Project description:Limited functional annotation of the Z. mobilis genome is a current barrier to both basic studies of Z. mobilis and its development as a synthetic-biology chassis. To gain insight, we collected sample-matched multiomics data including RNA-seq, transcription start site sequencing (TSS-seq), termination sequencing (term-seq), ribosome profiling, and label-free shotgun proteomic mass spectrometry across different growth conditions to improve annotation and assign functional sites in the Z. mobilis genome. Proteomics and ribosome profiling informed revisions of protein-coding genes, which included 44 start codon changes and 42 added proteins.
Project description:Investigation of the expression profiling of the ethanologenic Zymomonas mobilis in response to ethanol stress. A six chip study using total RNA recovered from three separate wild-type cultures of Zymomonas mobilis ATCC31821 and three separate cultures of a triple treated with 5% ethanol. Each chip measures the expression level of 1800 genes from Zymomonas mobilis ATCC31821 and the associated plasmids, with three-fold technical redundancy.
Project description:Investigation of the expression profiling of the ethanologenic Zymomonas mobilis in response to furfural stress. A six chip study using total RNA recovered from three separate wild-type cultures of Zymomonas mobilis ATCC31821 and three separate cultures of a triple treated with 1.0 g/l furfural. Each chip measures the expression level of 1800 genes from Zymomonas mobilis ATCC31821 and the associated plasmids, with three-fold technical redundancy.
Project description:High glucose concentrations were desirable for ethanol fermentation of Zymomonas mobilis, but it can lead to decrease in ethanol production and productivity. Sorbitol as a compatible solute can be absorbed or synthesized to counteract the detrimental osmotic stress caused from external high glucose concentrations by Z. mobilis. Currently, molecular mechanisms of tolerance to high glucose concentrations and sorbitol promoting ethanol fermentation are still unclear for Z. mobilis. To better understand mechanisms with which high concentrations of glucose and sorbitol affect physiology and metabolism of Z. mobilis ATCC31821 (ZM4), the global transcriptional responses of ZM4 to the challenge of high glucose concentration and sorbitol were profiled using whole genome microarray analysis. Swings J, Deley J. Bacterial Rev. 1977, 41(1): 1-46. Loos H, Kramer R, Sahm H and Sprenger GA. J Bacteriol. 1994, 176(24):7688–7693.
