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

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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

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28553270 AND SRC: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)

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21 March 2020

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Streptomyces ambofaciens

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transcriptomics

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2

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21 March 2020

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21 March 2020

Gianluca De Bellis

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21 March 2020

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21 March 2020

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21 March 2020

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Adelfia Talà

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21 March 2020

Clarissa Consolandi

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Clarissa Consolandi

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21 March 2020

author name string

Marco Fondi

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21 March 2020

Fabrizio Damiano

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21 March 2020

Benedetta Mattorre

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21 March 2020

Mariangela Testini

8

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21 March 2020

Giuseppe E De Benedetto

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21 March 2020

Luisa Siculella

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21 March 2020

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12 May 2017

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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/[email protected]

Frontiers in Microbiology

1 reference

Europe PubMed Central

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

21 March 2020

8

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Europe PubMed Central

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21 March 2020

835

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Europe PubMed Central

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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/[email protected]

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/FMICB.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/FMICB.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/FMICB.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/FMICB.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/FMICB.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/FMICB.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/FMICB.2017.00835

21 January 2018

Multidimensional optimality of microbial metabolism

1 reference

https://api.crossref.org/works/10.3389/FMICB.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

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

21 March 2020

PMC publication ID

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Europe PubMed Central

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21 March 2020

PubMed publication ID

1 reference

Europe PubMed Central

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

21 March 2020

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