Molecular modeling of glycosyltransferases involved in the biosynthesis of blood group A,blood group B,Forssman, and iGb3 antigens and their interaction with substrates

A terminal alpha1-3 linked Gal or GalNAc sugar residue is the common structure found in several oligosaccharide antigens, such as blood groups A and B, the xeno-antigen, the Forssman antigen, and the isogloboside 3 (iGb3) glycolipid. The enzymes involved in the addition of this residue display strong amino acid sequence similarities, suggesting a common fold. From a recently solved crystal structure of the bovine alpha3-galactosyltransferase complexed with UDP, homology modeling methods were used to build the four other enzymes of this family in their locked conformation. Nucleotide-sugars, the Mn2+ ion, and oligosaccharide acceptors were docked in the models. Nine different amino acid regions are involved in the substrate binding sites. After geometry optimization of the complexes and analysis of the predicted structures, the basis of the specificities can be rationalized. In the nucleotide-sugar binding site, the specificity between Gal or GalNAc transferase activity is due to the relative size of two clue amino acids. In the acceptor site, the presence of up to three tryptophan residues define the complexity of the oligosaccharide that can be specifically recognized. The modeling study helps in rationalizing the crystallographic data obtained in this family and provides insights on the basis of substrate and donor recognition.     

Mutagenesis of a bacteriophage lytic enzyme PlyGBS significantly increases its antibacterial activity against group B streptococci

Group B streptococci (GBS) are the leading cause of neonatal meningitis and sepsis worldwide. Intrapartum antibiotic prophylaxis (IAP) is the current prevention strategy given to pregnant women with confirmed vaginal GBS colonization. Due to antibiotic resistance identified in GBS, we previously developed another strategy using a bacteriophage lytic enzyme, PlyGBS, to reduce vaginal GBS colonization. In this study, various DNA mutagenesis methods were explored to produce PlyGBS mutants with increased lytic activity against GBS. Several hyperactive mutants were identified that contain only the endopeptidase domain found in the N-terminal region of PlyGBS and represent only about one-third of the wild-type PlyGBS in length. Significantly, these mutants not only have 18–28-fold increases in specific activities compared to PlyGBS, but they also have a similar activity spectrum against several streptococcal species. One of the hyperactive mutants, PlyGBS90-1, reduced the GBS colonization from >5 logs of growth per mouse to <50 colony-forming units (cfu) 4 h post treatment (∼4-log reduction) using a single dose in a mouse vaginal model. A reduction in GBS colonization before delivery should significantly reduce neonatal GBS infection providing a safe alternative to IAP.     

Isolation of constitutive variants of a subfamily 10 histidine protein kinase (SppK) from Lactobacillus using random mutagenesis

The histidine protein kinase SppK is a peptide pheromone-activated kinase that regulates the production of the bacteriocin sakacin P in Lactobacillus sakei. SppK belongs to subfamily 10 of histidine protein kinases (HPKs), which regulate important processes in Gram-positive bacteria, including virulence, competence and bacteriocin production. To obtain insight into the functional properties of this relatively unknown class of HPKs, we have subjected SppK to random mutagenesis by error-prone PCR, followed by selection for mutants displaying a constitutive phenotype. Most identified mutations were clustered in a predicted coiled coil-like region, which is an important part of the HPK dimer interface and which includes the autophosphorylated histidine. Other mutations were located in the junctions between the dimerization domain and the membrane receptor domain or the catalytic kinase domain. Interestingly, two previously identified constitutive variants of ComD, an SppK homologue involved in competence regulation in Streptococcus pneumoniae, contained single mutations in the same regions.     

Impact of ploughing on soil seed bank dynamics in temporary pools

We examined the impact of ploughing on soil seed banks of plant communities living in temporary marshes located in agricultural fields. The quantity, quality and vertical distribution of seeds were quantified under ploughed or unploughed treatment at community level. We also focussed on a typical semi-aquatic species, Damasonium alisma, to investigate the impact of ploughing at population level. We used two complementary techniques to study seed banks: hand sorting and seedling emergence. We found that species richness of seeds, seed abundance and germination ability were strongly affected by ploughing at community level. Concerning D. alisma, most of the seeds (56%) were stored in the two deepest soil layers among the four considered in ploughed pools. Moreover, the germination rate was higher for buried seeds (84%) than for seeds collected at the surface (33.6%). These patterns were almost inverted in unploughed pools. Our results agree with the temporal storage effect generally suggested to describe the seed bank property of plant communities. But in addition, we showed that ploughing induces a spatial storage effect in accumulating species and individuals in the seed banks that favourably influence community dynamics. We conclude that, in contrast to what is usually thought, ploughing disturbance can be of benefit for such ephemeral wetland vegetation.     

Amphioxus and tunicates as evolutionary model systems

One important question in evolutionary biology concerns the origin of vertebrates from invertebrates. The current consensus is that the proximate ancestor of vertebrates was an invertebrate chordate. Today, the invertebrate chordates comprise cephalochordates (amphioxus) and tunicates (each a subphylum in the phylum Chordata, which also includes the vertebrate subphylum). It was widely accepted that, within the chordates, tunicates represent the sister group of a clade of cephalochordates plus vertebrates. However, recent studies suggest that the evolutionary positions of tunicates and cephalochordates should be reversed, the implications of which are considered here. We also review the two major groups of invertebrate chordates and compare relative advantages (and disadvantages) of each as model systems for elucidating the origin of the vertebrates.     

Genetic structure of natural populations of the red-spotted newt,Notophthalmus viridescens

Genetic variation is described at 15 loci in 2 neotenic and 12 nonneotenic populations of red-spotted newts. Though high levels of genetic similarity (I=0.990) were found among all populations, allele frequencies at six of the eight most polymorphic loci show significant heterogeneity across populations. Change in allele frequencies at two of these loci (Pep-2 and Ldh-1) is significantly correlated with latitude. Interspecific homologies are established for newt peptidases based on substrate specificities and lactate dehydrogenases based on tissue distribution, thermal stability, and kinetic properties. Nonneotenic populations are highly variable (H=0.157) and neotenic populations are only slightly, but significantly, less variable (H=0.120). The high levels of heterozygosity detected in nonneotenic populations may result from large effective population size and/or environmental heterogeneity. The unexpectedly high heterozygosity values obtained for the neotenic populations may indicate adult dispersal or the presence of some previously undetected red efts at these localities. In any case, a major change in life history has apparently had little effect on the genetic structure of these populations.This research was supported by grants from the Blakeslee Fund of Smith College.     

Reproductive ecology of five pipefish species in one eelgrass meadow

Synopsis Synopsis Pipefishes have rarely been watched in the wild and have never before been followed in their common seagrass habitats. This study explores the reproductive ecology of five species of pipefishes living in a Swedish eelgrass meadow during parts of four breeding seasons, tagging four of the species. Pipefish are remarkable for their specialised paternal care: only males aerate, osmoregulate and nourish the developing embryos. Two of the species (Entelurus aequoreus andNerophis ophidion) have simple ventral gluing of eggs on the trunk while three species (Syngnathus acus, S. rostellatus andS. typhle) have fully enclosed brood pouches on their tails. Males of the former species receive eggs from one female while males of the genusSyngnathus receive partial clutches from several females. Sex ratios of adults on the site differed from equal to male-biased to female-biased, according to species.S. typhle were most numerous and were resighted most often. They were present throughout the breeding season whereas there were temporal shifts in the presence of the other species on the meadow and in some sex ratios. Most species occurred in the deeper, denser part of the meadow but there was some habitat separation by species and sex. All species tended to stay low in the eelgrass, primarily coming up above the eelgrass to display and mate. No species showed site fidelity either to a home range or to the meadow, withE. aequoreus adults spending least time on the meadow. Sexual size dimorphism differed: males were larger inS. rostellatus, the same size inS acus and smaller in the other species. Although the species overlap in habitat requirements and breeding season, the only observed interspecific interactions were abortive courtships betweenSyngnathus species.