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PROVIDER: PRJEB54794 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Birds and other reptiles possess a diversity of feather and scale-like skin appendages. Feathers are commonly assumed to have originated from ancestral scales in theropod dinosaurs. However, most birds also have scaled feet, indicating birds evolved the capacity to grow both ancestral and derived morphologies. This suggests a more complex evolutionary history than a simple linear transition between feathers and scales. We set out to investigate the evolution of feathers via the comparison of transcriptomes assembled from diverse skin appendages in chicken, emu, and alligator. Our data reveal that feathers and the overlapping ‘scutate’ scales of birds share more similar gene expression to each other, and to two types of alligator scales, than they do to the tuberculate ‘reticulate’ scales on bird footpads. Accordingly, we propose a history of skin appendage diversification, in which feathers and bird scutate scales arose from ancestral archosaur body scales, whereas reticulate scales arose earlier in tetrapod evolution. We also show that many “feather-specific genes” are also expressed in alligator scales. In-situ hybridization results in feather buds suggest that these genes represent ancestral scale genes that acquired novel roles in feather morphogenesis and were repressed in bird scales. Our findings suggest that the differential reuse, in feathers, and suppression, in bird scales, of genes ancestrally expressed in archosaur scales has been a key factor in the origin of feathers – and may represent an important mechanism for the origin of evolutionary novelties.
2019-05-01 | GSE120493 | GEO
Project description:Here, we address the transcriptional response to both novobiocin-induced rapid chromosome relaxation or long-term topological imbalance, both increased and decreased supercoiling, in environmental antibiotic-producing bacteria belonging to the Streptomyces genus.
2019-06-14 | GSE132702 | GEO
Project description:We address the transcriptional response to both novobiocin-induced rapid chromosome relaxation or long-term topological imbalance, both increased and decreased supercoiling, in environmental antibiotic-producing bacteria belonging to the Streptomyces genus.
2019-06-22 | E-MTAB-8071 | biostudies-arrayexpress
Project description:Chitin is the second most abundant biopolymer present in soils and is utilized by antibiotic-producing Streptomyces species. Its monomer, N-acetylglucosamine (NAG), regulates the developmental program of the model organism Streptomyces coelicolor. NAG blocks differentiation when growing on rich medium whilst it promotes development on poor culture media. We report here the negative effect of NAG on tacrolimus (FK506) production in Streptomyces tsukubaensis NRRL 18488 growing on a defined rich medium. Using microarrays technology, we found that GlcNAc represses the transcription of fkbN, encoding the main transcriptional activator of the tacrolimus biosynthetic cluster, and of ppt1, encoding a phosphopantheteinyltransferase involved in tacrolimus biosynthesis. On the contrary, NAG stimulated transcription of genes related to amino acid and nucleotide biosynthesis, DNA replication, RNA translation, glycolysis, pyruvate metabolism, and key gene members of the PHO regulon. The results obtained support those previously reported for S. coelicolor, but some important differences were observed
2020-02-08 | GSE110393 | GEO
Project description:We have integrated nucleotide resolution genome-scale measurements of the transcriptome and translatome of the Streptomyces coelicolor A3(2), the model antibiotic-producing actinomycete. Our systematic study determined 3,473 transcription start sites, leading to discovery of a high proportion (~21%) of leaderless mRNAs and 230 non-coding RNAs; this enabled deduction of promoter architecture on a genome-scale. Ribosome profiling analysis revealed that the translation efficiency was negatively correlated for secondary metabolic genes. These results provide novel fundamental insights into translational regulation of secondary metabolism that enables rational synthetic biology approaches to awaken such âsilentâ secondary metabolic pathways. Profiles of primary transcripts, whole transcripts, and ribosome protected fragments (RPFs) of Streptomyces coelicolor were generated by deep sequencing using Illumina Miseq.
2016-05-28 | E-GEOD-69350 | biostudies-arrayexpress
Project description:Specialised metabolites made by the genus Streptomyces form the basis of 55% of clinically used antibiotics as well as cancer therapeutics, immunosuppressants and other anti-infectives. Streptomyces venezuelae is a model for the genus because it is fast-growing, sporulates in liquid culture within 24 hours and coordinates production of the antibiotic chloramphenicol with sporulation. In this work we demonstrate that the conserved orphan response regulator OrrA directly controls the production of the conserved WhiB-like protein WblA which in turn binds to 90 target gene promoters, including genes required for aerial hyphae production and sporulation. We provide evidence that WblA directly controls the production of AdpA and BldN, key developmental regulators that are required for entry into sporulation and show that the cellular levels of the key developmental regulators AdpA, BldM, BldN, RsbN, WhiA, WhiB and WhiD are significantly altered in a ∆wblA mutant. Proteins encoded by 32 of the 33 predicted specialised metabolite biosynthetic gene clusters in S. venezuelae are also significantly affected by loss of WblA and we show that the ∆wblA mutant over produces the antibiotic chloramphenicol. This is the first time the WblA regulon has been defined in the genus Streptomyces and is consistent with previous reports that deletion of wblA has pleiotropic effects on antibiotic production and sporulation in diverse Streptomyces species.
2025-08-04 | GSE300101 | GEO
Project description:Global regulation by the Streptomyces coelicolor atypical MerR-like transcription factor BldC. BldC is a transcriptional regulator essential for morphological development and antibiotic production in Streptomyces coelicolor. Here we identify the BldC regulon by means of chromatin immunoprecipitation (ChIP) microarray analysis. The BldC regulon encompasses at least 201 transcriptional units, which include many genes that play key roles in Streptomyces development (e.g., bldC itself, bldB, bldM, whiB, whiD, whiI, sigF, smeA-sffA, hupS), antibiotic production (e.g., afsK) and stress response (e.g., clpB, nsrR, sigE, sigF). All BldC-binding sites identified by ChIP-chip are present in the promoters of the target genes. In vitro DNA-binding experiments show that BldC is capable of binding DNA specifically in the absence of other proteins and suggest that BldC is a minor-groove DNA-binding protein. The regulon of BldC partially overlaps with that of the pleiotropic regulator BldD. BldC and BldD bind to distinct sites in the promoter region of smeA, where they simultaneously repress its transcription.
2013-01-01 | GSE28908 | GEO
Project description:Antibiotic biosynthesis in Streptomyces species is controlled by a complex genetic and biochemical network of global and pathway specific regulators. Details of their precise interactions in mediating temporal and spatial expression of secondary metabolite genes remain poorly defined. In this study, we employed whole-genome microarrays to investigate the temporal transcriptome profiles of S. coelicolor A3(2) afsS::apr mutant strain (YSK4425) and compare it to wild-type M145 strain. The regulatory protein encoded by afsS is known to affect antibiotic biosynthesis (Floriano, B., Bibb, M. 1996. afsR is a pleiotropic but conditionally required regulatory gene for antibiotic production in Streptomyces coelicolor A3(2). Mol Microbiol, 21, 385-96). Keywords: Time course
2007-06-23 | GSE8160 | GEO
Project description:We have integrated nucleotide resolution genome-scale measurements of the transcriptome and translatome of the Streptomyces coelicolor A3(2), the model antibiotic-producing actinomycete. Our systematic study determined 3,473 transcription start sites, leading to discovery of a high proportion (~21%) of leaderless mRNAs and 230 non-coding RNAs; this enabled deduction of promoter architecture on a genome-scale. Ribosome profiling analysis revealed that the translation efficiency was negatively correlated for secondary metabolic genes. These results provide novel fundamental insights into translational regulation of secondary metabolism that enables rational synthetic biology approaches to awaken such ‘silent’ secondary metabolic pathways.
2016-05-28 | GSE69350 | GEO