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Variable genetic elements including plasmids, transposons and prophages are involved in pathogenesis and antibiotic resistance, and are an important component of the staphylococcal genome. This review covers a set of newly described variable chromosomal elements, pathogenicity and resistance islands, carrying superantigen and resistance genes, especially toxic shock and methicillin resistance, respectively.
In Drosophila, the Toll family of proteins are central to innate defense against microbial pathogens. Conserved throughout evolution, mammalian Toll-like receptors (TLRs) participate in innate immunity. TLRs mediate activation by microbial ligands including lipoproteins, resulting in the activation of IL-12 and nitric oxide synthase. Microbial lipoproteins also induce host cell apoptosis. In this manner, the ability of microbial lipoproteins to activate TLRs can contribute to host defense and immunopathology during infection.
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Microorganisms are well known for degrading numerous natural compounds. The synthesis of a multitude of chlorinated compounds by the chemical industry and their release into the natural environment have created major pollution problems. Part of the cause of such pollution is the inability of natural microorganisms to efficiently degrade synthetic chlorinated compounds. Microorganisms are, however, highly adaptable to changes in the environment and have consequently evolved the genes that specify the degradation of chlorinated compounds to varying degrees. Highly selective laboratory techniques have also enabled the isolation of microbial strains capable of utilizing normally recalcitrant highly chlorinated compounds as their sole source of carbon and energy. The evolution and role of microbial genes and enzymes, as well as their mode of regulation and genetic interrelationships, have therefore been the subjects of intense study. This review emphasizes the genetic organization and the regulation of gene expression, as well as evolutionary considerations, regarding the microbial degradation of chlorobenzoates, chlorocatechols, and chlorophenoxyacetic acids.
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Microbial carbamoyl phosphate synthetases (CPS) use glutamine as nitrogen donor and are composed of two subunits (or domains), one exhibiting glutaminase activity, the other able to synthesize carbamoyl phosphate (CP) from bicarbonate, ATP, and ammonia. The pseudodimeric organization of this synthetase suggested that it has evolved by duplication of a smaller kinase, possibly a carbamate kinase (CK). In contrast to other prokaryotes the hyperthermophilic archaeon Pyrococcus furiosus was found to synthesize CP by using ammonia and not glutamine. We have purified the cognate enzyme and found it to be a dimer of two identical subunits of Mr 32,000. Its thermostability is considerable, 50% activity being retained after 1 h at 100 degrees C or 3 h at 95 degrees C. The corresponding gene was cloned by PCR and found to present about 50% amino acid identity with known CKs. The stoichiometry of the reaction (two ATP consumed per CP synthesized) and the ability of the enzyme to catalyze at high rate a bicarbonate-dependent ATPase reaction however clearly distinguish P. furiosus CPS from ordinary CKs. Thus the CPS of P. furiosus could represent a primeval step in the evolution of CPS from CK. Our results suggest that the first event in this evolution was the emergence of a primeval synthetase composed of subunits able to synthesize both carboxyphosphate and CP; this step would have preceded the duplication assumed to have generated the two subdomains of modern CPSs. The gene coding for this CK-like CPS was called cpkA.
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).
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.
"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.
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.
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.
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.
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.
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.
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.
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.
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.