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In addition to the requirement for a respiratory terminal electron acceptor (invariably oxygen) for survival, aerobic phototrophic bacteria also differ from classical purple phototrophic bacteria by their cessation of photosynthetic pigment synthesis upon illumination. These differences raise important questions about the evolution and genetic regulation of photosynthesis in the aerobic phototrophic bacteria (Beatty 2002) .
In 16S rRNA phylogenetic trees, the aerobic phototrophic bacteria are interspersed with purple phototrophic and chemotrophic species. These relationships indicate that these bacteria may represent an intermediate evolutionary form between the purple phototrophic bacteria and chemotrophic relatives, or arose from an aerobic chemotroph by lateral gene transfer of photosynthesis genes from a purple bacterium (Beatty 2002; Yurkov and Beatty 1998) .
Synthesis of the photosynthetic apparatus in aerobic phototrophic bacteria occurs aerobically in darkness with illumination halting pigment synthesis, yet the photosystem produced in darkness synthesizes ATP and enhances growth when cells are illuminated. This was shown by increased growth yields of aerobic phototrophic bacteria in chemostat cultures exposed to alternating periods of illumination (Yurkov and van Gemerden 1993) , and by light-dependent ATP synthesis in cells that had been previously grown in darkness (Okamura et al. 1986) . However, nothing is known about how the aerobic phototrophic bacteria sense oxygen, or the intensity or wavelength of light, and how these sensations are coupled to gene expression. This is in contrast to purple bacterial signal transduction pathways that control photosystem synthesis during the transition from aerobic respiratory to anaerobic photosynthetic growth, and the transition from dark to light anaerobic growth (Masuda and Bauer 2002; Oh and Kaplan 2001) .
Thus, although the photosynthetic apparatus of the aerobic phototrophic bacteria is similar to those of the better-studied anoxygenic purple phototrophic bacteria (Yurkov and Beatty 1998) , the regulation and ecophysiological function of the photosynthetic apparatus are very different and genomic analysis should reveal the reasons for these differences.
Significance of the Roseobacter denitrificans Genome Sequence
The genome sequence of a representative aerobic phototrophic bacteria species is important for three compelling reasons.
1) The evolutionary genesis of photosynthesis genes. This is a difficult question (Gupta 2003; Xiong et al. 2000) , and yet, a genome sequence-based approach could provide remarkable insights by expansion of recent bioinformatic approaches (Raymond et al. 2002, 2003) that include the aerobic phototrophic bacteria. Furthermore, the true evolutionary position of the aerobic phototrophic bacteria vis á vis purple phototrophic bacteria and chemotrophs will be clarified by whole genome comparisons.
2) Pathways of carbon dioxide fixation and production. The aerobic phototrophic bacteria are thought to be incapable of autotrophic CO 2 fixation (Yurkov and Beatty 1998) , but Kolber et al. (2001) reported the incorporation of significant amounts of 14CO 2 into cell material. The genome sequence will reveal if there were the genetic potential for autotrophic CO 2 fixation via the Calvin-Benson-Bassham cycle (Tabita 1995) or, conceivably, the reverse citric acid cycle (Ormerod 2003) . Alternatively, perhaps the aerobic phototrophic bacteria encode only the potential for limited, heterotrophic CO 2 fixation. The genome sequence of an aerobic phototrophic bacterium will allow construction of metabolic pathways in silico (Larimer et al. 2004) , which could be tested in biochemical and molecular biology experiments. Because of their wide distribution and huge numbers in the oceans, the question of autotrophy is central to our understanding of the significance of the vast numbers of aerobic phototrophic bacteria as either net consumers or producers of CO 2 in the global carbon cycle.
3) Light and oxygen signal transduction in gene expression. Although high light intensity represses photosynthesis in a variety of organisms, the extreme repression found in the aerobic phototrophic bacteria offers an opportunity to use this exaggerated response to facilitate an understanding of pathways and mechanisms that have subtle, and hence difficult to study, effects in other species. The genome sequence could be used in bioinformatic approaches to identify homologous or potentially new light sensors and signal transducers (e.g.: phytochromes, PAS proteins and the AppA protein; see (Giraud et al. 2002; Larimer et al. 2004; Masuda and Bauer 2002) . Similarly, because the aerobic phototrophic bacteria produce the photosynthetic apparatus under aerobic conditions, in contrast to the purple phototrophic bacteria, an analysis of the presence or sequence of aerobic phototrophic bacteria homologues of genes that have been implicated in purple phototrophs (Bauer and Bird 1996; Oh and Kaplan 2001) would contribute to a general understanding of oxygen regulation. The genome sequence will allow the study of both the light- and oxygen-responsive pathways by cloning and over-expressing genes for biochemical and biophysical analysis of purified proteins, as well as by gene disruption.
We have chosen the aerobic phototrophic bacterium R. denitrificans for genome sequencing because: 1) it is readily cultivated in the laboratory; 2) work on respiratory and photosynthetic electron transfer pathways in this organism is establishing this species as the model aerobic phototrophic bacterium (Candela et al. 2001; Okamura et al. 1986; Schwarze et al. 2000) ; 3) it is the only aerobic phototrophic bacterium that is capable of anaerobic growth, by use of nitrate as a terminal electron acceptor (Yurkov and Beatty 1998) , which will facilitate subsequent studies of the effects of oxygen on photosynthetic and other metabolic processes; 4) it is a marine bacterium, and so may be representative of the globally huge population of aerobic phototrophic bacteria enumerated in oceanic samples (Kolber et al. 2001) ; 5) the G+C content of this organism is ~ 59% and the genome size is estimated to be ~4 Mb (unpublished), thus there should not be any significant technical obstacles to obtaining the sequence.
The R. denitrificans genome sequence and annotation will also greatly facilitate studies of the evolution of photosynthesis, experiments on carbon dioxide fixation and production, and experiments to elucidate why the expression of photosynthesis genes in the aerobic phototrophic bacteria is independent of oxygen yet extremely sensitive to illumination. The answers to these questions will contribute to a better understanding of fundamental aspects of the origin and dispersion of photosynthesis genes, the global carbon cycle, and general biological mechanisms for sensing and transducing the environmental signals of oxygen and light.
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