A novel rhodobacter sphaeroides expression system for real-time evaluation of heterologous protein expression levels

Heterologous protein expression levels can not be evaluated in real-time by experimental procedures commonly used for most expression systems during host cell culture. Rb. sphaeroides has provided an ideal system for studying both photosynthesis and membrane development and exhibited potential as a novel expression system. We constructed the puc1BA and puc2BA mutant strain Rb. sphaeroides CQU68 and used it as a novel expression system to heterologously express proteins fused to β-subunit of light-harvesting 2 complexes (LH2). The presence of LH2 with β-subunit fusion proteins was spectrally detected by the LH2 typical absorption at ~800 nm and ~850 nm, and the formation of these complexes were further confirmed by SDS-PAGE and Western blot analysis. The expression levels of heterologous protein measured by SDS-PAGE and Western blot turned out to be higher as the typical spectral peak heights increase. These findings suggested that the production of the heterologous protein could be rapidly detected through the LH2 absorption at ~800 nm and ~850 nm. Moreover, the typical absorption could be used as a monitor for rapid and real-time evaluation of heterologous protein expression levels.     

A monoclonal antibody against peripheral benzodiazepine receptor activities the human neutrophil NADPH-oxidase.

A murine monoclonal antibody, mAb 8523, raised against whole human pro-monocytic U937 cells recognizes an 18 kDa antigen in human neutrophils (PMN), as determined by immunoprecipitation and by immunodetection on Western blots of SDS-PAGE of PMN membrane fractions. That is 18 kDa antigen corresponds to the phagocyte peripheral benzodiazepine receptor (PBZDR) is evidenced by its co-migration with the 18 kDa covalently labeled PBZDR, detected by autoradiography, and their co-modulation upon phorbol-myristate-acetate activation of PMN. Purified mAb 8523 (IgG2b) is able to dose-dependently and specifically stimulate both the basal and the FMLP-induced oxidative burst of intact human PMN, assessed by luminol-amplified chemiluminescence. This property of the first described monoclonal antibody against PBZDR supports the implication of this receptor in NADPH-oxidase activation and consequently in phagocyte-dependent host defense mechanisms.     

Immunohistochemical assessment of the peripheral benzodiazepine receptor in human tissues.

Exhaustive analysis of the location of the peripheral benzodiazepine receptor (PBR) both at the subcellular and the tissue level is warranted to gain a better understanding of its biological roles. To date, many studies have been performed in animal models, such as rat, mouse, and pig, that yielded important information. However, only a few reports were dedicated to the analysis of PBR expression in humans. To enlarge on previous studies, we investigated PBR expression in different human organs using the monoclonal antibody 8D7 that specifically recognized the human PBR. First, we performed electron microscopic analysis that for the first time unambiguously demonstrated the localization of the PBR on the outer mitochondrial membrane. Second, focusing our analysis on human tissues for which information on PBR expression is sparse (lung, stomach, small intestine, colon, thyroid, adrenal gland, pancreas, breast, prostate, ovary), we found that PBR exhibits selective localization. This characterization of PBR localization in human tissues should provide important insights for the understanding of PBR functions.     

A structural model for the large subunit of the mammalian mitochondrial ribosome

Protein translation is essential for all forms of life and is conducted by a macromolecular complex, the ribosome. Evolutionary changes in protein and RNA sequences can affect the 3D organization of structural features in ribosomes in different species. The most dramatic changes occur in animal mitochondria, whose genomes have been reduced and altered significantly. The RNA component of the mitochondrial ribosome (mitoribosome) is reduced in size, with a compensatory increase in protein content. Until recently, it was unclear how these changes affect the 3D structure of the mitoribosome. Here, we present a structural model of the large subunit of the mammalian mitoribosome developed by combining molecular modeling techniques with cryo-electron microscopic data at 12.1A resolution. The model contains 93% of the mitochondrial rRNA sequence and 16 mitochondrial ribosomal proteins in the large subunit of the mitoribosome. Despite the smaller mitochondrial rRNA, the spatial positions of RNA domains known to be involved directly in protein synthesis are essentially the same as in bacterial and archaeal ribosomes. However, the dramatic reduction in rRNA content necessitates evolution of unique structural features to maintain connectivity between RNA domains. The smaller rRNA sequence also limits the likelihood of tRNA binding at the E-site of the mitoribosome, and correlates with the reduced size of D-loops and T-loops in some animal mitochondrial tRNAs, suggesting co-evolution of mitochondrial rRNA and tRNA structures.     

A structural and dynamic model for the nicotinic acetylcholine receptor

Folding of the five polypeptide subunits (alpha 2 beta gamma delta) of the nicotinic acetylcholine receptor (AChR) into a functional structural model is described. The principles used to arrange the sequences into a structure include: (1) hydrophobicity----membrane-crossing segments; (2) amphipathic character----ion-carrying segments (ion channel with single group rotations); (3) molecular shape (elongated, pentagonal cylinder)----folding dimensions of exobilayer portion; (4) choice of acetylcholine binding sites----specific folding of exobilayer segments; (5) location of reducible disulfides (near agonist binding site)----additional specification of exobilayer arrangement; (6) genetic homology----consistency of functional group choices; (7) noncompetitive antagonist labeling----arrangement of bilayer helices. The AChR model is divided into three parts: (a) exobilayer consisting of 11 antiparallel beta-strands from each subunit; (b) bilayer consisting of four hydrophobic and one amphiphilic alpha-helix from each subunit; (c) cytoplasmic consisting of one (folded) loop from each subunit. The exobilayer strands can form a closed 'flower' (the 'resting state') which is opened ('activated') by agonists bound perpendicular to the strands. Rearrangement of the agonists to a strand-parallel position and partial closing of the 'flower' leads to a desensitized receptor. The actions of acetylcholine and succinoyl and suberoyl bis-cholines are clarified by the model. The opening and closing of the exobilayer 'flower' controls access to the ion channel which is composed of the five amphiphilic bilayer helices. A molecular mechanism for ion flow in the channel is given. Openings interrupted by short duration closings (50 microseconds) depend upon channel group motions. The unusual photolabeling of intrabilayer serines in alpha, beta and delta subunits but not in gamma subunits near the binding site for non-competitive antagonists is explained along with a mechanism for the action of these antagonists such as phencyclidine. The unusual alpha 192Cys-193Cys disulfide may have a special peptide arrangement, such as a cis-peptide bond to a following proline (G.A. Petsko and E.M. Kosower, unpublished results). The position of phosphorylatable sites and proline-rich segments are noted for the cytoplasmic loops. The dynamic behavior of the AChR channel and many different experimental results can be interpreted in terms of the model. An example is the lowering of ionic conductivity on substitution of bovine for Torpedo delta M2 segment. The model represents a useful construct for the design of experiments on AChR.     

The disulfide bridge in the head domain of rhodobacter sphaeroides cytochrome c1 is needed to maintain its structural integrity

Cytochrome c(1) of Rhodobacter sphaeroides ubiquinol-cytochrome c oxidoreductase contains several insertions and deletions that distinguish it from the complex of other higher organisms. Additionally, this bacterial cytochrome c(1) contains two nonconserved cysteines, C145 and C169, with the latter included in the second long insertion located upstream of the sixth heme ligand, M185. The orientation of the insertions and the state of these non-heme binding cysteines remain unknown. Mutating one or both cysteines is found to have comparable effects on the functionality of the cytochrome bc(1) complex. Mutants show an electron transfer activity decreased to a rate that is still high enough to support delayed photosynthetic growth. The mutated cytochrome c(1) has a decreased E(m) without any alteration in the heme ligation environment since none of the mutants binds carbon monoxide. The low E(m) is believed to be caused by a structural modification in the head domain of cytochrome c(1). Analysis of the mutants reveals that the two cysteines form a disulfide bridge. Cleavage of cytochrome c(1) between the two cysteines followed by gel electrophoresis shows two fragments only under reducing conditions, confirming the existence of a disulfide bridge. The disulfide bridge is essential in maintaining the structural integrity of cytochrome c(1) and thus the functionality of the cytochrome bc(1) complex.     

A novel Arabidopsis thaliana protein is a functional peripheral-type benzodiazepine receptor

A key element in the regulation of mammalian steroid biosynthesis is the 18 kDa peripheral-type benzodiazepine receptor (PBR), which mediates mitochondrial cholesterol import. PBR also possess an affinity to the tetrapyrrole metabolite protoporphyrin. The bacterial homolog to the mammalian PBR, the Rhodobacter TspO (CrtK) protein, was shown to be involved in the bacterial tetrapyrrole metabolism. Looking for a similar mitochondrial import mechanism in plants, protein sequences from Arabidopsis and several other plants were found with significant similarities to the mammalian PBR and to the Rhodobacter TspO protein. A PBR-homologous Arabidopsis sequence was cloned and expressed in E. coli. The recombinant gene product showed specific high affinity benzodiazepine ligand binding. Moreover, the protein applied to E. coli protoplasts caused an equal benzodiazepine-stimulated uptake of cholesterol and protoporphyrin IX. These results suggest that the PBR like protein is involved in steroid import and is directing protoporphyrinogen IX to the mitochondrial site of protoheme formation.     

Putative endogenous ligands for the benzodiazepine receptor.

The recent discovery of pharmacologically relevant, high affinity, stereospecific binding sites for the benzodiazepines in the central nervous system (CNS) has rekindled investigations concerning the mechanism of action of these drugs. It has become increasingly clear that elucidation of benzodiazepine action will provide new and important insights into the neurochemical substances of seizure activity, centrally mediated muscle relaxation and anxiety, three major actions of this class of drugs.The existence of a functional receptor for the benzodiazepines, compounds not present $\text{in vivo}$, suggests that endogenous substances exist that serve as natural substrates for this receptor. Furthermore, the characterization of endogenous benzodiazepine receptor ligands affords an opportunity to determine the neurochemical mechanisms underlying the pharmacologic and behavioral effects manifested by the benzodiazepines.Using receptor binding methodology to assay tissue extracts for [³H] diazepam binding inhibitory activity, putative endogenous ligands for the benzodiazepine receptor have been isolated and identified as the purine nucleosides. Compounds such as inosine and hypoxanthine exhibit competitive inhibition of [³H] diazepam binding. The low affinity purinergic inhibition of diazepam binding is consistent with their $\text{in vivo}$ concentrations. Distinct structure-activity relationships exist for the purines with subtle structural alterations having marked effects on diazepam binding inhibitory potency. The methylxanthine stimulants, caffeine, theophylline, and theobromine, also competitively inhibit diazepam binding, suggesting that some of their actions may be mediated by the benzodiazepine receptor.The purines also have “benzodiazepine-like” pharmacologic properties, since they have been shown to antagonize pentylenetetrazol induced seizures in mice in a dose dependent manner. Neurophysiologic studies have also shown that iontophoresis of inosine on cultured mouse primary neurons produce neurotransmitter like effects. Furthermore, these effects are similar to those observed with flurazepam, a finding that provides additional evidence for the “benzodiazepine-like” properties of the purines.The preliminary studies outlined below indicate that the purines are good candidates as putative endogenous ligands for the benzodiazepine receptor and provide a foundation for future studies that concern the homeostatic mediation of seizure activity and anxiety.     

Pathways of energy flow through the light-harvesting antenna of the photosynthetic purple bacterium rhodobacter sphaeroides

Using low intensity picosecond absorption spectroscopy with independently tunable excitation and probing infrared pulses, we have studied the pathways of energy transport through the light-harvesting antenna pigments of the photosynthetic purple bacterium Rhodobacter sphaeroides. From the observed excited-state rise time of the red-most pigment B896 as a function of excitation wavelength it is concluded that the B850 pigment of LH2 is spectrally heterogeneous. For excitations originating in the B850 pigment this results in a fast channel (9 ps) that is mainly excited in the peak of the B850 absorption band, and a slow channel (35 ps) that is predominantly excited at ~840 nm. Upon excitation of B800, more than 90% of the excitations follow the fast path. From the observed kinetics it is concluded that the majority of the LH2 → LH1 energy transfer takes place within at most a few picoseconds. The rate-limiting step in the whole energy transfer sequence appears to be the B896 → reaction center transfer. The origin of the B850 heterogeneity and the slow 35-ps component is at the moment unclear. Possibly it represents a highly extended form of LH2 in which transfer to LH1 takes a relatively long time, due to a large number of transfer steps.     

A BchD (magnesium chelatase) mutant of rhodobacter sphaeroides synthesizes zinc bacteriochlorophyll through novel zinc-containing intermediates

Heme and bacteriochlorophyll a (BChl) biosyntheses share the same pathway to protoporphyrin IX, which then branches as follows. Fe(2+) chelation into the macrocycle by ferrochelatase results in heme formation, and Mg(2+) addition by Mg-chelatase commits the porphyrin to BChl synthesis. It was recently discovered that a bchD (Mg-chelatase) mutant of Rhodobacter sphaeroides produces an alternative BChl in which Mg(2+) is substituted by Zn(2+). Zn-BChl has been found in only one other organism before, the acidophilic Acidiphilium rubrum. Our objectives in this work on the bchD mutant were to 1) elucidate the Zn-BChl biosynthetic pathway in this organism and 2) understand causes for the low amounts of Zn-BChl produced. The bchD mutant was found to contain a Zn-protoporphyrin IX pool, analogous to the Mg-protoporphyrin IX pool found in the wild type strain. Inhibition of ferrochelatase with N-methylprotoporphyrin IX caused Zn-protoporphyrin IX and Zn-BChl levels to decline by 80-90% in the bchD mutant, whereas in the wild type strain, Mg-protoporphyrin IX and Mg-BChl levels increased by 170-240%. Two early metabolites of the Zn-BChl pathway were isolated from the bchD mutant and identified as Zn-protoporphyrin IX monomethyl ester and divinyl-Zn-protochlorophyllide. Our data support a model in which ferrochelatase synthesizes Zn-protoporphyrin IX, and this metabolite is acted on by enzymes of the BChl pathway to produce Zn-BChl. Finally, the low amounts of Zn-BChl in the bchD mutant may be due, at least in part, to a bottleneck upstream of the step where divinyl-Zn-protochlorophyllide is converted to monovinyl-Zn-protochlorophyllide.     

Neuropharmacological profile of peripheral benzodiazepine receptor agonists, DAA1097 and DAA1106.

Receptor binding and behavioral profiles of N-(4-chloro-2-phenoxyphenyl)-N-(2-isopropoxybenzyl)acetamide (DAA1097) and N-(2,5-dimethoxybenzyl)-N-(5-fluoro-2-phenoxyphenyl)acetamide (DAA1106), novel, selective agonists for the peripheral benzodiazepine receptor (PBR) were examined. DAA1097 and DAA1106 inhibited [3H]PK 11195 binding to crude mitochondrial preparations of rat whole brain, with IC50 values of 0.92 and 0.28 nM. Likewise, DAA1097 and DAA1106 inhibited [3H]Ro 5-4864 binding to the same mitochondrial preparation, with IC50 values of 0.64 and 0.21 nM. In contrast, DAA1097 and DAA1106 did not inhibit [3H]-flunitrazepam, the central benzodiazepine receptor (CBR) ligand, binding to membranes of rat whole brain (IC50>10,000nM). Oral administration of DAA1097 and DAA1106 had anxiolytic effects in the mouse light/dark exploration test and in the rat elevated plus- maze test. Oral administration of DAA1106, diazepam and buspirone but not DAA1097 significantly increased sleeping time in hexobarbital-induced anesthesia in mice. The order of potency of potentiation of hexobarbital anesthesia was diazepam> buspirone> DAA1106> DAA1097. Oral administration of DAA1097 and DAA1106 but not diazepam and buspirone did not affect spontaneous locomotor activity in mice. These findings indicate that DAA1097 and DAA1106 are PBR selective ligands with potent anxiolytic-like properties, in laboratory animals.     

Handling mammalian mitochondrial tRNAs and aminoacyl-tRNA synthetases for functional and structural characterization

The mammalian mitochondrial (mt) genome codes for only 13 proteins, which are essential components in the process of oxidative phosphorylation of ADP into ATP. Synthesis of these proteins relies on a proper mt translation machinery. While 22 tRNAs and 2 rRNAs are also coded by the mt genome, all other factors including the set of aminoacyl-tRNA synthetases (aaRSs) are encoded in the nucleus and imported. Investigation of mammalian mt aminoacylation systems (and mt translation in general) gains more and more interest not only in regard of evolutionary considerations but also with respect to the growing number of diseases linked to mutations in the genes of either mt-tRNAs, synthetases or other factors. Here we report on methodological approaches for biochemical, functional, and structural characterization of human/mammalian mt-tRNAs and aaRSs. Procedures for preparation of native and in vitro transcribed tRNAs are accompanied by recommendations for specific handling of tRNAs incline to structural instability and chemical fragility. Large-scale preparation of mg amounts of highly soluble recombinant synthetases is a prerequisite for structural investigations that requires particular optimizations. Successful examples leading to crystallization of four mt-aaRSs and high-resolution structures are recalled and limitations discussed. Finally, the need for and the state-of-the-art in setting up an in vitro mt translation system are emphasized. Biochemical characterization of a subset of mammalian aminoacylation systems has already revealed a number of unprecedented peculiarities of interest for the study of evolution and forensic research. Further efforts in this field will certainly be rewarded by many exciting discoveries.     

Comparative structural and functional studies of avian and mammalian hemoglobins

Thermal stabilities of chicken, grey lag goose (Anser anser), turkey as avian hemoglobins (Hbs); and human, bovine, sheep and horse as mammalian Hbs in hemolysate form were investigated and compared with oxygen affinities taken from literature. The thermal stability was obtained from thermal profiles using temperature scanning spectrophotometry. The buffer conditions were 50 mM Tris, pH 7.2, and 1 mM EDTA. The average of the inverse temperature transitions, average hydrophobicity, total van der Waals volume, partial molal volume and hydration potential were calculated by computational methods. The hemolysed avian Hbs have a lower oxygen affinity, higher thermal stability and higher self association than the mammalian Hbs. These observations are based on amino-acid composition, influence of ionic effectors, and the presence of Hb D in several avian Hbs. The results indicate that the avian Hbs have a more tense (T) conformation than the mammalian Hbs.     

Mechanism of action of RNase T. II. A structural and functional model of the enzyme

A detailed structural and functional model of E. coli RNase T was generated based on sequence analysis, homology modeling, and experimental observation. In the accompanying article, three short sequence segments (nucleic acid binding sequences (NBS)) important for RNase T substrate binding were identified. In the model, these segments cluster to form a positively charged surface patch. However, this patch is on the face of the RNase T monomer opposite the DEDD catalytic center. We propose that by dimerization, the NBS patch from one subunit is brought to the vicinity of the DEDD center of the second monomer to form a fully functional RNase T active site. In support of this model, mutagenetic studies show that one NBS1 residue, Arg(13), sits at the catalytic center despite being on the opposite side of the monomer. Second, the complementarity of the RNase T subunits through the formation of homodimers was demonstrated by reconstitution of partial RNase T activity from monomers derived from two inactive mutant proteins, one defective in catalysis and one in substrate binding. These data explain why RNase T must dimerize to function. The model provides a detailed framework on which to explain the mechanism of action of RNase T.     

A model for indication of DNA functional and structural changes at low-dose radiation

The work offers an "in vivo-in vitro" model which allows to identify DNA's both structural and functional damages caused by gamma-irradiation in doses from 0.02 to 0.25 Gy. As a donor the authors used an irradiated pTTQ 19 plasmide which had two marker genes: the ampicilline-resistant gene (amp(r)) and beta-galactosidase structural gene (lacZ alpha). E. coli GM 109 bacterial stamm transformed by the irradiated plasmide was used as a recipient. The structural damages of the irradiated plasmide were registered by DNA electrophoretic analysis in agarose gel. The plasmide DNA dysfunctions were assessed by its ability to pass on ampicilline resistance to E. coli bacterial cells as well as by beta-galactosidase level. The irradiated plasmide was found to have a tendency to decrease beta-galactosidase activity and number of E. coli ampicilline-resistant transformants depending on the received radiation dose: by 24.5% (0.05 Gy), 30.9% (0.19 Gy), and by 40.2% (0.25 Gy).     

Characterization of the rhodobacter sphaeroides 5-aminolaevulinic acid synthase isoenzymes, HemA and HemT, isolated from recombinant Escherichia coli.

The hemA and hemT genes encoding 5-aminolaevulinic acid synthase (ALAS) from the photosynthetic bacterium Rhodobacter sphaeroides, were cloned to allow high expression in Escherichia coli. Both HemA and HemT appeared to be active in vivo as plasmids carrying the respective genes complemented an E. coli hemA strain (glutamyl-tRNA reductase deficient). The over-expressed isoenzymes were isolated and purified to homogeneity. Isolated HemA was soluble and catalytically active whereas HemT was largely insoluble and failed to show any activity ex vivo. Pure HemA was recovered in yields of 5-7 mg x L-1 of starting bacterial culture and pure HemT at 10 mg x L-1 x HemA has a final specific activity of 13 U x mg-1 with 1 unit defined as 1 micromol of 5-aminolaevulinic acid formed per hour at 37 degrees C. The Km values for HemA are 1.9 mM for glycine and 17 microM for succinyl-CoA, with the enzyme showing a turnover number of 430 h-1. In common with other ALASs the recombinant R. sphaeroides HemA requires pyridoxal 5'-phosphate (PLP) as a cofactor for catalysis. Removal of this cofactor resulted in inactive apo-ALAS. Similarly, reduction of the HemA-PLP complex using sodium borohydride led to > 90% inactivation of the enzyme. Ultraviolet-visible spectroscopy with HemA suggested the presence of an aldimine linkage between the enzyme and pyridoxal 5'-phosphate that was not observed when HemT was incubated with the cofactor. HemA was found to be sensitive to reagents that modify histidine, arginine and cysteine amino acid residues and the enzyme was also highly sensitive to tryptic cleavage between Arg151 and Ser152 in the presence or absence of PLP and substrates. Antibodies were raised to both HemA and HemT but the respective antisera were not only found to bind both enzymes but also to cross-react with mouse ALAS, indicating that all of the proteins have conserved epitopes.