Experimental and computational analysis of the ancestry of an evolutionary young enzyme from histidine biosynthesis

The conservation of fold and chemistry of the enzymes associated with histidine biosynthesis suggests that this pathway evolved prior to the diversification of Bacteria, Archaea, and Eukaryotes. The only exception is the histidinol phosphate phosphatase (HolPase). So far, non-homologous HolPases that possess distinct folds and belong to three different protein superfamilies have been identified in various phylogenetic clades. However, their evolution has remained unknown to date. Here, we analyzed the evolutionary history of the HolPase from γ-Proteobacteria (HisB-N). It has been argued that HisB-N and its closest homologue d -glycero-d -manno-heptose-1,7-bisphosphate 7-phosphatase (GmhB) have emerged from the same promiscuous ancestral phosphatase. GmhB variants catalyze the hydrolysis of the anomeric d -glycero-d -manno-heptose-1,7-bisphosphate (αHBP or βHBP) with a strong preference for one anomer (αGmhB or βGmhB). We found that HisB-N from Escherichia coli shows promiscuous activity for βHBP but not αHBP, while βGmhB from Crassaminicella sp. shows promiscuous activity for HolP. Accordingly, a combined phylogenetic tree of αGmhBs, βGmhBs, and HisB-N sequences revealed that HisB-Ns form a compact subcluster derived from βGmhBs. Ancestral sequence reconstruction and in vitro analysis revealed a promiscuous HolPase activity in the resurrected enzymes prior to functional divergence of the successors. The following increase in catalytic efficiency of the HolP turnover is reflected in the shape and electrostatics of the active site predicted by AlphaFold. An analysis of the phylogenetic tree led to a revised evolutionary model that proposes the horizontal gene transfer of a promiscuous βGmhB from δ- to γ-Proteobacteria where it evolved to the modern HisB-N.     

The intrinsic electrophysiological characteristics of fly lobula plate tangential cells: I. Passive membrane properties

The passive membrane properties of the tangential cells in the fly lobula plate (CH, HS, and VS cells, Fig. 1) were determined by combining compartmental modeling and current injection experiments. As a prerequisite, we built a digital base of the cells by 3D-reconstructing individual tangential cells from cobalt-stained material including both CH cells (VCH and DCH cells), all three HS cells (HSN, HSE, and HSS cells) and most members of the VS cell family (Figs. 2, 3). In a first series of experiments, hyperpolarizing and depolarizing currents were injected to determine steady-state I-V curves (Fig. 4). At potentials more negative than resting, a linear relationship holds, whereas at potentials more positive than resting, an outward rectification is observed. Therefore, in all subsequent experiments, when a sinusoidal current of variable frequency was injected, a negative DC current was superimposed to keep the neurons in a hyperpolarized state. The resulting amplitude and phase spectra revealed an average steady-state input resistance of 4 to 5 M and a cut-off frequency between 40 and 80 Hz (Fig. 5). To determine the passive membrane parameters R _m (specific membrane resistance), R _i (specific internal resistivity), and C _m (specific membrane capacitance), the experiments were repeated in computer simulations on compartmental models of the cells (Fig. 6). Good fits between experimental and simulation data were obtained for the following values: R _m = 2.5 kcm², R _i = 60 cm, and C _m = 1.5 F/cm² for CH cells; R _m = 2.0 kcm², R _i = 40 cm, and C _m = 0.9 F/cm² for HS cells; R _m = 2.0 kcm², R _i = 40 cm, and C _m = 0.8 F/cm² for VS cells. An error analysis of the fitting procedure revealed an area of confidence in the R _m -R _i plane within which the R _m -R _i value pairs are still compatible with the experimental data given the statistical fluctuations inherent in the experiments (Figs. 7, 8). We also investigated whether there exist characteristic differences between different members of the same cell class and how much the exact placement of the electrode (within ±100 m along the axon) influences the result of the simulation (Fig. 9). The membrane parameters were further examined by injection of a hyperpolarizing current pulse (Fig. 10). The resulting compartmental models (Fig. 11) based on the passive membrane parameters determined in this way form the basis of forthcoming studies on dendritic integration and signal propagation in the fly tangential cells (Haag et al., 1997; Haag and Borst, 1997).     

The zygote and proembryo of alfalfa: quantitative,three-dimensional analysis and implications for biparental plastid inheritance

Summary Genetic studies have demonstrated biparental inheritance of plastids in alfalfa. The ratio of paternal to maternal plastids in the progeny varies according to the genotypes of the parents, which can be classified as strong or weak transmitters of plastids. Previous cytological investigations of generative cells and male gametes have provided no consistent explanation for plastid inheritance patterns among genotypes. However, plastids in the mature egg cells of a strong female genotype (6–4) were found to be more numerous and larger than in mature eggs of a weak female genotype (CUF-B), and the plastids in 6–4 eggs are positioned equally around the nucleus. In CUF-B, the majority of plastids are positioned below (toward the micropyle) the mid level of the nucleus, which is the future division plane of the zygote. Since only the apical portion of the zygote produces the embryo proper, plastids in the basal portion were predicted to become included in the suspensor cells and not be inherited. In the present study, we examined zygotes and a two-celled proembryo from a cross between CUF-B and a strong male genotype (301), a cross that results in over 90% of the progeny possessing paternal plastids only. Our results indicate that the distribution of plastids observed in the CUF-B egg cell is maintained through the first division of the zygote. Further, paternal plastids are similarly distributed; however, within the apical portion of the zygote and in the apical cell of the two-celled proembryo, the number of paternal plastids is typically much greater than the number of maternal plastids. These findings suggest that maternal and paternal plastid distribution within the zygote is a significant factor determining the inheritance of maternal and paternal plastids in alfalfa.     

Elemental signatures of human diets from the Georgia Bight

Multielement analysis was performed on bone samples extracted from the femora of 39 adults from three mortuary sites (Johns Mound, Santa Catalina de Guale, and Santa Catalina de Guale de Santa Meria) and time periods (late preagricultural, early contact, and late contact) in the Georgia Bight. This study was used to investigate whether elemental analysis would support or contradict other lines of data regarding diets and dietary change previously generated for the region. The data are in agreement with an earlier interpretation, based on stable isotopes, that dietary maize increases through time but fails to support the idea that marine resources decreased in importance. Rather, it appears that the wild plant food component of the diets decreases as maize increases in importance; throughout the sequence, marine resources comprise a significant portion of the diets. © 1995 Wiley-Liss, Inc.     

Sexual differences in the Golgi apparatus of rat hepatocytes: three-dimensional analysis

Lipid metabolism takes place in the Golgi apparatus, but at a higher rate in female than in male rats. I therefore examined the Golgi apparatus by morphometric means for differences between the sexes at the light-and electron-microscopic level. The Golgi apparatus was stained in situ by a zinc-iodide-osmium method. The counts of the Golgi apparatus in cross-sections in female hepatocytes by light microscopy were approximately twice that in male hepatocytes. Upon ovariectomy, these counts were greatly reduced but were reestablished after estrogen supplement. To clarify this phenomenon, three-dimensional reconstructions of the Golgi apparatus were produced from electron-microscopic images of serially cut 160-nm sections. The Golgi apparatus of both male and ovariectomized females had the shape of a small ring, whereas it took the form of a large elongated cylinder in normal females and in castrated males after treatment with estrogen. The numerical difference in Golgi apparatus counts by light microscopy of in males and females is, therefore, apparently attributable to the size and shape of the Golgi apparatus, and is controlled by the estrogen level.     

Diet and status at Chalcatzingo: some empirical and technical aspects of strontium analysis.

Determination of the levels of particular trace elements preserved in bone provides a potential pathway for reconstructing the diet of extinct primate species and archaic human groups. Strontium is one of the most useful trace elements for dietary reconstruction but several empirical properties of strontium must be considered during the interpretation of results. (1) Strontium is distributed unevenly throughout the physical environment. (2) Plants, in general, do not discriminate against strontium. (3) During ionic transfer across biological membranes, strontium is discriminated against by terrestrial vertebrates. (4) It is unlikely that strontium would be selectively removed from bone mineral during diagenesis. A particular difficulty in trace element analysis is caused by interaction between analytical technique and sample matrix. To assess this problem the skeletal population from Chalcatzingo was analyzed by two techniques: atomic absorption spectrometry and neutron activation analysis. The results from the two techniques compared favorably indicating that the pattern of bone strontium levels could be accepted as an accurate reflection of the distribution of bone strontium within the population. After demonstrating the internal accuracy of the results, the bone strontium level and position of social rank within Chalcatzingo were compared. Ethnographic and archaeological evidence on chiefdoms and states indicate that dietary differences in the amount of meat consumed occur between social ranks. The relative social ranks were reconstructed by using a "pattern analysis" of the burial goods accompanying each individual. The individuals accompanied by jade had the lowest mean bone strontium level (X = 532). Those individuals buried with a shallow dish had a slightly higher level (X = 635). A third group, which had no grave goods, had the highest mean bone strontium level (X = 700) which suggests that their diet contained less meat than was available to the rest of the community.     

Evolutionary diversification of structure and function in the family of intracellular calcium-binding proteins

Summary The maximum parsimony method was used to reconstruct the genealogical history of the family of intracellular calcium-binding proteins represented by six major present-day lineages, three of which - calcium dependent modulator protein, heart and skeletal muscle troponin Cs, and alkali light chains of myosin - were found to share a closer kinship with one another than with the other lineages. Similarly, parvalbumins and regulatory light chains of myosin were depicted as more closely related, whereas the branch of intestinal calcium-binding protein proved to have the most distant separation. The computer-generated amino acid sequence for the common ancestor of these six lineages described a four domain protein in which each domain of approximately 40 amino acid residues had a mid-region, 12 residue segment that bound calcium and had properties most resembling those of the calcium dependent modulator protein. It could then be deduced that parvalbumins evolved by deletion of domain I, inactivation of calcium-binding properties in domain II, and acquisition of increased affinity for Ca⁺⁺ and Mg⁺⁺ in domains III and IV. Regulatory light chains of myosin lost the cation binding property from three domains, retaining it in I, whereas alkali light chains of myosin lost this ability from each of the four domains. In skeletal muscle troponin C all domains retained their calcium-binding activity; however, like parvalbumins, domains III and IV acquired high affinity properties. Cardiac troponin C lost its binding activity from domain I but otherwise resembled the skeletal muscle form. Finally, intestinal calcium-binding protein evolved by deletion of domains III and IV.Positive selection could be implicated in these evolutionary changes in that the rate of fixation of mutations substantially increased in the mid portions of those domains which were loosing calcium-binding activity. Likewise, when the cation binding sites were changing from low to high affinity, an accelerated rate of fixed mutations was observed. Once this new functional parameter was selected these regions showed a remarkable conservatism, as did those binding sites which were maintaining the lower affinity. Moreover even in sequence regions not directly involved in cation binding, the lineage of troponin C became very conservative over the past 300 million years, perhaps because of the necessity for maintaining specific interfaces in order for the molecule to interact with troponin I and T in a functional thin myofilament. A similar phenomenon was observed in domain II of the regulatory light chains of the myosin lineage suggesting a possible binding site with the heavy chain of myosin.This paper is dedicated to the memory of Jean-Francois Pechère, deceased     

Ultrastructural characterization and three-dimensional reconstruction of isolated maize (Zea mays L.) egg cell protoplasts

Summary Isolated egg cell protoplasts ofZea mays L., inbred line A 188, have been studied at the transmission electron microscope level. Their preparation for electron microscopy has been performed by embedding in ultra-low gelling agarose as a preliminary step. Five isolated egg cell protoplasts were serially ultrathin sectioned and studied in detail. One of these protoplasts was reconstructed in three dimensions to provide additional information on its structure. After enzymatic digestion and microdissection, isolated egg cells are true, highly vacuolized protoplasts. The structure of their organelles agrees with in situ observations, indicating an ultrastructural intactness after isolation: the mitochondria are polymorphic, form reticulate networks, and have well developed cristae; the plastids contain starch grains; and the spherical nucleus is euchromatic. As in situ, the organelles of the isolated egg cell protoplasts are aggregated near the nucleus. The complete picture provided by this work should serve as a comparative base for studies on in vitro fertilization products.     

An ostracod-based calibration function for electrical conductivity reconstruction in lacustrine environments in Patagonia,Southern South America

In the Patagonian region (∼37–56°S) E of the Andes, the salinity and solute composition of lakes is strongly related to their location along the marked W-E decreasing precipitation gradient that is one of the main climatic features of the area. A calibration function (n = 34) based on 12 ostracod species (Ostracoda, Crustacea) was developed by WA-PLS to quantitatively reconstruct electrical conductivity (EC) values as a salinity proxy. The selected one component model had a r² = 0.74 and RMSEP and maximum bias equal to 16% and 31% of the sampled range, respectively, comparable to other published ostracod-based calibration functions. This model was applied to the ostracod record of the closed lake Laguna Cháltel (49°58′S, 71°07′W), comprising seven species and dominated by two species of the genus Limnocythere. In order to evaluate the calibration function’s robustness, the obtained EC values were compared with qualitative lake level and salinity variations inferred through a multiproxy hydrological reconstruction of the lake. Both reconstructions show good overall agreement, with reconstructed EC values in the oligo-mesohaline range (average: 11 060 ± 680 μS/cm) between 4570 and 3190 cal BP, corresponding to the ephemeral and shallow lake phases, and a marked decrease in EC concurrent with a lake level rise, reaching an average EC of 1140 ± 90 μS/cm during the deep lake phase (1720 cal BP to present). The variability in the reconstructed EC values for the ephemeral lake phase showed some inconsistency with the expected trend, which was attributed to time-averaging effects; for its part, the pace of the decrease in EC during the medium-depth phase (3190–1720 cal BP) differed from the expected, which could be due to autigenic effects (redissolution of salts) at the onset of this phase. This comparison not only lends support to the adequacy of the calibration function, but also suggests that its application in the context of a multiproxy study can greatly contribute to distinguish between autigenic and climatic-related controls of paleosalinity in closed lakes, allowing performing more accurate paleoenvironmental inferences on the basis of paleohydrological reconstructions.