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PubMed1999

Phylogeny and in situ identification of a morphologically conspicuous bacterium, Candidatus Magnospira bakii, present at very low frequency in activated sludge.

A morphologically conspicuous bacterium that constituted a very small fraction (< 0.01%) of the total microbial community of activated sludge was enriched and analysed phylogenetically by a combination of cultivation-independent molecular and physical methods. The large, corkscrew-shaped, filamentous bacteria were first detected in municipal activated sludge by light microscopy owing to their unusual rotating gliding motility. Various attempts at microbiological enrichment and pure culture isolation with traditional techniques failed, as did attempts to retrieve the morphotype of interest by micromanipulation. In situ hybridization with the group-specific, rRNA-targeted oligonucleotide probe CF319a indicated a phylogenetic affiliation to the Cytophaga-Flexibacter group of the Cytophaga-Flavobacterium-Bacteroides phylum. Based on strong morphological resemblance to members of the genus Saprospira, additional 16S rRNA-targeted oligonucleotides with more narrow specificity were designed and evaluated for in situ hybridization to the morphotype of interest. Flow cytometric cell sorting based on the fluorescence conferred by probe SGR1425 and forward scatter enabled a physical enrichment of the helical coiled cells. Subsequent polymerase chain reaction (PCR) amplification of 16S rDNA fragments from whole fixed sorted cells with a primer pair based on probes CF319a and SGR1425 resulted in the retrieval of 12 almost identical partial 16S rDNA fragments with sequence similarities among each other of more than 99.2%. In situ hybridizations proved that the sequences that showed the highest similarity (88.4%) to the 16S rRNA of Saprospira grandis were indeed retrieved from the corkscrew-shaped filaments. The bacterium is likely to be a member of a genus of which no species has been cultured hitherto. It was consequently tentatively named 'Magnospira bakii' and has the taxonomic rank of Candidatus Magnospira bakii, as the ultimate taxonomic placement has to await its cultivation. In this study, it was demonstrated that even bacteria occurring at very low frequencies in highly complex environmental samples can be retrieved selectively without cultivation for further molecular analysis.

Cloning, Molecular↗
PubMed2002

Stable augmentation of activated sludge with foreign catabolic genes harboured by an indigenous dominant bacterium.

Comamonas sp. rN7 is a phenol-degrading bacterium that represents the dominant catabolic population in activated sludge. The present study examined the utility of this bacterium for establishing foreign catabolic genes in phenol-digesting activated sludge. The phc genes coding for phenol hydroxylase and its transcriptional regulators of C. testosteroni R5 were integrated into the chromosome of strain rN7. The specific phenol-oxygenating activity of a resultant transformant designated rN7(R503) was three times higher than the activity of strain rN7, and the phc genes were stably inherited by rN7(R503) grown in a non-selective laboratory medium. Inoculation of phenol-acclimatized activated sludge with rN7(R503) resulted in a high phenol-oxygenating activity and improved resistance to phenol-shock loading compared to sludge inoculated with either no cells, rN7 or R5. Quantitative competitive polymerase chain reaction (PCR) showed that the phc genes were retained in the rN7(R503)-inoculated sludge at a density of more than 108 copies per ml of mixed liquor for more than 35 days, whereas those in the R5-inoculated sludge disappeared rapidly. No transfer of the phc genes to other indigenous populations was apparent in the rN7(R503)-harbouring sludge. From these results, we concluded that the phenol treatment of the activated sludge was enhanced by the phc genes harboured by the rN7(R503) population. This study suggests a possible bioaugmentation strategy for stably utilizing foreign catabolic genes in natural ecosystems.

Biodegradation, Environmental↗
PubMed1998

Prominent occurrence of ribosomes from an uncultured bacterium of the Verrucomicrobiales cluster in grassland soils.

An uncultured bacterium of the Verrucomicrobiales cluster was identified by its 16S rDNA sequence as a major bacterium in Dutch Drentse A grassland soils. Potential metabolic activity of the according organism was estimated by applying direct ribosome isolation from soil and partial amplification of the 16S rRNA via RT-PCR using bacteria-specific primers. Temperature gradient gel electrophoresis separated the amplicons sequence specifically into reproducible fingerprints. One of the fingerprint bands matched with the signal of clone DA101. Southern blot hybridization with a DA101-specific V6 probe confirmed sequence identity. It is the first time that an organism of the Verrucomicrobiales cluster has been indicated as a potential major metabolizer in environmental microbial communities.

Bacteria↗
PubMed2002

Fermentation of pectin and glucose, and activity of pectin-degrading enzymes in the rabbit caecal bacterium Bifidobacterium pseudolongum.

AIMS: In a rabbit caecal bacterium Bifidobacterium pseudolongum, metabolites of pectin and glucose, and activities of enzymes involved in the degradation of pectin were assayed. Simultaneously, activities of these enzymes were assayed in a rumen pectinolytic strain of Streptococcus bovis. METHODS AND RESULTS: A strain B. pseudolongum P6 which grew best on pectin was selected among bifidobacteria isolated from the rabbit caecum. Cultures of B. pseudolongum P6 grown on pectin produced significantly less formate, lactate and ethanol, and more acetate and succinate than cultures grown on glucose. No CO2 production on pectin was observed. Pectin macromolecule was degraded by extracellular pectinase (EC 3.2.1.15). Cell extracts possessed the activity of 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase (EC 4.1.2.14). Streptococcus bovis X4, possessed activity of exopectate lyase and pectinase, but not that of KDPG aldolase. CONCLUSIONS: Our results are consistent with the assumption that in B. pseudolongum P6 acidic products of pectin degradation are catabolized via a modified Entner-Doudoroff pathway, as shown previously in rumen pectin-utilizing bacteria. The missing KDPG aldolase activity in Strep. bovis X4 seems to be the reason for the absence of growth of this bacterium on pectin. SIGNIFICANCE AND IMPACT OF THE STUDY: Information on polysaccharide metabolism in bifidobacteria is fragmentary. This study extends the knowledge on pectin metabolism in intestinal bacteria.

Aldehyde-Lyases↗
PubMed2003

A quantitative method for measuring the mass concentration of the filamentous bacterium Type 021N in activated sludge using fluorescence in situ hybridization.

AIMS: This study aimed to develop a quantitative method for measuring mass concentrations of Type 021N, a bacterium causing bulking in activated sludge. METHODS AND RESULTS: Fluorescence in situ hybridization was used to determine the relationship between the concentration ratio of the mass of the bacterium Type 021N to mass of activated sludge, and the proportion of fluorescence area imparted by probe G123T specific for Type 021N to that obtained with probe EUB338 for bacteria. A linear relationship existed between the cube root of the mass concentration ratio and square root of this area proportion. CONCLUSIONS: A standard curve was obtained for quantifying Type 021N in activated sludge. SIGNIFICANCE AND IMPACT OF THE STUDY: This method may allow the determination of growth rate constant of filamentous bacteria in activated sludge, information that will help in understanding their ecology.

Bacteria↗
PubMed2003

Lactobacillus ruminis is a predominant lactic acid producing bacterium in the caecum and rectum of the pig.

AIMS: To identify the predominant lactic acid producing bacteria in the small intestine, caecum and the rectum of the healthy pig. METHODS AND RESULTS: Samples obtained from the large intestine of healthy pigs post-mortem were cultured using a modified agar-MRS medium in roll tubes. Thirteen isolates were selected on the basis of their morphological characteristics and Gram stain reaction for gene sequencing. These isolates were characterized by DNA sequence analysis of 16S rDNA. Eight isolates were identified as Lactobacillus ruminis, two as Enterococcus faecium, one as Mitsuokella multiacidus and two as Escherichia coli. CONCLUSION: This is the first report of Lact. ruminis as the dominant lactic acid bacteria in the large intestine of the pig. SIGNIFICANCE AND IMPACT OF THE STUDY: The results suggest that Lact. ruminis is a dominant bacterium in the large intestine of the healthy pig. Future work should focus on the role of this bacterium in relation to the physiological function of the intestine and the health of the animal.

Animals↗
PubMed2006

Discrete steps in sensing of beta-lactam antibiotics by the BlaR1 protein of the methicillin-resistant Staphylococcus aureus bacterium.

Chemical sensing by cell-surface receptors to effect signal transduction is a ubiquitous biological event. Despite extensive structural biochemical study, detailed knowledge of how signal transduction occurs is largely lacking. We report herein a kinetic and structural study, obtained by stopped-flow IR spectroscopy, of the activation of the BlaR1 receptor of the Staphylococcus aureus bacterium by beta-lactam antibiotics. The cell-surface BlaR1 receptor alerts the bacterium to the presence of beta-lactam antibiotics, resulting in expression of the gene for a beta-lactamase enzyme. This enzyme hydrolytically destroys the remaining beta-lactam antibiotics. IR spectroscopic interrogation of the beta-lactam-BlaR1 receptor reaction has allowed the simultaneous measurement of the chemical events of receptor recognition of the beta-lactam and the characterization of the conformational changes in the BlaR1 receptor that result. The key chemical events in beta-lactam recognition are serine acylation and subsequent irreversible decarboxylation of the BlaR1 active site lysine carbamate. Both events are observed by stopped-flow IR kinetics and (13)C isotope-edited IR spectroscopy. The secondary structural changes in the BlaR1 receptor conformation that occur as a consequence of this acylation/decarboxylation are predicted to correlate to the signal transduction event accomplished by this receptor.

Acylation↗
PubMed2006

Swimming efficiency of bacterium Escherichia coli.

We use measurements of swimming bacteria in an optical trap to determine fundamental properties of bacterial propulsion. In particular, we directly measure the force required to hold the bacterium in the optical trap and determine the propulsion matrix, which relates the translational and angular velocity of the flagellum to the torques and forces propelling the bacterium. From the propulsion matrix, dynamical properties such as torques, swimming speed, and power can be obtained by measuring the angular velocity of the motor. We find significant heterogeneities among different individuals even though all bacteria started from a single colony. The propulsive efficiency, defined as the ratio of the propulsive power output to the rotary power input provided by the motors, is found to be approximately 2%, which is consistent with the efficiency predicted theoretically for a rigid helical coil.

Escherichia coli↗
PubMed2003

Gene function analysis in environmental isolates: the nif regulon of the strict iron oxidizing bacterium Leptospirillum ferrooxidans.

A random genomic library from an environmental isolate of the Gram-negative bacterium Leptospirillum ferrooxidans has been printed on a microarray. Gene expression analysis was carried out with total RNA extracted from L. ferrooxidans cultures in the presence or absence of ammonium as nitrogen source under aerobic conditions. Although practically nothing is known about the genome sequence of this bacterium, this approach allowed us the selection and sequencing of only those clones bearing genes that showed an altered expression pattern. By sequence comparison, we have identified most of the genes of nitrogen fixation regulon in L. ferrooxidans, like the nifHDKENX operon, encoding the structural components of Mo-Fe nitrogenase; nifSU-hesB-hscBA-fdx operon, for Fe-S cluster assembly; the amtB gene (ammonium transporter); modA (molybdenum ABC type transporter); some regulatory genes like ntrC, nifA (the specific activator of nif genes); or two glnB-like genes (encoding the PII regulatory protein). Our results show that shotgun DNA microarrays are very powerful tools to accomplish gene expression studies with environmental bacteria whose genome sequence is still unknown, avoiding the time and effort necessary for whole genome sequencing projects.

Bacteria↗
PubMed1969

A bacterium capable of using phytol as its sole carbon source, isolated from algal sediment of Mud Lake, Florida.

A species of Flavobacterium that consistently attacks pure phytol and can use it as a sole source of carbon has been isolated from the blue-green algal sediment of Mud Lake, Florida. Biochemical tests demonstrate that this bacterium also readily uses various other organic compounds. This bacterium may account for the degradation products of chlorophyll and its side chain phytol, which have been found in the Mud Lake algal sediment. Phytol and its degradation products play a role in Refsum's disease, but phytol is also the most promising precursor of the isoprenoid hydrocarbons found in oil shale of the Green River Formation (Eocene) of Colorado, Utah, and Wyoming. The discovery of this species of Flavobacterium is a significant product of a protracted study of the bacteriology, phycology, zoology, and geochemistry of the algal sediment forming in Mud Lake, which is believed to be a modern analogue of the kind of algal sediment that, through geologic time, became oil shale.

Chlorophyll↗
PubMed1981

Regulation of glutamine synthetase activity by adenylylation in the Gram-positive bacterium Streptomyces cattleya.

The enzymatic activity of glutamine synthetase [GS; L-glutamate:ammonia ligase (ADP-forming), EC 6.3.1.2] from the Gram-positive bacterium Streptomyces cattleya is regulated by covalent modification. In whole cells containing high levels of GS the addition of ammonium chloride leads to a rapid decline in GS activity. Crude extracts prepared from such ammonia-shocked cells had very low levels of GS activity as measured by biosynthetic and gamma-glutamyltransferase assays. Incubation of the crude extracts with snake venom phosphodiesterase restored GS activity. In cell extracts, GS was also inactivated by an ATP- and glutamine-dependent reaction. Radioactive labeling studies demonstrated the incorporation of an AmP moiety into GS protein upon modification. Our results suggest a covalent modification of GS in a Gram-positive bacterium. This modification appears to be adenylylation of the GS subunit similar to that found in the Gram-negative bacteria.

Adenine↗
PubMed1985

The presence of a copper/zinc superoxide dismutase in the bacterium Photobacterium leiognathi: a likely case of gene transfer from eukaryotes to prokaryotes.

The free-living bacterium Photobacterium leiognathi is also known to be a symbiont of ponyfish. The presence of a copper/zinc superoxide dismutase in P. leiognathi has been considered to be a case of gene transfer from eukaryotes to prokaryotes because this form of superoxide dismutase is normally present only in higher eukaryotic species. However, the amino acid sequence of the enzyme from the bacterium exhibited low identities (25-30%) with the same enzyme from eukaryotes. When amino acid mutations are taken into consideration, the weighted sequence similarity increases significantly; furthermore, the bacterial enzyme has the same active site residues and similar predicted secondary structure as the eukaryotic enzymes. The possibility of convergence is ruled out and the case of divergence is considered unlikely because of the observed phylogenetic distribution of the enzyme. This indicates that the presence of the copper/zinc superoxide dismutase in P. leiognathi can indeed be considered a case of gene transfer from eukaryotic species to prokaryotic species.

Amino Acid Sequence↗
PubMed1987

Transposition of bacteriophage Mu in the Legionnaires disease bacterium.

Legionnaires disease is an acute respiratory disease that is often fatal for immunocompromised patients. The causative agent of this disease, Legionella pneumophila, is a Gram-negative bacterium that is present in a variety of aquatic environments. L. pneumophila is a facultative intracellular parasite; it grows within human phagocytic cells and eventually causes their destruction. In contrast to many other intracellular parasites, L. pneumophila is a Gram-negative bacterium that can be grown in standard microbiological culture medium. To determine the factors that enable this organism to enter, survive, and multiply within human mononuclear phagocytes, we chose bacteriophage Mu, a powerful genetic tool that transposes within the host cell genome, to generate insertion mutations and gene fusions in the Legionella genome. Certain derivatives of Mu are able to generate fusions between target genes and the lac operon from Escherichia coli. We have determined that although Mu is unable to attach to L. pneumophila or complete its life cycle within Legionella, it does transpose within the Legionella genome. Transposition was detected with a mini-Mu phage that carries the lac operon of E. coli.

Bacteriophage mu↗
PubMed1995

Purification and properties of periplasmic 3':5'-cyclic nucleotide phosphodiesterase. A novel zinc-containing enzyme from the marine symbiotic bacterium Vibrio fischeri.

The 3':5'-cyclic nucleotide phosphodiesterase (CNP) of Vibrio fischeri, due to its unusual location in the periplasm, allows this symbiotic bacterium to utilize extracellular 3':5'-cyclic nucleotides (e.g. cAMP) as sole sources of carbon and energy, nitrogen, and phosphorus for growth. The enzyme was purified to apparent homogeneity by a four-step procedure: chloroform shock, ammonium sulfate precipitation, and chromotography on DEAE-Sephacel and Cibacron Blue 3GA-agarose. The active enzyme consists of a single polypeptide with a mass of 34 kDa. At 25 degrees C, it has a pH optimum of 8.25, a Km for cAMP of 73 microns, and a Vmax of 3700 mumol of cAMP hydrolyzed/min/mg protein (turnover number of 1.24 x 10(5)/min). The specific activity of the V. fischeri enzyme is approximately 20-fold greater than that of any previously characterized CNP when comparisons of activity are made at the same assay temperature. Activity increases with temperature up to 60 degrees C. The CNP contains 2 atoms of zinc/monomer, and zinc, copper, magnesium, and calcium can restore activity of the apoenzyme to varying degrees. The exceptional specific activity of the enzyme and its unusual location in the periplasm support proposals that the enzyme enables the bacterium to scavenge 3':5'-cyclic nucleotides in seawater and that the enzyme plays a role in cAMP-mediated host-symbiont interactions.

3',5'-Cyclic-AMP Phosphodiesterases↗
PubMed2002

Structure and binding mode of a ribosome recycling factor (RRF) from mesophilic bacterium.

X-ray and NMR analyses on ribosome recycling factors (RRFs) from thermophilic bacteria showed that they display a tRNA-like L-shaped conformation consisting of two domains. Since then, it has been accepted that domain I, consisting of a three-helix bundle, corresponds to the anticodon arm of tRNA and domain II and a beta/alpha/beta sandwich structure, corresponds to the acceptor arm. In this study, we obtained a RRF from a mesophilic bacterium, Vibrio parahaemolyticus, by gene cloning and carried out an x-ray analysis on it at 2.2 A resolution. This RRF was shown to be active in an in vitro assay system using Escherichia coli polysomes and elongation factor G (EF-G). In contrast, the above-mentioned RRFs from thermophilic bacteria were inactive in such a system. Analysis of the relative orientations between the two domains in the structures of various RRFs, including this RRF from mesophilic bacterium, revealed that domain II rotates about the long axis of the helix bundle of domain I. To elucidate the ribosome binding site of RRF, the peptide fragment (RRF-DI) corresponding to domain I of RRF was expressed and characterized. RRF-DI is bound to 70 S ribosome and the 50 S subunit with an affinity similar to that of wild-type RRF. But it does not bind to the 30 S subunit. These findings caused us to reinvestigate the concept of the mimicry of RRF to tRNA and to propose a new model where domain I corresponds to the acceptor arm of tRNA and domain II corresponds to the anticodon arm. This is just the reverse of a model that is now widely accepted. However, the new model is in better agreement with published biological findings.

Amino Acid Sequence↗
PubMed2003

A Novel H-NS-like protein from an antarctic psychrophilic bacterium reveals a crucial role for the N-terminal domain in thermal stability.

We describe here new members of the H-NS protein family identified in a psychrotrophic Acinetobacter spp. bacterium collected in Siberia and in a psychrophilic Psychrobacter spp. bacterium collected in Antarctica. Both are phylogenetically closely related to the HvrA and SPB Rhodobacter transcriptional regulators. Their amino acid sequence shares 40% identity, and their predicted secondary structure displays a structural and functional organization in two modules similar to that of H-NS in Escherichia coli. Remarkably, the Acinetobacter protein fully restores to the wild-type H-NS-dependent phenotypes, whereas the Psychrobacter protein is no longer able to reverse the effects of H-NS deficiency in an E. coli mutant strain above 30 degrees C. Moreover, in vitro experiments demonstrate that the ability of the Psychrobacter H-NS protein to bind curved DNA and to form dimers is altered at 37 degrees C. The construction of hybrid proteins containing the N- or the C-terminal part of E. coli H-NS fused to the C- or N-terminal part of the Psychrobacter protein demonstrates the role of the N-terminal domain in this process. Finally, circular dichroism analysis of purified H-NS proteins suggests that, as compared with the E. coli and Acinetobacter proteins, the alpha-helical domain displays weaker intermolecular interactions in the Psychrobacter protein, which may account for the low thermal stability observed at 37 degrees C.

Acinetobacter↗
PubMed2005

Epidermal growth factor receptor acts as a negative regulator for bacterium nontypeable Haemophilus influenzae-induced Toll-like receptor 2 expression via an Src-dependent p38 mitogen-activated protein kinase signaling pathway.

Epidermal growth factor receptor (EGFR) has been shown to play important roles in regulating diverse biological processes, including cell growth, differentiation, apoptosis, adhesion, and migration. Its role in regulating human Toll-like receptors (TLRs), key host defense receptors that recognize invading bacterial pathogens, however, remains unknown. Here we show for the first time that EGFR acts as a negative regulator for TLR2 induction by the bacterium nontypeable Haemophilus influenzae (NTHi) in vitro and in vivo. The negative regulation of TLR2 induction by EGFR is mediated via an Src-MKK3/6-p38 alpha/beta MAP kinase-dependent mechanism. Moreover, direct activation of EGFR signaling by the bacterium NTHi-derived EGF-like factor appears to be responsible for triggering the downstream Src-MKK3/6-p38 MAPK signaling, which in turn leads to the negative regulation of TLR2 induction. Finally, exogenous EGF increases NTHi invasion of host epithelial cells, thereby demonstrating the biological significance of TLR2 regulation by EGFR signaling. The evidence we provided in the present study may suggest a novel strategy utilized by bacteria to attenuate host defensive and immune response by negatively regulating the expression of host defense receptor TLR2. These studies may bring new insight for fully understanding the important role of EGFR signaling in regulating host defense and immune response by tightly controlling TLR2 induction during bacterial infections.

Animals↗