Lysine Malonylome May Affect the Central Metabolism and Erythromycin Biosynthesis Pathway in Saccharopolyspora erythraea

Lysine
acylation is a dynamic, reversible post-translational modification
that can regulate cellular and organismal metabolism in bacteria.
Acetylome has been studied well in bacteria. However, to our knowledge,
there are no proteomic data on the lysine malonylation in prokaryotes,
especially in actinomycetes, which are the major producers of therapeutic
antibiotics. In our study, the first malonylome of the erythromycin-producing Saccharopolyspora erythraea was described by using
a high-resolution mass spectrometry-based proteomics approach and
high-affinity antimalonyllysine antibodies. We identified 192 malonylated
sites on 132 substrates. Malonylated proteins are enriched in many
biological processes such as protein synthesis, glycolysis and gluconeogenesis,
the TCA cycle, and the feeder metabolic pathways of erythromycin synthesis
according to GO analysis and KEGG pathway analysis. A total of 238
S/T/Y/H-phosphorylated sites on 158 proteins were also identified
in our study, which aimed to explore the potential cross-talk between
acylation and phosphorylation. After that, site-specific mutations
showed that malonylation is a negative regulatory modification on
the enzymatic activity of the acetyl–CoA synthetase (Acs) and
glutamine synthetase (Gs). Furthermore, we compared the malonylation
levels of the two-growth state to explore the potential effect of
malonylation on the erythromycin biosynthesis. These findings expand
our current knowledge of the actinomycetes malonylome and supplement
the acylproteome databases of the whole bacteria.