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PubMedDate not supplied

Betaine use by rhizosphere bacteria: genes essential for trigonelline, stachydrine, and carnitine catabolism in Rhizobium meliloti are located on pSym in the symbiotic region.

Rhizobium meliloti is known to use betaines synthesized by its host, Medicago sativa, as osmoprotectants and sources of energy. It is shown in the present report that the symbiotic megaplasmid (pSym) of R. meliloti RCR2011 encodes functions essential to the catabolism of three betaines, trigonelline (nicotinic acid N-methylbetaine), stachydrine (proline betaine or dimethylproline), and carnitine (gamma-trimethyl-beta-hydroxybutyrobetaine). Preliminary evidence is presented showing that functions on pSym also influence the catabolism of choline and its oxidative product, glycine betaine. Genes implicated in betaine catabolism are found in the symbiotic region of pSym. Trigonelline catabolism functions lie between two clusters of symbiotic genes, nifKDH and nok/fixVI'. Stachydrine and carnitine functions lie to the right of trigonelline catabolism functions, immediately to the right of fixVI'. Information necessary to choline and glycine betaine catabolism is probably encoded to the right of stachydrine catabolism functions.

Alkaloids↗
PubMed1998

Evaluation of immunogenicity and protective activity in BALB/c mice of the 25-kDa major outer-membrane protein of Brucella melitensis (Omp25) expressed in Escherichia coli.

The antibody response specific to the 25-kDa major outer-membrane protein (Omp25) of Brucella melitensis expressed in Escherichia coli was assessed in BALB/c mice. Groups of mice were immunised and boosted either with sonicated E. coli carrying plasmid pAC2533-E. coli (pAC2533)-expressing the gene coding for Omp25 (omp25 gene) of B. melitensis, or with E. coli carrying plasmid pUC19-E. coli (pUC19). One control group received saline. The evolution of antibody responses was investigated by indirect ELISA with whole rough (R) B. melitensis H38 cells as antigen. Serum antibody titres of mice immunised with E. coli (pAC2533) were appreciably higher than those of mice immunised with E. coli (pUC19). The specificity to Omp25 of murine antibodies induced by E. coli (pAC2533) was demonstrated by SDS-PAGE and immunoblotting of five B. melitensis strains. Binding of antibody in E. coli (pAC2533) immune sera to the surface of B. melitensis strains differing in their smooth lipopolysaccharide (S-LPS) expression was also studied by whole-cell ELISA and by flow cytometry. Antibody reactivity to R and smooth-rough (S-R) was much stronger than that to smooth (S) B. melitensis strains, indicating a much better accessibility of Omp25 to antibody on strains lacking or expressing less O-polysaccharide on their surface. The antibodies to Omp25 were predominantly of IgG2a isotype. The capacity of E. coli (pAC2533) to induce protective immune responses against four challenge strains of B. melitensis was further evaluated in mice. Significant reductions in splenic infections, in comparison with mice immunised with E. coli (pUC19) and unimmunised (saline injection) mice, were observed in R B. melitensis B115, S-R B. melitensis EP and S B. melitensis H38 infected mice. Protection against S B. melitensis 16M was not significant. The data from the present study, together with previous results, suggest that humoral immunity against probably conformational, well-exposed epitopes of the Omp25 could contribute to protective mechanisms against B. melitensis infection in mice.

Animals↗
PubMed1997

Molecular mechanisms of Nod factor diversity.

The rhizobia-legume symbiosis is highly specific. Major host specificity determinants are the bacterial Nod factor signals that trigger the nodulation programme in a compatible host. Nod factors are lipo-chitooligosaccharides (LCOs) varying in the oligosaccharide chain length, the nature of the fatty acids and substitutions on the oligosaccharide. The nod genotype of rhizobia, which forms the genetic basis for this structural variety, includes a set of nodulation genes encoding the enzymes that synthesize LCOs. Allelic and non-allelic variation in these genes ensures the synthesis of different LCO structures by the different rhizobia. The nod genotypes co-evolved with host plant divergence in contrast to the rhizobia, which followed a different evolution. Horizontal gene transfer probably played an important role during evolution of symbiosis. The nod genotypes are particularly well equipped for horizontal gene transfer because of their location on transmissible plasmids and/or on 'symbiosis islands', which are symbiotic regions associated with movable elements.

Evolution, Molecular↗
PubMed1998

In vivo definition of the functional origin of leading strand replication on the lactococcal plasmid pFX2.

The lactococcal plasmid pFX2 belongs to a family of plasmids, whose prototype is the streptococcal plasmid pMV158, that replicates by the rolling circle mechanism. Determination of the nucleotide sequence of the repX gene of pFX2 allowed us to make some minor corrections in the published sequence, and to show that the repX gene is identical to the rep gene of plasmid pWV01. We have established pFX2 in Escherichia coli and in Streptococcus pneumoniae. In the latter host, we have defined in vivo the nick site introduced by the RepX protein. Plasmid pFX2 and the pMV158 derivative pLS1 exhibit a moderate degree of incompatibility in S. pneumoniae. Cloning of the double strand origin (dso) of pFX2 into a high-copy-number plasmid that is compatible with the pMV158 replicon led to an increase in incompatibility toward pLS1. Plasmids pFX2 and pLS1 exhibit homologies in their Rep proteins and in their dso sequences, but not in their negative control elements. Thus, the observed incompatibility indicates that cross-recognition of Rep proteins and dso takes place.

Amino Acid Sequence↗
PubMed2006

Genotypic analyses of Escherichia coli isolated from chickens with colibacillosis and apparently healthy chickens in Japan.

A genotypic comparison using pulsed-field gel electrophoresis (PFGE), amplified ribosomal restriction analysis (ARDRA) as well as PCRs targeting virulence associated genes reported elsewhere in avian pathogenic Escherichia coli(APEC) was made between E. coli strains isolated from chickens with colibacillosis and those from the feces of apparently healthy chickens in Japan. The majority (67%) of clinical isolates belonged to a certain phylogenetic ARDRA but not PFGE cluster, with virulence-related genes carried by ColV plasmid being markedly prevalent. The result suggests that APEC strains originated from the same "ancestor" in the course of E. coli evolution.

Animals↗
PubMed2000

Genetic variation: molecular mechanisms and impact on microbial evolution.

On the basis of established knowledge of microbial genetics one can distinguish three major natural strategies in the spontaneous generation of genetic variations in bacteria. These strategies are: (1) small local changes in the nucleotide sequence of the genome, (2) intragenomic reshuffling of segments of genomic sequences and (3) the acquisition of DNA sequences from another organism. The three general strategies differ in the quality of their contribution to microbial evolution. Besides a number of non-genetic factors, various specific gene products are involved in the generation of genetic variation and in the modulation of the frequency of genetic variation. The underlying genes are called evolution genes. They act for the benefit of the biological evolution of populations as opposed to the action of housekeeping genes and accessory genes which are for the benefit of individuals. Examples of evolution genes acting as variation generators are found in the transposition of mobile genetic elements and in so-called site-specific recombination systems. DNA repair systems and restriction-modification systems are examples of modulators of the frequency of genetic variation. The involvement of bacterial viruses and of plasmids in DNA reshuffling and in horizontal gene transfer is a hint for their evolutionary functions. Evolution genes are thought to undergo biological evolution themselves, but natural selection for their functions is indirect, at the level of populations, and is called second-order selection. In spite of an involvement of gene products in the generation of genetic variations, evolution genes do not programmatically direct evolution towards a specific goal. Rather, a steady interplay between natural selection and mixed populations of genetic variants gives microbial evolution its direction.

Bacteria↗
PubMed1995

Evolution of the Enterococcus faecalis sex pheromone system.

In this article we present data that form the basis of a model of the evolution of the unique Enterococcus faecalis sex pheromone system. The data indicate tht sex pheromone plasmid-encoded genes/functions, which are essential for this highly efficient plasmid collection system, are common among all sex pheromone plasmids; pAM373 seems to be only distantly related to all other pheromone plasmids. These genes appear to be restricted to sex pheromone plasmids (but see below for possible exceptions). However, the ability to produce sex pheromone-like peptides is not restricted to E. faecalis. We argue that the sex pheromone system of E. faecalis developed only once--but into at least 19 different variants--to form a system which is highly specific for this bacterium and is related to virulence.

Adhesins, Bacterial↗
PubMed1999

Bacterial catabolic transposons.

The introduction of foreign organic hydrocarbons into the environment in recent years, as in the widespread use of antibiotics, has resulted in the evolution of novel adaptive mechanisms by bacteria for the biodegradation of the organic pollutants. Plasmids have been implicated in the catabolism of many of these complex xenobiotics. The catabolic genes are prone to undergo genetic rearrangement and this is due to their presence on transposons or their association with transposable elements. Most of the catabolic transposons have structural features of the class I (composite) elements. These include transposons for chlorobenzoate (Tn5271), chlorobenzene (Tn5280), the newly discovered benzene catabolic transposon (Tn5542), and transposons encoding halogenated alkanoates and nylon-oligomer-degradative genes. Transposons for the catabolism of toluene (Tn4651, Tn4653, Tn4656) and naphthalene (Tn4655) belong to class II (Tn3 family) elements. Many catabolic genes have been associated with insertion sequences, which suggests that these gene clusters could be rapidly disseminated among the bacterial populations. This greatly expands the substrate range of the microorganisms in the environment and aids the evolution of new and novel degradative pathways. This enhanced metabolic versatility can be exploited for and is believed to play a major part in the bioremediation of polluted environments.

Bacteria↗
PubMed1999

Generation of new transposons in vivo: an evolutionary role for the "staggered" head-to-head dimer and one-ended transposition.

From a plasmid carrying the tnpA gene and one inverted repeat sequence (IR) of transposon Tn3, plasmids containing a structure characteristic of transposons, i.e., two IRs flanking a tnpA gene, were generated spontaneously in vivo. They appear to have arisen either through the formation of a "staggered" head-to-head dimer or by so-called one-ended transposition. These putative transposons could indeed transpose to, or form cointegrates with, a recipient plasmid. Based on these findings it is proposed that a primeval transposase gene and its target site evolved first, and subsequently gave rise to a "fully-fledged" transposon by head-to-head dimerization or one-ended transposition.

Base Sequence↗
PubMedDate not supplied

Molecular symbionts and the evolution of sex.

The main focus of this article is on the evolutionary origin of sex rather than its maintenance in extant organisms. Sexual outbreeding involves a complex set of biological phenomena, and it is useful to consider the probable order in which the components of this process evolved. I propose that conjugation between cells was the initial stage in the evolution of sex. It has been shown that molecular symbionts (such as transposons and plasmids) derive a major selective advantage from conjugation and sexual outbreeding. This strongly suggests that the origin of conjugation between cells may best be understood as a symbiont-encoded adaptive function. In other words, conjugation between haploid cells evolved initially as a means of propagating molecular symbionts. Once efficient mechanisms of conjugation were in place, however, the subsequent elaboration of the other aspect of sex, particularly genetic recombination, were facilitated. Although the molecular symbiont theory is directly relevant only to the origin of sex, it also has implications for understanding the subsequent stages in the evolution of sex.

Biological Evolution↗
PubMed1999

Importance of illegitimate recombination and transposition in IS30-associated excision events.

In the present study we report on the excision of IS30 elements and IS30-derived composite transposons. Frequent loss of IS30 was observed during dissolution of dimeric IS30 structures, containing IR-IR junctions, leading to resealed donor molecules. In contrast, unambiguous transpositional excision resulting in resealed remainder products could not be identified in the case of a monomeric element. The bias in the excision of monomeric and dimeric IS30 structures indicates a difference in the molecular mechanism of transposition of IS30 monomers and dimers. Sequence data on the rarely detected plasmids missing full IS or Tn copies rather suggest that all products were derived from illegitimate recombination. The reaction occurred between short homologies and was independent of the transposase activity. Similar IS30 excision events accompanied by multiple plasmid or genome rearrangements were detected in Pseudomonas putida and Rhizobium meliloti, yielding stable replicons that retained the selective marker gene of the transposon. We provide evidence that both transposition and illegitimate recombination can contribute to the stabilization of replicons through the elimination of IS elements, which emphasizes the evolutionary significance of these events.

Base Sequence↗
PubMed2004

Molecular evolutionary relationships of enteroinvasive Escherichia coli and Shigella spp.

Enteroinvasive Escherichia coli (EIEC), a distinctive pathogenic form of E. coli causing dysentery, is similar in many properties to bacteria placed in the four species of Shigella. Shigella has been separated as a genus but in fact comprises several clones of E. coli. The evolutionary relationships of 32 EIEC strains of 12 serotypes have been determined by sequencing of four housekeeping genes and two plasmid genes which were used previously to determine the relationships of Shigella strains. The EIEC strains were grouped in four clusters with one outlier strain, indicating independent derivation of EIEC several times. Three of the four clusters contain more than one O antigen type. One EIEC strain (an O112ac:H- strain) was found in Shigella cluster 3 but is not identical to the Shigella cluster 3 D2 and B15 strains with the same O antigen. Two forms of the virulence plasmid pINV have been identified in Shigella strains by using the sequences of ipgD and mxiA genes, and all but two of our EIEC strains have pINV A. The EIEC strains were grouped in two subclusters with a very low level of variation, generally not intermingled with Shigella pINV A strains. The EIEC clusters based on housekeeping genes were reflected in the plasmid gene sequences, with some exceptions. Two strains were found in the pINV B form by using the ipgD sequence, with one strain having an mxiA sequence similar to the divergent sequence of D1. Clearly, EIEC and Shigella spp. form a pathovar of E. coli.

Bacterial Proteins↗
PubMed2002

Evolution of multiresistance in nontyphoid salmonella serovars from 1984 to 1998 in Argentina.

Molecular evolution of multiresistance in nontyphoid Salmonella spp. was investigated with 155 isolates obtained in Argentina from 1984 to 1998. In 74 isolates obtained from 1984 to 1988 resistance was associated with the presence of Tn3, Tn9, class I (In0) and II (Tn7) integrons, and the aac(3)-IIa gene. Extended-spectrum cephalosporin (ESC) resistance in Salmonella spp. emerged in 1989, and 81 isolates resistant to at least one ESC and one aminoglycoside were collected thereafter. Among these, two patterns of antimicrobial resistance mechanisms were found: from 1989 to 1992, resistance was related to the spreading of Tn1331 and bla(CTX-M-2), in addition to the persistence of In0 and Tn7. From 1993 to 1998, several integrons were added to the first pattern and three integron groups (IG), namely, IG1 (38% of the isolates), IG2 (51%), and IG3 (11%), were identified. At least two beta-lactamase genes were detected in 65% of the isolates (after 1989) by PCR analysis. Furthermore, five beta-lactamase genes, bla(CTX-M-(2)), bla(OXA-9), bla(OXA-2), bla(TEM-1), and bla(PER-2), were found in two isolates. The bla(CTX-M-2) gene was found in several complex sulI-type integrons with different rearrays within the variable region of class I integrons, suggesting evolution of these integrons in nontyphoid Salmonella. In conclusion, progressive acquisition and accumulation of plasmid-mediated resistance determinants occurred from 1984 to 1998 in nontyphoid Salmonella isolates of the most prevalent serovars from Argentina. It is suggested that antimicrobial resistance mechanisms in these bacteria may have been the consequence of plasmid exchange between Salmonella enterica serovar Typhimurium and Escherichia coli or Shigella flexneri and/or spreading of mobile elements from the nosocomial environment.

Argentina↗
PubMed1993

The 73-kb pIAA plasmid increases competitive fitness of Pseudomonas syringae subspecies savastanoi in oleander.

Pseudomonas syringae subsp. savastanoi causes tumors on olive and oleander by producing the plant growth regulators indoleacetic acid (IAA) and cytokinins following infection of the plant. The contribution of IAA production to the ability of P. syringae subsp. savastanoi to grow and survive in oleander leaf tissue was studied. Bacterial strains differing only with respect to IAA production were characterized. Growth and survival of wild-type and two mutant strains of P. syringae subsp. savastanoi in oleander leaf tissue were monitored by weekly colony counts and IAA plate assays. Growth rate of the three strains in culture and in planta did not differ significantly. However, the wild-type strain reached a higher population density and maintained its maximum density at least 9 weeks longer than either mutant population. An insertion mutant containing the IAA plasmid (pIAA), but incapable of IAA production, did not maintain a higher population density than a strain cured of the IAA plasmid. The pIAA-cured strain maintained a higher population density when coinoculated with an IAA-producing strain than when inoculated alone. These results suggest that IAA production may contribute to the fitness of P. syringae subsp. savastanoi in oleander tissue and that the iaa operon alone may be responsible for the competitive advantage of cells harboring pIAA.

Biological Evolution↗
PubMed2000

Anti-DNA antibodies exhibit different binding motif preferences for single stranded or double stranded DNA.

A common feature for most anti-DNA antibodies (Abs) is their induction in an antigen (Ag)-driven specific clonal expansion pattern though crossreactivity. However, the fine sequences in DNA Ags that interact directly with immune system and the ability of DNA to induce immune responses is poorly understood. In order to define the characteristics of possible antigenic determinants in DNA Ags, we immunized mice with the pBR322 plasmid and used antisera as source of anti-DNA Abs. A systemic evolution of ligands by exponential enrichment (SELEX) procedure was performed on an oligodeoxynucleotide library either in single stranded (ss-) or double stranded (ds-) form. The SELEXed fragments were cloned and sequenced. The resulting sequences were analyzed using the Multiple Alignment Construction and Analysis Workbench program. We show that the fragments of ss- or ds- form bound by a same stock of antibodies were different in their conserved sequences. ss-DNA fragments recognized by anti-DNA Abs were rich in cacc, caccc, accc or cccc blocks, while the same stock of Abs exhibited significant preference for the (5'gcg3'/3'cgc5') motif located in ds-DNA. At the same time sera from unimmunized control mice showed no sequence preference in either ss-DNA or ds-DNA. Future improvement of this work and the potential use of SELEX for studies of DNA Ags are also discussed.

Animals↗
PubMed1977

Aminoglycoside-modifying enzyme of an antibiotic-producing bacterium acts as a determinant of antibiotic resistance in Escherichia coli.

Bacillus circulans NRRL B-3312, a nonpathogenic bacterium that produces the aminoglycoside antibiotic butirosin, is known to contain an aminoglycoside phosphotransferase that is similar to the neomycin phosphotransferases of clinically isolated antibiotic-resistant bacteria. Purified DNAs from B. circulans and the plasmid ColE1-ApR were digested with EcoRI endonuclease and the resulting fragments covalently joined with polynucleotide ligase. The recombined DNA was used to transform E. coli and ampicillin-neomycin resistant colonies were selected. Analysis of several clones indicated that neomycin resistance in the E. coli transformants was due to the presence of the B. circulans phosphotransferase gene. This observation is consistent with the notion that anitbiotic-modifying enzymes from antibiotic-producing organisms may be the sources of antibiotic resistance in plasmid-containing bacteria.

Bacillus↗
PubMed1995

Natural plasmids of filamentous fungi.

Among eukaryotes, plasmids have been found in fungi and plants but not in animals. Most plasmids are mitochondrial. In filamentous fungi, plasmids are commonly encountered in isolates from natural populations. Individual populations may show a predominance of one type, but some plasmids have a global distribution, often crossing species boundaries. Surveys have shown that strains can contain more than one type of plasmid and that different types appear to be distributed independently. In crosses, plasmids are generally inherited maternally. Horizontal transmission is by cell contact. Circular plasmids are common only in Neurospora spp., but linear plasmids have been found in many fungi. Circular plasmids have one open reading frame (ORF) coding for a DNA polymerase or a reverse transcriptase. Linear plasmids generally have two ORFs, coding for presumptive DNA and RNA polymerases with amino acid motifs showing homology to viral polymerases. Plasmids often attain a high copy number, in excess of that of mitochondrial DNA. Linear plasmids have a protein attached to their 5' end, and this is presumed to act as a replication primer. Most plasmids are neutral passengers, but several linear plasmids integrate into mitochondrial DNA, causing death of the host culture. Inferred amino acid sequences of linear plasmid ORFs have been used to plot phylogenetic trees, which show a fair concordance with conventional trees. The circular Neurospora plasmids have replication systems that seem to be evolutionary intermediates between the RNA and the DNA worlds.

Ascomycota↗