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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↗

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↗

PubMed1979

Influence of a naturally occurring competing enzymic activity on studies of 3-hydroxy-3-methylglutaryl coenzyme A reductase activity.

An enzymic activity which competes with 3-hydroxy-3-methylglutaryl coenzyme A reductase for D-hydroxymethylglutaryl CoA has been found in isolated rat liver microsomes and in microsomal extracts. The presence of this activity in enzyme preparations causes a decrease in the rate of mevalonate formation leading to an underestimation of reductase activity and an overestimation of the apparent Km of the reductase. The product formed by this competing enzymic activity behaves similarly to, but not identically with, mevalonolactone when chromatographed on Bio-Rad AG 1-x8 formate, which is used in many reductase assay procedures to separate mevalonolactone from hydroxymethylglutaryl CoA. Removal of this competing enzymic activity from reductase preparations can be accomplished by gel filtration using Bio-Gel A 1.5m, by washing the microsomes or by incubating the microsomal extract at 37 degrees C. Using enzyme preparations free of this competing enzymic activity, the apparent Km values of the reductase for D-hydroxymethylglutaryl CoA and NADPH were found to be 1.3 and 26 micronM respectively.

Animals↗

PubMed2026

High-throughput recovery of integron cassettes for gene discovery screens.

Integrons capture functional genes in mobile genetic elements called integron cassettes, which represent an untapped source of genes of biotechnological interest. Here we present two tools, cassette gatherer and cassette hunter, that enable high-throughput establishment of gene libraries either from genetically tractable strains or directly from DNA. We re-engineered a class 1 integron into counterselection markers on a plasmid or on the chromosome of a naturally competent Vibrio cholerae, which enabled capture of single cassettes in a sequence- and function-independent manner. When applied to Vibrio strains and genomic libraries, our tools recovered hundreds of single cassettes per assay with more than 99% specificity. We further subjected the library of cassettes generated by the hunter and gatherer tools to screens against phages ICP2 and T4, and identified nine phage-defence systems, including five previously undescribed. These tools enable rapid and large-scale recovery of integron cassettes that could be leveraged for functional gene discovery.

Journal Article↗

PubMed2025

ComFB, a widespread family of c-di-NMP receptor proteins.

Cyclic dimeric-GMP (c-di-GMP) is a ubiquitous bacterial second messenger that regulates a variety of cellular processes, including motility, biofilm formation, secretion, cell cycle progression, and development, and also contributes to the virulence of many bacterial pathogens. While the genes encoding c-di-GMP cyclases and hydrolases are readily identifiable in microbial genomes, known c-di-GMP receptor domains are quite few, with only PilZ and MshEN broadly distributed across bacterial phyla. Recently, a new c-di-GMP receptor, named CdgR or ComFB, has been identified in cyanobacteria and shown to regulate cell size and natural competence. We demonstrated that CdgR proteins exhibit sequence and structural similarity to the Bacillus subtilis late competence development protein ComFB, a conserved protein of unknown function associated with bacterial competence. This prompted us to hypothesize that ComFB and ComFB-like proteins could also serve as c-di-GMP receptors. Here, we comprehensively investigated the ComFB protein family and demonstrated that ComFB proteins are evolutionarily widespread among bacteria and function as a novel family of c-di-GMP receptors. We showed that ComFB proteins from Gram-positive bacteria (B. subtilis, Thermoanaerobacter brockii) and Gram-negative pathogens (Vibrio cholerae, Treponema denticola) bind c-di-GMP with high affinity. Several ComFB proteins also bind cyclic di-adenosine monophosphate (c-di-AMP), suggesting that ComFB represents a widely distributed bacterial protein family with dual specificity for c-di-GMP and c-di-AMP. Our physiological studies further showed that ComFB plays vital roles in controlling motility in a c-di-GMP-dependent manner in two phylogenetically distant bacteria, B. subtilis and the gram-negative Shewanella oneidensis, attesting to the biological relevance of ComFB as a c-di-GMP binding protein.

Bacterial Proteins↗

PubMed2025

Protein overabundance is driven by growth robustness.

Protein expression levels optimize cell fitness: Too low an expression level of essential proteins will slow growth by compromising essential processes; whereas overexpression slows growth by increasing the metabolic load. This trade-off naïvely predicts that cells maximize their fitness by sufficiency, expressing just enough of each essential protein for function. We test this prediction in the naturally-competent bacterium Acinetobacter baylyi by characterizing the proliferation dynamics of essential-gene knockouts at a single-cell scale (by imaging) as well as at a genome-wide scale. In these experiments, cells proliferate for multiple generations as target protein levels are diluted from their endogenous levels. This approach facilitates a proteome-scale analysis of the fitness landscape with respect to protein abundance. We find that most essential proteins are subject to a threshold-like fitness landscape: growth is independent of protein abundance above a critical threshold and arrests below that threshold. We have recently analyzed the implications of this landscape for growth robustness. Confirming signature predictions of this model, we find that (i) roughly 70% of essential proteins are overabundant, (ii) overabundance increases as the expression level decreases and (iii) the lowest abundance proteins are in vast excess (>10×) of what is required for growth in the typical cell. These results reveal that robustness plays a fundamental role in determining the expression levels of essential genes and that overabundance is a key mechanism for ensuring robust growth.

Journal Article↗

PubMed2024

Development of SacB-based counterselection for efficient allelic exchange in Fusobacterium nucleatum.

Fusobacterium nucleatum, prevalent in the oral cavity, is significantly linked to overall human health. Our molecular comprehension of its role in oral biofilm formation and its interactions with the host under various pathological circumstances has seen considerable advancements in recent years, primarily due to the development of various genetic tools for DNA manipulation in this bacterium. Of these, counterselection-based unmarked in-frame mutation methods have proved notably effective. Under suitable growth conditions, cells carrying a counterselectable gene die, enabling efficient selection of rare, defined allelic exchange mutants. The sacB gene from Bacillus subtilis, encoding levansucrase, is a widely used counterselective marker partly due to the easy availability of sucrose. Yet, its potential application in F. nucleatum genetic study remains untested. We demonstrated that F. nucleatum cells expressing sacB in either a shuttle or suicide plasmid exhibit a lethal sensitivity to supplemental sucrose. Utilizing sucrose counterselection, we created an in-frame deletion of the F. nucleatum tonB gene, a critical gene for energy-dependent transport processes in Gram-negative bacteria, and a precise knock-in of the luciferase gene immediately following the stop codon of the hslO gene, the last gene of a five-gene operon possibly related to the natural competence of F. nucleatum. Post-counterselection with 5% sucrose, chromosomal plasmid loss occurred in all colonies, leading to gene alternations in half of the screened isolates. This sacB-based counterselection technique provides a reliable method for isolating unmarked gene mutations in wild-type F. nucleatum, enriching the toolkit for fusobacterial research.IMPORTANCEInvestigations into Fusobacterium nucleatum's role in related diseases significantly benefit from the strategies of creating unmarked gene mutations, which hinge on using a counterselective marker. Previously, the galk-based allelic exchange method, although effective, faced an inherent limitation-the need for a modified host. This study aims to surmount this limitation by substituting galK with sacB for gene modification in F. nucleatum. Our application of the sacB-based methodology successfully yielded a tonB in-frame deletion mutant and a luciferase gene knock-in at the precise chromosomal location in the wild-type background. The new method augments the existing toolkit for F. nucleatum research and has far-reaching implications due to the easy accessibility to the counterselection compound sucrose. We anticipate its broader adoption in further exploration, thereby reinforcing its critical role in propelling our understanding of F. nucleatum.

Fusobacterium nucleatum↗

PubMed1979

Binding specificity of the two major DNA-binding proteins in human serum.

The two major DNA-binding proteins of human serum (DNA-binding protein 1 and DNA-binding protein 2) were shown to bind preferentially to single-stranded polynucleotides rich in guanine residues. Equilibrium competition experiments using a nitrocellulose filter assay system containing labeled human lymphocyte DNA and various competing natural and synthetic polynucleotides indicated that both proteins recognized sequences of bases containing a keto group in either position 6 (purines) or 4 (pyrimidines) and that these keto groups must be readily accessible for effective binding to occur. Guanine was shown to be the preferred nucleotide through inhibition experiments using a series of synthetic homopolymers and a series of bacterial DNAs of differing G + C content. The relationship between protein affinity and G + C content was shown to be directly proportional. The equilibrium constants for the binding of the human lymphocyte DNA by both proteins were on the order of 10(-6) M, and the length of the nucleotide sequence necessary for effective binding was found to be 12 to 18 bases using a series of oligomers of poly(dG).

Carrier Proteins↗

PubMed1979

Competence for genetic transformation in pneumococcus depends on synthesis of a small set of proteins.

In bacterial genetic transformation the uptake of DNA and its integration into the resident chromosome is dependent on a special cellular state, termed competence. In those species where appearance of competence has been studied, specific (but often poorly defined) growth conditions lead to a simultaneous development of competence in a substantial fraction of the cells in a culture. In Bacillus subtilis, and in Haemophilus species, competence appears in the stationary phase of growth or in certain other growth-limiting conditions. Streptococcus pneumoniae (pneumococcus) is perhaps unusual in that virtually all cells of a culture become competent, for a short period at a specific cell density during logarithmic growth, without perturbing the growth rate. The synchronous appearance of competence in pneumococcal cultures results from an autocatalytic effect of a small protein released by the cells that induces competence. The response to competence factor has been shown to require protein synthesis. We report here additional information on the nature of competence in pneumococcus: pulse-labelling studies show that for the brief period of competence protein synthesis is restricted to a few specific polypeptides.

Bacterial Proteins↗

PubMed1976

Cyclic adenosine monophosphate and the development of Polysphondylium.

Centre formation in Polysphondylium violaceum is delayed for 2 h on buffered agar containing 10(-3) M c-AMP, and for up to 22 h on unbuffered agar with the same c-AMP concentration. With ambient c-AMP concentrations as low as 10(-6) M, P. pallidum forms numerous, small, atypical aggregates which do not fruit. This effect is independent of whether the agar is buffered. P. violaceum amoebae are weakly attracted to the tip of a microelectrole containing 10(-3) or 10(-4) M c-AMP, but the electrode cannot compete when natural centres form nearby. P. pallidum amoebae are not attracted. Aggregates of P. violaceum and of P. pallidum are strongly attracted to a microelectrode releasing c-AMP. The observation of Shaffer that Polysphondylium grex switch over from secreting an acrasin that attracts homologous amoebae to one that attracts the larger Dictyostelium species suggests that the second acrasin might by c-AMP. The above results strengthen this conjecture. As c-AMP inhibits centre formation, the secretion of c-AMP by older aggregates may explain an inhibition of centre formation in the 'overlay' experiments of Shaffer.

Cell Aggregation↗

PubMed1979

Determinants of 5-fluorouracil sensitivity in human tumors.

It is not apparent that advanced human carcinomas of the breast or the large bowel are conprised of at least two populations: those responding to treatment with 5-fluorouracil (approximately 20 per cent) and those unresponsive to this drug. This classification cannot be made before chemotherapy on the basis of any clinical parameter. Biochemical parameters to distinguish between responding and nonresponding tumors are being sought in this laboratory. Techniques have been developed to measure thymidylate synthetase, the target enzyme for 5-fluorouracil, 5-fluoro-2'-deoxyuridylate, the active form of the antimetabolite, and 2'-deoxyuridylate, the naturally occuring competing metabolite. These methods are sufficiently sensitive to permit analysis of these parameters in needle biopsy specimens, and do not require exposure of patients to radioisotopes.

Biopsy, Needle↗

PubMed1979

Influence of sex and handedness on hemispheric functioning.

Forty normal adult volunteers comprising an equal number of right- and left-handed males and females solved simple multiplication problems presented visually to one cerebral hemisphere while various competing stimuli were simultaneously presented to the other hemisphere. The contribution of sex of subject, handedness, hemisphere of presentation and the nature of the competing stimulus in relation to task performance was examined. Each of these variables was significantly associated with correct responses and errors, with few statistically significant interactions. Females and dextrals made more correct responses than males or sinistrals. Type of error depended upon which hemisphere received the problem, with the right hemisphere yielding more errors of commission and the left more errors of omission. Simultaneously presented identical or different arithmetic problems resulted in the most errors compared to the other competing stimuli.

Adult↗

PubMed1976

Formation of ternary complexes of thymidylate synthetase as followed by absorbance, fluorescence, and circular dichroic spectra and gel electrophoresis.

Ternary complexes of thymidylate synthetase (Form II and Form III), which are composed of the enzyme, 5-fluorodeoxyuridylate, and the natural isomer of methylenetetrahydrofolate, were generated by titrating thymidylate synthetase (Form I) in the presence of 5-fluorodeoxyuridylate with either the enzymatically prepared natural isomer or the chemically prepared racemic mixture of the diastereomers of methylenetetrahydrofolate. Such titrations were monitored by absorption, circular dichroic and fluorescence spectroscopy, and polyacrylamide gel electrophoresis. The results of these investigations suggest that the natural isomer of methylenetetrahydrofolate is primarily involved in the formation of stable ternary complexes with thymidylate synthetase and 5-fluorodeoxyuridylate but that the unnatural isomer of methylenetetrahydrofolate, when present in solution, may compete with the natural isomer by forming relatively weak complexes with the enzyme and the 5-fluorodeoxyuridylate.

Binding Sites↗

PubMed1975

Vulnerability of cell-surface receptors to autoimmune reactions.

A previous hypothesis in which myasthenia gravis was explained by an immune response to acetylcholine receptors has been validated, and is here extended to cell receptors in general. Receptors on target cells, being accessible to circulating trophic hormones or transmitters, must also be accessible to antibodies which compete with the natural mediator for access to the site. To detect anti-receptor antibodies, physiological assay systems would be more sensitive than conventional immunological assays. Autoimmune responses to receptor sites would require a genetic predisposition to failure of immunological tolerance such as occurs in various autoimmune diseases. This hypothesis is supported by recent findings in hyperthyroidism and a type of insulin-resistant diabetes mellitus, and is applicable to other endocrinopathies, diseases in which dysfunction at receptor sites can be postulated, and regulatory functions within the immune system itself.

Animals↗

PubMedDate not supplied

[Selective binding of tRNA by RNA dependent DNA-polymerase from Escherichia coli].

Highly purified RNA dependent DNA-polymerase was isolated recently from E. coli by Romashchenko et al. [8]. The present data demonstrate that total E. coli tRNA inhibits poly(dT) synthesis on poly (A): oligo (dT) catalyzed by the enzyme when the enzyme:tRNA ratio is about 1 : 80--100. The inhibition results from the binding of certain tRNA's by the enzyme. The enzyme tRNA complex was separated from the unbound tRNA's by gel-filtration of Sephadex G-100. The tRNA's extracted from the complex are able to inhibit completely poly(A):oligo(dT) templated synthesis of poly(dT) under the enzyme:tRNA ratio about 1 : 2--3. Aminoacylation of tRNA separated from the enzyme complex has shown that E. coli RNA dependent DNA-polymerase selectively binds tRNAThr and to a lesser extent tRNATyr and tRNALys. It is suggested that the enzyme bound tRNA's carry out the functions of natural primers which compete with oligo(dT) for the enzyme responsible for the primer binding.

Escherichia coli↗

PubMed1976

A conceptual framework for measuring clinical problem-solving.

Most attempts to measure clinical competence start by modeling the clinician's problem-solving process. The conflicting data from studies built around this approach suggest the need for rethinking the underlying concepts. Presented is a conceptual framework for clinical competence which is a natural expansion of earlier approaches. The framework is based upon defining the domain in which the clinician functions as the starting point for measuring clinical competence. There are three dimensions to the framework-problem-solving process, clinical discipline, and context of care. The intersection of the dimensions defines the clinical practice domain to be measured. For each domain specific problems can be identified and clinicians asked to demonstrate competence in resolving them.

Clinical Competence↗

PubMedDate not supplied

Lysolecithin induced membrane alterations in thymocytes. Effects of lysophosphatides possessing adjuvant and immuno-suppressive activities on cell agglutination by concanavalin A.

The effects of lysolecithin and of 2 synthetic ether-desoxy lysolecithin analogs, containing alkyl residues of 16 or 12 carbon atoms, on the agglutination kinetics of calf and rabbit thymocytes by concanavalin A (Con A) were investigated. Unlike the natural lysolecithin, these synthetic analogs are resistant to metabolism by membrane associated enzymes. It was found that pretreatment of thymocytes with lysolecithin or with the C16-analog leads to slightly increased agglutination rates. The C12-analog, in contrast, significantly inhibits thymocyte agglutination by Con A. Moreover, a comparison of these results with lysophosphatide effects on the agglutinability of erythrocytes of various species revealed that the inhibitory effect of the short-chain phosphatide is rather specific for thymocytes. The finding that long- and short-chain lysophosphatides, which have previously been shown to react as adjuvants or immunosuppressants, respectively, induce adserve alterations in thymocyte membranes indicates that these substances may affect the immune response by changing the membrane properties of immune competent cells. Concerning the nature of these membrane alterations it was shown that lysolecithin did not affect the number of Con A receptors per cell nor the affinity of lectin binding. It is therefore concluded that the lysophosphatide induced alterations of Con A agglutinability can not be caused by an uncovering or covering of lectin-receptors.

Agglutination↗

PubMed1978

The effects of bioregulators upon amino acid transport and protein synthesis in isolated rat hepatocytes.

Isolated rat hepatocytes prepared by an enzyme perfusion technique possess a functional amino acid transport system and retain the capacity to synthesize protein. Amino acid transport was studied using the non-metabolizable amino acid analog alpha-aminoisobutyric acid. The transport process was time, temperature and concentration dependent. Similarly, leucine incorporation into protein was time and temperature dependent being optimal at 3m degrees C. Amino acid, fetal calf serum, growth hormone and glucose all produced small, reproducible increases in protein synthesis rates. Bovine serum albumin diminished the uptake of alpha-aminoisobutyric acid and leucine incorporation into protein. The amino acid content on either side of the cell membrane was found to affect transport into or out of the cellular compartment (transconcentration effects). High cell concentrations decreased transport and protein synthesis as a result of isotopic dilution of labelled amino acids with those released by the hepatocytes. This was consistent with the capacity of naturally occurring amino aicds to compete with alpha-aminoisobutyric acid for uptake into the hepatocyte. In order to define more precisely the effects of bioregulators on transport and protein synthesis it will be necessary to define and subfractionate cellular compartments and proteins which are the specific targets of cellular regulation.

Amino Acids↗