Silent genes given voice

Cornish‐Bowden, Athel; Cárdenas, Marí­a Luz

doi:10.1038/35054646

Cited by 35 publications

(8 citation statements)

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“…In this specific example, the use of metabolomics to reveal similarities between yeast mutants was termed FANCY, for Functional ANalysis by Co-responses in Yeast, by Bas Teusink (Teusink et al 1998)—an acronym which, for better or worse, never caught on. For all that, the concept was robustly validated by the association of the metabolomes of pfk26 and pfk27 deletants, and also those of a number of nuclear petite mutants (Raamsdonk et al 2001; Cornish-Bowden and Cárdenas 2001). What was remarkable about this proof-of-principle study was that it worked at all, given the small number of metabolites identified in the NMR analyses.…”

Section: The Metabolomementioning

confidence: 99%

The metabolome 18 years on: a concept comes of age

Kell

Oliver

2016

Metabolomics

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Section: The Metabolomementioning

confidence: 99%

The metabolome 18 years on: a concept comes of age

Kell

Oliver

2016

Metabolomics

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“…Clearly the solution here is not simply to gather more observations, but to search for a better understanding of the observations already available; an important step is to recognize that metabolite concentrations are far more sensitive than fluxes to perturbations. Studying effects of gene deletion on concentrations, preferably combined effects on multiple concentrations, therefore provides a much more sensitive probe into gene function than studying effects on fluxes [2,3]. All of this implies a need for a biology of systems that studies an organism as an entity and not just as a collection of components.…”

Section: Introductionmentioning

confidence: 98%

Systems biology may work when we learn to understand the parts in terms of the whole

Cornish‐Bowden

Cárdenas

2005

Biochemical Society Transactions

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The first point to note about whether systems biology will work is that the essential idea of systems biology is not new: there has been interest in it, as well as efforts to apply it, since the middle of the 20th century. The difference now is that it has become fashionable, with an explosion in the number of publications using the two words, albeit not always with the same meaning. The reductionist approach remains dominant, however, and systems biology is often seen as no more than integration of diverse data into models of systems. This way of thinking needs to be changed if systems biology is to lead to an understanding of life and to provide the benefits that are expected from it. The emphasis ought to be on the needs of the system as a whole for understanding the components, not the converse. General properties of metabolic systems, such as feed-back inhibition, can be properly understood by taking account of supply and demand, i.e. the requirements of the system as a whole, but this is often overlooked. Metabolism tends to be viewed as static, although enzymes (and proteins in general) are continuously synthesized and degraded. The fact that they are themselves therefore metabolites introduces great complexity to metabolism, including an implication of infinite regress; understanding how living organisms escape from this will be an essential step towards understanding life.

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“…It was widely assumed, however, that the function of a previously unknown gene could be identified, or at least suggested, by doing appropriate genetic experiments to delete it from the genome and seeing what happened. In practice this rarely works, as a high proportion, maybe as many as 80%, of genes in yeast are "silent": when one of them is deleted the organism grows and multiplies quite normally, at the normal rate, and the rates of any metabolic processes that are measured usually prove to be normal as well (Cornish-Bowden and Cárdenas 2001a).…”

Section: -Henrik Kacser (1987)mentioning

confidence: 99%

Putting the Systems Back into Systems Biology

Cornish‐Bowden¹

2006

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P u t t i n g t h e S y s t e m sABSTRACT In recent years the term "systems biology" has become widespread in the biological literature, but most of the papers in which these words appear have surprisingly little to do with older notions of biological systems: they often seem to imply little more than reductionist biology applied on a large scale, with a little attention to interactions between some of the components, but with minimal attention to the kinetic properties of enzymes, which supplied much of the reductionist foundation of biochemistry. A systemic approach to biology ought to put the emphasis on the entire system; insofar as it is concerned with components at all, it is to explain their roles in meeting the needs of the system as a whole. Genuinely systemic thinking allows us to understand how biochemical systems are regulated, and why clumsy attempts to manipulate them for biotechnological purposes may fail. At a more abstract level, it is necessary for understanding the nature of life, because as long as an organism is treated as no more than a collection of components, one cannot ask the right questions, and certainly cannot answer them.

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Silent genes given voice

Cited by 35 publications

References 3 publications

The metabolome 18 years on: a concept comes of age

The metabolome 18 years on: a concept comes of age

Systems biology may work when we learn to understand the parts in terms of the whole

Putting the Systems Back into Systems Biology

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