title: The complete genome sequence of the algal symbiont Dinoroseobacter shibae: a hitchhiker's guide to life in the sea.
abstract: Dinoroseobacter shibae DFL12(T), a member of the globally important marine Roseobacter clade, comprises symbionts of cosmopolitan marine microalgae, including toxic dinoflagellates. Its annotated 4 417 868 bp genome sequence revealed a possible advantage of this symbiosis for the algal host. D. shibae DFL12(T) is able to synthesize the vitamins B(1) and B(12) for which its host is auxotrophic. Two pathways for the de novo synthesis of vitamin B(12) are present, one requiring oxygen and the other an oxygen-independent pathway. The de novo synthesis of vitamin B(12) was confirmed to be functional, and D. shibae DFL12(T) was shown to provide the growth-limiting vitamins B(1) and B(12) to its dinoflagellate host. The Roseobacter clade has been considered to comprise obligate aerobic bacteria. However, D. shibae DFL12(T) is able to grow anaerobically using the alternative electron acceptors nitrate and dimethylsulfoxide; it has the arginine deiminase survival fermentation pathway and a complex oxygen-dependent Fnr (fumarate and nitrate reduction) regulon. Many of these traits are shared with other members of the Roseobacter clade. D. shibae DFL12(T) has five plasmids, showing examples for vertical recruitment of chromosomal genes (thiC) and horizontal gene transfer (cox genes, gene cluster of 47 kb) possibly by conjugation (vir gene cluster). The long-range (80%) synteny between two sister plasmids provides insights into the emergence of novel plasmids. D. shibae DFL12(T) shows the most complex viral defense system of all Rhodobacterales sequenced to date.
authors.affiliation: Helmholtz-Centre for Infection Research, Braunschweig, Germany. iwd@helmholtz-hzi.de
authors.forename: Irene
authors.initials: I
authors.lastname: Wagner-Döbler
authors.forename: Britta
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authors.lastname: Ballhausen
authors.forename: Martine
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authors.lastname: Berger
authors.forename: Thorsten
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authors.lastname: Brinkhoff
authors.forename: Ina
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authors.lastname: Buchholz
authors.forename: Boyke
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authors.forename: Heribert
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authors.lastname: Cypionka
authors.forename: Rolf
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authors.forename: Thomas
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authors.lastname: Drepper
authors.forename: Gunnar
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authors.lastname: Gerdts
authors.forename: Sarah
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authors.lastname: Hahnke
authors.forename: Cliff
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authors.lastname: Han
authors.forename: Dieter
authors.initials: D
authors.lastname: Jahn
authors.forename: Daniela
authors.initials: D
authors.lastname: Kalhoefer
authors.forename: Hajnalka
authors.initials: H
authors.lastname: Kiss
authors.forename: Hans-Peter
authors.initials: HP
authors.lastname: Klenk
authors.forename: Nikos
authors.initials: N
authors.lastname: Kyrpides
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Liebl
authors.forename: Heiko
authors.initials: H
authors.lastname: Liesegang
authors.forename: Linda
authors.initials: L
authors.lastname: Meincke
authors.forename: Amrita
authors.initials: A
authors.lastname: Pati
authors.forename: Jörn
authors.initials: J
authors.lastname: Petersen
authors.forename: Tanja
authors.initials: T
authors.lastname: Piekarski
authors.forename: Claudia
authors.initials: C
authors.lastname: Pommerenke
authors.forename: Silke
authors.initials: S
authors.lastname: Pradella
authors.forename: Rüdiger
authors.initials: R
authors.lastname: Pukall
authors.forename: Ralf
authors.initials: R
authors.lastname: Rabus
authors.forename: Erko
authors.initials: E
authors.lastname: Stackebrandt
authors.forename: Sebastian
authors.initials: S
authors.lastname: Thole
authors.forename: Linda
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authors.lastname: Thompson
authors.forename: Petra
authors.initials: P
authors.lastname: Tielen
authors.forename: Jürgen
authors.initials: J
authors.lastname: Tomasch
authors.forename: Mathias
authors.initials: M
authors.lastname: von Jan
authors.forename: Nittaya
authors.initials: N
authors.lastname: Wanphrut
authors.forename: Antje
authors.initials: A
authors.lastname: Wichels
authors.forename: Hajo
authors.initials: H
authors.lastname: Zech
authors.forename: Meinhard
authors.initials: M
authors.lastname: Simon
mesh_terms: D000332:Aerobiosis; D000693:Anaerobiosis; D053898:Biosynthetic Pathways / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry* / Q000235:genetics*; D004121:Dimethyl Sulfoxide / Q000378:metabolism; D056890:Eukaryota / Q000254:growth & development / Q000382:microbiology; D016680:Genome, Bacterial; D008969:Molecular Sequence Data; D009566:Nitrates / Q000378:metabolism; D010957:Plasmids; D041902:Rhodobacteraceae / Q000235:genetics* / Q000302:isolation & purification / Q000502:physiology; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D013559:Symbiosis; D026801:Synteny; D013831:Thiamine / Q000096:biosynthesis; D014805:Vitamin B 12 / Q000096:biosynthesis
chemical_list: D004269:DNA, Bacterial; D009566:Nitrates; D014805:Vitamin B 12; D013831:Thiamine; D004121:Dimethyl Sulfoxide