Hydroxynonenal-generated crosslinking fluorophore accumulation in Alzheimer disease reveals a dichotomy of protein turnover

Lipid peroxidation generates reactive aldehydes, most notably hydroxynonenal (HNE), which covalently bind amino acid residue side chains leading to protein inactivation and insolubility. Specific adducts of lipid peroxidation have been demonstrated in intimate association with the pathological lesions of Alzheimer disease (AD), suggesting that oxidative stress is a major component of AD pathogenesis. Some HNE-protein products result in protein crosslinking through a fluorescent compound similar to lipofuscin, linking lipid peroxidation and the lipofuscin accumulation that commonly occurs in post-mitotic cells such as neurons. In this study, brain tissue from AD and control patients was examined by immunocytochemistry and immunoelectron microscopy for evidence of HNE-crosslinking modifications of the type that should accumulate in the lipofuscin pathway. Strong labeling of granulovacuolar degeneration (GVD) and Hirano bodies was noted but lipofuscin did not contain this specific HNE-fluorophore. These findings directly implicate lipid crosslinking peroxidation products as accumulating not in the lesions or the lipofuscin pathways, but instead in a distinct pathway, GVD, that accumulates cytosolic proteins.     

Holocene turnover of the French vertebrate fauna

Comparing available paleontological, archaeological, historical, and former distributional data with current natural history and distributions demonstrated a turnover in the French vertebrate fauna during the Holocene (subdivided into seven sub-periods). To this end, a network of 53 specialists gleaned information from more than 1300 documents, the majority never cited before in the academic literature. The designation of 699 species as native, vanished, or non-indigenous in France or in one or more of its biogeographical entities during the Holocene period was investigated. Among these 699 species, 585 were found to belong to one or more of these categories. Among the 154 species that fit the definition of non-indigenous, 86 species were new species for France during the Holocene. Fifty-one that were autochthonous vanished from France during this period. Among these 51 species, 10 (two birds and eight mammals) are now globally extinct. During the last 11 millennia, the turnover in the French vertebrate fauna yielded a net gain of 35 species. On a taxon-by-taxon basis, there was a gain in the sizes of the ichthyofauna (19 : 27%), the avifauna (10 : 3%) and the herpetofauna (7 : 9%) and a loss in the mammalian fauna (−1 : 1%). Values of a per-century invasion index were less than 1 between 9200 BC and 1600 AD but increased dramatically after this date. An exponential model fits the trajectory of this index well, reaching the value of 132 invasions per century for the last sub-period, which encompasses 1945–2002. Currently, the local ecological and economic impacts of populations of 116 species (75% of the 154 that satisfied the criteria for non-indigenous) are undocumented, and the non-indigenous populations of 107 vertebrate species (69%) are unmanaged. The delay in assessing the ecological and economical impact of non-indigenous species, which is related to a lack of interest of French academic scientists in the Science and Action programmes, prevents the public from becoming informed and hinders the debates needed to construct a global strategy. For such a strategy to be effective, it will have to be elaborated at a more global scale than in just France – definitely at least in Europe. This revised version was published online in July 2006 with corrections to the Cover Date.     

6种植物次生物质对斜纹夜蛾解毒酶活性的影响

草食性昆虫取食植物时遇到宿主植物中大量次生物质的化学防御,研究昆虫适应植物毒素的反防御策略具有重要的科学意义。分别添加0.01%肉桂酸、0.01%水杨酸、0.01%花椒毒素、0.02%槲皮素、0.05%黄酮和0.1%香豆素等6种植物次生物质的人工饲料饲养斜纹夜蛾(Spodoptera litura)五龄幼虫48 h后,测定斜纹夜蛾幼虫中肠和脂肪体中谷胱甘肽S-转移酶(GSTs)、羧酸酯酶(CarE)、P450的酶含量及头部乙酰胆碱酯酶(AChE)的活性,利用半定量RT-PCR检测中肠和脂肪体中CYP4M14和CYP4S9的基因表达水平。结果表明:取食肉桂酸和香豆素后,斜纹夜蛾中肠中CarE的酶活性分别提高了1.67和1.37倍,取食6种次生物质均能显著提高斜纹夜蛾脂肪体中GSTs酶活性。取食肉桂酸和香豆素48 h后,脂肪体中P450酶含量比对照增加2.93和14.50倍。取食肉桂酸、花椒毒素、槲皮素和香豆素后,斜纹夜蛾头部AchE酶活性与对照相比提高了1.53、1.80、2.36和1.56倍。6种次生物质均可诱导脂肪体中CYP4M14基因表达,槲皮素、肉桂酸和香豆素强烈诱导CYP4S9在脂肪体中表达。表明,斜纹夜蛾具有利用植物次生物质诱导其解毒酶的能力,进而提高其对毒素的抗性。     

Systems-wide proteomic analysis in mammalian cells reveals conserved, functional protein turnover

The turnover of each protein in the mammalian proteome is a functionally important characteristic. Here, we employed high-resolution mass spectrometry to quantify protein dynamics in nondividing mammalian cells. The ratio of externally supplied versus endogenous amino acids to de novo protein synthesis was about 17:1. Using subsaturating SILAC labeling, we obtained accurate turnover rates of 4106 proteins in HeLa and 3528 proteins in C2C12 cells. Comparison of these human and mouse cell lines revealed a highly significant turnover correlation of protein orthologs and thus high species conservation. Functionally, we observed statistically significant trends for the turnover of phosphoproteins and gene ontology categories that showed extensive covariation between mouse and human. Likewise, the members of some protein complexes, such as the proteasome, have highly similar turnover rates. The high species conservation and the low complex variances thus imply great regulatory fine-tuning of protein turnover.     

植物次生代谢物对甜菜夜蛾生长发育及解毒酶的影响

【目的】明确植物次生代谢物对甜菜夜蛾Spodoptera exigua生长发育及解毒酶的影响,探索利用植物次生物质防控甜菜夜蛾的潜在途径。【方法】本研究选用3种含量（0.01%、0.1%和1.0%）的槲皮素、山奈酚和香豆素,分别与人工饲料混合均匀后饲养甜菜夜蛾3龄初幼虫,观察植物次生代谢物对幼虫生长发育的影响;并测定幼虫取食添加0.1%的槲皮素、山奈酚和香豆素的人工饲料24、48和72 h后,幼虫羧酸酯酶（Caboxylesterase,CarE）、谷胱甘肽-S-转移酶（Glutathione-S-transferase,GSTs）和P450解毒酶活性。【结果】添加不同次生物质的人工饲料显著影响甜菜夜蛾幼虫生长和解毒酶活性。与对照组相比,3种次生代谢物均显著提高了幼虫死亡率。幼虫取食添加1%槲皮素的人工饲料后,蛹重显著降低,发育历期明显延长。而取食添加0.1%山奈酚的人工饲料后,可诱导幼虫CarE活性显著增强,0.1%槲皮素和0.1%香豆素对幼虫CarE活性均有显著抑制作用。添加槲皮素对幼虫GSTs活性无显著性影响,添加0.1%山奈酚和0.1%香豆素可诱导幼虫GSTs活性显著升高。0.1%槲皮素和0.1%香豆素可促进幼虫P450活性增强但未达到显著水平,但0.1%山奈酚处理48h后,幼虫P450活性显著降低。【结论】植物次生代谢物种类与含量对甜菜夜蛾生长发育及解毒酶活性存在不同程度的影响。     

Plasmodium falciparum antioxidant protein reveals a novel mechanism for balancing turnover and inactivation of peroxiredoxins

Life under aerobic conditions has shaped peroxiredoxins (Prx) as ubiquitous thiol-dependent hydroperoxidases and redox sensors. Structural features that balance the catalytically active or inactive redox states of Prx, and, therefore, their hydroperoxidase or sensor function, have so far been analyzed predominantly for Prx1-type enzymes. Here we identify and characterize two modulatory residues of the Prx5-type model enzyme PfAOP from the malaria parasite Plasmodium falciparum. Gain- and loss-of-function mutants reveal a correlation between the enzyme parameters and the inactivation susceptibility of PfAOP with the size of residue 109 and the presence or absence of a catalytically relevant but nonessential cysteine residue. Based on our kinetic data and the crystal structure of PfAOP^L109M, we suggest a novel mechanism for balancing the hydroperoxidase activity and inactivation susceptibility of Prx5-type enzymes. Our study provides unexpected insights into Prx structure–function relationships and contributes to our understanding of what makes Prx good enzymes or redox sensors.     

Amino acid racemization reveals differential protein turnover in osteoarthritic articular and meniscal cartilages

Introduction  

Certain amino acids within proteins have been reported to change from the L form to the D form over time. This process is known as racemization and is most likely to occur in long-lived low-turnover tissues such as normal cartilage. We hypothesized that diseased tissue, as found in an osteoarthritic (OA) joint, would have increased turnover reflected by a decrease in the racemized amino acid content.     

Genetic depletion reveals an essential role for an SR protein splicing factor in vertebrate cells

SR proteins are essential for the splicing of messenger RNA precursors in vitro, where they also alter splice site selection in a concentration-dependent manner. Although experiments involving overexpression or dominant mutations have confirmed that these proteins can influence RNA processing decisions in vivo, similar results with loss-of-function mutations have been lacking. Now, a system for genetic depletion of the chicken B cell line DT40 has revealed that the SR protein ASF/SF2 (alternative splicing factor/splicing factor 2) is essential for viability in these cells⁽¹⁾. This study opens the way for a complete functional dissection of this protein, and other SR proteins, in vivo.     

Dynamic behavior of GFP-CLIP-170 reveals fast protein turnover on microtubule plus ends

Microtubule (MT) plus end-tracking proteins (+TIPs) specifically recognize the ends of growing MTs. +TIPs are involved in diverse cellular processes such as cell division, cell migration, and cell polarity. Although +TIP tracking is important for these processes, the mechanisms underlying plus end specificity of mammalian +TIPs are not completely understood. Cytoplasmic linker protein 170 (CLIP-170), the prototype +TIP, was proposed to bind to MT ends with high affinity, possibly by copolymerization with tubulin, and to dissociate seconds later. However, using fluorescence-based approaches, we show that two +TIPs, CLIP-170 and end-binding protein 3 (EB3), turn over rapidly on MT ends. Diffusion of CLIP-170 and EB3 appears to be rate limiting for their binding to MT plus ends. We also report that the ends of growing MTs contain a surplus of sites to which CLIP-170 binds with relatively low affinity. We propose that the observed loss of fluorescent +TIPs at plus ends does not reflect the behavior of single molecules but is a result of overall structural changes of the MT end.     

Whole-genome sequencing of the endemic Antarctic fungus Antarctomyces pellizariae reveals an ice-binding protein,a scarce set of secondary metabolites gene clusters and provides insights on Thelebolales phylogeny

The snow-covered surfaces of Antarctica comprise an extreme environment that favors the development of life forms with adaptations to adverse low-temperature habitats. The ability to survive and such temperatures might involve the production of antifreeze proteins and ice-binding proteins that attenuate the effects of intense cold temperatures. He, we sequenced and reconstructed the nuclear and mitochondrial genomes of the endemic Antarctic fungus Antarctomyces pellizariae UFMGCB 12416. We then have identified a putative ice-binding protein-coding gene, mapped the presence of secondary metabolite gene clusters, and reconstructed the phylogenetic relationships of a A. pellizariae with others Leotiomycetes from the alignment of hundreds of orthologous single-copy proteins. Our results will deepen the understanding of microbial ice-binding proteins and the genomic aspects of psychrophilic fungi.DatasetThe GenBank/EMBL/DDBJ accession number for the gene sequence of ice-binding protein from A. pellizariae determined in this study is MN867686. The Whole Genome Shotgun project of strain A. pellizariae UFMGCB 12416 has been deposited at DDBJ/ENA/GenBank under accession WCAA00000000. The version described in this paper is version WCAA01000000. The mitochondrial genome has been deposited under accession MT197497.     

Metabolomic analysis reveals reliance on secondary plant metabolites to facilitate carnivory in the Cape sundew,Drosera capensis

Background and AimsSecondary metabolites are integral to multiple key plant processes (growth regulation, pollinator attraction and interactions with conspecifics, competitors and symbionts) yet their role in plant adaptation remains an underexplored area of research. Carnivorous plants use secondary metabolites to acquire nutrients from prey, but the extent of the role of secondary metabolites in plant carnivory is not known. We aimed to determine the extent of the role of secondary metabolites in facilitating carnivory of the Cape sundew, Drosera capensis.MethodsWe conducted metabolomic analysis of 72 plants in a time-series experiment before and after simulated prey capture. We used ultra-high-performance liquid chromatography–tandem mass spectrometry (UHPLC–MS/MS) and the retention time index to identify compounds in the leaf trap tissue that changed up to 72 h following simulated prey capture. We identified associated metabolic pathways, and cross-compared these compounds with metabolites previously known to be involved in carnivorous plants across taxa.Key ResultsFor the first time in a carnivorous plant, we have profiled the whole-leaf metabolome response to prey capture. Reliance on secondary plant metabolites was higher than previously thought – 2383 out of 3257 compounds in fed leaves had statistically significant concentration changes in comparison with unfed controls. Of these, ~34 compounds are also associated with carnivory in other species; 11 are unique to Nepenthales. At least 20 compounds had 10-fold changes in concentration, 12 of which had 30-fold changes and are typically associated with defence or attraction in non-carnivorous plants.ConclusionsSecondary plant metabolites are utilized in plant carnivory to an extent greater than previously thought – we found a whole-metabolome response to prey capture. Plant carnivory, at the metabolic level, likely evolved from at least two distinct functions: attraction and defence. Findings of this study support the hypothesis that secondary metabolites play an important role in plant diversification and adaptation to new environments.     

Increase in respiratory cost at high growth temperature is attributed to high protein turnover cost in Petunia x hybrida petals

It is widely believed that turnover of nitrogenous (N) compounds (especially proteins) incurs a high respiratory cost. Thus, if protein turnover costs change with temperature, this would influence the dependence of respiration rate on growth temperature. Here, we examined the extent to which protein turnover cost explained differences in N-utilization costs (nitrate uptake/reduction, ammonium assimilation, amino acid and protein syntheses, protein turnover and amino acid export) and in respiration rate with changes in growth temperature. By measurements and literature data, we evaluated each N-utilization cost in Petunia x hybrida petals grown at 20, 25 or 35 degrees C throughout their whole lifespans. Protein turnover cost accounted for 73% of the integrated N-utilization cost on a whole-petal basis at 35 degrees C. The difference in this cost on a dry weight basis between 25 and 35 degrees C accounted for 75% of the difference in N-utilization cost and 45% of the difference in respiratory cost. The cost of nitrate uptake/reduction was high at low growth temperatures. We concluded that respiratory cost in petals was strongly influenced by protein turnover and nitrate uptake/reduction, and on the shoot basis, C investment in biomass was highest at 25 degrees C.     

The effects of volatile microbial secondary metabolites on protein synthesis in Serpula lacrymans

The cyanobacterium Synechocystis sp. PCC 6803 is transformable at high efficiency and integrates DNA by homologous double recombination. However, several genetic mapping procedures depend on the ability to generate transformants even with very small amounts of added DNA. This study is aimed at optimizing the transformation efficiency at limiting concentrations of exogenous DNA. The transformation efficiency showed little sensitivity to experimental conditions. Transformation with circular plasmid DNA was found to be no more than 30% more efficient than with linearized plasmid DNA. The efficiency of transformation remained essentially the same in the presence of competing DNA, indicating that the capacity of DNA uptake by the cells is not limiting. The incubation time of cells with DNA before plating (0-8 h) affected the transformation efficiency by up to 3-fold. Only minor changes in the efficiency were observed as a function of the presence of a membrane filter on the plate or the presence of TAE or TBE gel buffer residues in the transformation mixture. However, transformability of the host strain of Synechocystis sp. PCC 6803 was increased by two orders of magnitude if the sll1354 gene encoding the exonuclease RecJ was deleted. Therefore, the transformation efficiency of Synechocystis sp. PCC 6803 with exogenous DNA appears to be determined primarily by intracellular processes such as the efficiency of DNA processing and homologous recombination.     

Effect of leucine and metabolites of branched chain amino acids on protein turnover in heart.

Leucine, but not isoleucine or valine, inhibited protein degradation and accelerated protein synthesis in hearts perfused with buffer that contained glucose (15 mM) and normal plasma levels of other amino acids, except for the branched chain compounds. Products of leucine, isoleucine, and valine metabolism also inhibited protein degradation and stimulated protein synthesis. These compounds included the transamination and decarboxylation products, as well as acetate, acetoacetate, and propionate. In some, but not all instances, inhibition of degradation and acceleration of synthesis were accompanied by an increase in intracellular leucine. When insulin was added to the perfusate, the rate of degradation was reduced by 40%, but addition of leucine was ineffective in the presence of the hormone. Insulin, leucine (2 mM) and a mixture of branched chain amino acids at normal plasma levels increased latency of cathepsin D in hearts that were perfused with buffer containing glucose. A combination of leucine and insulin increased latency more than either substance alone. These studies indicate that leucine as well as a variety of substrates that are oxidized in the citric acid cycle are involved in regulation of protein turnover in heart muscle.     

Whole-body autoradiography reveals that the Peptostreptococcus magnus immunoglobulin-binding domains of protein L preferentially target B lymphocytes in the spleen and lymph nodes in vivo

Protein L is an immunoglobulin (Ig)-binding protein produced by the Gram-positive bacterium Peptostreptococcus magnus that interacts with the variable region of Ig kappa light chains. The Ig light chain-binding capacity of protein L gives it the potential to interact with cells expressing surface Ig such as B cells. The present study was performed to address the in vivo trafficking of protein L at both the organ and the cellular level. Using the powerful technique of whole-body autoradiography in a murine model system, we demonstrate specific targeting of protein L to secondary lymphoid tissues in whole-animal analysis. The observed targeting depends on the capacity to interact with murine Ig, as tissue targeting was not apparent in mice given protein H, an Ig-binding protein produced by Streptococcus pyogenes with affinity for human but not murine Ig. Tissue targeting data were combined with flow cytometry analysis, which demonstrated the capacity of protein L to target and activate B lymphocytes in vivo. B cells targeted by protein L had increased surface expression of CD86 and MHC-II, and protein L was present in vacuolar compartments of B cells. Protein L did not bind T cells or natural killer cells but had some capacity to target dendritic cells and macrophages. The data show that protein L preferentially targets secondary lymphoid organs, and activates and is internalized by B cells in vivo. Furthermore, the observed tissue and cell targeting properties require an affinity for murine Ig. These data support the potential use of this Ig-binding protein as a targeting approach to deliver agents to defined cell populations in vivo.     

Cloning of the SNG1 gene of Arabidopsis reveals a role for a serine carboxypeptidase-like protein as an acyltransferase in secondary metabolism

Serine carboxypeptidases contain a conserved catalytic triad of serine, histidine, and aspartic acid active-site residues. These enzymes cleave the peptide bond between the penultimate and C-terminal amino acid residues of their protein or peptide substrates. The Arabidopsis Genome Initiative has revealed that the Arabidopsis genome encodes numerous proteins with homology to serine carboxypeptidases. Although many of these proteins may be involved in protein turnover or processing, the role of virtually all of these serine carboxypeptidase-like (SCPL) proteins in plant metabolism is unknown. We previously identified an Arabidopsis mutant, sng1 (sinapoylglucose accumulator 1), that is defective in synthesis of sinapoylmalate, one of the major phenylpropanoid secondary metabolites accumulated by Arabidopsis and some other members of the Brassicaceae. We have cloned the gene that is defective in sng1 and have found that it encodes a SCPL protein. Expression of SNG1 in Escherichia coli demonstrates that it encodes sinapoylglucose:malate sinapoyltransferase, an enzyme that catalyzes a transesterification instead of functioning like a hydrolase, as do the other carboxypeptidases. This finding suggests that SCPL proteins have acquired novel functions in plant metabolism and provides an insight into the evolution of secondary metabolic pathways in plants.     

On the regulation and turnover of progesterone metabolites in rat uterus

Recently the in vitro progesterone metabolism was shown to be inhibited in uterine tissue by association of the hormone with binding components. However, a dissociation of progesterone would impair the protection of the steroid hormone caused by complex formation. In order to study this effect, the influence of time was investigated on the metabolism of progesterone. Progesterone metabolites were analysed quantitatively from the recovered material of uteri and nutrient media by thin layer chromatography (TLC) at various time invervals. After finishing the incubation with the labelled steroid, the amount of progesterone metabolites produced increased continuously in the tissue during the following hour when the uteri were kept in nutrient medium. This indicated that the dissociation of progesterone from a hormone protein complex led to the subsequent metabolism of the unbound hormone. However, the metabolism was reduced markedly by an increase of the protein content in uterine tissue and with it by an increase of progesterone binding proteins in uterine cytosol as determined by charcoal adsorption technique. Additionally, the amount of progesterone metabolites was found to be much higher in uterine tissue than that released into nutrient medium during the time interval studied. Therefore, uterine tissue concentrates progesterone metabolites, and a rapid turnover of these substances does not occur.