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PubMed2025

Archaea produce peptidoglycan hydrolases that kill bacteria.

The social life of archaea is poorly understood. In particular, even though competition and conflict are common themes in microbial communities, there is scant evidence documenting antagonistic interactions between archaea and their abundant prokaryotic brethren: bacteria. Do archaea specifically target bacteria for destruction? If so, what molecular weaponry do they use? Here, we present an approach to infer antagonistic interactions between archaea and bacteria from genome sequence. We show that a large and diverse set of archaea encode peptidoglycan hydrolases, enzymes that recognize and cleave a structure-peptidoglycan-that is a ubiquitous component of bacterial cell walls but absent from archaea. We predict the bacterial targets of archaeal peptidoglycan hydrolases using a structural homology approach and demonstrate that the predicted target bacteria tend to inhabit a similar niche to the archaeal producer, indicative of ecologically relevant interactions. Using a heterologous expression system, we demonstrate that two peptidoglycan hydrolases from the halophilic archaeaon Halogranum salarium B-1 kill the halophilic bacterium Halalkalibacterium halodurans, a predicted target, and do so in a manner consistent with peptidoglycan hydrolase activity. Our results suggest that, even though the tools and rules of engagement remain largely unknown, archaeal-bacterial conflicts are likely common, and we present a roadmap for the discovery of additional antagonistic interactions between these two domains of life. Our work has implications for understanding mixed microbial communities that include archaea and suggests that archaea might represent a large untapped reservoir of novel antibacterials.

N-Acetylmuramoyl-L-alanine Amidase↗
PubMedDate not supplied

Comparison of fatty acid composition and kinetics of phosphorus-accumulating organisms and glycogen-accumulating organisms.

It was demonstrated that glycogen-accumulating organisms (GAOs) were able to compete with phosphorus-accumulating organisms (PAOs) for acetate in a biological phosphorus removal (BPR) process, leading to a loss of BPR capability. Cellular fatty acid composition, which serves as a fingerprint for microbial identification, was used to determine microbial population change and to investigate the competition mechanisms of PAOs and GAOs. Analysis of cellular fatty acid composition indicated that PAOs grown with acetate and glucose were different species and that GAOs and PAOs grown with the same substrate were also different species. Glycogen-accumulating organisms seemed to coexist with PAOs even in a well-developed BPR process. The GAOs were able to accumulate more poly-beta-hydroxybutyrate (PHB) and glycogen than PAOs during the anaerobic stage of the BPR process. The GAOs synthesized more in-cell glycogen than PAOs. The growth rate for PAOs was always greater than that for GAOs at various acetate or glucose concentrations, while GAOs had higher acetate uptake and PHB synthesis rates than PAOs. Therefore, GAOs are thought to compete with PAOs only at long solids retention times (> or = 20 days).

Bacteria↗
PubMed1993

Adequate iron stores and the 'Nil nocere' principle.

There is a need to change the policy of unselective iron supplementation during periods of life with physiologically increased cell proliferation. Levels of iron stores to be regarded as adequate during infancy and pregnancy are still not well established. Recent data support the view that it is not justified to interfere with physiological adaptations developed through millions of years by sophisticated and precisely coordinated regulation of iron absorption, utilization and storage. Recent data suggest that the chelatable intracellular iron pool regulates the expression of proteins with central importance in cellular iron metabolism (TfR, ferritin, and erythroid 5-aminolevulinic synthetase) in a coordinately controlled way through an iron dependent cytosolic mRNA binding protein, the iron regulating factor (IRF). This factor is simultaneously a sensor and a regulator of iron levels. The reduction of ferritin levels during highly increased cell proliferation is a mirror of the increased density of TfRs. An abundance of data support the vigorous competition for growth-essential iron between microbial pathogens and their vertebrate hosts. The highly coordinated regulation of iron metabolism is probably crucial in achieving a balance between the blockade of readily accessible iron to invading organisms and yet providing sufficient iron for the immune system of the host. The most evident adverse clinical effects of excess iron have been observed in immunodeficient patients in tropical countries and in AIDS patients. Excess iron also increases the risk of initiation and promotion of malignant processes by iron binding to DNA and by the iron-catalysed release of free radicals. Oxygen radicals were shown to damage critical biomolecules leading, apart from cancer, to a variety of human disease states, including inflammation and atherosclerosis. They are also involved in processes of aging and thrombosis. Recent clinical trials have suggested that the use of iron-chelators, natural and synthetic antioxidants, and anti-TfR monoclonal antibodies can contribute in retarding malignant cell proliferation. Hypoferraemia during pregnancy is--like haemodilution--an adaptation to the risks involved in the natural hypercoagulable state of pregnancy. It may also serve to prevent the risk of infections and mutagenicity in the highly proliferating tissues of the foetus. Blunted erythropoiesis has been revealed during the first 30 weeks of pregnancy by the use of the newly developed method of determining the soluble serum transferrin receptor. The lack of increase in erythropoietin levels proves that there is no hypoxia. Decreases in Hb and iron levels are parts of a physiological adaptation. As a consequence they should neither be treated nor prevented. It is stressed that whenever a widespread and ingrained routine medical intervention has to be changed it is essential to first monitor the potential health effects of the recommended change in a national policy.

Adult↗
PubMed1998

Microbial transglutaminase-mediated synthesis of hapten-protein conjugates for immunoassays.

Hapten-protein conjugates are essential in many immunochemical assays, in particular, in assays employing titration or competitive assay formats. By exploitation of the catalytic properties of the microbial transglutaminase from Streptoverticillium mobarense sp. (MTGase), i.e., acyl transfer between gamma-carboxamide groups and various primary amines, new techniques for the synthesis of hapten-protein conjugates were developed. This is demonstrated by two examples. The feasibility of MTGase for hapten-protein conjugate synthesis was studied by coupling the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) to casein. Different procedures for the synthesis and the immobilization of these 2,4-D-casein conjugates were evaluated, comprising (i) a batch procedure, (ii) coupling of 2,4-D to an already immobilized layer of casein, and (iii) a method for simultaneous immobilization and conjugation. Kinetic studies revealed that conjugate formation in the batch procedure was almost complete after approx 2 h. By employing the conjugates in a competitive ELISA, detection limits as low as 0.05 microgram/L 2,4-D were reached. Using the approach with simultaneous immobilization and conjugation, the time for the whole assay could be reduced to only 2 h. Finally, to demonstrate the versatility of the enzymatic synthesis of hapten-protein conjugates, an ELISA for 2,4,6-trinitrotoluene (TNT) determination based on transglutaminase-synthesized conjugates was developed. In this assay, a detection limit as low as 0.04 microgram/l TNT was obtained.

2,4,5-Trichlorophenoxyacetic Acid↗
PubMed1996

Are ruminal bacteria armed with bacteriocins?

The production of toxic compounds or antibiotics is a common component of intermicrobial competitive interactions, and many of these toxins have been adopted and adapted for the control of microbial populations. One class of these toxins, the bacteriocins, is a heterogeneous group of proteinaceous antibiotics that often display a high degree of target specificity, although many have a very wide spectrum of activity. To date, only limited information is available concerning the occurrence of bacteriocins among ruminal isolates or the sensitivity of ruminal microorganisms to exogenous bacteriocins. A survey of 50 strains of Butyrivibrio spp. isolated from a variety of sources (sheep, deer, and cattle) for bacteriocin production indicated a high incidence of bacteriocin-like activity (50%). Many of these inhibitory compounds appear to have a broad spectrum of activity, which suggests that bacteriocins may have a significant impact on both the competitive fitness of individual microbial strains within the rumen and on the overall structure of the microbial population within the rumen. Selected bacteriocins from lactic acid bacteria also were shown to have activity against Butyrivibrio spp. and may have application in ruminant systems. Bacteriocins may provide an alternative group of antibiotics for the manipulation of ruminal microbial populations. Bacteriocins have significant advantages over other antibiotics in target specificity, susceptibility to proteolytic digestion, possibility of genetic transfer and manipulation, and, in the case of some bacteriocins derived from lactic acid bacteria, a long history of safe use.

Animals↗
PubMed2003

[Mechanisms of plant disease resistance induced by arbuscular mycorrhizal fungi].

In recent years, the induced disease resistance of plant by Arbuscular Mycorrhizal Fungi (AMF) has become a hot spot in chemo-ecological study and in biocontrol of plant disease. There were many reports indicating that AMF had antagonistic function to soilborne disease pathogen, or could suppress the growth of pathogen, and increase the resistance or tolerance of mycorrhizal plants to soilborne disease. In mycorrhizosphere, there are interactions among microbial community, in which, AMF could suppress the growth of pathogen and promote the growth of beneficial microbe. Thus, AMF may use as biocontrol fungi with other antagonism microbe. There were several hypotheses about the mechanisms of the increased resistance in mycorrhizal plants: (1) improvement of plant nutrient status; (2) competition; (3) changed roots morphology and structure; (4) changed microbial flora in rhizosphere; (5) induced resistance or systematic resistance in plant. After colonized by AMF, phenolic compounds accumulate in plant, and local defense response or systemic defense response occurs. It is necessary to do intensive research on the mechanisms of increased resistance in mycorrhizal plants, because it may help us understand the function of disease resistance of mycorrhiza correctly, and let us use AMF as a new biocontrol method to control soilborne disease in eco-agriculture in the near future.

Ecology↗
PubMed1987

Determination of binding parameters of macrolides, lincosamides, and streptogramins to Legionella pneumophila.

Parameters of [3H]erythromycin binding to Legionella pneumophila were determined in vitro using both an equilibrium and a kinetic method. Different L. pneumophila serogroups, 1-3, and a virulent strain serogroup, 1, were tested. All strains of bacteria exhibited the same binding pattern, with a dissociation constant of 0.15 microM. Other macrolides, streptogramin B-types, and lincosamides competitively displaced bound erythromycin suggesting that these compounds share common binding sites on the bacteria. Minimum inhibitory concentration (MIC) values for macrolides, streptogramin B-types, and lincosamides were determined with buffered charcoal yeast extract (BCYE) medium. A good correlation (r = 0.994) was found between the corresponding inhibition constants of these antibiotics and their MIC. It was also noted that for lincosamides the microbiological inactivity was associated with a very low bacterium affinity. Thus, it is concluded that binding parameters of these antibiotics reflect their efficacy against L. pneumophila in vitro and may serve as a useful adjunct in developing new compounds.

Anti-Bacterial Agents↗
PubMed1992

Localization of epitopes for antibodies that differentially label sodium sodium channels in skeletal muscle surface and T-tubular membranes.

We previously characterized two monoclonal antibodies, A/B2 and L/D3, that bind to the amino-terminus of the sodium channel but produce distinct immunocytochemical patterns in innervated adult skeletal muscle. Because these findings suggested the presence of several channel isoforms, we sought to define the epitopes for each antibody. Five peptides encompassing the amino-terminal 126 residues of the adult skeletal muscle sodium channel were synthesized and tested by radioimmunoassay against each antibody. Both monoclonals bound only to a peptide comprising residues 1-30 (I1-30). A nested set of peptides within this region was then synthesized and used to compete for antibody binding to I1-30. L/D3 binding was quantitatively inhibited by oligopeptides 1-30, 7-30, 13-30, and 19-30 but not 25-30, while binding of A/B2 was blocked only by the intact I1-30 peptide. This data implies that the epitope for L/D3 lies within residues 19-25 while the epitope for A/B2 is contained within residues 1-6. These tentative epitope localizations were confirmed using both proteolytic cleavage of I1-30 and immunoreactivity of a peptide corresponding to residues 1-12 with A/B2 but not L/D3. Therefore, epitopes for each monoclonal antibody are present in the SkM-1 sequence and are in close proximity in the amino-terminus of the protein. Their characteristic immunocytochemical labeling patterns may reflect differing accessibility of the epitopes in various membrane environments.

Amino Acid Sequence↗
PubMed1981

Dual effects of type II collagen on the degradation of type I collagen by tadpole collagenase.

Kinetic analysis of the degradation of mixtures of type I and type II collagens by tadpole collagenase was performed, using [14C]glycine-labeled type I collagen and [3H]acetylated type II collagen as substrates. The degradation rate of type I collagen was decreased in the initial stage of the reaction, then further slowed down giving a constant rate independent of both the amounts of enzyme and type II collagen. The effect of type II collagen on the degradation of type I collagen is two-fold. First, competitive inhibition manifested only in the initial stage of the reaction due to higher (about 4-fold) affinity of type II collagen for the enzyme than type I collagen. Second, interference in step(s) following the formation of enzyme-substrate complex.

Animals↗
PubMed1998

Influence of temperature, pH and water activity on "in vitro" inhibition of Penicillium glabrum (Wehmer) Westling by yeasts.

Four different yeast species (Metschnikowia pulcherrima, Saccharomycopsis vini, Kluyveromyces marxianus, Cryptococcus albidus), isolated from surface of grapes, were evaluated for biocontrol potential against Penicillium glabrum. In order to investigate the influence of temperature, pH, water activity and yeast cell concentration on Penicillium glabrum inhibition, the individual effects and the interaction of these factors were analyzed by means of a Central Composite Design (CCD). All yeast species tested showed antagonistic effects which were more pronounced at high cell concentrations. The other variables affected the antagonistic effect differentially depending on the yeast species. Results of the experimental design showed that the selective success of a competitive microflora is under environmental control; moreover, when microbial cells are subjected to multiple factors, the effects and the reciprocal interactions of the individual variables cannot be independently evaluated.

Agar↗
PubMed2026

ALPAR: automated learning pipeline for antimicrobial resistance.

SUMMARY: The field of machine learning in antimicrobial resistance (AMR) research has experienced rapid growth, fueled by advancements in high-throughput genome sequencing and the growing capacity of computational resources. However, the complexity and lack of standardized data preparation and bioinformatic analyses present significant challenges, especially for newcomers to the domain. In response to these challenges, we introduce ALPAR (Automated Learning Pipeline for Antimicrobial Resistance), a comprehensive AMR data analysis tool covering the entire process from processing of raw genomic data to training machine learning models to interpretation of results. Our method relies on a reproducible pipeline that integrates widely used bioinformatics tools, presenting a simplified, automatic workflow specifically tailored for single-reference AMR analysis. Accepting genomic data in the form of FASTA files as input, ALPAR facilitates the generation of machine learning-ready data tables and both the training of machine learning and the execution of genome-wide association studies (GWAS) experiments. Additionally, our tool offers supplementary functionalities such as phylogeny-based analysis of the distribution of mutations, enhancing its utility for researchers. The tool has also proven its performance in competitive benchmarks, winning the 2024 CAMDA Anti-Microbial Resistance Prediction Challenge and placing third in the 2025 edition. AVAILABILITY AND IMPLEMENTATION: ALPAR is open-source and freely accessible via GitHub (https://github.com/kalininalab/ALPAR). The pipeline is fully reproducible and can be easily installed as a Conda package (https://anaconda.org/kalininalab/ALPAR).

Machine Learning↗
PubMed1986

Antagonistic interactions of macrolides and synergimycins on bacterial ribosomes.

The affinity of ribosomes for VS (virginiamycin S, a type B synergimycin) is known to be increased by VM (virginiamycin M, a type A synergimycin). Erythromycin, a macrolide, displaces ribosome-bound VS in the absence of VM, but is ineffective in its presence. In the present work, the ability of spiramycin and tylosin (macrolide subgroups) derivatives to displace ribosome-bound VS, in the presence and in the absence of VM, has been explored. All macrolides with in-vitro activity displaced ribosome-bound VS: the displacement curves produced by tylosin and spiramycin derivatives virtually overlapped. When VM was added to these systems, displaced VS became readily attached to ribosomes in the case of erythromycin, did not bind appreciably within 20 min incubation in the presence of tylosin, and underwent a slow binding in the case of an N-substituted tylosin. The 16-membered macrolides (leucomycin, spiramycin and tylosin subgroups) can therefore be distinguished from the 14-membered macrolides (erythromycin subgroup) by the antagonistic effect displayed toward VM.

Bacteria↗
PubMed1994

The pseudodisaccharides: a novel class of group I intron splicing inhibitors.

Lysinomicin, a naturally-occurring pseudodisaccharide, inhibits translation in prokaryotes. We report that lysinomicin (and three related compounds) are able to inhibit the self-splicing of group I introns, thus identifying pseudodisaccharides as a novel class of group I intron splicing inhibitors. Lysinomicin inhibited the self-splicing of the sunY intron of phage T4 with a Ki of 8.5 microM (+/- 5 microM) and was active against other group I introns. Inhibition was found to be competitive with the substrate guanosine, unlike aminoglycoside antibiotics, which act non-competitively to inhibit the splicing of group I introns. Competitive inhibitors of group I intron splicing known to date all contain a guanidino group that was thought to be required for inhibition; lysinomicin lacks a guanidino group.

Aminoglycosides↗
PubMed2003

Production of enterolysin A by a raw milk enterococcal isolate exhibiting multiple virulence factors.

Even though enterococci are a common cause of human infection they can readily be isolated from a range of food sources, including various meat and dairy products. An enterococcal strain, DPC5280, which exhibits a broad spectrum of inhibition against many Gram-positive bacteria was recently isolated from an Irish raw milk sample. Characterization of the inhibition revealed that the strain exhibits haemolytic activity characteristic of the two-component lantibiotic cytolysin and also produces a heat-labile antimicrobial protein of 34 kDa. The latter protein displayed cell wall hydrolytic activity, as evidenced by zymogram gels containing autoclaved lactococcal cells. N-terminal sequencing of the purified protein yielded the sequence ASNEWS which is 100 % identical to enterolysin A (accession no. AF249740), a protein which shares 28 and 29 % identity to the Gly-Gly endopeptidases, lysostaphin and zoocin A, respectively. Indeed, amplification of entL from DPC5280 and sequencing revealed that the protein is 100 % identical to enterolysin A. The DPC5280 strain also contained the determinants associated with multiple virulence factors, including gelatinase, aggregation substance and multiple antibiotic resistance. The linkage of this cell-wall-degrading enzyme to other virulence factors in enterococci may contribute to the competitiveness of pathogenic enterococci when found in complex microbial environments such as food and the gastrointestinal tract.

Amino Acid Sequence↗
PubMed1998

Physiology of organic nitrogen acquisition by ectomycorrhizal fungi and ectomycorrhizas.

Ectomycorrhizal fungi are symbiotically associated microorganisms which ecological importance has been repeatedly demonstrated. There has been a considerable amount of research aimed at assessing the ability of ectomycorrhizal fungi and ectomycorrhizas to utilize organic nitrogen sources. The fate of soil proteins, peptides and amino acids has been studied from a number of perspectives. Exocellular hydrolytic enzymes have been detected and characterized in a number of ectomycorrhizal and ericoid fungi. Studies on amino acid transport through the plasma membrane have demonstrated the ability of ectomycorrhizal fungi to take up the products of proteolytic activities. Investigations on intracellular metabolism of amino acids have allowed the identification of the metabolic pathways involved. Possible intracellular compartmentation of amino acids will be examined by immunocytochemistry. Further translocation of amino acids in symbiotic tissues has been established by experiments using isotopic tracers, although the exact nature of the nitrogenous compounds transferred at the symbiotic interface remained unclear. One of the main future challenges in the physiology of organic nitrogen acquisition is to determine the nature, the regulation and the location of N-compound transporters at the soil-fungus and fungus-plant interfaces. The molecular approach which is just emerging in this particular research area will greatly improve our knowledge. Future research should also address the extent of competition between different ectomycorrhizal species and between different microbial populations for organic nitrogen.

Amino Acids↗
PubMed1997

Molecular interactions of a semisynthetic glycopeptide antibiotic with D-alanyl-D-alanine and D-alanyl-D-lactate residues.

LY191145 is an N-alkylated glycopeptide antibiotic (the p-chlorobenzyl derivative of LY264826) with activity against vancomycin-susceptible and -resistant bacteria. Similar to vancomycin, LY191145 inhibited polymerization of peptidoglycan when muramyl pentapeptide served as a substrate but not when muramyl tetrapeptide was used, signifying a substrate-dependent mechanism of inhibition. Examination of ligand binding affinities for LY191145 and the effects of this agent on R39 D,D-carboxypeptidase action showed that, similar to vancomycin, LY191145 had an 800-fold greater affinity for N,N'-diacetyl-L-Lys-D-Ala-D-Ala than for N,N'-diacetyl-L-Lys-D-Ala-D-Lac. The antibacterial activity of LY191145 was antagonized by N,N'-diacetyl-L-Lys-D-Ala-D-Ala, but the molar excess required for complete suppression exceeded that needed to suppress inhibition by vancomycin. LY191145 is strongly dimerized and the p-chlorobenzyl side chain facilitates interactions with bacterial membranes. These findings are consistent with a mechanism of inhibition where interactions between antibiotic and D-Ala-D-Ala or D-Ala-D-Lac residues depend on intramolecular effects occurring at the subcellular target site.

Anti-Bacterial Agents↗
PubMed2005

Vertical and seasonal variations of bacterioplankton subgroups with different nucleic Acid contents: possible regulation by phosphorus.

We used flow cytometry to examine seasonal variations in basin-scale distributions of bacterioplankton in Lake Biwa, Japan, a large mesotrophic freshwater lake with an oxygenated hypolimnion. The bacterial communities were divided into three subgroups: bacteria with very high nucleic acid contents (VHNA bacteria), bacteria with high nucleic acid contents (HNA bacteria), and bacteria with low nucleic acid contents (LNA bacteria). During the thermal stratification period, the relative abundance of VHNA bacteria (%VHNA) increased with depth, while the reverse trend was evident for LNA bacteria. Seasonally, the %VHNA was strongly positively correlated (r = 0.87; P < 0.001) with the concentration of dissolved inorganic phosphorus, but not with the concentration of chlorophyll a. The growth of VHNA bacteria was significantly enhanced by addition of phosphate or phosphate plus glucose but not by addition of glucose alone. Although the growth of VHNA and HNA bacteria generally exceeded that of LNA bacteria, our data also revealed that LNA bacteria grew faster than and were grazed as fast as VHNA bacteria in late August, when nutrient limitation was presumably severe. Based on these results, we hypothesize that in severely P-limited environments such as Lake Biwa, P limitation exerts more severe constraints on the growth of bacterial groups with higher nucleic acid contents, which allows LNA bacteria to be competitive and become an important component of the microbial loop.

Animals↗