Ith a lambda-phage cI motif are also likely correlated with the extra recA (22, 24). The presence of multiples copies of recA and related enzymes could account for gene duplication and/or integration of foreign genes that would lead to genome expansion. Based on the comparative analysis of many genomes, Konstantinidis et al. (21) hypothesized that species with large genomes may dominate noncompeti
DsDNA Preparation. A. marina was grown as described (29) on 1.5 agar plates. Genomic DNA was isolated by using the U.S. Department of Energy Joint Genome Initiative ``DNA Isolation Bacterial CTAB Protocol'' (http:// my.jgi.doe.gov/general/index.html). Genome Sequencing. The A. marina genome was sequenced by using a pyrosequencing approach on a Roche-454 GS20 instrument at 454 Life Sciences. Appro
G chlorophyll.Fig. 3. A schematic of the putative carotenoid biosynthesis pathway in Acaryochloris. The reaction catalyzed by CrtR passes through the intermediate -cryptoxanthin.which likely provided the origin for CAO, and other poorly understood enzymes, such as the phylogenetically aberrant divinyl chlorophyllide reductase (33), which shows an unusual phylogenetic topology in A. marina (AM1 239
G chlorophyll.Fig. 3. A schematic of the putative carotenoid biosynthesis pathway in Acaryochloris. The reaction catalyzed by CrtR passes through the intermediate -cryptoxanthin.which likely provided the origin for CAO, and other poorly understood enzymes, such as the phylogenetically aberrant divinyl chlorophyllide reductase (33), which shows an unusual phylogenetic topology in A. marina (AM1 239
S coding for photosystem-associated proteins have been duplicated in A. marina. Two of four unique copies of psbU (AM1 G0114 and AM1 D0138) are plasmidencoded, with a protein identity ranging from 36 to 82 . Both psaK and psbE share a conserved duplication found in many other cyanobacteria, with 32 and 68 identity, respectively. Last, all genes responsible for coding cytochrome b6f are present
Of the A. marina chromosome nucleotide sequence (vs. itself) shows 18.7 of the sequence (not including the original, duplicated sequence) has a homology of greater than E 1 10 10 to another location on the chromosome. This is significantly higher than the 11.2 and 5.8 duplication in Synechocystis PCC6803 and Nostoc sp. PCC7120, respectively. A. marina actually has far fewer duplicated regions t
Synthesis (Fig. 3). There is no clear differentiation that would explain the near-complete conversion of -carotene to zeaxanthin by -carotene hydroxylase (CrtR), the enzyme responsible for zeaxanthin biosynthesis. We suggest a putative carotene biosynthesis pathway (Fig. 3) that accommodates the distinct complement of the carotenoid biosynthesis enzymes and their end products in A. marina.Light-Ha
Nit of PSII). Two of the psbA sequences (AM1 2166 and AM1 2889) share 97 nucleotide and 100 amino acid identity, whereas the third (AM1 0448) shares only 61 amino acid identity and is more closely related to a divergent PsbA in Anabaena variabilis (YP 324615) and Crocosphaera watsonii (ZP 00515211). Two of the psbD sequences (AM1 1083 and AM1 4084) share 99 nucleotide and 100 amino acid ident