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PubMed1995

Cellular fatty acids and aldehydes of oral Eubacterium.

The cellular fatty acids and aldehydes of oral Eubacterium species were determined by gas chromatography-mass spectrometry. E. brachy and E. lentum contained mainly branched-chain fatty acids, whereas the others contained straight-chain acids. E. brachy, E. lentum, E. yurii ssp. yurii, E. yurii spp. margaretiae, E. limosum, E. plauti and E. aerofaciens also contained aldehydes with even carbon numbers. In addition to species-specific components, the compositional ratios of fatty acids and aldehydes characterized each individual species. The 10 species tested were divided into 5 groups by the principal component analysis. Cellular fatty acids and aldehydes would be chemical markers for interspecies differentiation of oral Eubacterium.

Aldehydes↗

PubMed1988

Evidence for a multigene family involved in bile acid 7-dehydroxylation in Eubacterium sp. strain VPI 12708.

Eubacterium sp. strain VPI 12708 is a human intestinal isolate which has an inducible bile acid 7-dehydroxylation activity. At least two cholic acid-induced polypeptides, with molecular masses of 27,000 and 45,000 daltons, respectively, coelute with bile acid 7-dehydroxylation activity. The 45,000-dalton polypeptide appears to be encoded by a cholic acid-induced mRNA species of greater than 6 kilobases, which suggests that the gene coding for this polypeptide is part of a larger operon. A gene has been cloned which flanks the gene encoding the 45,000-dalton polypeptide, in the upstream (5') direction. This gene appears to encode a second 27,000-dalton polypeptide. The gene bears striking homology at both the nucleotide (80%) and deduced amino acid sequence (89%) levels with the gene which encodes the 27,000-dalton polypeptide that has been shown previously to be involved in the bile acid 7-dehydroxylation reaction sequence. The implications of this homology and the possible function(s) of the two homologous genes in bile acid 7-dehydroxylation are discussed. Evidence is presented which suggests that the two homologous genes involved in bile acid 7-dehydroxylation may be part of a larger multigene family in Eubacterium sp. strain VPI 12708.

Amino Acid Sequence↗

PubMed1990

Cloning and sequencing of a bile acid-inducible operon from Eubacterium sp. strain VPI 12708.

Two bile acid-inducible polypeptides from Eubacterium sp. strain VPI 12708 with molecular weights of 27,000 and approximately 45,000 have previously been shown to be encoded by genes residing on a 2.9-kb EcoRI fragment. We now report the cloning and sequencing of three additional overlapping DNA fragments upstream from this EcoRI fragment. Together, these four fragments contain a large segment of a bile acid-inducible operon which encodes the 27,000- and 45,000-Mr (now shown to be 47,500-Mr) polypeptides and open reading frames potentially coding for four additional polypeptides with molecular weights of 59,500, 58,000, 19,500, and 9,000 to 11,500. A bile acid-inducible polypeptide with an apparent Mr of 23,500, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, was purified to homogeneity, and the N-terminal amino acid sequence that was obtained matched the sequence deduced from the open reading frame coding for the 19,500-Mr polypeptide. A short DNA segment containing the 3' downstream end of the gene coding for the 47,500-Mr polypeptide was not successfully cloned but was directly sequenced from DNA fragments synthesized by polymerase chain reaction. The mRNA initiation site for the bile acid-inducible operon was shown by primer extension to be immediately upstream from the gene encoding the 58,000-Mr polypeptide. A potential promoter region upstream from the mRNA initiation site displayed significant homology with the promoter regions of previously identified bile acid-inducible genes from Eubacterium sp. strain VPI 12708. We hypothesize that this bile acid-inducible operon codes for most of the enzymes involved in the bile acid 7 alpha-dehydroxylation pathway in this bacterium.

Amino Acid Sequence↗

PubMed1990

Multiple copies of a bile acid-inducible gene in Eubacterium sp. strain VPI 12708.

Eubacterium sp. strain VPI 12708 is an anaerobic intestinal bacterium which possesses inducible bile acid 7-dehydroxylation activity. Several new polypeptides are produced in this strain following induction with cholic acid. Genes coding for two copies of a bile acid-inducible 27,000-dalton polypeptide (baiA1 and baiA2) have been previously cloned and sequenced. We now report on a gene coding for a third copy of this 27,000-dalton polypeptide (baiA3). The baiA3 gene has been cloned in lambda DASH on an 11.2-kilobase DNA fragment from a partial Sau3A digest of the Eubacterium DNA. DNA sequence analysis of the baiA3 gene revealed 100% homology with the baiA1 gene within the coding region of the 27,000-dalton polypeptides. The baiA2 gene shares 81% sequence identity with the other two genes at the nucleotide level. The flanking nucleotide sequences associated with the baiA1 and baiA3 genes are identical for 930 bases in the 5' direction from the initiation codon and for at least 325 bases in the 3' direction from the stop codon, including the putative promoter regions for the genes. An additional open reading frame (occupying from 621 to 648 bases, depending on the correct start codon) was found in the identical 5' regions associated with the baiA1 and baiA3 clones. The 5' sequence 930 bases upstream from the baiA1 and baiA3 genes was totally divergent. The baiA2 gene, which is part of a large bile acid-inducible operon, showed no homology with the other two genes either in the 5' or 3' direction from the polypeptide coding region, except for a 15-base-pair presumed ribosome-binding site in the 5' region. These studies strongly suggest that a gene duplication (baiA1 and baiA3) has occurred and is stably maintained in this bacterium.

Amino Acid Sequence↗

PubMed1992

The bile acid-inducible baiB gene from Eubacterium sp. strain VPI 12708 encodes a bile acid-coenzyme A ligase.

The baiB gene from Eubacterium sp. strain VPI 12708 was previously cloned, sequenced, and shown to be part of a large bile acid-inducible operon encoding polypeptides believed to be involved in bile acid 7 alpha-dehydroxylation. In the present study, the baiB gene was subcloned and expressed in Escherichia coli and shown to encode a bile acid-coenzyme A (CoA) ligase. This ligase required a C-24 bile acid with a free carboxyl group, ATP, Mg2+, and CoA for synthesis of the final bile acid-CoA conjugate. Product analysis by reverse-phase high-performance liquid chromatography revealed final reaction products that comigrated with cholyl-CoA and AMP. A putative bile acid-AMP intermediate was detected when CoA was omitted from the reaction mixture. The bile acid-CoA ligase has amino acid sequence similarity to several other polypeptides involved in the ATP-dependent linking of AMP or CoA to cyclic carboxylated compounds. The bile acid-CoA ligation is believed to be the initial step in the bile acid 7 alpha-dehydroxylation pathway in Eubacterium sp. strain VPI 12708.

Base Sequence↗

PubMed1993

Characterization of the baiH gene encoding a bile acid-inducible NADH:flavin oxidoreductase from Eubacterium sp. strain VPI 12708.

A cholate-inducible, NADH-dependent flavin oxidoreductase from the intestinal bacterium Eubacterium sp. strain VPI 12708 was purified 372-fold to apparent electrophoretic homogeneity. The subunit and native molecular weights were estimated to be 72,000 and 210,000, respectively, suggesting a homotrimeric organization. Three peaks of NADH:flavin oxidoreductase activity (forms I, II, and III) eluted from a DEAE-high-performance liquid chromatography column. Absorption spectra revealed that purified form III, but not form I, contained bound flavin, which dissociated during purification to generate form I. Enzyme activity was inhibited by sulfhydryl-reactive compounds, acriflavine, o-phenanthroline, and EDTA. Activity assays and Western blot (immunoblot) analysis confirmed that expression of the enzyme was cholate inducible. The first 25 N-terminal amino acid residues of purified NADH:flavin oxidoreductase were determined, and a corresponding oligonucleotide probe was synthesized for use in cloning of the associated gene, baiH. Restriction mapping, sequence data, and RNA blot analysis suggested that the baiH gene was located on a previously described, cholate-inducible operon > or = 10 kb long. The baiH gene encoded a 72,006-Da polypeptide containing 661 amino acids. The deduced amino acid sequence of the baiH gene was homologous to that of NADH oxidase from Thermoanaerobium brockii, trimethylamine dehydrogenase from methylotrophic bacterium W3A1, Old Yellow Enzyme from Saccharomyces carlsbergensis, and the product of the baiC gene of Eubacterium sp. strain VPI 12708, located upstream from the baiH gene in the cholate-inducible operon. Alignment of these five sequences revealed potential ligands for an iron-sulfur cluster, a putative flavin adenine dinucleotide-binding domain, and two other well-conserved domains of unknown function.

Amino Acid Sequence↗

PubMed1996

A purgative action of barbaloin is induced by Eubacterium sp. strain BAR, a human intestinal anaerobe, capable of transforming barbaloin to aloe-emodin anthrone.

Orally administered barbaloin (100 mg/kg) did not induce any diarrhea in male Wistar rats, in spite of severe diarrhea with sennoside B (40 mg/kg). Also, in gnotobiote rats mono-associated with Peptostreptococcus intermedius, a human intestinal anaerobe capable of reducing sennidins to rhein anthrone, barbaloin did not induce diarrhea; the faecal water content (71.9%) 8 h after the administration of barbaloin was not increased, compared with that (73.9%) just before the treatment. However, severe diarrhea was induced with barbaloin in gnotobiote rats mono-associated with Eubacterium sp. strain BAR, another human intestinal anaerobe capable of transforming barbaloin to aloe-emodin anthrone; the faecal water content was significantly increased to 85.5% 8 h after the administration, from 73.2% before the treatment. At this time, barbaloin was transformed to aloe-emodin anthrone in the feces from the gnotobiote rats mono-associated with the strain BAR, but not in feces from the conventional rats or the gnotobiote rats mono-associated with P. intermedius. These facts indicate that barbaloin is inactive as a laxative itself but is activated to aloe-emodin anthrone, a genuine purgative component, by Eubacterium sp. strain BAR.

Animals↗

PubMed1984

Eubacterium brachy. Reactivity in in vitro bone resorptive bioassay.

Recent studies have demonstrated an association of Eubacterium sp. with the subgingival microflora of patients with chronic periodontitis. One species, Eubacterium brachy, was evaluated to determine the possible mechanisms by which this microorganism may contribute to this disease. An extracellular antigen was identified in the culture supernatant which reacted with antibodies in human sera. This antigen was isolated by methanol precipitation and purified by gel filtration. The purified extracellular antigen was reacted in vitro with 45CaCl2-labeled fetal rat bone in a bone resorptive bioassay. This antigen was shown to have a molecular weight of 170,000, to share a line of identity with a sonicated preparation of E. brachy whole cells and to result in increased 45CaCl2 release from fetal rat bones when cultures were exposed to the purified extracellular antigen at concentrations of 10 to 53 micrograms/ml.

Animals↗

PubMed1998

Effect of feeding of a cholesterol-reducing bacterium, Eubacterium coprostanoligenes, to germ-free mice.

Twelve germ-free mice were used to evaluate the effect of orally administered Eubacterium coprostanoligenes (ATCC 51222) on serum cholesterol concentration. After 1 week of bacterial administration, serum cholesterol concentration of the experimental group (204.9 +/- 5.3 mg/dl, mean +/- SEM) tended to be lower than that of controls (213.7 +/- 5.9 mg/dl, mean +/- SEM). The hypocholesterolemic effect, however, was transient. Greater coprostanol-to-cholesterol ratios in feces of bacteria-fed mice also indicated a transient cholesterol-reducing action of E. coprostanoligenes in the intestine. Eubacterium coprostanoligenes did not colonize the intestine of E. coprostanoligenes-fed mice. Results indicate that the transient occurrence of E. coprostanoligenes in the digestive tract of E. coprostanoligenes-fed mice may decrease plasma cholesterol concentration, but colonization of the tract depends on monoassociation with another bacterium. Results also indicate that feeding of E. coprostanoligenes decreases blood cholesterol concentration.

Animals↗

PubMed1989

Isolation of Eubacterium suis from sows with cystitis.

Eubacterium suis was isolated from the bladders of 3 of 64 sows (4.7%) examined at slaughter. Two of the sows had cystitis similar to other descriptions of E suis infections in sows. There was no histologic evidence of cystitis in the third sow from which E suis was recovered. In all 3 instances, a mixed infection was present. Other bacteria present were predominantly gram-positive organisms. Eubacterium suis cystitis may be more prevalent than previously suspected. The special culture conditions required to grow this organism may account for the paucity of reports in the United States.

Abattoirs↗

PubMed1987

Biosynthesis of a novel bile acid nucleotide and mechanism of 7 alpha-dehydroxylation by an intestinal Eubacterium species.

Eubacterium species V.P.I. 12708 has inducible bile acid 7-dehydroxylase activity that can use either 7 alpha or 7 beta bile acids as substrates. Cell extracts prepared from bacteria grown in the presence of cholic acid catalyzed the rapid conversion of free bile acids into a highly polar bile acid metabolite (HPBA). This conjugation activity co-eluted with bile acid 7-dehydroxylase activity on high performance gel filtration chromatography (GFC). The HPBA was purified by a combination of high performance GFC and reverse-phase high performance liquid chromatography (HPLC). The intact HPBA eluted earlier from reverse-phase HPLC than deoxycholyl-CoA and had a Mr of 1102 by Bio-Gel P-2 (GFC). The HPBA had an absorption peak at 255 nm and was sensitive to treatment with phosphodiesterase I or nucleotide pyrophosphatase. The HPBA has a free phosphate as shown by an increase in elution volume on reverse-phase HPLC following treatment with alkaline phosphatase. Treatment of the purified HPBA with nucleotide pyrophosphate plus alkaline phosphatase yielded adenosine, whereas, treatment with nucleotide pyrophosphatase alone generated 5',3'-ADP. A bile acid metabolite was also generated by nucleotide pyrophosphatase treatment. The bile acid metabolite had different chromatographic properties (HPLC and TLC) than the corresponding free bile acid. Gas liquid chromatography-mass spectrometry showed the bile acid metabolite to be 12 alpha-hydroxy-3-oxo-4-cholenoic acid. We hypothesize that the HPBA is an intermediate in 7-dehydroxylation and consists of this compound linked at the C-24 with an anhydride bond to the beta phosphate (5') of ADP-3'-phosphate. These results suggest a novel mechanism of bile acid 7 alpha/7 beta-dehydroxylation in Eubacterium sp. V.P.I. 12708.

Adenosine Diphosphate↗

PubMed1993

Studies on the prevalence of Eubacterium suis in boars on farms in Brazil, Portugal and Argentina by indirect immunofluorescence technique.

The main habitat of Eubacterium suis (E. suis) is the preputial diverticulum of male pigs. E. suis can be transmitted from boars to the vestibule of sows at the time of mating and ascending urinary tract infections in sows may result. A total of 195 swabs of the preputial diverticulum was collected for prevalence studies of E. suis infections in adult breeding males on Brazilian (n = 96 boars), Portuguese (n = 78 boars) and Argentinian (n = 21 boars) farms. The fixed smears were stored at 4 degrees C for one to four months until indirect immunofluorescence test was performed. Eubacterium suis was found in 75 (78%), 52 (67%) and 16 (76%) boars, respectively. These results indicate that E. suis is present in Brazil, Argentina as well as in Portugal and may be involved in urinary tract infections of sows more frequently as it is known till now.

Animals↗

PubMed1999

The bile acid-inducible baiF gene from Eubacterium sp. strain VPI 12708 encodes a bile acid-coenzyme A hydrolase.

The human intestinal Eubacterium sp. strain VPI 12708 has been shown to have a multistep biochemical pathway for bile acid 7alpha-dehydroxylation. A bile acid-inducible operon encoding 9 open reading frames has been cloned and sequenced from this organism. Several of the genes in this operon have been shown to catalyze specific reactions in the 7alpha-dehydroxylation pathway. The baiF gene from this operon was cloned, expressed in Escherichia coli, and found to encode a novel bile acid-coenzyme A (CoA) hydrolase. The subunit molecular mass of the purified bile acid-CoA hydrolase was calculated to be 47,466 daltons and the native enzyme had a relative molecular weight of 72,000. The K m and Vmax for cholyl-coenzyme A (CoA) hydrolysis was approximately 175 microm and 374 micromol/min per mg protein, respectively. The enzyme used cholyl-CoA, 3-dehydrocholyl-CoA, and chenodeoxycholyl-CoA as substrates. No hydrolytic activity was detected using acetyl-CoA, isovaleryl-CoA, palmitoyl-CoA, or phenylacetyl-CoA as substrates. Amino acid sequence database searches showed no significant similarity of bile acid-CoA hydrolase to other thioesterases, but significant amino acid sequence identity was found with Escherichia coli carnitine dehydratase. The characteristic thioesterase active site Gly-X-Ser-X-Gly motif was not found in the amino acid sequence of this enzyme. Bile acid-CoA hydrolase from Eubacterium sp. strain VPI 12708 may represent a new family of thioesterases.

Acyltransferases↗

PubMed1998

Eubacterium aggreganssp. nov., a new homoacetogenic bacterium from olive mill wastewater treatment digestor.

A strictly anaerobic, homoacetogenic, gram-positive, non spore-forming bacterium, designated strain SR12(T) (T = type strain), was isolated from an anaerobic methanogenic digestor fed with olive mill wastewater. Yeast extract was required for growth but could also be used as sole carbon and energy source. Strain SR12(T) utilized a few carbohydrates (glucose, fructose and sucrose), organic compounds (lactate, crotonate, formate and betaine), alcohols (methanol), the methoxyl group of some methoxylated aromatic compounds, and H2 + CO2. The end-products of carbohydrate fermentation were acetate, formate, butyrate, H2 and CO2. End-products from lactate and methoxylated aromatic compounds were acetate and butyrate. Strain SR12(T) was non-motile, formed aggregates, had a G+C content of 55 mol % and grew optimally at 35 degrees C and pH 7.2 on a medium containing glucose. Phylogenetically, strain SR12(T) was related to Eubacterium barkeri, E. callanderi, and E. limosum with E. barkeri as the closest relative (similarity of 98%) with which it bears little phenotypic similarity or DNA homology (60%). On the basis of its phenotypic, genotypic, and phylogenetic characteristics, we propose to designate strain SR12(T) as Eubacterium aggregans sp. nov. The type strain is SR12(T) (= DSM 12183).

Journal Article↗

PubMed2004

Elongation factor Ts from the Antarctic eubacterium Pseudoalteromonas haloplanktis TAC 125: biochemical characterization and cloning of the encoding gene.

The elongation factor Ts was isolated from the psychrophilic Antarctic eubacterium Pseudoalteromonas haloplanktis TAC 125 strain (PhEF-Ts), and its functional properties were studied. At 0 degrees C PhEF-Ts enhanced the [(3)H]GDP/GDP exchange rate on the preformed PhEF-Tu.[(3)H]GDP complex by 2 orders of magnitude even at very low Tu:Ts ratio, by lowering the energy of activation of the exchange reaction. PhEF-Ts is a monomeric protein, and in solution it forms a stable dimeric complex with PhEF-Tu. The PhEF-Ts encoding gene was cloned and sequenced. Its structural organization was similar to that of Escherichia coli because it showed at its 5' end the gene encoding the ribosomal protein S2. The translated amino acid sequence had a calculated molecular weight of 30762, and showed a high sequence identity with E. coli (68%) and Thermus thermophilus (44%) EF-Ts. The PhEF-Ts primary structure contains well-preserved almost all the amino acid residues interacting at the interfaces of the E. coli EF-Ts.EF-Tu complex. Finally, the high concentration of PhEF-Ts in this psychrophilic eubacterium might represent an adaptive tool to ensure an efficient nucleotide exchange even at low temperature.

Amino Acid Sequence↗

PubMed2003

Active lipoprotein precursors in the Gram-positive eubacterium Lactococcus lactis.

Lipid-modified proteins play important roles at the interface between eubacterial cells and their environment. The importance of lipoprotein processing by signal peptidase II (SPase II) is underscored by the fact that this enzyme is essential for viability of the Gram-negative eubacterium Escherichia coli. In contrast, SPase II is not essential for growth and viability of the Gram-positive eubacterium Bacillus subtilis. This could be due to alternative amino-terminal lipoprotein processing, which was shown previously to occur in SPase II mutants of B. subtilis. Alternatively, uncleaved lipoprotein precursors might be functional. To explore further the importance of lipoprotein processing in Gram-positive eubacteria, an SPase II mutant strain of Lactococcus lactis was constructed. Although some of the 39 (predicted) lactococcal lipoproteins, such as PrtM and OppA, are essential for growth in milk, the growth of SPase II mutant L. lactis cells in this medium was not affected. Furthermore, the activity of the strictly PrtM-dependent extracellular protease PrtP, which is required for casein degradation, was not impaired in the absence of SPase II. Importantly, no alternative processing of pre-PrtM and pre-OppA was observed in cells lacking SPase II. Taken together, these findings show for the first time that authentic lipoprotein precursors retain biological activity.

Aspartic Acid Endopeptidases↗

PubMed1988

Ribosomes of the extremely thermophilic eubacterium Thermotoga maritima are uniquely insensitive to the miscoding-inducing action of aminoglycoside antibiotics.

Poly(U)- and poly(UG)-programmed cell-free systems were developed from the extreme thermophilic, anaerobic eubacterium Thermotoga maritima, and their susceptibility to aminoglycoside and other antibiotics was assayed at a temperature (75 degrees C) close to the physiological optimum (80 degrees C) for cell growth and in vitro polypeptide synthesis, using a Bacillus stearothermophilus system as the reference. The synthetic capacity of the Thermotoga assay mixture was abolished by the eubacterium-targeted drugs chloramphenicol, thiostrepton, and kirromycin. However, streptomycin, the disubstituted 2-deoxystreptamines (kanamycin, gentamicin, neomycin, and paromomycin), and the monosubstituted 2-deoxystreptamine (hygromycin) all failed to promote translational misreading of poly(U) on Thermotoga ribosomes; they also failed to block polyphenylalanine synthesis at a low (less than 10(-4) M) concentration and did not inhibit Thermotoga cell growth at a high (10 micrograms/ml) concentration even though Thermotoga ribosomes possess the 16S rRNA sequences required for aminoglycoside action. In contrast to the other eubacteria, Thermotoga elongation factor G was also refractory to the steroid inhibitor of peptidyl-tRNA translocation fusidic acid.

Aminoglycosides↗

PubMed1993

Eubacterial components similar to small nuclear ribonucleoproteins: identification of immunoprecipitable proteins and capped RNAs in a cyanobacterium and a gram-positive eubacterium.

Small nuclear ribonucleoprotein (snRNP) particles play an important role in the processing of pre-mRNA. snRNPs have been identified immunologically in a variety of cells, but none have ever been observed in prokaryotic systems. This report provides the first evidence for the presence of snRNP-like components in two types of prokaryotic cells: those of the cyanobacterium Synechococcus leopoliensis and those of the gram-positive eubacterium Bacillus subtilis. These components consist of snRNP-immunoreactive proteins and RNAs, including some with the snRNP-unique 5' m2,2,7G (m3G) cap. Immunoreactivity was determined by immunoprecipitation procedures, with either antinuclear-antibody-positive (RNP- and Sm-monospecific) patient sera or a m3G monoclonal antibody, with radiolabelled cell extracts that were preadsorbed with antinuclear-antibody-negative sera. S. leopoliensis immunoprecipitates showed the presence of high-molecular-mass proteins (14 to 70 kDa) and RNAs (138 to 243 nucleotides) that are analogous in size to proteins and RNAs found in human (HEp-2) cell immunoprecipitates but absent in Escherichia coli immunoprecipitates. Thin-layer chromatography of S. leopoliensis immunoprecipitates confirmed the presence of a capped nucleotide similar to a capped nucleotide in HEp-2 immunoprecipitates; no such nucleotide was observed in E. coli immunoprecipitates. Immunoreactive RNAs (117-170 nucleotides) were identified in a second eubacterium, B. subtilis, as well. This work suggests that snRNPs or their evolutionary predecessors predate the emergence of eukaryotic cells.

Antibodies, Antinuclear↗