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Detection of lateral gene transfer among microbial genomes.

An increasingly comprehensive assessment is being developed of the extent and potential significance of lateral gene transfer among microbial genomes. Genomic sequences can be identified as being of putatively lateral origin by their unexpected phyletic distribution, atypical sequence composition, differential presence or absence in closely related genomes, or incongruent phylogenetic trees. These complementary approaches sometimes yield inconsistent results. Not only more data but also quantitative models and simulations are needed urgently.

Evolution, Molecular↗

Genetic evolution of bacteriophage. I. Hybrids between unrelated bacteriophages P22 and Fels 2.

A new bacteriophage species, designated F22, was isolated from phage P22 stocks grown on Salmonella typhimurium Q1 lysogenic for Fels 2 at a frequency of less than 10(-11). P22 has a very short tail with a hexagonal base plate and six spikes. Phage Fels 2 is morphologically similar to E. coli T-even phages, having a long tail with a contractile sheath and carrying no genetic region related to P22. Phage F22 is morphologically and serologically indistinguishable from Fels 2, but carries the c(c(1), c(2), and c(3)) markers of P22. The color markers h(21), g, and m(3) of P22 do not appear in F22. Thus, F22 is evidently a recombinant between the unrelated bacteriophages P22 and Fels 2. The recombination between unrelated bacteriophages could play an important role in the evolution of bacteriophages.

Complement Fixation Tests↗

Symbiont acquisition as neoseme: origin of species and higher taxa.

We examine the hypothesis that, in the origin of species and higher taxa of eukaryotes, symbiont acquisition followed by partner integration has been equivalent to neoseme appearance leading to speciation. The formation of stable symbiotic associations involves partner-surface recognition, behavioral and metabolic interaction, and, in some cases, gene product (RNA, protein) and genic (RNA, DNA) integration. This analysis is applied here to examples of neosemes that define specific taxa and to neosemes in plants, fungi, and animals that involve the appearance of new types of tissue. If this hypothesis is correct--if the origin of major genetic variation leading to speciation and even higher taxa may occur through symbiont acquisition and integration--then the analysis of "origins of species and higher taxa" becomes analogous to the study of microbial community ecology.

Bacteria↗

Discovery and directed evolution of a glyphosate tolerance gene.

The herbicide glyphosate is effectively detoxified by N-acetylation. We screened a collection of microbial isolates and discovered enzymes exhibiting glyphosate N-acetyltransferase (GAT) activity. Kinetic properties of the discovered enzymes were insufficient to confer glyphosate tolerance to transgenic organisms. Eleven iterations of DNA shuffling improved enzyme efficiency by nearly four orders of magnitude from 0.87 mM-1 min-1 to 8320 mM-1 min-1. From the fifth iteration and beyond, GAT enzymes conferred increasing glyphosate tolerance to Escherichia coli, Arabidopsis, tobacco, and maize. Glyphosate acetylation provides an alternative strategy for supporting glyphosate use on crops.

Acetylation↗

Entropy balances of microbial product formation.

Considering the approach of Bermudez and Wagensberg (1986) devoted to the entropy balance of growing microorganisms some equations were developed which describe particularly the entropy balance of microbial product formation. The formula allows to determine the coefficients of resistance R(mn) and of coupling L(mn) according to rates of growth, product formation, maintenance metabolism and heat evolution assuming a linear relationship between thermodynamic fluxes and forces. In order to check the usefulness of the derived model appropriate experimental data of two microbial batch processes concerning production of L-lysine and the antibiotic nourseothricine were taken into account. The results showed similar courses of entropy balances despite different pathways of product formation which were characterized by an overshoot of entropy production at the beginning of biosynthesis of the primary and secondary metabolite. This fact was interpreted as a more general phenomenon for microorganisms under inbalanced nutritional conditions.

Journal Article↗

Combined effects of carbon dioxide addition and barrier films on microbial and sensory changes in pasteurized milk.

The growth of psychrotrophic microorganisms is an important factor in the deterioration of refrigerated pasteurized milk. Dissolved CO2 inhibits certain spoilage microorganisms in foods provided that the packaging offers a sufficient barrier to CO2 evolution. The objectives of this work were, first, to estimate the sensory threshold for dissolved CO2 in 2% milk and, second, to determine the relationship between microbial growth and package barrier properties for pasteurized milk to which CO2 had been added at concentrations near the flavor threshold. The sensory threshold, as determined by a trained panel, for CO2 in 2% pasteurized milk was > 2.8 mM and < 9.1 mM. Pasteurized milk was inoculated with a cocktail of spoilage microorganisms, packaged in different barrier film pouches, and stored at 6.1 degrees C for up to 28 d. The addition of CO2 at concentrations of 8.7 and 21.5 mM increased the time needed to reach 10(6) cfu/ml from 6.4 d (no CO2) to 8.0 and 10.9 d, respectively, in low barrier pouches. In high barrier pouches, the time needed to reach 10(6) cfu/ml was increased to 9.7 and 13.4 d, respectively, at CO2 concentrations of 8.7 and 21.5 mM. This increase represents an increase in shelf-life of approximately 25 to 200%. Microbial counts had longer lag times and lower growth rates and took longer to reach stationary growth as the concentration of CO2 increased in all films than did the control milk. The control milk curdled in less than 17 d, but the test milk in the high barrier packaging had not curdled at 28 d. These data suggest that the shelf-life of pasteurized refrigerated milk could be extended by at least 25 to 200% at CO2 concentrations near the sensory threshold. The major variables in shelf-life are the amount of added CO2 and the barrier properties of the package.

Animals↗

De Novo Genome Sequence Assembly of the Algal Endosymbiont Micractinium conductrix Derived From Its Host Paramecium bursaria 186b.

Endosymbiosis is a major driver of evolutionary innovation and underpins the function of diverse ecosystems. The origins and evolution of endosymbiosis are challenging to study experimentally due to the short-lived culturability of many microbial strains derived from endosymbiotic interactions. The facultative endosymbiosis between the ciliate, Paramecium bursaria, and the green alga, Micractinium conductrix (Chlorellaceae, Trebouxiophyceae), is ecologically widespread and has emerged as a powerful lab-tractable model system. This endosymbiosis is founded upon a reciprocal nutrient exchange, but each of the species can be cultured independently enabling quantification of symbiotic fitness effects, new partnerships to be generated in the lab, and co-associations to be subject to experimental evolution. To date, evolve-and-resequence approaches have been limited due to a lack of high-quality genome assemblies enabling gene variants to be identified. Here, we report a near telomere-to-telomere genome assembly for M. conductrix 186b, using a range of sequencing technologies. Comparative analysis shows that this is one of the most complete Chlorellaceae algal genome assemblies available to date. To aid accurate gene calling and annotation, we conducted both RNAseq and Iso-Seq transcriptome sequencing experiments. Collectively, these 'omics datasets will facilitate: (i) comparative genomics studies of endosymbiont evolution, (ii) evolve-and-resequence experiments, (iii) genome-scale metabolic modeling studies, and (iv) identification of targets for genetic modification experiments and biotechnological applications.

Symbiosis↗

Symbiosis and pathogenesis: evolution of the microbe-host interaction.

Symbiotic and pathogenic bacteria have in common that they live in or on host organisms or host cells. To make a successful living in eukaryotic hosts, bacteria must possess the traits to recognize a given host and establish adherence. When the bacterial location is internal or intracellular, they must further have the ability to invade, to establish a niche, and finally to multiply within a host. The underlying mechanisms which allow this form of existence show similarities between symbiotic and pathogenic bacteria. The final outcome, however, may result in a wide spectrum of consequences for the host ranging from the acquisition of novel metabolic pathways to damage or death. Despite the vastly different forms of interactions, symbiotic and pathogenic bacteria have in common that they are adapted to a particular environmental niche represented by the host organism or compartment thereof. This contribution reviews the evolutionary forces which have shaped the microbial-host interactions. Particular emphasis is placed on the genetic and molecular mechanisms that drive bacterial evolution in response to the selective pressures of the host environment.

Animals↗

Conserved protein folds underpin the diversification of secreted proteins in a fungal pathogen.

BACKGROUND: During host colonization, fungal plant pathogens secrete effector-like proteins that alter host cell physiology and target plant-associated microbes. However, rapid evolution and low sequence conservation hinder the study and characterization of these proteins. The fungus Zymoseptoria passerinii infects Hordeum spp. and includes lineages adapted to wild and domesticated barley. To date, the evolution of effector-like proteins in this species has not been addressed. RESULTS: We combined multiple structure-based and network analyses to unravel the secretome of Z. passerinii. We first compared AlphaFold2 and ESMFold predictions to establish the baseline for structural analyses. We identified 72 structural clusters in the secretome, revealing fold-level relationships across divergent sequences. We showed that effector-like proteins with predicted host immune-interfering functions evolved from a limited group of protein folds, whereas proteins with predicted antimicrobial properties were distributed across fold groups. Physicochemical comparisons indicate that putative antimicrobial effectors predominantly emerged through amino acid replacements on common effector-enriched scaffolds in Z. passerinii, reconfiguring surface charge and electrostatics. We analyzed intra- and interspecific variation in selected effector-enriched families by comparing Z. passerinii proteins and homologs across the genus Zymoseptoria. We describe constrained core folds, with local variation in loop and surface-exposed regions, consistent with fold stability while still enabling protein diversification. We further report that putative antimicrobial effector homologs are broadly distributed across the genus despite sequence divergence. CONCLUSIONS: The secretome of Z. passerinii is organized around common structural folds that support diverse biological roles, including host manipulation and host-associated microbial interactions. Conserved scaffolds combined with surface and physicochemical variation likely contribute to rapid adaptive evolution of effector-like proteins in Z. passerinii.

Fungal Proteins↗

Universal biases in protein composition of model prokaryotes.

The levels of cellular organization in living organisms are the results of a variety of selection pressures. We have investigated here the final outcome of this integrated selective process in proteins of the best known microbial models Escherichia coli, Bacillus subtilis, and Methanococcus jannaschii, supposed to have undergone separate evolution for more than 1 billion years. Using multivariate analysis methods, including correspondence analysis, we studied the overall amino acid composition of all proteins making a proteome. Starting from and further developing previous results that had pointed out some general forces driving the amino acid composition of the proteomes of these model bacteria, we explored the correlations existing between the structure and functions of the proteins forming a proteome and their amino acid composition. The electric charge of amino acids measured against hydrophobicity creates a highly homogeneous cluster, made exclusively of proteins that are core components of the cytoplasmic membrane of the cell (integral inner membrane proteins). A second bias is imposed by the G+C content of the genome, indicating that protein functions are so robust with respect to amino acid changes that they can accommodate a large shift in the nucleotide content of the genome. A remarkable role of aromatic amino acids was uncovered. Expressed orphan proteins are enriched in these residues, suggesting that they might participate in a process of gain of function during evolution.

Amino Acids↗

Nucleotide sequence of the kanamycin resistance determinant of the pneumococcal transposon Tn1545: evolutionary relationships and transcriptional analysis of aphA-3 genes.

The nucleotide sequence of the kanamycin resistance determinant aphA-3 encoded by transposon Tn1545 from Streptococcus pneumoniae was determined and compared to those of plasmids pJH1 and pIP1433 from Streptococcus faecalis and Campylobacter coli, respectively. The three sequences were found to be identical and differed by two substitutions and the deletion of a codon from that of plasmid pSH2 from Staphylococcus aureus. Comparison of the 5' noncoding sequences indicated that the regions containing the aphA-3 gene in pJH1 and in Tn1545 evolved independently by deletion from a sequence similar to that found in pIP1433. In the latter plasmid, aphA-3 is transcribed from a promoter, P1, which is flanked by two 12-base pair direct repeats. The rearrangement observed in pJH1 removed one of these recombinogenic sites and altered the -10 and 3' flanking sequences of P1. The promoter thus generated. P1', allows expression of similar level of kanamycin resistance as P1. However, fusion experiments carried out with a promotorless chloramphenicol acetyltransferase gene indicated that the canonical promoter P1 is significantly less efficient than P1'. From analysis of the thermodynamic properties of these promoters, we conclude that this difference in strength reflects the melting properties of the -10 sequences. The transition from pIP1433 to pJH1 may correspond to the progression of a molecule structurally unstable to a more stable one combined with the need to maintain an efficient promoter upstream of the aphA-3 gene. The deletion event in Tn1545, which occurred between the two 12-base pair directly repeated sequences, removed P1 in its entirety.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Sequence↗

Evolution of resistance in microorganisms of human origin.

Resistance to antimicrobials in bacteria results from either evolution of "new" DNA or from variation in existing DNA. Evidence suggests that new DNA did not originate since the use of antibiotics in medicine, but evolved long ago in soil bacteria. This evidence is based on functional and structural homologies of resistance proteins in human pathogens, and resistance proteins or physiological proteins of soil bacteria. Variation in existing DNA has been shown to comprise variations in structural or regulatory genes of the normal chromosome or mutations in already existing plasmid-mediated resistance genes modifying the resistance phenotype. The success of R-determinants in human pathogens was due to their horizontal spread by transformation, transduction and conjugation. Furthermore, transposition has enabled bacteria to efficiently distribute R-determinants between independent DNA-molecules. Since the genetic processes involved in the development of resistance are rare events, the selective pressure exerted by antibiotics has significantly contributed to the overall evolutionary picture. With few exceptions, experimental data about the role of antibiotic usage outside human medicine with respect to the resistance problem in human pathogens are missing. Epidemiological data about the occurrence of resistance in human pathogens seem to indicate that the major contributing factor to the problem we face today was the extensive use of antibiotics in medicine itself.

Anti-Bacterial Agents↗

Can thromboembolism be the result, rather than the inciting cause, of acute vascular events such as stroke, pulmonary embolism, mesenteric ischemia, and venous thrombosis?: a maladaptation of the prehistoric trauma response.

Thromboembolism is considered the inciting cause of many vascular disorders including acute coronary syndrome (ACS), ischemic stroke, pulmonary embolism (PE), deep vein thrombosis (DVT), and mesenteric ischemia. Adrenergia and inflammation are known to accompany these conditions, particularly among arterial thromboembolic disorders, but the teleologic basis of these associations remains poorly understood. We argue that thromboembolism may sometimes be the result, rather than the cause, of acute vascular events, and may be precipitated by underlying adrenergia. Thromboembolic events are most prone to occur during parts of the circadian, seasonal, lifespan, and reproductive cycles with sympathetic dominance, as well as during behavioral, exertional, physiologic, and iatrogenic activation of sympathetic stress. Molecular evidence suggests that adrenergia and inflammation can promote coagulation and lead to co-activation of the pathways. Acute vascular events that occur without angiographic evidence of occlusion suggest that some infarcts may be attributable to adrenergia alone. "Embolic" disorders may represent asynchronous systemic phenomena rather than clot migration. During acute thromboembolism, downstream tissue hypoxia can activate maladaptive self-propelling cycles of sympathetic bias, inflammation, and coagulation. The counterproductive co-activation of these pathways may reflect a maladaptive interlink forged during the primordial evolution of trauma physiology. Their rapid co-mobilization enables rapid control of hemorrhage, microbial defense, and perfusion maintenance during trauma, but the pathways may behave maladaptively in the setting of modern diseases where endothelial injury may be more often precipitated by smoking, diabetes, dyslipidemia, or hypertension. Sympathetic blockade is already employed in ACS, and beta-blockers are used as antihypertensives to prevent stroke. Our hypothesis suggests that the benefits of beta-blockers in stroke may be independent of antihypertensive effects, and that adrenergia may represent a target for managing all thromboembolic disorders, independent of anti-coagulative and thrombolytic therapies. Perhaps reducing adrenergia, rather than maintaining high cerebral perfusion pressure, may represent a counterintuitive strategy for treating stroke and for reducing reperfusion injury. Plausible mechanisms by which autonomic dysfunction may induce venous thrombosis are discussed, especially in those with baroreceptor dysfunction, immobilization, or dehydration. Unexplained hypercoagulability of cancer may also operate through tumor-induced adrenergia and inflammation.

Humans↗