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.