Enzyme dynamics and activity: time-scale dependence of dynamical transitions in glutamate dehydrogenase solution.

We have examined the temperature dependence of motions in a cryosolution of the enzyme glutamate dehydrogenase (GDH) and compared these with activity. Dynamic neutron scattering was performed with two instruments of different energy resolution, permitting the separate determination of the average dynamical mean square displacements on the sub-approximately 100 ps and sub-approximately 5 ns time scales. The results demonstrate a marked dependence on the time scale of the temperature profile of the mean square displacement. The lowest temperature at which anharmonic motion is observed is heavily dependent on the time window of the instrument used to observe the dynamics. Several dynamical transitions (inflexions of the mean squared displacement) are observed in the slower dynamics. Comparison with the temperature profile of the activity of the enzyme in the same solvent reveals dynamical transitions that have no effect on GDH function.     

Evolution of antifungal-drug resistance: mechanisms and pathogen fitness

Like other microorganisms, fungi exist in populations that are adaptable. Under the selection imposed by antifungal drugs, drug-sensitive fungal pathogens frequently evolve resistance. Although the molecular mechanisms of resistance are well-characterized, there are few measurements of the impact of these mechanisms on pathogen fitness in different environments. To predict resistance before a new drug is prescribed in the clinic, the full spectrum of potential resistance mutations and the interactions among combinations of divergent mechanisms can be determined in evolution experiments. In the search for new strategies to manage drug resistance, measuring the limits of adaptation might reveal methods for trapping fungal pathogens in evolutionary dead ends.     

Evolution in a flat fitness landscape

A simple model of a population of asexually reproducing individuals, evolving in a flat fitness landscape, is defined. It is shown that the model is equivalent to a dynamical system with stochastic dynamics, the Annealed Random Map Model. Thus, it is possible to solve exactly for the genealogy statistics and for the genetic variability of the population. Fluctuations of quantities, like the average relatedness and the variability, which also take place in the limit of an infinitely large population, are computed.     

Enzyme Evolution in the Enterobacteriaceae

An immunological approach has been used for the study of alkaline phosphatase evolution in bacteria of the family Enterobacteriaceae. Antisera were prepared against alkaline phosphatase from Escherichia coli and Klebsiella aerogenes and tested against the unpurified alkaline phosphatases of 32 strains of enterobacteria by double diffusion and quantitative micro-complement fixation. The immunological relationships detected among the alkaline phosphatases of enterobacteria agree approximately with those reported for five other enzymes, as well as with the tryptic peptide pattern similarities found for two other enzymes, and with the relationships detected by interspecific deoxyribonucleic acid hybridization tests.     

The Classification and Evolution of Enzyme Function

Enzymes are the proteins responsible for the catalysis of life. Enzymes sharing a common ancestor as defined by sequence and structure similarity are grouped into families and superfamilies. The molecular function of enzymes is defined as their ability to catalyze biochemical reactions; it is manually classified by the Enzyme Commission and robust approaches to quantitatively compare catalytic reactions are just beginning to appear. Here, we present an overview of studies at the interface of the evolution and function of enzymes.     

Evolution of polyembryony: Consequences to the fitness of mother and offspring

Polyembryony, referring here to situations where a nucellar embryo is formed along with the zygotic embryo, has different consequences for the fitness of the maternal parent and offspring. We have developed genetic and inclusive fitness models to derive the conditions that permit the evolution of polyembryony under maternal and offspring control. We have also derived expressions for the optimal allocation (evolutionarily stable strategy, ESS) of resources between zygotic and nucellar embryos. It is seen that (i) Polyembryony can evolve more easily under maternal control than under that of either the offspring or the ‘selfish’ endosperm. Under maternal regulation, evolution of polyembryony can occur for any clutch size. Under offspring control polyembryony is more likely to evolve for high clutch sizes, and is unlikely for low clutch sizes (<3). This conflict between mother and offspring decreases with increase in clutch size and favours the evolution of polyembryony at high clutch sizes, (ii) Polyembryony can evolve for values of “x” (the power of the function relating fitness to seed resource) greater than 0.5758; the possibility of its occurrence increases with “x”, indicating that a more efficient conversion of resource into fitness favours polyembryony. (iii) Under both maternal parent and offspring control, the evolution of polyembryony becomes increasingly unlikely as the level of inbreeding increases, (iv) The proportion of resources allocated to the nucellar embryo at ESS is always higher than that which maximizes the rate of spread of the allele against a non-polyembryonic allele.     

Evolution in Saccharomyces cerevisiae: identification of mutations increasing fitness in laboratory populations

Since the publication of the complete sequence of the genome of Saccharomyces cerevisiae, a number of comprehensive investigations have been initiated to gain insight into cellular function. The focus of these studies has been to identify genes essential for survival in specific environments or those that when mutated cause gross phenotypic defects in growth. Here we describe Ty1-based mutational approaches designed to identify genes, which when mutated generate evolutionarily significant phenotypes causing small but positive increments on fitness. As expected, Ty1 mutations with a positive fitness effect were in the minority. However, mutations in two loci, one inactivating FAR3 and one upstream of CYR1, identified in evolving populations, were shown to have small but significantly positive fitness effects.     

酶的分子定向进化及其应用

酶的分子定向进化是20世纪90年代初兴起的一种蛋白质工程的新策略,是一种在生物体外模拟自然进化过程的、具有一定目的性的快速改造蛋A质的方法.该方法引起了生物催化技术领域的又一次革命.目前分子定向进化技术已被广泛应用于工业、农业及制药业等的相关领域.本文详细综述了酶的分子定向进化的概念、过程、基本策略及其核心技术,并着重介绍了酶的分子定向进化技术在提高酶的活力、稳定性、底物特异性和对映体选择性等几方面的应用及取得的相关成果.     

Spatial Dynamics and the Evolution of Enzyme Production

We re-examine the problem of the evolution of protein synthesis or enzyme production using a stochastic cellular automaton model, where the replicators are fixed in the sites of a two-dimensional square lattice. In contrast with the classical chemical kinetics or mean-field predictions, we show that a small colony of mutant, protein-mediated (enzymatic) replicators has an appreciable probability to take over a resident population of simpler, direct-template replicators. In addition, we argue that the threshold phenomenon corresponding to the onset of invasion can be described quantitatively within the physics framework of nonequilibrium phase transitions. We study also the invasion of a resident population of enzymatic replicators by more efficient replicators of the same kind, and show that although slightly more efficient mutants cannot invade, invasion is a likely event if the productivity advantage of the mutants is large. In this sense, the establishment of a population of enzymatic replicators is not a `once-forever' evolutionary decision.     

Enzyme processing of textiles in reverse micellar solution

Scouring of cotton using pectinase enzyme, bioscouring, in reverse micellar system was studied. The effectiveness of bioscouring was evaluated by measuring weight loss of cotton, analyzing pectin and cotton wax remaining and by wetness testing. Pectinase enzyme showed excellent activity even in organic media, and the effectiveness of scouring was equivalent or better than that achieved by conventional alkaline process or bioscouring in aqueous media. Enzymatic modification of wool using protease enzyme in the same system was also studied. It has found that felting property and tensile strength of wool fabrics treated by protease in reverse micellar system were superior to those in aqueous media. Possibilities of utilization of the same system for the subsequent textile dyeing process were also investigated. It was found that cotton and polyester fabrics were dyed satisfactorily by reverse micellar system compared to conventional aqueous system.     

Physical activity and health-related physical fitness in Taiwanese adolescents

The relationship between physical activity and health-related physical fitness was evaluated in 282 Taiwanese adolescents 12-14 years of age. The subjects were randomly selected from the 7th, 8th and 9th grades in two junior high schools in Taiwan. Physical activity was estimated as total daily energy expenditure and energy expenditure in moderate-to-vigorous physical activity from 24-hour activity records for three days, two week days and one weekend day. Health-related fitness was assessed as the one-mile run (cardiorespiratory endurance), timed sit-ups (abdominal strength and endurance), sit-and-reach (lower back flexibility), and subcutaneous fatness (sum of the triceps, subscapular, suprailiac, and medial calf skinfolds). Physical activity is significantly and positively correlated with one-mile run performance and the sit-and-reach, but not with sit-ups and subcutaneous fatness. Overall, the strength of the relationships between estimated energy expenditure and specific fitness items in the total sample vary from low to moderate, with only 1% to 12% of the variance in fitness variables being explained by estimated energy expenditure. Comparisons of active versus inactive, and fit versus unfit adolescents provide additional insights. The more active (highest quartile) are also more fit in cardiorespiratory endurance and in the sit-and-reach than the less active (lowest quartile), and the more fit in the one-mile run (better time, lowest quartile) and the sit-and-reach (highest quartile) are more active than the less fit in each item, respectively.     

Evolution of total net fitness in thermal lines: Drosophila subobscura likes it 'warm'

Fisher's fundamental theorem states that heritable variation for net fitness sets a limit to the rate of response to natural selection. How will temperate (i.e. cold‐tolerant) species cope with contemporary rapid global warming? Using three‐fold replicated lines of Drosophila subobscura that had been allowed to evolve for 4 years (between 32 and 59 generations) at 13 °C (cold), 18 °C (the supposed optimum temperature), and 22 °C (warm) I assess here how net fitness changes according to thermal environments. Net fitness was estimated following the classical approach in population genetics of competing over a number of generation in outbred experimental populations multiple wild‐type O chromosomes (homologous to arm 3R in D. melanogaster) independently derived from each base thermal stock in an otherwise homogeneous genetic background against a balancer chromosome. Warm‐adapted populations (‘warm‐adapted O chromosomes’) performed comparatively well at all tested temperatures. However, net fitness was severely reduced in cold‐adapted populations when transferred to warmer conditions. It seems, therefore, that thermal fitness breath for D. subobscura flies is positively associated to temperature. These findings are discussed in relation to the fast world‐wide clinal shifts in the frequency of genetic markers correlated with current climate change.     

Evolution of transposable elements: an IS10 insertion increases fitness in Escherichia coli

Strains of Escherichia coli carrying Tn10, a transposon consisting of two IS10 insertion sequences flanking a segment encoding for a tetracycline-resistance determinant, gain a competitive advantage in chemostat cultures. All Tn10-bearing strains that increase in frequency during competition have a new IS10 insertion that is found in the same location in the genome of those strains. We mapped, by a gradient of transmission, the position of the new IS10 insertion. We examined 11 isolates whose IS10 insertion was deleted by recombinational crossing- over, and in all cases the competitive fitness of the isolates was decreased. These results show that the IS10-generated insertion increases fitness in chemostat cultures. We named the insertion fit::IS10 and suggest that transposable elements may speed the rate of evolution by promoting nonhomologous recombination between preexisting variations within a genome and thereby generating adaptive variation.      

改进酶稳定性的定向进化技术

酶作为一种生物催化剂,以其独特的优良特性,在绿色化学和清洁生产中得到了广泛的应用。随着酶定向进化技术的建立和发展,通过定向进化改进酶稳定性的研究越来越多。详细综述了各种定向进化方法的特点及在提高酶稳定性方面的应用,并从结构和功能的角度进一步解释了相关机理。