title: Niche adaptation and genome expansion in the chlorophyll d-producing cyanobacterium Acaryochloris marina.
abstract: Acaryochloris marina is a unique cyanobacterium that is able to produce chlorophyll d as its primary photosynthetic pigment and thus efficiently use far-red light for photosynthesis. Acaryochloris species have been isolated from marine environments in association with other oxygenic phototrophs, which may have driven the niche-filling introduction of chlorophyll d. To investigate these unique adaptations, we have sequenced the complete genome of A. marina. The DNA content of A. marina is composed of 8.3 million base pairs, which is among the largest bacterial genomes sequenced thus far. This large array of genomic data is distributed into nine single-copy plasmids that code for >25% of the putative ORFs. Heavy duplication of genes related to DNA repair and recombination (primarily recA) and transposable elements could account for genetic mobility and genome expansion. We discuss points of interest for the biosynthesis of the unusual pigments chlorophyll d and alpha-carotene and genes responsible for previously studied phycobilin aggregates. Our analysis also reveals that A. marina carries a unique complement of genes for these phycobiliproteins in relation to those coding for antenna proteins related to those in Prochlorococcus species. The global replacement of major photosynthetic pigments appears to have incurred only minimal specializations in reaction center proteins to accommodate these alternate pigments. These features clearly show that the genus Acaryochloris is a fitting candidate for understanding genome expansion, gene acquisition, ecological adaptation, and photosystem modification in the cyanobacteria.
authors.affiliation: Institute of Low Temperature Science, Hokkaido University, N19W8, Sapporo 060-0819, Japan.
authors.forename: Wesley D
authors.initials: WD
authors.lastname: Swingley
authors.forename: Min
authors.initials: M
authors.lastname: Chen
authors.forename: Patricia C
authors.initials: PC
authors.lastname: Cheung
authors.forename: Amber L
authors.initials: AL
authors.lastname: Conrad
authors.forename: Liza C
authors.initials: LC
authors.lastname: Dejesa
authors.forename: Jicheng
authors.initials: J
authors.lastname: Hao
authors.forename: Barbara M
authors.initials: BM
authors.lastname: Honchak
authors.forename: Lauren E
authors.initials: LE
authors.lastname: Karbach
authors.forename: Ahmet
authors.initials: A
authors.lastname: Kurdoglu
authors.forename: Surobhi
authors.initials: S
authors.lastname: Lahiri
authors.forename: Stephen D
authors.initials: SD
authors.lastname: Mastrian
authors.forename: Hideaki
authors.initials: H
authors.lastname: Miyashita
authors.forename: Lawrence
authors.initials: L
authors.lastname: Page
authors.forename: Pushpa
authors.initials: P
authors.lastname: Ramakrishna
authors.forename: Soichirou
authors.initials: S
authors.lastname: Satoh
authors.forename: W Matthew
authors.initials: WM
authors.lastname: Sattley
authors.forename: Yuichiro
authors.initials: Y
authors.lastname: Shimada
authors.forename: Heather L
authors.initials: HL
authors.lastname: Taylor
authors.forename: Tatsuya
authors.initials: T
authors.lastname: Tomo
authors.forename: Tohru
authors.initials: T
authors.lastname: Tsuchiya
authors.forename: Zi T
authors.initials: ZT
authors.lastname: Wang
authors.forename: Jason
authors.initials: J
authors.lastname: Raymond
authors.forename: Mamoru
authors.initials: M
authors.lastname: Mimuro
authors.forename: Robert E
authors.initials: RE
authors.lastname: Blankenship
authors.forename: Jeffrey W
authors.initials: JW
authors.lastname: Touchman
mesh_terms: D000222:Adaptation, Physiological; D002734:Chlorophyll / Q000096:biosynthesis*; D002876:Chromosomes, Bacterial; D000458:Cyanobacteria / Q000235:genetics* / Q000378:metabolism / Q000502:physiology*; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D008969:Molecular Sequence Data; D010802:Phylogeny
chemical_list: D002734:Chlorophyll; C107509:chlorophyll d