Inferring functional relationships of proteins from local sequence and spatial surface patterns

We describe a novel approach for inferring functional relationship of proteins by detecting sequence and spatial patterns of protein surfaces. Well-formed concave surface regions in the form of pockets and voids are examined to identify similarity relationship that might be directly related to protein function. We first exhaustively identify and measure analytically all 910,379 surface pockets and interior voids on 12,177 protein structures from the Protein Data Bank. The similarity of patterns of residues forming pockets and voids are then assessed in sequence, in spatial arrangement, and in orientational arrangement. Statistical significance in the form of E and p-values is then estimated for each of the three types of similarity measurements. Our method is fully automated without human intervention and can be used without input of query patterns. It does not assume any prior knowledge of functional residues of a protein, and can detect similarity based on surface patterns small and large. It also tolerates, to some extent, conformational flexibility of functional sites. We show with examples that this method can detect functional relationship with specificity for members of the same protein family and superfamily, as well as remotely related functional surfaces from proteins of different fold structures. We envision that this method can be used for discovering novel functional relationship of protein surfaces, for functional annotation of protein structures with unknown biological roles, and for further inquiries on evolutionary origins of structural elements important for protein function.     

Structure of a highly phosphorylated lipopolysaccharide core in the Delta algC mutants derived from Pseudomonas aeruginosa wild-type strains PAO1 (serogroup O5) and PAC1R (serogroup O3)

Lipopolysaccharides (LPS) were isolated from rough-type mutant strains of Pseudomonas aeruginosa (Delta algC) derived from wild-type strains PAO1 (serogroup O5) and PAC1R (serogroup O3). Structural studies of the LPS core region with a special focus on the phosphorylation pattern were performed by 2D NMR spectroscopy, including a 1H,(31)P HMQC-TOCSY experiment, MALDI-TOF MS, and Fourier-transform ion cyclotron resonance ESIMS using the capillary skimmer dissociation technique. Both LPS were found to contain two residues each of 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo) and L-glycero-D-manno-heptose (Hep), one residue of N-(L-alanyl)-D-galactosamine and one O-carbamoyl group (Cm) on the distal Hep residue. The following structures of a tetrasaccharide trisphosphate from strain PAC1R Delta algC and that carrying an additional ethanolamine phosphate group (PEtN) from strain PAO1 Delta algC were elucidated: [carbohydrate structre: see text] where R=P in PAC1R Delta algC and PPEtN in PAO1 Delta algC. To our knowledge, in this work the presence of ethanolamine diphosphate is unambiguously confirmed and its position established for the first time in the LPS core of a rough-type strain of P. aeruginosa. In addition, the structure of the complete LPS core of wild-type strain P. aeruginosa PAO1 was reinvestigated and the position of the phosphorylation sites was revised.     

Simultaneous selection on two fitness-related traits in the butterfly Bicyclus anynana

Abstract. Theory about the role of constraints in evolution is abundant, but few empirical data exist to describe the consequences a bias in phenotypic variation has for micro evolution. Responses to natural selection can be severely hampered by a genetic correlation among a suite of traits. Constraints can be studied using antagonistic selection experiments, that is, two-trait selection in opposition to this correlation. The two traits studied here were development time and wing pattern (eyespot size) in the butterfly Bicyclus anynana , both of which have a clear adaptive significance. Rates of response were higher for eyespot size than for development time, but were independent of the concurrent selection (either in the same direction as the correlation or perpendicular to it). Regimes differed in both traits in all directions after 11 generations of selection. The uncoupling lines had higher relative responses than the synergistic lines in development time and equal relative responses in eyespot size. The patterns for eyespot size (reaction norms) were consistent across different rearing temperatures. Differences in lines selected for fast and slow development time were more pronounced at lower temperatures, irrespective of the direction of joint wing pattern selection. Furthermore, correlated responses in pupal weight and growth rate were observed; lines selected for a slower development had higher pupal weights, especially at lower temperatures. The response of the uncoupling lines was not hampered by a lack of selectable genetic variation, and the relative response in the development time was larger than expected based on response in the coupled direction and quantitative genetic predictions. This suggests that the structure of the genetic architecture does not constrain the short-term, independent evolution of both wing pattern and development time.     

Assortative Mating and Fertility in two Drosophila subobscura Strains with different Mitochondrial DNA Haplotypes

The mating pattern and female fertility on the two main mitochondrial DNA haplotypes (I and II) of Drosophila subobscura were studied, in an attempt to find possible differences between them in relation to sexual selection or isolation that could explain the populational dynamics and the co-existence of these two strains in nature. The mating pattern indicated an assortative mating in population cages, where couples of the same haplotype, mainly those of haplotype I, mated more often. However, the significations detected in laboratory conditions disappeared in wild populations, where random mating was the rule. The female fertility also showed differences in the laboratory compared to the wild, since couples with haplotype I males were more efficient in the laboratory populations. These results, together with others that we previously obtained, either point to selection acting directly on the mtDNA or to the presence of some kind of cytonuclear co-adaptation in these two haplotypes, although this must be modulated by other factors that change with the seasons and time. The end result could well be a balance of opposite forces acting on both haplotypes.     

Auxin distribution and transport during embryonic pattern formation in wheat

Inhibitors of auxin polar transport disrupt normal embryogenesis and thus specific spatial auxin distribution due to auxin movement may be important in establishing embryonic pattern formation in plants. In the present study, the distribution of the photoaffinity labeling agent tritiated 5-azidoindole-3-acetic acid ([3H],5-N3IAA), an analog of indole-3-acetic acid (IAA), was visualized in zygotic wheat (Triticum aestivum L.) embryos grown in vitro and in planta, and used to deduce auxin transport pathways in these embryos. This study provides the first direct evidence that the distribution of auxin, here [3H],5-N3IAA, is heterogeneous and changes during embryo development. In particular, the shift from radial to bilateral symmetry was correlated with a redistribution of [3H],5-N3IAA in the embryo. Furthermore, in bilaterally symmetrical embryos, that is, embryos in the late transition stage or older, the localization of [3H],5-N3IAA was altered by N-1-naphthylphthalamic acid, a specific inhibitor of auxin polar transport. No significant effect was observed in radially symmetrical embryos, that is, globular embryos, or very early transition embryos. Thus, the shift from radial to bilateral symmetry is associated with the onset of active, directed auxin transport involved in auxin redistribution. A change in the distribution of [3H],5-N3IAA was also observed in morphologically abnormal embryos induced on media supplemented with auxin or auxin polar transport inhibitors. By means of a microscale technique, free IAA concentration was measured in in vitro- and in planta-grown embryos and was found to increase during development. Therefore, IAA may be synthesized or released from conjugates in bilaterally symmetrical embryos, although import from surrounding tissues cannot be excluded.     

Monoamine pharmacology of the lobster cardiac ganglion

Monoamine agonists and antagonists were applied to the lobster cardiac ganglion in an attempt to clarify the different actions of 5-hydroxytryptamine (5HT) and dopamine (DA) on this rhythmic pattern generator. Experiments were designed to determine whether the similar responses to 5HT and DA applied to the anterior region of the ganglion could be separated by pharmacological approaches, and whether the different responses to 5HT applied to the anterior and posterior regions of the ganglion could be attributed to mediation by different receptors. A small number of the 5HT agonists which were tested mimic the effects of 5HT, in that they increase the frequency of bursting and decrease burst duration when applied to the whole ganglion, but decrease burst frequency and increase burst duration when applied only to the posterior half. Other 5HT agonists decrease frequency and prolong bursts when applied to the whole ganglion. Of the DA agonists tested, none acts as DA itself does. Rather, they mimic the effects of 5HT applied to the posterior ganglion, by slowing bursting and prolonging bursts. The actions of agonists do not correspond in any clear way to the receptor specificities as defined in vertebrates. Most antagonists tested do not show similar specificities to their effects in vertebrates. In particular, most of the DA antagonists tested are more effective in blocking exogenous 5HT than DA. One monoamine agonist directly alters the properties of endogenous burst-organizing potentials (driver potentials) in the motorneurons of the ganglion.     

Foot formation in hydra: commitment of the basal disk cells in the lower peduncle

Foot regeneration in the freshwater hydra Pelmatohydra robusta was examined using a monoclonal antibody AE03 as a marker. This antibody specifically recognizes mucous-producing ectodermal epithelial cells in the basal disk, but not cells in the peduncle region located just above the basal disk in the foot. When the basal disk was removed by amputation at the upper or lower part of the peduncle, AE03-positive (basal disk) cells always appeared at the regenerating tip of the footless polyp approximately 12-16 h later. When a small piece of tissue was cut out from the upper or lower peduncle region, the tissue invariably turned into a smooth spherical or oblong shape within a few hours. AE03 signal appeared in these spheres variably depending on their origin: when tissue pieces were derived from the lower peduncle, the signal appeared in nearly all pieces and often covered the entire surface of the pieces within 24 h. In contrast, the signal appeared in less than 10% of pieces derived from the upper peduncle. Furthermore, the signal seldom covered more than half of the surface of these pieces. When maintained for many days, pieces derived from the upper peduncle often regenerated tentacles, whereas those from the lower peduncle seldom did. These and other observations suggest that epithelial cells in the peduncle can rapidly differentiate into basal disk cells when the basal tissue is removed. However, cells in the upper peduncle are not irreversibly committed to differentiate into basal disk cells because, when cut out as small tissue pieces, they could remain AE03 negative and become tentacle cells. In contrast, the cells in the lower peduncle apparently are irreversibly committed to differentiate into basal disk cells, as they always turned rapidly into AE03-positive cells once they were physically separated from (and freed from the influence of) the basal disk itself, regardless of the separation methods used.     

Refinement of wingless expression by a wingless- and notch-responsive homeodomain protein,defective proventriculus

Pattern formation during animal development is often induced by extracellular signaling molecules, known as morphogens, which are secreted from localized sources. During wing development in Drosophila, Wingless (Wg) is activated by Notch signaling along the dorsal-ventral boundary of the wing imaginal disc and acts as a morphogen to organize gene expression and cell growth. Expression of wg is restricted to a narrow stripe by Wg itself, repressing its own expression in adjacent cells. This refinement of wg expression is essential for specification of the wing margin. Here, we show that a homeodomain protein, Defective proventriculus (Dve), mediates the refinement of wg expression in both the wing disc and embryonic proventriculus, where dve expression requires Wg signaling. Our results provide evidence for a feedback mechanism that establishes the wg-expressing domain through the action of a Wg-induced gene product.     

Modulation of BMP activity in dorsal-ventral pattern formation by the chordin and ogon antagonists

We analyzed the interactions between mutations in antagonistic BMP pathway signaling components to examine the roles that the antagonists play in regulating BMP signaling activity. The dorsalized mutants swirl/bmp2b, snailhouse/bmp7, lost-a-fin/alk8, and mini fin/tolloid were each analyzed in double mutant combinations with the ventralized mutants chordino/chordin and ogon, whose molecular nature is not known. Similar to the BMP antagonist chordino, we found that the BMP ligand mutants swirl/bmp2b and snailhouse/bmp7 are also epistatic to the putative BMP pathway antagonist, ogon, excluding a class of intracellular antagonists as candidates for ogon. In ogon;mini fin double mutants, we observed a mutual suppression of the ogon and mini fin mutant phenotypes, frequently to a wild type phenotype. Thus, the Tolloid/Mini fin metalloprotease that normally cleaves and inhibits Chordin activity is dispensable, when Ogon antagonism is reduced. These results suggest that Ogon encodes a Tolloid and Chordin-independent antagonistic function. By analyzing genes whose expression is very sensitive to BMP signaling levels, we found that the absence of Ogon or Chordin antagonism did not increase the BMP activity remaining in swirl/bmp2b or hypomorphic snailhouse/bmp7 mutants. These results, together with other studies, suggest that additional molecules or mechanisms are essential in generating the presumptive gastrula BMP activity gradient that patterns the dorsal-ventral axis. Lastly we observed a striking increased penetrance of the swirl/bmp2b dominant dorsalized phenotype, when Chordin function is also absent. Loss of the BMP antagonist Chordin is expected to increase BMP signaling levels in a swirl heterozygote, but instead we observed an apparent decrease in BMP signaling levels and a loss of ventral tail tissue. As has been proposed for the fly orthologue of chordin, short gastrulation, our paradoxical results can be explained by a model whereby Chordin both antagonizes and promotes BMP activity.