Actinomycetales
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA350502 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR4720671.fastq.gz | Fastqsanger.gz | |||
| SRR4720642.fastq.gz | Fastqsanger.gz | |||
| SRR4720692.fastq.gz | Fastqsanger.gz | |||
| SRR4720694.fastq.gz | Fastqsanger.gz | |||
| SRR4720646.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 8 |
Similar Datasets
Project description:The genome of Mycobacterium tuberculosis harbors four copies of a cluster of genes termed mce operons. Despite extensive research that has demonstrated the importance of these operons on infection outcome, their physiological function remains obscure. Expanding databases of complete microbial genome sequences facilitate a comparative genomic approach that can provide valuable insight into the role of uncharacterized proteins.The M. tuberculosis mce loci each include two yrbE and six mce genes, which have homology to ABC transporter permeases and substrate-binding proteins, respectively. Operons with an identical structure were identified in all Mycobacterium species examined, as well as in five other Actinomycetales genera. Some of the Actinomycetales mce operons include an mkl gene, which encodes an ATPase resembling those of ABC uptake transporters. The phylogenetic profile of Mkl orthologs exactly matched that of the Mce and YrbE proteins. Through topology and motif analyses of YrbE homologs, we identified a region within the penultimate cytoplasmic loop that may serve as the site of interaction with the putative cognate Mkl ATPase. Homologs of the exported proteins encoded adjacent to the M. tuberculosis mce operons were detected in a conserved chromosomal location downstream of the majority of Actinomycetales operons. Operons containing linked mkl, yrbE and mce genes, resembling the classic organization of an ABC importer, were found to be common in Gram-negative bacteria and appear to be associated with changes in properties of the cell surface.Evidence presented suggests that the mce operons of Actinomycetales species and related operons in Gram-negative bacteria encode a subfamily of ABC uptake transporters with a possible role in remodeling the cell envelope.
| S-EPMC1810536 | biostudies-literature
Project description:Actinomycetales genome sequencing
| PRJNA421080 | ENA
Project description:Actinomycetales bacterium JB111 complete genome sequence
| PRJEB19043 | ENA
Project description:Phosphopantetheinyl transferases (PPTases) are a superfamily of essential enzymes required for the synthetic processes of many compounds including fatty acid, polyketide, and nonribosomal peptide metabolites. These enzymes activate carrier proteins in specific biosynthetic pathways via the transfer of a phosphopantetheinyl moiety to a serine residue in the conserved motif of carrier proteins. Since many Actinomycetales microorganisms produce a number of polyketide and nonribosomal peptide metabolites, the distribution of PPTase genes was investigated in these microorganisms. PPTases were found in bacterial protein databases using a hidden Markov model search with the PF01648 (4'-phosphopantetheinyl transferase superfamily) model. Actinomycetales microorganisms harbor several genes encoding AcpS-type and Sfp-type PPTases in individual genomes, many of which were associated with the biosynthetic gene cluster for polyketide or nonribosomal peptide metabolites. The properties of these PPTases were evaluated in the heterologous expression system using the biosynthetic gene clusters and genes encoding PPTases found in the present study. Sfp-type PPTases were classified into two subgroups, and although the substrate specificities of the enzymes in one subgroup were wide, the catalytic activities of enzymes in the other subgroup were low. SAV_1784 of Streptomyces avermitilis possessed the most characteristic broad-range activity against several type I polyketide synthases and nonribosomal peptide synthetases.
| S-EPMC6042109 | biostudies-literature
Project description:Bacteria regulate chromosome replication and segregation tightly with cell division to ensure faithful segregation of DNA to daughter generations. The underlying mechanisms have been addressed in several model species. It became apparent that bacteria have evolved quite different strategies to regulate DNA segregation and chromosomal organization. We have investigated here how the actinobacterium Corynebacterium glutamicum organizes chromosome segregation and DNA replication. Unexpectedly, we found that C. glutamicum cells are at least diploid under all of the conditions tested and that these organisms have overlapping C periods during replication, with both origins initiating replication simultaneously. On the basis of experimental data, we propose growth rate-dependent cell cycle models for C. glutamicumIMPORTANCE Bacterial cell cycles are known for few model organisms and can vary significantly between species. Here, we studied the cell cycle of Corynebacterium glutamicum, an emerging cell biological model organism for mycolic acid-containing bacteria, including mycobacteria. Our data suggest that C. glutamicum carries two pole-attached chromosomes that replicate with overlapping C periods, thus initiating a new round of DNA replication before the previous one is terminated. The newly replicated origins segregate to midcell positions, where cell division occurs between the two new origins. Even after long starvation or under extremely slow-growth conditions, C. glutamicum cells are at least diploid, likely as an adaptation to environmental stress that may cause DNA damage. The cell cycle of C. glutamicum combines features of slow-growing organisms, such as polar origin localization, and fast-growing organisms, such as overlapping C periods.
| S-EPMC5461407 | biostudies-literature
Project description:In this study we will compare the single cell transcriptomes of immune cells from asthmatics responding to steroids, those refractory to steroids, and a control population.
This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
| EGAS00001001755 | EGA
Project description:Two classes of F(420)-dependent reductases (FDR-A and FDR-B) that can reduce aflatoxins and thereby degrade them have previously been isolated from Mycobacterium smegmatis. One class, the FDR-A enzymes, has up to 100 times more activity than the other. F(420) is a cofactor with a low reduction potential that is largely confined to the Actinomycetales and some Archaea and Proteobacteria. We have heterologously expressed ten FDR-A enzymes from diverse Actinomycetales, finding that nine can also use F(420)H(2) to reduce aflatoxin. Thus FDR-As may be responsible for the previously observed degradation of aflatoxin in other Actinomycetales. The one FDR-A enzyme that we found not to reduce aflatoxin belonged to a distinct clade (herein denoted FDR-AA), and our subsequent expression and analysis of seven other FDR-AAs from M. smegmatis found that none could reduce aflatoxin. Certain FDR-A and FDR-B enzymes that could reduce aflatoxin also showed activity with coumarin and three furanocoumarins (angelicin, 8-methoxysporalen and imperatorin), but none of the FDR-AAs tested showed any of these activities. The shared feature of the compounds that were substrates was an α,β-unsaturated lactone moiety. This moiety occurs in a wide variety of otherwise recalcitrant xenobiotics and antibiotics, so the FDR-As and FDR-Bs may have evolved to harness the reducing power of F(420) to metabolise such compounds. Mass spectrometry on the products of the FDR-catalyzed reduction of coumarin and the other furanocoumarins shows their spontaneous hydrolysis to multiple products.
| S-EPMC3288000 | biostudies-literature
Project description:Commensal microbes are exposed to enterohepatically circulated steroids such as bile acids and hormones in the gastrointestinal, vaginal, and urinary tracts. Since commensal microbes are exposed to these molecules exclusively in association with their host, we hypothesized that they may serve as effectors to identify and characterize genetic pathways involved in the commensal-host relationship. Host specific and some ingested steroids (phytoestrogens) are enterohepatically circulated through the lumen of the small intestine. Bile acid steroids are present at high concentrations, approximating 4 to 20 mM in the duodenum, and are released in bile from the common bile duct. Steroid hormones are secreted in bile at levels approximating 6 to 13 mg per day once conjugated to glucuronide or sulfate by the liver. Re-absorption of steroids by the terminal ileum is an incomplete process: for example, 200 to 600 mg of bile acid steroids per day in humans escape to the colon where complex microbial populations exist. We have shown that steroid hormones estradiol, progesterone, and hydrocortisone serve as strong substrates for the major RND- and MFS-type (except hydrocortisone) tripartite multidrug efflux systems, AcrAB-TolC and EmrAB-TolC respectively, even though such molecules fail to demonstrate antimicrobial properties in this bacterial background (Elkins and Mullis [2006] J. Bacteriol. 188:1191-1195). Although bile acids are subject to efflux, they are also known to directly interact with intracellular global regulators such as MarR (Prouty et al. [2004] Microbiol. 150:775-783) and Rob (Rosenberg et al., [2003] Mol. Microbiol. 48:1609-1619) consequently altering antimicrobial and bile resistance profiles. In our present study, whole-genome DNA microarrays of E. coli were used to determine what general effect steroids, both bile acid and hormones, may have on the transcriptome in relation to the human commensal environment. Keywords: Comparative Chemical Class Treatment
2008-03-14 | GSE10811 | GEO
Project description:Recent metagenomic studies have revealed that microbial diversity in the atmosphere rivals that of surface environments. This indicates that the atmosphere may be worth bioprospecting in for novel microorganisms, especially those selected for by harsh atmospheric conditions. This is interesting in light of the antibiotic resistance crisis and renewed interests in bioprospecting for members of the Actinomycetales, which harbor novel secondary metabolite-producing pathways and produce spores that make them well suited for atmospheric travel. The latter leads to the hypothesis that the atmosphere may be a promising environment in which to search for novel Actinomycetales. Although ubiquitous in soils, where bioprospecting efforts for Actinomycetales have been and are largely still focused, we present novel data indicating that culturable members of this taxonomic order are 3-5.6 times more abundant in air samples collected at 1.5, 4.5, 7.5, and 18 m above the ground, than in the underlying soil. These results support the hypothesis that mining the vast and readily accessible lower atmosphere for novel Actinomycetales in the search for undescribed secondary metabolites could prove fruitful.
| S-EPMC4523828 | biostudies-literature
Project description:Actinomycetes are a heterogeneous group of gram positive filamentous bacteria that have been found to produce a wide range of valuable bioactive secondary metabolites, particularly antibiotics. Moreover, actinomycetes isolated from unexplored environments show an unprecedented potential to generate novel active compounds. Hence, in order to search for novel antibiotics, we isolated and characterized actinomycetes strains from plant samples collected from a mangrove in Macau. Within the class of actinobacteria, fourteen actinomycetes isolates have been isolated and identified belonging to the genus of Streptomyces, Micromonospora, Mycobacterium, Brevibacterium, Curtobacterium and Kineococcus based on their 16S rRNA sequences. Further whole genome sequencing analysis of one of the isolated Streptomyces sp., which presented 99.13% sequence similarity with Streptomyces parvulus strain 2297, showed that it consisted of 118 scaffolds, 8,348,559 base pairs and had a 72.28% G?+?C content. In addition, genome-mining revealed that the isolated Streptomyces sp. contains 109 gene clusters responsible for the biosynthesis of known and/or novel secondary metabolites, including different types of terpene, T1pks, T2pks, T3pks, Nrps, indole, siderophore, bacteriocin, thiopeptide, phosphonate, lanthipeptide, ectoine, butyrolactone, T3pks-Nrps, and T1pks-Nrps. Meanwhile, the small molecules present in ethyl acetate extract of the fermentation broth of this strain were analyzed by LC-MS. Predicted secondary metabolites of melanin and desferrioxamine B were identified and both of them were firstly found to be produced by the Streptomyces parvulus strain. Our study highlights that combining genome mining is an efficient method to detect potentially promising natural products from mangrove-derived actinomycetes.
| S-EPMC6155160 | biostudies-literature