Molecular analysis of an enigmatic Streptococcus pneumoniae virulence factor: The raffinose-family oligosaccharide utilization system

J Biol Chem. 2019 Nov 15;294(46):17197-17208. doi: 10.1074/jbc.RA119.010280. Epub 2019 Oct 7.


Streptococcus pneumoniae is an opportunistic respiratory pathogen that can spread to other body sites, including the ears, brain, and blood. The ability of this bacterium to break down, import, and metabolize a wide range of glycans is key to its virulence. Intriguingly, S. pneumoniae can utilize several plant oligosaccharides for growth in vitro, including raffinose-family oligosaccharides (RFOs, which are α-(1→6)-galactosyl extensions of sucrose). An RFO utilization locus has been identified in the pneumococcal genome; however, none of the proteins encoded by this locus have been biochemically characterized. The enigmatic ability of S. pneumoniae to utilize RFOs has recently received attention because mutations in two of the RFO locus genes have been linked to the tissue tropism of clinical pneumococcal isolates. Here, we use functional studies combined with X-ray crystallography to show that although the pneumococcal RFO locus encodes for all the machinery required for uptake and degradation of RFOs, the individual pathway components are biochemically inefficient. We also demonstrate that the initiating enzyme in this pathway, the α-galactosidase Aga (a family 36 glycoside hydrolase), can cleave α-(1→3)-linked galactose units from a linear blood group antigen. We propose that the pneumococcal RFO pathway is an evolutionary relic that is not utilized in this streptococcal species and, as such, is under no selection pressure to maintain binding affinity and/or catalytic efficiency. We speculate that the apparent contribution of RFO utilization to pneumococcal tissue tropism may, in fact, be due to the essential role the ATPase RafK plays in the transport of other carbohydrates.

Keywords: Streptococcus; X-ray crystallography; galactosidase; glycoside hydrolase; host-pathogen interaction; pneumococcus; raffinose-family oligosaccharide (RFO); structure-function; virulence factor.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Genetic Loci
  • Host-Pathogen Interactions
  • Humans
  • Models, Molecular
  • Pneumococcal Infections / metabolism
  • Pneumococcal Infections / microbiology
  • Raffinose / genetics
  • Raffinose / metabolism*
  • Streptococcus pneumoniae / genetics
  • Streptococcus pneumoniae / pathogenicity
  • Streptococcus pneumoniae / physiology*
  • alpha-Galactosidase / genetics
  • alpha-Galactosidase / metabolism


  • Bacterial Proteins
  • alpha-Galactosidase
  • Raffinose

Associated data

  • PDB/2I58
  • PDB/4ZZE
  • PDB/4FNU