From essential to persistent genes: a functional approach to constructing synthetic life

Area of Science:

• Synthetic biology
• Genomics
• Molecular biology

Background:

• The concept of a 'minimal genome' is a key goal in synthetic biology.
• Minimal gene sets are context-dependent and vary across prokaryotic genomes.
• Lack of consensus on gene essentiality criteria complicates defining a universal minimal genome.

Purpose of the Study:

• To propose an alternative concept to the 'minimal genome' for classifying essential genes.
• To identify criteria for genes crucial for robust long-term survival.
• To inform synthetic biology applications and the creation of artificial life-like forms.

Main Methods:

• Analysis of conserved genes across sequenced prokaryotic genomes.
• Evaluation of gene expression levels and DNA strand location.
• Development of the 'gene persistence' concept.

Main Results:

• No single protein-coding gene is conserved across all prokaryotic genomes studied.
• The concept of 'gene persistence' is introduced as a classification for essential genes.
• Persistent genes are conserved in most genomes, highly expressed, and often on the leading DNA strand.

Conclusions:

• A universal minimal genome remains elusive due to context-dependency and variations in essentiality criteria.
• Gene persistence offers a practical framework for identifying genes critical for cellular robustness.
• Understanding gene persistence has implications for genome engineering and synthetic life creation.