NDP-rhamnose biosynthesis and rhamnosyltransferases: building diverse glycoconjugates in nature

Abstract

Rhamnose is an important 6-deoxy sugar present in many natural products, glycoproteins, and structural polysaccharides. Whilst predominantly found as the l-enantiomer, instances of d-rhamnose are also found in nature, particularly in the Pseudomonads bacteria. Interestingly, rhamnose is notably absent from humans and other animals, which poses unique opportunities for drug discovery targeted towards rhamnose utilizing enzymes from pathogenic bacteria. Whilst the biosynthesis of nucleotide-activated rhamnose (NDP-rhamnose) is well studied, the study of rhamnosyltransferases that synthesize rhamnose-containing glycoconjugates is the current focus amongst the scientific community. In this review, we describe where rhamnose has been found in nature, as well as what is known about TDP-β-l-rhamnose, UDP-β-l-rhamnose, and GDP-α-d-rhamnose biosynthesis. We then focus on examples of rhamnosyltransferases that have been characterized using both in vivo and in vitro approaches from plants and bacteria, highlighting enzymes where 3D structures have been obtained. The ongoing study of rhamnose and rhamnosyltransferases, in particular in pathogenic organisms, is important to inform future drug discovery projects and vaccine development.

Discovery and biosynthesis of persiathiacins: Unusual polyglycosylated thiopeptides active against multi-drug resistant tuberculosis

“…17 Moreover, no 6-deoxysugar biosynthetic genes, beyond those hypothesised to be involved in the assembly of TDP-D-amicetose, TDP-D-olivose, and TDP-6-deoxy-β-D-glucose are present in the persiathiacin BGC (Figure 3 and Table S4). Because L-rhamnose is ubiquitously incorporated into bacterial cell surface carbohydrates, 44 dedicated genes for TDP-L-rhamnose biosynthesis are invariably absent from rhamnosylated natural product BGCs. Taken together, these observations are consistent with the assignment of sugar 1 as an O-dimethylated L-rhamnose derivative.…”

Nucleotide sugar dehydratases: Structure, mechanism, substrate specificity, and application potential

“…Not surprisingly, the pathways leading to the two most common deoxy sugars, namely Lfucose (L-Fuc) and L-rhamnose (L-Rha) (Figure 1 A-C), are highly conserved in all domains of life employing homologues of the same enzymes. While L-rhamnose can only be produced by bacteria, fungi, plants and large DNA-viruses, L-fucose is also synthesized by complex eukaryotes like mammals (11)(12)(13)(14)(15)(16)(17). For example, L-fucose can be found as a constituent of Lewis blood group antigens and several human milk oligosaccharides (HMO) but also in bacterial lipopolysaccharide layer (LPS) and plant N-glycan structures (15,(18)(19)(20)(21).…”

“…Plants, viruses and fungi are reported to utilize UDP-Glc as starting substrate, while bacteria and some microalgae prefer (deoxy)thymidine as nucleotide anchor, thus starting from (d)TDP-Glc (12,17,(24)(25)(26)(27)(28)(29). After the initial 4,6-dehydration step converting NDP-Glc to NDP-4-keto-6-deoxy Glc (NDP-4k6d-Glc) (17,29,33), consecutive 3,5-epimerization and 4-reduction steps are needed to yield NDP-L-Rha. These can be catalyzed by a single bifunctional (but two-domain) enzyme or by two separate enzymes.…”

“…1 , A – C ), are highly conserved in all domains of life using homologs of the same enzymes. l -Rha can only be produced by bacteria, fungi, plants, and large DNA viruses, whereas l -Fuc is also synthesized by complex eukaryote-like mammals ( 10 , 11 , 12 , 13 , 14 , 15 , 16 ). For example, l -Fuc can be found as a constituent of Lewis blood group antigens and several human milk oligosaccharides and also in bacterial lipopolysaccharide (LPS) layer and plant N -glycan structures ( 14 , 17 , 18 , 19 , 20 ).…”

“…Plants, viruses, and fungi are reported to utilize UDP-Glc as the starting substrate, whereas bacteria and some microalgae prefer (deoxy)thymidine as a nucleotide anchor, thus starting from (d)TDP-Glc ( 11 , 16 , 23 , 24 , 25 , 26 , 27 , 28 ). After the initial 4,6-dehydration step converting NDP-Glc to NDP-4k6d-Glc ( 16 , 28 , 32 ), consecutive 3,5-epimerization and 4-reduction steps are needed to yield NDP- l -Rha. These can be catalyzed by a single bifunctional (but two-domain) enzyme or by two separate enzymes.…”