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PubMed2006

The genome of Rhizobium leguminosarum has recognizable core and accessory components.

BACKGROUND: Rhizobium leguminosarum is an alpha-proteobacterial N2-fixing symbiont of legumes that has been the subject of more than a thousand publications. Genes for the symbiotic interaction with plants are well studied, but the adaptations that allow survival and growth in the soil environment are poorly understood. We have sequenced the genome of R. leguminosarum biovar viciae strain 3841. RESULTS: The 7.75 Mb genome comprises a circular chromosome and six circular plasmids, with 61% G+C overall. All three rRNA operons and 52 tRNA genes are on the chromosome; essential protein-encoding genes are largely chromosomal, but most functional classes occur on plasmids as well. Of the 7,263 protein-encoding genes, 2,056 had orthologs in each of three related genomes (Agrobacterium tumefaciens, Sinorhizobium meliloti, and Mesorhizobium loti), and these genes were over-represented in the chromosome and had above average G+C. Most supported the rRNA-based phylogeny, confirming A. tumefaciens to be the closest among these relatives, but 347 genes were incompatible with this phylogeny; these were scattered throughout the genome but were over-represented on the plasmids. An unexpectedly large number of genes were shared by all three rhizobia but were missing from A. tumefaciens. CONCLUSION: Overall, the genome can be considered to have two main components: a 'core', which is higher in G+C, is mostly chromosomal, is shared with related organisms, and has a consistent phylogeny; and an 'accessory' component, which is sporadic in distribution, lower in G+C, and located on the plasmids and chromosomal islands. The accessory genome has a different nucleotide composition from the core despite a long history of coexistence.

ATP-Binding Cassette Transporters↗
PubMed1999

Comparison between MRI, microbiology and histology in evaluation of antibiotics in a murine model of thigh infection.

Although in vivo magnetic resonance imaging (MRI) is rapidly becoming a recognised tool in experimental pharmacological research, at the best of our knowledge, scarce application in the field of antibacterial drug research has been reported so far. In this last field, animal models of bacterial infections are used to test the efficacy of novel compounds. In this paper we have explored the potential usefulness of MRI in monitoring the chronological evolution of experimental bacterial infections and the effect of different therapeutic treatments. A murine model of thigh infection induced by Staphylococcus aureus has been used and the efficacy of vancomycin and imipenem/cilastatin has been tested. Three groups of infected animals were studied by microbiology, histology and MRI methods. The results obtained show that in vivo MRI data are highly consistent with microbiological and histological data, allowing, similarly to these commonly used techniques, the efficacy of different antibacterial treatments to be quantified. Our findings suggest that MRI could be used to assess the efficacy of new chemical entities in antibacterial pharmacological research. The advantages of MRI, as a non invasive technique, in comparison with commonly used microbiological and histological methods are discussed.

Animals↗
PubMed1998

A chitin-binding domain in a marine bacterial chitinase and other microbial chitinases: implications for the ecology and evolution of 1,4-beta-glycanases.

To examine the ecology and evolution of microbial chitinases, especially the chitin-binding domain, one of the chitinase genes (chiA) from the marine bacterium Vibrio harveyi was analysed. The deduced amino acid sequence of ChiA is not very similar overall to other proteins, except for two regions, the putative catalytic and chitin-binding domains. Among all bacterial chitinases sequenced to date, there is no relationship between percentage similarity of catalytic domains and chitin-binding domains in pairwise comparisons, suggesting that these two domains have evolved separately. The chitin-binding domain appears to be evolutionarily conserved among many bacterial chitinases and is also somewhat similar to cellulose-binding domains found in microbial cellulases and xylanases. To investigate the role of the chitin-binding domain, clones producing versions of ChiA with or without this domain were examined. One version with the domain (ChiA1) bound to and hydrolysed chitin, whereas a truncated ChiA without the putative chitin-binding domain (ChiA2) did not bind to chitin, but it could hydrolyse chitin, although not as well. ChiA1 diffused more slowly in agarose containing colloidal chitin than ChiA2, but diffusion of the two proteins in agarose without colloidal chitin was similar. These results indicate that the chitin-binding domain helps determine the movement of chitinase along N-acetylglucosamine strands and within environments containing chitin.

Amino Acid Sequence↗
PubMed1999

Escherichia coli mutants lacking all possible combinations of eight penicillin binding proteins: viability, characteristics, and implications for peptidoglycan synthesis.

The penicillin binding proteins (PBPs) synthesize and remodel peptidoglycan, the structural component of the bacterial cell wall. Much is known about the biochemistry of these proteins, but little is known about their biological roles. To better understand the contributions these proteins make to the physiology of Escherichia coli, we constructed 192 mutants from which eight PBP genes were deleted in every possible combination. The genes encoding PBPs 1a, 1b, 4, 5, 6, and 7, AmpC, and AmpH were cloned, and from each gene an internal coding sequence was removed and replaced with a kanamycin resistance cassette flanked by two res sites from plasmid RP4. Deletion of individual genes was accomplished by transferring each interrupted gene onto the chromosome of E. coli via lambda phage transduction and selecting for kanamycin-resistant recombinants. Afterwards, the kanamycin resistance cassette was removed from each mutant strain by supplying ParA resolvase in trans, yielding a strain in which a long segment of the original PBP gene was deleted and replaced by an 8-bp res site. These kanamycin-sensitive mutants were used as recipients in further rounds of replacement mutagenesis, resulting in a set of strains lacking from one to seven PBPs. In addition, the dacD gene was deleted from two septuple mutants, creating strains lacking eight genes. The only deletion combinations not produced were those lacking both PBPs 1a and 1b because such a combination is lethal. Surprisingly, all other deletion mutants were viable even though, at the extreme, 8 of the 12 known PBPs had been eliminated. Furthermore, when both PBPs 2 and 3 were inactivated by the beta-lactams mecillinam and aztreonam, respectively, several mutants did not lyse but continued to grow as enlarged spheres, so that one mutant synthesized osmotically resistant peptidoglycan when only 2 of 12 PBPs (PBPs 1b and 1c) remained active. These results have important implications for current models of peptidoglycan biosynthesis, for understanding the evolution of the bacterial sacculus, and for interpreting results derived by mutating unknown open reading frames in genome projects. In addition, members of the set of PBP mutants will provide excellent starting points for answering fundamental questions about other aspects of cell wall metabolism.

Bacterial Proteins↗
PubMed2001

Perspective: reverse evolution.

For some time, the reversibility of evolution was primarily discussed in terms of comparative patterns. Only recently has this problem been studied using experimental evolution over shorter evolutionary time frames. This has raised questions of definition, experimental procedure, and the hypotheses being tested. Experimental evolution has provided evidence for multiple population genetic mechanisms in reverse evolution, including pleiotropy and mutation accumulation. It has also pointed to genetic factors that might prevent reverse evolution, such as a lack of genetic variability, epistasis, and differential genotype-by-environment interactions. The main focus of this perspective is on laboratory studies and their relevance to the genetics of reverse evolution. We discuss reverse evolution experiments with Drosophila, bacterial, and viral populations. Field studies of the reverse evolution of melanism in the peppered moth are also reviewed.

Animals↗
PubMed1993

Occurrence of chaperonin 60 and chaperonin 10 in primary and secondary bacterial symbionts of aphids: implications for the evolution of an endosymbiotic system in aphids.

All aphids harbor symbiotrophic prokaryotes ("primary symbionts") in a specialized-abdominal cell, the bacteriocyte. Chaperonin 60 (Cpn60, symbionin) and chaperonin 10 (Cpn10), which are high and low molecular weight heatshock proteins, were sought in tissues of more than 60 aphid species. The endosymbionts were compared immunologically and histologically. It was demonstrated that (1) there are two types of aphids in terms of the endosymbiotic system: some with only primary symbionts and others with, in addition, secondary symbionts; (2) the primary symbionts of various aphids are quite similar in morphology whereas the secondary symbionts vary; and (3) irrespective of the aphid species, Cpn60 is abundant in both the primary and secondary symbionts, while Cpn10 is abundant in the secondary symbionts but present in small amounts in the primary ones. Based on these results, we suggest that the primary symbionts have been derived from a prokaryote that was acquired by the common ancestor of aphids whereas the secondary symbionts have been acquired by various aphids independently after divergence of the aphid species. In addition, we point out the possibility that the prokaryotes under intracellular conditions have been subject to some common evolutionary pressures, and as a result, have come to resemble cell organelles.

Animals↗
PubMed1999

Lubricating bacteria model for branching growth of bacterial colonies.

Various bacterial strains (e.g., strains belonging to the genera Bacillus, Paenibacillus, Serratia, and Salmonella) exhibit colonial branching patterns during growth on poor semisolid substrates. These patterns reflect the bacterial cooperative self-organization. A central part of the cooperation is the collective formation of a lubricant on top of the agar which enables the bacteria to swim. Hence it provides the colony means to advance towards the food. One method of modeling the colonial development is via coupled reaction-diffusion equations which describe the time evolution of the bacterial density and the concentrations of the relevant chemical fields. This idea has been pursued by a number of groups. Here we present an additional model which specifically includes an evolution equation for the lubricant excreted by the bacteria. We show that when the diffusion of the fluid is governed by a nonlinear diffusion coefficient, branching patterns evolve. We study the effect of the rates of emission and decomposition of the lubricant fluid on the observed patterns. The results are compared with experimental observations. We also include fields of chemotactic agents and food chemotaxis and conclude that these features are needed in order to explain the observations.

Bacteria↗
PubMed1990

Non specific immunomodulation in respiratory infections.

The recent advances in immunology have opened the way for new therapeutic approaches aiming at modulating the various components of the immune system in man. Lyophilized bacterial lysate were studied in a large number of models and found, when given orally, or by aerosol to induce specific and non specific responses. They stimulate the systemic and local immune response and activates the macrophages which play a key role in the immune system, modulates the level of serum immunoglobulins and potentiates the lymphocyte response to PHA and other mitogens. Based on these data a trial was conducted on 332 patients with or without bronchial asthma and recurrent respiratory tract infections. These patients have been observed during 2 years, the first year without therapy the second with bacterial lysates. The evolution during these 2 winters have been analysed by a score method. Improvements were recorded in about 2/3 of the cases and the number of infections were reduced from 2.14/patients to 1.08/patient (p less than 0.001). Bacterial lysates could be considered as an effective therapy or a preventive measure for respiratory tract infections in patients with or without bronchial asthma. The levels of serum immunoglobulins IgG, IgA, IgM and IgE have been studied before and after oral immunotherapy with a bacterial lysate in 88 patients bronchial asthma, repeated respiratory infection, and 12 cases of IgA deficiency. A significant increase in IgA has been observed in nine patients presenting initially a decreased IgA serum level. In three patients without response to the standard treatment an increase in IgA was achieved by increasing the dosage of oral bacterial lysate.(ABSTRACT TRUNCATED AT 250 WORDS)

Adjuvants, Immunologic↗
PubMed1988

Oxidation of palmitic acid by Mycobacterium leprae in an axenic medium.

The ability of Mycobacterium leprae to oxidize palmitic acid during incubation in an axenic medium was studied. By using a Buddemeyer-type detection system, partially purified nude-mouse-derived M. leprae was found to produce 14CO2 from 14C-labeled palmitic acid in a linear fashion for at least 1 week. Procedures known to remove residual host tissue did not diminish the rate of 14CO2 evolution, indicating that bacterial metabolism was being measured. Palmitate oxidation was temperature sensitive, with an apparent optimum of 33 degrees C, but pH insensitive. Bacilli exposed to a variety of antileprosy drugs for 1 or 2 weeks displayed significantly reduced rates of 14CO2 evolution upon subsequent addition of 14C-labeled palmitic acid. This activity could be readily detected with 10(6) bacilli, thus indicating its potential for use in clinical susceptibility testing.

Carbon Dioxide↗
PubMed2002

Comparative analysis of ribosomal proteins in complete genomes: an example of reductive evolution at the domain scale.

A comprehensive investigation of ribosomal genes in complete genomes from 66 different species allows us to address the distribution of r-proteins between and within the three primary domains. Thirty-four r-protein families are represented in all domains but 33 families are specific to Archaea and Eucarya, providing evidence for specialisation at an early stage of evolution between the bacterial lineage and the lineage leading to Archaea and Eukaryotes. With only one specific r-protein, the archaeal ribosome appears to be a small-scale model of the eukaryotic one in terms of protein composition. However, the mechanism of evolution of the protein component of the ribosome appears dramatically different in Archaea. In Bacteria and Eucarya, a restricted number of ribosomal genes can be lost with a bias toward losses in intracellular pathogens. In Archaea, losses implicate 15% of the ribosomal genes revealing an unexpected plasticity of the translation apparatus and the pattern of gene losses indicates a progressive elimination of ribosomal genes in the course of archaeal evolution. This first documented case of reductive evolution at the domain scale provides a new framework for discussing the shape of the universal tree of life and the selective forces directing the evolution of prokaryotes.

Animals↗
PubMed2006

Evolution of surveillance methods for detection of bacterial contamination of platelets in a university hospital, 1991 through 2004.

BACKGROUND: Platelet (PLT) bacterial contamination (PBC) is the most common transfusion-associated infection. It is important to understand the impact of interventions addressing this problem. STUDY DESIGN AND METHODS: PBC was studied by prospective (active) and transfusion-reaction triggered (passive) surveillance from July 1991 to December 2004. Active surveillance, utilized for 10 years, included bacterial culture of all or 4- and 5-day-old PLTs at issue and intermittent use of Gram stain, pH measurements, and early (24-hr) culture of single-donor plateletpheresis (SDP) units. RESULTS: Active surveillance detected 38 instances of PBC, 7 in SDP units (1:2213) and 31 in random-donor PLT units (1:2090 units, p = 0.89; or 1:418 pools of 5 units, p < 0.001). Contaminants were coagulase-negative staphylococci (CONS; n = 27), Staphylococcus aureus (4), Bacillus cereus (1), Serratia marcescens (2), streptococci (2 S. bovis, 1 S. uberis), and CONS with viridans group streptococcus (1). Only one instance of contamination, caused by Pseudomonas aeruginosa, was detected by passive surveillance, with fatal outcome. Colony counts of contaminants ranged from 0.5 x 10(2) to 4 x 10(11) colony-forming units per mL at time of issue. PBC was interdicted before transfusion in 6 cases through Gram stain screening. Transfusion reactions occurred in 13 of 32 recipients (41%), with 9 severe reactions (28%) and 3 deaths (9%). pH testing failed to detect 5 contaminated units and resulted in discard of nearly 2 percent of units, whereas culture of SDP units at 24 hours failed to identify a contaminated unit. CONCLUSION: Improved active surveillance methods for detecting PBC are needed to improve the safety of PLT transfusions.

Bacterial Infections↗
PubMed1990

[Approximation of the dynamics of microbial contamination of the Segre River in Lérida].

The water rivers contains a basal autochthonus population of micro-organisms which is local and temporal and it is modified by the incoming sewage. In this paper a simple model is applied to estimate the faecal bacterial load poured from the town of Lérida to the Segre River and the downstream assimilation capacity of this river. In spite of the inherent limitations and imprecision due to sampling operations and calculations, the numerical results are related to other published results. The evolution of faecal bacterial population downstream of Lérida does not follow the theoretical model without a growth coefficient. The showed data on faecal pollution (bacteriological and viral detectors) are the only ones which have been published on the final section, the most disturbed, of the Segre River.

Bacteria↗
PubMed2000

Parallel evolution of virulence in pathogenic Escherichia coli.

The mechanisms underlying the evolution and emergence of new bacterial pathogens are not well understood. To elucidate the evolution of pathogenic Escherichia coli strains, here we sequenced seven housekeeping genes to build a phylogenetic tree and trace the history of the acquisition of virulence genes. Compatibility analysis indicates that more than 70% of the informative sites agree with a single phylogeny, suggesting that recombination has not completely obscured the remnants of ancestral chromosomes. On the basis of the rate of synonymous substitution for E. coli and Salmonella enterica (4.7 x 10(-9) per site per year), the radiation of clones began about 9 million years ago and the highly virulent pathogen responsible for epidemics of food poisoning, E. coli O157:H7, separated from a common ancestor of E. coli K-12 as long as 4.5 million years ago. Phylogenetic analysis reveals that old lineages of E. coli have acquired the same virulence factors in parallel, including a pathogenicity island involved in intestinal adhesion, a plasmid-borne haemolysin, and phage-encoded Shiga toxins. Such parallel evolution indicates that natural selection has favoured an ordered acquisition of genes and the progressive build-up of molecular mechanisms that increase virulence.

DNA, Bacterial↗