Structure,function and evolution of seryl-tRNA synthetases: Implications for the evolution of aminoacyl-tRNA synthetases and the genetic code

Two aspects of the evolution of aminoacyl-tRNA synthetases are discussed. Firstly, using recent crystal structure information on seryl-tRNA synthetase and its substrate complexes, the coevolution of the mode of recognition between seryl-tRNA synthetase and tRNA^ser in different organisms is reviewed. Secondly, using sequence alignments and phylogenetic trees, the early evolution of class 2 Amnoacyl-tRNA synthetases is traced. Arguments are presented to suggest that synthetases are not the oldest of protein enzymes, but survived as RNA enzymes during the early period of the evolution of protein catalysts. In this view, the relatedness of the current synthetases, as evidenced by the division into two classes with their associated subclasses, reflects the replacement of RNA synthetases by protein synthetases. This process would have been triggered by the acquisition of tRNA 3 end charging activity by early proteins capable of activating small molecules (e.g., amino acids) with ATP. If these arguments are correct, the genetic code was essentially frozen before the protein synthetases that we know today came into existence. Correspondence to: S. CusackBased on a presentation made at a workshop-Aminoacyl-tRNA Synthetases and the Evolution of the Genetic Code-held at Berkeley, CA, July 17–20, 1994     

Specific Activity of Brain Palmitoyl-CoA Pool Provides Rates of Incorporation of Palmitate in Brain Phospholipids in Awake Rats

Abstract: In vivo rates of palmitate incorporation into brain phospholipids were measured in awake rats following programmed intravenous infusion of unesterified [9,10-³H]palmitate to maintain constant plasma specific activity. Animals were killed after 2–10 min of infusion by microwave irradiation and analyzed for tracer distribution in brain phospholipid and phospholipid precursor, i.e., brain unesterified palmitate and palmitoyl-CoA, pools. [9,10-³H]Palmitate incorporation into brain phospholipids was linear with time and rapid, with >50% of brain tracer in choline-containing glycerophospholipids at 2 min of infusion. However, tracer specific activity in brain phospholipid precursor pools was low and averaged only 1.6–1.8% of plasma unesterified palmitate specific activity. Correction for brain palmitoyl-CoA specific activity increased the calculated rate of palmitate incorporation into brain phospholipids (0.52 nmol/s/g) by ∼60-fold. The results suggest that palmitate incorporation and turnover in brain phospholipids are far more rapid than generally assumed and that this rapid turnover dilutes tracer specific activity in brain palmitoyl-CoA pool owing to release and recycling of unlabeled fatty acid from phospholipid breakdown.     

Prostaglandin H Synthetase-Mediated Metabolism of Dopamine: Implication for Parkinson's Disease

Abstract: Differences in prostaglandin H synthetase (PHS) activity in the substantia nigra of age- and post-mortem interval-matched parkinsonian, Alzheimer's, and normal control brain tissue were assessed. Prostaglandin E₂ (PGE₂, an index of PHS activity) was higher in substantia nigra of parkinsonian brain tissue than Alzheimer's or control tissue. Incubation of substantia nigra slices with arachidonic acid (AA) increased PGE₂ synthesis. Dopamine stimulated PHS synthesis of PGE₂. [³H]Dopamine was activated by PHS to electrophilic intermediate(s) that covalently bound to DNA, microtubulin protein, bovine serum albumin, and sulfhydryl reagents. When AA was replaced by hydrogen peroxide, PHS/H₂O₂-supported binding proceeded at rates similar to those observed with PHS/AA. Indomethacin and aspirin inhibited AA-mediated cooxidation of dopamine but not H₂O₂-mediated metabolism. PHS-mediated metabolism of dopamine was not affected by monoamine oxidase inhibitors. Substrate requirements and effects of specific inhibitors suggest cooxidation of dopamine is mediated by the hydroperoxidase activity of PHS. ³²P-postlabeling was used to detect dopamine-DNA adducts. PHS/AA activation of dopamine in the presence of DNA resulted in the formation of five dopamine-DNA adducts, i.e., 23, 43, 114, 70, and 270 amol/µg DNA. DNA adduct formation was PHS, AA, and dopamine dependent. PHS catalyzed cooxidation of dopamine in dopaminergic neuronal degeneration is discussed.     

Conformation and interactions of bombolitin I analogues with SDS micelles and phospholipid vesicles: CD,fluorescence, two-dimensional NMR and computer simulations

Bombolitins are five structurally related heptadecapeptides acting at the membrane level able to lyse erythrocytes and liposomes and to enhance the activity of phospholipase A ₂(PLA₂). In the presence of SDS or phospholipid vesicles bombolitins are able to form amphiphilic α-helical structures and this property seems to be the major determinant of bioactivity. In order to test the model of interaction between bombolitin I and membranes, an analogue was synthesized in which all the lysines were replaced by arginines: ([Arg^2,9,12, Ile¹⁰] bornbolitin I). The design ofthis sequence allowed the synthesis of a second analogue through a specijic postsynthetic dansylation at the ?-amino group qf a lysine residue replacing the original leucine residue at position 7. The, first analogue was, fiilly characterized by CD and two-dimensional nmr in the presence of SDS or phospholipid vesicles. The peptide, folds into an amphiphilic α-helical confbrrnation with the helical segment spanning the central part of the sequencefrom Ile³ to His¹⁶. This behavior is identical to that observed for the native sequence. The replacement of Iysine residues by arginine hus no detectable effect on the conformational prderence of the peptide chain. By CD and fluorescence spectroscopy measurements, the fluorophore-containing analogue [Arg^2,9,12, Lys⁷(?-dansyl)] bombolitin I also folded into the α-helical conformation in the presence of SDS micelles or phospholipid vesicles. In particular, the dansyl fluorophore, which is located approximately in the middle of the apolar surface ojthe amphiphilic helix, is clearly buried in a hydrophobic environment when the peptide is bound to phospholipid vesicles. These findings support the hypothesis that the peptide helices are oriented parallel to the vesicle surface. © 1995 John Wiley & Sons, Inc.     

Impact of moisture on thermally induced denaturation and decomposition of lyophilized bovine somatotropin

The nonisothermal transitions of lyophilized recombinant bovine somatotropin (rbSt) as seen via differential scanning calorimetry were evaluated with respect to moisture content. The transition peak temperature of rbSt decreased with increasing moisture from 161°C in the dry state to a plateau of 65°C at 28% moisture, which is similar to that of rbSt in solution. Using high performance liquid chromatography, this irreversible endothermic transition consisted primarily of unfolding, hydrophobic aggregation, and some covalent modifications. In the dry state, covalent modifications, including polymerization into compounds of higher molecular weight, were more prominent, while in the presence of moisture, hydrophobic aggregation was most prominent. The irreversibility and scan rate dependence of the endothermic phenomena supports the kinetic nature of the transition rather than a simple equilibrium between globular and unfolded states. The apparent activation energy, for the net transition (i.e., unfolding, hydrophobic aggregation, and covalent modifications) was 57 kcal/mol for rbSt at 9.9% moisture. The observed enthalpy of the transition increased, decreased, then approximately leveled off as a function of increasing moisture content. This can be explained by the increasingly significant contribution of the exothermic aggregation at higher moisture contents. © 1995 John Wiley & Sons, Inc.     

Control of trophoblast cell differentiation: Lessons from the genetics of early pregnancy loss and trophoblast neoplasia

Trophoblast cell differentiation is crucial to the morphogenesis of the placenta and thus the establishment of pregnancy and the growth and development of the embryo/fetus. In the present review, we discuss current evidence for the existence of regulatory genes crucial to trophoblast cell differentiation and placental morphogenesis. The elucidation of regulatory pathways controlling normal differentiation of trophoblast cells will facilitate the identification of sensitive junctures in the regulatory pathways leading to various developmental disorders, including those associated with the initiation of pregnancy, fetal growth retardation and gestational trophoblast disease.     

VARIANCE-INDUCED PEAK SHIFTS

The increase in phenotypic variance that occurs in some populations as a result of bottlenecks and founder events can cause a dramatic increase in the probability of a peak shift from one adaptive state to another. Periods of small population size allow drift in the amount of phenotypic variance. Increases in phenotypic variance, coupled with a constant individual fitness function with multiple peaks, can cause the mean fitness landscape to change from bimodal to unimodal, thereby allowing the population's mean phenotype to change deterministically by selection. As the amount of phenotypic variance is returned to an equilibrium state, the multiple peaks reemerge, but the population has moved from one stable state to another. These variance-induced peak shifts allow punctuational evolution from one peak to another at a rate that can be much higher than that predicted by Wright's shifting-balance process alone.     

PERSPECTIVE: DARWIN,PROGRESS, AND ECONOMIC PRINCIPLES

Darwin's concept of progress was an economic one, with the accumulation of adaptations having a strong analogy to technological innovations. This interpretation makes it easier to understand his differences with Lamarck and others whose views he considered metaphysically objectionable. It also clarifies his relationship to Malthus and such features of his theory as the episodic nature of evolutionary change. His position is consistent with modern theories of biotic invasions and long-term evolutionary trends. It also accords well with current efforts to produce a synthesis between biology and economics.     

Stream-dwelling insects and extremely low frequency electromagnetic fields: a ten-year study

Changes in the structure of benthic insect communities at an experimental site and at a reference site in the Ford River, Michigan were monitored over a 10-year period to determine whether extremely low frequency electromagnetic fields (ELF) affected those communities. Five of 10 biotic parameters monitored are presented: taxon evenness (J), richness (S), numerical dominance of chironomids, and total insect mass. Data were separated into three seasons because coefficient of variation values were lower in the summer than in the spring and fall. Two-way ANOVA tests for the biotic variables were often significantly different between sites and among years, but the interaction terms were less frequently significant. Biotic parameters were regressed against stream discharge, water temperatures, years, and ELF cumulative ground field exposures. At the experimental site, discharge accounted for more variation than did water temperature or years for all biotic parameters except chironomid numerical dominance in the fall. Intervention analyses, using the B.A.C.I parametric or the R.I.A non-parametric showed significant differences in three of 15 cases; namely, for the highly varying chironomid numerical dominance values in the spring and fall and for the low varying total insect mass values in the summer. For those tests, the Before Impact period spanned April 1984 through May 1986. The After Impact period (full ELF power) spanned June 1989 through August 1993. Trend analysis for total insect mass at the experimental site in the summer showed discharge to be more important than water temperatures or ELF ground field exposures. Natural physical factors appear to be more important than the anthropogenic ELF fields in accounting for seasonal and yearly changes in the community.