Unbiased characterization of genotype-dependent metabolic regulations by metabolomic approach in Arabidopsis thaliana

Background  

Metabolites are not only the catalytic products of enzymatic reactions but also the active regulators or the ultimate phenotype of metabolic homeostasis in highly complex cellular processes. The modes of regulation at the metabolome level can be revealed by metabolic networks. We investigated the metabolic network between wild-type and 2 mutant (methionine-over accumulation 1 [mto1] and transparent testa4 [tt4]) plants regarding the alteration of metabolite accumulation in Arabidopsis thaliana.     

Membrane cofactor protein (MCP or CD46) is a cellular pilus receptor for pathogenic Neisseria

The Bacillus subtilis RecR protein is required for DNA repair and recombination in vivo . In its N-terminal portion, RecR possesses potential zinc-ligand structures associated with the multicysteine (C₄) superfamily. The number and arrangement of the cysteine residues is suggestive of RecR being a zinc-finger protein. One of the four cysteines (Cys-60) has been replaced by a Ser (C60S) or an Ala (C60A) residue to generate the recR60 and recR601 genes, respectively. B. subtilis recR60 , recR601 or Δ recR1 (a null-mutant allele) cells are 10-, 134- and 144-fold more sensitive to 10 mM methanesulphonate and 95-, 900- and 1100-fold more sensitive to the lethal effect of 100 μM 4-nitroquinoline-1-oxide (4NQO) than the wild-type strain, respectively. The RecR zinc-ligand C₄ motif does not seem to be accessible, because the protein is highly resistant to oxidation and moderately resistant to reduction. We have determined by different biochemical methods that RecR is a zinc metalloprotein whose cysteine residues have a structural and/or functional role.     

Concerted evolution of polymorphic MHC class II β loci: a comment to reviewer's reply

Address correspondence and offprint requests to: L. Andersson     

Isolation of two C-reactive protein homologues from cod (Gadus morhua L.) serum

Pentraxins are important molecules in innate defence and play a role in the acute phase response of both mammals and fish. Isolation of cod pentraxins by affinity chromatography using phosphorylcholine agarose revealed two pentraxin-like proteins, referred to as PI and PII proteins. These varied in their overall charge, pentameric and subunit molecular size, glycosylation and N-terminal amino acid sequences. The PI protein was homologous with the CRP-like pentraxin previously described in cod whereas the PII protein was a new CRP homologue, which was characterized by substantial individual heterogeneity with regard to subunit size and relative density. The results indicate considerable genetic variations in the cod pentraxins.     

Overexpression of a novel endogenous NADH kinase in Aspergillus nidulans enhances growth

The complete genome sequence of the filamentous fungi Aspergillus nidulans has paved the way for fundamental research on this industrially important species. To the best of our knowledge, this is the first time a gene encoding for ATP-dependent NADH kinase (ATP:NADH 2'-phosphotransferase, EC 2.7.1.86) has been identified. The enzyme has a predicted molecular weight of 49 kDa. We characterised the role of this NADH kinase by genomic integration of the putative gene AN8837.2 under a strong constitutive promoter. The physiological effects of overexpressed NADH kinase in combination with different aeration rates were studied in well-controlled glucose batch fermentations. Metabolite profiling and metabolic network analysis with [1-(13)C] glucose were used for characterisation of the strains, and the results demonstrated that NADH kinase activity has paramount influence on growth physiology. Biomass yield on glucose and the maximum specific growth rate increased from 0.47 g/g and 0.22 h(-1) (wild type) to 0.54 g/g and 0.26 h(-1) (NADH kinase overexpressed), respectively. The results suggest that overexpression of NADH kinase improves the growth efficiency of the cell by increasing the access to NADPH. Our findings indicate that A. nidulans is not optimised for growth in nutrient-rich conditions typically found in laboratory and industrial fermentors. This conclusion may impact the design of new strains capable of generating reducing power in the form of NADPH, which is crucial for efficient production of many industrially important metabolites and enzymes.     

Patterns of invertebrate density and taxonomic richness across gradients of area,isolation, and vegetation diversity in a lake‐island system

Over the past half century, ecologists have tried to unravel the factors that drive species richness patterns in ecological communities. One influential theory is island biogeography theory (IBT), which predicts that island or habitat area and isolation are drivers of species richness. However, relatively few studies testing IBT have considered invertebrate or belowground communities, and it is unclear as to whether the predictions made by IBT hold for these communities. Other theories predict that habitat characteristics such as vegetation diversity may be important drivers of invertebrate species richness. To investigate patterns of invertebrate density and species richness across gradients of area, isolation, and vegetation diversity, we used a system of 30 lake islands in the boreal zone of northern Sweden. We assessed density and taxonomic richness of ground‐dwelling spiders, web‐building spiders, beetles, collembolans, mites, and nematodes, for all islands during two consecutive summers. For all invertebrate groups, both density and taxonomic richness were either neutrally or negatively related to island size, and either neutrally or positively related to island isolation. Meanwhile the density and taxonomic richness for several groups was positively related to vegetation diversity (i.e. habitat heterogeneity). In multiple regression analyses, island size was often the single best predictor for both invertebrate density and taxonomic richness, but in some cases island size and isolation in combination explained more variation than each factor considered singly. Contrary to IBT predictions, invertebrate density and richness was never positively related to island size or negatively related to island isolation. Instead, our results suggest that plant diversity (and thus habitat heterogeneity) was the main driver of the patterns that we found, although other factors could have some influence. We conclude that several factors, but not necessarily those predicted as important by IBT, are important in determining invertebrate abundance and species richness in island systems.     

Physiological characterization of brewer’s yeast in high-gravity beer fermentations with glucose or maltose syrups as adjuncts

High-gravity brewing, which can decrease production costs by increasing brewery yields, has become an attractive alternative to traditional brewing methods. However, as higher sugar concentration is required, the yeast is exposed to various stresses during fermentation. We evaluated the influence of high-gravity brewing on the fermentation performance of the brewer’s yeast under model brewing conditions. The lager brewer’s strain Weihenstephan 34/70 strain was characterized at three different gravities by adding either glucose or maltose syrups to the basic wort. We observed that increased gravity resulted in a lower specific growth rate, a longer lag phase before initiation of ethanol production, incomplete sugar utilization, and an increase in the concentrations of ethyl acetate and isoamyl acetate in the final beer. Increasing the gravity by adding maltose syrup as opposed to glucose syrup resulted in more balanced fermentation performance in terms of higher cell numbers, respectively, higher wort fermentability and a more favorable flavor profile of the final beer. Our study underlines the effects of the various stress factors on brewer’s yeast metabolism and the influence of the type of sugar syrups on the fermentation performance and the flavor profile of the final beer.     

Smoking and nicotine exposure delay development of collagen-induced arthritis in mice

Introduction  

Recent epidemiologic studies have implicated smoking as an environmental risk factor for the development of rheumatoid arthritis (RA). The aim of the present study is the evaluation of the role of cigarette smoke (CS) in the pathogenesis of collagen-induced arthritis in mice.     

Changes in the Spinal Cord Proteome of an Amyotrophic Lateral Sclerosis Murine Model Determined by Differential In-gel Electrophoresis

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder characterized by loss of motor neurons resulting in progressive paralysis. To date, more than 140 different mutations in the gene encoding CuZn-superoxide dismutase (SOD1) have been associated with ALS. Several transgenic murine models exist in which various mutant SOD1s are expressed. We used DIGE to analyze the changes in the spinal cord proteome induced by expression of the unstable SOD1 truncation mutant G127insTGGG (G127X) in mice. Unlike mutants used in most other models, G127X lacks SOD activity and is present at low levels, thus reducing the risk of overexpression artifacts. The mice were analyzed at their peak body weights just before onset of symptoms. Variable importance plot analysis showed that 420 of 1,800 detected protein spots contributed significantly to the differences between the groups. By MALDI-TOF MS analysis, 54 differentially regulated proteins were identified. One spot was found to be a covalently linked mutant SOD1 dimer, apparently analogous to SOD1-immunoreactive bands migrating at double the molecular weight of SOD1 monomers previously detected in humans and mice carrying mutant SOD1s and in sporadic ALS cases. Analyses of affected functional pathways and the subcellular representation of alterations suggest that the toxicity exerted by mutant SODs induces oxidative stress and affects mitochondria, cellular assembly/organization, and protein degradation.Amyotrophic lateral sclerosis (ALS)¹ is a devastating neurodegenerative disease characterized by loss of motor neurons in the motor cortex, the brainstem, and the spinal cord. This results in progressive muscular atrophy, and the patients usually succumb to respiratory failure within a few years. About 10% of ALS cases are familial (1), and in some patients the disease is linked to mutations in the CuZn-superoxide dismutase (SOD1) gene (2). SOD1 is a ubiquitously expressed antioxidant enzyme. Overall about 6% of all cases with ALS show SOD1 mutations, and more than 140 such mutations have been identified (3). The mutations confer a cytotoxic gain of function of unknown character to the enzyme (4, 5). ALS caused by mutant SOD1s shows the same spectrum of disease phenotypes as is seen in sporadic cases lacking such mutations. This suggests that the pathogenesis of ALS induced by SOD1 mutations should show significant similarities with that in sporadic disease, e.g. similar pathogenic protein alterations.ALS has been modeled in mice via transgenic overexpression of mutant SOD1s (5–8). To cause disease within the short lifespan of a mouse, the mutant SOD1s have to be expressed at rates around 25-fold higher than the rate of expression of the endogenous murine enzyme (9). Mostly structurally stable mutants have been used, resulting in up to 10-fold increases in SOD activity and 20-fold increases in SOD1 protein levels in the CNS that may cause overexpression artifacts. Overloading of mitochondria with mutant SOD1s and vacuolization have been observed in such models (10).To explore ALS pathogenesis, we studied changes in the proteome of spinal cords of SOD1 transgenic mice using DIGE. To reduce the risk of overexpression artifacts, we used mice that express the unstable human SOD1 (hSOD1) truncation mutant G127insTGGG (G127X) (7). These mice develop an aggressive form of the disease, which is of short duration, despite the fact that the mutant lacks SOD activity and the fact that the level of G127X hSOD1 protein is less than half that of the endogenous murine SOD1. The mice were studied at their peak body weights just before development of paralytic symptoms. Here we present the identity of and discuss the possible significance of 53 proteins found to be differentially regulated in ALS transgenic mice.