title: Combining functional and structural genomics to sample the essential Burkholderia structome.
abstract: BACKGROUND
  The genus Burkholderia includes pathogenic gram-negative bacteria that cause melioidosis, glanders, and pulmonary infections of patients with cancer and cystic fibrosis. Drug resistance has made development of new antimicrobials critical. Many approaches to discovering new antimicrobials, such as structure-based drug design and whole cell phenotypic screens followed by lead refinement, require high-resolution structures of proteins essential to the parasite.
  
  
  RESULTS
  We experimentally identified 406 putative essential genes in B. thailandensis, a low-virulence species phylogenetically similar to B. pseudomallei, the causative agent of melioidosis, using saturation-level transposon mutagenesis and next-generation sequencing (Tn-seq). We selected 315 protein products of these genes based on structure-determination criteria, such as excluding very large and/or integral membrane proteins, and entered them into the Seattle Structural Genomics Center for Infection Disease (SSGCID) structure determination pipeline. To maximize structural coverage of these targets, we applied an "ortholog rescue" strategy for those producing insoluble or difficult to crystallize proteins, resulting in the addition of 387 orthologs (or paralogs) from seven other Burkholderia species into the SSGCID pipeline. This structural genomics approach yielded structures from 31 putative essential targets from B. thailandensis, and 25 orthologs from other Burkholderia species, yielding an overall structural coverage for 49 of the 406 essential gene families, with a total of 88 depositions into the Protein Data Bank. Of these, 25 proteins have properties of a potential antimicrobial drug target i.e., no close human homolog, part of an essential metabolic pathway, and a deep binding pocket. We describe the structures of several potential drug targets in detail.
  
  
  CONCLUSIONS
  This collection of structures, solubility and experimental essentiality data provides a resource for development of drugs against infections and diseases caused by Burkholderia. All expression clones and proteins created in this study are freely available by request.
authors: Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America.
authors: Loren
authors: L
authors: Baugh
authors: Larry A
authors: LA
authors: Gallagher
authors: Rapatbhorn
authors: R
authors: Patrapuvich
authors: Matthew C
authors: MC
authors: Clifton
authors: Anna S
authors: AS
authors: Gardberg
authors: Thomas E
authors: TE
authors: Edwards
authors: Brianna
authors: B
authors: Armour
authors: Darren W
authors: DW
authors: Begley
authors: Shellie H
authors: SH
authors: Dieterich
authors: David M
authors: DM
authors: Dranow
authors: Jan
authors: J
authors: Abendroth
authors: James W
authors: JW
authors: Fairman
authors: David
authors: D
authors: Fox
authors: Bart L
authors: BL
authors: Staker
authors: Isabelle
authors: I
authors: Phan
authors: Angela
authors: A
authors: Gillespie
authors: Ryan
authors: R
authors: Choi
authors: Steve
authors: S
authors: Nakazawa-Hewitt
authors: Mary Trang
authors: MT
authors: Nguyen
authors: Alberto
authors: A
authors: Napuli
authors: Lynn
authors: L
authors: Barrett
authors: Garry W
authors: GW
authors: Buchko
authors: Robin
authors: R
authors: Stacy
authors: Peter J
authors: PJ
authors: Myler
authors: Lance J
authors: LJ
authors: Stewart
authors: Colin
authors: C
authors: Manoil
authors: Wesley C
authors: WC
authors: Van Voorhis
mesh_terms: D019121:Burkholderia Infections / Q000188:drug therapy / Q000235:genetics*; D016957:Burkholderia pseudomallei / Q000235:genetics* / Q000472:pathogenicity; D019295:Computational Biology; D030562:Databases, Protein; D015195:Drug Design; D020043:Genes, Essential; D016680:Genome, Bacterial; D023281:Genomics; D006801:Humans; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D010802:Phylogeny; D011487:Protein Conformation
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