title: Genomic encyclopedia of sugar utilization pathways in the Shewanella genus.
abstract: BACKGROUND
  Carbohydrates are a primary source of carbon and energy for many bacteria. Accurate projection of known carbohydrate catabolic pathways across diverse bacteria with complete genomes constitutes a substantial challenge due to frequent variations in components of these pathways. To address a practically and fundamentally important challenge of reconstruction of carbohydrate utilization machinery in any microorganism directly from its genomic sequence, we combined a subsystems-based comparative genomic approach with experimental validation of selected bioinformatic predictions by a combination of biochemical, genetic and physiological experiments.
  
  
  RESULTS
  We applied this integrated approach to systematically map carbohydrate utilization pathways in 19 genomes from the Shewanella genus. The obtained genomic encyclopedia of sugar utilization includes ~170 protein families (mostly metabolic enzymes, transporters and transcriptional regulators) spanning 17 distinct pathways with a mosaic distribution across Shewanella species providing insights into their ecophysiology and adaptive evolution. Phenotypic assays revealed a remarkable consistency between predicted and observed phenotype, an ability to utilize an individual sugar as a sole source of carbon and energy, over the entire matrix of tested strains and sugars.Comparison of the reconstructed catabolic pathways with E. coli identified multiple differences that are manifested at various levels, from the presence or absence of certain sugar catabolic pathways, nonorthologous gene replacements and alternative biochemical routes to a different organization of transcription regulatory networks.
  
  
  CONCLUSIONS
  The reconstructed sugar catabolome in Shewanella spp includes 62 novel isofunctional families of enzymes, transporters, and regulators. In addition to improving our knowledge of genomics and functional organization of carbohydrate utilization in Shewanella, this study led to a substantial expansion of our current version of the Genomic Encyclopedia of Carbohydrate Utilization. A systematic and iterative application of this approach to multiple taxonomic groups of bacteria will further enhance it, creating a knowledge base adequate for the efficient analysis of any newly sequenced genome as well as of the emerging metagenomic data.
authors.affiliation: Burnham Institute for Medical Research, La Jolla, California 92037, USA.
authors.forename: Dmitry A
authors.initials: DA
authors.lastname: Rodionov
authors.forename: Chen
authors.initials: C
authors.lastname: Yang
authors.forename: Xiaoqing
authors.initials: X
authors.lastname: Li
authors.forename: Irina A
authors.initials: IA
authors.lastname: Rodionova
authors.forename: Yanbing
authors.initials: Y
authors.lastname: Wang
authors.forename: Anna Y
authors.initials: AY
authors.lastname: Obraztsova
authors.forename: Olga P
authors.initials: OP
authors.lastname: Zagnitko
authors.forename: Ross
authors.initials: R
authors.lastname: Overbeek
authors.forename: Margaret F
authors.initials: MF
authors.lastname: Romine
authors.forename: Samantha
authors.initials: S
authors.lastname: Reed
authors.forename: James K
authors.initials: JK
authors.lastname: Fredrickson
authors.forename: Kenneth H
authors.initials: KH
authors.lastname: Nealson
authors.forename: Andrei L
authors.initials: AL
authors.lastname: Osterman
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D050260:Carbohydrate Metabolism / Q000235:genetics*; D002244:Carbon / Q000378:metabolism; D004755:Enterobacteriaceae / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics*; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D008969:Molecular Sequence Data; D010641:Phenotype; D018085:Regulon / Q000235:genetics; D015203:Reproducibility of Results; D020592:Shewanella / Q000201:enzymology / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D001426:Bacterial Proteins; D002244:Carbon