Showing papers in "Fems Microbiology Letters in 2000"
TL;DR: Results indicate that 6.4% of toxigenic isolates of C. difficile referred to the Anaerobe Reference Unit from UK hospitals have cdtA and cdtB genes.
Abstract: In addition to the two large clostridial cytotoxins (TcdA and TcdB) certain strains of Clostridium difficile produce an actin-specific ADP-ribosyltransferase, or binary toxin. PCR reactions were developed to detect genes encoding the enzymatic (cdtA) and binding (cdtB) components of the binary toxin and 170 representative strains were tested to assess the prevalence of the toxin. Positive PCR results (n=59) were confirmed by immunoblotting and ADP-ribosyltransferase assay. PCR ribotype and toxinotype (restriction fragment length polymorphism analysis of genes for TcdA and TcdB) correlated with possession of binary toxin genes. All strains with cdtA and cdtB belonged to toxin-variable toxinotypes and five toxin-producing groups of strains have been described according to the presence or absence of TcdA, TcdB and binary toxin. Result indicate that ca. 6.4% of toxigenic isolates of C. difficile referred to the Anaerobe Reference Unit from UK hospitals have cdtA and cdtB genes.
457 citations
TL;DR: PCR-DGGE of a portion of the 26S rRNA gene was shown to distinguish most yeast genera associated with the production of wine and represents an attractive alternative to traditional plating schemes for analysis of the microbial successions inherent in the fermentation of wine.
Abstract: We present a method to directly characterize the yeast diversity present in wine fermentations by employing denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR)-amplified 26S ribosomal RNA (rRNA) genes. PCR-DGGE of a portion of the 26S rRNA gene was shown to distinguish most yeast genera associated with the production of wine. With this method the microbial dynamics in several model wine fermentations were profiled. PCR-DGGE provided a qualitative assessment of the yeast diversity in these fermentations accurately identifying populations as low as 1000 cells ml−1. PCR-DGGE represents an attractive alternative to traditional plating schemes for analysis of the microbial successions inherent in the fermentation of wine.
439 citations
TL;DR: Among the four strains, NBRI2601 was the most efficient strain in terms of its capability to solubilize phosphorus in the presence of 10% salt, pH 12, or 45 degrees C.
Abstract: Phosphate solubilizing bacteria NBRI0603, NBRI2601, NBRI3246 and NBRI4003 were isolated from the rhizosphere of chickpea and alkaline soils. All four strains demonstrated diverse levels of phosphate solubilization activity under in vitro conditions in the presence of various carbon and nitrogen sources. Acid production may have contributed to phosphate solubilization, but was not the only reason for phosphate release into the medium. Among the four strains, NBRI2601 was the most efficient strain in terms of its capability to solubilize phosphorus in the presence of 10% salt, pH 12, or 45°C. The strains showed varied levels of phosphate solubilization when the effects of different sources of nitrogen were examined during growth. The presence of low levels of Ca2+ and EDTA in the medium enhanced phosphate solubilization.
383 citations
TL;DR: Evidence is emerging that alkali generation, particularly through ammonia production from arginine and urea, plays major roles in pH homeostasis in oral biofilms and may moderate initiation and progression of dental caries.
Abstract: pH is a key environmental factor affecting the physiology, ecology and pathogenicity of the oral biofilms colonizing the hard tissues of the human mouth. Much attention has been focused on the production of organic acids through the metabolism of carbohydrates by pathogenic oral bacteria. Now, evidence is emerging that alkali generation, particularly through ammonia production from arginine and urea, plays major roles in pH homeostasis in oral biofilms and may moderate initiation and progression of dental caries. This short review highlights recent progress on understanding molecular genetic and physiologic aspects of ammonia generation by prominent oral bacteria.
354 citations
TL;DR: Hydrogen, methane and carbon dioxide gases are continuously generated in the interior of the authors' planet and probably constitute sustainable sources of carbon and energy for deep intraterrestrial biosphere ecosystems.
Abstract: Intraterrestrial life has been found at depths of several thousand metres in deep sub-sea floor sediments and in the basement crust beneath the sediments. It has also been found at up to 2800-m depth in continental sedimentary rocks, 5300-m depth in igneous rock aquifers and in fluid inclusions in ancient salt deposits from salt mines. The biomass of these intraterrestrial organisms may be equal to the total weight of all marine and terrestrial plants. The intraterrestrial microbes generally seem to be active at very low but significant rates and several investigations indicate chemolithoautotrophs to form a chemosynthetic base. Hydrogen, methane and carbon dioxide gases are continuously generated in the interior of our planet and probably constitute sustainable sources of carbon and energy for deep intraterrestrial biosphere ecosystems. Several prospective research areas are foreseen to focus on the importance of microbial communities for metabolic processes such as anaerobic utilisation of hydrocarbons and anaerobic methane oxidation.
348 citations
TL;DR: The established two-step multiplex PCR assays were applied to the identification of 84 Lactobacillus strains isolated from human stool specimens and the PCR results were consistent with the results from the DNA-DNA hybridization assay.
Abstract: Rapid and reliable two-step multiplex polymerase chain reaction (PCR) assays were established to identify human intestinal lactobacilli; a multiplex PCR was used for grouping of lactobacilli with a mixture of group-specific primers followed by four multiplex PCR assays with four sorts of species-specific primer mixtures for identification at the species level. Primers used were designed from nucleotide sequences of the 16S–23S rRNA intergenic spacer region and its flanking 23S rRNA gene of members of the genus Lactobacillus which are commonly isolated from human stool specimens: Lactobacillus acidophilus, Lactobacillus crispatus, Lactobacillus delbrueckii (ssp. bulgaricus and ssp. lactis), Lactobacillus fermentum, Lactobacillus gasseri, Lactobacillus jensenii, Lactobacillus paracasei (ssp. paracasei and ssp. tolerans), Lactobacillus plantarum, Lactobacillus reuteri, Lactobacillus rhamnosus and Lactobacillus salivarius (ssp. salicinius and ssp. salivarius). The established two-step multiplex PCR assays were applied to the identification of 84 Lactobacillus strains isolated from human stool specimens and the PCR results were consistent with the results from the DNA–DNA hybridization assay. These results suggest that the multiplex PCR system established in this study is a simple, rapid and reliable method for the identification of common Lactobacillus isolates from human stool samples.
320 citations
TL;DR: Phylogenetic analysis, using the deduced amino acid sequences of the Gram-positive hyaluronidases, suggests a relatedness among some of the enzymes, and molecular advances may lead to a more thorough understanding of the role of hyalons in bacterial physiology and pathogenesis.
Abstract: Bacterial hyaluronidases, enzymes capable of breaking down hyaluronate, are produced by a number of pathogenic Gram-positive bacteria that initiate infections at the skin or mucosal surfaces. Since reports of the hyaluronidases first appeared, there have been numerous suggestions as to the role of the enzyme in the disease process. Unlike some of the other more well studied virulence factors, much of the information on the role of hyaluronidase is speculative, with little or no data to substantiate proposed roles. Over the last 5 years, a number of these enzymes from Gram-positive organisms have been cloned, and the nucleotide sequence determined. Phylogenetic analysis, using the deduced amino acid sequences of the Gram-positive hyaluronidases, suggests a relatedness among some of the enzymes. Molecular advances may lead to a more thorough understanding of the role of hyaluronidases in bacterial physiology and pathogenesis.
310 citations
TL;DR: The assay was useful to identify cultures after in vitro cultivation and to detect and identify A. butlzeri and A. cryaerophilus from poultry samples present in 24-h old enrichment in Arcobacter broth with cefoperazone, amphotericin and teicoplanin (CAT)-supplement.
Abstract: A multiplex PCR assay with five primers targeting the 16S and 23S rRNA genes was developed for the simultaneous detection and identification of Arcobacter butzleri, Arcobacter cryaerophilus and Arcobacter skirrowii. The selected primers amplify a 257-bp fragment from A. cryaerophilus, a 401-bp fragment from A. butzleri and a 641-bp fragment from A. skirrowii. No PCR product was generated for closely related bacteria including Campylobacter and Helicobacter species. The assay was useful to identify cultures after in vitro cultivation and to detect and identify A. butlzeri and A. cryaerophilus from poultry samples present in 24-h old enrichment in Arcobacter broth with cefoperazone, amphotericin and teicoplanin (CAT)-supplement.
276 citations
TL;DR: Conventional cultivation and fluorescence in situ hybridization (FISH) using 16S rRNA-based probes were compared for the enumeration of human colonic bacteria and showed that plate counts of total anaerobes, bifidobacteria, lactobacilli and bacteroides were approximately ten-fold lower than the corresponding FISH counts.
Abstract: Conventional cultivation and fluorescence in situ hybridization (FISH) using 16S rRNA-based probes were compared for the enumeration of human colonic bacteria. Groups of common intestinal anaerobic bacteria were enumerated in slurries prepared from fecal samples of three healthy volunteers. To introduce variation between the samples, they were incubated for 48 h in batch culture (anaerobic) fermenters at 37 degrees C, and pure cultures of Bifidobacterium infantis, Clostridium perfringens, or Lactobacillus acidophilus were added. Samples were taken from the fermenters at different times. Total anaerobes, bifidobacteria, bacteroides, clostridia, and lactobacilli were enumerated by both plating and FISH. The results showed that plate counts of total anaerobes, bifidobacteria, lactobacilli and bacteroides were approximately ten-fold lower than the corresponding FISH counts. Numbers of clostridia were higher using the plating method, probably because the clostridia probe used in FISH analyses was designed to only detect part of the genus Clostridium. The introduced variation in the methods could be detected by both methods and was comparable.
228 citations
TL;DR: The fungal taxol had strong cytotoxic activity towards KB and P388 cancer cells in vitro, tested by the MTT assay, and enhanced microtubule stability and bundling in culture cells and induced tubulin polymerization in vitro similar to the authentic taxol.
Abstract: The diterpenoid taxol is an important anticancer agent used widely in the clinic. The purpose of this work was to identify a taxol-producing endophytic fungus (strain TF5) isolated from Taxus mairei and study its anticancer activities. Strain TF5 was identified as a Tubercularia sp. according to the morphology of the fungal culture, the mechanism of spore production and the characteristics of the spores. Strain TF5 produced taxol, when grown in potato dextrose liquid medium and analyzed by thin layer chromatography, high performance liquid chromatography, ultraviolet and mass spectrometry. The fungal taxol, which was isolated from the organic extract of the TF5 culture, had strong cytotoxic activity towards KB and P388 cancer cells in vitro, tested by the MTT assay. Observed with immunofluorescence and electron microscopy, the fungal taxol enhanced microtubule stability and bundling in culture cells and induced tubulin polymerization in vitro similar to the authentic taxol.
215 citations
TL;DR: A survey of extended-spectrum beta-lactamases among clinical isolates recovered from 196 separate medical institutions during the period January 1997 to January 1998 detected 15 E. coli and 34 K. pneumoniae isolates producing ESBLs, the first report characterizing TEM- and SHV-derived ESBLS in Japan.
Abstract: We conducted a survey of extended-spectrum β-lactamases (ESBLs) among 16 805 Escherichia coli and 9794 Klebsiella pneumoniae clinical isolates recovered from 196 separate medical institutions during the period January 1997 to January 1998. Using the criteria for minimal inhibitory concentrations (MICs) of oxyimino-cephalosporins of ≥8 μg ml−1 and confirmation by double-disk test, we detected 15 E. coli and 34 K. pneumoniae isolates producing ESBLs. Genotypes of ESBLs determined by PCR with type-specific primers included one TEM-derived and 24 SHV-derived ESBLs, in addition to 24 Toho-1-type ESBLs, one of the major types of ESBLs reported in Japan. Nucleotide sequence analysis of SHV-specific PCR products revealed that SHV-12 was the dominant type of SHV-derived ESBL. In addition, we also identified TEM-26 and SHV-2. This is the first report characterizing TEM- and SHV-derived ESBLs in Japan.
TL;DR: This review describes the metabolic alterations and adaptations of yeast cells in response to osmotic stress and hypothesised that the two pathways function as glycolytic safety valves during adaptation to stress.
Abstract: This review describes the metabolic alterations and adaptations of yeast cells in response to osmotic stress. The basic theme of the cellular response is known to be exclusion of the extracellular stress agent salt and intracellular accumulation of the compatible solute glycerol. Molecular details of these basic processes are currently rather well known. However, analysis of expression changes during adaptation to salt has revealed a number of metabolic surprises. These include the induced expression of genes involved in glycerol dissimilation as well as trehalose turnover. The physiological rationale for these responses to osmotic stress is discussed. A model is presented in which it is hypothesised that the two pathways function as glycolytic safety valves during adaptation to stress.
TL;DR: Osmoregulated periplasmic glucans appear to be important intrinsic components of the Gram-negative bacterial envelope, which can be essential in extreme conditions found in nature, and especially when bacteria must interact with an eukaryotic host.
Abstract: Large amounts of osmoregulated periplasmic glucans (OPGs) are found in the periplasmic space of Proteobacteria. Four families of OPGs are described on the basis of structural features of the polyglucose backbone. Depending on the species considered, OPGs can be modified to various extent by a variety of substituents. Genes governing the backbone synthesis are identified in a limited number of species. They belong to three unrelated families. OPG synthesis is subject to osmoregulation and feedback control. Osmoregulation can occur at the level of gene expression and/or at the level of enzyme activity. Mutants defective in OPG synthesis have a highly pleiotropic phenotype, indicative of an overall alteration of their envelope properties. Mutants of this kind were obtained as attenuated or avirulent derivatives of plant or animals pathogen. Thus, OPGs appear to be important intrinsic components of the Gram-negative bacterial envelope, which can be essential in extreme conditions found in nature, and especially when bacteria must interact with an eukaryotic host.
TL;DR: The total structure of a tripeptide siderophore synthesized by the non-ribosomal peptide synthetase within the cluster has been deduced from the translated sequence of its encoding gene, representing a novel method for the structural assignment of natural products from genome sequence data.
Abstract: A gene cluster for the non-ribosomal synthesis of a peptide of unknown structure has been identified in the partial genome sequence of Streptomyces coelicolor. Using molecular and computational analyses, the total structure of a tripeptide siderophore synthesized by the non-ribosomal peptide synthetase within the cluster has been deduced from the translated sequence of its encoding gene. This represents a novel method for the structural assignment of natural products from genome sequence data.
TL;DR: Cloning and expression of the cassette region demonstrated that dfrA17 conferred high level resistance to trimethoprim but aadA5 conferred resistance to spectinomycin but not to streptomycin.
Abstract: Escherichia coli INS33 was isolated from the urinary tract of an infected patient. It was resistant to ampicillin, chloramphenicol, spectinomycin, streptomycin, sulfafurazole, tetracycline and trimethoprim. PCR screening revealed the presence of a class 1 integron that harboured two new gene cassettes, designated dfrA17 and aadA5. The new dfrA17 cassette was 91% identical to the known dfrA7 cassette. The aadA5 cassette was 95% identical over the first 830 bp to aadA4, but lacked the IS26 element found at the 3′ end of this truncated cassette. Cloning and expression of the cassette region demonstrated that dfrA17 conferred high level resistance to trimethoprim but aadA5 conferred resistance to spectinomycin but not to streptomycin.
TL;DR: The results suggest that this anti-adhesive cell surface protein of Lactobacillus could protect against uropathogens by preventing their adhesion.
Abstract: Lactobacilli have been shown to be important in the maintenance of the healthy urogenital flora. One strain, Lactobacillus fermentum RC-14, releases surface-active components which can inhibit adhesion of uropathogenic bacteria. Using a quantitative method for determining inhibition of adhesion, a protein with high anti-adhesive properties against Enterococcus faecalis 1131 was purified. The N-terminal sequence of the 29-kDa protein was identical to that of a collagen-binding protein from Lactobacillus reuteri NCIB 11951, and exhibited close homology with a basic surface protein from L. fermentum BR11. The results suggest that this anti-adhesive cell surface protein of Lactobacillus could protect against uropathogens by preventing their adhesion.
TL;DR: Extracellular amylase production by the moderate halophile Halomonas meridiana was optimized and the enzyme was characterized biochemically, indicating an alpha-amylase activity.
Abstract: Extracellular amylase production by the moderate halophile Halomonas meridiana was optimized and the enzyme was characterized biochemically. The highest amylase production was achieved by growing H. meridiana cultures in media with 5% salts and starch, in the absence of glucose until the end of the exponential phase. The amylase exhibited maximal activity at pH 7.0, being relatively stable in alkaline conditions. Optimal temperature and salinity for activity were 37°C and 10% NaCl, respectively. Moreover, activity at salinity as high as 30% salts was detected. Maltose and maltotriose were the main end products of starch hydrolysis, indicating an α-amylase activity.
TL;DR: Several xylanase-producing cultures are isolated and characterised, one of which (an alkalophilic Bacillus SSP-34) produced more than 100 IU ml(-1) of xylan enzyme activity, which makes them less suitable for pulp and paper industries.
Abstract: Xylanases are used mainly in the pulp and paper industries for the pretreatment of Kraft pulp prior to bleaching to minimize use of chlorine, the conventional bleaching agent. This application has great potential as an environmentally safe method. Hydrolysis by xylanases of relocated and reprecipitated xylan on the surface of cellulose fibres formed during Kraft cooking facilitates the removal of lignin by increasing permeability to oxidising agents. Most of the xylanases reported in the literature contained significant cellulolytic activity, which make them less suitable for pulp and paper industries. The need for large quantities of xylanases which would be stable at higher temperatures and pH values and free of cellulase activity has necessitated a search for novel enzymes. We have isolated and characterised several xylanase-producing cultures, one of which (an alkalophilic Bacillus SSP-34) produced more than 100 IU ml−1 of xylanase activity. The SSP-34 xylanases have optimum activity at 50°C in a pH range 6–8, with only small amounts of cellulolytic activity (CMCase (0.4 IU ml−1, pH 7), FPase (0.2 IU ml−1, pH 7) and no activity at pH 9).
TL;DR: The Giardia genome project database provides an online resource forGiardia lamblia (WB strain, clone C6) genome sequence information, which includes edited single-pass reads, the results of BLASTX searches, and details of progress towards sequencing the entire 12 million-bp Giardian genome.
Abstract: The Giardia genome project database provides an online resource for Giardia lamblia (WB strain, clone C6) genome sequence information. The database includes edited single-pass reads, the results of BLASTX searches, and details of progress towards sequencing the entire 12 million-bp Giardia genome. Pre-sorted BLASTX results can be retrieved based on keyword searches and BLAST searches of the high throughput Giardia data can be initiated from the web site or through NCBI. Descriptions of the genomic DNA libraries, project protocols and summary statistics are also available. Although the Giardia genome project is ongoing, new sequences are made available on a bi-monthly basis to ensure that researchers have access to information that may assist them in the search for genes and their biological function. The current URL of the Giardia genome project database is www.mbl.edu/Giardia.
TL;DR: In vitro inoculation of grapevine plantlets induced a significant plant growth promotion which made them more hardy and vigorous when compared to non-inoculated plantlets, and this ability increased upon transplanting.
Abstract: The potential of a plant growth-promoting rhizobacterium, Pseudomonas sp. (strain PsJN), to stimulate the growth and enhancement of the resistance of grapevine (Vitis vinifera L.) transplants to gray mould caused by Botrytis cinerea has been investigated. In vitro inoculation of grapevine plantlets induced a significant plant growth promotion which made them more hardy and vigorous when compared to non-inoculated plantlets. This ability increased upon transplanting. When grown together with B. cinerea, the causal agent of gray mould, significant differences of aggressiveness were observed between the inoculated and non-inoculated plants. The presence of bacteria was accompanied by an induction of plant resistance to the pathogen. The beneficial effect from this plant–microbe association is being postulated.
TL;DR: Electron microscopy of gastric biopsies from infected individuals revealed blebbing of the H. pylori outer membrane, similar to the process of outer membrane vesicle shedding which occurs when the bacterium is grown in broth, which supports the hypothesis that these vesicles represent a vehicle for the delivery of damaging bacterial products to the gastric mucosa.
Abstract: Helicobacter pylori infection in humans is associated with diverse of clinical outcomes which are partly attributed to bacterial strain differences. Secreted bacterial products are thought to be involved in the pathogenesis caused by this non-invasive bacterium. Electron microscopy of gastric biopsies from infected individuals revealed blebbing of the H. pylori outer membrane, similar to the process of outer membrane vesicle shedding which occurs when the bacterium is grown in broth. Porins, a class of proinflammatory proteins, were observed in the outer membrane vesicles. The VacA cytotoxin, which is produced by 50–60% of H. pylori strains and associated with increased pathogenesis of infection, was also found to be vesicle-associated and biologically active. This supports the hypothesis that these vesicles represent a vehicle for the delivery of damaging bacterial products to the gastric mucosa.
SIDI1
TL;DR: The data showed that the concentration of nisin required for effective control of food-borne pathogenic bacteria could be considerably lowered by the use of thymol in combination, which could lead to a less favourable condition for the occurrence ofnisin-resistant bacterial sub-populations.
Abstract: Nisin Z and thymol were tested, alone and in combination, for antibacterial activity against Listeria monocytogenes ATCC 7644 and Bacillus subtilis ATCC 33712. The antibacterial effect of nisin Z, produced by Lactococcus lactis KE3 isolated from the traditional Moroccan fermented milk, was greatly potentiated by sub-inhibitory concentrations of thymol in both bacterial strains. Our data showed that the concentration of nisin required for effective control of food-borne pathogenic bacteria could be considerably lowered by the use of thymol in combination. The use of low concentrations of nisin could lead to a less favourable condition for the occurrence of nisin-resistant bacterial sub-populations.
TL;DR: Low-molecular-mass beta-(2,6)-linked fructose-oligosaccharides were examined as a new carbohydrate source for growth of bifidobacteria and showed the best growth, produced the highest amounts of organic acids and metabolized both short- and long-chain beta-FOS.
Abstract: Low-molecular-mass beta-(2,6)-linked fructose-oligosaccharides (beta-(2,6)-FOS) were examined as a new carbohydrate source for growth of bifidobacteria. beta-(2,6)-FOS were prepared from microbial high-molecular-mass levan by acid hydrolysis and refined by cation-exchange chromatography. (13)C-NMR spectroscopy confirmed the presence of predominantly beta-(2,6)-fructosyl linkages in the oligosaccharides. More than 80% beta-(2,6)-FOS was recovered after in vitro incubation with amylolytic and proteolytic enzymes, implying resistance to degradation in the upper intestinal tract. Bifidobacterium adolescentis, B. longum, B. breve, and B. pseudocatenulatum were studied in vitro for their ability to metabolize beta-(2,6)-FOS. Growth, decrease in pH, formation of short- chain fatty acids (lactate, acetate, formate) and degradation of beta-(2,6)-FOS were markedly different among species. B. adolescentis showed the best growth, produced the highest amounts of organic acids and metabolized both short- and long-chain beta-(2, 6)-FOS.
TL;DR: High performance liquid chromatography analysis of culture supernatants indicated that Remazol Black B was degraded by the fungus, however, complete mineralisation did not occur as a colourless organic breakdown product accumulated.
Abstract: Phlebia tremellosa decolourised eight synthetic textile dyes (200 mg l−1) by greater than 96% within 14 days under stationary incubation conditions. High performance liquid chromatography analysis of culture supernatants indicated that Remazol Black B was degraded by the fungus, however, complete mineralisation did not occur as a colourless organic breakdown product accumulated. Laccase activity was detectable in culture supernatants after 5 days when the fungus was grown in the presence of an artificial textile effluent, with activity reaching a maximum of 15 U l−1 on day 14.
TL;DR: The results suggest that IbpA and IbpB may be involved in the resistances to heat and oxidative stress.
Abstract: To investigate the function of Escherichia coli small heat shock proteins, IbpA and IbpB, we constructed ibpA-, ibpB- and ibpAB-overexpressing strains and also an ibpAB-disrupted strain. The ibpA-, ibpB- and ibpAB-overexpressing strains were found to be resistant not only to heat but also to superoxide stress. However, the ibpAB-disrupted strain was not more sensitive to these stresses than the wild-type strain. The heat sensitivity of a rpoH amber mutant was partially suppressed by the overexpression of plac::ibpAB. These results suggest that IbpA and IbpB may be involved in the resistances to heat and oxidative stress.
TL;DR: In this paper, the start sites for 13 new genes were determined and a total of 23 promoter regions upstream of the Bacteroides fragilis start sites were aligned and similarities were noted.
Abstract: There is little known about the sequences that mediate the initiation of transcription in Bacteroides fragilis, thus transcriptional start sites for 13 new genes were determined and a total of 23 promoter regions upstream of the start sites were aligned and similarities were noted. A region at about −7 contained a consensus sequence of TAnnTTTG and upstream in the region centered at about −33, another TTTG motif was found in the majority of promoters examined. Canonical, Escherichia coli, −10 and −35 consensus sequences were not readily apparent. Mutations within the −7 motif indicated the TTTG residues were essential since changes in this sequence reduced the promoter activity to that of a no promoter control in a chloramphenicol acetyl transferase transcriptional fusion model system. Additional fusion studies indicated that the −33 region was also necessary for full activity.
TL;DR: The success of HEGs in colonizing diverse genetic niches results from the flexibility of the encoded endonucleases in adopting new specificities, and the proteins have evolved activities that benefit their host organisms.
Abstract: Persistence of a mobile DNA element in a population reflects a balance between the ability of the host to eliminate the element and the ability of the element to survive and to disseminate to other individuals. In each of the three biological kingdoms, several families of a mobile DNA element have been identified which encode a single protein that acts on nucleic acids. Collectively termed homing endonuclease genes (HEGs), these elements employ varied strategies to ensure their survival. Some members of the HEG families have a minimal impact on host fitness because they associate with genes having self-splicing introns or inteins that remove the HEGs at the RNA or protein level. The HEG and the intron/intein gene spread throughout the population by a gene conversion process initiated by the HEG-encoded endonuclease called ‘homing’ in which the HEG and intron/intein genes are copied to cognate alleles that lack them. The endonuclease activity also contributes to a high frequency of lateral transmission of HEGs between species as has been documented in plants and other systems. Other HEGs have positive selection value because the proteins have evolved activities that benefit their host organisms. The success of HEGs in colonizing diverse genetic niches results from the flexibility of the encoded endonucleases in adopting new specificities.
TL;DR: The spread of the HPI among various members of the family Enterobacteriaceae is demonstrated, including Klebsiella of various species, as in Yersinia sp.
Abstract: A pathogenicity island termed high-pathogenicity island (HPI) is present in pathogenic Yersinia. This 35 to 45 kb island carries genes involved in synthesis, regulation and transport of the siderophore yersiniabactin. Recently, the HPI was also detected in various strains of Escherichia coli. In this study, the distribution of the HPI in the family Enterobacteriaceae was investigated. Among the 67 isolates pertaining to 18 genera and 52 species tested, nine (13.4%) harbored the island. These isolates were three E. coli, one Citrobacter diversus and five Klebsiella of various species (Klebsiella pneumoniae, Klebsiella rhinoscleromatis, Klebsiella ozaenae, Klebsiella planticola, and Klebsiella oxytoca). As in Yersinia sp., all nine isolates synthesized the HPI-encoded iron-repressible proteins HMWP1 and HMWP2. In the K. oxytoca strain, the right-end portion of the HPI was deleted, whereas the entire core region of the island was present in the eight other enterobacteria strains analyzed. In most of these isolates, the HPI was bordered by an asn tRNA locus, as in Yersinia sp. This report thus demonstrates the spread of the HPI among various members of the family Enterobacteriaceae.
TL;DR: It is suggested that Sphingomonas sp.
Abstract: Sphingomonas sp. strain P2, which is capable of utilizing phenanthrene as a sole carbon and energy source, was isolated from petroleum-contaminated soil in Thailand. Gas chromatography-mass spectrometry and 1H and 13C nuclear magnetic resonance analyses revealed two novel metabolites from the phenanthrene degradation pathway. One was identified as 5,6-benzocoumarin, which was derived by dioxygenation at the 1- and 2-positions of phenanthrene, and the other was determined to be 1,5-dihydroxy-2-naphthoic acid. Other metabolites from phenanthrene degradation were identified as 7,8-benzocoumarin, 1-hydroxy-2-naphthoic acid and coumarin. From these results, it is suggested that strain P2 can degrade phenanthrene via dioxygenation at both 1,2- and 3,4-positions followed by meta-cleavage.
TL;DR: The membrane condensing hopanoids possibly may alleviate stress in aerial mycelium by diminishing water permeability across the membrane.
Abstract: Streptomyces coelicolor A3(2) contains a cluster of putative isoprenoid and hopanoid biosynthetic genes. The strain does not produce the pentacyclic hopanoids in liquid culture but produces them on solid medium when sporulating. Mutants defective in the formation of aerial mycelium and spores (bld), with the exception of bldB, do not synthesize hopanoids, whereas mutants, which form aerial mycelium but no spores (whi), do. The membrane condensing hopanoids possibly may alleviate stress in aerial mycelium by diminishing water permeability across the membrane.