Copper proteomes, phylogenetics and evolution

This paper is a continuation of our study of the connection between the changing environment and the changing use of particular elements in organisms in the course of their combined evolution (Decaria, Bertini and Williams, Metallomics, 2010, 2, 706). Here we treat the changes in copper proteins in historically the same increasingly oxidising environmental conditions. The study is a bioinformatic analysis of the types and the numbers of copper domains of proteins from 435 DNA sequences of a wide range of organisms available in NCBI, using the method developed by Andreini, Bertini and Rosato in Accounts of Chemical Research 2009, 42, 1471. The copper domains of greatest interest are found predominantly in copper chaperones, homeostatic proteins and redox enzymes mainly used outside the cytoplasm which are in themselves somewhat diverse. The multiplicity of these proteins is strongly marked. The contrasting use of the iron and heme iron proteins in oxidations, mostly in the cytoplasm, is compared with them and with activity of zinc fingers during evolution. It is shown that evolution is a coordinated development of the chemistry of elements with use of novel and multiple copies of their proteins as their availability rises in the environment.     

Playing Darwin. Part A. Experimental Evolution in Drosophila

In 2009 we celebrate Charles Darwin’s second centenary, and 150 years since the publication of ‘The Origin of Species’. After so many years, what has changed in the way we understand Evolution? Obviously we have now a full understanding of the mechanisms underlying heritability. Many molecular tools are available, allowing among other things to reconstruct more accurately the evolutionary history of species and use a comparative approach to infer evolutionary processes. But we can also study evolution in action. Such studies—Experimental Evolution—help us to characterize in detail the evolutionary processes and patterns as a function of environmental challenges, the previous history and present state of populations, and the interactions between such factors. We have now a wide variety of organisms that have been studied with this approach, exploring a diversity of potentialities, in biological characteristics and genetic tools, and covering a variety of evolutionary questions. In this short article I will illustrate the potentialities of Experimental Evolution, focusing in three studies in Drosophila. These and other studies of Experimental Evolution illustrate that Evolution is often local, involving complex patterns and processes, which lead both to specific adaptations and to biological diversity, as Darwin already stated clearly in ‘The Origin of Species’.     

Histone formation, gene expression, and zinc deficiency in Euglena gracilis

Histones, and other basic proteins, have been isolated from zinc-sufficient (+Zn) Euglena gracilis by standard chromatographic methods. These cells contain 2.46 micrograms of histones and 1.96 micrograms of DNA per 10(6) organisms. Each of the histones, H1, H3, H2A, H2B, and H4, is present in both log- and stationary-phase +Zn cells and has been characterized according to its electrophoretic mobility and molecular weight. H1 has been further identified on the basis of its amino acid composition and its cross-reactivity with calf thymus histone H1 antibodies. Similarly, H3 has been recognized as well by its specific reaction with an H3 antibody. In contrast, log-phase zinc-deficient (-Zn) cells contain H1 and H3 while H2A, H2B, and H4 are absent. All of the histones vanish in stationary-phase-Zn organisms. The DNA content increases as the -Zn cells progress from log to stationary phase, reaching a value of 4.40 micrograms/10(6) cells, double that of comparable stationary-phase +Zn organisms. A 2000-3000-dalton polypeptide whose electrophoretic behavior differs from that of the known histones constitutes over 90% of the total basic proteins of -Zn cells. On addition of zinc to stationary -Zn cells, cell division resumes, and all the histones and other basic proteins reappear. Together with previous results, the data demonstrate that zinc significantly affects the metabolism of all major chromatin components, i.e., the RNA polymerases, DNA, and histones of E. gracilis [Vallee, B.L., & Falchuk, K.H. (1981) Philos. Trans. R. Soc. London, Ser. B 294, 185-197]. The implications of these effects of zinc on chromatin structure and function are discussed.     

Application of the biotic ligand model to predicting zinc toxicity to rainbow trout,fathead minnow,and Daphnia magna

The Biotic Ligand Model has been previously developed to explain and predict the effects of water chemistry on the toxicity of copper, silver, and cadmium. In this paper, we describe the development and application of a biotic ligand model for zinc (Zn BLM). The data used in the development of the Zn BLM includes acute zinc LC50 data for several aquatic organisms including rainbow trout, fathead minnow, and Daphnia magna. Important chemical effects were observed that influenced the measured zinc toxicity for these organisms including the effects of hardness and pH. A significant amount of the historical toxicity data for zinc includes concentrations that exceeded zinc solubility. These data exhibited very different responses to chemical adjustment than data that were within solubility limits. Toxicity data that were within solubility limits showed evidence of both zinc complexation, and zinc-proton competition and could be well described by a chemical equilibrium approach such as that used by the Zn BLM.     

Evolution of global regulatory networks during a long-term experiment with Escherichia coli

Evolution has shaped all living organisms on Earth, although many details of this process are shrouded in time. However, it is possible to see, with one's own eyes, evolution as it happens by performing experiments in defined laboratory conditions with microbes that have suitably fast generations. The longest-running microbial evolution experiment was started in 1988, at which time twelve populations were founded by the same strain of Escherichia coli. Since then, the populations have been serially propagated and have evolved for tens of thousands of generations in the same environment. The populations show numerous parallel phenotypic changes, and such parallelism is a hallmark of adaptive evolution. Many genetic targets of natural selection have been identified, revealing a high level of genetic parallelism as well. Beneficial mutations affect all levels of gene regulation in the cells including individual genes and operons all the way to global regulatory networks. Of particular interest, two highly interconnected networks -- governing DNA superhelicity and the stringent response -- have been demonstrated to be deeply involved in the phenotypic and genetic adaptation of these experimental populations.     

Structure, function, and regulation of a subfamily of mouse zinc transporter genes

Zinc is an essential metal for all eukaryotes, and cells have evolved a complex system of proteins to maintain the precise balance of zinc uptake, intracellular storage, and efflux. In mammals, zinc uptake appears to be mediated by members of the Zrt/Irt-like protein (ZIP) superfamily of metal ion transporters. Herein, we have studied a subfamily of zip genes (zip1, zip2, and zip3) that is conserved in mice and humans. These eight-transmembrane domain proteins contain a conserved 12-amino acid signature sequence within the fourth transmembrane domain. All three of these mouse ZIP proteins function to specifically increase the uptake of zinc in transfected cultured cells, similar to the previously demonstrated functions of human ZIP1 and ZIP2 (Gaither, L. A., and Eide, D. J. (2000) J. Biol. Chem. 275, 5560-5564; Gaither, L. A., and Eide, D. J. (2001) J. Biol. Chem. 276, 22258-22264). No ZIP3 orthologs have been previously studied. Furthermore, this first systematic comparative study of the in vivo expression and dietary zinc regulation of this subfamily of zip genes revealed that 1) zip1 mRNA is abundant in many mouse tissues, whereas zip2 and zip3 mRNAs are very rare or moderately rare, respectively, and tissue-restricted in their accumulation; and 2) unlike mouse metallothionein I and zip4 mRNAs (Dufner-Beattie, J., Wang, F., Kuo, Y.-M., Gitschier, J., Eide, D., and Andrews, G. K. (2003) J. Biol. Chem. 278, 33474-33481), the abundance of zip1, zip2, and zip3 mRNAs is not regulated by dietary zinc in the intestine and visceral endoderm, tissues involved in nutrient absorption. These studies suggest that all three of these ZIP proteins may play cell-specific roles in zinc homeostasis rather than primary roles in the acquisition of dietary zinc.     

Origin and evolution of chromosomal sperm proteins

In the eukaryotic cell, DNA compaction is achieved through its interaction with histones, constituting a nucleoprotein complex called chromatin. During metazoan evolution, the different structural and functional constraints imposed on the somatic and germinal cell lines led to a unique process of specialization of the sperm nuclear basic proteins (SNBPs) associated with chromatin in male germ cells. SNBPs encompass a heterogeneous group of proteins which, since their discovery in the nineteenth century, have been studied extensively in different organisms. However, the origin and controversial mechanisms driving the evolution of this group of proteins has only recently started to be understood. Here, we analyze in detail the histone hypothesis for the vertical parallel evolution of SNBPs, involving a “vertical” transition from a histone to a protamine‐like and finally protamine types (H → PL → P), the last one of which is present in the sperm of organisms at the uppermost tips of the phylogenetic tree. In particular, the common ancestry shared by the protamine‐like (PL)‐ and protamine (P)‐types with histone H1 is discussed within the context of the diverse structural and functional constraints acting upon these proteins during bilaterian evolution.     

PharmEcology: A pharmacological approach to understanding plant-herbivore interactions: an introduction to the symposium

A central goal in understanding the ecology and evolution of animals is to identify factors that constrain or expand breadth of diet. Selection of diet in many animals is often constrained by chemical deterrents (i.e., secondary metabolites) in available food items. The integration of chemistry and ecology has led to a significant understanding of the chemical complexity of prey (e.g., animals, plants, and algae) and the resultant foraging behavior of consumers. However, most of the literature on chemical defenses of marine and terrestrial prey lacks a mechanistic understanding of how consumers tolerate, or avoid, chemically-defended foods. In order to understand ecological patterns of foraging and co-evolutionary relationships between prey and consumers, we must advance our understanding of the physiological mechanisms responsible for chemical interactions. Such mechanistic studies require the integration of the discipline of pharmacology with ecology, which we call "PharmEcology." Pharmacology provides the tools and insight to investigate the fate (what the body does to a chemical) and action (what a chemical does to the body) of chemicals in living organisms, whereas ecology provides the insight into the interactions between organisms (e.g., herbivores) and their environment (e.g., plants). Although, the general concepts of pharmacology were introduced to ecologists studying plant-herbivore interactions over 30 years ago, the empirical use of pharmacology to understand mechanisms of chemical interactions has remained limited. Moreover, many of the recent biochemical, molecular and technical advances in pharmacology have yet to be utilized by ecologists. The PharmEcology symposium held at a meeting of the Society for Integrative and Comparative Biology in January of 2009 was developed to define novel research directions at the interface of pharmacology and ecology.     

Evolutionary remnants as widely accessible evidence for evolution: the structure of the argument for application to evolution education

Evolution education, in both schools and informal education, often focuses on natural selection and the fit of organisms through natural selection to their environment and way of life. Examples of evidence that evolution has occurred are therefore often limited to a modest number of classic but exotic cases, with little attention to how one might apply principles to more familiar organisms. Many of these classic examples are examples of adaptation; adaptation to local environments is, however, an outcome that could in principle also be explained by supernatural creation or design. A frequent result is the perception among the public is that examples of evolution are rare, and that the existence of well-adapted organisms may just as easily be explained metaphysically. We argue that among categories of evidence of evolution accessible to non-specialists in any environment, the most compelling evidence of common ancestry consists of remnants of evolutionary history evident in homologous features, particularly when those homologies are related to lack of fit of organisms to their way of life (“vestiges”) or to better fit that involves complicated combinations of parts usually assigned other functions (“contrivances”). Darwin emphasized the critical nature of this argument from imperfections, and it has been part of traditional catalogs of “evidence for evolution” for more than a century. Yet while remnants of history are widely used as a category of evidence for evolution, their utility in education of comparative anatomy to document body parts passed on through descent is underemphasized in evolution education at all levels. We explore the use of evolutionary remnants to document common ancestry and evidence for evolution, for application to evolution education.     

用于蛋白质体外分子进化研究的DNA随机突变技术

蛋白质体外分子进化是模拟自然的进化过程,利用基因随机突变和定向筛选（选择）技术,以获得具有预期新功能的突变体分子。虽然体外进化近几年才产生,但已成为医药和工业领域中筛选具有特殊催化性质的酶的最重要的方法之一。ＤＮＡ随机突变技术是蛋白质体外分子进化研究的基础,本文将对几种最重要的突变方法：倾向错误的ＰＣＲ、ＤＮＡ重排、模板交错延伸反应和随机延伸突变的原理和应用等加以介绍。     

Non-sequence-specific DNA binding by the FILAMENTOUS FLOWER protein from Arabidopsis thaliana is reduced by EDTA.

The FILAMENTOUS FLOWER protein has a zinc finger domain, hydrophobic region, proline-rich region, and a HMG box-like domain. We have reported that zinc release at the zinc finger is probably facilitated by the non-canonical cysteine residue at position 56, and that EDTA causes the structural change and enhances the self-assembly of the protein (Kanaya, E., Watanabe, K., Nakajima, N., Okada, K., and Shimura, Y. (2001) J. Biol. Chem. 276, 7383-7390). To investigate this aspect further we examined the DNA binding function of the FILAMENTOUS FLOWER protein. Gel retardation experiments showed that the FILAMENTOUS FLOWER protein binds to DNA without sequence specificity. Deletion analyses suggested that the zinc finger domain and the hydrophobic region are not required but the proline-rich region and the HMG box-like domain are indispensable for the DNA binding by the FILAMENTOUS FLOWER protein. The DNA binding by the protein consisting of the zinc finger domain and the rest of the regions was reduced with the addition of EDTA. This result probably suggests that the zinc release, the structural change probably occurring in the zinc finger domain, the intermolecular interaction, and the self-assembly of the protein are related to the dissociation of the FILAMENTOUS FLOWER protein from DNA.     

The nature of the last universal ancestor and the root of the tree of life, still open questions.

The nature of the last universal ancestor to all extent cellular organisms and the rooting of the universal tree of life are fundamental questions which can now be addressed by molecular evolutionists. Several scenarios have been proposed during the last years, based on the phylogenies of ribosomal RNA and of duplicated proteins, which suggest that the last universal ancestor was either an RNA progenote or an hyperthermophilic prokaryote. We discuss these hypotheses in the light of new data on the evolution of DNA metabolizing enzymes and of contradictions between different protein phylogenies. We conclude that the last universal ancestor was a member of the DNA world already containing several DNA polymerases and DNA topoisomerases. Furthermore, we criticize current data which suggest that the rooting of the universal tree of life is located in the eubacterial branch and we conclude that both rooting the universal tree and the nature of the last universal ancestor are still open questions.     

Recent advances in studies of evolutionary relationships between proteins and nucleic acids

Evolution depends upon the occurrence of occasional changes, large or small, in hereditary characteristics. Molecular genetics gave rise to the new field of molecular evolution, which is currently exploring the changes that take place in proteins and nucleic acids over long periods of time. The following are some of the fundamental assumptions:

1. The phenotypic characteristics of organisms depend directly on proteins.
2. Proteins are synthesized in accordance with information carried in molecules of DNA as sequences of the four bases, adenine, guanine, cytosine, and thymine. The information is transcribed into molecules of messenger RNA and is translated into proteins by the intervention of the genetic code.
3. Changes in the composition of the base sequences in DNA can take place in living organisms, and these changes can affect the phenotypic characteristics of the next generation.
4. The process of natural selection favors the perpetuation of organisms which compete successfully in the struggle for existence. This process leads to the elimination of all but a small fraction of the astronomical number of possible protein molecules that could result from genetic translation of the possible variants of DNA. Furthermore, the number of protein molecules was originally much smaller than it is to-day, and it has increased by hereditary processes rather than by the chance appearance of entirely new proteins.
5. The DNA present in any single cell contains the complete information for all the hereditary characteristics of the organism. The amount of DNA per cell may increase during evolution and this increase has produced modern organisms that are ‘higher’, more specialized, and more complex, from carlicr and simpler forms.
6. Protein molecules are slowly and steadily differentiated during evolution if their genes are physically separated from each other, by allopatric speciation or even by duplication and translocation, whether or not the function of the proteins are changed.
7. Mutations, together with recombination, contribute to changes in the genetic pool which provide the variability within populations that is necessary for evolution of species.

The field of molecular evolution should include a theory of the chemical events leading to the formation of the first living organism from molecules of non-living origin. The gentic code may have evolved through multiplication of transfer RNA molecules by gene duplication followed by differentiation. This proposal is supported by the similarities between all tRNA molecules of known structures. The DNA of higher organisms contains families of repetitive sequences. The families may contain thousands or hundreds of thousands of individual members. The ‘family resemblance’ within each group grows less with the passage of time because this leads to differentiation resulting from the accumulation of point mutations.     

Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle.

The Minimum Evolution (ME) approach to phylogeny estimation has been shown to be statistically consistent when it is used in conjunction with ordinary least-squares (OLS) fitting of a metric to a tree structure. The traditional approach to using ME has been to start with the Neighbor Joining (NJ) topology for a given matrix and then do a topological search from that starting point. The first stage requires O(n(3)) time, where n is the number of taxa, while the current implementations of the second are in O(p n(3)) or more, where p is the number of swaps performed by the program. In this paper, we examine a greedy approach to minimum evolution which produces a starting topology in O(n(2)) time. Moreover, we provide an algorithm that searches for the best topology using nearest neighbor interchanges (NNIs), where the cost of doing p NNIs is O(n(2) + p n), i.e., O(n(2)) in practice because p is always much smaller than n. The Greedy Minimum Evolution (GME) algorithm, when used in combination with NNIs, produces trees which are fairly close to NJ trees in terms of topological accuracy. We also examine ME under a balanced weighting scheme, where sibling subtrees have equal weight, as opposed to the standard "unweighted" OLS, where all taxa have the same weight so that the weight of a subtree is equal to the number of its taxa. The balanced minimum evolution scheme (BME) runs slower than the OLS version, requiring O(n(2) x diam(T)) operations to build the starting tree and O(p n x diam(T)) to perform the NNIs, where diam(T) is the topological diameter of the output tree. In the usual Yule-Harding distribution on phylogenetic trees, the diameter expectation is in log(n), so our algorithms are in practice faster that NJ. Moreover, this BME scheme yields a very significant improvement over NJ and other distance-based algorithms, especially with large trees, in terms of topological accuracy.     

Zinc finger proteins as templates for metal ion exchange and ligand reactivity. Chemical and biological consequences

Zinc finger reactions with inorganic ions and coordination compounds are as diverse as the zinc fingers themselves. Use of metal ions such as Co(2+) and Cd(2+) has given structural, thermodynamic and kinetic information on zinc fingers and zinc-finger-DNA/RNA interactions. It is a general truism that alteration of the coordination sphere in the finger environment will disrupt the recognition with DNA/RNA and this has implications for mechanism of toxicity and carcinogenesis of metal ions. Structural zinc fingers are susceptible to electrophilic attack and the recognition that the coordination sphere of inorganic compounds may be modulated for control of electrophilic attack on zinc fingers raises the possibility of systematic studies of zinc fingers as drug targets using inorganic chemistry. Some inorganic compounds such as those of As(III) and Au(I) may exert their biological effects through inactivation of zinc fingers and novel approaches to specifically attack the zinc-bound ligands using Co(III)-Schiff bases and Platinum(II)-Nucleobase compounds have been proposed. The genomic importance of zinc fingers suggests that the "coordination chemistry" of zinc fingers themselves is ripe for exploration to design new targets for medicinal inorganic chemistry.     

Searching for convergent evolution in manganese superoxidase dismutase using hydrophobic cluster analysis

There are numerous examples of convergent evolution in nature. Major ecological adaptations such as flight, loss of limbs in vertebrates, pesticide resistance, adaptation to a parasitic way of life, etc., have all evolved more than once, as seen by their analogous functions in separate taxa. But what about protein evolution? Does the environment have a strong enough influence on intracellular processes that enzymes and other functional proteins play, to evolve similar functional roles separately in different organisms? Manganese Superoxide Dismutase (MnSOD) is a manganesedependant metallo-enzyme which plays a crucial role in protecting cells from anti-oxidative stress by eliminating reactive (superoxide) oxygen species. It is a ubiquitous housekeeping enzyme found in nearly all organisms. In this study we compare phylogenies based on MnSOD protein sequences to those based on scores from Hydrophobic Cluster Analysis (HCA). We calculated HCA similarity values for each pair of taxa to obtain a pair-wise distance matrix. A UPGMA tree based on the HCA distance matrix and a common tree based on the primary protein sequence for MnSOD was constructed. Differences between these two trees within animals, enterobacteriaceae, planctomycetes and cyanobacteria are presented and cited as possible examples of convergence. We note that several residue changes result in changes in hydrophobicity at positions which apparently are under the effect of positive selection.     

Zinc finger of replication protein A, a non-DNA binding element, regulates its DNA binding activity through redox.

Eukaryotic replication protein A (RPA) is a single-stranded DNA-binding protein with multiple functions in DNA replication, repair, and genetic recombination. RPA contains an evolutionarily conserved 4-cysteine-type zinc finger motif (X(3)CX(2-4)CX(12-15)CX(2)C) that has a potential role in regulation of DNA replication and repair (Dong, J., Park, J-S., and Lee, S-H. (1999) Biochem. J. 337, 311-317 and Lin, Y.-L., Shivji, M. K. K., Chen, C., Kolodner, R., Wood, R. D., and Dutta, A. (1998) J. Biol. Chem. 273, 1453-1461), even though the zinc finger itself is not essential for its DNA binding activity (Kim, D. K., Stigger, E., and Lee, S.-H. (1996) J. Biol. Chem. 271, 15124-15129). Here, we show that RPA single-stranded DNA (ssDNA) binding activity is regulated by reduction-oxidation (redox) through its zinc finger domain. RPA-ssDNA interaction was stimulated 10-fold by the reducing agent, dithiothreitol (DTT), whereas treatment of RPA with oxidizing agent, diazene dicarboxylic acid bis[N,N-dimethylamide] (diamide), significantly reduced this interaction. The effect of diamide was reversed by the addition of excess DTT, suggesting that RPA ssDNA binding activity is regulated by redox. Redox regulation of RPA-ssDNA interaction was more effective in the presence of 0.2 M NaCl or higher. Cellular redox factor, thioredoxin, was able to replace DTT in stimulation of RPA DNA binding activity, suggesting that redox protein may be involved in RPA modulation in vivo. In contrast to wild-type RPA, zinc finger mutant (cysteine to alanine mutation at amino acid 486) did not require DTT for its ssDNA binding activity and is not affected by redox. Together, these results suggest a novel function for a putative zinc finger in the regulation of RPA DNA binding activity through cellular redox.     

Reviews

Bailey, W. J., & J. Ridsdill-Smith, eds. (1991): Reproductive behaviour of insects: Individuals and populations (Fortpflanzungsverhatten von Insekten: Individuen und Populationen). Hughes, R. N., (ed.) (1993): Diet selection: an interdisciplinary approach to foraging behaviour (Ergebnisse zur Theorie des optimalen Futtersuchverhaltens). Charnov, E. L. (1993): Life history invariants. Some explorations of symmetry in evolutionary ecology (Konstanten des Lebenszyklus. Krebs, J. R., & N. B. Davies (1993): An introduction to behavioural ecology (Eine Einführung in die Verhaltensökologie). Walossek, D. (1993): The upper Cambrian Rehbachiella and the phylogeny of Brachiopoda and Crustacea (Rehbachiella aus dem oberen Kambrium und die Stammesgeschichte der Brachiopoda und Crustacea) Fossils and Strata Scandinavian University Press, Toyen. McGrew, W. C. (1992): Chimpanzee material culture. Implications for human evolution (Materielle Kultur der Schimpansen und Folgerungen für die Evolution des Menschen). Kämpfe, L., Hrsg. (1992): Evolution und Stammesgeschichte der Organismen (Evolution and phylogenesis of organisms). Heiligenberg, W. (1991): Neural nets in electric fish (Neuronale Netzwerke bei elektrischen Fischen). Estes, R. D. (1993): The safari companion: a guide to watching African mammals (Der Safari-Begleiter: ein Feldführer zur Beobachtung afrikanischer Säugetiere).