Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genomics and metabolomics-based assessment of the biosynthetic potential of the sponge-associated microorganism Streptomyces cacaoi strain R2A-843A from the Philippines

ABSTRACT: The biosynthetic machinery of the sponge-associated Streptomyces cacaoi strain R2A-843A was assessed using a combined genomics and metabolomics approach. Whole genome sequencing and molecular networking showed the high biosynthetic potential of this actinomycete. A significant proportion of the genome is dedicated to secondary metabolite production, with biosynthetic gene clusters for nonribosomal peptides, polyketides and terpenes being the most represented. Seven cyclic pentapeptides, including a putative new analogue, and a glycosylated lanthipeptide were identified using HRMS and untargeted MSMS analysis. Chemistry-guided purification confirmed the production of the peptides BE-18257A (1) and BE-18257B (2). The production of 1 and 2 and the growth of the microorganism were monitored for eight days. Compound 2 was produced at higher concentration, starting at 48 h post-incubation.

INSTRUMENT(S): Xevo G2 XS Tof

ORGANISM(S): Streptomyces Cacaoi (ncbitaxon:1898)

SUBMITTER: Lilibeth A. Salvador-Reyes

PROVIDER: MSV000092786 | MassIVE | Tue Aug 29 23:44:00 BST 2023

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Similar Datasets

biosynthetic potential of three high microbial abundance marine sponge holobionts

Project description:marine sponge biosynthetic profiles

| PRJEB51534 | ENA

Biosynthetic genes Antarctica

Project description:Diversity of bacterial biosynthetic genes in maritime Antarctica

| PRJEB36337 | ENA

Generation of new compounds through unbalanced transcription of landomycin A cluster

Project description:On the example of the biosynthetically exhausted landomycin A cluster we demonstrate unbalancing of gene transcription as an efficient method for the generation of new compounds. Decoupled from the native regulators LanI and LanK, all landomycin A structural genes were set under the control of a single synthetic promoter and expressed in a heterologous host Streptomyces albus J1074. Previously being both temporarily and quantitatively regulated, these genes were transcribed as a single polycistronic mRNA leading to the production of four novel and two known compounds. No glycosylated landomycins were detected though the entire biosynthetic cluster was transcribed, showing the crucial role of the balanced gene expression for the production of landomycin A. Two new compounds, fridamycin F and G, isolated in this study were shown to originate from the interplay between the expressed biosynthetic pathway and metabolic network of the heterologous host. Structure activity studies of the isolated compounds as well as results of transcriptome sequencing are discussed in this article. Comparison of gene expression of the H2-26 cosmid (encoding landomycin A biosynthetic genes) with H2-26-act, where an additional constitutive promoter cassette was integrated to drive biosynthetic genes transcription.

2016-07-01 | E-GEOD-83137 | biostudies-arrayexpress

Global analysis of growth phase responsive gene expression and regulation of antibiotic biosynthetic pathways

Project description:The eubacterial species Streptomyces coelicolor proceeds through a complex growth cycle in which morphological differentiation/development is associated with a transition from primary to secondary metabolism and the production of antibiotics. We used DNA microarrays and mutational analysis to investigate the expression of individual genes and multigene antibiotic biosynthetic pathways during these events. We identified expression patterns in biosynthetic, regulatory, and ribosomal protein genes that were associated highly specifically with particular stages of development. A knowledge-based algorithm that correlates temporal changes in expression with chromosomal position identified groups of contiguous genes expressed at discrete stages of morphological development, inferred the boundaries of known antibiotic synthesis gene loci, and revealed novel physical clusters of coordinately regulated genes. Microarray analysis of RNA from cells mutated in genes regulating synthesis of the antibiotics actinorhodin (Act) and undecylprodigiosin (Red) identified proximate and distant sites that contain putative ABC transporter and two-component system genes expressed coordinately with genes of specific biosynthetic pathways and indicated the existence of two functionally and physically discrete regulons in the Red pathway. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Computed

2005-07-23 | E-GEOD-2983 | biostudies-arrayexpress

Surges in biosynthetic gene cluster transcription are accompanied by bursts in natural compound production in the myxobacterium Sorangium sp. So ce836

Project description:An improved understanding of the genome-wide regulation of natural compound biosynthesis in bacterial producers may accelerate the discovery of novel biologically active molecules and facilitate their production. To this end, we have investigated the time course of genome-wide transcription in the myxobacterium Sorangium sp. So ce836 in relation to its production of natural compounds. Time-resolved RNA sequencing revealed the dynamic temporal variation of transcriptional activity, indicating that core biosynthesis genes from 48 biosynthetic gene clusters (BGCs; 92% of all BGCs encoded in the genome) were actively transcribed at specific time points in a batch culture. The majority (80%) of polyketide synthase and nonribosomal peptide synthetase genes displayed distinct peaks of transcription during exponential bacterial growth. Strikingly, these surges in BGC transcriptional activity were associated with boosts in the production of known natural compounds, indicating that their biosynthesis was crucially regulated at the transcriptional level. In contrast, BGC read counts from single time points had limited predictive value about biosynthetic activity, since transcription levels varied >100-fold among BGCs with detected natural products. Taken together, our time-course data provided unique insights into the dynamics of natural compound biosynthesis and its regulation in a wild-type myxobacterium, challenging the commonly cited notion of preferential BGC expression under meager conditions for bacterial growth. The close association between BGC transcription and compound production suggested that the molecular manipulation of transcriptional activity may be a viable strategy to increase compound yields from myxobacterial producer strains, warranting increased efforts to develop genetic engineering tools for these organisms.

2023-05-03 | GSE217497 | GEO

Global analysis of growth phase responsive gene expression and regulation of antibiotic biosynthetic pathways

2005-07-23 | GSE2983 | GEO

Generation of new compounds through unbalanced transcription of landomycin A cluster

2016-07-01 | GSE83137 | GEO

Biosynthetic potential of the global ocean microbiome

Project description:Biosynthetic potential of the global ocean microbiome

| PRJEB45951 | ENA

Biosynthetic Gene Cluster regulatory sequence library profiled in S. albidoflavus

Project description:Here, we profiled the transcriptional capacity of a library of regulatory sequences mined from diverse Biosynthetic Gene Clusters in S. albidoflavus (S. albus J1074) to investigate BGC gene regulation.

2022-06-07 | E-MTAB-9223 | biostudies-arrayexpress

Sponge-derived Commensal Bacteria MassIVE submission

Project description:This dataset contains several sponge-derived bacteria, along with data from the sponges to enable the assignation of the biosynthetic source of detected metabolite features. Media controls and solvent blanks are also included. Please see metadata for the bacterial source sponge.

2022-10-28 | MSV000090609 | MassIVE

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data