The ability to acclimate to a continuously changing environment is critical for microorganisms. For microbes that rely on photosynthesis as their primary means of energy acquisition, acute responsiveness to changing light conditions can provide a selective advantage in many ecological settings. While numerous species are capable of acclimation to changes in light intensity, the ability to sense and respond to variations in light quality (color) is less common among prokaryotes. One group that is capable of complex responses to changes in both light intensity and quality are the cyanobacteria, and the best studied response of these organisms to changes in light quality is a process called complementary chromatic adaptation (CCA) (Engelmann 1902, Gaidukov 1903). CCA was originally characterized as a photoreversible change in color phenotype that was dependent upon the light quality in which the cells were grown. Later work determined that CCA was the result of shifts in the ratio of two chromophorylated proteins involved in photosynthetic light harvesting, phycocyanin (PC, absorbance maximum ~620 nm) and phycoerythrin (PE, absorbance maximum ~560 nm) (Boresch 1922; Bennett and Bogorad, 1971, 1973).

These two proteins have open chain tetrapyrroles (bilins) covalently attached and are located within photosynthetic light harvesting structures called phycobilisomes (PBS) (Gantt 1981, Glazer 1984, Sidler 1994). While the structures of PBS vary among species, the common hemidiscoidal forms are composed of two structurally discrete regions called cores and rods. Cores are in the central portion of the PBS, and keep the PBS associated with the photosynthetic thylakoid membrane and transfer light energy from the distal regions of the PBS to the photosynthetic reaction centers. Rods are cylindrical structures that are attached at one end to the core. Most typically, six rods radiate out from the core, capturing light energy and nearly unidirectionally transferring it to the core. PC and PE can be found in the rods, depending upon the species and ambient light conditions. In addition to chromophore containing proteins (phycobiliproteins), which always consist of an ? and ? subunit, both rods and cores contain linker peptides. These are small proteins that are typically not chromophorylated and have important structural roles in PBS.

By definition, CCA only occurs in species that contain both PC and PE, but not all cyanobacteria that contain these pigments undergo CCA (Boresch 1922, Tandeau de Marsac 1977). Three classes of chromatic adapters have been defined (Tandeau de Marsac 1977). PC and PE abundance in group I species is unaffected by light quality. In group II species, PC production is constant regardless of light quality but PE levels increase when cells are grown in green light (GL). Group III members modulate both PE and PC production in response to light quality: PC accumulates in red light (RL) and PE accumulates in GL.

Type III CCA has been best studied in the filamentous species Fremyella diplosiphon (also called Calothrix sp PCC 7601), where action spectra have demonstrated that this process is highly sensitive to RL and GL (Diakoff and Scheibe 1973; Haury and Bogorad 1977). The wealth of physiological data collected for CCA in this species has been supplemented by detailed molecular analyses that have traditionally been focused on the expression of genes encoding PBS components (reviewed in Bogorad 1975, Tandeau de Marsac 1983, Grossman et al. 1993, Grossman 2003). Allophycocyanin (AP) is the principle phycobiliprotein found in the core and is encoded by the apcAB operon and is approximately equally abundant in RL and GL (Conley et al., 1986). F. diplosiphon is capable of synthesizing two forms of PC under normal growth conditions (Bryant, 1981). Constitutive PC (PCc) is always located at the core proximal end of the rods, is encoded by the cpcB1A1 operon, and is present at similar levels in both RL and GL (Conley et al., 1986). Inducible PC (PCi), is not detectable in cells grown in GL but is synthesized at high levels and incorporated into the core distal regions of the rods during growth in RL (Conley et al., 1985). The genes that encode PCi (cpcB2A2) and the PCi linker peptides (cpcH2I2D2) are cotranscribed in the cpcB2A2H2I2D2 operon (hereafter abbreviated cpcB2A2) (Conley et al., 1985, 1988, Lomax et al., 1987). PE and its associated linkers are synthesized at high levels and incorporated into the core distal regions of the rods during growth in GL but are made at very low levels in RL (Gendel et al., 1979). Unlike PCi and its linkers, PE and the PE linkers are encoded by two unlinked operons, cpeBA and cpeCDE, respectively (Mazel et al., 1986, Federspiel and Grossman, 1990, Federspiel and Scott, 1992). All of these light mediated changes in protein abundance are mirrored by similar changes in the transcript accumulation patterns of genes encoding components of the PBS. RNA levels of both cpcB1A1 and apcAB are relatively unaffected by changes in light quality (Conley et al., 1986, 1988). In contrast, cpcB2A2 RNA is abundant in RL but not in GL, while cpeBA and cpeCDE RNAs accumulate in GL but not RL (Conley et al., 1985, Federspiel and Grossman, 1990, Federspiel and Scott, 1992, Mazel et al., 1986). For cpcB2A2 and cpeBA, the shifts in RNA levels mediated by light quality are primarily a result of changes in transcription (Oelmuller et al., 1988a,b). Recently, several genes that do not encode PBS components but are regulated by light quality have been identified in F. diplosiphon. GL upregulates the expression of both the pebAB operon, which encodes the enzymes involved in the conversion of biliverdin to phycoerythrobilin (the chromophore attached to PE) (Alvey et al. 2003), and the cpeSTR genes, which may have regulatory roles (see below) and appear to be cotranscribed with the cpeCDE genes (Cobley et al., 2002, Seib and Kehoe, 2002).

The signal transduction mechanisms controlling CCA are just beginning to be understood. Thus far only five genes have been isolated that directly or indirectly affect the levels of expression of CCA responsive genes in cells that are completely light acclimated. Three of the encoded proteins, RcaE, RcaF, and RcaC, appear to act within a single pathway. RcaE is a phytochrome class CCA photoreceptor with strong similarity to histidine kinases (Kehoe and Grossman 1996, Terauchi et al., 2003) while RcaF and RcaC are response regulators that appear, along with RcaE, to be part of a complex phosphorelay (Chiang et al., 1992, Kehoe and Grossman, 1996, 1997). Disruption of rcaE, rcaF, or rcaC dramatically affects CCA regulation of both PC and PE synthesis (Bruns et al., 1989, Chiang et al., 1992, Kehoe and Grossman, 1997). The fourth component, CpeR, is required for the expression of cpeBA, but not cpeCDE, in GL (Cobley et al., 2002, Seib and Kehoe, 2002) while the fifth component, CotB, is required for proper expression of both cpeBA and cpeCDE in GL (Balabas et al., 2003). The functions of CpeR and CotB have not yet been established.

It has been recognized for some time that the cellular responses of F. diplosiphon to changes in light quality involve much more than restructuring of the PBS during CCA. In 1973, Bennett and Bogorad noted several differences between filaments grown in RL and GL. Average filament lengths were longer and cells were larger and more cylindrical during growth in GL., and specialized cells called necridia were transiently created after a shift from GL to RL (Bennett and Bogorad, 1973). These mophological processes were proposed to be controlled by a different regulatory system than CCA responses (Bogorad, 1975). Also, electron transport, rather than a photoreceptor, appears to regulate two additional responses in F. diplosiphon; production of hormogonia (short, gas-vacuolated filaments) in RL and the synthesis of heterocysts (specialized cells for nitrogen fixation) during growth in GL in the absence of fixed nitrogen (Campbell et al., 1993)

As a first step towards a more complete perspective on both the cellular physiology and regulatory mechanisms involved in light quality adaptation in F. diplosiphon, we have used DNA microarrays to characterize genome wide differences in RNA levels between cells acclimated to RL and GL growth conditions. In prokaryotic systems, arrays are typically created by PCR amplification of or synthesis of oligonucleotides corresponding to specific open reading frames (ORFs) that have been previously identified in sequenced genomes. Because the F. diplosiphon genome has not yet been sequenced, we created and analyzed genomic DNA microarrays, which contained uncharacterized but indexed fragments of F. diplosiphon genomic DNA. Using this approach to analyze approximately half of the F. diplosiphon genome, we have successfully identified 19 novel genes that are differentially expressed in RL and GL.