Project description:The goal was to study the factionation of different lignocelullose (glucose, wheat bran, wheat straw) by Streptomyces coelicolor A3(2) and the corresponding production of secondary metabolites. This was performed by multi-omic experiment such as transcriptomic/metabolomic and leadsto the production of new metabolites. For that, the strain Streptomyces coelicolor A3(2) was subjected to three carbon sources in triplicate (wheat bran, wheat straw and finally glucose as control). Enzymatic activities were studied at different times and the expression of CAZYmes was studied by transcriptomic in order to detect which enzymes are needed for each carbon source
Project description:Investigation of whole genome gene expression level changes in Streptomyces avermitilis delta-aveI mutant, compared to the wild-type strain. The mutants analyzed in this study are further described in Chen L, Lu Y., Chen J, Zhang W, Shu D, Qin Z, Yang S, Jiang W. (2008) Characterization of a negative regulator AveI for avermectin biosynthesis in Streptomyces avermitilis NRRL8165. Appl Microbiol Biotechnol 80(2): 277-86. Overall design: A six chip study using total RNA recovered from three separate Streptomyces avermitilis NRRL8165 and three separate cultures of a Streptomyces avermitilis NRRL8165 delta-aveI (delta-l) mutant. 3 separate RMA normalizations performed, one for each pair of control and mutant samples.
Project description:Investigation of whole genome gene expression level changes in Streptomyces avermitilis delta-aveI mutant, compared to the wild-type strain. The mutants analyzed in this study are further described in Chen L, Lu Y., Chen J, Zhang W, Shu D, Qin Z, Yang S, Jiang W. (2008) Characterization of a negative regulator AveI for avermectin biosynthesis in Streptomyces avermitilis NRRL8165. Appl Microbiol Biotechnol 80(2): 277-86. A six chip study using total RNA recovered from three separate Streptomyces avermitilis NRRL8165 and three separate cultures of a Streptomyces avermitilis NRRL8165 delta-aveI (delta-l) mutant. 3 separate RMA normalizations performed, one for each pair of control and mutant samples.
Project description:Comparative genomic hybridization analysis of Streptomyces coelicolor A3(2) versus Streptomyces lividans 66 and Streptomyces lividans TK24 using high density 105,000 x 60-mer ink-jet in situ synthesized arrays.
Project description:This study compared the genome of Streptomyces rimosus rimosus against that of Streptomyces coelicolor. It also compared 4 strains with changes in oxytetracycline production and derived from G7, the type strain, against G7. Keywords: Comparative genomic hybridization Overall design: Duplicate samples, each replicate may be found in the corresponding supplementary file for the Sample
Project description:Peptidases are known to play key roles in multiple biological processes in all living organisms. In a model plant Arabidopsis, the vast majority of many putative aminopeptidases remain uncharacterized. We therefore aim to explore physiological function of uncharacterized aminopeptidase in higher plants using Arabidopsis as a model to study.We performed functional and expression analyses of the Arabidopsis LAP2 through cDNA cloning, isolation of T-DNA insertional mutants, characterization of the enzymatic activity, characterization of gene expression, and transcriptomic and metabolomic analyses of the mutants. We found that LAP2, one of the 28 aminopeptidases in Arabidopsis, regulates plant growth, leaf longevity and stress response by controlling intracellular protein turnover. Loss-of-function alleles of LAP2 reduced in vegetative growth, accelerated leaf senescence and rendered plants more sensitive to various stresses. LAP2 is highly expressed in the quiescent center cells in the root meristem, cotyledons and leaf veins. Integration of global gene expression and metabolite analyses suggest that LAP2 controlled intracellular protein turnover. The mutant maintained free leucine by up-regulating key genes for leucine biosynthesis, however, this influenced the flux of glutamate strikingly. As a result, gamma-aminobutyric acid, a metabolite which is derived from glutamate, was diminished in the mutant. Decrements in these nitrogen-rich compounds are associated with morphological alterations and stress sensitivity of the mutant.Our results provide molecular and biochemical evidence that LAP2 is indeed an enzymatically active aminopeptidase. LAP2 plays key roles in senescence, stress response and protein turnover. Regulated proteolysis is an important mechanism in all stages of the plant life cycle. The present study would contribute to further understanding of the aminopeptidases which have several implications in higher plants. Overall design: Comparison between wild-type and mutant (LAP2-1) plants was performed. Two biological replicates (20 pooled plants in each replicate) were used, and each replicate was dye-swaped.
Project description:Bacterial genomic plasticity and instability carry multiple functional genetic information in Streptomyces secondary metabolism. Our previously publication has reported an effective industrial Streptomyces strain, with a unique phenotype of the high clavulanic acid yield. The complete genome of strain F163-1 harboring a 136.9-kb giant region of plasticity (RGP) was sequenced. The chromosome and plasmid are densely packed by an exceptionally huge variety of potential secondary metabolic gene clusters, excluding production of putative antibiotics. Intriguingly, architecture and size differences of plasmid pSCL4 between F613-1 and ATCC 27064 suggest the pSCL4 plasmid evolving from pSCL4-like and pSCL2-like extrachromosomal replicons, in addition to the previously proposed ATCC 27064 mega-plasmid formation hypothesis through recombination between the smaller F613-1 pSCL4 plasmid arm regions and the linear chromosome. Comparative genomics systemically investigate secondary metabolism capacitates in this study indicates that frequent exchange of genetic materials between Streptomyces replicons may shape remarkable diversities of secondary metabolite repertoires. Consequently, the F613-1 strain seems to have evolved its specific genomic architectures and genetic patterns to meet the requirement in subsequent industrial processes. Overall design: mRNA profiles of S. clavuligerus F613-1 and ATCC27064 strains were generated by deep sequencing