A network-based approach to identify substrate classes of bacterial glycosyltransferases

Background

Bacterial interactions with the environment- and/or host largely depend on the bacterial glycome. The specificities of a bacterial glycome are largely determined by glycosyltransferases (GTs), the enzymes involved in transferring sugar moieties from an activated donor to a specific substrate. Of these GTs their coding regions, but mainly also their substrate specificity are still largely unannotated as most sequence-based annotation flows suffer from the lack of characterized sequence motifs that can aid in the prediction of the substrate specificity.

Results

In this work, we developed an analysis flow that uses sequence-based strategies to predict novel GTs, but also exploits a network-based approach to infer the putative substrate classes of these predicted GTs. Our analysis flow was benchmarked with the well-documented GT-repertoire of Campylobacter jejuni NCTC 11168 and applied to the probiotic model Lactobacillus rhamnosus GG to expand our insights in the glycosylation potential of this bacterium. In L. rhamnosus GG we could predict 48 GTs of which eight were not previously reported. For at least 20 of these GTs a substrate relation was inferred.

Conclusions

We confirmed through experimental validation our prediction of WelI acting upstream of WelE in the biosynthesis of exopolysaccharides. We further hypothesize to have identified in L. rhamnosus GG the yet undiscovered genes involved in the biosynthesis of glucose-rich glycans and novel GTs involved in the glycosylation of proteins. Interestingly, we also predict GTs with well-known functions in peptidoglycan synthesis to also play a role in protein glycosylation.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-349) contains supplementary material, which is available to authorized users.     

BEHAVIORAL AND PHYSIOLOGICAL MEASUREMENTS OF MATERNAL INVESTMENT IN THE STELLER SEA LION, EUMETOPIAS JUBATUS

The onshore and at-sea cycles of females, suckling behavior of pups and their milk intake were studied in Steller sea lions ( Eumetopias jubatus ) during 1983 at Año Nuevo Island, California. Females averaged approximately 21 h ashore and 36 h at sea. The trips to sea lengthened as pups aged, resulting in an overall decline in female time ashore to 30% by the sixth week following parturition. Activity budgets of pups showed no significant differences among suckling time, age and sex. Milk intake, estimated using labeled water studies, revealed that heavier pups consumed more milk than lighter ones (milk ingestion in ml/d = 4.26 + 0.0687 [Pup Mass in kg]). Mean milk intake was 1.78 ± 0.33 liters/d. Mean pup growth rate was 0.38 ± 0.1 kg/d. The results suggest that female attendance patterns are shaped by the increasing nutritional demands of growing pups and their increasing efficiency at suckling.     

Piperazinyl-glutamate-pyrimidines as potent P2Y12 antagonists for inhibition of platelet aggregation

Piperazinyl-glutamate-pyrimidines were prepared with oxygen, nitrogen, and sulfur substitution at the 4-position of the pyrimidine leading to highly potent P2Y₁₂ antagonists. In particular, 4-substituted piperidine-4-pyrimidines provided compounds with exceptional potency. Pharmacokinetic and physicochemical properties were fine-tuned through modifications at the 4-position of the piperidine ring leading to compounds with good human PRP potency, selectivity, clearance and oral bioavailability.     

Piperazinyl-glutamate-pyridines as potent orally bioavailable P2Y12 antagonists for inhibition of platelet aggregation

Polymer-assisted solution-phase (PASP) parallel library synthesis was used to discover a piperazinyl-glutamate-pyridine as a P2Y₁₂ antagonist. Exploitation of this lead provided compounds with excellent inhibition of platelet aggregation as measured in a human platelet rich plasma (PRP) assay. Pharmacokinetic and physiochemical properties were optimized leading to compound (4S)-4-[({4-[4-(methoxymethyl)piperidin-1-yl]-6-phenylpyridin-2-yl}carbonyl)amino]-5-oxo-5-{4-[(pentyloxy)carbonyl]piperazin-1-yl}pentanoic acid 22J with good human PRP potency, selectivity, in vivo efficacy and oral bioavailability.     

The subfossil occurrence and paleoecological implications of Macrotarsomys petteri (Rodentia: Nesomyidae) in extreme southeastern Madagascar

Remains of a large-bodied species of endemic nesomyid rodent, Macrotarsomys petteri Goodman and Soarimalala, 2005, were identified from subfossil deposits recovered from Andrahomana Cave in extreme southeastern Madagascar. This recently described extant species was previously only known from a single specimen collected at a site about 450 km northwest of Andrahomana and with distinctly different forest habitat than currently found in the vicinity of the cave. Radiocarbon dating of remains of M. petteri from the cave site indicates that it persisted in the region subsequent to human settlement. Previous reports of a large member of Macrotarsomys from other Quaternary sites in southern Madagascar are almost certainly of M. petteri. It is proposed that this species once had a broad distribution across the southern portion of the island during a more mesic period and subsequent aridification of the region has led to its local extirpation across most of its former range. To cite this article: S.M. Goodman et al., C. R. Palevol 5 (2006).     

Gene expression in cortex and hippocampus during acute pneumococcal meningitis

Background  

Pneumococcal meningitis is associated with high mortality (~30%) and morbidity. Up to 50% of survivors are affected by neurological sequelae due to a wide spectrum of brain injury mainly affecting the cortex and hippocampus. Despite this significant disease burden, the genetic program that regulates the host response leading to brain damage as a consequence of bacterial meningitis is largely unknown.     

Efficient adenovirus transduction of 3T3-L1 adipocytes stably expressing coxsackie-adenovirus receptor

3T3-L1 adipocytes have proven difficult to transfect with plasmid-encoded cDNAs or even infect with virally-derived cDNAs. We have developed and characterized a 3T3-L1 adipocyte cell line stably expressing the truncated receptor for coxsackievirus and adenovirus receptor (CAR) for its ability to be infected with adenoviruses at a low multiplicity of infection (m.o.i.). Using green fluorescent protein driven by the cytomegalovirus promoter in adenovirus fiber type 5 we compared infection efficiencies of CAR adipocytes versus the parental 3T3-L1 adipocytes. As assessed by immunofluorescence, CAR adipocytes were infected at approximately 100-fold greater efficiency than regular 3T3-L1 adipocytes. The efficiency of transduction for the CAR adipocytes was >90% at multiplicities of infection of 50 whereas standard adipocytes were poorly transduced even at an m.o.i. of 2000. Since many investigators studying insulin action use 3T3-L1 adipocytes, we compared CAR adipocytes versus regular adipocytes and showed that the two cell lines were similar with respect to insulin stimulation of insulin receptor, MAPK, and Akt phosphorylation and basal- and insulin-stimulated glucose transport. In addition, CAR adipocytes accumulated GLUT4 and SCD1 proteins during the adipogenesis program with the same time course as regular 3T3-L1 adipocytes. Lastly, CAR adipocytes produced and secreted the adipose-specific hormone Acrp30. These data suggest 3T3-L1CARDelta1 adipocytes are virtually indistinguishable from their parental cells, but demonstrate a significant advantage with improved efficiency of adenoviral transduction for gain or deletion of function studies.     

Biome reconstruction from pollen and plant macrofossil data for Africa and the Arabian peninsula at 0 and 6000 years

Biome reconstruction from pollen and plant macrofossil data provides an objective method to reconstruct past vegetation. Biomes for Africa and the Arabian peninsula have been mapped for 6000 years bp and provide a new standard for the evaluation of simulated palaeovegetation distributions. A test using modern pollen data shows the robustness of the biomization method, which is able to predict the major vegetation types with a high confidence level. The application of the procedure to the 6000 years data set (pollen and plant macrofossil analyses) shows systematic differences from the present that are consistent with the numerous previous regional and continental interpretations, while providing a more extensive and more objective basis for such interpretations. Madagascar, eastern, southern and central Africa show only minor changes in terms of biomes, compared to present. Major changes in biome distributions occur north of 15°N, with steppe in many low-elevation sites that are now desert, and temperate xerophytic woods/scrub and warm mixed forest in the Saharan mountains. These shifts in biome distributions imply significant changes in climate, especially precipitation, between 6000 years and present, reflecting a change in monsoon extent combined with a southward expansion of Mediterranean influence.