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PubMed1992

The alpha/beta hydrolase fold.

We have identified a new protein fold--the alpha/beta hydrolase fold--that is common to several hydrolytic enzymes of widely differing phylogenetic origin and catalytic function. The core of each enzyme is similar: an alpha/beta sheet, not barrel, of eight beta-sheets connected by alpha-helices. These enzymes have diverged from a common ancestor so as to preserve the arrangement of the catalytic residues, not the binding site. They all have a catalytic triad, the elements of which are borne on loops which are the best-conserved structural features in the fold. Only the histidine in the nucleophile-histidine-acid catalytic triad is completely conserved, with the nucleophile and acid loops accommodating more than one type of amino acid. The unique topological and sequence arrangement of the triad residues produces a catalytic triad which is, in a sense, a mirror-image of the serine protease catalytic triad. There are now four groups of enzymes which contain catalytic triads and which are related by convergent evolution towards a stable, useful active site: the eukaryotic serine proteases, the cysteine proteases, subtilisins and the alpha/beta hydrolase fold enzymes.

Acetylcholinesterase↗
PubMed2003

Common Structural Cliques: a tool for protein structure and function analysis.

Proposed is a method for locating functionally relevant atoms in protein structures and a representation of spatial arrangements of these atoms allowing for a flexible description of active sites in proteins. The search method is based on comparison of local structure features of proteins that share a common biochemical function. The method does not depend on overall similarity of structures and sequences of compared proteins or on previous knowledge about functionally relevant residues. The compared protein structures are condensed to a graph representation, with atoms as nodes and distances as edge labels. Protein graphs are then compared to extract all possible Common Structural Cliques. These cliques are merged to create Structural Templates: graphs that describe structural analogies between compared proteins. Structures of serine endopeptidases were compared in pairs using the presented algorithm with different geometrical parameters. Additionally, a Structural Template was extracted from the structures of aminotransferases, two different proteins that catalyze the same type of chemical reaction. The results presented show that the method works efficiently even in the case of large protein systems and allows for extraction of common structural features from proteins catalyzing a particular chemical reaction, but that evolved from different ancestors by convergent evolution.

Algorithms↗
PubMedDate not supplied

Effect of a virus on accumulation of a tissue-specific cell-surface protein of the fungus Cryphonectria (Endothia) parasitica.

Hypovirulence and decreased sporulation of the plant pathogenic fungus Cryphonectria (Endothia) parasitica is caused by double-stranded (ds)RNAs. These symptoms of dsRNA infection are correlated with down-regulation of at least nine major fungal polypeptides. One of the regulated polypeptides was purified to homogeneity and antibody to it was prepared. This polypeptide (cryparin) has a -glycine-serine-repeating sequence near the amino-terminal end that is typical of structural proteins and has properties of a lectin. Antibody-staining showed that this 18.6-kDa polypeptide is specific to aerial hyphae and fruiting bodies and that it accumulates in large amounts on hyphal cell surfaces. The dsRNA affects accumulation of this protein, both in the fugal hyphae and in the growth medium. Cryparin is similar in physical properties to those of the putative phytotoxin cerato-ulmin produced by the Dutch elm disease fungus. Toxicity of cryparin is not detectable, but the striking similarities between the physical properties and locations of accumulation of cryparin and cerato-ulmin in fungal fruiting structures suggest either conservation of structure or convergent evolution in function of these two proteins.

Amino Acid Sequence↗
PubMed2001

Polymorphism of the polyketide synthase gene phID in biocontrol fluorescent pseudomonads producing 2,4-diacetylphloroglucinol and comparison of PhID with plant polyketide synthases.

Many biocontrol fluorescent pseudomonads can protect plants from soilborne fungal pathogens through production of the antifungal secondary metabolite 2,4-diacetylphloroglucinol (Phl). One of the phl biosynthetic genes, phlD, encodes a polyketide synthase similar to plant chalcone synthases. Here, restriction analysis of phlD from 39 Phl+ biocontrol fluorescent pseudomonads yielded seven different banding patterns. The gene was sequenced in seven strains, representing the different restriction patterns. Cluster analysis of phlD restriction data or phlD sequences indicated that phlD polymorphism was high, and two main clusters were obtained when predicted PhlD sequences were compared. When the seven PhlD sequences were studied with those of other procaryotic polyketide synthases (gram-positive bacteria) and plant chalcone synthases, however, Phl+ pseudomonads, gram-positive bacteria, and plants clustered separately. Yet, sequence analysis of active site regions for PhlD and plant chalcone synthases revealed that PhlD can be considered a member of the chalcone synthase family, which may be interpreted as convergent evolution of key enzymes involved in secondary metabolism. For the 39 Phl+ pseudomonads, a relationship was found among phlD restriction patterns, phylogenetic groups defined by 16S rDNA restriction analysis (confirmed by 16S rDNA sequencing), and production levels of Phl in vitro.

Acyltransferases↗
PubMed2003

How estrogen-specific proteins discriminate estrogens from androgens: a common steroid binding site architecture.

Steroid hormones play an essential role in a wide range of physiological and pathological processes, such as growth, metabolism, aging, and hormone-sensitive cancers. Estrogens are no exception and influence growth, differentiation, and functioning of many target tissues, such as the mammary gland, uterus, hypothalamus, pituitary, bone, and liver. Although very similar in structure, each steroid class (i.e., estrogens, androgens, progestins, mineral corticoids, or glucocorticoids) is responsible for distinct physiological processes. To permit specific biological responses for a given steroid class, specific proteins are responsible for steroid bioactivation, action, and inactivation, yet they have low or no affinity to other classes. Estrogens make no exception and possess their own set of related proteins. To understand the molecular basis underlying estrogen recognition from other steroids, structural features of estrogen-specific proteins were analyzed along with their ability to discriminate between steroid hormones belonging to different classes. Hence, the study of all estrogen-specific proteins for which an atomic structure has been determined demonstrated that a common steroid-binding pocket architecture is shared by these proteins. This architecture is composed of the following elements: i) a glutamate residue acting as a proton acceptor coupled with a proton donor that interact with the steroid O3; ii) a proton donor (His or Ser) that interacts with O17; iii) a highly conserved sandwich-like structure providing steric hindrance and preventing C19 steroid from binding; and iv) several amino acid residues interacting with the C18. As these different estrogen-specific proteins are not related in overall sequence, the inference is that the steroid binding site in these proteins has originated by convergent evolution.

17-Hydroxysteroid Dehydrogenases↗
PubMed2004

Novel phylogenetic relationships of the enigmatic brevicipitine and scaphiophrynine toads as revealed by sequences from the nuclear Rag-1 gene.

Owing to a general paucity of characters and an apparently high level of homoplasy, the systematics of frogs have remained disputed. A phylogeny based on the single-copy nuclear Rag-1 gene revealed unexpected placements of scaphiophrynine and brevicipitine toads. The former have usually been considered as sister group to all other extant microhylids or are even classified as a separate family. Their basal position among microhylids was weakly indicated in our analysis; but they clearly are part of a strongly supported clade composed of representatives from five other microhylid subfamilies. By contrast, the brevicipitines, a group that hitherto was unanimously considered to belong to the Microhylidae, were highly divergent and placed as a sister group to the arthroleptoid clade. These novel phylogenetic placements are best reflected by a classificatory status of the Scaphiophryninae as a subfamily of the Microhylidae, whereas the brevicipitines may merit recognition as a distinct family. Our findings seem to corroborate a high degree of morphological homoplasy in frogs and suggest that even highly derived morphological states, such as the hydrostatic tongue of microhylids, hemisotids and brevicipitines, may be subject to convergent evolution, parallelism or character reversal.

Animals↗
PubMed2006

An archaic crested plesiosaur in opal from the Lower Cretaceous high-latitude deposits of Australia.

Umoonasaurus demoscyllus gen. et sp. nov. is a new small-bodied (approx. 2.5m) pliosauroid plesiosaur from the Lower Cretaceous (Aptian-Albian) of southern Australia. It is represented by several partial skeletons (one with a near complete skull is the most complete opalized vertebrate fossil yet known), and is unique in having large crests on the skull midline and above the orbits. Umoonasaurus is surprisingly archaic despite its relatively late age (approx. 115 Myr ago)--being simultaneously the most basal (primitive) and last surviving rhomaleosaurid. Notably, it lacks the 'pliosauromorph' features (large head, short neck, gigantism) typically characterizing many more derived Jurassic rhomaleosaurids; thus, reinforcing the suspected convergent evolution of the 'pliosauromorph' hypercarnivore body plan. Umoonasaurus inhabited an Early Cretaceous high-latitude (approx. 70 degrees S) inland seaway subject to seasonally near-freezing climatic conditions. This extreme environment supported a diverse range of plesiosaur taxa, suggesting that these marine reptiles might have possessed adaptations (e.g. heightened metabolic levels) to cope with cold-water temperatures. Indeed, survival of ancient endemic lineages such as Umoonasaurus is a common phenomenon in Australian Cretaceous vertebrate assemblages and might have been facilitated by isolation in low-temperature high-latitude regions.

Animals↗
PubMed1979

Ultrastructure of graniferous tracheary elements in the haustorium of Exocarpus bidwillii, a root hemi-parasite of the Santalaceae.

The xylem in the body of the haustorium of E. bidwillii has the shape of an inverted conical flask with the expanded portion being known as the vascular core. The tracheary elements of the vascular core are notable for the occurrence of numerous granules within their lumina and the presence of mostly imperforate walls. Elsewhere in the haustorium graniferous tracheary elements are absent and the cells are usually ordinary vessel elements. Thin sections for transmission electron microscopy, post-stained in potassium permanganate, show that the secondary wall thickenings of the graniferous tracheary elements consist of eccentric layers in which the microfibrils of each successive layer run alternately longitudinally and transversely. The granules of the tracheary elements average 2 micrometer in diameter and consist of a homogeneous matrix which shows a fine fibrillar structure on high resolution. The granules are naked and mostly remain as separate structures within the lumen of the cell, but occasionally they fuse into small groups or irregular masses. In some cells the granules become transformed into fibrillar material that disperses throughout the lumen. This dispersed material may accumulate in vessels of the interrupted zone proximal to the vascular core. Occasionally, the granules also change into compacted amorphous masses that adhere to the walls of the cell. Ultrastructural cytochemistry confirms that the granules are protein and not starch as was originally believed for the Santalaceae. The function of the vascular core and its graniferous tracheary elements is discussed and we suggest that it might help regulate the pressure and flow of xylem sap entering the parasite from the host. Graniferous tracheary elements in the Santalaceae and in root parasites of the Serophulariaceae are compared and it is concluded that they represent examples of convergent evolution.

Histocytochemistry↗
PubMed1993

The molecular basis of a spectral shift in the rhodopsins of two species of squid from different photic environments.

The molecular basis of spectral tuning of rhodopsin pigments in two squid species is examined. The absorbance spectra of rhodopsin extracts from Alloteuthis subulata (lambda max 499 nm) showed a 5 nm red shift compared with Loligo forbesi (lambda max 494 nm). The rhodopsin gene sequence of A. subulata opsin was determined from polymerase chain reaction (PCR) amplified fragments by using genomic DNA as template. The deduced amino acid sequence was compared with that obtained from the previously published cDNA sequence of Loligo forbesi. A total of 22 amino acid differences are present, although only seven can be considered to be non-homologous substitutions. Three of these changes occur in helical transmembrane regions but only one, the substitution of phenylalanine by serine at site 270 in Alloteuthis subulata, involves the replacement of an apolar with a hydroxyl-bearing residue at a site located near the centre of helix VI and on the inner face of the retinal-binding pocket. The equivalent site is also used for the spectral tuning of primate cone pigments, an example of convergent evolution. It is proposed that substitution at this site is responsible for the 5 nm red shift. The relation between this spectral shift and the maximum depth distribution of Alloteuthis subulata of about 200 m, compared with about 360 m for Loligo forbesi, is discussed. An unexpected finding was that the rhodopsin gene of both species appears to lack introns.

Amino Acid Sequence↗
PubMed1997

Enigmatic phylogeny of skuas (Aves:Stercorariidae)

Multiple sources of evidence show that the skuas (Aves:Stercorariidae) are a monophyletic group, closely related to gulls (Laridae. On morphological and behavioural evidence the Stercorariidae are divided into two widely divergent genera, Catharacta and Stercorarius, consistent with observed levels of nuclear and mitochondrial gene divergence. Catharacta skuas are large-bodied and with one exception breed in the Southern Hemisphere. Stercorarius skuas otherwise known as jaegers) are smaller bodied and breed exclusively in the Northern Hemisphere. Evidence from both mitochondrial and nuclear genomes and from ectoparasitic lice (Insecta:Phthiraptera) shows that the Pomarine skua, S. pomarinus, which has been recognized as being somewhat intermediate in certain morphological and behavioural characteristics, is much more closely related to species in the genus Catharacta, especially to the Northern Hemisphere-breeding Great skua, C. skua, than it is to the other two Stercorarius skuas, the Arctic skua, S. parasiticus and the Longtailed skua, S. longicaudus. Three possible explanations that might account for this discordant aspect of skua phylogeny are explored. These involve (i) the segregation of ancestral polymorphism, (ii) convergent evolution of morphology and behaviour or (iii) inter-generic hybridization. The available evidence from both nuclear and mitochondrial genomes does not exclude any of these hypotheses. Thus, resolution of this enigma of skua phylogeny awaits further work.

Animals↗
PubMed2000

Polymorphic growth rates in myrmecophilous insects.

A polymorphism in growth rates was recently described affecting the larval development of the myrmecophilous butterfly Maculinea rebeli, spanning different years in a single insect population. The close integration of M. rebeli into the host ant colonies, facilitated by adaptations in behaviour and chemical mimicry, make extended larval development a successful strategy. Here we present additional data for M. rebeli and new data for Maculinea alcon (another cuckoo-feeding lycaenid) and the two myrmecophilous predators Maculinea arion and Microdon mutabilis (Diptera: Syrphidae). As predicted, M. alcon shows the same growth pattern as M. rebeli with a proportion of caterpillars developing in one year and the remainder over two years. This pattern holds in both northern and southern European populations, where M. alcon exploits different species of host. Against expectation, the same bimodal distribution of pre-pupation body weights, indicating one and two year developers, was found for the larvae of M. arion and M. mutabilis. As predators, both species are less closely integrated in their host ant colonies, suggesting that the polymorphism in growth rates is a more general adaptation to a myrmecophilous life style, arrived at by convergent evolution between the Maculinea and Microdon species. For predatory species we suggest that biennialism is an adaptation to the migratory behaviour of the host made possible by the predators' ability to fast over extended periods. We also hypothesize that M. arion represents an ancestral strategy in Maculinea butterflies and that the growth polymorphism might have become genetically fixed in the cuckoo-feeding species.

Animals↗
PubMed2001

Molecular evolutionary relationships between partulid land snails of the Pacific.

Adaptive radiation of partulid land snails in the tropical Pacific has produced an extraordinary array of distinctive morphological, ecological and behavioural types. Here we use part of the nuclear ribosomal RNA gene cluster to investigate the relationships within and between the three partulid genera, Partula, Samoana and Eua. The genera cluster separately, with Samoana and Partula forming monophyletic groups. With one exception, the molecular data generally support the previous generic classification based on genital morphology, even in species that show a number of characteristics otherwise atypical of the genus. Convergent evolution explains morphological similarities between members of different genera. The phylogeny suggests that Samoana has colonized the Pacific from west to east, originating in the area where Eua, believed to be the most ancient partulid genus, is found. An unexplained anomaly is the reported occurrence of a single species of Samoana in the Mariana Islands of the western Pacific. The genus Partula has a disjunct distribution, encompassing islands both to the east and west of the range occupied by Eua. Partula seems to have spread both eastward and westward after the splitting of the Partula lineage.

Animals↗
PubMed1994

Natural selection at the class II major histocompatibility complex loci of mammals.

The role of natural selection at major histocompatibility complex (MHC) loci was studied by analysis of molecular sequence data from mammalian class II MHC loci. As found previously for the class I MHC molecule and a hypothetical model of the class II molecule, the rate of non-synonymous nucleotide substitution exceeded that of synonymous substitution in the codons encoding the antigen recognition site of polymorphic class II molecules. This pattern is evidence that the polymorphism at these loci is maintained by a form of balancing selection, such as overdominant selection. By contrast, in the case of monomorphic class II loci, no such enhancement of the rate of non-synonymous substitution was observed. Phylogenetic analysis indicates that, in contrast to monomorphic ('non-classical') class I MHC loci, some monomorphic class II loci of mammals are quite ancient. The DMA and DMB loci, for example, diverged before all other known mammalian class II loci, possibly before the divergence of tetrapods from bony fishes. Analysis of the patterns of sharing of polymorphic residues at class II MHC loci by mammals of different species revealed that extensive convergent evolution has occurred at these loci; but no support was found for the hypothesis that MHC polymorphisms have been maintained since before the divergence of orders of eutherian mammals.

Animals↗
PubMed1996

Mitochondrial phylogeography of rock-dwelling cichlid fishes reveals evolutionary influence of historical lake level fluctuations of Lake Tanganyika, Africa.

The East African Lakes Tanganyika, Malawi and Victoria each harbour hundreds of endemic invertebrate and vertebrate species. Inferences about the ecological and evolutionary processes responsible for the origin of these species flocks will only be possible when they are made within historical and comparative frameworks. Specifically, the relative importance of intrinsic characteristics and extrinsic factors may offer information about the processes that drive diversification and speciation in these species. We investigated the sequence variation of a segment of the mitochondrial DNA control region of 32 populations representing all four nominal species in the three genera of eretmodine cichlids from Lake Tanganyika. Based on a phylogenetic analysis of these data we attempted to evaluate the importance of major lake level fluctuations on patterns of intralacustrine speciation. The geography of genetic variation reveals a high degree of within-lake endemism among genetically well-separated lineages distributed along the inferred shore lines of three historically intermittent lake basins. Seismic data indicate that extreme lowering of water levels in the Pleistocene caused the single Lake Tanganyika basin to split into three isolated ones. The strong phylogeographic structure of the Eretmodini, and the observation that some closely related populations occur on opposite shores of the lake, agree with this geological scenario. The three-clade-three-basin phylogeographic pattern was repeated twice within this tribe of cichlids. The phylogeographic pattern of eretmodine cichlids suggests that major fluctuations in the level of the lake have been important in shaping their adaptive radiation and speciation. The mitochondrially defined clades are in conflict with the current taxonomy of the group and suggest that there has been convergent evolution in trophic morphology, particularly in the shapes of oral teeth, taxonomically the most diagnostic characters of the three genera.

Age Factors↗
PubMed2003

Regulative germ cell specification in axolotl embryos: a primitive trait conserved in the mammalian lineage.

How germ cells are specified in the embryos of animals has been a mystery for decades. Unlike most developmental processes, which are highly conserved, embryos specify germ cells in very different ways. Curiously, in mouse embryos germ cells are specified by extracellular signals; they are not autonomously specified by maternal germ cell determinants (germ plasm), as are the germ cells in most animal model systems. We have developed the axolotl (Ambystoma mexicanum), a salamander, as an experimental system, because classic experiments have shown that the germ cells in this species are induced by extracellular signals in the absence of germ plasm. Here, we provide evidence that the germ cells in axolotls arise from naive mesoderm in response to simple inducing agents. In addition, by analysing the sequences of axolotl germ-cell-specific genes, we provide evidence that mice and urodele amphibians share a common mechanism of germ cell development that is ancestral to tetrapods. Our results imply that germ plasm, as found in species such as frogs and teleosts, is the result of convergent evolution. We discuss the evolutionary implications of our findings.

Ambystoma↗
PubMed1979

The strategy of infection as a criterion for phylogenetic relationships of non-coli phages morphologically similar to phage T7.

Five phages which are morphologically similar to coliphage T7 but attack other host bacteria have been compared to T7 and to its relative, T3, by the following criteria: (a) cross-reactivity with antisera against T7 and T3, (b) DNA base sequence homologies, as determined by the C0t technique, (c) synthesis of two phage-coded enzymes: RNA polymerase and SAMase, (d) patterns of phage-directed protein synthesis, as determined by SDS-polyacrylamide gel electrophoresis of phage coat subunits. As judged by all these criteria, Pseudomonas phage PX3 is not related to T7; thus, morphological similarity was attributed to convergent evolution. The other phages, i.e. Serratia phage IV, Psuedomonas phage gh-1, Citrobacter phage ViIII and Klebsiella phage No. 11, were considered to be related to T7 on the basis of similarities in the patterns of phage-coded proteins and because, early after infection, these phages induced, as T7 does, an RNA polymerase which specifically transcribes the DNA of thehomologous phage. Phages IV and No. 11 also induced the early synthesis of SAMase (previously only known to occur upon T3 infection). With the exception of phage IV, however, DNA base sequence homologies with T7 or T3 seem to be poor or non-existent. The tested phages, again with the exception of phage IV, did not react with antiserum against T3 or T7. It is concluded that a particular pattern of phage-directed protein synthesis (as characterized by polyacrylamide gel electrophoresis and enzyme tests) may provide evidence for phylogenetic relationships between phages, even in cases where other criteria, such as genetic recombination, serological cross-reaction, and DNA base sequence homologies, fail to indicate relatedness.

Adenosylmethionine Decarboxylase↗
PubMed1997

Role of p53 mutation in polyomavirus-induced tumorigenesis.

Small DNA tumour viruses, such as simian virus 40 (SV40), papilloma viruses and adenoviruses, encode proteins that form complexes with and inactivate the p53 and retinoblastoma (RB) proteins. This convergent evolution reflects the common need of these viruses to inactivate these two important regulators of cell cycle progression and cell survival. Polyomavirus, a close relative of SV40, is different. Its large T protein complexes only with RB, not with p53. We have examined whether this is compensated by the frequent appearance of p53 mutations in polyomavirus-induced tumours. We tested the p53 status of 15 polyomavirus-induced sarcomas. Two sarcomas were p53-negative while six carried mutant p53. Another six sarcomas expressed low levels of wild-type p53. One tumour expressed high levels of wild-type p53 protein as shown by DNA sequencing and immunofluorescence staining. MDM2 amplification was not detected in any of the tumours, but Northern blotting showed that MDM2 was overexpressed in at least two tumours that expressed wild-type p53 and in one tumour that expressed both wild-type and mutant p53. Treatment with the DNA-damaging agent mitomycin C caused p53 protein accumulation followed by induction of MDM2 and WAF1/p21 mRNA in four of the tumours expressing wild-type p53, indicating that p53-mediated transcriptional activation was unaltered in these tumours. However, p53-mediated transactivation of WAF1/p21 was impaired in the wild-type p53-expressing tumours that expressed elevated levels of MDM2. These results demonstrate that p53 mutation and inactivation are frequently but not invariably involved in polyomavirus-induced tumorigenesis.

Animals↗
PubMed2003

Missing links in the divergence of Chlamydophila abortus from Chlamydophila psittaci.

Pathological and serological evidence and DNA-DNA reassociation data indicate that Chlamydophila psittaci and Chlamydophila abortus are separate species. C. psittaci causes avian systemic disease and C. abortus causes abortion. Both previously belonged to Chlamydia psittaci are associated with zoonotic and enzootic outbreaks. Genetic studies suggest that they are closely related and because of the recent availability of diverse C. psittaci strains and comparative data for several genes, it was possible to explore this relationship. The parrot C. psittaci strain 84/2334 was found to have DNA sequences that were identical to an extrachromosomal plasmid in duck C. psittaci strain N352, to rnpB in strain R54 from a brown skua and to the rrn intergenic spacer in parakeet strain Prk/Daruma (from Germany, Antarctica and Japan, respectively). Analysis of ompA and the rrn spacer revealed progressive diversification of the strains, with 84/2334 resembling what might have been a recent ancestor of C. abortus. Another C. psittaci strain (VS225) showed evidence of having undergone convergent evolution towards the C. abortus-like genotype, whereas strain R54 diverged independently. For the first time, these studies link C. abortus in an evolutionary context to the C. psittaci lineage. It has been concluded that C. abortus diverged from C. psittaci, and so strain R54 was designated a C. psittaci strain. It is recommended that characterization of C. psittaci and C. abortus strains should utilize more than a single method and more than a single gene.

Abortion, Veterinary↗