The nucleotide sequence of the entire genome of a cyanobacterium Gloeobacter violaceus PCC 7421 was determined. The genome of G. violaceus was a single circular chromosome 4,659,019 bp long with an average GC content of 62%. No plasmid was detected. The chromosome comprises 4430 potential protein-encoding genes, one set of rRNA genes, 45 tRNA genes representing 44 tRNA species and genes for tmRNA, B subunit of RNase P, SRP RNA and 6Sa RNA. Forty-one percent of the potential protein-encoding genes showed sequence similarity to genes of known function, 37% to hypothetical genes, and the remaining 22% had no apparent similarity to reported genes. Comparison of the assigned gene components with those of other cyanobacteria has unveiled distinctive features of the G. violaceus genome. Genes for PsaI, PsaJ, PsaK, and PsaX for Photosystem I and PsbY, PsbZ and Psb27 for Photosystem II were missing, and those for PsaF, PsbO, PsbU, and PsbV were poorly conserved. cpcG for a rod core linker peptide for phycobilisomes and nblA related to the degradation of phycobilisomes were also missing. Potential signal peptides of the presumptive products of petJ and petE for soluble electron transfer catalysts were less conserved than the remaining portions. These observations may be related to the fact that photosynthesis in G. violaceus takes place not in thylakoid membranes but in the cytoplasmic membrane. A large number of genes for sigma factors and transcription factors in the LuxR, LysR, PadR, TetR, and MarR families could be identified, while those for major elements for circadian clock, kaiABC were not found. These differences may reflect the phylogenetic distance between G. violaceus and other cyanobacteria.

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 ␣-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.comparative microbial genomics ͉ photosynthesis ͉ oxygenic phototrophs ͉ evolution

Formalism of the excitation transfer matrix element applicable for any multiconfigurational wave functions is made. On the basis of the resultant formulas, the excitation transfer matrix elements between the S2 or S1 state of a carotenoid, neurosporene, and the S2 or S1 state of bacteriochlorophyll a are calculated at various stacked configurations of the two molecules. The results show that the excitation transfer from the carotenoid S1 state to the bacteriochlorophyll S1 state via the Coulomb mechanism including multipole–multipole interactions takes place very efficiently in a speed more rapid than that via the electron-exchange mechanism. The results also show that the excitation transfer from carotenoid to bacteriochlorophyll occurs directly from the carotenoid S2 state, as well as from the carotenoid S1 state. Furthermore, it is shown that the excitation transfer matrix element due to the electron-exchange interaction has an oscillatory dependence on the displacement of one molecule from the other when the distance between the planes of the π systems is kept constant. Based on these results, a possible mechanism of the excitation transfer from carotenoid to bacteriochlorophyll in vivo is discussed.

The composition of photosystem II (PSII) in the chlorophyll (Chl) d-dominated cyanobacterium Acaryochloris marina MBIC 11017 was investigated to enhance the general understanding of the energetics of the PSII reaction center. We first purified photochemically active complexes consisting of a 47-kDa Chl protein (CP47), CP43 (PcbC), D1, D2, cytochrome b 559, PsbI, and a small polypeptide. The pigment composition per two pheophytin (Phe) a molecules was 55 ؎ 7 Chl d, 3.0 ؎ 0.4 Chl a, 17 ؎ 3 ␣-carotene, and 1.4 ؎ 0.2 plastoquinone-9. The special pair was detected by a reversible absorption change at 713 nm (P713) together with a cation radical band at 842 nm. FTIR difference spectra of the specific bands of a 3-formyl group allowed assignment of the special pair. The combined results indicate that the special pair comprises a Chl d homodimer. The primary electron acceptor was shown by photoaccumulation to be Phe a, and its potential was shifted to a higher value than that in the Chl a/Phe a system. The overall energetics of PSII in the Chl d system are adjusted to changes in the redox potentials, with P713 as the special pair using a lower light energy at 713 nm. Taking into account the reported downward shift in the potential of the special pair of photosystem I (P740) in A. marina, our findings lend support to the idea that changes in photosynthetic pigments combine with a modification of the redox potentials of electron transfer components to give rise to an energetic adjustment of the total reaction system. Acaryochloris marina ͉ FTIR ͉ reaction center ͉ photosynthesis ͉ electron transfer C hlorophyll (Chl) a has a ubiquitous role as an electron donor in the photochemical reactions of oxygenic photosynthesis, in which two kinds of photosystem, namely photosystem I (PSI) and photosystem II (PSII), cooperatively drive photosynthetic electron flow from water to NADP ϩ . The reduced cofactor, NADPH, is then used for CO 2 fixation. Chl a is a key pigment that serves as an electron donor called the special pair in PSI and PSII. Acaryochloris spp. are unique cyanobacteria that differ from the majority of photosynthetic organisms by having Chl d (3-desvinyl-3-formyl Chl a) (1-4) as the major pigment (Ͼ95%); Chl a is a minor component but is never absent (5, 6). In photosynthetic organisms, changes in pigment composition affect both the function of pigments and their reaction environments, including the modified proteins that accommodate them. Photosynthetic pigments function in two roles: as lightharvesting components and as electron transfer components. Light harvesting is mainly governed by the orientation and energy levels of pigments, and, in this context, a particular excitation energy level is not an absolute precondition for function, but a relative one. On the other hand, electron transfer reactions are governed by an absolute redox potential, because the photosynthetic oxidation of water requires a very high potential, whereas reduction of NADP ϩ requires a very low potential. For this reason, it is of particul...

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