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PubMed1999

Beneficial mutations, hitchhiking and the evolution of mutation rates in sexual populations.

Natural selection acts in three ways on heritable variation for mutation rates. A modifier allele that increases the mutation rate is (i) disfavored due to association with deleterious mutations, but is also favored due to (ii) association with beneficial mutations and (iii) the reduced costs of lower fidelity replication. When a unique beneficial mutation arises and sweeps to fixation, genetic hitchhiking may cause a substantial change in the frequency of a modifier of mutation rate. In previous studies of the evolution of mutation rates in sexual populations, this effect has been underestimated. This article models the long-term effect of a series of such hitchhiking events and determines the resulting strength of indirect selection on the modifier. This is compared to the indirect selection due to deleterious mutations, when both types of mutations are randomly scattered over a given genetic map. Relative to an asexual population, increased levels of recombination reduce the effects of beneficial mutations more rapidly than those of deleterious mutations. However, the role of beneficial mutations in determining the evolutionarily stable mutation rate may still be significant if the function describing the cost of high-fidelity replication has a shallow gradient.

Alleles↗

PubMed1998

Molecular evolution of an imprinted gene: repeatability of patterns of evolution within the mammalian insulin-like growth factor type II receptor.

The repeatability of patterns of variation in Ka/Ks and Ks is expected if such patterns are the result of deterministic forces. We have contrasted the molecular evolution of the mammalian insulin-like growth factor type II receptor (Igf2r) in the mouse-rat comparison with that in the human-cow comparison. In so doing, we investigate explanations for both the evolution of genomic imprinting and for Ks variation (and hence putatively for mutation rate evolution). Previous analysis of Igf2r, in the mouse-rat comparison, found Ka/Ks patterns that were suggested to be contrary to those expected under the conflict theory of imprinting. We find that Ka/Ks variation is repeatable and hence confirm these patterns. However, we also find that the molecular evolution of Igf2r signal sequences suggests that positive selection, and hence conflict, may be affecting this region. The variation in Ks across Igf2r is also repeatable. To the best of our knowledge this is the first demonstration of such repeatability. We consider three explanations for the variation in Ks across the gene: (1) that it is the result of mutational biases, (2) that it is the result of selection on the mutation rate, and (3) that it is the product of selection on codon usage. Explanations 2 and 3 predict a Ka-Ks correlation, which is not found. Explanation 3 also predicts a negative correlation between codon bias and Ks, which is also not found. However, in support of explanation 1 we do find that in rodents the rate of silent C --> T mutations at CpG sites does covary with Ks, suggesting that methylation-induced mutational patterns can explain some of the variation in Ks. We find evidence to suggest that this CpG effect is due to both variation in CpG density, and to variation in the frequency with which CpGs mutate. Interestingly, however, a GC4 analysis shows no covariance with Ks, suggesting that to eliminate methyl-associated effects CpG rates themselves must be analyzed. These results suggest that, in contrast to previous studies of intragenic variation, Ks patterns are not simply caused by the same forces responsible for Ka/Ks correlations.

Animals↗

PubMed2007

Growth of Rhodospirillum rubrum on synthesis gas: conversion of CO to H2 and poly-beta-hydroxyalkanoate.

To examine the potential use of synthesis gas as a carbon and energy source in fermentation processes, Rhodospirillum rubrum was cultured on synthesis gas generated from discarded seed corn. The growth rates, growth and poly-beta-hydroxyalkanoates (PHA) yields, and CO oxidation/H(2) evolution rates were evaluated in comparison to the rates observed with an artificial synthesis gas mixture. Depending on the gas conditioning system used, synthesis gas either stimulated or inhibited CO-oxidation rates compared to the observations with the artificial synthesis gas mixture. Inhibitory and stimulatory compounds in synthesis gas could be removed by the addition of activated charcoal, char-tar, or char-ash filters (char, tar, and ash are gasification residues). In batch fermentations, approximately 1.4 mol CO was oxidized per day per g cell protein with the production of 0.75 mol H(2) and 340 mg PHA per day per g cell protein. The PHA produced from R. rubrum grown on synthesis gas was composed of 86% beta-hydroxybutyrate and 14% beta-hydroxyvalerate. Mass transfer of CO into the liquid phase was determined as the rate-limiting step in the fermentation.

Aldehyde Oxidoreductases↗

PubMed2001

Use of dynamic step response for control of fed-batch conversion of lignocellulosic hydrolyzates to ethanol.

Optimization of fed-batch conversion of lignocellulosic hydrolyzates by the yeast Saccharomyces cerevisiae was studied. The feed rate was controlled using a step response strategy, in which the carbon dioxide evolution rate was used as input variable. The performance of the control strategy was examined using both an untreated and a detoxified dilute acid hydrolyzate, and the performance was compared to that obtained with a synthetic medium. In batch cultivation of the untreated hydrolyzate, only 23% of the hexose sugars were assimilated. However, by using the feed-back controlled fed-batch technique, it was possible to obtain complete conversion of the hexose sugars. Furthermore, the maximal specific ethanol productivity (q(E,max)) increased more than 10-fold, from 0.06 to 0.70 g g(-1) h(-1). In addition, the viability of the yeast cells decreased by more than 99% in batch cultivation, whereas a viability of more than 40% could be maintained during fed-batch cultivation. In contrast to untreated hydrolyzate, it was possible to convert the sugars in the detoxified hydrolyzate also in batch cultivation. However, a 50% higher specific ethanol productivity was obtained using fed-batch cultivation. During batch cultivation of both untreated and detoxified hydrolyzate a gradual decrease in specific ethanol productivity was observed. This decrease could largely be avoided in fed-batch cultivations.

Cellulose↗

PubMed2004

Male-biased mutation, sex linkage, and the rate of adaptive evolution.

An interaction between sex-linked inheritance and sex-biased mutation rates may affect the rate of adaptive evolution. Males have much higher mutation rates than females in several vertebrate and plant taxa. When evolutionary rates are limited by the supply of favorable new mutations, then genes will evolve faster when located on sex chromosomes that spend more time in males. For mutations with additive effects, Y-linked genes evolve fastest, followed by Z-linked genes, autosomal genes, X-linked genes, and finally W-linked and cytoplasmic genes. This ordering can change when mutations show dominance. The predicted differences in substitution rates may be detectable at the molecular level. Male-biased mutation could cause adaptive changes to accumulate more readily on certain kinds of chromosomes and favor animals with Z-W sex determination to have rapidly evolving male sexual displays.

Adaptation, Biological↗

PubMed2003

Testing the link between the latitudinal gradient in species richness and rates of molecular evolution.

Numerous hypotheses have been proposed to explain latitudinal gradients in species richness, but all are subject to ongoing debate. Here we examine Rohde's (1978, 1992) hypothesis, which proposes that climatic conditions at low latitudes lead to elevated rates of speciation. This hypothesis predicts that rates of molecular evolution should increase towards lower latitudes, but this prediction has never been tested. We discuss potential links between rates of molecular evolution and latitudinal diversity gradients, and present the first test of latitudinal variation in rates of molecular evolution. Using 45 phylogenetically independent, latitudinally separated pairs of bird species and higher taxa, we compare rates of evolution of two mitochondrial genes and DNA-DNA hybridization distances. We find no support for an effect of latitude on rate of molecular evolution. This result casts doubt on the generality of a key component of Rohde's hypothesis linking climate and speciation.

Animals↗

PubMed2000

Oxygen transfer and uptake rates during xanthan gum production.

Oxygen uptake rate and oxygen mass transfer rate have been studied during xanthan gum production process in stirred tank bioreactor. Empirical equations for the oxygen mass transfer coefficient have been obtained taking into account several variables such as air flow rate, stirrer speed and apparent viscosity. Oxygen uptake rate evolution in the course fermentation has been measured, obtaining an equation as a function of biomass concentration, including overall growth and non growth-associated oxygen uptake. A metabolic kinetic model has been employed for xanthan gum production description including oxygen mass transfer and uptake rates. The results point out that this model is able to describe adequately not only oxygen dissolved evolution, but also of the production of xanthan and substrate consumption. Also, the influence of several parameters (k(L)a, air flow rate and dissolved oxygen) in the evolution of the key compounds of the system have been studied. The results of the simulation shown that an increasing of dissolved oxygen concentration favor the xanthan gum production.

Journal Article↗

PubMed1999

Random mutagenesis in the large extrinsic loop E and transmembrane alpha-helix VI of the CP 47 protein of Photosystem II.

The intrinsic chlorophyll-protein CP 47 is a component of Photosystem II which functions in both light-harvesting and oxygen evolution. Using the Escherichia coli mutator strain XL-1 Red, we introduced mutations at 14 sites in the large extrinsic loop E of CP 47 and its adjacent transmembrane alpha-helix VI. Four mutant cell lines were recovered in which the histidyl residues 455H, 466H and 469H were altered. The cell lines H455T, H455Y, H469Y, and the double mutant F432L,H466R exhibited phenotypes that supported the identification of the histidyl residues 455H, 466H and 469H as chlorophyll ligands. Four additional mutant cell lines were recovered which contained mutations at positions 448R in the large extrinsic loop of CP 47. These mutants, R448K, R448Q, R448S, and R448W, exhibited variable phenotypes ranging from moderate alteration of photoautotrophic growth and oxygen evolution rates to a complete inhibition of these parameters. Those mutants exhibiting photoautotrophic growth and oxygen evolution capability under standard conditions were unable to grow photoautotrophically or evolve oxygen when grown at low chloride concentrations. Finally, a mutant cell line exhibiting a substitution at position 342G was recovered. The mutant G342D exhibited moderate alterations of photoautotrophic growth and oxygen evolution. In addition to these alterations, mutants were recovered in which deletions and insertions (leading to frame shifts) and stop codons were introduced. These mutants uniformly lacked the ability to either grow photoautotrophically or evolve oxygen.

Escherichia coli↗

PubMed2005

Water-photolysis properties of micron-length highly-ordered titania nanotube-arrays.

We report the water photoelectrolysis and photoelectrochemical properties of the titania nanotube arrays as a function of nanotube crystallinity, length (up to 6.4 microm), and pore size. Most noteworthy of our results, under 320-400 nm illumination (98 mW/cm2) the titania nanotube-array photoanodes (area 1 cm2), pore size 110 nm, wall thickness 20 nm, and 6 microm length, generate hydrogen by water photoelectrolysis at a rate of 7.6 mL/hr, with a photoconversion efficiency of 12.25%. The energy-time normalized hydrogen evolution rate is 80 mL/hrW, the largest reported hydrogen photoelectrolysis generation rate for any material system by a factor of four. The highly-ordered nanotubular architecture appears to allow for superior charge separation and charge transport, with a calculated quantum efficiency of over 80% for incident photons with energies larger than the titania bandgap.

Electrochemistry↗

PubMed2000

Spatiotemporal reorganization of growth rates in the evolution of ontogeny.

Heterochrony, evolutionary changes in rate or timing of development producing parallelism between ontogeny and phylogeny, is viewed as the most common type of evolutionary change in development. Alternative hypotheses such as heterotopy, evolutionary change in the spatial patterning of development, are rarely entertained. We examine the evidence for heterochrony and heterotopy in the evolution of body shape in two clades of piranhas. One of these is the sole case of heterochrony previously reported in the group; the others were previously interpreted as cases of heterotopy. To compare ontogenies of shape, we computed ontogenetic trajectories of shape by multivariate regression of geometric shape variables (i.e., partial warp scores and shape coordinates) on centroid size. Rates of development relative to developmental age and angles between the trajectories were compared statistically. We found a significant difference in developmental rate between species of Serrasalmus, suggesting that heterochrony is a partial explanation for the evolution of body shape, but we also found a significant difference between their ontogenetic transformations; the direction of the difference between them suggests that heterotopy also plays a role in this group. In Pygocentrus we found no difference in developmental rate among species, but we did find a difference in the ontogenies, suggesting that heterotopy, but not heterochrony, is the developmental basis for shape diversification in this group. The prevalence of heterotopy as a source of evolutionary novelty remains largely unexplored and will not become clear until the search for developmental explanations looks beyond heterochrony.

Animals↗

PubMed2002

Alterations of the oxygen-evolving apparatus induced by a 305Arg --> 305Ser mutation in the CP43 protein of photosystem II from Synechocystis sp. PCC 6803 under chloride-limiting conditions.

The psbC gene encodes CP43, a component of Photosystem II (PSII) in higher plants, algae, and cyanobacteria. Previous work demonstrated that alteration of an arginine residue occurring at position 305 to serine produced a strain (R305S) with altered PSII activity (Knoepfle, N., Bricker, T. M., and Putnam-Evans, C. (1999) Biochemistry 38, 1582-1588). This strain grew at wild-type rates in complete BG-11 media (480 microM chloride) and evolved oxygen at rates that were 60-70% of the observed wild-type rates. The R305S strain assembled approximately 70-80% of the functional PSII centers contained in the control strain, and these PSII centers were very sensitive to photoinactivation at high light intensities. We recently observed that the R305S mutant exhibited a pronounced chloride effect. When this mutant was grown in media depleted of chloride (30 microM chloride), it exhibited a severely reduced photoautotrophic growth rate. The effect of chloride depletion on the growth rate of the mutant was reversed by the addition of 480 microM bromide to the chloride-depleted BG-11 media. Oxygen evolution rates for the mutant were further depressed to about 22% of that observed in control cells under chloride-limiting conditions. Addition of bromide restored these rates to those observed under chloride-sufficient conditions. The mutant exhibited a significantly lower relative quantum yield for oxygen evolution than did the control strain, and this was exacerbated under chloride-limiting conditions. Fluorescence yield measurements indicated that both the mutant and the control strains assembled fewer PSII reaction centers under chloride-limiting conditions. The reaction centers assembled by the mutant exhibited an enhanced sensitivity to photoinactivation under chloride-limiting conditions, with a t(1/2) of photoinactivation of 2.6 min under chloride-limiting conditions as compared to a t(1/2) of 4.7 min under normal growth conditions. The mutant also exhibited an enhanced stability of its S(2) state and increased number of centers in the S(1) state following dark incubation. These results indicate that the mutant R305S exhibits a defect in its ability to utilize chloride in support of efficient oxygen evolution in PSII. This is the first mutant of this type described in the CP43 protein.

Arginine↗

PubMed1969

The rate of molecular evolution considered from the standpoint of population genetics.

The rate of amino acid substitutions in the evolution of homologous proteins is remarkably constant. Furthermore, estimated rates of amino acid substitutions based on comparisons of the alpha hemoglobin chains of various mammals with that of the carp are about the same as those based on comparisons of the carp alpha and mammalian beta or the alpha and beta chains in mammals. These uniformities are regarded as evidence for the hypothesis that a majority of amino acid substitutions that occurred in these proteins are the result of random fixation of selectively neutral or nearly neutral mutations. TWO IMPLICATIONS OF THIS POSSIBILITY ARE DISCUSSED: (a) Random gene frequency drift is playing an important role in determining the genetic structure of biological populations and (b) genes in "living fossils" may be expected to have undergone as many DNA base (and therefore amino acid) substitutions as corresponding genes (proteins) in more rapidly evolving species.

Amino Acid Sequence↗

PubMed1996

Dynamics of ammonia uptake in nitrogen limited anaerobic cultures of Saccharomyces cerevisiae.

Dynamics of the ammonia uptake by Saccharomyces cerevisiae under anaerobic conditions was studied in ammonia limited continuous cultures. A large number of pulse additions of ammonia (25-100 mg 1(-1)) were made at different dilution rates (0.05-0.20 h-1). The response was followed by on-line monitoring of the carbon dioxide evolution rate (CER), optical density, and by frequent analysis of extra- and intracellular metabolites. The uptake of a pulse of ammonia proceeded in a qualitatively highly reproducible pattern. Initially, a rapid and growth rate dependent uptake of ammonia was observed (lasting for about 10-15 min). Next followed a phase with little uptake (approx. 5 min). Finally, the rest of the ammonia pulse was taken up at a somewhat smaller rate which also depended on the growth rate. The first phase coincided with an increase in CER caused by mobilization of the intracellular carbohydrate trehalose and subsequently of glycogen. Regardless of dilution rate and the amount of ammonia added, the initial high uptake rate of ammonia was maintained until approximately the same amount of ammonia had been taken up. Transition from the first to the second uptake phase was associated with an increased glycerol production, indicating an elevated anabolic activity.

Ammonia↗

PubMed2006

Low rates of expression profile divergence in highly expressed genes and tissue-specific genes during mammalian evolution.

Evolutionary rates provide important information about the pattern and mechanism of evolution. Although the rate of gene sequence evolution has been well studied, the rate of gene expression evolution is poorly understood. In particular, it is unclear whether the gene expression level and tissue specificity influence the divergence of expression profiles between orthologous genes. Here we address this question using a microarray data set comprising the expression signals of 10,607 pairs of orthologous human and mouse genes from over 60 tissues per species. We show that the level of gene expression and the degree of tissue specificity are generally conserved between the human and mouse orthologs. The rate of gene expression profile change during evolution is negatively correlated with the level of gene expression, measured by either the average or the highest level among all tissues examined. This is analogous to the observation that the rate of gene (or protein) sequence evolution is negatively correlated with the gene expression level. The impacts of the degree of tissue specificity on the evolutionary rate of gene sequence and that of expression profile, however, are opposite. Highly tissue-specific genes tend to evolve rapidly at the gene sequence level but slowly at the expression profile level. Thus, different forces and selective constraints must underlie the evolution of gene sequence and that of gene expression.

Animals↗

PubMed1991

Arginine residues in the D2 polypeptide may stabilize bicarbonate binding in photosystem II of Synechocystis sp. PCC.

Bicarbonate (HCO3-) causes a significant and reversible stimulation of anion-inhibited electron flow in photosystem II of higher plants and cyanobacteria. To test if selected arginine (Arg) residues are involved in the binding of HCO3-, we utilized oligonucleotide-directed mutagenesis to construct Synechocystis sp. PCC 6803 mutants carrying mutations in Arg residues in the D2 protein. Measurements of oxygen evolution showed that the D2 mutants R233Q (arginine-233----glutamine) and R251S (arginine-251----serine) were 10-fold more sensitive to formate than the wild type. The formate concentration giving half-maximal inhibition of the steady-state oxygen evolution rate was 48 mM, 4.5 mM and 4 mM for the wild type, R233Q and R251S, respectively. Measurements of oxygen evolution in single-turnover flashes confirm that the mutants are more sensitive to formate than the wild type. Measurements of chlorophyll a fluorescence decay kinetics after the second saturating actinic flash indicated that, after formate treatment, the halftime of QA- oxidation was decreased by approximately a factor of 2, 4 and 6 in the wild type, R251S and R233Q, respectively. The recombination rate between QA- and S2 was approx. 2-fold slower in R251S and R233Q than in the wild type. In the presence of 100 mM sodium formate, reactivation of the Hill reaction by bicarbonate showed that the wild type had an apparent Km for bicarbonate of 0.5 mM, while the Km values for R233Q and R251S were 1.4 and 1.5 mM, respectively. We suggest that Arg-233 and Arg-251 in the D2 polypeptide contribute to stabilization of HCO3- binding in Photosystem II.

Arginine↗

PubMed2004

Enhanced stem cell survival in familial adenomatous polyposis.

Individuals with heterozygous germline adenomatous polyposis coli (APC) mutations or familial adenomatous polyposis (FAP) are born with normal appearing colons but later develop hundreds to thousands of polyps. Tumor progression apparently starts after somatic loss of the normal APC allele, but germline APC mutations may potentially alter niche stem cell survival through dominant-negative interactions or haploinsufficiency. Although morphologically occult, altered stem cell turnover or clonal evolution rates may be detected by measuring the diversity of crypt sequences, with greater diversity expected with longer lived stem cell lineages. Methylation pattern diversity (numbers of unique patterns per crypt) was higher in normal appearing crypts from four of five FAP colons compared to six non-FAP colons and one attenuated FAP colon. Simulations indicate higher FAP crypt diversity is consistent with slower clonal evolution from enhanced stem cell survival, either through increased stem cell numbers or decreased stem cell lineage extinction, which is predicted to increase progression rates to cancer. Enhanced stem cell survival was associated with APC mutations that remove some but not all catenin-binding repeats. Therefore, some APC mutations may be common in colorectal cancers because they confer occult pretumor "caretaker" and "gatekeeper" defects. FAP crypts accumulate more alterations from slower stem cell clonal evolution rather than increased error rates. In non-FAP crypts, enhanced stem cell survival conferred by somatic heterozygous APC mutations would favor fixation through occult clonal niche expansions. Heterozygous APC mutations may change stem cell survival during colorectal pretumor progression.

Adenomatous Polyposis Coli↗

PubMed1978

Calcium and photosynthetic oxygen evolution in cyanobacteria.

Calcium activation of oxygen evolution from French-press preparations of Phormidium luridum is largely reversible upon removal of added Ca(2+). Activation occurs via a first-order binding with a dissociation constant of 2.8 mM. An 8-fold increase in oxygen evolution rate observed upon Ca(2+) addition is accounted for by a 4-fold increase in the number of active photosynthetic units, and a doubling of turnover rate. While both Ca(2+) and Mg(2+) stimulate turnover, unit activation is Ca(2+) specific. Under optimal conditions, 30% of the units functioning in the intact cell can be recovered in the Ca(2+) -activated preparation. The Ca(2+) requirement of P. luridum preparations is not relieved by proton-carrying uncouplers, or by rate-saturating concentrations of the Hill acceptor, ferricyanide. Taken together with the reported stimulation by Ca(2+) of oxygen evolution in the presence of DCMU (Piccioni, R.G. and Mauzerall, D.C. (1976) Biochim. Biophys. Acta 423, 605--609) these observations strongly suggest a site of Ca(2+) action within Photosystem II. The pronounced specificity of the Ca(2+) requirement appears in preparations of other cyanobacteria (Anabaena flos-aquae and Anacystis nidulans) but not in the eucaryote Chlorella vulgaris. While milder cell-disruption methods bring about some Ca(2+) dependence in P. luridum, French-press treatment is required for maximal expression of Ca(2+) -specific effects. French-press breakage causes a release of endogenous Ca(2+) from cells, supporting the view that added Ca(2+) restores oxygen evolution by satisfying a physiological requirement for the cation.

Binding Sites↗

PubMed1977

Effect of Light Intensity on Efficiency of Carbon Dioxide and Nitrogen Reduction in Pisum sativum L.

Photosynthetic efficiency, primary productivity, and N(2) reduction were determined in peas (Pisum sativum L. var. Alaska) grown at light intensities ranging from severely limiting to saturating. Plants grown under higher light intensities showed greater carboxylation and light capture potential and higher rates of net C exchange. Uptake of N(2), computed from measured C(2)H(2) reduction and H(2) evolution rates, also increased with growth light intensity, while the previously proposed relative efficiency of N(2) fixation, based on these same parameters, declined. The plot of N/C ratios (total nitrogen content/plant dry weight) increased hyperbolically with light intensity, and the plot of N(2)/CO(2) uptake ratios (N(2) uptake rate/net CO(2) uptake rate) increased linearly. Both plots extrapolated to the light compensation point. The data indicate that the relative efficiency of N(2) fixation is not necessarily correlated with maximum plant productivity and that evaluation of a plant's capacity to reduce N(2) is related directly to concurrent CO(2) reduction. A measure of whole plant N(2) fixation efficiency based on the N(2)/CO(2) uptake ratio is proposed.

Journal Article↗