Intestinal Microbiota Regulate Xenobiotic Metabolism in the Liver

Background

The liver is the central organ for xenobiotic metabolism (XM) and is regulated by nuclear receptors such as CAR and PXR, which control the metabolism of drugs. Here we report that gut microbiota influences liver gene expression and alters xenobiotic metabolism in animals exposed to barbiturates.

Principal findings

By comparing hepatic gene expression on microarrays from germfree (GF) and conventionally-raised mice (SPF), we identified a cluster of 112 differentially expressed target genes predominantly connected to xenobiotic metabolism and pathways inhibiting RXR function. These findings were functionally validated by exposing GF and SPF mice to pentobarbital which confirmed that xenobiotic metabolism in GF mice is significantly more efficient (shorter time of anesthesia) when compared to the SPF group.

Conclusion

Our data demonstrate that gut microbiota modulates hepatic gene expression and function by altering its xenobiotic response to drugs without direct contact with the liver.     

High-Throughput Multiplex Single-Nucleotide Polymorphism (SNP) Analysis in Genes Involved in Methionine Metabolism

Hyperhomocysteinemia is a well-known independent marker factor for atherothrombotic diseases and may result from acquired and genetic influences. Several polymorphisms are suspected to be associated with hyperhomocysteinemia, but data are limited and inconsistent. High-throughput genotyping technologies, such as GenomeLab SNPStream, are now available. Moreover, an appropriate selection of SNPs to be analyzed could represent a strong resource to define the role of genetic risk factors. We developed a multiplex PCR-oligonucleotide extension approach by GenomeLab platform. We selected 72 SNPs based on their putative function and frequency in the candidate genes AHCY, BHMT, BHMT2, CBS, ENOSF1, FOLH1, MTHFD1, MTHFR, MTR, MTRR, NNMT, PON1, PON2, SLC19A1, SHMT1, TCN2, and TYMS. We were able to analyze 57 of the SNPs (79%). For MTHFR C677T and A1298C and MTR A2756G SNPs, we compared data obtained with an electronic microchip technology and found 99.2% concordance. We also performed a haplotype analysis. This approach could represent a useful tool to investigate the genotype-phenotype correlation and the association of these genes with hyperhomocysteinemia and correlated diseases.     

Conjugating Enzymes Involved in Xenobiotic Metabolism of Organic Xenobiotics in Plants

Phytoremediation of organic pollutants has become a topic of great interest in many countries due to the increasing number of recorded spill sites. When applying plant remediation techniques to unknown pollutant mixtures, information on the uptake rates as well as on the final fate of the compounds is generally lacking. A range of compounds are easily taken up by plants, whereas others may stay motionless and recalcitrant in the soil or sediment. Uptake is a necessary prerequisite for close contact between the pollutant and the detoxifying enzymes of plants that are localized in the cytosol of living cells. The presence and activity of these enzymes is crucial for a potential metabolization and further degradation of the chemicals under consideration. Conjugation to biomolecules is regarded as a beneficial detoxification reaction. The present review summarizes several prerequisites for pollutant uptake and discusses information on conjugating detoxification reactions. The final fate of compounds is critically discussed and perspectives for phytoremediation are given.     

Polymorphism in Genes That Influence Sperm Displacement

Paternity of offspring of multiply inseminated females is in many organisms highly skewed, with an advantage generally going to the male that most recently mated. Variation in sperm competitive ability can result in strong natural selection, and one expects that a gene that offers an advantage in sperm displacement would, all else being equal, be rapidly fixed, leaving low equilibrium levels of variability in sperm competition. However, empirical studies have demonstrated genetic variation in sperm displacement, begging the question of how this variation can be maintained. Here we develop a population genetic model to find conditions that maintain polymorphism in alleles that influence sperm displacement. We consider a one-locus model in which allelic variants have pleiotropic effects on fecundity and mating ability in addition to sperm displacement. This model can admit more than one stable polymorphism, and we find conditions for protected polymorphism. Induced overdominance is not necessary for stable polymorphism. These results have direct bearing on the observed variation in the ability of resident sperm to defend against displacement.     

Rapid Birth–Death Evolution Specific to Xenobiotic Cytochrome P450 Genes in Vertebrates

Genes vary greatly in their long-term phylogenetic stability and there exists no general explanation for these differences. The cytochrome P450 (CYP450) gene superfamily is well suited to investigating this problem because it is large and well studied, and it includes both stable and unstable genes. CYP450 genes encode oxidase enzymes that function in metabolism of endogenous small molecules and in detoxification of xenobiotic compounds. Both types of enzymes have been intensively studied. My analysis of ten nearly complete vertebrate genomes indicates that each genome contains 50–80 CYP450 genes, which are about evenly divided between phylogenetically stable and unstable genes. The stable genes are characterized by few or no gene duplications or losses in species ranging from bony fish to mammals, whereas unstable genes are characterized by frequent gene duplications and losses (birth–death evolution) even among closely related species. All of the CYP450 genes that encode enzymes with known endogenous substrates are phylogenetically stable. In contrast, most of the unstable genes encode enzymes that function as xenobiotic detoxifiers. Nearly all unstable CYP450 genes in the mouse and human genomes reside in a few dense gene clusters, forming unstable gene islands that arose by recurrent local gene duplication. Evidence for positive selection in amino acid sequence is restricted to these unstable CYP450 genes, and sites of selection are associated with substrate-binding regions in the protein structure. These results can be explained by a general model in which phylogenetically stable genes have core functions in development and physiology, whereas unstable genes have accessory functions associated with unstable environmental interactions such as toxin and pathogen exposure. Unstable gene islands in vertebrates share some functional properties with bacterial genomic islands, though they arise by local gene duplication rather than horizontal gene transfer.     

Expression of Xenobiotic Metabolizing Cytochrome P450 Genes in a Spinosad-Resistant Musca domestica L. Strain

Background

Spinosad is important in pest management strategies of multiple insect pests. However, spinosad resistance is emerging in various pest species. Resistance has in some species been associated with alterations of the target-site receptor, but in others P450s seems to be involved. We test the possible importance of nine cytochrome P450 genes in the spinosad-resistant housefly strain 791spin and investigate the influence of spinosad on P450 expression in four other housefly strains.

Results

Significant differences in P450 expression of the nine P450 genes in the four strains after spinosad treatment were identified in 40% of cases, most of these as induction. The highly expressed CYP4G2 was induced 6.6-fold in the insecticide susceptible WHO-SRS females, but decreased 2-fold in resistant 791spin males. CYP6G4 was constitutively higher expressed in the resistant strain compared to the susceptible strain. Furthermore, CYP6G4 gene expression was increased in susceptible WHO-SRS flies by spinosad while the expression level did not alter significantly in resistant fly strains. Expression of CYP6A1 and male CYP6D3 was constitutively higher in the resistant strain compared to the susceptible. However, in both cases male expression was higher than female expression.

Conclusion

CYP4G2, CYP6A1, CYP6D3 and CYP6G4 have expressions patterns approaching the expectations of a hypothesized sex specific spinosad resistance gene. CYP4G2 fit requirements of a spinosad resistance gene best, making it the most likely candidate. The overall high expression level of CYP4G2 throughout the strains also indicates importance of this gene. However, the data on 791spin are not conclusive concerning spinosad resistance and small contributions from multiple P450s with different enzymatic capabilities could be speculated to do the job in 791spin. Differential expression of P450s between sexes is more a rule than an exception. Noteworthy differences between spinosad influenced expression of P450 genes between a field population and established laboratory strains were shown.     

Polymorphism of the Serotonin System Genes in Some Finno-Ugric Populations

Polymorphic sites in the genes encoding monoamine oxidase A (MAO-A), serotonin transporter (hSERT) and 5-HT_2A receptor were typed in Khant and Komi ethnic groups with the purpose of revealing possible inerpopulation differences in genotype and allele frequencies. No statistically significant differences in the hSERT and 5-HT_2A gene frequencies were detected. At the same time, the populations examined had statistically significantly different MAO-A genotype and allele frequencies. These results obtained indicate the prevalence of the site gain alleles of theEcoRV and Fnu4HI RFLP loci at the MAO-A gene in Komis and the of the corresponding site loss alleles in Khants.     

Natural Polymorphism of Pectinase PGU Genes in the Saccharomyces Yeasts

Microbiology - The distribution and properties of the pectinase-encoding PGU genes in different species of Saccharomyces yeasts was studied. Application of molecular karyotyping and Southern...     

Rb and p53 Liver Functions Are Essential for Xenobiotic Metabolism and Tumor Suppression

The tumor suppressors Retinoblastoma (Rb) and p53 are frequently inactivated in liver diseases, such as hepatocellular carcinomas (HCC) or infections with Hepatitis B or C viruses. Here, we discovered a novel role for Rb and p53 in xenobiotic metabolism, which represent a key function of the liver for metabolizing therapeutic drugs or toxins. We demonstrate that Rb and p53 cooperate to metabolize the xenobiotic 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC). DDC is metabolized mainly by cytochrome P450 (Cyp)3a enzymes resulting in inhibition of heme synthesis and accumulation of protoporphyrin, an intermediate of heme pathway. Protoporphyrin accumulation causes bile injury and ductular reaction. We show that loss of Rb and p53 resulted in reduced Cyp3a expression decreased accumulation of protoporphyrin and consequently less ductular reaction in livers of mice fed with DDC for 3 weeks. These findings provide strong evidence that synergistic functions of Rb and p53 are essential for metabolism of DDC. Because Rb and p53 functions are frequently disabled in liver diseases, our results suggest that liver patients might have altered ability to remove toxins or properly metabolize therapeutic drugs. Strikingly the reduced biliary injury towards the oxidative stress inducer DCC was accompanied by enhanced hepatocellular injury and formation of HCCs in Rb and p53 deficient livers. The increase in hepatocellular injury might be related to reduce protoporphyrin accumulation, because protoporphrin is well known for its anti-oxidative activity. Furthermore our results indicate that Rb and p53 not only function as tumor suppressors in response to carcinogenic injury, but also in response to non-carcinogenic injury such as DDC.     

Xenobiotic metabolism in helminths

During its life cycle a parasite, like mammals and other organisms, comes into contact with a variety of toxic molecules. In mammals the main line of defence against such compounds is a group of oxidative enzymes that occur predominantly in the liver. Many of these oxidations are dependent on the haemoprotein cytochrome P-450 which serves as a terminal oxidase accepting electrons from NADPH and cytochrome [Formula: see text] . This review by Wendy Precious and John Barrett illustrates that in contrast to mammals, xenobiotic metabolism in both parasitic and free-living platyhelminths and nematodes is predominantly reductive and hydrolytic as the cytochrome P-450 system is absent. This is surprising since it is present in many groups including bacteria, fungi and protozoa, which suggests an ancient origin. The absence of the cytochrome P-450 system not only severely limits the ability of helminths to detoxify compounds but also limits their ability to activate prodrugs.     

Xenobiotic metabolism in bivalves

Xenobiotic metabolism is the aim of many studies concerning the development of pollution biomarkers. Enzymatic pathways of this metabolism in bivalves are similar to those previously described in vertebrates, each of them showing their own biochemical characteristics and sometimes specific mechanisms. Laboratory or in-situ induction experiments frequently lead to delicate interpretations. The analysis of these results displays a tendency for the induction of P-450 activities by hydrocarbons in marine bivalves, and a proportional induction of xenobiotic membranar elimination mechanisms to the level of in-situ pollution in Mytilus galloprovincialis. This synthesis confirms the possible use of enzymatic activities from xenobiotic metabolism as pollution biomarkers in bivalves. The lack of fundamental data and the low number of in-situ studies have prevented, until now, the establishment of a systematic correlation between an enzymatic behaviour and a level of pollution.     

DNA Polymorphism of Drosophila Genes and Factors Determining It

The data on variation of DNA sequences in genes of Drosophilidae are reviewed. Intraspecific polymorphism and interspecific divergence of DNA nucleotide sequences are shown to be characteristic of most genes. The level of intraspecific polymorphism and interspecific DNA divergence and the degree of correlation between them depend on the mode, intensity, and direction of natural selection, as well as on the evolutionary history of the genes and species. The evolutionary role of synonymous and nonsynonymous nucleotide substitutions in DNA is analyzed. Genes responsible for the reproduction and genes controlling other functions are compared in respect to their variation.     

蚯蚓纤溶酶组分及其基因的多态性

生化制备证明,蚯蚓纤溶酶为一组含有10个以上同工酶组分的混合酶.为了研究这些组分的DNA和蛋白质序列的异同,本文通过对数据库中已报道的28条蚯蚓纤溶酶基因按相似性进行归类,将它们分为4组(基因型).同一组中的序列具有共同特征,即保守的N-末端、C-末端和相同的结构域,而且这些结构域在序列中分布的位置也相同;但它们之间在中间部分存在明显差异,这些差异说明了基因型中存在多态性.这种多态性可能是它们在体内溶栓的药理药效作用存在差异的结构基础.     

Absence of Protein Polymorphism in the Ras Genes of Drosophila melanogaster

Sequence analysis of 27 alleles of each of the three Ras-related genes in Drosophila melanogaster indicates that they all have low levels of polymorphism but may experience slightly different evolutionary pressures. No amino acid replacement substitutions were indicated in any of the sequences, or in the sibling species D. simulans and D. mauritiana. The Dras1 gene, which is the major ras homologue in Drosophila, has less within-species variation in D. melanogaster relative to the amount of divergence from the sibling species than does Dras2, although the contrast was not significant by the HKA test. Dras2 appears to be maintaining two classes of haplotype in D. melanogaster, one of which is closer to the alleles observed in the sibling species, suggesting that this is not likely to be a pseudogene despite the absence of a mutant phenotype. Although differences in level of expression may affect the function of the genes, it is concluded that genetic variation in the Ras signal transduction pathways cannot be attributed to catalytic variation in the Ras proteins. Received: 5 November 1998 / Accepted: 26 March 1999     

S－美芬妥英羟化代谢多态性的分子机制研究进展

人群中存在着Ｓ－美芬妥英羟化代谢多态性。从人肝微粒体已分离出Ｓ－美芬妥英羟化酶。在基因克隆研究中已分离出与该羟化酶活性有关的Ｐ４５０ｃＤＮＡ,属Ｐ４５０２Ｃ１９。最近报道,人肝中Ｐ４５０２Ｃ１９的含量和催活Ｓ－美芬妥英羟化活性密切相关,其弱代谢者主要由于ＣＹＰ２Ｃ１９的外显子５单碱基对（Ｇ→Ａ）的变异,使核苷酸序列错位而产生无功能的Ｐ４５０蛋白的结果。     

Three Signatures of Adaptive Polymorphism Exemplified by Malaria-Associated Genes

Malaria has been one of the strongest selective pressures on our species. Many of the best-characterized cases of adaptive evolution in humans are in genes tied to malaria resistance. However, the complex evolutionary patterns at these genes are poorly captured by standard scans for nonneutral evolution. Here, we present three new statistical tests for selection based on population genetic patterns that are observed more than once among key malaria resistance loci. We assess these tests using forward-time evolutionary simulations and apply them to global whole-genome sequencing data from humans, and thus we show that they are effective at distinguishing selection from neutrality. Each test captures a distinct evolutionary pattern, here called Divergent Haplotypes, Repeated Shifts, and Arrested Sweeps, associated with a particular period of human prehistory. We clarify the selective signatures at known malaria-relevant genes and identify additional genes showing similar adaptive evolutionary patterns. Among our top outliers, we see a particular enrichment for genes involved in erythropoiesis and for genes previously associated with malaria resistance, consistent with a major role for malaria in shaping these patterns of genetic diversity. Polymorphisms at these genes are likely to impact resistance to malaria infection and contribute to ongoing host–parasite coevolutionary dynamics.     

Sequence Polymorphism and Evolution of Three Cetacean MHC Genes

Sequence variability at three major histocompatibility complex (MHC) genes (DQB, DRA, and MHC-I) of cetaceans was investigated in order to get an overall understanding of cetacean MHC evolution. Little sequence variation was detected at the DRA locus, while extensive and considerable variability were found at the MHC-I and DQB loci. Phylogenetic reconstruction and sequence comparison revealed extensive sharing of identical MHC alleles among different species at the three MHC loci examined. Comparisons of phylogenetic trees for these MHC loci with the trees reconstructed only based on non-PBR sites revealed that allelic similarity/identity possibly reflected common ancestry and were not due to adaptive convergence. At the same time, trans-species evolution was also evidenced that the allelic diversity of the three MHC loci clearly pre-dated species divergence events according to the relaxed molecular clock. It may be the forces of balancing selection acting to maintain the high sequence variability and identical alleles in trans-specific manner at the MHC-I and DQB loci.