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.     

Microbial Community Profile and Water Quality in a Protected Area of the Caatinga Biome

The Caatinga is a semi-arid biome in northeast Brazil. The Paraguaçú River is located in the Caatinga biome, and part of its course is protected by the National Park of Chapada Diamantina (PNCD). In this study we evaluated the effect of PNCD protection on the water quality and microbial community diversity of this river by analyzing water samples obtained from points located inside and outside the PNCD in both wet and dry seasons. Results of water quality analysis showed higher levels of silicate, ammonia, particulate organic carbon, and nitrite in samples from the unprotected area compared with those from protected areas. Pyrosequencing of the 16S rRNA genes revealed that Burkholderiales was abundant in samples from all three sites during both seasons and was represented primarily by the genus Polynucleobacter and members of the Comamonadaceae family (e.g., genus Limnohabitans). During the dry season, the unprotected area showed a higher abundance of Flavobacterium sp. and Arthrobacter sp., which are frequently associated with the presence and/or degradation of arsenic and pesticide compounds. In addition, genes that appear to be related to agricultural impacts on the environment, as well as those involved in arsenic and cadmium resistance, copper homeostasis, and propanediol utilization, were detected in the unprotected areas by metagenomic sequencing. Although PNCD protection improves water quality, agricultural activities around the park may affect water quality within the park and may account for the presence of bacteria capable of pesticide degradation and assimilation, evidencing possible anthropogenic impacts on the Caatinga.     

Effects of cyclohexane, an industrial solvent, on the yeast Saccharomyces cerevisiae and on isolated yeast mitochondria

Little information on the effects of cyclohexane at the cellular or subcellular level is available. In Saccharomyces cerevisiae, cyclohexane inhibited respiration and diverse energy-dependent processes. In mitochondria isolated from S. cerevisiae, oxygen uptake and ATP synthesis were inhibited, although ATPase activity was not affected. Cyclohexane effects were similar to those reported for beta-pinene and limonene, suggesting that the cyclohexane ring in these monoterpenes may be a determinant for their biological activities.     

Flagellates in the malpighian tubules of laboratory-bred Lutzomyia longipalpis fed on a hamster experimentally infected with Leishmania mexicana amazonensis

As a preparatory stage for a study aiming at identifying the species and subspecies of local Leishmania in naturally infected sandflies through immunoradiometric assay with monoclonal antibodies, we tried to obtain experimental infections of phlebotomines with well characterized stocks of parasites, in order to test the effectiveness of the method.     

Responses of entomopathogenic fungi to the mutagen 4-nitroquinoline 1-oxide

Survival of entomopathogenic fungi under solar ultraviolet (UV) radiation is paramount to the success of biological control of insect pests and disease vectors. The mutagenic compound 4-nitroquinoline 1-oxide (4-NQO) is often used to mimic the biological effects of UV radiation on organisms. Therefore, we asked whether tolerance to 4-NQO could predict tolerance to UV radiation in thirty isolates of entomopathogenic fungi and one isolate of a xerophilic fungus. A dendrogram obtained from cluster analyses based on the 50 and 90 % inhibitory concentrations (IC₅₀ and IC₉₀, respectively) divided the fungal isolates into six clusters numbered consecutively based on their tolerance to 4-NQO. Cluster 6 contained species with highest tolerance to 4-NQO (IC₅₀ > 4.7 μM), including Mariannaea pruinosa, Lecanicillium aphanocladii, and Torrubiella homopterorum. Cluster 1 contained species least tolerant to 4-NQO (IC₅₀ < 0.2 μM), such as Metarhizium acridum (ARSEF 324), Tolypocladium geodes, and Metarhizium brunneum (ARSEF 7711). With few exceptions, the majority of Metarhizium species showed moderate to low tolerances (IC₅₀ between 0.4 and 0.9 μM) and were placed in cluster 2. Cluster 3 included species with moderate tolerance (IC₅₀ between 1.0 and 1.2 μM). In cluster 4 were species with moderate to high tolerance (IC₅₀ between 1.3 and 1.6 μM). Cluster 5 contained the species with high tolerance (IC₅₀ between 1.9 and 4.0 μM). The most UV tolerant isolate of M. acridum, ARSEF 324, was the least tolerant to 4-NQO. Also, L. aphanocladii, which is very susceptible to UV radiation, showed high tolerance to 4-NQO. Our results indicate that tolerance to 4-NQO does not correlate with tolerance to UV radiation. Therefore this chemical compound is not a predictor of UV tolerance in entomopathogenic fungi.     

<Emphasis Type="Italic">Syndesmis</Emphasis> François, 1886 (Rhabdocoela: Umagillidae): a revisitation,with a synopsis and an identification key to species,and new molecular evidence for ascertaining the phylogeny of the group

Syndesmis François, 1886 is a genus of umagillid turbellarians comprising species which are typically endosymbionts of echinoids, i.e. sea urchins. This group is likely key in addressing the issue of transition between a free-living and a parasitic mode of life in the Platyhelminthes. Accordingly, its phylogeny should be considered for detailed analysis, namely by addressing molecular evidence for its different species. At the present time, a revisitation of Syndesmis is required and fully justified by the following lines of argument: (i) the body of knowledge on Syndesmis is large, but the information is scattered through many different works in the literature; (ii) for about 60 years, it was a common practice to assign the umagillids isolated from sea urchins as a single species, i.e. the type-species, Syndesmis echinorum François, 1886, which was later split into several species on morphological grounds; and (iii) the type-species - for which no molecular information is available - was redescribed and new species were described in recent years but the generic diagnosis of Syndesmis was not emended accordingly. The present state of art additionally justifies the necessity of (i) an updated synopsis of species and (ii) an identification key to the 26 species described from different hosts and geographical locations. All these aspects define the aims of the present study. It is proposed that S. antillarum is attributed to Stunkard & Corliss (1951) and not to Powers (1936).