Quantitative and spatio-temporal features of protein aggregation in Escherichia coli and consequences on protein quality control and cellular ageing

Abstract

The aggregation of proteins as a result of intrinsic or environmental stress may be cytoprotective, but is also linked to pathophysiological states and cellular ageing. We analysed the principles of aggregate formation and the cellular strategies to cope with aggregates in Escherichia coli using fluorescence microscopy of thermolabile reporters, EM tomography and mathematical modelling. Misfolded proteins deposited at the cell poles lead to selective re-localization of the DnaK/DnaJ/ClpB disaggregating chaperones, but not of GroEL and Lon to these sites. Polar aggregation of cytosolic proteins is mainly driven by nucleoid occlusion and not by an active targeting mechanism. Accordingly, cytosolic aggregation can be efficiently re-targeted to alternative sites such as the inner membrane in the presence of site-specific aggregation seeds. Polar positioning of aggregates allows for asymmetric inheritance of damaged proteins, resulting in higher growth rates of damage-free daughter cells. In contrast, symmetric damage inheritance of randomly distributed aggregates at the inner membrane abrogates this rejuvenation process, indicating that asymmetric deposition of protein aggregates is important for increasing the fitness of bacterial cell populations.

Bacterial Inclusion Bodies: Discovering Their Better Half

“…However, there are also reports stating that exclusion of aggregates from mid-cell to the pole is energy-free, and simply results from nucleoid exclusion [17,20,[28][29][30]. Restriction of aggregates to the pole was also observed during treatment with substances disrupting the protein motive force, suggesting an energy independent process of aggregation [20]. Energy-independent polar localization was also confirmed by others [30] but also convincing opposite results were obtained [15].…”

“…There are claims that transport of aggregates to the poles is energy-driven as studies on reassembly of pressure dissociated IBs revealed that confinement to the pole is caused by the presence of the nucleoid but reassembly of smaller aggregates into large IBs does not occur in energy and nutrient depleted cells [16]. However, there are also reports stating that exclusion of aggregates from mid-cell to the pole is energy-free, and simply results from nucleoid exclusion [17,20,[28][29][30]. Restriction of aggregates to the pole was also observed during treatment with substances disrupting the protein motive force, suggesting an energy independent process of aggregation [20].…”

“…Thus, it is not absolutely clear if active ATP-dependent transport of smaller particles is required or if the fluidizing properties of active metabolism are responsible for the polar preference of protein aggregates [16]. IBs and aggregation foci are not only found at the polar sites but also in mid-cells presumably at the place of future septation sites [20,30,31]. The major disaggregating chaperones (DnaK, ClpB) also co-localize at the poles [20] and are required for disaggregation of polar aggregates [15].…”

“…Thus, it is possible that IB formation occurs passively but only when biochemical reactions and active metabolism are disturbing the glassy structure of the cytoplasm. On the other hand there is no doubt that protein disaggregation is an ATP-driven process [20]. For example, HtpG can interact with DnaK/DnaJ/GrpE to further promote refolding of aggregated proteins in an ATP-dependent manner [21].…”

“…For example, HtpG can interact with DnaK/DnaJ/GrpE to further promote refolding of aggregated proteins in an ATP-dependent manner [21]. Alternatively, ClpB can also assist in cooperation with DnaK/DnaJ/GrpE in ATP-driven refolding of aggregated proteins [20,22,23]. The small heat shock proteins (sHSPs) IbpA and IbpB stabilize and decrease the size of protein aggregates [24] thereby promoting DnaK/DnaJ/GrpE and ClpB mediated refolding [25] and further possible proteolysis.…”