Initial Characterization of the FlgE Hook High Molecular Weight Complex of Borrelia burgdorferi

The spirochete periplasmic flagellum has many unique attributes. One unusual characteristic is the flagellar hook. This structure serves as a universal joint coupling rotation of the membrane-bound motor to the flagellar filament. The hook is comprised of about 120 FlgE monomers, and in most bacteria these structures readily dissociate to monomers (∼ 50 kDa) when treated with heat and detergent. However, in spirochetes the FlgE monomers form a large mass of over 250 kDa [referred to as a high molecular weight complex (HMWC)] that is stable to these and other denaturing conditions. In this communication, we examined specific aspects with respect to the formation and structure of this complex. We found that the Lyme disease spirochete Borrelia burgdorferi synthesized the HMWC throughout the in vitro growth cycle, and also in vivo when implanted in dialysis membrane chambers in rats. The HMWC was stable to formic acid, which supports the concept that the stability of the HMWC is dependent on covalent cross-linking of individual FlgE subunits. Mass spectrometry analysis of the HMWC from both wild type periplasmic flagella and polyhooks from a newly constructed ΔfliK mutant indicated that other proteins besides FlgE were not covalently joined to the complex, and that FlgE was the sole component of the complex. In addition, mass spectrometry analysis also indicated that the HMWC was composed of a polymer of the FlgE protein with both the N- and C-terminal regions remaining intact. These initial studies set the stage for a detailed characterization of the HMWC. Covalent cross-linking of FlgE with the accompanying formation of the HMWC we propose strengthens the hook structure for optimal spirochete motility.     

A new method for determination of parity in optical diffraction patterns from the structures with helical symmetry

In optical diffraction patterns from the structures with helical symmetry, the reflections appear as layer-lines. The Bessel function orders (n) of the layer-lines are not easily determined, because the radial co-ordinates of the principal maxima on the layer-lines cannot be measured precisely. We developed a method to find whether n is even or odd (parity of n) by superposing two identical images of a particle back to back with the two axes aligned. The method was successfully applied to analysis of the structure of straight polyhooks isolated from the mutant SJW880 of Salmonella typhimurium.     

Biofilm Formation by Psychrobacter arcticus and the Role of a Large Adhesin in Attachment to Surfaces

Psychrobacter arcticus strain 273-4, an isolate from a Siberian permafrost core, is capable of forming biofilms when grown in minimal medium under laboratory conditions. Biofilms form at 4 to 22°C when acetate is supplied as the lone carbon source and with 1 to 7% sea salt. P. arcticus is also capable of colonizing quartz sand. Transposon mutagenesis identified a gene important for biofilm formation by P. arcticus. Four transposon mutants were mapped to a 20.1-kbp gene, which is predicted to encode a protein of 6,715 amino acids (Psyc_1601). We refer to this open reading frame as cat1, for cold attachment gene 1. The cat1 mutants are unable to form biofilms at levels equivalent to that of the wild type, and there is no impact on the planktonic growth characteristics of the strains, indicating a specific role in biofilm formation. Through time course studies of the static microtiter plate assay, we determined that cat1 mutants are unable to form biofilms equivalent to that of the wild type under all conditions tested. In flow cell experiments, cat1 mutants initially are unable to attach to the surface. Over time, however, they form microcolonies, an architecture very different from that produced by wild-type biofilms. Our results demonstrate that Cat1 is involved in the initial stages of bacterial attachment to surfaces.     

Light-dependent conformational change of neoxanthin in a siphonous green alga,Codium intricatum,revealed by Raman spectroscopy

Siphonous green algae, a type of deep-sea green algae, appear olive drab and utilize blue–green light for photosynthesis. A siphonous green alga, Codium (C.) intricatum, was isolated from Okinawa prefecture in Japan, and a clonal algal culture in filamentous form was established. The major light-harvesting antenna was analogous to the trimeric LHCII found in higher plants, but the C. intricatum complex contained an unusual carbonyl carotenoid siphonaxanthin. Culture conditions were optimized to achieve high siphonaxanthin content in intact lyophilized filamentous bodies. Interestingly, the carotenoid composition was different when cultured under high irradiance: all-trans neoxanthin was accumulated in addition to the normal 9′-cis form in whole cell extract. Resonance Raman spectra of intact filamentous bodies, cultured under high- and low-light conditions, confirmed the accumulation of all-trans neoxanthin under high irradiance conditions. A plausible function of the presence of all-trans neoxanthin will be discussed in relation to the regulation against high light stress.     

Medium-dependent phenotypes of Streptomyces coelicolor with mutations in ftsI or ftsW

Streptomyces coelicolor A3(2) ftsI- and ftsW-null mutants produced aerial hyphae with no evidence of septation when grown on a traditional osmotically enhanced medium. This phenotype was partially suppressed when cultures were grown on media prepared without sucrose. We infer that functional FtsZ rings can form in ftsI- and ftsW-null mutants under certain growth conditions.     

Production of Antibacterial Compounds and Biofilm Formation by Roseobacter Species Are Influenced by Culture Conditions

Bacterial communities associated with marine algae are often dominated by members of the Roseobacter clade, and in the present study, we describe Roseobacter phenotypes that may provide this group of bacteria with selective advantages when colonizing this niche. Nine of 14 members of the Roseobacter clade, of which half were isolated from cultures of the dinoflagellate Pfiesteria piscicida, produced antibacterial compounds. Many non-Roseobacter marine bacteria were inhibited by sterile filtered supernatants of Silicibacter sp. TM1040 and Phaeobacter (formerly Roseobacter) strain 27-4, which had the highest production of antibacterial compound. In contrast, Roseobacter strains were susceptible only when exposed to concentrated compound. The production of antibacterial compound was influenced by the growth conditions, as production was most pronounced when bacteria were grown in liquid medium under static conditions. Under these conditions, Silicibacter sp. TM1040 cells attached to one another, forming rosettes, as has previously been reported for Phaeobacter 27-4. A spontaneous Phaeobacter 27-4 mutant unable to form rosettes was also defective in biofilm formation and the production of antibacterial compound, indicating a possible link between these phenotypes. Rosette formation was observed in 8 of 14 Roseobacter clade strains examined and was very pronounced under static growth in 5 of these strains. Attachment to surfaces and biofilm formation at the air-liquid interface by these five strains was greatly facilitated by growth conditions that favored rosette formation, and rosette-forming strains were 13 to 30 times more efficient in attaching to glass compared to strains under conditions where rosette formation was not pronounced. We hypothesize that the ability to produce antibacterial compounds that principally inhibit non-Roseobacter species, combined with an enhancement in biofilm formation, may give members of the Roseobacter clade a selective advantage and help to explain the dominance of members of this clade in association with marine algal microbiota.     

l-Cystine transport by papain-treated rat renal brush-border membrane vesicles

In papain-treated rat renal brush-border membrane vesicles, cystine uptake was enhanced under sodium gradient conditions. This effect was not observed when sodium was equilibrated across the vesicle membrane or when sodium was completely absent from the incubation medium. The increased rate of cystine uptake occurred within the first two minutes of incubation and coincided with the period of increased flux of sodium known to occur after papain treatment. Under sodium gradient conditions, the V_max of cystine uptake by treated vesicles was 65% greater while the K_m was 25% lower than the value observed in untreated membranes. The increased cystine uptake after papain treatment occurred when medium cystine was in the electroneutral form. In the absence of a sodium gradient, cystine uptake by control membranes was insensitive to changes in membrane potential and this was unaltered after papain treatment. Exposure of the membranes to papain also resulted in a profound decrease in cystine binding which occurs in native membranes incubated with cystine. The fact that cystine uptake is unchanged under sodium equilibration and even enhanced under sodium gradient conditions suggests that the component of cystine binding is not essential for cystine transport and may represent non-specific binding to membrane proteins.     

Effects of O2 stress on tomato alcohol dehydrogenase activity: Description of a second ADH coding gene

Subjecting tomato seedlings to anaerobic conditions results in expression of a previously undescribed Adh gene, Adh-2. Induction profiles were similar for all tissues, including roots, hypocotyls, cotyledons, and true leaves. In sharp contrast to ADH-1, ADH-2 showed no induction under anaerobic stress. The only time ADH-2 activity was expressed (under noninduced conditions) was during the early stages of embryogenesis. By late embryogenesis, ADH-2 activity approached a zero level, concomitant with a sharp rise in ADH-1 activity, which is found in the cotyledons of quiescent embryo. Despite striking differences in the regulation of these two genes, their homology is demonstrated in the ability of their enzyme subunits to form presumed intergenic heterodimers, which are visible during the transient period of embryogenesis when the polypeptides encoded by both genes are expressed. A multiple point linkage test using isozymic marker genes places the Adh-2 locus on chromosome 6 near Aps-1, whereas Adh-1 resides on chromosome 4.     

Sorption of some ions by algae related to their trophic conditions

The unicellular algaeScenedesmus obliquus (125),Chlorella pyrenoidosa (82) andCoccomyxa solorinae saccatae (111) were studied with respect to the form of uptake of potassium, phosphate, calcium and zinc ions and to the energy sources involved: light under autotrophic conditions, glucose under mixotrophic or heterotrophic conditions (in light and in darkness or together with yeast extract as an auxotrophic substrate). We respected the trophic conditions of algae when preparing the experimental material (precultivation). The following conditions were reached:

1. (1)
   The three algae grow faster in a glucose medium under mixotrophic conditions and are capable of growing on it also heterotrophically:Ch. pyrenoidosa andSc. obliquus grow substantially better thanC. solorinae saccatae. The first two algae grow more intensively in a glucose medium containing yeast extract whileCoccomyxa does not. After cultivation under mixotrophic conditions the first two diminish endogenous respiration, the third raises it. Glucose stimulates respiration in the first two when grown autotrophically, while after mixotrophic cultivation the effect of glucose is suppressed inCh. pyrenoidosa and in the other two only after growth on glucose with yeast extract.     
   
   

Dimorphism and hydrocarbon metabolism in Yarrowia lipolytica var. indica

Yarrowia lipolytica is able to metabolize high Mr hydrophobic natural compounds such as fatty acids and hydrocarbons. Characteristically, strains of Y. lipolytica can grow as populations with variable proportions of yeast and filamentous forms. In the present study, we describe the dimorphic characteristics of a variant designated as Y. lipolytica var. indica isolated from petroleum contaminated sea water and the effect of cell morphology on hydrocarbon metabolism. The variant behaved as a yeast monomorphic strain, under conditions at which terrestrial Y. lipolytica strain W29 and its derived strains, grow as almost uniform populations of mycelial cells. Using organic nitrogen sources and N-acetylglucosamine as carbon source, var. indica was able to form mycelial cells, the proportion of which increased when incubated under semi-anaerobic conditions. The cell surface characteristics of var. indica and W29 were found to be different with respect to contact angle and percent hydrophobicity. For instance, percent hydrophobicity of var. indica was 89.93 ± 1.95 while that of W29 was 70.78 ± 1.1. Furthermore, while all tested strains metabolize hydrocarbons, only var. indica was able to use it as a carbon source. Yeast cells of var. indica metabolized hexadecane with higher efficiency than the mycelial form, whereas the mycelial form of the terrestrial strain metabolized the hydrocarbon more efficiently, as occurred with the mycelial monomorphic mutant AC11, compared to the yeast monomorphic mutant AC1.     

Carbon monoxide-dependent evolution of hydrogen by the homoacetate-fermenting bacteriumClostridium thermoaceticum

Clostridium thermoaceticum was found to form H₂ when cultivated heterotrophically on dextrose under a carbon monoxide (CO) gas phase. In contrast, when cultivated under CO₂, only minimal levels of hydrogen were detected. Resting cells from the CO-grown cultures also formed H₂ when incubated under CO with dextrose, while a comparative study with resting cells from CO₂-grown cultures demonstrated that the CO₂-grown cells were not competent in H₂ formation when incubated under CO. When dextrose was deleted, CO-cultivated resting cells did not form H₂ when incubated under CO.     

Photosynthesis in Chromera velia Represents a Simple System with High Efficiency

Chromera velia (Alveolata) is a close relative to apicomplexan parasites with a functional photosynthetic plastid. Even though C. velia has a primitive complement of pigments (lacks chlorophyll c) and uses an ancient type II form of RuBISCO, we found that its photosynthesis is very efficient with the ability to acclimate to a wide range of irradiances. C. velia maintain similar maximal photosynthetic rates when grown under continual light-limited (low light) or light-saturated (high light) conditions. This flexible acclimation to continuous light is provided by an increase of the chlorophyll content and photosystem II connectivity under light limited conditions and by an increase in the content of protective carotenoids together with stimulation of effective non-photochemical quenching under high light. C. velia is able to significantly increase photosynthetic rates when grown under a light-dark cycle with sinusoidal changes in light intensity. Photosynthetic activities were nonlinearly related to light intensity, with maximum performance measured at mid-morning. C. velia efficiently acclimates to changing irradiance by stimulation of photorespiration and non-photochemical quenching, thus avoiding any measurable photoinhibition. We suggest that the very high CO₂ assimilation rates under sinusoidal light regime are allowed by activation of the oxygen consuming process (possibly chlororespiration) that maintains high efficiency of RuBISCO (type II). Despite the overall simplicity of the C. velia photosynthetic system, it operates with great efficiency.     

RegB Kinase Activity Is Repressed by Oxidative Formation of Cysteine Sulfenic Acid

RegB/RegA comprise a global redox-sensing signal transduction system utilized by a wide range of proteobacteria to sense environmental changes in oxygen tension. The conserved cysteine 265 in the sensor kinase RegB was previously reported to form an intermolecular disulfide bond under oxidizing conditions that converts RegB from an active dimer into an inactive tetramer. In this study, we demonstrate that a stable sulfenic acid (-SOH) derivative also forms at Cys-265 in vitro and in vivo when RegB is exposed to oxygen. This sulfenic acid modification is reversible and stable in the air. Autophosphorylation assay shows that reduction of the SOH at Cys-265 to a free thiol (SH) can increase RegB kinase activity in vitro. Our results suggest that a sulfenic acid modification at Cys-265 performs a regulatory role in vivo and that it may be the major oxidation state of Cys-265 under aerobic conditions. Cys-265 thus functions as a complex redox switch that can form multiple thiol modifications in response to different redox signals to control the kinase activity of RegB.     

Growth-based Determination and Biochemical Confirmation of Genetic Requirements for Protein Degradation in Saccharomyces cerevisiae

Regulated protein degradation is crucial for virtually every cellular function. Much of what is known about the molecular mechanisms and genetic requirements for eukaryotic protein degradation was initially established in Saccharomyces cerevisiae. Classical analyses of protein degradation have relied on biochemical pulse-chase and cycloheximide-chase methodologies. While these techniques provide sensitive means for observing protein degradation, they are laborious, time-consuming, and low-throughput. These approaches are not amenable to rapid or large-scale screening for mutations that prevent protein degradation. Here, a yeast growth-based assay for the facile identification of genetic requirements for protein degradation is described. In this assay, a reporter enzyme required for growth under specific selective conditions is fused to an unstable protein. Cells lacking the endogenous reporter enzyme but expressing the fusion protein can grow under selective conditions only when the fusion protein is stabilized (i.e. when protein degradation is compromised). In the growth assay described here, serial dilutions of wild-type and mutant yeast cells harboring a plasmid encoding a fusion protein are spotted onto selective and non-selective medium. Growth under selective conditions is consistent with degradation impairment by a given mutation. Increased protein abundance should be biochemically confirmed. A method for the rapid extraction of yeast proteins in a form suitable for electrophoresis and western blotting is also demonstrated. A growth-based readout for protein stability, combined with a simple protocol for protein extraction for biochemical analysis, facilitates rapid identification of genetic requirements for protein degradation. These techniques can be adapted to monitor degradation of a variety of short-lived proteins. In the example presented, the His3 enzyme, which is required for histidine biosynthesis, was fused to Deg1-Sec62. Deg1-Sec62 is targeted for degradation after it aberrantly engages the endoplasmic reticulum translocon. Cells harboring Deg1-Sec62-His3 were able to grow under selective conditions when the protein was stabilized.     

Biomechanical responses of aquatic plants to aerial conditions

Background and Aims

Wetlands are impacted by changes in hydrological regimes that can lead to periods of low water levels. During these periods, aquatic plants experience a drastic change in the mechanical conditions that they encounter, from low gravitational and tensile hydrodynamic forces when exposed to flow under aquatic conditions, to high gravitational and bending forces under terrestrial conditions. The objective of this study was to test the capacity of aquatic plants to produce self-supporting growth forms when growing under aerial conditions by assessing their resistance to terrestrial mechanical conditions and the associated morpho-anatomical changes.

Methods

Plastic responses to aerial conditions were assessed by sampling Berula erecta, Hippuris vulgaris, Juncus articulatus, Lythrum salicaria, Mentha aquatica, Myosotis scorpioides, Nuphar lutea and Sparganium emersum under submerged and emergent conditions. The cross-sectional area and dry matter content (DMC) were measured in the plant organs that bear the mechanical forces, and their biomechanical properties in tension and bending were assessed.

Key Results

All of the species except for two had significantly higher stiffness in bending and thus an increased resistance to terrestrial mechanical conditions when growing under emergent conditions. This response was determined either by an increased allocation to strengthening tissues and thus a higher DMC, or by an increased cross-sectional area. These morpho-anatomical changes also resulted in increased strength and stiffness in tension.

Conclusions

The capacity of the studied species to colonize this fluctuating environment can be accounted for by a high degree of phenotypic plasticity in response to emersion. Further investigation is however needed to disentangle the finer mechanisms behind these responses (e.g. allometric relations, tissue make-up), their costs and adaptive value.     

Respiratory Succession and Community Succession of Bacterioplankton in Seasonally Anoxic Estuarine Waters

Anoxia occurs in bottom waters of stratified estuaries when respiratory consumption of oxygen, primarily by bacteria, outpaces atmospheric and photosynthetic reoxygenation. Once water becomes anoxic, bacterioplankton must change their metabolism to some form of anaerobic respiration. Analysis of redox chemistry in water samples spanning the oxycline of Chesapeake Bay during the summer of 2004 suggested that there was a succession of respiratory metabolism following the loss of oxygen. Bacterial community doubling time, calculated from bacterial abundance (direct counts) and production (anaerobic leucine incorporation), ranged from 0.36 to 0.75 day and was always much shorter than estimates of the time that the bottom water was anoxic (18 to 44 days), indicating that there was adequate time for bacterial community composition to shift in response to changing redox conditions. However, community composition (as determined by PCR-denaturing gradient gel electrophoresis analysis of 16S rRNA genes) in anoxic waters was very similar to that in surface waters in June when nitrate respiration was apparent in the water column and only partially shifted away from the composition of the surface community after nitrate was depleted. Anoxic water communities did not change dramatically until August, when sulfate respiration appeared to dominate. Surface water populations that remained dominant in anoxic waters were Synechococcus sp., Gammaproteobacteria in the SAR86 clade, and Alphaproteobacteria relatives of Pelagibacter ubique, including a putative estuarine-specific Pelagibacter cluster. Populations that developed in anoxic water were most similar (<92% similarity) to uncultivated Firmicutes, uncultivated Bacteroidetes, Gammaproteobacteria in the genus Thioalcalovibrio, and the uncultivated SAR406 cluster. These results indicate that typical estuarine bacterioplankton switch to anaerobic metabolism under anoxic conditions but are ultimately replaced by different organisms under sulfidic conditions.     

Acid-Sensitive Enteric Pathogens Are Protected from Killing under Extremely Acidic Conditions of pH 2.5 when They Are Inoculated onto Certain Solid Food Sources

Gastric acidity is recognized as the first line of defense against food-borne pathogens, and the ability of pathogens to resist this pH corresponds to their oral infective dose (ID). Naturally occurring and genetically engineered acid-sensitive enteric pathogens were examined for their ability to survive under acidic conditions of pH 2.5 for 2 h at 37°C when inoculated onto ground beef. Each of the strains displayed significantly high survival rates under these normally lethal conditions. The acid-sensitive pathogens Campylobacter jejuni and Vibrio cholerae, which were protected at lower levels from acid-induced killing by ground beef under these conditions, were sensitive to killing in acidified media at pH 5.0 but survived at pH 6.0. Salmonella inoculated onto the surface of preacidified ground beef could not survive if the pH on the surface of the beef was 2.61 or lower but was viable if the surface pH was 3.27. This implies that the pH of the microenvironment occupied by the bacteria on the surface of the food source is critical for their survival. Salmonella was also shown to be protected from killing when inoculated onto boiled egg white, a food source high in protein and low in fat. These results may explain why Salmonella species have a higher oral ID of approximately 10⁵ cells when administered under defined conditions but have been observed to cause disease at doses as low as 50 to 100 organisms when consumed as part of a contaminated food source. They may also help explain why some pathogens are associated primarily with food-borne modes of transmission rather than fecal-oral transmission.