ArticleBMC systems biology2014
Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale.
Article in BMC systems biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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48 citing papers in PubMed, 94 citations in OpenAlex.
- Coarse-grained resource allocation modeling for decoding and rewiring microbial metabolism.Trends in microbiology · 2026Review
- Integration of proteomic data with genome-scale metabolic models: A methodological overview.Protein science : a publication of the Protein Society · 2024Review
- Cardinality optimization in constraint-based modelling: application to human metabolism.Bioinformatics (Oxford, England) · 2023Article
- Predicting stress response and improved protein overproduction in Bacillus subtilis.NPJ systems biology and applications · 2022Article
- Construction and Analysis of an Enzyme-Constrained Metabolic Model ofBiomolecules · 2022Article
- Characterizing the Interplay of Rubisco and Nitrogenase Enzymes in Anaerobic-Photoheterotrophically Grown Rhodopseudomonas palustris CGA009 through a Genome-Scale Metabolic and Expression Model.Microbiology spectrum · 2022Article
- Construction of Multiscale Genome-Scale Metabolic Models: Frameworks and Challenges.Biomolecules · 2022Review
- Review
- Constraint-based modeling of yeast mitochondria reveals the dynamics of protein import and iron-sulfur cluster biogenesis.iScience · 2021Article
- Genome-Scale Reconstruction of Microbial Dynamic Phenotype: Successes and Challenges.Microorganisms · 2021Review
- Genome-scale metabolic modeling reveals key features of a minimal gene set.Molecular systems biology · 2021Article
- Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth.PLoS computational biology · 2021Article
- Addressing uncertainty in genome-scale metabolic model reconstruction and analysis.Genome biology · 2021Review
- Modeling of nitrogen fixation and polymer production in the heterotrophic diazotrophMetabolic engineering communications · 2020Article
- Reconstructing organisms in silico: genome-scale models and their emerging applications.Nature reviews. Microbiology · 2020Review
- Review
- Metabolic Modelling as a Framework for Metabolomics Data Integration and Analysis.Metabolites · 2020Review
- Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes.BMC bioinformatics · 2020Article
- Genome-scale reconstructions of the mammalian secretory pathway predict metabolic costs and limitations of protein secretion.Nature communications · 2020Article
- Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli.PLoS computational biology · 2019Article
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundMembranes play a crucial role in cellular functions. Membranes provide a physical barrier, control the trafficking of substances entering and leaving the cell, and are a major determinant of cellular ultra-structure. In addition, components embedded within the membrane participate in cell signaling, energy transduction, and other critical cellular functions. All these processes must share the limited space in the membrane; thus it represents a notable constraint on cellular functions. Membrane- and location-based processes have not yet been reconstructed and explicitly integrated into genome-scale models.
resultsThe recent genome-scale model of metabolism and protein expression in Escherichia coli (called a ME-model) computes the complete composition of the proteome required to perform whole cell functions. Here we expand the ME-model to include (1) a reconstruction of protein translocation pathways, (2) assignment of all cellular proteins to one of four compartments (cytoplasm, inner membrane, periplasm, and outer membrane) and a translocation pathway, (3) experimentally determined translocase catalytic and porin diffusion rates, and (4) a novel membrane constraint that reflects cell morphology. Comparison of computations performed with this expanded ME-model, named iJL1678-ME, against available experimental data reveals that the model accurately describes translocation pathway expression and the functional proteome by compartmentalized mass.
conclusioniJL1678-ME enables the computation of cellular phenotypes through an integrated computation of proteome composition, abundance, and activity in four cellular compartments (cytoplasm, periplasm, inner and outer membrane). Reconstruction and validation of the model has demonstrated that the iJL1678-ME is capable of capturing the functional content of membranes, cellular compartment-specific composition, and that it can be utilized to examine the effect of perturbing an expanded set of network components. iJL1678-ME takes a notable step towards the inclusion of cellular ultra-structure in genome-scale models.
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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.