Carbon upshift in Lactococcus cremoris elicits immediate initiation of proteome-wide adaptation, coinciding with growth acceleration and pyruvate dissipation switching.

Abstract

Fitness optimization in a dynamic environment requires bacteria to adapt their proteome in a tightly regulated manner by altering protein production and/or degradation. Here, we investigate proteome adaptation in Lactococcus cremoris following a sudden nutrient upshift (e.g., nutrients that allow faster growth) and focus especially on the fate of redundant proteins after the shift. Protein turnover analysis demonstrated that L. cremoris cultures shifted from galactose to glucose, immediately accelerate growth and initiate proteome-wide adjustment toward glucose-optimized composition. Redundant proteins were predominantly adjusted by lowering (or stopping) protein production combined with dilution by growth. However, pyruvate formate lyase activator (PflA) was actively degraded, which appears correlated to reduced 4Fe-4S cofactor availability. Active PflA removal induces the shutdown of galactose-associated mixed acid fermentation to accelerate the switch toward glucose-associated homolactic fermentation. Our work deciphers molecular adjustments upon environmental change that drive physiological adaptation, including growth rate and central energy metabolism.IMPORTANCEBacteria adapt to their environment by adjusting their molecular makeup, in particular their proteome, which ensures fitness optimization under the newly encountered environmental condition. We present a detailed analysis of proteome adaptation kinetics in Lactococcus cremoris following its acute transition from galactose to glucose media, as an example of a sudden nutrient quality upshift. Analysis of the replacement times of individual proteins after the nutrient upshift established that the entire proteome is instantly adjusting to the new condition, which coincides with immediate growth rate acceleration and metabolic adaptation. The latter is driven by the active removal of the pyruvate formate lyase activator protein that is pivotal in controlling pyruvate dissipation in L. cremoris. Our work exemplifies the amazing rate of molecular adaptation in bacteria that underlies physiological adjustments, including growth rate and carbon metabolism. This mechanistic study contributes to our understanding of adaptation in L. cremoris during the dynamic conditions it encounters during (industrial) fermentation, even though environmental transitions in these processes are mostly more gradual than the acute shift studied here.