphila and C. rubra strains revealed the presence of many biosynthetic gene clusters with the potential to synthesize novel drug-like metabolites. In vitro screens showed that the isolates inhibited the growth of Gram-positive bacteria and wheat pathogens belonging to the genus Fusarium.
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Affiliation(s)
- Magdalena Świecimska
- Department of Microbiology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87 100 Toruń, Poland.
| | - Patrycja Golińska
- Department of Microbiology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87 100 Toruń, Poland.
| | - Magdalena Wypij
- Department of Microbiology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87 100 Toruń, Poland.
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom.
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Thompson D, Cognat V, Goodfellow M, Koechler S, Heintz D, Carapito C, Van Dorsselaer A, Mahmoud H, Sangal V, Ismail W. Phylogenomic Classification and Biosynthetic Potential of the Fossil Fuel-Biodesulfurizing Rhodococcus Strain IGTS8. Front Microbiol 2020; 11:1417. [PMID: 32733398 PMCID: PMC7358434 DOI: 10.3389/fmicb.2020.01417] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 06/02/2020] [Indexed: 01/02/2023] Open
Abstract
Rhodococcus strain IGTS8 is the most extensively studied model bacterium for biodesulfurization of fossil fuels via the non–destructive sulfur–specific 4S pathway. This strain was initially assigned to Rhodococcus rhodochrous and later to Rhodococcus erythropolis thus making its taxonomic status debatable and reflecting the limited resolution of methods available at the time. In this study, phylogenomic analyses of the whole genome sequences of strain IGTS8 and closely related rhodococci showed that R. erythropolis and Rhodococcus qingshengii are very closely related species, that Rhodococcus strain IGTS8 is a R. qingshengii strain and that several strains identified as R. erythropolis should be re-classified as R. qingshengii. The genomes of strains assigned to these species contain potentially novel biosynthetic gene clusters showing that members of these taxa should be given greater importance in the search for new antimicrobials and other industrially important biomolecules. The plasmid-borne dsz operon encoding fossil fuel desulfurization enzymes was present in R. qingshengii IGTS8 and R. erythropolis XP suggesting that it might be transferable between members of these species.
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Affiliation(s)
- Dean Thompson
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Valérie Cognat
- Institut de Biologie Moléculaire des Plantes, Centre National de Recherche Scientifique (CNRS), Université de Strasbourg, Strasbourg, France
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Sandrine Koechler
- Institut de Biologie Moléculaire des Plantes, Centre National de Recherche Scientifique (CNRS), Université de Strasbourg, Strasbourg, France
| | - Dimitri Heintz
- Institut de Biologie Moléculaire des Plantes, Centre National de Recherche Scientifique (CNRS), Université de Strasbourg, Strasbourg, France
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse Bio-organique, Institut Pluridisciplinaire Hubert Curien, UMR 7178 CNRS, Université de Strasbourg, Strasbourg, France
| | - Alain Van Dorsselaer
- Laboratoire de Spectrométrie de Masse Bio-organique, Institut Pluridisciplinaire Hubert Curien, UMR 7178 CNRS, Université de Strasbourg, Strasbourg, France
| | - Huda Mahmoud
- Department of Biological Sciences, College of Science, Kuwait University, Safat, Kuwait
| | - Vartul Sangal
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Wael Ismail
- Environmental Biotechnology Program, Life Sciences Department, College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
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The Degradative Capabilities of New Amycolatopsis Isolates on Polylactic Acid. Microorganisms 2019; 7:microorganisms7120590. [PMID: 31757055 PMCID: PMC6955660 DOI: 10.3390/microorganisms7120590] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/08/2019] [Accepted: 11/18/2019] [Indexed: 11/27/2022] Open
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. The PLA-degrading capability of the four strains was investigated by testing their ability to assimilate lactic acid, fragment PLA polymers, and deteriorate PLA films. The strain SNC was the best PLA degrader—it was able to assimilate lactic acid, constitutively cleave PLA, and form a thick and widespread biofilm on PLA film. The activity of this strain extensively eroded the polymer, leading to a weight loss of 36% in one month in mesophilic conditions.
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Sangal V, Goodfellow M, Blom J, Tan GYA, Klenk HP, Sutcliffe IC. Revisiting the Taxonomic Status of the Biomedically and Industrially Important Genus Amycolatopsis, Using a Phylogenomic Approach. Front Microbiol 2018; 9:2281. [PMID: 30319584 PMCID: PMC6171478 DOI: 10.3389/fmicb.2018.02281] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 09/06/2018] [Indexed: 12/21/2022] Open
Abstract
Strains belonging to the genus Amycolatopsis are well known for the production of a number of important antimicrobials and other bioactive molecules. In this study, we have sequenced the genomes of five Amycolatopsis strains including Amycolatopsis circi DSM 45561T, Amycolatopsis palatopharyngis DSM 44832T and Amycolatopsis thermalba NRRL B-24845T. The genome sequences were analyzed with 52 other publically available Amycolatopsis genomes, representing 34 species, and 12 representatives from related genera including Saccharomonospora, Saccharopolyspora, Saccharothrix, Pseudonocardia and Thermobispora. Based on the core genome phylogeny, Amycolatopsis strains were subdivided into four major clades and several singletons. The genus Amycolatopsis is homogeneous with only three strains noted to group with other genera. Amycolatopsis halophila YIM93223T is quite distinct from other Amycolatopsis strains, both phylogenetically and taxonomically, and belongs to a distinct genus. In addition, Amycolatopsis palatopharyngis DSM 44832T and Amycolatopsis marina CGMCC4 3568T grouped in a clade with Saccharomonospora strains and showed similar taxogenomic differences to this genus as well as other Amycolatopsis strains. The study found a number of strains, particularly those identified as Amycolatopsis orientalis, whose incorrect identification could be resolved by taxogenomic analyses. Similarly, some unclassified strains could be assigned with species designations. The genome sequences of some strains that were independently sequenced by different laboratories were almost identical (99-100% average nucleotide and amino acid identities) consistent with them being the same strain, and confirming the reproducibility and robustness of genomic data. These analyses further demonstrate that whole genome sequencing can reliably resolve intra- and, inter-generic structures and should be incorporated into prokaryotic systematics.
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Affiliation(s)
- Vartul Sangal
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-Universität, Gießen, Germany
| | - Geok Yuan Annie Tan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Iain C Sutcliffe
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
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Genilloud O. Mining Actinomycetes for Novel Antibiotics in the Omics Era: Are We Ready to Exploit This New Paradigm? Antibiotics (Basel) 2018; 7:E85. [PMID: 30257490 PMCID: PMC6316141 DOI: 10.3390/antibiotics7040085] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 09/20/2018] [Accepted: 09/21/2018] [Indexed: 12/28/2022] Open
Abstract
The current spread of multi-drug resistance in a number of key pathogens and the lack of therapeutic solutions in development to address most of the emerging infections in the clinic that are difficult to treat have become major concerns. Microbial natural products represent one of the most important sources for the discovery of potential new antibiotics and actinomycetes have been one of the most relevant groups that are prolific producers of these bioactive compounds. Advances in genome sequencing and bioinformatic tools have collected a wealth of knowledge on the biosynthesis of these molecules. This has revealed the broad untapped biosynthetic diversity of actinomycetes, with large genomes and the capacity to produce more molecules than previously estimated, opening new opportunities to identify the novel classes of compounds that are awaiting to be discovered. Comparative genomics, metabolomics and proteomics and the development of new analysis and genetic engineering tools provide access to the integration of new knowledge and better understanding of the physiology of actinomycetes and their tight regulation of the production of natural products antibiotics. This new paradigm is fostering the development of new genomic-driven and culture-based strategies, which aims to deliver new chemical classes of antibiotics to be developed to the clinic and replenish the exhausted pipeline of drugs for fighting the progression of infection diseases in the near future.
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Affiliation(s)
- Olga Genilloud
- Fundación MEDINA, Avda Conocimiento 34, 18016 Granada, Spain.
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