Starvation induces shrinkage of the bacterial cytoplasm

Abstract

Environmental fluctuations are a common challenge for single-celled organisms; enteric bacteria such as Escherichia coli experience dramatic changes in nutrient availability, pH, and temperature during their journey into and out of the host. While the effects of altered nutrient availability on gene expression and protein synthesis are well known, their impacts on cytoplasmic dynamics and cell morphology have been largely overlooked. Here, we discover that depletion of utilizable nutrients results in shrinkage of E. coli’s inner membrane from the cell wall. Shrinkage was accompanied by a ∼17% reduction in cytoplasmic volume and a concurrent increase in periplasmic volume. Inner membrane retraction occurred almost exclusively at the new cell pole. This phenomenon was distinct from turgor-mediated plasmolysis and independent of new transcription, translation, or canonical starvation-sensing pathways. Cytoplasmic dry-mass density increased during shrinkage, suggesting that it is driven primarily by loss of water. Shrinkage was reversible: upon a shift to nutrient-rich medium, expansion started almost immediately at a rate dependent on carbon-source quality. Robust recovery from starvation required the Tol-Pal system, highlighting the importance of envelope coupling during recovery. Klebsiella pneumoniae also exhibited shrinkage when shifted to carbon-free conditions, suggesting a conserved phenomenon. These findings demonstrate that even when Gram-negative bacterial growth is arrested, cell morphology and physiology are still dynamic.Significance statementBacterial cells constantly face nutrient fluctuations in their natural environments. While previous studies have identified gene expression changes upon nutrient depletion, it is much less well known how cellular morphology and cytoplasmic properties respond to shifts in nutrient availability. Here, we discovered that switching fast-growing Escherichia coli cells to nutrient-free conditions results in substantial shrinkage of the inner membrane away from the cell wall, especially at the new pole. Shrinkage was primarily driven by loss of cytoplasmic water contents. Shrinkage was also exhibited by cells naturally entering stationary phase, highlighting its biological relevance across starvation conditions. The membrane-spanning Tol-Pal system was critical for robust entry into and recovery from shrinkage, indicating the importance of cell-envelope homeostasis in surviving nutrient starvation.

Polar accumulation of pyoverdin and exit from stationary phase

“…Certain of the dynamics observed by Shi et al (2021) [37] are consistent with our observations, however, some observations are difficult to reconcile with experimental details and the known biology of pyoverdin. For example, polarization of mCherry occurred in the periplasm of E. coli soon after starvation, but these cells maintained high ATP levels typical of exponentially growing cells.…”

“…Lack of location specificity hints at a connection to more general biophysical aspects of cell biology. Interestingly, a recent study of E. coli under starvation conditions showed polar accumulation of fluorescent markers, including mCherry [37]. Accumulation was connected to shrinkage of the cytoplasm, with shrinkage creating additional space in the polar region of the periplasm.…”

Transition of Vibrio cholerae through a natural host induces resistance to environmental changes

“…Upon introduction to artificial fresh water, the bacteria morphologically change, most notably by increasing distance between the inner and the outer membrane. Dehiscence within bacteria, including V. cholerae, has previously been described and it has been associated with the transition to viable but non-culturable states, in which cells have a very low metabolic activity (Brenzinger et al, 2019;Shi et al, 2021). As noted in previous research, V. cholerae also expresses unknown structures in response to stressful environments (Dobro et al, 2017).…”

“…How are V. cholerae cells able to thrive during these drastic changes in environmental conditions of the infection process? Previous studies have shown that the cells alter their shape in response to changing environments (Bartlett et al, 2017;Brenzinger et al, 2019;Shi et al, 2021). In addition to its shape, V. cholerae may also adapt its molecular machines, altering their availability and quantity, to levels that support success in the new environment.…”

Bacterial transcription during growth arrest

“…The resulting changes in gross morphology have the potential to impact transcription during the growth arrest that follows the completion of the reductive divisions, because the DNA becomes denser and more compacted even though the nucleoid occupies a slightly greater fraction of the cellular volume as growth rates slow toward growth arrest [30,31]. Recent studies have suggested that nutrient downshift can result in a modest decrease in cytoplasmic volume even in the absence of reductive divisions, leading to a further increase in cellular density [32]. Similar phenomena have also been observed in eukaryotic microbes such as yeast and have been proposed in both systems to contribute to increased macromolecular crowding, decreased mobility, and increased rigidity of both the chromosome(s) and the cytoplasm [33,34].…”