Evolution of glutamate dehydrogenase genes: Evidence for two paralogous protein families and unusual branching patterns of the archaebacteria in the universal tree of life

Summary The existence of two families of genes coding for hexameric glutamate dehydrogenases has been deduced from the alignment of 21 primary sequences and the determination of the percentages of similarity between each pair of proteins. Each family could also be characterized by specific motifs. One family (Family 1) was composed of gdh genes from six eubacteria and six lower eukaryotes (the primitive protozoan Giardia lamblia, the green alga Chlorella sorokiniana, and several fungi and yeasts). The other one (Family 11) was composed of gdh genes from two eubacteria, two archaebacteria, and five higher eukaryotes (vertebrates). Reconstruction of phylogenetic trees using several parsimony and distance methods confirmed the existence of these two families. Therefore, these results reinforced our previously proposed hypothesis that two close but already different gdh genes were present in the last common ancestor to the three Ur-kingdoms (eubacteria, archaebacteria, and eukaryotes). The branching order of the different species of Family I was found to be the same whatever the method of tree reconstruction although it varied slightly according the region analyzed. Similarly, the topological positions of eubacteria and eukaryotes of Family II were independent of the method used. However, the branching of the two archaebacteria in Family II appeared to be unexpected: (1) the thermoacidophilic Sulfolobus solfataricus was found clustered with the two eubacteria of this family both in parsimony and distance trees, a situation not predicted by either one of the contradictory trees recently proposed; and (2) the branching of the halophilic Halobacterium salinarium varied according to the method of tree construction: it was closer to the eubacteria in the maximum parsimony tree and to eukaryotesin distance trees. Therefore, whatever the actual position of the halophilic species, archaebacteria did not appear to be monophyletic in these gdh gene trees. This result questions the firmness of the presently accepted interpretation of previous protein trees which were supposed to root unambiguously the universal tree of life and place the archaebacteria in this tree. Offprint requests to: B. Labedan     

Ecology of Soil Erosion in Ecosystems

Each year, about 75 billion tons of soil are eroded from the world's terrestrial ecosystems. Most agricultural land in the world is losing soil at rates ranging from 13 tons/ha/year to 40 tons/ha/year. Because soil is formed very slowly, this means that soil is being lost 13–40 times faster than the rate of renewal and sustainability. Rain and wind energy are the two prime causes of erosion from tilled or bare land. Erosion occurs when the soil lacks protective vegetative cover. Soil erosion reduces the productivity of the land by loss of water, soil organic matter, nutrients, biota, and depth of soil. The greatest threat to providing food for a rapidly growing human population is soil erosion. Abandoned, eroded agricultural land is replaced by clearing forested ecosystems. Received 17 February 1998; accepted 26 May 1998.     

Postnatal Evolution of the γ-Aminobutyric Acid/Benzodiazepine Receptor Complex in a Model of Inherited Epilepsy: The Quaking Mouse

Binding assays of [3H]muscimol and [3H]-flunitrazepam have been performed on brain homogenates of brainstem, cerebellum, and forebrain of genetically epileptic quaking (qk) mutant mice 20, 40, 70, and 90 days old and their corresponding controls of the same strain (C57BL/6J). The endogenous gamma-aminobutyric acid (GABA) content has been determined in various brain regions of 70-day-old qk and control mice. Finally, the behavioral effects of diazepam, of the mixed GABAA/GABAB receptor agonist progabide, and of the selective GABAB receptor agonist baclofen have been assessed in adult qk mutants. Our results strongly suggest a lack of involvement of GABAergic neurotransmission in the inherited epilepsy of the qk mutant mouse.     

Speciation history of the North American funnel web spiders, Agelenopsis (Araneae: Agelenidae): phylogenetic inferences at the population-species interface

Intra- and interspecific relationships of 12 out of 13 described species as well as a potential new species in the spider genus Agelenopsis (Araneae: Agelenidae) were analyzed using sequence data from two mitochondrial genes, cytochrome oxidase I (COI) and 16S ribosomal RNA. Approximately half of the species examined formed well-supported monophyletic groups, whereas the rest of the species were part of well-supported monophyletic species groups. Rather than viewing cases where species were not identified as being monophyletic as poor taxonomy, these cases more likely represent recent speciation and offer insights into the process of speciation. The clade with the lowest levels of interspecific sequence divergence was found in eastern North America, whereas western species displayed much higher levels of interspecific divergence. These patterns appear to extend below the species level as well, with southwestern species exhibiting the highest levels of intraspecific sequence divergence and geographic structuring. The relationship between Agelenopsis and Barronopsis, a genus once considered a sub-genus of Agelenopsis, was also examined. The two genera are reciprocally monophyletic but more generic level sampling is needed to confirm an apparent sister relationship between the two.     

Social Cues and Following Behavior in the Forest Tent Caterpillar

Colonies of the social caterpillar Malacosoma disstria Hubner (Lepidoptera: Lasiocampidae) travel in groups following silk trails marked with pher-omone. This study examined first, the cues involved in following behavior and second, the responses to these cues at different larval stadia. Both second and fourth instar larvae discriminated between fresh and older trails, and travelled faster in the presence of trails. In addition to trail following, young caterpillars exhibited leader following, which might be particularly important in exploring unmarked territory. Indeed, second instar caterpillars were more likely to travel together when trails were absent. Fourth instar larvae exhibited greater independent locomotion in the absence of trails than did younger larvae. These findings help explain patterns of social behavior observed in forest tent caterpillar colonies in the field.     

Neisseria gonorrhoeae secretes chromosomal DNA via a novel type IV secretion system

The process of DNA donation for natural transformation of bacteria is poorly understood and has been assumed to involve bacterial cell death. Recently in Neisseria gonorrhoeae we found that mutations in three genes in the gonococcal genetic island (GGI) reduced the ability of a strain to act as a donor in transformation and to release DNA into the culture. To better characterize the GGI and the process of DNA donation, the 57 kb genetic island was cloned, sequenced and subjected to insertional mutagenesis. DNA sequencing revealed that the GGI has characteristics of a horizontally acquired genomic island and encodes homologues of type IV secretion system proteins. The GGI was found to be incorporated near the chromosomal replication terminus at the dif site, a sequence targeted by the site-specific recombinase XerCD. Using a plasmid carrying a small region of the GGI and the associated dif site, we demonstrated that this model island could be integrated at the dif site in strains not carrying the GGI and was spontaneously excised from that site. Also, we were able to delete the entire 57 kb region by transformation with DNA from a strain lacking the GGI. Thus the GGI was likely acquired and integrated into the gonococcal chromosome by site-specific recombination and may be lost by site-specific recombination or natural transformation. We made mutations in six putative type IV secretion system genes and assayed these strains for the ability to secrete DNA. Five of the mutations greatly reduced or completely eliminated DNA secretion. Our data indicate that N. gonorrhoeae secretes DNA via a specific process. Donated DNA may be used in natural transformation, contributing to antigenic variation and the spread of antibiotic resistance, and it may modulate the host immune response.     

Using 2H2O to study the influence of feeding on protein synthesis: effect of isotope equilibration in vivo vs. in cell culture

We previously reported that 2H2O can be used to measure rates of protein synthesis during prolonged steady-state conditions (Previs SF, Fatica R, Chandramouli V, Alexander JC, Brunengraber H, and Landau BR. Am J Physiol Endocrinol Metab 286: E665-E672, 2004). The underlying premise of our method is that following the administration of 2H2O, 2H atoms in body water rapidly equilibrate with free alanine before it is incorporated into newly synthesized proteins. We have now directly examined whether 2H2O can be used to measure the influence of a single meal on protein synthesis. In addition, we have compared the use of 2H2O for measuring rates of protein synthesis in vivo vs. in cell culture. Using a rat model, we observed rapid equilibration between 2H in body water and free alanine; therefore we were able to study the response of protein synthesis to a single meal. We observed that approximately 50% of the plasma albumin that is synthesized over the course of 24 h is made within approximately 5 h after eating (in rats trained to eat a complete 24-h ration of food in a single meal). Contrary to what we observed in vivo, feeding (the replenishment of cell culture medium) does influence the use of 2H2O for in vitro studies. In particular, since there can be slow equilibration of 2H between water and alanine in the cell culture medium, special consideration must be made to avoid underestimating the rate of protein synthesis in vitro.     

Differences in the neurotoxicity profile induced by ATP and ATPgammaS in cultured cerebellar granule neurons

Extracellular ATP and P2 receptors may play a crucial role in the neurodegeneration of the CNS. Here, we investigated in neuronal cerebellar granule cultures the biological effect of the quite stable P2 receptor agonist ATPgammaS and compare it to the cytotoxic action of ATP. Time-course experiments showed that 500 microM ATPgammaS causes 50-100% cell death in 15-24 h. As proved by pharmacological means, ATPgammaS toxicity apparently involves neither indirect activation of NMDA receptors, nor ectonucleotidase activities, nor nucleoside transport and intracellular purine metabolism. Moreover, ATPgammaS induces detrimental effects without modifying the expression of several P2X and P2Y receptor proteins. Cell death instead occurs after extracellular release of the cytosolic enzyme lactic dehydrogenase and inhibition of the overall activity of the intracellular dehydrogenases. Moreover, ATPgammaS causes transient outflow of cytochrome c from mitochondria (maximal 2.5-fold stimulation in 4 h), it raises the intracellular reactive oxygen species (about four-fold in 1 h) and cAMP levels (about 40% in 15 min-4 h). Among several P2 receptor antagonists, only pyridoxal-phosphate-6-azophenyl-2',4'-disulphonic acid 4-sodium promotes 80-100% neuroprotection.