Biosynthesis of landomycin E deoxysugar part in Streptomyces globisporus 1912: sequencing and analysis of lndZ1 and lndZ3 genes

DNA fragment of landomycin E biosynthesis gene cluster 1.5 kb in size has been completely sequenced and two open reading frames were identified. Gene lndZ1 resembles NDP-hexose-3,5-epimerase and lndZ3 is similar to NDP-hexose-4-ketoreductases. LndZ1 and LndZ3 proteins are suggested to accomplish two last catalytic steps towards deoxysugar L-rhodinose present in landomycin E carbohydrate moietyThis work was supported by grant BG-117b from Ministry of Education and Science of Ukraine (to V.F). We are gratefull to the staff of DNA sequencing facility at the Dept. of Biochemistry of Cambridge University (John Lester, Tania Mironenko, Nataliya Scott) for help in sequencing

SEQUENCING AND ANALYSIS OF PUTATIVE 3D-4H RING CYCLASE GENE lndF OF STREPTOMYCES GLOBISPORUS 1912 LANDOMYCIN E BIOSYNTHETIC GENE CLUSTER

DNA fragment of landomycin E biosynthesis gene cluster 700 bp in size has been completely sequenced. 3?-end of lndE (oxygenase) was identified, 5?-end of lndA (ketosynthase) and entire ORF for previously not sequenced lanF homologue, lndF. Analysis of lndF putative translation product revealed that it is highly conservative in comparison with other known cyclases from antibiotic biosynthesis gene clusters. Unlike urdamycin, jadomycin biosynthetic clusters, lndF and lndA are uncoupled, as well as genes lanF and lanA. Genes lndF and lndA are not preceded by direct or inverted repeats, putative sites for binding of transcriptional activator LndI. In contrast, lanF is flanked at it's 5?-end by three direct repeats, possible target for regulatory protein LanI.L. Castro is acknowledged for help in sequencing. This work was supported by INTAS grant YSF 00-208 to B.O

Chemical Approaches To Perturb, Profile, and Perceive Glycans

Glycosylation is an essential form of post-translational modification that regulates intracellular and extracellular processes. Regrettably, conventional biochemical and genetic methods often fall short for the study of glycans, because their structures are often not precisely defined at the genetic level. To address this deficiency, chemists have developed technologies to perturb glycan biosynthesis, profile their presentation at the systems level, and perceive their spatial distribution. These tools have identified potential disease biomarkers and ways to monitor dynamic changes to the glycome in living organisms. Still, glycosylation remains the underexplored frontier of many biological systems. In this Account, we focus on research in our laboratory that seeks to transform the study of glycan function from a challenge to routine practice

MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration

Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broaderinvolvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/

Minimum Information about a Biosynthetic Gene cluster

A wide variety of enzymatic pathways that produce specialized metabolites in bacteria, fungi and plants are known to be encoded in biosynthetic gene clusters. Information about these clusters, pathways and metabolites is currently dispersed throughout the literature, making it difficult to exploit. To facilitate consistent and systematic deposition and retrieval of data on biosynthetic gene clusters, we propose the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard.Chemistry and Chemical Biolog

MIBiG 4.0 : advancing biosynthetic gene cluster curation through global collaboration

Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/

raw LC-MS data associated with the paper of Melnyk S et al. Genetic approaches to improving clorobiocin production in Streptomyces roseochromogenes NRRL 3504

Zipped folder containing raw LC-MS files which were used to measure the clorobiocin production leves in recombinant S. roseochromogenes strainsTHIS DATASET IS ARCHIVED AT DANS/EASY, BUT NOT ACCESSIBLE HERE. TO VIEW A LIST OF FILES AND ACCESS THE FILES IN THIS DATASET CLICK ON THE DOI-LINK ABOV