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PubMed2005

Genes for utilization of deoxyfructosyl glutamine (DFG), an amadori compound, are widely dispersed in the family Rhizobiaceae.

Amadori compounds form spontaneously in decomposing plant material and can be found in the rhizosphere. As such, these compounds could influence microbial populations by serving as sources of carbon, nitrogen and energy to microorganisms expressing suitable catabolic pathways. Two distinct sets of genes for utilization of deoxyfructosyl glutamine (DFG), an Amadori compound, have been identified in isolates of Agrobacterium spp. One, the soc gene set, is encoded by pAtC58, a 543 kb plasmid in A. tumefaciens strain C58. The second, mocD dissimilates DFG formed in the pathway for catabolism of mannopine (MOP) a non-Amadori, imine-type member of the mannityl opine family characteristic of certain Ti and Ri plasmids. To assess the level of dispersal of these two Amadori-utilizing systems, isolates of Agrobacterium spp. and related bacteria in the family Rhizobiaceae were examined by Southern analysis for homologs of socD and mocD. Homologs of mocD were associated only with Ti plasmid-encoded pathways for catabolism of MOP. Homologs of socD were more widely distributed, being detectable in many but not all of the isolates of Agrobacterium, Sinorhizobium, and Rhizobium spp. tested. However, this gene was never associated with the virulence elements, such as the Ti and Ri plasmids, in these strains. Regardless of genus most of the isolates containing socD homologs could utilize DFG as sole source of carbon, nitrogen and energy. Correlation studies suggested that mocD has evolved uniquely as part of the mannityl opine catabolic pathway while socD has evolved for the general utilization of Amadori compounds. Certain isolates of Agrobacterium and Rhizobium that lacked detectable homologs of socD and mocD also could utilize DFG suggesting the existence of additional, unrelated pathways for the catabolism of this Amadori compound. These results suggest that Amadori compounds constitute a source of nutrition that is important to microflora in the rhizosphere.

Biological Evolution↗

PubMed2005

Crystallization of the C-terminal domain of the addiction antidote CcdA in complex with its toxin CcdB.

CcdA and CcdB are the antidote and toxin of the ccd addiction module of Escherichia coli plasmid F. The CcdA C-terminal domain (CcdAC36; 36 amino acids) was crystallized in complex with CcdB (dimer of 2 x 101 amino acids) in three different crystal forms, two of which diffract to high resolution. Form II belongs to space group P2(1)2(1)2(1), with unit-cell parameters a = 37.6, b = 60.5, c = 83.8 A and diffracts to 1.8 A resolution. Form III belongs to space group P2(1), with unit-cell parameters a = 41.0, b = 37.9, c = 69.6 A, beta = 96.9 degrees, and diffracts to 1.9 A resolution.

Bacterial Proteins↗

PubMed1999

Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA.

Our basic observation is that each genome has a characteristic "signature" defined as the ratios between the observed dinucleotide frequencies and the frequencies expected if neighbors were chosen at random (dinucleotide relative abundances). The remarkable fact is that the signature is relatively constant throughout the genome; i.e. , the patterns and levels of dinucleotide relative abundances of every 50-kb segment of the genome are about the same. Comparison of the signatures of different genomes provides a measure of similarity which has the advantage that it looks at all the DNA of an organism and does not depend on the ability to align homologous sequences of specific genes. Genome signature comparisons show that plasmids, both specialized and broad-range, and their hosts have substantially compatible (similar) genome signatures. Mammalian mitochondrial (Mt) genomes are very similar, and animal and fungal Mt are generally moderately similar, but they diverge significantly from plant and protist Mt sets. Moreover, Mt genome signature differences between species parallel the corresponding nuclear genome signature differences, despite large differences between Mt and host nuclear signatures. In signature terms, we find that the archaea are not a coherent clade. For example, Sulfolobus and Halobacterium are extremely divergent. There is no consistent pattern of signature differences among thermophiles. More generally, grouping prokaryotes by environmental criteria (e.g., habitat propensities, osmolarity tolerance, chemical conditions) reveals no correlations in genome signature.

Animals↗

PubMed2006

Identification of the plasmid-borne quinolone resistance gene qnrS in Salmonella enterica serovar Infantis.

OBJECTIVES: A Salmonella enterica serovar Infantis isolate of avian origin was investigated for the presence of the gene qnrS, its transferability and its association with other resistance genes. METHODS: The Salmonella Infantis isolate was investigated for its susceptibility to antimicrobial agents and its plasmid content. Hybridization experiments and PCR assays were performed to identify the resistance genes while transformation and conjugation studies were conducted to show their transferability. The quinolone resistance-determining regions of the genes gyrA, gyrB, parC and parE were sequenced. Moreover, extended sequence analysis was performed to gain insight into the structure and organization of the qnrS gene area. RESULTS: The Salmonella Infantis isolate exhibited the Asp87-->Tyr87 mutation in gyrA, but no resistance-mediating mutations in the other target genes. It carried a conjugative plasmid, pINF5, on which a qnrS gene was detected in close proximity to a Tn3-like, blaTEM-1-carrying transposon. Homology to the qnrS-carrying plasmid pAH0376 of Shigella flexneri was limited to the Tn3-qnrS region. Sequence analysis of an approximately 13.4 kb region of pINF5 identified truncated insertion sequences of types IS26 and IS2 as well as an internal segment of the CS12 fimbrial gene cluster of Escherichia coli up- and downstream of the qnrS gene. CONCLUSIONS: This is to the best of our knowledge the first report of a qnrS gene in a Salmonella isolate. The analysis of the regions flanking the qnrS gene suggested that this region developed in multiple steps that included not only the integration of insertion sequences and a Tn3-like transposon, but also interplasmid recombination events.

Ampicillin↗

PubMed1996

Change of a catalytic reaction carried out by a DNA replication protein.

The RepA protein of plasmid pC194 initiates and terminates rolling circle replication. At initiation, it forms a 5'-phosphotyrosyl DNA link, whereas at termination, a glutamate residue directs hydrolytic cleavage of the newly synthesized origin, and the resulting 3'-hydroxyl group undergoes transesterification with the phosphotyrosine link. The protein is thus released from DNA, and the termination is uncoupled from reinitiation of replication. Replacement of the glutamate with tyrosine in RepA altered this mechanism, so that termination occurred by two successive transesterifications and became coupled to reinitiation. This result suggests that various enzymes involved in DNA cleavage and rejoining may have similar mechanistic and evolutionary roots.

Bacteriophage phi X 174↗

PubMed1987

Bacterial viruses, prophages, and plasmids, reconsidered.

Prophages and plasmids offer to the bacterial cells generalized access to each other's genes. The result is an extremely rich, available gene bank. It has successfully supported the original bacterial life since its beginnings and therefore it has conditioned all bacterial cells. Thus, most of the basic mechanisms for the living world, the richest variety of new genes, and particularly the improved ways of using DNA as an extremely adaptable genetic material happened in bacteria with the help of prophages and plasmids. This fact has profoundly marked all the biosphere. The ancestor of the nucleus probably started as an accumulation of prophages and plasmids integrated in the growing "chromosome" of the outer symbiont of the first eukaryotes. Many bacterial vestiges were probably retained in eukaryotes, mostly those related to the dominant and lasting role of small replicons in all their bacterial precursors. These vestiges may, for example, serve as an endogenic source for some DNA viruses in eukaryotes. The other animal and plant viruses seem to derive directly or indirectly from prophages or plasmids. In the case of RNA viruses they may have originated from probable RNA small replicons present in the first forms of life on earth. Some confusion arose in biology, as viruses were discovered first and therefore their most probable ancestors, the plasmids and the prophages which were discovered later, were thought to be viruslike, or viruses, as is the case with prophages.

Bacteria↗

PubMed2004

Complete sequence of virulence plasmid pEIB1 from the marine fish pathogen Vibrio anguillarum strain MVM425 and location of its replication region.

AIMS: The aim of this study was to determine the whole DNA sequence of pEIB1, one pJM1-like virulence plasmid from Vibrio anguillarum MVM425 and locate the replication region. METHODS AND RESULTS: DNA sequence of virulence plasmid pEIB1 from V. anguillarum MVM425 was determined using the methods of restriction endonuclease digestion, subcloning, and primer walking. The whole nucleotide sequence of pEIB1 comprises 66,164 bp, encoding 44 open reading frames (>400 bp) containing the genes of DNA replication, biosynthesis and regulation of the siderophore anguibactin and transport of ferric-anguibactin complexes. With no demonstrated replication origin, the Sau3AI partial digested plasmid DNA fragments of pEIB1 were ligated into the BamHI-fragment containing the kanamycin-resistance gene (Kmr). For there is no effective transformation in V. anguillarum, the ligated DNA was first introduced into E. coli JM83, and the transfomants were selected for resistance to kanamycin. It was demonstrated with southern blotting and DNA sequencing that plasmid pEIB7 containing the Sau3AI DNA fragment of pEIB1 (from 12516 to 13957) has the ability to replicate in E. coli JM83 and V. anguillarum MVM425sh. The segregational stability of plasmid pEIB7 kept in 100 and 4% in E. coli JM83 and V. anguillarum MVM425sh respectively when the cells were cultured in 200th generation. In following experiments, we also found that plasmid pEIB7 replicated at a middle-copy number of 10-40 in JM83, while at a high-copy number of 100-300 in MVM425sh. Moreover, pEIB7 can survive in V. alginolyticus, another fish pathogenic. CONCLUSIONS: With the whole DNA sequence of pEIB1 determining, it was found that pEIB1 showed microheterogeneity in its restriction endonuclease patterns with pJM1 though their DNA sequences had slight difference. According to the complete DNA sequence of pEIB1, its replication region was located from 12516 to 13957. And this replication region is compatible to pUC18 (pMB1), pKA3 (pSC101) and p15A: caiE (p15A). SIGNIFICANCE AND IMPACT OF THE STUDY: The worldwide vibriosis marine pathogen V. anguillarum strains contain common virulence, pJM1-like plasmids, independent on the geographical source. The pEIB1 was the second common virulence plasmid, which sequence was determined. Its sequence is highly homologous to pJM1 as they both encode biosynthesis and regulation of the siderophore anguibactin and transport of ferric-anguibactin complexes. Some interesting features as in pJM1 were also identified, such as transposon-like structures. So it can be deferred that the whole DNA sequences of virulent plasmid pEIB1 will be great helpful to future revealing these V. anguillarum virulence-related genes derived during evolution from transposition events or horizontal transfer of genes potentially originating in other organisms. Another result, replication region of pEIB1 locating is the first report about replication of pJM1-like plasmid. This work will be useful for researching pJM1-like plasmid replication mechanism in V. anguillarum.

Animals↗

PubMed1986

Cytological, flow cytometric, and molecular analysis of the rapid evolution of mammalian chromosomes containing highly amplified DNA sequences.

Transfection of a mouse dihydrofolate reductase (DHFR) cDNA contained in a plasmid "expression vector" into DHFR deficient Chinese hamster cells, followed by progressive selection of cells in increasing concentrations of methotrexate (MTX), leads to marked amplification of the exogenous DHFR sequences in the recipient hamster cells. This gene amplification is evident at the cytological level, in the form of homogeneously staining chromosomal regions (HSRs), at a gene expression level, in the form of fluorescein-methotrexate binding, and at the DNA level. Flow sorting, based on variable fluorescein-MTX binding, or direct cellular cloning, followed by chromosome analysis, revealed intercellular heterogeneity of HSRs in size and distribution. This suggested that there was a rapid evolution of HSRs in MTX-resistant transfectants. Chromosomal analysis of HSR evolution in situ, by examining individual colonies presumably derived from one or a few cells, underscored this impression of chromosome structural fluidity. Rates of HSR change in excess of 0.01 per cell division, increased by low doses of the recombinogen, mitomycin C, were detected. The Chinese hamster DHFR transfectants described should be amenable to detailed, coordinate cytological and molecular characterization. Such an analysis should contribute to an understanding of processes such as homologous recombination in mediating HSR evolution in mammalian chromosomes.

Animals↗

PubMed2002

Once the circle has been broken: dynamics and evolution of Streptomyces chromosomes.

Chromosomal instability has been a hallmark of Streptomyces genetics. Deletions and circularization often occur in the less-conserved terminal sequences of the linear chromosomes, which contain swarms of transposable elements and other horizontally transferred elements. Intermolecular recombination involving these regions also generates gross exchanges, resulting in terminal inverted repeats of heterogeneous size and context. The structural instability is evidently related to evolution of the Streptomyces chromosomes, which is postulated to involve linearization of hypothetical circular progenitors via integration of a linear plasmid. This scenario is supported by several bioinformatic analyses.

Biological Evolution↗

PubMed1997

Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi.

The genome of the bacterium Borrelia burgdorferi B31, the aetiologic agent of Lyme disease, contains a linear chromosome of 910,725 base pairs and at least 17 linear and circular plasmids with a combined size of more than 533,000 base pairs. The chromosome contains 853 genes encoding a basic set of proteins for DNA replication, transcription, translation, solute transport and energy metabolism, but, like Mycoplasma genitalium, it contains no genes for cellular biosynthetic reactions. Because B. burgdorferi and M. genitalium are distantly related eubacteria, we suggest that their limited metabolic capacities reflect convergent evolution by gene loss from more metabolically competent progenitors. Of 430 genes on 11 plasmids, most have no known biological function; 39% of plasmid genes are paralogues that form 47 gene families. The biological significance of the multiple plasmid-encoded genes is not clear, although they may be involved in antigenic variation or immune evasion.

Biological Transport↗

PubMed1994

Genetic analysis of a plasmid-encoded, host genotype-specific enhancement of bacterial fitness.

In the absence of antibiotics, carriage of pACYC184 reduces the competitive fitness of an Escherichia coli B genotype that was not previously selected for plasmid carriage, relative to that of an isogenic plasmid-free competitor. However, a host genotype propagated with the plasmid for 500 generations evolved an unexpected competitive advantage from plasmid carriage, relative to its own isogenic plasmid-free segregant. We manipulated the pACYC184 genome in order to identify the plasmid-encoded function that was required for the enhancement of the coevolved host genotype's competitive fitness. Inactivation of the plasmid-encoded tetracycline resistance gene, by deletion of either the promoter region or the entire gene, eliminated the beneficial effect of plasmid carriage for the coevolved host. This beneficial effect for the coevolved host was also manifest with pBR322, which contains a tetracycline resistance gene identical to that of pACYC184 but is otherwise heterologous.

Biological Evolution↗

PubMed1988

Mutations restoring import of a yeast mitochondrial protein with a nonfunctional presequence.

An internal deletion in the presequence of the precursor to yeast cytochrome oxidase subunit IV blocks import of the protein into mitochondria. We have identified two mechanisms by which yeast cells can suppress the defect of the plasmid-borne defective gene. One mechanism creates a new functional presequence by point mutations, or local DNA rearrangements, within the open reading frame or its 5'-untranslated region. The second mechanism compensates for the defective presequence by recessive mutations in single nuclear genes. The plasmid-linked mutations may mimic the mechanism(s) by which mitochondrial presequences arose during evolution whereas the chromosomal mutations may help to identify components of the mitochondrial import machinery.

Amino Acid Sequence↗

PubMed1996

Molecular aspects of pesticide degradation by microorganisms.

Microorganisms are able to degrade a large variety of compounds, including pesticides under laboratory conditions. However, methods have yet to be developed to decontaminate the environment from residues of pesticides. Pesticidal degradative genes in microbes have been found to be located on plasmids, transposons, and/or on chromosomes. Recent studies have provided clues to the evolution of degradative pathways and the organization of catabolic genes, thus making it much easier to develop genetically engineered microbes for the purpose of decontamination. Genetic manipulation offers a way of engineering microorganisms to deal with a pollutant, including pesticides that may be present in the contaminated sites. The simplest approach is to extend the degradative capabilities of existing metabolic pathways within an organism either by introducing additional enzymes from other organisms or by modifying the specificity of the catabolic genes already present. Continuous efforts are required in this direction, and at present several bacteria capable of degrading pesticides have been isolated from the natural environment. Catabolic genes responsible for the degradation of several xenobiotics, including pesticides, have been identified, isolated, and cloned into various other organisms such as Streptomyces, algae, fungi, etc. In addition, recombinant DNA studies have made it possible to develop DNA probes that are being used to identify microbes from diverse environmental communities with an unique ability to degrade pesticides.

Ascomycota↗

PubMed1997

Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution.

Virulence genes of pathogenic bacteria, which code for toxins, adhesins, invasins or other virulence factors, may be located on transmissible genetic elements such as transposons, plasmids or bacteriophages. In addition, such genes may be part of particular regions on the bacterial chromosomes, termed 'pathogenicity islands' (Pais). Pathogenicity islands are found in Gram-negative as well as in Gram-positive bacteria. They are present in the genome of pathogenic strains of a given species but absent or only rarely present in those of non-pathogenic variants of the same or related species. They comprise large DNA regions (up to 200 kb of DNA) and often carry more than one virulence gene, the G + C contents of which often differ from those of the remaining bacterial genome. In most cases, Pais are flanked by specific DNA sequences, such as direct repeats or insertion sequence (IS) elements. In addition, Pais of certain bacteria (e,g. uropathogenic Escherichia coli, Yersinia spp., Helicobacter pylori) have the tendency to delete with high frequencies or may undergo duplications and amplifications. Pais are often associated with tRNA loci, which may represent target sites for the chromosomal integration of these elements. Bacteriophage attachment sites and cryptic genes on Pais, which are homologous to phage integrase genes, plasmid origins of replication of IS elements, indicate that these particular genetic elements were previously able to spread among bacterial populations by horizontal gene transfer, a process known to contribute to microbial evolution.

Biological Evolution↗

PubMed2000

Adaptive mutation: implications for evolution.

Adaptive mutation is defined as a process that, during nonlethal selections, produces mutations that relieve the selective pressure whether or not other, nonselected mutations are also produced. Examples of adaptive mutation or related phenomena have been reported in bacteria and yeast but not yet outside of microorganisms. A decade of research on adaptive mutation has revealed mechanisms that may increase mutation rates under adverse conditions. This article focuses on mechanisms that produce adaptive mutations in one strain of Escherichia coli, FC40. These mechanisms include recombination-induced DNA replication, the placement of genes on a conjugal plasmid, and a transient mutator state. The implications of these various phenomena for adaptive evolution in microorganisms are discussed.

Adaptation, Physiological↗

PubMedDate not supplied

Multiple antimicrobial resistance region of a putative virulence plasmid from an Escherichia coli isolate incriminated in avian colibacillosis.

Infections due to Escherichia coli have been costly to the poultry industry, but the exact virulence mechanisms used by these organisms to cause disease in birds remain undefined. Several factors have been shown to contribute to the virulence of avian E. coli, and many of the genes encoding these factors have been found on large conjugative plasmids. Because of the occurrence of antimicrobial resistance genes on these same plasmids, it is possible that the use of antimicrobial agents may select for persistence of E. coli containing such plasmids. In the present study, a subclone of one of these plasmids was identified as likely containing some virulence and antimicrobial resistance genes. In an effort to better understand the relationship between virulence and resistance in these plasmids, this subclone was sequenced and the sequence analyzed. Analysis of this 30-kilobase (kb) region of plasmid pTJ100 revealed a mosaic of virulence genes, insertion sequences, antimicrobial resistance cassettes, and their remnants. Many of the resistance genes found in this region were expressed under laboratory conditions, indicating that certain antimicrobial agents, including disinfectants, antibiotics, and heavy metals, could promote selection of E. coli containing such plasmids in the production environment. Also, analysis of the G + C content of this clone indicated that it is the likely consequence of a complex evolution with components derived from various sources. The occurrence of many mobile elements in conjunction with antimicrobial resistance and virulence genes in this 30-kb region may indicate that the genetic constitution of the clone is quite plastic. Although further study will be required to better define this plasmid's role in avian E. coli virulence, the sequence described here is, to our knowledge, the longest known contiguous sequence of a ColV plasmid yet presented. Analysis of this sequence indicates that this clone and its parent plasmid may be important to the pathogenesis of avian colibacillosis and the evolution of avian E. coli virulence.

Animals↗

PubMed2000

Evolution of microbial pathogens.

Various genetic mechanisms including point mutations, genetic rearrangements and lateral gene transfer processes contribute to the evolution of microbes. Long-term processes leading to the development of new species or subspecies are termed macroevolution, and short-term developments, which occur during days or weeks, are considered as microevolution. Both processes, macro- and microevolution need horizontal gene transfer, which is particularly important for the development of pathogenic microorganisms. Plasmids, bacteriophages and so-called pathogenicity islands (PAIs) play a crucial role in the evolution of pathogens. During microevolution, genome variability of pathogenic microbes leads to new phenotypes, which play an important role in the acute development of an infectious disease. Infections due to Staphylococcus epidermidis, Candida albicans and Escherichia coli will be described with special emphasis on processes of microevolution. In contrast, the development of PAIs is a process involved in macroevolution. PAIs are especially important in processes leading to new pathotypes or even species. In this review, particular attention will be given to the fact that the evolution of pathogenic microbes can be considered as a specific example for microbial evolution in general.

Candida albicans↗

PubMed1998

Heterologous gene expression in an Escherichia coli population under starvation stress conditions.

A novel system to study the evolution of transcription signals in heterologous systems under selective starvation conditions is described. It is based on the plasmid-mediated transfer of his biosynthetic genes from Azospirillum brasilense into a heterologous Escherichia coli mutant population lacking histidine biosynthetic ability. We show that under highly selective stressful conditions, genetic changes in the donor plasmid lead to mutated sequences that are efficiently recognized as promoters by the E. coli RNA polymerase.

Adaptation, Physiological↗