title: Phylogenomic analysis of glycogen branching and debranching enzymatic duo.
abstract: BACKGROUND
  Branched polymers of glucose are universally used for energy storage in cells, taking the form of glycogen in animals, fungi, Bacteria, and Archaea, and of amylopectin in plants. Some enzymes involved in glycogen and amylopectin metabolism are similarly conserved in all forms of life, but some, interestingly, are not. In this paper we focus on the phylogeny of glycogen branching and debranching enzymes, respectively involved in introducing and removing of the α(1-6) bonds in glucose polymers, bonds that provide the unique branching structure to glucose polymers.
  
  
  RESULTS
  We performed a large-scale phylogenomic analysis of branching and debranching enzymes in over 400 completely sequenced genomes, including more than 200 from eukaryotes. We show that branching and debranching enzymes can be found in all kingdoms of life, including all major groups of eukaryotes, and thus were likely to have been present in the last universal common ancestor (LUCA) but have been lost in seemingly random fashion in numerous single-celled eukaryotes. We also show how animal branching and debranching enzymes evolved from their LUCA ancestors by acquiring additional domains. Furthermore, we show that enzymes commonly perceived as orthologous, such as human branching enzyme GBE1 and E. coli branching enzyme GlgB, are in fact related by a gene duplication and consequently paralogous.
  
  
  CONCLUSIONS
  Despite being usually associated with animal liver glycogen and plant starch, energy storage in the form of branched glucose polymers is clearly an ancient process and has probably been present in the last universal common ancestor of all present life. The evolution of the enzymes enabling this form of energy storage is more complex than previously thought and illustrates the need for explicit phylogenomic analysis in the study of even seemingly "simple" metabolic enzymes. Patterns of conservation in the evolution of the glycogen/starch branching and debranching enzymes hint at some as yet unknown mechanisms, as mutations disrupting these patterns lead to a variety of genetic diseases in humans and other mammals.
authors.affiliation: Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, 10901 N, Torrey Pines Road, La Jolla 92037, CA, USA. czmasek@sanfordburnham.org.
authors.forename: Christian M
authors.initials: CM
authors.lastname: Zmasek
authors.forename: Adam
authors.initials: A
authors.lastname: Godzik
mesh_terms: D015061:1,4-alpha-Glucan Branching Enzyme / Q000235:genetics*; D000818:Animals; D001419:Bacteria / Q000235:genetics; D056890:Eukaryota / Q000145:classification / Q000201:enzymology / Q000378:metabolism; D019143:Evolution, Molecular; D006003:Glycogen / Q000378:metabolism; D006008:Glycogen Storage Disease / Q000201:enzymology; D006801:Humans; D010802:Phylogeny; D010944:Plants / Q000201:enzymology / Q000235:genetics; D013213:Starch / Q000378:metabolism
chemical_list: D013213:Starch; D006003:Glycogen; D015061:1,4-alpha-Glucan Branching Enzyme