In Silico Classification of Proteins from Acidic and Neutral Cytoplasms

Protein acidostability is a common problem in biopharmaceutical and other industries. However, it remains a great challenge to engineer proteins for enhanced acidostability because our knowledge of protein acidostabilization is still very limited. In this paper, we present a comparative study of proteins from bacteria with acidic (AP) and neutral cytoplasms (NP) using an integrated statistical and machine learning approach. We construct a set of 393 non-redundant AP-NP ortholog pairs and calculate a total of 889 sequence based features for these proteins. The pairwise alignments of these ortholog pairs are used to build a residue substitution propensity matrix between APs and NPs. We use Gini importance provided by the Random Forest algorithm to rank the relative importance of these features. A scoring function using the 10 most significant features is developed and optimized using a hill climbing algorithm. The accuracy of the score function is 86.01% in predicting AP-NP ortholog pairs and is 76.65% in predicting non-ortholog AP-NP pairs, suggesting that there are significant differences between APs and NPs which can be used to predict relative acidostability of proteins. The overall trends uncovered in the study can be used as general guidelines for designing acidostable proteins. To best of our knowledge, this work represents the first systematic comparative study of the acidostable proteins and their non-acidostable orthologs.     

Spheroplast induction inAnabaena variabilis Kütz andA. azollae stras

Summary Spheroplasts were obtained by lysozyme treatment of 48 hour (4– 8cells) akinete germlings of the cultured cyanobacteriaAnabaena variabilis andA. azollae originally isolated from the leaf cavity of the fernAzolla pinnata. The osmotic stabilizer was 0.5 M sucrose. At least 50% of the cells in a short filament became spheroplasts after 1–4 hours in lysozyme (1 mg/ml) in incubation medium at 34 °C, with greater than 75% viability after 2 hours. The spheroplasts were osmotically fragile and showed intense chlorophyll autofluorescence in UV light. In phase microscopy, treated cells appeared larger, became spherical and lost some of their optical refraction. Transmission electron microscopy confirmed the loss of the peptidoglycan layer and the partial remains of the outer membrane after lysozyme exposure. We previously obtained protoplasts ofAzolla fern leaf cells so that we now can study the recognition sites in both members of theAzolla/Anabaena nitrogen fixing symbiosis during cell wall degradation and regeneration.     

The major soluble cytochromes of the obligately aerobic sulfur bacterium,Thiobacillus neapolitanus

Four cytochromes were isolated from soluble extracts of the aerobic sulfur bacterium, Thiobacillus neapolitanus. The two most abundant proteins were purified to homogeneity and thoroughly characterized. Cytochrome c-554 (547) is a monomeric, small molecular weight protein which is unusual in having two well-resolved alpha peaks in UV-visible absorption spectra. The redox potential is 208 mV. Native cytochrome c-549 is oligometric, but has a subunit size of about 26.000. The yield of this protein could be improved dramatically by washing membranes with 30% ammonium sulfate, but the material solubilized by this method had a larger native molecular weight than that in the initial 0.1 M Tris-Cl extract and behaved differently on chromatography. The properties of cytochrome c-549 including subunit size and UV-visible absorption spectra are similar to mitochondrial cytochrome c ₁ and chloroplast cytochrome f, which suggests that it may be a modified form of the predominant membrane cytochrome. Based on cytochrome content, it is suggested that T. neapolitanus is not closely related to other thiobacilli.Dedicated to Prof. Dr. G. Drews on the occasion of his sixtieth birthday     

Characterization of a new platelet-forming purple sulfur bacterium,Amoebobacter pedioformis sp. nov.

The dominant purple sulfur bacterium of a reddish-colored waste water pond near Taichung, Taiwan, was isolated in pure culture, strain CML2. Individual cells were nearly spherical, nonmotile, and contained in their peripheral parts was vacuoles that appeared like elongated, curved tubes. Four to sixteen cells formed platelet-like aggregates reminiscent of Thiopedia rosea. The intracellular photosynthetic membrane system of the cells was of vesicular type; the photosynthetic pigments consisted of bacteriochlorophyll a and spirilloxanthin as the major carotenoid. The color of cell suspensions was pink to rosered. Under anaerobic conditions photolithoautotrophic growth occurred with sulfide, elemental sulfur or thiosulfate; sulfur globules were stored as an intermediary oxidation product. In the presence of sulfide, acetate, lactate and pyruvate were photoassimilated; strain CML2 lacked assimilatory sulfate reduction. Fastest photoautotrophic growth (11 h doubling time) was obtained at pH 7.5, 35°C and a light intensity of about 1000 lux (tungsten lamp). Chemolithoautotrophic growth in the dark was possible under reduced oxygen partial pressure with reduced sulfur compounds as respiratory substrates. The DNA base composition of strain CML2 was 65.5 mol% G+C. Strain CML2 is described as type strain of a new species, Amoebobacter pedioformis sp. nov., in the family Chromatiaceae.     

Intracellular salt and solute concentrations in Ectothiorhodospira marismortui: glycine betaine and Nα-carbamoyl glutamineamide as osmotic solutes

Ectothiorhodospira marismortui, a moderately halophilic purple sulfur bacterium from a hypersaline sulfur spring, contains glycine betaine and N-carbamoyl glutamineamide (CGA) as the main intracellular osmotic solutes, with sucrose as a minor component. The concentration of glycine betaine was found to increase with increasing salt concentration of the medium, from 0.47 M to 1.29 M in cells grown from 0.85 to 2.56 M NaCl, while the estimated CGA concentration rose from about 0.2 M to 0.5 M. The concentration of sucrose remained constant at a value of around 0.05 M. Intracellular sodium and potassium concentrations were relatively low (around 0.5 and 0.3 M, respectively, at an external NaCl concentration of 1.8 M). The concentration of the novel compound N-carbamoyl glutamineamide was enhanced when l-glutamine was added to the growth medium, suggesting that glutamine served as a precursor for the synthesis of the compound.Abbreviations CGA N-carbamoyl glutamineamide     

Isolation of totally inverted submitochondrial particles by sonication of beef heart mitochondria

A novel procedure for isolating totally inverted preparations of submitochondrial particles by sonication of beef heart mitochondria is described. The procedure involves only differential centrifugation in 0.25 M sucrose containing 0.15 M KCl. The submitochondrial particles have 96% of their cytoplasmic face cytochromec-binding sites sequestered within the particles. Mild sonication exposes cytochromec-binding sites to the medium. The oligomycin-sensitive ATPase of sonic-derived submitochondrial particles, like that of electron transport particles, is inhibited 98% by exogenous isolated ATPase inhibitor protein. NADH oxidase activity in these particles is inhibited by oligomycin. The respiratory control index (uncoupled rate/oligomycin-inhibited rate) is approximately 3.4 and can be increased by washing the particles with medium containing bovine serum albumin.     

Localization of acid and alkaline phosphatases in Myxococcus coralloides D

Myxococcus coralloides produces two different phosphatases, one acid and the other alkaline. Both enzymes were localized by physical and biochemical techniques. Spheroplasts from M. coralloides released 20–30% of the phosphatase activities. Osmotic shock or treatment with high MgCl₂ or LiCl concentrations did not produce a greater release. Cytochemical localization situated the phosphatases in the outer membrane and the periplasmic space. Separation of the cytoplasmic membrane and outer membrane of the cells by sucrose gradient centrifugation showed that phosphatases are located primarily in the outer membrane. membrane.     

Respiratory oxidation of reduced sulfur compounds by intact cells of Thiobacillus tepidarius (type strain)

Thiobacillus tepidarius (type strain) was grown in microaerophilic conditions, on tetrathionate, thiosulfate or crystalline S^o. The rates of tetrathionate, thiosulfate, elemental sulfur (S^o) and sulfite oxidation of the different cultures were measured respirometrically, using exponentially growing cells, with an oxygen electrode. Cells growing on the three different sulfur compounds retain thiosulfate-, tetrathionate, and S^o-oxidizing activities (SOA), but lack respiratory sulfite-oxidizing activity. The SOA for all the cultures was almost totally inhibited by 50 M myxothiazol, an inhibitor of the quinone-cytochrome b region, and by 10 M of the uncoupler carbonyl cyanide m-chlorophenylhydrazone (CCCP). Tetrathionate- and thiosulfate-oxidizing activities were moderately and weakly inhibited by 50 M totally inhibited (>95%) all respiratory activities. This study suggests that electrons released by S^o oxidation enter the respiratory chain in the quinone-cytochrome b region.Abbreviation SOA sulfur-oxidizing activity     

Periplasmic electron carriers and photo-induced electron transfer in the photosynthetic bacterium Ectothiorhodospira sp.

A detailed analysis of the periplasmic electron carriers of the photosynthetic bacterium Ectothiorhodospira sp. has been performed. Two low mid-point redox potential electron carriers, cytochrome c′ and cytochrome c, are detected. A high potential iron–sulfur protein is the only high mid-point redox potential electron transfer component present in the periplasm. Analysis of light-induced absorption changes shows that this high potential iron–sulfur protein acts in vivo as efficient electron donor to the photo-oxidized high potential heme of the Ectothiorhodospira sp. reaction center. This revised version was published online in June 2006 with corrections to the Cover Date.     

Lateral heterogeneity of bacterial membranes]

Isolated membranes of M. lysodeikticus were rapidly frozen and disrupted in a Hughes press. After disruption the fragments were centrifuged at 144000 g for 1 hour and part of the supernatant just above the pellet was subjected to isopycnic centrifugation in a continuous sucrose density gradient. It was found that the material tested was a mixture of fragments differing in their buoyant densities. These fragments also differed in their protein/lipid ratios, cytochrome content and dehydrogenase activities calculated per protein and lipid as well as in proportion of the respiratory chain enzymes. The results obtained are indicative of lateral heterogeneity of the bacterial membrane and the existence of areas in the membrane having high concentration of the respiratory chain enzymes. The latter may suggest that the system of substrate oxidation is segregated in the membrane. It is assumed that there exists in the membrane an exchange of components between different electron-transporting chains operated due to their lateral diffusion.     

Analysing the outer membrane subproteome of Methylococcus capsulatus (Bath) using proteomics and novel biocomputing tools

High-resolution two-dimensional gel electrophoresis and mass spectrometry has been used to identify the outer membrane (OM) subproteome of the Gram-negative bacterium Methylococcus capsulatus (Bath). Twenty-eight unique polypeptide sequences were identified from protein samples enriched in OMs. Only six of these polypeptides had previously been identified. The predictions from novel bioinformatic methods predicting β-barrel outer membrane proteins (OMPs) and OM lipoproteins were compared to proteins identified experimentally. BOMP () predicted 43 β-barrel OMPs (1.45%) from the 2,959 annotated open reading frames. This was a lower percentage than predicted from other Gram-negative proteomes (1.8–3%). More than half of the predicted BOMPs in M. capsulatus were annotated as (conserved) hypothetical proteins with significant similarity to very few sequences in Swiss-Prot or TrEMBL. The experimental data and the computer predictions indicated that the protein composition of the M. capsulatus OM subproteome was different from that of other Gram-negative bacteria studied in a similar manner. A new program, Lipo, was developed that can analyse entire predicted proteomes and give a list of recognised lipoproteins categorised according to their lipo-box similarity to known Gram-negative lipoproteins (). This report is the first using a proteomics and bioinformatics approach to identify the OM subproteome of an obligate methanotroph.     

Genetic transformation and transfection ofBacillus subtilis spheroplasts

Genetic transformation and transfection of lysozyme-treatedBacillus subtilis spheroplasts 168M ind occurs only if they are stabilized with 0.5m phosphate buffer and not if they are stabilized with 0.5m sucrose. Spheroplasts prepared from maximally competent cells give maximum transformation and transfection results. The results indicate that the DNA receptors must also be intact in the spheroplasts.     

Membrane-anchored cytochrome c as an electron carrier in photosynthesis and respiration: past,present and future of an unexpected discovery

In the mid 1980s, it was observed that photosynthesis could still occur in the absence of the diffusible electron carrier cytochrome c ₂ in the purple non-sulfur facultative phototrophic bacterium Rhodobacter capsulatus. This serendipic finding led to the discovery of a novel class of membrane-anchored electron carrier cytochromes and their associated electron transfer pathways. Studies of cytochrome c _y of R. capsulatus (and its homologues in other species) have modified the previous dogma of electron transfer between photosynthetic and respiratory membrane protein complexes with a new paradigm, in which these proteins and their electron carriers can form `hard-wired' structural super-complexes. Here, we reminisce on the early days of this discovery, its impacts on our understanding of cellular energy transduction pathways and the physiological roles played by the electron carrier cytochromes c, and discuss the current knowledge and emerging future challenges of this field. This revised version was published online in August 2006 with corrections to the Cover Date.     

Immune response of rainbow trout (Oncorhynchus mykiss) to antigenic preparations fromVibrio anguillarumserogroup O1

The humoral and cellular immune responses of rainbow trout were investigated following injection with formalin-killedVibrio anguillarumin Freund's incomplete adjuvant (FIA) in terms of reactivity towards different antigen preparations of the bacterium. Vaccinated fish were compared with control fish that had been injected only with FIA. The antigen preparations used for the comparative studies were formalin-killed bacteria, extracellular products (ECP), outer membrane proteins (OMP) and cytoplasmic membrane proteins (CMP). Humoral antibody as measured by ELISA was detected with all antigen preparations. As evaluated by ELISPOT and by proliferation assays, leucocytes isolated from vaccinated fish reacted most strongly with the OMP preparation. This observation suggests the existence of undefined potent antigenic components among these proteins. In proliferation assays, the tested antigen preparations contained components that were mitogenic to cell cultures from unvaccinated fish. However, in terms of antibodies measured by ELISA and ELISPOT techniques, only vaccinated fish reacted with theV. anguillarumpreparations.     

Assimilatory sulfur metabolism in marine microorganisms: Sulfur metabolism,growth, and protein synthesis of Pseudomonas halodurans and Alteromonas luteo-violaceus during sulfate limitation

Sulfate concentration in the growth medium exerted a strong influence on the sulfur content of protein in two marine bacteria, Pseudomonas halodurans and Alteromonasluteo-violaceus, but the distribution of sulfur in major biochemical fractions was not affected. 90% of the total cellular sulfur was contained in low molecular weight organic compounds and protein; inorganic sulfate was not an important component. The sulfur content of isolated protein and total cellular sulfur increased in proportion to the external sulfate concentration for both bacteria, reaching a maximum at about 100–250 M. The growth rate of P. halodurans only was dependent on the sulfate concentration.Sulfur starvation of cells labeled to equilibrium with ³⁵S-sulfate resulted in a rapid decrease in low molecular weight organic S with a concommitant increase in alcohol soluble (P. halodurans) or residue protein (A. luteo-violaceus). Although cell division was prevented, total protein increased in both bacteria, resulting in synthesis of sulfur-deficient protein. This effect was most pronounced in P. halodurans.Addition of ³⁵S-sulfate to sulfur-starved A. luteo-violaceus further demonstrated that sulfur metabolism was restricted primarily to the synthesis and utilization of sulfurcontaining protein precursors. The low molecular weight organic S pool was replenished rapidly, and the pool size per cell reached twice the normal value before cell division resumed. Incorporation into protein was very rapid.Abbreviations L.M.W. low molecular weight - TCA trichloroacetic acid     

蔗糖添加对杉木低磷胁迫响应和蔗糖代谢的影响

为了揭示低磷胁迫下蔗糖对杉木低磷胁迫响应和蔗糖代谢的影响,选用两种不同磷效率杉木家系M32和M28进行低磷胁迫下的蔗糖添加试验,分析蔗糖添加对低磷胁迫下杉木形态特征、生理特性和低磷诱导相关基因表达的影响。结果表明：蔗糖添加促进了低磷胁迫下杉木苗高、根长、根表面积、根平均直径、根体积、根叶组织蔗糖含量和根叶组织无机磷含量的增加,但仍明显低于正常供磷处理下添加蔗糖处理的杉木增量。低磷促进杉木叶中花青素的积累,而正常供磷和低磷胁迫下的蔗糖添加处理都显著促进了叶片花青素含量的增加。随着胁迫时间的延长,M28与M32在根、叶组织的蔗糖含量存在显著差异,且M28根叶组织中的蔗糖合成酶活性和蔗糖磷酸合成酶活性都高于M32。蔗糖合成酶ClSuSy在M28和M32根系中受低磷胁迫诱导下调表达,但蔗糖添加处理明显诱导ClSuSy表达量升高,M28在正常供磷并添加蔗糖处理下的ClSuSy表达量显著高于其它处理。蔗糖转运蛋白SUT4、磷转运蛋白ClPht1;4、紫色酸性磷酸酶PAP1和PAP11在M28和M32根系中总体上受低磷胁迫诱导上调表达,且受蔗糖添加处理诱导下调表达。低磷胁迫下,添加或不添加蔗糖处理的M32根系SUT4的表达量均在15d时显著升高,并在45d时回落到正常水平。ClPht1;4和PAP1在低磷胁迫15d的表达量显著高于45d时的表达量,且ClPht1;4在M32根系中的表达量远高于M28。本研究表明,蔗糖对杉木低磷胁迫响应和糖代谢有重要的影响作用,低磷胁迫下添加蔗糖处理能够在一定程度上缓解杉木低磷胁迫响应。     

Structural analysis of the HiPIP from the acidophilic bacteria: Acidithiobacillus ferrooxidans

Hip is a high-potential iron–sulfur protein (HiPIP) isolated from the acidophilic bacterium, Acidithiobacillus ferrooxidans. In the present work, a structural model of Hip suggests that the role of proline residues is essential to stabilize the protein folding at very low pH. The presence of an unusual disulfide bridge in Hip is demonstrated using mass spectrometry and nuclear magnetic resonance. This disulfide bridge is necessary to anchor the N-terminal extremity of the protein, but is not involved in the acid stability of Hip. The structural parameters correlated with the pH dependence of Hip redox potential are also analysed on the basis of this model. Given that the same structural features can enhance acidic stability and lead to elevated redox potentials, modulation of the redox potentials of electron carriers may be necessary to achieve electron transfer at very low pH.     

Electron Microscopy of the Major Outer Membrane Protein of Campylobacter jejuni

The surfaces of the disrupted-cell surfaces of the Campylobacter jejuni strains FUM158432 and M1 were examined using the negative-staining technique and electron microscopy. The surfaces of the whole cells and the outer membranes were covered with small dark dots which, in some areas, were arranged in hexagonal patterns. The hexagonal arrangement was more clearly seen in extracted outer membrane. The size of each structure was measured based on a center-to-center distance with the adjacent structure, and was determined to be 9.9±0.9 nm. A profile of the proteins in the outer membrane by SDS-PAGE, performed in 0.1% SDS and at 100 C, showed 42 kDa proteins to comprise the major outer membrane protein of this bacterium. Digestion of the outer membrane materials with proteinase reduced this protein band in the SDS-PAGE, and the amount of dark dots on the electron micrograph indicated the structure to be the major outer membrane protein (porin) of this bacterium. The power spectrogram of a computer-assisted Fourier transformation of the hexagonally arranged porin proteins suggests that the porin has a trimeric structure rather than a monomeric one.     

Evidence for plasma membrane-associated forms of sucrose synthase in maize

Plasma membrane fractions were isolated from maize (Zea mays L.) endosperms and etiolated kernels to investigate the possible membrane location of the sucrose synthase (SS) protein. Endosperms from seedlings at both 12 and 21 days after pollination (DAP), representing early and mid-developmental stages, were used, in addition to etiolated leaf and elongation zones from seedlings. Plasma membrane fractions were isolated from this material using differential centrifugation and aqueous two-phase partitioning. The plasma membrane-enriched fraction obtained was then analyzed for the presence of sucrose synthase using protein blots and activity measurements. Both isozymes SS1 and SS2, encoded by the lociSh1 andSus1, respectively, were detected in the plasma membrane-enriched fraction using polyclonal and monoclonal antisera to SS1 and SS2 isozymes. In addition, measurements of sucrose synthase activity in plasma membrane fractions of endosperm revealed high levels of specific activity. The sucrose synthase enzyme is tightly associated with the membrane, as shown by Triton X-100 treatment of the plasma membrane-enriched fraction. It is noteworthy that the gene products of bothSh1 andSus1 were detectable as both soluble and plasma membrane-associated forms.     

Carbohydrate metabolism during postharvest ripening in kiwifruit

Mature fruit (kiwifruit) of Actinidia deliciosa var. deliciosa (A. Chev.), (C.F.) Liang and Ferguson cv. Haywood (Chinese gooseberry) were harvested and allowed to ripen in the dark at 20° C. Changes were recorded in metabolites, starch and sugars, adenine nucleotides, respiration, and sucrose and glycolytic enzymes during the initiation of starch degradation, net starch-to-sucrose conversion and the respiratory climacteric. The conversion of starch to sucrose was not accompanied by a consistent increase in hexose-phosphates, and UDP-glucose declined. The activity of sucrose phosphate synthase (SPS) measured with saturating substrate rose soon after harvesting and long before net sucrose synthesis commenced. The onset of sugar accumulation correlated with an increase in SPS activity measured with limiting substrates. Throughout ripening, until sucrose accumulation ceased, feeding [¹⁴C] glucose led to labelling of sucrose and fructose, providing evidence for a cycle of sucrose synthesis and degradation. It is suggested that activation of SPS, amplified by futile cycles, may regulate the conversion of starch to sugars. The respiratory climacteric was delayed, compared with net starchsugar interconversion, and was accompanied by a general decline of pyruvate and all the glycolytic intermediates except fructose-1,6-bisphosphate. The ATP/ ADP ratio was maintained or even increased. It is argued that the respiratory climacteric cannot be simply a consequence of increased availability of respiratory substrate during starch-sugar conversion, nor can it result from an increased demand for ATP during this process.Abbreviations Frul,6bisP fructose-1,6-bisphosphate - Frul,6Pase fructose-1,6-bisphosphatase - Fru6P fructose-6-phosphate - PEP phosphoenolpyruvate - PFK phosphofructokinase - PFP pyrophosphate: fructose-6-phosphate phosphotransferase - SPS sucrose phosphate synthase - UDPGlc uridine 5'-diphosphoglucose We thank Professor G. Costa, University of Udine and Flavia Succhi, University of Bologna for their help in obtaining the fruit in Italy. E.A.M. was the recipient of a travel grant through the NZ/German Technological Agreement.