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PubMed1997

Experimental surgery to create subgenomes of Bacillus subtilis 168.

The 4,188-kb circular genome of Bacillus subtilis 168 was artificially dissected into two stable circular chromosomes in vivo, one being the 3,878-kb main genome and the other the 310-kb subgenome that was recovered as covalently closed circular DNA in CsCl-ethidium bromide ultracentrifugation. The minimal requirements to physically separate the 310-kb DNA segment out of the genome were two interrepeat homologous sequences and an origin of DNA replication between them. The subgenome originated from the 1,255-1, 551-kb region of the B. subtilis genome was essential for the cell to survive because the subgenome was not lost from the cell. The finding that the B. subtilis genome has a potential to be divided and the resulting two replicons stably maintained may shed light on origins and formation mechanisms of giant plasmids or second chromosomes present in many bacteria. Similar excision or its reversal process, i.e., integration of large sized covalently closed circular DNA pieces into the main genome, implies significant roles of subgenomes in the exchange of genetic information and size variation of bacterial genomes in bacterial evolution.

Bacillus subtilis↗
PubMed2005

Bacterial phytopathogens and genome science.

There are now fourteen completed genomes of bacterial phytopathogens, all of which have been generated in the past six years. These genomes come from a phylogenetically diverse set of organisms, and range in size from 870 kb to more than 6Mb. The publication of these annotated genomes has significantly helped our understanding of bacterial plant disease. These genomes have also provided important information about bacterial evolution. Examples of recently completed genomes include: Pseudomonas syringae pv tomato, which is notable for its large repertoire of effector proteins; Leifsonia xyli subsp. xyli, the first Gram-positive bacterial genome to be sequenced; and Phytoplasma asteris, the small genome that lacks important functions previously thought to be essential in a bacterium.

Actinomycetales↗
PubMedDate not supplied

[Plasticity of bacterial genomes: pathogenicity islands and the locus of enterocyte effacement (LEE)].

Many bacterial virulence attributes, like toxins, adhesins, invasins, iron uptake systems, are encoded within specific regions of the bacterial genome. These in size varying regions are termed pathogenicity islands (PAIs) since they confer pathogenic properties to the respective micro-organism. Per definition PAIs are exclusively found in pathogenic strains and are often inserted near transfer-RNA genes. Nevertheless, non-pathogenic bacteria also possess foreign DNA elements that confer advantageous features, leading to improved fitness. These additional DNA elements as well as PAIs are termed genomic islands and were acquired during bacterial evolution. Significant G+C content deviation in pathogenicity islands with respect to the rest of the genome, the presence of direct repeat sequences at the flanking regions, the presence of integrase gene determinants as other mobility features,the particular insertion site (tRNA gene) as well as the observed genetic instability suggests that pathogenicity islands were acquired by horizontal gene transfer. PAIs are the fascinating proof of the plasticity of bacterial genomes. PAIs were originally described in human pathogenic Escherichia (E.) coli strains. In the meantime PAIs have been found in various pathogenic bacteria of humans, animals and even plants. The Locus of Enterocyte Effacement (LEE) is one particular widely distributed PAI of E coli. In addition, it also confers pathogenicity to the related species Citrobacter (C.) rodentium and Escherichia (E.) alvei. The LEE is an important virulence feature of several animal pathogens. It is an obligate PAI of all animal and human enteropathogenic E. coli (EPEC), and most enterohaemorrhegic E. coli (EHEC) also harbor the LEE. The LEE encodes a type III secretion system, an adhesion (intimin) that mediates the intimate contact between the bacterium and the epithelial cell, as well as various proteins which are secreted via the type III secretion system. The LEE encoded virulence features are responsible for the formation of so called attaching and effacing (AE) lesions in the intestinal epithelium. Due to its wide distribution in animal pathogens, LEE encoded antigens are suitable vaccine antigens. Acquisition and structure of the LEE pathogenicity island is the crucial point of numerous investigations. However, the evolution of the LEE, its origin and further spread in E. coli, are far from being resolved.

Bacteria↗
PubMed2005

Off the hook--how bacteria survive protozoan grazing.

Bacterial growth and survival in numerous environments are constrained by the action of bacteria-consuming protozoa. Recent findings suggest that bacterial adaptations against protozoan predation might have a significant role in bacterial persistence and diversification. We argue that selective predation has given rise to diverse routes of bacterial defense, including adaptive mechanisms in bacterial biofilms, and has promoted major transitions in bacterial evolution, such as multicellularity and pathogenesis. We propose that studying predation-driven adaptations will provide an exciting frontier for microbial ecology and evolution at the interface of prokaryotes and eukaryotes.

Adaptation, Biological↗
PubMed1994

Bacterial gene transfer by natural genetic transformation in the environment.

Natural genetic transformation is the active uptake of free DNA by bacterial cells and the heritable incorporation of its genetic information. Since the famous discovery of transformation in Streptococcus pneumoniae by Griffith in 1928 and the demonstration of DNA as the transforming principle by Avery and coworkers in 1944, cellular processes involved in transformation have been studied extensively by in vitro experimentation with a few transformable species. Only more recently has it been considered that transformation may be a powerful mechanism of horizontal gene transfer in natural bacterial populations. In this review the current understanding of the biology of transformation is summarized to provide the platform on which aspects of bacterial transformation in water, soil, and sediments and the habitat of pathogens are discussed. Direct and indirect evidence for gene transfer routes by transformation within species and between different species will be presented, along with data suggesting that plasmids as well as chromosomal DNA are subject to genetic exchange via transformation. Experiments exploring the prerequisites for transformation in the environment, including the production and persistence of free DNA and factors important for the uptake of DNA by cells, will be compiled, as well as possible natural barriers to transformation. The efficiency of gene transfer by transformation in bacterial habitats is possibly genetically adjusted to submaximal levels. The fact that natural transformation has been detected among bacteria from all trophic and taxonomic groups including archaebacteria suggests that transformability evolved early in phylogeny. Probable functions of DNA uptake other than gene acquisition will be discussed. The body of information presently available suggests that transformation has a great impact on bacterial population dynamics as well as on bacterial evolution and speciation.

DNA, Bacterial↗
PubMed2000

Symbiosis and pathogenesis: evolution of the microbe-host interaction.

Symbiotic and pathogenic bacteria have in common that they live in or on host organisms or host cells. To make a successful living in eukaryotic hosts, bacteria must possess the traits to recognize a given host and establish adherence. When the bacterial location is internal or intracellular, they must further have the ability to invade, to establish a niche, and finally to multiply within a host. The underlying mechanisms which allow this form of existence show similarities between symbiotic and pathogenic bacteria. The final outcome, however, may result in a wide spectrum of consequences for the host ranging from the acquisition of novel metabolic pathways to damage or death. Despite the vastly different forms of interactions, symbiotic and pathogenic bacteria have in common that they are adapted to a particular environmental niche represented by the host organism or compartment thereof. This contribution reviews the evolutionary forces which have shaped the microbial-host interactions. Particular emphasis is placed on the genetic and molecular mechanisms that drive bacterial evolution in response to the selective pressures of the host environment.

Animals↗
PubMed1991

Natural transfer of conjugative transposon Tn916 between gram-positive and gram-negative bacteria.

The conjugative streptococcal transposon Tn916 was found to transfer naturally between a variety of gram-positive and gram-negative eubacteria. Enterococcus faecalis hosting the transposon could serve as a donor for Alcaligenes eutrophus, Citrobacter freundii, and Escherichia coli at frequencies of 10(-6) to 10(-8). No transfer was observed with several phototrophic species. Mating of an E. coli strain carrying Tn916 yielded transconjugants with Bacillus subtilis, Clostridium acetobutylicum, Enterococcus faecalis, and Streptococcus lactis subsp. diacetylactis at frequencies of 10(-4) to 10(-6). Acetobacterium woodii was the only gram-positive organism tested that did not accept the transposon from a gram-negative donor. The results prove the ability of conjugative transposable elements such as Tn916 for natural cross-species gene transfer, thus potentially contributing to bacterial evolution.

Bacillus subtilis↗
PubMed2003

Widespread horizontal transfer of mitochondrial genes in flowering plants.

Horizontal gene transfer--the exchange of genes across mating barriers--is recognized as a major force in bacterial evolution. However, in eukaryotes it is prevalent only in certain phagotrophic protists and limited largely to the ancient acquisition of bacterial genes. Although the human genome was initially reported to contain over 100 genes acquired during vertebrate evolution from bacteria, this claim was immediately and repeatedly rebutted. Moreover, horizontal transfer is unknown within the evolution of animals, plants and fungi except in the special context of mobile genetic elements. Here we show, however, that standard mitochondrial genes, encoding ribosomal and respiratory proteins, are subject to evolutionarily frequent horizontal transfer between distantly related flowering plants. These transfers have created a variety of genomic outcomes, including gene duplication, recapture of genes lost through transfer to the nucleus, and chimaeric, half-monocot, half-dicot genes. These results imply the existence of mechanisms for the delivery of DNA between unrelated plants, indicate that horizontal transfer is also a force in plant nuclear genomes, and are discussed in the contexts of plant molecular phylogeny and genetically modified plants.

Base Sequence↗
PubMed2006

Gene gain and gene loss in streptococcus: is it driven by habitat?

Bacterial genomes can evolve either by gene gain, gene loss, mutating existing genes, and/or by duplication of existing genes. Recent studies have clearly demonstrated that the acquisition of new genes by lateral gene transfer (LGT) is a predominant force in bacterial evolution. To better understand the significance of LGT, we employed a comparative genomics approach to model species-specific and intraspecies gene insertions/deletions (ins/del among 12 sequenced streptococcal genomes using a maximum likelihood method. This study indicates that the rate of gene ins/del is higher on the external branches and varies dramatically for each species. We have analyzed here some of the experimentally characterized species-specific genes that have been acquired by LGT and conclude that at least a portion of these genes have a role in adaptation.

Adaptation, Biological↗
PubMed2006

Shuffling bacterial metabolomes.

Horizontal gene transfer (HGT) has a far more significant role than gene duplication in bacterial evolution. This has recently been illustrated by work demonstrating the importance of HGT in the emergence of bacterial metabolic networks, with horizontally acquired genes being placed in peripheral pathways at the outer branches of the networks.

Bacteria↗
PubMedDate not supplied

Bacterial meningitis in hemodialyzed patients.

BACKGROUND: To analyze the clinical features, causative pathogens and therapeutic outcomes of bacterial meningitis in hemodialyzed patients. PATIENTS AND METHODS: Two hundred and sixty-seven patients, > or = 16 yrs, were identified with culture-proven bacterial meningitis. In addition, the causative pathogens and therapeutic outcomes between uremic and non-uremic patients with adult bacterial meningitis were analyzed. RESULTS: Nine uremic patients with bacterial meningitis, accounting for 3% (9/267) of our adult patients with culture-proven bacterial meningitis had fever, disturbed consciousness and seizures. These were the three most common manifestations in our patients. The interval between the onset of symptoms and therapy start was 5-11 days (mean: 9 days). No patients were initially diagnosed with bacterial meningitis, two patients were initially suspected of having infection of unknown origin. In the non-uremic patient group, klebsiella pneumoniae, Staphylococcus aureus, and Streptococcus pneumoniae were the most frequently detected pathogens, while pseudomonas aeruginosa and coagulase-negative Staphylococcus were the most prevalent in the uremic patients group. The overall mortality rates for the non-uremic and uremic patient groups were 33 and 78% respectively. CONCLUSION: The mortality rate for bacterial meningitis in the uremic patients group remained high. Due to non-specific manifestations and slow evolution, bacterial meningitis was commonly misdiagnosed as uremic encephalopathy. Therefore, effective treatment was usually delayed. To avoid treatment failure, early diagnosis, careful monitoring of clinical condition and appropriate antibiotic choices are necessary.

Adult↗
PubMed1991

A correlation of phylogenetic diversity in the Proteobacteria with the influences of ecological forces.

The Proteobacteria are physiologically and morphologically diverse, although they form a coherent set of four main lineages on phylogenetic analysis of ribosomal RNA. A rational and consistent taxonomic arrangement bringing today's phenotypic and phylogenetic conclusions about them into register is not yet possible. It is also difficult to understand the selective forces involved in their evolution that fostered such diversity. This latter problem is addressed in this essay and is based on the assumption that bacterial evolution could only have occurred in ecological consortia whose products of metabolism modified the environment, provided nutrition, and have a basis for selection of new capabilities.

Bacteria↗
PubMed2005

Genome plasticity and ori-ter rebalancing in Salmonella typhi.

Genome plasticity resulting from frequent rearrangement of the bacterial genome is a fascinating but poorly understood phenomenon. First reported in Salmonella typhi, it has been observed only in a small number of Salmonella serovars, although the over 2,500 known Salmonella serovars are all very closely related. To gain insights into this phenomenon and elucidate its roles in bacterial evolution, especially those involved in the formation of particular pathogens, we systematically analyzed the genomes of 127 wild-type S. typhi strains isolated from many places of the world and compared them with the two sequenced strains, Ty2 and CT18, attempting to find possible associations between genome rearrangement and other significant genomic features. Like other host-adapted Salmonella serovars, S. typhi contained large genome insertions, including the 134 kb Salmonella pathogenicity island, SPI7. Our analyses showed that SPI7 disrupted the physical balance of the bacterial genome between the replication origin (ori) and terminus (ter) when this DNA segment was inserted into the genome, and rearrangement in individual strains further changed the genome balance status, with a general tendency toward a better balanced genome structure. In a given S. typhi strain, genome diversification occurred and resulted in different structures among cells in the culture. Under a stressed condition, bacterial cells with better balanced genome structures were selected to greatly increase in proportion; in such cases, bacteria with better balanced genomes formed larger colonies and grew with shorter generation times. Our results support the hypothesis that genome plasticity as a result of frequent rearrangement provides the opportunity for the bacterial genome to adopt a better balanced structure and thus eventually stabilizes the genome during evolution.

Evolution, Molecular↗
PubMed1997

Conserved clusters of functionally related genes in two bacterial genomes.

An approach for genome comparison, combining function classification of gene products and sequence comparison, is presented. The genomes of Haemophilus influenzae and Escherichia coli are analyzed, and all genes are classified into nine major functional classes, corresponding to important cellular processes. To study gene order relationships and genome organization in the two bacteria, we performed statistics on neighboring pairs of genes. To estimate the significance of the observations, a statistical model based on binomial distributions has been developed. Significant patterns of gene order are observed within, as well as between, the two bacterial genomes: Functionally related genes tend to be neighbors more often than do unrelated genes. Some of these groups represent well-known operons, but additional gene clusters are identified. These clusters correspond to genomic elements that have been conserved during bacterial evolution. In addition to nearest-neighbor relationships, the method is also useful to study the relative direction of transcription in genomes, which is also highly conserved between homologous gene pairs. This new approach combines the high-level description of molecular function with pair statistics that express genome organization. It is expected to complement traditional methods of sequence analysis in the study of genomic structure, function, and evolution.

Binomial Distribution↗
PubMed2004

Patterns of bacterial gene movement.

Lateral gene transfer has emerged as an important force in bacterial evolution. A substantial number of genes can be inserted into or deleted from genomes through the process of lateral transfer. In this study, we looked for atypical occurrence of genes among related organisms to detect laterally transferred genes. We have analyzed 50 bacterial complete genomes from nine groups. For each group we use a 16s rRNA phylogeny and a comparison of protein similarity to map gene insertions/deletions onto their species phylogeny. The results reveal that there is poor correlation of genes inserted, deleted, and duplicated with evolutionary branch length. In addition, the numbers of genes inserted, deleted, or duplicated within the same branch are not always correlated with each other. Nor is there any similarity within groups. For example, in the Rhizobiales group, the ratio of insertions to deletions in the evolutionary branch leading to Agrobacterium tumefaciens str. C58 (Cereon) is 0.52, but it is 39.52 for Mesorhizobium loti. Most strikingly, the number of insertions of foreign genes is much larger in the external branches of the trees. These insertions also greatly outnumber the occurrence of deletions, and yet the genome sizes of these bacteria remain roughly constant. This indicates that many of the insertions are specific to each organism and are lost before related species can evolve. Simulations of the process of insertion and deletion, tailored to each phylogeny, support this conclusion.

Evolution, Molecular↗
PubMed1993

Rapid divergence of Agrobacterium vitis octopine-cucumopine Ti plasmids from a recent common ancestor.

The octopine/cucumopine (o/c) Ti plasmids of the grapevine-associated Agrobacterium vitis strains constitute a family of related DNA molecules. Restriction maps were established of two limited-host-range o/c Ti plasmids, pTiAg57 and pTiAB3, and of the wide-host-range o/c Ti plasmid pTiHm1. Together with the previously obtained map of the wide-host-range o/c Ti plasmid pTiTm4, about 1000 kb were mapped with a resolution of 0.2 kb, allowing a detailed comparison of the various structures. One region of the o/c Ti plasmids is highly conserved and differs mainly by the presence or absence of relatively small DNA fragments (0.9-2.7 kb); the other region has been modified more extensively and carries large sequences specific for each Ti plasmid type. The sequence similarity within large conserved regions shows that these plasmids have diverged recently and that their evolution was driven by large-scale genetic events rather than single nucleotide changes. These results have important implications for studies on bacterial evolution.

Arginine↗
PubMed2007

An H-NS-like stealth protein aids horizontal DNA transmission in bacteria.

The Sfh protein is encoded by self-transmissible plasmids involved in human typhoid and is closely related to the global regulator H-NS. We have found that Sfh provides a stealth function that allows the plasmids to be transmitted to new bacterial hosts with minimal effects on their fitness. Introducing the plasmid without the sfh gene imposes a mild H-NS(-) phenotype and a severe loss of fitness due to titration of the cellular pool of H-NS by the A+T-rich plasmid. This stealth strategy seems to be used widely to aid horizontal DNA transmission and has important implications for bacterial evolution.

Bacterial Proteins↗
PubMed2002

Mobility of a restriction-modification system revealed by its genetic contexts in three hosts.

The flow of genes among prokaryotes plays a fundamental role in shaping bacterial evolution, and restriction-modification systems can modulate this flow. However, relatively little is known about the distribution and movement of restriction-modification systems themselves. We have isolated and characterized the genes for restriction-modification systems from two species of Salmonella, S. enterica serovar Paratyphi A and S. enterica serovar Bareilly. Both systems are closely related to the PvuII restriction-modification system and share its target specificity. In the case of S. enterica serovar Paratyphi A, the restriction endonuclease is inactive, apparently due to a mutation in the subunit interface region. Unlike the chromosomally located Salmonella systems, the PvuII system is plasmid borne. We have completed the sequence characterization of the PvuII plasmid pPvu1, originally from Proteus vulgaris, making this the first completely sequenced plasmid from the genus Proteus. Despite the pronounced similarity of the three restriction-modification systems, the flanking sequences in Proteus and Salmonella are completely different. The SptAI and SbaI genes lie between an equivalent pair of bacteriophage P4-related open reading frames, one of which is a putative integrase gene, while the PvuII genes are adjacent to a mob operon and a XerCD recombination (cer) site.

Amino Acid Sequence↗