This paper investigates the case of enzyme classification to evaluate different ideals for regulating values in science. I show that epistemic and non-epistemic considerations are inevitably and untraceably entangled in enzyme classification, and argue that this has significant implications for the two main kinds of views on values in science, namely, Epistemic Priority Views and Joint Satisfaction Views. More precisely, I argue that the case of enzyme classification poses a problem for the usability and descriptive accuracy of (...) these two views. The paper ends by suggesting that these two views provide different but complementary perspectives, and that both are useful for evaluating values in science. (shrink)

The multiplicity of deubiquitinating enzymes (DUBs) encoded by vertebrate genomes is partly attributable to whole genome duplication events that occurred early in chordate evolution. By surveying the literature for the largest family of DUBs (the ubiquitin-specific proteases), extensive functional redundancy for duplicated genes has been confirmed as opposed to singletons. Dramatically conflicting results have been reported for loss of function studies conducted through RNA interference as opposed to inactivating mutations, but the contradictory findings can be reconciled by a recently proposed (...) compensatory mechanism involving nonsense-mediated RNA degradation. Duplicated genes are often inactivated to become pseudogenes, and it is proposed that such is the fate of the USP15 gene of zebrafish, a commonly used model system. As it is reviewed here, these observations have implications not only for the interpretation of model system phenotypes but also for therapeutic interventions designed to target DUBs. (shrink)

Specificities of enzymes involved in plant specialized metabolism, including flavonoid biosynthesis, are generally promiscuous. This enzyme promiscuity has served as an evolutionary basis for new enzyme functions and metabolic pathways in land plants adapting to environmental challenges. This phenomenon may lead, however, to inefficiency in specialized metabolism and adversely affect metabolite‐mediated plant survival. How plants manage enzyme promiscuity for efficient specialized metabolism is, thus, an open question. Recent studies of flavonoid biosynthesis addressing this issue have revealed a (...) conserved strategy, namely, a homolog of chalcone isomerase with no catalytic activity binds to chalcone synthase, a key flavonoid pathway enzyme, to narrow (or rectify) the enzyme's highly promiscuous product specificity. Reducing promiscuity via specific protein–protein interactions among metabolic enzymes and proteins may be a solution adopted by land plants to achieve efficient operation of specialized metabolism, while the intrinsic promiscuity of enzymes has likely been retained incidentally. (shrink)

A set of amino acid side chains that confer specificity for the coenzyme NADPH and the substrate glutathione in the flavoprotein disulphide oxidoreductase, glutathione reductase, has been identified. Systematic replacement of these amino acid residues in the coenzyme‐binding site switches the specificity of the enzyme from its natural strong preference for NADPH to a marked preference For NADH. The amino acids replaced all lie in a structural motif within the dinucleotide‐binding domain of the protein. Since this domain is a (...) feature common to most dehydrogenases (reductases) that use nicotinamide coenzymes, it may be that the coenzyme specificities of all such enzymes can be manipulated in this way. Similarly, amino acid residues involved in the selective recognition of trypanothione by trypanothione reductase, an enzyme related to glutathione reductase and exclusive to trypanosomatids, were identified. Suitable mutation of the corresponding residues in E. coli glutathione reductase switched its substrate specificity towards trypanothione. A better understanding of the substrate specificity of these enzymes could open up a route to the chemotherapy of trypanosomal infections. (shrink)

A companion paper explored the role of intuition in the genesis of an alternative theory for the secretion of pancreatic digestive enzymes, looking through the lens of three philosophers/historians of science. Gerald Holton, the last scholar, proposed that scientific imagination is shaped by a number of thematic presuppositions, which function largely below awareness. They come in pairs of opposites that alternately gain cultural preeminence. The current paper examines three thematic presuppositions inherent to both the generally accepted model for digestive (...) class='Hi'>enzyme secretion and most consciousness-centered views of higher-level cognition—discreteness, reduction, and simplicity. Since they often build on each other, together they are referred to as the simplicity worldview . Also considered are the three opposite thematic assumptions inherent to both the alternative model for digestive enzyme secretion and intuition-friendly views of higher-level cognition—the continuum, holism, and complexity—together referred to as the complexity worldview . The article highlights the potential importance to scientific knowledge of this currently less favored worldview. (shrink)

The aim of this paper is to compare various methods for the quantification of metabolic pathways dynamics. A Yates-Pardee metabolic pathway with enzyme organization, i.e. with spatial localization of the enzymes in a specific cellular compartment, was studied using: (i) the classical Henri-Michaelis-Menten (HMM) equations, (ii) linearization of the HMM equations in the vicinity of a steady state (linearized formalism), and (iii) Biochemical Systems Theory formalism (BST formalism). It is shown that transient solutions computed via either the linearized formalism (...) or the BST formalism can greatly differ from transient solutions computed with the HMM equations. However, in the studied example, results remain qualitatively the same for the three formalisms. This suggests that the study of the topology of the system may give useful insights into the metabolic pathways dynamics. (shrink)

Enzyme engineering allows to explore sequence diversity in search for new properties. The scientific literature is populated with methods to create enzyme libraries for engineering purposes, however, choosing a suitable method for the creation of mutant libraries can be daunting, in particular for the novices. Here, we address both novices and experts: how can one enter the arena of enzyme library design and what guidelines can advanced users apply to select strategies best suited to their purpose? Section (...) I is dedicated to the novices and presents an overview of established and standard methods for library creation, as well as available commercial solutions. The expert will discover an up‐to‐date tool to freshen up their repertoire (Section I) and learn of the newest methods that are likely to become a mainstay (Section II). We focus primarily on in vitro methods, presenting the advantages of each method. Our ultimate aim is to offer a selection of methods/strategies that we believe to be most useful to the enzyme engineer, whether a first‐timer or a seasoned user. (shrink)

Context can determine whether a given gene acts as an oncogene or a tumor suppressor. Deubiquitinating enzymes (DUBs) regulate the stability of many components of the pathways dictating cell fate so it would be expected that alterations in the levels or activity of these enzymes may have oncogenic or tumor suppressive consequences. In the current review we survey publications reporting that genes encoding DUBs are oncogenes or tumor suppressors. For many DUBs both claims have been made. For such “double agents,” (...) the effects of gain or loss of function will depend on the overall status of a complex of molecular signaling networks subject to extensive crosstalk. As the TGF‐β paradox makes clear context is critical in cell fate decisions, and the disconnect between experimental findings and patient survival outcomes can in part be attributed to disparities between culture conditions and the microenvironment in vivo. Convincing claims for oncogene or tumor suppressor roles require the documentation of gene alterations in patient samples; survival curves are alone inadequate. (shrink)

RésuméĽenzymologie est une discipline scientifique apparue au debut du siècle dernier. Les techniques de plus en plus élaborées qui en ont depuis lors permis le développement, faisant appel à une rigueur expérimentale toujours plus évidente, pourraient suggérer un recul de la réalite biologique et physiologique au profit de modéles abstraits. La présentation de quelques exemples montre que ce point de vue n'est pas fondé.SummaryThe infancy of enzymology dates back to the beginning of the 19th century. The experimental techniques which have (...) subsequently been developed in this field of biochemistry might now suggest a prevalence of abstract models over biological and physiological relevance.Several pertinent examples show that such a view is unjustified.ZusammenfassungDie Anfänge der Enzymologie als wissenschaftliche Disziplin gehen bis auf das frühe 19. Jahrhundert zurück. Die experimentelle Methodik, die auf diesem Gebiet der Biochemie entwickelt wurde, deutet auf eine Bevorzugung abstrakter Modelle gegenüber der biologischen Wirklichkeit.Einige Beispiele sollen zeigen, dass diese Ansicht unbegründet ist. (shrink)

tRNA nucleotidyltransferase adds the invariant CCA‐terminus to the tRNA 3′‐end, a central step in tRNA maturation. This CCA‐adding enzyme is a specialized RNA polymerase that synthesizes the CCA sequence at high fidelity in all kingdoms of life. Recently, an additional function of this enzyme was identified, where it generates a specific degradation tag on structurally unstable tRNAs. This tag consists of an additional repeat of the CCA triplet, leading to a 3′‐terminal CCACCA sequence. In order to explain how (...) the enzyme catalyzes this extended polymerization reaction, Kuhn et al. solved a series of co‐crystal structures of the CCA‐adding enzyme from Archaeoglobus fulgidus in complex with different tRNA substrates. They show that the enzyme forces a bound unstable tRNA to refold the acceptor stem for a second round of CCA‐addition, while stable transcripts are robust enough to resist this isomerization. In this review, we discuss how the CCA‐adding enzyme uses a simple yet very elegant way to scrutinize its substrates for sufficient structural stability and, consequently, functionality. (shrink)

Enzymes are protein catalysts of extraordinary efficiency, capable of bringing about rate enhancements of their biochemical reactions that can approach factors of 1020. Theories of enzyme catalysis, which seek to explain the means by which enzymes effect catalytic transformation of the substrate molecules on which they work, have evolved over the past century from the “lock-and-key” model proposed by Emil Fischer in 1894 to models that explicitly rely on transition state theory to the most recent theories that strive to (...) provide accounts that stress the essential role of protein dynamics. In this paper, I attempt to construct a metaphysical framework within which these new models of enzyme catalysis can be developed. This framework is constructed from key doctrines of process thought, which gives ontologic priority to becoming over being, as well as tenets of a process philosophy of chemistry, which stresses environmentally responsive molecular transformation. Enzyme catalysis can now be seen not as enzyme acting on its substrate, but rather as enzyme and substrate entering into a relation which allows them to traverse the reaction coordinate as an ontologic unity. (shrink)

Enzymes are remarkable molecules which make metabolism possible. Their processing powers are considerable for not only are they catalysts they also contribute to information processing, integration, coherence and memory in the cell. This complex of attributes suggests that a complementary perspective to enzyme nature and activity is needed related to what enzymes and verbs have in common. The value of this kind of thinking is that it shifts the focus from objects and mechanisms to processes and information. In order (...) to support this idea a number of features which enzymes and verbs share are discussed including, context-dependence, occurrence, cases, voice, mood and glue/integrative capacities. The paper concludes with some reflections on the utility of a view of enzymes as verbs. (shrink)

Free radicals are generally perceived as highly reactive species which are harmful to biological systems. There are, however, a number of enzymes that use carbon‐based radicals to catalyse a variety of important and unusual reactions. The most prominent example is ribonucleotide reductase, an enzyme which is crucial for the synthesis of DNA. In general, radicals are used to remove hydrogen from unreactive positions in the substrate, and in this way the substrate is activated to undergo chemical transformations that would (...) otherwise be difficult to achieve. Several different mechanisms have evolved which allow enzymes to generate and maintain radicals in increasingly aerobic enviroments. An unexpected finding is the existance of stable protein‐based radicals, residing on a variety of amino‐acid side chains, which serve to link the radical‐generating and catalytic sites and to store the radical between turnovers. (shrink)

It is proposed in this paper that enzymes, by virtue of a number of correctly positioned sites of interaction with substrates, can force the compression of hydrogen bonds, increasing the probability of proton transfer by quantum mechanical tunneling. By such a catalytic mechanism a rate enhancement of many orders of magnitude may be obtained with a very low energy input requirement. The mechanism would, however, require a highly structured catalyst.Pertinent aspects of hydrogen bond theory and of tunneling theory are briefly (...) reviewed. (shrink)

In this article C. L. Tsou, of the Institute of Biophysics, Beijing, criticizes the use of the expression I50, the inhibitor concentration to produce 50% inhibition of a particular enzyme as a ‘most unfortunate’ parameter, when screening enzyme inhibitors designed as drugs. Comments on Dr Tsou's point of view will be welcomed from readers.

Many kinds of multifunctional regulatory proteins have been identified that perform distinct biochemical functions in the nucleus, the cytoplasm, or both. Here we describe the recent discovery by Hall et al. (2004)1 of a new type of multifunctional protein: a metabolic enzyme that doubles as a transcription factor. This enzyme, Arg5,6, functions as a catalytic enzyme in ornithine biosynthesis and also binds and regulates the promoters of nuclear and mitochondrial genes. It may also regulate precursor mRNA metabolism. (...) We discuss how proteins that serve as both metabolic enzymes and transcription factors might have evolved. BioEssays 27:467–471, 2005. © 2005 Wiley Periodicals, Inc. (shrink)

Recently, it has been argued that the phenomenon of direct transfer of intermediate metabolites between adjacent enzymes, also known as metabolic channelling, would not decrease the concentration of those intermediates in the bulk solution. However, this conclusion has been drawn by extrapolation from the results of simulations with a rather restricted set of parameters. We show that, for a number of kinetic cases, the existence of metabolic channelling can decrease the size of the soluble pool of intermediates. When the (...) class='Hi'>enzyme(s) downstream of the channel have a catalytic capacity that is large relative to the enzymes upstream of the channel, the decrease of concentration can be substantial (3 orders of magnitude). (shrink)

In the metabolic control theory, the control coefficient is a key parameter in quantifying the sensitivity of the flux towards an infinitesimal variation of enzyme activity. This concept does not apply just as it is for variations of enzyme concentrations whenever there is spatial, energy or resources limitations in the cell. Due to constraint on total enzyme concentration, the variation of concentration of any given enzyme may affect the concentrations of other enzymes. To take into account (...) these correlations between enzyme concentrations, we propose the concept of "combined response coefficient". Its definition is similar to that of the control coefficient, but its mathematical expression is different. Its range of variation is from – + 1, the null value corresponding to optimum enzyme concentration, i.e. to concentrations that maximise the flux, and the negative values to concentrations beyond the optimum value. A summation property could be derived using a simple weighting of the combined response coefficients, the sum of the weighed coefficient being 0. (shrink)

Endo‐exonucleases from E. coli to man, although very different proteins, are multifunctional enzymes with similar enzymatic activities. They probably have two common but opposing biological roles. On the one hand, they promote survival of the organism by acting in recombination and recombinational DNA repair to diversify and help preserve the genome intact. On the other hand, they degrade the genomic DNA when it is damaged beyond repair. This ensures elimination of heavily mutagenized cells from the population.

The importance of drug‐metabolizing enzymes in developing mammals has been recently reevaluated in view of the activities and potential inducibilities of these enzymes. The role of endogenous factors raises the question of whether there is a positive regulation of the expression of drug‐metabolizing enzymes by hormones. In humans, among the different isoenzymes of cytochrome P‐450 described in adult liver, only one is absent in 20‐week‐old fetuses. Epoxide hydrolase and glutathione S‐transferases are active while UDP‐glucuronidation develops postnatally. The consequence of this (...) asynchronous rise of activities is briefly discussed. (shrink)

Purified nuclei are being used as a test system to study the regulation of nuclear enzymes in plants. Regulatory agents such as light, hormones and polyamines can stimulate kinases or phosphatases that control nuclear protein phosphorylation and they can modulate the activity of as yet unidentified enzymes required for transcript synthesis and/or stabilization. This essay summarizes current findings and discusses the advantages and pitfalls of using isolated nuclei to investigate how nuclear functions are controlled.

The Enzymatic control reactions model was presented within the scope of fractional calculus. In order to accommodate the usual initial conditions, the fractional derivative used is in Caputo sense. The methodologies of the three analytical methods were used to derive approximate solution of the fractional nonlinear system of differential equations. Two methods use integral operator and the other one uses just an integral. Numerical results obtained exhibit biological behavior of real world problem.

The Enzymatic control reactions model was presented within the scope of fractional calculus. In order to accommodate the usual initial conditions, the fractional derivative used is in Caputo sense. The methodologies of the three analytical methods were used to derive approximate solution of the fractional nonlinear system of differential equations. Two methods use integral operator and the other one uses just an integral. Numerical results obtained exhibit biological behavior of real world problem.

DNA helicases catalyze the disruption of the hydrogen bonds that hold the two strands of double‐stranded DNA together. This energy‐requiring unwinding reaction results in the formation of the single‐stranded DNA required as a template or reaction intermediate in DNA replication, repair and recombination. A combination of biochemical and genetic studies have been used to probe and define the roles of the multiple DNA helicases found in E. coli. This work and similar efforts in eukaryotic cells, although far from complete, have (...) established that DNA helicases are essential components of the machinery that interacts with the DNA molecule. (shrink)

Numerous eukaryotic DNA processing enzymes, such as DNA polymerases and ligases, bind the processivity factor PCNA, which acts as a platform to recruit and regulate the binding of enzymes to their DNA substrate. Multiple PCNA‐interacting motifs (PIPs) are present in these enzymes, but their individual structural and functional role has been a matter of debate. Recent cryo‐EM reconstructions of high‐fidelity DNA polymerase Pol δ (Pol δ), translesion synthesis DNA polymerase κ (Pol κ) and Ligase 1 (Lig1) bound to a DNA (...) substrate and PCNA demonstrate that the critical interaction with PCNA involves the internal PIP proximal to the catalytic domain. The ancillary PIPs, located in long disordered regions, are instead invisible in the reconstructions, and appear to function as flexible tethers when the enzymes fall off the DNA. In this review, we discuss the recent structural advancements and propose a functional hierarchy for the PIPs in Pol δ, Pol κ, and Lig1. (shrink)

RésuméĽétude du développement?on;un organisme fait appel à diverses approches choisies en fonction des objectifs fixés par ľexpérimentateur. Ainsi, la mise en évidence?on;une corrélation entre deux paramétres, par exemple biochimique et morphologique, permet de les considérer comme associés, sans nécessairement dégager entre eux un lien direct de causalité. Ce dernier peut être explicité par une autre approche, comme ľillustre une étude portant sur la relation entre une enzyme ‐glycohydrolase) et la différentiation sporale chez Neurospora crassa.SummaryThe study of the development of (...) an organism requires diverse approaches selected on the basis of experimental objectives. For instance, the finding of a correlation between two parameters, i.e. biochemical and morphological, allows them to be considered as associated without necessarily pointing to a direct causal relationship. This latter may be brought out by another approach, as illustrated by this study bearing on the relation between an enzyme ‐gly‐cohydrolase) and differentiation of spores in Neurospora crassa.ZusammenfassungDas Studium der Entwicklung eines Organismus erfordert verschiedenartige Annäherungen, je nach den vom Experimendierenden gestellten Ziele. Daher erlaubt der Nachweis einer Korrela‐tion zwischen zwei Parametern, zum Beispiel einem biochemischen und einem morphologischen, sie als verbunden zu betrachten ohne notwendigerweise eine Kausalbeziehung zwischen Ihnen zu beweisen. Eine solche kann von einer anderen Seite geklärt werden, wie es eine Studie der Beziehung zwischen einem Enzym ‐glycohydrolase) und der Sporendifferenzierung bei Neurospora crassa zeigt. (shrink)

Roots presents articles on landmark discoveries that laid the basis for contemporary molecular and cellular biology. In this article, N. H. Horowitz, Professor Emeritus at the California Institute of Technology, and a former associate of George Beadle's, reviews the work that led to the one gene–one enzyme hypothesis.

Abstractα/β barrels have an ill‐defined origin. Evidence exists which favours their divergent evolution from a common ancestral barrel and convergent evolution to a stable fold. However, recent sequence and structural information for the flavin oxidase/dehydrogenase family of barrel enzymes indicate that sub‐families of α/β barrels have evolved divergently. The modular fusion of barrel domains with core structures from other gene families has also contributed to the evolution of related but catalytically distinct enzyme molecules within each sub‐family of the flavin (...) oxidases/dehydrogenases. An analysis of the structures and sequences of the flavin oxidases/dehydrogenases has now enabled studies focusing on the evolutionary origins and modular assembly of this important family of proteins to be initiated. (shrink)

The role of intuition in scientific endeavor is examined through the lens of three philosophers/historians of science—Karl Popper, Thomas Kuhn, and Gerald Holton. All three attribute an important role to imagination/intuition in scientific endeavor. As a case study, the article examines the controversy between the generally accepted Vesicular Sequestration/Exocytosis Model of pancreatic digestive enzyme secretion and an alternative view called the Equilibrium Model. It highlights the intertwining of intuition and reason in the genesis of the Equilibrium Model developed in (...) response to findings that could not readily be explained by the consensus view. It suggests that tacit knowledge/understanding works in conjunction with philosophical and aesthetic presuppositions that function to a greater or lesser extent below awareness. Together they guide judgments about whether falsification has occurred and help frame alternative theories. (shrink)

We review here some recent data about glucose‐6‐phosphate dehydrogenase (G6PD), the first and key regulatory enzyme of the pentose phosphate pathway. New evidence has been presented to suggest that malaria is a selective agent for G6PD deficiency, which is the most common enzymopathy in man, and that G6PD deficiency, generally considered to be a mild and benign condition, is significantly disadvantageous in certain environmental conditions. At the molecular level, the enzyme structure has recently been elucidated and mechanisms regulating (...) G6PD gene expression have been determined. A G6PD knock‐out mutation introduced in mouse cells makes them exquisitely sensitive to oxidative stress, indicating that this ubiquitous metabolic enzyme has a major role in the defence against oxidative stress, even in eukaryotic nucleated cells, which have several alternative routes for providing the same protection. Because of the high prevalence of G6PD deficiency in many populations, it is expected that these findings will prompt further studies to ascertain the putative role of G6PD deficiency in conditions such as carcinogenesis and ageing. (shrink)

Intracellular bacteria were recently shown to employ eukaryotic prenylation system for modifying activity and ensuring proper intracellular localization of their own proteins. Following the same logic, the proteins of viruses may also serve as prenylation substrates. Using extensively validated high-confidence prenylation predictions by PrePS with a cut-off for experimentally confirmed farnesylation of hepatitis delta virus antigen, we compiled in silico evidence for several new prenylation candidates, including IRL9 and few other proteins encoded by Herpesviridae, Nef, E1A, NS5A, PB2, HN, L83L, (...) MC155R, other Poxviridae proteins, and some bacteriophages of human associated bacteria. If confirmed experimentally, these findings may aid in dissection of molecular functions of uncharacterized viral proteins and provide a novel rationale for statin and FT/GGT1-based inhibition of viral infections. Prenylation of bacteriophage proteins may aid in moderation of microbial infections. Many human viruses, including HCV, HIV1, ASFV, and a number of Adeno-, Pox-, and herpesviruses, including CMV, encode the substrates for mammalian prenylation enzymes. Prenylation is advantageous for viral infection; its suppression by FT/GGT and FPPS inhibitors has antiviral effects. In bacteriophages, prenylation may aid in moderation of microbial infections. (shrink)

Intracellular bacteria were recently shown to employ eukaryotic prenylation system for modifying activity and ensuring proper intracellular localization of their own proteins. Following the same logic, the proteins of viruses may also serve as prenylation substrates. Using extensively validated high-confidence prenylation predictions by PrePS with a cut-off for experimentally confirmed farnesylation of hepatitis delta virus antigen, we compiled in silico evidence for several new prenylation candidates, including IRL9 and few other proteins encoded by Herpesviridae, Nef, E1A, NS5A, PB2, HN, L83L, (...) MC155R, other Poxviridae proteins, and some bacteriophages of human associated bacteria. If confirmed experimentally, these findings may aid in dissection of molecular functions of uncharacterized viral proteins and provide a novel rationale for statin and FT/GGT1-based inhibition of viral infections. Prenylation of bacteriophage proteins may aid in moderation of microbial infections. Many human viruses, including HCV, HIV1, ASFV, and a number of Adeno-, Pox-, and herpesviruses, including CMV, encode the substrates for mammalian prenylation enzymes. Prenylation is advantageous for viral infection; its suppression by FT/GGT and FPPS inhibitors has antiviral effects. In bacteriophages, prenylation may aid in moderation of microbial infections. (shrink)

Phosphatidylinositol 3 kinase (PI 3-kinase) is an important enzyme that is involved in the regulation of a variety of biological processes such as apoptosis, cell division, and ion channel activity and can play a role in the pathological development of a number of diseases, including AIDS and cancer. The authors’ data indicate that external qi of Yan Xin Life Science Technology (YXLST) can modulate enzyme activity in two directions. Within a time window of 3 days of the initial (...) emission of external qi of YXLST, PI 3-kinase activity was restored in an outdated enzyme sample that had lost activity, and PI 3-kinase activity was suppressed in a freshly purified sample relative to an untreated control sample so that its activity was nearly undetectable. The data presented are consistent with the hypothesis that external qi of YXLST can alter molecular events. The uniqueness of this and other observations mandates further study. (shrink)

Some metabolic pathways are nearly ubiquitous among organisms: the genes encoding the enzymes for such pathways must therefore be ancient and essential. De novo pyrimidine biosynthesis is an example of one such metabolic pathway. In animals a single protein called CADAbbreviations: CAD, trifunctional protein catalyzing the first three steps of de novo pyrimidine biosynthesis in higher eukaryotes; CPS, carbamyl phosphate synthetase domain; CPSase, carbamyl phosphate synthetase activity; ATC, aspartate transcarbamylase domain; ATCase, aspartate transcarbamylase activity; DHO, dihydroorotase domain; DHOase, dihydroorotase activity; (...) GLN, glutaminase subdomain or subunit of carbamyl phosphate synthetase, GL Nase, glutaminase activity; SYN, synthetase subdomain or subunit of carbamyl phosphate synthetase; SYNase, synthetase activity. carries the first three steps of this pathway. The same three enzymes in prokaryotes are associated with separate proteins. The CAD gene appears to have evolved through a process of gene duplication and DNA rearrangement, leading to an in‐frame gene fusion encoding a chimeric protein. A driving force for the creation of eukaryotic genes encoding multienzymatic proteins such as CAD may be the advantage of coordinate expression of enzymes catalyzing steps in a biosynthetic pathway. The analogous structure in bacteria is the operon. Differences in the translational mechanisms of eukaryotes and prokaryotes may have dictated the different strategies used by organisms to evolve coordinately regulated genes. (shrink)

Uncoupling proteins (UCPs) regulate mitochondrial function, and thus cellular metabolism. Angiotensin‐converting enzyme (ACE) is the central component of endocrine and local tissue renin–angiotensin systems (RAS), which also regulate diverse aspects of whole‐body metabolism and mitochondrial function (partly through altering mitochondrial UCP expression). We show that ACE expression also appears to be regulated by mitochondrial UCPs. In genetic analysis of two unrelated populations (healthy young UK men and Scandinavian diabetic patients) serum ACE (sACE) activity was significantly higher amongst UCP3‐55C (rather (...) than T) and UCP2 I (rather than D) allele carriers. RNA interference against UCP2 in human umbilical vein endothelial cells reduced UCP2 mRNA sixfold (P < 0·01) whilst increasing ACE expression within a physiological range (<1·8‐fold at 48 h; P < 0·01). Our findings suggest novel hypotheses. Firstly, cellular feedback regulation may occur between UCPs and ACE. Secondly, cellular UCP regulation of sACE suggests a novel means of crosstalk between (and mutual regulation of) cellular and endocrine metabolism. This might partly explain the reduced risk of developing diabetes and metabolic syndrome with RAS antagonists and offer insight into the origins of cardiovascular disease in which UCPs and ACE both play a role. (shrink)

The present account spans the history of arginine regulation from its discovery in 1955 until the present. In 1957 I demonstrated that not only added arginine but also internally produced arginine represses enzyme formation and that the potential for enzyme synthesis is in excess of what is required for growth. In 1959 I located the regulatory gene argR encoding the arginine repressor. An unusual feature of this research was the finding that in E. coli B, in contrast to (...) E. coli K12, arginine synthesis is permanently repressed, independent of arginine. This was due to a single amino acid difference between the two repressors. Recent studies showed that, in natural populations of E. coli, K12‐type regulation is much more frequent than B‐type regulation, and that E. coli B evolved from a strain with K12‐type regulation. In competition experiments, E. coli K12 was found to be favored in the presence of arginine and E. coli B in its absence, showing that contrary to expectations permanently turned off regulation is favored over negative regulation in some environments. BioEssays 29:484–488, 2007. © 2007 Wiley Periodicals, Inc. (shrink)