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The fermenting bacterium Malonomonas rubra is phylogenetically related to sulfur-reducing bacteria and contains a c-type cytochrome similar to those of sulfur and sulfate reducers.

Malonomonas rubra is a microaerotolerant fermenting bacterium which can maintain its energy metabolism for growth by decarboxylation of malonate to acetate. 16S rRNA sequence analysis revealed that M. rubra is closely related to the cluster of mesophilic sulfur-reducing bacteria within the delta subclass of the Proteobacteria, with the fermenting bacterium Pelobacter acidigallici and the sulfur reducers Desulfuromusa kysingii, D. bakii and D. succinoxidans as closest relatives. The cells contain high amounts (up to 12% of the total cell protein content) of a c-type cytochrome which is present mainly (> 60%) in the cytoplasm and to minor parts in the periplasm (> 20%) and associated with the membrane fraction (> 10%), independent of the growth substrate. This cytochrome is a tetraheme cytochrome of 13,700 Da molecular mass with a midpoint redox potential of -0.210 V.M. rubra does not reduce sulfur or ferric iron compounds. Since this cytochrome appears not to be involved in the energy metabolism it is concluded that it is a remnant of sulfur-reducing ancestors of this bacterium, without a conceivable physiological function in its present energy metabolism.

Cytochrome c Group↗

Halomonas campisalis sp. nov., a denitrifying, moderately haloalkaliphilic bacterium.

The isolation and characterization of a denitrifying bacterium that is both moderately halophilic and alkaliphilic is described. The organism was isolated for use in the development of a bioprocess that could potentially reduce the costs of ion exchange resin regenerant disposal. The process of ion exchange, after resin regeneration, produces a briny, alkaline waste that is difficult and expensive to dispose. The biological removal of nitrate and subsequent reuse of these brines can potentially provide a cost-saving alternative to disposing of this waste product. To achieve our objective, a moderately halophilic, alkaliphilic bacterium was isolated from sediment samples taken from the salt plain of Alkali Lake in Washington State (USA). The haloalkaliphilic bacterium, designated strain 4A, is motile with rod-shaped cells that are 3 to 5 microm long and 1 microm wide. Electron acceptors used include oxygen, nitrate, and nitrite. In addition, it has similar specific nitrate reduction rates and biomass yields as non-halophilic denitrifying bacteria. It is capable of using a variety of electron donors. This organism can grow at NaCl concentrations ranging from 0.2 to 4.5 M with optimum growth occurring at 1.5 M and pH values ranging from 6 to 12 with 9.5 being the optimum pH. The temperature range for growth of strain 4A is 4-50 degrees C with optimal growth occurring at 30 degrees C. The G + C content is 66 mol%. Phylogenetic analyses based upon 16S rDNA gene sequence placed isolate 4A in the genus Halomonas. In addition, DNA-DNA hybridization experiments clearly indicate that it is a unique species. Phenotypic and phylogenetic studies indicate that isolate 4A represents a new species. We propose the name Halomonas campisalis for this species and strain 4A (ATCC 700597) as the type strain. Due to its denitrification ability, broad carbon utilization range and its high salinity and pH tolerance this organism, and similar ones, hold promise for the treatment of saline, alkaline waste.

Biodegradation, Environmental↗

Degradation of pectic substances by two pectate lyases from a human intestinal bacterium, Clostridium butyricum-beijerinckii group.

Clostridium butyricum-beijerinckii group, an anaerobic human intestinal bacterium, produced exo-pectate lyase, endo-pectate lyase, and pectin methylesterase, but not polygalacturonase. The production of the two pectate lyases was strongly influenced by the composition of the carbon sources added to the medium. The enzymes secreted by the bacterium into the human large intestine cooperatively digested pectic substances, producing mainly 4,5-unsaturated digalacturonic acid with the participation of the pectin methylesterase. The findings suggest that in the human intestine the bacterium contributes to the digestion of ingested pectic substances.

Journal Article↗

Constitutive synthesis, purification, and characterization of catechol 1,2-dioxygenase from the aniline-assimilating bacterium Rhodococcus sp. AN-22.

A catechol 1,2-dioxygenase (CD) was found, which was synthesized constitutively in the aniline-assimilating bacterium Rhodococcus sp. AN-22 grown on a medium without aniline, as well as on aniline medium. The bacterium synthesized CD in its cells grown on all the 21 non-aromatic substrates examined, including four natural media such as meat and yeast extracts, one sugar, six organic acids, and 10 amino acids as carbon, energy, and nitrogen sources. When the bacterium was incubated on a medium with D-glucose, L-malate, isoleucine, leucine, etc., it synthesized more CD than that in cells grown on aniline. Two CDs, which were prepared from cells grown on aniline and L-malate, were purified separately to homogeneity and characterized. The two enzymes were apparently identical in molecular and catalytic properties including molecular mass, optimal pH, stability to heating, and substrate specificity for catechol analogues. However, they differed in the substrate specificity and resistance to sulfhydryl and chelating agents from the inducible CDs produced by other aniline-assimilating bacteria reported previously.

Journal Article↗

[Analysis of the impurity of bacterium source of standard endotoxin by gas chromatography/mass spectrometry].

To analyse the impurity of bacterium source of standard endotoxin, 3-hydroxy fatty acid species in different endotoxin standards was determined by gas chromatography/mass spectrometry (GC/MS) using N, O-bis (trimethylsilyl) trifluoroacetamide as the silanizing reagent. GC/MS analysis was performed using a gas chromatograph equipped with a 60 m x 0.25 mm i. d. DB-5 fused silica capillary column and an injector at 250 degrees C. Helium was used as the carrier gas under a constant pressure of 206 kPa. The oven was programmed at a rate of 5 degrees C /min from 90 degrees C (held for 5 min) to 280 degrees C (held for 5 min). The sample size was 1 microL. The transfer line was kept at 280 degrees C. The quadrupole mass spectrometer was operated in electron impact (EI) ionization mode, and the temperature of the source was kept at 250 degrees C. The kind of 3-hydroxy fatty acids in 9 000 EU/tube national standard endotoxin, 20 EU/tube working standard endotoxin, Escherichia coli, Pseudomonas aeruginosa and deionized water were determined to study the purity of bacterium source of the standard endotoxin. It was shown that 9 000 EU/tube endotoxin standard and Escherichia coli only contained 3-hydroxytetradecanoic acid. There was 3-hydroxydodecanoic acid in 20 EU/tube working standard endotoxin, which indicated the presence of impurity of bacterium source.

Bacteria↗

The butterfly Danaus chrysippus is infected by a male-killing Spiroplasma bacterium.

Many insects carry maternally inherited bacteria which kill male offspring. Such bacteria will spread if male death benefits the female siblings who transmit the bacterium, and they are therefore expected in insects with antagonistic sibling interactions. We report that the butterfly Danaus chrysippus is host to a maternally inherited male-killing bacterium. Using diagnostic PCR and rDNA sequence, the bacterium was identified as a Spiroplasma closely related to 2 ladybird beetle male-killers and the tick symbiont Spiroplasma ixodetis. The male-killer was found to have a geographically restricted distribution, with up to 40% of females being infected in East Africa, but no detectable infection in small samples from other populations. Danaus chrysippus is a surprising host for a male-killer as its eggs are laid singly. This suggests that the ecological conditions permitting male-killers to invade may be more widespread than previously realized.

Animals↗

Detection of green fluorescent protein in a single bacterium by capillary electrophoresis with laser-induced fluorescence.

Green fluorescence protein (GFP) is a common reporter used to monitor protein expression in single cells. However, autofluorescence from endogenous components can mask the signal from GFP, particularly at low expression levels in prokaryotes. We employ capillary electrophoresis with laser-induced fluorescence for the analysis of the expression of green fluorescent protein in a single bacterium. Capillary electrophoresis separates GFP from native cellular autofluorescent components, reducing the background signal and improving detection limits. Our system provides 100 ymol (60 copies) limits of detection for GFP. To demonstrate the performance of this instrument, we employ a model system of Deinococcus radiodurans that has been engineered to express GFP under the control of the recA promoter. We report resolution and detection of GFP and autofluorescent components in a single D. radiodurans bacterium. This paper presents the first example of expression of GFP in D. radiodurans and the first detection of GFP in a single bacterium by capillary electrophoresis.

Deinococcus↗

Membrane-bound electron transfer chain of the thermohalophilic bacterium Rhodothermus marinus: characterization of the iron-sulfur centers from the dehydrogenases and investigation of the high-potential iron-sulfur protein function by in vitro reconstitution of the respiratory chain.

Rhodothermus marinus, a thermohalophilic bacterium, has a unique electron-transfer chain, containing, besides a cbb3 and a caa3 terminal oxidases, a novel cytochrome bc complex [Pereira, M. M., Carita, J. N., and Teixeira, M. (1999) Biochemistry 38, 1268-1275]. The membrane-bound iron-sulfur centers of this bacterium were studied by electron paramagnetic resonance (EPR) spectroscopy, leading to the identification of its main electron-transfer complexes. The resonances typical for the Rieske-type centers are not detected. Clusters S1 and S3 from succinate dehydrogenase were identified; interestingly, center S3 is shown to be present in two different conformations, with g values at 2.035, 2.009, and 2.001 and at 2.025, 2.002, and 2.000. Upon addition of NADH and dithionite, EPR signals assigned to resonances characteristic of binuclear and tetranuclear clusters develop and are attributed to the iron-sulfur centers of complexes I and II. A high-potential iron-sulfur protein- (HiPIP-) type center previously detected in the membranes of this bacterium [Pereira et al. (1994) FEBS Lett. 352, 327-330] is shown to belong indeed to a canonical HiPIP. This protein was purified and extensively characterized. It is a small water-soluble protein of approximately 10 kDa, containing a single [4Fe-4S]3+/2+ cluster. The reduction potential, determined by EPR redox titrations in intact and detergent-solubilized membranes as well as by cyclic voltammetry in solution, has a pH-independent value of 260 +/- 20 mV, in the range 6-9. In vitro reconstitution of the R. marinus electron-transfer chain shows that the HiPIP plays a fundamental role in the chain, as the electron shuttle between R. marinus cytochrome bc complex and the caa3 terminal oxidase, being thus simultaneously identified a HiPIP reductase and a HiPIP oxidase.

Bacterial Proteins↗

Dechlorination of chlorobenzenes by a culture containing bacterium DF-1, a PCB dechlorinating microorganism.

Polychlorinated benzenes were reductively dechlorinated by an enrichment culture containing the polychlorinated biphenyl (PCB) dechlorinating bacterium DF-1. The culture dechlorinated hexachlorobenzene (hexa-CB) --> pentachlorobenzene (penta-CB) --> 1,2,3,5-tetrachlorobenzene (1,2,3,5-CB) --> 1,3,5-trichlorobenzene (1,3,5-CB) and did not dechlorinate other tetrachlorobenzenes or any trichlorobenzenes. This restricted series of reactions is the most predominant and frequently reported pathway for the dechlorination of hexa-CB and penta-CB by enrichment cultures inoculated with either freshwater or estuarine sediments. The culture did not dechlorinate hydroxylated and methoxylated polychlorinated benzenes or a hydroxylated PCB. Bacterium DF-1 was detected by PCR/DGGE analysis following dechlorination of penta-CB but was not detected when a chlorinated benzene (CB) was not dechlorinated; detection of other members in the communitywas unaffected by the presence or absence of CB dechlorination. This is the first report of a bacterium that reductively dechlorinates both PCBs and CBs and the first identification of an organism that can dechlorinate a CB with more than four chlorines.

Bacteria↗

Reductive dechlorination of tetrachloroethene to trans-dichloroethene and cis-dichloroethene by PCB-dechlorinating bacterium DF-1.

Polychlorinated biphenyls (PCBs) and chlorinated ethenes (CEs) are known to pollute sediment, soil, and groundwater. The anaerobic dechlorination of these compounds is an integral part of their biodegradation in polluted environments. We report for the first time the dechlorination of tetrachloroethene (PCE) and trichloroethene (TCE) by bacterium DF-1. This PCB and chlorobenzene dechlorinating bacterium dechlorinated PCE to TCE, which was then converted into trans-1,2-dichloroethene (trans-DCE) and cis-1,2-dichloroethene (cis-DCE). The ratio of trans-DCE to cis-DCE produced by the culture had a range of 1.2-1.7. Bacterium DF-1 has been enriched in co-culture with a desulfovibrio-like microorganism. PCR-denaturing gradient gel electrophoresis (PCR-DGGE) analysis of the 16S rRNA genes of the co-culture demonstrated that DF-1 was enriched during the dechlorination of PCE, PCB, and chlorobenzene. DF-1 was not detected in the absence of PCE dechlorination and the desulfovibrio-like organism, isolated in pure culture, did not dechlorinate PCE. This is the first identification of a microorganism capable of producing high amounts of trans-DCE from PCE and indicates that microorganisms such as DF-1 are a possible biological source of trans-DCE in the environment.

Anaerobiosis↗

Stimulatory and inhibitory effects of organohalides on the dehalogenating activities of PCB-dechlorinating bacterium o-17.

Bacterium o-17, a microorganism capable of the ortho dechlorination of 2,3,5,6-polychlorinated biphenyl (PCB), is a member of a sediment-free, nonmethanogenic mixed culture. The culture was examined for the ability to dechlorinate 26 PCB congeners, 12 chlorobenzenes (CBZs), and 6 chlorinated ethenes (CEs). Eight of the PCBs and 4 of the CBZs were dechlorinated including single-flanked ortho PCB chlorines, but double-flanked chlorines of PCBs and CBZs were preferentially dechlorinated. The dechlorination of three of the PCBs (2,3,4,5,6-, 2,3,4,6-, and 2,3,5,6-PCB), three of the CBZs (hexa-, penta-, and 1,2,3-CBZ), and PCE could be sustained for three or more sequential transfers of the bacterial community. Two PCBs (2,3,4- and 2,3,5-PCB), two CBZs (1,2,3,5- and 1,2,4,5-CBZ), and trichloroethene were dechlorinated only when a more extensively chlorinated parent compound was present. Aroclor 1260 and 2,4,6-PCB, not dechlorinated by the culture, inhibited the dechlorination of 2,3,5,6-PCB. Within the culture only bacterium o-17 was linked to dechlorination by PCR-DGGE analysis, confirming that this dehalogenating species was the catalyst for the dechlorination of the compounds tested. The microorganism is capable of dechlorinating several different congeners of PCBs, CBZs, and CEs, and it remains a rare example of an ortho-PCB dechlorinator. However, its limited ability to dechlorinate more extensively chlorinated congeners and Aroclor plus the inhibitory effects of some PCB congeners upon the bacterium is consistent with the observed infrequency of this reaction in the environment. An assessment of bioremediation potential of this microorganism in situ will require a greater understanding of the synergistic, cometabolic and competitive interactions of PCB dechlorinating microbial communities.

Bacteria↗

Strain variability and the effects of organic compounds on the growth of the chemolithotrophic bacterium Thiobacillus ferrooxidans.

The effects of naturally-occurring organic compounds on ferrous iron oxidation by the bacterium Thiobacillus ferrooxidans were examined with a view to using these compounds to treat or prevent acid mine/rock drainage. The compounds glucose, cellobiose, galacturonic acid, and citric acid were added to the growth medium of five different strains of the bacterium and growth studies were done to determine whether or not strain differences existed with respect to organic compound sensitivity. The effects of these compounds were compared to the effects of sodium dodecyl sulfate (SDS) an anionic detergent. Each of the compounds tested had an inhibitory effect on the strains of the bacterium and sensitivity to these compounds was strain dependent. All strains appeared to be equally susceptible to SDS. Inhibitory concentrations ranged from 70 mM to >280 mM for glucose, 7.5 mM to 150 mM for cellobiose, 20 mM to 230 mM for galacturonic acid, and 50 mM to 130 mM for citric acid. SDS effectively inhibited iron oxidation for all strains at a concentration of 0.3 mM, the lowest concentration tested. Some naturally-occurring organic compounds, therefore, might be candidates for the growth control of T. ferrooxidans.

Carbohydrate Metabolism↗

Thermodynamic characterization of a tetrahaem cytochrome isolated from a facultative aerobic bacterium, Shewanella frigidimarina: a putative redox model for flavocytochrome c3.

The facultative aerobic bacterium Shewanella frigidimarina produces a small c-type tetrahaem cytochrome (86 residues) under anaerobic growth conditions. This protein is involved in the respiration of iron and shares 42% sequence identity with the N-terminal domain of a soluble flavocytochrome, isolated from the periplasm of the same bacterium, which also contains four c -type haem groups. The thermodynamic properties of the redox centres and of an ionizable centre in the tetrahaem cytochrome were determined using NMR and visible spectroscopy techniques. This is the first detailed thermodynamic study performed on a tetrahaem cytochrome isolated from a facultative aerobic bacterium and reveals that this protein presents unique features. The redox centres have negative and different redox potentials, which are modulated by redox interactions between the four haems (covering a range of 8-56 mV) and by redox-Bohr interactions between the haems and an ionizable centre (-4 to -36 mV) located in close proximity to haem III. All of the interactions between the five centres are clearly dominated by electrostatic effects and the microscopic reduction potential of haem III is the one most affected by the oxidation of the other haems and by the protonation state of the molecule. Altogether, this study indicates that the tetrahaem cytochrome isolated from S. frigidimarina (Sfc) has the thermodynamic properties to work as an electron wire between its redox partners. Considering the high degree of sequence identity between Sfc and the cytochrome domain of flavocytochrome c(3), the structural similarities of the haem core, and that the macroscopic potentials are also identical, the results obtained in this work are rationalized in order to put forward a putative redox model for flavocytochrome c(3).

Cytochrome c Group↗

Constitutive expression of catABC genes in the aniline-assimilating bacterium Rhodococcus species AN-22: production, purification, characterization and gene analysis of CatA, CatB and CatC.

The aniline-assimilating bacterium Rhodococcus sp. AN-22 was found to constitutively synthesize CatB (cis,cis-muconate cycloisomerase) and CatC (muconolactone isomerase) in its cells growing on non-aromatic substrates, in addition to the previously reported CatA (catechol 1,2-dioxygenase). The bacterium maintained the specific activity of the three enzymes at an almost equal level during cultivation on succinate. CatB and CatC were purified to homogeneity and characterized. CatB was a monomer with a molecular mass of 44 kDa. The enzyme was activated by Mn2+, Co2+ and Mg2+. Native CatC was a homo-octamer with a molecular mass of 100 kDa. The enzyme was stable between pH 7.0 and 10.5 and was resistant to heating up to 90 degrees C. Genes coding for CatA, CatB and CatC were cloned and named catA, catB and catC respectively. The catABC genes were transcribed as one operon. The deduced amino acid sequences of CatA, CatB and CatC showed high identities with those from other Gram-positive micro-organisms. A regulator gene such as catR encoding a regulatory protein was not observed around the cat gene cluster of Rhodococcus sp. AN-22, but a possible relic of catR was found in the upstream region of catA. Reverse transcriptase-PCR and primer extension analyses showed that the transcriptional start site of the cat gene cluster was located 891 bp upstream of the catA initiation codon in the AN-22 strain growing on both aniline and succinate. Based on these data, we concluded that the bacterium constitutively transcribed the catABC genes and translated its mRNA into CatA, CatB and CatC.

Aniline Compounds↗

The role of histidine-118 of inorganic pyrophosphatase from thermophilic bacterium PS-3.

Treatment of the inorganic pyrophosphatase from thermophilic bacterium PS-3 with diethyl pyrocarbonate resulted in the almost complete loss of its activity, which followed pseudo-first-order kinetics. The presence of Mg2+ prevented the inactivation. Enzyme inactivated with diethyl pyrocarbonate was re-activated by hydroxylamine. The inactivation parallelled the amount of modified histidine residue, and a plot of the activity remaining against the amount of modified histidine residue suggested that the modification of one of two histidine residues totally inactivated the enzyme. The site involved was found to be located in a single lysyl endopeptidase-digest peptide derived from the ethoxy[14C]carbonylated enzyme. Amino acid analysis and sequence analysis of the peptide revealed that it comprised residues 96-119 of the inorganic pyrophosphatase from thermophilic bacterium PS-3. These results, when compared with those reported for the Escherichia coli and yeast enzymes, imply that His-118 of the inorganic pyrophosphatase from thermophilic bacterium PS-3 is located near the Mg(2+)-binding site and thus affects the binding of Mg2+.

Amino Acids↗

Assessment of the fructanolytic activities in the rumen bacterium Treponema saccharophilum strain S.

AIMS: To characterize the fructose polymer degrading enzymes of rumen bacterium Treponema saccharophilum strain S. METHODS AND RESULTS: Conventional methods were used to examine bacterial growth and enzyme activities. Electrophoretic zymogram under native conditions, and thin layer chromatography, were applied to identify and characterize the enzymes. Treponema saccharophilum utilized Timothy grass fructan, inulin and sucrose but not free fructose. Timothy grass fructan was degraded at a significantly higher rate than sucrose and inulin. Two fructanolytic enzymes were found in the soluble, and one in the membrane fraction of bacterial cell extract. The first degraded each mentioned carbohydrate to monosaccharides. The second released oligosaccharides only from Timothy grass fructan. CONCLUSIONS: The bacterium T. saccharophilum strain S is capable of synthesizing non-specific beta-fructofuranosidases and 2,6-beta-D-fructan fructanohydrolase. The enzymes are of constitutive character. SIGNIFICANCE AND IMPACT OF THE STUDY: It has been stated for the first time that the 2,6-beta-D-fructan fructanohydrolase is synthesized by the rumen bacterium T. saccharophilum. This organism appears to be responsible for grass fructan degradation in the rumen.

Animals↗

A novel polymer produced by a bacterium isolated from a deep-sea hydrothermal vent polychaete annelid.

AIMS: The objective of the present work was to describe an aerobic, mesophilic and heterotrophic marine bacterium, designated HYD657, able to produce an exopolysaccharide (EPS). It was isolated from a East Pacific Rise deep-sea hydrothermal vent polychaete annelid. METHODS AND RESULTS: This micro-organism, on the basis of the phenotypical features and genotypic investigations, can be clearly assigned to the Alteromonas macleodii species and the name A. macleodii subsp. fijiensis biovar deepsane is proposed. Optimal growth occurs between 30 and 35 degrees C, at pH between 6.5 and 7.5 and at ionic strengths between 20 and 40 g x l(-1) NaCl. The G + C content of DNA was 46.5%. This bacterium excreted, under laboratory conditions, an EPS consisting of glucose, galactose, rhamnose, fucose and mannose as neutral sugars along with glucuronic and galacturonic acids and a diacidic hexose identified as a 3-0-(1 carboxyethyl)-D-glucuronic acid. Its average molecular mass was 1.6 x 10(6) Da. CONCLUSIONS: The bacterium HYD657, for which the name A. macleodii subsp. fijiensis biovar deepsane is proposed, produces an unusual EPS in specific medium. SIGNIFICANCE AND IMPACT OF THE STUDY: Due to its interesting biological activities, applications have been found in cosmetics. Its probable contribution to the filamentous microbial mat in the Alvinella pompejana microenvironment can be also mentioned.

Alteromonas↗

Platelet activation by a relapsing fever spirochaete results in enhanced bacterium-platelet interaction via integrin alphaIIbbeta3 activation.

Borrelia hermsii, a spirochaete responsible for relapsing fever in humans, grows to high density in the bloodstream and causes thrombocytopenia. We show here that B. hermsii binds to human platelets. Extended culture in bacteriological medium resulted in both diminished infectivity in vivo and diminished platelet binding in vitro. Platelet binding was promoted by the platelet integrin alphaIIbbeta3: the bacterium bound to purified integrin alphaIIbbeta3, and bacterial binding to platelets was diminished by alphaIIbbeta3 antagonists or by a genetic defect in this integrin. Integrin alphaIIbbeta3 undergoes a conformational change upon platelet activation, and bacteria bound more efficiently to activated rather than resting platelets. Nevertheless, B. hermsii bound at detectable levels to preparations of resting platelets. The bacterium did not recognize a point mutant of alphaIIbbeta3 that cannot acquire an active conformation. Rather, B. hermsii was capable of triggering platelet and integrin alphaIIbbeta3 activation, as indicated by the expression of the platelet activation marker P-selectin and integrin alphaIIbbeta3 in its active conformation. The degree of platelet activation varied depending upon bacterial strain and growth conditions. Prostacyclin I2, an inhibitor of platelet activation, diminished bacterial attachment, indicating that activation enhanced bacterial binding. Thus, B. hermsii signals the host cell to activate a critical receptor for the bacterium, thereby promoting high-level bacterial attachment.

Animals↗