Distribution of dTDP-glucose-4,6-dehydratase gene and diversity of potential glycosylated natural products in marine sediment-derived bacteria

Abstract

To investigate the distribution of dTDP-glucose-4,6-dehydratase (dTGD) gene and diversity of the potential 6-deoxyhexose (6DOH) glycosylated compounds in marine microorganisms, a total of 91 marine sediment-derived bacteria, representing 48 operational taxonomic units and belonging to 25 genera, were screened by polymerase chain reaction. In total, 84% of the strains were dTGD gene positive, suggesting 6DOH biosynthetic pathway is widespread in these marine sediment-derived bacteria. BLASTp results of dTGD gene fragments indicate a high chemical diversity of the potential 6DOH glycosylated compounds. Close phylogenetic relationship occurred between dTGDs involved in the production of same or similar 6DOH glycosylated compounds, suggesting dTGD can be used to predict the structure of potential 6DOH glycosylated compounds produced by new strains. In two cases, where dTGD shared ≥85% amino acid identity and close phylogenetic relationship with their counterparts, 6DOH glycosylated compounds were accurately predicted. Our results demonstrate that phylogenetic analysis of dTGD gene is useful for structure prediction of glycosylated compounds from newly isolated strains and can therefore guide the chemical purification and structure identification process. The rapid identification of strains that possess dTGD gene provides a bioinformatics assessment of the greatest potential to produce glycosylated compounds despite the absence of fully biosynthetic pathways or genome sequences.

Analysis of proteomic changes in roots of soybean seedlings during recovery after flooding

“…During post-flooding recovery, de novo protein synthesis may be activated, thereby increasing the demand for synthesis of immunophilins. The conversion of dTDP-D-glucose into dTDP-4-keto-6-deoxy-Dglucose, a key intermediate for most deoxysugars, is catalyzed by dTDP-glucose 4-6 dehydratase [35]. In plants, deoxysugars such as deoxyribose, fucose, and rhamnose are involved in a number of critical cellular processes.…”

Glycogenomics as a mass spectrometry-guided genome-mining method for microbial glycosylated molecules

“…Specific glycosylation genes such as dehydratases, deoxygenases, dehydrogenases, methyltransferases, aminotransferases, and epimerases modify the common deoxysugar intermediate to yield the large diversity of sugar monomers in microbial GNPs (11,12). Phylogenetically, the highest GNP sugar diversity is found in actinobacteria (13). Among these bacteria, the families of Micromonosporaceae, Pseudonocardiaceae, Streptomycetaceae, and Thermomonosporaceae have the highest genetic potential to produce GNPs (Dataset S1).…”

Recent Advances in the Discovery and Development of Marine Microbial Natural Products

“…To identify new sources of bioactive secondary metabolites, gene-guided screening has been deployed to search target genes associated with NPs biosynthetic pathways, e.g., the fragments between ketosynthase and methylmalonyl-CoA transferase of polyketides (PKS) type I [51], enediyne PKS ketosynthase gene [52], O -methyltransferase gene [53], P450 monooxygenase gene [54], polyether epoxidase gene [55], 3-hydroxyl-3-methylglutaryl coenzyme A reductase gene [56], dTDP-glucose-4,6-dehydratase (dTGD) gene [48], and halogenase gene [57]. When combined with homology-based searches and phylogenetic analyses, gene-based screening offers the greatest potential to predict the production of interesting, new secondary metabolites harbored by isolates or environments.…”

“…This predictive capability provides a simple and rapid method to avoid the isolation of known compounds or to identify strains that produce compounds within a desired structural class [58]. Chen et al [48] investigated the distribution of dTGD gene and diversity of the potential 6-deoxyhexose (6DOH) glycosylated compounds from 91 marine sediment-derived bacteria, representing 48 OTUs and belonging to 25 genera, by PCR. Eighty-four percent of the strains were dTGD gene positive, suggesting that 6DOH biosynthetic pathway is widespread in these marine sediment-derived bacteria.…”

“…BLASTp results also indicated a high chemical diversity of the potential 6DOH glycosylated compounds. The results demonstrated that phylogenetic analysis of dTGD gene is useful for structure prediction of glycosylated compounds from newly isolated strains and can therefore guide the chemical purification and structure identification process such as medermycin and chromomycin A3 [48]. Hence, gene-guided screening provides a bioinformatic assessment of the secondary metabolite biosynthetic potential in the absence of fully assembled pathways or genome sequences.…”