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MRNA-seq of Physcomitrella protonema responding to 1 hr red light in wild type and the phytochrome-deficient mutant

ABSTRACT: The red/far-red light photoreceptor phytochrome mediates photomorphological responses in plants. For light sensing and signaling, phytochromes need to associate with open-chain tetrapyrrole molecules as the chromophore. Biosynthesis of tetrapyrrole chromophores requires members of ferredoxin-dependent bilin reductases (FDBRs). There are two FDBRs in Physcomitrella patens, HY2 and PUBS. Knocking out both generates the phytochrome-deficient mutant. Datasets here provides the transcriptome profiling of Physcomitrella protonema grown in the dark and exposed to one hour red light. Wild type and the hy2 pubs double mutant were used to dissect the regulated genes of moss phytochromes. For details, please see PMID: .

ORGANISM(S): Physcomitrium patens

PROVIDER: GSE36274 | GEO | 2012/05/08

SECONDARY ACCESSION(S): PRJNA153109

REPOSITORIES: GEO

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mRNA-seq of Physcomitrella protonema responding to 1 hr red light in wild type and the phytochrome-deficient mutant

Project description:The red/far-red light photoreceptor phytochrome mediates photomorphological responses in plants. For light sensing and signaling, phytochromes need to associate with open-chain tetrapyrrole molecules as the chromophore. Biosynthesis of tetrapyrrole chromophores requires members of ferredoxin-dependent bilin reductases (FDBRs). There are two FDBRs in Physcomitrella patens, HY2 and PUBS. Knocking out both generates the phytochrome-deficient mutant. Datasets here provides the transcriptome profiling of Physcomitrella protonema grown in the dark and exposed to one hour red light. Wild type and the hy2 pubs double mutant were used to dissect the regulated genes of moss phytochromes. 4 samples, dark-grown wild-type and pubs hy2 protonema as time 0 control, followed by red light irradiation for one hour respectively

2012-05-08 | E-GEOD-36274 | biostudies-arrayexpress

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Project description:Here we show that the phytochrome-less chlorophyte Chlamydomonas reinhardtii retains a functional pathway to synthesize the linear tetrapyrrole (bilin) precursor of the phytochrome chromophore. Reverse genetic, metabolic inactivation and bilin rescue experiments establish that this pathway is needed for heme iron acquisition and for the diurnal transition to phototrophic growth. RNA-Seq measurements reveal a bilin-dependent signaling network that is necessary for the heterotrophic to phototrophic transition. These results imply the presence of a novel bilin sensor pathway that may be widely distributed amongst oxygenic photosynthetic organisms. We isolated RNA from heterotrophic suspension cultures of 4A+ WT and the hmox1 mutant grown in the presence or absence of 0.1 mM BV IXM-NM-1 before and after transfer to low light.

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Retrograde bilin signaling enables Chlamydomonas greening and phototrophic survival

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Diatom phytochromes reveal the existence of far-red light based sensing in the ocean

Project description:The absorption of visible light in aquatic environments has led to the common assumption that aquatic organisms sense and adapt to penetrative blue/green light wavelengths, but show little or no response to the more attenuated red/far-red wavelengths. Here we show that two marine diatom species, Phaeodactylum tricornutum and Thalassiosira pseudonana, possess a bona fide red/far-red light sensing phytochrome (DPH) that uses biliverdin as a chromophore and displays accentuated red-shifted absorbance peaks compared to other characterized plant and algal phytochromes. Exposure to both red and far-red light causes changes in gene expression in P. tricornutum and the responses to far-red light disappear in DPH knockout cells, demonstrating that P. tricornutum DPH mediates far-red light signaling. The identification of DPH genes in diverse diatom species widely distributed along the water column further emphasizes the ecological significance of far-red light sensing, raising questions about the sources of far-red light. Our analyses indicate that, although far-red wavelengths from sunlight are only detectable at the ocean surface, chlorophyll fluorescence and Raman scattering can generate red/far-red photons in deeper layers. This study opens up novel perspectives on phytochrome-mediated far-red light signaling in the ocean and on the light sensing and adaptive capabilities of marine phototrophs.

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Structural basis for the Pr-Pfr long-range signaling mechanism of a full-length bacterial phytochrome at the atomic level

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2021-12-17 | PXD026829 | Pride

Small RNAs from the moss Physcomitrella patens

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Bilin-dependent photoacclimation in Chlamydomonas reinhardtii

Project description:Linear tetrapyrrole (bilin)-based phytochrome sensors optimize photosynthetic light capture by mediating massive gene reprogramming in land plants, yet surprisingly, many sequenced chlorophyte (green) algae lack phytochrome genes. Previous studies on the heme oxygenase (hmox1) mutant of Chlamydomonas reinhardtii suggest that bilin biosynthesis in plastids is needed for regulation of a limited nuclear gene network implicated in oxygen detoxification during dark to light transitions. The hmox1 mutant is unable to grow photoautotrophically and poorly acclimates to increased illumination even in the presence of acetate. Here we show that these phenotypes reflect the reduced accumulation of PSI reaction centers as well as a loss of PSI and PSII antennae complexes during photoacclimation. Phenotypically, the hmox1 mutant is similar to the chlorophyll biosynthesis mutants, gun4, crd1 and cth1. However, many of the hmox1 phenotypes can be rescued by the application of exogenous biliverdin IXα, the bilin product of HMOX1; this rescue is independent of photosynthesis but strongly dependent upon blue light. RNA-Seq comparisons of hmox1, 4A+ wild type and two genetically complemented lines also reveal that bilins restore regulation of a small network of photosynthesis-associated nuclear genes. These include genes responsible for chlorophyll biosynthesis (CHLI1/2), PSI light-harvesting (LHCA4) and naphthoquinone metabolism (MEN2), all of which show reduced photoinduction in the hmox1 mutant. We propose that a bilin-based, blue light sensory system is responsible for the maintenance of a functional photosynthetic apparatus in light-grown C. reinhardtii. This critical and possibly ancestral role for bilins may be responsible for retention of bilin biosynthesis in all eukaryotic photosynthetic species.

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The Physcomitrella Degradome

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Project description:The phytochromes (PHYs) are a family of photoreceptors which absorb red and far-red light to modulate developmental responses in photosynthetic organisms. We developed knockout mutants of PHYB and PHYC in tetraploid wheat and performed RNA-seq studies to analyze and compare the regulons of each phytochrome under short day photoperiods.

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