Project description:Streptomyces tsukubaensis NRRL 18488 is the preferred strain for the production of immunosuppressant agent tacrolimus (FK506). To take full advantage of its genetic potential, systematic understanding of secondary metabolism and related regulatory mechanisms is highly demanded. Here, to this end, we complete its 7.9 Mbp linear genome sequence followed by integrating with multi-omics measurements. With accurate reannotation of FK506 gene cluster, total 2,389 transcription start sites were determined by using primary transcriptome analysis. Integrated analysis of transcriptome and translatome data revealed that secondary metabolic gene clusters, especially FK506 cluster, undergo translational control with decrease in translational efficiency according to the growth. Furthermore, we demonstrated that SD motif has little correlation with ribosome pausing but AT-rich codons delay the translational elongation. Strong ribosome pausing was observed in the rare TTA codon in FK506 cluster. This comprehensive genome-scale analysis provides insight to the translational regulation of secondary metabolism in S. tsukubaensis.

2019-10-16 | GSE97637 | GEO

Detoxins S1, N1, N2, N3, P1, P2, P3 source strain raw UHPLC-MS data and representative MS2

Project description:detoxin S1 source strain Streptomyces sp. S-325 (JOIW01) raw UHPLC-MS data and representative MS2 detoxins N1, N2, N3 source strain Streptomyces spectabilis NRRL 2792 raw UHPLC-MS data and representative MS2 detoxins N2, N3 source strain Streptomyces sp. NRRL B-1347 (JOJM01) raw UHPLC-MS data detoxins P1, P2, P3 source strain Amycolatopsis jujuensis NRRL B-24427 raw UHPLC-MS data and representative MS2

2019-04-01 | MSV000083648 | MassIVE

Expression analysis of Spathaspora passalidarum NRRL Y-27907 grown in glucose or xylose

Project description:Investigation of whole genome gene expression level changes in Spathaspora passalidarum NRRL Y-27907 grown aerobically in xylose, compared to the same strain grown aerobically in glucose.

2011-10-20 | GSE24853 | GEO

Expression analysis of Candida tenuis NRRL Y-1498 grown in glucose or xylose

Project description:Investigation of whole genome gene expression level changes in Candida tenuis NRRL Y-1498 grown aerobically in xylose, compared to the same strain grown aerobically in glucose.

2011-10-20 | GSE24856 | GEO

Expression analysis of Lodderomyces elongisporus NRRL YB-4239 grown in glucose or xylose

Project description:Investigation of whole genome gene expression level changes in Lodderomyces elongisporus NRRL YB-4239 grown aerobically in xylose, compared to the same strain grown aerobically in glucose.

2011-10-20 | GSE24855 | GEO

Transcriptome data involved in Japanese flounder (Paralichthys olivaceus) albinism

Project description:In this study, a high-throughput sequencing strategy was employed to identify the mRNA involved in P. olivaceus albinism. Based on P. olivaceus genome, RNA-seq identified 21,787 know genes and 711 new genes by transcripts assembly. Of those, 235 genes exhibited significantly different expression pattern (fold change ≥2 or ≤0.5 and q-value≤0.05), including 194 down-regulated genes and 41 up-regulated genes in albino versus normally pigmented individuals. These genes were enriched to 81 GO terms and 9 KEGG pathways (p≤0.05). Among those, the pigmentation related pathways-Melanogenesis and tyrosine metabolism were contained.

2017-07-13 | GSE99341 | GEO

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