1
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Nofiani R, Ardiningsih P, Zahra STA, Sukito A, Weisberg AJ, Chang JH, Mahmud T. Genome features and secondary metabolite potential of the marine symbiont Streptomyces sp. RS2. Arch Microbiol 2023; 205:244. [PMID: 37209150 DOI: 10.1007/s00203-023-03556-2] [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: 01/09/2023] [Revised: 04/14/2023] [Accepted: 04/15/2023] [Indexed: 05/22/2023]
Abstract
Streptomyces sp. RS2 was isolated from an unidentified sponge collected around Randayan Island, Indonesia. The genome of Streptomyces sp. RS2 consists of a linear chromosome of 9,391,717 base pairs with 71.9% of G + C content, 8270 protein-coding genes, as well as 18 rRNA and 85 tRNA loci. Twenty-eight putative secondary metabolites biosynthetic gene clusters (BGCs) were identified in the genome sequence. Nine of them have 100% similarity to BGCs for albaflavenone, α-lipomycin, coelibactin, coelichelin, ectoine, geosmin, germicidin, hopene, and lanthionine (SapB). The remaining 19 BGCs have low (< 50%) or moderate (50-80%) similarity to other known secondary metabolite BGCs. Biological activity assays of extracts from 21 different cultures of the RS2 strain showed that SCB ASW was the best medium for the production of antimicrobial and cytotoxic compounds. Streptomyces sp. RS2 has great potential to be a producer of novel secondary metabolites, particularly those with antimicrobial and antitumor activities.
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Affiliation(s)
- Risa Nofiani
- Department of Chemistry, Universitas Tanjungpura, Pontianak, 78124, Indonesia.
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, 97331, USA.
| | - Puji Ardiningsih
- Department of Chemistry, Universitas Tanjungpura, Pontianak, 78124, Indonesia
| | | | - Agus Sukito
- Research Center for Applied Microbiology, National Research and Innovation Agency, Bogor, 16458, Indonesia
| | - Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Taifo Mahmud
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, 97331, USA
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2
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Goel N, Singh R, Sood S, Khare SK. Investigation of Streptomyces sp. Strain EMB24 Secondary Metabolite Profile Has Unraveled Its Extraordinary Antibacterial Potency Against Drug-Resistant Bacteria. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:1168-1175. [PMID: 36220897 PMCID: PMC9553293 DOI: 10.1007/s10126-022-10168-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
With the overuse and misuse of antibiotics amid COVID-19 pandemic, the antimicrobial resistance, which is already a global challenge, has accelerated its pace significantly. Finding novel and potential antibiotics seems one of the probable solutions. In this work, a novel Streptomyces sp. strain EMB24 was isolated and found to be an excellent source of antimicrobials as confirmed by agar-plug assay. It showed antibacterial activity against infection-causing bacteria, namely Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa. In addition, Streptomyces sp. strain EMB24 inhibited the growth methicillin-resistant Staphylococcus aureus (MRSA), tetracycline-resistant Neisseria gonorrhoeae, and ampicillin-resistant Neisseria gonorrhoeae. Furthermore, to get deep insights about the genome and biosynthetic gene clusters producing antibiotics, whole genome sequencing was done. The strain EMB24 is closely related to the Streptomyces longispororuber as revealed by phylogenetic analysis which is a potential source of antibiotics and pigments as undecylprodigiosin and metacycloprodigiosin belonging to the class prodigiosin. Naphthyridinomycin, alkylresorcinols, desferrioxamine B and E, venezuelin, aborycin, MS-271, and siamycin are potent therapeutics that shared 100% similarity with the reference strain as revealed by the online antiSMASH tool.
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Affiliation(s)
- Nikky Goel
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Rajendra Singh
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Seema Sood
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Sunil Kumar Khare
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
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3
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Ngashangva N, Mukherjee PK, Sharma C, Kalita MC, Sarangthem I. Integrated genomics and proteomics analysis of Paenibacillus peoriae IBSD35 and insights into its antimicrobial characteristics. Sci Rep 2022; 12:18861. [PMID: 36344671 PMCID: PMC9640621 DOI: 10.1038/s41598-022-23613-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022] Open
Abstract
Antimicrobial resistance has been developing fast and incurring a loss of human life, and there is a need for new antimicrobial agents. Naturally occurring antimicrobial peptides offer the characteristics to counter AMR because the resistance development is low or no resistance. Antimicrobial peptides from Paenibacillus peoriae IBSD35 cell-free supernatant were salted out and purified using chromatography and characterized with liquid chromatography-tandem-mass spectrometry. The extract has shown a high and broad spectrum of antimicrobial activity. Combining the strain IBSD35 genome sequence with its proteomic data enabled the prediction of biosynthetic gene clusters by connecting the peptide from LC-MS/MS data to the gene that encode. Antimicrobial peptide databases offered a platform for the effective search, prediction, and design of AMPs and expanded the studies on their isolation, structure elucidation, biological evaluation, and pathway engineering. The genome-based taxonomy and comparisons have shown that P. peoriae IBSD35 is closely related to Paenibacillus peoriae FSL J3-0120. P. peoriae IBSD35 harbored endophytic trait genes and nonribosomal peptide synthases biosynthetic gene clusters. The comparative genomics revealed evolutionary insights and facilitated the discovery of novel SMs using proteomics from the extract of P. peoriae IBSD35. It will increase the potential to find novel bio-molecules to counter AMR.
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Affiliation(s)
- Ng Ngashangva
- grid.464584.f0000 0004 0640 0101A National Institute of Department of Biotechnology, Institute of Bioresources and Sustainable Development (IBSD), Govt. of India, Takyelpat, Imphal, Manipur 795001 India
| | - Pulok K. Mukherjee
- grid.464584.f0000 0004 0640 0101A National Institute of Department of Biotechnology, Institute of Bioresources and Sustainable Development (IBSD), Govt. of India, Takyelpat, Imphal, Manipur 795001 India
| | - Chandradev Sharma
- grid.464584.f0000 0004 0640 0101A National Institute of Department of Biotechnology, Institute of Bioresources and Sustainable Development (IBSD), Govt. of India, Takyelpat, Imphal, Manipur 795001 India
| | - Mohan C. Kalita
- grid.411779.d0000 0001 2109 4622Department of Biotechnology, Gauhati University, Jalukbari, Guwahati, Assam 781014 India
| | - Indira Sarangthem
- grid.464584.f0000 0004 0640 0101A National Institute of Department of Biotechnology, Institute of Bioresources and Sustainable Development (IBSD), Govt. of India, Takyelpat, Imphal, Manipur 795001 India
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4
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Kirsch SH, Haeckl FPJ, Müller R. Beyond the approved: target sites and inhibitors of bacterial RNA polymerase from bacteria and fungi. Nat Prod Rep 2022; 39:1226-1263. [PMID: 35507039 DOI: 10.1039/d1np00067e] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covering: 2016 to 2022RNA polymerase (RNAP) is the central enzyme in bacterial gene expression representing an attractive and validated target for antibiotics. Two well-known and clinically approved classes of natural product RNAP inhibitors are the rifamycins and the fidaxomycins. Rifampicin (Rif), a semi-synthetic derivative of rifamycin, plays a crucial role as a first line antibiotic in the treatment of tuberculosis and a broad range of bacterial infections. However, more and more pathogens such as Mycobacterium tuberculosis develop resistance, not only against Rif and other RNAP inhibitors. To overcome this problem, novel RNAP inhibitors exhibiting different target sites are urgently needed. This review includes recent developments published between 2016 and today. Particular focus is placed on novel findings concerning already known bacterial RNAP inhibitors, the characterization and development of new compounds isolated from bacteria and fungi, and providing brief insights into promising new synthetic compounds.
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Affiliation(s)
- Susanne H Kirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany. .,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - F P Jake Haeckl
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany. .,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany. .,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.,Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany
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5
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Yuan C, Li P, Qing C, Kou Z, Wang H. Different Regulatory Strategies of Arsenite Oxidation by Two Isolated Thermus tengchongensis Strains From Hot Springs. Front Microbiol 2022; 13:817891. [PMID: 35359718 PMCID: PMC8963470 DOI: 10.3389/fmicb.2022.817891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/17/2022] [Indexed: 11/13/2022] Open
Abstract
Arsenic is a ubiquitous constituent in geothermal fluids. Thermophiles represented by Thermus play vital roles in its transformation in geothermal fluids. In this study, two Thermus tengchongensis strains, named as 15Y and 15W, were isolated from arsenic-rich geothermal springs and found different arsenite oxidation behaviors with different oxidation strategies. Arsenite oxidation of both strains occurred at different growth stages, and two enzyme-catalyzed reaction kinetic models were observed. The arsenite oxidase of Thermus strain 15W performed better oxidation activity, exhibiting typical Michaelis–Menten kinetics. The kinetic parameter of arsenite oxidation in whole cell showed a Vmax of 18.48 μM min–1 and KM of 343 μM. Both of them possessed the arsenite oxidase-coding genes aioB and aioA. However, the expression of gene aioBA was constitutive in strain 15W, whereas it was induced by arsenite in strain 15Y. Furthermore, strain 15Y harbored an intact aio operon including the regulatory gene of the ArsR family, whereas a genetic inversion of an around 128-kbp fragment produced the inactivation of this regulator in strain 15W, leading to the constitutive expression of aioBA genes. This study provides a valuable insight into the adaption of thermophiles to extreme environments.
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Affiliation(s)
- Changguo Yuan
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan, China
| | - Ping Li
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan, China
- *Correspondence: Ping Li,
| | - Chun Qing
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan, China
| | - Zhu Kou
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan, China
| | - Helin Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan, China
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6
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Barry CP, Gillane R, Talbo GH, Plan M, Palfreyman R, Haber-Stuk AK, Power J, Nielsen LK, Marcellin E. Multi-omic characterisation of Streptomyces hygroscopicus NRRL 30439: detailed assessment of its secondary metabolic potential. Mol Omics 2022; 18:226-236. [PMID: 34989730 DOI: 10.1039/d1mo00150g] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The emergence of multidrug-resistant pathogenic bacteria creates a demand for novel antibiotics with distinct mechanisms of action. Advances in next-generation genome sequencing promised a paradigm shift in the quest to find new bioactive secondary metabolites. Genome mining has proven successful for predicting putative biosynthetic elements in secondary metabolite superproducers such as Streptomycetes. However, genome mining approaches do not inform whether biosynthetic gene clusters are dormant or active under given culture conditions. Here we show that using a multi-omics approach in combination with antiSMASH, it is possible to assess the secondary metabolic potential of a Streptomyces strain capable of producing mannopeptimycin, an important cyclic peptide effective against Gram-positive infections. The genome of Streptomyces hygroscopicus NRRL 30439 was first sequenced using PacBio RSII to obtain a closed genome. A chemically defined medium was then used to elicit a nutrient stress response in S. hygroscopicus NRRL 30439. Detailed extracellular metabolomics and intracellular proteomics were used to profile and segregate primary and secondary metabolism. Our results demonstrate that the combination of genomics, proteomics and metabolomics enables rapid evaluation of a strain's performance in bioreactors for industrial production of secondary metabolites.
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Affiliation(s)
- Craig P Barry
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia.
| | - Rosemary Gillane
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia.
| | - Gert H Talbo
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia. .,The Queensland Node of Metabolomics Australia, AIBN, The University of Queensland, 4072 St. Lucia, Australia
| | - Manual Plan
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia. .,The Queensland Node of Metabolomics Australia, AIBN, The University of Queensland, 4072 St. Lucia, Australia
| | - Robin Palfreyman
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia. .,The Queensland Node of Metabolomics Australia, AIBN, The University of Queensland, 4072 St. Lucia, Australia
| | | | - John Power
- Zoetis, 333 Portage Street, Kalamazoo, MI 49007, USA
| | - Lars K Nielsen
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia. .,The Queensland Node of Metabolomics Australia, AIBN, The University of Queensland, 4072 St. Lucia, Australia.,The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia. .,The Queensland Node of Metabolomics Australia, AIBN, The University of Queensland, 4072 St. Lucia, Australia
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7
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Pathak A, Nowell RW, Wilson CG, Ryan MJ, Barraclough TG. Comparative genomics of Alexander Fleming's original Penicillium isolate (IMI 15378) reveals sequence divergence of penicillin synthesis genes. Sci Rep 2020; 10:15705. [PMID: 32973216 PMCID: PMC7515868 DOI: 10.1038/s41598-020-72584-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 09/03/2020] [Indexed: 11/18/2022] Open
Abstract
Antibiotics were derived originally from wild organisms and therefore understanding how these compounds evolve among different lineages might help with the design of new antimicrobial drugs. We report the draft genome sequence of Alexander Fleming’s original fungal isolate behind the discovery of penicillin, now classified as Penicillium rubens Biourge (1923) (IMI 15378). We compare the structure of the genome and genes involved in penicillin synthesis with those in two ‘high producing’ industrial strains of P. rubens and the closely related species P. nalgiovense. The main effector genes for producing penicillin G (pcbAB, pcbC and penDE) show amino acid divergence between the Fleming strain and both industrial strains, whereas a suite of regulatory genes are conserved. Homologs of penicillin N effector genes cefD1 and cefD2 were also found and the latter displayed amino acid divergence between the Fleming strain and industrial strains. The draft assemblies contain several partial duplications of penicillin-pathway genes in all three P. rubens strains, to differing degrees, which we hypothesise might be involved in regulation of the pathway. The two industrial strains are identical in sequence across all effector and regulatory genes but differ in duplication of the pcbAB–pcbC–penDE complex and partial duplication of fragments of regulatory genes. We conclude that evolution in the wild encompassed both sequence changes of the effector genes and gene duplication, whereas human-mediated changes through mutagenesis and artificial selection led to duplication of the penicillin pathway genes.
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Affiliation(s)
- Ayush Pathak
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, SL5 7PY, UK
| | - Reuben W Nowell
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, SL5 7PY, UK.,Department of Zoology, University of Oxford, 11a Mansfield Rd, Oxford, OX1 3SZ, UK
| | - Christopher G Wilson
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, SL5 7PY, UK.,Department of Zoology, University of Oxford, 11a Mansfield Rd, Oxford, OX1 3SZ, UK
| | | | - Timothy G Barraclough
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, SL5 7PY, UK. .,Department of Zoology, University of Oxford, 11a Mansfield Rd, Oxford, OX1 3SZ, UK.
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8
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Wang M, Xue J, Ma J, Feng X, Ying H, Xu H. Streptomyces lydicus M01 Regulates Soil Microbial Community and Alleviates Foliar Disease Caused by Alternaria alternata on Cucumbers. Front Microbiol 2020; 11:942. [PMID: 32499771 PMCID: PMC7243425 DOI: 10.3389/fmicb.2020.00942] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 04/20/2020] [Indexed: 01/22/2023] Open
Abstract
Due to the adverse effect on the environment caused by excessive use of chemical fertilizers, the development of sustainable agriculture attracts a growing demand of biological based fertilizers composed of living microorganisms. In this study, an Actinobacteria Streptomyces lydicus M01 was isolated from the rhizosphere soil of Pyrus calleryana. This strain effectively promoted the plant growth and suppressed a foliar disease caused by Alternaria alternata on cucumbers. S. lydicus M01 exhibited growth promoting characteristics such as phosphate solubilization, IAA secretion, siderophore and ACC deaminase production. Through Illumina sequencing of the 16S rRNA gene and ITS gene of the soil microbes, we found that the application of S. lydicus M01 altered the composition of the microbial community by promoting beneficial groups, including bacteria genera Pseudarthrobacter, Sphingomonas, Rhodanobacter, and Pseudomonas, fungi genera Fusicolla, Humicola, Solicoccozyma, and Paraphaeosphaeria. Most of these bacteria and eukaryotes exhibit positive effects on growth promotion, such as nutrient accumulation, auxin secretion, abiotic stress alleviation, biological control, or bioremediation. Furthermore, studies on the reactive oxygen species (ROS) level and antioxidants of cucumber leaves revealed that S. lydicus M01 treatment reduced the ROS accumulation and increased the activities of antioxidases related with ROS scavenging, which indicated an enhanced disease resistance of cucumbers under biotic stress. Thus, our results suggest that the application of S. lydicus M01 can systemically affect plant microbiome interactions and represent a promising sustainable solution to improve agricultural production instead of chemical fertilizers.
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Affiliation(s)
- Mingxuan Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Jian Xue
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Junjie Ma
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Xiaohai Feng
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Hanjie Ying
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China.,College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Hong Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
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9
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Núñez-Montero K, Lamilla C, Abanto M, Maruyama F, Jorquera MA, Santos A, Martinez-Urtaza J, Barrientos L. Antarctic Streptomyces fildesensis So13.3 strain as a promising source for antimicrobials discovery. Sci Rep 2019; 9:7488. [PMID: 31097761 PMCID: PMC6522549 DOI: 10.1038/s41598-019-43960-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 05/01/2019] [Indexed: 12/29/2022] Open
Abstract
Antarctic have been suggested as an attractive source for antibiotics discovery and members of Streptomyces genus have historically been studied as natural producers of antimicrobial metabolites. Nonetheless, our knowledge on antibiotic-producing Streptomyces from Antarctic is very limited. In this study, the antimicrobial activity of organic extracts from Antarctic Streptomyces strains was evaluated by disk diffusion assays and minimum inhibitory concentration. The strain Streptomyces sp. So13.3 showed the greatest antibiotic activity (MIC = 15.6 μg/mL) against Gram-positive bacteria and growth reduction of Gram‒negative pathogens. The bioactive fraction in the crude extract was revealed by TLC‒bioautography at Rf = 0.78 with molecular weight between 148 and 624 m/z detected by LC-ESI-MS/MS. The strain So13.3 was taxonomically affiliated as Streptomyces fildesensis. Whole genome sequencing and analysis suggested a 9.47 Mb genome size with 42 predicted biosynthetic gene clusters (BGCs) and 56 putative clusters representing a 22% of total genome content. Interestingly, a large number of them (11 of 42 BGCs and 40 of 56 putative BGCs), did not show similarities with other known BGCs. Our results highlight the potential of the Antarctic Streptomyces strains as a promising source of novel antimicrobials, particularly the strain Streptomyces fildesensis So13.3, which first draft genome is reported in this work.
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Affiliation(s)
- Kattia Núñez-Montero
- Laboratorio de Biología Molecular Aplicada, Centro de Excelencia en Medicina Traslacional, Universidad de La Frontera, Temuco, Chile.,Núcleo Científico y Tecnológico en Biorecursos (BIOREN), Universidad de La Frontera, Temuco, Chile.,Centro de Investigación en Biotecnología, Escuela de Biología, Instituto Tecnológico de Costa Rica, Cartago, Costa Rica
| | - Claudio Lamilla
- Laboratorio de Biología Molecular Aplicada, Centro de Excelencia en Medicina Traslacional, Universidad de La Frontera, Temuco, Chile.,Núcleo Científico y Tecnológico en Biorecursos (BIOREN), Universidad de La Frontera, Temuco, Chile
| | - Michel Abanto
- Núcleo Científico y Tecnológico en Biorecursos (BIOREN), Universidad de La Frontera, Temuco, Chile
| | - Fumito Maruyama
- Núcleo Científico y Tecnológico en Biorecursos (BIOREN), Universidad de La Frontera, Temuco, Chile.,Department of Microbiology, Graduate School of Medicine, Kyoto University, Yoshida‒Konoe‒cho, Sakyo‒ku, Kyoto, Japan
| | - Milko A Jorquera
- Núcleo Científico y Tecnológico en Biorecursos (BIOREN), Universidad de La Frontera, Temuco, Chile.,Laboratorio de Ecología Microbiana Aplicada, Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile
| | - Andrés Santos
- Laboratorio de Biología Molecular Aplicada, Centro de Excelencia en Medicina Traslacional, Universidad de La Frontera, Temuco, Chile.,Núcleo Científico y Tecnológico en Biorecursos (BIOREN), Universidad de La Frontera, Temuco, Chile.,Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Barrack Road, Weymouth, Dorset, DT4 8UB, UK
| | - Jaime Martinez-Urtaza
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Barrack Road, Weymouth, Dorset, DT4 8UB, UK
| | - Leticia Barrientos
- Laboratorio de Biología Molecular Aplicada, Centro de Excelencia en Medicina Traslacional, Universidad de La Frontera, Temuco, Chile. .,Núcleo Científico y Tecnológico en Biorecursos (BIOREN), Universidad de La Frontera, Temuco, Chile.
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10
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Zhan W, Yao J, Tang K, Li Y, Guo Y, Wang X. Characterization of Two Toxin-Antitoxin Systems in Deep-Sea Streptomyces sp. SCSIO 02999. Mar Drugs 2019; 17:md17040211. [PMID: 30987346 PMCID: PMC6521030 DOI: 10.3390/md17040211] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 03/26/2019] [Accepted: 04/01/2019] [Indexed: 12/20/2022] Open
Abstract
Toxin-antitoxin (TA) systems are ubiquitous and abundant genetic elements in bacteria and archaea. Most previous TA studies have focused on commensal and pathogenic bacteria, but have rarely focused on marine bacteria, especially those isolated from the deep sea. Here, we identified and characterized three putative TA pairs in the deep-sea-derived Streptomyces sp. strain SCSIO 02999. Our results showed that Orf5461/Orf5462 and Orf2769/Orf2770 are bona fide TA pairs. We provide several lines of evidence to demonstrate that Orf5461 and Orf5462 constitute a type-II TA pair that are homologous to the YoeB/YefM TA pair from Escherichia coli. Although YoeB from SCSIO 02999 was toxic to an E. coli host, the homologous YefM antitoxin from SCSIO 02999 did not neutralize the toxic effect of YoeB from E. coli. For the Orf2769/Orf2770 TA pair, Orf2769 overexpression caused significant cell elongation and could lead to cell death in E. coli, and the neighboring Orf2770 could neutralize the toxic effect of Orf2769. However, no homologous toxin or antitoxin was found for this pair, and no direct interaction was found between Orf2769 and Orf2770. These results suggest that Orf2769 and Orf2770 may constitute a novel TA pair. Thus, deep-sea bacteria harbor typical and novel TA pairs. The biochemical and physiological functions of different TAs in deep-sea bacteria warrant further investigation.
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Affiliation(s)
- Waner Zhan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Jianyun Yao
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
| | - Kaihao Tang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
| | - Yangmei Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yunxue Guo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
| | - Xiaoxue Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
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11
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Impacts of horizontal gene transfer on the compact genome of the clavulanic acid-producing Streptomyces strain F613-1. 3 Biotech 2018; 8:472. [PMID: 30456006 DOI: 10.1007/s13205-018-1498-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 11/01/2018] [Indexed: 12/27/2022] Open
Abstract
Mobile genetic elements involved in mediating horizontal transfer events contribute to bacterial evolution, and bacterial genomic plasticity and instability result in variation in functional genetic information in Streptomyces secondary metabolism. In a previous study, we reported the complete genome sequence of the industrial Streptomyces strain F613-1, which produces high yields of clavulanic acid. In this study, we used comparative genomics and bioinformatics to investigate the unique genomic features of this strain. Taken together, comparative genomics were used to systematically investigate secondary metabolism capabilities and indicated that frequent exchange of genetic materials between Streptomyces replicons may shape the remarkable diversities in their secondary metabolite repertoires. Moreover, a 136.9-kb giant region of plasticity (RGP) was found in the F613-1 chromosome, and the chromosome and plasmid pSCL4 are densely packed with an exceptionally large variety of potential secondary metabolic gene clusters, involving several determinants putatively accounting for antibiotic production. In addition, the differences in the architecture and size of plasmid pSCL4 between F613-1 and ATCC 27064 suggest that the pSCL4 plasmid could evolve from pSCL4-like and pSCL2-like extrachromosomal replicons. Furthermore, the genomic analyses revealed that strain F613-1 has developed specific genomic architectures and genetic patterns that are well suited to meet the requirements of industrial innovation processes.
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12
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Palazzotto E, Weber T. Omics and multi-omics approaches to study the biosynthesis of secondary metabolites in microorganisms. Curr Opin Microbiol 2018; 45:109-116. [PMID: 29656009 DOI: 10.1016/j.mib.2018.03.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 03/28/2018] [Accepted: 03/30/2018] [Indexed: 10/17/2022]
Abstract
Natural products produced by microorganisms represent the main source of bioactive molecules. The development of high-throughput (omics) techniques have importantly contributed to the renaissance of new antibiotic discovery increasing our understanding of complex mechanisms controlling the expression of biosynthetic gene clusters (BGCs) encoding secondary metabolites. In this context this review highlights recent progress in the use and integration of 'omics' approaches with focuses on genomics, transcriptomics, proteomics metabolomics meta-omics and combined omics as powerful strategy to discover new antibiotics.
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Affiliation(s)
- Emilia Palazzotto
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs., Lyngby, Denmark
| | - Tilmann Weber
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs., Lyngby, Denmark.
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13
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Wu H, Liu W, Shi L, Si K, Liu T, Dong D, Zhang T, Zhao J, Liu D, Tian Z, Yue Y, Zhang H, Xuelian B, Liang Y. Comparative Genomic and Regulatory Analyses of Natamycin Production of Streptomyces lydicus A02. Sci Rep 2017; 7:9114. [PMID: 28831190 PMCID: PMC5567329 DOI: 10.1038/s41598-017-09532-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 07/17/2017] [Indexed: 11/16/2022] Open
Abstract
Streptomyces lydicus A02 is used by industry because it has a higher natamycin-producing capacity than the reference strain S. natalensis ATCC 27448. We sequenced the complete genome of A02 using next-generation sequencing platforms, and to achieve better sequence coverage and genome assembly, we utilized single-molecule real-time (SMRT) sequencing. The assembled genome comprises a 9,307,519-bp linear chromosome with a GC content of 70.67%, and contained 8,888 predicted genes. Comparative genomics and natamycin biosynthetic gene cluster (BGC) analysis showed that BGC are highly conserved among evolutionarily diverse strains, and they also shared closer genome evolution compared with other Streptomyces species. Forty gene clusters were predicted to involve in the secondary metabolism of A02, and it was richly displayed in two-component signal transduction systems (TCS) in the genome, indicating a complex regulatory systems and high diversity of metabolites. Disruption of the phoP gene of the phoR-phoP TCS and nsdA gene confirmed phosphate sensitivity and global negative regulation of natamycin production. The genome sequence and analyses presented in this study provide an important molecular basis for research on natamycin production in Streptomyces, which could facilitate rational genome modification to improve the industrial use of A02.
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Affiliation(s)
- Huiling Wu
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Weicheng Liu
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Lingling Shi
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Kaiwei Si
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Ting Liu
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Dan Dong
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Taotao Zhang
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Juan Zhao
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Dewen Liu
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Zhaofeng Tian
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Yuesen Yue
- Beijing Research and Development Center for Grass and Environment, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Hong Zhang
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Bai Xuelian
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Yong Liang
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
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14
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Zhu D, Xiao S, Yu J, Ai Q, He Y, Cheng C, Zhang Y, Pan Y. Effects of One-Week Empirical Antibiotic Therapy on the Early Development of Gut Microbiota and Metabolites in Preterm Infants. Sci Rep 2017; 7:8025. [PMID: 28808302 PMCID: PMC5556106 DOI: 10.1038/s41598-017-08530-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 07/13/2017] [Indexed: 12/11/2022] Open
Abstract
The early postnatal period is the most dynamic and vulnerable stage in the assembly of intestinal microbiota. Antibiotics are commonly prescribed to newborn preterm babies and are frequently used for a prolonged duration in China. We hypothesized that the prolonged antibiotic therapy would affect the early development of intestinal microbiota and their metabolites. To test this hypothesis, we analyzed the stool microbiota and metabolites in 36 preterm babies with or without antibiotic treatment. These babies were divided into three groups, including two groups treated with the combination of penicillin and moxalactam or piperacillin-tazobactam for 7 days, and the other group was free of antibiotics. Compared to the antibiotic-free group, both antibiotic-treated groups had distinct gut microbial communities and metabolites, including a reduction of bacterial diversity and an enrichment of harmful bacteria such as Streptococcus and Pseudomonas. In addition, there was a significant difference in the composition of gut microbiota and their metabolites between the two antibiotic-treated groups, where the piperacillin-tazobactam treatment group showed an overgrowth of Enterococcus. These findings suggest that prolonged antibiotic therapy affects the early development of gut microbiota in preterm infants, which should be considered when prescribing antibiotics for this population.
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Affiliation(s)
- Danping Zhu
- Department of Neonatology, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China.,China International Science and Technology Cooperation Base of Child development and Critical Disorders, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Chongqing, China
| | - Sa Xiao
- Department of Neonatology, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China.,China International Science and Technology Cooperation Base of Child development and Critical Disorders, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Chongqing, China
| | - Jialin Yu
- Department of Neonatology, Children's Hospital of Chongqing Medical University, Chongqing, China. .,Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China. .,China International Science and Technology Cooperation Base of Child development and Critical Disorders, Chongqing, China. .,Chongqing Key Laboratory of Child Infection and Immunity, Chongqing, China. .,Department of Pediatric, The Affiliated Hospital of Shenzhen University, Shenzhen, China.
| | - Qing Ai
- Department of Neonatology, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China.,China International Science and Technology Cooperation Base of Child development and Critical Disorders, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Chongqing, China
| | - Yu He
- Department of Neonatology, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China.,China International Science and Technology Cooperation Base of Child development and Critical Disorders, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Chongqing, China
| | - Chen Cheng
- Department of Neonatology, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China.,China International Science and Technology Cooperation Base of Child development and Critical Disorders, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Chongqing, China
| | - Yunhui Zhang
- Department of Neonatology, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China.,China International Science and Technology Cooperation Base of Child development and Critical Disorders, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Chongqing, China
| | - Yun Pan
- Department of Neonatology, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China.,China International Science and Technology Cooperation Base of Child development and Critical Disorders, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Chongqing, China
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