Project description:Representatives of the genus Beijerinckia are known as heterotrophic, dinitrogen-fixing bacteria which utilize a wide range of multicarbon compounds. Here we show that at least one of the currently known species of this genus, i.e., Beijerinckia mobilis, is also capable of methylotrophic metabolism coupled with the ribulose bisphosphate (RuBP) pathway of C1 assimilation. A complete suite of dehydrogenases commonly involved in the sequential oxidation of methanol via formaldehyde and formate to CO2 was detected in cell extracts of B. mobilis grown on CH3OH. Carbon dioxide produced by oxidation of methanol was further assimilated via the RuBP pathway as evidenced by reasonably high activities of phosphoribulokinase and ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO). Detection and partial sequence analysis of genes encoding the large subunits of methanol dehydrogenase (mxaF) and form I RubisCO (cbbL) provided genotypic evidence for methylotrophic autotrophy in B. mobilis.
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.