Pathways and Mechanisms for Product Release in the Engineered Haloalkane Dehalogenases Explored Using Classical and Random Acceleration Molecular Dynamics Simulations

Eight mutants of the DhaA haloalkane dehalogenase carrying mutations at the residues lining two tunnels, previously observed by protein X-ray crystallography, were constructed and biochemically characterized. The mutants showed distinct catalytic efficiencies with the halogenated substrate 1,2,3-trichloropropane. Release pathways for the two dehalogenation products, 2,3-dichloropropane-1-ol and the chloride ion, and exchange pathways for water molecules, were studied using classical and random acceleration molecular dynamics simulations. Five different pathways, denoted p1, p2a, p2b, p2c, and p3, were identified. The individual pathways showed differing selectivity for the products: the chloride ion releases solely through p1, whereas the alcohol releases through all five pathways. Water molecules play a crucial role for release of both products by breakage of their hydrogen-bonding interactions with the active-site residues and shielding the charged chloride ion during its passage through a hydrophobic tunnel. Exchange of the chloride ions, the alcohol product, and the waters between the buried active site and the bulk solvent can be realized by three different mechanisms: (i) passage through a permanent tunnel, (ii) passage through a transient tunnel, and (iii) migration through a protein matrix. We demonstrate that the accessibility of the pathways and the mechanisms of ligand exchange were modified by mutations. Insertion of bulky aromatic residues in the tunnel corresponding to pathway p1 leads to reduced accessibility to the ligands and a change in mechanism of opening from permanent to transient. We propose that engineering the accessibility of tunnels and the mechanisms of ligand exchange is a powerful strategy for modification of the functional properties of enzymes with buried active sites.     

Flagellar formation in Escherichia coli electron transport mutants.

Mutants of Escherichia coli lacking ubiquinone or heme have been tested for motility and found to be essentially immotile. The loss of motility is identified with the loss of flagellum synthesis.     

Sex: Is Giardia Doing It in the Dark?

The protist Giardia has long been considered strictly asexual. Now genes specific for meiotic recombination have been found in the Giardia genome, but their consequences for genetics, epidemiology and evolution remain unknown.     

Population Structure of and Conservation Strategies for Wild Pyrus ussuriensis Maxim. in China

Pyrus ussriensis Maxim. is native to the northern part of China, but whose habitats are currently being destroyed by environmental changes and human deforestation. An investigation of population structure and genetic diversity of wild Ussurian pear is a priority in order to acquire fundamental knowledge for conservation. A total of 153 individuals of wild Ussurian pear from the main habitats, Heilongjiang, Jilin, and Inner Mongolia in China, possessed low genetic diversity as a result of habitat fragmentation. The genetic diversity of the populations in Inner Mongolia and north east of Heilongjiang was especially low and there was the possibility of inbreeding. Wild Ussurian pears were divided into 5 groups based on the Bayesian clustering method using 20 nuclear SSRs (nSSRs) and 5 groups by haplotype distributions using 16 chloroplast SSRs (cpSSRs), and the populations in Inner Mongolia and north east of Heilongjiang represented unique genotypes. AMOVA indicated there was a 20.05% variation in nSSRs and a 44.40% variation in cpSSRs among populations. These values are relatively high when compared to those of other tree species. Haplotype E, positioned in the center of the cpSSR analysis network and showed the largest number of connections with other haplotypes, represented the most important haplotype. Inner Mongolia and the north east of Heilongjiang are two areas that need urgent conservation because of their genetic vulnerability and peculiarity. We determined 4 conservation units based on the clustering by nSSRs and cpSSRs, and geographic factor. This information is helpful in deciding the conservation strategies for wild Ussurian pear in China.     

Biochemical characterization of a novel haloalkane dehalogenase from a cold-adapted bacterium

A haloalkane dehalogenase, DpcA, from Psychrobacter cryohalolentis K5, representing a novel psychrophilic member of the haloalkane dehalogenase family, was identified and biochemically characterized. DpcA exhibited a unique temperature profile with exceptionally high activities at low temperatures. The psychrophilic properties of DpcA make this enzyme promising for various environmental applications.     

Frequency distributions for chloroplast genes in Chlamydomonas zygote clones: Evidence for random drift

Mitochondria and chloroplasts of eucaryotic cells contain populations of DNA molecules. In certain cases, e.g., the chloroplasts of Chlamydomonas reinhardtii and the mitochondria of Saccharomyces cerevisiae, organelles contributed by the two parents are known to fuse in the zygote, creating a single population of DNA molecules. In a cross, this population will include molecules of both parental genotypes. There is reason to suspect that organelle DNA molecules in this population are selected randomly for replication and recombination. This would result in random changes in the frequency of a particular allele or genotype within the organelle gene pool of a single zygote and also within its clone of progeny cells. A given gene frequency would increase in some zygote clones and decrease in others, analogous to random drift of gene frequencies in small Mendelian populations. To test this, we have examined the distribution of chloroplast gene frequencies among the zygote clones produced in each of a number of crosses of Chlamydomonas. These distributions are typically U or L shaped as predicted by the random drift hypothesis. They include uniparental zygote clones, in which a chloroplast allele from one parent has been fixed (frequency 100%) and the alternative allele from the other parent has been lost (frequency 0%). Among the remaining (biparental) zygote clones, there is a linear distribution of allele frequencies, showing a great increase in variance over the input frequencies. In these experiments both biparental and uniparental zygotes show a bias favoring chloroplast alleles from the mt⁺ (maternal) parent, and there is no statistically significant mode at the allele frequency of 0.5 corresponding to the equal input of alleles from the maternal and paternal (mt^?) parents. The observed distributions support the hypothesis that both uniparental inheritance and the high variance of allele frequencies among zygote clones are due to random drift of allele frequencies, coupled with a directional force which favors fixation of the maternal allele. In addition, statistical analysis of the data shows a strong but incomplete tendency for linked chloroplast markers to be fixed or lost together in uniparental zygotes. Possible cellular and molecular mechanisms for these observations are discussed.     

On the Origin of Mitochondrial Mutants: Evidence for Intracellular Selection of Mitochondria in the Origin of Antibiotic-Resistant Cells in Yeast

In wild-type Saccharomyces cerevisiae, erythromycin and certain other antibacterial antibiotics inhibit the formation of respiratory enzymes in mitochondria by inhibiting translation on mitochondrial ribosomes. This paper is concerned with the origin of mutant cells, resistant to erythromycin by virtue of having a homogeneous population of mutant mitochondrial DNA molecules. Such mutant cells are obtained by plating wild-type (sensitive) cells on a nonfermentable substrate plus the antibiotic. Colonies of mutant cells appear first about four days after the time of appearance of established mutant cells; new colonies continue to appear, often at a constant rate, for many days. Application of the Newcombe respreading experiment demonstrates that most or all of the mutant cells which form the resistant colonies on selective medium arise only after exposure of the population to erythromycin. It is suggested that this result is most probably due to intracellular selection for mitochondrial genomes. Resistant mitochondria arising from spontaneous mutation are postulated to be at a selective disadvantage in the absence of erythromycin; reproducing more slowly than wild-type sensitive mitochondria, they cannot easily accumulate in sufficient numbers in a cell to render it resistant as a whole. In the presence of erythromycin, resistant mitochondria can continue to reproduce while sensitive mitochondria cannot, until there is a sufficient number to make the cell resistant, i.e. to permit normal cell growth. The same phenomenon is seen with respect to chloramphenicol resistance. Intracellular selection is considered more likely than direct induction of mutation by the antibiotic, since mutant cells do not accumulate in the presence of erythromycin if the mitochondrial genome is rendered non-essential by growth on glucose or nontranslatable by chloramphenicol. Intra-cellular selection provides a mechanism for direct adaptation at the cell level, compatible with currently acceptable ideas of spontaneous mutation and selection at the organelle level.     

Destruction of aflatoxins B1 and G1 in bread making

The effect of processing steps as well preservatives used in French bread making namely propionic acid and/or potassium sorbate (0.2%) on the destruction of aflatoxins B₁ and G₁ was studied. Mixing and baking processes showed marked destruction of aflatoxins B₁ and G₁; being 71.2% and 52.5% for aflatoxin B₁ after mixing and baking steps, while reaching 73.9% and 54.5% for aflatoxin G₁. Fermentation step caused additional 15.3% and 15.0% destruction of aflatoxins B₁ and G₁. On the other hand, aflatoxin B₁ destruction was 79.2% and 50.7% when propionic acid was used and 75.3 and 56.7% in the presence of potassium sorbate and after mixing and baking steps respectively. Concerning aflatoxins G₁ it was found that mixing and baking steps showed destruction of 81.9% and 53.4% in the presence of propionic acid and 75.1 and 49.4% in the presence of potassium sorbate in this respective order. Generally, it can be concluded that using propionic acid as preservative appeared to be more effective on the destruction of aflatoxins B₁ and G₁ than potassium sorbate in French bread making.     

内蒙古山杏种群表型变异

为明确内蒙古山杏(Armeniaca sibirica)种群间和种群内的表型变异程度和变异规律, 以内蒙古山杏自然分布区的13个种群的23个表型性状为研究对象, 采用巢式方差分析、多重比较、变异分析、相关性分析和主成分分析等多种分析方法, 对种群间和种群内的表型多样性及其与地理生态因子的相关性进行了讨论。研究结果表明: 内蒙古山杏的表型性状在种群间和种群内均存在丰富的变异, 种群间的变异大于种群内的变异, 表型性状的平均分化系数为73.03%, 种群间变异是山杏表型变异的主要变异来源。各性状的平均变异系数为14.28%, 变异幅度为7.01%-27.23%, 其中核的变异系数最大, 果的变异系数最小。土默特左旗万家沟种群表型多样性最丰富, 科尔沁右翼前旗察尔森种群表型多样性最小。表型性状主要受经度、年降水量以及年日照时间3个主要地理生态因子影响。通过主成分分析可以把13个种源区划为四大类, 其中乌拉山种群的叶性状和阿鲁科尔沁旗种群的核性状受地理生态因子影响最大。     

Altered climate leads to positive density‐dependent feedbacks in a tropical wet forest

Climate change is predicted to result in warmer and drier Neotropical forests relative to current conditions. Negative density‐dependent feedbacks, mediated by natural enemies, are key to maintaining the high diversity of tree species found in the tropics, yet we have little understanding of how projected changes in climate are likely to affect these critical controls. Over 3 years, we evaluated the effects of a natural drought and in situ experimental warming on density‐dependent feedbacks on seedling demography in a wet tropical forest in Puerto Rico. In the +4°C warming treatment, we found that seedling survival increased with increasing density of the same species (conspecific). These positive density‐dependent feedbacks were not associated with a decrease in aboveground natural enemy pressure. If positive density‐dependent feedbacks are not transient, the diversity of tropical wet forests, which may rely on negative density dependence to drive diversity, could decline in a future warmer, drier world.