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PubMed2001

Multiple causation of phylogeographical pattern as revealed by nested clade analysis of the bamboo viper (Trimeresurus stejnegeri) within Taiwan.

In order to assess the utility of nested clade analysis, both standard phylogenetic algorithms and nested clade analysis were performed on a geographically widespread survey of mitochondrial DNA haplotypes of the bamboo viper, Trimeresurus stejnegeri, within Taiwan. Gross tree topologies were congruent for all analyses and indicated the presence of two geographically overlapping clades within Taiwan. The smaller lineage was restricted to the north and east coasts, whereas the larger lineage occupied all but the northern range of the species within Taiwan including the Pacific offshore populations of Green and Orchid Islands. The phylogeographical pattern supports the existence of at least one colonization event from the continent since the initial isolation of Taiwan from the mainland in the Pliocene. However, determining the exact number of colonization events was not possible due to the simultaneous vicariant forces of hypothesized continental landbridge connections and the occurrence of dramatic in situ orogenesis throughout the Pleistocene. Nested clade analysis provided multiple temporal and spatial population historical inferences that are not possible with standard analyses and therefore should become widely applied to future phylogeographical studies.

Animals↗
PubMed2001

The use of amplified fragment length polymorphism in determining species trees at fine taxonomic levels: analysis of a medically important snake, Trimeresurus albolabris.

There are a huge number of phylogenetic studies based on mitochondrial DNA (mtDNA); however, these may represent gene trees that may not be congruent with the species tree. A solution to this problem is to include additional, independent, loci from the nuclear genome. At fine taxonomic levels, i.e. between populations and closely related species, previously suggested nuclear markers such as intron sequence data may not be appropriate. In this study we investigate the use of amplified fragment length polymorphisms (AFLP) to aid determination of the species tree for 24 specimens of a medically important snake, Trimeresurus albolabris. This is of particular importance for many venomous snakes as venom often varies intraspecifically. Five different primer combinations produced 434 bands and were analysed by constructing a phylogenetic tree using neighbour joining and principal component analysis. Results were similar across all methods and found distinct groupings. The results were compared with mtDNA data and a reconciled tree was constructed in order to determine the species tree for T. albolabris. We found that T. albolabris (sensu lato) is not monophyletic. Specimens from the Indonesian islands (except West Java) form a distinct clade and we propose elevation to species level. A specimen from Nepal is also distinct and suggests that this population also deserves specific status. We suggest that AFLPs may prove a valuable aid in determining species trees as opposed to gene trees at fine taxonomic levels and this should facilitate the incorporation of molecular data into such activities as antivenom production and conservation management.

Animals↗
PubMed2004

The utility of AFLPs for supporting mitochondrial DNA phylogeographical analyses in the Taiwanese bamboo viper, Trimeresurus stejnegeri.

An amplified fragment length polymorphism (AFLP) assay was performed on individuals representing discrete haplotypes from two genetically distinct mtDNA lineages of the bamboo viper, Trimeresurus stejnegeri (Schmidt), within Taiwan. AFLP (525 polymorphic markers from five primer pairs) and mtDNA genetic distances were highly correlated and an analysis of molecular variance, and a Bayesian approach similarly partitioned estimates of genetic similarity according to the mtDNA phylogeographical pattern. These results are discussed in relation to biogeographical hypotheses, comparative rates of mtDNA molecular evolution, and in the identification of evolutionary significant units of Taiwanese T. stejnegeri. In spite of the high degree of congruence between the genetic datasets, the AFLP phylogenetic analysis did not support the mtDNA tree, suggesting that no contemporary barriers to gene flow exist between individuals from the two mtDNA lineages.

Analysis of Variance↗
PubMed2001

Purification, cDNA cloning and characterization of the vascular apoptosis-inducing protein, HV1, from Trimeresurus flavoviridis.

Hemorrhagic snake venom induces apoptosis in vascular endothelial cells (VEC). In previous reports, we described the purification and cDNA cloning from Crotalus atrox of a vascular apoptosis-inducing protein (VAP1) that specifically induces apoptosis in vascular endothelial cells. We report here the purification and cDNA cloning of another vascular apoptosis-inducing protein, HV1, from crude venom of Trimeresurus flavoviridis. The protein, namely HV1, was purified as an inducer of apoptosis in cultured vascular endothelial cells. HV1 was a homodimeric protein with a molecular mass of 110 kDa. HV1 cDNA encoded a protein with 612 amino-acid residues. The amino-acid sequence predicted from the cDNA was highly homologous to VAP1. The amino-acid sequence of HV1 indicated that HV1 belongs to the metalloprotease/disintegrin family, and that it is a multidomain polypeptide with a proprotein domain, a metalloprotease domain, a disintegrin-like domain and a cysteine-rich domain. In the disintegrin-like domain, the sequence DECD, replaces the RGD sequence that has frequently been found in such domains. This replacement also occurs in VAP1. Our results indicate HV1 as the first identified homolog of VAP1.

Amino Acid Sequence↗
PubMed2005

cDNA cloning and functional expression of jerdostatin, a novel RTS-disintegrin from Trimeresurus jerdonii and a specific antagonist of the alpha1beta1 integrin.

Jerdostatin represents a novel RTS-containing short disintegrin cloned by reverse transcriptase-PCR from the venom gland mRNA of the Chinese Jerdons pit viper Trimeresurus jerdonii. The jerdostatins precursor cDNA contained a 333-bp open reading frame encoding a signal peptide, a pre-peptide, and a 43-amino acid disintegrin domain, whose amino acid sequence displayed 80% identity with that of the KTS-disintegrins obtustatin and viperistatin. The jerdostatin cDNA structure represents the first complete open reading frame of a short disintegrin and points to the emergence of jerdostatin from a short-coding gene. The different residues between jerdostatin and obtustatin/viperistatin are segregated within the integrin-recognition loop and the C-terminal tail. Native jerdostatin (r-jerdostatin-R21) and a R21K mutant (r-jerdostatin-K21) were produced in Escherichia coli. In each case, two conformers were isolated. One-dimensional (1)H NMR showed that conformers 1 and 2 of r-jerdostatin-R21 represent, respectively, well folded and unfolded proteins. The two conformers of the wild-type and the R21K mutant inhibited the adhesion of alpha(1)-K562 cells to collagen IV with IC(50) values of 180 and 703 nm, respectively. The IC(50) values of conformers 2 of r-jerdostatin-R21 and r-jerdostatin-K21 were, respectively, 5.95 and 12.5 microm. Neither r-jerdostatin-R21 nor r-jerdostatin-K21 showed inhibitory activity toward other integrins, including alpha(IIb)beta(3), alpha(v)beta(3), alpha(2)beta(1), alpha(5)beta(1), alpha(4)beta(1), alpha(6)beta(1), and alpha(9)beta(1) up to a concentration of 24 mum. Although the RTS motif appears to be more potent than KTS inhibiting the alpha(1)beta(1) integrin, r-jerdostatin-R21 is less active than the KTS-disintegrins, strongly suggesting that substitutions outside the integrin-binding motif and/or C-terminal proteolytic processing are responsible for the decreased inhibitory activity.

Amino Acid Sequence↗
PubMed2003

Assessing the phylogenetic utility of four mitochondrial genes and a nuclear intron in the asian pit viper genus, Trimeresurus: separate, simultaneous, and conditional data combination analyses.

A number of methods have been proposed for addressing how to optimize the analysis of multiple data sets from diverse mitochondrial and nuclear gene partitions in the pursuit of robust organismal phylogenies. The present study used separate, simultaneous, and conditional data combination methods to analyze 3,135 bp of data from four mitochondrial partitions and the seventh intron of the beta fibrinogen gene in the Asian pit viper genus, Trimeresurus sensu stricto. The phylogenetic utility and homogeneity of all partitions were estimated via a combination of homogeneity partition tests, homoplasy indices, and partitioned Bremer support. Despite the detection of significant heterogeneity of phylogenetic signal between the mitochondrial and nuclear partitions, the simultaneous analysis represented the best-supported topology of all the data. The relatively slow rate (approximately one quarter of the rate of mtDNA) and functionally unconstrained molecular evolution of the intron resulted in much lower levels of homoplasy compared with the mitochondrial partitions. This was further shown via partitioned Bremer support, which, when considered throughout hierarchical clade levels, highlighted the phylogenetic strength and limitations of the intron at deeper and shallower phylogenetic levels, respectively. The simultaneous analysis helped to resolve the phylogenetic relationships of taxa that were unresolved throughout all individual gene trees and tentatively supports the existence of morphologically and genetically distinct clades within the genus. Topological appraisals of the mitochondrial gene partitions suggest that the cytochrome b and the NADH subunit 4 gene partitions are better estimators of phylogenetic relationships than are the 12S and 16S ribosomal RNA partitions at the taxonomic levels under consideration.

Animals↗
PubMed1996

Crystal structure of H2-proteinase from the venom of Trimeresurus flavoviridis.

The crystal structure of the zinc-protease, H2-proteinase, isolated from the venom of Trimeresurus flavoviridis has been determined. The crystallographic R factor is 0.176 for 10,635 reflections with Fobs > 2sigma(Fobs) in the 8.0 to 2.2 Angstrom resolution range. The enzyme has two domains with a cleft in which a catalytic zinc atom is located. The N-terminal domain is composed of four helices around a central five-stranded beta-sheet. The irregularly folded C-terminal domain contains one helix and two disulfide bridges. These two domains are linked by a disulfide bridge. In the zinc environment, the catalytic zinc atom forms a distorted tetrahedral coordination with three histidines and one catalytic water molecule, and the methionine-containing turn is structurally conserved. These are distinctive features of the metzincins, one of the zinc metalloprotease superfamilies. The entire structure shows good agreement with that of two Crotalus snake venom proteases, adamalysin II and atrolysin C. The H2-proteinase, however, contains no structural calcium ions, and differences of disulfide configurations and the coordination of the catalytic water molecule exist as compared with the other two proteases.

Amino Acid Sequence↗
PubMed2000

Isolation and characterization of pepsinogen from Trimeresurus flavoviridis (Habu snake).

Pepsinogen was isolated from the gastric mucosa of Trimeresurus flavoviridis (Habu snake) by DEAE-cellulose and DEAE-Sepharose ion-exchange chromatographies, and Sephacryl S-200 gel-chromatography. The yield calculated from the crude extract was 29% with 6.2-fold purification. The purified pepsinogen gave a single band on both native- and SDS-PAGE. As no other active enzyme was detected on the chromatographies, it was concluded that the Habu snake has one major pepsinogen. The molecular mass of the pepsinogen was estimated to be 38 kDa by SDS-PAGE. The sequence of the N-terminal 26 amino acid residues was determined and compared with those of other pepsinogens. The N-terminal structure of Habu snake pepsinogen was more homologous with those of mammalian pepsinogens C than those of mammalian pepsinogens A. The pepsinogen was rapidly converted to pepsin by way of an intermediate form induced by acidification. The optimum pH of Habu snake pepsin for bovine hemoglobin was 1.5-2.0, and it retained full activity at pH 6.2 and 30 degrees C on incubation for 30 min. The optimum temperature for the snake pepsin was 50 degrees C and it was stable at 40 degrees C on incubation for 10 min. The proteolytic activity of the pepsin toward bovine hemoglobin was about two times higher than that of porcine pepsin A, however, the activity toward oxidized bovine insulin B-chain was lower than that of porcine pepsin A, and it did not hydrolyze oligopeptides. The specificity for oxidized bovine insulin B-chain of the pepsin was different from that of porcine pepsin A. Habu snake pepsin was inhibited by pepstatin A but not by serine, cysteine, or metallo protease inhibitors.

Amino Acid Sequence↗
PubMed1995

Crystal structure analysis of phospholipase A2 from trimeresurus flavoviridis (Habu snake) venom at 1.5 A resolution.

The crystal structure of dimeric phospholipase A2 (PLA2) from the venom of Habu snake, Trimeresurus flavoviridis, has been determined by the molecular replacement method, and has been refined at 1.5 A resolution to an R-factor of 0.175. In the crystal, T. flavoviridis PLA2 forms a dimer using two 14 kDa subunits related by a pseudo 2-fold axis. Along the axis, the dimer has a narrow channel passing through it. Although no calcium ion is present in the calcium binding site, the peptide-chain folding of the subunits, the conformation of the catalytic residues, and the hydrogen-bonding network around the active sites are almost identical to those of the group I/II monomeric or dimeric PLA2s. The catalytic residues in both subunits are buried in the interior of the dimer and are inaccessible to substrate from the bulk solvent. In addition, the subunits of the dimer interact with each other at the hydrophobic region of the molecular surface where the entrance to the active site opens and where PLA2 is presumed to interact with the phospholipid of the substrate. Therefore, it is inferred that dimerization of T. flavoviridis PLA2 is the result of free-energy minimization by excluding the hydrophobic molecular surface from the aqueous solvent, rather than being required for the enzymatic function.

Amino Acid Sequence↗
PubMed1995

Crystallization and preliminary X-ray study of H2-proteinase from the venom of Trimeresurus flavoviridis.

H2-proteinase, a non-hemorrhagic metalloproteinase from the venom of Trimeresurus flavoviridis, has been crystallized by vapor diffusion from solutions containing ammonium sulfate. The crystals belong to the tetragonal space group, P41212 or P43212, with unit cell dimensions of a = b = 77.8 A and c = 82.3 A. The asymmetric unit contains one protein molecule. Diffraction data for a native crystal were collected up to 2.0 A resolution.

Animals↗
PubMed2004

Purification, partial characterization, crystallization and preliminary X-ray diffraction of two cysteine-rich secretory proteins from Naja atra and Trimeresurus stejnegeri venoms.

Cysteine-rich secretory proteins (CRISPs) are widely distributed in mammals and snake venoms. They possess apparent homology but varying functions. The structure of CRISPs has remained elusive. Two novel members of the family, natrin and stecrisp, have been purified from Naja atra and Trimeresurus stejnegeri venoms, respectively. Their crystals diffract X-rays to resolution limits of 2.1 and 1.6 angstroms, respectively, and belong to the orthorhombic system with different space groups, unit-cell parameters and numbers of molecules per asymmetric unit. Their structures will contribute a structural basis for further functional studies of this family.

Amino Acid Sequence↗
PubMed2004

Ecological diversification in a group of Indomalayan pitvipers (Trimeresurus): convergence in taxonomically important traits has implications for species identification.

We analyse molecular and phenotypic evolution in a group of taxonomically problematic Indomalayan pitvipers, the Trimeresurus sumatranus group. Mitochondrial DNA sequencing provides a well-resolved phylogeny, with each species representing a distinct lineage. Multivariate morphological analysis reveals a high level of phenotypic differentiation, which is congruent between the sexes but does not reflect phylogenetic history. An adaptive explanation for the observed pattern of differentiation is supported by independent contrasts analysis, which shows significant correlations between current ecology and the characters that most account for the variation between taxa, including those that are presently used to identify the species. Reduced precipitation and altitude, and increased temperature, are correlated with higher numbers of scales on the head, body and tail. It is hypothesized that scale number plays an important role in heat and water exchange by influencing the area of exposed of interstitial skin, and that colour pattern variation reflects selection pressures involving camouflage and thermoregulation. Ecological convergence in traits used for classification is found to have important implications for species identification where taxa are distributed over varying environments.

Animals↗
PubMed1994

Binding properties of the coagulation factor IX/factor X-binding protein isolated from the venom of Trimeresurus flavoviridis.

The binding properties of the coagulation factor IX/factor X-binding anticoagulant protein (IX/X-bp) isolated from the venom of Trimeresurus flavoviridis (habu snake) were investigated with an enzyme-linked immunosorbent assay. The half-maximal binding and maximal binding of IX/X-bp to both factors IX and X were observed at concentrations of Ca2+ ions of 0.4 mM and 1 mM, respectively. Concentration of IX/X-bp at half-maximal binding to solid-phase bovine factor IX and solid-phase bovine factor X were 0.4 +/- 0.1 nM and 1.1 +/- 0.4 nM, respectively, in the presence of 1 mM Ca2+ ions. The kinetics of binding activity of IX/X-bp to bovine factors IXa and Xa and to human factors IX and X resembled those of the binding to bovine factors IX and X. IX/X-bp did not bind to solid-phase coagulation factors other than factor IX/IXa and factor X/Xa, for example, prothrombin, factor VII, protein C, and protein Z, under the conditions of the experiment. To localize the binding sites of IX/X-bp on the coagulation factors, the ability of IX/X-bp to bind to various fragments derived from factors IX and X was examined. The binding of IX/X-bp to solid-phase factor IX was inhibited by a peptide containing the 4-carboxyglutamic acid (Gla) domain derived from factor IXa beta' (residues 1-42) in the liquid phase, but the binding was not inhibited by Gla-domainless factor IXa beta'. Half-maximal binding of IX/X-bp to solid-phase Gla-domain peptide of factor IX occurred at 9.2 +/- 1.9 nM. Factor X was partially reduced and the S-carboxymethylated light and heavy chains of factor X were prepared. IX/X-bp bound to the S-carboxymethylated light chain of factor X but not to the heavy chain. The binding of IX/X-bp to solid-phase factor X was inhibited by the Gla-domain peptide of factor X (residues 1-44) but not by Gla-domainless factor X. IX/X-bp bound to PCGFX, a recombinant human protein C whose Gla-domain region (residues 1-43) had been replaced by residues 1-43 of human factor X. The affinity of binding was about one tenth of that to intact human factor X. IX/X-bp was unable to bind at all to human protein C. These data indicate that IX/X-bp is a protein that binds to the Gla-domain regions of factors IX and X in the presence of Ca2+ ions.

Animals↗
PubMed1997

Characterization and evolution of a gene encoding a Trimeresurus flavoviridis serum protein that inhibits basic phospholipase A2 isozymes in the snake's venom.

The proteins that bind phospholipase A2 (PLA2) isozymes of Trimeresurus flavoviridis (habu snake, crotalinae) venom were fractionated from sera on four columns, each conjugated with one of four PLA2 isozymes. Five proteins, termed PLA2 inhibitors (PLI) I-V, were obtained as the binding components. The combinations of the binding components differed depending on the PLA2 isozymes. PLI-IV and PLI-V correspond to PLI-A and PLI-B, respectively, which were known to bind to a major [Asp49]PLA2, PLA2, and contained a segment similar to the carbohydrate-recognition domain of C-type lectins. PLI-I, which is a major component of inhibitory proteins against three basic PLA2 isozymes, PLA-B (a basic [Asp49]PLA2) and basic proteins I and II (both [Lys49]PLA2s), has been isolated, and its partial amino acid sequence has been determined. A cDNA encoding PLI-I was isolated from a T. flavoviridis liver cDNA library and sequenced. PLI-I cDNA encoded 200 amino acid residues, including a signal peptide of 19 amino acid residues. One sugar chain was predicted to occur at position 157. A gene coding for PLI-I was isolated. It is 9.6-kb long and consists of five exons and four introns. Comparison of the exon-intron structure of the PLI-I gene with those of genes encoding urokinase-type-plasminogen-activator receptor (uPAR), Ly-6, CD59 and neurotoxins showed that they have characteristic unit encoding approximately 90 amino acid residues, which is divided over two exons. This strongly suggests that the PLI-I gene belongs to the uPAR, Ly-6, CD59 and neurotoxin gene family. There are two types of structurally different inhibitors against PLA2 isozymes in T. flavoviridis serum with different evolutionary origins.

Amino Acid Sequence↗
PubMed1999

Himehabu lectin, a novel inducer of Ca2+-release from the venom of the snake Trimeresurus okinavensis, in sarcoplasmic reticulum.

The lectin himehabu lectin (HHL) has recently been isolated from crude venom of the snake Trimeresurus okinavensis. Ca2+ -electrode and fluorescent Ca2+ -indicator experiments showed that HHL induced release of Ca2+ from the heavy fraction of skeletal muscle sarcoplasmic reticulum (HSR). The release of Ca2+ induced by caffeine from HSR was abolished by ryanodine, Mg2+ and ruthenium red, typical inhibitors of Ca2+ -release channels, whereas that induced by HHL was only partially reduced by these inhibitors. HHL, unlike caffeine, had no effect on [3H]ryanodine binding to HSR. These results suggest that HHL induces release of Ca2+ which is at least partially mediated through Ca2+ -release channels with novel pharmacological properties.

Animals↗
PubMed1994

Polymorphisms of Trimeresurus flavoviridis venom gland phospholipase A2 isozyme genes.

Trimeresurus flavoviridis venom gland phospholipase A2 (PLA2) genes pgPLA 1a and pgPLA 2a encode Asp-49-PLA2 and genes pgPLA 1b and pgPLA 2b encode an isozyme of Asp-49-PLA2. Polymorphisms were found in pairs of pgPLA 1a and pgPLA 2a and of pgPLA 1b and pgPLA 2b for individuals of T. flavoviridis. The occurrence of both homozygotes and heterozygotes was demonstrated.

Animals↗
PubMed2004

Immunohistochemical study of endothelial nitric oxide synthase in the trigeminal ganglia of a crotaline snake Trimeresurus flavoviridis.

The immunoreactivity of constitutive endothelial nitric oxide synthase (eNOS) was studied in the trigeminal ganglia (TG) of a crotaline snake, Trimeresurus flavoviridis. eNOS immunoreactivity was found in TG neurons of different sizes. The percentage of eNOS-positive TG neurons was significantly higher in the mandibular division than in the infrared-related divisions, the maxillary division and ophthalmic ganglion (p<0.001). These findings suggest that eNOS in the TG of crotaline snakes is involved in constitutive neurotransmission in the TG, and is minimally involved in processing in the infrared-sensory system.

Animals↗
PubMed2002

Offshore insular variation in the diet of the Taiwanese bamboo viper Trimeresurus stejnegeri (Schmidt).

Dietary data were ascertained for 229 T. stejnegeri (snout vent length >300mm) from 36 localities throughout the main island of Taiwan and the outlying Orchid (Lanyu) and Green (Ludau) Islands. Twenty nine percent of the snakes were devoid of any prey, and of the snakes containing prey, 43% of the cases were unidentifiable. This relatively large proportion of unidentifiable prey items (observed in the hindgut) may reflect either rapid digestion of amphibian prey and/or rapid venting of feces as an evolutionary adaptation to arboreal life. Trimeresurus stejnegeri appears euryphagous, taking primarily amphibians, but additionally reptilian, mammalian and insect prey. There was no discrepancy in prey composition based on comparisons of where the prey item was recorded in the digestive tract. No sexual variation in diet composition was evident, although males were more likely to contain prey than females, indicating the utilisation of different foraging strategies on similar sympatric prey items. Variation in diet composition was observed between mainland Taiwan and offshore islands, which is most likely the result of differences in prey availability.

Amphibians↗