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PubMed2004

Impact of replacement of D1 C-terminal alanine with glycine on structure and function of photosynthetic oxygen-evolving complex.

The C-terminal alanine 344 (Ala-344) in the D1 protein of photosystem II is conserved in all of the organisms performing oxygenic photosynthesis. A free alpha-COO(-) of Ala-344 has been proposed to be responsible for ligating the Mn cluster. Here, we constructed a mutant having D1 in which D1-Ala-344 was replaced with glycine (Gly) in cyanobacterium Synechocystis sp. PCC 6803. The effects of this minimal change in the side group from methyl to hydrogen on the properties of the oxygen-evolving complex were comprehensively investigated using purified core particles. The mutant grew photoautotrophically, and little change was observed in the protein composition of the oxygen-evolving core particles. The Gly-substituted oxygen-evolving complex showed small but normal S(2) multiline and enhanced g = 4.1 electron spin resonance signals and S(2)-state thermoluminescence bands with slightly elevated peak temperature. The Gly substitution resulted in distinct but relatively small changes in a few bands arising from the putative carboxylate ligand for the Mn cluster in the mid-frequency (1800-1000 cm(-1)) S(2)/S(1) Fourier transform infrared difference spectrum. In contrast, the low frequency (670-350 cm(-1)) S(2)/S(1) Fourier transform infrared difference spectrum was markedly changed by the substitution. The results indicate that the internal structure of the Mn cluster and/or the interaction between the Mn cluster and its ligand are considerably altered by a simple change in the side group, from methyl to hydrogen, at the C-terminal of the D1 protein.

Alanine↗

PubMed1987

Structural localization of the O2-evolving apparatus to multimeric (tetrameric) particles on the lumenal surface of freeze-etched photosynthetic membranes.

Isolated appressed chloroplast membranes, highly enriched in photosystem II (PSII) activity, were examined by freeze-etch electron microscopy. The exposed surfaces of these Triton X-100 solubilized membrane fragments correspond to the lumenal or ESs surface of intact stacked thylakoid membrane regions (Dunahay, T. G., L. A. Staehelin, M. Seibert, P. D. Ogilvie, and S. P. Berg. 1984. Biochim. Biophys. Acta. 764:179-193). The sequential removal from this sample of three extrinsic proteins (17, 23, and 33 kD) associated with the O2-evolving apparatus and the concomitant loss of O2 evolution, was related to subtle changes in the height and substructure of characteristic multimeric (often tetrameric) particles that protrude from the ESs membrane surface. After removal of these proteins, the multimeric particles disappeared and dimeric particles of similar diameter but of lesser height (6.1 vs. 8.2 nm in the controls) were observed. Reconstitution of the depleted membrane fragments with the extrinsic proteins led to rebinding of the three proteins, to a 63% recovery of the control rates of O2 evolution, and to the reappearance of the larger multimeric particles. Analysis of the structural changes associated with the loss and rebinding of the extrinsic proteins is consistent with a stoichiometry of one PSII complex for either one or two copies of the 17-, 23-, and 33-kD proteins, and these are symmetrically arranged on the lumenal surface of the complex. These results demonstrate that the multimeric ESs particles correspond to part of the intact O2-evolving apparatus of PSII, thus confirming previous indirect studies relating these particles to PSII. The dimeric particles probably contain the rest of the O2-evolving complex.

Chlorophyll↗

PubMed2005

Equivalent binding sites reveal convergently evolved interaction motifs.

MOTIVATION: Much research has been devoted to the characterization of interaction interfaces found in complexes with known structure. In this context, the interactions of non-homologous domains at equivalent binding sites are of particular interest, as they can reveal convergently evolved interface motifs. Such motifs are an important source of information to formulate rules for interaction specificity and to design ligands based on the common features shared among diverse partners. RESULTS: We develop a novel method to identify non-homologous structural domains which bind at equivalent sites when interacting with a common partner. We systematically apply this method to all pairs of interactions with known structure and derive a comprehensive database for these interactions. Of all non-homologous domains, which bind with a common interaction partner, 4.2% use the same interface of the common interaction partner (excluding immunoglobulins and proteases). This rises to 16% if immunoglobulin and proteases are included. We demonstrate two applications of our database: first, the systematic screening for viral protein interfaces, which can mimic native interfaces and thus interfere; and second, structural motifs in enzymes and its inhibitors. We highlight several cases of virus protein mimicry: viral M3 protein interferes with a chemokine dimer interface. The virus has evolved the motif SVSPLP, which mimics the native SSDTTP motif. A second example is the regulatory factor Nef in HIV which can mimic a kinase when interacting with SH3. Among others the virus has evolved the kinase's PxxP motif. Further, we elucidate motif resemblances in Baculovirus p35 and HIV capsid proteins. Finally, chymotrypsin is subject to scrutiny wrt. its structural similarity to subtilisin and wrt. its inhibitor's similar recognition sites. SUPPLEMENTARY INFORMATION: A database is online at scoppi.biotec.tu-dresden.de/abac/.

Algorithms↗

PubMed1991

Identification of adaptive changes in an evolving population of Escherichia coli: the role of changes with regulatory and highly pleiotropic effects.

A population of Escherichia coli initiated with a single clone developed extensive morphological and physiological polymorphism after being maintained for 773 generations in glucose-limited continuous culture. To understand the mechanisms of adaptation to this environment, total protein patterns of four adaptive clones and of the parent strains were examined by two-dimensional gel electrophoresis. Approximately 20% of the proteins (approximately 160 in absolute numbers) showed significantly different levels of expression in pairwise comparisons of parent and adapted clones. The extent of these changes points to the importance of mutations with regulatory and/or highly pleiotropic effects in the adaptive process. The four evolved clones all expressed fewer proteins than did the parent strain, supporting the hypothesis of energy conservation during evolutionary change. Forty-two proteins that could be assigned to known cellular functions were identified. The changes in some of them indicated that the evolved clones developed different adaptive mechanisms to glucose-limited environment. Changes were observed in the expression levels of proteins associated with translation, membrane composition, shock response, and active transport. A fraction of the changes could not be either explained or predicted from a consideration of the nature of the environment in which the clones evolved.

Adaptation, Biological↗

PubMed2004

Isolation and characterization of oxygen-evolving photosystem II complexes retaining the PsbO, P and Q proteins from Euglena gracilis.

Oxygen-evolving photosystem II (PSII) complexes of Euglena gracilis were isolated and characterized. (1) The PSII complexes contained three extrinsic proteins of 33 kDa (PsbO), 23 kDa (PsbP) and 17 kDa (PsbQ), and showed oxygen-evolving activity of around 700 micromol O2 (mg Chl)(-1) h(-1) even in the absence of Cl- and Ca2+ ions. (2) NaCl-treatment removed not only PsbP and PsbQ but also a part of PsbO from Euglena PSII, indicating that PsbO binds to Euglena PSII more loosely than those of other organisms. Treatments by urea/NaCl, alkaline Tris or CaCl2 completely removed the three extrinsic proteins from Euglena PSII. (3) Each of the Euglena extrinsic proteins bound directly to PSII independent of the other extrinsic proteins, which is similar to the binding properties of the extrinsic proteins in a green alga, Chlamydomonas reinhardtii. (4) One of the significant features of Euglena PSII is that the oxygen evolution was not enhanced by Ca2+. When CaCl2-treated Euglena PSII was reconstituted with PsbO, the oxygen-evolving activity was stimulated by the addition of NaCl, but no further stimulation was observed by CaCl2. (5) Oxygen evolution of Euglena PSII reconstituted with PsbO from C. reinhardtii or spinach instead of that from Euglena also showed no enhancement by Ca2+, whereas a significant enhancement of oxygen evolution was observed by Ca2+ when the green algal or higher plant PSII was reconstituted with Euglena PsbO instead of their own PsbO. These results indicate that the PSII intrinsic proteins instead of the extrinsic PsbO protein, are responsible for the stimulation of oxygen evolution by Ca2+. Sequence comparison of major PSII intrinsic proteins revealed that PsbI of Euglena PSII is remarkably different from other organisms in that Euglena PsbI possesses extra 16-17 residues exposed to the luminal side. This may be related to the loss of enhancement of oxygen evolution by Ca2+ ion.

Algal Proteins↗

PubMedDate not supplied

Thromboxane A2 does not contribute to arrhythmogenesis during evolving canine myocardial infarction.

During the healing phase of evolving myocardial infarction, inflammatory cells invade the affected region and produce metabolites that may influence electrophysiological parameters and the genesis of malignant arrhythmias. We have recently shown an increased synthetic capacity within an evolving infarct for thromboxane A2 (TXA2), a metabolite that has been implicated in arrhythmias associated with early ischemia. The present study used both in vivo and in vitro procedures to define the electrophysiological and arrhythmogenic effects, if any, of thromboxane during evolving myocardial infarction. Thirty-three dogs divided into three groups were studied 3-7 days after transient left anterior descending coronary artery ligation. One group (n = 24) was examined by programmed electrical stimulation in the conscious state and, of the five dogs in this group with sustained ventricular tachycardia (VT), none demonstrated consistent limitation of inducibility by selective inhibition of thromboxane synthetase using three different agents. In the second group, (n = 5) regional conduction velocity was assessed using detailed three-dimensional activation analysis from 232 simultaneous intramyocardial sites, and no change was induced by the thromboxane synthetase inhibitor OKY-1581 in either normal or infarcted myocardial zones during sinus rhythm or with pacing. In the third group (n = 4), isolated ventricular muscle was studied in vitro using both intracellular transmembrane action potential recordings and surface extracellular maps from 48 simultaneous points. Neither intracellular action potential parameters nor extracellularly recorded activation patterns were altered by superfusion with the stable thromboxane analog STA2, the activity of which was verified by bioassay. Thus, despite increased synthetic capacity for thromboxane generation, the presence of TXA2 does not directly influence either electrophysiological indices or arrhythmogenesis.

Action Potentials↗

PubMed2006

The evolving structure of orthopaedic residency education.

Orthopaedic residency has undergone continual evolution since the early 1900s. Training has evolved from a preceptorship to a highly evolved and structured educational system which largely standardizes training throughout the United States. Approval and accreditation of training programs, as well as content, is now overseen by a hierarchical group of organizations with representations from a variety of medical societies and boards. The evolving process has served the public well, providing competent care of the musculoskeletal system.

History, 20th Century↗

PubMed1996

Analysis of the beta' subunit of DNA-dependent RNA polymerase does not support the hypothesis inferred from 16S rRNA analysis that Oenococcus oeni (formerly Leuconostoc oenos) is a tachytelic (fast-evolving) bacterium.

rRNA sequencing has shown that leuconostocs comprise three distinct phylogenetic lineages which have been designated separate genera (viz., the genera Leuconostoc sensu stricto, Oenococcus, and Weissella). In addition, the 16S rRNA line formed by Oenococcus oeni (formerly Leuconostoc oenos) is exceptionally long; this fact, together with variations in the compositions of conserved positions in the 16S rRNA, has led to the hypothesis (D. Yang and C. R. Woese, Syst. Appl. Microbiol. 12:145-149, 1989) that this organism is a fast-evolving bacterium. Previous evidence that the leuconostocs should be divided into three genera and that O. oeni is an example of tachytelic evolution has come solely from rRNA analyses. In this study we seqenced the rpoC gene encoding the beta' subunit of DNA-dependent RNA polymerase of leuconostocs and performed a comparative phylogenetic analysis. The subdivision of the leuconostocs into three distinct lineages was confirmed by the rpoC gene data, but no evidence that indicated that O. oeni is evolving at an extraordinary rate was found. If O. oeni is truly tachytelic, then fast-evolving phenomena would be expected to occur throughout the whole genome, including this independent molecular chronometer.

Amino Acid Sequence↗

PubMed2003

Sexual isolation evolves faster than hybrid inviability in a diverse and sexually dimorphic genus of fish (Percidae: Etheostoma).

Theory predicts that sexual (or behavioral) isolation will be the first form of reproductive isolation to evolve in lineages characterized by sexual selection. Here I directly compare the rate of evolution of sexual isolation with that of hybrid inviability in a diverse and sexually dimorphic genus of freshwater fish. The magnitude of both sexual isolation and hybrid inviability were quantified for multiple pairs of allopatric species. Rates of evolution were inferred by comparing genetic distances of these species pairs with the magnitude of each form of reproductive isolation: the slope of the regression of genetic distance on the magnitude of reproductive isolation represents the rate of evolution. Of the two forms of isolation, the magnitude of sexual isolation exhibited the steeper slope of regression, indicating that sexual isolation will tend to evolve to completion earlier than hybrid inviability, strictly as a by-product of evolution in geographically isolated populations. Additional evidence from the literature is used to qualitatively compare rates of evolution of sexual isolation with that of other forms of reproductive isolation. Preliminary comparisons support the prediction that sexual isolation will evolve more rapidly than other forms. Because Etheostoma is characterized by striking sexual dimorphism, these results are consistent with the hypothesis that sexual selection for exaggerated mate-recognition characters causes the relatively rapid evolution of sexual isolation.

Animals↗

PubMed1995

Distinct and differently regulated Mo-dependent nitrogen-fixing systems evolved for heterocysts and vegetative cells of Anabaena variabilis ATCC 29413: characterization of the fdxH1/2 gene regions as part of the nif1/2 gene clusters.

Two different fdxH genes (fdxH1, fdxH2) have been isolated from the nitrogen-fixing, heterocyst-forming cyanobacterium Anabaena variabilis ATCC 29413. They are part of two different nif gene clusters, nif1 and nif2. fdxH1 encodes the [2Fe-2S] ferredoxin that is known as the direct electron donor to nitrogenase in heterocysts, and is very similar to FdxH from Anabaena sp. PCC 7120. FdxH2 has more residues in common and shares its oxygen sensitivity with the single FdxH from the non-heterocystous, filamentous cyanobacterium Plectonema boryanum PCC 73110. The latter expresses nitrogenase early (< or = 3-4h) after nitrogen depletion in vegetative cells and exclusively under anaerobic conditions. fdxH2 and the nif2 genes of Anabaena 29413 are also transcribed < or = 4 h after onset of nitrogen-stepdown, exclusively under anaerobic growth conditions and long before functional heterocysts appear. At this time, no fdxH1 and nif1 gene transcription was observed. It occurred later and was associated with nitrogen fixation under aerobic conditions, i.e. within heterocysts. fdxH2 and nifHDK2 were not transcribed during aerobic, nitrogen-fixing growth. In addition, neither was an fdxH2-type gene found nor an anaerobically and early inducible Nif2 system detectable in Anabaena 7120. These data reveal that in filamentous cyanobacteria two different Nif systems have evolved based on molybdenum nitrogenases. It is concluded that a Nif2-type system operates in vegetative cells of non-heterocystous and some, but not all, heterocyst-forming filamentous cyanobacteria. It is environmentally regulated by the levels of both oxygen and combined nitrogen in the habitat. To simultaneously allow for oxygen-evolving photosynthesis and oxygen-sensitive nitrogen fixation, the Nif1-type system probably branched from an ancestral Nif2-type system and has evolved for an exclusive operation within heterocysts. Accordingly, its expression has become an obligate late event in the developmental programme of heterocyst differentiation, irrespective of aerobic or anaerobic growth conditions.

Amino Acid Sequence↗

PubMed1998

The evolved basis and adaptive functions of cognitive distortions.

This paper explores common cognitive distortions from the perspective of evolutionary psychology. It is suggested that cognitive distortions are natural consequences of using fast track defensive algorithms that are sensitive to threat. In various contexts, especially those of threat, humans evolved to think adaptively rather than logically. Hence cognitive distortions are not strictly errors in brain functioning and it can be useful to inform patients that 'negative thinking' may be dysfunctional but is a reflection of basic brain design and not personal irrationality. The evolved nature of cognitive distortions has been implicit in cognitive therapy from its early days (Beck, 1963; Ellis, 1962) but has not been fully articulated in what is now known about evolved mental processes. Many forms of cognitive distortion can be seen to use the (previously) adaptive heuristic of better safe than sorry.

Adaptation, Psychological↗

PubMed2025

Multi-Omics Analysis of Experimentally Evolved Candida auris Isolates Reveals Modulation of Sterols, Sphingolipids, and Oxidative Stress in Acquired Amphotericin B Resistance.

Clinical isolates of Candida auris show a high prevalence of resistance to Amphotericin B (AmB)-an uncommon trait in most Candida species. Alterations in ergosterol biosynthesis can contribute to acquired AmB resistance in C. auris laboratory strains but are rarely seen in clinical isolates. In this study, we experimentally evolved two drug-susceptible Clade II isolates of C. auris to develop AmB resistance. The evolved strains displayed a four to eight fold increase in MIC50 compared to the parental cells. We analyzed changes in their karyotype, genome, lipidome, and transcriptome associated with this acquired resistance. In one lineage, AOX2 was upregulated, and its deletion reversed the AmB resistance phenotype. The aox2Δ mutant also failed to evolve AmB resistance under experimental conditions. In the same lineage, restoring the UPC2 S332R and RTG3 S101T mutations to the wild-type allele restored AmB susceptibility. In another lineage, the ergosterol and sphingolipid pathways were observed to play a critical role, and upregulation of the ERG genes elevated the total sterol content, while significant downregulation of HSX11 (glucosylceramide synthase) resulted in lower levels of glucosylceramides. To our knowledge, this study is the first to show that AmB resistance in C. auris can be acquired through mechanisms both dependent on or independent of sterol content modulation, highlighting Aox2 and Upc2 as key regulators of amphotericin resistance.

Amphotericin B↗

PubMed2004

Architecture of the photosynthetic oxygen-evolving center.

Photosynthesis uses light energy to drive the oxidation of water at an oxygen-evolving catalytic site within photosystem II (PSII). We report the structure of PSII of the cyanobacterium Thermosynechococcus elongatus at 3.5 angstrom resolution. We have assigned most of the amino acid residues of this 650-kilodalton dimeric multisubunit complex and refined the structure to reveal its molecular architecture. Consequently, we are able to describe details of the binding sites for cofactors and propose a structure of the oxygen-evolving center (OEC). The data strongly suggest that the OEC contains a cubane-like Mn3CaO4 cluster linked to a fourth Mn by a mono-micro-oxo bridge. The details of the surrounding coordination sphere of the metal cluster and the implications for a possible oxygen-evolving mechanism are discussed.

Binding Sites↗

PubMed1986

Enrichment for Hydrogen-Oxidizing Acinetobacter spp. in the Rhizosphere of Hydrogen-Evolving Soybean Root Nodules.

Field soybean plants were inoculated with Hup wild-type or H(2) uptake-negative (Hup) mutants of Bradyrhizobium japonicum. For two consecutive summers we found an enrichment for acinetobacters associated with the surfaces of the H(2)-evolving nodules. Soybean root nodules that evolved H(2) had up to 12 times more Acinetobacter spp. bacteria associated with their surfaces than did nodules incapable of evolving H(2). All of the newly isolated strains identified as Acinetobacter obtained from the surfaces of root nodules, as well as known established Acinetobacter strains, were capable of oxidizing H(2), a property not previously described for this alkane-degrading soil bacterium.

Journal Article↗

PubMed2002

Codenitrification and denitrification are dual metabolic pathways through which dinitrogen evolves from nitrate in Streptomyces antibioticus.

We screened actinomycete strains for dinitrogen (N(2))-producing activity and discovered that Streptomyces antibioticus B-546 evolves N(2) and some nitrous oxide (N(2)O) from nitrate (NO(3)(-)). Most of the N(2) that evolved from the heavy isotope ([(15)N]NO(3)(-)) was (15)N(14)N, indicating that this nitrogen species consists of two atoms, one arising from NO(3)(-) and the other from different sources. This phenomenon is similar to codenitrification in fungi. The strain also evolved less, but significant, amounts of (15)N(15)N from [(15)N]NO(3)(-) in addition to (15)N(15)NO with concomitant cell growth. Prior to the production of N(2) and N(2)O, NO(3)(-) was rapidly reduced to nitrite (NO(2)(-)) accompanied by distinct cell growth, showing that the actinomycete strain is a facultative anaerobe that depends on denitrification and nitrate respiration for anoxic growth. The cell-free activities of denitrifying enzymes could be reconstituted, supporting the notion that the (15)N(15)N and (15)N(15)NO species are produced by denitrification from NO(3)(-) via NO(2)(-). We therefore demonstrated a unique system in an actinomycete that produces gaseous nitrogen (N(2) and N(2)O) through both denitrification and codenitrification. The predominance of codenitrification over denitrification along with oxygen tolerance is the key feature of nitrate metabolism in this actinomycete.

Aerobiosis↗

PubMed2001

Emergence of memory-driven command neurons in evolved artificial agents.

Using evolutionary simulations, we develop autonomous agents controlled by artificial neural networks (ANNs). In simple lifelike tasks of foraging and navigation, high performance levels are attained by agents equipped with fully recurrent ANN controllers. In a set of experiments sharing the same behavioral task but differing in the sensory input available to the agents, we find a common structure of a command neuron switching the dynamics of the network between radically different behavioral modes. When sensory position information is available, the command neuron reflects a map of the environment, acting as a location-dependent cell sensitive to the location and orientation of the agent. When such information is unavailable, the command neuron's activity is based on a spontaneously evolving short-term memory mechanism, which underlies its apparent place-sensitive activity. A two-parameter stochastic model for this memory mechanism is proposed. We show that the parameter values emerging from the evolutionary simulations are near optimal; evolution takes advantage of seemingly harmful features of the environment to maximize the agent's foraging efficiency. The accessibility of evolved ANNs for a detailed inspection, together with the resemblance of some of the results to known findings from neurobiology, places evolved ANNs as an excellent candidate model for the study of structure and function relationship in complex nervous systems.

Biological Evolution↗

PubMed2000

Cooperative coevolution: an architecture for evolving coadapted subcomponents.

To successfully apply evolutionary algorithms to the solution of increasingly complex problems, we must develop effective techniques for evolving solutions in the form of interacting coadapted subcomponents. One of the major difficulties is finding computational extensions to our current evolutionary paradigms that will enable such subcomponents to "emerge" rather than being hand designed. In this paper, we describe an architecture for evolving such subcomponents as a collection of cooperating species. Given a simple string-matching task, we show that evolutionary pressure to increase the overall fitness of the ecosystem can provide the needed stimulus for the emergence of an appropriate number of interdependent subcomponents that cover multiple niches, evolve to an appropriate level of generality, and adapt as the number and roles of their fellow subcomponents change over time. We then explore these issues within the context of a more complicated domain through a case study involving the evolution of artificial neural networks.

Adaptation, Physiological↗

PubMed2005

Evolving evolutionary algorithms using linear genetic programming.

A new model for evolving Evolutionary Algorithms is proposed in this paper. The model is based on the Linear Genetic Programming (LGP) technique. Every LGP chromosome encodes an EA which is used for solving a particular problem. Several Evolutionary Algorithms for function optimization, the Traveling Salesman Problem and the Quadratic Assignment Problem are evolved by using the considered model. Numerical experiments show that the evolved Evolutionary Algorithms perform similarly and sometimes even better than standard approaches for several well-known benchmarking problems.

Algorithms↗