Molecular evolution of the bacterial pseudouridine‐5′‐phosphate glycosidase protein family

Abstract

Pseudouridine is a noncanonical C–nucleoside commonly present in RNA, which is not metabolized in mammals, but can be recycled by the unique enzyme family of bacterial pseudouridine glycosidases such as YeiN from Escherichia coli. Here, we present rigorous bioinformatic and biochemical analyses of the protein family in order to find sequences that might code for nonpseudouridine glycosidase activities. To date, the only other function reported for the enzyme family occurs during the biosynthesis of the antibiotic alnumycin A in Streptomyces species, where AlnA functions as an unusual C–glycosynthase. Bioinformatics analysis of 755 protein sequences identified one group of sequences that were unlikely to harbour pseudouridine glycosidase activities. This observation was confirmed in vitro with one representative protein, IdgA from Streptomyces albus, which was unable to synthesize pseudouridine monophosphate, but was able to attach d–ribose‐5‐phosphate to juglone. Furthermore, our analyses provide evidence for horizontal gene transfer of pseudouridine glycosidases that may have occurred in Streptomyces and Doria species. Inspection of the genomic loci in the vicinity of pseudouridine glycosidases revealed that in 77% of the strains a kinase gene putatively involved in the phosphorylation of pseudouridine was found nearby, whereas the sequences encoding nonpseudouridine glycosidases coexisted with a phosphatase of the haloacid dehalogenase enzyme family. The investigation suggested that these unknown sequences might be involved in the biosynthesis of soluble blue pigments because of the presence of genes homologous to nonribosomal peptide synthetases.

Reverse C-glycosidase reaction provides C-nucleotide building blocks of xenobiotic nucleic acids

“…CM020, that catalyze β-C-riboside formation from D-Rib5P (1) and different naphthoquinones (Supplementary Fig. 7) 53,54,87 . The herein developed idea of modular phosphorylation-glycosylation cascades could be analogously applied to AlnA-type C-glycosynthases, to also harness these enzymes' catalytic proficiency and substrate promiscuity for practical synthesis.…”

Investigation of Indigoidine Synthetase Reveals a Conserved Active-Site Base Residue of Nonribosomal Peptide Synthetase Oxidases

“…[12][13][14][15] Indigoidine synthetase genes have been engineered and introduced into living systems to construct a cross-kingdom reporter system 16 , generate blue rose 17 , and produce 2 as a promising water-insoluble dye 18,19 . Interestingly, indigoidine synthetase genes are widely distributed in bacteria, including Actinobacteria and Proteobacteria ( Figure S1), and frequently colocalized with genes encoding enzymes that glycosylate C-5 of 1, leading to the water-soluble blue pigment indochrome 20,21 , and the C-nucleoside antibiotic, minimycin 13 (Figure 1b). As such, indigoidine synthetases are involved in biosynthesis of a broad range of bacterial secondary metabolites.…”

MU-PseUDeep: A deep learning method for prediction of pseudouridine sites

“…It is known that Ψ and other modified ribonucleosides play an important role in inter-nucleotide bond formation by means of guanyl-specific ribonucleases [42] . Ψ is also known to bind protein phosphatase in some bacterial species [43] , [44] , [45] . Previous research has also indicated the importance of Ψ in regulating neuronal functions [46] , which is corroborated by the enrichment of biological processes shown in Fig.…”