Phylogenetic origin of LI-cadherin revealed by protein and gene structure analysis

The intestine specific LI-cadherin differs in its overall structure from classical and desmosomal cadherins by the presence of seven instead of five cadherin repeats and a short cytoplasmic domain. Despite the low sequence similarity, a comparative protein structure analysis revealed that LI-cadherin may have originated from a five-repeat predecessor cadherin by a duplication of the first two aminoterminal repeats. To test this hypothesis, we cloned the murine LI-cadherin gene and compared its structure to that of other cadherins. The intron-exon organization, including the intron positions and phases, is perfectly conserved between repeats 3–7 of LI-cadherin and 1–5 of classical cadherins. Moreover, the genomic structure of the repeats 1–2 and 3–4 is identical for LI-cadherin and highly similar to that of the repeats 1–2 of classical cadherins. These findings strengthen our assumption that LI-cadherin originated from an ancestral cadherin with five domains by a partial gene duplication event.Received 22 December 2003; received after revision 9 February 2004; accepted 27 February 2004     

Misacylation of tRNA in prokaryotes: a re-evaluation

Misacylation of tRNA by a non-cognate amino acid is a natural phenomenon and occurs with a frequency of approximately 1 in 10,000 due to occasional mistakes in aminoacyl transfer RNA (tRNA) synthesis. In a number of prokaryotic organisms, misacylation of selenocysteinyl tRNA, glutaminyl tRNA and aspartyl tRNAs has particular physiological meaning. Recently, misacylation has emerged as a powerful tool for studying specific interactions between aa-tRNAs and associated protein factors. The present review provides an overview of the application of misacylated tRNA in research. Received 27 April 2005; received after revision 2 November 2005; accepted 5 December 2005     

Histories of molecules: Reconciling the past

Molecular data and methods have become centrally important to evolutionary analysis, largely because they have enabled global phylogenetic reconstructions of the relationships between organisms in the tree of life. Often, however, molecular stories conflict dramatically with morphology-based histories of lineages. The evolutionary origin of animal groups provides one such case. In other instances, different molecular analyses have so far proved irreconcilable. The ancient and major divergence of eukaryotes from prokaryotic ancestors is an example of this sort of problem. Efforts to overcome these conflicts highlight the role models play in phylogenetic reconstruction. One crucial model is the molecular clock; another is that of ‘simple-to-complex’ modification. I will examine animal and eukaryote evolution against a backdrop of increasing methodological sophistication in molecular phylogeny, and conclude with some reflections on the nature of historical science in the molecular era of phylogeny.     

Retroelements and their impact on genome evolution and functioning

Retroelements comprise a considerable fraction of eukaryotic genomes. Since their initial discovery by Barbara McClintock in maize DNA, retroelements have been found in genomes of almost all organisms. First considered as a “junk DNA” or genomic parasites, they were shown to influence genome functioning and to promote genetic innovations. For this reason, they were suggested as an important creative force in the genome evolution and adaptation of an organism to altered environmental conditions. In this review, we summarize the up-to-date knowledge of different ways of retroelement involvement in structural and functional evolution of genes and genomes, as well as the mechanisms generated by cells to control their retrotransposition.     

Genomic revelations of a mutualism: the pea aphid and its obligate bacterial symbiont

The symbiosis of the pea aphid Acyrthosphion pisum with the bacterium Buchnera aphidicola APS represents the best-studied insect obligate symbiosis. Here we present a refined picture of this symbiosis by linking pre-genomic observations to new genomic data that includes the complete genomes of the eukaryotic and prokaryotic symbiotic partners. In doing so, we address four issues central to understanding the patterns and processes operating at the A. pisum/Buchnera APS interface. These four issues include: (1) lateral gene transfer, (2) host immunity, (3) symbiotic metabolism, and (4) regulation.     

Lipid transport in microorganisms

Summary Microorganisms are useful model systems for the study of intracellular transport of lipids. Eukaryotic microorganisms, such as the yeastSaccharomyces cerevisiae, are similar to higher eukaryotes with respect to organelle structure and membrane assembly. Experiments in vivo showed that transport of phosphatidylcholine between yeast microsomes and mitochondria is energy independent; transfer of phosphatidylinositol to the plasma membrane and the flux of secretory vesicles take place by different mechanisms. Linkage of transfer and biosynthesis of phospholipids was demonstrated in the case of intramitochondrial phospholipid transfer. A yeast phosphatidylinositol/phosphatidylcholine transfer protein, which is essential for cell viability, was isolated and characterized. Another phospholipid transfer protein present in yeast cytosol, which has a different specificity, is currently under investigation. Transfer of phospholipids between cellular membranes was also demonstrated with prokaryotes. The cytoplasm and the periplasma of the gram-negative facultative photosynthetic bacteriumRhodopseudomonas sphaeroides contain phospholipid transfer proteins; these seem to be involved in the biosynthesis of prokaryotic membranes.     

Acetyl-coenzyme A synthetase (AMP forming)

Acetyl-coenzyme A synthetase (AMP forming; Acs) is an enzyme whose activity is central to the metabolism of prokaryotic and eukaryotic cells. The physiological role of this enzyme is to activate acetate to acetyl-coenzyme A (Ac-CoA). The importance of Acs has been recognized for decades, since it provides the cell the two-carbon metabolite used in many anabolic and energy generation processes. In the last decade researchers have learned how carefully the cell monitors the synthesis and activity of this enzyme. In eukaryotes and prokaryotes, complex regulatory systems control acs gene expression as a function carbon flux, with a second layer of regulation exerted posttranslationally by the NAD⁺/sirtuin-dependent protein acetylation/deacetylation system. Recent structural work provides snapshots of the dramatic conformational changes Acs undergoes during catalysis. Future work on the regulation of acs gene expression will expand our understanding of metabolic integration, while structure/function studies will reveal more details of the function of this splendid molecular machine.Received 4 December 2003; received after revision 2 March 2004; accepted 16 March 2004     

Homologous recombination in plants

In plants three different approaches have been used to study homologous DNA recombination; extrachromosomal recombination (ECR) between transfected DNA molecules, intrachromosomal recombination (ICR) between repeated genes integrated into and resident at the genome and recombination between introduced DNA and homologous sequences in the genome (gene targeting). ECR is efficient (10^–1 to 10^–3) and occurs mainly during a limited time period early after transfection. It proceeds predominantly via nonconservative single-strand annealing. ICR, which in most cases is described best by the double-strand break repair model of recombination, occurs at frequencies of one event in 10⁵ to 10⁷ cells. ICR takes place throughout the whole life-cycle of a plant, in all organs and at different developmental stages. As there exists no predetermined germline in plants, somatic recombination events can be transferred to the next generation. Recombination frequencies are enhanced by DNA damage. Gene targeting, like ICR, occurs at low rates in plant cells. Almost nothing is known about the enzymes involved in homologous recombination in plants.     

Operons

Operons (clusters of co-regulated genes with related functions) are common features of bacterial genomes. More recently, functional gene clustering has been reported in eukaryotes, from yeasts to filamentous fungi, plants, and animals. Gene clusters can consist of paralogous genes that have most likely arisen by gene duplication. However, there are now many examples of eukaryotic gene clusters that contain functionally related but non-homologous genes and that represent functional gene organizations with operon-like features (physical clustering and co-regulation). These include gene clusters for use of different carbon and nitrogen sources in yeasts, for production of antibiotics, toxins, and virulence determinants in filamentous fungi, for production of defense compounds in plants, and for innate and adaptive immunity in animals (the major histocompatibility locus). The aim of this article is to review features of functional gene clusters in prokaryotes and eukaryotes and the significance of clustering for effective function.     

Age and evolution of bacteria

Summary Age and evolution of bacteria can be estimated, including facts and hypotheses belonging to morphology, biochemistry, paleontology, ecology and pathogenicity. The corresponding dates are summarized in the following.About 3.5×10⁹ years: Origin of heterotrophic eobiontes.—About 3.0×10⁹ years: The increasing lack of prebiogenic substances is due to the evolution of the respiratory pathway, that is due to the evolution of the photoautotrophy and now released O₂ is due to the evolution of strictly aerobic cells. There is, simultaneously, a transition of spheres to long forms, development of an amoebalike motility, the evolution of spirochetes and the substitution of cholesterol for cardiolipin in the more evolved cells (i.e. strictly aerobic cells etc.).—About 2.0×1.0×10⁹ years: Evolution of the eucyte by symbiosis of a great, primitive, anaerobic, cholesterol-containing cell with a little, strictly aerobic, cardiolipin-containing cell, with a spirochete and in some extent also with photoautotrophic cell.—About 1.0×10⁹ years (maximum: 1.8–1.5×10⁹ years, minimum: 7×10⁸ years): Evolution of metazoa and begin of cell differentiation.—About 2.0–1.0×10⁹ years: Evolution of the bacterial murein sacculus and then development of flagella mediated motility.—About 6×10⁸ years (maximum:1.0×10⁹ years, minimum: 4.5×10⁸ years): Evolution of the gram-negative cell wall.—About 4.0×10⁸ years: Evolution of the gram-positive cell wall.—About 5.0×10⁸ years: Gram-negative, strictly anaerobic bacteria become the first enteric bacteria in coelenterates. About 4.0×10⁸ years: gram-negative, microaerophilic bacteria become Enterobacteriaceae in vertebrates in addition to the strictly anaerobic organisms.—About 3.0–2.0×10⁸ years: Consolidation of the Salmonella in reptiles.—About 2.0–1.5×10⁸ years: Consolidation of Escherichia and other coliform species in mammals.—About 10⁶ years: Evolution of typically human pathogenic organisms, transmitted in homogeneous-homonomous infection ways, i.e. N. gonorrhoeae, S. typhi, T. pallidum, etc.Dedicated to Prof. H. Habs, Bonn, to his 75th anniversary on 11 September 1977.Acknowledgment. I thank Prof. F. Müller, Hamburg, and Prof. P. Sitte, Freiburg i. Br., for stimulating discussions.     

Retrotransposable elements in the Dictyostelium discoideum genome

Repetitive DNA is a major component of any living cell. In eukaryotes retrotransposable elements make up several percent of the genome size, and consequently, retroelements are often identified in experiments aimed at establishing physical maps and whole genome sequences. In this review, recent progress in the characterization of retrotransposable elements in the genome of the eukaryotic mi croorganism Dictyostelium discoideum is summarized with a focus on retroelements which integrate near transfer RNA genes with intriguing position specificity. Received 21 November 1997; received after revision 6 January 1998; accepted 6 January 1998     

Flavodoxins: sequence, folding, binding, function and beyond

Flavodoxins are electron-transfer proteins involved in a variety of photosynthetic and non-photosynthetic reactions in bacteria, whereas, in eukaryotes, a descendant of the flavodoxin gene helps build multidomain proteins. The redox activity of flavodoxin derives from its bound flavin mononucleotide cofactor (FMN), whose intrinsic properties are profoundly modified by the host apoprotein. This review covers the very exciting last decade of flavodoxin research, in which the folding pathway, the structure and stability of the apoprotein, the mechanism of FMN recognition, the interactions that stabilize the functional complex and tailor the redox potentials, and many details of the binding and electron transfer to partner proteins have been revealed. The next decade should witness an even deeper understanding of the flavodoxin molecule and a greater comprehension of its many physiological roles. The fact that flavodoxin is essential for the survival of some human pathogens could make it a drug target on its own. Received 26 October 2005; received after revision 20 November 2005; accepted 14 December 2005     

Microbial legradation of bitumen

Summary Bitumen is commonly employed as a matrix for the long-term storage of low and intermediate level radioactive waste. As bitumen can be degraded by microbial activity, it is of great significance to determine the rates at which it may occur in nuclear waste repositories.Experiments have been carried out under optimal culture conditions using bitumen with a highly increased surface area. The potential of different microbial consortia to degrade bitumen has been examined. The investigations showed clearly that bitumen-degrading organisms are ubiquitous. In general the organisms formed biofilms on the accessible substrate surface area. Under oxic culture conditions a bitumen degradation rate of 20–50 g bitumen · m^–2· y^–1 leading to a CO₂ liberation of 15–40 l was observed. Anoxic conditions yielded a 100 times smaller degradation rate of 0.2–0.6 g bitumen · m^–2 · y^–1 and a CO₂ production of 0.15–0.45 l.Based on linear extrapolation the experimentally determined degradation rates would lead to a 25–70% deterioration of the bitumen matrix under oxic and 0.3–0.8% under anoxic conditions within 1000 years.