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Integrated omics studies delineate the formation and dynamics of lipid droplets in Rhodococcus opacus PD630 for biofuel feedstock

ABSTRACT: Purpose: To delineate mechanisms underlying lipid storage in LDs, we compared the transcriptomes of cells cultivated under three lipid-accumulating conditions. Methods: PD630 mRNA profiles of 3 different conditions (normal condition and LDs acculation conditions) were generated by deep sequencing, using Solid platform. The sequence reads were mapped by using Bowtie followed by Cufflinks. Results: Most genes were either expressed under all three conditions (6,759 genes) or under at least one condition (7,770 genes), but 1,177 genes were not expressed under any of these conditions. We observed a marked response 3 h after cells were transferred from NB to MSM; 56.99% of the genes were up-regulated and 30.32% were down-regulated, with 21.15% being up-regulated more than 2-fold and 9.36% being down-regulated more than 2-fold Conclusions: Genes in category J (translation, ribosomal structure and biogenesis) were significantly up-regulated (p-value 5.05E-20, two-tailed Chi-square test), while genes in category K (transcription), G (carbohydrate transport and metabolism) and C (energy production and conversion) were down-regulated (p-values: 6.0E-07, 8.08E-06 and 4.56E-05, respectively, two-tailed Chi-square test). Increased expression of ribosomal proteins is consistent with number of genes (56.99%) up-regulated in the MSM3 treatment. This decrease in energy production and conversion is consistent with inhibition of cell division and lipid accumulation in MSM.

ORGANISM(S): Rhodococcus opacus

PROVIDER: GSE42381 | GEO | 2013/11/04

SECONDARY ACCESSION(S): PRJNA181257

REPOSITORIES: GEO

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Integrated omics studies delineate the formation and dynamics of lipid droplets in Rhodococcus opacus PD630 for biofuel feedstock

Project description:Purpose: To delineate mechanisms underlying lipid storage in LDs, we compared the transcriptomes of cells cultivated under three lipid-accumulating conditions. Methods: PD630 mRNA profiles of 3 different conditions (normal condition and LDs acculation conditions) were generated by deep sequencing, using Solid platform. The sequence reads were mapped by using Bowtie followed by Cufflinks. Results: Most genes were either expressed under all three conditions (6,759 genes) or under at least one condition (7,770 genes), but 1,177 genes were not expressed under any of these conditions. We observed a marked response 3 h after cells were transferred from NB to MSM; 56.99% of the genes were up-regulated and 30.32% were down-regulated, with 21.15% being up-regulated more than 2-fold and 9.36% being down-regulated more than 2-fold Conclusions: Genes in category J (translation, ribosomal structure and biogenesis) were significantly up-regulated (p-value 5.05E-20, two-tailed Chi-square test), while genes in category K (transcription), G (carbohydrate transport and metabolism) and C (energy production and conversion) were down-regulated (p-values: 6.0E-07, 8.08E-06 and 4.56E-05, respectively, two-tailed Chi-square test). Increased expression of ribosomal proteins is consistent with number of genes (56.99%) up-regulated in the MSM3 treatment. This decrease in energy production and conversion is consistent with inhibition of cell division and lipid accumulation in MSM. PD630 mRNA profiles of 3 different conditions (normal condition and LDs acculation conditions) were generated by deep sequencing, using Solid platform.

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