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Learning to read and write in evolution: From static pseudoenzymes and pseudosignalers to dynamic gear shifters

Abudukelimu, A., Mondeel, T.D.G.A., Barberis, Matteo and Westerhoff, H.V. (2017) Learning to read and write in evolution: From static pseudoenzymes and pseudosignalers to dynamic gear shifters Biochemical Society Transactions, 45 (3). pp. 635-652.

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We present a systems biology view on pseudoenzymes that acknowledges that genes are not selfish: the genome is. With network function as the selectable unit, there has been an evolutionary bonus for recombination of functions of and within proteins. Many proteins house a functionality by which they 'read' the cell's state, and one by which they 'write' and thereby change that state. Should the writer domain lose its cognate function, a 'pseudoenzyme' or 'pseudosignaler' arises. GlnK involved in Escherichia coli ammonia assimilation may well be a pseudosignaler, associating 'reading' the nitrogen state of the cell to 'writing' the ammonium uptake activity. We identify functional pseudosignalers in the cyclin-dependent kinase complexes regulating cell-cycle progression. For the mitogen-activated protein kinase pathway, we illustrate how a 'dead' pseudosignaler could produce potentially selectable functionalities. Four billion years ago, bioenergetics may have shuffled 'electron-writers', producing various networks that all served the same function of anaerobic ATP synthesis and carbon assimilation from hydrogen and carbon dioxide, but at different ATP/acetate ratios. This would have enabled organisms to deal with variable challenges of energy need and substrate supply. The same principle might enable 'gear-shifting' in real time, by dynamically generating different pseudo-redox enzymes, reshuffling their coenzymes, and rerouting network fluxes. Non-stationary pH gradients in thermal vents together with similar such shuffling mechanisms may have produced a first selectable proton-motivated pyrophosphate synthase and subsequent ATP synthase. A combination of functionalities into enzymes, signalers, and the pseudoversions thereof may offer fitness in terms of plasticity, both in real time and in evolution.

Item Type: Article
Divisions : Faculty of Health and Medical Sciences > School of Biosciences and Medicine
Authors :
Abudukelimu, A.
Mondeel, T.D.G.A.
Westerhoff, H.V.
Date : 15 June 2017
DOI : 10.1042/BST20160281
Copyright Disclaimer : © 2017 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society
Depositing User : Clive Harris
Date Deposited : 12 Apr 2019 13:13
Last Modified : 12 Apr 2019 13:13

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