In vivo transposition of mariner-based elements in enteric bacteria and mycobacteria

mariner family transposons are widespread among eukaryotic organisms. These transposons are apparently horizontally transmitted among diverse eukaryotes and can also transpose in vitro in the absence of added cofactors. Here we show that transposons derived from the mariner element Himar1 can efficiently transpose in bacteria in vivo. We have developed simple transposition systems by using minitransposons, made up of short inverted repeats flanking antibiotic resistance markers. These elements can efficiently transpose after expression of transposase from an appropriate bacterial promoter. We found that transposition of mariner-based elements in Escherichia coli produces diverse insertion mutations in either a targeted plasmid or a chromosomal gene. With Himar1-derived transposons we were able to isolate phage-resistant mutants of both E. coli and Mycobacterium smegmatis. mariner-based transposons will provide valuable tools for mutagenesis and genetic manipulation of bacteria that currently lack well developed genetic systems.     

Structure of the Shigella dysenteriae haem transport locus and its phylogenetic distribution in enteric bacteria

The ability to transport and use haemin as an iron source is frequently observed in clinical isolates of Shigella spp. and pathogenic Escherichia coli. We found that many of these haem-utilizing E. coli strains contain a gene that hybridizes at high stringency to the S. dysenteriae type 1 haem receptor gene, shuA. These shuA-positive strains belong to multiple phylogenetic groups and include clinical isolates from enteric, urinary tract and systemic infections. The distribution of shuA in these strains suggests horizontal transfer of the haem transport locus. Some haem-utilizing pathogenic E. coli strains did not hybridize with shuA, so at least one other haem transport system is present in this group. We also characterized the chromosomal region containing shuA in S. dysenteriae. The shuA gene is present in a discrete locus, designated the haem transport locus, containing eight open reading frames. Several of the proteins encoded in this locus participate with ShuA in haem transport, as a Salmonella typhimurium strain containing the entire haem transport locus used haem much more efficiently than the same strain containing only shuA. The haem transport locus is not present in E. coli K-12 strains, but the sequences flanking the haem transport locus in S. dysenteriae matched those at the 78.7 minute region of E. coli K-12. The junctions and flanking sequences in the shuA-positive pathogenic E. coli strains tested were nearly identical to those in S. dysenteriae, indicating that, in these strains, the haem transport locus has an organization similar to that in S. dysenteriae, and it is located in the same relative position on the chromosome.     

Fimbrial expression in enteric bacteria: a critical step in intestinal pathogenesis

The ability of species of enteric bacteria to recognize and colonize unique niches along the intestine is mainly based on receptor distribution and interpretation of a combination of environmental signals leading to the expression of specific adherence factors. Such elaborate orchestration of events is critical during the initial steps of pathogenesis.     

Genetic characterization of the pdu operon: use of 1,2-propanediol in Salmonella typhimurium

Salmonella typhimurium is able to catabolize 1,2-propanediol for use as the sole carbon and energy source; the first enzyme of this pathway requires the cofactor adenosyl cobalamin (Ado-B12). Surprisingly, Salmonella can use propanediol as the sole carbon source only in the presence of oxygen but can synthesize Ado-B12 only anaerobically. To understand this situation, we have studied the pdu operon, which encodes proteins for propanediol degradation. A set of pdu mutants defective in aerobic degradation of propanediol (with exogenous vitamin B12) defines four distinct complementation groups. Mutations in two of these groups (pduC and pduD) eliminate propanediol dehydratase activity. Based on mutant phenotypes, a third complementation group (pduG) appears to encode a cobalamin adenosyl transferase activity. No function has been assigned to the pduJ complementation group. Propionaldehyde dehydrogenase activity is eliminated by mutations in any of the four identified complementation groups, suggesting that this activity may require a complex of proteins encoded by the operon. None of the mutations analyzed affects either of the first two genes of the operon (pduA and pduB), which were identified by DNA sequence analysis. Available data suggest that the pdu operon includes enough DNA for about 15 genes and that the four genetically identified genes are the only ones required for aerobic use of propanediol.     

Isolation and characterization of phenol-degrading denitrifying bacteria

Phenol is a man-made as well as a naturally occurring aromatic compound and an important intermediate in the biodegradation of natural and industrial aromatic compounds. Whereas many microorganisms that are capable of aerobic phenol degradation have been isolated, only a few phenol-degrading anaerobic organisms have been described to date. In this study, three novel nitrate-reducing microorganisms that are capable of using phenol as a sole source of carbon were isolated and characterized. Phenol-degrading denitrifying pure cultures were obtained by enrichment culture from anaerobic sediments obtained from three different geographic locations, the East River in New York, N.Y., a Florida orange grove, and a rain forest in Costa Rica. The three strains were shown to be different from each other based on physiologic and metabolic properties. Even though analysis of membrane fatty acids did not result in identification of the organisms, the fatty acid profiles were found to be similar to those of Azoarcus species. Sequence analysis of 16S ribosomal DNA also indicated that the phenol-degrading isolates were closely related to members of the genus Azoarcus. The results of this study add three new members to the genus Azoarcus, which previously comprised only nitrogen-fixing species associated with plant roots and denitrifying toluene degraders.     

Identification of novel intergenic repetitive units in a mycobacterial two-component system operon

Mycobacterial interspersed repetitive units (MIRUs), a novel class of repeated sequences, were identified within the intercistronic region of an operon coding for a mycobacterial two-component system, named senX3-regX3. Southern blot analysis and homology searches revealed the presence of several homologous sequences in intergenic regions dispersed throughout the genomes of Mycobacterium bovis BCG, Mycobacterium tuberculosis and Mycobacterium leprae. These could be grouped into three major families, containing elements of 77-101 bp, 46-53 bp and 58-101 bp. Based on the available mycobacterial sequences, the total number of MIRUs is estimated to be about 40-50 per genome. Similar to previously identified small repetitive sequences, the MIRUs of the two-component operon are transcribed on a polycistronic mRNA. Unlike previously identified small repetitive sequences, however, MIRUs do not contain dyad symmetries, comprise small open reading frames (ORFs) whose extremities overlap those of the contiguous ORFs and are oriented in the same translational direction as those of the adjacent genes. Analyses of the sequences at the insertion sites suggest that MIRUs disseminate by transposition into DTGA sites involved in translational coupling in polycistronic operons.     

Bacteriophages of enteric bacteria in drinking water, comparison of their distribution in two countries

The presence of bacteriophages infecting enteric bacteria was tested in more than 1500 drinking water samples in Israel and Spain. Bacteriophages tested were somatic coliphages, F-specific bacteriophages and Bacteroides fragilis bacteriophages. The three groups of bacteriophage were isolated in 100 ml water samples by the presence/absence test with similar frequencies, which ranged from 4.4% for somatic coliphages to 6.1% for bacteriophages infecting Bact. fragilis. In contrast, the frequency of isolation of bacteriophages was significantly higher than the frequency of isolation of faecal coliforms, which averaged only 1.9%. No significant differences were observed between the frequencies of isolation between the samples tested in Spain and those tested in Israel. The percentage of groundwater samples containing faecal coliforms and somatic coliphages was reduced significantly by chlorination, despite known deficiencies. However, there was no effect on the occurrence of F-specific bacteriophages and Bact. fragilis bacteriophages.     

An evaluation of lectin-mediated magnetic bead cell sorting for the targeted separation of enteric bacteria

Lectin-labelled magnetic beads were assessed and compared with antisera as an alternative approach for the targeted separation and isolation of enteric bacteria. Of the 16 lectins tested against a range of bacterial species, concanavalin A (conA) showed the greatest potential. Agglutination of bacterial cells in suspension using conA and methods for effective labelling of the magnetic beads with the lectin were optimized. ConA-labelled magnetic beads were compared with antibody-labelled beads for recovery of bacterial cells from pure or mixed laboratory cultures and from natural populations in river water. Recovered cell populations were free from environmental impurities and a high percentage of the culturable cells was extracted. Specific cell recovery was found to be variable, but the use of lectins offers some promise as an alternative cell discriminator.     

Assessment of a new four-hour diagnostic kit--RapID onE system for the identification of enteric bacteria

RapID onE System is a newly developed four-hour rapid diagnostic kit for the identification of enteric bacteria. To know the effectiveness of this system, we used 125 strains of oxidase-negative, gram-negative bacilli for this evaluation. Except for Acinetobacter calcoaceticus, all the bacilli belong to family Enterobacteriaceae. The bacterial strains of this assessment belong to 12 genera and 20 species. Among them, 84 strains were freshly isolated from clinical specimens and 41 strains were frozen (-70 degrees C) stock clinical isolates. The results show that 115 (92.0%) strains were correctly identifed to the species level. It yielded 92.9% and 90.2% of correct identification of fresh isolates and frozen stocks, respectively. In this paper, the reading criteria of RapID onE System would also be discussed.     

Phylogenetic characterization of bacteria in the subsurface microbial culture collection

The Subsurface Microbial Culture Collection (SMCC) was established by the U.S. Dept. of Energy (DOE) and contains nearly 10,000 strains of microorganisms (mostly bacteria) isolated from terrestrial subsurface environments. Selected groups of bacterial isolates from three sample sites situated above geochemically and hydrologically different subsurface environments have been characterized by phylogenetic analysis of 16S ribosomal RNA (rRNA) gene nucleotide sequences. Among these isolates were members of six major phylogenetic groups of bacteria: the high-G+C and low-G+C Gram-positive bacteria; the alpha-, beta-, and gamma-subdivisions of the Proteobacteria; and the Flexibacter/Cytophaga/Bacteroides group. A small number of the SMCC strains may be members of new bacterial genera, but most of them could be placed with reasonable confidence into more than 35 previously described genera. The majority of the Gram-positive isolates were species of Arthrobacter, Bacillus, or Streptococcus, whereas Acinetobacter, Comamonas, Pseudomonas, Sphingomonas, and Variovorax were among the most frequently encountered Gram-negative genera. A high proportion of the strains were placed in fewer than 10 genera, implying that there is substantial duplication within the SMCC at the genus level. When groups of isolates assigned to Acinetobacter, Arthrobacter, or Sphingomonas were analyzed in more detail, however, it was found that each group consisted of subgroups of strains that probably differed at the species level. Restriction endonuclease analysis (applied to the strains from one sample site) indicated that additional diversity was present at the strain level. Most of the SMCC isolates assigned to some genera (e.g., Acinetobacter) were very closely related to previously described species in those genera, but most of the isolates assigned to other genera (e.g., Arthrobacter and Sphingomonas) appeared (or were shown) to be new species, thereby indicating that a reasonable amount of novelty is present within the SMCC at the species level.     

Development and maintenance of the gut-associated lymphoid tissue (GALT): the roles of enteric bacteria and viruses

Hydrogen peroxide (H2O2) is considered to be a mediator of apoptotic cell death but the mechanism by which it induces apoptosis is unclear. Here, we show that cells undergoing apoptosis from exposure to H2O2 display a significant decrease in intracellular concentration of superoxide (O2-) which is associated with a reduction of the intracellular milieu, as measured by an increase in the GSH/GSSG ratio and a decrease in intracellular pH. The notion that a decrease in intracellular O2- concentration triggers apoptosis is supported by the observation that H2O2-mediated apoptosis could be retarded in cells in which the intracellular O2- concentration is maintained at or above the cellular baseline level by inhibition of the major O2- scavenger superoxide dismutase (Cu/Zn SOD). Taken together, our observations indicate that a decrease in the intracellular O2- concentration, reduction and acidification of the intracellular milieu constitute a signal for H2O2-mediated apoptosis, thereby inducing a reductive as opposed to an oxidative stress.     

Alterations in intestinal barrier function do not predispose to translocation of enteric bacteria in gastroenterologic patients

The potential of electrospray mass spectrometry (ESMS) for the sequencing of glycopeptides was evaluated using quadrupole time-of-flight (QTOF) technology in the MS/MS mode. The location of O-glycosylation sites was possible in the positive ion (+) mode by detection of prominent y- and b-fragment ions from the underivatized TAP25-2 [T1APPAHGVT9S10APDT14RPAPGS20T21APPA], an overlapping sequence of MUC1 tandem repeats which had been glycosylated in vitro by two GalNAc residues in the positions T9 and T21. The high mass resolution and accuracy of QTOF-(+)ESMS allowed reliable structural assignments. The reduced complexity of the fragment spectra and the higher signal-to-noise ratio render QTOF-(+)ESMS an alternative mass spectrometric approach to the identification of O-glycosylation sites when compared with sequencing by post-source decay matrix-assisted laser desorption/ionization MS. Diagnostic ions from the N-terminus in the b-series offered direct evidence, which was supported by indirect evidence from the C-terminus ions of the y-series. The higher glycosylated GalNAc2-substituted fragments were mainly observed as multiply ionized species.     

Identification of a novel enteric Helicobacter species in a kitten with severe diarrhea

A previously undescribed Helicobacter sp. was recovered from a cat with severe diarrhea. Based upon the absence of any other identifiable cause of diarrhea, this helicobacter may be involved in the development of the disease signs. The organism could not be cultured but was described on the basis of 16S rRNA gene sequence analysis and morphology and appeared to be a new species, with Helicobacter canis being the most genetically similar species. The presence of a diarrhea-inducing helicobacter in a companion animal may pose a risk of zoonosis.     

Identification and sequence analysis of lpfABCDE, a putative fimbrial operon of Salmonella typhimurium

A chromosomal region present in Salmonella typhimurium but absent from related species was identified by hybridization. A DNA probe originating from 78 min on the S. typhimurium chromosome hybridized with DNA from Salmonella enteritidis, Salmonella heidelberg, and Salmonella dublin but not with DNA from Salmonella typhi, Salmonella arizonae, Escherichia coli, and Shigella serotypes. Cloning and sequence analysis revealed that the corresponding region of the S. typhimurium chromosome encodes a fimbrial operon. Long fimbriae inserted at the poles of the bacterium were observed by electron microscopy when this fimbrial operon was introduced into a nonpiliated E. coli strain. The genes encoding these fimbriae were therefore termed lpfABCDE, for long polar fimbriae. Genetically, the lpf operon was found to be most closely related to the fim operon of S. typhimurium, both in gene order and in conservation of the deduced amino acid sequences.