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At least 973 records · Page 54Linked to original sources
PubMed2003

Thermostabilization of bacterial fructosyl-amino acid oxidase by directed evolution.

We succeeded in isolating several thermostable mutant fructosyl-amino acid oxidase (FAOX; EC 1.5.3) without reduction of productivity by directed evolution that combined an in vivo mutagenesis and membrane assay screening system. Five amino acid substitutions (T60A, A188G, M244L, N257S, and L261M) occurred in the most thermostable mutant obtained by a fourth round of directed evolution. This altered enzyme, FAOX-TE, was stable at 45 degrees C, whereas the wild-type enzyme was not stable above 37 degrees C. The K(m) values of FAOX-TE for D-fructosyl-L-valine and D-fructosyl-glycine were 1.50 and 0.58 mM, respectively, in contrast with corresponding values of 1.61 and 0.74 mM for the wild-type enzyme. This altered FAOX-TE will be useful in the diagnosis of diabetes.

Amino Acid Oxidoreductases↗
PubMed2005

Evolutionary origins of genomic repertoires in bacteria.

Explaining the diversity of gene repertoires has been a major problem in modern evolutionary biology. In eukaryotes, this diversity is believed to result mainly from gene duplication and loss, but in prokaryotes, lateral gene transfer (LGT) can also contribute substantially to genome contents. To determine the histories of gene inventories, we conducted an exhaustive analysis of gene phylogenies for all gene families in a widely sampled group, the gamma-Proteobacteria. We show that, although these bacterial genomes display striking differences in gene repertoires, most gene families having representatives in several species have congruent histories. Other than the few vast multigene families, gene duplication has contributed relatively little to the contents of these genomes; instead, LGT, over time, provides most of the diversity in genomic repertoires. Most such acquired genes are lost, but the majority of those that persist in genomes are transmitted strictly vertically. Although our analyses are limited to the gamma-Proteobacteria, these results resolve a long-standing paradox-i.e., the ability to make robust phylogenetic inferences in light of substantial LGT.

Bacteria↗
PubMed1996

Are bacterial biofilms constrained to Darwin's concept of evolution through natural selection?

Numerous antimicrobial agents have been developed which act at the molecular, cellular, and organismal levels. However, few have been developed which act at the community-level. This results largely from the failure of Darwinian selection theory to envision communities as units of proliferation and evolution. It is thus difficult to conceive of microbial communities as causative agents and to develop antimicrobials which are effective against them. Consequently, we find it necessary to consider a more comprehensive biological paradigm which envisions biofilm communities and other microbial associations (e.g. mixed infections, food spoilage, tooth decay) as units of existence, activity, ecology, proliferation, survival, and evolution. These communities exist in the same sense that organisms exist as units of ecological activity. This is a simpler, more comprehensive, and more unifying theory of ecology. It is simpler in that it no longer requires convoluted explanations of altruistic behavior in terms of individual selection. It is more comprehensive by not constraining evolution to the selection of any single level of biological organization (genes, races, lineages, or groups). It unifies in that it bridges the boundaries between microbial ecology, evolutionary ecology and ecosystem ecology. The basis for this theory lies in recognizing that life consists of various forms of information (order) which evolve not only through genetic recombination and mutation, but also through the recombination of organisms within communities (as well as other mechanisms, some of which are considered beyond the realm of biology). It also involves setting aside the concept of evolution through selection and competition, in favor of evolution through proliferation and association.

Bacteria↗
PubMed1981

[Acute neutropenia in adult severe bacterial infections. Six cases (author's transl)].

A transient neutropenia (duration : less than 48 hours) occurred in 6 patients with severe bacterial infections. The bone marrow myeloïd cellularity was high or normal; a maturation arrest of the myeloïd cells - at a variable stage - was present in each case, as well as circulating granulocyte precursors. Other causes of neutropenia were excluded. A general survey of the literature is made and the mechanisms of this bacterial neutropenia are considered : bone marrow failure seems mostly improbable ; the few previously reported cases, the experimental bacterial neutropenias, the peculiar, transient, evolution we observed, all favor a peripheral mechanism ; the bacterial infection seems to act by; two ways : in septicemia (especially during septic shock) by enhancing leucocyte margination along vascular walls ; in large septic foci (mostly pulmonary) by an important destruction of polymorphonuclear neutrophils. Such bacterial infections share a bad prognosis but the neutropenia itself needs no specific treatment.

Acute Disease↗
PubMed1995

Horizontal gene transfer: regulated expression of a tobacco homologue of the Agrobacterium rhizogenes rolC gene.

A tobacco homologue (trolC) of the rolC gene of the Agrobacterium rhizogenes Ri-plasmid was cloned and sequenced from Nicotiana tabacum L. cv. Havana 425. The coding region of trolC is similar in sequence (69-87% for DNA and 54-89% for the deduced amino acid sequence) to rolC genes of the agropine, mannopine, and mikimopine strains of Ri-plasmids and the N. glauca rolC homologue. Southern analyses showed that trolC is encoded by a small gene family derived from the tomentosiformis ancestor of tobacco. This suggests that trolC resulted from an ancient transfer of DNA between A. rhizogenes and a progenitor of modern tobacco. Transcripts of trolC were detected in three morphologically distinct cultivars of tobacco. trolC mRNA accumulated in young leaves and shoot tips, but not in lower leaves and roots of mature plants. Accumulation of trolC mRNA in cultured leaf tissues was strongly down-regulated by auxin and induced by cytokinin. These results are of particular interest because they suggest that a gene of bacterial origin introduced during evolution can have a function in a modern plant.

Amino Acid Sequence↗
PubMed1998

Purification and characterization of a monomeric isocitrate dehydrogenase from the sulfate-reducing bacterium Desulfobacter vibrioformis and demonstration of the presence of a monomeric enzyme in other bacteria.

NADP(+)-specific isocitrate dehydrogenase (EC 1.1.1.42) was purified to homogeneity from the sulfate-reducing bacterium Desulfobacter vibrioformis, and shown to be a monomeric protein with a molecular mass of 80 kDa. The pH and temperature optima were 8.5 and 45 degrees C, respectively. The N-terminal amino acid sequence (Thr, Glu, Thr, Ile, Arg, Trp, Thr, X, Thr, Asp, Glu, Ala, Pro, Leu, Leu, Ala, Thr) showed similarity with that of other known monomeric isocitrate dehydrogenases. Catalytically active isocitrate dehydrogenase from D. vibrioformis was obtained by activity staining after SDS-PAGE and removal of SDS from the gel. This technique revealed a NADP(+)-dependent monomeric enzyme in other Desulfobacter spp., Desulfuromonas acetoxidans and Chlorobium tepidium. These findings imply that monomeric isocitrate dehydrogenases are present in distantly related bacteria and indicate an early evolution of monomeric isocitrate dehydrogenases in the bacterial lineage.

Bacterial Proteins↗
PubMed2006

Origin of the bacterial SET domain genes: vertical or horizontal?

The presence of Supressor of variegation-Enhanser of zeste-Trithorax (SET) domain genes in bacteria is a current paradigm for lateral genetic exchange between eukaryotes and prokaryotes. Because a major function of SET domain proteins is the chemical modification of chromatin and bacteria do not have chromatin, there is no apparent functional requirement for the existence of bacterial SET domain genes. Consequently, their finding in only a small fraction of pathogenic and symbiotic bacteria was taken as evidence that bacteria have obtained the SET domain genes from their hosts. Furthermore, it was proposed that the products of the genes would, most likely, be involved in bacteria-host interactions. The broadened scope of sequenced bacterial genomes to include also free-living and environmental species provided a larger sample to analyze the bacterial SET domain genes. By phylogenetic analysis, examination of individual chromosomal regions for signs of insertion, and evaluating the chromosomal versus SET domain genes' GC contents, we provide evidence that SET domain genes have existed in the bacterial domain of life independently of eukaryotes. The bacterial genes have undergone an evolution of their own unconnected to the evolution of the eukaryotic SET domain genes. Initial finding of SET domain genes in predominantly pathogenic and symbiotic bacteria resulted, most probably, from a biased sample. However, a lateral transfer of SET domain genes may have occurred between some bacteria and a family of Archaea. A model for the evolution and distribution of SET domain genes in bacteria is proposed.

Amino Acid Sequence↗
PubMed2006

Genetic and functional analyses of the lgtH gene, a member of the beta-1,4-galactosyltransferase gene family in the genus Neisseria.

Lipooligosaccharide (LOS) is a major virulence factor of the pathogenic Neisseria. Three galactosyltransferase genes, lgtB, lgtE and lgtH, responsible for the biosynthesis of LOS oligosaccharide chains, were analysed in five Neisseria species. The function of lgtH in Neisseria meningitidis 6,275 was determined by mutagenesis and chemical characterization of the parent and mutant LOS chains. The chemical characterization included SDS-PAGE, immunoblot, hexose and mass spectrometry analyses. Compared with the parent LOS, the mutant LOS lacked galactose, and its oligosaccharide decreased by three or four sugar units in matrix-assisted laser desorption ionization (MALDI)-MS analysis. The results show that lgtH encodes a beta-1,4-galactosyltransferase, and that the glucose moiety linked to heptose (Hep) in the alpha chain is the acceptor site in the biosynthesis of Neisseria LOS. To understand the sequence diversity and relationships of lgtB, lgtE and lgtH, the entire lgt-1 locus was further sequenced in three N. meningitidis strains and three commensal Neisseria strains, and compared with the previously reported lgt genes from Neisseria species. Comparison of the protein sequences of the three enzymes LgtB, LgtE and LgtH showed a conserved N-terminal region, and a highly variable C-terminal region, suggesting functional constraint for substrate and acceptor specificity, respectively. The analyses of allelic variation and evolution of 23 lgtB, 12 lgtE and 14 lgtH sequences revealed a distinct evolutionary history of these genes in Neisseria. For example, the splits graph of lgtE displayed a network evolution, indicating frequent DNA recombination, whereas splits graphs of lgtB and lgtH displayed star-tree-like evolution, indicating the accumulation of point mutations. The data presented here represent examples of the evolution and variation of prokaryotic glycosyltransferase gene families. These imply the existence of multiple enzyme isoforms for biosynthesis of a great diversity of oligosaccharides in nature.

Alleles↗
PubMed2004

To BAC or not to BAC: marine ecogenomics.

Most microbes in the ocean are still resistant to our collective cultivation efforts. Environmental microbial genomics provides science with the means for accessing and assessing the genomes, diversity, evolution and population dynamics of uncultured microorganisms--the ocean's hidden majority.

Chromosomes, Artificial, Bacterial↗
PubMed1999

Evolutionary changes reflected by the cellular amino acid composition.

Comparison of the amino acid composition of cell-proteins using 17 amino acids has been used to investigate the biological evolution of organisms such as bacteria, blue-green alga, green alga, fungi, slime mold, protozoa and vertebrates. The degree of difference in the amino acid ratios between any two groups reflects the degree of divergency in biological evolution. The amino acid composition of the Gram-negative bacteria (Escherichia coli, Klebsiella, Proteus, and Vibrio alginolyticus) was identical. However, the amino acid composition of Staphylococcus aureus and Bacillus subtilis, which are Gram-positive bacteria, differed from each other and from the Gram-negative bacteria. The amino acid composition of the blue-green alga (Cyanobacterium, Chroococidiopsis) was quite similar to that of E. coli. A marked difference in the amino acid composition was observed between E. coli and green alga (Chlorella), and significant differences were observed between E. coli and other organisms, such as fungi, protozoa (Tetrahymena), slime mold (Dictyostelium discoideum) and vertebrates. In conclusion, the change in cellular amino acid composition reflects the divergence which has occurred during biological evolution, whereas a basic pattern of amino acid composition is maintained in spite of a long period of evolutional divergence among the various organisms. Thus, it is proposed that the primitive life forms established at the end of prebiotic evolution had a similar amino acid composition.

Amino Acids↗
PubMed2005

Type I polyketide synthases may have evolved through horizontal gene transfer.

Type I polyketide synthases (PKSI) are modular multidomain enzymes involved in the biosynthesis of many natural products of industrial interest. PKSI modules are minimally organized in three domains: ketosynthase (KS), acyltransferase (AT), and acyl carrier protein. The KS domain phylogeny of 23 PKSI clusters was determined. The results obtained suggest that many horizontal transfers of PKSI genes have occurred between actinomycetales species. Such gene transfers may explain the homogeneity and the robustness of the actinomycetales group since gene transfers between closely related species could mimic patterns generated by vertical inheritance. We suggest that the linearity and instability of actinomycetales chromosomes associated with their large quantity of genetic mobile elements have favored such horizontal gene transfers.

Acyltransferases↗
PubMed2005

The many faces of the helix-turn-helix domain: transcription regulation and beyond.

The helix-turn-helix (HTH) domain is a common denominator in basal and specific transcription factors from the three super-kingdoms of life. At its core, the domain comprises of an open tri-helical bundle, which typically binds DNA with the 3rd helix. Drawing on the wealth of data that has accumulated over two decades since the discovery of the domain, we present an overview of the natural history of the HTH domain from the viewpoint of structural analysis and comparative genomics. In structural terms, the HTH domains have developed several elaborations on the basic 3-helical core, such as the tetra-helical bundle, the winged-helix and the ribbon-helix-helix type configurations. In functional terms, the HTH domains are present in the most prevalent transcription factors of all prokaryotic genomes and some eukaryotic genomes. They have been recruited to a wide range of functions beyond transcription regulation, which include DNA repair and replication, RNA metabolism and protein-protein interactions in diverse signaling contexts. Beyond their basic role in mediating macromolecular interactions, the HTH domains have also been incorporated into the catalytic domains of diverse enzymes. We discuss the general domain architectural themes that have arisen amongst the HTH domains as a result of their recruitment to these diverse functions. We present a natural classification, higher-order relationships and phyletic pattern analysis of all the major families of HTH domains. This reconstruction suggests that there were at least 6-11 different HTH domains in the last universal common ancestor of all life forms, which covered much of the structural diversity and part of the functional versatility of the extant representatives of this domain. In prokaryotes the total number of HTH domains per genome shows a strong power-equation type scaling with the gene number per genome. However, the HTH domains in two-component signaling pathways show a linear scaling with gene number, in contrast to the non-linear scaling of HTH domains in single-component systems and sigma factors. These observations point to distinct evolutionary forces in the emergence of different signaling systems with HTH transcription factors. The archaea and bacteria share a number of ancient families of specific HTH transcription factors. However, they do not share any orthologous HTH proteins in the basal transcription apparatus. This differential relationship of their basal and specific transcriptional machinery poses an apparent conundrum regarding the origins of their transcription apparatus.

Amino Acid Sequence↗
PubMed2025

Bacterial immune systems as causes and consequences of microbiome structure.

Attacks from molecular parasites such as mobile genetic elements (MGEs) have driven the evolution of defense systems in bacterial genomes. Yet, despite significant advances in understanding the molecular mechanisms of these bacterial immune systems, we have only a rudimentary understanding of their ecology and evolution. Bacteria exist as part of complex microbiomes, but community ecology and microbiome research has yet to characterize the impacts of interactions between MGEs and defense mechanisms upon the structure, dynamics and evolution of microbiomes. This Essay introduces and discusses the interplay between bacterial community dynamics and bacterial immune systems, speculating about how these reciprocal interactions may shape microbial community structure and function.

Bacteria↗
PubMed1999

Functional classes in the three domains of life.

The evolutionary divergence among the three major domains of life can now be addressed through the first set of complete genomes from representative species. These model species from the three domains of life, Haemophilus influenzae for Bacteria, Saccharomyces cerevisiae for Eukarya, and Methanococcus jannaschii for Archaea, provide the basis for a universal functional classification and analysis. We have chosen 13 functional classes and three superclasses (ENERGY, COMMUNICATION and INFORMATION) as global descriptors of protein function. Compositional comparison of the three complete genomes reveals that functional classes are ubiquitous yet diverse in the three domains of life. Proteins related with ENERGY processes are generally represented in all three domains, while those related with COMMUNICATION represent the most distinctive functional feature of each single domain. Finally, functions related with INFORMATION processing (translation, transcription, and replication) show a complex behaviour. In Archaea, proteins in this superclass are related with proteins in either Eukarya or Bacteria, as recognized previously. The distribution of functional classes in the three domains accurately reflects the principal characteristics of cellular life forms.

Archaeal Proteins↗
PubMed2004

Evolutionary relationships of Fusobacterium nucleatum based on phylogenetic analysis and comparative genomics.

BACKGROUND: The phylogenetic position and evolutionary relationships of Fusobacteria remain uncertain. Especially intriguing is their relatedness to low G+C Gram positive bacteria (Firmicutes) by ribosomal molecular phylogenies, but their possession of a typical gram negative outer membrane. Taking advantage of the recent completion of the Fusobacterium nucleatum genome sequence we have examined the evolutionary relationships of Fusobacterium genes by phylogenetic analysis and comparative genomics tools. RESULTS: The data indicate that Fusobacterium has a core genome of a very different nature to other bacterial lineages, and branches out at the base of Firmicutes. However, depending on the method used, 35-56% of Fusobacterium genes appear to have a xenologous origin from bacteroidetes, proteobacteria, spirochaetes and the Firmicutes themselves. A high number of hypothetical ORFs with unusual codon usage and short lengths were found and hypothesized to be remnants of transferred genes that were discarded. Some proteins and operons are also hypothesized to be of mixed ancestry. A large portion of the Gram-negative cell wall-related genes seems to have been transferred from proteobacteria. CONCLUSIONS: Many instances of similarity to other inhabitants of the dental plaque that have been sequenced were found. This suggests that the close physical contact found in this environment might facilitate horizontal gene transfer, supporting the idea of niche-specific gene pools. We hypothesize that at a point in time, probably associated to the rise of mammals, a strong selective pressure might have existed for a cell with a Clostridia-like metabolic apparatus but with the adhesive and immune camouflage features of Proteobacteria.

Bacterial Proteins↗
PubMed2005

Prokaryotic phylogenies inferred from protein structural domains.

The determination of the phylogenetic relationships among microorganisms has long relied primarily on gene sequence information. Given that prokaryotic organisms often lack morphological characteristics amenable to phylogenetic analysis, prokaryotic phylogenies, in particular, are often based on sequence data. In this work, we explore a new source of phylogenetic information, the distribution of protein structural domains within fully sequenced prokaryotic genomes. The evolution of the structural domains we use has been studied extensively, allowing us to base our phylogenetic methods on testable theoretical models of structural evolution. We find that the methods that produce reasonable phylogenetic relationships are indeed the methods that are most consistent with theoretical evolutionary models. This work represents, to our knowledge, the first such theoretically motivated phylogeny, as well as the first application of structural information to phylogeny on this scale. Our results have strong implications for the phylogenetic relationships among prokaryotic organisms and for the understanding of protein evolution as a whole.

Archaeal Proteins↗