Intracellular glutamine fluctuates with nitrogen availability and regulates Mycobacterium smegmatis biofilm formation

Biofilm formation allows pathogenic nontuberculous mycobacteria (NTM) to adhere to household plumbing systems and has been observed in vivo during human infection. Glucose drives NTM aggregation in vitro, and ammonium inhibits it, but the regulatory systems controlling this early step in biofilm formation are not understood. Here, we show that a variety of carbon and nitrogen sources have similar impacts on aggregation in the model NTM Mycobacterium smegmatis as glucose and ammonium, suggesting that the response to these nutrients is general and likely sensed through downstream, integrated signals. Next, we performed a transposon screen in M. smegmatis to uncover these putative regulatory nodes. Our screen revealed that mutating specific genes in the purine and pyrimidine biosynthesis pathways caused an aggregation defect, but supplementing with adenosine and guanosine had no impact on aggregation either in a purF mutant or WT. Realizing that the only genes we hit in purine or pyrimidine biosynthesis were those that utilized glutamine as a nitrogen donor, we pivoted to the hypothesis that intracellular glutamine could be a nitrogen-responsive node affecting aggregation. We tested this hypothesis in defined M63 medium using targeted mass spectrometry. Indeed, intracellular glutamine increased with nitrogen availability and correlated with planktonic growth. Furthermore, a garA mutant, which has an artificially expanded glutamine pool in growth phase, grew solely as planktonic cells even without nitrogen supplementation. Altogether these results establish that intracellular glutamine controls M. smegmatis aggregation, and they introduce flux-dependent sensors as key components of the NTM biofilm regulatory system.