title: Comparative genomics and transcriptional profiles of Saccharopolyspora erythraea NRRL 2338 and a classically improved erythromycin over-producing strain.
abstract: BACKGROUND
  The molecular mechanisms altered by the traditional mutation and screening approach during the improvement of antibiotic-producing microorganisms are still poorly understood although this information is essential to design rational strategies for industrial strain improvement. In this study, we applied comparative genomics to identify all genetic changes occurring during the development of an erythromycin overproducer obtained using the traditional mutate-and- screen method.
  
  
  RESULTS
  Compared with the parental Saccharopolyspora erythraea NRRL 2338, the genome of the overproducing strain presents 117 deletion, 78 insertion and 12 transposition sites, with 71 insertion/deletion sites mapping within coding sequences (CDSs) and generating frame-shift mutations. Single nucleotide variations are present in 144 CDSs. Overall, the genomic variations affect 227 proteins of the overproducing strain and a considerable number of mutations alter genes of key enzymes in the central carbon and nitrogen metabolism and in the biosynthesis of secondary metabolites, resulting in the redirection of common precursors toward erythromycin biosynthesis. Interestingly, several mutations inactivate genes coding for proteins that play fundamental roles in basic transcription and translation machineries including the transcription anti-termination factor NusB and the transcription elongation factor Efp. These mutations, along with those affecting genes coding for pleiotropic or pathway-specific regulators, affect global expression profile as demonstrated by a comparative analysis of the parental and overproducer expression profiles. Genomic data, finally, suggest that the mutate-and-screen process might have been accelerated by mutations in DNA repair genes.
  
  
  CONCLUSIONS
  This study helps to clarify the mechanisms underlying antibiotic overproduction providing valuable information about new possible molecular targets for rationale strain improvement.
authors.affiliation: Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20090 Segrate, Milano, Italy.
authors.forename: Clelia
authors.initials: C
authors.lastname: Peano
authors.forename: Adelfia
authors.initials: A
authors.lastname: Talà
authors.forename: Giorgio
authors.initials: G
authors.lastname: Corti
authors.forename: Daniela
authors.initials: D
authors.lastname: Pasanisi
authors.forename: Miriana
authors.initials: M
authors.lastname: Durante
authors.forename: Giovanni
authors.initials: G
authors.lastname: Mita
authors.forename: Silvio
authors.initials: S
authors.lastname: Bicciato
authors.forename: Gianluca
authors.initials: G
authors.lastname: De Bellis
authors.forename: Pietro
authors.initials: P
authors.lastname: Alifano
mesh_terms: D000900:Anti-Bacterial Agents / Q000096:biosynthesis*; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D002244:Carbon / Q000378:metabolism; D004917:Erythromycin / Q000096:biosynthesis*; D005798:Genes, Bacterial; D023281:Genomics; D009154:Mutation; D016366:Open Reading Frames; D016930:Saccharopolyspora / Q000235:genetics* / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins; D004917:Erythromycin; D002244:Carbon