title: Prediction and biochemical demonstration of a catabolic pathway for the osmoprotectant proline betaine.
abstract: Through the use of genetic, enzymatic, metabolomic, and structural analyses, we have discovered the catabolic pathway for proline betaine, an osmoprotectant, in Paracoccus denitrificans and Rhodobacter sphaeroides. Genetic and enzymatic analyses showed that several of the key enzymes of the hydroxyproline betaine degradation pathway also function in proline betaine degradation. Metabolomic analyses detected each of the metabolic intermediates of the pathway. The proline betaine catabolic pathway was repressed by osmotic stress and cold stress, and a regulatory transcription factor was identified. We also report crystal structure complexes of the P. denitrificans HpbD hydroxyproline betaine epimerase/proline betaine racemase with l-proline betaine and cis-hydroxyproline betaine.
  
  
  OBJECTIVE
  At least half of the extant protein annotations are incorrect, and the errors propagate as the number of genome sequences increases exponentially. A large-scale, multidisciplinary sequence- and structure-based strategy for functional assignment of bacterial enzymes of unknown function has demonstrated the pathway for catabolism of the osmoprotectant proline betaine.
authors: Ritesh
authors: R
authors: Kumar
authors: Suwen
authors: S
authors: Zhao
authors: Matthew W
authors: MW
authors: Vetting
authors: B McKay
authors: BM
authors: Wood
authors: Ayano
authors: A
authors: Sakai
authors: Kyuil
authors: K
authors: Cho
authors: José
authors: J
authors: Solbiati
authors: Steven C
authors: SC
authors: Almo
authors: Jonathan V
authors: JV
authors: Sweedler
authors: Matthew P
authors: MP
authors: Jacobson
authors: John A
authors: JA
authors: Gerlt
authors: John E
authors: JE
authors: Cronan
mesh_terms: D000591:Amino Acid Isomerases / Q000737:chemistry; D003080:Cold Temperature; D018360:Crystallography, X-Ray; D015964:Gene Expression Regulation, Bacterial; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D055442:Metabolome; D009997:Osmotic Pressure; D010231:Paracoccus denitrificans / Q000187:drug effects / Q000235:genetics* / Q000378:metabolism* / Q000528:radiation effects; D011392:Proline / Q000031:analogs & derivatives* / Q000378:metabolism; D011487:Protein Conformation; D012242:Rhodobacter sphaeroides / Q000187:drug effects / Q000235:genetics* / Q000378:metabolism* / Q000528:radiation effects; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism
chemical_list: D014157:Transcription Factors; D011392:Proline; D000591:Amino Acid Isomerases; C021420:hydroxyproline epimerase; C003342:stachydrine