The interaction of an anti-tumour platinum complex with DNA.

The interaction of the anti-tumour active cis platinum (II) complexes with DNA has been investigated using dichloro(ethylenediamine)platinum(II) and E. coli DNA. Equilibrium dialysis studies indicate that Pt(en)Cl2 binds reversibly to DNA to a saturation value of 0.57 Pt: P, which is consistent with the platinum being bound both monofunctionally and bifunctionally. Pt(en)Cl2 inhibits the intercalation of 9-aminoacridine (9AA) by cross-linking the bases of the double helix, but at no stage does all the bound platinum cross-link. It is suggested that this inhibition of intercalation is due to intrastrand cross-linking.     

A C4-oxidizing Lytic Polysaccharide Monooxygenase Cleaving Both Cellulose and Cello-oligosaccharides

Lignocellulosic biomass is a renewable resource that significantly can substitute fossil resources for the production of fuels, chemicals, and materials. Efficient saccharification of this biomass to fermentable sugars will be a key technology in future biorefineries. Traditionally, saccharification was thought to be accomplished by mixtures of hydrolytic enzymes. However, recently it has been shown that lytic polysaccharide monooxygenases (LPMOs) contribute to this process by catalyzing oxidative cleavage of insoluble polysaccharides utilizing a mechanism involving molecular oxygen and an electron donor. These enzymes thus represent novel tools for the saccharification of plant biomass. Most characterized LPMOs, including all reported bacterial LPMOs, form aldonic acids, i.e., products oxidized in the C1 position of the terminal sugar. Oxidation at other positions has been observed, and there has been some debate concerning the nature of this position (C4 or C6). In this study, we have characterized an LPMO from Neurospora crassa (NcLPMO9C; also known as NCU02916 and NcGH61–3). Remarkably, and in contrast to all previously characterized LPMOs, which are active only on polysaccharides, NcLPMO9C is able to cleave soluble cello-oligosaccharides as short as a tetramer, a property that allowed detailed product analysis. Using mass spectrometry and NMR, we show that the cello-oligosaccharide products released by this enzyme contain a C4 gemdiol/keto group at the nonreducing end.     

Thematic minireview series on enzyme evolution in the post-genomic era

The emergence of genomics; ongoing computational advances; and the development of large-scale sequence, structural, and functional databases have created important new interdisciplinary linkages between molecular evolution, molecular biology, and enzymology. The five minireviews in this series survey advances and challenges in this burgeoning field from complementary perspectives. The series has three major themes. The first is the evolution of enzyme superfamilies, in which members exhibit increasing sequence, structural, and functional divergence with increasing time of divergence from a common ancestor. The second is the evolutionary role of promiscuous enzymes, which, in addition to their primary function, have adventitious secondary activities that frequently provide the starting point for the evolution of new enzymes. The third is the importance of in silico approaches to the daunting challenge of assigning and predicting the functions of the many uncharacterized proteins in the large-scale sequence and structural databases that are now available. A recent computational advance, the use of protein similarity networks that map functional data onto proteins clustered by similarity, is presented as an approach that can improve functional insight and inference. The three themes are illustrated with several examples of enzyme superfamilies, including the amidohydrolase, metallo-β-lactamase, and enolase superfamilies.     

Evolutionary Aspects of Enzyme Dynamics

The role of evolutionary pressure on the chemical step catalyzed by enzymes is somewhat enigmatic, in part because chemistry is not rate-limiting for many optimized systems. Herein, we present studies that examine various aspects of the evolutionary relationship between protein dynamics and the chemical step in two paradigmatic enzyme families, dihydrofolate reductases and alcohol dehydrogenases. Molecular details of both convergent and divergent evolution are beginning to emerge. The findings suggest that protein dynamics across an entire enzyme can play a role in adaptation to differing physiological conditions. The growing tool kit of kinetics, kinetic isotope effects, molecular biology, biophysics, and bioinformatics provides means to link evolutionary changes in structure-dynamics function to the vibrational and conformational states of each protein.     

人类线粒体DNA世系的系统发育关系研究

本文以人类线粒体DNA为例,回顾了其系统发育关系的重建的研究历史,进而总结介绍了该分析方法在人类进化历史研究、线粒体DNA数据质量评估以及疾病相关线粒体DNA突变的甄别等方面的应用,以期对该方法在国内的推广应用有所裨益。     

Investigating age‐dependency of species extinction rates using dynamic survivorship analysis

Survivorship curves with taxon lifespans normalised to variations in the real‐time extinction rate (the ‘Corrected Survivorship Score’ technique) are plotted for various fossil groups. Of five groups tested at the ‘species level’ (strictly speaking, Linnean morphospecies), only the calcareous nannoplankton are found to have had a constant extinction probability with respect to morphospecies age. The planktonic foraminifer, trilobite, conodont and graptolite data all show a significant age‐dependent effect (convexity of survivorship curves), which reveals in each case a progressively increasing extinction probability as morphospecies became older. This effect is found to be much reduced for trilobite genera and absent for ammonoid families, suggesting that age‐dependency of extinction probability is primarily a characteristic of the species level in some, but not all groups. However, the pattern may be partly an artefact of taxonomic methodology. Morphospecies range data, which are gathered primarily for biostratigraphic purposes, are far from ideal for the purpose of survivorship analysis. Therefore, survivorship curves for a specially‐developed lineage phylogeny of Palaeogene planktonic foraminifera are also presented. These do not indicate a similar age‐dependency to the extinction probability with respect to either the terminal or non‐terminal lineages.     

Escherichia coli d-Malate Dehydrogenase,a Generalist Enzyme Active in the Leucine Biosynthesis Pathway

The enzymes of the β-decarboxylating dehydrogenase superfamily catalyze the oxidative decarboxylation of d-malate-based substrates with various specificities. Here, we show that, in addition to its natural function affording bacterial growth on d-malate as a carbon source, the d-malate dehydrogenase of Escherichia coli (EcDmlA) naturally expressed from its chromosomal gene is capable of complementing leucine auxotrophy in a leuB⁻ strain lacking the paralogous isopropylmalate dehydrogenase enzyme. To our knowledge, this is the first example of an enzyme that contributes with a physiologically relevant level of activity to two distinct pathways of the core metabolism while expressed from its chromosomal locus. EcDmlA features relatively high catalytic activity on at least three different substrates (l(+)-tartrate, d-malate, and 3-isopropylmalate). Because of these properties both in vivo and in vitro, EcDmlA may be defined as a generalist enzyme. Phylogenetic analysis highlights an ancient origin of DmlA, indicating that the enzyme has maintained its generalist character throughout evolution. We discuss the implication of these findings for protein evolution.     

Directed evolution of a thermostable quorum-quenching lactonase from the amidohydrolase superfamily

A thermostable quorum-quenching lactonase from Geobacillus kaustophilus HTA426 (GI: 56420041) was used as an initial template for in vitro directed evolution experiments. This enzyme belongs to the phosphotriesterase-like lactonase (PLL) group of enzymes within the amidohydrolase superfamily that hydrolyze N-acylhomoserine lactones (AHLs) that are involved in virulence pathways of quorum-sensing pathogenic bacteria. Here we have determined the N-butyryl-l-homoserine lactone-liganded structure of the catalytically inactive D266N mutant of this enzyme to a resolution of 1.6 Å. Using a tunable, bioluminescence-based quorum-quenching molecular circuit, the catalytic efficiency was enhanced, and the AHL substrate range increased through two point mutations on the loops at the C-terminal ends of the third and seventh β-strands. This E101N/R230I mutant had an increased value of k_cat/K_m of 72-fold toward 3-oxo-N-dodecanoyl-l-homoserine lactone. The evolved mutant also exhibited lactonase activity toward N-butyryl-l-homoserine lactone, an AHL that was previously not hydrolyzed by the wild-type enzyme. Both the purified wild-type and mutant enzymes contain a mixture of zinc and iron and are colored purple and brown, respectively, at high concentrations. The origin of this coloration is suggested to be because of a charge transfer complex involving the β-cation and Tyr-99 within the enzyme active site. Modulation of the charge transfer complex alters the lactonase activity of the mutant enzymes and is reflected in enzyme coloration changes. We attribute the observed enhancement in catalytic reactivity of the evolved enzyme to favorable modulations of the active site architecture toward productive geometries required for chemical catalysis.     

Divergence and convergence in enzyme evolution

Comparative analysis of the sequences of enzymes encoded in a variety of prokaryotic and eukaryotic genomes reveals convergence and divergence at several levels. Functional convergence can be inferred when structurally distinct and hence non-homologous enzymes show the ability to catalyze the same biochemical reaction. In contrast, as a result of functional diversification, many structurally similar enzyme molecules act on substantially distinct substrates and catalyze diverse biochemical reactions. Here, we present updates on the ATP-grasp, alkaline phosphatase, cupin, HD hydrolase, and N-terminal nucleophile (Ntn) hydrolase enzyme superfamilies and discuss the patterns of sequence and structural conservation and diversity within these superfamilies. Typically, enzymes within a superfamily possess common sequence motifs and key active site residues, as well as (predicted) reaction mechanisms. These observations suggest that the strained conformation (the entatic state) of the active site, which is responsible for the substrate binding and formation of the transition complex, tends to be conserved within enzyme superfamilies. The subsequent fate of the transition complex is not necessarily conserved and depends on the details of the structures of the enzyme and the substrate. This variability of reaction outcomes limits the ability of sequence analysis to predict the exact enzymatic activities of newly sequenced gene products. Nevertheless, sequence-based (super)family assignments and generic functional predictions, even if imprecise, provide valuable leads for experimental studies and remain the best approach to the functional annotation of uncharacterized proteins from new genomes.     

Molecular analysis of heterochronic changes in the evolution of direct developing sea urchins

The sea urchin Heliocidaris erythrogramma is a direct developer; it progresses directly from the gastrula to the juvenile adult without forming a pluteus larva. No larval skeleton is formed by mesenchyme cells, but formation of the juvenile skeleton is accelerated. We have examined two alterations in mesenchyme cell behavior that accompany this striking change in developmental pattern. 1) Rapid cell proliferation produces 1700–2200 mesenchyme cells by mid-gastrula, compared to 30–60 primary mesenchyme cells in species with typical larval development. This change may reflect the accelerated production of adult structures in H. erythrogramma. 2) B2C2 is a monoclonal antibody that recognizes primary (Anstrom et al., 1987) and adult mesenchyme cells associated with skeleton formation in typical developers. The altered pattern of B2C2 staining in H. erythrogramma (e.g., a later initial appearance of the B2C2 antigen) suggests that H. erythrogramma has deleted part of a larval program of development and accelerated its adult program of development. These results indicate that cellular and molecular heterochronies accompany the morphological changes in H. erythrogramma development.     

Evolution of the nauplius stage in malacostracan crustaceans*

This article gives an overview on some aspects of malacostracan development at the levels of gene expression, cell division, and shape of embryos and larvae. The various modes of development found in malacostracans are discussed in a phylogenetic and an evolutionary framework. It is suggested that the plesiomorphic condition within the Malacostraca is an embryonized egg‐nauplius which is characterised by a yolky egg, precocious development of the three anteriormost head segments, an antero‐ventrally folded caudal papilla, and a growth zone formed by rings of 19 ecto‐ and eight mesoteloblasts. Several alterations of this malacostracan ground pattern occurred concerning the arrangement and the number of teloblasts, the shape of the embryo and the timing of segmentation with respect to the naupliar segments. From their distribution within the phylogenetic tree and from their larval characteristics it is concluded that the free‐living nauplius larvae of euphausiids and dendrobranchiate decapods are secondarily evolved from ontogenies without a free‐living nauplius. Because the nauplius stage is lost in several malacostracan taxa, the concept of the nauplius as a phylotypic stage of crustaceans is refuted. In addition, the nauplius as an example of the recapitulation of ancestral characters is discussed.