Talk:Phytochrome

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The notations Pr and Pfr were recently changed to P_r and P_fr. Is that standard? In published papers, I keep seeing the non-subscripted version: [1], [2]. Cheers, AxelBoldt 15:07, 8 May 2006 (UTC)[reply]

You're right. The non-supscripted versions are standard. Also, the P in Pr / Pfr stands for "pigment" not "phytochrome" - I changed that (but left subscripts for now).

Indeed, subscripting is not mandatory. I removed the archaeic structure illustration of phytochromobilin and the poor diagram showing the UV-Vis absorbance spectra of Pr and "Pfr" (which was the spectrum of a Pr / Pfr mixture). Also I have changed "form" and "isoform" to "state" (thus "ground state", "signalling state") which is more in line with current useage in photobiology and photochemistry.

130.15.30.116 (talk) 14:49, 12 May 2008 (UTC) Some problems: This article does not use properly embedded references, can this be fixed? Also, the "Isoforms or states" section appears to be referencing a non-existent chart or figure in the text (refers to "left" and "right").[reply]

Wiki Education Foundation-supported course assignment

This article was the subject of a Wiki Education Foundation-supported course assignment, between 20 March 2019 and 30 April 2019. Further details are available on the course page. Student editor(s): M02odel, F29gall.

Above undated message substituted from Template:Dashboard.wikiedu.org assignment by PrimeBOT (talk) 06:37, 17 January 2022 (UTC)[reply]

Isoform conversion

Should this section mention that Pfr will slowly convert to Pr if there is no external stimuli? At the moment, all it mentions is conversion due to light wavelengths. I would edit it myself, but I'm far from an expert on the subject, I'm not sure if this conversion is real or one of the various over-simplifications school syllabuses seem to love.Matt The Sixth (talk) 18:59, 30 January 2012 (UTC)[reply]

Phytochromobiline structure

The images appear to be at a early level of phytochrom research - indeed the conformations of the pigment during photoisomerization are more or less known. There appears to be a rotation of the D-ring of the tetrapyrrole, a E/Z-isomerisation at the C15-C16 double bond. There have been experiments with synthetic sterically locked pigments to characterise their conformational states. Pfr structure is still partly hypothetical though. Look for the Review Articles by Rockwell in Annu. Rev. of Plant Biol of 2006 and 2008.I uploaded updated images to german wikipedia, maybe you want to use these. --85.178.47.222 (talk) 12:34, 28 May 2008 (UTC)[reply]

Genetic engineering

I'm only about 80% sure of this so someone double-check me.

If phytochrome A (Pr) absorbs red light and is converted to phytochrome B (Pfr) which absorbs far-red light and is converted back to phyA then a plant exposed to more far-red light will have mroe phyA and a plant exposed to more red light will have more phyb. If direct sunlight has a R:FR ratio of 1.2 and sunlight under a canopy of leaves has a R:FR ratio of 0.13^[1] then it seems there is more far-red light in the shade where a plant would want to grow taller to seek the light. Or, a plant in the shade will recieve more far-red light and grow taller where a plant which recieved more red light (the opposite) should not grow as tall. Therefore, A shaded plant will have more phyA, causing it to grow taller, where an unshaded plant will have more phyB, causing it to not grow as tall. Finally, these sentences: "Harry Smith and co-workers at Leicester University in England showed that by increasing the expression level of phytochrome A (which responds to far-red light) shade avoidance responses can be altered. As a result, plants can expend less energy on growing as tall as possible and have more resources for growing seeds and expanding their root systems." wrongly state that phyA absorbs far-red light instead of red and imply that a plant with more phyA will not grow as tall as a plant with more phyB where the opposite is actually true.^[2]Thepaan (talk) 04:48, 26 January 2010 (UTC)[reply]

No, this is not correct. Only the Pfr (red absorbing) form is biologically active. Since this form is degraded as phyA, and not as rapidly as phyB, an overexpression of phyA will alter the Pr:Pfr ratio (photoequilibrium) in favor of Pfr, causing shorter plants.

I don't think phytochrome A = Pr and phytochrome B = Pfr. Phytochrome A and B are different homologues of phyotchrome; they are not the same protein. Arabidopsis has 5 phytochrome homologues. Phytochrome is photoreversible and can exist in 2 conformers, Pr and Pfr, depending on the light conditions. Duxenaz (talk) 22:05, 3 March 2010 (UTC)[reply]

They are not the same protein but they are homologs sharing (most likely) the same biological output pathway. Thus, all phytochromes in the Pfr form can probably transmit the same signal.

References

Phytochrome evolution

"Presumably plant phytochromes are derived from an ancestral cyanobacterial phytochrome, perhaps by gene migration from the chloroplast to the nucleus." This has no citation. In the literature it is sometimes asserted but rarely with evidence. For example, Karniol et al. (2005) ^[1] states: "The evolution of plant phys remains unclear given the absence of prokaryotic versions with a similar C-terminal architecture (e.g. tandem internal PAS domains), although their derivation from a Cph obtained during chloroplast endosymbiosis is most likely." They do not provide any evidence for this. Lamparter ^[2] suggests that cyanobacterial and plant phytochromes evolved independently and are a result of convergent evolution. Evidence of this includes: - it would take few mutations for a bacterial phytochrome (BphP) to bind phytochromobilin or pycocyanobilin. - biliverdin (the most common chromophore of BphPs) is a precursor to phytochromobilin and phycocyanobilin, but phytochromobilin and pycocyanobilin are not involved in eachother's biosynthesis. - a clade comprised of plant and cyanobacterial phytochromes is polyphyletic (although this depends on the domain used for the multiple sequence alignment) ^[3]^[4].

Also, isn't it convention to write genes in lower case italics? So this: ". . .Arabidopsis has five phytochrome genes (PHYA - E). . ." Should be phyA-E?

Duxenaz (talk) 22:36, 3 March 2010 (UTC)[reply]

No, it is convention to write mutant gene names in lower case in many plant systems. Functional / wild type genes are generally upper case.

References

^ Karniol, Wagner, Walker and Vierstra (2005) Phylogenetic analysis of the phytochrome superfamily reveals distinct microbial subfamilies of photoreceptors. Biochem. J. 392, 103-116.
^ Lamparter, T. (2004) Evolution of cyanobacterial and plant phytochromes. FEBS Letters 573, 1-5
^ Karniol, Wagner, Walker and Vierstra (2005) Phylogenetic analysis of the phytochrome superfamily reveals distinct microbial subfamilies of photoreceptors. Biochem. J. 392, 103-116.
^ Montgomery and Lagarias (2002) Phytochrome ancestry: sensors of bilins and light

[1] ttp://www.mobot.org/jwcross/duckweed/phytochrome.htm

[2] ttp://www.mcdb.ucla.edu/Research/Tobin/lab/Research/research.html

[3] Karniol, Wagner, Walker and Vierstra (2005) Phylogenetic analysis of the phytochrome superfamily reveals distinct microbial subfamilies of photoreceptors. Biochem. J. 392, 103-116.

[4] Lamparter, T. (2004) Evolution of cyanobacterial and plant phytochromes. FEBS Letters 573, 1-5

[5] Karniol, Wagner, Walker and Vierstra (2005) Phylogenetic analysis of the phytochrome superfamily reveals distinct microbial subfamilies of photoreceptors. Biochem. J. 392, 103-116.

[6] Montgomery and Lagarias (2002) Phytochrome ancestry: sensors of bilins and light

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