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Functional metabolomics: from biomarker discovery to metabolome reprogramming.

Peng B, Li H, Peng XX - Protein Cell (2015)

Bottom Line: Metabolomics is emerging as a powerful tool for studying metabolic processes, identifying crucial biomarkers responsible for metabolic characteristics and revealing metabolic mechanisms, which construct the content of discovery metabolomics.The striking feature on the similarity of the basic metabolic pathways and components among vastly different species makes the reprogramming metabolomics possible when the engineered metabolites play biological roles in cellular activity as a substrate of enzymes and a regulator to other molecules including proteins.This review introduces the current state and trends of discovery metabolomics and reprogramming metabolomics and highlights the importance of reprogramming metabolomics.

View Article: PubMed Central - PubMed

Affiliation: Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.

ABSTRACT
Metabolomics is emerging as a powerful tool for studying metabolic processes, identifying crucial biomarkers responsible for metabolic characteristics and revealing metabolic mechanisms, which construct the content of discovery metabolomics. The crucial biomarkers can be used to reprogram a metabolome, leading to an aimed metabolic strategy to cope with alteration of internal and external environments, naming reprogramming metabolomics here. The striking feature on the similarity of the basic metabolic pathways and components among vastly different species makes the reprogramming metabolomics possible when the engineered metabolites play biological roles in cellular activity as a substrate of enzymes and a regulator to other molecules including proteins. The reprogramming metabolomics approach can be used to clarify metabolic mechanisms of responding to changed internal and external environmental factors and to establish a framework to develop targeted tools for dealing with the changes such as controlling and/or preventing infection with pathogens and enhancing host immunity against pathogens. This review introduces the current state and trends of discovery metabolomics and reprogramming metabolomics and highlights the importance of reprogramming metabolomics.

No MeSH data available.


Related in: MedlinePlus

Outline of reprogramming metabolome
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Related In: Results  -  Collection


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Fig3: Outline of reprogramming metabolome

Mentions: Reprogramming metabolomics identifies crucial biomarkers and pathways while discovery metabolomics does to provide potential metabolic modulators, reprogramming metabolites, for modulating an existing metabolome to a targeted metabolome. This leads to reconstitution of metabolic strategy. The reconstitution can be demonstrated by metabolomics analysis and functional assays (Peng et al., 2015a). The metabolomics analysis is used to validate the effect of exogenous metabolite boosting on varied metabolites and pathways and identify the metabolic flux magnitudes into each metabolite pool by determining the mass isotopomer distribution for all labeled compounds (Peng et al., 2015a). The functional assays provide proofs on whether the reconstituted metabolic strategy may show the similar phenotypes and the mechanism of action (Peng et al., 2015a; Su et al., 2015; Cheng et al., 2014; Zhao et al., 2014; Ma et al., 2015). Thus, reprogramming metabolomics reveal the response and reconstituted mechanisms by analysis of the response metabolome and reconstituted metabolome, respectively, in which methods on molecular biology and biochemistry, cell biology and immunology will become basic tool to elucidate these mechanisms. The general methodologies of the reprogramming metabolomics are outlined in Fig. 3.Figure 3


Functional metabolomics: from biomarker discovery to metabolome reprogramming.

Peng B, Li H, Peng XX - Protein Cell (2015)

Outline of reprogramming metabolome
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4537470&req=5

Fig3: Outline of reprogramming metabolome
Mentions: Reprogramming metabolomics identifies crucial biomarkers and pathways while discovery metabolomics does to provide potential metabolic modulators, reprogramming metabolites, for modulating an existing metabolome to a targeted metabolome. This leads to reconstitution of metabolic strategy. The reconstitution can be demonstrated by metabolomics analysis and functional assays (Peng et al., 2015a). The metabolomics analysis is used to validate the effect of exogenous metabolite boosting on varied metabolites and pathways and identify the metabolic flux magnitudes into each metabolite pool by determining the mass isotopomer distribution for all labeled compounds (Peng et al., 2015a). The functional assays provide proofs on whether the reconstituted metabolic strategy may show the similar phenotypes and the mechanism of action (Peng et al., 2015a; Su et al., 2015; Cheng et al., 2014; Zhao et al., 2014; Ma et al., 2015). Thus, reprogramming metabolomics reveal the response and reconstituted mechanisms by analysis of the response metabolome and reconstituted metabolome, respectively, in which methods on molecular biology and biochemistry, cell biology and immunology will become basic tool to elucidate these mechanisms. The general methodologies of the reprogramming metabolomics are outlined in Fig. 3.Figure 3

Bottom Line: Metabolomics is emerging as a powerful tool for studying metabolic processes, identifying crucial biomarkers responsible for metabolic characteristics and revealing metabolic mechanisms, which construct the content of discovery metabolomics.The striking feature on the similarity of the basic metabolic pathways and components among vastly different species makes the reprogramming metabolomics possible when the engineered metabolites play biological roles in cellular activity as a substrate of enzymes and a regulator to other molecules including proteins.This review introduces the current state and trends of discovery metabolomics and reprogramming metabolomics and highlights the importance of reprogramming metabolomics.

View Article: PubMed Central - PubMed

Affiliation: Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.

ABSTRACT
Metabolomics is emerging as a powerful tool for studying metabolic processes, identifying crucial biomarkers responsible for metabolic characteristics and revealing metabolic mechanisms, which construct the content of discovery metabolomics. The crucial biomarkers can be used to reprogram a metabolome, leading to an aimed metabolic strategy to cope with alteration of internal and external environments, naming reprogramming metabolomics here. The striking feature on the similarity of the basic metabolic pathways and components among vastly different species makes the reprogramming metabolomics possible when the engineered metabolites play biological roles in cellular activity as a substrate of enzymes and a regulator to other molecules including proteins. The reprogramming metabolomics approach can be used to clarify metabolic mechanisms of responding to changed internal and external environmental factors and to establish a framework to develop targeted tools for dealing with the changes such as controlling and/or preventing infection with pathogens and enhancing host immunity against pathogens. This review introduces the current state and trends of discovery metabolomics and reprogramming metabolomics and highlights the importance of reprogramming metabolomics.

No MeSH data available.


Related in: MedlinePlus