Effects of arcA and arcB genes knockout on the metabolism in Escherichia coli under anaerobic and microaerobic conditions

Nizam, Syed Asif; Shimizu, Kazuyuki

doi:10.1016/j.bej.2008.06.021

Cited by 39 publications

(26 citation statements)

References 38 publications

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“…Different types of mutations in components of global regulatory systems, such as arcA and creB (39)(40)(41)43), have been shown to influence both carbon and redox balances in E. coli, mainly under microoxic growth conditions. The current study focused on the manipulation of global regulators as a relevant tool to modulate central metabolic fluxes under anoxic conditions and harnessing the reducing power availability for biotechnological purposes.…”

Section: Discussionmentioning

confidence: 99%

Manipulation of the Anoxic Metabolism in Escherichia coli by ArcB Deletion Variants in the ArcBA Two-Component System

Bidart

Ruiz

Almeida

et al. 2012

Appl Environ Microbiol

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Bioprocesses conducted under conditions with restricted O 2 supply are increasingly exploited for the synthesis of reduced biochemicals using different biocatalysts. The model facultative anaerobe Escherichia coli has elaborate sensing and signal transduction mechanisms for redox control in response to the availability of O 2 and other electron acceptors. The ArcBA two-component system consists of ArcB, a membrane-associated sensor kinase, and ArcA, the cognate response regulator. The tripartite hybrid kinase ArcB possesses a transmembrane, a PAS, a primary transmitter (H1), a receiver (D1), and a phosphotransfer (H2) domain. Metabolic fluxes were compared under anoxic conditions in a wild-type E. coli strain, its ⌬arcB derivative, and two partial arcB deletion mutants in which ArcB lacked either the H1 domain or the PAS-H1-D1 domains. These analyses revealed that elimination of different segments in ArcB determines a distinctive distribution of D-glucose catabolic fluxes, different from that observed in the ⌬arcB background. Metabolite profiles, enzyme activity levels, and gene expression patterns were also investigated in these strains. Relevant alterations were observed at the P-enol-pyruvate/pyruvate and acetyl coenzyme A metabolic nodes, and the formation of reduced fermentation metabolites, such as succinate, D-lactate, and ethanol, was favored in the mutant strains to different extents compared to the wild-type strain. These phenotypic traits were associated with altered levels of the enzymatic activities operating at these nodes, as well as with elevated NADH/NAD ؉ ratios. Thus, targeted modification of global regulators to obtain different metabolic flux distributions under anoxic conditions is emerging as an attractive tool for metabolic engineering purposes.A noxic fermentation of different carbon sources by Escherichia coli is increasingly gaining momentum in biotechnological setups designed to obtain reduced biochemicals. Relevant examples in this sense include (but are certainly not limited to) the production of ethanol (31, 58, 69), succinate (64), D-lactate (45), and polyhydroxyalkanoates (24, 40), often by using redox and/or regulatory E. coli mutants as the biocatalyst. These metabolic engineering approaches underscore the need for a complete understanding of the cell physiology and metabolic network operativity under anoxic growth conditions. In fact, the relative lack of knowledge on the cellular wiring of these regulatory networks under conditions relevant to both laboratory and industrial applications represents a hurdle that has to be overcome for the efficient design of industrial processes. Metabolic fluxes through the central carbon pathways constitute the backbone of cell metabolism and represent the in vivo reaction rates of cognate enzymatic steps (62). The observed fluxome is the phenotypic consequence of both gene transcription and translation, as well as of the enzymatic activity and the regulation exerted at the metabolite level (48). Fluxome analysis is thus a useful approach to...

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Section: Discussionmentioning

confidence: 99%

Manipulation of the Anoxic Metabolism in Escherichia coli by ArcB Deletion Variants in the ArcBA Two-Component System

Bidart

Ruiz

Almeida

et al. 2012

Appl Environ Microbiol

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“…The goals of these studies have been to explore specific parts of the metabolic and regulatory network, and to assess the general perturbation response. Examples of the former are studies which combine genetic and environmental perturbations to study oxygen sensing and aerobic regulatory response [25–27]. Another example is a study by Nakahigashi et al, in which a novel hidden reaction in the pentose phosphate pathway was discovered by studying sets of double knockouts [28].…”

Section: Metabolic Flux Analysis Studies Of E Coli Knockoutsmentioning

confidence: 99%

Metabolic flux analysis of Escherichia coli knockouts: lessons from the Keio collection and future outlook

Long¹,

Antoniewicz²

2014

Current Opinion in Biotechnology

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Cellular metabolic and regulatory systems are of fundamental interest to biologists and engineers. Incomplete understanding of these complex systems remains an obstacle to progress in biotechnology and metabolic engineering. An established method for obtaining new information on network structure, regulation and dynamics is to study the cellular system following a perturbation such as a genetic knockout. The Keio collection of all viable E. coli single-gene knockouts is facilitating a systematic investigation of the regulation and metabolism of E. coli. Of all omics measurements available, the metabolic flux profile (the fluxome) provides the most direct and relevant representation of the cellular phenotype. Recent advances in 13C-metabolic flux analysis are now permitting highly precise and accurate flux measurements for investigating cellular systems and guiding metabolic engineering efforts.

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“…In addition, as expected from the aforementioned regulation, the TCA cycle is activated when the arcA/B gene is knocked out, causing high NADH/NAD ratios, which in turn represses the activity of the TCA cycle [261]. Vemuri et al [262,263] considered expressing the heterologous nox gene to oxidize NADH, thereby activating the TCA cycle, whereas we have used nicotinic acid and sodium nitrate to activate the TCA cycle [264].…”

Section: Global Regulators In Relation To the Cultural Environmentmentioning

confidence: 97%

Effects of arcA and arcB genes knockout on the metabolism in Escherichia coli under anaerobic and microaerobic conditions

Cited by 39 publications

References 38 publications

Manipulation of the Anoxic Metabolism in Escherichia coli by ArcB Deletion Variants in the ArcBA Two-Component System

Manipulation of the Anoxic Metabolism in Escherichia coli by ArcB Deletion Variants in the ArcBA Two-Component System

Metabolic flux analysis of Escherichia coli knockouts: lessons from the Keio collection and future outlook

Toward systematic metabolic engineering based on the analysis of metabolic regulation by the integration of different levels of information

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