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Streptomyces

Streptomyces: A genus of actinobacteria known for their diverse secondary metabolite production.
These soil-dwelling, filamentous bacteria are a rich source of clinically important antibiotics, antitumor agents, and other bioactive compounds.
Streptomyces research is crucial for the discovery and optimization of novel therapeutic leads.
PubCompare.ai is an innovative tool that leverages AI to streamline Streptomyces experimentation, enhacing reproducibility and unlocking new insights through comparisons of literature, preprints, and patents.
Optimize your Streptomyces reserch with this powerful platform and elevate your discoveries.

Most cited protocols related to «Streptomyces»

A set of 2,831 Actinobacterial genomes was downloaded from NCBI by querying for "Whole genome shotgun sequencing project" or "Complete genome" in combination with the taxonomic identifier for actinobacteria. The Propionibacteriales, Micrococcales, Corynebacteriales and Bifidobacteriales orders were excluded, as they contain large numbers of genomes without relevant natural product-producing capacity, except the Nocardiaceae family from the Corynebacteriales (see next section). To these set, 249 additional draft assemblies from the Metcalf lab were added (e.g. Streptomyces sp. B-1348. See BioProject PRJNA488366). Draft genome assemblies from this BioProject were obtained by using SPAdes50 (link) with default options.
All files were processed with antiSMASH v417 (link) (parameters: --minimal). The antiSMASH-annotated genome sequences are available as Online Data (antiSMASH_results_Metcalf_B, antiSMASH_results_Metcalf_J and antiSMASH_results_NCBI).
To the resulting 73,260 predicted Biosynthetic Gene Clusters (BGCs), 1,393 more were added from the Minimum Information about a Biosynthetic Gene Cluster database (MIBiG21 (link), release 1.3, August 2016, antiSMASH-analyzed versions from each entry) as reference data.
This final BGC set was then analyzed with BiG-SCAPE using version 31 of the Pfam database. The “hybrids” mode, which allows BGCs with mixed annotations be analyzed in their individual Class sets (e.g. a BGC annotated as lantipeptide-t1pks will be analyzed as both a RiPP and a PKSI) was enabled. Two results sets were created (Online Data: BiG-SCAPE Results network files): one with the default "global" mode enabled, and the other with "glocal" mode enabled (See Fig. 2).
Publication 2019
Actinomycetes Anabolism Gene Clusters Genome Hybrids Natural Products Nocardiaceae Streptomyces
MS/MS spectra for crude extracts of S. roseosporus and Streptomyces sp. DSM were collected as previously described37 (link). Briefly, MS/MS spectra were collected using direct infusion using an Advion nanomate-electrospray robot and capillary liquid chromatography using a manually pulled 10 cm silica capillary packed with C18 reverse phase resin. Samples were introduced for capillary LC using a Surveyor system using a 10mL injection (10 ng/μL in 10% ACN). Metabolites were separated using a time variant gradient [(minutes, % of solvent B): (20, 5), (30, 60), (75, 95) where solvent A is water with 0.1% AcOH and B is ACN with 0.1% AcOH] using a 200mL flowrate (1% to instrument source with 1.8kV source voltage). Both methods utilized detection by a Thermo Finnigan LTQ/FT-ICR mass spectrometer. The mass spectrometer was operated in data dependent positive ion mode; automatically switching between full scan high resolution FT MS and low resolution LTQ MS/MS acquisitions. Full scan MS spectra were acquired in the FT and the top six most intense ions in a particular scan were fragmented using collision induced dissociation (CID) at a constant collision energy of 35eV, an activation Q of 0.25, and an activation time of 50 to 80 ms. RAW files were converted to .mzXML using ReAdW.
Publication 2016
Capillaries Complex Extracts Ions Liquid Chromatography Radionuclide Imaging Resins, Plant Silicon Dioxide Solvents Streptomyces Tandem Mass Spectrometry
A molecular network was created at GNPS data from the S. roseosporus and Streptomyces sp. DSM5940 MS/MS data. The specific job is browse-able online (link). Full parameters can be found in Supplementary Table 11.
Publication 2016
Streptomyces Tandem Mass Spectrometry
Plasmid pCRISPomyces-1 was constructed via yeast homologous recombination28 (link) from the following fragments: promoter rpsLp(XC),18 (link) synthesized as a gBlock (Integrated DNA Technologies, Coralville, IA) to remove BbsI recognition sites; codon-optimized Spcas9, along with the wild-type fd terminator, synthesized by GenScript (Piscataway, NJ); promoter rpsLp(CF), PCR amplified from a previous construct;18 (link) tracrRNA, oop terminator, promoter gapdhp(EL),18 (link) a lacZ expression cassette flanked by BbsI recognition sites and direct repeat sequences, and a T7 terminator, synthesized as a gBlock (IDT); yeast helper fragment containing URA3 and CEN6/ARS4 flanked by XbaI recognition sites, PCR amplified from pRS416 (Stratagene, La Jolla, CA); and an E. coli/Streptomyces helper fragment containing origin colE1, selection marker aac(3)IV, pSG5 rep origin, and origin of transfer oriT, PCR amplified in two pieces from plasmid pJVD52.126 (link) to remove a BbsI recognition site in pSG5 rep. The resulting intermediate plasmid was then digested with XbaI to liberate the yeast helper fragment, and the backbone was re-ligated to yield pCRISPomyces-1. Plasmid pCRISPomyces-2 was constructed via isothermal assembly of the EcoRI/XbaI-digested pCRISPomyces-1 backbone with two synthetic gBlocks (IDT) comprising a guide RNA expression cassette (with a BbsI-flanked lacZ cassette in place of the spacer sequence). All targeting constructs were assembled by a combination of Golden Gate assembly29 (link) (for insertion of spacers) and traditional digestion/ligation or isothermal assembly30 (link) (for insertion of editing templates). Single spacer inserts were generated by annealing two 24 nt oligonucleotides (offset by 4 nt to generate sticky ends), while double spacer inserts were synthesized as gBlocks (IDT). The 1 kb left and right arms of each editing template were amplified from purified genomic DNA, spliced by overlap-extension PCR,31 (link) and ligated into the XbaI site of the desired plasmid. Correct plasmid assembly was confirmed by diagnostic digestion and sequencing (GeneWiz, South Plainfield, NJ). Plasmid maps were generated with Vector NTI (Invitrogen, Carlsbad, CA).
Publication 2014
Arm, Upper Cloning Vectors Codon crRNA, Transactivating Deoxyribonuclease EcoRI Diagnosis Digestion Direct Repeat Gene Transfer, Horizontal Genome LacZ Genes Ligation Microtubule-Associated Proteins Oligonucleotides Plasmids Saccharomyces cerevisiae Streptomyces Transcription, Genetic Vertebral Column
I used the NCBI BLAST 16S rRNA database (BLAST16S) (Sayers et al., 2012 (link)), downloaded July 1, 2017, the RDP 16S rRNA training set v16 (RDP16S) and the Warcup fungal ITS training set v2 (WITS) (Deshpande et al., 2015 (link)). The sequences and taxonomy annotations for these databases were mostly obtained from authoritatively named isolate strains. While there could be some errors in the taxonomy annotations, I pragmatically considered them to be authoritative and used them as truth standards for the benchmark tests. BLAST16S and the RDP 16S rRNA training set have highly uneven numbers of sequences per genus. For example, ∼40% (950/2,273) of the genera in BLAST16S have only a single sequence while the most abundant genus, Streptomyces, has 1,162 sequences, more than all singletons combined. To investigate the effects of uneven representation and create a more balanced reference, I created a subset (BLAST16S/10) by imposing a maximum of 10 sequences per genus; sequences were discarded at random as needed to meet this constraint. I also considered two larger databases: the subset of Greengenes clustered at 97% identity (GG97) which is the default 16S rRNA reference database in QIIME v1, and UNITE (Kõljalg et al., 2013 (link)). GG97 and UNITE were not used as truth standards because most of their taxonomy annotations are computational or manual predictions. To investigate prediction performance with shorter sequences, I extracted the V4 and V3–V5 segments from BLAST16S and BLAST16S/10 using V4 primer sequences from Kozich et al. (2013) (link) and V3–V5 primer sequences from Methé et al. (2012) (link). Sequence error was not modeled because state-of-the-art methods are able to extract highly accurate sequences from noisy next-generation reads (Edgar, 2013 (link); Callahan et al., 2016 (link)).
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Publication 2018
Oligonucleotide Primers RNA, Ribosomal, 16S Strains Streptomyces Unite resin

Most recents protocols related to «Streptomyces»

Centrifuge the cells (3000 rpm,
10 min) and then collect the supernatant
to remove cell debris. Add a mixture containing 20 μL of the
bead mixture, 20 μL of the sample solution, and 20 μL
of the assay antibody mixture incubated for a 96-well filter plate
and for 2 h at 500 rpm in the dark environment. Then, 20 μL
of PE-labeled Streptomyces-plant cyanate
(SA-PE) solution is put in the wells for 30 min (500 rpm) at room
temperature. Lastly, the corresponding fluorescence is measured by
flow cytometry and the level of intracellular cytokines in the sample
is obtained by analyzing the fluorescence intensity of the immune
complex; fluorescence data were collected using BD FACS Diva software
and intracellular cytokine levels were evaluated using FCAP Array
3.0 analysis software.31 (link)
Publication 2023
Biological Assay Cells Complex, Immune Cyanates Cytokine Fluorescence Immunoglobulins Plants Protoplasm Streptomyces
Fragile genomic sites, such as inverted repeats or transposable elements are common in the genome of Streptomyces. Because they are easily copied (or translocated) we assume that they can also be spontaneously generated with a small probability μn (independent of genome size). The new fragile site is inserted at a random location in the genome.
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Publication 2023
Chromosome Fragile Sites DNA Transposable Elements Genome Streptomyces
Fragile sites are the cause of genome instability in the model. We let fragile sites cause large‐scale chromosomal mutations with a per‐fragile site probability μf. We take into account that large‐scale mutations in Streptomyces preferentially disrupt telomeric regions (Chen et al, 2002 (link); Hopwood, 2006 (link); Hoff et al, 2018 (link); Tidjani et al, 2020 (link)) by letting fragile site‐induced mutations delete the entire chromosomal region downstream (i.e., to the right) of the genomic location of the fragile site (see Fig 1C). Effectively, this means that we model one arm of the chromosome, and that the model centromere and telomere result from the asymmetric effect of fragile site deletions. No other type of mutation has any left/right preference in the model.
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Publication 2023
Centromere Chromosome Fragile Sites Chromosomes Gene Deletion Genome Genomic Instability Mutation Streptomyces Telomere
Isotopically labeled reagents and OminPur® Pronase E (4,000 U/mg) were purchased from Sigma Aldrich. GCMS data were acquired with an Agilent 7890 GC with a 30-m × 250-μm × 0.25-mm HP 5-ms UI capillary column and Agilent G7081B MSD. High-resolution mass spectrometry data were acquired with an Agilent 6230 TOF LC/MS System (Agilent Technologies) equipped with a ZORBAX Eclipse XDB C18 column (5 μm, 150 × 4.6 mm). NMR data were recorded at 400 MHz for 1H and 100 MHz for 13C with a Varian Inova NMR spectrometer (Agilent). 13C NMR for [2,4,6,8,10,12,14,17,19,21,23,25,27-13C]TNM A was acquired using a Bruker NEO 600 MHz (14.1 T) NMR spectrometer equipped with four-channel, 24 slot SampleCase, and a triple resonance (HCN) CryoProbe. The gene encoding SgcE was coexpressed in pET30Xa-LIC vector with SgcE10 in pCDF-F2-EK-LIC vector as previously described (19 (link)). The gene encoding DynE8 was coexpressed in pET30Xa-LIC vector with SgcE10 in pCDF-2-EK-LIC vector. The TNM A-producing strain Streptomyces sp. CB03234 and the generation of the PKSE (ΔtmnE) mutant strain SB20001 were previously described (16 (link)). The DYN A-producing strain Micromonospora chersina ATCC 53710 and the generation of the PKSE (ΔdynE7) mutant strain were previously described (15 ).
Publication 2023
Capillaries Carbon-13 Magnetic Resonance Spectroscopy Cloning Vectors Gas Chromatography-Mass Spectrometry Genes Mass Spectrometry Micromonospora chersina Pronase E Strains Streptomyces Vibration
Streptomyces sp. R2 (MTCC5597; DSM26035) (hereafter mentioned as R2) was maintained as slant stock in yeast extract & malt extract (YEME-Himedia, India) agar comprised of50% seawater, glycerol stock in 30% glycerol as well as in lyophilized form. Cultures were revived on fresh YEME agar plates after incubation for 7–10 days at 28°C. The crude ethyl acetate extracts fromR2 grown agar media were purified by adopting the preparative HPLC to yield TR with more than 98% purity. Mycobacterial clinical and laboratory standard strain H37Rv were grown on Lowenstein Jenson (LJ) egg-based media. While testing the in-vitro anti-TB Middlebrook 7H9 liquid media supplemented with oleic acid, albumin, dextrose, and catalase (OADC) (BD Biosciences) were used. All the Mtb cultures were incubated at 37°C unless stated otherwise.
Balb/c / Swiss Albino Mice weighing 20–25g, Duncan Hartley Guinea pigs weighing 350–400g and Sprague Dawley rats weighing 180–200g were used. In all the experiments, an equal number of male and female animals were used. The animals were maintained at 24 ± 2°C, 50 to 60% relative humidity, with a 12 hours light-dark cycle. All the animals were acclimatized to laboratory conditions, at least 7 days before conducting tests. Entire in-vivo studies were carried out in the BSL3 animal house of the National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, India. Each group of animals was kept in separate isolators to prevent cross-infection between the animals. This study was approved by the Institutional Ethics Committee (IEC) of the National Institute for Research in Tuberculosis (001/NIRT-IEC/2019 dt.02.01.2019) and Institutional Animal Ethics committee of National JALMA Institute for Leprosy and Other Mycobacterial Diseases (NJIL&OMD/3-IAEC/2019-01 dt. 26.07.2019).
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Publication 2023
Agar Albinism Albumins Animals Catalase Cavia Cross Infection ethyl acetate Females Glucose Glycerin High-Performance Liquid Chromatographies Humidity Institutional Ethics Committees Leprosy Males Mice, Inbred BALB C Mycobacterium Mycobacterium Infections Oleic Acid Rats, Sprague-Dawley Strains Streptomyces Tuberculosis Yeast, Dried

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Hyaluronidase from Streptomyces hyalurolyticus is an enzyme that catalyzes the hydrolysis of hyaluronic acid, a major component of the extracellular matrix. This enzyme is produced by the bacterium Streptomyces hyalurolyticus.
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Tunicamycin is a natural product isolated from the bacterium Streptomyces sp. It functions as an inhibitor of N-linked glycosylation, a process involved in the synthesis of glycoproteins.
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Streptomyces hyaluronidase is an enzyme derived from the bacterium Streptomyces species. It functions by catalyzing the hydrolysis of hyaluronic acid, a major component of the extracellular matrix.

More about "Streptomyces"

Streptomyces are a genus of Actinobacteria, a diverse group of soil-dwelling, filamentous bacteria renowned for their remarkable ability to produce a wide array of secondary metabolites.
These microorganisms are a rich source of clinically important compounds, including antibiotics, antitumor agents, and other bioactive molecules.
Streptomyces research is crucial for the discovery and optimization of novel therapeutic leads.
The Streptomyces genus encompasses a vast array of species, each with the potential to unlock new and exciting discoveries.
For example, Streptomyces hyalurolyticus is a well-known producer of the enzyme hyaluronidase, which has various applications in the life sciences.
Similarly, Streptomyces sp. are known to produce the antifungal compound tunicamycin, which has been widely used in research.
To streamline Streptomyces experimentation and enhance reproducibility, researchers can utilize innovative tools like PubCompare.ai.
This AI-driven platform enables the comparison of literature, preprints, and patents, allowing scientists to identify the best protocols and products for their Streptomyces research.
By leveraging the power of artificial intelligence, PubCompare.ai can help unlock new insights and elevate the discoveries made in Streptomyces research.
In addition to PubCompare.ai, researchers working with Streptomyces may also employ a variety of common laboratory tools and reagents, such as the Wizard Genomic DNA Purification Kit for extracting high-quality genomic DNA, the QIAquick Gel Extraction Kit for purifying DNA fragments from agarose gels, and restriction endonucleases for precise genetic manipulation.
The QIAprep Spin Miniprep Kit can be used for plasmid purification, while bovine serum albumin (BSA) is a versatile protein often used in buffer solutions.
By combining the insights gained from the MeSH term description, the metadescription, and the additional information provided, researchers can optimize their Streptomyces research and unlock new possibilities in the realm of secondary metabolite discovery and therapeutic development.
Remember, even the most experienced scientists can make a typo now and then, so don't be surprised if you find one in this text.