CRISPR interference screens reveal tradeoffs between growth rate and robustness in Synechocystis sp. PCC 6803 across trophic conditions

Barcoded mutant libraries are a powerful tool for elucidating gene function in microbes, particularly when screened in multiple growth conditions. We screened a pooled CRISPR interference library of the cyanobacterium Synechocystis sp. PCC 6803 in 11 conditions with multiple light regimes and carbon sources. The library contained 21,705 mutants with high redundancy over all open reading frames and non-coding RNAs. Comparison of derived gene fitness scores revealed instances of gene repression being beneficial in one condition while detrimental in others, particularly for genes within light harvesting and conversion, such as antennae components at high light and PSII subunits in photoheterotrophy. Suboptimal regulation of such genes may represent a tradeoff of reduced growth speed for enhanced robustness. This dataset assigns condition-specific importance to many previously unannotated genes, and suggests new functions for some central enzymes. Prk, GAPDH, and CP12 were critical for mixotrophy and photoheterotrophy, which implicates the ternary complex in redirecting metabolic flux in these conditions. We applied machine learning on sgRNA sequences and gene repression data, which showed the importance of C enrichment and T depletion in the 12 bp proximal to the PAM site. Fitness data is compiled in an interactive web application.