Proteasomes from Structure to Function: Perspectives from Archaea

Insight into the world of proteolysis has expanded considerably over the past decade. Energy-dependent proteases, such as the proteasome, are no longer viewed as nonspecific degradative enzymes associated solely with protein catabolism but are intimately involved in controlling biological processes that span life to death. The proteasome maintains this exquisite control by catalyzing the precisely timed and rapid turnover of key regulatory proteins. Proteasomes also interplay with chaperones to ensure protein quality and to readjust the composition of the proteome following stress. Archaea encode proteasomes that are highly related to those of eukaryotes in basic structure and function. Investigations of archaeal proteasomes coupled with those of eukaryotes has greatly facilitated our understanding of the molecular mechanisms that govern regulated protein degradation by this elaborate nanocompartmentalized machine.

Molecular variability of the coat protein gene of Potato virus Y from tobacco in China

Thirty-three tobacco samples showing typical symptoms of Potato virus Y (PVY) infection were obtained from tobacco fields in various regions of China. The results of indirect ELISA confirmed the infection with PVY. All the isolates had a capacity to infect tobacco systemically in greenhouse, causing either of two main symptoms: veinal necrosis and mosaic. The nucleotide and amino acid sequences of the coat protein (CP) gene and protein, respectively, of the isolates were determined. Comparison of the isolates revealed a high conservation of the CP gene with an identity of 83.2%. A phylogenetic tree of 41 Chinese isolates of PVY, based on complete CP gene, showed 3 groups corresponding to the strains PVYNTN (A group), PVYO (C group) and a putative new strain similar to PVYN (B group). The amino acid sequences of complete CP protein of the isolates showed an identity of 87.6%. The highest identity was observed in the C-terminal half of the CP protein, where only 11 amino acid differences could be observed, in contrast to the N-terminal half with 22 differences.

Herpes simplex virus 1 recombinant virions exhibiting the amino terminal fragment of urokinase-type plasminogen activator can enter cells via the cognate receptor

Earlier this laboratory constructed a herpes simplex virus 1 recombinant (R5111) that carries a IL13 ligand inserted into glycoprotein D and can enter cells via the IL13Ralpha2 receptor commonly expressed on the surface of malignant glioma cells. In this report, we describe the properties of two recombinant viruses carrying chiemric gD genes. In R5181 recombinant virus the chimeric gene consisted on the residues 20-155 of urokinase plaminogen activator (uPA) inserted between residues 24 and 25 of gD. In R5182 the insert consisted of a 23-residue sequence encoding the uPA binding domain for the urokinase plaminogen activator receptor (uPAR). These viruses were constructed for three reasons, to increase the number of viruses that specifically target receptors on the surface of malignant glioma cells, to determine whether viruses exhibiting novel ligands could enter cells via receptors anchored to the cell surface via glycosylphosphatidylinositol anchor as has been recently demonstrated for nectin1, and to determine whether receptors other than IL13Ralpha2 could be targeted by genetic engineering of the virus. We report that R5181 but not R5182 recombinant virus was able to enter cells expressing uPAR. The results indicate that HSV-1 recombinant viruses can be engineered to enter cells via a variety of unrelated nonviral receptors, including receptors that are anchored to the cells surface but without transmembrane domains.

A cross-sectional study of smoking risk factors in junior high school students in Henan, China

This study was conducted to determine the predictors of tobacco use among junior high school students in Henan. Two thousand seven hundred sixty-three students (from grades 7 to 9) were studied. Demographic, smoking-related, and other predictor variables was investigated. Overall, 6.6% of students were current smokers; 8.7% students reported having tried cigarettes before; and 42.1% of current smokers and 34.2% of triers experimented with smoking during ages 10-12. Of the factors associated with student tobacco use, mother and peer smoking were the strongest independent predictors. The school's negative attitude towards smoking was an important protective factor for preventing student smoking behavior. These findings revealed that effective smoking prevention interventions needed to be comprehensive.

Single nucleotide polymorphisms and haplotypes of histamine N-methyltransferase in patients with gastric ulcer

INTRODUCTION

Histamine plays a crucial role in the regulation of gastric acid secretion, which is involved in the pathogenesis of peptic ulcer. Histamine N-methyltransferase (HNMT) is the major metabolizing enzyme for histamine inactivation in human stomach.

OBJECTIVE

This study aims to determine whether there exists a relationship between HNMT gene polymorphisms and the risk for gastric ulcer (GU).

METHODS

118 GU patients and 154 ethnically matched control subjects were enrolled and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assays were developed to genotype all these subjects for the T-1637C, C-411T, C314T and A1097T point mutations in HNMT gene. Haplotypes were reconstructed from the genotype data.

RESULTS

Frequencies of the variant alleles in cases and controls were 0.398 vs 0.396 for T-1637C, 0.144 vs 0.110 for C-411T, 0.034 vs 0.042 for C314T, and 0.242 vs 0.273 for A1097T, respectively, with no significant difference for any locus between the two groups (all P > 0.05). Also the frequencies of genotypes, haplotypes and haplotype pairs based on these polymorphisms did not differ significantly between cases and controls.

CONCLUSION

This study provided no evidence for the involvement of HNMT polymorphisms in the susceptibility to GU.

Linkage Disequilibrium and Haplotype Architecture for two ABC Transporter Genes (ABCC1 and ABCG2) in Chinese Population: Implications for Pharmacogenomic Association Studies

Information about linkage disequilibrium (LD) patterns and haplotype structures for candidate genes is instructive for the design and analysis of genetic association studies for complex diseases and drug response. ABCC1 and ABCG2 are genes coding for two multidrug resistance (MDR) associated transporters; they are also related to some pathophysiological traits. To pinpoint the LD profiles of these MDR genes in Chinese, we systemically screened 27 unrelated individuals for single nucleotide polymorphisms (SNPs) in the coding and regulatory regions of these genes, and thereby characterized their haplotype structures. Despite marked variations in haplotype diversity, LD pattern and intragenic recombination intensity between the two genes, both loci could be partitioned into several LD blocks, in which a modest number of haplotypes accounted for a high fraction of the sampled chromosomes. We concluded that each locus has its own genomic LD profile, but that they still share a common segmental LD architecture with low haplotype diversity. Our data will benefit genetic association studies of complex traits and drug response possibly related to these genes.

Identification of systemically expanded activated T cell clones in MRL/lpr and NZB/W F1 lupus model mice

CD4(+) T lymphocytes play an important role in the pathogenesis of systemic lupus erythematosus (SLE). To characterize the clonal expansion of CD4(+) T cells in murine lupus models, we analysed the T cell clonality in various organs of young and nephritic MRL/lpr and NZB/W F1 mice using reverse transcription-polymerase chain reaction (RT-PCR) and subsequent single-strand conformation polymorphism (SSCP) analysis. We demonstrated that some identical T cell clonotypes expanded and accumulated in different organs (the bilateral kidneys, brain, lung and intestine) in nephritic diseased mice, and that a number of these identical clonotypes were CD4(+) T cells. In contrast, young mice exhibited little accumulation of common clones in different organs. The T cell receptor (TCR) V beta usage of these identical clonotypes was limited to V beta 2, 6, 8.1, 10, 16 and 18 in MRL/lpr mice and to V beta 6 and 7 in NZB/W F1 mice. Furthermore, some conserved amino acid motifs such as I, D or E and G were observed in CDR3 loops of TCR beta chains from these identical CD4(+) clonotypes. The existence of systemically expanding CD4(+) T cell clones in the central nervous system (CNS) suggests the involvement of the systemic autoimmunity in CNS lesions of lupus. FACS-sorted CD4(+)CD69(+) cells from the kidney displayed expanded clonotypes identical to those obtained from the whole kidney and other organs from the same individual. These findings suggest that activated and clonally expanded CD4(+) T cells accumulate in different tissues of nephritic lupus mice, and these clonotypes might recognize restricted T cell epitopes on autoantigens involved in specific immune responses of SLE, thus playing a pathogenic role in these lupus mice.

Complete nucleotide sequence of a potyvirus causing maize dwarf mosaic disease in central China

The full-length nucleotide sequence of a potyvirus causing the maize dwarf mosaic (MDM) disease in Henan province, central China, was obtained by reverse transcription-polymerase chain reaction (RT-PCR) and rapid amplification of the cDNA 5'-end (5'-RACE). The viral genome comprised of 9596 nucleotides except the polyA tail and encoded a putative polyprotein of 3603 amino acids. The entire genomic sequence of this isolate shared identities of 94.2% and 98.3% with Sugarcane mosaic virus (SCMV) HZ isolate at the nucleotide and deduced amino acid levels, respectively, but only a 69.1% identity with MDM virus (MDMV) Bulgarian isolate (MDMV-Bg) at the nucleotide level. Phylogenetical tree analysis of the complete nucleotide sequences indicated that the Henan isolate of a potyvirus causing MDM disease is in fact a Henan strain of SCMV (SCMV-HN).

Nucleotide sequences of the coat protein and readthrough protein genes of the Chinese GAV isolate of barley yellow dwarf virus

The nucleotide sequences of the coat protein (CP) and readthrough protein (RTP) genes of the Chinese GAV isolate of Barley yellow dwarf virus (BYDV) were determined. The CP and RTP genes of GAV isolate comprised 600 and 1374 nucleotides, respectively. When the CP and RTP gene sequences of GAV isolate were compared with those of BYDV isolates MAV-PS1, P-PAV, NY-SGV and Cereal yellow dwarf virus RPV (CYDV-RPV), the highest similarity (97.2%) between the CP genes of GAV and MAV-PS1 isolates was observed, while the RTP genes of these two isolates shared a lower similarity (87.8%). The results of the alignment of the deduced amino acid sequences of RTP showed that the sequence diversity observed was located at the C terminus.

Dual mechanisms of ABCA1 regulation by geranylgeranyl pyrophosphate

ATP-binding cassette transporter A1 (ABCA1) mediates an active efflux of cholesterol and phospholipids and is mutated in patients with Tangier disease. Expression of ABCA1 may be increased by certain oxysterols such as 22(R)-hydroxycholesterol via activation of the nuclear hormone receptor liver X receptor (LXR). In searching for potential modulators of ABCA1 expression, we have studied the effects of various mevalonate metabolites on the expression of ABCA1 in two human cell lines, THP-1 and Caco-2 cells. Most of the tested metabolites, including mevalonate, geranyl pyrophosphate, farnesyl pyrophosphate, and ubiquinone, failed to significantly change the expression levels of ABCA1. However, treatment with geranylgeranyl pyrophosphate resulted in a dose- and time-dependent reduction of ABCA1 expression. Geranylgeranyl pyrophosphate appears to reduce ABCA1 expression via two different mechanisms. One of these mechanisms is by acting directly as an antagonist of LXR since it reduces the interaction between LXR alpha or -beta with nuclear coactivator SRC-1. Another mechanism appears to involve activation of the Rho GTP-binding proteins since treatment of Caco-2 cells with inhibitors of geranylgeranyl transferase or the Rho proteins significantly increased the expression and promoter activity of ABCA1. Further studies showed that mutations in the DR4 element of the ABCA1 promoter completely eliminate the inducible activities of these inhibitors. These data indicate that activation of the Rho proteins may change the activation status of LXR.

Role of AMP-activated protein kinase in mechanism of metformin action

Metformin is a widely used drug for treatment of type 2 diabetes with no defined cellular mechanism of action. Its glucose-lowering effect results from decreased hepatic glucose production and increased glucose utilization. Metformin's beneficial effects on circulating lipids have been linked to reduced fatty liver. AMP-activated protein kinase (AMPK) is a major cellular regulator of lipid and glucose metabolism. Here we report that metformin activates AMPK in hepatocytes; as a result, acetyl-CoA carboxylase (ACC) activity is reduced, fatty acid oxidation is induced, and expression of lipogenic enzymes is suppressed. Activation of AMPK by metformin or an adenosine analogue suppresses expression of SREBP-1, a key lipogenic transcription factor. In metformin-treated rats, hepatic expression of SREBP-1 (and other lipogenic) mRNAs and protein is reduced; activity of the AMPK target, ACC, is also reduced. Using a novel AMPK inhibitor, we find that AMPK activation is required for metformin's inhibitory effect on glucose production by hepatocytes. In isolated rat skeletal muscles, metformin stimulates glucose uptake coincident with AMPK activation. Activation of AMPK provides a unified explanation for the pleiotropic beneficial effects of this drug; these results also suggest that alternative means of modulating AMPK should be useful for the treatment of metabolic disorders.

[External irradiation combined with intracavitary brachytherapy for esophageal cancer]

OBJECTIVE

To study the long-term treatment results and acute irradiation response as well as complications following external irradiation combined with intracavitary brachytherapy.

METHODS

After loading intracavitary brachytherapy was used for patients with esophageal cancer. In 92 patients with esophageal cancer, 47 (group A) were treated with external irradiation only, and 45 (group B) with external irradiation and brachytherapy. The doses were 60.0 Gy - 70.0 Gy per 6-7 week for external irradiation, using 8 or 10 MV liner accelerator, and 5.0-8.0 Gy per fraction for intracavitary therapy.

RESULTS

There was a significant difference in acute response and complications as well as local recurrence rate between the two groups (P < 0.05). The survival rates of groups A and B at 1,3 and 5 years were 59.6%, 25.6%, 10.6% and 80.0%, 46.7%, 26.7% respectively (P < 0.05 respectively, using chi2 test). The complications related to intracavitary irradiation were esophageal perforation, esophagorrhagia, esophagotracheal fistula and esophageal narrowing. 66 patients died and 9 lost follow-up, giving a follow up rate of 90.2%.

CONCLUSION

External irradiation combined with afterloading intracavitary brachytherapy for esophageal cancer can reduce the local recurrence and enhance the long-term survival but with an increase of complications compared with the patients treated with external irradiation alone.

Serotonin modulates locomotory behavior and coordinates egg-laying and movement in Caenorhabditis elegans

Biogenic amines have been implicated in the modulation of neural circuits involved in diverse behaviors in a wide variety of organisms. In the nematode C. elegans, serotonin has been shown to modulate the temporal pattern of egg-laying behavior. Here we show that serotonergic neurotransmission is also required for modulation of the timing of behavioral events associated with locomotion and for coordinating locomotive behavior with egg-laying. Using an automated tracking system to record locomotory behavior over long time periods, we determined that both the direction and velocity of movement fluctuate in a stochastic pattern in wild-type worms. During periods of active egg-laying, the patterns of reversals and velocity were altered: velocity increased transiently before egg-laying events, while reversals increased in frequency following egg-laying events. The temporal coordination between egg-laying and locomotion was dependent on the serotonergic HSN egg-laying motorneurons as well as the decision-making AVF interneurons, which receive synaptic input from the HSNs. Serotonin-deficient mutants also failed to coordinate egg-laying and locomotion and exhibited an abnormally low overall reversal frequency. Thus, serotonin appears to function specifically to facilitate increased locomotion during periods of active egg-laying, and to function generally to modulate decision-making neurons that promote forward movement.

The pattern of gene expression in human CD34(+) stem/progenitor cells

We have analyzed the pattern of gene expression in human primary CD34(+) stem/progenitor cells. We identified 42,399 unique serial analysis of gene expression (SAGE) tags among 106,021 SAGE tags collected from 2.5 x 10(6) CD34(+) cells purified from bone marrow. Of these unique SAGE tags, 21,546 matched known expressed sequences, including 3,687 known genes, and 20,854 were novel without a match. The SAGE tags that matched known sequences tended to be at higher levels, whereas the novel SAGE tags tended to be at lower levels. By using the generation of longer sequences from SAGE tags for gene identification (GLGI) method, we identified the correct gene for 385 of 440 high-copy SAGE tags that matched multiple genes and we generated 198 novel 3' expressed sequence tags from 138 high-copy novel SAGE tags. We observed that many different SAGE tags were derived from the same genes, reflecting the high heterogeneity of the 3' untranslated region in the expressed genes. We compared the quantitative relationship for genes known to be important in hematopoiesis. The qualitative identification and quantitative measure for each known gene, expressed sequence tag, and novel SAGE tag provide a base for studying normal gene expression in hematopoietic stem/progenitor cells and for studying abnormal gene expression in hematopoietic diseases.

Modulation of retinal cell populations and eye size in retinoic acid receptor knockout mice

PURPOSE

The retinoic acid receptors are expressed from early stages of development in the diverse tissues that make up the vertebrate eye. Their loss has subtle effects on eye development. We adapted sensitive quantitative trait locus (QTL) mapping methods to assess consequences of inactivating alleles of the alpha and beta receptors, Rara and Rarb, on eye and retinal development. Rara is of particular interest because this gene is a candidate for Nnc1, a QTL that controls retinal ganglion cell proliferation.

METHODS

We studied lines of mice in which expression of the a1 isoform of Rara or all isoforms of Rarb had been disrupted by gene targeting. We measured eye weight, lens weight, retinal area, and retinal ganglion cell number in each of six genotypes (Rara and Rarb -/-, +/-, +/+; 10-25 cases/genotype).

RESULTS

Loss of either protein is associated with a small but significant loss of eye weight and retinal area. However, only the Rarb knockout has a significant effect on the ganglion cell population and the loss of both wildtype alleles leads to an 8,000 cell deficit. Surprisingly, loss of the Rara a1 isoform that is expressed in this cell population from early stages has no effect on number. Null alleles of both genes have little if any effect on lens growth.

CONCLUSIONS

Despite its expression in embryonic retina, Rara is unlikely to be the Nnc1 QTL. In contrast, Rarb, a gene that maps to Chr 14 and which is not an Nnc1 candidate gene, has a significant effect on cell number and is therefore a QTL controlling this key population. This raises the intriguing possibility that normal allelic variants of Rarb modulate the ganglion cell population in other vertebrates, including humans.

Uroplakin Ia is the urothelial receptor for uropathogenicEscherichia coli: evidence from in vitro FimH binding

The binding of uropathogenic Escherichia coli to the urothelial surface is a crucial initial event for establishing urinary tract infection because it allows the bacteria to gain a foothold on the urothelial surface, thus preventing them from being removed by micturition. In addition, it triggers bacterial invasion as well as host urothelial defense. This binding is mediated by the FimH adhesin located at the tip of the bacterial type 1-fimbrium, a filamentous attachment apparatus, and its urothelial receptor. We have prepared a biotinylated, recombinant FimH-FimC adhesin:chaperone complex and used it to identify its mouse urothelial receptor. The FimH-FimC complex binds specifically to a single 24 kDa major mouse urothelial plaque protein, which we identified as uroplakin Ia by mass spectrometry, cDNA cloning and immunoreactivity. The terminal mannosyl moieties on Asn-169 of uroplakin Ia are responsible for FimH as well as concanavalin A binding. Although FimH binds to uroplakin Ia with only moderate strength (Kd ∼100 nM between pH 4 and 9), the binding between multiple fimbriae of a bacterium and the crystalline array of polymerized uroplakin receptors should achieve high avidity and stable bacterial attachment. The FimH-FimC complex binds preferentially to the mouse urothelial umbrella cells in a pattern similar to uroplakin staining. Our results indicate that the structurally related uroplakins Ia and Ib are glycosylated differently, that uroplakin Ia serves as the urothelial receptor for the type 1-fimbriated E. coli, and that the binding of uropathogenic bacteria to uroplakin Ia may play a key role in mediating the urothelial responses to bacterial attachment.

27-hydroxycholesterol is an endogenous ligand for liver X receptor in cholesterol-loaded cells

The nuclear receptors liver X receptor alpha (LXRalpha) (NR1H3) and LXRbeta (NR1H2) are important regulators of genes involved in lipid metabolism, including ABCA1, ABCG1, and sterol regulatory element-binding protein-1c (SREBP-1c). Although it has been demonstrated that oxysterols are LXR ligands, little is known about the identity of the physiological activators of these receptors. Here we confirm earlier studies demonstrating a dose-dependent induction of ABCA1 and ABCG1 in human monocyte-derived macrophages by cholesterol loading. In addition, we show that formation of 27-hydroxycholesterol and cholestenoic acid, products of CYP27 action on cholesterol, is dependent on the dose of cholesterol used to load the cells. Other proposed LXR ligands, including 20(S)-hydroxycholesterol, 22(R)-hydroxycholesterol, and 24(S),25-epoxycholesterol, could not be detected under these conditions. A role for CYP27 in regulation of cholesterol-induced genes was demonstrated by the following findings. 1) Introduction of CYP27 into HEK-293 cells conferred an induction of ABCG1 and SREBP-1c; 2) upon cholesterol loading, CYP27-expressing cells induce these genes to a greater extent than in control cells; 3) in CYP27-deficient human skin fibroblasts, the induction of ABCA1 in response to cholesterol loading was ablated; and 4) in a coactivator association assay, 27-hydroxycholesterol functionally activated LXR. We conclude that 27-hydroxylation of cholesterol is an important pathway for LXR activation in response to cholesterol overload.

Role of AMP-activated protein kinase in mechanism of metformin action

Metformin is a widely used drug for treatment of type 2 diabetes with no defined cellular mechanism of action. Its glucose-lowering effect results from decreased hepatic glucose production and increased glucose utilization. Metformin's beneficial effects on circulating lipids have been linked to reduced fatty liver. AMP-activated protein kinase (AMPK) is a major cellular regulator of lipid and glucose metabolism. Here we report that metformin activates AMPK in hepatocytes; as a result, acetyl-CoA carboxylase (ACC) activity is reduced, fatty acid oxidation is induced, and expression of lipogenic enzymes is suppressed. Activation of AMPK by metformin or an adenosine analogue suppresses expression of SREBP-1, a key lipogenic transcription factor. In metformin-treated rats, hepatic expression of SREBP-1 (and other lipogenic) mRNAs and protein is reduced; activity of the AMPK target, ACC, is also reduced. Using a novel AMPK inhibitor, we find that AMPK activation is required for metformin's inhibitory effect on glucose production by hepatocytes. In isolated rat skeletal muscles, metformin stimulates glucose uptake coincident with AMPK activation. Activation of AMPK provides a unified explanation for the pleiotropic beneficial effects of this drug; these results also suggest that alternative means of modulating AMPK should be useful for the treatment of metabolic disorders.

[Pharmacological study on the extracts from Typhonium flagelliforme Blume]

OBJECTIVE

To study the pharmacological action of Typhonium flagelliforme Blune(TFB).

METHODS

Relieving a cough and eliminating expectoration were observed by strong aqua spray and pheol red determining methods. The antiasthmatic action was observed by whole spraying method. The analgesia and anti-inflammation were studied by the twisting test induced by acetic acid and ear swelling induced by xylene. The sedation was determined by autonomic action test. The toxicity of TFB was studied through the acute toxicity test in mice.

RESULTS

All the water, alcohol and ester extracts of TFB could significantly decrease cough times, increase phenol red outage in trachea, prolong asthma incubation period, decrease twisting times, inhibit ear swelling and decrease autonomic action times.

CONCLUSION

All water, alcohol and ester extracts of TFB have effects of relieving a cough, eliminating expectoration, antiasthmatic, analgesia, anti-inflammation and sedation. The maximum tolerances of TFB for acute toxicity were 720 g/kg(water extract), 900 g/kg (alcohol extract) 3240 g/kg(ester extract) respectively.

Miniaturized pyrosequencer for DNA analysis with capillaries to deliver deoxynucleotides

As the human genome project proceeds, various types of DNA analysis tools are required for life sciences and medical sciences including DNA diagnostics. For example, a small DNA sequencer for sequencing a short DNA is required for bed-side DNA testing as well as DNA analysis in a small laboratory. Here, a new handy DNA sequencing system (pyrosequencer) based on the detection of inorganic pyrophosphate (PPi) released by polymerase incorporation is demonstrated. The system uses the bioluminescence detection system. The key point for the miniaturized DNA sequencer is to make a deoxynucleotide triphosphate (dNTP) delivery system small and inexpensive. It has been realized by using narrow capillaries to connect a reaction chamber and four dNTP reservoirs. Each dNTP is introduced into the reaction chamber by applying a pressure to the reservoir. Compared with other microdispensers, it is much cheaper and easier. By optimizing the conditions, an excellent sequencing ability is achieved while it is a simple and inexpensive system. In most cases, more than 40 bases can be successfully sequenced. A homopolymeric region, which can not be easily sequenced by a conventional gel-based DNA sequencer, is readily sequenced with this system. The new system is successfully applied to sequence a GC rich region or a region close to a priming region where misreading frequently occurs. A rapid analysis for a short DNA was easily achieved with this small instrument.