1
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Jaffal H, Kortebi M, Misson P, Tavares P, Ouldali M, Leh H, Lautru S, Lioy VS, Lecointe F, Bury-Moné SG. Prophage induction can facilitate the in vitro dispersal of multicellular Streptomyces structures. PLoS Biol 2024; 22:e3002725. [PMID: 39052683 DOI: 10.1371/journal.pbio.3002725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 08/06/2024] [Accepted: 06/28/2024] [Indexed: 07/27/2024] Open
Abstract
Streptomyces are renowned for their prolific production of specialized metabolites with applications in medicine and agriculture. These multicellular bacteria present a sophisticated developmental cycle and play a key role in soil ecology. Little is known about the impact of Streptomyces phage on bacterial physiology. In this study, we investigated the conditions governing the expression and production of "Samy", a prophage found in Streptomyces ambofaciens ATCC 23877. This siphoprophage is produced simultaneously with the activation of other mobile genetic elements. Remarkably, the presence and production of Samy increases bacterial dispersal under in vitro stress conditions. Altogether, this study unveiled a new property of a bacteriophage infection in the context of multicellular aggregate dynamics.
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Affiliation(s)
- Hoda Jaffal
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Mounia Kortebi
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Pauline Misson
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Paulo Tavares
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Malika Ouldali
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Hervé Leh
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Sylvie Lautru
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Virginia S Lioy
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - François Lecointe
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Stéphanie G Bury-Moné
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
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2
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Pinatel E, Calcagnile M, Talà A, Damiano F, Siculella L, Peano C, De Benedetto GE, Pennetta A, De Bellis G, Alifano P. Interplay between non-coding RNA transcription, stringent phenotype and antibiotic production in Streptomyces. J Biotechnol 2022:S0168-1656(22)00029-3. [PMID: 35182607 DOI: 10.1016/j.jbiotec.2022.02.006] [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: 01/15/2021] [Accepted: 02/12/2022] [Indexed: 11/26/2022]
Abstract
While in recent years the key role of non-coding RNAs (ncRNAs) in regulation of gene expression has become increasingly evident, their interaction with the global regulatory circuits is still obscure. Here we analyzed the structure and organization of the transcriptome of Streptomyces ambofaciens, the producer of spiramycin. We identified ncRNAs including 45 small-RNAs (sRNAs) and 119 antisense-RNAs (asRNAs I) that appear transcribed from dedicated promoters. Some sRNAs and asRNAs are unprecedented in Streptomyces, and were predicted to target mRNAs encoding proteins involved in transcription, translation, ribosomal structure and biogenesis, and regulation of morphological and biochemical differentiation. We then compared ncRNA expression in three strains: i.) the wild type strain; ii.) an isogenic pirA-defective mutant with central carbon metabolism imbalance, "relaxed" phenotype, and repression of antibiotic production; iii.) a pirA-derivative strain harboring a "stringent" RNA polymerase that suppresses pirA-associated phenotypes. Data indicated that expression of most ncRNAs was correlated to the stringent/relaxed phenotype suggesting novel effector mechanisms of the stringent response.
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Affiliation(s)
- Eva Pinatel
- Institute of Biomedical Technologies, National Research Council, Segrate, Milan, Italy
| | - Matteo Calcagnile
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Via Monteroni, 73100 Lecce, Italy
| | - Adelfia Talà
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Via Monteroni, 73100 Lecce, Italy
| | - Fabrizio Damiano
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Via Monteroni, 73100 Lecce, Italy
| | - Luisa Siculella
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Via Monteroni, 73100 Lecce, Italy
| | - Clelia Peano
- Genomic Unit, IRCCS Humanitas Clinical and Research Center, Rozzano, Milan, Italy; Institute of Genetic and Biomedical Research, UoS of Milan, National Research Council, Rozzano, Milan, Italy
| | | | - Antonio Pennetta
- Department of Cultural Heritage, University of Salento, Via Monteroni, 73100 Lecce, Italy
| | - Gianluca De Bellis
- Institute of Biomedical Technologies, National Research Council, Segrate, Milan, Italy
| | - Pietro Alifano
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Via Monteroni, 73100 Lecce, Italy.
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3
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Baltz RH. Genome mining for drug discovery: progress at the front end. J Ind Microbiol Biotechnol 2021; 48:6324007. [PMID: 34279640 PMCID: PMC8788784 DOI: 10.1093/jimb/kuab044] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 07/11/2021] [Indexed: 12/12/2022]
Abstract
Microbial genome mining for drug discovery and development has been accelerating in recent years, driven by technical advancements in genome sequencing, bioinformatics, metabolomics/metabologenomics, and synthetic biology. Microbial genome mining is a multistep process that starts with the sequencing of microbes that encode multiple secondary metabolites and identifying new and novel secondary metabolite biosynthetic gene clusters (BGCs) to pursue. The initial steps in the process are critical for the overall success, and they encompass the most innovative new technologies to revitalize natural product discovery. As microbial genome mining has matured in recent years, unvalidated conjectures about what microbes to pursue, how to identify legitimate secondary metabolite BGCs, and how to sequence DNA to satisfactory levels of completion have been identified. The solutions to correct the misconceptions around these topics are beginning to be implemented.
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Affiliation(s)
- Richard H Baltz
- CognoGen Biotechnology Consulting, 7757 Uliva Way, Sarasota, FL 34238, USA
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4
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Guo HY, Chen ZA, Shen QK, Quan ZS. Application of triazoles in the structural modification of natural products. J Enzyme Inhib Med Chem 2021; 36:1115-1144. [PMID: 34167422 PMCID: PMC8231395 DOI: 10.1080/14756366.2021.1890066] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 01/30/2021] [Accepted: 02/08/2021] [Indexed: 02/07/2023] Open
Abstract
Nature products have been extensively used in the discovery and development of new drugs, as the most important source of drugs. The triazole ring is one of main pharmacophore of the nitrogen-containing heterocycles. Thus, a new class of triazole-containing natural product conjugates has been synthesised. These compounds reportedly exert anticancer, anti-inflammatory, antimicrobial, antiparasitic, antiviral, antioxidant, anti-Alzheimer, and enzyme inhibitory effects. This review summarises the research progress of triazole-containing natural product derivatives involved in medicinal chemistry in the past six years. This review provides insights and perspectives that will help scientists in the fields of organic synthesis, medicinal chemistry, phytochemistry, and pharmacology.
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Affiliation(s)
- Hong-Yan Guo
- Key Laboratory of Natural Medicines of the Changbai Mountain, Affifiliated Ministry of Education, College of Pharmacy, Yanbian University, Affiliated Hospital of Yanbian University, Yanji, Jilin, China
| | - Zheng-Ai Chen
- Department of Pharmacology, Medical School of Yanbian University, Yanji, Jilin, China
| | - Qing-Kun Shen
- Key Laboratory of Natural Medicines of the Changbai Mountain, Affifiliated Ministry of Education, College of Pharmacy, Yanbian University, Affiliated Hospital of Yanbian University, Yanji, Jilin, China
| | - Zhe-Shan Quan
- Department of Pharmacology, Medical School of Yanbian University, Yanji, Jilin, China
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5
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Interplay between Non-Coding RNA Transcription, Stringent/Relaxed Phenotype and Antibiotic Production in Streptomyces ambofaciens. Antibiotics (Basel) 2021; 10:antibiotics10080947. [PMID: 34438997 PMCID: PMC8388888 DOI: 10.3390/antibiotics10080947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/28/2021] [Accepted: 08/02/2021] [Indexed: 11/25/2022] Open
Abstract
While in recent years the key role of non-coding RNAs (ncRNAs) in the regulation of gene expression has become increasingly evident, their interaction with the global regulatory circuits is still obscure. Here we analyzed the structure and organization of the transcriptome of Streptomyces ambofaciens, the producer of spiramycin. We identified ncRNAs including 45 small-RNAs (sRNAs) and 119 antisense-RNAs (asRNAs I) that appear transcribed from dedicated promoters. Some sRNAs and asRNAs are unprecedented in Streptomyces and were predicted to target mRNAs encoding proteins involved in transcription, translation, ribosomal structure and biogenesis, and regulation of morphological and biochemical differentiation. We then compared ncRNA expression in three strains: (i) the wild-type strain; (ii) an isogenic pirA-defective mutant with central carbon metabolism imbalance, “relaxed” phenotype, and repression of antibiotic production; and (iii) a pirA-derivative strain harboring a “stringent” RNA polymerase that suppresses pirA-associated phenotypes. Data indicated that the expression of most ncRNAs was correlated to the stringent/relaxed phenotype suggesting novel effector mechanisms of the stringent response.
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6
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Al-shaibani MM, Radin Mohamed RMS, Sidik NM, Enshasy HAE, Al-Gheethi A, Noman E, Al-Mekhlafi NA, Zin NM. Biodiversity of Secondary Metabolites Compounds Isolated from Phylum Actinobacteria and Its Therapeutic Applications. Molecules 2021; 26:molecules26154504. [PMID: 34361657 PMCID: PMC8347454 DOI: 10.3390/molecules26154504] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 07/14/2021] [Accepted: 07/22/2021] [Indexed: 12/08/2022] Open
Abstract
The current review aims to summarise the biodiversity and biosynthesis of novel secondary metabolites compounds, of the phylum Actinobacteria and the diverse range of secondary metabolites produced that vary depending on its ecological environments they inhabit. Actinobacteria creates a wide range of bioactive substances that can be of great value to public health and the pharmaceutical industry. The literature analysis process for this review was conducted using the VOSviewer software tool to visualise the bibliometric networks of the most relevant databases from the Scopus database in the period between 2010 and 22 March 2021. Screening and exploring the available literature relating to the extreme environments and ecosystems that Actinobacteria inhabit aims to identify new strains of this major microorganism class, producing unique novel bioactive compounds. The knowledge gained from these studies is intended to encourage scientists in the natural product discovery field to identify and characterise novel strains containing various bioactive gene clusters with potential clinical applications. It is evident that Actinobacteria adapted to survive in extreme environments represent an important source of a wide range of bioactive compounds. Actinobacteria have a large number of secondary metabolite biosynthetic gene clusters. They can synthesise thousands of subordinate metabolites with different biological actions such as anti-bacterial, anti-parasitic, anti-fungal, anti-virus, anti-cancer and growth-promoting compounds. These are highly significant economically due to their potential applications in the food, nutrition and health industries and thus support our communities' well-being.
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Affiliation(s)
- Muhanna Mohammed Al-shaibani
- Micro-Pollutant Research Centre (MPRC), Faculty of Civil Engineering and Built Environment, Universiti Tun Hussein Onn Malaysia, Parit Raja 86400, Johor, Malaysia;
- Center for Diagnostic, Therapeutic and Investigative Studies, Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Kuala Lumpur 50300, Malaysia;
| | - Radin Maya Saphira Radin Mohamed
- Micro-Pollutant Research Centre (MPRC), Faculty of Civil Engineering and Built Environment, Universiti Tun Hussein Onn Malaysia, Parit Raja 86400, Johor, Malaysia;
- Correspondence: (R.M.S.R.M.); (N.M.S.); (A.A.-G.)
| | - Nik Marzuki Sidik
- Faculty of Agro-Based Industry, Universiti Malaysia Kelantan, Jeli 17600, Kelantan, Malaysia
- Correspondence: (R.M.S.R.M.); (N.M.S.); (A.A.-G.)
| | - Hesham Ali El Enshasy
- Institute of Bioproducts Development (IBD), Universiti Teknologi Malaysia (UTM), Skudai 81310, Johor, Malaysia;
- City of Scientific Research and Technology Applications (SRTA), 21934 New Burg Al Arab, Alexandria, Egypt
| | - Adel Al-Gheethi
- Micro-Pollutant Research Centre (MPRC), Faculty of Civil Engineering and Built Environment, Universiti Tun Hussein Onn Malaysia, Parit Raja 86400, Johor, Malaysia;
- Correspondence: (R.M.S.R.M.); (N.M.S.); (A.A.-G.)
| | - Efaq Noman
- Applied Microbiology Department, Faculty of Applied Sciences, Taiz University, Taiz 6803, Yemen;
| | - Nabil Ali Al-Mekhlafi
- Atta-ur-Rahman Institute for Natural Product Discovery, UiTM, Puncak Alam Campus, Bandar Puncak Alam 42300, Selangor, Malaysia;
- Biochemical Technology Program, Department of Chemistry Faculty of Applied Science, Thamar University, Thamar P.O. Box 87246, Yemen
| | - Noraziah Mohamad Zin
- Center for Diagnostic, Therapeutic and Investigative Studies, Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Kuala Lumpur 50300, Malaysia;
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7
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Baltz RH. Genome mining for drug discovery: cyclic lipopeptides related to daptomycin. J Ind Microbiol Biotechnol 2021; 48:6178872. [PMID: 33739403 PMCID: PMC9113097 DOI: 10.1093/jimb/kuab020] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 11/17/2020] [Indexed: 11/25/2022]
Abstract
The cyclic lipopeptide antibiotics structurally related to daptomycin were first reported in the 1950s. Several have common lipopeptide initiation, elongation, and termination mechanisms. Initiation requires the use of a fatty acyl-AMP ligase (FAAL), a free-standing acyl carrier protein (ACP), and a specialized condensation (CIII) domain on the first NRPS elongation module to couple the long chain fatty acid to the first amino acid. Termination is carried out by a dimodular NRPS that contains a terminal thioesterase (Te) domain (CAT-CATTe). Lipopeptide BGCs also encode ABC transporters, apparently for export and resistance. The use of this mechanism of initiation, elongation, and termination, coupled with molecular target-agnostic resistance, has provided a unique basis for robust natural and experimental combinatorial biosynthesis to generate a large variety of structurally related compounds, some with altered or different antibacterial mechanisms of action. The FAAL, ACP, and dimodular NRPS genes were used as molecular beacons to identify phylogenetically related BGCs by BLASTp analysis of finished and draft genome sequences. These and other molecular beacons have identified: (i) known, but previously unsequenced lipopeptide BGCs in draft genomes; (ii) a new daptomycin family BGC in a draft genome of Streptomyces sedi; and (iii) novel lipopeptide BGCs in the finished genome of Streptomyces ambofaciens and the draft genome of Streptomyces zhaozhouensis.
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Affiliation(s)
- Richard H Baltz
- CognoGen Biotechnology Consulting, 7757 Uliva Way, Sarasota, FL 34238, USA
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8
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Mining the Biosynthetic Potential for Specialized Metabolism of a Streptomyces Soil Community. Antibiotics (Basel) 2020; 9:antibiotics9050271. [PMID: 32456220 PMCID: PMC7277575 DOI: 10.3390/antibiotics9050271] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 05/18/2020] [Accepted: 05/20/2020] [Indexed: 12/22/2022] Open
Abstract
The diversity and distribution of specialized metabolite gene clusters within a community of bacteria living in the same soil habitat are poorly documented. Here we analyzed the genomes of 8 Streptomyces isolated at micro-scale from a forest soil that belong to the same species or to different species. The results reveal high levels of diversity, with a total of 261 biosynthesis gene clusters (BGCs) encoding metabolites such as terpenes, polyketides (PKs), non-ribosomal peptides (NRPs) and ribosomally synthesized and post-translationally modified peptides (RiPPs) with potential bioactivities. A significant part of these BGCs (n = 53) were unique to only one strain when only 5 were common to all strains. The metabolites belong to very diverse chemical families and revealed that a large diversity of metabolites can potentially be produced in the community. Although that analysis of the global metabolome using GC-MS revealed that most of the metabolites were shared between the strains, they exhibited a specific metabolic pattern. We also observed that the presence of these accessory pathways might result from frequent loss and gain of genes (horizontal transfer), showing that the potential of metabolite production is a dynamic phenomenon in the community. Sampling Streptomyces at the community level constitutes a good frame to discover new biosynthetic pathways and it appears as a promising reservoir for the discovery of new bioactive compounds.
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9
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Zhang H, Dong S, Lou T, Wang S. Complete genome sequence unveiled cellulose degradation enzymes and secondary metabolic potentials in Streptomyces sp. CC0208. J Basic Microbiol 2018; 59:267-276. [PMID: 30589093 DOI: 10.1002/jobm.201800563] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 11/19/2018] [Accepted: 11/30/2018] [Indexed: 11/10/2022]
Abstract
Marine Streptomyces sp. CC0208 isolated from the Bohai Bay showed high efficiency of cellulose degradation under optimized fermentation parameters. Also, as one of the bioinformatics-based approaches for the discovery of novel natural product and enzyme effectively, genome mining has been developed and applied widely. Herein, we reported the complete genome sequence of Streptomyces sp. CC0208.Whole-genome sequencing analysis revealed a genome size of 9,325,981 bp with a linear chromosome, GC content of 70.59% and 8487 protein-coding genes. Abundant genes have predicted functions in antibiotic metabolism and enzymes. A 20 enzymes closely associated with cellulose degradation were discovered. A total of 25 biosynthetic gene clusters (BGCs) of secondary metabolites were identified, including diverse classes of natural products. The availability of genome sequence of Streptomyces sp. CC0208 not only will assist in cracking the mechanism of cellulose degradation but also will provide the insights into the significant secondary metabolic potentials for the production of diverse compound classes based on rational strategies.
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Affiliation(s)
- Hongyu Zhang
- Tianjin Key Laboratory of Food Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China.,State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shirui Dong
- Tianjin Key Laboratory of Food Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
| | - Tingting Lou
- Tianjin Entry and Exit Inspection and Quarantine Bureau, Tianjin, China
| | - Suying Wang
- Tianjin Key Laboratory of Food Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
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10
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Comparative Genomics among Closely Related Streptomyces Strains Revealed Specialized Metabolite Biosynthetic Gene Cluster Diversity. Antibiotics (Basel) 2018; 7:antibiotics7040086. [PMID: 30279346 PMCID: PMC6315706 DOI: 10.3390/antibiotics7040086] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 09/27/2018] [Accepted: 09/28/2018] [Indexed: 02/06/2023] Open
Abstract
Specialized metabolites are of great interest due to their possible industrial and clinical applications. The increasing number of antimicrobial resistant infectious agents is a major health threat and therefore, the discovery of chemical diversity and new antimicrobials is crucial. Extensive genomic data from Streptomyces spp. confirm their production potential and great importance. Genome sequencing of the same species strains indicates that specialized metabolite biosynthetic gene cluster (SMBGC) diversity is not exhausted, and instead, a pool of novel specialized metabolites still exists. Here, we analyze the genome sequence data from six phylogenetically close Streptomyces strains. The results reveal that the closer strains are phylogenetically, the number of shared gene clusters is higher. Eight specialized metabolites comprise the core metabolome, although some strains have only six core gene clusters. The number of conserved gene clusters common between the isolated strains and their closest phylogenetic counterparts varies from nine to 23 SMBGCs. However, the analysis of these phylogenetic relationships is not affected by the acquisition of gene clusters, probably by horizontal gene transfer events, as each strain also harbors strain-specific SMBGCs. Between one and 15 strain-specific gene clusters were identified, of which up to six gene clusters in a single strain are unknown and have no identifiable orthologs in other species, attesting to the existing SMBGC novelty at the strain level.
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11
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Draft Whole-Genome Shotgun Sequence of Streptomyces sp. Strain ETH9427. Microbiol Resour Announc 2018; 7:MRA01197-18. [PMID: 30533680 PMCID: PMC6256703 DOI: 10.1128/mra.01197-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 08/31/2018] [Indexed: 11/20/2022] Open
Abstract
The draft genome of Streptomyces sp. strain ETH9427 was sequenced and assembled into three large scaffolds, a 7.745-Mb linear chromosome with terminal inverted repeats of 201 kb and two probable extrachromosomal elements. The draft genome of Streptomyces sp. strain ETH9427 was sequenced and assembled into three large scaffolds, a 7.745-Mb linear chromosome with terminal inverted repeats of 201 kb and two probable extrachromosomal elements. Thirty-two biosynthetic gene clusters (BGCs) were identified, out of which four are duplicated in the terminal inverted repeats.
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12
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Rigali S, Anderssen S, Naômé A, van Wezel GP. Cracking the regulatory code of biosynthetic gene clusters as a strategy for natural product discovery. Biochem Pharmacol 2018; 153:24-34. [DOI: 10.1016/j.bcp.2018.01.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 01/03/2018] [Indexed: 12/19/2022]
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13
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Talà A, Damiano F, Gallo G, Pinatel E, Calcagnile M, Testini M, Fico D, Rizzo D, Sutera A, Renzone G, Scaloni A, De Bellis G, Siculella L, De Benedetto GE, Puglia AM, Peano C, Alifano P. Pirin: A novel redox-sensitive modulator of primary and secondary metabolism in Streptomyces. Metab Eng 2018; 48:254-268. [PMID: 29944936 DOI: 10.1016/j.ymben.2018.06.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 06/21/2018] [Accepted: 06/22/2018] [Indexed: 10/28/2022]
Abstract
Pirins are evolutionarily conserved iron-containing proteins that are found in all kingdoms of life, and have been implicated in diverse molecular processes, mostly associated with cellular stress. In the present study, we started from the evidence that the insertional inactivation of pirin-like gene SAM23877_RS18305 (pirA) by ΦC31 Att/Int system-based vectors in spiramycin-producing strain Streptomyces ambofaciens ATCC 23877 resulted in marked effects on central carbon and energy metabolism gene expression, high sensitivity to oxidative injury and repression of polyketide antibiotic production. By using integrated transcriptomic, proteomic and metabolite profiling, together with genetic complementation, we here show that most of these effects could be traced to the inability of the pirA-defective strain to modulate beta-oxidation pathway, leading to an unbalanced supply of precursor monomers for polyketide biosynthesis. Indeed, in silico protein-protein interaction modeling and in vitro experimental validation allowed us to demonstrate that PirA is a novel redox-sensitive negative modulator of very long-chain acyl-CoA dehydrogenase, which catalyzes the first committed step of the beta-oxidation pathway.
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Affiliation(s)
- Adelfia Talà
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Fabrizio Damiano
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Giuseppe Gallo
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy; Advanced Technologies Network (ATeN) Center, University of Palermo, Palermo, Italy
| | - Eva Pinatel
- Institute of Biomedical Technologies, National Research Council, Segrate, Italy
| | - Matteo Calcagnile
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Mariangela Testini
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Daniela Fico
- Laboratory of Analytical and Isotopic Mass Spectrometry, Department of Cultural Heritage, University of Salento, Lecce, Italy
| | - Daniela Rizzo
- Laboratory of Analytical and Isotopic Mass Spectrometry, Department of Cultural Heritage, University of Salento, Lecce, Italy
| | - Alberto Sutera
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy; Advanced Technologies Network (ATeN) Center, University of Palermo, Palermo, Italy
| | - Giovanni Renzone
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, Naples, Italy
| | - Andrea Scaloni
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, Naples, Italy
| | - Gianluca De Bellis
- Institute of Biomedical Technologies, National Research Council, Segrate, Italy
| | - Luisa Siculella
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Giuseppe Egidio De Benedetto
- Laboratory of Analytical and Isotopic Mass Spectrometry, Department of Cultural Heritage, University of Salento, Lecce, Italy
| | - Anna Maria Puglia
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
| | - Clelia Peano
- Institute of Biomedical Technologies, National Research Council, Segrate, Italy; Institute of Genetic and Biomedical Research, UoS Milan, National Research Council, Rozzano, Milan, Italy; Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Pietro Alifano
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy.
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14
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Dettori L, Ferrari F, Framboisier X, Paris C, Guiavarc'h Y, Hôtel L, Aymes A, Leblond P, Humeau C, Kapel R, Chevalot I, Aigle B, Delaunay S. An aminoacylase activity from Streptomyces ambofaciens catalyzes the acylation of lysine on α-position and peptides on N-terminal position. Eng Life Sci 2018; 18:589-599. [PMID: 32624939 DOI: 10.1002/elsc.201700173] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 03/16/2018] [Accepted: 04/12/2018] [Indexed: 11/11/2022] Open
Abstract
The presence of aminoacylase activities was investigated in a crude extract of Streptomyces ambofaciens ATCC23877. First activities catalyzing the hydrolysis of N-α or ε-acetyl-L-lysine were identified. Furthermore, the acylation of lysine and different peptides was studied and compared with results obtained with lipase B of Candida antarctica (CALB). Different regioselectivities were demonstrated for the two classes of enzymes. CALB was able to catalyze acylation only on the ε-position whereas the crude extract from S. ambofaciens possessed the rare ability to catalyze the N-acylation on the α-position of the lysine or of the amino-acid in N-terminal position of peptides. Two genes, SAM23877_1485 and SAM23877_1734, were identified in the genome of Streptomyces ambofaciens ATCC23877 whose products show similarities with the previously identified aminoacylases from Streptomyces mobaraensis. The proteins encoded by these two genes were responsible for the major aminoacylase hydrolytic activities. Furthermore, we show that the hydrolysis of N-α-acetyl-L-lysine could be attributed to the product of SAM23877_1734 gene.
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Affiliation(s)
| | | | | | - Cédric Paris
- Université de Lorraine Plateau d'Analyse Structurale et Métabolomique Nancy France
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15
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Calcagnile M, Bettini S, Damiano F, Talà A, Tredici SM, Pagano R, Di Salvo M, Siculella L, Fico D, De Benedetto GE, Valli L, Alifano P. Stimulatory Effects of Methyl-β-cyclodextrin on Spiramycin Production and Physical-Chemical Characterization of Nonhost@Guest Complexes. ACS OMEGA 2018; 3:2470-2478. [PMID: 30221219 PMCID: PMC6130790 DOI: 10.1021/acsomega.7b01766] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 01/08/2018] [Indexed: 06/08/2023]
Abstract
Spiramycin is a macrolide antibiotic and antiparasitic that is used to treat toxoplasmosis and various other infections of soft tissues. In the current study, we evaluated the effects of α-cyclodextrin, β-cyclodextrin, or methyl-β-cyclodextrin supplementation to a synthetic culture medium on biomass and spiramycin production by Streptomyces ambofaciens ATCC 23877. We found a high stimulatory effect on spiramycin production when the culture medium was supplemented with 0.5% (w/v) methyl-β-cyclodextrin, whereas α-cyclodextrin or β-cyclodextrin weakly enhanced antibiotic yields. As the stimulation of antibiotic production could be because of spiramycin complexation with cyclodextrins with effects on antibiotic stability and/or efflux, we analyzed the possible formation of complexes by physical-chemical methods. The results of Job plot experiment highlighted the formation of a nonhost@guest complex methyl-β-cyclodextrin@spiramycin I in the stoichiometric ratio of 3:1 while they excluded the formation of complex between spiramycin I and α- or β-cyclodextrin. Fourier-transform infrared spectroscopy measurements were then carried out to characterize the methyl-β-cyclodextrin@spiramycin I complex and individuate the chemical groups involved in the binding mechanism. These findings may help to improve the spiramycin fermentation process, providing at the same time a new device for better delivery of the antibiotic at the site of infection by methyl-β-cyclodextrin complexation, as it has been well-documented for other bioactive molecules.
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Affiliation(s)
- Matteo Calcagnile
- Department of Biological
and Environmental Sciences and Technologies, Department of Engineering
for Innovation, and Department of Cultural Heritage, University
of Salento, Via Monteroni, 73100 Lecce, Italy
| | - Simona Bettini
- Department of Biological
and Environmental Sciences and Technologies, Department of Engineering
for Innovation, and Department of Cultural Heritage, University
of Salento, Via Monteroni, 73100 Lecce, Italy
| | - Fabrizio Damiano
- Department of Biological
and Environmental Sciences and Technologies, Department of Engineering
for Innovation, and Department of Cultural Heritage, University
of Salento, Via Monteroni, 73100 Lecce, Italy
| | - Adelfia Talà
- Department of Biological
and Environmental Sciences and Technologies, Department of Engineering
for Innovation, and Department of Cultural Heritage, University
of Salento, Via Monteroni, 73100 Lecce, Italy
| | - Salvatore M. Tredici
- Department of Biological
and Environmental Sciences and Technologies, Department of Engineering
for Innovation, and Department of Cultural Heritage, University
of Salento, Via Monteroni, 73100 Lecce, Italy
| | - Rosanna Pagano
- Department of Biological
and Environmental Sciences and Technologies, Department of Engineering
for Innovation, and Department of Cultural Heritage, University
of Salento, Via Monteroni, 73100 Lecce, Italy
| | - Marco Di Salvo
- Department of Biological
and Environmental Sciences and Technologies, Department of Engineering
for Innovation, and Department of Cultural Heritage, University
of Salento, Via Monteroni, 73100 Lecce, Italy
| | - Luisa Siculella
- Department of Biological
and Environmental Sciences and Technologies, Department of Engineering
for Innovation, and Department of Cultural Heritage, University
of Salento, Via Monteroni, 73100 Lecce, Italy
| | - Daniela Fico
- Department of Biological
and Environmental Sciences and Technologies, Department of Engineering
for Innovation, and Department of Cultural Heritage, University
of Salento, Via Monteroni, 73100 Lecce, Italy
| | - Giuseppe E. De Benedetto
- Department of Biological
and Environmental Sciences and Technologies, Department of Engineering
for Innovation, and Department of Cultural Heritage, University
of Salento, Via Monteroni, 73100 Lecce, Italy
| | - Ludovico Valli
- Department of Biological
and Environmental Sciences and Technologies, Department of Engineering
for Innovation, and Department of Cultural Heritage, University
of Salento, Via Monteroni, 73100 Lecce, Italy
| | - Pietro Alifano
- Department of Biological
and Environmental Sciences and Technologies, Department of Engineering
for Innovation, and Department of Cultural Heritage, University
of Salento, Via Monteroni, 73100 Lecce, Italy
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16
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Genome plasticity is governed by double strand break DNA repair in Streptomyces. Sci Rep 2018; 8:5272. [PMID: 29588483 PMCID: PMC5869714 DOI: 10.1038/s41598-018-23622-w] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 03/12/2018] [Indexed: 12/22/2022] Open
Abstract
The linear chromosome of the bacterium Streptomyces exhibits a remarkable genetic organization with grossly a central conserved region flanked by variable chromosomal arms. The terminal diversity co-locates with an intense DNA plasticity including the occurrence of large deletions associated to circularization and chromosomal arm exchange. These observations prompted us to assess the role of double strand break (DSB) repair in chromosome plasticity following. For that purpose, DSBs were induced along the chromosome using the meganuclease I-SceI. DSB repair in the central region of the chromosome was mutagenic at the healing site but kept intact the whole genome structure. In contrast, DSB repair in the chromosomal arms was mostly associated to the loss of the targeted chromosomal arm and extensive deletions beyond the cleavage sites. While homologous recombination occurring between copies of DNA sequences accounted for the most part of the chromosome rescue events, Non Homologous End Joining was involved in mutagenic repair as well as in huge genome rearrangements (i.e. circularization). Further, NHEJ repair was concomitant with the integration of genetic material at the healing site. We postulate that DSB repair drives genome plasticity and evolution in Streptomyces and that NHEJ may foster horizontal transfer in the environment.
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17
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Valenzuela SV, Ferreres G, Margalef G, Pastor FJ. Fast purification method of functional LPMOs from Streptomyces ambofaciens by affinity adsorption. Carbohydr Res 2017; 448:205-211. [DOI: 10.1016/j.carres.2017.02.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 02/17/2017] [Accepted: 02/18/2017] [Indexed: 01/03/2023]
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18
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Draft Genome Sequence of Streptomyces sp. M1013, a Close Relative of Streptomyces ambofaciens and Streptomyces coelicolor. GENOME ANNOUNCEMENTS 2017; 5:5/29/e00643-17. [PMID: 28729266 PMCID: PMC5522933 DOI: 10.1128/genomea.00643-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report the draft genome sequence of Streptomyces sp. M1013, a strain isolated from the Medicago arborea rhizosphere in Izmir, Turkey. An average nucleotide identity (ANI) analysis reveals that this strain belongs to the same species as Streptomyces canus ATCC12647 and is closely related to Streptomyces ambofaciens and Streptomyces coelicolor.
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19
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Feijoo-Siota L, Rama JLR, Sánchez-Pérez A, Villa TG. Considerations on bacterial nucleoids. Appl Microbiol Biotechnol 2017; 101:5591-5602. [PMID: 28664324 DOI: 10.1007/s00253-017-8381-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 06/01/2017] [Accepted: 06/02/2017] [Indexed: 12/21/2022]
Abstract
The classic genome organization of the bacterial chromosome is normally envisaged with all its genetic markers linked, thus forming a closed genetic circle of duplex stranded DNA (dsDNA) and several proteins in what it is called as "the bacterial nucleoid." This structure may be more or less corrugated depending on the physiological state of the bacterium (i.e., resting state or active growth) and is not surrounded by a double membrane as in eukayotic cells. The universality of the closed circle model in bacteria is however slowly changing, as new data emerge in different bacterial groups such as in Planctomycetes and related microorganisms, species of Borrelia, Streptomyces, Agrobacterium, or Phytoplasma. In these and possibly other microorganisms, the existence of complex formations of intracellular membranes or linear chromosomes is typical; all of these situations contributing to weakening the current cellular organization paradigm, i.e., prokaryotic vs eukaryotic cells.
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Affiliation(s)
- Lucía Feijoo-Siota
- Department of Microbiology, Biotechnology Unit, Faculty of Pharmacy, University of Santiago de Compostela, 15706, Santiago de Compostela, Spain
| | - José Luis R Rama
- Department of Microbiology, Biotechnology Unit, Faculty of Pharmacy, University of Santiago de Compostela, 15706, Santiago de Compostela, Spain
| | - Angeles Sánchez-Pérez
- Discipline of Physiology and Bosch Institute, School of Medical Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Tomás G Villa
- Department of Microbiology, Biotechnology Unit, Faculty of Pharmacy, University of Santiago de Compostela, 15706, Santiago de Compostela, Spain.
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20
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Fondi M, Pinatel E, Talà A, Damiano F, Consolandi C, Mattorre B, Fico D, Testini M, De Benedetto GE, Siculella L, De Bellis G, Alifano P, Peano C. Time-Resolved Transcriptomics and Constraint-Based Modeling Identify System-Level Metabolic Features and Overexpression Targets to Increase Spiramycin Production in Streptomyces ambofaciens. Front Microbiol 2017; 8:835. [PMID: 28553270 PMCID: PMC5427115 DOI: 10.3389/fmicb.2017.00835] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 04/24/2017] [Indexed: 12/22/2022] Open
Abstract
In this study we have applied an integrated system biology approach to characterize the metabolic landscape of Streptomyces ambofaciens and to identify a list of potential metabolic engineering targets for the overproduction of the secondary metabolites in this microorganism. We focused on an often overlooked growth period (i.e., post-first rapid growth phase) and, by integrating constraint-based metabolic modeling with time resolved RNA-seq data, we depicted the main effects of changes in gene expression on the overall metabolic reprogramming occurring in S. ambofaciens. Moreover, through metabolic modeling, we unraveled a set of candidate overexpression gene targets hypothetically leading to spiramycin overproduction. Model predictions were experimentally validated by genetic manipulation of the recently described ethylmalonyl-CoA metabolic node, providing evidence that spiramycin productivity may be increased by enhancing the carbon flow through this pathway. The goal was achieved by over-expressing the ccr paralog srm4 in an ad hoc engineered plasmid. This work embeds the first metabolic reconstruction of S. ambofaciens and the successful experimental validation of model predictions and demonstrates the validity and the importance of in silico modeling tools for the overproduction of molecules with a biotechnological interest. Finally, the proposed metabolic reconstruction, which includes manually refined pathways for several secondary metabolites with antimicrobial activity, represents a solid platform for the future exploitation of S. ambofaciens biotechnological potential.
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Affiliation(s)
- Marco Fondi
- Department of Biology, University of FlorenceFlorence, Italy
| | - Eva Pinatel
- Institute of Biomedical Technologies, National Research CouncilSegrate, Italy
| | - Adelfia Talà
- Department of Biological and Environmental Sciences and Technologies, University of SalentoLecce, Italy
| | - Fabrizio Damiano
- Department of Biological and Environmental Sciences and Technologies, University of SalentoLecce, Italy
| | - Clarissa Consolandi
- Institute of Biomedical Technologies, National Research CouncilSegrate, Italy
| | | | - Daniela Fico
- Laboratory of Analytical and Isotopic Mass Spectrometry, Department of Cultural Heritage, University of SalentoLecce, Italy
| | - Mariangela Testini
- Department of Biological and Environmental Sciences and Technologies, University of SalentoLecce, Italy
| | - Giuseppe E De Benedetto
- Laboratory of Analytical and Isotopic Mass Spectrometry, Department of Cultural Heritage, University of SalentoLecce, Italy
| | - Luisa Siculella
- Department of Biological and Environmental Sciences and Technologies, University of SalentoLecce, Italy
| | - Gianluca De Bellis
- Institute of Biomedical Technologies, National Research CouncilSegrate, Italy
| | - Pietro Alifano
- Department of Biological and Environmental Sciences and Technologies, University of SalentoLecce, Italy
| | - Clelia Peano
- Institute of Biomedical Technologies, National Research CouncilSegrate, Italy
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21
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Toussaint M, Bontemps C, Besserer A, Hotel L, Gérardin P, Leblond P. Whole-cell biosensor of cellobiose and application to wood decay detection. J Biotechnol 2016; 239:39-46. [DOI: 10.1016/j.jbiotec.2016.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 10/03/2016] [Accepted: 10/06/2016] [Indexed: 12/18/2022]
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22
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Hoff G, Bertrand C, Zhang L, Piotrowski E, Chipot L, Bontemps C, Confalonieri F, McGovern S, Lecointe F, Thibessard A, Leblond P. Multiple and Variable NHEJ-Like Genes Are Involved in Resistance to DNA Damage in Streptomyces ambofaciens. Front Microbiol 2016; 7:1901. [PMID: 27965636 PMCID: PMC5124664 DOI: 10.3389/fmicb.2016.01901] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 11/14/2016] [Indexed: 11/26/2022] Open
Abstract
Non-homologous end-joining (NHEJ) is a double strand break (DSB) repair pathway which does not require any homologous template and can ligate two DNA ends together. The basic bacterial NHEJ machinery involves two partners: the Ku protein, a DNA end binding protein for DSB recognition and the multifunctional LigD protein composed a ligase, a nuclease and a polymerase domain, for end processing and ligation of the broken ends. In silico analyses performed in the 38 sequenced genomes of Streptomyces species revealed the existence of a large panel of NHEJ-like genes. Indeed, ku genes or ligD domain homologues are scattered throughout the genome in multiple copies and can be distinguished in two categories: the “core” NHEJ gene set constituted of conserved loci and the “variable” NHEJ gene set constituted of NHEJ-like genes present in only a part of the species. In Streptomyces ambofaciens ATCC23877, not only the deletion of “core” genes but also that of “variable” genes led to an increased sensitivity to DNA damage induced by electron beam irradiation. Multiple mutants of ku, ligase or polymerase encoding genes showed an aggravated phenotype compared to single mutants. Biochemical assays revealed the ability of Ku-like proteins to protect and to stimulate ligation of DNA ends. RT-qPCR and GFP fusion experiments suggested that ku-like genes show a growth phase dependent expression profile consistent with their involvement in DNA repair during spores formation and/or germination.
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Affiliation(s)
- Grégory Hoff
- UMR 1128, Dynamique des Génomes et Adaptation Microbienne, Université de LorraineVandœuvre-lès-Nancy, France; UMR 1128, Institut National de la Recherche Agronomique, Dynamique des Génomes et Adaptation MicrobienneVandœuvre-lès-Nancy, France
| | - Claire Bertrand
- UMR 1128, Dynamique des Génomes et Adaptation Microbienne, Université de LorraineVandœuvre-lès-Nancy, France; UMR 1128, Institut National de la Recherche Agronomique, Dynamique des Génomes et Adaptation MicrobienneVandœuvre-lès-Nancy, France
| | - Lingli Zhang
- UMR 1128, Dynamique des Génomes et Adaptation Microbienne, Université de LorraineVandœuvre-lès-Nancy, France; UMR 1128, Institut National de la Recherche Agronomique, Dynamique des Génomes et Adaptation MicrobienneVandœuvre-lès-Nancy, France
| | - Emilie Piotrowski
- UMR 1128, Dynamique des Génomes et Adaptation Microbienne, Université de LorraineVandœuvre-lès-Nancy, France; UMR 1128, Institut National de la Recherche Agronomique, Dynamique des Génomes et Adaptation MicrobienneVandœuvre-lès-Nancy, France
| | - Ludovic Chipot
- UMR 1128, Dynamique des Génomes et Adaptation Microbienne, Université de LorraineVandœuvre-lès-Nancy, France; UMR 1128, Institut National de la Recherche Agronomique, Dynamique des Génomes et Adaptation MicrobienneVandœuvre-lès-Nancy, France
| | - Cyril Bontemps
- UMR 1128, Dynamique des Génomes et Adaptation Microbienne, Université de LorraineVandœuvre-lès-Nancy, France; UMR 1128, Institut National de la Recherche Agronomique, Dynamique des Génomes et Adaptation MicrobienneVandœuvre-lès-Nancy, France
| | - Fabrice Confalonieri
- Institute for Integrative Biology of the Cell (I2BC), CEA, Centre National de la Recherche Scientifique, Université Paris-Sud Orsay, France
| | - Stephen McGovern
- Institut Micalis, INRA, AgroParisTech, Université Paris-Saclay Jouy-en-Josas, France
| | - François Lecointe
- Institut Micalis, INRA, AgroParisTech, Université Paris-Saclay Jouy-en-Josas, France
| | - Annabelle Thibessard
- UMR 1128, Dynamique des Génomes et Adaptation Microbienne, Université de LorraineVandœuvre-lès-Nancy, France; UMR 1128, Institut National de la Recherche Agronomique, Dynamique des Génomes et Adaptation MicrobienneVandœuvre-lès-Nancy, France
| | - Pierre Leblond
- UMR 1128, Dynamique des Génomes et Adaptation Microbienne, Université de LorraineVandœuvre-lès-Nancy, France; UMR 1128, Institut National de la Recherche Agronomique, Dynamique des Génomes et Adaptation MicrobienneVandœuvre-lès-Nancy, France
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23
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Klich K, Pyta K, Kubicka MM, Ruszkowski P, Celewicz L, Gajecka M, Przybylski P. Synthesis, Antibacterial, and Anticancer Evaluation of Novel Spiramycin-Like Conjugates Containing C(5) Triazole Arm. J Med Chem 2016; 59:7963-73. [PMID: 27501415 DOI: 10.1021/acs.jmedchem.6b00764] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Huisgen cycloaddition allowed obtaining of novel triazole-bridged antibiotics (6-16) with the reconstructed C(5) arm of spiramycin. (1)H-(1)H NOESY couplings indicated the structure of novel derivatives in solution and demonstrated that the rebuilt C(5) arm is slightly differently oriented relative to the aglycone part if compared to that of spiramycin (1). Combined analysis of biological data together with experimentally determined lipophilicity (clogP) and solubility show the importance of the chemical nature of the newly introduced triazole C(5) arm in the presence of attractive antibacterial and anticancer potency. The most cytotoxic active triazole conjugates having a hydrophobic and bulky C(5) arm showed higher selectivity toward cancer cell lines (HeLa, KB, MCF-7, Hep-G2, and U87) relative to HDF normal cells than that of the parent spiramycin. Our studies have demonstrated that the aldehyde group is not crucial for the presence of interesting antibacterial [MIC(S. pneumoniae) ∼ 1.2 μM] and anticancer [IC50(HepG2) ∼ 6 μM] properties of 16-membered lactone macrolides based on spiramycin's aglycone.
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Affiliation(s)
- Katarzyna Klich
- Faculty of Chemistry, Adam Mickiewicz University , Umultowska 89b, 61-614 Poznan, Poland
| | - Krystian Pyta
- Faculty of Chemistry, Adam Mickiewicz University , Umultowska 89b, 61-614 Poznan, Poland
| | - Marcelina M Kubicka
- Department of Genetics and Pharmaceutical Microbiology, University of Medical Sciences , Swiecickiego 4, 60-781 Poznan, Poland
| | - Piotr Ruszkowski
- Department of Pharmacology, University of Medical Sciences , Rokietnicka 5a, 60-806 Poznan, Poland
| | - Lech Celewicz
- Faculty of Chemistry, Adam Mickiewicz University , Umultowska 89b, 61-614 Poznan, Poland
| | - Marzena Gajecka
- Department of Genetics and Pharmaceutical Microbiology, University of Medical Sciences , Swiecickiego 4, 60-781 Poznan, Poland.,Institute of Human Genetics, Polish Academy of Sciences , Strzeszynska 32, 60-479 Poznan, Poland
| | - Piotr Przybylski
- Faculty of Chemistry, Adam Mickiewicz University , Umultowska 89b, 61-614 Poznan, Poland
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Gifted microbes for genome mining and natural product discovery. J Ind Microbiol Biotechnol 2016; 44:573-588. [PMID: 27520548 DOI: 10.1007/s10295-016-1815-x] [Citation(s) in RCA: 170] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 07/30/2016] [Indexed: 10/21/2022]
Abstract
Actinomycetes are historically important sources for secondary metabolites (SMs) with applications in human medicine, animal health, and plant crop protection. It is now clear that actinomycetes and other microorganisms with large genomes have the capacity to produce many more SMs than was anticipated from standard fermentation studies. Indeed ~90 % of SM gene clusters (SMGCs) predicted from genome sequencing are cryptic under conventional fermentation and analytical analyses. Previous studies have suggested that among the actinomycetes with large genomes, some have the coding capacity to produce many more SMs than others, and that strains with the largest genomes tend to be the most gifted. These contentions have been evaluated more quantitatively by antiSMASH 3.0 analyses of microbial genomes, and the results indicate that many actinomycetes with large genomes are gifted for SM production, encoding 20-50 SMGCs, and devoting 0.8-3.0 Mb of coding capacity to SM production. Several Proteobacteria and Firmacutes with large genomes encode 20-30 SMGCs and devote 0.8-1.3 Mb of DNA to SM production, whereas cultured bacteria and archaea with small genomes devote insignificant coding capacity to SM production. Fully sequenced genomes of uncultured bacteria and archaea have small genomes nearly devoid of SMGCs.
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25
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Complete Genome Sequence of Streptomyces ambofaciens DSM 40697, a Paradigm for Genome Plasticity Studies. GENOME ANNOUNCEMENTS 2016; 4:4/3/e00470-16. [PMID: 27257195 PMCID: PMC4891641 DOI: 10.1128/genomea.00470-16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The sequence of Streptomyces ambofaciens DSM 40697 was completely determined. The genome consists of an 8.1-Mbp linear chromosome with terminal inverted repeats of 210 kb. Genomic islands were identified, one of which corresponds to a new putative integrative and conjugative element (ICE) called pSAM3.
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