Time-Resolved Transcriptomics and Constraint-Based Modeling Identify System-Level Metabolic Features and Overexpression Targets to Increase Spiramycin Production in Streptomyces ambofaciens (Q33665576)

From Wikidata

Jump to navigation Jump to search

scientific article

Language	Label	Description	Also known as
English	Time-Resolved Transcriptomics and Constraint-Based Modeling Identify System-Level Metabolic Features and Overexpression Targets to Increase Spiramycin Production in Streptomyces ambofaciens	scientific article

Statements

scholarly article

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28553270%20AND%20SRC:MED&resulttype=core&format=json

21 March 2020

Time-Resolved Transcriptomics and Constraint-Based Modeling Identify System-Level Metabolic Features and Overexpression Targets to Increase Spiramycin Production in Streptomyces ambofaciens (English)

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28553270%20AND%20SRC:MED&resulttype=core&format=json

21 March 2020

0 references

1 reference

based on heuristic

inferred from title

Streptomyces ambofaciens

1 reference

1 reference

transcriptomics

1 reference

based on heuristic

inferred from title

2

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28553270%20AND%20SRC:MED&resulttype=core&format=json

21 March 2020

7

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28553270%20AND%20SRC:MED&resulttype=core&format=json

21 March 2020

Gianluca De Bellis

11

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28553270%20AND%20SRC:MED&resulttype=core&format=json

21 March 2020

12

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28553270%20AND%20SRC:MED&resulttype=core&format=json

21 March 2020

13

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28553270%20AND%20SRC:MED&resulttype=core&format=json

21 March 2020

3

object named as

Adelfia Talà

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28553270%20AND%20SRC:MED&resulttype=core&format=json

21 March 2020

Clarissa Consolandi

5

object named as

Clarissa Consolandi

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28553270%20AND%20SRC:MED&resulttype=core&format=json

21 March 2020

author name string

Marco Fondi

1

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28553270%20AND%20SRC:MED&resulttype=core&format=json

21 March 2020

Fabrizio Damiano

4

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28553270%20AND%20SRC:MED&resulttype=core&format=json

21 March 2020

Benedetta Mattorre

6

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28553270%20AND%20SRC:MED&resulttype=core&format=json

21 March 2020

Mariangela Testini

8

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28553270%20AND%20SRC:MED&resulttype=core&format=json

21 March 2020

Giuseppe E De Benedetto

9

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28553270%20AND%20SRC:MED&resulttype=core&format=json

21 March 2020

Luisa Siculella

10

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28553270%20AND%20SRC:MED&resulttype=core&format=json

21 March 2020

publication date

12 May 2017

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28553270%20AND%20SRC:MED&resulttype=core&format=json

21 March 2020

full work available at URL

https://www.frontiersin.org/articles/10.3389/fmicb.2017.00835/pdf

1 reference

19 March 2024

https://api.unpaywall.org/v2/10.3389/fmicb.2017.00835?email=unpaywall_01@example.com

Frontiers in Microbiology

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28553270%20AND%20SRC:MED&resulttype=core&format=json

21 March 2020

8

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28553270%20AND%20SRC:MED&resulttype=core&format=json

21 March 2020

835

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28553270%20AND%20SRC:MED&resulttype=core&format=json

21 March 2020

describes a project that uses

object named as

DESeq2

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

online access status

1 reference

19 March 2024

https://api.unpaywall.org/v2/10.3389/fmicb.2017.00835?email=unpaywall_01@example.com

access restriction status

1 reference

based on heuristic

inferred from online access status

Applications of Genome-Scale Metabolic Models in Biotechnology and Systems Medicine

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

Predictive analytics of environmental adaptability in multi-omic network models.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

Transcriptomics-based strain optimization tool for designing secondary metabolite overproducing strains of Streptomyces coelicolor

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

Genetic manipulation of secondary metabolite biosynthesis for improved production in Streptomyces and other actinomycetes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

Next-generation genome-scale models for metabolic engineering.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

The transporter classification database

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

Genome-scale metabolic network guided engineering of Streptomyces tsukubaensis for FK506 production improvement

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

Reconstruction of the Saccharopolyspora erythraea genome-scale model and its use for enhancing erythromycin production

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

A systems biology approach to drug targets in Pseudomonas aeruginosa biofilm

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

Fast gapped-read alignment with Bowtie 2

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

Significant reduction of brain cysts caused by Toxoplasma gondii after treatment with spiramycin coadministered with metronidazole in a mouse model of chronic toxoplasmosis.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

Beyond ethylmalonyl-CoA: the functional role of crotonyl-CoA carboxylase/reductase homologs in expanding polyketide diversity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

Identification of a bioactive 51-membered macrolide complex by activation of a silent polyketide synthase in Streptomyces ambofaciens

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

SurreyFBA: a command line tool and graphics user interface for constraint-based modeling of genome-scale metabolic reaction networks

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

BRENDA, the enzyme information system in 2011

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

High-throughput generation, optimization and analysis of genome-scale metabolic models

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

Glycosylation steps during spiramycin biosynthesis in Streptomyces ambofaciens: involvement of three glycosyltransferases and their interplay with two auxiliary proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

Utilizing elementary mode analysis, pathway thermodynamics, and a genetic algorithm for metabolic flux determination and optimal metabolic network design

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

In silico identification of gene amplification targets for improvement of lycopene production

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

What is flux balance analysis?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

BEDTools: a flexible suite of utilities for comparing genomic features

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

A protocol for generating a high-quality genome-scale metabolic reconstruction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

The Sequence Alignment/Map format and SAMtools

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

Organization of the biosynthetic gene cluster for the macrolide antibiotic spiramycin in Streptomyces ambofaciens

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

Synthesis of C5-dicarboxylic acids from C2-units involving crotonyl-CoA carboxylase/reductase: the ethylmalonyl-CoA pathway

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

Metabolic modeling of a mutualistic microbial community.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

MetaCyc: a multiorganism database of metabolic pathways and enzymes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

[A new species of Streptomyces producing antibiotics Streptomyces ambofaciens n. sp., cultural characteristics].

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

Posttranslational processing of the xylanase Xys1L from Streptomyces halstedii JM8 is carried out by secreted serine proteases.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2−ΔΔCT Method

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

KEGG: kyoto encyclopedia of genes and genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

Role of crotonyl coenzyme A reductase in determining the ratio of polyketides monensin A and monensin B produced by Streptomyces cinnamonensis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

Microbial ecology and evolution: a ribosomal RNA approach

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

Basic local alignment search tool

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

Cloning of spiramycin biosynthetic genes and their use in constructing Streptomyces ambofaciens mutants defective in spiramycin biosynthesis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

21 June 2018

Effects of glucose limitation on biomass and spiramycin production by Streptomyces ambofaciens

1 reference

https://api.crossref.org/works/10.3389%2FFMICB.2017.00835

21 January 2018

maSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments

1 reference

https://api.crossref.org/works/10.3389%2FFMICB.2017.00835

21 January 2018

Genome-scale metabolic flux analysis of Streptomyces lividans growing on a complex medium.

1 reference

https://api.crossref.org/works/10.3389%2FFMICB.2017.00835

21 January 2018

Genome-scale metabolic reconstruction and constraint-based modelling of the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125.

1 reference

https://api.crossref.org/works/10.3389%2FFMICB.2017.00835

21 January 2018

Production of a novel polyketide through the construction of a hybrid polyketide synthase.

1 reference

https://api.crossref.org/works/10.3389%2FFMICB.2017.00835

21 January 2018

Systematic Identification of a Panel of Strong Constitutive Promoters from Streptomyces albus.

1 reference

https://api.crossref.org/works/10.3389%2FFMICB.2017.00835

21 January 2018

Concentrations and in vivo antibacterial activity of spiramycin and metronidazole in patients with periodontitis treated with high-dose metronidazole and the spiramycin/metronidazole combination

1 reference

https://api.crossref.org/works/10.3389%2FFMICB.2017.00835

21 January 2018

Multidimensional optimality of microbial metabolism

1 reference

https://api.crossref.org/works/10.3389%2FFMICB.2017.00835

21 January 2018

pTOYAMAcos, pTYM18, and pTYM19, actinomycete-Escherichia coli integrating vectors for heterologous gene expression

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5427115

30 October 2018

Complete genome sequence of Streptomyces ambofaciens ATCC 23877, the spiramycin producer

1 reference

https://pubmed.ncbi.nlm.nih.gov/28553270

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Glycerol effect on spiramycin production and valine catabolism in Streptomyces ambofaciens

1 reference

https://pubmed.ncbi.nlm.nih.gov/28553270

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

In silico aided metabolic engineering of Streptomyces roseosporus for daptomycin yield improvement

1 reference

https://pubmed.ncbi.nlm.nih.gov/28553270

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Network-based prediction of human tissue-specific metabolism

1 reference

https://pubmed.ncbi.nlm.nih.gov/28553270

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

[Trypanocide action of an antibiotic produced by a Streptomyces]

1 reference

https://pubmed.ncbi.nlm.nih.gov/28553270

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Regulation of spiramycin synthesis in Streptomyces ambofaciens: effects of glucose and inorganic phosphate

1 reference

https://pubmed.ncbi.nlm.nih.gov/28553270

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Role of Crotonyl Coenzyme A Reductase in Determining the Ratio of Polyketides Monensin A and Monensin B Produced byStreptomyces cinnamonensis

2 references

12 April 2024

https://opencitations.net/index/api/v1/references/10.3389/FMICB.2017.00835

12 April 2024

https://opencitations.net/index/api/v1/citations/10.1128/JB.181.21.6806-6813.1999

Identifiers

10.3389/FMICB.2017.00835

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28553270%20AND%20SRC:MED&resulttype=core&format=json

21 March 2020

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28553270%20AND%20SRC:MED&resulttype=core&format=json

21 March 2020

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28553270%20AND%20SRC:MED&resulttype=core&format=json

21 March 2020

Sitelinks

Wikipedia(0 entries)

Wikibooks(0 entries)

Wikinews(0 entries)

Wikiquote(0 entries)

Wikisource(0 entries)

Wikiversity(0 entries)

Wikivoyage(0 entries)

Wiktionary(0 entries)

Multilingual sites(0 entries)

Retrieved from "https://www.wikidata.org/w/index.php?title=Q33665576&oldid=2134294236"