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Journal ArticleDOI

Biochemical systems analysis: A study of function and design in molecular biology

01 Mar 1978-International Journal of Bio-medical Computing (Elsevier)-Vol. 9, Iss: 2, pp 163-164
About: This article is published in International Journal of Bio-medical Computing.The article was published on 1978-03-01. It has received 379 citations till now.
Citations
More filters
Journal ArticleDOI
TL;DR: This work states that rapid advances in network biology indicate that cellular networks are governed by universal laws and offer a new conceptual framework that could potentially revolutionize the view of biology and disease pathologies in the twenty-first century.
Abstract: A key aim of postgenomic biomedical research is to systematically catalogue all molecules and their interactions within a living cell. There is a clear need to understand how these molecules and the interactions between them determine the function of this enormously complex machinery, both in isolation and when surrounded by other cells. Rapid advances in network biology indicate that cellular networks are governed by universal laws and offer a new conceptual framework that could potentially revolutionize our view of biology and disease pathologies in the twenty-first century.

7,475 citations


Cites background from "Biochemical systems analysis: A stu..."

  • ...Therefore, an ultimate description of cellular networks requires that both the intensity (that is, strength) and the temporal aspects of the interactions are considere...

    [...]

Journal ArticleDOI
TL;DR: This study defines the function of one of the most significant recurring circuit elements in transcription networks, the feed-forward loop (FFL), which is a three-gene pattern composed of two input transcription factors, both jointly regulating a target gene.
Abstract: Engineered systems are often built of recurring circuit modules that carry out key functions. Transcription networks that regulate the responses of living cells were recently found to obey similar principles: they contain several biochemical wiring patterns, termed network motifs, which recur throughout the network. One of these motifs is the feed-forward loop (FFL). The FFL, a three-gene pattern, is composed of two input transcription factors, one of which regulates the other, both jointly regulating a target gene. The FFL has eight possible structural types, because each of the three interactions in the FFL can be activating or repressing. Here, we theoretically analyze the functions of these eight structural types. We find that four of the FFL types, termed incoherent FFLs, act as sign-sensitive accelerators: they speed up the response time of the target gene expression following stimulus steps in one direction (e.g., off to on) but not in the other direction (on to off). The other four types, coherent FFLs, act as sign-sensitive delays. We find that some FFL types appear in transcription network databases much more frequently than others. In some cases, the rare FFL types have reduced functionality (responding to only one of their two input stimuli), which may partially explain why they are selected against. Additional features, such as pulse generation and cooperativity, are discussed. This study defines the function of one of the most significant recurring circuit elements in transcription networks.

1,774 citations

Journal ArticleDOI
19 Nov 2010-Science
TL;DR: A phenomenological study is described that reveals intrinsic constraints governing the allocation of resources toward protein synthesis and other aspects of cell growth, and may facilitate the understanding and manipulation of complex biological systems before underlying regulatory circuits are elucidated.
Abstract: In bacteria, the rate of cell proliferation and the level of gene expression are intimately intertwined. Elucidating these relations is important both for understanding the physiological functions of endogenous genetic circuits and for designing robust synthetic systems. We describe a phenomenological study that reveals intrinsic constraints governing the allocation of resources toward protein synthesis and other aspects of cell growth. A theory incorporating these constraints can accurately predict how cell proliferation and gene expression affect one another, quantitatively accounting for the effect of translation-inhibiting antibiotics on gene expression and the effect of gratuitous protein expression on cell growth. The use of such empirical relations, analogous to phenomenological laws, may facilitate our understanding and manipulation of complex biological systems before underlying regulatory circuits are elucidated.

1,229 citations


Cites background from "Biochemical systems analysis: A stu..."

  • ...(B) The RNA/protein ratio for a family of translational mutants SmR (triangles) and SmP (inverted triangles) and their parent strain Xac (circles) (27), grown with various nutrients (see key at lower left) (table S2)....

    [...]

Book
14 Feb 2002
TL;DR: A comprehensive review of the theory of genetic programming can be found in this paper, where the authors provide a coherent consolidation of recent work on the theoretical foundations of GP and genetic algorithms.
Abstract: This is one of the only books to provide a complete and coherent review of the theory of genetic programming (GP). In doing so, it provides a coherent consolidation of recent work on the theoretical foundations of GP. A concise introduction to GP and genetic algorithms (GA) is followed by a discussion of fitness landscapes and other theoretical approaches to natural and artificial evolution. Having surveyed early approaches to GP theory it presents new exact schema analysis, showing that it applies to GP as well as to the simpler GAs. New results on the potentially infinite number of possible programs are followed by two chapters applying these new techniques.

829 citations

Journal ArticleDOI
TL;DR: The discoveries of feedback inhibition, co-operativity and covalent modification in enzymes, and of mechanisms for the control of enzyme synthesis and degradation, have disclosed a repertoire of molecular effects that potentially alter the fluxes in metabolic pathways.
Abstract: As the details of the chemical transformations in metabolism have become increasingly clear, and the enzymes catalysing many of the reactions have been characterized, it is understandable that biochemists should want to explain at the molecular level the metabolic homeostasis observed at the physiological level. How are the rates of synthesis and degradation of metabolites kept in close balance over a very wide range of external conditions without catastrophic rises or falls in the metabolite concentrations? The discoveries of feedback inhibition, co-operativity and covalent modification in enzymes, and of mechanisms for the control of enzyme synthesis and degradation, have disclosed a repertoire of molecular effects that potentially alter the fluxes in metabolic pathways. With such a range of effects to choose from, it is not surprising that disputes arise over explanations for the changes in flux through particular pathways under given circumstances. Since the explanations are usually verbal and qualitative, discrimination between different explanations, or assessment of their adequacy, is difficult. More recently, several groups have attempted theoretical analysis of the potential of these different molecular mechanisms to contribute to the control of metabolic flux. Since these theories can be given a mathematical formulation, they can be used in combination with appropriate experimental measurements to provide quantitative explanations and, potentially, predictions. The theories have often been controversial. Matters at issue have included the extent to which it is feasible to perform experiments to obtain the necessary data, the adequacy of the theories for making useful predictions, and the degree to which the quantitative measures of the theories do actually capture the relevant aspects of regulation and control. To some extent, this is a matter of semantics; a mathematical theory is more explicit about its underlying assumptions and the meaning of its statements, but regulation and control are two terms that have been used without strict adherence to any agreed definition in many different contexts (as noted in [1]). It is therefore inevitable that some will find that the use of these terms in the context of a mathematical theory places a narrower construction on them than they would like. These theories all include a form of sensitivity analysis; that is, the magnitude of the effect of some small change in a parameter (such as an enzyme activity) on a metabolic system property (such as the flux or the concentration of a metabolite) is mathematically related to the properties of the components of the system. Sensitivity analysis is widely used for analogous problems in other fields, including economics, ecology [2], engineering [3] and chemical kinetics [4-6]. Its application in biochemistry was pioneered by Higgins [7], but three variants subsequently arose: Metabolic Control Analysis, Biochemical Systems Theory and Crabtree and Newsholme's 'flux-oriented' theory (the term used in [8]). It is not possible to give a succinct account of the differences between the approaches, which is a controversial area [9-18] even though the underlying mathematics is equivalent to a considerable extent. One area of difference is the choice of the type of parameter that is changed for the determination of sensitivities. In Metabolic Control Analysis, enzyme concentration (or activity) is usually chosen; the response to an external modifier of a metabolic pathway is derived from the resulting sensitivities. In Biochemical Systems Theory [19-25], the primary parameters for the sensitivities are the 'rate constants' for synthesis and degradation of metabolite pools. Savageau has given many reasons for this choice of parameter; Cornish-Bowden has articulated some of the problems with it [15]. Although using these 'rate constants' simplifies the analysis procedures within Biochemical Systems Theory, there is not a one-to-one relationship between them and the enzymes of the system, which can create a slight complication in determining the sensitivity to variation of an enzyme activity. Savageau's theory is part of an integrated system for stability analysis and simulation, in addition to sensitivity analysis. Crabtree and Newsholme's theory [8,10,26-30] is intermediate between the two others, and the primary sensitivities are to an external modifier (a hypothetical one if necessary), but its mathematical development is less rigorous. In this review, I shall concentrate on Metabolic Control Analysis. This is because, apart from considerations of space, approximately two-thirds of the literature citations of theories of metabolic regulation in the past 5 years have been to Metabolic Control Analysis. This may relate to perceived ease of use, which has been compared using the different approaches on the same set of experimental results [31]. In the following review, I will not give a complete derivation and description of the basic concepts of Metabolic Control Analysis; clear accounts can be found in previous articles and reviews [9,32-39]. Instead I will try to indicate areas of disagreement, the scope of the basic theory and where it has been modified or extended, and recent approaches to experimental applications.

788 citations

References
More filters
Journal ArticleDOI
TL;DR: This work states that rapid advances in network biology indicate that cellular networks are governed by universal laws and offer a new conceptual framework that could potentially revolutionize the view of biology and disease pathologies in the twenty-first century.
Abstract: A key aim of postgenomic biomedical research is to systematically catalogue all molecules and their interactions within a living cell. There is a clear need to understand how these molecules and the interactions between them determine the function of this enormously complex machinery, both in isolation and when surrounded by other cells. Rapid advances in network biology indicate that cellular networks are governed by universal laws and offer a new conceptual framework that could potentially revolutionize our view of biology and disease pathologies in the twenty-first century.

7,475 citations

Journal ArticleDOI
TL;DR: This study defines the function of one of the most significant recurring circuit elements in transcription networks, the feed-forward loop (FFL), which is a three-gene pattern composed of two input transcription factors, both jointly regulating a target gene.
Abstract: Engineered systems are often built of recurring circuit modules that carry out key functions. Transcription networks that regulate the responses of living cells were recently found to obey similar principles: they contain several biochemical wiring patterns, termed network motifs, which recur throughout the network. One of these motifs is the feed-forward loop (FFL). The FFL, a three-gene pattern, is composed of two input transcription factors, one of which regulates the other, both jointly regulating a target gene. The FFL has eight possible structural types, because each of the three interactions in the FFL can be activating or repressing. Here, we theoretically analyze the functions of these eight structural types. We find that four of the FFL types, termed incoherent FFLs, act as sign-sensitive accelerators: they speed up the response time of the target gene expression following stimulus steps in one direction (e.g., off to on) but not in the other direction (on to off). The other four types, coherent FFLs, act as sign-sensitive delays. We find that some FFL types appear in transcription network databases much more frequently than others. In some cases, the rare FFL types have reduced functionality (responding to only one of their two input stimuli), which may partially explain why they are selected against. Additional features, such as pulse generation and cooperativity, are discussed. This study defines the function of one of the most significant recurring circuit elements in transcription networks.

1,774 citations

Journal ArticleDOI
19 Nov 2010-Science
TL;DR: A phenomenological study is described that reveals intrinsic constraints governing the allocation of resources toward protein synthesis and other aspects of cell growth, and may facilitate the understanding and manipulation of complex biological systems before underlying regulatory circuits are elucidated.
Abstract: In bacteria, the rate of cell proliferation and the level of gene expression are intimately intertwined. Elucidating these relations is important both for understanding the physiological functions of endogenous genetic circuits and for designing robust synthetic systems. We describe a phenomenological study that reveals intrinsic constraints governing the allocation of resources toward protein synthesis and other aspects of cell growth. A theory incorporating these constraints can accurately predict how cell proliferation and gene expression affect one another, quantitatively accounting for the effect of translation-inhibiting antibiotics on gene expression and the effect of gratuitous protein expression on cell growth. The use of such empirical relations, analogous to phenomenological laws, may facilitate our understanding and manipulation of complex biological systems before underlying regulatory circuits are elucidated.

1,229 citations

Journal ArticleDOI
TL;DR: The discoveries of feedback inhibition, co-operativity and covalent modification in enzymes, and of mechanisms for the control of enzyme synthesis and degradation, have disclosed a repertoire of molecular effects that potentially alter the fluxes in metabolic pathways.
Abstract: As the details of the chemical transformations in metabolism have become increasingly clear, and the enzymes catalysing many of the reactions have been characterized, it is understandable that biochemists should want to explain at the molecular level the metabolic homeostasis observed at the physiological level. How are the rates of synthesis and degradation of metabolites kept in close balance over a very wide range of external conditions without catastrophic rises or falls in the metabolite concentrations? The discoveries of feedback inhibition, co-operativity and covalent modification in enzymes, and of mechanisms for the control of enzyme synthesis and degradation, have disclosed a repertoire of molecular effects that potentially alter the fluxes in metabolic pathways. With such a range of effects to choose from, it is not surprising that disputes arise over explanations for the changes in flux through particular pathways under given circumstances. Since the explanations are usually verbal and qualitative, discrimination between different explanations, or assessment of their adequacy, is difficult. More recently, several groups have attempted theoretical analysis of the potential of these different molecular mechanisms to contribute to the control of metabolic flux. Since these theories can be given a mathematical formulation, they can be used in combination with appropriate experimental measurements to provide quantitative explanations and, potentially, predictions. The theories have often been controversial. Matters at issue have included the extent to which it is feasible to perform experiments to obtain the necessary data, the adequacy of the theories for making useful predictions, and the degree to which the quantitative measures of the theories do actually capture the relevant aspects of regulation and control. To some extent, this is a matter of semantics; a mathematical theory is more explicit about its underlying assumptions and the meaning of its statements, but regulation and control are two terms that have been used without strict adherence to any agreed definition in many different contexts (as noted in [1]). It is therefore inevitable that some will find that the use of these terms in the context of a mathematical theory places a narrower construction on them than they would like. These theories all include a form of sensitivity analysis; that is, the magnitude of the effect of some small change in a parameter (such as an enzyme activity) on a metabolic system property (such as the flux or the concentration of a metabolite) is mathematically related to the properties of the components of the system. Sensitivity analysis is widely used for analogous problems in other fields, including economics, ecology [2], engineering [3] and chemical kinetics [4-6]. Its application in biochemistry was pioneered by Higgins [7], but three variants subsequently arose: Metabolic Control Analysis, Biochemical Systems Theory and Crabtree and Newsholme's 'flux-oriented' theory (the term used in [8]). It is not possible to give a succinct account of the differences between the approaches, which is a controversial area [9-18] even though the underlying mathematics is equivalent to a considerable extent. One area of difference is the choice of the type of parameter that is changed for the determination of sensitivities. In Metabolic Control Analysis, enzyme concentration (or activity) is usually chosen; the response to an external modifier of a metabolic pathway is derived from the resulting sensitivities. In Biochemical Systems Theory [19-25], the primary parameters for the sensitivities are the 'rate constants' for synthesis and degradation of metabolite pools. Savageau has given many reasons for this choice of parameter; Cornish-Bowden has articulated some of the problems with it [15]. Although using these 'rate constants' simplifies the analysis procedures within Biochemical Systems Theory, there is not a one-to-one relationship between them and the enzymes of the system, which can create a slight complication in determining the sensitivity to variation of an enzyme activity. Savageau's theory is part of an integrated system for stability analysis and simulation, in addition to sensitivity analysis. Crabtree and Newsholme's theory [8,10,26-30] is intermediate between the two others, and the primary sensitivities are to an external modifier (a hypothetical one if necessary), but its mathematical development is less rigorous. In this review, I shall concentrate on Metabolic Control Analysis. This is because, apart from considerations of space, approximately two-thirds of the literature citations of theories of metabolic regulation in the past 5 years have been to Metabolic Control Analysis. This may relate to perceived ease of use, which has been compared using the different approaches on the same set of experimental results [31]. In the following review, I will not give a complete derivation and description of the basic concepts of Metabolic Control Analysis; clear accounts can be found in previous articles and reviews [9,32-39]. Instead I will try to indicate areas of disagreement, the scope of the basic theory and where it has been modified or extended, and recent approaches to experimental applications.

788 citations

Journal ArticleDOI
26 Feb 2004-Nature
TL;DR: A flux balance analysis of the metabolism of Escherichia coli strain MG1655 shows that network use is highly uneven, which probably represents a universal feature of metabolic activity in all cells, with potential implications for metabolic engineering.
Abstract: Cellular metabolism, the integrated interconversion of thousands of metabolic substrates through enzyme-catalysed biochemical reactions, is the most investigated complex intracellular web of molecular interactions. Although the topological organization of individual reactions into metabolic networks is well understood, the principles that govern their global functional use under different growth conditions raise many unanswered questions. By implementing a flux balance analysis of the metabolism of Escherichia coli strain MG1655, here we show that network use is highly uneven. Whereas most metabolic reactions have low fluxes, the overall activity of the metabolism is dominated by several reactions with very high fluxes. E. coli responds to changes in growth conditions by reorganizing the rates of selected fluxes predominantly within this high-flux backbone. This behaviour probably represents a universal feature of metabolic activity in all cells, with potential implications for metabolic engineering.

694 citations