title: Polynucleobacter necessarius, a model for genome reduction in both free-living and symbiotic bacteria.
abstract: We present the complete genomic sequence of the essential symbiont Polynucleobacter necessarius (Betaproteobacteria), which is a valuable case study for several reasons. First, it is hosted by a ciliated protist, Euplotes; bacterial symbionts of ciliates are still poorly known because of a lack of extensive molecular data. Second, the single species P. necessarius contains both symbiotic and free-living strains, allowing for a comparison between closely related organisms with different ecologies. Third, free-living P. necessarius strains are exceptional by themselves because of their small genome size, reduced metabolic flexibility, and high worldwide abundance in freshwater systems. We provide a comparative analysis of P. necessarius metabolism and explore the peculiar features of a genome reduction that occurred on an already streamlined genome. We compare this unusual system with current hypotheses for genome erosion in symbionts and free-living bacteria, propose modifications to the presently accepted model, and discuss the potential consequences of translesion DNA polymerase loss.
authors.affiliation: Department of Biology, Pisa University, 56126 Pisa, Italy.
authors.forename: Vittorio
authors.initials: V
authors.lastname: Boscaro
authors.forename: Michele
authors.initials: M
authors.lastname: Felletti
authors.forename: Claudia
authors.initials: C
authors.lastname: Vannini
authors.forename: Matthew S
authors.initials: MS
authors.lastname: Ackerman
authors.forename: Patrick S G
authors.initials: PS
authors.lastname: Chain
authors.forename: Stephanie
authors.initials: S
authors.lastname: Malfatti
authors.forename: Lisa M
authors.initials: LM
authors.lastname: Vergez
authors.forename: Maria
authors.initials: M
authors.lastname: Shin
authors.forename: Thomas G
authors.initials: TG
authors.lastname: Doak
authors.forename: Michael
authors.initials: M
authors.lastname: Lynch
authors.forename: Giulio
authors.initials: G
authors.lastname: Petroni
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D042521:Burkholderiaceae / Q000235:genetics*; D019295:Computational Biology; D016812:Euplotes / Q000382:microbiology*; D019143:Evolution, Molecular; D059646:Genome Size / Q000235:genetics*; D016680:Genome, Bacterial / Q000235:genetics*; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D013559:Symbiosis / Q000235:genetics*
keywords: Burkholderiales; genome streamlining; nonsynonymous mutation rates; protozoa; symbiosis