Comparative genomic analysis of azasugar biosynthesis

Azasugars are monosaccharide analogs in which the ring oxygen is replaced with a nitrogen atom. These well-known glycosidase inhibitors are of interest as therapeutics, yet several aspects of azasugars remain unknown including their distribution, structural diversity, and chemical ecology. The hallmark signature of bacterial azasugar biosynthesis is a three gene cluster (3GC) coding for aminotransferase, phosphatase, and dehydrogenase enzymes. Using the bioinformatics platform Enzyme Similarity Tool (EST), we identified hundreds of putative three gene clusters coding for azasugar production in microbial species. In the course of this work, we also report a consensus sequence for the aminotransferase involved in azasugar biosynthesis as being: SGNXFRXXXFPNXXXXXXXLXVPXPYCXRC. Most clusters are found in Bacillus and Streptomyces species which typically inhabit soil and the rhizosphere, but some clusters are found with diverse species representation such as Photorhabdus and Xenorhabdus which are symbiotic with entomopathogenic nematodes; the human skin commensal Cutibacterium acnes, and the marine Bacillus rugosus SPB7, a symbiont to the sea sponge Spongia officinalis. This pan-taxonomic survey of the azasugar 3GC signature may lead to the identification of new azasugar producers, facilitate studies of their natural functions, and lead to new potential therapeutics.

Draft Genome Sequence of Bacillus sp. Strain SPB7, Isolated from the Marine Sponge Spongia officinalis

ABSTRACT The draft genome of Bacillus sp. SPB7, which was isolated from the marine sponge Spongia officinalis, is presented. This bacterium is a producer of an antimicrobial cyclic diketopiperazine, (3S,6S)-3,6-diisobutylpiperazine-2,5-dione. The genome consists of 4,511 protein-coding genes, 63 tRNAs, 2 16S rRNAs, 3 23S rRNAs, and a single copy of 5S rRNA.

Antimicrobial and Antioxidant Activities of Novel Marine Bacteria (Bacillus 2011SOCCUF3) Isolated from Marine Sponge (Spongia officinalis)

Background : Bacillus species represent a rich source of new bioactive metabolites that can combat diseases. Methods: Bacillus strain was isolated from the marine sponge Spongia officinalis and routinely maintained on marine broth. The bacteria strain was identified as Bacillus 2011SOCCUF3 using 16S rDNA sequencing. The strain was cultured on Tryptone Casein Oat Soluble Starch (TCOATSS) media with continuous agitation for 4 days. The fermented broth was centrifuged, and the supernatant was mixed with 10% (w/v) of adsorbent resin (XAD-7HP and XAD-16N, 1:1) and shaken continuously at a reduced speed for 7 h; and the resin was collected by filtration through sintered glass funnel and washed with MilliQ water, and then eluted with methanol to obtain the extract. The extract was evaporated in vacuo at reduced temperature and pressure to obtain the dry extract. The dry extract was purified by vacuum liquid chromatography, eluting with methanol in acetone gradient. The in vitro antimicrobial and antioxidant activities were investigated using the agar-well diffusion, DPPH scavenging and the phosphomolybdate methods respectively. Results: The extract and fractions showed good antimicrobial activities with minimum inhibitory concentration range of <1.0 mg/mL. The extract and fractions also exhibited good antioxidant activities with their IC50 values been comparable to the standard. Conclusion: Thus, a novel Bacillus strain isolated from the marine sponge (Spongia officinalis) obtained from Cortiou and Riou, France, exhibited promising antimicrobial and antioxidant activities.

A de novo transcriptome assembly for the bath sponge Spongia officinalis, adjusting for microsymbionts

Objectives We report a transcriptome acquisition for the bath sponge Spongia officinalis, a non-model marine organism that hosts rich symbiotic microbial communities. To this end, a pipeline was developed to efficiently separate between bacterial expressed genes from those of eukaryotic origin. The transcriptome was produced to support the assessment of gene expression and, thus, the response of the sponge, to elevated temperatures, replicating conditions currently occurring in its native habitat. Data description We describe the assembled transcriptome along with the bioinformatic pipeline used to discriminate between signals of metazoan and prokaryotic origin. The pipeline involves standard read pre-processing steps and incorporates extra analyses to identify and filter prokaryotic reads out of the analysis. The proposed pipeline can be followed to overcome the technical RNASeq problems characteristic for symbiont-rich metazoan organisms with low or non-existent tissue differentiation, such as sponges and cnidarians. At the same time, it can be valuable towards the development of approaches for parallel transcriptomic studies of symbiotic communities and the host.