Glycoconjugate pathway connections revealed by sequence similarity network analysis of the monotopic phosphoglycosyl transferases

Proc Natl Acad Sci U S A. 2021 Jan 26;118(4):e2018289118. doi: 10.1073/pnas.2018289118.

Abstract

The monotopic phosphoglycosyl transferase (monoPGT) superfamily comprises over 38,000 nonredundant sequences represented in bacterial and archaeal domains of life. Members of the superfamily catalyze the first membrane-committed step in en bloc oligosaccharide biosynthetic pathways, transferring a phosphosugar from a soluble nucleoside diphosphosugar to a membrane-resident polyprenol phosphate. The singularity of the monoPGT fold and its employment in the pivotal first membrane-committed step allows confident assignment of both protein and corresponding pathway. The diversity of the family is revealed by the generation and analysis of a sequence similarity network for the superfamily, with fusion of monoPGTs with other pathway members being the most frequent and extensive elaboration. Three common fusions were identified: sugar-modifying enzymes, glycosyl transferases, and regulatory domains. Additionally, unexpected fusions of the monoPGT with members of the polytopic PGT superfamily were discovered, implying a possible evolutionary link through the shared polyprenol phosphate substrate. Notably, a phylogenetic reconstruction of the monoPGT superfamily shows a radial burst of functionalization, with a minority of members comprising only the minimal PGT catalytic domain. The commonality and identity of the fusion partners in the monoPGT superfamily is consistent with advantageous colocalization of pathway members at membrane interfaces.

Keywords: enzyme evolution; glycan biosynthetic pathway; membrane-associated pathway; phylogenetic reconstruction; sequence similarity network.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Amino Acid Sequence
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Binding Sites
  • Cytoplasm / enzymology
  • Cytoplasm / genetics
  • Evolution, Molecular
  • Gene Expression
  • Gene Regulatory Networks
  • Glycoconjugates / chemistry*
  • Glycoconjugates / metabolism
  • Glycosyltransferases / chemistry*
  • Glycosyltransferases / genetics
  • Glycosyltransferases / metabolism
  • Gram-Negative Bacteria / classification
  • Gram-Negative Bacteria / enzymology*
  • Gram-Negative Bacteria / genetics
  • Gram-Positive Bacteria / classification
  • Gram-Positive Bacteria / enzymology*
  • Gram-Positive Bacteria / genetics
  • Metabolic Networks and Pathways / genetics
  • Models, Molecular
  • Periplasm / enzymology
  • Periplasm / genetics
  • Phylogeny
  • Polysaccharides / chemistry*
  • Polysaccharides / metabolism
  • Protein Binding
  • Protein Conformation, alpha-Helical
  • Protein Conformation, beta-Strand
  • Protein Interaction Domains and Motifs
  • Sequence Alignment
  • Sequence Homology, Amino Acid
  • Substrate Specificity

Substances

  • Bacterial Proteins
  • Glycoconjugates
  • Polysaccharides
  • Glycosyltransferases