Genome-scale transcription–translation mapping reveals novel features of Zymomonas mobilis promoters and transcription units

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 Zymomonas mobilis subsp. mobilils ZM4 genome. Proteomics and ribosome profiling informed revisions of protein-coding genes, which included 44 start codon changes and 42 added proteins. We developed statistical methods for annotating transcript 5′ and 3′ ends enabling identification of 3940 TSSs and their corresponding promoters and 2091 transcription termination sites, which were distinguished from RNA processing sites by lack of an adjacent RNA 5′ end. 3 or 4 biological replicate samples of cells grown aerobically or anaerobically in rich media and anaerobically in minimal media. Samples were collected at growing phase and stationary phase time points.