Distant Families Research Articles

Evolutionary relationships among G protein-coupled receptors using a clustered database approach.

Guanine nucleotide-binding protein-coupled receptors (GPCRs) comprise large and diverse gene families in fungi, plants, and the animal kingdom. GPCRs appear to share a common structure with 7 transmembrane segments, but sequence similarity is minimal among the most distant GPCRs. To reevaluate the question of evolutionary relationships among the disparate GPCR families, this study takes advantage of the dramatically increased number of cloned GPCRs. Sequences were selected from the National Center for Biotechnology Information (NCBI) nonredundant peptide database using iterative BLAST (Basic Local Alignment Search Tool) searches to yield a database of approximately 1700 GPCRs and unrelated membrane proteins as controls, divided into 34 distinct clusters. For each cluster, separate position-specific matrices were established to optimize sequence comparisons among GPCRs. This approach resulted in significant alignments between distant GPCR families, including receptors for the biogenic amine/peptide, VIP/secretin, cAMP, STE3/MAP3 fungal pheromones, latrophilin, developmental receptors frizzled and smoothened, as well as the more distant metabotrobic glutamate receptors, the STE2/MAM2 fungal pheromone receptors, and GPR1, a fungal glucose receptor. On the other hand, alignment scores between these recognized GPCR clades with p40 (putative GPCR) and pm1 (putative GPCR), as well as bacteriorhodopsins, failed to support a finding of homology. This study provides a refined view of GPCR ancestry and serves as a reference database with hyperlinks to other sources. Moreover, it may facilitate database annotation and the assignment of orphan receptors to GPCR families.

The molecular evolutionary history of a winged bean alpha-chymotrypsin inhibitor and modeling of its mutations through structural analyses.

A serine protease inhibitor of the Kunitz-STI (soybean trypsin inhibitor) family, isolated from the legume seeds of winged bean, was found to inhibit chymotrypsin at a 1:2 stoichiometric ratio. When the structure was determined in our laboratory, it was found to form a characteristic beta-trefoil fold, which is also seen in other proteins from distant families and sources. The folding organization divides the protein into three approximately equal subdomains related by a pseudo-threefold axis of symmetry passing parallel to the barrel axis of the trefoil. Following the now established idea that the present-day genes originated from ancestral minigenes through evolution, the origin of the proteins having this beta-trefoil organization is scrutinized using its subdomain motif as the search probe. The results, based mainly on structural analyses, indicate the independent existence of such a motif, mimicking the unknown ancestral protein(s) that might have been distributed in nature, not only by gene duplication, but also by insertion and permutation in other folds. The understanding led to a hypothesis for the possible origin of the Kunitz-STI family. On the basis of this model of evolution, structurally hypervariable regions were located on the protein where mutations could be designed and a broad range of engineering of the protein's activity could be conceived.

Twilight zone of protein sequence alignments.

Sequence alignments unambiguously distinguish between protein pairs of similar and non-similar structure when the pairwise sequence identity is high (>40% for long alignments). The signal gets blurred in the twilight zone of 20-35% sequence identity. Here, more than a million sequence alignments were analysed between protein pairs of known structures to re-define a line distinguishing between true and false positives for low levels of similarity. Four results stood out. (i) The transition from the safe zone of sequence alignment into the twilight zone is described by an explosion of false negatives. More than 95% of all pairs detected in the twilight zone had different structures. More precisely, above a cut-off roughly corresponding to 30% sequence identity, 90% of the pairs were homologous; below 25% less than 10% were. (ii) Whether or not sequence homology implied structural identity depended crucially on the alignment length. For example, if 10 residues were similar in an alignment of length 16 (>60%), structural similarity could not be inferred. (iii) The 'more similar than identical' rule (discarding all pairs for which percentage similarity was lower than percentage identity) reduced false positives significantly. (iv) Using intermediate sequences for finding links between more distant families was almost as successful: pairs were predicted to be homologous when the respective sequence families had proteins in common. All findings are applicable to automatic database searches.

A phylogenetic analysis of higher‐level gall wasp relationships (Hymenoptera: Cynipidae)

We present the most comprehensive analysis of higher‐level relationships in gall wasps conducted thus far. The analysis was based on detailed study of the skeletal morphology of adults, resulting in 164 phylogenetically informative characters, complemented with a few biological characters. Thirty‐seven cynipid species from thirty‐one genera, including four genera of the apparently monophyletic Cynipini and almost all of the genera in the other tribes, were examined. The outgroup included exemplar species from three successively more distant cynipoid families: Figitidae (the sister group of the Cynipidae), Liopteridae and Ibaliidae. There was considerable homoplasy in the data, but many groupings in the shortest tree were nonetheless well supported, as indicated by bootstrap proportions and decay indices. Partitioning of the data suggested that the high level of homoplasy is characteristic of the Cynipidae and not the result of the amount of available phylogenetically conservative characters being exhausted. The analysis supported the monophyly of the Cynipini (oak gall wasps) which, together with the Rhoditini (the rose gall wasps), Eschatocerini and Pediaspidini formed a larger monophyletic group of gall inducers restricted to woody representatives of the eudicot subclass Rosidae. The inquilines (Synergini) were indicated to be monophyletic, whereas the Aylacini, primarily herb gall inducers, appeared as a paraphyletic assemblage of basal cynipid groups. The shortest tree suggests that the Cynipidae can be divided into three major lineages: one including the inquilines, the Aylacini genera associated with Rosaceae, and Liposthenes; one consisting entirely of Aylacini genera, among them Aulacidea, Isocolus and Neaylax; and one comprising the woody rosid gallers (the oak and rose gall wasps and allies), the Phanacis‐Timaspis complex and the Aylacini genera associated with Papaveraceae.

Seasonal Interactions Among Genotype, Root Regeneration Potential, and Field Performance of Transplanted Container-grown Sycamore

Seven half-sib families of Platanus occidentalis L., either genetically improved selections (TFS-09, TFS-24, WV-10, WV-14) or non-improved selections (Brazos-C, Brazos-D, Putnam), were grown outdoors in 2.3-L to 9.1-L containers, then transplanted in fall, spring, or summer to assess root regeneration potential (RRP) and initial (2 year) post-transplant landscape growth. TFS-09, TFS-24, Brazos-C, and Brazos-D were Texas selections, while WV-10, WV-14, and Putnam were from Tennessee and Kentucky. Generally, local half-sib families grew more rapidly than geographically distant families and some genetically improved selections grew more rapidly than non-improved selections, both in the landscape and nursery. Rapid growth of new roots and transplanted root dry matter were more consistently associated with successful transplant establishment across families than other measures of RRP. Survival was reduced after summer vs. spring or fall transplant.

Sequence alignments of the H(+)-dependent oligopeptide transporter family PTR: inferences on structure and function of the intestinal PET1 transporter.

To study the structure and function of the intestinal H+/ peptide transporter PET1, we compared its amino acid sequence with those of related transporters belonging to the oligopeptide transporter family PTR, and with more distant transporter families. We have developed a new approach to the sequence analysis of proteins with multiple transmembrane domains (TMDs) which takes into account the repeated TMD-loop topology. In addition to conventional analyses of the entire sequence, each TMD and its adjacent loop residues (= TMD segments) were analyzed separately as independent structural units. In combination with hydropathy analysis, this approach reveals any changes in the order of the TMD segments in the primary structure and permits TMD alignments among divergent structures even if rearrangements of the order of TMD segments have occurred in the course of evolution. Alignments of TMD segments indicate that the TMD order in PTR transporters may have changed in the process of evolution. Consideration of such changes permits the alignment of homologous TMD segments from PTR transporters belonging to distant akaryotic and eukaryotic phyla. Multiple alignments of TMDs reveal several highly conserved regions that may play a role in transporter function. In comparing the PTR transporters with other transporter gene families, alignment scores using the entire primary structure are too low to support a finding of probable homology. However, statistically significant alignments were observed among individual TMD segments if one disregards the order in which they occur in the primary structure. Our results support the hypothesis that the PTR transporters may have evolved by rearrangement, duplication, or insertions and deletions of TMD segments as independent modules. This modular structure suggests new alignment strategies for determining functional domains and testing relationship among distant transporter families.

Sequence and structural links between distant ADP-ribosyltransferase families.

The low resolution structure of the Pseudomonas aeroginosa exotoxin A (ETA) presented in 1986 provided the first tantalizing three-dimensional view of an ADP-ribosyl-transferase (ADPRT) catalytic domain. The major features of this protein fold have recurred in the more recently solved crystal structures of the cholera toxin-related heat-labile enterotoxin (LT), diphtheria toxin (DT) and pertussis toxin (PT). A core set of alpha + beta elements define a minimal, conserved scaffold with remarkably plastic sequence requirements-only a single glutamic acid residue critical to catalytic activity is invariant. Other interchangeable residues in locations important for catalysis and binding are suggested by the cocrystal structures of DT with the inhibitor ApUp, ETA with bound AMP and nicotinamide, and DT with substrate NAD-in close accord with labeling and mutagenic data. Faint sequence resemblances that were earlier noticed among prokaryotic ADPRTs have now been securely extended by the structural concordance between toxin folds; more recently, eukaryotic ADPRTs have surfaced and their sequences can be reliably threaded into the conserved core fold. We will briefly summarize efforts in Palo Alto and Hamburg to explore these latter relationships, and to mount a rigorous search for new ADPRT families in the growing sequence databases.

Application of a recombinant cichlid growth hormone radioimmunoassay to measure native GH in tilapia(Oreochromis niloticus)bred at different temperatures

Resume This work descnbes the application of a homologous radioimmunoassay (RIA) in the measurement of plasma and pituitary growth hormone levels of tilapia maintained at 20 and 26C, using recombinant tilapia growth hormone (rtiGH). RIA sensitivity (EDYo) was 0.08 nglml and ED5 was 0.6210.02 nglml. Intra- and inter-assay coefficients of variation were 3.3 and 10.6% respectively, for a plasma sample of 1 ng/ml of tiGH. Mammalian or salmonids growth hormones, thyrotropins or tilapia prolactins did not show cross-reactivity with rtiGH antiserum. Plasma and pituitary extract of Oreochromis niloticus gave inhibition curves parallel to the rtiGH standard curve without interaction with serial dilutions either of tissue extracts or plasma from hypophysectomized tilapia. Pituitary extracts from other cichlid fish showed parallel competitive binding curves. Pituitary extracts of perciform fish exhibited a lower affinity to antirtiGH serum, while extracts of species from more distant families showed only negligible cross-reactivity or none at al]. The effects of water temperature on plasma concentrations and pituitary contents of GH were investigated in tilapia acclimatized to 26 and to 20°C. Measurements have been performed at the beginning and at the end of a two-week experiment. Whereas in fish from colder water plasma GH mean values were decreased, only a similar tendency was obsemed in pituitary GH contents. These results emphasize the hypothesis wich reports that the increase of growth with temperature is, at least in part, controlled by GH.

Polymorphism of pollen in the genusAcer(Aceraceae)

Abstract In 31 species of Acer different deviative pollen grains with a quite regular arrangement of apertures were found. Tetrads with a different structure were also found. It was shown that no single dependence between structure of tetrad and arrangement of deviative pollen exists. Deviative pollen forms with a similar arrangement of apertures were also found in distant angiosperm families but only in those which usually have 3-colpate pollen grains.

Weakly coupled Gibbs measures

We formulate an abstract functional-analytic framework for the study of Gibbs measures on infinite product spaces. Working in this frame-work, we present a detailed analysis of the weak-coupling regime. Specifically, we derive general theorems on existence of the Gibbs measure, analyticity in its component Gibbs factors, and exponential decay of correlations and truncated expectations in the spread of distant families of random variables. In translation-invariant situations we obtain a central limit theorem. Our main tool is a series expansion in truncated expectations, which we analyze with L p methods.

A Peculiar Ericalean Pollen, Grain

IN the genus Styphelia Sm., the Epacridaceae include a pollen form previously not known in this or related families. I have examined the patterns of ektexine ornamentation in pollen from all genera of the Epacridaceae. The grains are mostly similar to those of allied families, in that they are either smooth or have an ornamentation which is inconspicuous except under oil immersion. Those of Styphelia, however, are strikingly different. Of the eleven species recognized by Bentham1, I have been able to investigate ten, and in these the grains are always provided with warts (Fig. 1), the largest of which are usually conspicuous at quite low magnifications and may be more than 10µ in diameter. As can be seen in the photograph, the warts are rather easily detached, and at first sight they could be mistaken for oil droplets. The grains of S. tenuiflora and S. melaleucoides have smaller warts than do the other species, but even here they are easily distinguished from those of related groups. Similar forms occur in distant families (for example, Nymphaeaceae), but the pollen of Styphelia appears to be without parallel in the Ericales.