Streptomyces leeuwenhoekii C34 genome
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REPOSITORIES: ENA
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Project description:Bacterial genomic plasticity and instability carry multiple functional genetic information in Streptomyces secondary metabolism. Our previously publication has reported an effective industrial Streptomyces strain, with a unique phenotype of the high clavulanic acid yield. The complete genome of strain F163-1 harboring a 136.9-kb giant region of plasticity (RGP) was sequenced. The chromosome and plasmid are densely packed by an exceptionally huge variety of potential secondary metabolic gene clusters, excluding production of putative antibiotics. Intriguingly, architecture and size differences of plasmid pSCL4 between F613-1 and ATCC 27064 suggest the pSCL4 plasmid evolving from pSCL4-like and pSCL2-like extrachromosomal replicons, in addition to the previously proposed ATCC 27064 mega-plasmid formation hypothesis through recombination between the smaller F613-1 pSCL4 plasmid arm regions and the linear chromosome. Comparative genomics systemically investigate secondary metabolism capacitates in this study indicates that frequent exchange of genetic materials between Streptomyces replicons may shape remarkable diversities of secondary metabolite repertoires. Consequently, the F613-1 strain seems to have evolved its specific genomic architectures and genetic patterns to meet the requirement in subsequent industrial processes.
2017-10-10 | GSE104738 | GEO
Project description:Streptomyces are among the most prolific bacterial producers of specialized metabolites, including antibiotics. The linear genome is partitioned into a central region harboring core genes and two extremities enriched in specialized metabolite biosynthetic gene clusters (SMBGCs). The molecular mechanisms governing structure and function of these compartmentalized genomes remain mostly unknown. Here we show that in exponential phase, chromosome structure correlates with genetics compartmentalization: conserved, large and highly transcribed genes form boundaries that segment the central part of the genome into domains, whereas the terminal ends are transcriptionally, largely quiescent compartments with different structural features. Onset of metabolic differentiation is accompanied by remodeling of chromosome architecture from an ‘open’ to a rather ‘closed’ conformation, in which the SMBGCs are expressed forming new boundaries. Altogether, our results reveal that S. ambofacien's linear chromosome is partitioned into structurally distinct entities, indicating a link between chromosome folding, gene expression and genome evolution
2021-07-01 | GSE162865 | GEO
Project description:We used an approach combining PacBio data and published Illumina reads to de novo assemble D. busckii contigs. We generated Hi-C data from D. busckii embryos to order these contigs into chromosome-length scaffolds. For D. virilis we generated Hi-C data to order and orient the published Dvir_caf1 scaffolds into chromosome-length assemblies. Furthermore, we compared Hi-C matrices from these two new assemblies with D. melanogaster with respect to synteny blocks and dosage compensation as a chromosome-wide gene-regulatory mechanism.
2019-10-14 | GSE120750 | GEO
Project description:We used an approach combining PacBio data and published Illumina reads to de novo assemble D. busckii contigs. We generated Hi-C data from D. busckii embryos to order these contigs into chromosome-length scaffolds. For D. virilis we generated Hi-C data to order and orient the published Dvir_caf1 scaffolds into chromosome-length assemblies. Furthermore, we compared Hi-C matrices from these two new assemblies with D. melanogaster with respect to synteny blocks and dosage compensation as a chromosome-wide gene-regulatory mechanism.
2019-10-14 | GSE120751 | GEO
Project description:Compared with HKE9, HKE9-M-rpoS (rpoS knockout in hypervirulent Klebsiella pneumoniae strain HKE9) had 624 genes expressed significantly different, among which 148 genes were significantly up-regulated and 476 genes were significantly down-regulated, 586 genes on chromosomes, 10 genes on circular plasmid and 28 genes on linear plasmid; HKE9-C-M-rpoS had 746 genes expressed significantly different, among which 286 genes were significantly up-regulated and 460 genes were significantly down-regulated, 727 genes on chromosomes, 11 genes on circular plasmid and 8 genes on linear plasmid. Compared with HKE9-M-rpoS, HKE9-C-M-rpoS (rpoS complement in strain HKE9-M-rpoS) had 509 genes expressed significantly different, among which 324 genes were significantly up-regulated and 185 genes were significantly down-regulated, 458 genes on chromosomes, 3 genes on circular plasmid and 48 genes on linear plasmid.
2023-11-15 | GSE224709 | GEO
Project description:Raw reads of RNA products generated upon incubation of circular and linear pLac-Tet plasmid in human cell-free extract.
2017-12-16 | GSE75512 | GEO
Project description:The gene aml encoding alpha-amylase in Streptomyces lividans was cloned in the multicopy plasmid pIJ486, generating plasmid pAMI11. Plasmid pAMI11 and pIJ486 were propagated in S. lividans TK21 to obtain S. lividans TK21(pAMI11) and its isogenic strain S. lividans TK21(pIJ486). Transcriptional profiling of the bacterium that overproduces alpha-amylase mainly resulted in the upregulation of genes involved in the biogenesis and function of ribosomes, together with the upregulation of the genes involved in the redox processes, the ABC transporters, the central carbon, aminoacid and purine /pyrimidine metabolism. Moreover, some genes involved in oxidative stress were upregulated. The number of genes downregulated was much lower than the upregulated ones. Therefore, bacteria respond by favouring alpha-amylase overproduction that apparently does not cause damage to the cell.
2015-07-23 | GSE61448 | GEO
Project description:The gene dagA encoding agarase in Streptomyces coelicolor was cloned in the multicopy plasmid pIJ486 generating plasmid pAGAs5. Plasmid pAGAs5 and pIJ486 were propagated in S. lividans TK21 to obtain S. lividans TK21(pAGAs5) and its isogenic strain S. lividans TK21(pIJ486). Transcriptional profiling of the bacterium that overproduces agarase mainly resulted in the downregulation of the genes involved in the biogenesis and function of ribosomes, together with the downregulation of the genes involved in nitrogen, aminoacids, purine/pyrimidine and central carbon metabolism as well as ABC transporters, redox processes and fatty acids biosynthesis. The number of genes upregulated in the agarase overproducer strain is lower than in the downregulated ones. Almost 50% of the dowregulated genes have been described as forming part of the stringent response in streptomycetes. Therefore, the overproduction of agarase may lead to a condition of nutrient depletion that triggers the stringent response.
2015-07-23 | GSE61447 | GEO
Project description:Contigs metagenomic, de novo assembly of consortium reads
| PRJNA413159 | ENA
Project description:NGPS is a method for de-novo, full-length protein sequencing in high throughput. The method is based on cleavage of the protein at semi-random sites by microwave-assisted acid hydrolysis (MAAH), enrichment of LC-MS/MS amenable peptides from the hydrolysate by solid-phase-extraction, LC-MS/MS analysis, de-novo long peptide tag sequencing of resulting peptides and assembly of peptide tags into consensus contigs.
2017-04-03 | PXD003804 | Pride