ArticleBMC systems biology2013
Mapping global effects of the anti-sigma factor MucA in Pseudomonas fluorescens SBW25 through genome-scale metabolic modeling.
Article in BMC systems biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
15 citing papers in PubMed, 39 citations in OpenAlex.
- A widely-occurring family of pore-forming effectors broadens the impact of the Serratia Type VI secretion system.The EMBO journal · 2025Article
- Multi-Omics Analysis Revealed Increased De Novo Synthesis of Serine and Lower Activity of the Methionine Cycle in Breast Cancer Cell Lines.Molecules (Basel, Switzerland) · 2023Article
- Metabolic reconstruction of Pseudomonas chlororaphis ATCC 9446 to understand its metabolic potential as a phenazine-1-carboxamide-producing strain.Applied microbiology and biotechnology · 2020Article
- Pseudomonad reverse carbon catabolite repression, interspecies metabolite exchange, and consortial division of labor.Cellular and molecular life sciences : CMLS · 2020Review
- Fatty Acid Synthesis and Degradation Interplay to Regulate the Oxidative Stress in Cancer Cells.International journal of molecular sciences · 2019Article
- Genome-Scale Metabolic Network Models of Bacillus Species Suggest that Model Improvement is Necessary for Biotechnological Applications.Iranian journal of biotechnology · 2018Article
- Identification of a New Phosphatase Enzyme Potentially Involved in the Sugar Phosphate Stress Response in Pseudomonas fluorescens.Applied and environmental microbiology · 2017Article
- Comparison of 432 Pseudomonas strains through integration of genomic, functional, metabolic and expression data.Scientific reports · 2016Article
- Alginate Biosynthesis Factories in Pseudomonas fluorescens: Localization and Correlation with Alginate Production Level.Applied and environmental microbiology · 2016Article
- Mutational Analyses of Glucose Dehydrogenase and Glucose-6-Phosphate Dehydrogenase Genes in Pseudomonas fluorescens Reveal Their Effects on Growth and Alginate Production.Applied and environmental microbiology · 2015Article
- Fluxome study of Pseudomonas fluorescens reveals major reorganisation of carbon flux through central metabolic pathways in response to inactivation of the anti-sigma factor MucA.BMC systems biology · 2015Article
- Bacterial exopolysaccharides: biosynthesis pathways and engineering strategies.Frontiers in microbiology · 2015Review
- Modeling the differences in biochemical capabilities of pseudomonas species by flux balance analysis: how good are genome-scale metabolic networks at predicting the differences?TheScientificWorldJournal · 2014Article
- Bacterial sigma factors as targets for engineered or synthetic transcriptional control.Frontiers in bioengineering and biotechnology · 2014Review
- MEMOSys 2.0: an update of the bioinformatics database for genome-scale models and genomic data.Database : the journal of biological databases and curation · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAlginate is an industrially important polysaccharide, currently produced commercially by harvesting of marine brown sea-weeds. The polymer is also synthesized as an exo-polysaccharide by bacteria belonging to the genera Pseudomonas and Azotobacter, and these organisms may represent an alternative alginate source in the future. The current work describes an attempt to rationally develop a biological system tuned for very high levels of alginate production, based on a fundamental understanding of the system through metabolic modeling supported by transcriptomics studies and carefully controlled fermentations.
resultsAlginate biosynthesis in Pseudomonas fluorescens was studied in a genomics perspective, using an alginate over-producing strain carrying a mutation in the anti-sigma factor gene mucA. Cells were cultivated in chemostats under nitrogen limitation on fructose or glycerol as carbon sources, and cell mass, growth rate, sugar uptake, alginate and CO(2) production were monitored. In addition a genome scale metabolic model was constructed and samples were collected for transcriptome analyses. The analyses show that polymer production operates in a close to optimal way with respect to stoichiometric utilization of the carbon source and that the cells increase the uptake of carbon source to compensate for the additional needs following from alginate synthesis. The transcriptome studies show that in the presence of the mucA mutation, the alg operon is upregulated together with genes involved in energy generation, genes on both sides of the succinate node of the TCA cycle and genes encoding ribosomal and other translation-related proteins. Strains expressing a functional MucA protein (no alginate production) synthesize cellular biomass in an inefficient way, apparently due to a cycle that involves oxidation of NADPH without ATP production. The results of this study indicate that the most efficient way of using a mucA mutant as a cell factory for alginate production would be to use non-growing conditions and nitrogen deprivation.
conclusionsThe insights gained in this study should be very useful for a future efficient production of microbial alginates.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.