6 CONTROL OF METABOLIC HOMEOSTASIS
Bacteria are exposed to an ever-changing environment. This forces the cells to constantly sense their surroundings and to adapt to it by regulation of their proteome and metabolome. In this way, bacteria can use their scarce energy resources sparingly and in a targeted manner. Many of the underlying regulatory processes that involve the control of gene expression and enzyme activities are well understood. In contrast, much less is known about the fine-tuning of metabolism which is often achieved by rapidly evolving interactions with regulatory proteins or RNA molecules. As regulation of gene expression is rather slow, direct control of enzyme activities by regulatory interactions seems to be the way of choice for fine-tuning. Indeed, it has been demonstrated that transcription regulation is not sufficient to explain metabolic adaptation (Schilling et al., 2007; Chubukov et al., 2013). One of these examples has recently been identified: the so far unknown B. subtilis protein YneR (see Table 1) was found to interact with two subunits of pyruvate dehydrogenase. Further investigation revealed that this protein inhibits the activity of the pyruvate dehydrogenase (see above; O’Reilly et al., 2023). Similar, the potential control of lipid acquisition by the paralogous proteins YqhY and YloU (Table 1, see above) is an excellent example for the need to study regulatory interactions in metabolism in more details.
A well-established mechanism for fine-tuning a pathway is mediated by regulatory proteins of the PII superfamily. These relatively small proteins can be found in all domains of life and belong to one of the largest family in the group of signal transduction proteins (Forchhammer & Lüddecke, 2016; Forchhammer et al., 2022). Typically, PII proteins bind small molecules to sense the cell’s environment and subsequently interact with a wide variety of proteins in the cell. In the first few years after the discovery of the PII protein, it was already shown to be involved in numerous processes of nitrogen anabolism (Ninfa & Jiang, 2005). Through advances in protein structure research, it became apparent that the family of canonical PII proteins has not only to be expanded to include the PII-like proteins but that these proteins are also involved in many novel regulatory interactions (Forchhammer et al., 2022).
Although the sequence similarity of PII-like proteins is rather low, their trimeric structure is highly conserved and characteristic of this protein family. Excitingly, this has allowed the identification of numerous new sensors that can bind a range of different ligands. For example, the cyanobacterial PII-like signaling protein SbtB was shown to bind numerous adenine nucleotides, including second the messenger molecules cAMP and c-di-AMP. Thus, SbtB not only regulates the bicarbonate transporter SbtA, but also controls the activity of the glycogen-branching enzyme GlgB (Selim et al., 2018; Selim et al., 2021; Fang et al., 2021). Another example is the carboxysome-associated PII-like protein CPII, which binds bicarbonate in addition to ADP/AMP and is thought to regulate carbon metabolism in response to bicarbonate availability (Wheatley et al., 2016). Numerous other PII (-like) proteins, such as the B. subtilis DarA protein or CutA fromE. coli and cyanobacteria, have already been identified and are still waiting to be explored (Gundlach et al., 2015; Selim et al., 2021). Interestingly, DarA binds the essential second messenger molecule c-di-AMP in B. subtilis and related gram-positive bacteria (Campeotto et al., 2015; Sureka et al., 2014; Gundlach et al., 2015); however, the function has still not been identified. For CutA, it has long been assumed that it is involved in copper homeostasis; however, a recent study excludes this possibility, thus leaving both the nature of the ligand of CutA and its molecular function an open question (Selim et al., 2021). The fact, that both mutations in darA and cutAdo not yield clear phenotypes supports the idea that these proteins play a role in fine-control of metabolic homeostasis.
Certainly, we are only at the beginning of understanding the mechanisms by which bacterial metabolism can be adapted to subtle changes in the environment. This is important not only to understand the mechanisms that underly the robustness of metabolic networks, but also - due to the ever-growing demand for industrial products, such as drugs, chemicals or vitamins - underlines the importance of developing pathways that are as efficient as possible and thus of our knowledge of metabolic fine-control.