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At least 415 records · Page 23Linked to original sources
PubMed1999

The caa3 terminal oxidase of the thermohalophilic bacterium Rhodothermus marinus: a HiPIP:oxygen oxidoreductase lacking the key glutamate of the D-channel.

The respiratory chain of the thermohalophilic bacterium Rhodothermus marinus contains a novel complex III and a high potential iron-sulfur protein (HiPIP) as the main electron shuttle (Pereira et al., Biochemistry 38 (1999) 1268-1275 and 1276-1283). In this paper, one of the terminal oxidases expressed in this bacterium is extensively characterised. It is a caa3-type oxidase, isolated with four subunits (apparent molecular masses of 42, 19 and 15 kDa and a C-haem containing subunit of 35 kDa), which has haems of the A(s) type. This oxidase is capable of using TMPD and horse heart cytochrome c as substrates, but has a higher turnover with HiPIP, being the first example of a HiPIP:oxygen oxidoreductase. The oxidase has unusually low reduction potentials of 260 (haem C), 255 (haem A) and 180 mV (haem A3). Subunit I of R. marinus caa3 oxidase has an overall significant homology with the subunits I of the COX type oxidases, namely the metal binding sites and most residues considered to be functionally important for proton uptake and pumping (K- and D-channels). However, a major difference is present: the putative essential glutamate (E278 in Paraccocus denitrificans) of the D-channel is missing in the R. marinus oxidase. Homology modelling of the R. marinus oxidase shows that the phenol group of a tyrosine residue may occupy a similar spatial position as the glutamate carboxyl, in relation to the binuclear centre. Moreover, sequence comparisons reveal that several enzymes lacking that glutamate have a conserved substitution pattern in helix VI: -YSHPXV- instead of -XGHPEV-. These observations are discussed in terms of the mechanisms for proton uptake and it is suggested that, in these enzymes, tyrosine may play the role of the glutamate in the proton channel.

Amino Acid Sequence↗
PubMed1997

Cloning and expression of superoxide dismutase from Aquifex pyrophilus, a hyperthermophilic bacterium.

A superoxide dismutase (SOD) gene of Aquifex pyrophilus, a marine hyperthermophilic bacterium, was cloned, sequenced, expressed in Escherichia coli, and its gene product characterized. This is the first SOD from a hyperthermophilic bacterium that has been cloned. It is an iron-containing homo-oligomeric protein with a monomeric molecular mass of 24.2 kDa. The DNA-derived amino acid sequence is more similar to those of known Mn- and Fe-SODs from thermophilic archaea than of Cu, Zn-SODs. The metal binding residues found in all SOD sequences from different species are also conserved in A. pyrophilus SOD. The protein is biochemically active only as an oligomer and is resistant to thermal denaturation.

Amino Acid Sequence↗
PubMed1999

A RNA polymerase with transcriptional activity at 0 degrees C from the Antarctic bacterium Pseudomonas syringae.

A DNA-dependent RNA polymerase was purified from the Antarctic psychrotrophic bacterium Pseudomonas syringae. The RNA polymerase showed a typical eubacterial subunit composition with beta, beta', alpha2 and sigma subunits. The subunits cross-reacted with antibodies raised against holoenzyme and the individual subunits of the RNA polymerase of Escherichia coli. However, the enzyme was considered unique, since unlike the RNA polymerase of mesophilic E. coli it exhibited significant and consistent transcriptional activity (10-15%) even at 0 degrees C. But, similar to the enzyme from the mesophilic bacterium, the RNA polymerase from P. syringae exhibited optimum activity at 37 degrees C. The study also demonstrates that the RNA polymerase of P. syringae could preferentially transcribe the cold-inducible gene cspA of E. coli only at lower temperatures (0-22 degrees C). The polymerase was also observed to be relatively more rifampicin-resistant during transcription at lower temperature.

Adaptation, Biological↗
PubMed2002

Crystal structure of a transcarbamylase-like protein from the anaerobic bacterium Bacteroides fragilis at 2.0 A resolution.

A transcarbamylase-like protein essential for arginine biosynthesis in the anaerobic bacterium Bacteroides fragilis has been purified and crystallized in space group P4(3)2(1)2 (a=b=153.4 A, c=94.8 A). The structure was solved using a single isomorphous replacement with anomalous scattering (SIRAS) and was refined at 2.0 A resolution to an R-factor of 20.6% (R-free=25.2%). The molecular model is trimeric and comprises 960 amino acid residues, two phosphate groups and 422 water molecules. The monomer has the consensus transcarbamylase fold with two structural domains linked by two long interdomain helices: the putative carbamoyl phosphate-binding domain and a binding domain for the second substrate. Each domain has a central parallel beta-sheet surrounded by alpha-helices and loops with alpha/beta topology. The putative carbamoyl phosphate-binding site is similar to those in ornithine transcarbamylases (OTCases) and aspartate transcarbamylases (ATCases); however, the second substrate-binding site is strikingly different. This site has several insertions and deletions, and residues critical to substrate binding and catalysis in other known transcarbamylases are not conserved. The three-dimensional structure and the fact that this protein is essential for arginine biosynthesis suggest strongly that it is a new member of the transcarbamylase family. A similar protein has been found in Xylella fastidiosa, a bacterium that infects grapes, citrus and other plants.

Amino Acid Sequence↗
PubMed2002

Bioaugmentation with the resin acid-degrading bacterium Zoogloea resiniphila DhA-35 to counteract pH stress in an aerated lagoon treating pulp and paper mill effluent.

Efficient and reliable removal of resin acids such as dehydroabietic acid (DhA), which are the major toxicants in pulp and paper mill effluents and form pitch interfering with papermaking, is critically important to prevent toxicity discharge and failure of paper machines. Low- and high-pH stresses sometimes occur in effluent treatment systems due to the use of large amounts of acids and alkalines in the pulping processes. We found that both low- and high-pH stresses (pH 3 and 10, respectively) decreased the removal of total organic carbon and completely inhibited the removal of DhA by the biomass of an aerated lagoon treating pulp mill effluent. The pH stresses caused changes in the bacterial community structure as assessed by ribosomal intergenic spacer length polymorphism. The pH stresses greatly reduced the indigenous DhA-degrading populations in the lagoon community. Bioaugmentation with Zoogloea resiniphila DhA-35, a DhA-degrading bacterium originally isolated from a pulp mill treatment system, restored the DhA removal by both the low- and high-pH-stressed lagoon biomass. This bacterium was persistent after introduction into the lagoon microbial community, and its cellular rRNA:rDNA ratio increased during the period of DhA removal. The introduction of strain DhA-35 changed the microbial community structure, but did not adversely affect the TOC removal by the community. This study suggests that it is feasible and potentially useful to use bioaugmentation with resin-acid-degrading bacteria such as DhA-35 to restore and enhance resin acid removal by aerated lagoon microbial communities.

Biodegradation, Environmental↗
PubMed1998

Effect of selected environmental factors on degradation and mineralization of biaryl compounds by the bacterium Ralstonia pickettii in soil and compost.

By varying selected environmental factors, the degradation and mineralization of biaryl compounds by the bacterium Ralstonia pickettii in soil and compost were investigated. An optimized soil moisture and enhanced bioavailability by using the nonionic surfactant Tween 80 were of great importance for the degradation rates of biaryl compounds like biphenyl and 4-chlorobiphenyl by cells of Ralstonia picketti SBUG 290 inoculated into soil. Additionally, degradation of these compounds by the investigated strain in soil was strongly dependent upon the medium of precultivation. Also the influence of temperature and soil pH-value was tested. In contrast to the used soil, the autochthonous flora of the compost seemed to have a higher physiological activity. All investigated compounds (biphenyl, 4-chlorobiphenyl and dibenzofuran) were degraded quickly in compost. Inoculation with the investigated bacterium did not enhance the degradation rates significantly.

Air Pollutants, Occupational↗
PubMed2003

Nucleotide sequence based characterizations of two cryptic plasmids from the marine bacterium Ruegeria isolate PR1b.

Two plasmids, 76 and 148 kb in size, isolated from Ruegeria strain PR1b were entirely sequenced. These are the first plasmids to be characterized from this genus of marine bacteria. Sequence analysis revealed a biased distribution of function among the putative proteins encoded on the two plasmids. The smaller plasmid, designated pSD20, encodes a large number of putative proteins involved in polysaccharide biosynthesis and export. The larger plasmid, designated pSD25, primarily encodes putative proteins involved in the transport of small molecules and in DNA mobilization. Sequence analysis revealed uncommon potential replication systems on both plasmids. pSD25, the first repABC-type replicon isolated from the marine environment, actually contains two repABC-type replicons. pSD20 contains a complex replication region, including a replication origin and initiation protein similar to iteron-containing plasmids (such as pSW500 from the plant pathogen Erwinia stewartii) linked to putative RepA and RepB stabilization proteins of a repABC-type replicon and is highly homologous to a plasmid from the phototrophic bacterium Rhodobacter sphaeroides. Given the nature of the putative proteins encoded by both plasmids it is possible that these plasmids enhance the metabolic and physiological flexibility of the host bacterium, and thus its adaptation to the marine sediment environment.

ATP-Binding Cassette Transporters↗
PubMed2001

Histamine formation by Tetragenococcus muriaticus, a halophilic lactic acid bacterium isolated from fish sauce.

We examined histamine formation in cultures of Tetragenococcus muriaticus, a halophilic lactic acid bacterium isolated from fish sauce. T. muriaticus formed histamine in low acidity (pH 5.8), O2 limiting conditions with optimal NaCl and glucose concentrations of 5-7% (w/v) and above 1%, respectively. Histamine formation could not be prevented even at 20% (w/v) NaCl, indicating that NaCl could not prevent histamine formation by this bacterium. A conspicuous amount of histamine accumulated only during the late stationary phase regardless of the growth conditions. Studies of cell suspension experiments confirmed the results obtained from cultured cells.

Animals↗
PubMed2001

Biological control of postharvest pear diseases using a bacterium, Pantoea agglomerans CPA-2.

Epiphytic microorganisms isolated from the fruits and leaf surfaces of apples and pears were screened for antagonistic activity against Penicillium expansum on pears. From 247 microorganisms tested for antagonistic properties against P. expansum, a bacterium strain identified as Pantoea agglomerans (CPA-2) was selected. This bacterium was very effective against Botrytis cinerea, P. expansum and Rhizopus stolonifer. Complete control at the three tested concentrations (2 x 10(7), 8 x 10(7) and 1 x 10(8) CFU ml(-1)) was obtained on wounded pears inoculated with 10(3), 10(4) and 10(5) conidia ml(-1) of P. expansum and R. stolonifer. At 8 x 10(7) CFU ml(-1), Pan. agglomerans reduced B. cinerea decay by more than 80% at the three concentrations of the pathogen. In over 3 years of experiments in semicommercial trials, Pan. agglomerans provided excellent control against B. cinerea and P. expansum under cold storage, either in air or in low oxygen atmospheres. Equal control was obtained with Pan. agglomerans at 8 x 10(7) CFU ml(-1), as with the fungicide imazalil at commercial doses, against both pathogens. Pan. agglomerans grew well inside wounds on pears at both room and cold temperatures and under modified atmospheres. In contrast, it grew poorly on the surface of intact fruit.

Cold Temperature↗
PubMed1999

Effect of rapid cooling and acidic pH on cellular homeostasis of Pectinatus frisingensis, a strictly anaerobic beer-spoilage bacterium.

Pectinatus frisingensis is a strictly anaerobic mesophilic bacterium involved in bottled beer spoilage. Cellular volume, adenylate energy charge, intracellular pH and intracellular potassium concentration measurements were performed in late exponential-phase cell suspensions placed in different physiological conditions, to evaluate the capability of this bacterium to maintain cellular homeostasis. The intracellular pH was calculated from the intracellular accumulation of a [carboxyl-14C]benzoic acid. Optimum physiological conditions were the presence of a carbon source and pH of 6.2, hostile conditions were a pH 4.5, absence of a carbon source, and rapid cooling treatment. The cell was able to maintain a higher intracellular pH than the external pH under all conditions. Intracellular volume was lower at pH 4.5 than at pH 6.2. A low net potassium efflux rate was routinely measured in starving cells, while glucose addition promoted immediate net potassium uptake from the medium. Cooling treatment resulted in sudden net potassium efflux from the cell, a decrease of the intracellular pH, and low modifications of the adenylate energy charge in metabolizing-glucose cell suspensions. Thus, cold treatment perturbs the P. frisingensis homeostasis but the bacteria were able to restore their homeostasis in the presence of a carbon source, and under warm conditions.

Adenosine Monophosphate↗
PubMed1997

Improvement of expression and secretion of a fungal xylanase in the rumen bacterium Butyrivibrio fibrisolvens OB156 by manipulation of promoter and signal sequences.

Promoters and signal sequences for expression and secretion of a fungal xylanase encoded by a modified Neocallimastix patriciarum xynA cDNA in the rumen bacterium, Butyrivibrio fibrisolvens OB156, were investigated. Successful expression of the fungal xylanase in OB156 was obtained using the putative xylanase promoter from B. fibrisolvens strain 49. Replacing the putative -35 region sequence (TTGCAC) of the xylanase promoter with the sequence TTGACA by mutagenesis reduced the fungal xylanase expression level 4-fold in OB156, indicating that this B. fibrisolvens strain did not efficiently recognise the E. coli consensus -35 sequence. Reduction of the spacer length between the -35 and -10 regions of the xylanase promoter from 18 to 17 base-pairs (bp) considerably increased the expression levels of the fungal enzyme in both E. coli and OB156. Insertion of a pUB110 mob promoter upstream of the xylanase promoter also significantly improved the fungal xylanase expression. Secretion of the fungal xylanase mediated by the alpha-amylase signal peptide from B. fibrisolvens strain H17c was efficient in E. coli, but very poor in OB156. An increase in the hydrophobicity of the signal sequence resulted in a 4-fold increase in the extracellular portion of the fungal xylanase in OB156, indicating marked improvement in xylanase secretion efficiency. The recombinant plasmids and xylanase expression/secretion cassettes were found to be stable in OB156 after prolonged cultivation (100 generations) in the absence of antibiotic selection. These results suggest that the rumen bacterium B. fibrisolvens can be manipulated to produce and secrete a eukaryotic extracellular protein with stable maintenance of the expression cassette in plasmid form.

Amino Acid Sequence↗
PubMed1988

A new species of fish-pathogenic bacterium antigenically related to classical Brucellae.

A bacterial epizootic in trout (Salmo gairneri, Richardson) characterized by haemorrhagic diathesis is described in its acute and subacute form. The disease could be reproduced with the isolated new bacterial species. Two basic features characterize this bacterium: I. growth at 41 degrees C (water bath) on cultivation in solid and liquid media and 2. antigenic relationship to the classical brucellae. Immunoelectrophoretic analysis revealed a common antigenic determinant in the LPS of the isolated fish-pathogenic bacterium and that of classical brucellae (S form).

Agglutination Tests↗
PubMed1997

N-acyl amino acid biosynthesis in marine bacterium, Deleya marina.

We reported previously that the marine bacterium, Deleya marina (ATCC 25374), produced N-acyl leucine and isoleucine, in which nonhydroxy fatty acid was linked to alpha-amino group of amino acid. Further analysis of bacterium lipids revealed the additional production of N-acyl ornithine. The N-acyl ornithine had a 3-hydroxy fatty acid linked by an amide bond to a-amino group of ornithine and a nonhydroxy fatty acid esterified to the hydroxy group of the 3-hydroxy fatty acid. N-acyl ornithine was located in the cell membrane and N-acyl leucine and isoleucine in cytoplasm. N-acyl ornithine is thought to be a functional analogue of phosphatidylethanolamine (PE) because of their similar structure. PE replacement into N-acyl ornithine in the cell membrane under phosphate-limited conditions was observed with other bacteria, so we anticipated the nonbiosynthesis of N-acyl ornithine under phosphate-sufficient conditions. We did not anticipate that N-acyl leucine and isoleucine in cytoplasm, whose structure is dissimilar to that of PE, would be replaced into PE in the cell membrane. Neither N-acyl leucine, N-acyl isoleucine, nor N-acyl ornithine was biosynthesized under phosphate-sufficient condition. Thus, we report here for the first time that N-acyl amino acids in cytoplasm were not biosynthesized under phosphate-sufficient conditions.

Bacteria↗
PubMed2003

Deep desulfurization of hydrodesulfurization-treated diesel oil by a facultative thermophilic bacterium Mycobacterium sp. X7B.

The dibenzothiophene (DBT) desulfurization pathway of a facultative thermophilic bacterium Mycobacterium sp. X7B was investigated. Metabolites were identified by gas chromatography-mass spectrometry, and the results showed that 2-hydroxybiphenyl, the end product of the previously reported sulfur-specific pathway (also called 4S pathway), was further converted to 2-methoxybiphenyl. This is the first strain to possess this ability and therefore, an extended 4S pathway was determined. In addition, the DBT-desulfurizing bacterium Mycobacterium sp. X7B was able to grow on DBT derivatives such as 4-methylDBT and 4,6-dimethylDBT. Resting cells could desulfurize diesel oil (total sulfur, 535 ppm) after hydrodesulfurization. GC flame ionization detection and GC atomic emission detection analyses were used to qualitatively evaluate the effect of Mycobacterium sp. X7B treatment on the content of the diesel oil. The total sulfur content of the diesel oil was reduced 86% using resting cell biocatalysts for 24 h at 45 degrees C.

Air Pollutants↗
PubMed1999

Cloning and sequence analysis of two catechol-degrading gene clusters from the aniline-assimilating bacterium Frateuria species ANA-18.

The aniline-assimilating bacterium Frateuria species ANA-18 produced two catechol 1,2-dioxygenases, CD I and CD II, and two muconate cycloisomerases, MC I and MC II. The catA genes catA1 and catA2 encoding CD I and CD II, respectively, were cloned from a gene library of this bacterium. The catA1 gene was clustered with catB1 encoding MC I, catC1 encoding muconolactone isomerase (MI), catD encoding beta-ketoadipate enol-lactone hydrolase (ELH), and ORFR1 encoding a putative LysR-type regulator. The organization of these genes was ORFR1catB1C1D. The catA2 gene also constructed a gene cluster involving catB2 encoding MC II, catC2 encoding MI, and ORFR2 encoding a putative LysR-type regulator with the alignment of ORFR2catB2A2C2. The intergenic regions of ORFR1-catB1 and ORFR2-catB2 contained homologous sequences with the catR-catB intergenic region containing a repression binding site and activation binding site of CatR in Pseudomonas putida. These findings suggest that the two cat clusters were regulated independently in their expression. When a product of cloned catD was added to a reaction mixture containing beta-ketoadipate enol-lactone, beta-ketoadipate was produced. This observation showed that the cloned catD encoded ELH and was expressed in Escherichia coli. We found that Frateuria sp. ANA-18 had a large plasmid with a molecular size more than 100kb. Polymerase chain reaction amplifying partial catA genes and Southern hybridization analyses with probes containing catA genes were conducted, to examine the localization of the two catA genes. We concluded that the catA1 and catA2 genes were located on the chromosomal and large plasmid DNAs, respectively, in Frateuria sp. ANA-18.

Amino Acid Sequence↗
PubMed1999

Characterization of a new xylanolytic bacterium, Clostridium xylanovorans sp. nov.

A new xylanolytic bacterium designated strain HESP1T (T = type strain) was isolated from a methanogenic digester. Strain HESP1T was a motile, rod shaped, spore-forming bacterium, which possessed a Gram-positive type cell wall. Glucose, fructose, lactose, trehalose, maltose, raffinose, sucrose, xylan, mannitol, cellobiose, galactose, mannose, melibiose, ribose were fermented to produce, acetate, butyrate, H2, CO2, formate, isobutyrate, and ethanol. Fumarate was fermented to acetate. Glycerol and methanol were also utilized. Sulfate, thiosulfate, nitrate, sulfur and fumarate were not used as electron acceptors. Strain HESP1T had a G + C content of 40 mol% and grew optimally at 37 degrees C and pH 7 on a fructose containing medium. Phylogenetically, strain HESP1T was most related to Clostridium aminovalericum (similarity of 94%) than to C. populeti, C. herbivorans and Eubacterium xylanophilum (average similarity of 92%), all members of subcluster XIVa of the low G + C containing Gram-positive branch. However, strain HESP1T shared little phenotypic and genotypic traits with C. aminovalericum and on the basis of this and phylogenetic evidence, we propose to tentatively designate strain HESP1T as a new species of the genus Clostridium, Clostridium xylanovorans sp. nov. The type strain is HESP1T (= DSM 12503).

Base Sequence↗
PubMed1999

Enrichment, phylogenetic analysis and detection of a bacterium that performs enhanced biological phosphate removal in activated sludge.

Activated sludge communities which performed enhanced biological phosphate removal (EBPR) were phylogenetically analyzed by 16S rRNA-targeted molecular methods. Two anaerobic-aerobic sequencing batch reactors were operated with two different carbon sources (acetate vs. a complex mixture) for three years and showed anaerobic-aerobic cycles of polyhydroxybutyrate- (PHB) and phosphate-accumulation characteristic for EBPR-systems. In situ hybridization showed that the reactor fed with the acetate medium was dominated by bacteria phylogenetically related to the Rhodocyclus-group within the beta-Proteobacteria (81% of DAPI-stained cells). The reactor with the complex medium was also predominated by this phylogenetic group albeit at a lesser extent (23% of DAPI-stained cells). More detailed taxonomic information on the dominant bacteria in the acetate-reactor was obtained by constructing clone libraries of 16S rDNA fragments. Two different types of Rhodocyclus-like clones (R1 and R6) were retrieved. Type-specific in situ hybridization and direct rRNA-sequencing revealed that R6 was the type of the dominant bacteria. Staining of intracellular polyphosphate- and PHB-granules confirmed that the R6-type bacterium accumulates PHB and polyphosphate just as predicted by the metabolic models for EBPR. High similarities to 16S rDNA fragments from other EBPR-sludges suggest that R6-type organisms were present and may play an important role in EBPR in general. Although the R6-type bacterium is closely related to the genus Rhodocyclus, it did not grow phototrophically. Therefore, we propose a provisional new genus and species Candidatus Accumulibacter phosphatis.

Aerobiosis↗
PubMed2003

"Bacillus hackensackii" sp. nov., a novel carbon dioxide sensitive bacterium isolated from blood culture.

An endospore-forming, gram-positive bacillus was isolated from a patient's blood culture. This bacillus did not grow in the presence of 5% carbon dioxide although it grew well in ambient air at 37 degrees C. Although the organism thus is an aerobic bacterium, its sensitivity to increased carbon dioxide concentration places it in a distinct category of gaseous atmospheric requirement: capnophobic. Based on its morphology, growth characteristics, biochemical reactions and a complete 16S rRNA gene nucleotide sequence analysis, this microorganism represents a novel Bacillus species. The clinical significance of this isolate is unknown. It is proposed that the bacterium be classified in the genus Bacillus as "Bacillus hackensackii".

Adult↗