Project description:Time course intracellular proteomics of Streptomyces hygroscopicus NRRL 30439 (S. inhibens NRRL30439, CP084681) during submerged culture fermentation. Label free quantification of LC-MSMS spectra was used for protein expression profiling to support primary and secondary metabolic functionalities.
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.
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.
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.
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. A six array study using total RNA recovered from three separate cultures of Spathaspora passalidarum NRRL Y-27907 grown in glucose and three separate cultures of Spathaspora passalidarum NRRL Y-27907 grown in xylose. Each array measures the expression level of 362,487 probes (average probe length 54.5 +/- 4.0 nt) tiled across the Spathaspora passalidarum NRRL Y-27907 genome with a median spacing distance of 29 nt. During data processing, probes are filtered to include only those probes corresponding to annotated protein-coding genes.
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. A six array study using total RNA recovered from three separate cultures of Candida tenuis NRRL Y-1498 grown in glucose and three separate cultures of Candida tenuis NRRL Y-1498 grown in xylose. Each array measures the expression level of 363,196 probes (average probe length 53.1 +/- 3.8 nt) tiled across the Candida tenuis NRRL Y-1498 genome with a median spacing distance of 24 nt. During data processing, probes are filtered to include only those probes corresponding to annotated protein-coding genes.
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. A six array study using total RNA recovered from three separate cultures of Lodderomyces elongisporus NRRL YB-4239 grown in glucose and three separate cultures of Lodderomyces elongisporus NRRL YB-4239 grown in xylose. Each array measures the expression level of 371,451 probes (average probe length 54.1 +/- 4.1 nt) tiled across the Lodderomyces elongisporus NRRL YB-4239 genome with a median spacing distance of 33 nt. During data processing, probes are filtered to include only those probes corresponding to annotated protein-coding genes.
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.