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At least 1,153 records · Page 64Linked to original sources
PubMed1979

Symbionticism revisited: a discussion of the evolutionary impact of intracellular symbioses.

Wallin (1927) first published the notion that the fusion of bacteria with host cells was the principal source of genetic novelty for speciation. He suggested that mitochondria are transitional elements in this process. While the significance that he attributed to symbiosis now seem excessive, he was one of the first authors to be aware of the evolutionary potential of symbiotic events and his view of mitochondria may not seem strange to many cell biologist today. The most significant evolutionary development which has been attributed to intracellular symbiosis is the origin of eukaryotic cellular organization. The current status of the 'serial endosymbiosis hypothesis' is briefly review. The case for the symbiotic origin of the chloroplast, based principally on 16 S RNA oligonucleotide cataloguing, is very strong. Mitochondrial origins are more obscure but also appear to be symbiotic due to recent 18 S cataloguing from wheat embryos. The probablility of the multiple origin of some eukaryotic organelles is also examined, the processes in question being the acquisition of distinct stocks of chloroplasts from disparate photosynthetic prokaryotes and the secondary donation of organelles from degenerate eukaryotic endosymbionts to their hosts, with specific reference to the dinoflagellates Peridinium balticum, Kryptoperidinium foliaceum and the ciliate Mesodinium rubrum. It is concluded that the evolutionary potential of intracellular symbiosis ('cytobiosis': a term introduced in this paper) is great, with the best established influence being on the origin of eukaryotic chloroplasts. Together with the potential effects of viral vectors, symbiosis serves as a supplementary speciation mechanism capable of producing directed evolutionary changes. It is likely that these processes will explain some of the apparent anomalies in evolutionary rates and direction which are not readily explicable by the conventional synthetic theory of evolution.

Animals↗
PubMed2001

Detecting changes in the functional constraints of paralogous genes.

We describe a new procedure to determine whether regional alterations in the evolutionary constraints imposed on paralogous proteins have occurred. We used as models the A and B (alternatively called alpha and beta) subunits of V/F/A-ATPases, originated by a gene duplication more than 3 billion years ago. Changes associated to three major splits (eubacteria versus Archaea-eukaryotes; Archaea versus eukaryotes; and among free-living bacteria and symbiotic mitochondria) were studied. Only in the first case, when we compared eubacterial or mitochondrial F-ATPases versus eukaryotic vacuolar V-ATPases or archaeal A-ATPases, constraint changes were observed. Modifications in the degree of regional constraining were not detected for the other two types of comparisons (V-ATPases versus A-ATPases and within F-ATPases, respectively). When the rates of evolution of the two subunits were compared, it was found that F-ATPases regulatory subunits evolved faster than catalytic subunits, but the opposite was true for A- and V-ATPases. Our results suggest that, even for universal and essential proteins, selective constraints may be occasionally altered. On the other hand, in some cases no changes were detected after periods of more than 2.2 billion years.

Adenosine Triphosphatases↗
PubMedDate not supplied

Environmentally constrained mutation and adaptive evolution in Salmonella.

The relationship between environment and mutation is complex [1]. Claims of Lamarkian mutation [2] have proved unfounded [3-5]; it is apparent, however, that the external environment can influence the generation of heritable variation, through either direct effects on DNA sequence [6] or DNA maintenance and copying mechanisms [7-10], or as a consequence of evolutionary processes [11-16]. The spectrum of mutational events subject to environmental influence is unknown [6] and precisely how environmental signals modulate mutation is unclear. Evidence from bacteria suggests that a transient recombination-dependent hypermutational state can be induced by starvation [5]. It is also apparent that changes in the mutability of specific loci can be influenced by alterations in DNA topology [10,17]. Here we describe a remarkable instance of adaptive evolution in Salmonella which is caused by a mutation that occurs in intermediate-strength osmotic environments. We show that the mutation is not 'directed' and describe its genetic basis. We also present compelling evidence in support of the hypothesis that the mutational event is constrained by signals transmitted from the external environment via changes in the activity of DNA gyrase.

Adaptation, Physiological↗
PubMed1996

Penicillin and beyond: evolution, protein fold, multimodular polypeptides, and multiprotein complexes.

As the protein sequence and structure databases expand, the relationships between proteins, the notion of protein superfamily, and the driving forces of evolution are better understood. Key steps of the synthesis of the bacterial cell wall peptidoglycan are revisited in light of these advances. The reactions through which the D-alanyl-D-alanine depeptide is formed, utilized, and hydrolyzed and the sites of action of the glycopeptide and beta-lactam antibiotics illustrate the concept according to which new enzyme functions evolve as a result of tinkering of existing proteins. This occurs by the acquisition of local structural changes, the fusion into multimodular polypeptides, and the association into multiprotein complexes.

Bacterial Proteins↗
PubMed1991

Nucleotide sequence of the Rhodobacter capsulatus fruK gene, which encodes fructose-1-phosphate kinase: evidence for a kinase superfamily including both phosphofructokinases of Escherichia coli.

The fruK gene encoding fructose-1-phosphate kinase (FruK), located within the fructose (fru)-catabolic operon of Rhodobacter capsulatus, was sequenced. FruK of R. capsulatus (316 amino acids; molecular weight = 31,232) is the same size as and is homologous to FruK of Escherichia coli, phosphofructokinase B (PfkB) of E. coli, phosphotagatokinase of Staphylococcus aureus, and ribokinase of E. coli. These proteins therefore make up a family of homologous proteins, termed the PfkB family. A phylogenetic tree for this new family was constructed. Sequence comparisons plus chemical inactivation studies suggested the lack of involvement of specific residues in catalysis. Although the Rhodobacter FruK differed markedly from the other enzymes within the PfkB family with respect to amino acid composition, these enzymes exhibited similar predicted secondary structural features. A large internal segment of the Rhodobacter FruK was found to be similar in sequence to the domain bearing the sugar bisphosphate-binding region of the large subunit of ribulose 1,5-bisphosphate carboxylase/oxygenase of plants and bacteria. Proteins of the PfkB family did not exhibit statistically significant sequence identity with PfkA of E. coli. PfkA, however, is homologous to other prokaryotic and eukaryotic ATP- and PPi-dependent Pfks (the PfkA family). These eukaryotic, ATP-dependent enzymes each consist of a homotetramer (mammalian) or a heterooctamer (yeasts), with each subunit containing an internal duplication of the size of the entire PfkA protein of E. coli. In some of these enzymes, additional domains are present. A phylogenetic tree was constructed for the PfkA family and revealed that the bacterial enzymes closely resemble the N-terminal domains of the eukaryotic enzyme subunits whereas the C-terminal domains have diverged more extensively. The PPi-dependent Pfk of potato is only distantly related to the ATP-dependent enzymes. On the basis of their similar functions, sizes, predicted secondary structures, and sequences, we suggest that the PfkA and PfkB families share a common evolutionary origin.

Amino Acid Sequence↗
PubMed1990

Sequences of isopenicillin N synthetase genes suggest horizontal gene transfer from prokaryotes to eukaryotes.

Evolutionary distances between bacterial and fungal isopenicillin N synthetase (IPNS) genes have been compared to distances between the corresponding 5S rRNA genes. The presence of sequences homologous to the IPNS gene has been examined in DNAs from representative prokaryotic organisms and Ascomycotina. The results of both analyses strongly support two different events of horizontal transfer of the IPNS gene from bacteria to filamentous fungi. This is the first example of such a type of transfer from prokaryotes to eukaryotes.

Acremonium↗
PubMed1995

Revival and identification of bacterial spores in 25- to 40-million-year-old Dominican amber.

A bacterial spore was revived, cultured, and identified from the abdominal contents of extinct bees preserved for 25 to 40 million years in buried Dominican amber. Rigorous surface decontamination of the amber and aseptic procedures were used during the recovery of the bacterium. Several lines of evidence indicated that the isolated bacterium was of ancient origin and not an extant contaminant. The characteristic enzymatic, biochemical, and 16S ribosomal DNA profiles indicated that the ancient bacterium is most closely related to extant Bacillus sphaericus.

Amber↗
PubMed2006

Molecular evolution of peptide methionine sulfoxide reductases (MsrA and MsrB): on the early development of a mechanism that protects against oxidative damage.

Methionine sulfoxide reductases, enzymes that reverse the oxidation of methionine residues, have been described in a wide range of species. The reduction of the diastereoisomers of oxidized methionine is catalyzed by two different monomeric methionine sulfoxide reductases (MsrA and MsrB) and is best understood as an evolutionary response to high levels of oxygen either in the Earth's atmosphere or possibly in more localized environments. Phylogenetic analyses of these proteins suggest that their distribution is the outcome of a complex history including many paralogy and lateral gene transfer events.

Animals↗
PubMed1990

A novel repeated DNA sequence located in the intergenic regions of bacterial chromosomes.

We report the discovery of a novel group of highly conserved DNA sequences located within the intergenic regions of the chromosomes of Escherichia coli, Salmonella typhimurium and other bacteria. These intergenic repeat units (IRUs) are 124-127 nucleotides long and have the potential to form stable stem-loop structures. The location of these sequences within the intergenic regions is variable with respect to known or putative signals for transcription and translation of the flanking genes. Some of the IRU sequences are transcribed, others are probably not. The structure and possible functions of these sequences are discussed in relation to palindromic units and other repeated DNA sequences in bacteria.

Base Sequence↗
PubMed1987

Bacterial viruses, prophages, and plasmids, reconsidered.

Prophages and plasmids offer to the bacterial cells generalized access to each other's genes. The result is an extremely rich, available gene bank. It has successfully supported the original bacterial life since its beginnings and therefore it has conditioned all bacterial cells. Thus, most of the basic mechanisms for the living world, the richest variety of new genes, and particularly the improved ways of using DNA as an extremely adaptable genetic material happened in bacteria with the help of prophages and plasmids. This fact has profoundly marked all the biosphere. The ancestor of the nucleus probably started as an accumulation of prophages and plasmids integrated in the growing "chromosome" of the outer symbiont of the first eukaryotes. Many bacterial vestiges were probably retained in eukaryotes, mostly those related to the dominant and lasting role of small replicons in all their bacterial precursors. These vestiges may, for example, serve as an endogenic source for some DNA viruses in eukaryotes. The other animal and plant viruses seem to derive directly or indirectly from prophages or plasmids. In the case of RNA viruses they may have originated from probable RNA small replicons present in the first forms of life on earth. Some confusion arose in biology, as viruses were discovered first and therefore their most probable ancestors, the plasmids and the prophages which were discovered later, were thought to be viruslike, or viruses, as is the case with prophages.

Bacteria↗
PubMed2005

Intra- and interspecific comparisons of bacterial diversity and community structure support coevolution of gut microbiota and termite host.

We investigated the bacterial gut microbiota from 32 colonies of wood-feeding termites, comprising four Microcerotermes species (Termitidae) and four Reticulitermes species (Rhinotermitidae), using terminal restriction fragment length polymorphism analysis and clonal analysis of 16S rRNA. The obtained molecular community profiles were compared statistically between individuals, colonies, locations, and species of termites. Both analyses revealed that the bacterial community structure was remarkably similar within each termite genus, with small but significant differences between sampling sites and/or termite species. In contrast, considerable differences were found between the two termite genera. Only one bacterial phylotype (defined with 97% sequence identity) was shared between the two termite genera, while 18% and 50% of the phylotypes were shared between two congeneric species in the genera Microcerotermes and Reticulitermes, respectively. Nevertheless, a phylogenetic analysis of 228 phylotypes from Microcerotermes spp. and 367 phylotypes from Reticulitermes spp. with other termite gut clones available in public databases demonstrated the monophyly of many phylotypes from distantly related termites. The monophyletic "termite clusters" comprised of phylotypes from more than one termite species were distributed among 15 bacterial phyla, including the novel candidate phyla TG2 and TG3. These termite clusters accounted for 95% of the 960 clones analyzed in this study. Moreover, the clusters in 12 phyla comprised phylotypes from more than one termite (sub)family, accounting for 75% of the analyzed clones. Our results suggest that the majority of gut bacteria are not allochthonous but are specific symbionts that have coevolved with termites and that their community structure is basically consistent within a genus of termites.

Animals↗
PubMed2004

Evidence of positively selected sites in mammalian alpha-defensins.

Alpha-defensins are a family of mammalian antimicrobial peptides that exhibit variable activity against a panel of microbes, including bacteria, fungi, and enveloped viruses. We have employed a maximum-likelihood approach to detect evidence of positive selection (adaptive evolution) in the evolution of these important molecules of the innate immune response. We have identified 14 amino acid sites that are predicted to be subject to positive selection. Furthermore, we show that all these sites are located in the mature antimicrobial peptide and not in the prepropeptide region of the molecule, implying that they are of functional importance. These results suggest that mammalian alpha-defensins have been under selective pressure to evolve in response to potentially infectious challenges by fast-evolving microbes.

Amino Acid Sequence↗
PubMed1999

Mosaic bacterial chromosomes: a challenge en route to a tree of genomes.

In a recent analysis J.G. Lawrence and H. Ochman [Proc Natl Acad Sci USA 1998;95:9413-9417 (Reference 1)] surmised that about 10% of the current E. coli genome consists of genes that were acquired in over 200 events of lateral gene transfer, which occurred subsequent to the divergence of E. coli and Salmonella some 100 million years ago. Overall, the data suggest that no less than 18% of E. coli's genes might be relatively recent foreign acquisitions, and that the average rate of acquisition may be close to about 16 kb per million years. These quantitative estimates of comparatively recent genome flux have profound impact on evolutionary genome comparisons. They tend to suggest that a search should be on to identify principles that might ultimately govern gene distribution patterns across prokaryotic genomes.

Biological Evolution↗
PubMed1995

Heterogeneity of genome sizes among natural isolates of Escherichia coli.

Comparisons of the genetic maps of Escherichia coli K-12 and Salmonella typhimurium LT2 suggest that the size and organization of bacterial chromosomes are highly conserved. Employing pulsed-field gel electrophoresis, we have estimated the extent of variation in genome size among 14 natural isolates of E. coli. The BlnI and NotI restriction fragment patterns were highly variable among isolates, and genome sizes ranged from 4,660 to 5,300 kb, which is several hundred kilobases larger than the variation detected between enteric species. Genome size differences increase with the evolutionary genetic distance between lineages of E. coli, and there are differences in genome size among the major subgroups of E. coli. In general, the genomes of natural isolates are larger than those of laboratory strains, largely because of the fact that laboratory strains were derived from the subgroup of E. coli with the smallest genomes.

Biological Evolution↗
PubMed2003

Functional cooperation between exonucleases and endonucleases--basis for the evolution of restriction enzymes.

Many types of restriction enzymes cleave DNA away from their recognition site. Using the type III restriction enzyme, EcoP15I, which cleaves DNA 25-27 bp away from its recognition site, we provide evidence to show that an intact recognition site on the cleaved DNA sequesters the restriction enzyme and decreases the effective concentration of the enzyme. EcoP15I restriction enzyme is shown here to perform only a single round of DNA cleavage. Significantly, we show that an exonuclease activity is essential for EcoP15I restriction enzyme to perform multiple rounds of DNA cleavage. This observation may hold true for all restriction enzymes cleaving DNA sufficiently far away from their recognition site. Our results highlight the importance of functional cooperation in the modulation of enzyme activity. Based on results presented here and other data on well-characterised restriction enzymes, a functional evolutionary hierarchy of restriction enzymes is discussed.

Binding Sites↗
PubMed2003

Genome evolution in an insect cell: distinct features of an ant-bacterial partnership.

Bacteria that live exclusively within eukaryotic host cells include not only well-known pathogens, but also obligate mutualists, many of which occur in diverse insect groups such as aphids, psyllids, tsetse flies, and the ant genus Camponotus (Buchner, 1965; Douglas, 1998; Moran and Telang, 1998; Baumann et al., 2000; Moran and Baumann, 2000). In contrast to intracellular pathogens, these primary (P) endosymbionts of insects are required for the survival and reproduction of the host, exist within specialized host cells called bacteriocytes, and undergo stable maternal transmission through host lineages (Buchner, 1965; McLean and Houk, 1973). Due to their long-term host associations and close phylogenetic relationship with well-characterized enterobacteria (Fig. 1), P-endosymbionts of insects are ideal model systems to examine changes in genome content and architecture that occur in the context of beneficial, intracellular associations. Since these bacteria have not been cultured outside of the host cell, they are difficult to study with traditional genetic or physiological approaches. However, in recent years, molecular and computational approaches have provided important insights into their genetic diversity and ecological significance. This review describes some recent insights into the evolutionary genetics of obligate insect-bacteria symbioses, with a particular focus on an intriguing association between the bacterial endosymbiont Blochmannia and its ant hosts.

Animals↗
PubMed2006

Domain deletions and substitutions in the modular protein evolution.

The main mechanisms shaping the modular evolution of proteins are gene duplication, fusion and fission, recombination and loss of fragments. While a large body of research has focused on duplications and fusions, we concentrated, in this study, on how domains are lost. We investigated motif databases and introduced a measure of protein similarity that is based on domain arrangements. Proteins are represented as strings of domains and comparison was based on the classic dynamic alignment scheme. We found that domain losses and duplications were more frequent at the ends of proteins. We showed that losses can be explained by the introduction of start and stop codons which render the terminal domains nonfunctional, such that further shortening, until the whole domain is lost, is not evolutionarily selected against. We demonstrated that domains which also occur as single-domain proteins are less likely to be lost at the N terminus and in the middle, than at the C terminus. We conclude that fission/fusion events with single-domain proteins occur mostly at the C terminus. We found that domain substitutions are rare, in particular in the middle of proteins. We also showed that many cases of substitutions or losses result from erroneous annotations, but we were also able to find courses of evolutionary events where domains vanish over time. This is explained by a case study on the bacterial formate dehydrogenases.

Amino Acid Motifs↗
PubMed2004

Simulation, experiment, and evolution: understanding nucleation in protein S6 folding.

In this study, we explore nucleation and the transition state ensemble of the ribosomal protein S6 using a Monte Carlo (MC) Go model in conjunction with restraints from experiment. The results are analyzed in the context of extensive experimental and evolutionary data. The roles of individual residues in the folding nucleus are identified, and the order of events in the S6 folding mechanism is explored in detail. Interpretation of our results agrees with, and extends the utility of, experiments that shift phi-values by modulating denaturant concentration and presents strong evidence for the realism of the mechanistic details in our MC Go model and the structural interpretation of experimental phi-values. We also observe plasticity in the contacts of the hydrophobic core that support the specific nucleus. For S6, which binds to RNA and protein after folding, this plasticity may result from the conformational flexibility required to achieve biological function. These results present a theoretical and conceptual picture that is relevant in understanding the mechanism of nucleation in protein folding.

Bacterial Proteins↗