Streptomyces sp. B-S-A12
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA962462 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Ralstonia sp. A12 Genome sequencing and assembly
| PRJNA266745 | ENA
Project description:BACKGROUND: While substantial advances have been made to understand the nature and significance of interspecies interaction in oral microbial communities, much remains to be learned about how commensal species contribute to the maintenance of health-associated biofilm communities. We report that successful competition of Streptococcus sp. A12 with the dental pathogen Streptococcus mutans requires many different factors. While A12 can directly inhibit the growth of S. mutans, A12 harbors several genes (i.e. pcfFEGRK) that are required to be able to tolerate antagonistic factors of S. mutans, and these gene products are critical to the competitive fitness of A12. Here, we delve deeper in the role of the pcfFEG, a predicted lantibiotic immunity transporter, and the pcfRK, its genetically-linked two-component system (TCS) in A12. METHODS: RNA-Seq was utilized to compare the transcriptomes of A12 wild-type strain and A12 lacking the response regulator (pcfR) or histidine kinase (pcfK) of pcfRK, a TCS directly regulating pcfFEG. Each strains were prepared in 3 biological replicates. Strains were grown to OD600 nm = 0.4 in BHI medium before harvest. Deep sequencing was performed at the University of Florida ICBR facilities (Gainesville, FL). Approximately 15 million short-reads were obtained for each sample. After removing adapter sequences from each short-read and trimming of the 3’-ends by quality scores, the resulting sequences were mapped onto the reference genome of strain Streptococcus sp. A12 (NCBI Reference Sequence: NZ_CP013651.1) using the short-read aligner. Mapped short-read alignments were then converted into readable formats using SAMTOOLS. RESULTS: Using an optimized data analysis workflow, we mapped 13-16 million reads per sample to the genome of A12. For viewing of the mapped reads aligned to the genome, .bam files were uploaded into the Integrative Genomics Viewer (IGV – version 2.3.55). A .csv file containing raw read counts for each replicate (3) was then uploaded to Degust (http://degust.erc.monash.edu/) and edgeR analysis performed to determine Log2 fold change and a false discovery rate (FDR). When compared to the wild-type A12 strain, 61 genes were differentially expressed in A12 lacking pcfR and 35 genes were differentially expressed in A12 lacking pcfK (Log2 fold change > (-)1.5, -log10 P-value > 4). Interestingly, a subset of the same genes was found to be upregulated in both pcfR and pcfK deletion strains, including ATM98_04215, ATM98_04220 and ATM98_03625, annotated as a protease, a dipeptidase (both co-transcribed), and an aminopeptidase, respectively. Another interesting finding was a cluster of genes predicted to be the mannose PTS system was downregulated in the pcfK mutant strain, and a two-component ABC transporter annotated as ABC-type CcmA multidrug resistance system was found to be upregulated in the pcfR mutant strain. The pcfK mutant strain showed an upregulation of the pcfFEG genes and the cognate response regulator gene, pcfR. In the pcfR mutant, pcfK was also upregulated, compared to the parental A12 strain. CONCLUSIONS: Transcriptional profiling of pcfR and pcfK mutant strains revealed the scope of the pcfRK regulon. When supplemented with functional genomics, we uncovered additional genes shown to function independently or cooperatively with PcfFEGRK in tolerating the lantibiotic nisin. Together these results highlight additional mechanisms beneficial species may be utilizing to remain competitive when existing in complex microbial communities.
2020-08-24 | GSE156714 | GEO
Project description:Vibrio parahaemolyticus strain:A12 | isolate:A12 Genome sequencing and assembly
| PRJNA913564 | ENA
Project description:Streptomyces sp. M7 has demonstrated ability to remove lindane from culture media and soils. In this study, we used MS-based label-free quantitative proteomic to understand lindane degradation and its metabolic context in Streptomyces sp. M7. We identified the proteins involved in the up-stream degradation pathway. Our results demonstrated that mineralization of lindane is feasible since proteins from an unusual down-stream degradation pathway were also identified. Degradative steps were supported by an active catabolism that supplied energy and reducing equivalents in the form of NADPH. This is the first study in which degradation steps of an organochlorine compound and metabolic context are elucidate in a biotechnological genus as Streptomyces. These results serve as basement to study other degradative actinobacteria and to improve the degradation processes of Streptomyces sp. M7.
2018-08-10 | PXD010607 | Pride
Project description:This study aimed to investigate the variations in the protein composition of Streptomyces sp. PU10 when cultivated with either Impranil (polyestere-polyurethane) or glucose as the carbon source. We analyzed both the intracellular and extracellular protein fractions to gain insights into the intricate processes involving PU degradation, intermediate metabolic pathways in PU degradation, and the connection between primary and secondary metabolism within Streptomyces sp. PU10.
2024-03-29 | PXD047534 | Pride
Project description:Actinomycete genomes contain a plethora of orphan gene clusters encoding unknown secondary metabolites, and representing a huge unexploited pool of chemical diversity. The explosive increase in genome sequencing and the massive advance of bioinformatic tools have revolutionized the rationale for natural product discovery from actinomycetes. In this context, we applied a genome mining approach to discover a group of unique catecholate-hydroxamate siderophores termed as qinichelins from Streptomyces sp. MBT76. Quantitative proteomics statistically correlated a gene cluster of interest (qch) to its unknown chemotype (qinichelin), after which structural elucidation of isolated qinichelin was assisted by bioinformatics analysis and verified by MS2 and NMR experiments. Strikingly, intertwined functional crosstalk among four separately located gene clusters was implicated in the biosynthesis of qinichelins.
2018-10-24 | PXD006577 | Pride
Project description:Pedobacter arcticus A12 Genome sequencing and assembly
| PRJNA169846 | ENA
Project description:Streptomyces sp. MB42 produces antimicrobial compound under the pressence of specific compounds. This experiment is to see which gene cluster upregulated during the treatment of target compound.
2022-02-04 | PXD029669 | Pride
Project description:The aim of this work was to understand the response of Streptomyces sp. MC1 when exposed to Cr(VI) and phenantrene.
2020-11-25 | PXD018877 | Pride
Project description:Pelosinus fermentans A12 Genome sequencing
| PRJNA84233 | ENA