Structure and evolution of the apolipoprotein multigene family

We present the complementary DNA and deduced amino acid sequence of rat apolipoprotein A-II (apoA-II), and the results of a detailed statistical analysis of the nucleotide and amino acid sequences of all the apolipoprotein gene sequences published to date: namely, those of human and rat apoA-I, apoA-II and apoE, rat apoA-IV, and human apoC-I, C-II and C-III. Our results indicate that the apolipoprotein genes have very similar genomic structures, each having a total of three introns at the same locations. Using the exon/intron junctions as reference points, we have obtained an alignment of the coding regions of all the genes studied. It appears that the mature peptide regions of these genes are almost completely made up of tandem repeats of 11 codons. The part of mature peptide region encoded by exon 3 contains a common block of 33 codons, whereas the part encoded by exon 4 contains a much more variable number of internal repeats of 11 codons. These genes have apparently evolved from a primordial gene through multiple partial (internal) and complete gene duplications. On the basis of the degree of homology of the various sequences, and the pattern of the internal repeats in these genes, we propose an evolutionary tree for the apolipoprotein genes and give rough estimates of the divergence times between these genes. Our results show that apoA-II has evolved extremely rapidly and that apoA-I and apoE also have evolved at high rates but some regions are better conserved than the others. The rate of evolution of individual regions seems to be related to the stringency of their functional requirements.     

The paraoxonase gene family and atherosclerosis

Epidemiologic, genetic, and biochemical studies support an antiatherogenic role for paraoxonase (PON) 1. While the precise mechanism by which PON1 protects against the development of atherosclerosis is unclear, in vitro studies and the results from PON1 knockout and transgenic mice suggest that this protective effect may be attributed to PON1's ability to attenuate the oxidative modification of lipoprotein particles. The two other members of the PON gene family, namely, PON2 and PON3, have also been reported to possess antioxidant properties and may exhibit antiatherogenic capacities as well. Previous studies have demonstrated that PON1 expression is downregulated by oxidative stress. In contrast, more recent studies have shown that PON2 expression is upregulated in response to oxidative stress-inducing agents, while PON3 expression remains unchanged. While the physiological function of these proteins is unknown, studies currently underway using PON2 and PON3 knockout and transgenic mice should enable us to tease out the apparently redundant functions of these three proteins and yield clues as to their physiological function as well as their role in atherogenesis.     

Antioxidant and detoxifying fish enzymes as biomarkers of river pollution

The activity of several antioxidant and detoxifying enzymes, superoxide dismutase SOD , GSH peroxidase GSHPx , GSSG reductase GSR and GSH S transferase GST , the contents of thiobarbituric acid reactive substances TBARS , and the SOD and GST isoenzyme patterns were studied in the livers of chubs Leuciscus cephalus from reference river areas and polluted urban sites. Livers of polluted fish contained higher concentrations of transition metals, especially copper and iron. Total GSHPx activity was 1.8 fold higher in the polluted fish than in reference animals, while the SOD and GSR activities and the TBARS content were not significantly changed. Three new SOD isoforms pI 4.45, 5.1, 5.2 and a higher intensity of the band pI 4.2 were observed after isoelectrofocusing of polluted fish extracts. Total GST activity was higher in fish from polluted areas. The GST isoenzyme pattern was studied using subunit specific substrates DCNB, EPNP, EA, NPB, NBC and by Western blot using antibodies specific to rat GST subunits 1, 8 Alpha class , 3 Mu class and 7 Pi class . Reference and polluted fish lacked cross reactivity towards Alpha class GSTs. Reference fish displayed weaker cross reactivity towards CST 7 and 2.3 fold lower activity with EA, while higher cross reaction with GST 3 was observed in polluted fish.     

Novel family shuffling methods for the in vitro evolution of enzymes.

It has recently been shown that shuffling of the amino acid sequences of family enzymes allows the generation of improved enzymes. Family shuffling is generally achieved by a DNase I treatment and then by PCR. Shuffling of the xylE and nahH genes, both encoding catechol 2,3-dioxygenases, was carried out by the published method. However, nahH-xylE hybrids were only formed at a very low frequency (less than 1%). Therefore, we developed improved methods for family shuffling by which DNA was cleaved by restriction enzymes instead of by DNase I. With the first improved method, five nahH fragments and five xylE fragments that had been generated by restriction enzyme digestion were subjected to the PCR reactions in two steps, the first being without a primer and the second with a set of primers. This method enabled nahH-xylE hybrid genes to be formed at a high frequency (almost 100%). With the second improved method, nahH and xylE were cleaved by several sets of restriction enzymes, and these digests were then reassembled in two steps. The nahH and xylE DNAs were each cleaved by two (or three) sets of restriction enzymes, and one type of nahH digest and one type of xylE digest were mixed, thus making four (or nine) different mixtures of the nahH and xylE digests. These mixtures were used as templates to carry out PCR without a primer. After the first PCR reaction, all the mixtures were combined, and a second PCR reaction was carried out without a primer. Following these two PCR assembly steps, a third PCR reaction was carried out with two primers to amplify the full-length nahH-xylE hybrid genes. This second method also yielded nahH-xylE hybrids at a frequency of 100%. The degree of recombination of the products with the second method was higher than that with the first method. These methods were used to isolate catechol 2,3-dioxygenases exhibiting relatively high stability at high temperature, one of them being respectively 13- and 26-fold more thermostable than XylE and NahH at 50 degrees C.     

Structure and evolution of the Cinful retrotransposon family of maize.

A maize cDNA clone was isolated by virtue of its intense hybridization to total maize genomic DNA, indicating homology to highly repetitive sequences. Genomic homologues were identified and subcloned from an adh1-bearing maize yeast artificial chromosome (YAC). Sequencing revealed that the expressed sequence was part of a Ty3-gypsy-type retrotransposon. We discovered and sequenced two complete retrotransposons of this family, and named them Cinful elements because they are members of a family of maize retrotransposons including Zeon-1 and the first plant transposable element sequenced, the solo long terminal repeat (LTR) called Cin1. All are defective, as Cinful-1 and Cinful-2 elements lack gag and Zeon-1 lacks pol homology. Despite the apparent lack of an intact "autonomous" element, the Cinful family has expanded to a copy number of about 18 000, representing just under 9% of the maize genome. Both point mutations and major rearrangements, including possible gene acquisition, differentiate members of the Cinful family. Cinful family members were found to have an unusual feature that we also observed in two other Ty3-class retrotransposons of teosinte and tobacco: related tandem repeats that separate their internal domains with a gag- or pol-containing homology from a 3' segment of unknown function. The conserved and variable features identified provide insights into the origin, mutational history, and functional components of this major constituent of the maize genome.     

Antioxidant and detoxifying fish enzymes as biomarkers of river pollution

The activity of several antioxidant and detoxifying enzymes, superoxide dismutase SOD, GSH peroxidase GSHPx, GSSG reductase GSR and GSH S transferase GST, the contents of thiobarbituric acid reactive substances TBARS, and the SOD and GST isoenzyme patterns were studied in the livers of chubs Leuciscus cephalus from reference river areas and polluted urban sites. Livers of polluted fish contained higher concentrations of transition metals, especially copper and iron. Total GSHPx activity was 1.8 fold higher in the polluted fish than in reference animals, while the SOD and GSR activities and the TBARS content were not significantly changed. Three new SOD isoforms pI 4.45, 5.1, 5.2 and a higher intensity of the band pI 4.2 were observed after isoelectrofocusing of polluted fish extracts. Total GST activity was higher in fish from polluted areas. The GST isoenzyme pattern was studied using subunit specific substrates DCNB, EPNP, EA, NPB, NBC and by Western blot using antibodies specific to rat GST subunits 1, 8 Alpha class, 3 Mu class and 7 Pi class. Reference and polluted fish lacked cross reactivity towards Alpha class GSTs. Reference fish displayed weaker cross reactivity towards CST 7 and 2.3 fold lower activity with EA, while higher cross reaction with GST 3 was observed in polluted fish.     

Forced evolution of a herbicide detoxifying glutathione transferase

Plant Tau class glutathione transferases (GSTUs) detoxify diphenylether herbicides such as fluorodifen, determining their selectivity in crops and weeds. Using reconstructive PCR, a series of mutant GSTUs were generated from in vitro recombination and mutagenesis of the maize sequences ZmGSTU1 and ZmGSTU2 (with the prefix Zm designating Zea mays L.). A screen of 5000 mutant GSTUs identified seven enzymes with enhanced fluorodifen detoxifying activity. The best performing enhanced fluorodifen detoxifying mutant (EFD) had activity 19-fold higher than the parent enzymes, with a single point mutation conferring this enhancement. Further mutagenesis of this residue generated an EFD with a 29-fold higher catalytic efficiency toward fluorodifen as compared with the parents but with unaltered catalysis toward other substrates. When expressed in Arabidopsis thaliana, the optimized EFD, but not the parent enzymes, conferred enhanced tolerance to fluorodifen. Molecular modeling predicts that the serendipitous mutation giving the improvement in detoxification is due to the removal of an unfavorable interaction together with the introduction of a favorable change in conformation of residues 107-119, which contribute to herbicide binding.     

The paraoxonase gene family and coronary heart disease

PURPOSE OF REVIEW: The antioxidant activity of high-density lipoprotein is largely due to the paraoxonase 1 located on it. Experiments with transgenic paraoxonase 1 knock-out mice indicate the potential for this enzyme to protect against atherogenesis. This effect of high-density lipoprotein in decreasing low-density lipoprotein lipid peroxidation is maintained for longer than that of antioxidant vitamins and could thus be more protective. Several important advances in the field of paraoxonase research have occurred during this review period, not least the discovery that two other members of the paraoxonase gene family, PON2 and PON3, may also have important antioxidant properties. Significant advances have been made in understanding the basic biochemical function of paraoxonase 1 and the discovery of possible modulators of its activity. RECENT FINDINGS: Decreased coronary heart disease risk associated with polymorphisms of paraoxonase 1, which are most active in lipid peroxide hydrolysis, as revealed by meta-analysis is likely to be an underestimate of the true contribution of paraoxonase 1 to coronary heart disease because these polymorphisms explain only a small component of the variation in paraoxonase 1 activity. It is a very important observation, however, because genetic influences are not likely to be confounded by other factors linked with both coronary heart disease and diminished paraoxonase 1 activity. SUMMARY: Although advances have been made in research into the paraoxonase family and atherosclerosis, much more needs to be done. Paraoxonase 1 is much the most extensively researched and strategies will hopefully emerge to increase its activity and provide a more satisfactory test of the antioxidant hypothesis of atherosclerosis than antioxidant vitamins have done.     

Purification of rabbit and human serum paraoxonase.

Rabbit serum paraoxonase/arylesterase has been purified to homogeneity by Cibacron Blue-agarose chromatography, gel filtration, DEAE-Trisacryl M chromatography, and preparative SDS gel electrophoresis. Renaturation (Copeland et al., 1982) and activity staining of the enzyme resolved by SDS gel electrophoresis allowed for identification and purification of paraoxonase. Two bands of active enzyme were purified by this procedure (35,000 and 38,000). Enzyme electroeluted from the preparative gels was reanalyzed by analytical SDS gel electrophoresis, and two higher molecular weight bands (43,000 and 48,000) were observed in addition to the original bands. This suggested that repeat electrophoresis resulted in an unfolding or other modification and slower migration of some of the purified protein. The lower mobility bands stained weakly for paraoxonase activity in preparative gels. Bands of each molecular weight species were electroblotted onto PVDF membranes and sequenced. The gas-phase sequence analysis showed that both the active bands and apparent molecular weight bands had identical amino-terminal sequences. Amino acid analysis of the four electrophoretic components from PVDF membranes also indicated compositional similarity. The amino-terminal sequences are typical of the leader sequences of secreted proteins. Human serum paraoxonase was purified by a similar procedure, and ten residues of the amino terminus were sequenced by gas-phase procedures. One amino acid difference between the first ten residues of human and rabbit was observed.     

Insect fungal symbionts: A promising source of detoxifying enzymes

Summary Many species of insects cultivate, inoculate, or contain symbiotic fungi. Insects feed on plant materials that contain plant-produced defensive toxins, or are exposed to insecticides or other pesticides when they become economically important pests. Therefore, it is likely that the symbiotic fungi are also exposed to these toxins and may actually contribute to detoxification of these compounds. Fungi associated with bark beetles, ambrosia beetles, termites, leaf-cutting ants, long-horned beetles, wood wasps, and drug store beetles can variously metabolize/detoxify tannins, lignins, terpenes, esters, chlorinated hydrocarbons, and other toxins. The fungi (Attamyces) cultivated by the ants and the yeast (Symbiotaphrina) contained in the cigarette beetle gut appear to have broad-spectrum detoxifying abilities. The present limiting factor for using many of these fungi for large scale detoxification of, for example, contaminated soils or agricultural commodities is their slow growth rate, but conventional strain selection techniques or biotechnological approaches should overcome this problem.Presented at the Symposium on Fungal Detoxification at the 48th Annual Meeting of the Society for Industrial Microbiology, Philadelphia, PA, August 4–9, 1991.     

乙基多杀菌素抗性小菜蛾代谢解毒酶酶活性研究

【目的】阐明小菜蛾Plutella xylostella(L.)对乙基多杀菌素的代谢抗性机理,为延缓小菜蛾对乙基多杀菌素抗药性发展及抗性治理技术提供支持。【方法】通过酶动力学方法测定了小菜蛾对乙基多杀菌素高抗、中抗和敏感种群的谷胱甘肽-S-转移酶、羧酸酯酶、乙酰胆碱酯酶和多功能氧化酶4种代谢解毒酶的比活力。【结果】乙基多杀菌素高抗小菜蛾种群的谷胱甘肽-S-转移酶、羧酸酯酶、乙酰胆碱酯酶的比活力分别为15.38、3.15和7.30 OD·min~(-1)·mg~(-1)pro,显著高于敏感种群;但乙酰胆碱酯酶在中抗种群和敏感种群中比活力差异不显著;多功能氧化酶在高抗、中抗和敏感种群中的比活力分别为4.97、4.08和4.23 OD·min~(-1)·mg~(-1)pro,差异不显著。【结论】谷胱甘肽-S-转移酶、羧酸酯酶和乙酰胆碱酯酶的酶活随着小菜蛾对乙基多杀菌素抗性的增强而增强,而多功能氧化酶的酶活在抗性种群与敏感种群间差异不显著,因此小菜蛾对乙基多杀菌素的代谢抗性机理研究应重点关注这3种酶。     

Structure and evolution of the plant cation diffusion facilitator family of ion transporters

Background  

Members of the cation diffusion facilitator (CDF) family are integral membrane divalent cation transporters that transport metal ions out of the cytoplasm either into the extracellular space or into internal compartments such as the vacuole. The spectrum of cations known to be transported by proteins of the CDF family include Zn, Fe, Co, Cd, and Mn. Members of this family have been identified in prokaryotes, eukaryotes, and archaea, and in sequenced plant genomes. CDF families range in size from nine members in Selaginella moellendorffii to 19 members in Populus trichocarpa. Phylogenetic analysis suggests that the CDF family has expanded within plants, but a definitive plant CDF family phylogeny has not been constructed.     

Role of pro-oxidant properties of flavonoids in the induction of detoxifying enzymes gene expression

Flavonoids are one of the most important components of human daily diet. In recent years flavonoids have became the subject of extensive investigations mostly due to their heath-promoting properties. Beneficial health effects of flavonoids are mainly ascribed to their antioxidant activity. However, there is increasing evidence of the positive role of pro-oxidant properties of flavonoids, considered previously as highly unfavorable, through the induction of detoxifying enzymes gene expression. The article discusses recent reports on the EpRE-mediated induction of NQO1 (NAD(P)H: quinone oxidoreductase) gene expression by the flavonoids (flavonols, flavones and flavan-3-oles) and the role of pro-oxidant properties of the flavonoids in the mechanism of this induction.     

Determinants of variation in human serum paraoxonase activity

Paraoxonase-1 (PON1) is associated with high-density lipoprotein (HDL) particles and is believed to contribute to antiatherogenic properties of HDLs. We assessed the determinants of PON1 activity variation using different substrates of the enzyme. PON1 activity in serum samples from 922 participants in the San Antonio Family Heart Study was assayed using a reliable microplate format with three substrates: paraoxon, phenyl acetate and the lactone dihydrocoumarin. There were major differences among results from the three substrates in degree of effect by various environmental and genetic factors, suggesting that knowledge of one substrate activity alone may not provide a complete sense of PON1 metabolism. Three significant demographic covariates (age, smoking status and contraceptive usage) together explained 1-6% of phenotypic variance, whereas four metabolic covariates representing lipoprotein metabolism (apoAII, apoAI, triglycerides and non-HDL cholesterol) explained 4-19%. Genes explained 65-92% of phenotypic variance and the dominant genetic effect was exerted by a locus mapping at or near the protein structural locus (PON1) on chromosome 7. Additional genes influencing PON1 activity were localized to chromosomes 3 and 14. Our study identified environmental and genetic determinants of PON1 activity that accounted for 88-97% of total phenotypic variance, suggesting that few, if any, major biological determinants are unrepresented in the models.     

Structure and functional features of enzymes from the Ca2+-phospholipid-dependent protein kinase family

Present day scientific data about the Ca(2+)-phospholipid-dependent protein kinases structure and molecular mechanisms of their activity are summarized and analyzed in this review. Ca(2+)-phospholipid-dependent protein kinases family is well known to include a whole series of enzymes which are homologous by their structure. They play an important role in cell differentiation, growth and proliferation as well as signal transduction through the cytoplasmic membrane. They also take part in cell response realization by phosphorylation of target proteins. Now application of modern biochemical and biophysical methods provided for possibility of the clarification of these enzymes structure features. The great lot of experimental data about the molecular mechanisms of Ca(2+)-phospholipid-dependent protein kinases activity regulation by phosphatydyle serine, phorbol ethers, saturated and unsaturated fatty acids, calcium iones, autophosphorylation and holoferment phosphorylation by other kinases was obtained. As a model of Ca(2+)-phospholipide-dependent protein kinases regulation was their development on the base of the scientific data about this problem.     

Structure, evolution and action of vitamin B6-dependent enzymes

The number of known three-dimensional structures of vitamin B₆-dependent enzymes has doubled in the past two years. A fourth type of fold for B₆-dependent enzymes, involving a TIM-barrel domain, has been discovered. Alanine racemase is the first known representative of this new fold. Significant progress has been made in understanding the allosteric effects in the tryptophan synthase reaction.     

Structure, function, and evolution of the PsbP protein family in higher plants

The PsbP is a thylakoid lumenal subunit of photosystem II (PSII), which has developed specifically in higher plants and green algae. In higher plants, the molecular function of PsbP has been intensively investigated by release-reconstitution experiments in vitro. Recently, solution of a high-resolution structure of PsbP has enabled investigation of structure-function relationships, and efficient gene-silencing techniques have demonstrated the crucial role of PsbP in PSII activity in vivo. Furthermore, genomic and proteomic studies have shown that PsbP belongs to the divergent PsbP protein family, which consists of about 10 members in model plants such as Arabidopsis and rice. Characterization of the molecular function of PsbP homologs using Arabidopsis mutants suggests that each plays a distinct and important function in maintaining photosynthetic electron transfer. In this review, recent findings regarding the molecular functions of PsbP and other PsbP homologs in higher plants are summarized, and the molecular evolution of these proteins is discussed.     

Baculovirus-mediated expression and purification of human serum paraoxonase 1A

Human paraoxonase 1 (hPON1) is a lipid-associated enzyme transported on HDL. There is considerable interest in hPON1 because of its putative antioxidative/antiatherogenic properties. We have created a recombinant baculovirus (BV) to generate hPON1A in large quantities for structure-function studies and here describe the method for production and isolation of the enzyme. A high level of recombinant hPON1 type A (rPON1A) was produced by Hi-5 insect cells (40 mg/l); a fraction ( approximately 10 mg/l) was secreted into the cell culture medium, but the majority ( approximately 30 mg/l) remained associated with the host insect cells. Cell-associated rPON1A was purified by detergent extraction (Tergitol NP-10) followed by three simple chromatography steps (DEAE-Sepharose, Sephacryl S-200, and concanavalin A). The purified enzyme bound to concanavalin A and was converted to a lower molecular mass by endoglycosidase H digestion, suggesting that rPON1A contained high-mannose N-glycan chains. There was a significant decrease in arylesterase activity (>99%) concomitant with enzymatic deglycosylation. rPON1A was dependent on Ca(2+) for arylesterase activity, exhibiting kinetic parameters similar to native hPON1A (K(m) = 3.8 +/- 2.1 vs. 3.7 +/- 2.0 mM and V(max) = 1,305 +/- 668 vs. 1,361 +/- 591 U/mg protein, rPON1A and hPON1A, respectively). Both rPON1A and hPON1A efficiently inhibited lipoxygenase-mediated peroxidation of phospholipid. In contrast to the arylesterase activity, which was sensitive to endoglycosidase H treatment, enzymatic deglycosylation did not inhibit the antioxidant activity of rPON1A. In conclusion, our BV-mediated PON1A expression system appears ideally suited for the production of relatively large quantities of rPON1A for structure-function studies.     

Molecular evolution of the reactive oxygen-generating NADPH oxidase (Nox/Duox) family of enzymes

Background  

NADPH-oxidases (Nox) and the related Dual oxidases (Duox) play varied biological and pathological roles via regulated generation of reactive oxygen species (ROS). Members of the Nox/Duox family have been identified in a wide variety of organisms, including mammals, nematodes, fruit fly, green plants, fungi, and slime molds; however, little is known about the molecular evolutionary history of these enzymes.