Cytochrome c in the microbial world.
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Bacterial Physiological Phenomena↗
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[Cephalosporins: 4 generations of structural evolution].
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Bacteria↗
[A comparative analysis of molecular-genetic peculiarities of the genomes of cholera, plague and anthrax agents and their evolutional transformations].
Cholera, plague, and anthrax, the diseases that have accounted for millions of human victims, still endanger the entire mankind by possible development of epidemic outbreaks due to their spread or application as bioterrorist agents. Generalized results of research into the genomic features of the Vibrio cholerae, Yersinia pestis, and Bacillus anthracis are discussed. Despite different frequencies of evolutional transformations occurring in their genomes, that are likely to be associated with diverse life cycles of the pathogens, clones with altered diagnostic, and virulence characteristics were shown to have a fair probability of formation. Also presented in the review, are literature data concerning the main evolutional stages for any of these pathogens, determination of new genetic variants, consideration of the mechanisms facilitating maintenance of the microbial agents during the interepidemic periods.
Anthrax↗
Evolution of HIV-1 multidrug-resistant genotypes during combination therapy and after the cessation of antiretroviral drugs.
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Anti-HIV Agents↗
Miniaturized test system for soil respiration induced by volatile pollutants.
A miniaturized method based on 96-well microtitre plates was developed and used to study respiration in pristine and contaminated soils following addition of volatile substrates. Small soil samples were exposed to fuel components, which were volatilized from spatially separate reservoirs of 2,2,4,4,6,8,8-heptamethylnonane (HMN) as an organic carrier. Respiration was determined as CO(2) production by means of a pH-indicator and bicarbonate-containing agar, or as (14)CO(2) evolution from (14)C-labelled substrates. Substrate concentrations inducing maximum microbial activity or inhibition were determined and CO(2) production profiles examined by multivariate analysis. When high concentrations of fuel components were applied, distinction of hydrocarbon exposed soils from unexposed soil was achieved within 6 h of incubation. With low concentrations, adequate distinction was achieved after 24 h, probably as a result of community adaptation. Nutrient limitation was identified with the (14)C method for toluene, and the optimal N and P amendment determined. Further potential applications of this rapid and inexpensive method are outlined.
Bacterial Physiological Phenomena↗
Structure and function of the low Mr phosphotyrosine protein phosphatases.
Phosphotyrosine protein phosphatases (PTPases) catalyse the hydrolysis of phosphotyrosine residues in proteins and are hence implicated in the complex mechanism of the control of cell proliferation and differentiation. The low Mr PTPases are a group of soluble PTPases displaying a reduced molecular mass; in addition, a group of low molecular mass dual specificity (ds)PTPases which hydrolyse phosphotyrosine and phosphoserine/threonine residues in proteins are known. The enzymes belonging to the two groups are unrelated to each other and to other PTPase classes except for the presence of a CXXXXXRS/T sequence motif containing some of the catalytic residues (active site signature) and for the common catalytic mechanism, clearly indicating convergent evolution. The low Mr PTPases have a long evolutionary history since microbial (prokaryotic and eukaryotic) counterparts of both tyrosine-specific and dsPTPases have been described. Despite the relevant number of data reported on the structural and catalytic features of a number of low Mr PTPases, only limited information is presently available on the substrate specificity and the true biological roles of these enzymes, in prokaryotic, yeast and eukaryotic cells.
Amino Acid Sequence↗
Redesigning metabolic routes: manipulation of TOL plasmid pathway for catabolism of alkylbenzoates.
Increasing quantities of man-made organic chemicals are released each year into the biosphere. Some of these compounds are both toxic and relatively resistant to physical, chemical, or biological degradation, and they thus constitute an environmental burden of considerable magnitude. Genetic manipulation of microbial catabolic pathways offers a powerful means by which to accelerate evolution of biodegradative routes through which such compounds might be eliminated from the environment. In the experiments described here, a catabolic pathway for alkylbenzoates specified by the TOL plasmid of Pseudomonas was restructured to produce a pathway capable of processing a new substrate, 4-ethylbenzoate. Analysis of critical steps in the TOL pathway that prevent metabolism of 4-ethylbenzoate revealed that this compound fails to induce synthesis of the catabolic enzymes and that one of its metabolic intermediates inactivates catechol 2,3-dioxygenase (C23O), the enzyme that cleaves the aromatic ring. Consequently, the pathway was sequentially modified by recruitment of genes from mutant bacteria selected for their production of either an altered pathway operon regulator that is activated by 4-ethylbenzoate or an altered C23O that is less sensitive to metabolite inactivation. The redesigned pathway was stably expressed and enabled host bacteria to degrade 4-ethylbenzoate in addition to the normal substrates of the TOL pathway.
Benzoates↗
Life in sediments fosters 'sexual' speciation in the Shewanella baltica complex.
Understanding how intra- and interspecific differentiation arises in natural microbial populations is central to explaining the processes that drive bacterial evolution. Motivated by the co-occurrence of multiple putative genospecies closely related to Shewanella baltica in Baltic Sea sediments, we investigated the genomic structure of this species complex across fine spatial scales. We analyzed 112 genome sequences from strains collected across several sediment cores and depths (0-6 cm) at Vaxön (Stockholm archipelago, Sweden) as well as earlier isolates from this site and allopatric strains from surrounding locations obtained from both sediments and the water column. Using a reverse-ecology population genomics approach, we found unprecedented genomic diversification among sediment-associated strains, which form a species complex resolving into three cohesive evolutionary groups (G1, G2, and G3) with distinct signatures of metabolic specialization including sulfite respiration. While G1 consists predominantly of a single species (S. baltica) with high gene turnover, G2 and G3 comprise an array of divergent putative genospecies and previously reported species consistently recovered from sediments. Patterns of homologous recombination indicate that diversification of the lineages within G2 and G3 is primarily recombination-driven ('sexual') and is associated with specialization in sulfite reduction and utilization of certain carbon sources. The extent of diversity uncovered here far exceeds that reported for S. baltica from other environments, suggesting that a sediment-associated lifestyle promotes the emergence of novel genotypes. These findings expand the known limits of sympatric speciation in prokaryotes beyond subspecific ecotypes, demonstrating that bacterial species can diverge and persist as distinct lineages in the absence of spatial segregation and at microgeographic scales. Furthermore, our results suggest that collective interactions and ecological differentiation can structure sediment-associated bacterial populations strongly enough to drive divergence at the species level.
Journal Article↗
Bordetella species are distinguished by patterns of substantial gene loss and host adaptation.
Pathogens of the bacterial genus Bordetella cause respiratory disease in humans and animals. Although virulence and host specificity vary across the genus, the genetic determinants of this diversity remain unidentified. To identify genes that may underlie key phenotypic differences between these species and clarify their evolutionary relationships, we performed a comparative analysis of genome content in 42 Bordetella strains by hybridization of genomic DNA to a microarray representing the genomes of three Bordetella species and by subtractive hybridization. Here we show that B. pertussis and B. parapertussis are predominantly differentiated from B. bronchiseptica by large, species-specific regions of difference, many of which encode or direct synthesis of surface structures, including lipopolysaccharide O antigen, which may be important determinants of host specificity. The species also exhibit sequence diversity at a number of surface protein-encoding loci, including the fimbrial major subunit gene, fim2. Gene loss, rather than gene acquisition, accompanied by the proliferation of transposons, has played a fundamental role in the evolution of the pathogenic bordetellae and may represent a conserved evolutionary mechanism among other groups of microbial pathogens.
Animals↗
Evolutionary aspects of urea cycle enzyme genes.
The functions and expression pattern of urea cycle enzymes have undergone considerable changes during the course of evolution. Sequence analyses shows that urea cycle enzymes from mammals are homologous to microbial enzymes of the arginine-metabolic pathway. Recently, an unexpected relationship was found between argininosuccinate lyase (EC 4.3.2.1), the fourth enzyme of the cycle, and delta-crystallin, a lens structural protein of birds and reptiles.
Animals↗
Characterization of the drug resistance plasmid R2418: restriction map and role of insertion and deletion in its evolution.
Escherichia coli 2418 strain is resistant to beta-lactam antibiotics (ampicillin, carbenicillin, and cephalothin), streptomycin, tetracycline, kanamycin, and chloramphenicol. This strain contains at least two conjugative plasmids (R2418 and R2418S) encoding resistance to beta lactam antibiotics and resistance to both beta-lactam antibiotics and streptomycin, respectively. Restriction endonuclease mapping of plasmid DNAs indicates that the plasmid R2418S has evolved from R2418 DNA by the insertion of 2.5-kb DNA between BamHI and PvuII sites, and deletion of 0.5-kb DNA within the EcoRI-EcoRV region. The 2.5-kb DNA insert is responsible for streptomycin resistance. This evolution is also associated with a reduction in the efficiency of conjugal transfer for the plasmid R2418S. The conjugal transfer of streptomycin resistance occurs only through the coresidence of the conjugative plasmid R2418 or R2418S in the donor cell. In accordance with the hypothesis that the Smr determinant is due to a putative transposon, plasmid-free transconjugants resistant to streptomycin only were isolated. Southern blot analysis of HindIII chromosomal digests extracted from these transconjugants shows that the Smr determinant is inserted into different sites in chromosomal DNA.
Anti-Bacterial Agents↗
Effect of high pressure homogenisation of milk on cheese yield and microbiology, lipolysis and proteolysis during ripening of Caciotta cheese.
The principal aim of this work was to compare Caciotta cheeses obtained from cow milk previously subjected to high pressure homogenisation (HPH) at 100 MPa with those produced from raw (R) or heat-treated (P) cow milk. HPH had both direct and indirect effects on cheese characteristics and their evolution during ripening. In particular, HPH treatment of milk induced a significant increase of the cheese yield; moreover, it affected the microbial ecology of both curd and cheese. Compared with the thermal treatment, the HPH treatment resulted in a decrease of about one log cfu/g of yeast and lactobacilli cell loads of the curd. The initial milk treatment also affected the evolution over time and the levels attained at the end of ripening of all the microbial groups studied. In fact, lactobacilli, microstaphylococci and yeast cell loads remained at lower levels in the cheeses obtained from HPH milk with respect to the other cheese types over the whole ripening period. Moreover, HPH of milk induced marked and extensive lipolysis. Cheeses from HPH milk showed the presence of high amounts of free fatty acids immediately after brining. The electrophoretic patterns of the different cheese types showed that Caciotta made from HPH-treated milk was characterized by a more extensive and faster proteolysis as well as a significant modification of its volatile molecule profile. The results obtained and the sensory analysis indicated that HPH treatment of milk was able to differentiate Caciotta cheese or to modify its ripening patterns.
Animals↗
Coordinated amino acid changes in the evolution of mammalian defensins.
The mammalian defensin molecule is a short, highly cationic peptide cytotoxic to both microbial and mammalian cells which is cleaved from a precursor including a signal peptide and a highly anionic propiece. A phylogenetic analysis of 28 complete sequences from five mammalian species (mouse, rat, guinea pig, rabbit, and human) showed species-specific clusters of sequences, indicating that the genes duplicated after divergence of these species. Comparison of rates of synonymous and nonsynonymous nucleotide substitution suggested that gene duplication has often been followed by a period in which diversification of the mature defensins at the amino acid level has been selectively favored. In some comparisons, it appeared that amino acid differences in this region have appeared in a nonrandom fashion so as to change the pattern of residue charges. Because it has been hypothesized that the negative charge in the propiece serves to balance the positive charge in the mature defensin and thus to prevent cytotoxicity prior to cleavage, we used a maximum likelihood method of reconstructing ancestral states in order to test whether this balance has been maintained over evolutionary time in spite of rapid diversification of the mature defensin at the amino acid level. Reconstructed ancestral sequences always maintained a charge balance between mature defensin and propiece, and changes in the net positive charge of the mature defensin were balanced by corresponding changes in the propiece. The results support the hypothesis that, in the evolution of these proteins, amino acid changes have occurred in a coordinated fashion so as to preserve an adaptive phenotype.
Amino Acid Sequence↗
The evolution of the ribonucleotide reductases: much ado about oxygen.
Ribonucleotide reduction is the only known biological means for de novo production of deoxyribonucleotides, the building blocks of DNA. These are produced from ribonucleotides, the building blocks of RNA, and the direction of this reaction has been taken to support the idea that, in evolution, RNA preceded DNA as genetic material. However, an understanding of the evolutionary relationships among the three modern-day classes of ribonucleotide reductase and how the first reductase arose early in evolution is still far off. We propose that the diversification of this class of enzymes is inherently tied to microbial colonization of aerobic and anaerobic niches. The work is of broader interest, as it also sheds light on the process of adaptation to oxygenic environments consequent to the evolution of atmospheric oxygen.
Allosteric Regulation↗
Common themes in microbial pathogenicity.
A bacterial pathogen is a highly adapted microorganism which has the capacity to cause disease. The mechanisms used by pathogenic bacteria to cause infection and disease usually include an interactive group of virulence determinants, sometimes coregulated, which are suited for the interaction of a particular microorganism with a specific host. Because pathogens must overcome similar host barriers, common themes in microbial pathogenesis have evolved. However, these mechanisms are diverse between species and not necessarily conserved; instead, convergent evolution has developed several different mechanisms to overcome host barriers. The success of a bacterial pathogen can be measured by the degree with which it replicates after entering the host and reaching its specific niche. Successful microbial infection reflects persistence within a host and avoidance or neutralization of the specific and nonspecific defense mechanisms of the host. The degree of success of a pathogen is dependent upon the status of the host. As pathogens pass through a host, they are exposed to new environments. Highly adapted pathogenic organisms have developed biochemical sensors exquisitely designed to measure and respond to such environmental stimuli and accordingly to regulate a cascade of virulence determinants essential for life within the host. The pathogenic state is the product of dynamic selective pressures on microbial populations.
Animals↗
The conscious cell.
The evolutionary antecedent of the nervous system is "microbial consciousness." In my description of the origin of the eukaryotic cell via bacterial cell merger, the components fused via symbiogenesis are already "conscious" entities. I have reconstructed an aspect of the origin of the neurotubule system by a hypothesis that can be directly tested. The idea is that the system of microtubules that became neurotubules has as its origin once-independent eubacteria of a very specific kind. Nothing, I claim, has ever been lost without a trace in evolution. The remains of the evolutionary process, the sequence that occurred that produced Cajal's neuron and other cells, live today. By study of obscure protists that we take to be extant decendants of steps in the evolution of cells, we reconstruct the past directly from living organisms. Even remnants of "microbial mind" can be inferred from behaviors of thriving microorganisms. All of the eukaryotes, not just lichens or an animal's neurons, are products of symbiogenesis among formerly free-living bacteria, some highly motile. Eukaryotes have evolved by the inheritance of acquired genomes; they have gained all their new features by ingesting and not digesting whole bacterial cells with complete genomes.
Animals↗
Molecular evolution of an arsenate detoxification pathway by DNA shuffling.
Functional evolution of an arsenic resistance operon has been accomplished by DNA shuffling, involving multiple rounds of in vitro recombination and mutation of a pool of related sequences, followed by selection for increased resistance in vivo. Homologous recombination is achieved by random fragmentation of the PCR templates and reassembly by primerless PCR. Plasmid-determined arsenate resistance from plasmid pl258 encoded by genes arsR, arsB, and arsC was evolved in Escherichia coli. Three rounds of shuffling and selection resulted in cells that grew in up to 0.5 M arsenate, a 40-fold increase in resistance. Whereas the native plasmid remained episomal, the evolved operon reproducibly integrated into the bacterial chromosome. In the absence of shuffling, no increase in resistance was observed after four selection cycles, and the control plasmid remained episomal. The integrated ars operon had 13 mutations. Ten mutations were located in arsB, encoding the arsenite membrane pump, resulting in a fourfold to sixfold increase in arsenite resistance. While arsC, the arsenate reductase gene, contained no mutations, its expression level was increased, and the rate of arsenate reduction was increased 12-fold. These results show that DNA shuffling can improve the function of pathways by complex and unexpected mutational mechanisms that may be activated by point mutation. These mechanisms may be difficult to explain and are likely to be overlooked by rational design.
Adenosine Triphosphatases↗
Eco-evolutionary dynamics sustain a potent yet rare antibiotic gene cluster in Streptomyces.
Microbial secondary metabolites have been recognized and utilized for nearly a century. Nevertheless, the eco-evolutionary mechanisms governing their distribution among microorganisms remain largely unresolved. In this study, we examined intraspecific interactions within Streptomyces albidoflavus and identified a strain exhibiting potent antagonistic activity against conspecifics. This "killer" phenotype was attributed to the production of kosinostatin, a hybrid aromatic polyketide antibiotic. Evolutionary genomic analyses provided strong evidence that the kosinostatin biosynthetic gene cluster was horizontally acquired in S. albidoflavus over a relatively short evolutionary timescale, a finding consistent with its sparse distribution within this species, across the genus Streptomyces, and even throughout the phylum Actinomycetota. Using microcosm assays, we demonstrated that the kosinostatin producer outcompeted sensitive conspecifics in liquid culture but not in soil, indicating that environmental context plays a key role in altering the fitness benefits of this cluster. Moreover, the competitive advantage was observed only in the presence of sensitive strains, revealing a trade-off between fitness benefits and metabolic costs. These results highlight the role of context-dependent selection in shaping the evolutionary persistence of the kosinostatin cluster. The current distribution pattern of this cluster in S. albidoflavus likely results from a dynamic interplay of intraspecific horizontal gene transfer, vertical inheritance, and recurrent gene loss. Overall, our findings establish an eco-evolutionary framework that explains the rarity of a potent antibiotic gene cluster in Streptomyces, illustrating how environmental constraints, fitness trade-offs, and gene flux collectively orchestrate the biosynthetic architecture of Streptomyces species.
Streptomyces↗