Improving solubility of catalytic domain of human beta-1,4-galactosyltransferase 1 through rationally designed amino acid replacements.

beta-1,4-galactosyltransferase 1 (beta4gal-T1, EC 2.4.1.38) transfers galactose from UDP-galactose to free N-acetyl-D-glucosamine or bound N-acetyl-D-glucosamine-R. Soluble beta4gal-T1, purified from human milk has been refractory to structural studies by X-ray or NMR. In a previous study (Malissard et al. 1996, Eur. J. Biochem. 239, 340-348) we produced in the yeast Saccaromyces cerevisiae an N-deglycosylated form of soluble beta4gal-T1 that was much more homogeneous than the human enzyme, as it displayed only two isoforms when analysed by IEF as compared to 13 isoforms for the native beta4gal-T1. The propensity of recombinant beta4gal-T1 to aggregate at concentrations > 1 mg.mL(-1) prevented structural and biophysical studies. In an attempt to produce a beta4gal-T1 form suitable for structural studies, we combined site-directed mutagenesis and heterologous expression in Escherichia coli. We produced a mutated form of the catalytic domain of beta4gal-T1 (sfbeta4gal-T1mut) in which seven mutations were introduced at nonconserved sites (A155E, N160K, M163T, A168T, T242N, N255D and A259T). Sfbeta4gal-T1mut was shown to be much more soluble than beta4gal-T1 expressed in S. cerevisiae (8.5 mg.mL(-1) vs. 1 mg.mL(-1)). Catalytic activity and kinetic parameters of sfbeta4gal-T1mut produced in E. coli were shown not to differ to any significant extent from those of the native enzyme.     

Colocalization of β1,4galactosyltransferase with mannose 6-phosphate receptor in monensin-induced TGN-derived structures

Previously, we demonstrated that beta 1,4galactosyltransferase (gal-T1) reversibly segregates from alpha 2,6sialyltransferase (ST6Gal) to swollen vesicles after monensin treatment of the cells. To further explore this phenomenon, we investigated the response to monensin of various Golgi proteins. Within 30 min of monensin treatment, gal-T1 moved from the Golgi apparatus, as defined by localization of giantin, to swollen vesicles whereas ST6Gal, alpha 2,3(N)sialyltransferase, mannosidase II, and N-acetylgalactosaminyltransferase 2 remained associated with the Golgi apparatus. Stably transfected CHO cells exhibited a similar phenomenon of monensin-induced displacement of recombinant gal-T1 to swollen vesicles while recombinant ST6Gal remained colocalized with endogenously expressed giantin. Gal-T1 and the cation-insensitive mannose 6-phosphate receptor colocalized in swollen vesicles as observed at both light and electron microscopic levels. When monensin was replaced by chloroquine, gal-T1 remained arrested in swollen vesicles. Brefeldin A treatment known to cause relocation of Golgi-associated gal-T1 to the endoplasmic reticulum had no effect on gal-T1 trapped in swollen vesicles. This evidence suggests that monensin blocks gal-T1 trafficking in post-Golgi structures and argues against swelling of gal-T1-containing trans Golgi cisternae as previously assumed.     

Species interactions and plant polyploidy

Polyploidy is a common mode of speciation that can have far‐reaching consequences for plant ecology and evolution. Because polyploidy can induce an array of phenotypic changes, there can be cascading effects on interactions with other species. These interactions, in turn, can have reciprocal effects on polyploid plants, potentially impacting their establishment and persistence. Although there is a wealth of information on the genetic and phenotypic effects of polyploidy, the study of species interactions in polyploid plants remains a comparatively young field. Here we reviewed the available evidence for how polyploidy may impact many types of species interactions that range from mutualism to antagonism. Specifically, we focused on three main questions: (1) Does polyploidy directly cause the formation of novel interactions not experienced by diploids, or does it create an opportunity for natural selection to then form novel interactions? (2) Does polyploidy cause consistent, predictable changes in species interactions vs. the evolution of idiosyncratic differences? (3) Does polyploidy lead to greater evolvability in species interactions? From the scarce evidence available, we found that novel interactions are rare but that polyploidy can induce changes in pollinator, herbivore, and pathogen interactions. Although further tests are needed, it is likely that selection following whole‐genome duplication is important in all types of species interaction and that there are circumstances in which polyploidy can enhance the evolvability of interactions with other species.     

Reflections on searching for a postdoctoral position: three points to ponder

Choosing the right laboratory in which to do postdoctoral training is perhaps one of the most important decisions that a scientist makes in his or her career. Does one choose a laboratory based on the research topic or the research style of the mentor? Does one choose a large laboratory or a small one? How does one fit the selection of a postdoctoral laboratory into the context of one’s long-range career goals? Here, I briefly discuss three points worth considering in seeking a research laboratory for postdoctoral training after the completion of a graduate degree.     

Functional studies of the mammalian Sac1 phosphoinositide phosphatase

The Sac1 PIP phosphatase is an enigmatic enzyme in that it occupies an intracellular location (ER) that is not normally associated with PIP signaling. Yet, genetic experiments in mice and silencing experiments in cultured cells report an essential housekeeping function for this protein. Detailed cellular analyses report maintenance of proper organization of the Golgi system, and of the mitotic spindle apparatus, are compromised when Sac1 functional thresholds are breached. While the Golgi derangements do not obviously affect protein transport through the organelle, the mitotic defects result in defects in progression through the G2/M stage of the cell cycle. Finally, both the catalytic PIP phosphatase activity, and its ability to be recycled back to the ER, represent essential functional features of the Sac1 enzyme.We expect that current insights for Sac1 will set the blueprint for future analyses of its functions. Many questions remain to be answered in this field: does Sac1 have important roles in ER and plasma membranes connections since ySac1 only degrades the plasma membrane-localized PtdIns 4-OH kinase Stt4 generated PtdIns-4-P? Does the ER-localized Sac1 play critical roles in regulating nuclear PIP signaling since ER is continuous with the nuclear envelope, and does it specifically happen in a certain stage during cell cycle progression? Does anchoring the Sac1-catalytic domain to other cellular membranes affect its function and what effects will be generated by mislocalizing the Sac1-catalytic domain to exotic membrane locations? Does the Golgi dispersion phenotype herald a crosstalk of the organelle with the mitotic apparatus (i.e. does Golgi disorganization provide ectopic nucleation sites for the γ-tubulin ring complex)? Clearly, there is much to be learned regarding the biological functions of Sac1-like lipid phosphatases, and we anticipate the discoveries yet to come will rival those derived from studies of the kinases – both in impact and in scope.     

Adaptation genomics: the next generation

Understanding the genetics of how organisms adapt to changing environments is a fundamental topic in modern evolutionary ecology. The field is currently progressing rapidly because of advances in genomics technologies, especially DNA sequencing. The aim of this review is to first briefly summarise how next generation sequencing (NGS) has transformed our ability to identify the genes underpinning adaptation. We then demonstrate how the application of these genomic tools to ecological model species means that we can start addressing some of the questions that have puzzled ecological geneticists for decades such as: How many genes are involved in adaptation? What types of genetic variation are responsible for adaptation? Does adaptation utilise pre-existing genetic variation or does it require new mutations to arise following an environmental change?     

Aurora kinases, aneuploidy and cancer, a coincidence or a real link?

As Aurora kinases are overexpressed in a large number of cancers, and ectopic expression of Aurora generates polyploid cells containing multiple centrosomes, it has been tempting to suggest that Aurora overexpression provokes genetic instability underlying the tumorigenesis. However, examination of the evidence suggests a more complex relationship. Overexpression of Aurora-A readily transforms rat-1 and NIH3T3 cells, but not primary cells, whereas overexpression of Aurora-B induces metastasis after implantation of tumors in nude mice. Why do polyploid cells containing abnormal centrosome numbers induced by Aurora not get eliminated at cell-cycle checkpoints? Does this phenotype determine the origin of cancer or does it only promote tumor progression? Would drugs against Aurora family members be of any help for cancer treatment? These and related questions are addressed in this review (which is part of the Chromosome Segregation and Aneuploidy series).     

基因流存在条件下的物种形成研究述评:生殖隔离机制进化

物种形成过程是生物多样性形成的基础, 长期以来一直是进化生物学的中心议题之一。传统的异域物种形成理论认为, 地理隔离是物种分化的主要决定因子, 物种形成只有在种群之间存在地理隔离的情况下才能发生。近年来, 随着种群基因组学的发展和溯祖理论分析方法的完善, 种群间存在基因流情况下的物种形成成为进化生物学领域新的研究焦点。物种形成过程中是否有基因流的发生?基因流如何影响物种的形成与分化?基因流存在条件下物种形成的生殖隔离机制是什么?根据已发表的相关文献资料, 作者综述了当前物种形成研究中基因流的时间和空间分布模式、基因流对物种分化的影响以及生殖隔离机制形成等问题, 指出基因流存在条件下的物种形成可能是自然界普遍发生的一种模式。     

Metastatic potential: generic predisposition of the primary tumor or rare,metastatic variants-or both?

Metastasis is a rare event. Does it arise from rare, variant, highly metastatic cells or does a primary tumor progress to a premalignant state from which metastases arise stochastically without further changes in gene expression? Arguments and evidence have been adduced to support either position. A paper in this month's Cancer Cell and other arguments instead suggest models combining features of both.     

Double immunofluorescent staining of α2,6 sialyltransferase and β1,4 galactosyltransferase in monensin-treated cells: Evidence for different Golgi compartments?

β1,4 galactosyl- and α2,6 sialyltransferase (gal-T EC 2.4.1.22 and sialyl-T EC 2.4.99.1) sequentially elongate and terminate complex N-glycan chains of glycoproteins. Both enzymes reside in trans Golgi cisternae; their ultrastructural relationship, however, is unknown. To delineate their respective Golgi compartment(s) we conducted a double label immunofluorescent study by conventional and confocal laser scanning microscopy in HepG2, HeLa, and other cells in presence of Golgi-disturbing agents. Polyclonal, peptide-specific antibodies to human sialyl-T expressed as a β-galactosidase-sialyl-T fusion protein in E. coli were developed and applied together with mABs to human milk gal-T. In untreated HepG2 and HeLa cells Golgi morphology identified by immunofluorescent labeling of sialyl-T and gal-T, respectively, was nearly identical. Treatment of cells with brefeldin A (BFA) led to rapid and coordinated disappearance of immunostaining of both enzymes; after BFA washout, vesicular structures reappeared which first stained for gal-T followed by sialyl-T; in the reassembled Golgi apparatus sialyl-T and gal-T were co-localized again. In contrast, monensin treatment produced a reversible swelling and scattering of gal-T positive Golgi elements while sialyl-T positive structures showed little change. Treatment with nocodazole led to dispersal of Golgi elements in which gal-T and sialyl-T remained co-localized. Treatment with chloroquine affected Golgi structure less than monensin and led to condensation of gal-T positive and to slight enlargement of sialyl-T positive structures. Sequential recovery from BFA of gal-T and sialyl-T and their segregation by monensin suggest that these enzymes are targeted to different Golgi subcompartments.     

Brefeldin A induces endoplasmic reticulum-associated O-glycosylation of galactosyltransferase

Recent data from several laboratories show that Brefeldin A (BFA) induces a microtubule-dependent back-flow of Golgi components to the endoplasmic reticulum (ER) thereby causing disassembly of the Golgi apparatus and its fusion with ER membranes. In order to delineate the effect of BFA on resident Golgi proteins, we investigated its effect on biosynthesis, maturation and intracellular transport of galactosyltransferase (gal-T), an established trans-Golgi enzyme. Using a protocol of metabolic labeling/immunoprecipitation followed by electrophoretic/fluorographic analysis, we show that in the presence of BFA, gal-T matures to a molecular form of 48.5 kD, a size intermediate between the 2 precursor forms of 44 and 47 and the mature form of 54 kD (Strous and Berger: J. Biol. Chem., 257:7623-28, 1982). Little mature form was detectable in the presence of BFA even after prolonged chase times of up to 28 hr. The intermediate form was sensitive to O-glycanase and endoglycosidase H, indicating early O-glycosylation without sialylation and lack of complex N-glycosylation, respectively. In order to define the compartment responsible for O-glycosylation in the presence of BFA, a temperature block of 25 degrees C was applied which inhibited recovery of Golgi elements from BFA-induced fusion with ER. At this temperature and in absence of BFA, biosynthesis of gal-T was not appreciably affected, while maturation was completely inhibited as indicated by the presence of unmodified precursor forms of gal-T. After 60 min preincubation with BFA, a time period sufficient to demonstrate complete fusion of Golgi with ER, subsequent biosynthesis of gal-T at 25 degrees C in absence of BFA led to the intermediate form, while precursor forms were not detectable. These data provide direct evidence for BFA-induced redistribution to the EF of Golgi enzymes involved in O-glycosylation and their early functional involvement in biosynthesis of newly synthesized gal-T.     

Future trypanosomatid phylogenies: refined homologies, supertrees and networks

There has been good progress in inferring the evolutionary relationships within trypanosomes from DNA data as until relatively recently, many relationships have remained rather speculative. Ongoing molecular studies have provided data that have adequately shown Trypanosoma to be monophyletic and, rather surprisingly, that there are sharply contrasting levels of genetic variation within and between the major trypanosomatid groups. There are still, however, areas of research that could benefit from further development and resolution that broadly fall upon three questions. Are the current statements of evolutionary homology within ribosomal small sub-unit genes in need of refinement? Can the published phylograms be expanded upon to form 'supertrees' depicting further relationships? Does a bifurcating tree structure impose an untenable dogma upon trypanosomatid phylogeny where hybridisation or reticulate evolutionary steps have played a part? This article briefly addresses these three questions and, in so doing, hopes to stimulate further interest in the molecular evolution of the group.     

A model of evolution for accumulating genetic information

By taking into account recent knowledge of multigene families and other repetitive DNA sequences, a model of evolution by gene duplication for accumulating genetic information is studied. Genetic information is defined as the sum of distinct functions that the gene family can perform. A coefficient, "genetic diversity" is defined and used in this study, that is highly correlated with genetic information. Initially, a multigene family with a few gene copies is assumed, and natural selection starts to work on this gene family to increase genetic diversity contained in the gene family. As an important mechanism, unequal crossing-over is incorporated. Together with mutation, it is responsible for supplying genetic variability among individuals for selection to work. A specific model, in which individuals with less genetic diversity are selectively disadvantageous, has been studied in detail. Through approximate theoretical analysis and extensive Monte Carlo studies, it has been shown that the system is an extremely efficient way to accumulate genetic information. For attaining one gene, the genetic load is much smaller under this model than under the traditional model of natural selection. The model may be applied to the process of origin of multigene families with diverse copy members such as those of immunoglobulin or cytochrome P450. In general, the process of creating new genes by duplication might be somewhere between the present and the traditional models.     

猪雌激素受体基因（ESR）一个新多态位点的发现

ESR基因是影响猪产仔数的主效基因,而且与猪的生长发育性状及胴体性状之间不存在负的基因多效性影响。目前对它的研究大都局限于Rothschild等人发现的PvuⅡ酶切位点。本实验采用PCR-SSCP方法,对ESR基因的外显子7进行检测,发现了一个新多态性位点,得到3种基因型,可以作为一个新的标记位点进一步研究。     

Is there a pattern of gene differentiation in the Indian populations

Summary Indian populations divided into a number of endogamous groups consisting of different castes, languages, religions, and tribes provide unique opportunities for examining the extent and nature of genetic differentiation at a microevolutionary stage. The genetic relationships between some of these Indian population groups have been examined using electrophoretic data from several biochemical loci in a gene diversity analysis. Does this type of analysis provide any insight into what causes such gene differentiation? What patterns of genetic variation emerge from these empirical findings? Answers are sought by relating the observed heterozygosity, genetic distance, and allied statistics to a mutation-drift hypothesis. The statistics used are: (1) interlocus mean and variance of heterozygosity, (2) mean and variance of genetic distance, and (3) correlation of heterozygosity and gene identity. The observed relationships between these sets of statistics agree well with the ones predicted by the hypothesis that different alleles at protein loci are selectively equivalent and gene frequency change occurs predominantly due to genetic drift     

基因工程微生物合成鼠李糖脂表面活性剂的研究进展

鼠李糖脂是一类重要的生物表面活性剂。相比于化学合成的表面活性剂,其具有更优秀的理化性质及环境友好等特点,被广泛应用于微生物采油、环境污染修复等工程中。目前,鼠李糖脂的工业生产主要采用铜绿假单胞菌这一具有致病性的天然合成菌株,与此同时,受菌株遗传背景的限制,优化发酵过程等方法在产量提升方面遇到了一些瓶颈问题。利用基因工程方法对菌株进行改良有望进一步提高鼠李糖脂生产的安全性、产量、产物性能等多项指标,因此受到了越来越广泛的关注。本文综述了近年来利用基因工程方法优化鼠李糖脂生物合成的最新进展,讨论了异源合成、代谢通路改造、基因表达优化、蛋白质工程、底盘工程等多种策略的应用,并展望了一系列可行的研究方向。     

Identification of the aceA gene encoding isocitrate lyase required for the growth of Pseudomonas aeruginosa on acetate, acyclic terpenes and leucine

Pseudomonas aeruginosa PAO1 mutants affected in acyclic monoterpenes, n-octanol, and acetate assimilation were isolated using transposon mutagenesis. The isocitrate lyase gene (aceA) corresponding to ORF PA2634 of the PAO1 strain genome was identified in one of these mutants. The aceA gene encodes a protein that is 72% identical to the isocitrate lyase (ICL) characterized from Colwellia maris, but is less than 30% identical to their homologues from pseudomonads. The genetic arrangement of aceA suggests that it is a monocistronic gene, and no adjacent related genes were found. The ICL protein was detected as a 60-kDa band in sodium dodecyl sulfate polyacrylamide gel electrophoresis from cultures grown on acetate, but not in glucose-grown PAO1 cultures. Genetic complementation further confirmed that the aceA gene encodes the ICL enzyme. The ICL enzyme activity in crude extracts from cultures of the PAO1 strain was induced by acetate, citronellol and leucine, and repressed by growth on glucose or citrate. These results suggest that ICL is involved in the assimilation of acetate, acyclic monoterpenes of the citronellol family, alkanols, and leucine, in which the final intermediary acetyl-coenzyme A may be channelled to the glyoxylate shunt.     

Does It Really Pay to Be Green? An Empirical Study of Firm Environmental and Financial Performance: An Empirical Study of Firm Environmental and Financial Performance

Previous empirical work suggests that firms with high environmental performance tend to be profitable, but questions persist about the nature of the relationship. Does stronger environmental performance really lead to better financial performance, or is the observed relationship the outcome of some other underlying firm attribute? Does it pay to have cleanrunning facilities or to have facilities in relatively clean industries? To explore these questions, we analyze 652 U.S. manufacturing firms over the time period 1987–1996. Although we find evidence of an association between lower pollution and higher financial valuation, we find that a firm's fixed characteristics and strategic position might cause this association. Our findings suggest that “When does it pay to be green?” may be a more important question than “Does it pay to be green?”