Chemical-genetic interrogation of RNA polymerase mutants reveals structure-function relationships and physiological tradeoffs

The multi-subunit bacterial RNA polymerase (RNAP) and its associated
regulators carry out transcription and integrate myriad regulatory
signals. Numerous studies have interrogated the inner workings of RNAP,
and mutations in genes encoding RNAP drive adaptation of Escherichia coli
to many health- and industry-relevant environments, yet a paucity of
systematic analyses has hampered our understanding of the fitness benefits
and trade-offs from altering RNAP function. Here, we conduct a
chemical-genetic analysis of a library of RNAP mutants. We discover
phenotypes for non-essential insertions, show that clustering mutant
phenotypes increases their predictive power for drawing functional
inferences, and demonstrate that some RNA polymerase mutants both decrease
average cell length and confer insensitivity to killing by cell-wall
targeting antibiotics. Our findings demonstrate that RNAP chemical-genetic
interactions provide a general platform for interrogating
structure-function relationships in vivo and for identifying physiological
trade-offs of mutations, including those relevant for disease and
biotechnology. This strategy should have broad utility for illuminating
the role of other important protein complexes.