Adaptation of Bacillus subtilis carbon core metabolism to simultaneous nutrient limitation and osmotic challenge: a multi‐omics perspective

Abstract

The Gram-positive bacterium Bacillus subtilis encounters nutrient limitations and osmotic stress in its natural soil ecosystem. To ensure survival and sustain growth, highly integrated adaptive responses are required. Here, we investigated the system-wide response of B. subtilis to different, simultaneously imposed stresses. To address the anticipated complexity of the cellular response networks, we combined chemostat experiments under conditions of carbon limitation, salt stress and osmoprotection with multi-omics analyses of the transcriptome, proteome, metabolome and fluxome. Surprisingly, the flux through central carbon and energy metabolism is very robust under all conditions studied. The key to achieve this robustness is the adjustment of the biocatalytic machinery to compensate for solvent-induced impairment of enzymatic activities during osmotic stress. Specifically, increased production of several enzymes of central carbon metabolism compensates for their reduced activity in the presence of high salt. A major response of the cell during osmotic stress is the production of the compatible solute proline. This is achieved through the concerted adjustment of multiple reactions around the 2-oxoglutarate node, which drives metabolism towards the proline precursor glutamate. The fine-tuning of the transcriptional and metabolic networks involves functional modules that overarch the individual pathways.

Plant-derived compatible solutes proline betaine and betonicine confer enhanced osmotic and temperature stress tolerance to Bacillus subtilis

“…1) could be used by B. subtilis as nutrients, either as sole carbon or as sole nitrogen sources. We also tested the potential use of these compounds as nutrients under high salinity (0.6 M NaCl) growth conditions as we considered the possibility that their uptake would be stimulated by increased osmolarity of the growth medium von Blohn et al, 1997;Zaprasis et al, 2014). Catabolic routes for trans-4-hydroxy-L-proline, L-proline betaine and betonicine have been identified in a variety of micro-organisms (Kumar et al, 2014;Watanabe et al, 2012;White et al, 2012;Zhao et al, 2013), but we found that B. subtilis cannot use any of the studied L-proline derivatives as nutrients (Fig.…”

“…Attesting to the critical role of compatible solute synthesis by micro-organisms for managing osmotic stress (Csonka, 1989;Kempf & Bremer, 1998), the genetic disruption of the osmotically inducible L-proline biosynthesis route causes an osmotically sensitive growth phenotype (Brill et al, 2011a). Osmostress protection of B. subtilis can also be achieved through L-proline uptake and the osmotically inducible OpuE transporter is key to this process von Blohn et al, 1997;Zaprasis et al, 2014). However, compared with the metabolically inert compatible solute glycine betaine (Boch et al, 1994), an exogenous supply of L-proline is not a particularly effective osmoprotectant for B. subtilis (Zaprasis et al, 2013).…”

Uptake of Amino Acids and Their Metabolic Conversion into the Compatible Solute Proline Confers Osmoprotection to Bacillus subtilis

“…We are thus led to the conclusion that the higher growth yield of osmotically stressed cells cultured in the presence of Glu, Gln, Asp, Asn, Arg, Orn, and Cit than of those that did not receive an osmoprotective amino acid (Fig. 2) rests on the saving of precious biosynthetic building blocks and energy sources that would otherwise have to be devoted under high-osmolarity growth conditions (61) to the synthesis of the proline precursor glutamate (31,32) or of proline itself (31,51). The highly interconnected proline and arginine synthesis and degradation pathways of B. subtilis (34,48,49) (Fig.…”

“…The cellular adjustment of B. subtilis to high-osmolarity environments is a well-staged and complex process (61,(69)(70)(71). However, the effective management of water fluxes in or out of the cell (12,72) and the fine-tuning of the solvent properties of the cytoplasm (19,73) are key events that allow cell proliferation under otherwise growth-inhibiting conditions (7,11,13).…”

Current Knowledge and Recent Advances in Marine Dinoflagellate Transcriptomic Research

“…Network analysis from various levels of "omics" data (transcriptomics, proteomic and metabolomics) is essential for understanding the entire behavior of cells during complex biological interactions [114]. Currently, this multi-omics approach has been used widely to study stress response in various organisms such as fungi, plants and bacteria [115][116][117]. However, to the best of our knowledge, there is no study that has been done that utilized multi-omic approaches to unravel dinoflagellates' complexity.…”