Software to Visualize Proteins and Perform Structural Alignments

Availability of protein structural data is accelerating at an astounding rate, facilitating in silico biochemical and biophysical analyses that require visualization methods. In particular, increased accessibility of representatives within respective protein families is empowering investigators to perform structural model comparisons that provide both functional and evolutionary insights at much more refined levels than previously possible. Numerous software platforms, including several free and open source versions, are available for users to interrogate protein structural models. In this article, three structural alignment protocols are described using freely available software to investigate aspects of protein structure evolution at quaternary, tertiary, and domain levels, respectively. Mapping distinct subunit interfaces and active site positioning within the PfpI/DJ-1 protein superfamily reveals quaternary structure that can have a prominent role in determination of distinct enzyme activities. In contrast, cytochrome c proteins are under strong evolutionary constraints due to their critical role in energy generation, and as a result, structural conservation is observed. However, substitutions within these conserved folds occur in distinct species, presumably to influence interactions with protein complexes involved in electron transport. Lastly, evolution of distinct allosteric mechanisms within winged helix-turn-helix transcriptional regulators, as well as protein dynamics, are revealed through visualization of metal- and redox-responsive DNA-binding proteins. The software platforms used in these protocols are Swiss-PDBViewer and PyMOL. Swiss-PDBViewer is an easy to implement, end-user software that is excellent for entry into protein visualization methods. PyMOL is also easy to implement, but offers greater depth for advanced investigations and visualizations, as well as the ability to capture protein structure conformational changes. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Exploring quaternary structure evolution with Swiss-PDBViewer Alternate Protocol: Exploring tertiary structure evolution with Swiss-PDBViewer Basic Protocol 2: Visualizing allostery using PyMOL.

Characterization of a Rhodobacter sphaeroides primary fatty acid kinase

Widely distributed among prokaryotes, short chain fatty acid kinases provide a path for fatty acid entry into central metabolic pathways. These enzymes catalyze the reversible, ATP-dependent synthesis of acyl-phosphates, which leads to the production of acyl-CoA derivatives by a coordinate acyltransferase. To date, characterized representatives of short chain fatty acid kinases exhibit relatively narrow substrate specificity. In this work, biochemical characterization of a predicted acetate kinase from Rhodobacter sphaeroides reveals a novel enzyme with broad substrate specificity for primary fatty acids of varying lengths (C2--C8).

Characterization of a butyrate kinase from Desulfovibrio vulgaris str. Hildenborough

Short and branched chain fatty acid kinases participate in both bacterial anabolic and catabolic processes, including fermentation, through the reversible, ATP-dependent synthesis of acyl phosphates. This study reports biochemical properties of a predicted butyrate kinase from Desulfovibrio vulgaris str. Hildenborough (DvBuk) expressed heterologously and purified from Escherichia coli. Gel filtration chromatography indicates purified DvBuk is active as a dimer. The optimum temperature and pH for DvBuk activity is 44°C and 7.5, respectively. The enzyme displays enhanced thermal stability in the presence of substrates as observed for similar enzymes. Measurement of kcat and KM for various substrates reveals DvBuk exhibits the highest catalytic efficiencies for butyrate, valerate and isobutyrate. In particular, these measurements reveal this enzyme's apparent high affinity for C4 fatty acids relative to other butyrate kinases. These results have implications on structure and function relationships within the ASKHA superfamily of phosphotransferases, particularly regarding the acyl binding pocket, as well as potential physiological roles for this enzyme in Desulfovibrio vulgaris str. Hildenborough.

Identification of SmtB/ArsR cis elements and proteins in archaea using the Prokaryotic InterGenic Exploration Database (PIGED)

Microbial genome sequencing projects have revealed an apparently wide distribution of SmtB/ArsR metal-responsive transcriptional regulators among prokaryotes. Using a position-dependent weight matrix approach, prokaryotic genome sequences were screened for SmtB/ArsR DNA binding sites using data derived from intergenic sequences upstream of orthologous genes encoding these regulators. Sixty SmtB/ArsR operators linked to metal detoxification genes, including nine among various archaeal species, are predicted among 230 annotated and draft prokaryotic genome sequences. Independent multiple sequence alignments of putative operator sites and corresponding winged helix-turn-helix motifs define sequence signatures for the DNA binding activity of this SmtB/ArsR subfamily. Prediction of an archaeal SmtB/ArsR based upon these signature sequences is confirmed using purified Methanosarcina acetivorans C2A protein and electrophoretic mobility shift assays. Tools used in this study have been incorporated into a web application, the Prokaryotic InterGenic Exploration Database (PIGED; http://bioinformatics.uwp.edu/~PIGED/home.htm), facilitating comparable studies. Use of this tool and establishment of orthology based on DNA binding signatures holds promise for deciphering potential cellular roles of various archaeal winged helix-turn-helix transcriptional regulators.

Prophage Finder: a prophage loci prediction tool for prokaryotic genome sequences

Prophage loci often remain under-annotated or even unrecognized in prokaryotic genome sequencing projects. A PHP application, Prophage Finder, has been developed and implemented to predict prophage loci, based upon clusters of phage-related gene products encoded within DNA sequences. This application provides results detailing several facets of these clusters to facilitate rapid prediction and analysis of prophage sequences. Prophage Finder was tested using previously annotated prokaryotic genomic sequences with manually curated prophage loci as benchmarks. Additional analyses from Prophage Finder searches of several draft prokaryotic genome sequences are available through the Web site (http://bioinformatics.uwp.edu/~phage/DOEResults.php) to illustrate the potential of this application.

GAPDH as a housekeeping gene: analysis of GAPDH mRNA expression in a panel of 72 human tissues

Quantitative gene expression data are often normalized to the expression levels of control or so-called “housekeeping” genes. An inherent assumption in the use of housekeeping genes is that expression of the genes remains constant in the cells or tissues under investigation. Although exceptions to this assumption are well documented, housekeeping genes are of value in fully characterized systems. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is one of the most commonly used housekeeping genes used in comparisons of gene expression data. To investigate the value of GAPDH as a housekeeping gene in human tissues, the expression of GAPDH mRNA was measured in a panel of 72 different pathologically normal human tissue types. Measurements were obtained from 371,088 multiplexed, quantitative real-time RT-PCRs with specific target genes. Significant differences in the expression levels of GAPDH mRNA were observed between tissue types and between donors of the same tissue. A 15-fold difference in GAPDH mRNA copy numbers was observed between the highest and lowest expressing tissue types, skeletal muscle and breast, respectively. No specific effect of either age or gender was observed on GAPDH mRNA expression. These data provide an extensive analysis of GAPDH mRNA expression in human tissues and confirm previous reports of the marked variability of GAPDH expression between tissue types. These data establish comparative levels of expression and can be used to add value to gene expression data in which GAPDH is used as the internal control.

Neuroprotection in a rat Parkinson model by GDNF gene therapy using EIAV vector

Vectors based on lentiviruses are opening up new approaches for the treatment of neurodegenerative diseases. Currently, the equine infectious anaemia virus (EIAV) vector is one of the most attractive gene delivery systems with respect to neuronal tropism. The aim was to validate EIAV-lentiviral vectors as a gene delivery system for neurotrophic factor genes in an animal model of Parkinson's disease. EIAV carrying the glial cell line-derived neurotrophic factor (GDNF) gene was unilaterally injected into rat striatum and above the substantia nigra (SN). One week later, the rats received a 6-OHDA lesion into the ipsilateral striatum. GDNF delivery led to extensive expression of GDNF protein within the striatum. In addition, near complete protection against dopaminergic cell death was observed in the GDNF-treated group.

Identification of potential stroke targets by lentiviral vector mediated overexpression of HIF-1 alpha and HIF-2 alpha in a primary neuronal model of hypoxia

The identification of genes differentially regulated by ischemia will lead to an improved understanding of cell death pathways such as those involved in the neuronal loss observed following a stroke. Furthermore, the characterization of such pathways could facilitate the identification of novel targets for stroke therapy. We have used a novel approach to amplify differential gene expression patterns in a primary neuronal model of stroke by employing a lentiviral vector system to specifically bias the transcriptional activation of hypoxically regulated genes. Overexpression of the hypoxia-induced transcription factor subunits HIF-1 alpha and HIF-2 alpha elevated hypoxia-mediated transcription of many known HIF-regulated genes well above control levels. Furthermore, many potentially novel HIF-regulated genes were discovered that were not previously identified as hypoxically regulated. Most of the novel genes identified were activated by a combination of HIF-2 alpha overexpression and hypoxic insult. These included several genes with particular importance in cell survival pathways and of potential therapeutic value. Hypoxic induction of HIF-2 alpha may therefore be a critical factor in mediating protective responses against ischemic injury. Further investigation of the genes identified in this study may provide increased understanding of the neuronal response to hypoxia and may uncover novel therapeutic targets for the treatment of cerebral ischemia.

Multicistronic lentiviral vector-mediated striatal gene transfer of aromatic L-amino acid decarboxylase, tyrosine hydroxylase, and GTP cyclohydrolase I induces sustained transgene expression, dopamine production, and functional improvement in a rat model of Parkinson's disease

Parkinson's disease (PD) is a neurodegenerative disorder characterized by the selective loss of dopaminergic neurons in the substantia nigra. This loss leads to complete dopamine depletion in the striatum and severe motor impairment. It has been demonstrated previously that a lentiviral vector system based on equine infectious anemia virus (EIAV) gives rise to highly efficient and sustained transduction of neurons in the rat brain. Therefore, a dopamine replacement strategy using EIAV has been investigated as a treatment in the 6-hydroxydopamine (6-OHDA) animal model of PD. A self-inactivating EIAV minimal lentiviral vector that expresses tyrosine hydroxylase (TH), aromatic amino acid dopa decarboxylase (AADC), and GTP cyclohydrolase 1 (CH1) in a single transcription unit has been generated. In cultured striatal neurons transduced with this vector, TH, AADC, and CH1 proteins can all be detected. After stereotactic delivery into the dopamine-denervated striatum of the 6-OHDA-lesioned rat, sustained expression of each enzyme and effective production of catecholamines were detected, resulting in significant reduction of apomorphine-induced motor asymmetry compared with control animals (p < 0.003). Expression of each enzyme in the striatum was observed for up to 5 months after injection. These data indicate that the delivery of three catecholaminergic synthetic enzymes by a single lentiviral vector can achieve functional improvement and thus open the potential for the use of this vector for gene therapy of late-stage PD patients.

Retinoic acid receptor beta2 and neurite outgrowth in the adult mouse spinal cord in vitro

Retinoic acid, acting through the nuclear retinoic acid receptor beta2 (RARbeta2), stimulates neurite outgrowth from peripheral nervous system tissue that has the capacity to regenerate neurites, namely, embryonic and adult dorsal root ganglia. Similarly, in central nervous system tissue that can regenerate, namely, embryonic mouse spinal cord, retinoic acid also stimulates neurite outgrowth and RARbeta2 is upregulated. By contrast, in the adult mouse spinal cord, which cannot regenerate, no such upregulation of RARbeta2 by retinoic acid is observed and no neurites are extended in vitro. To test our hypothesis that the upregulation of RARbeta2 is crucial to neurite regeneration, we have transduced adult mouse or rat spinal cord in vitro with a minimal equine infectious anaemia virus vector expressing RARbeta2. After transduction, prolific neurite outgrowth occurs. Outgrowth does not occur when the cord is transduced with a different isoform of RARbeta nor does it occur following treatment with nerve growth factor. These data demonstrate that RARbeta2 is involved in neurite outgrowth, at least in vitro, and that this gene may in the future be of some therapeutic use.

The genome of M. acetivorans reveals extensive metabolic and physiological diversity

Methanogenesis, the biological production of methane, plays a pivotal role in the global carbon cycle and contributes significantly to global warming. The majority of methane in nature is derived from acetate. Here we report the complete genome sequence of an acetate-utilizing methanogen, Methanosarcina acetivorans C2A. Methanosarcineae are the most metabolically diverse methanogens, thrive in a broad range of environments, and are unique among the Archaea in forming complex multicellular structures. This diversity is reflected in the genome of M. acetivorans. At 5,751,492 base pairs it is by far the largest known archaeal genome. The 4524 open reading frames code for a strikingly wide and unanticipated variety of metabolic and cellular capabilities. The presence of novel methyltransferases indicates the likelihood of undiscovered natural energy sources for methanogenesis, whereas the presence of single-subunit carbon monoxide dehydrogenases raises the possibility of nonmethanogenic growth. Although motility has not been observed in any Methanosarcineae, a flagellin gene cluster and two complete chemotaxis gene clusters were identified. The availability of genetic methods, coupled with its physiological and metabolic diversity, makes M. acetivorans a powerful model organism for the study of archaeal biology. [Sequence, data, annotations and analyses are available at http://www-genome.wi.mit.edu/.]

Link between the membrane-bound pyridine nucleotide transhydrogenase and glutathione-dependent processes in Rhodobacter sphaeroides

The presence of a glutathione-dependent pathway for formaldehyde oxidation in the facultative phototroph Rhodobacter sphaeroides has allowed the identification of gene products that contribute to formaldehyde metabolism. Mutants lacking the glutathione-dependent formaldehyde dehydrogenase (GSH-FDH) are sensitive to metabolic sources of formaldehyde, like methanol. This growth phenotype is correlated with a defect in formaldehyde oxidation. Additional methanol-sensitive mutants were isolated that contained Tn5 insertions in pntA, which encodes the alpha subunit of the membrane-bound pyridine nucleotide transhydrogenase. Mutants lacking transhydrogenase activity have phenotypic and physiological characteristics that are different from those that lack GSH-FDH activity. For example, cells lacking transhydrogenase activity can utilize methanol as a sole carbon source in the absence of oxygen and do not display a formaldehyde oxidation defect, as determined by whole-cell (13)C-nuclear magnetic resonance. Since transhydrogenase can be a major source of NADPH, loss of this enzyme could result in a requirement for another source for this compound. Evidence supporting this hypothesis includes increased specific activities of other NADPH-producing enzymes and the finding that glucose utilization by the Entner-Doudoroff pathway restores aerobic methanol resistance to cells lacking transhydrogenase activity. Mutants lacking transhydrogenase activity also have higher levels of glutathione disulfide under aerobic conditions, so it is consistent that this strain has increased sensitivity to oxidative stress agents like diamide, which are known to alter the oxidation reduction state of the glutathione pool. A model will be presented to explain the role of transhydrogenase under aerobic conditions when cells need glutathione both for GSH-FDH activity and to repair oxidatively damaged proteins.

Rabies virus glycoprotein pseudotyping of lentiviral vectors enables retrograde axonal transport and access to the nervous system after peripheral delivery

In this report it is demonstrated for the first time that rabies-G envelope of the rabies virus is sufficient to confer retrograde axonal transport to a heterologous virus/vector. After delivery of rabies-G pseudotyped equine infectious anaemia virus (EIAV) based vectors encoding a marker gene to the rat striatum, neurons in regions distal from but projecting to the injection site, such as the dopaminergic neurons of the substantia nigra pars compacta, become transduced. This retrograde transport to appropriate distal neurons was also demonstrated after delivery to substantia nigra, hippocampus and spinal cord and did not occur when vesicular stomatitis virus glycoprotein (VSV-G) pseudotyped vectors were delivered to these sites. In addition, peripheral administration of rabies-G pseudotyped vectors to the rat gastrocnemius muscle leads to gene transfer in motoneurons of lumbar spinal cord. In contrast the same vector pseudotyped with VSV-G transduced muscle cells surrounding the injection site, but did not result in expression in any cells in the spinal cord. Long-term expression was observed after gene transfer in the nervous system and a minimal immune response which, together with the possibility of non-invasive administration, greatly extends the utility of lentiviral vectors for gene therapy of human neurological disease.

The home stretch, a first analysis of the nearly completed genome of Rhodobacter sphaeroides 2.4.1

Rhodobacter sphaeroides 2.4.1 is an alpha-3 purple nonsulfur eubacterium with an extensive metabolic repertoire. Under anaerobic conditions, it is able to grow by photosynthesis, respiration and fermentation. Photosynthesis may be photoheterotrophic using organic compounds as both a carbon and a reducing source, or photoautotrophic using carbon dioxide as the sole carbon source and hydrogen as the source of reducing power. In addition, R. sphaeroides can grow both chemoheterotrophically and chemoautotrophically. The structural components of this metabolically diverse organism and their modes of integrated regulation are encoded by a genome of approximately 4.5 Mb in size. The genome comprises two chromosomes CI and CII (2.9 and 0.9 Mb, respectively) and five other replicons. Sequencing of the genome has been carried out by two groups, the Joint Genome Institute, which carried out shotgun-sequencing of the entire genome and The University of Texas-Houston Medical School, which carried out a targeted sequencing strategy of CII. Here we describe our current understanding of the genome when data from both of these groups are combined. Previous work had suggested that the two chromosomes are equal partners sharing responsibilities for fundamental cellular processes. This view has been reinforced by our preliminary analysis of the virtually completed genome sequence. We also have some evidence to suggest that two of the plasmids, pRS241a and pRS241b encode chromosomal type functions and their role may be more than that of accessory elements, perhaps representing replicons in a transition state.

The role of histidines in the acetate kinase from Methanosarcina thermophila

The role of histidine in the catalytic mechanism of acetate kinase from Methanosarcina thermophila was investigated by diethylpyrocarbonate inactivation and site-directed mutagenesis. Inactivation was accompanied by an increase in absorbance at 240 nm with no change in absorbance at 280 nm, and treatment of the inactivated enzyme with hydroxylamine restored 95% activity, results that indicated diethylpyrocarbonate inactivates the enzyme by the specific modification of histidine. The substrates ATP, ADP, acetate, and acetyl phosphate protected against inactivation suggesting at least one active site where histidine is modified. Correlation of residual activity with the number of histidines modified, as determined by absorbance at 240 nm, indicated that a maximum of three histidines are modified per subunit, two of which are essential for full inactivation. Comparison of the M. thermophila acetate kinase sequence with 56 putative acetate kinase sequences revealed eight highly conserved histidines, three of which (His-123, His-180, and His-208) are perfectly conserved. Diethylpyrocarbonate inactivation of the eight histidine --> alanine variants indicated that His-180 and His-123 are in the active site and that the modification of both is necessary for full inactivation. Kinetic analyses of the eight variants showed that no other histidines are important for activity. Analysis of additional His-180 variants indicated that phosphorylation of His-180 is not essential for catalysis. Possible functions of His-180 are discussed.

Reconstructing smell

Odorant signal transduction and neurogenesis are fundamental properties of the olfactory epithelium. Many preparations have been used to elucidate some of the mechanisms underlying these properties. In this article, we briefly review these research areas and describe some of the techniques used to obtain the data. We focus specifically on the cell-culture paradigm and the data obtained from various immortal cell lines in their attempts to reconstruct the olfactory epithelium in vitro.

Isolation and in vitro differentiation of conditionally immortalized murine olfactory receptor neurons

Two major challenges exist in our understanding of the olfactory system. One concerns the enormous combinatorial code underlying odorant discrimination by odorant receptors. The other relates to neurogenesis and neuronal development in the olfactory epithelium. To address these issues, continuous cell cultures containing olfactory receptor neurons (ORNs) were obtained from olfactory epithelia of H-2K(b)-tsA58 transgenic mice. ORNs were detected and characterized by immunocytochemistry, RT-PCR, and Western blot for the markers Galpha(olf), adenylyl cyclase III, the olfactory cyclic nucleotide-gated channel subunits, and olfactory marker protein. In culture, epidermal growth factor and nerve growth factor stimulated proliferation, and brain-derived neurotrophic factor and neurotrophin-3 induced cellular maturation. Clonal cell lines were isolated by fluorescence-activated cell sorting with anti-neural cell adhesion molecule antibodies, and of 144 single cells plated, 39 clones were expanded, propagated, and stored in liquid nitrogen. All attempts at recovery of clonal lines from frozen stocks have been successful. The most thoroughly characterized clone, 3NA12, expressed ORN markers and responded to stimulation by single odorants. Each odorant activated approximately 1% of cells in a clonal line, and this suggests that many different odorant receptors may be expressed by these clonal cells. Therefore, these cell lines and the method by which they have been obtained represent a significant advance in the generation of olfactory cell cultures and provide a system to investigate odorant coding and olfactory neurogenesis.

Pathways for transcriptional activation of a glutathione-dependent formaldehyde dehydrogenase gene

The widespread occurrence of glutathione-dependent formaldehyde dehydrogenases (GSH-FDH) suggests that this enzyme serves a conserved function in preventing the cytogenetic and potentially lethal interaction of formaldehyde with nucleic acids, proteins and other cell constituents. Despite this potential role of GSH-FDH, little is known about how its expression is regulated. Here, we identify metabolic and genetic signals that activate transcription of a GSH-FDH gene (adhI) in the bacterium Rhodobacter sphaeroides. Activity of the adhI promoter is increased by both exogenous formaldehyde and metabolic sources of this toxin. Elevated adhI promoter activity in DeltaGSH-FDH mutants implicates formaldehyde or the glutathione adduct that serves as a GSH-FDH substrate, S-hydroxymethylglutathione, as a transcriptional effector. From studying adhI expression in different host mutants, we find that the photosynthetic response regulator PrrA and the trans-acting spd-7 mutation increase function of this promoter. The behavior of a nested set of adhI::lacZ fusions indicates that activation by formaldehyde, PrrA and spd-7 requires only sequences 55 bp upstream of the start of transcription. A working model is presented to explain how GSH-FDH expression responds to formaldehyde and global signals generated from the reduced pyridine nucleotide produced by the activity of this enzyme.

Function of a glutathione-dependent formaldehyde dehydrogenase in Rhodobacter sphaeroides formaldehyde oxidation and assimilation

Despite its reactivity with many biological molecules, formaldehyde can be commonly encountered by virtually all cells. The widespread existence of glutathione-dependent formaldehyde dehydrogenases (GSH-FDH) in procaryotes and eucaryotes suggests this enzyme plays a central and universal role in biological formaldehyde oxidation. This work sought to determine the role of GSH-FDH in the facultative phototrophic bacterium Rhodobacter sphaeroides. Growth phenotypes of wild-type and mutant cells, changes in enzyme specific activities, and the pattern of 13C-labeled compounds detected by NMR spectroscopy cumulatively suggest that R. sphaeroides GSH-FDH can play a critical role in formaldehyde metabolism under both photosynthetic and aerobic respiratory conditions. In photosynthetic cells, the data indicate that GSH-FDH generates reducing power, in the form of NADH, and one-carbon skeletons that are oxidized to carbon dioxide for subsequent assimilation by the Calvin-Benson-Bassham cycle. For example, use of methanol as a sole photosynthetic carbon source increases the specific activities of GSH-FDH, an NAD-dependent formate dehydrogenase, and the key Calvin-Benson-Bassham cycle enzyme, ribulose-1,5-bisphosphate carboxylase. This role of GSH-FDH is also supported by the pattern of [13C]formaldehyde oxidation products that accumulate in photosynthetic cells and the inability of defined GSH-FDH or Calvin cycle mutants to use methanol as a sole carbon source. Our data also suggest that GSH-FDH acts in formaldehyde dissimilation when aerobic respiratory cultures cometabolize methanol and succinate.

Potassium conductances and proliferation in conditionally immortalized renal glomerular mesangial cells from the H-2Kb-tsA58 transgenic mouse

The effects of the temperature-sensitive, immortalizing Simian Virus 40 T antigen, tsA58, on whole-cell potassium conductances were assessed in renal glomerular mesangial cells from H-2Kb-tsA58 transgenic mice [1]. MTT cell viability assay data indicated that in permissive (33 degrees C, 50 U ml-1 gamma-interferon, IFN+) and non-permissive (37 degrees C, without gamma-interferon, IFN-) culture conditions the oncogene was active and inactive respectively. In IFN+ cells whole-cell currents were inhibited by 10 mM 4-aminopyridine, 1 mM ATP and glibenclamide (glyburide, IC50 = 0.4 microM) and stimulated by cromakalim (EC50 = 40 microM). Furthermore, increases in pipette free calcium activity stimulated the potassium conductance (EC50 = 0.5 microM). Apamin inhibited this conductance (IC50 = 9 nM). None of these effects were observed in IFN- cells. The potassium conductance in IFN- cells was activated by a hyposmotic shock and this was inhibited by Gd3. These data indicate that (1) conductances consistent with ATP-sensitive and small, calcium-activated potassium channels are found in IFN+ cells, (2) an osmotically-sensitive channel is found in IFN- cells and (3) channel expression is dependent upon the activation of tsA58.

Inhibition by P1075 and pinacidil of a calcium-independent chloride conductance in conditionally-immortal renal glomerular mesangial cells

1. Depolarization of mesangial cells has been shown to occur following an outward movement of chloride ions from the cell. We have shown previously that mesangial cells from the H-2Kb-tsA58 transgenic mouse possess a significant whole-cell chloride conductance and consequently are a suitable preparation for the study of potential chloride channel inhibitors. 2. The effects on the whole-cell chloride conductance of the chloride channel inhibitor, 5-nitro-2-(3-phenylpropylamino)-benzoate (NPPB) and the potassium channel openers, (KCOs) P1075 and pinacidil were investigated in mesangial cells from the H-2Kb-tsA58 transgenic mouse cultured in permissive conditions (at 33 degrees C in the presence of 50 u ml-1 murine gamma-interferon). 3. In symmetrical solutions of 140 mM tetramethylammonium chloride (TMAC1) the whole-cell chloride conductance was 1.08 +/- 0.05 nS (n = 63) and this could be reversibly inhibited by 5 x 10(-5) M NPPB. 4. Both P1075 and pinacidil inhibited the whole-cell chloride conductance. This inhibition was not reversible after drug washout and was demonstrated only when drugs were applied to the extracellular surface of the cells. Very low concentrations of the drugs were found to reduce the chloride conductance after 16 h incubation but under no circumstances studied was the conductance totally inhibited, leaving a mean residual current of 0.33 +/- 0.03 nS (n = 12). 5. The effects of different peptide calcium concentrations on the magnitude of the residual current in the presence of the drugs were investigated. The residual current was reduced with 10(-8) M calcium in the pipette and increased with 10(-3) M pipette calcium. Therefore, these data suggest that P1075 and pinacidil selectively inhibit a calcium-independent chloride conductance in mesangial cells from the H-2Kb-tsA58 transgenic mouse.

Insulin restores the calcium-activated chloride conductance in dedifferentiated renal glomerular mesangial cells from the H-2KB-TSA58 [corrected] transgenic mouse

The effects of duration in culture were assessed in mesangial cells from the H-2Kb-tsA58 transgenic mouse using the whole-cell configuration of the patch clamp technique. The whole-cell potassium conductance remained constant in cells from passages 8-17 while the chloride conductance was found to decrease in cells after passage 15. This reduction of the chloride conductance, indicating cell dedifferentiation, was the result of complete loss of the calcium-activated component of the conductance and loss of part of the calcium-insensitive component. Insulin, which increases the calcium-sensitivity of the calcium-activated component of the chloride conductance in early passage cells, restored part of the calcium-sensitive component of the chloride conductance in dedifferentiated cells. Vasoactive agonists such as arginine vasopressin and angiotensin II stimulate a chloride-dependent depolarization in mesangial cells that initiates cell contraction. In view of the importance of the chloride flux it is possible that the loss of a significant magnitude of chloride conductance may underlie mesangial cell pathology to some degree. This is supported by data that show insulin can reverse many of the early renal changes observed in diabetic nephropathy and, as shown in this study, that insulin enhances the chloride conductance in dedifferentiated, cultured mesangial cells.

Characterization of a glutathione-dependent formaldehyde dehydrogenase from Rhodobacter sphaeroides

Glutathione-dependent formaldehyde dehydrogenases (GSH-FDH) represent a ubiquitous class of enzymes, found in both prokaryotes and eukaryotes. During the course of studying energy-generating pathways in the photosynthetic bacterium Rhodobacter sphaeroides, a gene (adhI) encoding a GSH-FDH homolog has been identified as part of an operon (adhI-cycI) that also encodes an isoform of the cytochrome c2 family of electron transport proteins (isocytochrome c2). Enzyme assays with crude Escherichia coli extracts expressing AdhI show that this protein has the characteristic substrate preference of a GSH-FDH. Ferguson plot analysis with zymograms suggests that the functional form of AdhI is a homodimer of approximately40-kDa subunits, analogous to other GSH-FDH enzymes. These properties of AdhI were used to show that mutations which increase or decrease adhI expression change the specific activity of GSH-FDH in R. sphaeroides extracts. In addition, expression of the presumed adhI-cycI operon appears to be transcriptionally regulated, since the abundance of the major adhI-specific primer extension product is increased by the trans-acting spd-7 mutation, which increases the level of both isocytochrome c2 and AdhI activity. While transcriptional linkage of adhI and cycI could suggest a function in a common metabolic pathway, isocytochrome c2 (periplasm) and AdhI (cytoplasm) are localized in separate compartments of R. sphaeroides. Potential roles for AdhI in carbon and energy generation and the possible relationship of GSH-FDH activity to isocytochrome c2 will be discussed based on the commonly accepted physiological functions of GSH-FDH enzymes in prokaryotes and eukaryotes.

A characterization of the chloride conductance in mesangial cells from the H-2Kb-tsA58 transgenic mouse

The chloride conductance of conditionally immortalized mesangial cells isolated from the H-2Kb-tsA58 transgenic mouse was studied in cells grown in permissive and non-permissive culture conditions. No differences were found in the magnitude of the chloride conductance in 140 mM tetramethyl ammonium chloride between cells grown in permissive and non-permissive culture conditions (1.08 +/- 0.05 nS and 1.02 +/- 0.05 nS). Selectivity sequences were defined as 1.8I- > 1.2Br- > lCl- and 1.3I- > 1.1Br- > lCl- respectively and both the anion channel inhibitors niflumic acid and ochratoxin A inhibited the chloride conductance in a dose-dependent manner. The chloride conductance was made up from calcium-dependent and calcium-independent components and in the presence of 1 microM free calcium in the pipette this could be increased by the presence of 100 U ml-1 insulin added to the incubation medium. This appeared to increase the sensitivity of the conductance to levels of intracellular calcium as no differences were observed in the presence of either 1 mM or 100 nM pipette calcium. These data indicate that there is a significant chloride conductance in mesangial cells from the H-2Kb-tsA58 transgenic mouse and minimal changes are observed with changes from permissive to non-permissive culture conditions.

Evidence for regular sporulation by Haplosporidium nelsoni (MSX) (Ascetospora; Haplosporidiidae) in spat of the American oyster, Crassostrea virginica

The spore stage of Haplosporidium nelsoni, the ascetosporan parasite causing multinucleated sphere unknown (MSX) disease in oysters, Crassostrea virginica, has been reported so rarely (less than 0.01% of infected oysters) that a second host has been postulated. However, recent intensive sampling of young (less than 1 year) oysters in Delaware Bay, U.S. suggests that spore formation occurs regularly in this group and that spores are produced in at least 75-85% of all infections reaching the advanced stage. Sporulation was seasonal, occurring over two to three weeks in late June/early July and again in late summer/early fall. Our data indicate that sporulation by H. nelsoni in oysters is more common than previously suspected, occurring in a segment of the host population that may not have been sufficiently sampled in the past, and that a direct life cycle should be reconsidered.

Cloning and characterization of a Bacteroides conjugal tetracycline-erythromycin resistance element by using a shuttle cosmid vector

The Bacteroides conjugal tetracycline resistance (Tcr) elements appear not to be plasmids. In many cases, resistance to erythromycin (Emr) is cotransferred with Tcr. Using a newly constructed shuttle cosmid, pNJR1, we cloned 44 to 50 kilobase pairs of a conjugal Tcr Emr element on overlapping cosmid clones. Cosmid libraries were made in Escherichia coli with DNA from the original clinical Bacteroides thetaiotaomicron DOT strain containing Tcr Emr-DOT or from a Bacteroides uniformis Tcr Emr-DOT transconjugant strain. The cosmid clones were mobilized from E. coli into B. uniformis in groups of 10 to 20 per filter mating, with selection for Tcr or Emr transconjugants. The Tcr and Emr genes were cloned both separately and together on 30-kilobase-pair fragments. Several of the Tcr clones also contained transfer genes that permitted self-transfer of the cosmid from B. uniformis donors to E. coli or B. uniformis recipients. Neither the Tcr nor the Emr gene conferred resistance on E. coli, and the transfer-proficient clones did not self-transfer out of E. coli. Southern blot analysis was used to compare DNA from independently isolated Bacteroides strains carrying conjugal Tcr or Tcr Emr elements and their respective B. uniformis transconjugants. Results of these analyses indicate that there are large regions of homology, including regions outside the Tcr and Emr genes, but that the elements are not identical. Some Tcr clones contained a region which hybridized to chromosomal DNA from the wild-type B. uniformis recipient strain that did not carry the Tcr Emr-DOT element. This region of homology appeared not to be a junction fragment. It was not required in a Bacteroides recipient for successful transfer of the Tcr Emr element. Although we are not sure we have cloned a junction fragment between the Tcr Emr-DOT element and the B. uniformis chromosome, the preliminary function and restriction map appears to be linear.