Noncontiguous operon atlas for the Staphylococcus aureus genome

Area of Science:

• Bacterial genetics and molecular biology
• Transcriptomics and gene regulation

Background:

• Bacteria organize genes into operons for coordinated gene expression via polycistronic mRNA.
• Some cellular processes require coordinated protein production and antagonist gene inhibition, leading to the evolution of noncontiguous operons (NcOs).
• NcOs feature genes transcribed in opposite directions, resulting in overlapping transcripts and mutual repression, but are difficult to predict computationally.

Purpose of the Study:

• To identify and map noncontiguous operons (NcOs) in the Staphylococcus aureus genome using direct RNA sequencing.
• To investigate the physiological significance of NcO structures in bacterial gene regulation and function.

Main Methods:

• Direct RNA sequencing methodology was employed to analyze the transcriptome of Staphylococcus aureus.
• Identification and mapping of NcOs within the S. aureus genome and the lysogenic prophage 80α.
• Functional analysis using the menaquinone operon to assess the impact of NcO disruption on bacterial fitness.

Main Results:

• 18 NcOs were identified in the Staphylococcus aureus genome and 4 in the lysogenic prophage 80α.
• The identified NcOs include genes related to energy metabolism, metal transport, toxin-antitoxin systems, and phage lifecycle control.
• Disruption of NcO architecture in the menaquinone operon led to reduced bacterial fitness, increased menaquinone levels, and decreased oxygen consumption.

Conclusions:

• Noncontiguous operons (NcOs) are significant structures in bacterial physiology, enabling coordinated gene expression and functional regulation.
• Combining operon mapping with transcriptomic data is crucial for uncovering functional relationships between neighboring genes.
• The study highlights the importance of NcO architecture for maintaining bacterial fitness and cellular processes.