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PubMed2003

Structure-based design of agents targeting the bacterial ribosome.

Rational structure-based drug design has been applied to the antibiotic thiostrepton, in an attempt to overcome some of its' limitations. The identification of a proposed binding fragment allowed construction of a number of key fragments, which were derivatised to generate a library of potential antibiotics. These were then evaluated to determine their ability to bind to the L11 binding domain of the prokaryotic ribosome and inhibit bacterial protein translation.

Anti-Bacterial Agents↗
PubMed1997

Bacterial diversity in Adirondack mountain lakes as revealed by 16S rRNA gene sequences.

Bacterial communities of seven lakes in the Adirondack Mountains of New York State were characterized by amplification and sequencing of 16S ribosomal DNA. Analysis of over 100 partial sequences revealed a diverse collection of lineages, largely of the class Proteobacteria (19% alpha subdivision, 31% beta subdivision, and 9% gamma subdivision), the phylum Cytophaga-Flavobacteria-Bacteroides (15%), and the order Actinomycetales (18%). Additionally, a number of the sequences were similar to those of the order Verrucomicrobiales. However, few of the sequence types are closely related to those of characterized species. The relative contributions of the groups of sequences differed among the lakes, suggesting that bacterial population structure varies and that it may be possible to relate aquatic bacterial community structure to water chemistry.

Bacteria↗
PubMed2002

Modelling of activated sludge processes with structured biomass.

Bacterial communities when subjected to feast-famine conditions as occurring in many wastewater treatment systems store substrates as reserve polymers. Including storage polymers in a description of microbial growth processes makes important the choice of kinetic relations. Presently there is no sound description for the diversion of substrate towards biomass growth or substrate storage. Based on observations with pure cultures and mixed cultures growing under dynamic conditions a model is proposed to describe such behaviour. This description is based on the observation that bacteria in order to grow fast have to induce a high level of RNA and proteins in order to allow fast growth. We assume that this protein synthesising system is only induced in the presence of external substrates. Based on this assumption a model structure is proposed and evaluated. It seems that this model can predict the turnover of PHA in the cells correctly, and describes well the overall behaviour mixed culture SBR systems. However especially the growth rate in the famine phase seems to be overestimated. The model defined here is a contribution to a further development of mechanistically based models for activated sludge processes.

Biomass↗
PubMed2006

Structure and activity of bacterial community inhabiting rice roots and the rhizosphere.

Root-derived carbon provides a major source for microbial production and emission of CH4 from rice field soils. Therefore, we characterized the structure and activity of the bacterial community inhabiting rice roots and the rhizosphere. In the first experiment, DNA retrieved from rice roots was analysed for bacterial 16S rRNA genes using cloning, sequencing and in situ hybridization. In the second experiment, rice plants were pulse-labelled with 13CO2 (99% of atom 13C) for 7 days, and the bacterial RNA was isolated from rhizosphere soil and subjected to density gradient centrifugation. RNA samples from density fractions were analysed by terminal restriction fragment length polymorphism fingerprinting, cloning and sequencing. The experiments showed that the dominant bacteria inhabiting rice roots and the rhizosphere particularly belonged to the Alphaproteobacteria, Betaproteobacteria and Firmicutes. The RNA stable isotope probing revealed that the bacteria actively assimilating C derived from the pulse-labelled rice plants were Azospirillum spp. (Alphaproteobacteria) and members of Burkholderiaceae (Betaproteobacteria). Both anaerobic (e.g. Clostridia) and aerobic (e.g. Comamonas) degraders were present at high abundance, indicating that root environments and degradation processes were highly heterogeneous. The relative importance of iron and sulfate reducers suggested that cycling of iron and sulfur is active in the rhizosphere.

Bacteria, Aerobic↗
PubMed1995

Structure and partitioning of bacterial DNA: determined by a balance of compaction and expansion forces?

The mechanisms that determine chromosome structure and chromosome partitioning in bacteria are largely unknown. Here we discuss two hypotheses: (i) the structure of the Escherichia coli nucleoid is determined by DNA binding proteins and DNA supercoiling, representing a compaction force on the one hand, and by the coupled transcription/translation/translocation of plasma membrane and cell wall proteins, representing an expansion force on the other hand; (ii) the two forces are important for the partitioning process of chromosomes.

Chromosomes, Bacterial↗
PubMed1985

Detection of fine spiral structures (spirosomes) by weak sonication in some bacterial strains.

Fine spiral structures (spirosomes) were observed in cell suspensions of five species of bacteria just after weak sonication. The structure is morphologically indistinguishable from the spirosome reported for Lactobacillus species. The molecular weight of the protein of the spirosomes from nine strains was about 94,000 to 95,000 as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The difference in the molecular weight among these spirosomes was not very great, but there were slight differences among the strains from which the spirosomes were derived.

Bacteria↗
PubMed2001

Bacterial polypeptide release factor RF2 is structurally distinct from eukaryotic eRF1.

Bacterial release factor RF2 promotes termination of protein synthesis, specifically recognizing stop codons UAA or UGA. The crystal structure of Escherichia coli RF2 has been determined to a resolution of 1.8 A. RF2 is structurally distinct from its eukaryotic counterpart eRF1. The tripeptide SPF motif, thought to confer RF2 stop codon specificity, and the universally conserved GGQ motif, proposed to be involved with the peptidyl transferase center, are exposed in loops only 23 A apart, and the structure suggests that stop signal recognition is more complex than generally believed.

Amino Acid Sequence↗
PubMed1992

A naturally occurring tyrosine to histidine replacement at residue 33 of human thymidylate synthase confers resistance to 5-fluoro-2'-deoxyuridine in mammalian and bacterial cells.

Structural changes in the macromolecular targets of pharmacological agents can result in alterations in the efficacy of these agents. In previous studies, we identified a variant structural form of thymidylate synthase (TS) that is associated with relative resistance to 5-fluoro-2'-deoxyuridine, in a human colonic tumor cell line. We now report on the use of DNA transfer techniques to examine directly the effects of each TS form on drug response. TS cDNA constructs, corresponding to the normal or variant TS mRNA, were expressed in Chinese hamster lung cells or in Escherichia coli, and response to 5-fluoro-2'-deoxyuridine was determined. We observed that expression of the variant TS, which differs from the normal form by a tyrosine to histidine substitution at residue 33, confers a 4-fold level of drug resistance in the mammalian cells, as well as in bacteria. The possible role of Tyr-33 in 5-fluoropyrimidine-mediated inhibition of TS is discussed.

Amino Acid Sequence↗
PubMed2004

Bacterial population dynamics and community structure in a pharmaceutical manufacturing water supply system determined by real-time PCR and PCR-denaturing gradient gel electrophoresis.

AIMS: To control bacteria in the pharmaceutical water supply system. METHODS AND RESULTS: Bacteria were enumerated by conventional culture method and fluorescent vital staining. Activated carbon treatment and storage in a tank provided favourable environments for bacterial growth. The bacterial population of the water in both the post-activated carbon treatment and the tank was analysed by denaturing gradient gel electrophoresis (DGGE) with PCR-amplified 16S rDNA fragments including V6, -7, and -8 regions. The bacterial community structure in activated carbon treated water was stable throughout the year. Several kinds of bacteria such as genus Aquaspirillum and Methylobacterium were found in the water after activated carbon treatment. The bacterial community structure was changed and other bacteria such as mycobacteria were detected after storage. Mycobacteria were quantified in water samples using real-time PCR targeting the 16S rDNA gene. Mycobacteria were also detected in tap water and their number was increased 10(3)-10(4)-fold higher after storage. CONCLUSION: These data suggest the importance of culture-independent methods for quality control of water used in pharmaceutical manufacturing. SIGNIFICANCE AND IMPACT OF THE STUDY: Critical steps and specified bacteria that should be controlled in the water supply system were recognized by culture-independent methods. These data will enable effective control of water used in the pharmaceutical industry.

Bacteria↗
PubMed2006

Composition and dynamics of bacterial communities of a drinking water supply system as assessed by RNA- and DNA-based 16S rRNA gene fingerprinting.

Bacterial community dynamics of a whole drinking water supply system (DWSS) were studied from source to tap. Raw water for this DWSS is provided by two reservoirs with different water characteristics in the Harz mountains of Northern Germany. Samples were taken after different steps of treatment of raw water (i.e., flocculation, sand filtration, and chlorination) and at different points along the supply system to the tap. RNA and DNA were extracted from the sampled water. The 16S rRNA or its genes were partially amplified by reverse transcription-PCR or PCR and analyzed by single-strand conformation polymorphism community fingerprints. The bacterial community structures of the raw water samples from the two reservoirs were very different, but no major changes of these structures occurred after flocculation and sand filtration. Chlorination of the processed raw water strongly affected bacterial community structure, as reflected by the RNA-based fingerprints. This effect was less pronounced for the DNA-based fingerprints. After chlorination, the bacterial community remained rather constant from the storage containers to the tap. Furthermore, the community structure of the tap water did not change substantially for several months. Community composition was assessed by sequencing of abundant bands and phylogenetic analysis of the sequences obtained. The taxonomic compositions of the bacterial communities from both reservoirs were very different at the species level due to their different limnologies. On the other hand, major taxonomic groups, well known to occur in freshwater, such as Alphaproteobacteria, Betaproteobacteria, and Bacteroidetes, were found in both reservoirs. Significant differences in the detection of the major groups were observed between DNA-based and RNA-based fingerprints irrespective of the reservoir. Chlorination of the drinking water seemed to promote growth of nitrifying bacteria. Detailed analysis of the community dynamics of the whole DWSS revealed a significant influence of both source waters on the overall composition of the drinking water microflora and demonstrated the relevance of the raw water microflora for the drinking water microflora provided to the end user.

Bacteria↗
PubMed2002

Structure and function of bacterial initiation factors.

Bacteria require three initiation factors, IF1, IF2 and IF3, to start protein synthesis. In the last few years the elucidation of both structural and mechanistic aspects pertaining to these proteins has made substantial progress. In this article we outline the translation initiation process in bacteria and review these recent developments giving a summary of the main features of the structure and function of the initiation factors.

Bacterial Proteins↗
PubMed1999

Changes in bacterial and eukaryotic community structure after mass lysis of filamentous cyanobacteria associated with viruses.

During an experiment in two laboratory-scale enclosures filled with lake water (130 liters each) we noticed the almost-complete lysis of the cyanobacterial population. Based on electron microscopic observations of viral particles inside cyanobacterial filaments and counts of virus-like particles, we concluded that a viral lysis of the filamentous cyanobacteria had taken place. Denaturing gradient gel electrophoresis (DGGE) of 16S ribosomal DNA fragments qualitatively monitored the removal of the cyanobacterial species from the community and the appearance of newly emerging bacterial species. The majority of these bacteria were related to the Cytophagales and actinomycetes, bacterial divisions known to contain species capable of degrading complex organic molecules. A few days after the cyanobacteria started to lyse, a rotifer species became dominant in the DGGE profile of the eukaryotic community. Since rotifers play an important role in the carbon transfer between the microbial loop and higher trophic levels, these observations confirm the role of viruses in channeling carbon through food webs. Multidimensional scaling analysis of the DGGE profiles showed large changes in the structures of both the bacterial and eukaryotic communities at the time of lysis. These changes were remarkably similar in the two enclosures, indicating that such community structure changes are not random but occur according to a fixed pattern. Our findings strongly support the idea that viruses can structure microbial communities.

Animals↗
PubMed1999

Bacterial chemoreceptors: recent progress in structure and function.

The behavior of a bacterial cell is determined by the interplay between transmembrane receptor molecules and a cytoplasmic kinase that is linked to the flagellar apparatus. In the absence of external stimulus, a balance exists between stresses in the periplasmic region of receptor molecules, and compensating cytoplasmic forces. A response, positive or negative, is due to a temporary disturbance in this balance, with corresponding alterations in kinase activity, and ultimately, of swimming behavior. Methylation acts to restore the balance by changing the properties of the receptor. Because methylation is slow, a response will continue for a period of time following stimulation. The mechanisms by which these processes occur are now being elucidated at the molecular level, and should soon make bacterial chemotaxis the first available picture of a complete sensory system.

Bacterial Proteins↗
PubMed2003

Structure of the O-polysaccharide from Proteus myxofaciens. Classification of the bacterium into a new Proteus-O-serogroup.

The O-polysaccharide (O-antigen) was obtained from the lipopolysaccharide of Proteus myxofaciens, a Proteus strain producing copious amounts of slime, which was isolated from the gypsy moth larvae. The structure of the polysaccharide was studied by chemical analysis and 1H and 13C NMR spectroscopy, including 2D COSY, TOCSY, ROESY and H-detected 1H,13C HMQC experiments. It was found that the polysaccharide contains an amide of glucuronic acid (GlcA) with an unusual alpha-linked amino acid, Nepsilon-[(R)-1-carboxyethyl]-l-lysine (2S,8R-alaninolysine, 2S,8R-AlaLys), and has a linear tetrasaccharide repeating unit of the following structure: This structure is unique among known bacterial polysaccharide structures. On the basis of these and serological data, it is proposed that P. myxofaciens be classified into a new Proteus serogroup, O60, of which this strain is the single representative. Structural and serological relatedness of P. myxofaciens to other AlaLys-containing O-antigens of Proteus and Providencia is discussed.

Amides↗
PubMed1994

Ranalexin. A novel antimicrobial peptide from bullfrog (Rana catesbeiana) skin, structurally related to the bacterial antibiotic, polymyxin.

Antimicrobial peptides comprise a diverse class of molecules used in host defense by plants, insects, and animals. In this study we have isolated a novel antimicrobial peptide from the skin of the bullfrog, Rana catesbeiana. This 20 amino acid peptide, which we have termed Ranalexin, has the amino acid sequence: NH2-Phe-Leu-Gly-Gly-Leu-Ile-Lys-Ile-Val-Pro-Ala-Met-Ile-Cys-Ala-Val-Thr- Lys-Lys - Cys-COOH, and it contains a single intramolecular disulfide bond which forms a heptapeptide ring within the molecule. Structurally, Ranalexin resembles the bacterial antibiotic, polymyxin, which contains a similar heptapeptide ring. We have also cloned the cDNA for Ranalexin from a metamorphic R. catesbeiana tadpole cDNA library. Based on the cDNA sequence, it appears that Ranalexin is initially synthesized as a propeptide with a putative signal sequence and an acidic amino acid-rich region at its amino-terminal end. Interestingly, the putative signal sequence of the Ranalexin cDNA is strikingly similar to the signal sequence of opioid peptide precursors isolated from the skin of the South American frogs Phyllomedusa sauvagei and Phyllomedusa bicolor. Northern blot analysis and in situ hybridization experiments demonstrated that Ranalexin mRNA is first expressed in R. catesbeiana skin at metamorphosis and continues to be expressed into adulthood.

Amino Acid Sequence↗
PubMed1988

Tertiary structure of Bacillus thermoproteolyticus [4Fe-4S] ferredoxin. Evolutionary implications for bacterial ferredoxins.

The structure of a low-potential [4Fe-4S] ferredoxin from Bacillus thermoproteolyticus has been solved using anomalous scattering data from iron atoms in the diffraction data of native crystals and refined partially to a crystallographic R-factor of 0.33, with 2.3 A (1 A = 0.1 nm) resolution data. The least-squares refinement based on the Bijvoet differences has determined that the four iron atoms in the cluster are an equal distance, approximately 2.8 A, apart. The NH ... S hydrogen bonds between polypeptide nitrogen atoms, and both cysteine and inorganic sulfur atoms, are present, as in ferrodoxin from Peptococcus aerogenes. The polypeptide chain of the B. thermoproteolyticus ferredoxin has a fold closely similar to that of 2[4Fe-4S] ferredoxin from P. aerogenes. The structural correspondence indicates strongly that both types of ferredoxin evolved from a common ancestor. The second cluster-binding region in P. aerogenes ferredoxin corresponds to the alpha-helix in B. thermoproteolyticus ferredoxin. The secondary-structure predictions strongly suggest that the alpha-helix is generally present in the monocluster-type ferredoxins. The conformational change to alpha-helix, insertions of a loop and a protrusion, as well as the absence of the second cluster in B. thermoproteolyticus ferredoxin, result in the lack of 2-fold symmetry present in P. aerogenes ferredoxin. So, the track of gene duplication is no longer detectable in the tertiary structure alone. The evolutionary events that may have occurred in the ferredoxins with the [4Fe-4S] cluster are discussed.

Amino Acid Sequence↗
PubMed2004

Potassium, sodium, calcium and glutamate-gated channels: pore architecture and ligand action.

In the last decade, the idea of common organization of certain ion channel families exhibiting diverse physiological and pharmacological properties has received strong experimental support. Transmembrane topologies and patterns of the pore-facing residues are conserved in P-loop channels that include high-selective cation channels and certain ligand-gated channels. X-ray structures of bacterial K+ channels, KcsA, MthK and KvAP, help to understand structure-function relationships of other P-loop channels. Data on binding sites and mechanisms of action of ligands of K+, Na+, Ca2+ and glutamate gated ion channels are considered in view of their possible structural similarity to the bacterial K+ channels. Emphasized are structural determinants of ligand-receptor interactions within the channels and mechanisms of state-dependent action of the ligands.

Amino Acid Sequence↗
PubMed2002

The bacterial ribosome, a promising focus for structure-based drug design.

Recent crystal structures of the bacterial ribosome have identified the complex molecular interactions involved in antibiotic-ribosome recognition. Insights into the binding of aminoglycosides, macrolides, tetracyclines and other antibiotics provide opportunities for computational, structure-based approaches to be used in the design of appropriate modifications to existing antibiotics as well as in the discovery of completely new drug classes.

Anti-Bacterial Agents↗