Effect of Bacteria on Chemotaxis in the Cellular Slime Molds

The effect of chemotactic substances, secreted by Escherichia coli, on the cellular slime molds was studied by deposition of bacteria near myxamoebae populations. Droplets of a bacterial suspension and a myxamoebae suspension were placed separately, at predetermined distances from each other, on a hydrophobic agar surface of low rigidity. Myxamoebae remained confined inside the droplets, except when they were activated by the bacterial products. The sphere of attraction increased at higher bacterial concentrations. Myxamoebae could be attracted over distances as great as 5 mm. Myxamoebae in droplets close to dense bacterial populations not only were attracted toward the bacteria but also moved out in an opposite direction from the bacteria. There was a gradual decrease of attraction at increasing distances between amoebae and bacteria. The attraction by bacteria or bacterial products was reduced at lower temperatures. Light did not affect the distance over which attraction could be observed. Myxamoebae close to their aggregation phase were most sensitive to the bacterial attractants. Bacterial attractants at high concentrations could disperse aggregates, even when they were in an advanced stage. At still higher concentrations of the bacterial products, cells stopped moving altogether. The bacterial attractants activated different species of cellular slime molds. They appeared to be present not only in E. coli but also in all other bacterial species that were tested. These results are discussed in the light of earlier observations on the attraction of cells by aggregates of myxamoebae.     

Inhibition of growth and cell wall morphogenesis of Bacillus subtilis by extracellular slime produced by Physarum flavicomum.

Slime secreted by microplasmodia of the myxomycete Physarum flavicomum inhibited the uptake of glucose and amino acids, as well as growth and cell division of the bacterium Bacillus subtilis. Morphological changes such as production of chains, swollen cells, and/or cell lysis, occurred coincident with these physiological inhibitory events. These phenomena were all dependent on the concentration of slime present in the growth medium. Electron microscopy revealed that the cell walls of slime-inhibited cells were undergoing degradation and the process was most pronounced in the swollen cells. Isolated cell walls of B. subtilis were also found to undergo degradation upon incubation with slime. Boiled slime did not exhibit lytic activity on native cell walls, but boiled cell walls were degraded by native slime. The inhibitory effect of slime seemed to be, at least in part, due to an inherent peptidase (protease) activity. B. subtilis eventually overcomes the inhibition exhibited by slime due to the production of an antagonist of slime.     

Production and utilization of extracellular slime by Pseudomonas solanacearum and its role on survival at different relative humidities

Pseudomonas solanacearum produced maximum slime with glucose and least with glycerol. With increasing concentration of glucose, slime production increased. The maximum slime production was observed in the medium containing 1% glucose. The slime contained sugars, sugar acids and amino acids. The bacterium utilized the slime as a sole source of carbon. The growth on slime was more or less comparable to the growth on 0.1% glucose. The viability of the bacterium in slime increased as the relative humidity (RH) decreased. At higher RH the slime absorbed moisture and the viability was reduced. The bacterium could survive only for short period at higher RH under sunlight not in shade. The sunlight seemed to accentuate the harmful effect of RH on the bacterium.     

Cloning, expression, and substrate specificity of a fungal chymotrypsin. Evidence for lateral gene transfer from an actinomycete bacterium

Unlike trypsins, chymotrypsins have not until now been found in fungi. Expressed sequence tag analysis of the deuteromycete Metarhizium anisopliae identified two trypsins (family S1) and a novel chymotrypsin (CHY1). CHY1 resembles actinomycete (bacterial) chymotrypsins (family S2) rather than other eukaryote enzymes (family S1) in being synthesized as a precursor species (374 amino acids, pI/MW: 5.07/38,279) containing a large N-terminal fragment (186 amino acids). Chy1 was expressed in Pichia pastoris yielding an enzyme with a chymotrypsin specificity for branched aliphatic and aromatic C-terminal amino acids. This is predictable as key catalytic residues determining the specificity of Streptomyces griseus chymotrypsins are conserved with CHY1. Mature (secreted) CHY1 (pI/MW: 8.29/18,499) shows closest overall amino acid identity to S. griseus protease C (55%) and clustered with other secreted bacterial S2 chymotrypsins that diverged widely from animal and endocellular bacterial enzymes in phylogenetic trees of the chymotrypsin superfamily. Conversely, actinomycete chymotrypsins are much more closely related to fungal proteases than to other eubacterial sequences. Complete genomes of yeast, gram eubacteria, archaebacteria, and mitochondria do not contain paralogous genes. Expressed sequence tag data bases from other fungi also lack chymotrypsin homologs. In light of this patchy distribution, we conclude that chy1 probably arose by lateral gene transfer from an actinomycete bacterium.     

Characterization of a Novel PepF-Like Oligopeptidase Secreted by Bacillus amyloliquefaciens 23-7A

An oligopeptidase from Bacillus amyloliquefaciens 23-7A was characterized along with its biochemical activities and structural gene. The protein's amino acid sequence and enzymatic activities were similar to those of other bacterial PepFs, which belong to metallopeptidase family M3. While most bacterial PepFs are cytoplasmic endopeptidases, the identified PepF_Ba oligopeptidase is a secreted protein and may facilitate the process of sporulation.     

Fate of the 63-kDa periplasmic protein of the infectious form of the endonuclear symbiotic bacterium Holospora obtusa during the infection process

Holospora obtusa is a macronucleus-specific endosymbiotic bacterium of the ciliate Paramecium caudatum. We report the secretion of a 63-kDa periplasmic protein of an infectious form of the bacterium into the macronucleus of its host. Indirect immunofluorescence microscopy with five monoclonal antibodies against the 63-kDa protein demonstrated that, soon after the bacterial invasion into the host macronucleus, the protein was detected in the infected macronucleus and that levels of the protein increased dramatically within one day of infection. The use of inhibitors for host and bacterial protein synthesis illustrated that, in early infection of H. obtusa, not only the pre-existing but also a newly synthesized 63-kDa protein was secreted into the host macronucleus. A partial amino acid sequence of the protein was determined, and a gene encoding the 63-kDa protein was cloned. The deduced amino acid sequence shows that this protein is a novel protein.     

A reassessment of the structure of Paracoccus cytochrome c-550

An amino acid sequence and a three-dimensional structure of cytochrome c-550 from the facultatively denitrifying aerobic bacterium Paracoccus denitrificans have been reported (Timkovich et al., 1976; Timkovich &; Dickerson, 1976). The amino acid sequence showed considerable similarity to Rhodospirillaceae (purple phototrophic bacterial) cytochrome c₂, but also had some unexpected features. We have reexamined the amino acid sequence and have found five discrepancies. The molecule contains an additional tryptophan residue, which was not detected in either the 2.5 Å crystallographic analysis or the original sequence investigation.     

Synthesis of amino acid conjugates to 2-imino-3-methylene-5-carboxypyrrolidine and 2-imino-3-methylene-6-carboxypiperidine

The four stereomers of 2-imino-3-methylene-5-l(carboxy-l-valyl)pyrrolidine, a bacterial metabolite that is inhibitory to the fire blight bacterium Erwinia amylovora, were synthesised and compared for antibacterial activity. Several alternative amino acid conjugates with l,l-stereochemistry were also prepared, and the synthesis was extended to 3-methylenepiperidine-6-l-carboxylic acid and a selection of 2-imino-3-methylenepiperidine-6-l-carboxy-l-amino acid conjugates. All synthetic amino acid conjugates (l,l-stereomers) were inhibitory to the growth of E. amylovora. The likely participation of the conjugated iminomethylene moiety as a Michael acceptor is implicated.     

Amino acid sequence of the cytochrome subunit of the photosynthetic reaction centre from the purple bacterium Rhodopseudomonas viridis

The complete nucleotide sequence of the gene encoding the cytochrome subunit of the photosynthetic reaction centre from the purple bacterium Rhodopseudomonas viridis, and the derived amino acid sequence are presented. The nucleotide sequence of the gene reveals the existence of a typical bacterial signal peptide of 20 amino acid residues which is not found in the mature cytochrome subunit. The gene encoding the cytochrome subunit is preceded by the gene encoding the M subunit. Both genes overlap by 1 bp. The mature cytochrome subunit consists of 336 amino acid residues; 73% of its amino acid sequence was confirmed by protein sequencing work. The mol. wt of the cytochrome subunit including the covalently bound fatty acids and the bound heme groups is 40 500. The internal sequence homology is low, despite the symmetric structure of the cytochrome subunit previously shown by X-ray crystallographic analysis of the intact photosynthetic reaction centre. Sequence homologies to other cytochromes were not found.     

Structure and Composition of Biological Slimes on Paper and Board Machines

Biological slimes (biofilms) collected from the wet end of paper and board machines were examined by electron microscopy and analyzed for fatty acid composition, neutral sugar composition, and ATP. Electron microscopy revealed minuscule prokaryotic organisms (diameter, 0.2 to 0.4 μm). Larger cells morphologically resembling Sphaerotilus and Leptothrix spp. were found in slimes from machines using recycled fiber or unbleached pulp. The bacteria were embedded in a slimy matrix and often contained reserve materials microscopically resembling poly-β-hydroxybutyrate and glycogen. Fatty acid analysis of the slimes revealed bacterial signature fatty acids in concentrations equivalent to the presence of 2 × 10¹⁰ to 2.6 × 10¹² (average, 7 × 10¹¹) bacterial cells (live and dead) per g (dry weight) of slime. The slimes contained several known components of bacterial polysaccharides in addition to glucose, indicating that the slime body consisted of bacterial polysaccharides. The slimes contained uronic acids equivalent to a binding capacity of 12.5 to 50 μmol of divalent cations per g (dry weight) of slime. The uronic acid-containing polysaccharides may be responsible for the accumulation of heavy metals in the slime. Calculation of the ATP contents of the slimes resulted in an estimate of 5 × 10¹² cells per g (dry weight) of slime when calibrated with pure bacterial cultures isolated from the slimes. From electron micrographs, an estimate ranging from 1 × 10¹⁰ to 1.5 × 10¹² (average, 4 × 10¹¹) cells per g (dry weight) of slime was obtained.     

Isolation and characterization of a bacterial dipeptidyl carboxypeptidase inhibitor from Bacillus subtilis 3-16-20

A bacterial dipeptidyl carboxypeptidase inhibitor was isolated from the culture broth of a bacterium identified as Bacillus subtilis. The inhibitor was purified 33-fold from the culture supernatant of B. subtillis 3-16-20 strain by Q-, and S-Sepharose fast flow, C₁₈ column chromatography, ethanol treatment, and ODS column chromatography. The purified inhibitor has an amino acid sequence of glycyl-prolyl-phenylalanyl-prolylisoleucine. IC₅₀ values of the inhibitor were 177 μM (rabbit lung ACE) and 35 μM (bacterial DCP).     

Entropy-driven motility of Sinorhizobium meliloti on a semi-solid surface

Sinorhizobium meliloti growing on soft agar can exhibit an unusual surface spreading behaviour that differs from other bacterial surface motilities. Bacteria in the colony secrete an exopolysaccharide-rich mucoid fluid that expands outward on the surface, carrying within it a suspension of actively dividing cells. The moving slime disperses the cells in complex and dynamic patterns indicative of simultaneous bacterial growth, swimming and aggregation. We find that while flagellar swimming is required to maintain the cells in suspension, the spreading and the associated pattern formation are primarily driven by the secreted exopolysaccharide EPS II, which creates two entropy-increasing effects: an osmotic flow of water from the agar to the mucoid fluid and a crowding or depletion attraction between the cells. Activation of these physical/chemical phenomena may be a useful function for the high molecular weight EPS II, a galactoglucan whose biosynthesis is tightly regulated by the ExpR/SinI/SinR quorum-sensing system: unlike bacterial colonies that spread via bacterium-generated, physical propulsive forces, S. meliloti under quorum conditions may use EPS II to activate purely entropic forces within its environment, so that it can disperse by passively ‘surfing’ on those forces.     

Characteristics of Gloeophyllum trabeum Alcohol Oxidase, an Extracellular Source of H2O2 in Brown Rot Decay of Wood

A novel alcohol oxidase (AOX) has been purified from mycelial pellets of the wood-degrading basidiomycete Gloeophyllum trabeum and characterized as a homooctameric nonglycosylated protein with native and subunit molecular masses of 628 and 72.4 kDa, containing noncovalently bonded flavin adenine dinucleotide. The isolated AOX cDNA contained an open reading frame of 1,953 bp translating into a polypeptide of 651 amino acids displaying 51 to 53% identity with other published fungal AOX amino acid sequences. The enzyme catalyzed the oxidation of short-chain primary aliphatic alcohols with a preference for methanol (K_m = 2.3 mM, k_cat = 15.6 s⁻¹). Using polyclonal antibodies and immunofluorescence staining, AOX was localized on liquid culture hyphae and extracellular slime in sections from degraded wood and on cotton fibers. Transmission electron microscopy immunogold labeling localized the enzyme in the hyphal periplasmic space and wall and on extracellular tripartite membranes and slime, while there was no labeling of hyphal peroxisomes. AOX was further shown to be associated with membranous or slime structures secreted by hyphae in wood fiber lumina and within the secondary cell walls of degraded wood fibers. The differences in AOX targeting compared to the known yeast peroxisomal localization were traced to a unique C-terminal sequence of the G. trabeum oxidase, which is apparently responsible for the protein's different translocation. The extracellular distribution and the enzyme's abundance and preference for methanol, potentially available from the demethylation of lignin, all point to a possible role for AOX as a major source of H₂O₂, a component of Fenton's reagent implicated in the generally accepted mechanisms for brown rot through the production of highly destructive hydroxyl radicals.     

Effect of Protozoa on Bacterial Degradation of an Aromatic Compound

Prototrophic and growth factor-requiring strains of Alcaligenes spp. were used to study the effect of a protozoan, Tetrahymena pyriformis, on the degradation of p-aminobenzoate. The protozoan inhibited activity of the prototrophic bacterium by reducing its population size. For the growth factor-requiring strain of Alcaligenes, T. pyriformis provided the required growth factors so that the predator permitted the bacteria to grow and to continue p-aminobenzoate degradation. T. pyriformis inhibited bacterial activity when the amino acid supply was in excess, but activity of the auxotrophic strain of Alcaligenes was stimulated by the protozoan when the amino acid supply was limiting, although the bacterial population size was reduced by the protozoan.     

The Bacterivorous Soil Flagellate Heteromita globosa Reduces Bacterial Clogging under Denitrifying Conditions in Sand-Filled Aquifer Columns

An exopolymer (slime)-producing soil bacterium Pseudomonas sp. (strain PS+) rapidly clogged sand-filled columns supplied with air-saturated artificial groundwater containing glucose (500 mg liter⁻¹) as a sole carbon source and nitrate (300 mg liter⁻¹) as an alternative electron acceptor. After 80 days of operation under denitrifying conditions, the effective porosity and saturated hydraulic conductivity (permeability) of sand in these columns had fallen by 2.5- and 26-fold, respectively. Bacterial biofilms appeared to induce clogging by occluding pore spaces with secreted exopolymer, although there may also have been a contribution from biogas generated during denitrification. The bacterivorous soil flagellate Heteromita globosa minimized reductions in effective porosity (1.6-fold) and permeability (13-fold), presumably due to grazing control of biofilms. Grazing may have limited growth of bacterial biomass and hence the rate of exopolymer and biogas secretion into pore spaces. Evidence for reduction in biogas production is suggested by increased nitrite efflux from columns containing flagellates, without a concomitant increase in nitrate consumption. There was no evidence that flagellates could improve flow conditions if added once clogging had occurred (60 days). Presumably, bacterial biofilms and their secretions were well established at that time. Nevertheless, this study provides evidence that bacterivorous flagellates may play a positive role in maintaining permeability in aquifers undergoing remediation treatments.     

Genetic aspects of aromatic amino acid biosynthesis in Lactococcus lactic

Polymerase chain reaction (PCR) primers designed from a multiple alignment of predicted amino acid sequences from bacterial aroA genes were used to amplify a fragment of Lactococcus lactis DNA. An 8 kb fragment was then cloned from a lambda library and the DNA sequence of a 4.4 kb region determined. This region was found to contain the genes tyrA, aroA, aroK, and pheA, which are involved in aromatic amino acid biosynthesis and folate metabolism. TyrA has been shown to be secreted and AroK also has a signal sequence, suggesting that these proteins have a secondary function, possibly in the transport of amino acids. The aroA gene from L. lactis has been shown to complement an E. coli mutant strain deficient in this gene. The arrangement of genes involved in aromatic amino acid biosynthesis in L. lactis appears to differ from that in other organisms.     

Characterization of Bacteria That Suppress Rhizoctonia Damping-Off in Bark Compost Media by Analysis of Fatty Acid Biomarkers

Examination of cucumber roots (Cucumis sativus L.) grown in bark compost media and of the surrounding edaphic substrate showed profiles of polar lipid fatty acids commonly found in bacteria. The composition of fatty acids in these profiles differed significantly between roots grown in a medium naturally suppressive to Rhizoctonia damping-off and roots from a conducive medium. Cucumber roots from the suppressive medium had higher proportions of cis-vaccenic acid (18:1 ω 7c) and the iso-branched monoenoic fatty acid i17:1 ω 8 but lower proportions of several iso- and anteiso-branched fatty acids compared with roots from the conducive medium. The concentrations of the bacterial fatty acids were significantly lower in the surrounding media. However, the suppressive and conducive growth substrates had differences in the composition of the bacterial fatty acids similar to those found between the cucumber roots proper. These results suggest major differences in bacterial community composition between suppressive and conducive systems. Fatty acid analyses were also utilized to examine the effects on bacterial community composition of root colonization by Flavobacterium balustinum 299, a biocontrol agent. The concentration of the most prominent fatty acid in this bacterium, i17:1 ω 8, was increased on roots produced from inoculated seeds in a medium rendered suppressive by the treatment. This change was concomitant with a significant increase in the concentration of 18:1 ω 7c, not present in the lipids of the antagonist, indicating a shift in the microflora from a conducive to a suppressive bacterial community.     

Schistosoma mansoni: histochemical analysis of the postacetabular gland secretion of cercariae

Contents of the funduses and ducts of the postacetabular glands of Schistosoma mansoni cercariae, the secreted deposits, and the surface film were compared by their histochemical reactions. Techniques for carbohydrate-containing substances, neutral and acid mucosubstance, proteins and amino acids, and enzymes were used. The secretion reacted differently before (within the glands) and after (in secreted deposits) emission.Before emission, the postacetabular gland contents reacted as a neutral mucosubstance containing periodate-engendered and periodate-reactive aldehydes rich in vic-glycols or their substituted amines, probably hexoses other than glucose, such as fucose or galactose. No reactions of significance were observed for acid groups or for glycogen or lipids. In this state, the secretion is termed mucigen.After emission, the secretion stained not only as mucigen, but also as acid mucosubstance, apparently sialomucin. After emission, it is termed mucin.It is probable that acid radicals were present in mucigen but were masked stearically by the presence of adjacent neutral radicals or basic proteins. The surface film reacted as both a neutral and an acid mucosubstance. Evidence suggested that the film itself was neutral and that the reaction for acid mucosubstance was from an overlay of mucin secreted from the postacetabular glands.Proteins and amino acids, especially arginine, and some tyrosine and tryptophan were indicated in mucigen and in mucin by the histochemical tests. There was no histochemical evidence of enzymes. Secretion of the postacetabular glands is concluded from histochemical reactions, as from earlier chromatographic data (Stirewalt and Evans 1960), to be a carbohydrate-protein-lipid complex.     

Purification and molecular properties of a soluble ferredoxin from Rhodopseudomonas capsulata

A soluble ferredoxin was purified from the photosynthetic bacterium Rhodopseudomonas capsulata and characterized. Unlike Rhodospirillum rubrum, where two soluble ferredoxins have been found, only a single species was found in Rps. capsulata. The amino acid composition, ultraviolet-visible spectral properties, molecular weight (12000) and biological activity were determined. The ultraviolet-visible spectrum is similar to that of other bacterial ferredoxins, with a maximum when oxidized at 380 nm (? = 26.1 · 10³ M^-1 · cm^-1). The possible roles of this ferredoxin in the cellular metabolism are discussed.     

Crystal structures of mutant ribosomal proteins L1

Nine mutant ribosomal proteins L1 from the bacterium Thermus thermophilus and archaeon Methanococcus jannaschii were obtained and their crystal structures were determined and analyzed. The structure of the S179C TthL1 mutant, determined earlier, was also analyzed. In half of the proteins studied, point mutations of the amino acid residues exposed on the protein surface essentially changed the spatial structure of the protein. This proves that a correct study of biological processes with the help of site-directed mutagenesis requires a preliminary determination or, at least, modeling of the structures of mutant proteins. A detailed comparison of the structures of the L1 mutants and the corresponding wild-type L1 proteins demonstrated that the side chain of a mutated amino acid residue tends to adopt a location similar to that of the side chain of the corresponding residue in the wild-type protein. This observation assists in modeling the structure of mutant proteins.