A conservative distribution of tridomain NDP-heptose synthetases in actinobacteria

Heptose moieties not only act as building blocks of lipopolysaccharides (LPSs) and capsular polysaccharides (CPSs), which are important for the infection, colonization, and immune recognition of Gram-negative bacteria, but also are components of a variety of natural products with fascinating bioactivities from Gram-positive bacteria. Most of the heptose units are derived from the same precursor, d-sedoheptulose 7-phosphate (S7-P), an intermediate of the pentose phosphate pathway. In principle, S7-P is converted to NDP-heptose via a four-step process sequentially catalyzed by enzymes with isomerase, kinase, phosphatase, and nucleotidyltransferase activities. ADP-d-glycero-β-d-manno-heptose is a common intermediate of ADP-activated heptoses and its biosynthesis has been extensively studied in Gram-negative bacterium. Recently, the research group of this work discovered the first tridomain NDP-heptose synthesis enzyme SepB with isomerase, kinase, and nucleotidyltransferase activities during elucidating the biosynthesis of septacidins, a group of antifungal antibiotics from Gram-positive bacterium. SepB, together with phosphatase SepL, synthesizes ADP-d-glycero-β-d-manno-heptose via the same process as that in Gram-negative strain E. coli.

“The special tridomain feature of SepB aroused our interests to investigate its distribution.” said Dr. Yue Tang, the first author of this work. It is surprising that all the 86 tridomain homologues (including SepB) are conservative to the Actinobacteria class of Gram-positive bacterium. “Discovery of 85 SepB homologues, which are most likely to catalyze NDP-heptose formation, serves a good chance to take a glance at the biological meaning of heptose in Gram-positive bacteria.” said Tang. The related gene clusters of tridomain NDP-heptose synthetase genes belonging to could be categorized into three types, with type I gene clusters encoding septacidin analogues, type II gene clusters dictating natural products with decorated heptose moieties, and type III gene clusters responsible for the installation of glycan chains. “Moreover, homologous proteins of bifunctional kinase/nucleotidyltransferase HldE commonly found in Gram-negative bacterium like E. coli strains were observed in type III clusters. Taken the single domain GDP-heptose synthetase from Aneurinibacillus thermoaerophilus into account, all three forms of NDP-heptose synthetases are present in Gram-positive bacteria, suggesting that the roles of heptoses in Gram-positive bacteria are worthy of attention.” said Professor Yihua, Chen, the corresponding author. Enzymatical characterization of four selected tridomain proteins, Be-6, Cth-2, No-5, and Sa-4, showed that all of them are involved in the biosynthesis of ADP-d-glycero-β-d-manno-heptose, while the kinase domains of the latter three proteins are dysfunctional unexpectedly.  

These results showed that, as Gram-negative bacterium, Gram-positive bacterium is also a rich source of heptoses that are derived from S7-P. This research updates the current knowledge of NDP-heptose biosynthesis in Gram-positive bacterium and set a stage for further works toward heptose-containing natural products mining and their physiological function explorations.

This work was supported in part by the National Key R&D Program of China (2020YFA0907700), the National Natural Science Foundation of China (32025002), and the Center for Ocean Mega-Science, CAS (KEXUE2019GZ05).

See the article:

Tang, Y., Tang, W., Wang, M., et al. (2021). A conservative distribution of tridomain NDP-heptose synthetases in actinobacteria. Sci China Life Sci, in press, https://doi.org/10.1007/s11427-021-2000-2. https://engine.scichina.com/doi/10.1007/s11427-021-2000-2

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