Deciphering the influence of genome architecture in a minimized bacterial genome*

Probabilistic interactions of RNA polymerase with DNA dictate transcription, the process which evolves the bacterial transcriptome composed of rRNA, tRNA, mRNA, and sRNA. The boundaries of the transcriptional events are outlined by the genome architecture defined as the local arrangement of genetic features identified via sequence motifs (promoters, gene coding regions, and transcription termination sites, etc.) along the genome.  The local arrangement of these sequence motifs form operon-like regions, transcriptional units,  directly controlling the expression of encoded RNA species. Using bioinformatic analysis of these genetic features, their locations were predicted computationally, and integrated together to define transcriptional units in the minimized genomes of the minimal cell, JCVI-syn3A, and its previous iteration, JCVI-syn1.0. The computational predictions correlate well or strongly agree with an equivalent experimental genome architecture identification approach using Oxford Nanopore Technologies which provide long read native RNA sequencing. Comparison between the two genome architectures has resolved factors influencing the evolution of the transcriptome and potential downstream impacts on cellular processes.