photosynthesis defs

[gocentral]

Hi,

I've noticed that a whole lot of the children of photosynthesis are undefined. I'd like to use this sourceforge item to get feedback on some definitions before I implement them.

Terms:

photosynthesis, dark reaction C4 photosynthesis NAD-malic enzyme C4 photosynthesis NADP-malic enzyme C4 photosynthesis PEP carboxykinase C4 photosynthesis CAM photosynthesis photosynthesis, light reaction NADP+ reduction (Should this be in function?) photosynthetic water oxidation

There are more but I'll start by making defs for these. Any suggestions would also be gratefully received.

Thanks,

Jen

Reported by: jenclark

Original Ticket: "geneontology/ontology-requests/1727":https://sourceforge.net/p/geneontology/ontology-requests/1727

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photosynthesis, dark reaction The dark reaction of photosynthesis is also known as the calvin cycle. In plants, a cyclical series of carbon-fixing, sugar-producing reactions in the chloroplasts. Some of the sugars (triose phosphates) are recycled, others are stored as carbohydrates. Light is not needed for these reactions, they use the carbon dioxide and energy produced in the light reactions of photosynthesis. http://cancerweb.ncl.ac.uk

C4 photosynthesis Carried out in plants found principally in hot climates whose initial fixation of carbon dioxide in photosynthesis is by the Hatch Slack Kortshak (HSK) pathway. In the HSK pathway the enzymes that are found in mesophyll chloroplasts include PEP carboxylase, which adds carbon dioxide to phosphoenolpyruvate to give the 4 carbon compound, oxaloacetate. Four carbon compounds are transferred to bundle sheath chloroplasts, where the carbon dioxide is liberated and re-fixed by the Calvin Benson cycle. The presence of the HSK pathway permits efficient photosynthesis at high light intensities and low carbon dioxide concentrations. most species of this type have little or no photorespiration.

Original comment by: jenclark

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CAM photosynthesis Physiological adaptation of certain succulent plants, in which carbon dioxide can be fixed (nonphotosynthetically) at night into malic and other acids. During the day the carbon dioxide is regenerated and then fixed photosynthetically into the Calvin Benson cycle. This adaptation permits the stomata to remain closed during the day, conserving water. http://cancerweb.ncl.ac.uk

Original comment by: jenclark

[gocentral]

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> The dark reaction of photosynthesis is also known as the
> calvin cycle.

this is synonym territory; doesn't need to be in the def

> In plants, a cyclical series of carbon-fixing, > sugar-producing reactions in the chloroplasts. [snip]

does this term also have to be used/usable for photosynthetic bacteria?

Also, there should be a semicolon, not a comma here: > Light is not needed for these reactions, > they use the carbon dioxide and energy [...]

> C4 photosynthesis

Does this mean that HSK pathway is a synonym or C4 photosynthesis? Or part of?

This def could be edited for style -- it could be somewhat shorter, and would work best if it started off with something like ' A photosynthetic pathway in which ...' followed by biochemical features of the pathway that distingiush it from 'ordinary' photosynthesis. The part about which plants use this pathway can go at the end.

> CAM photosynthesis

Again, make sure the distinguishing biochemical features are prominent.

> carbon dioxide is ... fixed photosynthetically > into the Calvin Benson cycle.

sounds weird ... isn't it fixed BY the Calvin-Benson cycle? or via the cycle? I'd expect to see 'into' in front of 'glucose' or whatever the plant makes with the carbon...

m

Original comment by: mah11

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Hi mIdori,

Thanks for the feedback. I'll have a look at that. While you're there can I ask a quick question?

I found:

NADP+ reduction Currently GO:0009780 in process as child of photosynthesis, light reaction ; GO:0019684 I would have thought that this should be obsoleted and a new term created in function but I have looked and there are no 'x' reduction terms in function and lots of undefined ones in process.

I think NADP+ reduction must be the opposite of oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, with NADH or NADPH as one donor, and the other dehydrogenated GO:0046996 which is a term in function.

Have I got the right track there, and should I do something about those other 'x' reduction terms in process?

Jen

Original comment by: jenclark

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tricarboxylic acid cycle ; GO:0006099 A pathway that is a central feature of oxidative metabolism. It includes cyclic reactions whereby acetyl CoA is oxidized to carbon dioxide providing reducing equivalents (NADH or FADH2) to power the electron transport chain. Also provides intermediates for biosynthetic processes.

Not sure what these are about: reductive citric acid pathway ; GO:0019644 reductive tricarboxylic acid cycle ; GO:0019643

Original comment by: jenclark

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Entner-Doudoroff pathway ; GO:0009255 A pathway that converts glucose to pyruvate and glyceraldehyde-3 phosphate by producing 6-phosphogluconate and then dehydrating it.

Original comment by: jenclark

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photosynthetic water oxidation ; GO:0009781 is a bit like the reduction term. There are lots of undefined oxidation terms in process. I will try to find out what to do about this.

Original comment by: jenclark

[gocentral]

this the file containing the defs I'm working on

Original comment by: jenclark

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Jen,

Please look at the definition in MetaCyc or AraCyc. If you want more help with this, contact Peifen Zhang. She is our metabolism curator at TAIR and I believe she worked on these terms. Her email is: peifenz@acoma.stanford.edu Also, you can look at the online Arabidopsis book published by ASPB. If you go to ASPB and search for TAB or The Arabidopsis Book, you will get to the articles. There is a chapter on Photosynthesis.

Original comment by: syrhee

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Jen,

I'd agree with your assessment of the NADP+ reduction term. If there isn't something already existing in GO to represent it, I'd suggest adding a function term along the lines of this reaction from MetaCyc: http://biocyc.org/META/new-image?type=REACTION-IN- PATHWAY&object=RXN-924

Most of the other reduction terms look like they need to be rehomed under obsolete, too.

Original comment by: girlwithglasses

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Hi Amelia,

Thanks for looking at that. If any of the reduction terms have no annotations then can I just obsolete them without making a replacement or do I need to make replacements for all of them?

Jen

Original comment by: jenclark

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I've just had a look at the reduction terms - there's a new SF item about them - SF:955301.

Original comment by: girlwithglasses

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Noting urls:

light reaction: http://www.arabidopsis.org:1555/ARA/new-image?type=PATHWAY&object=PWY-101

photorespiration: http://www.arabidopsis.org:1555/ARA/new-image?type=PATHWAY&object=PWY-181

Original comment by: jenclark

[gocentral]

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Defs for:

C4 photosynthesis CAM photosynthesis

added.

Can we add an edited version of the 'photosynthesis, dark reaction' def:

A cyclical series of carbon-fixing, sugar-producing reactions in the chloroplasts. Some of the sugars (triose phosphates) are recycled, others are stored as carbohydrates. Light is not needed for these reactions as they use the carbon dioxide and energy produced in the light reactions of photosynthesis. http://cancerweb.ncl.ac.uk

Original comment by: jl242

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For 'photosynthesis, dark reaction' how about def: The 'dark' reactions comprise a complex cycle of enzyme-mediated reactions (the Calvin cycle) which catalyzes the reduction of carbon dioxide to sugar. As well as carbon dioxide the cycle requires reducing power in the form of reduced nicotinamide adenine dinucleotide phosphare (NADP) and chemical energy in the form of adenosine triphosphate (ATP). The reduced NADP (NADPH) and ATP are produced by the 'light' reactions.

Jen

Original comment by: jenclark

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ref for that is ISBN:0582015952

Original comment by: jenclark

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Looks fine to me.

Original comment by: syrhee

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Added the 'photosynthesis, dark reaction' def.

Original comment by: jl242

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Added a definition for 'photosynthesis, light reaction' which I got from TAIR website:

The light reactions of photosynthesis, which take place in photosystems II and I. Light energy is harvested and used to power the transfer of electrons among a series of electron donors and acceptors. The final electron acceptor is NADP+, which is reduced to NADPH. NADPH generated from light reactions is used in sugar synthesis in dark reactions. Light reactions also generate a proton motive force across the thylakoid membrane, and the proton gradient is used to synthesize ATP. There are two chemical reactions involved in the light reactions: water oxidation in photosystem II, and NADP reduction in photosystem I.

Original comment by: jl242

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added definitions:

photosynthetic NADP+ reduction GO:0009780 def: Processes by which NADP+ is reduced to NADPH. The light reactions of photosynthesis use energy from photons to generate high-energy electrons. These electrons are used directly to reduce NADP+ to NADPH. NADPH is a relatively stable molecule and can pass on its hydrogen atom to other molecules in chemical reactions. dbxref: [GO:jic, ISBN:0816017360, ISBN:0716746840]

photosynthetic water oxidation GO:0009781 def: Processes by which a molecule of water is oxidised during photosynthesis. P680+, the photochemically oxidized reaction-center chlorophyll of PSII, is a strong biological oxidant. The reduction potential of P680+ is more positive than that of water, and thus it can oxidize water to give O2 and H+ ions. The oxygen escapes as a gas while the H+ ions remain in solution inside the thylakoid vesicle.

dbxref: [ISBN:0716743663, ISBN:0816017360, GO:jic]

Jen

Original comment by: jenclark

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This is finished now.

Jen

Original comment by: jenclark

[gocentral]

• status: open --> closed-accepted

Original comment by: jenclark