Talk:Phytochrome

message: The notations Pr and Pfr were recently changed to Pr and Pfr. Is that standard? In published papers, I keep seeing the non-subscripted version: , . Cheers, AxelBoldt 15:07, 8 May 2006 (UTC)
thread_title: Untitled

message: 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)
thread_title:  Isoform conversion 

message: 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)
thread_title:  Phytochromobiline structure 

message: 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 0.13http://www.mobot.org/jwcross/duckweed/phytochrome.htm 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.http://www.mcdb.ucla.edu/Research/Tobin/lab/Research/research.htmlThepaan (talk) 04:48, 26 January 2010 (UTC)
thread_title:  Genetic engineering 

message: "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) Karniol, Wagner, Walker and Vierstra (2005) Phylogenetic analysis of the phytochrome superfamily reveals distinct
microbial subfamilies of photoreceptors. Biochem. J. 392, 103-116.  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 Lamparter, T. (2004) Evolution of cyanobacterial and plant phytochromes. FEBS Letters 573, 1-5 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) 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.
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)
thread_title:  Phytochrome evolution