Dissecting the Functional Role of Key Residues in Triheme Cytochrome PpcA: A Path to Rational Design of G. sulfurreducens Strains with Enhanced Electron Transfer Capabilities

PpcA is the most abundant member of a family of five triheme cytochromes c ₇ in the bacterium Geobacter sulfurreducens (Gs) and is the most likely carrier of electrons destined for outer surface during respiration on solid metal oxides, a process that requires extracellular electron transfer. This cytochrome has the highest content of lysine residues (24%) among the family, and it was suggested to be involved in e⁻/H⁺ energy transduction processes. In the present work, we investigated the functional role of lysine residues strategically located in the vicinity of each heme group. Each lysine was replaced by glutamine or glutamic acid to evaluate the effects of a neutral or negatively charged residue in each position. The results showed that replacing Lys⁹ (located near heme IV), Lys¹⁸ (near heme I) or Lys²² (between hemes I and III) has essentially no effect on the redox properties of the heme groups and are probably involved in redox partner recognition. On the other hand, Lys⁴³ (near heme IV), Lys⁵² (between hemes III and IV) and Lys⁶⁰ (near heme III) are crucial in the regulation of the functional mechanism of PpcA, namely in the selection of microstates that allow the protein to establish preferential e⁻/H⁺ transfer pathways. The results showed that the preferred e⁻/H⁺ transfer pathways are only established when heme III is the last heme to oxidize, a feature reinforced by a higher difference between its reduction potential and that of its predecessor in the order of oxidation. We also showed that K43 and K52 mutants keep the mechanistic features of PpcA by establishing preferential e⁻/H⁺ transfer pathways at lower reduction potential values than the wild-type protein, a property that can enable rational design of Gs strains with optimized extracellular electron transfer capabilities.     

Diagnostic Accuracy of Computer-Aided Detection of Pulmonary Tuberculosis in Chest Radiographs: A Validation Study from Sub-Saharan Africa

Background

Chest radiography to diagnose and screen for pulmonary tuberculosis has limitations, especially due to inter-reader variability. Automating the interpretation has the potential to overcome this drawback and to deliver objective and reproducible results. The CAD4TB software is a computer-aided detection system that has shown promising preliminary findings. Evaluation studies in different settings are needed to assess diagnostic accuracy and practicability of use.

Methods

CAD4TB was evaluated on chest radiographs of patients with symptoms suggestive of pulmonary tuberculosis enrolled in two cohort studies in Tanzania. All patients were characterized by sputum smear microscopy and culture including subsequent antigen or molecular confirmation of Mycobacterium tuberculosis (M.tb) to determine the reference standard. Chest radiographs were read by the software and two human readers, one expert reader and one clinical officer. The sensitivity and specificity of CAD4TB was depicted using receiver operating characteristic (ROC) curves, the area under the curve calculated and the performance of the software compared to the results of human readers.

Results

Of 861 study participants, 194 (23%) were culture-positive for M.tb. The area under the ROC curve of CAD4TB for the detection of culture-positive pulmonary tuberculosis was 0.84 (95% CI 0.80–0.88). CAD4TB was significantly more accurate for the discrimination of smear-positive cases against non TB patients than for smear-negative cases (p-value<0.01). It differentiated better between TB cases and non TB patients among HIV-negative compared to HIV-positive individuals (p<0.01). CAD4TB significantly outperformed the clinical officer, but did not reach the accuracy of the expert reader (p = 0.02), for a tuberculosis specific reading threshold.

Conclusion

CAD4TB accurately distinguished between the chest radiographs of culture-positive TB cases and controls. Further studies on cost-effectiveness, operational and ethical aspects should determine its place in diagnostic and screening algorithms.     

GTP,as well as ATP,can act as a substrate for the intrinsic protein kinase activity of synaptic plasma membranes

Summary GTP as well as ATP can act as phosphate donor for the intrinsic protein kinase activity of synaptic plasma membranes. There are many similarities between the activities observed with ATP or GTP. Both need a divalent cation, Mg²⁺ being preferred, both are slightly inhibited by Na⁺, and more strongly by K⁺, both are inhibited by theophylline and adenosine. The K_m for GTP (0.13 mM) is similar to that ATP (0.12 mM). There are, however, some differences in properties. When GTP instead of ATP is the phosphate donor the pH optimum is 6.5 instead of 7.4. In addition NH ₄ ⁺ inhibits the transfer of phosphate from GTP but not from ATP. More importantly, cyclic AMP only stimulates the transfer of phosphate from ATP not from GTP. SDS gel electrophoresis reveals that similar membrane proteins are phosphorylated by GTP and ATP in the presence or absence of cyclic AMP. This suggests that there may be two different types of protein kinase in the synaptic plasma membrane which act on similar membrane proteins. One is stimulated by cyclic AMP and is specific to ATP while the other is unaffected by cyclic nucleotides and can use either ATP or GTP as phosphate donor.Deceased     

Comparative measurements of chlorophyll a fluorescence, acid accumulation and gas exchange in exposed and shaded plants of Clusia minor L. and Clusia multiflora H. B. K. in the field

 Changes in chlorophyll a fluorescence during the day and diurnal-changes of net CO₂-exchange and organic acid contents were determined in two species of the genus Clusia during the dry season in Venezuela. The investigations included plants of the C₃/CAM intermediate species Clusia minor and the C₃ species C. multiflora growing at exposed and shaded sites. Both species showed a C₃ pattern of net CO₂-exchange at the exposed site. In the shade under extreme drought stress C. minor showed a weak expression of CAM without CO₂-uptake during the afternoon (phase IV of CAM). C. multiflora growing in the shade exhibited a C₃-pattern of net CO₂-exchange and a small but significant nocturnal accumulation of citrate. Shaded plants of C. minor were able to double their light utilisation for electron transport and to reduce non-photochemical quenching during phase III compared to phase II of CAM. Furthermore, increase of electron transport rate through photosystem II in phase III of CAM is correlated to decarboxylation of malate. At the exposed site C. multiflora was less negatively affected by high PPFD than C. minor. This was shown by a lower reduction of potential electron quantum yield (F_v/F_m) and higher light utilisation of electron transport of C. multiflora compared to C. minor. At the exposed site C. minor did not make use of the CAM option to increase light utilisation of electron transport and to reduce non-photochemical quenching as did the plants growing in the shade. Received: 20 March 1996 / Accepted: 24 June 1996     

Engineering for drought avoidance: expression of maize NADP-malic enzyme in tobacco results in altered stomatal function

Water is a principal limitation to agricultural production during drought and in arid regions of the world. Mechanisms that plants use to cope with drought can be grouped into two different strategies: drought tolerance and drought avoidance. Previous efforts toward engineering plants for improved performance during drought have focused on drought tolerance, the ability to adjust to dry conditions. This report addresses the engineering of a drought-avoidance phenotype, which allows for the conservation of water during plant growth. The majority of water lost from plants occurs through stomata. When stomata are open, potassium, chloride and/or malate are present at high concentrations in guard cells. The accumulation of large numbers of ions during stomatal opening increases the turgor pressure of the guard cells, which results in increased pore size. Expression of a single gene from maize, NADP-malic enzyme (ME), which converts malate and NADP to pyruvate, NADPH, and CO(2), resulted in altered stomatal behaviour and water relations in tobacco. The ME-transformed plants had decreased stomatal conductance and gained more fresh mass per unit water consumed than did the wild type, but they were similar to the wild type in their growth and rate of development. Providing chloride via the transpiration stream partially reversed the effects of ME expression on stomatal aperture size, which is consistent with the interpretation that expression of ME altered malate metabolism in guard cells. These results suggest a role for malic enzyme in the mechanism of stomatal closure, as well as a potential mechanism for genetically altering plant water use.     

Alcoholysis catalyzed by Candida antarctica lipase B in a gas/solid system: effects of water on kinetic parameters

The influence of water on the kinetics of alcoholysis of methyl propionate and n-propanol catalyzed by immobilized lipase B from Candida antarctica was studied in a continuous solid/gas reactor. In this reactor, the solid phase is composed of a packed enzymatic sample which is percolated by gaseous nitrogen, simultaneously carrying gaseous substrates to the enzyme while removing reaction products. In this system, interactions between the enzyme and nonreacting molecules are avoided, since no solvent is present, and it is thus more easy to assess the role of water. To this end, alcohol inhibition constant, substrates dissociation constants as well as acylation rate constant and ratio of acylation to deacylation rate constants have been determined as a function of water activity (a(w)). Data obtained highlight that n-propanol inhibition constant and dissociation constant of methyl propionate are a lot affected by a(w) variations whereas water has no significant effect on the catalytic acylation step nor on the ratio of acylation to deacylation rate constants. These results suggest the water-independent character of the transition step.     

Competitive reactions of a ruthenium arene anticancer complex with histidine, cytochrome c and an oligonucleotide

The ruthenium arene anticancer complex [(⁶-bip)Ru(en)Cl][PF₆] (1) (bip is biphenyl, en is ethylenediamine) reacted slowly with the amino acid L-histidine (L-His) in aqueous solution at 310 K. Two L-His adducts of 1 were separated by high-performance liquid chromatography and identified by electrospray ionisation mass spectrometry and NMR: an imidazole N-bound complex [(⁶-bip)Ru(en)(N–L-His)]²⁺, and an N-bound complex [(⁶-bip)Ru(en)(N–L-His)]²⁺. At 310 K, after 24 h only about 22% of complex 1 (2 mM) reacted with L-His, and of the unreacted 1, 59% had hydrolysed. In the presence of 100 mM NaCl, approximately 90% of 1 remained unreacted. In aqueous solution or triethylammonium acetate (TEAA) buffer (pH 7.6), ¹⁵N-labelled 1 reacted with cytochrome c to give two monoruthenated protein adducts. The reaction reached equilibrium within 2 h by which time approximately 50% of cytochrome c was ruthenated. On the basis of [¹H, ¹⁵N] NMR data, one adduct may have Ru bound to the N-terminus, and the other to a carboxylate group on the protein. In TEAA buffer and at 310 K, more than 90% of the 14-mer oligonucleotide d(TATGTACCATGTAT) reacted with 2 mol Eq of 1 to give rise to monoruthenated and diruthenated oligonucleotide adducts. The presence of cytochrome c (1 mol Eq) or L-His (4 mol Eq) had little effect on the course of the reaction with the oligonucleotide. In cells, DNA (or RNA) may be a favoured reaction site for this Ru anticancer complex.Electronic supplementary material is available for this article at .

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Limnology of 46 lakes and ponds on Banks Island, N.W.T., Canadian Arctic Archipelago

The goal of this study was to describe and quantify the physical and chemical limnological properties of 46 lakes and ponds on Banks Island, to explore the effects of ecoclimatic differences on the water chemistry of these study sites, and to establish baseline conditions for this previously unexplored limnological region, which could then be used in subsequent long-term environmental monitoring programs. A key finding was that the study sites on Banks Island represented a large nutrient concentration gradient from ultra-oligotrophic to hypereutrophic waters. In general, the study sites were relatively nutrient rich by Arctic standards (i.e. mean total nitrogen (TN_mean)=504.2μg/l and mean total phosphorus (TPU_mean)=18.0μg/l); concentrations that are amongst the highest of any previous limnological survey from similar latitudes. Dissolved organic carbon (DOC) concentrations were also some of the highest reported to date amongst all other Canadian Arctic island limnological surveys. These values reflect the milder climate, concentrated animal life and lushness of Banks Island, as compared to other Canadian Arctic Archipelago islands. Principal components analysis (PCA) separated sites along a conductivity/ionic and elevation gradient on Axis 1 (λ₁=0.343), and a metal (Fe, Zn, Al) and alkalinity-related (DIC, pH) gradient on the second axis (λ₂=0.187). Canonical variate analysis (CVA) was used to explore the classification of the study sites into Low Arctic, Mid Arctic or High Arctic designations based on their limnological characteristics.     

Chironomid assemblages from seabird-affected High Arctic ponds

Seabirds can shunt nutrients and contaminants from marine to terrestrial ecosystems by forming dense breeding colonies and releasing wastes to these sites. A large colony of seabirds at Cape Vera (Devon Island, High Arctic Canada) has resulted in eutrophic conditions and potentially toxic concentrations of sedimentary metals in several freshwater ponds that drain their nesting sites. Here, we investigated the effects of elevated nutrient and sedimentary metal concentrations on the distribution of subfossil chironomids in surface sediments from 21 ponds that span a gradient of seabird influence. Although many ponds registered high nutrient concentrations (e.g., mean TP = 45 μg l ⁻¹), eutrophic taxa typical of temperate waters were not common, with most assemblages being dominated by morphotypes of Psectrocladius and Tanytarsina, as well as Corynoneura arctica-type, and Metriocnemus hygropetricus-type. Although the ponds within and outside the area influenced by seabirds contained largely similar taxa, variations did exist in the relative abundances of the different species. Lakewater pH was the only measured environmental variable that explained statistically significant amounts of variation in the chironomid assemblages. Although direct effects of pH on chironomids cannot be ruled out, pH is likely tracking production-related changes driven by limnetic dissolved inorganic carbon dynamics. Sediment cores collected from seabird-affected and seabird-free ponds showed a greater number of chironomid taxa and higher head capsule abundances in the pond receiving seabird inputs. Chironomid assemblages in both cores recorded increased abundances in recent decades, likely in response to warmer conditions and lengthened growing seasons.     

The HtrA protease of Campylobacter jejuni is required for heat and oxygen tolerance and for optimal interaction with human epithelial cells

Campylobacter jejuni is a predominant cause of food-borne bacterial gastroenteritis in the developed world. We have investigated the importance of a homologue of the periplasmic HtrA protease in C. jejuni stress tolerance. A C. jejuni htrA mutant was constructed and compared to the parental strain, and we found that growth of the mutant was severely impaired both at 44 degrees C and in the presence of the tRNA analogue puromycin. Under both conditions, the level of misfolded protein is known to increase, and we propose that the heat-sensitive phenotype of the htrA mutant is caused by an accumulation of misfolded protein in the periplasm. Interestingly, we observed that the level of the molecular chaperones DnaK and ClpB was increased in the htrA mutant, suggesting that accumulation of non-native proteins in the periplasm induces the expression of cytoplasmic chaperones. While lack of HtrA reduces the oxygen tolerance of C. jejuni, the htrA mutant was not sensitive to compounds that increase the formation of oxygen radicals, such as paraquat, cumene hydroperoxide, and H2O2. Using tissue cultures of human epithelial cells (INT407), we found that the htrA mutant adhered to and invaded human epithelial cells with a decreased frequency compared to the wild-type strain. This defect may be a consequence of the observed altered morphology of the htrA mutant. Thus, our results suggest that in C. jejuni, HtrA is important for growth during stressful conditions and has an impact on virulence.