Similar and divergent features in mammalian and yeast prions

Mammalian transmissible spongiform encephalopathies are likely due to the propagation of an abnormal form of a constitutive protein instead of traditional genetic material (nucleic acids). Such infectious proteins, which are termed prions, exist in yeast. They are at the origin of a number of phenotypes that are inherited in a non-Mendelian manner. These prions are very useful to dissect the molecular events at the origin of this structure-based inheritance. The properties of mammalian and yeast prions are presented and compared. This review highlights a number of similarities and differences.     

Four homologous domains in the primary structure of GrsB are related to domains in a superfamily of adenylate-forming enzymes

The entire nucleotide sequence of the Bacillus brevis grsB gene encoding the gramicidin S synthetase 2, which activates and condenses the four amino acids proline, valine, ornithine and leucine has been determined. The gene contains an open reading frame of 13,359 bp which encodes a protein of 4453 amino acids with a predicted Mr of 510,287. The gene is located within the gramicidin S biosynthetic operon, also containing the genes grsT and grsA, whose nucleotide sequences have been determined previously. Within the GrsB amino acid sequence four conserved and repeated domains of about 600 amino acids (45-50% identity) have been identified. The four domains are separated by non-homologous sequences of about 500 amino acids. The domains also share a high degree of similarity (20-70%) with eight peptide synthetases of bacterial and fungal origin as well as with conserved sequences of nine other adenylate-forming enzymes of diverse origin. On the basis of sequence homology and functional similarities, we infer that those enzymes share a common evolutionary origin and present a phylogenetic tree for this superfamily of domain-bearing enzymes.     

Sugars in hydrolysates of fungal melanins and soil humic acids

Humic acids from four Brazilian topsoils of different origin and four fungal melanins, synthesized under two cultural conditions were subjected to a two step hydrolysis procedure and the released monosaccharides qualitatively and quantitatively determined by gas-liquid chromatography. The neutral sugars, glucose, galactose, mannose, arabinose, xylose, fucose, rhamnose and the alcohol sugar inositol, were detected in most of the soil humic acid samples. The fungal melanins showed the presence of glucose, galactose, mannose and arabinose. Ribose was present in two out of the eight samples tested. Some quantitative differences in the two types of humic polymers were noted and expected considering their origins. However, similarities were more apparent than differences and give further indication that melanic fungi may play a significant role in the formation of soil humic acids.     

Enzymatic activity of albumin shown by coelenterazine chemiluminescence

Bioluminescence, the emission of light from live organisms, occurs in 18 phyla and is the major communication system in the deep sea. It has appeared independently many times during evolution but its origins remain unknown. Coelenterazine bioluminescence discovered in luminous jellyfish is the most common chemistry causing bioluminescence in the sea, occurring in seven phyla. Sequence similarities between coelenterazine luciferases and photoproteins from different phyla are poor (often < 5%). The aim of this study was to examine albumin that binds organic substances as a coelenterazine luciferase to test the hypothesis that the evolutionary origin of a bioluminescent protein was the result of the formation of a solvent cage containing just a few key amino acids. The results show for the first time that bovine and human albumin catalysed coelenterazine chemiluminescence consistent with a mono-oxygenase, whereas gelatin and haemoglobin, an oxygen carrier, had very weak activity. Insulin also catalysed coelenterazine chemiluminescence and was increased by Zn(2+). Albumin chemiluminescence was heat denaturable, exhibited saturable substrate characteristics and was inhibited by cations that bound these proteins and by drugs that bind to human albumin drug site I. Molecular modelling confirmed the coelenterazine binding site and identified four basic amino acids: lys195, arg222, his242 and arg257, potentially important in binding and catalysis similar to naturally occurring coelenterazine bioluminescent proteins. These results support the 'solvent cage' hypothesis for the evolutionary origin of enzymatic coelenterazine bioluminescent proteins. They also have important consequences in diseases such as diabetes, gut disorders and food intolerance where a mono-oxygenase could affect cell surface proteins.     

The Historical Factor: The Biosynthetic Relationships Between Amino Acids and Their Physicochemical Properties in the Origin of the Genetic Code

Two forces are in general, hypothesized to have influenced the origin of the organization of the genetic code: the physicochemical properties of amino acids and their biosynthetic relationships. In view of this, we have considered a model incorporating these two forces. In particular, we have studied the optimization level of the physicochemical properties of amino acids in the set of amino acid permutation codes that respects the biosynthetic relationships between amino acids. Where the properties of amino acids are represented by polarity and molecular volume we obtain indetermination percentages in the organization of the genetic code of approximately 40%. This indicates that the contingent factor played a significant role in structuring the genetic code. Furthermore, this result is in agreement with the genetic code coevolution hypothesis, which attributes a merely ancillary role to the properties of amino acids while it suggests that it was their biosynthetic relationships that organized the code. Furthermore, this result does not favor the stereochemical models proposed to explain the origin of the genetic code. On the other hand, where the properties of amino acids are represented by polarity alone, we obtain an indetermination percentage of at least 21.5%. This might suggest that the polarity distances played an important role and would therefore provide evidence in favor of the physicochemical hypothesis of genetic code origin. Although, overall, the analysis might have given stronger support to the latter hypothesis, this did not actually occur. The results are therefore discussed in the context of the different theories proposed to explain the origin of the genetic code. Received: 10 September 1996 / Accepted: 3 March 1997     

Floristic relationships among vegetation types of new zealand and the southern andes: similarities and biogeographic implications

Background and Aims

Similarities between the floras of geographically comparable regions of New Zealand (NZ) and the southern Andes (SA) have interested biologists for over 150 years. The present work selects vegetation types that are physiognomically similar between the two regions, compares their floristic composition, assesses the environmental factors that characterize these matching vegetation types, and determines whether phylogenetic groups of ancestral versus modern origin are represented in different proportions in their floras, in the context of their biogeographic history.

Methods

Floristic relationships based on 369 genera of ten vegetation types present in both regions were investigated with correspondence analysis (CA) and ascending hierarchical clustering (AHC). The resulting ordination and classification were related to the environmental characteristics of the different vegetation types. The proportions of different phylogenetic groups between the regions (NZ, SA) were also compared, and between forest and non-forest communities.

Key Results

Floristic similarities between NZ and SA tend to increase from forest to non-forest vegetation, and are highest in coastal vegetation and bog. The floras of NZ and SA also differ in their phylogenetic origin, NZ being characterized by an ‘excess’ of genera of basal origin, especially in forests.

Conclusions

The relatively low similarities between forests of SA and NZ are related to the former being largely of in situ South American and Gondwanan origin, whereas the latter have been mostly reconstituted though transoceanic dispersal of propagules since the Oligocene. The greater similarities among non-forest plant communities of the two regions result from varied dispersal routes, including relatively recent transoceanic dispersal for coastal vegetation, possible dispersal via a still-vegetated Antarctica especially for bog plants, and independent immigration from Northern Hemisphere sources for many genera of alpine vegetation and grassland.Key words: Biogeographic history, floristic similarities, generic composition, local floras, New Zealand, phylogenetic origin, southern Andes, vegetation types     

Fatty acid composition in deep hydrothermal vent symbiotic bivalves.

Fatty acids in deep hydrothermal vent bivalves have been analyzed. Their composition is completely different from that of a littoral mussel collected in the Mediterranean sea. The distribution of fatty acids in the littoral mussel is characterized by a predominance of polyunsaturated fatty acids (20:5n-3, 22:6n-3) reflecting the planktonic origin of the food. Vent bivalve fatty acid distribution is dominated by an abundance of the monounsaturated acids (double bond in the n-7 position) 16:1n-7, 18:1n-7, and 20:1n-7 which are clearly of bacterial origin and give an indication of the symbiotic bacterial activity in the bivalves. Differences between the fatty acid composition of the bivalves from two hydrothermal sites (13 degrees N and Galapagos) and differences between the mantle and the gill were observed and are discussed with respect to vent activities at the two sites and species metabolic capacities as a function of ecological conditions.     

Insulin-like growth factor (IGF) binding protein complementary deoxyribonucleic acid from human HEP G2 hepatoma cells: predicted protein sequence suggests an IGF binding domain different from those of the IGF-I and IGF-II receptors

The primary structure of an insulin-like growth factor (IGF) binding protein produced by human HEP G2 hepatoma cells has been deduced from the cDNA sequence. The 234 amino acid protein has a predicted molecular mass of 25,274 and contains a single, distinctive cysteine-rich region. The N-terminal sequence of this protein is quite similar to the limited sequence data available for a rat IGF binding protein produced by BRL-3A cells and suggests a common ancestral origin. In contrast, the HEP G2 IGF binding protein sequence bears no similarity to the N-terminal 15 amino acids of a 53 kilodalton binding protein purified from human plasma. Comparison of full-length protein sequences for the IGF-I and IGF-II receptors with that of the HEP G2 IGF binding protein also fails to demonstrate any significant similarities among these three proteins, and suggests that each contains a unique binding domain for the IGF peptides.     

Evolution of sialic acid-binding proteins: molecular cloning and expression of fish siglec-4

Siglecs are the largest family of sialic acid-recognizing lectins identified so far with 11 members in the human genome. Most of these siglecs are exclusively expressed by cells of the immune system. Comparison of different mammalian species has revealed differential and complex evolutionary paths for this protein family, even within the primate lineage. To understand the evolution of siglecs, in particular the origin of this family, we investigated the occurrence of corresponding genes in bony fish. Interestingly, only unambiguous orthologs of mammalian siglec-4, a cell adhesion molecule expressed exclusively in the nervous system, could be identified in the genomes of fugu and zebrafish, whereas no obvious orthologs of the other mammalian siglecs were found. As in mammals, fish siglec-4 expression is restricted to nervous tissues as demonstrated by northern blot. Expressed as recombinant protein, fish siglec-4 binds to sialic acids with a specificity similar to the mammalian orthologs. Relatively low sequence similarities in the cytoplasmic tail as well as an additional splice variant found in fish siglec-4 suggest alternative signaling pathways compared to mammalian species. Our observations suggest that this siglec occurs at least in the nervous system of all vertebrates.     

Striking structural and functional similarities suggest that intestinal sucrase-isomaltase, human lysosomal alpha-glucosidase and Schwanniomyces occidentalis glucoamylase are derived from a common ancestral gene.

Sequence comparison of the primary structure of the yeast Schwanniomyces occidentalis glucoamylase (GAM) with GAMs in different microorganisms did not reveal significant similarities. By contrast, striking similarities were, surprisingly, found with 3 mammalian secretory and integral membrane proteins: the 2 subunits of intestinal brush border sucrase-isomaltase and human lysosomal alpha-glucosidase. The similarities among these proteins are found as clusters of up to 8 amino acids and distributed all over the protein sequences. The major sequence differences are found in the N-terminal regions accounting, probably, for the different cellular locations of these proteins. The high level of similarities between sucrase, isomaltase, Sch. occidentalis GAM and human lysosomal alpha-glucosidase suggest that these proteins are derived from the same ancestral gene. To our knowledge, this is the first report that describes similarities between a yeast secretory protein and mammalian secretory and integral membrane proteins.     

Extracting Hydrogen-Bond Signature Patterns from Protein Structure Data

Classification of protein sequences and structures into families is a fundamental task in biology, and it is often used as a basis for designing experiments for gaining further knowledge. Some relationships between proteins are detected by the similarities in their sequences, and many more by the similarities in their structures. Despite this, there are a number of examples of functionally similar molecules without any recognisable sequence or structure similarities, and there are also a number of protein molecules that share common structural scaffolds but exhibit different functions. Newer methods of comparing molecules are required in order to detect similarities and dissimilarities in protein molecules. In this article, it is proposed that the precise 3-dimensional disposition of key residues in a protein molecule is what matters for its function, or what conveys the "meaning" for a biological system, but not what means it uses to achieve this. The concept of comparing two molecules through their intramolecular interaction networks is explored, since these networks dictate the disposition of amino acids in a protein structure. First, signature patterns, or fingerprints, of interaction networks in pre-classified protein structural families are computed using an approach to find structural equivalences and consensus hydrogen bonds. Five examples from different structural classes are illustrated. These patterns are then used to search the entire Protein Data Bank, an approach through which new, unexpected similarities have been found. The potential for finding relationships through this approach is highlighted. The use of hydrogen-bond fingerprints as a new metric for measuring similarities in protein structures is also described.     

Genetic and molecular investigations on the endogenous mobile elements of non-drosophilid fruitflies

A syndrome of abnormal genetic effects, resembling Drosophila hybrid dysgenesis, occurs in Ceratitis capitata when strains of different origin are mated. The pattern of abnormal traits observed appears to be the phenotypic expression of a complex interacting dysgenic system of inducer and suppressor effects; probably more than one system is activated in the crosses. This suggests that different systems of mobile elements occur in different strains and populations of C. capitata. Using a PCR primer specific to the ITR sequence of a deleted element, full length mariner elements were isolated from C. capitata, Ceratitis rosa, and Trirhithrum coffeae. Very high similarities were found in inter- and intraspecific comparisons of the elements. The majority of these elements contained deletions and frame-shifts. However, one clone Ccmar1.18, from C. capitata, was found to possess an uninterrupted ORF coding for 338 amino acids with ∼60% similarity to the Mos1 element of Drosophila mauritiana. Database searches and phylogenetic analyses showed that the mariner elements isolated in the present study are representatives of Robertson's mellifera mariner subfamily. The copy numbers of the elements within each species are very different, ranging from about 10 in T. coffeae to 5000 in C. rosa. This revised version was published online in August 2006 with corrections to the Cover Date.     

Conservation of average hydrophobicity of apolar aminoacids in polypeptides constituting same glycosyl hydrolase sub-family enzymes

Polypeptides constituting the same functional enzyme in cells of different origins have small sequence similarities among themselves. Amino acid analysis reveals that each glycosyl hydrolase sub-family polypeptides conserves an average hydrophobicity value for total constituent apolar amino acids. The value may be a measure of the driving force present in the polypeptide for designed primary collapse for three-dimensional active site formation.     

The determination of similarities in amino acid composition among proteins separated by two-dimensional gel electrophoresis

A simple and rapid procedure has been developed to determine similarities in amino acid composition among cellular proteins separated by two-dimensional gel electrophoresis. Cells in tissue culture are simultaneously labeled with two different amino acids each tagged with a different radioisotope. The proteins are then separated on two-dimensional gels and their location on the gels determined by Coomassie-blue staining or autoradiography. Elution of the protein from the appropriate region of the gel followed by liquid scintillation counting yields an isotope ratio which reflects the ratio of the two amino acids in the protein. Examples of the use of this technique in analyzing mutant proteins, proteins altered by carbamylation, and cell proteins with similar amino acid composition (e.g., actin and tubulin) are given.     

Meiosis: inducing variation by reduction

A brief introduction is presented with some thought on the origin of meiosis. Subsequently, a sequential overview of the diverse processes that take place during meiosis is provided, with an eye to similarities and differences between the different eukaryotic systems. In the final part, we try to summarize the available core meiotic mutants and make a comprehensive comparison for orthologous genes between fungal, plant, and animal systems.     

Segmentation

The three major taxa with metameric segmentation (annelids, arthropods, and chordates) appear to use three very different molecular strategies to generate segments. However, unexpected similarities are starting to emerge from characterization of pair-rule patterning and segmental border formation. Moreover, the existence of an ancestral segmentation clock based on Notch signaling has become likely. An old concept of comparative anatomy, the enterocoele theory, is compatible with a single origin of segmentation mechanisms and could therefore provide a conceptual framework for assessing these molecular similarities.     

Helical Antifreeze Proteins Have Independently Evolved in Fishes on Four Occasions

Alanine-rich α-helical (type I) antifreeze proteins (AFPs) are produced by a variety of fish species from three different orders to protect against freezing in icy seawater. Interspersed amongst and within these orders are fishes making AFPs that are completely different in both sequence and structure. The origin of this variety of types I, II, III and antifreeze glycoproteins (AFGPs) has been attributed to adaptation following sea-level glaciations that occurred after the divergence of most of the extant families of fish. The presence of similar types of AFPs in distantly related fishes has been ascribed to lateral gene transfer in the case of the structurally complex globular type II lectin-like AFPs and to convergent evolution for the AFGPs, which consist of a well-conserved tripeptide repeat. In this paper, we examine the genesis of the type I AFPs, which are intermediate in complexity. These predominantly α-helical peptides share many features, such as putative capping structures, Ala-richness and amphipathic character. We have added to the type I repertoire by cloning additional sequences from sculpin and have found that the similarities between the type I AFPs of the four distinct groups of fishes are not borne out at the nucleotide level. Both the non-coding sequences and the codon usage patterns are strikingly different. We propose that these AFPs arose via convergence from different progenitor helices with a weak affinity for ice and that their similarity is dictated by the propensity of specific amino acids to form helices and to align water on one side of the helix into an ice-like pattern.     

DNA methylation: evolution of a bacterial immune function into a regulator of gene expression and genome structure in higher eukaryotes

The amino acid sequence of mammalian DNA methyltransferase has been deduced from the nucleotide sequence of a cloned cDNA. It appears that the mammalian enzyme arose during evolution via fusion of a prokaryotic restriction methyltransferase gene and a second gene of unknown function. Mammalian DNA methyltransferase currently comprises an N-terminal domain of about 1000 amino acids that may have a regulatory role and a C-terminal 570 amino acid domain that retains similarities to bacterial restriction methyltransferases. The sequence similarities among mammalian and bacterial DNA cytosine methyltransferases suggest a common evolutionary origin. DNA methylation is uncommon among those eukaryotes having genomes of less than 10(8) base pairs, but nearly universal among large-genome eukaryotes. This and other considerations make it likely that sequence inactivation by DNA methylation has evolved to compensate for the expansion of the genome that has accompanied the development of higher plants and animals. As methylated sequences are usually propagated in the repressed, nuclease-insensitive state, it is likely that DNA methylation compartmentalizes the genome to facilitate gene regulation by reducing the total amount of DNA sequence that must be scanned by DNA-binding regulatory proteins. DNA methylation is involved in immune recognition in bacteria but appears to regulate the structure and expression of the genome in complex higher eukaryotes. I suggest that the DNA-methylating system of mammals was derived from that of bacteria by way of a hypothetical intermediate that carried out selective de novo methylation of exogenous DNA and propagated the methylated DNA in the repressed state within its own genome.(ABSTRACT TRUNCATED AT 250 WORDS)     

Inducing effect of plant cells on nitrogenase activity by Spirillum and Rhizobium in vitro

Eleven different plant cell tissue cultures of both legume and non-legume origin have been grown in direct association, and in separate but close proximal association with both Spirillum lipoferum and Rhizobium sp. 32H1. Basic similarities were found in the nutritional requirement for the induction of nitrogenase activity (C2H2) in both organisms. In the absence of plant cell cultures both organisms need to be provided with a pentose sugar and a tricarboxylic acid to induce high levels of nitrogen-fixing activity. Plant cell callus tissue appears only capable of supplying the tricarboxylic acid to induce high levels of nitrogen-fixing activity. Plant cell callus tissue appears only capable of supplying the tricarboxylic acids needed but not the sugar component. The plant tissue, however, seems able to activate certain carbohydrates, which in themselves are incapable of substituting for the pentose additive.