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Microbial Genomics Jan 2022The development of spots or lesions symptomatic of common scab on root and tuber crops is caused by few pathogenic with 87-22 as the model species. Thaxtomin... (Comparative Study)
Comparative Study
The development of spots or lesions symptomatic of common scab on root and tuber crops is caused by few pathogenic with 87-22 as the model species. Thaxtomin phytotoxins are the primary virulence determinants, mainly acting by impairing cellulose synthesis, and their production in is in turn boosted by cello-oligosaccharides released from host plants. In this work we aimed to determine which molecules and which biosynthetic gene clusters (BGCs) of the specialized metabolism of 87-22 show a production and/or a transcriptional response to cello-oligosaccharides. Comparative metabolomic analyses revealed that molecules of the virulome of induced by cellobiose and cellotriose include (i) thaxtomin and concanamycin phytotoxins, (ii) desferrioxamines, scabichelin and turgichelin siderophores in order to acquire iron essential for housekeeping functions, (iii) ectoine for protection against osmotic shock once inside the host, and (iv) bottromycin and concanamycin antimicrobials possibly to prevent other microorganisms from colonizing the same niche. Importantly, both cello-oligosaccharides reduced the production of the spore germination inhibitors germicidins thereby giving the 'green light' to escape dormancy and trigger the onset of the pathogenic lifestyle. For most metabolites - either with induced or reduced production - cellotriose was revealed to be a slightly stronger elicitor compared to cellobiose, supporting an earlier hypothesis which suggested the trisaccharide was the real trigger for virulence released from the plant cell wall through the action of thaxtomins. Interestingly, except for thaxtomins, none of these BGCs' expression seems to be under direct control of the cellulose utilization repressor CebR suggesting the existence of a yet unknown mechanism for switching on the virulome. Finally, a transcriptomic analysis revealed nine additional cryptic BGCs that have their expression awakened by cello-oligosaccharides, suggesting that other and yet to be discovered metabolites could be part of the virulome of .
Topics: Biosynthetic Pathways; Cellobiose; Cellulose; Gene Expression Profiling; Gene Expression Regulation, Bacterial; Macrolides; Metabolomics; Multigene Family; Piperazines; Plant Tubers; RNA-Seq; Streptomyces; Trioses; Virulence Factors
PubMed: 35040428
DOI: 10.1099/mgen.0.000760 -
Microbiological Research Jan 2017Biological Nitrogen Fixation is critical for ecosystem productivity. Select members of Bacteria and Archaea express a nitrogenase enzyme complex that reduces atmospheric...
Biological Nitrogen Fixation is critical for ecosystem productivity. Select members of Bacteria and Archaea express a nitrogenase enzyme complex that reduces atmospheric nitrogen to ammonia. Several nitrogen fixing bacteria form symbiotic associations with plants, but free-living diazotrophs also contribute a substantial amount of nitrogen to ecosystems. The aim of this study was to isolate and characterize free-living diazotrophs in arid lands of South Dakota Badlands. Samples were obtained from sod tables and the surrounding base in spring and fall. Diazotrophs were isolated on solid nitrogen free medium (NFM) under hypoxic conditions, and their16S rRNA and nifH genes sequenced. nifH was also amplified directly from soil DNA extracts. The 16S rRNA gene data indicated a diversity of putative free-living diazotrophs across 4 phyla (Actinomycetes, Proteobacteria, Bacteroidetes, and Firmicutes), but ∼50% of these clustered with Streptomyces. These Streptomyces isolates grew in liquid NFM in an ammonia-depleted environment. Only 5 of these yielded a nifH gene product using the PolF/PolR primer set. Four of these aligned with nifH of the cyanobacteria Scytonema and Nostoc, and the other one aligned with nifH of Bradyrhizobium. Six selected Streptomyces isolates, three of which were nifH positive by PCR, all indicated N incorporation, providing strong support of nitrogen fixation. All nifH amplicons from soil DNA extract resembled Cyanobacteria. This is the first known report of diazotrophic Streptomyces, other than the thermophilic, autotrophic S. thermoautotrophicus. nifH genes of these Streptomyces were related to those from Cyanobacteria. It is possible that the cyanobacteria-like nifH amplicons obtained from soil DNA were associated with Streptomyces.
Topics: Biodiversity; Cluster Analysis; Culture Media; DNA, Bacterial; DNA, Ribosomal; Nitrogen Fixation; Oxidoreductases; Phylogeny; Polymerase Chain Reaction; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; South Dakota; Streptomyces
PubMed: 28024524
DOI: 10.1016/j.micres.2016.11.004 -
Brazilian Journal of Microbiology :... 2018A bacterium isolated from Sterkfontein dam was confirmed to produce bioflocculant with excellent flocculation activity. The 16S rDNA nucleotide sequence analyses...
A bacterium isolated from Sterkfontein dam was confirmed to produce bioflocculant with excellent flocculation activity. The 16S rDNA nucleotide sequence analyses revealed the bacteria to have 99% similarity to Streptomyces platensis strain HBUM174787 and the sequence was deposited in the Genbank as Streptomyces platensis with accession number FJ 486385.1. Culture conditions for optimal production of the bioflocculant included glucose as a sole carbon source, resulting in flocculating activity of 90%. Other optimal conditions included: peptone as nitrogen source; presence of Mg as cations and inoculum size of 1.0% (v/v) at neutral pH of 7. Optimum dose of the purified bioflocculant for the clarification of 4g/L kaolin clay suspension at neutral pH was 0.2mg/mL. Energy Dispersive X-ray analysis confirmed elemental composition of the purified bioflocculant in mass proportion (%w/w): carbon (21.41), oxygen (35.59), sulphur (26.16), nitrogen (0.62) and potassium (7.48). Fourier Transform Infrared Spectroscopy (FTIR) indicated the presence of hydroxyl, carboxyl, methoxyl and amino group in the bioflocculant. The bioflocculant produced by S. platensis removed chemical oxygen demand (COD) in river water and meat processing wastewater at efficiencies of 63.1 and 46.6% respectively and reduced their turbidity by 84.3 and 75.6% respectively. The high flocculating rate and removal efficiencies displayed by S. platensis suggests its industrial application in wastewater treatment.
Topics: Bacterial Proteins; Carbon; Flocculation; Nitrogen; Rivers; Streptomyces; Wastewater; Water Microbiology; Water Purification
PubMed: 29674102
DOI: 10.1016/j.bjm.2017.02.013 -
Journal of Bacteriology Jul 2016We recently described 13-deoxytetrodecamycin, a new member of the tetrodecamycin family of antibiotics. A defining feature of these molecules is the presence of a...
UNLABELLED
We recently described 13-deoxytetrodecamycin, a new member of the tetrodecamycin family of antibiotics. A defining feature of these molecules is the presence of a five-membered lactone called a tetronate ring. By sequencing the genome of a producer strain, Streptomyces sp. strain WAC04657, and searching for a gene previously implicated in tetronate ring formation, we identified the biosynthetic genes responsible for producing 13-deoxytetrodecamycin (the ted genes). Using the ted cluster in WAC04657 as a reference, we found related clusters in three other organisms: Streptomyces atroolivaceus ATCC 19725, Streptomyces globisporus NRRL B-2293, and Streptomyces sp. strain LaPpAH-202. Comparing the four clusters allowed us to identify the cluster boundaries. Genetic manipulation of the cluster confirmed the involvement of the ted genes in 13-deoxytetrodecamycin biosynthesis and revealed several additional molecules produced through the ted biosynthetic pathway, including tetrodecamycin, dihydrotetrodecamycin, and another, W5.9, a novel molecule. Comparison of the bioactivities of these four molecules suggests that they may act through the covalent modification of their target(s).
IMPORTANCE
The tetrodecamycins are a distinct subgroup of the tetronate family of secondary metabolites. Little is known about their biosynthesis or mechanisms of action, making them an attractive subject for investigation. In this paper we present the biosynthetic gene cluster for 13-deoxytetrodecamycin in Streptomyces sp. strain WAC04657. We identify related clusters in several other organisms and show that they produce related molecules.
Topics: Anti-Bacterial Agents; Bacterial Proteins; Biosynthetic Pathways; Furans; Multigene Family; Streptomyces
PubMed: 27137499
DOI: 10.1128/JB.00140-16 -
Archives of Razi Institute Oct 2021The bacterial isolates were obtained from the soil and cultivated in a wheat bran medium, which was used to produce the L-glutamate oxidase enzyme. The extracellular...
The bacterial isolates were obtained from the soil and cultivated in a wheat bran medium, which was used to produce the L-glutamate oxidase enzyme. The extracellular enzyme was then extracted using a cooling centrifugation process to obtain the filtrate that represents the crude enzyme. Afterward, the enzyme purification processes were carried out which included precipitation with ammonium sulfate as a preliminary purification step followed by dialysis to remove the salts. Next, ion-exchange chromatography and gel filtration were used to finish the purification process, and the enzyme activity was determined for each purification step. The results of purification of L-glutamate oxidase enzyme from using ammonium sulfate showed that the specific activity was 8.25 units/mg protein with a saturation ratio of 60%. Moreover, the results of purification using a dialysis tube indicated that the specific activity was 9.5 units/mg protein. In addition, the result of purification using diethylaminoethyl cellulose ion column revealed that the specific activity was 25 unit/mg protein and the results of purification using gel filtration showed that the specific activity was 56 units/mg protein which was the best step in the purification process due to high specific activity of the enzyme. The optimum temperature and pH for the activity and stability of the enzyme were tested. Based on the findings, the optimum temperature for the activity of the enzyme was 37 °C. In addition, it was found that the optimum temperature range for the stability of the enzyme was 30-50 °C. Besides, the optimum pH for the activity was 7.0 and the optimum pH range for the enzyme stability was 5.0-7.0.
Topics: Amino Acid Oxidoreductases; Animals; Bacterial Proteins; Enzyme Stability; Hydrogen-Ion Concentration; Streptomyces
PubMed: 35096313
DOI: 10.22092/ari.2021.355928.1738 -
BMC Microbiology Jun 2024Antimicrobial resistance (AMR) is a serious worldwide public health concern that needs immediate action. Probiotics could be a promising alternative for fighting...
BACKGROUND
Antimicrobial resistance (AMR) is a serious worldwide public health concern that needs immediate action. Probiotics could be a promising alternative for fighting antibiotic resistance, displaying beneficial effects to the host by combating diseases, improving growth, and stimulating the host immune responses against infection. This study was conducted to evaluate the probiotic, antibacterial, and antibiofilm potential of Streptomyces levis strain HFM-2 isolated from the healthy human gut.
RESULTS
In vitro antibacterial activity in the cell-free supernatant of S. levis strain HFM-2 was evaluated against different pathogens viz. K. pneumoniae sub sp. pneumoniae, S. aureus, B. subtilis, VRE, S. typhi, S. epidermidis, MRSA, V. cholerae, M. smegmatis, E. coli, P. aeruginosa and E. aerogenes. Further, the ethyl acetate extract from S. levis strain HFM-2 showed strong biofilm inhibition against S. typhi, K. pneumoniae sub sp. pneumoniae, P. aeruginosa and E. coli. Fluorescence microscopy was used to detect biofilm inhibition properties. MIC and MBC values of EtOAc extract were determined at 500 and 1000 µg/mL, respectively. Further, strain HFM-2 showed high tolerance in gastric juice, pancreatin, bile, and at low pH. It exhibited efficient adhesion properties, displaying auto-aggregation (97.0%), hydrophobicity (95.71%, 88.96%, and 81.15% for ethyl acetate, chloroform and xylene, respectively), and showed 89.75%, 86.53%, 83.06% and 76.13% co-aggregation with S. typhi, MRSA, S. pyogenes and E. coli, respectively after 60 min of incubation. The S. levis strain HFM-2 was susceptible to different antibiotics such as tetracycline, streptomycin, kanamycin, ciprofloxacin, erythromycin, linezolid, meropenem, amikacin, gentamycin, clindamycin, moxifloxacin and vancomycin, but resistant to ampicillin and penicillin G.
CONCLUSION
The study shows that S. levis strain HFM-2 has significant probiotic properties such as good viability in bile, gastric juice, pancreatin environment, and at low pH; proficient adhesion properties, and antibiotic susceptibility. Further, the EtOAc extract of Streptomyces levis strain HFM-2 has a potent antibiofilm and antibacterial activity against antibacterial-resistant clinical pathogens.
Topics: Biofilms; Humans; Probiotics; Streptomyces; Microbial Sensitivity Tests; Anti-Bacterial Agents; Bacteria; Gastrointestinal Tract
PubMed: 38862894
DOI: 10.1186/s12866-024-03353-x -
Journal of Industrial Microbiology &... Jan 2024The demand for discovering novel microbial secondary metabolites is growing to address the limitations in bioactivities such as antibacterial, antifungal, anticancer,... (Review)
Review
UNLABELLED
The demand for discovering novel microbial secondary metabolites is growing to address the limitations in bioactivities such as antibacterial, antifungal, anticancer, anthelmintic, and immunosuppressive functions. Among microbes, the genus Streptomyces holds particular significance for secondary metabolite discovery. Each Streptomyces species typically encodes approximately 30 secondary metabolite biosynthetic gene clusters (smBGCs) within its genome, which are mostly uncharacterized in terms of their products and bioactivities. The development of next-generation sequencing has enabled the identification of a large number of potent smBGCs for novel secondary metabolites that are imbalanced in number compared with discovered secondary metabolites. The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) system has revolutionized the translation of enormous genomic potential into the discovery of secondary metabolites as the most efficient genetic engineering tool for Streptomyces. In this review, the current status of CRISPR/Cas applications in Streptomyces is summarized, with particular focus on the identification of secondary metabolite biosynthesis gene clusters and their potential applications.This review summarizes the broad range of CRISPR/Cas applications in Streptomyces for natural product discovery and production.
ONE-SENTENCE SUMMARY
This review summarizes the broad range of CRISPR/Cas applications in Streptomyces for natural product discovery and production.
Topics: Streptomyces; CRISPR-Cas Systems; Genetic Engineering; Genome, Bacterial; Biological Products; Gene Editing
PubMed: 38439699
DOI: 10.1093/jimb/kuae009 -
Molecular Plant Pathology Sep 2009SUMMARY Common scab is a severe disease worldwide affecting tap root crops and potato tubers. It is caused by soil-borne filamentous bacteria belonging to the genus... (Review)
Review
UNLABELLED
SUMMARY Common scab is a severe disease worldwide affecting tap root crops and potato tubers. It is caused by soil-borne filamentous bacteria belonging to the genus Streptomyces. Streptomycetes usually are saprophytic microorganisms, but a few species have acquired the ability to infect underground plant tissues. The predominant causal agent of potato scab worldwide is Streptomyces scabies. The production of phytotoxins called thaxtomins is essential for the virulence of common scab-causing agents. The genes involved in the biosynthetic pathway of thaxtomins and other virulence genes are clustered on a large pathogenicity island. The pathogenicity island can be mobilized and transferred to nonpathogenic relatives, leading to the emergence of new pathogenic streptomycetes. In most pathogenic Streptomyces species, thaxtomin A is the predominant form found. The regulation of thaxtomin A synthesis is complex. Although the plant-derived compound cellobiose is now recognized as the inducer of thaxtomin A synthesis at a genetic level, other molecules (including aromatic amino acids and some secondary metabolites) show inhibitory effects on the production of the toxin. This paper is an overview of common scab with a focus on S. scabies and its virulence mechanisms.
TAXONOMY
Streptomyces scabies (Thaxt.) Lambert and Loria; Kingdom Bacteria; Phylum Actinobacteria; Class Actinomycetes; Order Actinomycetales; Family Streptomycetaceae; genus Streptomyces; species scabies or scabiei.
HOST RANGE
Streptomyces scabies (syn. S. scabiei) has a broad host range comprising tuber vegetables and most tap root crops. Streptomyces scabies causes common scab on potato (Solanum tuberosum), beet (Beta vulgaris), carrot (Daucus carota), parsnip (Pastinaca sativa), radish (Raphanus sativus), rutabaga (Brassica napobrassica) and turnip (Brassica rapa). Disease symptoms: Common scab symptoms appear as randomly distributed shallow, raised or deep-pitted corky lesions. Their size and colour are quite variable, but lesions typically are brown with a diameter of a few millimetres. No above-ground symptoms disclose the presence of the disease as aerial tissues of scab-infected plants remain healthy. Streptomyces scabies also inhibits the growth of seedlings in monocot and dicot plants.
USEFUL WEBSITES
http://www.sanger.ac.uk/Projects/S_scabies, http://www.potatodiseases.org/scab.html, http://www.uri.edu/ce/factsheets/sheets/potatoscab.html.
Topics: Amino Acids, Aromatic; Genes, Bacterial; Plant Diseases; Streptomyces; Virulence
PubMed: 19694949
DOI: 10.1111/j.1364-3703.2009.00561.x -
Molecular Microbiology Jan 1998The Streptomyces wild-type chromosome is linear in all examples studied. The ends of the chromosome or telomeres consist of terminal inverted repeats of various sizes... (Review)
Review
The Streptomyces wild-type chromosome is linear in all examples studied. The ends of the chromosome or telomeres consist of terminal inverted repeats of various sizes with proteins covalently bound to their 5' ends. The chromosome is very unstable and undergoes very large deletions spontaneously at rates higher than 0.1% of spores. Frequently, the telomeres are included in the deletions. Loss of both telomeres leads to circularization of the chromosome. The wild-type chromosome can also be circularized artificially by targeted recombination. Spontaneously or artificially circularized chromosomes are even more unstable than the linear ones. High-copy-number tandem amplifications of specific chromosomal regions are frequently associated with the deletions. RecA seems to be involved in the amplification mechanism and control of genetic instability.
Topics: Chromosome Deletion; Chromosomes, Bacterial; DNA, Bacterial; Gene Amplification; Gene Dosage; Streptomyces
PubMed: 9484880
DOI: 10.1046/j.1365-2958.1998.00652.x -
Antonie Van Leeuwenhoek Dec 2020A putative novel clade within the genus Streptomyces was discovered following antifungal screening against Pseudogymnoascus destructans, the causative agent of...
A putative novel clade within the genus Streptomyces was discovered following antifungal screening against Pseudogymnoascus destructans, the causative agent of white-nose syndrome, and described using multi-locus sequencing analysis. Swabs from both the cave myotis bat (Myotis velifer) and the Brazilian free-tailed bat (Tadarida brasiliensis) in southern New Mexico bore isolates AC536, AC541 and AC563, which were characterised using phylogenetic, morphological, and phenotypic analyses. Multi-locus sequence analysis positions AC541 with neighbors Streptomyces rubidus (NRRL B-24619), Streptomyces guanduensis (NRRL B-24617), and Streptomyces yeochonensis (NRRL B-24245). A complete genome of the type strain was assembled to determine its taxonomy and secondary metabolite potential. ANI comparisons between all closely related types strains are shown to be well below the 95-96% species delineation. DNA-DNA relatedness between AC541 and its nearest neighbors ranged between 23.7 and 24.1% confirming novelty. Approximately 1.49 Mb or 17.76% of the whole genome is devoted to natural product biosynthesis. The DNA G + C content of the genomic DNA of the type strain is 73.13 mol %. Micromorphology depicts ovoid spores with smooth surfaces in flexuous chains. Strains presented an ivory to yellow hue on most ISP media except inorganic salts-starch agar (ISP4) and can grow on D-glucose, mannitol, and D-fructose, but exhibited little to no growth on L-arabinose, sucrose, D-xylose, inositol, L-rhamnose, D-raffinose, and cellulose. This clade possesses the capability to grow from 10 to 45 °C and 12.5% (w/v) NaCl. There was strain growth variation in pH, but all isolates thrive at alkaline levels. Based on our polyphasic study of AC541, the strain warrants the assignment to a novel species, for which the name Streptomyces buecherae sp. nov. is proposed. The type strain is AC541 (= JCM 34263, = ATCC TSD201).
Topics: Animals; Ascomycota; Bacterial Typing Techniques; Base Composition; Chiroptera; DNA, Bacterial; New Mexico; Phylogeny; Sequence Analysis, DNA; Streptomyces
PubMed: 33200278
DOI: 10.1007/s10482-020-01493-4