Changes In Expression Of Enzymes Research Articles

Zonation of Nitrogen and Glucose Metabolism Gene Expression upon Acute Liver Damage in Mouse

Zonation of metabolic activities within specific structures and cell types is a phenomenon of liver organization and ensures complementarity of variant liver functions like protein production, glucose homeostasis and detoxification. To analyze damage and regeneration of liver tissue in response to a toxic agent, expression of liver specific enzymes was analyzed by in situ hybridization in mouse over a 6 days time course following carbon tetrachloride (CCl4) injection. CCl4 mixed with mineral oil was administered to BALB/c mice by intraperitoneal injection, and mice were sacrificed at different time points post injection. Changes in the expression of albumin (Alb), arginase (Arg1), glutaminase 2 (Gls2), Glutamine synthetase (Gs), glucose-6-phosphatase (G6pc), glycogen synthase 2 (Gys2), Glycerinaldehyd-3-phosphat-Dehydrogenase (Gapdh), Cytochrom p450 2E1 (Cyp2e1) and glucagon receptor (Gcgr) genes in the liver were studied by in situ hybridization and qPCR. We observed significant changes in gene expression of enzymes involved in nitrogen and glucose metabolism and their local distribution following CCl4 injury. We also found that Cyp2e1, the primary metabolizing enzyme for CCl4, was strongly expressed in the pericentral zone during recovery. Furthermore, cells in the damaged area displayed distinct gene expression profiles during the analyzed time course and showed complete recovery with strong albumin production 6 days after CCl4 injection. Our results indicate that despite severe damage, liver cells in the damaged area do not simply die but instead display locally adjusted gene expression supporting damage response and recovery.

Liver Fatty Acid-Binding Protein (L-Fabp) Modifies Intestinal Fatty Acid Composition and Adenoma Formation in ApcMin/+ Mice

Evidence suggests a relationship between dietary fat intake, obesity, and colorectal cancer, implying a role for fatty acid metabolism in intestinal tumorigenesis that is incompletely understood. Liver fatty acid-binding protein (L-Fabp), a dominant intestinal fatty acid-binding protein, regulates intestinal fatty acid trafficking and metabolism, and L-Fabp deletion attenuates diet-induced obesity. Here, we examined whether changes in intestinal fatty acid metabolism following L-Fabp deletion modify adenoma development in Apc(Min)(/+) mice. Compound L-Fabp(-/-)Apc(Min)(/+) mice were generated and fed a 10% fat diet balanced equally between saturated, monounsaturated, and polyunsaturated fat. L-Fabp(-/-)Apc(Min)(/+) mice displayed significant reductions in adenoma number and total polyp area compared with Apc(Min)(/+)controls, reflecting a significant shift in distribution toward smaller polyps. Adenomas from L-Fabp(-/-)Apc(Min)(/+) mice exhibited reductions in cellular proliferation, high-grade dysplasia, and nuclear β-catenin translocation. Intestinal fatty acid content was increased in L-Fabp(-/-)Apc(Min)(/+) mice, and lipidomic profiling of intestinal mucosa revealed significant shifts to polyunsaturated fatty acid species with reduced saturated fatty acid species. L-Fabp(-/-)Apc(Min)(/+) mice also showed corresponding changes in mRNA expression of enzymes involved in fatty acid elongation and desaturation. Furthermore, adenomas from L-Fabp(-/-)Apc(Min)(/+) mice displayed significant reductions in mRNA abundance of nuclear hormone receptors involved in cellular proliferation and in enzymes involved in lipogenesis. These findings collectively implicate L-Fabp as an important genetic modifier of intestinal tumorigenesis, and identify fatty acid trafficking and metabolic compartmentalization as an important pathway linking dietary fat intake, obesity, and intestinal tumor formation.

TGFβ1 alters androgenic metabolites and hydroxysteroid dehydrogenase enzyme expression in human prostate reactive stromal primary cells: Is steroid metabolism altered by prostate reactive stromal microenvironment?

The inflammatory tissue microenvironment can be an active promoter in preneoplastic cancer lesions. Altered steroid hormone metabolism as induced by the inflammatory microenvironment may contribute to epithelial cancer progression. Dehydroepiandrosterone sulfate (DHEAS) is the most abundant endogenous steroid hormone present in human serum and can be metabolized to DHEA, androgens and/or estrogens in peripheral tissues. We have previously reported that TGFβ1-induced reactive prostate stromal cells increase DHEA metabolism to active androgens and alter prostate cancer cell gene expression. While much of the focus on mechanisms of prostate cancer and steroid metabolism is in the epithelial cancer cells, this study focuses on TGFβ1-induced effects on DHEA metabolic pathways and enzymes in human prostate stromal cells. In DHEA-treated primary prostate stromal cells, TGFβ1 produced time- and dose-dependent increases in metabolism of DHEA to androstenedione and testosterone. Also TGFβ1-treated prostate stromal cells exhibited changes in the gene expression of enzymes involved in steroid metabolism including up-regulation of 3β hydroxysteroid dehydrogenase (HSD), and down-regulation of 17βHSD5, and 17βHSD2. These studies suggest that reactive prostate stroma and the inflammatory microenvironment may contribute to altered steroid metabolism and increased intratumoral androgens.

Modeling the Effect of Climate Change on Rare Genotypes in Nature

Numerical simulations are employed to model the impact of rare genetic types (or genotypes) experiencing climate change over a long time scale. The physical appearance of many genotypes is impacted by enzymatic functioning. Some enzymes are temperature sensitive and may therefore be impacted by global warming. When enzyme expression changes traits like pigmentation, can be affected dramatically.Genetic polymorphism, where at least two different types of the same species exist, are often maintained by natural selection. There are two color types of mosquitofish (Gambusia holbrooki), melanic (black spotted) and silver. Even though the mosquitofish are one of the most abundant fish species in the southeastern US, the melanic genotype is quite rare.All the progeny of silver mosquitofish are born silver and on average about 20% of the progeny of melanic fish are also silver. However in some populations cold exposure is required for the progeny of melanic fish to develop melanism. Without cold exposure these fish remain silver. Climate change, resulting in rising water temperatures may affect the expression patterns of the rare genotypes that require cold exposure to turn melanic. To simulate the effect of the rising temperature on the inheritance of melanism parameter we used three different functions as a linear function, a step function, and a random function. In each case simulations reveal that the climate change will have a devastating effect on the melanic genotypes that require cold exposure to express melanism - they will go extinct after a finite number of years. We also report on the effect of a variety of initial conditions on the population growth/decay and the sensitivity of the population to fitness changes.

Expression of antioxidant oxidoreductases and protein profile of seedling tissues of winter and spring forms of cereals under extreme temperature fluctuations

Cultivation of seedlings of soft wheat and barley under extreme temperature fluctuations led to a decrease in the total content of acidic proteins in tissues by more than 25% and reduced the total activity of peroxidases and superoxide dismutases. Against the background of changes in the general expression of enzymes, there was a redistribution of activities between their individual isoforms. Extreme ambient temperatures did not lead to a significant change in the ratio of peroxidase activity to the activity of superoxide dismutase in the cells of seedlings, but it caused a change in the ratio of peroxidase and oxidase activity in individual fractions of the electrophoretic spectrum. The dependence of the expression of structural oxidoreductase genes from the genetically determined type of development (winter or spring) was determined by the “organism-environment” definite situation. When growing cereals at a constant optimum temperature, there was no correlation between the type of development (winter or spring) and quantitative and qualitative indicators of the oxidoreductase spectra. However, when forming a plant stress response to extreme fluctuations in temperature, the degree of expression of some isoforms of enzymes in winter and spring genotypes was different, which indicates the dependence of the functional state of the studied enzymes on the allelic composition of the Vrn1 locus.

Systemic remodeling of the redox regulatory network due to RNAi perturbations of glutaredoxin 1, thioredoxin 1, and glucose-6-phosphate dehydrogenase

BackgroundCellular clearance of reactive oxygen species is dependent on a network of tightly coupled redox enzymes; this network rapidly adapts to oxidative conditions such as aging, viral entry, or inflammation. Current widespread use of shRNA as a means to perturb specific redox couples may be misinterpreted if the targeted effects are not monitored in the context of potential global remodeling of the redox enzyme network.ResultsStable cell lines containing shRNA targets for glutaredoxin 1, thioredoxin 1, or glucose-6-phosphate dehydrogenase were generated in order to examine the changes in expression associated with altering cytosolic redox couples. A qRT PCR array revealed systemic off-target effects of altered antioxidant capacity and reactive oxygen species formation. Empty lentiviral particles generated numerous enzyme expression changes in comparison to uninfected cells, indicating an alteration in antioxidant capacity irrespective of a shRNA target. Of the three redox couples perturbed, glutaredoxin 1, attenuation produced the most numerous off-target effects with 10/28 genes assayed showing statistically significant changes. A multivariate analysis extracted strong co-variance between glutaredoxin 1 and peroxiredoxin 2 which was subsequently experimentally verified. Computational modeling of the peroxide clearance dynamics associated with the remodeling of the redox network indicated that the compromised antioxidant capacity compared across the knockdown cell lines was unequally affected by the changes in expression of off-target proteins.ConclusionsOur results suggest that targeted reduction of redox enzyme expression leads to widespread changes in off-target protein expression, changes that are well-insulated between sub-cellular compartments, but compensatory in both the production of and protection against intracellular reactive oxygen species. Our observations suggest that the use of lentivirus can in itself have off-target effects on dynamic responses to oxidative stress due to the changes in species concentrations.

Ubiquitin Enzymes, Ubiquitin and Proteasome Activity in Blood Mononuclear Cells of MCI, Alzheimer and Parkinson Patients

Alzheimer's disease (AD) is a severe chronic neurodegenerative disease. During aging and neurodegeneration, misfolded proteins accumulate and activate the ubiquitin-proteasome system. The aim of the present study is to explore whether ubiquitin-activating enzyme E1, ubiquitin-conjugating enzyme E2, ubiquitin or proteasome activity are affected in peripheral blood mononuclear cells (PBMC) of AD, mild cognitive impairment (MCI) and Parkinson's disease (PD) patients compared to healthy subjects. PBMCs were isolated from EDTA blood samples and extracts were analyzed by Western Blot. Proteasome activity was measured with fluorogenic substrates. When compared to healthy subjects, the concentration of enzyme E1 was increased in PBMCs of AD patients, whereas the concentration of the enzyme E2 was decreased in these same patients. Ubiquitin levels and proteasome activity were unchanged in AD patients. No changes in enzyme expression or proteasome activity was observed in MCI patients compared to healthy and AD subjects. In PD patients E2 levels and proteasomal activity were significantly reduced, while ubiquitin and E1 levels were unchanged. The present investigation demonstrates the differences in enzyme and proteasome activity patterns of AD and PD patients. These results suggest that different mechanisms are involved in regulating the ubiquitin-proteasomal system in different neurodegenerative diseases.

Androgen profiles during pubertal Leydig cell development in mice

Postnatal Leydig cell (LC) development in mice has been assumed empirically to resemble that of rats, which have characteristic hormonal profiles at well-defined maturational stages. To characterize the changes in LC function and gene expression in mice, we examined reproductive hormone expression from birth to 180 days, and quantified in vivo and in vitro production of androgens during sexual maturation. Although the overall plasma androgen and LH profiles from birth through puberty were comparable to that of rats, the timing of developmental changes in androgen production and steroidogenic capacity of isolated LCs differed. In mice, onset of androgen biosynthetic capacity, distinguished by an acute rise in androstenedione and testosterone production and an increased expression of the steroidogenic enzymes, cytochrome P450 cholesterol side-chain cleavage enzyme and 17alpha-hydroxylase, occurred at day 24 (d24) rather than at d21 as reported in rats. Moreover, in contrast to persistently high testosterone production by pubertal and adult rat LCs, testosterone production was maximal at d45 in mice, and then declined in mature LCs. The murine LCs also respond more robustly to LH stimulation, with a greater increment in LH-stimulated testosterone production. Collectively, these data suggest that the mouse LC lineage has a delayed onset, and that it has an accelerated pace of maturation compared with the rat LC lineage. Across comparable maturational stages, LCs exhibit species-specific developmental changes in enzyme expression and capacity for androgen production. Our results demonstrate distinct differences in LC differentiation between mice and rats, and provide informative data for assessing reproductive phenotypes of recombinant mouse models.

Structure and function of the blood-brain barrier

Structure and function of the blood-brain barrier

Sodium lauryl sulphate alters the mRNA expression of lipid‐metabolizing enzymes and PPAR signalling in normal human skin in vivo

Detergents irritate skin and affect skin barrier homeostasis. In this study, healthy skin was exposed to 1% sodium lauryl sulphate (SLS) in water for 24 h. Biopsies were taken 6 h to 8 days post exposure. Lipid patterns were stained in situ and real-time polymerase chain reaction (PCR) was used to examine mRNA expression of enzymes synthesizing barrier lipids, peroxisome proliferator-activated receptors (PPAR) and lipoxygenases. The lipid pattern was disorganized from 6 h to 3 days after SLS exposure. Concomitant changes in mRNA expression included: (i) reduction, followed by induction, of ceramide-generating beta-glucocerebrosidase, (ii) increase on day 1 of two other enzymes for ceramide biosynthesis and (iii) persistent reduction of acetyl-CoA carboxylase-B, a key enzyme in fatty acid synthesis. Surprisingly, the rate-limiting enzyme in cholesterol synthesis, HMG-CoA reductase, was unaltered. Among putative regulators of barrier lipids synthesis, PPARalpha and PPARgamma exhibited reduced mRNA expression, while PPARbeta/delta and LXRbeta were unaltered. Epidermal lipoxygenase-3, which may generate PPARalpha agonists, exhibited reduced expression. In conclusion, SLS induces reorganization of lipids in the stratum corneum, which play a role in detergents' destruction of the barrier. The changes in mRNA expression of enzymes involved in synthesizing barrier lipids are probably important for the restoration of the barrier.

Misregulation of the arginase pathway in tissues of spontaneously hypertensive rats

There is a growing evidence that arginase has a role in the pathophysiology of cardiovascular diseases including hypertension. We recently reported arginase upregulation in aortas from hypertensive spontaneously hypertensive rats (SHRs). The aim of this study was to determine whether arginase abnormalities occur in other tissues of SHR, including the target organs of hypertension. Experiments were conducted on 5-, 10-, 19- and 26-week-old SHRs and Wistar-Kyoto (WKY) rats. Arginase activity and expression were evaluated in heart, kidney, liver, lung and brain tissue extracts. To investigate the role of blood pressure by itself in arginase abnormalities, arginase activity was determined in 10-week-old SHRs previously treated with hydralazine (20 mg kg(-1) per day, for 5 weeks). Compared with WKY rats, cardiac arginase activity was higher in hypertensive SHRs aged 10 weeks (+46%, P<0.05), 19 weeks (+29%, P<0.05) and 26 weeks (+23%, NS). Similar results were found in lungs in which arginase activity was increased in SHRs aged 10 weeks (+39%, P<0.05), 19 weeks (+49%, P<0.05) and 26 weeks (+36%, P<0.05) compared with WKY rats. The changes in arginase activity in these tissues were not associated with changes in enzyme expression. The prevention of hypertension by hydralazine blunted the increase in arginase activity in the hearts but not in the lungs. No change in arginase activity/expression was found in the kidney, liver or brain. In conclusion, this study shows that increased arginase activity is not restricted to large vessels in SHRs and suggests that cardiac arginase activity is hemodynamic sensitive.

Enhanced levels of mitochondrial enzyme 17β-hydroxysteroid dehydrogenase type 10 in patients with Alzheimer disease and multiple sclerosis

The multifunctional mitochondrial enzyme 17beta-hydroxysteroid dehydrogenase type 10 might play a role in the development of Alzheimer disease via its high-affinity binding to amyloid beta peptides and its neuronal over-expression. It is suggested that the cerebrospinal fluid levels of the enzyme, free or bound to amyloid beta peptides, are a potential specific biomarker of Alzheimer disease. However, mitochondrial dysfunction seems to play a role in many neurological diseases including multiple sclerosis. In this study, the specificity of changes in relation to the enzyme over-expression was evaluated using enzyme-linked immunosorbent and surface plasmon resonance sensors. The data indicated pronounced increases in the enzyme levels, specifically to 179% in multiple sclerosis and to 573% in Alzheimer disease when compared to the age-matched controls. Although the differences between both diseases were statistically significant, enzyme levels do not appear to be a highly specific biomarker of Alzheimer disease. On the other hand, enhancement in levels of the enzyme bound to amyloid beta peptides was only observed in people with Alzheimer disease, which suggests that the complex should be further considered as a possible biomarker. In patients with multiple sclerosis, our results are the first to demonstrate significant changes in enzyme expression and to suggest possible alterations in amyloid beta peptides.

Expression of Enzymes Involved in the Prostanoid Metabolism by Cortical Astrocytes after LPS-induced Inflammation

Neuroinflammatory processes are a common epiphenomenon for a number of neurological and neurodegenerative diseases. Besides microglia, astrocytes are implicated in brain inflammation in response to harmful stimuli and pathological processes. Bacterial endotoxins can induce the synthesis and release of proinflammatory mediators, i.e., cytokines and chemokines, by astroglia. In this study, we have investigated the effect of lipopolysaccharide (LPS) treatment on the expression of enzymes of prostanoid synthesis and degradation in cultured mouse cortical astrocytes using an Affymetrix Gene Chip array, quantitative reverse transcriptase polymerase chain reaction (RT-PCR), and an enzyme-immunosorbent assay. LPS treatment induced an upregulation of enzymes responsible for prostaglandin E2 synthesis, a downregulation of enzymes that catalyzes prostaglandin E2 (PGE2) degradation and production of proinflammatory leukotrienes. Changes in enzyme expression were accompanied by a highly significant increase in extracellular PGE2. Our data demonstrate that astrocytes are directly involved in the complex regulation of proinflammatory prostanoids in the CNS under pathological processes, thus being of potential interest as targets for therapeutical interventions. Further studies are required to unravel the different roles and interactions between astroglia and other cells of the brain-intrinsic innate immune system during inflammation.

Monocyte Differentiation, Activation, and Mycobacterial Killing Are Linked to Transsulfuration-dependent Redox Metabolism

Modulation of the ambient redox status by mononuclear phagocytes is central to their role in health and disease. However, little is known about the mechanism of redox regulation during mononuclear phagocyte differentiation and activation, critical cellular steps in innate immunity, and microbial clearance. An important intermediate in GSH-based redox metabolism is homocysteine, which can undergo transmethylation via methionine synthase (MS) or transsulfuration via cystathionine beta-synthase (CBS). The transsulfuration pathway generates cysteine, the limiting reagent in GSH biosynthesis. We now demonstrate that expression of CBS and MS are strongly induced during differentiation of human monocytes and are regulated at the transcriptional and posttranscriptional levels, respectively. The changes in enzyme expression are paralleled by an approximately 150% increase in S-adenosylmethionine (accompanied by a corresponding increase in phospholipid methylation) and a similar increase in GSH. Activation with lipopolysachharide or infection with Mycobacterium smegmatis diminished expression of both enzymes to a significant extent and decreased S-adenosylmethionine concentration by approximately 30% of the control value while GSH and cysteine concentrations increased approximately 100 and 300%, respectively. Blockade of the transsulfuration pathway with propargylglycine suppressed clearance of M. smegmatis by macrophages and inhibited phagolysosomal fusion, whereas N-acetylcysteine promoted phagolysosomal fusion and enhanced mycobacterial clearance 3-fold compared with untreated cells. We posit that regulation of the transsulfuration pathway during monocyte differentiation, activation, and infection can boost host defense against invading pathogens and may represent a heretofore unrecognized antimicrobial therapeutic target.

Up‐regulation of ectonucleotidase activity after cortical stab injury in rats

The objective of this study was to examine the changes in the activity and expression of ectonucleotidase enzymes in the model of unilateral cortical stab injury (CSI) in rat. The activities of ecto-nucleoside triphosphate diphosphohydrolase 1 (NTPDase 1) and ecto 5'-nucleotidase were assessed by measuring the levels of ATP, ADP and AMP hydrolysis in the crude membrane preparations obtained from injured left cortex, right cortex, left and right caudate nucleus, whole hippocampus and cerebellum. Significant increase in NTPDase and ecto 5'-nucleotidase activities was observed in the injured cortex following CSI, whereas in other brain areas only an increase in ecto 5'-nucleotidase activity was seen. Immunohistochemical analysis performed using antibodies specific to NTPDase 1 and ecto 5'-nucleotidase demonstrated that CSI induced significant changes in enzyme expression around the injury site. Immunoreactivity patterns obtained for NTPDase 1 and ecto 5'-nucleotidase were compared with those obtained for glial fibrillary acidic protein, as a marker of astrocytes and complement receptor type 3 (OX42), as a marker of microglia. Results suggest that up-regulation of ectonucleotidase after CSI is catalyzed by cells that activate in response to injury, i.e. cells immunopositive for NTPDase 1 were predominantly microglial cells, whereas cells immunopositive for ecto 5'-nucleotidase were predominantly astrocytes.

NOS expression and activity in cerebral resistance arteries: Effects of age and exercise training

We have previously shown that endothelium-dependent vasodilation to acetylcholine (ACh) is preserved in cerebral resistance arteries from aged rats; however, the role of specific isozymes of nitric oxide synthase (NOS) in mediating dilation to ACh changes with age and exercise training. In the present study, we investigated the effects of age and exercise training on expression and activity of NOS isoforms. Young (4 months) and old (24 months) male Fischer-344 rats underwent exercise training or remained sedentary for 10 weeks. Posterior communicating arteries (PCoA) were isolated for assessment of ACh-stimulated NO production and protein levels of NOS isozymes. ACh-stimulated NO production was similar in PCoA from young and old rats. Treatment with aminoguanidine, an inhibitor of iNOS significantly reduced NO production in PCoA from young but not old rats; however, iNOS protein was not detectable in PCoA from rats in any of the groups. Although protein levels for endothelial NOS (eNOS) and neuronal NOS (nNOS) were not altered by age or exercise training; calcium-free production of NO was significantly lower in PCoA from old rats. These data indicate that NOS activity differs in PCoA from young and old rats; however, alterations of NO production that occur with age and training are likely related to changes in NOS regulatory mechanisms rather than changes in enzyme expression.

7H-Dibenzo[ c, g]carbazole and 5,9-dimethyldibenzo[ c, g]carbazole exert multiple toxic events contributing to tumor promotion in rat liver epithelial ‘stem-like’ cells

Immature liver progenitor cells have been suggested to be an important target of hepatotoxins and hepatocarcinogens. The goal of the present study was to assess the impact of 7H-dibenzo[ c, g]carbazole (DBC) and its tissue-specific carcinogenic N-methyl ( N-MeDBC) and 5,9-dimethyl (DiMeDBC) derivatives on rat liver epithelial WB-F344 cells, in vitro model of liver progenitor cells. We investigated the cellular events associated with both tumor initiation and promotion, such as activation of aryl hydrocarbon receptor (AhR), changes in expression of enzymes involved in metabolic activation of DBC and its derivatives, effects on cell cycle, cell proliferation/apoptosis and inhibition of gap junctional intercellular communication (GJIC). N-MeDBC, a tissue-specific sarcomagen, was only a weak inhibitor of GJIC or inducer of AhR-mediated activity, and it did not affect either cell proliferation or apoptosis. DBC was efficient GJIC inhibitor, while DiMeDBC manifested the strongest AhR inducing activity. Accordingly, DiMeDBC was also the most potent inducer of cytochrome P450 1A1 (CYP1A1) and CYP1A2 expression among the three compounds tested. Both DBC and DiMeDBC induced expression of CYP1B1 and aldo-keto reductase 1C9 (AKR1C9). N-MeDBC failed to significantly upregulate CYP1A1/2 and it only moderately increased CYP1B1 or AKR1C9. Only the potent liver carcinogens, DBC and DiMeDBC, caused a significant increase of p53 phosphorylation at Ser15, an increased accumulation of cells in S-phase and apoptosis at micromolar concentrations. In addition, DiMeDBC was found to stimulate cell proliferation of contact-inhibited WB-F344 cells at 1 μM concentration, which is a mode of action that might further contribute to its hepatocarcinogenicity. The present data seem to suggest that the AhR activation, induction of enzymes involved in metabolic activation, inhibition of GJIC or stimulation of cell proliferation might all contribute to the hepatocarcinogenic effects of DBC and DiMeDBC.

Expression of mRNA for Inducible NO Synthase in Human Brain

We studied expression of inducible NO synthase gene in human brain under conditions of acute or chronic intoxication. Acute alcohol intoxication was accompanied by changes in enzyme expression in certain brain structures.

Combined Proteome and Metabolite-profiling Analyses Reveal Surprising Insights into Yeast Sulfur Metabolism

Metabolomics is considered as an emerging new tool for functional proteomics in the identification of new protein function or in projects aiming at modeling whole cell metabolism. When combined with proteome studies, metabolite-profiling analyses revealed unanticipated insights into the yeast sulfur pathway. In response to cadmium, the observed overproduction of glutathione, essential for the detoxification of the metal, can be entirely accounted for by a marked drop in sulfur-containing protein synthesis and a redirection of sulfur metabolite fluxes to the glutathione pathway. A kinetic analysis showed sequential and dramatic changes in intermediate sulfur metabolite pools within the first hours of the treatment. Strikingly, whereas proteome and metabolic data were positively correlated under cadmium conditions, proteome and metabolic data were negatively correlated during other growth conditions, i.e. methionine supplementation or sulfate starvation. These differences can be explained by alternative mechanisms in the regulation of Met4, the activator of the sulfur pathway. Whereas Met4 activity is controlled by the cellular cysteine content in response to sulfur source and availability, the present study suggests that Met4 activation under cadmium conditions is cysteine-independent. The results clearly indicate that the metabolic state of a cell cannot be safely predicted based solely on proteomic and/or gene expression data. Combined metabolome and proteome studies are necessary to draw a comprehensive and integrated view of cell metabolism.

Biogeochemical signatures through time as inferred from whole microbial genomes

Throughout geologic time, a strong feedback has existed between the geosphere and the biosphere; therefore biological evolution and innovation can be linked to the evolution of ancient environments on Earth. Here we deduce geochemi- cal signatures and phylogenetic relationships of prokaryotes from whole genome sequences and use this link to infer geochemical aspects of the biosphere through time. In particular, we have investigated two potential biosignatures for modern and ancient biochemistry: the magnitude of microbial carbon isotopic fractionation, and the use of metals in microbial cells. The distribution of carbon fixation pathways on microbial phylogenies suggests that: (1) both low and moderate carbon isotope fractionation were established quickly in the early evolution of life; and (2) methanotrophic and ethanotrophic metabolisms capable of producing biomass with extreme 13 C depletions are not primitive, but rather evolved after the major groups of Prokaryotes had already diverged. The universal importance of the TCA cycle, which results in low carbon isotopic fractionation, indicates it may have evolved especially early making it perhaps the most likely carbon fixation pathway for the last common ancestor (LCA). Low isotopic fractionation by the reductive TCA cycle can be considered consistent with carbon isotope ratios found in 3,800 million year old Isua sediments. Additionally, moderately fractionated biomass from up to 3,500 million years ago can now likely be attributed to carbon fixation by anoxygenic photoautotrophs using the reductive pentose phosphate cycle (Calvin cycle). In addition to carbon, cells require a number of other elements that could potentially provide biosignatures, including bioactive trace metals. We calculated for 52 prokaryotes based on the number of atoms of trace metals required to express one molecule of each metallo-enzyme coded for in the correspond- ing genomes. Our results suggest that the use of metals in prokaryotes as a group generally follows the hierarchy: Fe Zn > Mn Mo, Co, Cu Ni > W, V. However, model metallomes vary with metabolism, oxygen tolerance, optimum growth tempera- ture, and phylogeny. The model metallome of methanogens shows a unique metal signature, suggesting that elevated requirements of nickel and tungsten might be translated to the expressed metallome providing a biosignature for methanogenesis. The model metallomes of diazotrophs and cyanobacteria do not show unique signa- tures; however changes in enzyme expression under some conditions could still translate into a metal biosignature in the expressed cellular metal content. In a separate analysis, we made inferences about the timing of the evolution of individual metallo-enzymes based on their function and occurrence in modern organ- isms. The results suggest that fluctuations in the redox state of the Earth's oceans and atmosphere have forced changes in the proportions of metals used in biology. In this model, biological use of copper and molybdenum has developed along with bioavail- ability; biological use of iron and manganese has developed counter to bioavailability; and biological use of zinc, cobalt, and nickel has not changed significantly through time. Using this technique, we estimated a model metallome for the LCA based on the metallo-enzymes we infer to have been present at that time. This metallome for the LCA differs greatly from one extrapolated from the distribution of model metallomes on microbial phylogenies, supporting the idea that gene loss, metal substitution, and lateral gene transfer have been important in shaping the enzymatic composition of extant organisms.