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At least 19 recordsLinked to original sources
PubMed2026

Unveiling a missing component of the atypical type IV secretion system required for natural transformation of Helicobacter pylori.

Exchange of genetic information by natural transformation shapes bacterial evolution. In Helicobacter pylori it is thought to drive its unusually high recombination rate, which has a crucial role in the evolution of virulence and the propagation of antibiotics resistance genes. While in most cases uptake of the incoming DNA into the periplasm is mediated by type IV pili, in H. pylori this initial step of natural transformation requires ComB, a unique competence-specific type IV secretion system (T4SS). The mechanisms by which ComB mediates DNA uptake are still poorly understood, since T4SS are usually involved in an opposite process of DNA export. Here, we identify a gene (hp1421) that is absolutely required for uptake of the transforming DNA into the periplasm, although distant from the comB operons. We show that hp1421 codes for a hexameric ATPase from the VirB11 family. HP1421 is present in the cytoplasm and interacts with ComB4, another ATPase of the T4SS inner membrane subcomplex. The structural modelling and functional analysis of HP1421 and its interaction with ComB4 indicate that HP1421 is a missing component of the ComB inner-membrane subcomplex that we propose to name ComB11. Phylogenetic analyses show that comB11 is a H. pylori core gene and suggest that the competence-dedicated ComB T4SS was a recent acquisition within Helicobacteraceae. Hence, co-option of the T4SS for DNA transformation requires nearly all the proteins that were previously essential for DNA conjugation.

Helicobacter pylori↗
PubMed2026

Unveiling a missing component of the atypical type IV secretion system required for natural transformation of Helicobacter pylori.

Exchange of genetic information by natural transformation shapes bacterial evolution. In Helicobacter pylori it is thought to drive its unusually high recombination rate, which has a crucial role in the evolution of virulence and the propagation of antibiotics resistance genes. While in most cases uptake of the incoming DNA into the periplasm is mediated by type IV pili, in H. pylori this initial step of natural transformation requires ComB, a unique competence-specific type IV secretion system (T4SS). The mechanisms by which ComB mediates DNA uptake are still poorly understood, since T4SS are usually involved in an opposite process of DNA export. Here, we identify a gene (hp1421) that is absolutely required for uptake of the transforming DNA into the periplasm, although distant from the comB operons. We show that hp1421 codes for a hexameric ATPase from the VirB11 family. HP1421 is present in the cytoplasm and interacts with ComB4, another ATPase of the T4SS inner membrane subcomplex. The structural modelling and functional analysis of HP1421 and its interaction with ComB4 indicate that HP1421 is a missing component of the ComB inner-membrane subcomplex that we propose to name ComB11. Phylogenetic analyses show that comB11 is a H. pylori core gene and suggest that the competence-dedicated ComB T4SS was a recent acquisition within Helicobacteraceae. Hence, co-option of the T4SS for DNA transformation requires nearly all the proteins that were previously essential for DNA conjugation.

Journal Article↗
PubMed2025

Accumulation of numerous cellular T-DNA sequences in the genus Diospyros by multiple rounds of natural transformation.

Horizontal gene transfer (HGT) is an important phenomenon in the evolutionary history of plants. Natural transformation by Agrobacterium is a special case of HGT and leads to the insertion of cellular T-DNA (cT-DNA) sequences, for example, in Diospyros lotus. The genus Diospyros contains about 795 species with economically important members, like different types of persimmon (D. kaki, D. lotus, and D. virginiana) and ebony (e.g., D. ebenum). Whole genome sequences (WGS) from D. kaki, D. oleifera, D. lotus, and D. virginiana were investigated for cT-DNAs. These four species belong to one clade and contain 15 different cT-DNAs (DiTA to DiTO). The hexaploid species D. kaki cv. "Xiaoguo-tianshi" contains seven types of cT-DNA (DiTA to DiTG) on 27 of 42 homeologs, adding up to 628 kb of cT-DNA. Five of these seven cT-DNAs are non-fixed, as shown by empty chromosomal insertion sites. The evolutionary history of the Diospyros cT-DNAs was reconstructed using the divergence of their inverted repeats. Insert age varied from 3 to 12 million years. Partial cT-DNA sequences were detected in 35 additional species from five Diospyros clades. Our data highlight the unexpectedly large scale of natural Agrobacterium transformation in Diospyros and demonstrate the necessity of whole genome approaches for studies on the origin and evolution of cT-DNAs.

Diospyros↗
PubMedDate not supplied

Microbial transformations of natural antitumor agents. VIII. Formation of 8- and 9-hydroxyellipticines.

Microbial transformations of ellipticine with Aspergillus alliaceus (NRRL 315) yielded two phenolic metabolites which were isolated and characterized as 8- and 9-hydroxyellipticines. The latter is a major metabolite and its structure was determined by NMR and mass-spectometric analyses, and by comparison with authentic 9-hydroxyellipticine prepared by chemical demethylation of 9-methoxyellipticine. The structure of 8-hydroxyellipticine was determined primarily by NMR spectrometry. Whereas 8-hydroxyellipticine is a new derivative, 9-hydroxyellipticine has been described, and it is one of the major mammalian metabolites of the antitumor alkaloid ellipticine.

Alkaloids↗
PubMed1977

Microbial transformations of natural antitumor agents. 3. Conversion of thalicarpine to (+)-hernandalinol by Streptomyces punipalus.

Microbial transformation studies were conducted with the antitumor alkaloid thalicarpine. Streptomyces punipalus (NRRL 3529) converted thalicarpine to (+)-hernandalinol, the structure of which was determined spectroscopically and by synthesis from the known alkaloid hernandaline. This unusual biotransformation reaction most likely occurs by oxidative cleavage of the isoquinoline ring from thalicarpine through the intermediate hernandaline, which then undergoes further reduction to hernandalinol.

Antineoplastic Agents, Phytogenic↗
PubMed1978

Microbial transformations of natural antitumor agents: O-demethylation of vindoline by Sepedonium chrysospermum.

Vindoline (1a) was transformed to O-demethylvindoline (1b) by Sepedonium chrysospermum ATCC 13378 in 33% yield. Thin-layer and high-pressure liquid chromatographic methods distinguished 1b from previously reported microbial metabolites of vindoline. The structural proof of 1b was based on its mass spectral fragmentation pattern and on its chemical and nuclear magnetic resonance spectral properties.

Dealkylation↗
PubMed2026

Embryophyte-wide detection of natural Agrobacterium-mediated horizontal gene transfer reveals an ancient role for mini T-DNAs.

Agrobacterium transfers DNA into plant cells, leading to tumors, hairy roots (HR), and natural genetically modified organisms (nGMOs). Transferred DNAs (T-DNAs) from agrobacteria and T-DNA-derived cellular T-DNAs (cT-DNAs) from nGMOs vary considerably and may carry up to 15 different genes. Among these, opine synthase (ops) genes encode the synthesis of opines used as nutrients by the agrobacteria. Earlier studies predicted large numbers of naturally transformed plant species, but only few have been identified and studied so far. We therefore developed a general method to detect cT-DNAs in all publicly available whole genome sequences (WGS) and Sequence Read Archive (SRA) data from land plants. To avoid false positives, we only retained DNA sequences coding for T-DNA proteins. A total of 2614 nGMO species were identified, most are eudicots. However, cT-DNAs were also found in 82 mosses and 75 ferns, showing that Agrobacterium can also generate natural transformants among the early land plants. Analysis of 149 cT-DNA maps revealed different types of T-DNAs. Most notably, these included small T-DNAs (mini T-DNAs) with a single opine synthase gene. Mini T-DNAs are not expected to induce tumors or HRs. The predominance of mini cT-DNAs in mosses and ferns, and the presence of more complex cT-DNAs in spermatophytes, indicate that mini T-DNAs represent the earliest types of T-DNA. Our study also detected unusual T-DNA integration patterns, with multiple copies spread out over several hundreds of kilobases.

DNA, Bacterial↗
PubMed2025

LytF contributes to pilus extrusion during natural competence in Streptococcus sanguinis SK36.

Streptococci may enter a physiological state called competence, during which they express a specific set of genes required for exogenous DNA uptake and its subsequent integration into the genome through homologous recombination. This process, termed natural transformation, facilitates the horizontal acquisition of genetic material, potentially conferring adaptive advantages that enhance bacterial survival under selective pressures. To make homologous DNA available in the surrounding environment, Streptococcus pneumoniae expresses a cell wall hydrolase (CbpD) that lyses and kills closely related species. This process has been coined fratricide, and the acting hydrolase a fratricin. A significant fraction of streptococcal species does not encode a CbpD-like protein, but another competence-induced peptidoglycan hydrolase LytF. It has been speculated that LytF serves the same purpose as CbpD, however, our investigations into the role of LytF in Streptococcus sanguinis revealed no evidence supporting LytF as a fratricin. Instead, we show that LytF is involved in natural transformation by promoting DNA uptake. An essential part of DNA uptake is the competence-induced type IV pilus, which facilitates DNA uptake by pulling nearby DNA toward the cell. By immunoblotting and microscopy imaging, we found that LytF increases the extracellular levels of the major pilus component ComGC, suggesting that LytF may modify peptidoglycan to promote pilus extrusion across the cell wall, thereby enhancing the efficiency of DNA uptake.

Journal Article↗
PubMedDate not supplied

Nature of transformation of hydrocortisone by cells incorporated into polyacrylamide gel.

The ability of Mycobacterium globiforme 193 cells immobilized in polyacrylamide gel (Paag) to transform soluble and microcrystalline hydrocortisone was investigated under conditions to periodic aeration. It was found that the specific 3-oxosteroid-delta'-dehydrogenase activity of immobilized cells hardly differs from that of free cells and averages 0.06 mumole/mg cells . min; the quantitative and qualitative composition of the transformation products formed by free and immobilized cells was identical. The linear relation between the accumulation of the reaction product, prednisolone, and the transformation time, the absence of an activating effect of SAA [surface-active agents] on the 3-oxosteroid-delta'-dehydrogenase activity, the correlation between enzymatic activity and viability, and the absence of an increase in activity during repeated transformations indicate that the cytoplasmic membrane of Myc. globiforme is not a significant diffusion barrier for the reaction substrate and product. Maintenance of immobilized cells in a viable state is a necessary condition of the retention of enzymatic activity by these cells. "Activation" of immobilized cells is achieved by incubating the granules in nutrient medium. The cause of the "activation," in our opinion, is the appearance of a new surface and, probably, internal cell population.

3-Hydroxysteroid Dehydrogenases↗
PubMed2025

Global diversity of integrating conjugative elements (ICEs) in Helicobacter pylori and their influence on genome architecture.

Integrating conjugative elements (ICEs) are mobile genetic elements conferring a wide range of beneficial functions upon their bacterial hosts. Generally, they can be activated from their integrated states to undergo horizontal gene transfer via conjugation. In the case of the human gastric pathogen Helicobacter pylori, a paradigm for extensive genetic diversity, highly efficient natural transformation and recombination processes may superimpose canonical transfer of its two ICEs termed ICEHptfs3 and ICEHptfs4, and thus shape their composition substantially. Here, as a part of the Helicobacter pylori Genome Project (HpGP) initiative, we have analyzed high-quality genome sequences from 1011 clinical strains with respect to their ICE content and variability. We show that both elements are highly prevalent in all H. pylori populations, but have a strong tendency for gene erosion. ICE sequence variations reflect the population structure and show a clear signature of increased horizontal transfer. A detailed map of ICE integration sites revealed local preferences, but also how recombination processes result in hybrid elements or genome rearrangements. Population-specific differences in ICE cargo genes might reflect distinct requirements in the biological functions provided by these mobile elements.

Journal Article↗
PubMed2003

How clonal is Staphylococcus aureus?

Staphylococcus aureus is an important human pathogen and represents a growing public health burden owing to the emergence and spread of antibiotic-resistant clones, particularly within the hospital environment. Despite this, basic questions about the evolution and population biology of the species, particularly with regard to the extent and impact of homologous recombination, remain unanswered. We address these issues through an analysis of sequence data obtained from the characterization by multilocus sequence typing (MLST) of 334 isolates of S. aureus, recovered from a well-defined population, over a limited time span. We find no significant differences in the distribution of multilocus genotypes between strains isolated from carriers and those from patients with invasive disease; there is, therefore, no evidence from MLST data, which index variation within the stable "core" genome, for the existence of hypervirulent clones of this pathogen. Examination of the sequence changes at MLST loci during clonal diversification shows that point mutations give rise to new alleles at least 15-fold more frequently than does recombination. This contrasts with the naturally transformable species Neisseria meningitidis and Streptococcus pneumoniae, in which alleles change between 5- and 10-fold more frequently by recombination than by mutation. However, phylogenetic analysis suggests that homologous recombination does contribute toward the evolution of this species over the long term. Finally, we note a striking excess of nonsynonymous substitutions in comparisons between isolates belonging to the same clonal complex compared to isolates belonging to different clonal complexes, suggesting that the removal of deleterious mutations by purifying selection may be relatively slow.

Alleles↗
PubMed2025

Naturally competent bacteria and their genetic parasites-a battle for control over horizontal gene transfer?

Host-mediated natural competence for transformation of DNA and mobile genetic element (MGE)-driven conjugation and transduction are key modes of horizontal gene transfer. While these mechanisms are traditionally believed to shape bacterial evolution by enabling the acquisition of new genetic traits, numerous studies have elucidated an antagonistic relationship between natural transformation and MGEs. A new role of natural transformation as a chromosome-curing mechanism has now been proposed. Experimental data, along with mathematical models, suggest that transformation can eliminate deleterious MGEs. Supporting this hypothesis, MGEs have been shown to use various mechanisms to decrease or block transformability, such as disrupting competence genes, regulating the development of competence, hindering DNA uptake machinery, producing DNases that target the exogenous (transforming) DNA, and causing lysis of competent cells. A few examples of synergistic relationships between natural transformation and MGEs have also been reported, with natural transformation facilitating MGE transfer and phages enhancing transformation by supplying extracellular DNA through lysis and promoting competence via kin discrimination. Given the complexity of the relationships between natural transformation and MGEs, the balance between antagonism and synergy likely depends on specific selection pressures in a given context. The evidence collected here indicates a continuous conflict over horizontal gene transfer in bacteria, with semiautonomous MGEs attempting to disrupt host-controlled DNA acquisition, while host competence mechanisms work to resist MGE interference.

Gene Transfer, Horizontal↗
PubMed1978

Evidence for the progressive nature of neoplastic transformation in vitro.

The temporal acquisition of in vitro phenotypes associated with neoplasia were examined after exposure of Syrian hamster embryo cells to a chemical carcinogen. Quantitative assays measuring morphological changes, enhanced fibrinolytic activity, and anchorage independent growth were used to detect the development of transformed cells within a population of normal hamster embryo cells. Morphological transformation and enhanced fibrinolytic activity were early changes observed after treatment with benzo[alpha]-pyrene, whereas the ability to grow in semisolid agar was delayed 32-75 population doublings after carcinogen exposure. This delay was not due to selection of a small number of cells that were present early after treatment but at a level below detection, because a large percentage of the cells isolated at early passage (10(3)-fold above the level of detection) developed the potential for anchorage independent growth at later passages. This development of the anchorage independent growth phenotype was induced by the carcinogen treatment, because spontaneous transformation was rare. These observation suggest that multiple cellular changes are required for the acquisition of the capacity for anchorage independent growth and that neoplastic transformation in vitro is a progressive process through qualitatively different stages. Thus, an analogy can be drawn to the progressive nature of in vivo carcinogenesis. These results strongly justify the study of oncogenesis in cell culture as a model for neoplastic transformation in vivo.

Animals↗