Introduction and Overview of the Phototrophic Genome Project

Photosynthesis is the conversion of light energy to chemical energy as mediated by living organisms. This central biological process provides energy that sustains almost all life on Earth and is also the basis of all agriculture. Understanding how this complex process works at a molecular, cellular and ecosystem level, as well as how it originated and evolved are fundamental problems that are essential to obtaining the deep understanding required to lead to practical results to improve agriculture and complex environmental interactions.

Chlorophyll-based photosynthesis is confined to the domain Bacteria, with the exception of chloroplasts from eukaryotic algae and plants, which have unquestionably been derived from bacterial forms via endosymbiosis (Margulis 1993; Douglas 1998). Anoxygenic (non-oxygen-evolving) photosynthetic bacteria contain much simpler photosynthetic complexes that are the evolutionary ancestors of the two linked photosystems found in cyanobacteria, algae and plants. Analysis of these simpler organisms gives insights into the evolutionary processes that took place during the later development of the photosynthetic process. Most anoxygenic photosynthetic bacteria also can fix nitrogen, and evolutionary analysis has shown a deep linkage between these two essential processes (Burke et al. 1993; Raymond et al. 2004).

The process of photosynthesis involves several phases, including photon absorption and energy trapping by an antenna system, primary photochemistry in reaction center complexes, energy stabilization by secondary processes, and long-term energy storage in terms of synthesis of stable products, in most cases resulting from CO 2 fixation (Blankenship 2002). Fig. 1 schematically illustrates the patchy distribution of photosynthesis on the 16S rRNA bacterial tree of life. Five widely separated phyla of bacteria contain photosynthetic representatives, including the proteobacteria, the heliobacteria, the green sulfur bacteria, the filamentous anoxygenic phototrophs and the cyanobacteria. All the oxygenic prokaryotic photosynthetic organisms are included in the cyanobacteria, because they form a coherent group based on 16S rRNA analysis. The bacteriorhodopsin-based form of photosynthesis is not considered here, as it is clearly a separate evolutionary invention and is mechanistically unrelated to chlorophyll-based photosynthesis.

The four organisms selected for inclusion in this proposal were chosen for a variety of reasons, explained in detail below. However, in all cases they have unique aspects of their metabolism, physiology and ecology that are substantially different from any other sequenced genomes. Obtaining genome sequences for these organisms will greatly expand the available database on anoxygenic photosynthetic bacteria, including for the first time a heliobacterium, two proteobacteria with very different physiologies and ecology from any others whose genomes have been sequenced, and a cyanobacterium with unique pigment composition that may be an evolutionary missing link between anoxygenic and oxygenic photosynthetic organisms.

Understanding the evolutionary path of photosynthesis has long been a subject of great interest (Olson and Blankenship 2004). Previous phylogenetic analyses of photosynthetic bacteria have necessarily used a limited subset of genes to infer relationships among these organisms, often resulting in incongruent results. For example, molecular evolution analysis of several genes encoding chlorophyll biosynthesis enzymes suggests that the two groups of green bacteria, the green sulfur and the filamentous anoxygenic phototrophs, are closely related, as well as indicating that the heliobacteria and cyanobacteria are sister groups (Xiong et al., 2000). However, analysis of complete genomes (Raymond et al. 2002, 2003), as well as comparisons of other characteristics such as reaction centers or carbon fixation pathways or conserved insertions and deletions (Gupta 2003) indicates a very different pattern of relationships.

It is now clear that no single branching diagram can explain all these disparate patterns, probably because horizontal gene transfer has played a significant role in the evolutionary history of photosynthesis (Raymond et al. 2002, 2003). However, our current understanding of the evolution of photosynthesis is also very much limited by incomplete data in respect to diversity. In some cases only a single genome or a partial genome is available for sequence analysis. As more genomes become sequenced, it is becoming abundantly clear that it is necessary to have multiple genome sequences in order to detect and understand subtle patterns that may reflect ancient evolutionary processes. The addition of genome sequences for the microorganisms underway here will greatly improve our ability to detect such effects.