Protein evolution. How far can sequences diverge?
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Bacterial Proteins↗
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Prophages and bacterial genomics: what have we learned so far?
Bacterial genome nucleotide sequences are being completed at a rapid and increasing rate. Integrated virus genomes (prophages) are common in such genomes. Fifty-one of the 82 such genomes published to date carry prophages, and these contain 230 recognizable putative prophages. Prophages can constitute as much as 10-20% of a bacterium's genome and are major contributors to differences between individuals within species. Many of these prophages appear to be defective and are in a state of mutational decay. Prophages, including defective ones, can contribute important biological properties to their bacterial hosts. Therefore, if we are to comprehend bacterial genomes fully, it is essential that we are able to recognize accurately and understand their prophages from nucleotide sequence analysis. Analysis of the evolution of prophages can shed light on the evolution of both bacteriophages and their hosts. Comparison of the Rac prophages in the sequenced genomes of three Escherichia coli strains and the Pnm prophages in two Neisseria meningitidis strains suggests that some prophages can lie in residence for very long times, perhaps millions of years, and that recombination events have occurred between related prophages that reside at different locations in a bacterium's genome. In addition, many genes in defective prophages remain functional, so a significant portion of the temperate bacteriophage gene pool resides in prophages.
Base Sequence↗
Complete genome sequence of the marine planctomycete Pirellula sp. strain 1.
Pirellula sp. strain 1 ("Rhodopirellula baltica") is a marine representative of the globally distributed and environmentally important bacterial order Planctomycetales. Here we report the complete genome sequence of a member of this independent phylum. With 7.145 megabases, Pirellula sp. strain 1 has the largest circular bacterial genome sequenced so far. The presence of all genes required for heterolactic acid fermentation, key genes for the interconversion of C1 compounds, and 110 sulfatases were unexpected for this aerobic heterotrophic isolate. Although Pirellula sp. strain 1 has a proteinaceous cell wall, remnants of genes for peptidoglycan synthesis were found. Genes for lipid A biosynthesis and homologues to the flagellar L- and P-ring protein indicate a former Gram-negative type of cell wall. Phylogenetic analysis of all relevant markers clearly affiliates the Planctomycetales to the domain Bacteria as a distinct phylum, but a deepest branching is not supported by our analyses.
Adaptation, Physiological↗
Salmonellae of serotypes gallinarum and pullorum grouped by biotyping and fimbrial-gene probing.
When salmonellae of serotypes Gallinarum (50 isolates) and Pullorum (36 isolates), that produce non-adhesive (type-2) fimbriae, were tested for their reactions in biochemical tests, 81 (94%) were found to belong to three distinct biochemical groups, I-III. Interaction of HinfI-digested DNA of both Gallinarum and Pullorum with a probe of accessory genes of type-1 fimbriation in serotype Typhimurium gave one type of Southern hybridisation pattern that was readily distinguished from that of Typhimurium strains. With a probe of the Typhimurium fimbrial subunit gene, Pullorum isolates were separated into strongly and weakly probe-reactive groups which showed restriction fragment-length polymorphism; these latter groups corresponded to biochemical groups II and III, respectively.
Bacterial Typing Techniques↗
Microbiology and evolution. Modulating mutation rates in the wild.
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Adaptation, Physiological↗
Bacterial resistance to ultraviolet irradiation under anaerobiosis: implications for pre-phanerozoic evolution.
The concept that low concentrations of atmospheric oxygen and consequent unattenuated ultraviolet irradiation limited the emergence of Phanerozoic life, the Berkner-Marshall hypothesis, is no longer tenable. Anaerobic bacteria, which probably evolved far earlier than Metazoa, were irradiated in a special chamber under strictly anaerobic conditions. Both intrinsic resistance and photoreactivation by visible light were discovered in obligately and facultatively anaeroboc microbes. Atmospheric scientists have shown that small amounts of oxygen would have limied pre-Phanerozoic surface ultraviolet irradiation to fluxes well below those used in the anaerobic experiments described. Since adequate ultraviolet protection mechanisms evolved early, the late Proterozoic appearance of Metazoa probably was not related to high fluxes of solar ultraviolet radiation.
Anaerobiosis↗
Molecular structure and immunity specificity of colicin E6, an evolutionary intermediate between E-group colicins and cloacin DF13.
The primary structure of a 3.1-kilobase E6 or E3 segment carrying colicin and related genes was determined. Plasmid ColE6-CT14 showed striking homology to ColE3-CA38 throughout this segment, including homology to the secondary immunity gene, immE8, downstream of the E6 or E3 immunity gene. The ColE3-CA38 and ColE6-CT14 sequences, however, contained an exceptional hot spot region encoding both the colicin-active domain (RNase region) and the immunity protein, reflecting their different immunity specificities. On the other hand, some chimeric plasmids were constructed through homologous recombination between colicin E3 and cloacin DF13 operons. The resulting plasmids were deduced to produce chimeric colicins with a colicin E3-type N-terminal part, a cloacin DF13-type C-terminal-active domain, and the DF13 immunity protein. The killing spectra of the chimeric colicins and the immunities of the plasmids were identical to those of colicin E6 and ColE6-CT14, respectively, showing that the colicin E6 immunity specificity is completely equivalent to that of cloacin DF13. Nevertheless, colicin E6 has been found to show a sequence diversity from cloacin DF13 almost to the same extent as that from colicin E3 in their RNase and immunity regions, indicating that only a small number of amino acids defines the immunity specificity for discrimination between colicins E3 and E6 (or cloacin DF13).
Amino Acid Sequence↗
Structural, functional, and evolutionary analysis of moeZ, a gene encoding an enzyme required for the synthesis of the Pseudomonas metabolite, pyridine-2,6-bis(thiocarboxylic acid).
BACKGROUND: Pyridine-2,6-bis(thiocarboxylic acid) (pdtc) is a small secreted metabolite that has a high affinity for transition metals, increases iron uptake efficiency by 20% in Pseudomonas stutzeri, has the ability to reduce both soluble and mineral forms of iron, and has antimicrobial activity towards several species of bacteria. Six GenBank sequences code for proteins similar in structure to MoeZ, a P. stutzeri protein necessary for the synthesis of pdtc. RESULTS: Analysis of sequences similar to P. stutzeri MoeZ revealed that it is a member of a superfamily consisting of related but structurally distinct proteins that are members of pathways involved in the transfer of sulfur-containing moieties to metabolites. Members of this family of enzymes are referred to here as MoeB, MoeBR, MoeZ, and MoeZdR. MoeB, the molybdopterin synthase activating enzyme in the molybdopterin cofactor biosynthesis pathway, is the most characterized protein from this family. Remarkably, lengths of greater than 73% nucleic acid homology ranging from 35 to 486 bp exist between Pseudomonas stutzeri moeZ and genomic sequences found in some Mycobacterium, Mesorhizobium, Pseudomonas, Streptomyces, and cyanobacteria species. CONCLUSIONS: The phylogenetic relationship among moeZ sequences suggests that P. stutzeri may have acquired moeZ through lateral gene transfer from a donor more closely related to mycobacteria and cyanobacteria than to proteobacteria. The importance of this relationship lies in the fact that pdtc, the product of the P. stutzeri pathway that includes moeZ, has an impressive set of capabilities, some of which could make it a potent pathogenicity factor.
Amino Acid Sequence↗
Automatic selection of representative proteins for bacterial phylogeny.
BACKGROUND: Although there are now about 200 complete bacterial genomes in GenBank, deep bacterial phylogeny remains a difficult problem, due to confounding horizontal gene transfers and other phylogenetic "noise". Previous methods have relied primarily upon biological intuition or manual curation for choosing genomic sequences unlikely to be horizontally transferred, and have given inconsistent phylogenies with poor bootstrap confidence. RESULTS: We describe an algorithm that automatically picks "representative" protein families from entire genomes for use as phylogenetic characters. A representative protein family is one that, taken alone, gives an organismal distance matrix in good agreement with a distance matrix computed from all sufficiently conserved proteins. We then use maximum-likelihood methods to compute phylogenetic trees from a concatenation of representative sequences. We validate the use of representative proteins on a number of small phylogenetic questions with accepted answers. We then use our methodology to compute a robust and well-resolved phylogenetic tree for a diverse set of sequenced bacteria. The tree agrees closely with a recently published tree computed using manually curated proteins, and supports two proposed high-level clades: one containing Actinobacteria, Deinococcus, and Cyanobacteria ("Terrabacteria"), and another containing Planctomycetes and Chlamydiales. CONCLUSION: Representative proteins provide an effective solution to the problem of selecting phylogenetic characters.
Algorithms↗
The multidrug transporters belonging to major facilitator superfamily in Mycobacterium tuberculosis.
BACKGROUND: Both intrinsic and acquired multidrug resistance play an important role in the insurgence of tuberculosis. Detailed knowledge of the molecular basis of drug recognition and transport by multidrug transport systems is required for the development of new antibiotics that are not extruded or of inhibitors that block the multidrug transporter and allow traditional antibiotics to be effective. MATERIALS AND METHODS: We have undertaken the inventory of the drug transporters subfamily, included in the major facilitator superfamily (MFS), encoded by the complete genome of Mycobacterium tuberculosis (MTB). These proteins were identified on the basis of their characteristic stretches of amino acids and transmembrane segments (TMS) number. CONCLUSIONS: Genome analysis and searches of homology between the identified transporters and proteins characterized in other organisms revealed 16 open reading frames encoding putative drug efflux pumps belonging to MFS. In the case of two of them, we also have demonstrated that they function as drug efflux proteins.
Amino Acid Sequence↗
[Infective endocarditis. 7 decades of evolution].
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Endocarditis, Bacterial↗
The mesosome--a clue to the evolution of the plasma membrane.
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Actinomycetales↗
[Population composition of Actinomyces tumemacerans and Actinomyces albus var. fungatus].
The population analysis of Actinomyces tumemacerans and Actinomyces albus var. fungatus has revealed identical homologous series of spontaneous variants, this suggesting the genetical relationship of the cultures. Variants of the same type (basic, oligosporous, asporogenous and proactinomycete-like) are identical not only according to their individual properties (Kuznetsov, 1973) but also in total characteristics typical of the variants of a given species. Populations of the studied cultures comprise variants synthesizing several antibiotics, i.e. albofungin, albonursin and tetraene (basic and oligosporous variants), albofungin and tetraene (asprogenous green variants), as well as variants producing only one tetraene antibiotic (proactinomycete-like variants). Therefore, the population analysis based on the law of homologous series in hereditary variability of actinomycetes can be used as a new approach to the taxonomy of these microorganisms.
Anti-Bacterial Agents↗
The "domino theory" of gene death: gradual and mass gene extinction events in three lineages of obligate symbiotic bacterial pathogens.
During the adaptation of an organism to a parasitic lifestyle, various gene functions may be rendered superfluous due to the fact that the host may supply these needs. As a consequence, obligate symbiotic bacterial pathogens tend to undergo reductive genomic evolution through gene death (nonfunctionalization or pseudogenization) and deletion. Here, we examine the evolutionary sequence of gene-death events during the process of genome miniaturization in three bacterial species that have experienced extensive genome reduction: Mycobacterium leprae, Shigella flexneri, and Salmonella typhi. We infer that in all three lineages, the distribution of functional categories is similar in pseudogenes and genes but different from that of absent genes. Based on an analysis of evolutionary distances, we propose a two-step "domino effect" model for reductive genome evolution. The process starts with a gradual gene-by-gene-death sequence of events. Eventually, a crucial gene within a complex pathway or network is rendered nonfunctional triggering a "mass gene extinction" of the dependent genes. In contrast to published reports according to which genes belonging to certain functional categories are prone to nonfunctionalization more frequently and earlier than genes belonging to other functional categories, we could discern no characteristic regularity in the temporal order of function loss.
Bacteria↗
Pathoadaptive mutations: gene loss and variation in bacterial pathogens.
Pathogenicity-adaptive, or pathoadaptive, mutations represent a genetic mechanism for enhancing bacterial virulence without horizontal transfer of specific virulence factors. Pathoadaptive evolution can be important within single infections and for defining the population structure of a pathogenic species.
Adaptation, Physiological↗
The Garrod Lecture. Evasion of antibiotic action by bacteria.
Antibiotics have reduced the mortality from infectious diseases but not the prevalence of these diseases. Use, and often abuse, of antimicrobial agents encourages the evolution of bacteria toward resistance, often resulting in therapeutic failure. This evolution is due to the emergence of "new' resistance mechanisms and to the spread of well-characterized mechanisms of resistance to the majority of bacterial species. Bacterial resistance can be intrinsic or acquired. Intrinsic resistance is species or genus specific and delineates the spectrum of activity of the antibiotic. Acquired resistance is present in only certain strains of a species or of a genus. The latter results from mutation in a gene located in the host chromosome or a plasmid or from acquisition of new genetic information by a bacterium, mainly by conjugation or transformation. In this review, recent developments in the understanding of biochemical mechanisms and the genetics of resistance is considered for the clinically important antibiotic families.
Anti-Bacterial Agents↗
Evolution of serum prealbumin, C-reactive protein, and orosomucoid in neonates with bacterial infection.
The simultaneous changes in serum prealbumin, orosomucoid (alpha-acidglycoprotein, AGP), and C-reactive protein (CRP) were evaluated in 36 newborn infants with septicemia (n = 20), meningitis (n = 10), arthritis (n = 5), and peritonitis (n = 1). In 29 patients with a favorable outcome the values for serum prealbumin and CRP showed a rapid return toward normal: in 2 to 3 days serum prealbumin increased by 84% from the basal value and remained at (mean +/- 1 SD) 0.11 +/- 0.02 gm/L. Serum CRP decreased from 85 +/- 75 mg/L (range 0.15 to 206 mg/L) to 49 +/- 64 mg/L (2 to 210 mg/L) at 3 to 4 days of evolution and to normal values at day 13 to 16. The changes in serum orosomucoid values were slower, from 1.33 +/- 0.75 gm/L to 1.16 +/- 0.75 gm/L at day 13 to 16, with normalization after 20 to 30 days. Serum orosomucoid values returned to the normal range with the clinical improvement. In some patients the orosomucoid/prealbumin ratio decreased earlier than the serum orosomucoid concentration. Seven patients died, and in four of these in whom at least three values could be determined serum CRP and orosomucoid remained very high, whereas serum prealbumin did not increase or subsequently decreased. These data show an inverse change in serum CRP and prealbumin concentrations in infected neonates. The immediate decrease in CRP reflects the effect of treatment, whereas the later decrease in serum AGP parallels the clinical course of the infection. Thus the determination of these proteins can help to guide the treatment of infection in newborn infants.
Acute-Phase Proteins↗
The origin and evolution of human pathogens.
What are the genetic origins of human pathogens? An international group of scientists discussed this topic at a workshop that took place in late October 2004 in Baeza (Spain). Focusing primarily on bacterial pathogens, they examined the role that pathogenicity islands and bacteriophages play on determining the virulence properties that distinguish closely related members of a given species, such as host range and tissue specificity. They also discussed an instance in which closely related bacterial species differ in the production of a cell surface modification mediating resistance to an antibiotic as a result of the disparate regulation of homologous genes. In certain pathogens, genes normally carrying out housekeeping functions may adopt new functions, whereas in other organisms, genes that respond to stresses associated with non-host environments are silenced during infection to prevent the expression of products that interfere with the normal colonization process. The adaptive behaviour of certain pathogens relies on gene variation at certain loci that by virtue of containing polymeric repeats in regulatory or coding regions, can generate variants that may or may not express products that modify the cell surface of the organism. The meeting also addressed the properties of ORFan genes, which have no homologues in the sequence databases, as well as the creation of genes de novo by duplication and divergence.
Bacteria↗