Sociality changes Gene Essentiality

Abstract

Transposon insertion sequencing (Tn-seq) has become a powerful tool for assigning gene fitness and essentiality in bacteria, and has recently been extended to bacteriophages. A core but rarely examined assumption of these screens is that fitness is measured in an asocial environment, where each mutant succeeds or fails on its own. Yet many genes act socially: their products can be shared among neighbors, allowing defective mutants to be complemented in trans. In phages multiple genotypes routinely coinfect the same cell. Here we show that social interactions distort gene essentiality. Using paired quorum-sensing microarray and Tn-seq data from Pseudomonas aeruginosa, we find that quorum-sensing-regulated genes are over-represented among genes scored as non-essential, confirming that social genes are under-reported as essential. We then build a stochastic, agent-based model of phage Tn-seq across an MOI gradient, assigning each gene an intrinsic fitness effect and a complementation fraction. Complementable ("social") genes rise in frequency as MOI increases, masking their true fitness cost, whereas non-complementable ("private") genes, do not. Partitioning genes by life-cycle stage and applying a two-round high-then-low-MOI design, further separates gene functions by life cycle stage. We argue that deliberate MOI manipulation turns a confound into a tool, enabling systematic classification of phage sociality.