Mitochondrial ribosomal proteins in Xenopus laevis/X. mulleri interspecific hybrids.

The large subunits of mitochondrial ribosomes were isolated from two related frog species, Xenopus laevis and X. mulleri, and their proteins were compared by two-dimensional polyacrylamide gel electrophoresis. Three of the proteins observed in X. laevis are absent from X. mulleri, and four of the proteins observed in X. mulleri are absent from X. laevis. More than these seven such species-specific proteins may occur.Reciprocal crosses between frogs of the two species gave two groups of F1 hybrids. Nuclear genes in these hybrids derive equally from both species, while mitochondrial DNA (and therefore mitochondrial rRNA) derived exclusively from the maternal species. Electrophoretic analyses of the large subunit proteins of these F1 animals revealed that four of the species-specific proteins are present only when their corresponding species was the mother. While this result is consistent with the coding of these four proteins by mitochondrial DNA, it does not provide evidence against nuclear coding of these proteins. A fifth protein is absent from both F1 hybrids. A sixth is present in both F1 hybrids, and a seventh is present only when its corresponding species was the father. We conclude that at least these latter two mitochondrial ribosomal proteins are encoded by nuclear genes.     

Synthesis patterns of a set of follicle cell proteins in Drosophila melanogaster sibling species

The protein synthesis pattern of a set of stage and tissue specific proteins has previously been described in Drosophila melanogaster. The analysis of this set of follicle cell proteins (Fc proteins) is here extended to cover several sibling species of Drosophila melanogaster, namely D. simulans, D. mauritiana, D. erecta and D. yakuba. Even though a similar set of proteins were synthesized in these species, minor differences in size of the proteins were found between the species. Some of the species exhibited variation within species.     

Homologous gene expression in intergeneric fox hybrids (Alopex lagopus x Vulpes vulpes). I. Comparative electrophoretic analysis of blood proteins and enzymes in Arctic and silver foxes]

A comparative study of 27 enzymes and proteins in blue and silver foxes was carried out by means of starch gel electrophoresis. The structure of these enzymes and proteins is determined by about 33 genes. It is shown that a number of blood enzymes and proteins of these species is represented by a single electrophoretic form, while lactate dehydrogenase, carboanhydrase, arylesterase, carboxylesterase, diaphorase, hexokinase and tetrasolium oxidase have several forms. It is also found that these species differ in seven enzymes and proteins: diaphorase, G-6-PD, adenylate kinase, carboxylesterase, albumin, prealbumin, transferrins. Other enzymes and proteins are similar in their electrophoretic mobility. The data obtained afford the evidence that the two species (Vulpes vulpes and Alopex lagopus) differ in a set of enzymes and proteins.     

Synthesis patterns of a set of follicle cell proteins in Drosophila melanogaster sibling species

The protein synthesis pattern of a set of stage and tissue specific proteins has previously been described in Drosophila melanogaster. The analysis of this set of follicle cell proteins (Fc proteins) is here extended to cover several sibling species of Drosophila melanogaster, namely D. simulans, D. mauritiana, D. erecta and D. yakuba. Even though a similar set of proteins were synthesized in these species, minor differences in size of the proteins were found between the species. Some of the species exhibited variation within species.     

The effects on tubulin polymerization and associated guanosine triphosphate hydrolysis of aluminum ion, fluoride and fluoroaluminate species

The effects of aluminum ion, fluoride, and fluoroaluminate species on the assembly of tubulin in the presence of guanine nucleotides and the consequences of these ions on the associated GTPase of microtubules was investigated. Combinations of GDP and fluoroaluminate species were incapable of activating tubulin for polymerization, in contrast to other guanine nucleotide binding proteins, in which these species produce a functional GTP equivalent. Fluoride alone has an effect on GTP-magnesium-promoted microtubule assembly, causing an increased amount of polymer formation and a reduced rate of associated GTP hydrolysis. It is concluded that aluminum ion and fluoroaluminate species possess distinct mechanisms in inhibiting GTP hydrolysis of GTP-binding proteins and that subpopulations of GTP-binding proteins must exist based on differential sensitivities to these ions.     

Identification of signature proteins that are distinctive of the Deinococcus-Thermus phylum.

The members of the Deinococcus-Thermus phylum, which include many species that are resistant to extreme radiation, as well as several thermophiles, have been recognized solely on the basis of their branching patterns in 16S rRNA and other phylogenetic trees. No biochemical or physiological characteristic is currently known that is unique to this group of species. To identify genes/proteins that are exclusive of this group of species, systematic protein basic local alignment tool (Blastp) searches were carried out on each open reading frame (ORF) in the genome of Deinococcus radiodurans. These studies identified 65 proteins that were only found in all three sequenced Deinococcus-Thermus genomes (viz. D. radiodurans, D. geothermalis and Thermus thermophilus), but not in any other bacteria. In addition, these studies also identified 206 proteins that are exclusively found in the two Deinocococci species, and 399 proteins that are unique to D. radiodurans. The identified proteins, which represent a genetic repertoire distinctive to the Deinococcus-Thermus group, or to Deinococci species, provide novel molecular markers for their identification and characterization. The cellular functions of most of these proteins are not known and their studies should prove useful in identifying novel biochemical and physiological characteristics that are exclusive of these groups of bacteria and also those responsible for the extreme radiation resistance of Deinococci.     

FtsZ and the division of bacterial cell

In this review we have tried to describe proteins and supermolecular structures which take part in the division of bacterial cell. The principal cell division protein of the most of prokaryotes is FtsZ, a homologue of eukaryotic tubulin. FtsZ just as tubulin is capable to bind and hydrolyze GTP. The division of bacterial cell begins with forming of so called divisome. The basis of such divisome is a contractile ring (Z ring); the ring encircles the cell about midcell. Z ring consists of a bundle of laterally bound protofilaments, which have been formed as a result of FtsZ polymerization. Z ring is rigidly bounded to cytozolic side of inner membrane with participation of FtsA, ZipA, FtsW and many other cell division proteins of divisome. The ring directs the process of cytokinesis transmitting power of constriction to membrane. Primary structures of members of the family of prokaryotic FtsZs differ from eukaryotic tubulines significantly except the region, where the site of GTP binding is placed. There is high degree of homology between structures of these proteins in the region. FtsZ is one of the most conservative proteins in prokaryotes, but ftsZ genes have not been found in completely sequenced genomes of several species of microorganisms. There are 2 species of mycoplasmas (Ureaplasma parvum and Mycoplasma mobile), Prostecobacter dejongeii, 10 species of chlamydia and 5 species of archaea among them. So these organisms divide without FtsZ. There are many open reading frames which encode proteins with unknown functions in genomes of U. parvum and M. mobile. The comparison of primary structures of these hypothetical proteins with structures of cell division proteins did not allow researchers to find similar proteins among them. We suppose that the process of cell division of these organisms should recruit proteins with function similar to FtsZ and having homologous with FtsZ or other cell division proteins spatial structures.     

Physical Features of Intracellular Proteins that Moonlight on the Cell Surface

Moonlighting proteins comprise a subset of multifunctional proteins that perform two or more biochemical functions that are not due to gene fusions, multiple splice variants, proteolytic fragments, or promiscuous enzyme activities. The project described herein focuses on a sub-set of moonlighting proteins that have a canonical biochemical function inside the cell and perform a second biochemical function on the cell surface in at least one species. The goal of this project is to consider the biophysical features of these moonlighting proteins to determine whether they have shared characteristics or defining features that might suggest why these particular proteins were adopted for a second function on the cell surface, or if these proteins resemble typical intracellular proteins. The latter might suggest that many other normally intracellular proteins found on the cell surface might also be moonlighting in this fashion. We have identified 30 types of proteins that have different functions inside the cell and on the cell surface. Some of these proteins are found to moonlight on the surface of multiple species, sometimes with different extracellular functions in different species, so there are a total of 98 proteins in the study set. Although a variety of intracellular proteins (enzymes, chaperones, etc.) are observed to be re-used on the cell surface, for the most part, these proteins were found to have physical characteristics typical of intracellular proteins. Many other intracellular proteins have also been found on the surface of bacterial pathogens and other organisms in proteomics experiments. It is quite possible that many of those proteins also have a moonlighting function on the cell surface. The increasing number and variety of known moonlighting proteins suggest that there may be more moonlighting proteins than previously thought, and moonlighting might be a common feature of many more proteins.     

Comparative Analysis of Rapidly Transported Axonal Proteins in Sensory Neurons of the Frog and Rat

³⁵S-labeled proteins carried by fast axonal transport in sciatic sensory axons of bullfrog and rat were separated electrophoretically on discontinuous polyacrylamide gradient slab gels. In contrast to the previously reported similarity in the electrophoretic profiles of rapidly transported proteins from functionally different neurons, we have found that there is very little correspondence in the profiles of these proteins in functionally similar neurons from two widely studied species. We also found very little correspondence between the two species in the profiles of locally synthesized sciatic nerve protein. The results demonstrate the difficulty inherent in comparing the electrophoretic profiles obtained using these two model systems for the study of rapidly transported axonal proteins. In particular, relationships between the major rapidly transported proteins in the two species could_not be analyzed with this technique.     

The host defense proteome of human and bovine milk

Milk is the single source of nutrients for the newborn mammal. The composition of milk of different mammals has been adapted during evolution of the species to fulfill the needs of the offspring. Milk not only provides nutrients, but it also serves as a medium for transfer of host defense components to the offspring. The host defense proteins in the milk of different mammalian species are expected to reveal signatures of evolution. The aim of this study is therefore to study the difference in the host defense proteome of human and bovine milk. We analyzed human and bovine milk using a shot-gun proteomics approach focusing on host defense-related proteins. In total, 268 proteins in human milk and 269 proteins in bovine milk were identified. Of these, 44 from human milk and 51 from bovine milk are related to the host defense system. Of these proteins, 33 were found in both species but with significantly different quantities. High concentrations of proteins involved in the mucosal immune system, immunoglobulin A, CD14, lactoferrin, and lysozyme, were present in human milk. The human newborn is known to be deficient for at least two of these proteins (immunoglobulin A and CD14). On the other hand, antimicrobial proteins (5 cathelicidins and lactoperoxidase) were abundant in bovine milk. The high concentration of lactoperoxidase is probably linked to the high amount of thiocyanate in the plant-based diet of cows. This first detailed analysis of host defense proteins in human and bovine milk is an important step in understanding the function of milk in the development of the immune system of these two mammals.     

Molecular mechanisms underlying thermal adaptation of xeric animals

For many years, we and our collaborators have investigated the adaptive role of heat shock proteins in different animals, including the representatives of homothermic and poikilothermic species that inhabit regions with contrasting thermal conditions. Adaptive evolution of the response to hyperthermia has led to different results depending upon the species. The thermal threshold of induction of heat shock proteins in desert thermophylic species is, as a rule, higher than in the species from less extreme climates. In addition, thermoresistant poikilothermic species often exhibit a certain level of heat shock proteins in cells even at a physiologically normal temperature. Furthermore, there is often a positive correlation between the characteristic temperature of the ecological niche of a given species and the amount of Hsp70-like proteins in the cells at normal temperature. Although in most cases adaptation to hyperthermia occurs without changes in the number of heat shock genes, these genes can be amplified in some xeric species. It was shown that mobile genetic elements may play an important role in the evolution and fine-tuning of the heat shock response system, and can be used for direct introduction of mutations in the promoter regions of these genes.     

An anticarbohydrate monoclonal antibody inhibits cell-cell adhesion in many species of Dictyostelium but not of Polysphondylium.

The anticarbohydrate monoclonal antibody d-41 inhibits the adhesion of aggregating cells, as measured by an in vitro assay, in every species of Dictyostelium tested but in none of the species from the genus Polysphondylium. Although d-41 binds significantly to the surface of cells from both genera, the ability to inhibit adhesion correlates with the binding of the antibody to a few, mostly developmentally regulated, membrane-associated proteins in each of the species affected. Previous work in D. discoideum and D. purpureum have shown that the major d-41-b binding proteins from these species at this time in development are directly involved in the adhesion process. Therefore, the presence of the epitope on these proteins in the other species of Dictyostelium implicates them in the adhesion mechanism. The function of the carbohydrates containing the epitope is yet to be determined.     

Identification of centromere proteins in different mammalian cells

The characterization of centromeric proteins is facilitated using anti-centromere antibodies present in the sera of patients with the CREST variant of scleroderma. We have employed these sera to determine whether or not those proteins are present in different mammalian species, as well as to study their tissue distribution. Here, we describe the immunofluorescent pattern and the proteins recognized by CREST sera in dividing and resting cells from mouse, rat, swine, hamster, rabbit, and man. In nuclear preparations from cultured cells, thymocytes and spermatozoa from these species, the antigens recognized by CREST sera are proteins of 18 to 20 kDa in all species tested, except in rat. Additionally, two peptides of 80 and 140 kDa were observed in human preparations. In contrast, a 50 kDa peptide is the primary protein detected by the sera in rat nuclei.     

Two highly diverged New World Artemia species, A. franciscana and A. persimilis, from contrasting hypersaline habitats express a conserved stress protein complement

The brine shrimp Artemia is a well known animal extremophile adapted to survive in very harsh hypersaline environments. We compared the small stress proteins artemin and p26, and the chaperone hsc70 in encysted embryos (cysts) of the New World species, A. franciscana and A. persimilis. Cysts of the former, from San Francisco Bay, USA (SFB), were used essentially as a reference for these proteins, while both species were from locations in Chile where they occur in habitats at latitudinal extremes, the Atacama desert and Patagonia. These two species are phylogenetically distant, A. persimilis being closer to the Old World species, whilst A. franciscana is considered younger and undergoing evolutionary expansion. Using western blotting we found all three stress proteins in cysts from these five populations in substantial although variable amounts. The protein profiles revealed by Coomassie staining after electrophoresis (SDS-PAGE) were similar qualitatively, in spite of marked differences in the habitats from which these populations originated, and the long time since they diverged. We interpret these findings as further evidence for the adaptive importance of these three conserved proteins in coping with the variable, but severe stresses these encysted embryos endure.     

Endocytic pathways of pathogenic protein aggregates in neurodegenerative diseases

Endocytosis is the fundamental uptake process through which cells internalize extracellular materials and species. Neurodegenerative diseases (NDs) are characterized by a progressive accumulation of intrinsically disordered protein species, leading to neuronal death. Misfolding in many proteins leads to various NDs such as Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), amyotrophic lateral sclerosis (ALS) and other disorders. Despite the significance of disordered protein species in neurodegeneration, their spread between cells and the cellular uptake of extracellular species is not entirely understood. This review discusses the major internalization mechanisms of the different conformer species of these proteins and their endocytic mechanisms. We briefly introduce the broad types of endocytic mechanisms found in cells and then summarize what is known about the endocytosis of monomeric, oligomeric and aggregated conformations of tau, Aβ, α-Syn, Huntingtin, Prions, SOD1, TDP-43 and other proteins associated with neurodegeneration. We also highlight the key players involved in internalizing these disordered proteins and the several techniques and approaches to identify their endocytic mechanisms. Finally, we discuss the obstacles involved in studying the endocytosis of these protein species and the need to develop better techniques to elucidate the uptake mechanisms of a particular disordered protein species.     

Identification and Characterization of the Major Proteins of Mammalian Brain Synaptic Vesicles

Highly purified rat and cow brain synaptic vesicles contain major proteins with molecular weights of approximately 74,000, 60,000, 57,000, 40,000, 38,000, and 34,000 by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The presence of the major proteins on synaptic vesicles was confirmed by immunoprecipitation of intact rat brain synaptic vesicles with a synaptic vesicle-specific monoclonal antibody. The 40,000-Mr protein appeared to be identical to the 38,000-Mr integral membrane glycoprotein, p38 or synaptophysin, previously identified as a major component of mammalian synaptic vesicles. The isoelectric point of the 75,000-Mr proteins from either rat or cow brain synaptic vesicles is 5.0, and the pI of the 57,000-Mr protein is approximately 5.1 in both species. The similarity in size and charge of several major proteins in rat and cow synaptic vesicles suggests a high degree of structure conservation of these proteins in diverse mammalian species and raises the possibility that a set of functions common to most or all mammalian synaptic vesicles is mediated by these proteins.     

Penicillin-binding proteins in Proteus species.

Penicillin-binding proteins in three species of Proteus, Proteus mirabilis, P. morganii, and P. rettgeri, were investigated by sodium dodecyl sulfate-polyacrylamide slab gel electrophoresis. Penicillin-binding proteins in these Proteus species were compared with those in Escherichia coli K-12. An approximate correlation between penicillin-binding proteins in E. coli and those in Proteus species was shown by several criteria: electrophoretic mobilities; affinities of several beta-lactam antibiotics which show characteristic patterns of binding to penicillin-binding proteins in E. coli; relation between affinities of antibiotics to the proteins and effects on morphological changes in Proteus species; location of beta-lactamase activity among penicillin-binding proteins; and thermostability. The electrophoretic mobilities and several other characteristics of penicillin-binding proteins among the Proteus species examined were found to be similar from species to species and differed only slightly from those of E. coli.     

Analysis of the protein composition of yeast ribosomal subunits by two-dimensional polyacrylamide gel electrophoresis

The number of proteins in yeast ribosomal subunits was determined by two-dimensional polyacrylamide gel electrophoresis. The 40S subunit obtained after dissociation of ribosomes at high ionic strength contains 30 different protein species (including six acidic proteins). The 60S subunit, obtained in the same way contains 39 different species (including 1 acidic protein). While the total number of protein species found in yeast ribosomes, thus, is in close agreement with those reported for other eukaryotic organisms, the distribution between acidic and basic proteins is quite different. When the ribosomes were dissociated at low ionic strength, four extra protein spots appeared in the electropherograms of both 40S and 60S subunits. We consider these proteins to be nonribosomal.     

The nature of the proteins present in the 'relaxed particles' from methionine-starved Escherichia coli A19 (Hfr rel met rns).

The 'relaxed particles' formed during methionine starvation of Escherichia coli A19 (Hfr rel met rns) have been isolated by large-scale rate-zonal density gradient ultracentrifugation. The proteins and rRNA species associated with these particles have been examined. The rRNA species present are precursor and mature forms of 16S and 23S rRNA. The bulk of the rRNA which accumulates during starvation is found within the particles. The proteins prepared directly from the particles give strong multiple immunoprecipitates with antisera specific to 30S and 50S ribosomal proteins. The soluble proteins, prepared and examined in the same manner, do not give this immunological reaction. Two-dimensional electrophoresis patterns of the proteins from the particles show that the proteins co-migrate with proteins from 30S and 50S ribosomes and are entirely dissimilar to the proteins prepared by the same methods from the soluble fraction of the cells. On the basis of these and other observations, it is concluded that the 'relaxed particles' are not artefacts but are arrested ribosome precursors containing both rRNA and certain ribosomal proteins. The free pool of ribosomal proteins is low in exponential-phase cells and is not significantly increased by a 2 h period of starvation for glucose. The implications of these observations concerning the proteins associated with 'relaxed' and 'chloramphenicol particles' are discussed in raltion to ribosome biogenesis and the stabilization of rRNA.     

Protein-protein interaction network-based detection of functionally similar proteins within species

Although functionally similar proteins across species have been widely studied, functionally similar proteins within species showing low sequence similarity have not been examined in detail. Identification of these proteins is of significant importance for understanding biological functions, evolution of protein families, progression of co-evolution, and convergent evolution and others which cannot be obtained by detection of functionally similar proteins across species. Here, we explored a method of detecting functionally similar proteins within species based on graph theory. After denoting protein-protein interaction networks using graphs, we split the graphs into subgraphs using the 1-hop method. Proteins with functional similarities in a species were detected using a method of modified shortest path to compare these subgraphs and to find the eligible optimal results. Using seven protein-protein interaction networks and this method, some functionally similar proteins with low sequence similarity that cannot detected by sequence alignment were identified. By analyzing the results, we found that, sometimes, it is difficult to separate homologous from convergent evolution. Evaluation of the performance of our method by gene ontology term overlap showed that the precision of our method was excellent.