Retrograde bilin signaling enables Chlamydomonas greening and phototrophic survival

Abstract

The maintenance of functional chloroplasts in photosynthetic eukaryotes requires real-time coordination of the nuclear and plastid genomes. Tetrapyrroles play a significant role in plastid-tonucleus retrograde signaling in plants to ensure that nuclear gene expression is attuned to the needs of the chloroplast. Well-known sites of synthesis of chlorophyll for photosynthesis, plant chloroplasts also export heme and heme-derived linear tetrapyrroles (bilins), two critical metabolites respectively required for essential cellular activities and for light sensing by phytochromes. Here we establish that Chlamydomonas reinhardtii, one of many chlorophyte species that lack phytochromes, can synthesize bilins in both plastid and cytosol compartments. Genetic analyses show that both pathways contribute to iron acquisition from extracellular heme, whereas the plastid-localized pathway is essential for light-dependent greening and phototrophic growth. Our discovery of a bilin-dependent nuclear gene network implicates a widespread use of bilins as retrograde signals in oxygenic photosynthetic species. Our studies also suggest that bilins trigger critical metabolic pathways to detoxify molecular oxygen produced by photosynthesis, thereby permitting survival and phototrophic growth during the light period.biliverdin | heme oxygenase | iron homeostasis | oxidative stress | RNA-Seq analysisT he daily light-dark cycle requires all oxygenic photosynthetic species to survive the repeated transition from prolonged darkness to phototrophic metabolism at dawn. Most plants are unable to synthesize chlorophyll in darkness and therefore accumulate photosensitizing chlorophyll precursors at night (1). Sunrise induces an oxidative burst as photosynthesis resumes, so the transition to daylight requires careful coordination of many lightdependent processes. Multiple photoreceptors perform such roles in plants, the most notable being the red-sensing, linear tetrapyrrole (bilin)-based phytochromes and the blue-sensing, flavin-based cryptochromes and phototropins (2-5). Bilins are well-established plant retrograde signals, synthesized in plastids but enabling light sensing by cytosolic phytochromes. Phytochrome photoconversion then triggers nuclear translocation to positively regulate photosynthesis-associated nuclear gene (PhANG) expression (6, 7).Genetic studies suggest that plastids also export negative retrograde signals, metabolites that suppress nuclear gene networks targeted by phytochromes (8-10). Among these metabolites are abscisic acid (ABA) (11), tetrapyrroles (12-14), 3′-phosphoadenosine 5′-phosphate (PAP) (15), β-cyclocitral (16), and methylerythritol cyclodiphosphate (MEcPP) (17). Although hypothetical export of a negative tetrapyrrole signal has received considerable support, biochemical evidence for such a retrograde signal remains equivocal in plants (18)(19)(20). Chlorophyte algae diverged from the streptophyte plant lineage over 500 million years ago but share a common chlorophyll a/b-based photosynthetic lightharvesting app...

UV-B Perception and Acclimation in Chlamydomonas reinhardtii

“…It is of note that a significant number of genes we report as differentially expressed in response to acclimatory UV-B have been previously identified as differentially expressed within 30 min when Chlamydomonas cells were transferred from dark to white light (Duanmu et al, 2013) (Supplemental Figure 5). Similar to supplemental UV-B exposure, the transition from darkness to white light may result in an acclimatory response that, among other processes, promotes protection of the photosynthetic machinery.…”

“…Coverage of RNA-seq data is shown in Supplemental Table 2. For transcriptome comparison, genes with significantly altered expression (FDR # 0.05 and FC $ 2 or FC # 22) resulting from UV-B treatment were compared with those genes with significant differential regulation following a dark-to-light transition, as previously described (Duanmu et al, 2013). Genes that were updated in Phytozome 10 compared with Phytozome 9 have been updated using the Phytozome 10 transfer tables as far as possible.…”

Surprising roles for bilins in a green alga

“…Duanmu et al first show that HMOX1, HMOX2, and PCYA are catalytically active and produce bilins in vitro (6). They also demonstrate in a very elegant way that these proteins are functional in vivo by expressing a cyanobacteriochrome in the chloroplast of C. reinhardtii, where, remarkably, the photoreceptor is assembled with bound phytochromobilin chromophore.…”

“…These genes include several oxygen-dependent redox enzymes (monoand dioxygenases, proteins containing redox cofactors and enzymes associated with oxidative amino acid metabolism). A shift of an algal culture from dark to light is accompanied by a sudden increase in oxygen evolution and, as Duanmu et al suggest, by the release of heme from damaged hemoproteins (6). In contrast, in the light, the plastid-derived bilins appear to have an inhibitory action on nuclear genes involved in photosynthesis.…”

“…An intriguing feature of all sequenced chlorophyte genomes is that, although they lack phytochromes, their genomes encode two HMOXs, HMOX1 and HMOX2, and PCYA. In PNAS, Duanmu et al (6) investigate the role of these genes in the green alga Chlamydomonas reinhardtii and made unexpected findings.…”