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PubMed1995

Significance of bacteriophages for controlling bacterioplankton growth in a mesotrophic lake.

Bacterium-specific viruses have attracted much interest in aquatic microbial ecology because they have been shown to be about 10 times more abundant than planktonic bacteria. So far most of the studies of interactions of planktonic bacteria and viruses have been done in marine environments, and very little is known about these interactions in lakes. Therefore, we studied phage proliferation in Lake Constance, a large mesotrophic lake in Germany. We enumerated bacteria and quantified the fraction of bacteria with mature intracellular phage particles and the number of free viruses by transmission electron microscopy. Between the end of March and early August 1992, peaks of bacterial abundance were followed in 1 to 2 weeks by peaks in the fraction of bacteria containing visible phage particles (0 to 1.7%) and in the number of free viruses (1 x 10(sup7) to 4 x 10(sup7) ml(sup-1)). We estimated that 1 to 17% +/- 12% of all bacteria were phage infected, implying that phage-induced mortality was <34% +/- 24% of total mortality. A direct comparison between phage-induced mortality, the net decrease of bacterial numbers, and bacterial growth rates indicated that phage-induced mortality accounted for <11% of total bacterial mortality during the phytoplankton spring bloom and 18 to 21% following the bloom. Estimated burst sizes ranged from 21 to 121 phages. Phage production rates of 0.5 x 10(sup6) to 2.5 x 10(sup6) ml(sup-1) day(sup-1) accounted for 70 to 380% of the observed net increase rates of free phages, implying high rates of simultaneous phage decay. The cyclic dynamics between bacteria and phages and the varying size structure of the intracellular mature phage particles suggested that phage infection was important in structuring the bacterial host assemblage during the study period.

Journal Article↗
PubMed1984

Effects of physical configuration and chemical structure of suture materials on bacterial adhesion. A possible link to wound infection.

The purpose of this study was to examine the effects of physical configuration and the chemical nature of suture materials on the preferential adherence of bacteria. Ten suture materials of 2-0 (chromic catgut, Dexon, Vicryl, PDS, Mersilene, Tycron, Ethibond, Surgilon, Ethilon, and Prolene) were used. The bacterial strains tested were Staph. aureus and E. coli. The level of bacterial adherence was determined quantitatively by radiolabelled cells and qualitatively by scanning electron microscopy. It was found that the amount of adhered bacteria depended on the type of suture material, the type of bacteria, and the duration of contact. In the group of absorbable sutures, the new PDS sutures exhibited the smallest affinity toward the adherence of both E. coli and Staph. aureus. Dexon sutures had the highest affinity toward these two bacteria. With nonabsorbable sutures, the physical configuration of the sutures contributed more to their ability to attract bacteria than the surface finish. The bacterial adherence on suture materials was also time dependent. Scanning electron microscope morphologic observation also indicated that Staph. aureus adhered on the suture surface in clusters whereas E. coli tended to adhere individually.

Absorption↗
PubMedDate not supplied

On structural aspects of peptidoglycan of bacterial cell wall with special attention on mycobacteria by computer modelling.

The cell wall components of mycobacteria are said to be vitally linked with their pathogenicity. Peptidoglycan, one of the major cell wall component in most of the bacteria are multilayered in gram positive bacteria and it is diverse in nature for the Gram positive strain rather than gram negative. The cell wall of bacteria are primary targets for many drugs and antibiotics and conformation of the major cell wall components provide invaluable information and understanding at molecular level to medicinal chemists and drug designers. Mycobacterial peptidoglycan has been studied critically by computer modelling on various aspects. A plausible structure and conformation has been identified and glycan chain is found to have a pseudo two fold symmetry taking disaccharide unit as monomer with Knox & Murthy H-bond scheme. This paper attempts to clarify the understanding of organisation and possible interaction mode of peptidoglycan of organisation in complex mycobacterial cell wall structure.

Amino Acid Sequence↗
PubMed2003

Arming the enemy: the evolution of resistance to self-proteins.

A remarkable range of novel antibiotics is attracting increasing interest as a major new weapon in the campaign against bacterial infection. They are based on the toxic peptides that provide the innate immune system of animals, and it is claimed that bacteria will be unable to evolve resistance to them because they attack the 'Achilles' heel' of bacterial membrane structure. Both experimental evidence and theoretical arguments suggest that this claim is doubtful. If so, the introduction of these substances into general use may provoke the evolution of resistance to our own defence proteins and thus compromise our natural defences against infection.

Animals↗
PubMed1983

The primary structure of rat liver ribosomal protein L37. Homology with yeast and bacterial ribosomal proteins.

The covalent structure of the rat liver 60 S ribosomal subunit protein L37 was determined. Twenty-four tryptic peptides were purified and the sequence of each was established; they accounted for all 111 residues of L37. The sequence of the first 30 residues of L37, obtained previously by automated Edman degradation of the intact protein, provided the alignment of the first 9 tryptic peptides. Three peptides (CN1, CN2, and CN3) were produced by cleavage of protein L37 with cyanogen bromide. The sequence of CN1 (65 residues) was established from the sequence of secondary peptides resulting from cleavage with trypsin and chymotrypsin. The sequence of CN1 in turn served to order tryptic peptides 1 through 14. The sequence of CN2 (15 residues) was determined entirely by a micromanual procedure and allowed the alignment of tryptic peptides 14 through 18. The sequence of the NH2-terminal 28 amino acids of CN3 (31 residues) was determined; in addition the complete sequences of the secondary tryptic and chymotryptic peptides were done. The sequence of CN3 provided the order of tryptic peptides 18 through 24. Thus the sequence of the three cyanogen bromide peptides also accounted for the 111 residues of protein L37. The carboxyl-terminal amino acids were identified after carboxypeptidase A treatment. There is a disulfide bridge between half-cystinyl residues at positions 40 and 69. Rat liver ribosomal protein L37 is homologous with yeast YP55 and with Escherichia coli L34. Moreover, there is a segment of 17 residues in rat L37 that occurs, albeit with modifications, in yeast YP55 and in E. coli S4, L20, and L34.

Amino Acid Sequence↗
PubMed1990

The primary structure of a halorhodopsin from Natronobacterium pharaonis. Structural, functional and evolutionary implications for bacterial rhodopsins and halorhodopsins.

We cloned and sequenced the gene coding for the polypeptide of a halorhodopsin in Natronobacterium pharaonis (named here pharaonis halorhodopsin). Peptide sequencing of cyanogen bromide fragments, and immunoreactions of the protein and synthetic peptides derived from the COOH-terminal gene sequence, confirmed that the open reading frame is the structural gene for the pharaonis halorhodopsin polypeptide. The flanking DNA sequences, as well as those for other bacterial rhodopsins, were compared to previously proposed archaebacterial consensus sequences. In pairwise comparisons of the open reading frame with DNA sequences for bacterio-opsin and halo-opsin from Halobacterium halobium, silent divergences (mutations/nucleotide at codon positions which do not result in amino acid changes) were calculated. These indicate very considerable evolutionary distance between each pair of genes. In spite of this, the three protein sequences show extensive similarities, indicating strong selective pressures. Conserved and conservatively replaced amino acid residues in all three proteins identify general features essential for ion-motive bacterial rhodopsins, responsible for overall structure and chromophore properties. Comparison of the bacteriorhodopsin sequence with those of the two halorhodopsins, on the other hand, identifies features involved in their specific (proton and chloride ion) transport functions.

Amino Acid Sequence↗
PubMed2005

Soil microbial community response to land use change in an agricultural landscape of western Kenya.

Tropical agroecosystems are subject to degradation processes such as losses in soil carbon, nutrient depletion, and reduced water holding capacity that occur rapidly resulting in a reduction in soil fertility that can be difficult to reverse. In this research, a polyphasic methodology has been used to investigate changes in microbial community structure and function in a series of tropical soils in western Kenya. These soils have different land usage with both wooded and agricultural soils at Kakamega and Ochinga, whereas at Ochinga, Leuro, Teso, and Ugunja a replicated field experiment compared traditional continuous maize cropping against an improved N-fixing fallow system. For all sites, principal component analysis of 16S rRNA gene denaturing gradient gel electrophoresis (DGGE) profiles revealed that soil type was the key determinant of total bacterial community structure, with secondary variation found between wooded and agricultural soils. Similarly, phospholipid fatty acid (PLFA) analysis also separated wooded from agricultural soils, primarily on the basis of higher abundance of monounsaturated fatty acids, anteiso- and iso-branched fatty acids, and methyl-branched fatty acids in the wooded soils. At Kakamega and Ochinga wooded soils had between five 5 and 10-fold higher levels of soil carbon and microbial biomass carbon than agricultural soils from the same location, whereas total enzyme activities were also lower in the agricultural sites. Soils with woody vegetation had a lower percentage of phosphatase activity and higher cellulase and chitinase activities than the agricultural soils. BIOLOG analysis showed woodland soils to have the greatest substrate diversity. Throughout the study the two functional indicators (enzyme activity and BIOLOG), however, showed lower specificity with respect to soil type and land usage than did the compositional indicators (DGGE and PLFA). In the field experiment comparing two types of maize cropping, both the maize yields and total microbial biomass were found to increase with the fallow system. Moreover, 16S rRNA gene and PLFA analyses revealed shifts in the total microbial community in response to the different management regimes, indicating that deliberate management of soils can have considerable impact on microbial community structure and function in tropical soils.

Agriculture↗
PubMed2005

Structural basis for the interaction of Bordetella pertussis adenylyl cyclase toxin with calmodulin.

CyaA is crucial for colonization by Bordetella pertussis, the etiologic agent of whooping cough. Here we report crystal structures of the adenylyl cyclase domain (ACD) of CyaA with the C-terminal domain of calmodulin. Four discrete regions of CyaA bind calcium-loaded calmodulin with a large buried contact surface. Of those, a tryptophan residue (W242) at an alpha-helix of CyaA makes extensive contacts with the calcium-induced, hydrophobic pocket of calmodulin. Mutagenic analyses show that all four regions of CyaA contribute to calmodulin binding and the calmodulin-induced conformational change of CyaA is crucial for catalytic activation. A crystal structure of CyaA-calmodulin with adefovir diphosphate, the metabolite of an approved antiviral drug, reveals the location of catalytic site of CyaA and how adefovir diphosphate tightly binds CyaA. The ACD of CyaA shares a similar structure and mechanism of activation with anthrax edema factor (EF). However, the interactions of CyaA with calmodulin completely diverge from those of EF. This provides molecular details of how two structurally homologous bacterial toxins evolved divergently to bind calmodulin, an evolutionarily conserved calcium sensor.

Adenylate Cyclase Toxin↗
PubMedDate not supplied

[Experimental study of Microcystis-associated and free-living cyanobacteria].

In the experiment with water from the hypereutrophic Lake Frederiksborg Slotso (Denmark) sampled during the autumn peak of Microcystis growth, the quantity and production of free-living and cyanobacteria-associated heterotrophic bacteria were determined, as well as the extracellular enzymatic (aminopeptidase) activity. The functional diversities of associated and free-living bacterial communities were additionally compared using BIOLOG GN microplates to reveal the possible export of Microcystis-attached bacteria into ambient water. It has been shown that the cell size, production values, and growth rates of associated bacteria were less than those of free-living bacteria. At the same time, the potential aminopeptidase activity of associated bacteria was always higher than that of free-living bacteria. The experimental results have shown significant compositional differences in the structure of bacterial communities from different habitats.

Aminopeptidases↗
PubMed1984

Elimination of plasmid pMG110 from Escherichia coli by novobiocin and other inhibitors of DNA gyrase.

The ability of novobiocin to eliminate (cure) the wild-type plasmid pMG110 from Escherichia coli has been compared with that of other inhibitors of the gyrase B subunit and of the gyrase A subunit. Novobiocin eliminated pMG110 , producing over 99% plasmid loss at concentrations two- to eightfold below the MIC for bacterial growth. Structurally related compounds ( clorobiocin , coumermycin A1, isobutyryl novenamine , and decarbamyl novobiocin) varied in their ability to eliminate pMG110 . Higher concentrations of drugs were required to eliminate pMG110 from a gyrB( Cour ) strain, implicating DNA gyrase in the curing phenomenon. For these drugs, the ratio of the concentration effecting maximal plasmid elimination to the MIC varied from 0.16 to 1.1, indicating that curing cannot be explained simply by inhibition of a pool of DNA gyrase equally available for replication of the bacterial chromosome and the plasmid DNA molecule. Inhibitors of the gyrase A subunit, nalidixic acid and oxolinic acid, eliminated pMG110 only to variable low levels. The differences in the ability of the gyrase A and B subunit antagonists to eliminate plasmids are discussed.

Escherichia coli↗
PubMed1997

Crystal structure of the anti-bacterial sulfonamide drug target dihydropteroate synthase.

Sulfonamides were amongst the first clinically useful antibacterial agents to be discovered. The identification of sulfanilamide as the active component of the dye Prontosil rubrum led to the synthesis of clinically useful analogues. Today sulfamethoxazole (in combination with trimethoprim), is used to treat urinary tract infections caused by bacteria such as Escherichia coli and is also a first-line treatment for pneumonia caused by the fungus Pneumocystis carinii, a common condition in AIDS patients. The site of action is the de novo folate biosynthesis enzyme dihydropteroate synthase (DHPS) where sulfonamides act as analogues of one of the substrates, para-aminobenzoic acid (pABA). We report here the crystal structure of E.coli DHPS at 2.0 A resolution refined to an R-factor of 0.185. The single domain of 282 residues forms an eight-stranded alpha/beta-barrel. The 7,8-dihydropterin pyrophosphate (DHPPP) substrate binds in a deep cleft in the barrel, whilst sulfanilamide binds closer to the surface. The DHPPP ligand site is highly conserved amongst prokaryotic and eukaryotic DHPSs.

Amino Acid Sequence↗
PubMed2003

Dynamics of microcystin-degrading bacteria in mucilage of Microcystis.

To reveal the process of degradation of hepatotoxic microcystin produced in Microcystis cells during the Microcystis bloom period, we used fluorescence in situ hybridization (FISH) to analyze the population dynamics of microcystin-degrading bacteria in Microcystis mucilage. We designed and applied an oligonucleotide probe targeted to the 16S rRNA sequence of strain Y2 of a microcystin-degrading bacterium (MCD-bacterium), which was isolated from Lake Suwa, Japan. In both the 1998 and 1999 tests, FISH clearly showed that MCD-bacteria existed in the mucilage and that, when a high concentration of cell-bound microcystin was detected, MCD-bacteria exceeded 10% of the sum of bacteria hybridized with group-specific probes. The concentration of MCD-bacteria was highest in summer 1998, when a toxic species, M. viridis, was dominant. There was a high correlation between the number of MCD-bacteria in the mucilage and the concentration of cell-bound microcystin in the lake. Our results suggest that MCD-bacteria responded to changes in the concentration of microcystin and degraded the microcystin when it was released from Microcystis cells. We also analyzed changes in the bacterial community structure associated with the Microcystis colonies by using domain- and group-specific oligonucleotide probes. Changes in the concentrations of the Cytophaga/Flavobacterium group and delta-Proteobacteria, which can degrade macromolecules derived from Microcystis cells, were synchronized with changes in the concentration of Microcystis. The results not only suggest the significant role of MCD-bacteria in detoxification, but also demonstrate a possible sequence of degradation from Microcystis cells to microcystin maintained in the cell, which is then carried out by bacterial consortia in the mucilage.

Adhesives↗
PubMed2006

Analysis of the composition of bacterial communities in oil reservoirs from a southern offshore Brazilian basin.

The aim of this study was to characterize and compare the bacterial community structure of two distinct oil samples from a petroleum field in Brazil by using both molecular, based on the construction of 16S rRNA gene libraries, and cultivation methods. Statistical comparisons of libraries based on Amplified Ribosomal DNA Restriction Analysis (ARDRA) data revealed no significant differences between the communities recovered in the non-biodegraded (NBD) and highly biodegraded oils (HBD). BlastN analysis of the 16S rRNA gene sequences representative of distinct ribotypes from both oils showed the presence of nine different bacterial genera in these samples, encompassing members of the genera Arcobacter, Halanaerobium, Marinobacter, Propionibacterium, Streptomyces, Leuconostoc, Acinetobacter, Bacillus and Streptococcus. Enrichments obtained using oil as inoculum and sole carbon source yielded bacterial isolates showing high 16S rRNA gene sequence similarity with Achromobacter xylosoxidans, Bacillus subtilis, Brevibacillus sp., Dietzia sp. and Methylobacterium sp. Comparison between the data obtained using cultivation-independent and enrichment cultures suggests that different selection of community members may occur when using distinct approaches. All the organisms found, except for Leuconostoc sp. and Streptococus sp., have been previously reported in the literature as hydrocarbon degraders and/or associated to oil field environments.

Bacteria↗
PubMed1996

Novel polysaccharide capsular serotypes in Porphyromonas gingivalis.

Recently van Winkelhoff et al. (1) described 3 novel serotypes in virulent Porphyromonas gingivalis strains, which were based on different polysaccharide antigens. These antigens probably represent capsular structures and have been designated K1, K2 and K3. In the present study we report on 3 novel capsular serotypes, which are represented by P. gingivalis strains ATCC 49417, HG 1690 and HG 1691. The strains, isolated from patients with periodontitis, showed obvious encapsulation in wet India ink preparations. Thermostable antigens could be detected in the supernatant fractions of autoclaved cells. These antigens appeared to be negatively charged, sensitive to periodate degradation, and resistant to proteinase K treatment. On the basis of these characteristics we conclude that the antigens are probably extra-cellular polysaccharides representing a bacterial capsular structure. These K-antigens did not cross-react with K1, K2 or K3 immune-sera of P. gingivalis, with the exception of the K2 antiserum, which partially recognized K5- and K6-antigens. In contrast, K5 and K6 antisera did not react with the K2-antigen. After absorbtion of the K2 antiserum with cells of strains HG 1690 (K5) and HG 1691 (K6) cross-reactivity was no longer present. We propose these novel serotypes to be designated: K4 (ATCC 49417), K5 (HG 1960) and K6 (HG 1691).

Adult↗
PubMedDate not supplied

Structural and dynamic properties of bacterial type IV secretion systems (review).

The type IV secretion systems (T4SS) are widely distributed among the gram-negative and -positive bacteria. These systems mediate the transfer of DNA and protein substrates across the cell envelope to bacterial or eukaryotic cells generally through a process requiring direct cell-to-cell contact. Bacteria have evolved T4SS for survival during establishment of pathogenic or symbiotic relationships with eukaryotic hosts. The Agrobacterium tumefaciens VirB/D4 T4SS and related conjugation machines serve as models for detailed mechanistic studies aimed at elucidating the nature of translocation signals, machine assembly pathways and architectures, and the dynamics of substrate translocation. The A. tumefaciens VirB/D4 T4SS are polar-localized organelles composed of a secretion channel and an extracellular T pilus. These T4SS are assembled from 11 or more subunits. whose membrane topologies, intersubunit contacts and, in some cases, 3-dimensional structures are known. Recently, powerful in vivo assays have identified C-terminal translocation signals, defined for the first time the translocation route for a DNA substrate through a type IV secretion channel, and supplied evidence that ATP energy consumption contributes to a late stage of machine morphogenesis. Together, these recent findings describe the mechanics of type IV secretion in unprecedented detail.

Adenosine Triphosphate↗
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↗
PubMed2003

Application of denaturing gradient gel electrophoresis (DGGE) to the analysis of microbial communities of subgingival plaque.

OBJECTIVES: Denaturing gradient gel electrophoresis (DGGE) was applied to the microbiologic examination of subgingival plaque. MATERIALS AND METHODS: The PCR primers were designed from conserved nucleotide sequences on 16S ribosomal RNA gene (16SrDNA) with GC rich clamp at the 5'-end. Polymerase chain reaction (PCR) was performed using the primers and genomic DNAs of typical periodontal bacteria. The generated 16SrDNA fragments were separated by denaturing gel. RESULTS: Although the sizes of the amplified DNA fragments were almost the same among the species, 16SrDNAs of the periodontal bacteria were distinguished according to their specific sequences. The microflora of clinical plaque samples were profiled by the PCR-DGGE method, and the dominant 16SrDNA bands were cloned and sequenced. Simultaneously, Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis and Prevotella intermedia were detected by an ordinary PCR method. In the deep periodontal pockets, the bacterial community structures were complicated and P. gingivalis was the most dominant species, whereas the DGGE profiles were simple and Streptococcus or Neisseria species were dominant in the shallow pockets. The species-specific PCR method revealed the presence of A. actinomycetemcomitans, P. gingivalis and P. intermedia in the clinical samples. However, corresponding bands were not always observed in the DGGE profiles, indicating a lower sensitivity of the DGGE method. CONCLUSION: Although the DGGE method may have a lower sensitivity than the ordinary PCR methods, it could visualize the bacterial qualitative compositions and reveal the major species of the plaque. The DGGE analysis and following sequencing may have the potential to be a promising bacterial examination procedure in periodontal diseases.

5' Flanking Region↗