Genomics to fluxomics and physiomics — pathway engineering

Sanford, Karl; Soucaille, Phillipe; Whited, Gregg; Chotani, Gopal

doi:10.1016/s1369-5274(02)00318-1

Cited by 58 publications

(27 citation statements)

References 45 publications

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“…The excretion of by-products and depletion of nutrients from the medium result in an undefined environment, which has an unpredictable impact on the physiology and growth rate of the organism. In addition, batch cultivations yield no information about how the macromolecular content varies with the growth rate and specific environmental conditions and are therefore not amenable to systems biology approaches to modeling cellular physiology such as metabolic flux analysis (MFA) (48). MFA is a key technique in metabolic engineering, allowing metabolic phenotypes to be defined in terms of the carbon flux through a metabolic network by the use of mathematical modeling and computer simulation.…”

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confidence: 99%

Compiling a Molecular Inventory for Mycobacterium bovis BCG at Two Growth Rates: Evidence for Growth Rate-Mediated Regulation of Ribosome Biosynthesis and Lipid Metabolism

et al. 2005

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An experimental system of Mycobacterium tuberculosis growth in a carbon-limited chemostat has been established by the use of Mycobacterium bovis BCG as a model organism. For this model, carbon-limited chemostats with low concentrations of glycerol were used to simulate possible growth rates during different stages of tuberculosis. A doubling time of 23 h (D ‫؍‬ 0.03 h ؊1 ) was adopted to represent cells during the acute phase of infection, whereas a lower dilution rate equivalent to a doubling time of 69 h (D ‫؍‬ 0.01 h ؊1 ) was used to model mycobacterial persistence. This chemostat model allowed the specific response of the mycobacterial cell to carbon limitation at different growth rates to be elucidated. The macromolecular (RNA, DNA, carbohydrate, and lipid) and elemental (C, H, and N) compositions of the biomass were determined for steady-state cultures, revealing that carbohydrates and lipids comprised more than half of the dry mass of the BCG cell, with only a quarter of the dry weight consisting of protein and RNA. Consistent with studies of other bacteria, the specific growth rate impacts on the macromolecular content of BCG and the proportions of lipid, RNA, and protein increased significantly with the growth rate. The correlation of RNA content with the growth rate indicates that ribosome production in carbon-limited M. bovis BCG cells is subject to growth rate-dependent control. The results also clearly show that the proportion of lipids in the mycobacterial cell is very sensitive to changes in the growth rate, probably reflecting changes in the amounts of storage lipids. Finally, this study demonstrates the utility of the chemostat model of mycobacterial growth for functional genomic, physiology, and systems biology studies.With three million people dying from tuberculosis (TB) annually, Mycobacterium tuberculosis remains a formidable pathogen. Tuberculosis ranks among the top 10 causes of global mortality and morbidity and is the leading cause of infectious disease (66). The ability of M. tuberculosis to adapt to and survive harsh environmental conditions in order to establish and maintain long-term infections within its human host is fundamental to this organism's success. Modification of the mycobacterial cell in response to changes in the environment is crucial to this adaptive process, but detailed information about how M. tuberculosis changes its macromolecular composition in response to its environment and growth rate is lacking.The genome sequence of M. tuberculosis has been available since 1998 (9). Although information obtained from the genome sequence provided new and valuable insights into the biology of the tubercle bacillus, the genome itself provides few clues regarding how the pathogen responds to its environment by changing its cellular composition. One of the principal tasks of postgenomic biological studies of M. tuberculosis is to understand how the genome orchestrates the structure and dynamics of the cell in response to changes in the environment. This task requires an integrat...

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confidence: 99%

Compiling a Molecular Inventory for Mycobacterium bovis BCG at Two Growth Rates: Evidence for Growth Rate-Mediated Regulation of Ribosome Biosynthesis and Lipid Metabolism

et al. 2005

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“…Hence, any cellular behavior is a direct or indirect product of its metabolism. The enzymes/metabolites participating in metabolism provide a precise snapshot of a cellular phenotype (1,2). As part of our study on molecular adaptation, we have uncovered an interesting model system that allows deciphering the metabolic reconfiguration evoked by metal stress.…”

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confidence: 99%

Aluminum Triggers Decreased Aconitase Activity via Fe-S Cluster Disruption and the Overexpression of Isocitrate Dehydrogenase and Isocitrate Lyase

Middaugh

Hamel

Jean-Baptiste

et al. 2005

Journal of Biological Chemistry

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Although aluminum is known to be toxic to most organisms, its precise biochemical interactions are not fully understood. In the present study, we demonstrate that aluminum promotes the inhibition of aconitase (Acn) activity via the perturbation of the Fe-S cluster in Pseudomonas fluorescens. Despite the significant decrease in citrate isomerization activity, cellular survival is assured by the overexpression of isocitrate lyase and isocitrate dehydrogenase (IDH)-NADP ؉ . 13 C NMR spectroscopic studies, Blue Native PAGE, and Western blot analyses indicated that although the decrease in Acn activity is concomitant with the increase of aluminum in the culture, the amount of Acn expressed is not sensitive to the concentration of the trivalent metal. A 6-fold decrease in Acn activity and no discernable change in protein content in aluminum-stressed cultures were observed. The addition of Fe(NH 4 ) 2 (SO 4 ) 2 in a reducing environment led to a significant recovery in Acn activity. This enzymatic activity reverted to normal levels when aluminum-stressed cells were transferred to either a control or an iron-supplemented medium. The overexpression of the two isocitrate-metabolizing enzymes isocitrate lyase and IDH-NADP ؉ appears to mitigate the deficit in Acn activity. The levels of these enzymes are dependent on the aluminum content of the culture and appear to be under transcriptional control. Hence, the regulation of the enzymes involved in the homeostasis of isocitrate constitutes a pivotal component of the global metabolic strategy that ensures the survival of this organism in an aluminum citrate environment.Metabolism is the foundation of all living organisms, and any biological function is the manifestation of the global cellular metabolism. Hence, any cellular behavior is a direct or indirect product of its metabolism. The enzymes/metabolites participating in metabolism provide a precise snapshot of a cellular phenotype (1, 2). As part of our study on molecular adaptation, we have uncovered an interesting model system that allows deciphering the metabolic reconfiguration evoked by metal stress. The metal toxicant was supplied to the microbe Pseudomonas fluorescens, complexed to citrate, the only carbon source. The role of oxalate and phosphatidylethanolamine in the immobilization of aluminum has been demonstrated recently (3, 4). It appears that the cellular metabolism is reconfigured with the aim of providing the metabolic precursors that allow for the survival of the organism in an aluminum environment. Hence, an aluminum-adapted phenotype with an entirely different set of metabolic pathways than in the wild type is promoted.Citrate, the sole carbon source utilized in this system, is known to be cleaved in various organisms, primarily by the enzymes citrate-lyase (CL), 1 ATP-citrate-lyase (ATP-CL), and Acn. Whereas CL mediates the cleavage of citrate to acetate and oxaloacetate, ATP-CL catalyzes the degradation of tricarboxylic acid into acetyl-CoA and oxaloacetate (5, 6). The latter is also referred to as a l...

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“…Combination of constraint-based modeling framework with isotopic label tracing on a large scale [3,10,12] b. Construction genome-scale atom mapping model for MFA calculations enables the complete tracking of labeled atoms through pathways [4,7].…”

Section: Overview and Current Status Of 13 C Labeling Metabolic Flux mentioning

confidence: 99%

Metabolic flux analysis of Escherichia coli MG1655 under octanoic acid (C8) stress

Yoon

Jarboe

et al. 2015

Appl Microbiol Biotechnol

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Genomics to fluxomics and physiomics — pathway engineering

Cited by 58 publications

References 45 publications

Compiling a Molecular Inventory for Mycobacterium bovis BCG at Two Growth Rates: Evidence for Growth Rate-Mediated Regulation of Ribosome Biosynthesis and Lipid Metabolism

Compiling a Molecular Inventory for Mycobacterium bovis BCG at Two Growth Rates: Evidence for Growth Rate-Mediated Regulation of Ribosome Biosynthesis and Lipid Metabolism

Aluminum Triggers Decreased Aconitase Activity via Fe-S Cluster Disruption and the Overexpression of Isocitrate Dehydrogenase and Isocitrate Lyase

Metabolic flux analysis of Escherichia coli MG1655 under octanoic acid (C8) stress

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