The origins and evolution of eukaryotic proteins

The common ancestry of eukaryotes, archaebacteria and eubacteria is well demonstrated by amino acid sequence comparisons of numerous proteins that are common to all three groups. On the other hand, there are a few proteins, like ubiquitin, that are common to eukaryotes and archaebacteria and which have yet to be observed in eubacteria. Some proteins appear to be wholly restricted to eukaryotes; this is especially true of cytoskeletal proteins. Recently, actin has been found by crystallography to be homologous with an ATP-binding domain found in a heat shock protein and several other proteins common to all three urkingdoms. This observation is puzzling on several counts. Most cytoskeletal proteins like actin and tubulin are very slow changing and must have been so for a very long time. How is it, then, that no sequence resemblance can be discerned with their alledged prokaryotic antecedents? The question is addressed by considering two bacterial fts proteins which appear to be related to actin, on the one hand, and tubulin, on the other. One answer may be that the rate of change of these proteins changed dramatically at a key point in their history. Another possibility is that eukaryotes are much older than some of their other proteins indicate.     

Novel homologs of replication protein A in archaea: implications for the evolution of ssDNA-binding proteins

In Bacteria and Eukarya, ssDNA-binding proteins are central to most aspects of DNA metabolism. Until recently, however, no counterpart of an ssDNA-binding protein had been identified in the third domain of life, Archaea. Here, we report the discovery of a novel type of ssDNA-binding protein in the genomes of several archaeons. These proteins, in contrast to all known members of this protein family, possess four conserved DNA-binding sites within a single polypeptide or, in one case, two polypeptides. This peculiar structural organization allows us to propose a model for the evolution of this class of proteins.     

Mammalian heterotrimeric G-protein-like proteins in mycobacteria: implications for cell signalling and survival in eukaryotic host cells

Selectively-infective phage (SIP) is a novel methodology for the in vivo selection of interacting protein-ligand pairs. It consists of two components, (1) a phage particle made non-infective by replacing its N-terminal domains of geneIII protein (gIIIp) with a ligand-binding protein, and (2) an "adapter" molecule in which the ligand is linked to those N-terminal domains of gIIIp which are missing from the phage particle. Infectivity is restored when the displayed protein binds to the ligand and thereby attaches the missing N-terminal domains of gIIIp to the phage particle. Phage propagation is thus strictly dependent on the protein-ligand interaction. We have shown that the insertion of beta-lactamase into different positions of gIIIp, mimicking the insertion of a protein-ligand pair, led to highly infective phage particles. Any phages lacking the first N-terminal domain were not infective at all. In contrast, those lacking only the second N-terminal domain showed low infectivity irrespective of the presence or absence of the F-pilus on the recipient cell, which could be enhanced by addition of calcium. An anti-fluorescein scFv antibody and its antigen fluorescein were examined as a protein-ligand model system for SIP experiments. Adapter molecules, synthesized by chemical coupling of fluorescein to the purified N-terminal domains, were mixed with non-infective anti-fluorescein scFv-displaying phages. Infection events were strictly dependent on fluorescein being coupled to the N-terminal domains and showed a strong dependence on the adapter concentration. Up to 10(6) antigen-specific events could be obtained from 10(10) input phages, compared to only one antigen-independent event. Since no separation of binders and non-binders is necessary, SIP is promising as a rapid procedure to select for high affinity interactions.     

Comparison of circumsporozoite proteins from avian and mammalian malarias: biological and phylogenetic implications

The circumsporozoite (CS) protein of malaria parasites (Plasmodium) covers the surface of sporozoites that invade hepatocytes in mammalian hosts and macrophages in avian hosts. CS genes have been characterized from many Plasmodium that infect mammals; two domains of the corresponding proteins, identified initially by their conservation (region I and region II), have been implicated in binding to hepatocytes. The CS gene from the avian parasite Plasmodium gallinaceum was characterized to compare these functional domains to those of mammalian Plasmodium and for the study of Plasmodium evolution. The P. gallinaceum protein has the characteristics of CS proteins, including a secretory signal sequence, central repeat region, regions of charged amino acids, and an anchor sequence. Comparison with CS signal sequences reveals four distinct groupings, with P. gallinaceum most closely related to the human malaria Plasmodium falciparum. The 5-amino acid sequence designated region I, which is identical in all mammalian CS and implicated in hepatocyte invasion, is different in the avian protein. The P. gallinaceum repeat region consists of 9-amino acid repeats with the consensus sequence QP(A/V)GGNGG(A/V). The conserved motif designated region II-plus, which is associated with targeting the invasion of liver cells, is also conserved in the avian protein. Phylogenetic analysis of the aligned Plasmodium CS sequences yields a tree with a topology similar to the one obtained using sequence data from the small subunit rRNA gene. The phylogeny using the CS gene supports the proposal that the human malaria P. falciparum is significantly more related to avian parasites than to other parasites infecting mammals, although the biology of sporozoite invasion is different between the avian and mammalian species.     

Predicting the topology of eukaryotic membrane proteins

We show that the so-called 'positive inside' rule, i.e. the observation that positively charged amino acids tend to be more prevalent in cytoplasmic than in extra-cytoplasmic segments in transmembrane proteins [von Heijne, G. (1986) EMBO J. 5, 3021-3027], seems to hold for all polar segments in multi-spanning eukaryotic membrane proteins irrespective of their position in the sequence and hence can be used in conjunction with hydrophobicity analysis to predict their transmembrane topology. Further, as suggested by others, we confirm that the net charge difference across the first transmembrane segment correlates well with its orientation [Hartmann, E., Rapoport, T. A. and Lodish H. F. (1989) Proc. Natl Acad. Sci. USA 86, 5786-5790], and that the overall amino-acid composition of long polar segments can also be used to predict their cytoplasmic or extra-cytoplasmic location [Nakashima, H. and Nishikawa, K. (1992) FEBS Lett. 303, 141-146]. We present an approach to the topology prediction problem for eukaryotic membrane proteins based on a combination of these methods.     

LTR retrotransposons and the evolution of eukaryotic enhancers

Since LTR retrotransposons and retroviruses are especially prone to regional duplications and recombination events, these viral-like systems may be especially conducive to the evolution of closely spaced combinatorial regulatory motifs. Using the Drosophila copia LTR retrotransposon as a model, we show that a regulatory region contained within the element's untranslated leader region (ULR) consists of multiple copies of an 8 bp motif (TTGTGAAA) with similarity to the core sequence of the SV40 enhancer. Naturally occurring variation in the number of these motifs is correlated with the enhancer strength of the ULR. Our results indicate that inter-element selection may favor the evolution of more active enhancers within permissive genetic backgrounds. We propose that LTR retroelements and perhaps other retrotransposons constitute drive mechanisms for the evolution of eukaryotic enhancers which can be subsequently distributed throughout host genomes to play a role in regulatory evolution.     

Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms

The aim of this study was to study innervation and angiogenesis in response to grafts of dermis and cultured keratinocytes using immunohistochemical techniques. In a porcine model, fresh autologous de-epidermalized dermis and cultured autologous keratinocytes were combined using a two-stage technique, to produce keratodermal grafts. Wounds were encased within skin graft chambers that prevented the influence of the surrounding skin. As grafts contracted, a peripheral rim of granulation tissue became exposed, allowing us to compare the wound bed beneath grafts with that beneath the raw granulating surface. Grafts were studied for 6 weeks. Angiogenesis was studied using antisera to von Willebrand factor to detect endothelial cells. Nerve growth was studied using antisera to S-100, a Schwann cell marker, and to four axonal markers: protein gene product 9.5, C-flanking peptide of neuropeptide Y, calcitonin gene-related peptide, and vasoactive intestinal peptide. In kerato-dermal grafts (n = 28), organization of blood vessels and nerve growth occurred only beneath areas with epidermal cover as compared with the surrounding granulation tissue. Initially, the immunoreactivity to von Willebrand factor was high, but in areas with epidermal cover it assumed a more orderly pattern with fewer blood vessels. Innervation was first detected by S-100 immunoreactivity seen at 1 to 2 weeks, closely followed by that to protein gene product 9.5 and much later to calcitonin gene-related peptide. C-flanking peptide of neuropeptide Y and vasoactive intestinal peptide immunoreactivity were detected in the wound depth surrounding large blood vessels at 4 to 6 weeks. In control wounds that had been either grafted with de-epidermalized dermis alone (n = 10) or allowed to granulate (n = 10), persistently there was high immunoreactivity to von Willebrand factor but minimal immunoreactivity to the neural markers. In conclusion, kerato-dermal grafts become innervated, and beneath their surface there is also vascular organization to resemble normal skin. Keratinocytes themselves may influence angiogenesis and innervation, as both processes failed to occur beneath granulating areas.     

Modification of a hydrogen bond to a bacteriochlorophyll a molecule in the light-harvesting 1 antenna of Rhodobacter sphaeroides

Site-directed mutagenesis has been used to examine the function of a highly conserved aromatic residue, alpha Trp43, in the light-harvesting 1 antenna of the photosynthetic bacterium Rhodobacter sphaeroides. In this antenna alpha Trp43 is thought to be located near the putative binding site for bacteriochlorophyll; in this work it was changed to both Tyr and Phe, and in each case the main near-infrared absorbance peak was shifted to the blue, from 876 nm to 865 nm and then to 853 nm, respectively. Resonance Raman spectroscopy of the resulting complexes shows a shift of one component of the 1640-cm-1 peak to 1632 cm-1 for the Tyr mutant and to 1660 cm-1 for the Phe mutant. This demonstrates a strengthening of an existing H bond for the Tyr change and a breakage of this bond for the change to Phe. The 1640-cm-1 peak has been previously assigned to H-bonded C2 acetyl carbonyl groups of both bacteriochlorophylls in the light-harvesting 1 antenna dimer [Robert, B. & Lutz, M. (1985) Biochim. Biophys. Acta 807, 10-21]. These results indicate that one of these H bonds is to alpha Trp43, placing this residue in close proximity to the bacteriochlorophyll a macrocycle with which it interacts. The existence of this bond places constraints on the conformation of the alpha polypeptide, and a model of an alpha beta heterodimer is presented incorporating these data.     

A gonococcal porA pseudogene: implications for understanding the evolution and pathogenicity of Neisseria gonorrhoeae

There is an unanswered question from previous studies of 1H/2H-exchange of amide protons of barnase. Under certain conditions, there is a relatively abrupt change from EX2 towards EX1 kinetics as the temperature is slightly increased. The change in kinetics for different mutants is not directly related to their changes in stability. We have measured the stability of the folding intermediate of barnase (I) in 2H2O under a variety of conditions and calculated its population at different temperatures. The change in kinetics correlates with the change in the population of the folding intermediate. At higher temperatures and pH, the free energy of I becomes higher than that of the denatured state, D, and the kinetics becomes EX1. The data fit a simple kinetic scheme. Such changes in kinetics may be used to detect the presence of intermediates in the folding reaction at equilibrium in native conditions, but cannot distinguish whether they are on or off-pathway.     

A new symmetrodont mammal from China and its implications for mammalian evolution

A new symmetrodont mammal has been discovered in the Mesozoic era (Late Jurassic or Early Cretaceous period) of Liaoning Province, China. Archaic therian mammals, including symmetrodonts, are extinct relatives of the living marsupial and placental therians. However, these archaic therians have been mostly documented by fragmentary fossils. This newfossil taxon, represented by a nearly complete postcranial skeleton and a partial skull with dentition, is the best-preserved symmetrodont mammal yet discovered. It provides a new insight into the relationships of the major lineages of mammals and the evolution of the mammalian skeleton. Our analysis suggests that this new taxon represents a part of the early therian radiation before the divergence of living marsupials and placentals; that therians and multituberculates are more closely related to each other than either group is to other mammalian lineages; that archaic therians lacked the more parasagittal posture of the forelimb of most living therian mammals; and that archaic therians, such as symmetrodonts, retained the primitive feature of a finger-like promontorium (possibly with a straight cochlea) of the non-therian mammals. The fully coiled cochlea evolved later in more derived therian mammals, and is therefore convergent to the partially coiled cochlea of monotremes.     

Molecular phylogenetic approach for studying life-history evolution: the ambiguous example of the genus Medicago L

We present a molecular phylogeny including most species of the genus Medicago L. (Fabaceae). Based on the consensus of the 48 most parsimonious trees, life-history and mating-system characters are mapped, and a putative history of the genus is suggested. The most parsimonious reconstruction suggests an ancestral annual and selfing state, and recurrent evolution towards perenniality and outcrossing. Based on theoretical predictions and classical hypotheses of the history of the genus, different assumptions about the ancestral state and different weighting schemes of evolution between the character states are made. Assuming an outcrossing, perennial ancestral state (partly supported by morphological features) does not fundamentally change the reconstruction. To meet theoretical expectations, various weighting schemes favouring evolution towards annuality and selfing are applied. Influence and validity of such weighting schemes are discussed with regard to other studies.     

In vitro testing of susceptibilities of filamentous ascomycetes to voriconazole, itraconazole, and amphotericin B, with consideration of phylogenetic implications

The in vitro susceptibilities of three hundred eighty-one isolates representing two classes, five orders, nine families, 30 genera, and 51 species of ascomycetous fungi to voriconazole, itraconazole, and amphotericin B were tested by using a modification of the National Committee for Clinical Laboratory Standards M27-A reference method. For those fungi of known phylogenetic relatedness, drug MICs were consistently low for isolates among all clades, except for members of the family Microascaceae. The highest MICs of all drugs tested were consistently for the Microascaceae, supporting the observation of fungal phylogeny and corresponding susceptibility to antifungal drugs. Itraconazole and voriconazole have a broad range of activity against phylogenetically similar agents of hyalohyphomycosis, phaeohyphomycosis, chromoblastomycosis, and mycetoma.     

Heat-shock proteins and molecular chaperones: implications for pathogenesis, diagnostics, and therapeutics

Cells react to physical (e.g., heat) or chemical (e.g., anoxia, low pH) stressors, mounting a stress (heat-shock) response. Most genes are turned down or off, while a few are activated. The latter encode the stress or heat-shock proteins (Hsps), whose levels increase in stressed cells. Various Hsps are molecular chaperones. These, and other molecular chaperones that are not Hsps, help the other cellular proteins to achieve their native state (correct folding or functional conformation), reach their final destination (e.g., the endoplasmic reticulum or the mitochondria), resist denaturing by stressors, and regain the native state after partial denaturation. Thus the Hsps and molecular chaperones occupy the stage's center whenever and wherever there is cellular and tissue injury caused by local or systemic stressors via protein damage. This feature, their participation in protein folding and transport, and their evolutionary conservation within the three phylogenetic domains, strongly suggest a vital role for Hsps and molecular chaperones. Their importance in pathogenesis, and as diagnostic markers and prognostic indicators, is beginning to be appreciated. The role of Hsps and molecular chaperones in cell recovery from injury by a variety of noxae of clinical and surgical relevance is also being assessed. Consequently, the potential of these molecules (and corresponding genes) as targets for treatment or as therapeutic tools is emerging and is being explored. Stroke, myocardial infarction, inflammatory syndromes, infectious and parasitic diseases, autoimmune disorders, cancer, and aging are but some examples of conditions in which Hsps and molecular chaperones are being scrutinized. The era of Hsp and molecular chaperone pathology has dawned. It is likely that genetic and acquired defects of Hsp and molecular chaperone structure and function will be identified, and will play a primary, or auxiliary but determinant, role in disease.     

Mitochondrial phylogeny of the European cyprinids: implications for their systematics, reticulate evolution, and colonization time

Two different mitochondrial genes, the cytochrome b and the 16S rDNA, support the same European cyprinid molecular phylogeny: the most basal subfamily is the paraphyletic Rasborinae, the Cyprininae are monophyletic, the Tincinae and Gobioninae are close to the Cyprininae or more basal lineages but not close to Leuciscinae or Alburninae, and the Leuciscinae are paraphyletic but can become monophyletic if we include the biphyletic alburninae and exclude the Phoxinini. The relationship of the Acheilognathinae remains obscure. Natural intergeneric and interspecific hybridizations are clearly demonstrated within the Leuciscinae, both from high bootstrap proportions and intermediate morphological features: Chondrostoma toxostoma and Rutilus rutilus, Scardinius erythrophthalmus and R. rutilus, and Leuciscus multicellus and Leuciscus soufia. Finally, the use of the nonsaturated and clockwise 16S mtDNA sequences have been used to infer from nonintrogressive taxa the time of the first European cyprinid cladogeneses. The estimation confirms the hypothesis of Alma?a and Banarescu that European cyprinid subfamilies started to diversify 35 mya and confirms the hypothesis of Bianco on the diversification of European leuciscines in the Mediterranean area during the late Messinian (6.5 to 5.3 mya).     

Cytoskeletal proteins: the evolution of cell division

The prokaryotic cell division protein FtsZ and eukaryotic tubulin have been shown to have very similar structures and are most likely homologs. The evolutionary transition from FtsZ to tubulin could provide a window into the transition from prokaryotic cells to eukaryotic cells.     

Research on chronic, low-level exposure to formaldehyde: implications for neuropsychological assessment

Findings from empirical research serve as the foundation for neuropsychological assessment of individuals suspected of exposure to formaldehyde. Insofar as conclusions regarding causal relationships between exposure and neuropsychological deficits are based on research methodologies that are reliable, findings can be informative. Unfortunately, existing research is not rooted in sound methodology and findings may mislead rather than enlighten clinicians. Two prominent shortcomings in formaldehyde research are discussed: selection bias in recruitment of research participants and unreliability of participant recall for obtaining data on important background variables and exposure levels. Selected examples illustrate the influence of these shortcomings on research showing a causal relationship between long-term, low-level exposure to formaldehyde and chronic neurobehavioral deficiencies. The implications of these weaknesses for assessment of individual patients are discussed.     

Manipulation of lyophilization-induced phase separation: implications for pharmaceutical proteins

Lyophilization, or freeze-drying, of pharmaceutical proteins is often the only processing method that provides requisite long-term product stability. Freezing and drying, however, can cause acute damage to proteins. To alleviate damage, formulations frequently include protein stabilizers (often polymers and/or sugars), as well as buffering salts and "inert" bulking agents. While great efforts are placed on developing a formulation and suitable lyophilization cycle, incompatibilities among components through freezing and drying have been almost completely ignored. We demonstrate that solutions of poly(ethylene glycol) (PEG) and dextran, initially below critical concentrations for phase separation, do indeed experience a liquid-liquid phase separation induced by freeze concentration during the lyophilization cycle. The separation is shown to evolve with annealing at -7 degrees C and can be effectively inhibited simply by replacing NaCl with KCl in the formulation buffer. In addition, we show that phase separation causes unfolding of a model protein, recombinant hemoglobin, when freeze-dried in the PEG/dextran system. When the phase separation is averted by switching to KCl, the protein structural damage is also avoided. Measurements of pH in the frozen solutions show that the structural damage is not a result of pH changes. We suggest that KCl forms a glass with rapid cooling which kinetically prevents the phase separation and thus the protein structural damage.