Activity-assembled nBAF complex mediates rapid immediate early gene transcription by regulating RNA Polymerase II productive elongation

Signal-dependent RNA Polymerase II (Pol2) productive elongation is an integral component of gene transcription, including those of immediate early genes (IEGs) induced by neuronal activity. However, it remains unclear how productively elongating Pol2 overcome nucleosomal barriers. Using RNAi, three degraders, and several small molecule inhibitors, we show that the mammalian SWI/SNF complex of neurons (neuronal BAF, or nBAF) is required for activity-induced transcription of neuronal IEGs, including Arc . The nBAF complex facilitates promoter-proximal Pol2 pausing, signal-dependent Pol2 recruitment (loading), and importantly, mediates productive elongation in the gene body via interaction with the elongation complex and elongation-competent Pol2. Mechanistically, Pol2 elongation is mediated by activity-induced nBAF assembly (especially, ARID1A recruitment) and its ATPase activity. Together, our data demonstrate that the nBAF complex regulates several aspects of Pol2 transcription and reveal mechanisms underlying activity-induced Pol2 elongation. These findings may offer insights into human maladies etiologically associated with mutational interdiction of BAF functions.

The role of sex in daily levels of high-risk alcohol and cannabis co-use

Background

Co-use of alcohol and cannabis is highly prevalent and may be associated with negative outcomes. The intersection between alcohol and cannabis use remains poorly understood. The present study assessed this intersection and the moderating effects of sex on the daily levels of high-risk alcohol and cannabis co-use.

Methods

A secondary analysis of an experimental pharmacology study specifically designed to recruit individuals using both alcohol and cannabis was conducted. Thirty-three non-treatment seeking subjects (19 M/14F) reporting high-risk levels of alcohol and cannabis use completed a 30-day Timeline Follow-back (TLFB) assessment for alcohol and cannabis use, resulting in a total of N = 990 observations. Logistic models tested the probability of same day cannabis use as predicted by alcohol use (any use, total drinking, and binge drinking), sex, and alcohol use by sex interactions.

Results

Drinking any alcohol on a given day was associated with a significant increase in the likelihood of same-day cannabis use (b = 0.61, p = 0.001) as was amount of alcohol consumed on a given day (b = 0.083, p = 0.012). These relations were significantly moderated by sex (b = 1.58, p<0.001; b = 0.14, p = 0.044). Male-identifying individuals demonstrated an increased probability of concurrent cannabis use with any alcohol use on a given day, and this relationship increased linearly as the number of drinks consumed increased.

Conclusions

The present study investigated the patterns associated with co-using alcohol and cannabis in individuals reporting high-risk levels of both alcohol and cannabis use. The sex-dependent findings suggest that males are at higher risk for co-using alcohol and cannabis compared with females.

POS0985 DISEASE CONTROL PERCEPTION BY PHYSICIANS AND PATIENTS WITH ANKYLOSING SPONDYLITIS AND PSORIATIC ARTHRITIS IN REAL CLINICAL PRACTICE IN SPAIN: MIDAS STUDY RESULTS

Background:

There are few published data regarding physician’ and patient’ perception of the disease control for ankylosing spondylitis (AS) and psoriatic arthritis (PsA).

Objectives:

To evaluate the relationship between physician’ and patient’ disease control perception compared to clinical outcomes for controlled disease (BASDAI<4 in AS or DAPSA≤14 in PsA).

Methods:

MIDAS is an observational, non-interventional, cross-sectional, multicenter study. Patients ≥18 years with ≥6 months AS or PsA diagnosis according to ASAS and modified New York criteria or CASPAR criteria, respectively, undergoing treatment ≥3 months before inclusion. The endpoint of this analysis was the relationship between disease control perception by physicians and patients and disease control (BASDAI<4 in AS or DAPSA≤14 in PsA).

Results:

313 AS patients included: 75.7% male, 78.5% HLA-B*27+, a mean (SD) age of 50.4 (12.0) years, a mean (SD) disease duration of 15.5 (11.6) years and a mean (SD) CRP of 5.1 (8.2) mg/l. 313 PsA patients included: 54.3% male, 17.95% HLA-B*27+, a mean (SD) age of 54.1 (12.2) years, a mean (SD) disease duration of 10.5 (9.0) years and a mean (SD) CRP of 4.91 (7.3) mg/l. AS group: in 95.5% of AS patients with BASDAI<4, physician’s perception matched the clinical evaluation, while only 42.3% of the patients with BASDAI≥4 matched physician’s perception. Positive Predictive Value (PPV) was 75.1%, Negative Predictive Value (NPV) was 83.9% and precision was 76.7%. Patients perceived their own disease as controlled in 95.0% of cases with BASDAI scores <4 and as not controlled in 29.7% of cases with BASDAI score ≥4. PPV was 71.1%, NPV was 76.7% and precision was 71.9%. The same trend was observed when assessing disease control through ASDAS-CRP index. PsA group: in 96.2% of patients with DAPSA≤14, physician’s perception matched the clinical evaluation, while only 47.6% of patients with DAPSA>14 matched the physician’s perception. PPV was 73.1%, NPV was 89.6% and precision was 76.4%. Patients perceived their own disease as controlled in 93.5% of the cases with DAPSA scores ≤14 and as not controlled in 32.3% of the cases with DAPSA>14. PPV was 66.8%, NPV was 77.4% and precision was 68.4%. The same trend was observed when assessing disease control through the MDA criteria (Table 1).

Table 1.

Physician’s and patient’s perception of the disease control related to disease control variables in AS and PsA

Controlled disease by physician’s perception?Controlled disease by patient’s perception?Valid NYesN (%)NoN (%)Valid NYesN (%)NoN (%)ASDisease control(BASDAI)Controlled(BASDAI<4)202 (100%)193 (95.5%)9 (4.5%)202 (100%)192 (95.0%)10 (5.0%)Not controlled(BASDAI≥4)111 (100%)64 (57.7%)47 (42.3%)111 (100%)78 (70.3%)33 (29.7%)Disease activity(ASDAS-CRP)Inactive(ASDAS-CRP<1.3)92 (100%)90 (97.8%)2 (2.2%)92 (100%)91 (98.9%)1 (1.1%)Active(ASDAS-CRP≥1.3)221 (100%)167 (75.6%)54 (24.4%)221 (100%)179 (81.0%)42 (19.0%)PsADisease control(DAPSA)Controlled(DAPSA≤14)186 (100%)179 (96.2%)7 (3.8%)185 (100%)173 (93.5%)12 (6.5%)Not controlled(DAPSA>14)126 (100%)66 (52.4%)60 (47.6%)127 (100%)86 (67.7%)41 (32.3%)Active disease (MDA)Inactive(MDA criteria ≥5)161 (100%)154 (95.7%)7 (4.3%)160 (100%)152 (95.0%)8 (5.0%)Active(MDA criteria<5)151 (100%)91 (60.3%)60 (39.7%)152 (100%)107 (70.4%)45 (29.6%)

AS, ankylosing spondylitis; ASDAS-CRP, Ankylosing Spondylitis Disease Activity Score- C-reactive protein; BASDAI, Bath Ankylosing Spondylitis Disease Activity Index; DAPSA, Disease Activity in Psoriatic Arthritis; MDA, Minimal Disease Activity; PsA, psoriatic arthritis.

Conclusion:

A higher agreement between physician’s and patient’ perception with the current clinical evaluation was observed when patients were controlled. MiDAS study showed that in real clinical practice in Spain, physicians perceived more disease control than the patients

Acknowledgements:

We thank to MIDAS group investigators and patients included in the study.

Disclosure of Interests:

José Luis Pablos Speakers bureau: Janssen, Pfizer, Lilly, Novartis, Roche, Celgene, Bristol, Abbvie, Sanofi, Consultant of: Janssen, Pfizer, Lilly, Novartis, Roche, Celgene, Bristol, Abbvie, Sanofi, Gilead, Galápagos, Xavier Juanola Speakers bureau: Novartis, Abbvie, Pfizer, Lilly, Consultant of: Novartis, Lilly, Abbvie, Ceferino Barbazán Speakers bureau: Sanofi, Pfizer, Novartis, Amgen, Abbvie, Roche, Galápagos, Lilly, BMS, Biogen, UCB, Consultant of: Sanofi, Pfizer, Novartis, Amgen, Abbvie, Roche, Galápagos, Lilly, BMS, Biogen, UCB, María L. García Vivar Speakers bureau: Lilly, Novartis, Pfizer, Amgen, Bristol, Abbvie, Sanofi, Janssen and UCB, Consultant of: Lilly, Novartis, Pfizer, Amgen, Bristol, Abbvie, Sanofi, Janssen and UCB, Ana Cruz Valenciano Speakers bureau: Novartis, Consultant of: Novartis, Carlos Rodriguez-Lozano: None declared, Maria Estadella Employee of: I’m employed at Syneos Health providing services for Novartis., Ana Venegas Employee of: employee at Novartis, Cristina Sanabra Employee of: Novartis employee, Carlos Sastré Employee of: Novartis employee.

Poly(ADP-Ribose) Polymerase-3 Regulates Regeneration in Planarians

Protein ADP-ribosylation is a reversible post-translational modification (PTM) process that plays fundamental roles in cell signaling. The covalent attachment of ADP ribose polymers is executed by PAR polymerases (PARP) and it is essential for chromatin organization, DNA repair, cell cycle, transcription, and replication, among other critical cellular events. The process of PARylation or polyADP-ribosylation is dynamic and takes place across many tissues undergoing renewal and repair, but the molecular mechanisms regulating this PTM remain mostly unknown. Here, we introduce the use of the planarian Schmidtea mediterranea as a tractable model to study PARylation in the complexity of the adult body that is under constant renewal and is capable of regenerating damaged tissues. We identified the evolutionary conservation of PARP signaling that is expressed in planarian stem cells and differentiated tissues. We also demonstrate that Smed-PARP-3 homolog is required for proper regeneration of tissues in the anterior region of the animal. Furthermore, our results demonstrate, Smed-PARP-3(RNAi) disrupts the timely location of injury-induced cell death near the anterior facing wounds and also affects the regeneration of the central nervous system. Our work reveals novel roles for PARylation in large-scale regeneration and provides a simplified platform to investigate PARP signaling in the complexity of the adult body.

Effect of ageing on the availability of heavy metals in soils amended with compost and biochar: evaluation of changes in soil and amendment properties

Remediation strategies using soil amendments should consider the time dependence of metal availability to identify amendments that can sustainably reduce available pollutant concentrations over time. Drying-wetting cycles were applied on amendments, soils and soil + amendment mixtures, to mimic ageing at field level and investigate its effect on extractable Cd, Cu, Ni, Pb and Zn concentrations from three contaminated soils. The amendments investigated were municipal waste organic compost and biochars. The amendments, soils and mixtures were characterised by their physicochemical properties at different ageing times. The amendments were also characterised in terms of sorption capacity for Cd and Cu. The sorption capacity and the physicochemical properties of the amendments remained constant over the period examined. When mixed with the soils, amendments, especially the compost, immediately reduced the extractable metals in the soils with low pH and acid neutralisation capacity, due to the increase in pH and buffering capacity of the mixtures. The amendments had a relatively minor impact on the metal availability concentrations for the soil with substantially high acid neutralisation capacity. The most important changes in extractable metal concentrations were observed at the beginning of the experiments, ageing having a minor effect on metal concentrations when compared with the initial effect of amendments.

Viability of organic wastes and biochars as amendments for the remediation of heavy metal-contaminated soils

Composts derived from municipal (MOW and MSW) and domestic wastes (DOM), wastes from the olive oil industry (OWH and OP), green waste (GW), and biochars (BF and BS) were investigated to test their viability for remediating metal-contaminated soils. In addition to common analyses, the characterisation included structural analyses (FTIR and (13)C NMR), determination of the acid neutralisation capacity (ANC) and the construction of sorption isotherms for target metals (Pb, Zn, Cd, Ni and Cu). MOW and GW had the highest ANC values (4280 and 7100 meq kg(-1), respectively), and MOW, GW, DOM, BF and BS exhibited the highest solid-liquid distribution coefficients (Kd) with maximum values in the 10(4) L kg(-1) range. Sorption isotherms were fitted using linear and Freundlich models for better comparison of the sorption capacities of the materials. Based on their basic pH, high ANC and high sorption capacity, MOW, GW and biochars are the most promising materials.

Arg113His mutation of vanishing white matter is not present in multiple sclerosis

Vanishing white matter (VWM) is a childhood leukoencephalopathy with central hypomyelination, white matter rarefaction, and cystic degeneration. Adult onset, variable phenotype, and high frequency characterize Arg113His mutation caused by G338A polymorphism associated with VWM. A patient with trauma-associated onset, and clinical features compatible with multiple sclerosis (MS), was homozygous for G338A mutation of eukaryotic translation initiation factor (eIF2B5). The authors checked a cohort of 101 MS patients, including 19 with head/neck trauma-associated onset, and failed to find the mutation, described above, in MS chromosomes. Our report does not exclude the presence in MS chromosomes of other mutations in the eIF2B gene family. Multiple Sclerosis 2007; 13: 424-427. http://msj.sagepub.com

Helicobacter pylori vacA s1a and s1b alleles from clinical isolates from different regions of Chile show a distinct geographic distribution

AIM

To establish the most common vacA alleles in Helicobacter pylori (H pylori) strains isolated from Chilean patients and its relationship with gastritis and gastroduodenal ulcers.

METHODS

Two hundred and forty five H pylori clinical isolates were obtained from 79 biopsies from Chilean infected patients suffering from gastrointestinal diseases. An average of 2-3 strains per patient was isolated and the vacA genotype was analyzed by PCR and 3% agarose electrophoresis. Some genotypes were checked by DNA sequencing.

RESULTS

The most prevalent vacA genotype in Chilean patients was s1b m1 (76%), followed by s1a m1 (21%). In contrast, the s2 m2 genotype was scarcely represented (3%). The s1b m1 genotype was found most frequently linked to gastropathies (P<0.05) rather than ulcers. Ulcers were found more commonly in male and older patients. Curiously, patients living in cities located North and far South of Santiago, the capital and largest Chilean city, carried almost exclusively strains with the s1b m1 genotype. In contrast, patients from Santiago and cities located South of Santiago carried strains with either one or both s1a m1 and s1b m1 genotypes. Regarding the s2 m2 genotype, comparison with GenBank sequences revealed that Chilean s2 sequence was identical to those of Australian, American, and Colombian strains but quite different from those of Alaska and India.

CONCLUSION

Differences in geographic distribution of the s and m vacA alleles in Chile and a relationship of s1b m1 genotype with gastritis were found. Sequence data in part support a hispanic origin for the vacA genotype. Asymmetric distribution of genotypes s1b m1 and s2 m2 recedes H Pylori strain distribution in Spain and Portugal.

Subset of hybrid eukaryotic proteins is exported by the type I secretion system of Erwinia chrysanthemi

Erwinia chrysanthemi exports degradative enzymes by using a type I protein secretion system. The proteases secreted by this system lack an N-terminal signal peptide but contain a C-terminal secretion signal. To explore the substrate specificity of this system, we have expressed the E. chrysanthemi transporter system (prtDEF genes) in Escherichia coli and tested the ability of this ABC transporter to export hybrid proteins carrying C-terminal fragments of E. chrysanthemi protease B. The C terminus contains six glycine-rich repeated motifs, followed by two repeats of the sequences DFLV and DIIV. Two types of hybrid proteins were assayed for transport, proteins with the 93-residue-protease-B C terminus containing one glycine-rich repeat and both hydrophobic terminal repeats and proteins with the 181-residue C terminus containing all repeat motifs. Although the shorter C terminus is unable to export the hybrids, the longer C terminus can promote the secretion of hybrid proteins with N termini as large as 424 amino acids, showing that the glycine-rich motifs are required for the efficient secretion of these hybrids. However, the secretion of hybrids occurs only if these proteins do not carry disulfide bonds in their mature structures. These latter results suggest that disulfide bond formation can occur prior to or during the secretion. Disulfide bonds may prevent type I secretion of hybrids. One simple hypothesis to explain these results is that the type I channel is too narrow to permit the export of proteins with secondary structures stabilized by disulfide bonds.

Chromogenic plate assay distinguishing bacteriolytic from bacteriostatic activity of an antibiotic agent

A solid agar plate assay was devised to discriminate bacteriolytic from bacteriostatic activity for a given antibacterial agent. The assay uses a bacterial culture harboring beta-galactosidase enzyme as reporter of cellular lysis. When a drop of bacteriolytic compound is placed on the agar, beta-galactosidase is released from the bacteria to the external solid medium where it hydrolyzes X-Gal substrate analogue, developing a blue halo at the edge of the inhibition growth zone. The assay was successfully evaluated against several antibiotics with well-known mechanism of action. It was found that bacteriostatic compounds consistently did not display blue halo at the inhibition zone.

Serological response to Helicobacter pylori recombinant antigens in Chilean infected patients with duodenal ulcer, non-ulcer dyspepsia and gastric cancer

We have previously cloned 10 Helicobacter pylori antigen genes from a Chilean strain including: cytotoxin VacA, a truncated region of CagA (called A17), a species-specific protein (Ag26), urease subunits (UreA, UreB), a flagellin, (FlaB), heat shock proteins (HspA and HspB), an adhesin (HpaA) and a lipoprotein (Lpp20). Immunogenicity of these antigens was tested by immunoblot with sera of Chilean infected patients, revealing that HpaA, A17, HspB and VacA were more frequently recognized (86%, 82%, 68% and 68%, respectively). According to the clinical condition, it was determined that Lpp20 was preferentially recognized by sera from non-ulcer dyspepsia patients (80%), A17 and VacA by patients with duodenal ulcer (92% and 83% respectively), and HspB by patients with duodenal ulcer (83%) and gastric cancer (90%). An ELISA was developed with a purified mixture of A17 and VacA antigens to test the different groups of patients. It was found that sera from duodenal ulcer patients showed higher values than those from non-ulcer dyspepsia patients, but this difference was not significant (p<0.2). Moreover, sera from gastric cancer patients showed values lower than those from non-ulcer dyspepsia patients (p<0.019). These results indicate that, in the Chilean population, antibodies raised against VacA and A 7 are not markers either for duodenal ulcer or for gastric cancer.

Varicocele-associated decrease in antioxidant defenses

Varicocele is associated with an oxidative stress condition. We have measured the antioxidant defenses of varicocele patients both at the local (seminal plasma) and systemic (blood plasma) levels. The antioxidant defenses, as evaluated by the total reactive antioxidant potential parameter, decrease both in the seminal (controls 676+/-128; patients = 386+/-186) and blood (controls = 519+/-63; patients = 268+/-110) plasma of varicocele patients. Compared with controls, patients with both normal spermiograms and spermiograms altered in motility or morphology demonstrated lower values. The results obtained suggest that varicocele-associated oxidative stress is evidenced both at the local and systemic levels. This conclusion is supported by results showing that urinary spontaneous chemiluminescence is also significantly increased in the patients.

Selective regulation of integrin--cytoskeleton interactions by the tyrosine kinase Src

Cell motility on extracellular-matrix (ECM) substrates depends on the regulated generation of force against the substrate through adhesion receptors known as integrins. Here we show that integrin-mediated traction forces can be selectively modulated by the tyrosine kinase Src. In Src-deficient fibroblasts, cell spreading on the ECM component vitronectin is inhibited, while the strengthening of linkages between integrin vitronectin receptors and the force-generating cytoskeleton in response to substrate rigidity is dramatically increased. In contrast, Src deficiency has no detectable effects on fibronectin-receptor function. Finally, truncated Src (lacking the kinase domain) co-localizes to focal-adhesion sites with alpha v but not with beta 1 integrins. These data are consistent with a selective, functional interaction between Src and the vitronectin receptor that acts at the integrin-cytoskeleton interface to regulate cell spreading and migration.

Construction of a gene encoding the insect bactericidal protein attacin. Studies on its expression in Escherichia coli

Attacin, a bactericidal small protein is produced by the giant silk moth Hyalophora cecropia. This paper deals with our efforts to clone the attacin cDNA in a bacterial vector to express it in Escherichia coli and produce the protein in sufficient amount, for further studies. We chose two inducible expression vector/bacterial cell systems: pPL-lambda/N99cI+ cells which is able to be induced by nalidixic acid, and pET3d/BL21(DE3) cells carrying a T7 RNA polymerase gene which is IPTG-inducible. After cloning in the pPL-lambda system and under no addition of the inducer, isolated transformants carried this plasmid with at least 2 concurrent deletions that drastically affected attacin expression, even though attacin gene seems to be intact as deduced by its PCR amplification. It was concluded that basal attacin expression occurred in this system and bacterial growth was limited. Plasmid deletions may have emerged by selection pressure as a way to avoid bactericidal expression and allow bacteria survival. The second cloning attempt was done in pET3d vector/BL21 cells, that should not express the cloned sequence (they lack T7 RNA polymerase gene). Transformed BL21 cells gave 3 recombinant plasmids, 2 of them presented a C deletion that generated an early stop signal in the attacin coding region. The third clone, pET-ATT18, carrying an intact gene, was transferred to BL21(DE3)-IPTG inducible cells in order to be expressed. Attacin was undetectable in stained gels or by Western blot analysis. However, expression was visualized in grown cells after 30 min of IPTG induction and 5 min of [35S]-methionine labeling, as a 22.5 kDa protein band by using gel electrophoresis and fluorography. This low level of expression drastically affected bacterial growth. Considering that attacin has no lytic activity, these results suggest that this molecule should block bacterial growth directly at the cytoplasm by an unknown mechanism, since no signal peptide coding sequence was incorporated in this gene construction, precluding periplasmic or external destination of this protein.

NMDA-NR1 receptor subunit mRNA expression in rat brain after 6-OH-dopamine induced lesions: a non-isotopic in situ hybridization study

Antisense digoxigenin-labeled deoxyoligonucleotides probes and non-isotopic in situ hybridization (HIS) techniques have been used to explore the NMDA-NR1 receptor subunit mRNA distribution in different brain areas of rats which had their dopaminergic nigrostriatal pathway previously lesioned with intracerebral administration of 6-OH-dopamine (6-OH-DA). Intense and significant hybridization signals for NR1 mRNA were found in dentate gyrus and regions CA1-CA2-CA3 of the hippocampus, in layers II-III and V-VI of the cerebral cortex, and in the cerebellum of sham-treated rats. Basal ganglia structures such as the striatum exhibited few NR1 mRNA hybridization signals as compared to the hippocampus and cerebral cortex. In contrast, both zona compacta and reticulata of substantia nigra (SN) showed a reduced number of cells with nevertheless intense NR1 mRNA HIS signals. The NR1 mRNA distribution in the brain was affected in a brain regional selective manner by 6-OH-DA induced lesions of DA neuronal systems. A striking increase in NR1 mRNA HIS signals was observed in both striata after unilateral lesioning with 6-OH-DA. Instead, in SN compacta but not in reticulata, a moderate but significant bilateral reduction of NR1 mRNA was observed after unilateral 6-OH-DA injection. No significant changes in NR1 mRNA were detected in cerebral cortex and other brain regions after 6-OH-DA treatment. These studies, and others reported in the literature, support the view that extensive lesions of nigrostriatal DA-containing neurons in the brain may trigger compensatory or adaptative responses in basal ganglia structures such as striatum and substantia nigra which involve glutamateric neurons and the genic expression of NMDA receptors.

Discrete transcripts encode multiple chitinase isoforms in Brugian microfilariae

The blood-borne microfilariae of the Brugian nematodes produce multiple isoforms of chitinase, whose expression is coincident with the onset of microfilarial infectivity for mosquitoes. A single cDNA sequence was previously obtained by screening a Brugia malayi microfilarial cDNA library, yet two chitinase isozymes are readily distinguished in this species. In this paper, we present evidence for the existence of multiple transcripts encoding Brugian microfilarial chitinases. Using primers based on the previously-sequenced cDNA clone, we amplified and sequenced two discrete products from B. malayi microfilarial RNA by RT-PCR. While the shorter fragment was nearly identical to the previously sequenced cDNA, the larger fragment contained an extra copy of a serine/threonine-rich repeat. RNAse protection assays were used to demonstrate that both sequences represent true transcripts, and not PCR artifacts. Using primers based on the B.malayi sequence, two novel sequences were generated by RT-PCR from B. pahangi microfilariae. Homologous and cross-species RNAse protection assays verified that multiple transcripts also encode chitinase isozymes in B. pahangi microfilariae.

Expression of recombinant microfilarial chitinase and analysis of domain function

A family of chitinase isozymes was previously characterized from the microfilariae of Brugia malayi and Brugia pahangi. The expression of these enzymes correlates with the onset of microfilarial infectivity for the mosquito vector. To study the role of chitinase activity in filarial transmission, the p70 chitinase from Brugia malayi was cloned and expressed in two forms: a full-length product of approximately 62 kDa and a truncated product of 43 kDa containing only the N-terminal catalytic domain. Two epitopes defined by monoclonal antibodies were preserved only in the full-length recombinant enzyme. It was found that deletion of the cysteine-rich C-terminal domain increased the yield of the recombinant expression product, and did not affect the K(m) for di- or trisaccharide substrates. However, affinity for high molecular weight chitin was specific to the full-length molecule, and is apparently mediated by the cysteine-rich domain, suggesting a role for this part of the protein in targeting the secreted enzyme to its substrate.

Rotavirus detection by dot blot hybridization assay using a non-radioactive synthetic oligodeoxynucleotide probe

A synthetic oligodeoxynucleotide of 40 nucleotides corresponding to nucleotides 33-72 of the gene coding for the viral protein VP7 of rotavirus, was used as a nucleic acid probe to develop a non-radioactive hybridization method for rotavirus detection. The probe was labelled at the 3' end with biotin-7-dATP. The sensitivity and specificity of the dot blot hybridization assay for rotavirus detection was evaluated with 303 stool specimens. The results indicate that the hybridization assay has a higher sensitivity than both PAGE and EIA. Among the rotavirus strains tested 37 different electropherotypes were found. The results suggest that rotavirus diagnosis by dot hybridization using a non-radioactive probe may become routine laboratory procedure because it is simple, highly specific and very sensitive.

[Isolation of transcription promoters from Thiobacillus ferrooxidans and T. acidophilus and its introduction by conjugation to T. intermedius]

The chemolithotrophic acidophilic bacteria, Thiobacillus ferrooxidans is considered as the most important microorganism in relation to copper and uranium bioleaching ability. Since T. ferrooxidans is a strict chemolithotrophic microorganism, its genetic manipulation is a very hard task. Until now, all efforts have been unsuccessful. Therefore, we decided to approach the problem in steps, trying initially to manipulate some T. ferrooxidans related strains. We chose Thiobacillus acidophilus that shares its habitat with T. ferrooxidans and Thiobacillus intermedius, for its heterotrophic nature that makes them easier to grow and suitable for heterologous conjugation. The main objective of this work was directed towards the isolation and characterization of transcription promoters from T. acidophilus and T. ferrooxidans genomic DNA. Four different promoters from T. acidophilus and four from T. ferrooxidans were isolated and sequenced. In order to test their functional capacity in bacterial systems different from E. coli, they were subcloned and transferred to other bacteria. One of these recombinant plasmids was successfully transferred to T. intermedius and from it to Ps. putida. The subcloned promoter was able to confer streptomycin resistance to Ps. putida.

[Synthesis and secretion of the surface antigen from hepatitis B virus in animal cell cultures]

Stable mammalian cell lines synthesizing and secreting Hepatitis B surface particles have been obtained through genetic engineering techniques. These particles show by electron microscopy a size of 22 nm, they are structurally and immunochemically similar to the particles present in the plasma from chronic hepatitis B patients. Therefore these particles are an excellent source for the preparation of a vaccine against the virus.

Molecular cloning and expression in E. coli of a Salmonella typhi porin gene

Immunoscreening of a Salmonella typhi cosmid library in E. coli allowed the detection of clones producing a 36 kDa porin from S. typhi. The gene is efficiently expressed in an E. coli porin-less mutant and the protein is exported to the outer membrane envelope. Two clones which markedly differ in their level of expression have been isolated.

The yeast tRNA(Phe) gene family: structures and transcriptional activities reveal member differences not explained by intragenic promoters

Several cloned members of the yeast tRNA(Phe) gene family were transcribed in vitro using a HeLa extract and a yeast extract. The optimum DNA concentration was determined and kinetic experiments were performed for each clone to compare transcription levels. Both extract systems were able to splice the intervening sequence, but only the yeast extract produced the mature product. Some genes were not transcribed with the homologous system while they were transcribed with the HeLa extract, suggesting a control mechanism that is not operating in the heterologous system. Competition experiments demonstrated that the intragenic promoters of the inactive genes were able to bind transcription factor(s), but not as efficiently as active genes. This binding was not so strong when using linear DNA and was dependent on the presence of the 3' intragenic control region. DNA sequencing and computer analysis indicated the presence of short conserved sequences upstream from the genes. These sequences, which are not related to the intragenic promoters, are direct repeats of part of the 3' coding region in those genes that are transcribed in the homologous system. The relevance of these sequences on homologous transcription in vitro remains to be established.

Nucleotide sequence of a yeast tRNAArg3A gene and its transcription in a homologous in vitro system

Twelve bacterial clones containing complementary sequences to yeast tRNAArg3 were isolated from a gene library. The size of the yeast BamHI inserts ranges from 5.4 to 10 MDa. There are at least 6 copies of this gene in different loci of the yeast genome. Insert from clone pYAT-3 was mapped, and the presence of a tRNAArg3A gene was confirmed by DNA sequence. The coding region is colinear with the transcriptional product. Unlike other reported tRNAArg3A genes, this one is not linked to a tRNAAsp gene. In vitro transcription using a yeast extract produces a transcript of 76 +/- 1 bases.

Isolation and structure of a yeast initiator tRNAmet gene

Sixteen bacterial clones containing yeast initiator tRNAmet genes have been isolated. The size of the BamHI fragments encoding these genes ranges from 4,000 to 23,000 base pairs. The nucleotide sequence of one member of this group has been determined. It has no intervening sequences.

Yeast tRNA3Leu gene transcribed and spliced in a HeLa cell extract

A cloned yeast tRNA3Leu gene containing a 33-base intervening sequence (IVS) is selectively transcribed by a soluble extract from HeLa cells. The 130-nucleotide tRNA3Leu precursor RNA formed is colinear with the gene and contains approximately 4 leader nucleotides and up to 9 trailer nucleotides. The IVS is accurately and efficiently removed by an endogenous HeLa excision-ligase activity to yield the spliced tRNA, the free IVS, and the half-tRNA intermediates. The splicing reaction occurs without prior 5' and 3' maturation of the precursor but, with this exception, this pattern of synthesis and subsequent maturation of the tRNA3Leu precursor conforms to the scheme for tRNA biosynthesis deduced for the xenopus system. Indeed, the two systems utilize similar or identical tRNA3Leu precursors. Our results stress the extraordinary conservation of tRNA biosynthesis in eukaryotes and demonstrate that a HeLa extract provides a useful system for investigating this process.

The pH dependence of rat liver RNA polymerases I and II

The effect of pH on the stability and activity of rat liver RNA polymerases I (A) and II (B) has been studied. Both enzymes are irreversibly inactivated in buffer solutions below pH 5.0. Km values of the two enzymes are constant between pH 6.5 and 8.7 but a two -to three- fold increase is observed between pH 8.7 and 9.7. The Vmax versus pH profiles are bell-shaped curves indicating the participation of two ionizing groups with apparent pKa values of 6.5 and 9.8 for enzyme I and 6.7 and 9.9 for enzyme II. Both enzymes are inactivated by photooxidation in the presence of Rose Bengal. It is suggested that the above pKa corresponds to the imidazole of a histidine residue and a amino group of a lysine residue.

Isolation of yeast tRNALeu genes. DNA sequence of a cloned tRNALeu3 gene

A library of cloned yeast DNA fragments generated by digestion of yeast DNA with the restriction endonuclease Bam HI has been screened by colony hybridization to total yeast [32P]tRNA. Four hundred colonies carrying yeast tRNA genes were isolated. By hybridization to 125I-tRNALeu3, we have isolated from this collection 14 colonies carrying fragments containing yeast tRNALeu genes. The size of the yeast Bam HI inserts ranged from 2.45 x 10(6) to 14 x 10(6) daltons. One of these fragments was mapped in detail by restriction endonuclease digestion and hybridization to 125I-tRNALeu3. The presence of a tRNALeu3 gene was confirmed by DNA sequence. The results indicate that the tRNALeu3 coding region is not co-linear with the tRNALeu3. An intervening tract of 33 base pairs interrupts the coding sequences 1 base pair past the anticodon coding region. The putative structure of a tRNALeu3 precursor is deduced in which the anticodon base pairs with residues from the intervening sequence.

Structure of yeast phenylalanine-tRNA genes: an intervening DNA segment within the region coding for the tRNA

Sixteen bacterial clones containing sequences complementary to yeast PhetRNA were isolated from a collection of hybrid plasmids containing BamHI restriction endonuclease-generated yeast DNA fragments inserted in the plasmid vector pBR315. Ten of these clones contained hybrid plasmids with distinct BamHI fragments. The sequence of the Phe-tRNA structural genes and adjacent regions of three of these clones is reported here. In the region flanking the tRNA gene, the sequence of two of the cloned DNAs is similar; the sequence of the third varies considerably. All three of the tRNA genes are bordered by A,T-rich regions. In particular, near the region coding for the 3' end of the tRNA there is a long sequence of As in the coding strand. This is reminiscent of the region of termination of transcription of the yeast 5S rRNA gene. The sequences coding for the Phe-tRNA contain an additional segment of 18 or 19 base pairs (depending upon the clone) not predicted by the yeast Phe-tRNA sequence. These intervening segments are nearly identical in the three clones and are located within the structural gene, two base pairs from the nucleotides coding for the tRNA anticodon.

Ribosomal RNA genes of Saccharomyces cerevisiae. II. Physical map and nucleotide sequence of the 5 S ribosomal RNA gene and adjacent intergenic regions

A DNA fragment containing the structural gene for the 5 S ribosomal RNA and intergenic regions before and after the 35 S ribosomal RNA precursor gene of Saccharomyces cerevisiae has been amplified in a bacterial plasmid and physically mapped by restriction endonuclease cleavage and hybridization to purified yeast 5 S ribosomal RNA. The nucleotide sequence of the DNA fragments carrying the 5 S ribosomal RNA gene and adjacent regions has been determined. The sequence unambiguously identifies the 5 S ribosomal RNA gene, determines its polarity within the ribosomal DNA repeating unit, and reveals the structure of its promoter and termination regions. Partial DNA sequence of the regions near the beginning and end of the 35 S ribosomal RNA gene has also been determined as a preliminary step in establishing the structure of promoter and termination regions for the 35 S ribosomal RNA gene.

Inactivation of rat liver RNA polymerases I and II and yeast RNA polymerase I by pyrodixal 5'-phosphate. Evidence for the participation of lysyl residues at the active site

Purified DNA-dependent RNA polymerase forms I (A) and II (B) from rat liver and form I from yeast are rapidly inactivated by pyridoxal 5'-phosphate at pH 8.0. The inhibition is relatively specific since pyridoxamine 5'-phosphate is not an inhibitor and pyridoxal is about 12 times less effective than pyridoxal 5'-phosphate. The inactivation is reversed by high concentrations of amines, and can be made irreversible by reduction with NaBH4. Spectral analysis of the inhibited enzyme and its NaBH4 reduction product indicates that a Schiff base forms between the aldehyde group of pyridoxal 5'-phosphate and one or more amino groups of the protein. Nepsilon-Pyridoxyllysine was identified as the only product in acid hydrolysates of the reduced yeast RNA polymerase I-pyridoxal 5'-phosphate complex. Complete inactivation of yeast polymerase I results in the incorporation of 3-4 mol of pyridoxal 5'-phosphate/1 mol of enzyme. DNA and nucleotide substrates partially protect the enzymes from inactivation. These results suggest that one or more lysyl amino groups are critical for the activity of animal RNA polymerases and show that pyridoxal 5'-phosphate is a suitable probe for studying the active sites of these enzymes. Comparison of the present results with those previously obtained with Eschericha coli RNA polymerase in this laboratory suggest a new degree of structural homology between eucaryotic and procaryotic RNA polymerases.