Research in our lab is focused on the mechanisms that allow bacteria to control their own growth and reproduction under fluctuating environmental conditions, for example changes in nutrient availability or at the onset of environmental stress. As our primary model organism we use the fresh water bacterium Caulobacter crescentus, which divides asymmetrically and has well-defined cell cycle phases. In addition, we do some of our work in Escherichia coli and Pseudomonas aeruginosa to study how the C. crescentus cell cycle and stress response pathways relate to the ones of other bacteria, and to investigate how precise regulation of cell cycle progression contributes to bacterial persistence and pathogenesis. Our research can be divided into the following subareas:

Regulation of bacterial DNA replication by environmental cues

One of the key events in the cell cycle of all organisms is the initiation of DNA replication. In all bacteria it depends on the conserved replication initiator DnaA. Our recent work in C. crescentus revealed that the environmental control of DNA replication depends on precisely regulated production and degradation rates of DnaA. While conditions inducing unfolded protein stress stimulate DnaA proteolysis by the protease Lon (Jonas et al. 2013), nutrient depletion leads to a reduced rate of DnaA synthesis (Leslie et al. 2015). We have recently identified a post-transcriptional mechanisms involving the N-terminal amino acid sequence of DnaA that tunes DnaA translation elongation in response to nutrient availability (Felletti et al. 2021). We have also studied how DNA replication control is coordinated with cell differentiation under distinct starvation conditions (Hallgren et al. 2023).

Chaperones and cell cycle control

Chaperones have well-documented functions in maintaining protein homeostasis, but they can also have specific regulatory roles in diverse cellular processes by affecting the conformation, stability and function of protein substrates. In bacteria, the major molecular chaperones include the DnaK (Hsp70) and GroEL (Hsp60) systems. We are interested in the precise cellular mechanisms by which major chaperones like DnaK and GroEL are connected with cell cycle and growth control in the model bacterium Caulobacter crescentus. Our findings show that DnaK is essential for growth and DNA replication under non-stress conditions due to its critical function in inhibiting the heat shock sigma factor σ32 (Schramm et al. 2017). On the other hand, we found that the chaperonin GroEL promotes cell division by supporting the functions of critical cell division proteins (Schroeder et al. 2021). We are also interested in understanding how the protein quality control network of C. crescentus manages protein aggregation at the onset of stress and during stress recovery and how the presence of protein aggregates affects cell growth and reproduction (Schramm & Schroeder et al. 2019, Schramm et al. 2020).

Regulated proteolysis in cell cycle control and stress adaptation

Intracellular proteolysis represents an efficient way to regulate the levels of specific proteins. Lon is a highly conserved ATP-dependent protease that has important regulatory and protein quality control functions in cells from the three domains of life. Although Lon has been identified more than 40 years ago, only few native substrate proteins have been identified in most organisms. We have established proteomics approaches that have enabled the identification of > 150 novel putative Lon substrates in C. crescentus (Omnus & Fink et al. 2021), including regulators of cell cycle progression and cell differentiation as well as stress response proteins (Omnus & Fink et al. 2021, Akar et al. 2023). Additionally, we have identified a novel regulator of Lon, called LarA, that tunes the degradation of specific groups of substrates at the onset of proteotoxic stress (Omnus & Fink et al. 2023). Currently, we work towards a better general understanding of how Lon recognizes its substrates and how Lon regulators, such as LarA, modulate the activity and substrate specificity of Lon. We have also begun to expand our work on Lon to other species, including the opportunistic pathogen Pseudomonas aeruginosa.