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PubMed2003

How does an enzyme evolved in vitro compare to naturally occurring homologs possessing the targeted function? Tyrosine aminotransferase from aspartate aminotransferase.

Aspartate aminotransferase (AATase) and tyrosine aminotransferase (TATase) are Escherichia coli paralogs that share 43% sequence identity. A plausible model posits that TATase arose from a duplication of an ancestral AATase-like enzyme. Directed evolution of AATase to an enzyme having TATase activity was undertaken in order to compare the evolved AATase variants with homologous TATases. Eight rounds of DNA shuffling and in vivo selection followed by a backcross with WT AATase produced enzymes that exhibited 100-270-fold increases in k(cat)/K(m)(Phe) and had as much as 11% of the tyrosine aminotransferase activity of WT E.coli TATase. Amino acid substitutions in 11 clones from rounds 7 and 8 were compared with conserved residues in AATases and TATases. The findings are conveniently and compactly illustrated by the use of Venn diagrams and set theory notation. A statistically significant (0.001 or=75% identical) in AATases and variable (<75% identical) in TATases. Very few mutations occur in the intersection (set AAT intersection TAT) of amino acid residues that are conserved in both enzyme types. Seven mutations from set AAT-TAT were combined by site-directed mutagenesis to give a construct that is 60% as active as the best round 8 enzyme, which has 13 amino acid replacements. The Venn diagrams may provide a generally useful tool to highlight the most important specificity determinants for rational redesign. Amino acid replacements were mapped onto the crystal structure of a hydrocinnamate complex of a designed TATase. Five of the seven positions most frequently substituted in the evolved clones are within 15 A of the phenyl side-chain, but only six of the 48 positions that were mutated once or twice are within that radius. Context dependence, neutral mutations, different selective pressures, and stochastic components provide explanations for the observation that many of the substitutions found in the directly evolved enzymes differ from the corresponding amino acids found in the modern natural TATases.

Amino Acid Sequence↗

PubMed2003

Evolved mechanisms in depression: the role and interaction of attachment and social rank in depression.

Evolved mechanisms underpinning attachment and social rank behavior may be the basis for some forms of major depression, especially those associated with chronic stress. We note the heterogeneity of depression, but suggest that some of its core symptoms, such as behavioral withdrawal, low self-esteem and anhedonia, may have evolved in order to regulate behavior and mood and convey sensitivity to threats and safety. Focusing on the evolved mental mechanisms for attachment and social rank helps to make sense of (1) depression's common early vulnerability factors (e.g., attachment disruptions, neglect and abuse), (2) the triggering events (e.g., loss of close relationships, being defeated and/or trapped in low socially rewarding or hostile environments), and (3) the psychological preoccupations of depressed people (e.g., sense of unlovableness, self as inferior and a failure). This focus offers clues as to how these two systems interact and on how to intervene.

Achievement↗

PubMedDate not supplied

Self-evolving microstructured systems upon enzymatic catalysis.

The consequences of cell microstructuration on enzyme functions is discussed in the framework of self-evolving microstructured systems. Molecular assemblies of amphiphiles or lipids are spontaneously formed by self-organisation. Among these different structures, reversed micelles, liquid crystalline mesophases and vesicles are hosts for enzymatic reaction studies. Inside a living cell, phospholipid metabolism is responsible for membrane structural modifications; the catalytic behaviour of lipolytic enzymes, mainly phospholipase (PL) A2, is described in relation with structural aspects of biological membranes. The implication in cellular regulation events of PLC and PLD is discussed in relation with the role of their reaction products as second messengers in membrane fusion processes. The in vitro synthesis of dialkyl phosphatidylcholines, via the enzymatic 'salvage pathway' which leads to the formation of vesicles upon phospholipid formation, is considered in relation with autopoiesis. More recent studies on self-evolving systems based on enzyme-surfactants reactions are detailed. The interactions between amphiphilic aggregates and enzymes allow to explore the OG/octanol/water phase diagram. Enzymatic formation of dipalmitoylphosphatidylcholine (DPPC) liposomes and non-ionic surfactant vesicles (NSV), starting from mixed micelles or open structures, finally sets an example of a biomimetic self-evolving system.

Cholesterol↗

PubMed2001

Evolving hardware as model of enzyme evolution.

Organism growth and survival is based on thousands of enzymes organized in networks. The motivation to understand how a large number of enzymes evolved so fast inside cells may be relevant to explaining the origin and maintenance of life on Earth. This paper presents electronic circuits called 'electronic enzymes' that model the catalytic function performed by biological enzymes. Electronic enzymes are the hardware realization of enzymes defined as molecular automata with a finite number of internal conformational states and a set of Boolean operators modelling the active groups of the active site. One of the main features of electronic enzymes is the possibility of evolution finding the proper active site by means of a genetic algorithm yielding a metabolic ring or k-cycle that bears a resemblance to Krebs (k=7) or Calvin (k=4) cycles present in organisms. The simulations are consistent with those results obtained in vitro evolving enzymes based on polymerase chain reaction (PCR) as well as with the general view that suggests the main role of recombination during enzyme evolution. The proposed methodology shows how molecular automata with evolvable features that model enzymes or other processing molecules provide an experimental framework for simulation of the principles governing metabolic pathways evolution and self-organization.

Algorithms↗

PubMed2003

Enhancing evolvability with mutation buffering mediated through multiple weak interactions.

The evolutionary adaptability of a system is dependent on three organizational properties, self-organizing dynamics that are hierarchically organized, component redundancy, and multiple weak interactions [Towards high evolvability dynamics, in: G. van de Vijver, S. Salthe, M. Delpos (Eds.), Evolutionary Systems, Kluwer Academic Publishers, Dordrecht, 1998, pp. 147-169]. This study reports on the use of the dual dynamics network model as an aid in understanding the role multiple weak interactions play in enhancing evolutionary adaptability. Dual dynamics networks are self-organizing systems that consist of simple components that change local state due to the coupled influences from connected components exerting strong discrete decision-making influences and from groups of components exerting multiple weak influences [J. Theor. Biol. 193 (1998) 287]. The dual dynamics model has been enhanced to support investigations of properties relevant to a system's capacity for evolvability, such as structure-function relationships, neutrality, adaptive tolerance, and evolutionary search performance. Three network types are investigated, each utilizing a different method of coupling strong and weak influences. The results demonstrate that the manner of coupling multiple weak interactions into the systems dynamics significantly affects the structure-function maps and the consequent evolvability characteristics. Specifically it is found that a form of coupling, denoted as linear modulation, enhances evolutionary adaptability. Linear modulation coupling requires that the weak interactions be integrated with strong interactions in a manner that implies a linear ordered relation between the possible state values of the components of the systems. When coupling functions that do not imply such an ordering of local state values are used, evolutionary adaptability is decreased.

Adaptation, Physiological↗

PubMed2003

Evolution of evolvability via adaptation of mutation rates.

We examine a simple form of the evolution of evolvability-the evolution of mutation rates-in a simple model system. The system is composed of many agents moving, reproducing, and dying in a two-dimensional resource-limited world. We first examine various macroscopic quantities (three types of genetic diversity, a measure of population fitness, and a measure of evolutionary activity) as a function of fixed mutation rates. The results suggest that (i) mutation rate is a control parameter that governs a transition between two qualitatively different phases of evolution, an ordered phase characterized by punctuated equilibria of diversity, and a disordered phase of characterized by noisy fluctuations around an equilibrium diversity, and (ii) the ability of evolution to create adaptive structure is maximized when the mutation rate is just below the transition between these two phases of evolution. We hypothesize that this transition occurs when the demands for evolutionary memory and evolutionary novelty are typically balanced. We next allow the mutation rate itself to evolve, and we observe that evolving mutation rates adapt to values at this transition. Furthermore, the mutation rates adapt up (or down) as the evolutionary demands for novelty (or memory) increase, thus supporting the balance hypothesis.

Adaptation, Physiological↗

PubMed2003

Local evolvability of statistically neutral GasNet robot controllers.

In this paper we introduce and apply the concept of local evolvability to investigate the behaviour of populations during evolutionary search. We focus on the evolution of GasNet neural network controllers for a robotic visual discrimination problem, showing that the evolutionary process undergoes long neutral fitness epochs. We show that the local evolvability properties of the search space surrounding a group of statistically neutral solutions do vary across the course of an evolutionary run, especially during periods of population takeover. However, once takeover is complete there is no evidence for further increase in local evolvability across fitness epochs. We also see no evidence for the neutral evolution of increased solution robustness, but show that this may be due to the ability of evolutionary algorithms to focus search on volumes of the fitness landscape with above average robustness.

Adaptation, Physiological↗

PubMed2003

Bacterial type III secretion systems are ancient and evolved by multiple horizontal-transfer events.

Type III secretion systems (TTSS) are unique bacterial mechanisms that mediate elaborate interactions with their hosts. The fact that several of the TTSS proteins are closely related to flagellar export proteins has led to the suggestion that TTSS had evolved from flagella. Here we reconstruct the evolutionary history of four conserved type III secretion proteins and their phylogenetic relationships with flagellar paralogs. Our analysis indicates that the TTSS and the flagellar export mechanism share a common ancestor, but have evolved independently from one another. The suggestion that TTSS genes have evolved from genes encoding flagellar proteins is effectively refuted. A comparison of the species tree, as deduced from 16S rDNA sequences, to the protein phylogenetic trees has led to the identification of several major lateral transfer events involving clusters of TTSS genes. It is hypothesized that horizontal gene transfer has occurred much earlier and more frequently than previously inferred for TTSS genes and is, consequently, a major force shaping the evolution of species that harbor type III secretion systems.

Bacteria↗

PubMed2000

Evolving changes in Doppler mitral flow velocity pattern in rats with hypertensive hypertrophy.

OBJECTIVES: The aim of our study was to explore evolving changes in a mitral flow velocity pattern (MFVP) and its hemodynamic and pathological correlates in hypertensive rats in an isolated diastolic heart failure model. BACKGROUND: Development of left ventricular (LV) hypertrophy and concomitant diastolic dysfunction cause heart failure in hypertensive hearts even with normal systolic function; however, associated evolving change in MFVP is still unclear. METHODS: Mitral flow velocity pattern was recorded every 2 weeks from 7 to 19 weeks in six hypertensive rats. Hemodynamic and pathological correlates of Doppler mitral flow indexes were examined as an additional part of the study using the hypertensive rats at the age of 13 weeks (compensatory stage, n = 7) and at 19 weeks (heart failure stage, n = 8). RESULTS: Initial development of pressure overload LV hypertrophy resulted in a decrease in early diastolic filling wave (E), a reciprocal increase in the filling wave due to atrial contraction (A) and prolongation of deceleration time of E wave (relaxation abnormality pattern). These changes were associated with an increase in tau, an index of LV relaxation, but without a change in LV end-diastolic pressure. Transition to congestive heart failure caused an increase in E, a decrease in A and shortening of deceleration time. These changes were not associated with further increase in tau but with elevation of LV end-diastolic pressure, reflecting marked LV hypertrophy and myocardial fibrosis. CONCLUSIONS: Development of pressure overload LV hypertrophy is associated with evolving changes in MFVP from normal to relaxation abnormality pattern and, in turn, to pseudonormalized to restrictive pattern. Analysis of MFVP may be useful to follow not only functional but also constitutional changes of the myocardium in hypertensive hearts.

Animals↗

PubMed1999

Do essential genes evolve slowly?

Approximately two thirds of all knockouts of individual mouse genes give rise to viable fertile mice. These genes have thus been termed 'non-essential' in contrast to 'essential' genes, the knockouts of which result in death or infertility. Although non-essential genes are likely to be under selection that favours sequence conservation [1], it is predicted that they are less subject to such stabilising selection than essential genes, and hence evolve faster [2]. We have addressed this issue by analysing the molecular evolution of 108 non-essential and 67 essential genes that have been sequenced in both mouse and rat. On preliminary analysis, the non-essential genes appeared to be faster evolving than the essential ones. We found, however, that the non-essential class contains a disproportionate number of immune-system genes that may be under directional selection (that is, selection favouring change) because of host-parasite coevolution. After correction for this bias, we found that the rate at which genes evolve does not correlate with the severity of the knockout phenotype. This was corroborated by the finding that, whereas neuron-specific genes have significantly lower rates of change than other genes, essential and non-essential neuronal genes have comparable rates of evolution. Our findings most probably reflect strong selection acting against even very subtle deleterious phenotypes, and indicate that the putative involvement of directional selection in host-parasite coevolution and gene expression within the nervous system explains much more of the variance in rates of gene evolution than does the knockout phenotype.

Algorithms↗

PubMed2002

Automatic detection and segmentation of evolving processes in 3D medical images: Application to multiple sclerosis.

The study of temporal series of medical images can be helpful for physicians to perform pertinent diagnoses and to help them in the follow-up of a patient: in some diseases, lesions, tumors or anatomical structures vary over time in size, position, composition, etc., either because of a natural pathological process or under the effect of a drug or a therapy. It is a laborious and subjective task to visually and manually analyze such images. Thus the objective of this work was to automatically detect regions with apparent local volume variation with a vector field operator applied to the local displacement field obtained after a non-rigid registration between two successive temporal images. On the other hand, quantitative measurements, such as the volume variation of lesions or segmentation of evolving lesions, are important. By studying the information of apparent shrinking areas in the direct and reverse displacement fields between images, we are able to segment evolving lesions. Then we propose a method to segment lesions in a whole temporal series of images. In this article we apply this approach to automatically detect and segment multiple sclerosis lesions that evolve in time series of MRI scans of the brain. At this stage, we have only applied the approach to a few experimental cases to demonstrate its potential. A clinical validation remains to be done, which will require important additional work.

Automation↗

PubMed2001

An exploration of evolved mental mechanisms for dominant and subordinate behaviour in relation to auditory hallucinations in schizophrenia and critical thoughts in depression.

BACKGROUND: Mental mechanisms have evolved to enable animals (and humans) to be able to function in various social roles. It is suggested that the nature and functions of the mental mechanisms that enable animals to act as a hostile-dominant or threatened-subordinate can be distinguished. It is further suggested these can be internally activated and 'play off' against each other, such that a person 'attacks' themselves and then responds to their own internal attacks with subordinate defences. Hence, a depressed person can submit, feel defeated, belittled, beaten down, or want to run away (escape) from their own self-attacking thoughts, while psychotic voice hearers can feel similarly to their hostile voices. Such internal interactions may relate to depression in both psychotic voice hearers and depressed people. METHOD: A group of 66 voice hearers with a diagnosis of schizophrenia and 50 depressed patients were compared on a series of self-report questionnaires measuring the power of hostile self-directed thoughts/voices and the activation of defensive responses, especially fight/flight. RESULTS: We present evidence that schizophrenic, malevolent voice hearers and self-critical depressed people experience their hostile, internally generated voices/thoughts as powerful, dominating and controlling (i.e. have typical characteristics of a hostile dominant). Moreover, these voices/thoughts activate evolved subordinate defences such as fight/flight and these are associated with depression in both depression and schizophrenia. CONCLUSION: Conceptualizing aspects of depressed and psychotic thinking as relating to evolved mental mechanisms, which are role serving, but can internally play off against each other, may open new ways of investigating certain aspects of severe pathologies.

Adult↗

PubMed1992

Comparative properties of hydroquinone and hydroxylamine reduction of the Ca(2+)-stabilized O2-evolving complex of photosystem II: reductant-dependent Mn2+ formation and activity inhibition.

Calcium binding to photosystem II slows NH2OH inhibition of O2 evolution; Mn2+ is retained by the O2-evolving complex [Mei, R., & Yocum, C. F. (1991) Biochemistry 30, 7836-7842]. This Ca(2+)-induced stability has been further characterized using the large reductant hydroquinone. Salt-washed photosystem II membranes reduced by hydroquinone in the presence of Ca2+ retain 80% of steady-state O2 evolution activity and contain about 2 Mn2+/reaction center that can be detected at room temperature by electron paramagnetic resonance. This Mn2+ produces a weak enhancement of H2O proton spin-lattice relaxation rates, cannot be easily extracted by a chelator, and is reincorporated into the O2-evolving complex upon illumination. A comparison of the properties of Ca(2+)-supplemented photosystem II samples reduced by hydroquinone or NH2OH alone or in sequence reveals the presence of a subpopulation of manganese atoms at the active site of H2O oxidation that is not accessible to facile hydroquinone reduction. At least one of these manganese atoms can be readily reduced by NH2OH following a noninhibitory hydroquinone reduction step. Under these conditions, about 3 Mn2+/reaction center are lost and O2 evolution activity is irreversibly inhibited. We interpret the existence of distinct sites of reductant action on manganese as further evidence that the Ca(2+)-binding site in photosystem II participates in regulation of the organization of manganese-binding ligands and the overall structure of the O2-evolving complex.

Binding Sites↗

PubMed1994

Site-directed photosystem II mutants with perturbed oxygen-evolving properties. 1. Instability or inefficient assembly of the manganese cluster in vivo.

Several site-directed photosystem II mutants with substitutions at Asp-170 of the D1 polypeptide were characterized by noninvasive methods in vivo. In several mutants, including some that evolve oxygen, a significant fraction of photosystem II reaction centers are shown to lack photooxidizable Mn ions. In this fraction of reaction centers, either the high-affinity site from which Mn ions rapidly reduce the oxidized secondary electron donor, YZ+, is devoid of Mn ions or the Mn ion(s) bound at this site are unable to reduce YZ+. It is concluded that the Mn clusters in these mutants are unstable or are assembled inefficiently in vivo. Mutants were constructed in the unicellular cyanobacterium Synechocystis sp. PCC 6803. The in vivo characterization procedures employed in this study involved measuring changes in the yield of variable chlorophyll a fluorescence following a saturating flash or brief illumination given in the presence of the electron transfer inhibitor 3-(3,4-dichlorophenyl)-1,1-dimethylurea, or following each of a series of saturating flashes given in the absence of this inhibitor. These procedures are easily applied to mutants that evolve little or no oxygen, facilitate the characterization of mutants with labile oxygen-evolving complexes, permit photosystem II isolation efforts to be concentrated on mutants having the stablest Mn clusters, and guide systematic spectroscopic studies of isolated photosystem II particles to mutants of particular interest.

Aspartic Acid↗

PubMed1994

Purification and characterization of oxygen-evolving photosystem II core complexes from the green alga Chlamydomonas reinhardtii.

Oxygen-evolving photosystem II complexes were isolated from the green alga Chlamydomonas reinhardtii by selective solubilization of thylakoid membranes with dodecyl maltoside followed by density gradient centrifugation and anion-exchange chromatography. In the presence of CaCl2 and K3[Fe(CN)6] the complexes evolved oxygen at rates exceeding 1000 mumol (mg of chl)-1 h-1. The particles contained 40 chlorophylls a and had properties very similar to those of PSII isolated from higher plants. Chlamydomonas reinhardtii is now the first organism which can be used for both site-directed mutagenesis and detailed biochemical and biophysical characterization of oxygen-evolving photosystem II. It seems therefore to be an ideal model organism for investigation of structure-function relationships in photosynthetic oxygen evolution.

Animals↗

PubMed1991

Nitrogen ligation to manganese in the photosynthetic oxygen-evolving complex: continuous-wave and pulsed EPR studies of photosystem II particles containing 14N or 15N.

The possibility of nitrogen ligation to the Mn in the oxygen-evolving complex from photosystem II was investigated with electron paramagnetic resonance (EPR) and electron spin echo envelope modulation (ESEEM) spectroscopies using 14N- and 15N-labeled preparations. Oxygen-evolving preparations were isolated from a thermophilic cyanobacterium, Synechococcus sp., grown on a medium containing either 14NO3- or 15NO3- as the sole source of nitrogen. the substructure on the "multiline" EPR signal, which arises from Mn in the S2 state of the enzyme, was measured with continuous-wave EPR. No changes were detected in the substructure peak positions upon substitution of 15N for 14N, indicating that this substructure is not due to superhyperfine coupling from nitrogen ligands. To detect potential nitrogen ligands with superhyperfine couplings of lesser magnitude than could be observed with conventional EPR methods, electron spin-echo envelope modulation experiments were also performed on the multiline EPR signal. The Fourier transform of the light-minus-dark time domain ESEEM data shows a peak at 4.8 MHz in 14N samples which is absent upon substitution with 15N. This gives unambiguous evidence for weak hyperfine coupling of nitrogen to the Mn of the oxygen-evolving complex. Possible origins of this nitrogen interaction are discussed.

Cyanobacteria↗

PubMed2001

A novel protein involved in the functional assembly of the oxygen-evolving complex of photosystem II in Synechocystis sp. PCC 6803.

Mutation of Glu69 to Gln in the D2 protein of photosystem II is known to lead to a loss of photoautotrophic growth in Synechocystis sp. PCC 6803. However, second-site mutants (pseudorevertants) with restored photoautotrophic growth but still maintaining the E69Q mutation in D2 are easily obtained. Using a genomic mapping technique involving functional complementation, the secondary mutation was mapped to slr0286 in two independent mutants. The mutations in Slr0286 were R42M or R394H. To study the function of Slr0286, mutants of E69Q and of the wild-type strain were made that lacked slr0286. Deletion of slr0286 did not affect photoautotrophic capacity in wild type but led to a marked decrease in the apparent affinity of Ca(2+) to its binding site at the water-splitting system of photosystem II and to a reduced heat tolerance of the oxygen-evolving system, particularly in E69Q. Moreover, a small increase in the half-time for photoactivation of the oxygen-evolving complex of photosystem II for both wild type and the E69Q mutant was observed in the absence of Slr0286. The accumulation of photosystem II reaction centers, dark stability of the oxygen-evolving apparatus, stability of oxygen evolution, and the kinetics of charge recombination between Q(A)(-) and the donor side were not affected by deletion of slr0286. Slr0286 lacks clear functional motifs, and no homologues are apparent in other organisms, even not in other cyanobacteria. In any case, Slr0286 appears to help the functional assembly and stability of the water-splitting system of photosystem II.

Amino Acid Sequence↗

PubMed1999

Site-directed mutagenesis of basic arginine residues 305 and 342 in the CP 43 protein of photosystem II affects oxygen-evolving activity in Synechocystis 6803.

The intrinsic chlorophyll protein CP 43, a component of photosystem II (PS II) in higher plants, green algae, and cyanobacteria, is encoded by the psbC gene. Oligonucleotide-directed mutagenesis was employed to introduce mutations into a segment of psbC that encodes the large extrinsic loop E of CP 43 in the cyanobacterium Synechocystis 6803. Two mutations, R305S and R342S, each produced a strain with impaired photosystem II activity. The R305S mutant strain grew photoautotrophically at rates comparable to the control strain. Immunological analyses of a number of PSII components indicated that this mutant accumulated normal quantities of PSII proteins. However, this mutant evolved oxygen to only 70% of control rates at saturating light intensities. Measurements of total variable fluorescence yield indicated that this mutant assembled approximately 70% of the PSII centers found in the control strain. The R342S mutant failed to grow photoautotrophically and exhibited no capacity for oxygen evolution. However, when grown photoheterotrophically in medium containing both glucose and 3-(3, 4-dichlorophenyl)-1,1-dimethylurea (DCMU), oxygen-evolving activity was observed in the R342S mutant, but at a low level of approximately 10% of the control rate. Immunological analysis of isolated thylakoid membranes from this mutant also indicated that this strain accumulated normal amounts of PSII core proteins. Total variable fluorescence yields for the R342S mutant indicated that it assembled a severely reduced number of fully functional PSII centers. R305S and R342S mutant strains exhibited, respectively, 2.7- and 4-fold increased sensitivity to photoinactivation. The fluorescence rise times for both mutants were comparable to the control when hydroxylamine was used as electron donor. However, both strains exhibited an increase (2.5- and 8-fold, respectively, for R305S and R342S) in fluorescence rise times with water as an electron donor. These results suggest that the mutations R305S and R342S each produce a defect associated with the oxygen-evolving complex of photosystem II. These are the first site-directed mutations in CP 43 to show such an effect.

Arginine↗