Nucleotide sequence based characterizations of two cryptic plasmids from the marine bacterium Ruegeria isolate PR1b Zhenping Zhong, a,1 Ron Caspi, a,2 Donald Helinski, a Vic Knauf, b,3 Sean Sykes, c Colleen OÕByrne, c Terrance P. Shea, c Jane E. Wilkinson, c,4 Craig DeLoughery, c,5 and Aresa Toukdarian a, * a Division of Biology and Center for Molecular Genetics, University of California, San Diego, La Jolla, CA 92093-0322, USA b Calgene Inc, Davis, CA 95616, USA c Cereon Genomics, Cambridge, MA 02139, USA Received 4 September 2002, revised 19 November 2002 Abstract Twoplasmids,76and148kbinsize,isolatedfrom Ruegeria strainPR1bwereentirelysequenced.Thesearethefirst plasmids to be characterized from this genus of marine bacteria. Sequence analysis revealed a biased distribution of functionamongtheputativeproteinsencodedonthetwoplasmids.Thesmallerplasmid,designatedpSD20,encodesa large number of putative proteins involved in polysaccharide biosynthesis and export. The larger plasmid, designated pSD25, primarily encodes putative proteins involved in the transport of small molecules and in DNA mobilization. Sequence analysis revealed uncommon potential replication systems on both plasmids. pSD25, the first repABC-type replicon isolated from the marine environment, actually contains two repABC-type replicons. pSD20 contains a complex replication region, including a replication origin and initiation protein similar to iteron-containing plasmids (suchaspSW500fromtheplantpathogen Erwinia stewartii)linkedtoputativeRepAandRepBstabilizationproteinsof a repABC-type replicon and is highly homologous to a plasmid from the phototrophic bacterium Rhodobacter sph- aeroides.Giventhenatureoftheputativeproteinsencodedbybothplasmidsitispossiblethattheseplasmidsenhance the metabolic and physiological flexibility of the host bacterium, and thus its adaptation to the marine sediment environment. Ó 2003 Elsevier Science (USA). All rights reserved. Keywords: Biased putative functions; Environmental adaptation; Polysaccharide biosynthesis; ABC transporter; repABC replicon Plasmid 49 (2003) 233–252 www.elsevier.com/locate/yplas * Corresponding author. Fax: 1-858-534-0559. E-mail address: atoukdar@uscd.edu (A. Toukdarian). 1 Present address: Texas A&M University, College Station, TX 77840. 2 Present address: Pangene Corporation, 5500 Stewart Avenue, Fremont, CA 94538. 3 Present address: Tilligen Inc., 1000 Seneca Street Suite 200, Seattle, WA 98101. 4 Present address: Whitehead Institute, Nine Cambridge Center, Cambridge, MA 02142. 5 Present address: Aventis, 26 Lansdowne St., Cambridge, MA 02139. 0147-619X/03/$ - see front matter Ó 2003 Elsevier Science (USA). All rights reserved. doi:10.1016/S0147-619X(03)00014-3