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PubMed2003

Eukaryotic cells and microbial pathogens: a familiar couple take centre stage.

The interaction of a microbial pathogen with its host is a highly dynamic process shaped by evolution. Understanding cellular responses to microbial products is essential for a complete understanding of virulence. Similarly, studies aimed at determining how a particular virulence factor functions have helped unravel molecular mechanisms that govern eukaryotic cellular events. These two seemingly diverse areas were brought together on the beautiful Spanish Costa Brava in a recent meeting (October 13-17, 2002) sponsored by European Research Conferences (EURESCO) and the European Molecular Biology Organization (EMBO).

Animals↗
PubMed2004

Comparative immunopeptidomics of humans and their pathogens.

Major histocompatibility complex class I molecules present peptides of 8-10 residues to CD8+ T cells. We used 19 predicted proteomes to determine the influence of CD8+ T cell immune surveillance on protein evolution in humans and microbial pathogens by predicting immunopeptidomes, i.e., sets of class I binding peptides present in proteomes. We find that class I peptide binding specificities (i) have had little, if any, influence on the evolution of immunopeptidomes and (ii) do not take advantage of biases in amino acid distribution in proteins other than the concentration of hydrophobic residues in NH(2)-terminal leader sequences.

Animals↗
PubMed1990

Microbial isopenicillin N synthase genes: structure, function, diversity and evolution.

Clinically and economically, penicillins and cephalosporins are the most important class of the beta-lactam antibiotics. They are produced by a wide variety of microorganisms including numerous species of Streptomyces, some unicellular bacteria and several filamentous fungi. A key step common to their biosynthetic pathways is the conversion of a linear, cysteine-containing tripeptide to a bicyclic beta-lactam antibiotic by isopenicillin N synthase. Recent successes in the cloning and expression of isopenicillin N synthase genes now permit production of a plentiful supply of this enzyme, which may be used for structural and mechanistic studies, or for biotechnological applications in the creation of novel beta-lactam compounds from peptide analogues. New ideas concerning the evolution and prevalence of the penicillin and cephalosporin biosynthetic genes have emerged from studies of isopenicillin N synthase genes.

Amino Acid Sequence↗
PubMed1997

The public health threat of emerging viral disease.

"Emerging diseases" are those that either have newly appeared in the population or are rapidly increasing their incidence or expanding their geographic range. Emerging viruses usually have identifiable sources, often existing viruses of animals or humans that have been given opportunities to infect new host populations ("viral traffic"). Environmental and social changes, frequently the result of human activities, can accelerate viral traffic, with consequent increases in disease emergence. Host factors, including nutrition, have often received less attention in the past but are of considerable importance. These factors, combined with the ongoing evolution of viral and microbial variants, make it likely that emerging infections will continue to appear and probably increase, emphasizing the need for effective surveillance.

Animals↗
PubMed2001

The role of Toll-like receptors in host defense against microbial infection.

The Toll family of proteins is central to Drosophila host defense against microbial infection. Maintained throughout evolution, mammalian Toll-like receptors (TLRs) are proteins that participate in innate immunity to bacteria in at least four ways. First, TLRs participate in the recognition of molecular patterns present on microorganisms. Second, TLRs are expressed at the interface with the environment, the site of microbial invasion. Third, activation of TLRs induces expression of co-stimulatory molecules and the release of cytokines that instruct the adaptive immune response. Fourth, activation of TLRs leads to direct antimicrobial effector pathways that can result in elimination of the foreign invader. The recent investigation of TLRs in these areas has provided new insights into mechanisms of innate immunity.

Animals↗
PubMed2001

Lung dendritic cells and host immunity to infection.

The lung is a portal of entry for numerous microbial pathogens, against which evolution has created an adequate innate and adaptive immune response. Dendritic cells (DCs) are central to the integration of innate and specific immunity. These cells are located within the epithelium and interstitium of the lung where they are influenced by the innate immune system. Upon recognition and internalization of microbial antigens, DCs migrate to the draining lymph nodes of the lung to initiate the specific cellular and humoral immune response. By their capacity to integrate stimuli derived from the pathogen, the host and the environment, they are specialized to induce a protective immune response while at the same time avoiding damage to the host. It is becoming increasingly clear that dendritic cells are involved in the induction of immunity to viruses, bacteria, mycobacteria and fungi. Some pathogens subvert the function of dendritic cells to escape immune recognition. Not surprisingly, if dendritic cell function fails, the consequence for the host is immunodeficiency.

Animals↗
PubMed1982

Assessment of the human and ecological hazards of microbial insecticides.

A comprehensive account is given of the evolution of registration guidelines and safety testing procedures for microbial insecticidal agents. Particular emphasis is given to the use of viruses for pest control and the various guidelines developed to assess their possible hazards. The likely gains and risks associated with using viruses are discussed. Several meetings have been held in the last 10 years to assess the hazards of virus insecticides. Some of these meetings have produced recommendations, some have developed guidelines for safety testing. These meetings are reviewed. The various guidelines developed for safety testing are critically evaluated and the UK Registration Criteria for Biological Agents used as Pesticides are reproduced in full. Examples of viruses that have been safety tested and registered for use are given and the criteria used are described. Conclusions are drawn on the merits of the guidelines presently available and the likely future development of safety testing schemes is considered.

Animals↗
PubMed2002

Lateral gene transfers and the evolution of eukaryotes: theories and data.

Vertical transmission of heritable material, a cornerstone of the Darwinian theory of evolution, is inadequate to describe the evolution of eukaryotes, particularly microbial eukaryotes. This is because eukaryotic cells and eukaryotic genomes are chimeric, having evolved through a combination of vertical (parent to offspring) and lateral (trans-species) transmission. Observations on widespread chimerism in eukaryotes have led to new and revised hypothesis for the origin and diversification of eukaryotes that provide specific predictions on the tempo (early vs continuous transfers) and mode (nature of donor and recipient lineages) of lateral gene transfers (LGTs). Analyses of available data indicate that LGTs in eukaryotes largely fall into two categories: (1) LGTs from organelles to the nucleus, only a few of which appear to have occurred at the time of the origin of eukaryotes, and (2) anomalous LGTs involving diverse donor and recipient lineages. Further testing of hypotheses on the origin and diversification of eukaryotes will require complete genome sequences from a number of diverse eukaryotes and prokaryotes combined with sequences of targeted genes from a broad phylogenetic sample.

Animals↗
PubMed2001

Predicting the emergence of antibiotic resistance by directed evolution and structural analysis.

Directed evolution can be a powerful tool to predict antibiotic resistance. Resistance involves the accumulation of mutations beneficial to the pathogen while maintaining residue interactions and core packing that are critical for preserving function. The constraint of maintaining stability, while increasing activity, drastically reduces the number of possible mutational combination pathways. To test this theory, TEM-1 beta-lactamase was evolved using a hypermutator E. coli-based directed evolution technique with cefotaxime selection. The selected mutants were compared to two previous directed evolution studies and a database of clinical isolates. In all cases, evolution resulted in the generation of the E104K/M182T/G238S combination of mutations ( approximately 500-fold increased resistance), which is equivalent to clinical isolate TEM-52. The structure of TEM-52 was determined to 2.4 A. G238S widens access to the active site by 2.8 A whereas E104K stabilizes the reorganized topology. The M182T mutation is located 17 A from the active site and appears to be a global suppressor mutation that acts to stabilize the new enzyme structure. Our results demonstrate that directed evolution coupled with structural analysis can be used to predict future mutations that lead to increased antibiotic resistance.

Amino Acid Sequence↗
PubMed2004

Anaerobic microbial dehalogenation.

The natural production and anthropogenic release of halogenated hydrocarbons into the environment has been the likely driving force for the evolution of an unexpectedly high microbial capacity to dehalogenate different classes of xenobiotic haloorganics. This contribution provides an update on the current knowledge on metabolic and phylogenetic diversity of anaerobic microorganisms that are capable of dehalogenating--or completely mineralizing--halogenated hydrocarbons by fermentative, oxidative, or reductive pathways. In particular, research of the past decade has focused on halorespiring anaerobes, which couple the dehalogenation by dedicated enzyme systems to the generation of energy by electron transport-driven phosphorylation. Significant advances in the biochemistry and molecular genetics of degradation pathways have revealed mechanistic and structural similarities between dehalogenating enzymes from phylogenetically distinct anaerobes. The availability of two almost complete genome sequences of halorespiring isolates recently enabled comparative and functional genomics approaches, setting the stage for the further exploitation of halorespiring and other anaerobic dehalogenating microbes as dedicated degraders in biological remediation processes.

Amino Acid Sequence↗
PubMed2025

Laboratory Evolution Reveals Transcriptional Mechanisms Underlying Thermal Adaptation of Escherichia coli.

Adaptive laboratory evolution is able to generate microbial strains, which exhibit extreme phenotypes, revealing fundamental biological adaptation mechanisms. Here, we use adaptive laboratory evolution to evolve Escherichia coli strains that grow at temperatures as high as 45.3 °C, a temperature lethal to wild-type cells. The strains adopted a hypermutator phenotype and employed multiple systems-level adaptations that made global analysis of the DNA mutations difficult. Given the challenge at the genomic level, we were motivated to uncover high-temperature tolerance adaptation mechanisms at the transcriptomic level. We employed independently modulated gene set (iModulon) analysis to reveal five transcriptional mechanisms underlying growth at high temperatures. These mechanisms were connected to acquired mutations, changes in transcriptome composition, sensory inputs, phenotypes, and protein structures. They are as follows: (i) downregulation of general stress responses while upregulating the specific heat stress responses, (ii) upregulation of flagellar basal bodies without upregulating motility and upregulation fimbriae, (iii) shift toward anaerobic metabolism, (iv) shift in regulation of iron uptake away from siderophore production, and (v) upregulation of yjfIJKL, a novel heat tolerance operon whose structures we predicted with AlphaFold. iModulons associated with these five mechanisms explain nearly half of all variance in the gene expression in the adapted strains. These thermotolerance strategies reveal that optimal coordination of known stress responses and metabolism can be achieved with a small number of regulatory mutations and may suggest a new role for large protein export systems. Adaptive laboratory evolution with transcriptomic characterization is a productive approach for elucidating and interpreting adaptation to otherwise lethal stresses.

Escherichia coli↗
PubMed2004

Recognition of commensal microflora by toll-like receptors is required for intestinal homeostasis.

Toll-like receptors (TLRs) play a crucial role in host defense against microbial infection. The microbial ligands recognized by TLRs are not unique to pathogens, however, and are produced by both pathogenic and commensal microorganisms. It is thought that an inflammatory response to commensal bacteria is avoided due to sequestration of microflora by surface epithelia. Here, we show that commensal bacteria are recognized by TLRs under normal steady-state conditions, and this interaction plays a crucial role in the maintenance of intestinal epithelial homeostasis. Furthermore, we find that activation of TLRs by commensal microflora is critical for the protection against gut injury and associated mortality. These findings reveal a novel function of TLRs-control of intestinal epithelial homeostasis and protection from injury-and provide a new perspective on the evolution of host-microbial interactions.

Adaptor Proteins, Signal Transducing↗
PubMed2002

Effect of potassium salts and distillery effluent on carbon mineralization in soil.

Distillery effluent, a rich source of potassium, is used for irrigation at many places in the world. A laboratory experiment was conducted to study the influence of potassium salts present in post-methanation distillery effluent (PME) along with two other salts, KCl and K2SO4, on mineralization of carbon in soil. PME oxidized with H2O2, raw PME, KCl and K2SO4 solutions containing K equivalent to 10%, 20%, 40% and 100% of K present in PME were added to the soil separately, maintaining four replications for each treatment and control. Addition of salts up to a certain concentration stimulated C mineralization but a decline was noticed at higher concentrations. All the levels of salts caused higher CO2 evolution than the control suggesting that the presence of K salts enhanced the microbial activity resulting in increased CO2 evolution. The influence of K2SO4 was significantly higher than KCl in stimulating C mineralization in soil. Oxidized effluent had a higher stimulating effect than inorganic salts, showing the influence of other salts accompanying K in the PME. Raw PME, which contained excess organic C, increased CO2 evolution even at the highest salt level (100% PME) signifying the effect of added C on alleviating the salt stress on microbial activity.

Carbon↗
PubMed2001

Activation of toll-like receptors by microbial lipoproteins: role in host defense.

Conserved throughout evolution, mammalian toll-like receptors (TLRs) participate in innate immune response to microbial pathogens. The TLRs mediate activation by microbial ligands, resulting in cytokine activation as well as other host defense mechanisms. Activation of TLRs also can result in tissue injury including manifestations of septic shock and host cell apoptosis. In this manner, the activation of mammalian TLRs in the context of infectious disease can contribute to host defense and immunopathology.

Animals↗
PubMed1999

Disposition of D-[U-14C]tagatose in the rat.

The purpose of this experiment was to determine the disposition of D-tagatose, under development as a low-calorie sweetener, in conventional and germ-free male rats. One group of conventional rats was fed a diet containing D-tagatose (100 g/kg) mixed with the nonpurified diet (900 g/kg) for 28 days. Then, [U-14C]-labeled D-tagatose was administered as a single dose (approximately 220-380 kBq) to 4 of these adapted rats, as well as to 15 conventional and germ-free rats with no prior exposure (i.e., unadapted) to D-tagatose. Eleven of the 19 dosed animals (4 adapted conventional, 3 unadapted conventional and 2 unadapted germ-free, all dosed orally, plus 2 unadapted conventional dosed intravenously) were placed in metabolism chambers and samples of CO2, urine, and feces taken at regular intervals. At termination, a complete material balance was obtained based on the recovery of 14C. Over the 6-h digestive period, D-tagatose was metabolized to release 39.9 and 13.9% of the oral dose as CO2 in the adapted conventional rats and in the unadapted germ-free rats, respectively. Total releases approximated 68 and 22%, respectively. The difference in CO2 evolution is ascribed to microbial fermentation of D-tagatose in the gut of the conventional rats. The role of adaptation was confirmed by finding 93% less D-tagatose in the feces of the adapted conventional rat than in the feces of the unadapted conventional rat. The intestinal absorption of D-tagatose in the rat is estimated to be 20%. The results demonstrate that D-tagatose is metabolized primarily by microorganisms in the gut of the rat, with an upper limit between 15 and 20% of oral dose metabolized by the host.

Administration, Oral↗
PubMed2026

Transmission dynamics and driving mechanisms of antibiotic resistance genes through a chronosequence of saline-sodic rice cultivation.

Rice cultivation reclaims saline-sodic soils and improves fertility, but may also promote antibiotic resistance genes (ARGs) accumulation and horizontal transfer, posing ecological risks. This study investigated long-term co-evolution of soil properties, microbial communities, ARGs, and mobile genetic elements (MGEs) across a 1-78 year cultivation chronosequence in saline-sodic fields. Results indicated that prolonged cultivation effectively alleviated soil salinization and increased fertility. Microbial communities shifted directionally, with functional taxa enriched, while opportunistic pathogen-containing genera peaked during 5-20 years. ARGs abundance and diversity increased markedly after five years and peaked at 10-20 years. Multidrug efflux pump genes persisted throughout the chronosequence, whereas aminoglycoside resistance genes declined after 30 years. MGEs activity increased over time and was significantly correlated with key ARGs. Path analysis identified improved soil properties as the primary direct driver of ARGs accumulation, while cultivation-induced declines in microbial diversity indirectly promoted ARGs dissemination by weakening the community's suppression of MGEs-mediated horizontal transfer. Collectively, long-term rice cultivation not only ameliorated saline-sodic soils but also created a dynamic, stage-specific resistome, with the 5-20 year period representing a critical risk window for ARGs propagation. These findings highlight the need to integrate ARGs monitoring into soil health assessments for sustainable management of reclaimed saline-sodic lands.

Oryza↗
PubMed2001

Metal and radionuclide bioremediation: issues, considerations and potentials.

Recent demonstrations of the removal and immobilization of inorganic contaminants by microbial transformations, sorption and mineralization show the potential of both natural and engineered microbes as bioremedial tools. Demonstrations of microbe-mediated mineral formation in biofilms implicate this mode of microbial life in geological evolution and remediation of inorganic contaminants.

Bacteria↗