Talk:RuBisCO

Rubisco was a science collaboration of the week.
View the changes made during that week.

Article name

Since when has this enzyme been called rubisCO instead of rubisco? It was rubisco (or usually, its long name) when I was in grad school working on photosynthesis, and the website linked to from the article calls it rubisco. Can we change it back so that rubisco has the article and rubisCO is the redirect? -- Marj 18:28, 6 Oct 2004 (UTC)

I have moved the article to the short from of the name since that's what people call it in practice and since there is some technical issues with / in titles.--nixie 05:32, 11 August 2005 (UTC)

Calvin Cycle diagram

Hey I just made/added an overview of the calvin cycle for this page and the calvin cycle page, I was wondering what everybody thinks. I'm worried it's to complicated/busy, I am wondering if i should dumb it down (ie get rid of the molecule diagrams). Anything else to change, I really want it to be great. Adenosine | Talk 08:34, September 2, 2005 (UTC)

I think it is good to include such a diagram on this page. Please check the structure of 3-phosphoglycerate; I think you have a carbon with 5 bonds and an extra hydrogen. Is it reasonable to show the carboxyl group as protonated at physiological pH? I like the idea of science articles that start simple and then have the details towards the end. Maybe there could be a simplified figure right at the start of the article. --JWSchmidt 13:35, 2 September 2005 (UTC)

Questions about Figure 2:

File:TwoRuBisCOquestions.png --JWSchmidt 20:41, 2 September 2005 (UTC)

You'd start to think I don't study this stuff every day in school... fixed. Adenosine | Talk 20:52, September 3, 2005 (UTC)

I tried making a new version (Image:Calvin-cycle3.png) that emphasizes the labels for RuBisCO and "Phase 1". It allows my old eyes to better see "RuBisCO" in the thumbnail view. If you think the modified version is okay, it probably could be compressed to a smaller file size. --JWSchmidt 09:12, 5 September 2005 (UTC)

I like that edit very much Adenosine | Talk 09:19, September 5, 2005 (UTC)

Many changes

I'm trying to learn the editing procedures/protocols (so patience please) and I have started to make many changes to this entry to hopefully improve it, based on the latest literature and consensus views on this enzyme. More to come, including references to better document the changes I have made. Need to create a User name - ARP for now 130.126.53.185 23:49, 29 November 2005 (UTC)

Thanks for all of your work on this article. --JWSchmidt 01:28, 30 November 2005 (UTC)

Added figure.

Added a figure showing the complete enzyme. I think this image should replace or at least accompany figure 1, but I'm just learning this whole system.

Made some minor changes in the text - links. Will add refs soon. ARP 17:16, 30 November 2005 (UTC)

Feel free to change the image for Figure 1. Figure 1 resides withing a "protein information box". The information box is generated by a "template": Template:Protbox_start. You can edit the "Photo" and "Caption" parameters for the template where it is used right at the start of the RuBisCO edit window:

{{Protbox start|Name=[[RuBisCO]]|Photo=RuBisCO.jpg|Caption='''Figure 1'''. Charged domains [<span style="color:#ff0000;">red</span>(<big>-</big>), <span style="color:#0000ff;">blue</span>(+)] on [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?form=6&db=t&Dopt=s&uid=30476 RuBisCO] allow it to assemble into tightly packed multi-meric complexes, maximizing the number of copies of this inefficient enzyme inside plant cells.....

Just replace "RuBisCO.jpg" with the name of a better image and add a descriptive caption for the new image. --JWSchmidt 19:47, 30 November 2005 (UTC)

The "molecular structure" link for figure 1 is broken and should be updated. Was any specific PDB structure used for this image? Sahrendt (talk) 15:17, 16 October 2009 (UTC)

Added references and some text changes

I'll have to mess around with replacing/switching Figs 1&4.ARP 21:59, 30 November 2005 (UTC)

Switched figures

OK, I've switched figs 1 and 4. Added one more ref to 'genetic engineering' section and made some small text changes. Also note that in Fig 2, Ribulose 1-phosphate (& its structure) should be replaced by Ribulose 5-phosphate - I've emailed the original author and hopefully he will change it.ARP 16:22, 1 December 2005 (UTC)

Switched figures

OK, I've switched figs 1 and 4. Added one more ref to 'genetic engineering' section and made some small text changes. Also note that in Fig 2, Ribulose 1-phosphate (& its structure) should be replaced by Ribulose 5-phosphate - I've emailed the original author and hopefully he will change it.ARP 16:22, 1 December 2005 (UTC)

rubiscos structure

Rubisco consists of eight large L chains (56 kd) and eight small S chains (14 kd) giving an L8S8 octo-dimer. NOT four L chains and eight S chains!

Metabolic control

The article states that "RuBisCO is the primary rate-limiting enzyme of the Calvin cycle." - NO NO NO! Under normal physiological conditions, according to Quick et al (1991), Rubisco has a control coefficient of 0.05-0.15 (the sum total of the control coefficients of every enzyme in a given pathway being 1). Only when growth has taken place in low light, and light intensity is suddenly increased (or CO2 is suddenly decreased), does rubisco's control coefficient increase to coefficient ranges where this statement might be accurate (>0.5).

Under the "normal" high light intensities typical of outdoors on sunny days, the rubisco control coefficient is 0.8 - see the paper following Quick (Stitt et al., 1991). Studies in the Quick paper were conducted using growth chamber conditions - low light!!!. Thus the statement is correct. ARP 19:22, 20 December 2006 (UTC)

RuBisCo engineered to have all the essential amino acids

has anyone engineered rubisco to have a wider variety of amino acids as structural aspects That is making the essential amino acids part of rubisco while maintaining rubisco function If rubisco was full of things like methionine phenylalanine, valine, threonine, tryptophan, isoleucine, leucine, and lysine Cysteine, tyrosine, histidine and arginine then eating plants with this Rubiscos presence would provide all the essential amino acids Considering that RuBisCo makes up a majority of the protein on Earth I think that it should be upgraded to deliver all the amino acids necessary to live People could get all of their protein from engineered rubisco leaves n grass —Preceding unsigned comment added by 169.237.215.179 (talk) 21:26, 15 June 2009 (UTC)

People can already get all the protein they need, and other things, from spinach leaves. --Agesworth 05:52, 17 June 2009 (UTC) —Preceding unsigned comment added by Agesworth (talk • contribs)

These people want to have it as a future food additive: https://www.newsroom.co.nz/sustainable-future/rod-climate-series-6 If they succeed, then the amino-acid composition of specifically this protein will matter to the food-value of the resulting foods. New Zealand, where they're exploring it, is not a good candidate for putting genetically engineered plants into open growing conditions. 222.154.121.175 (talk) 22:31, 26 June 2023 (UTC)

Importance

Considering that RuBisCo makes up a majority of the protein on Earth I think that it should be upgraded to high/top level importance. Anyone else agree? —The preceding unsigned comment was added by R-Bowen J (talk • contribs) 08:11, 19 December 2006 (UTC).

Even if it is the most common protein, that does not mean it "makes up a majority of the protein on Earth". --JWSchmidt 02:58, 1 February 2007 (UTC)

I agree with the 1st guy - high or even top importance! Aaadddaaammm (talk) 15:02, 3 November 2008 (UTC)

I've changed the importance to high as it is the single most abundant protein on Earth. Smartse (talk) 00:48, 23 May 2009 (UTC)

Beautifully referenced

I came across today an article referring to RuBisCo in the journal Nature (Vol 447; 14 June 2007; pp. 781-782), and looked RuBisCo up on Wikipedia. This Wiki on RuBisCo reads quite well, and the referencing, detailed as it is, is impressive. Keep up the good job, contributors. AppleJuggler 03:34, 26 June 2007 (UTC)

Removed last section, "RuBisCO and carbon sequestration"

I removed the last section, because I think the connection between carbon sequestration RuBisCO specifically (as opposed to other proteins in photoautotrophs) is a red herring. The idea that addition of nutrients to ecosystems increases carbon sequestration is old and important. But there's nothing special about RuBisCO to this phenomenon: photoautotrophs require lots of proteins to successfully convert CO₂ into organic matter in a form that will not rapidly be converted back to CO₂ by heterotrophic organisms. Furthermore, I know of no evidence that in nitrogen-limited plants, added nitrogen is preferentially assimilated into RuBisCO as opposed to other biomolecules. So I don't think this section is really on-topic.

I have retained the reference to the carbon cycle under "Further reading", although I guess using my logic above it could be removed.

Otherwise, I think this is a first-rate article! Asteen (talk) 14:59, 20 April 2008 (UTC)

RuBisCO vs Rubisco

I propose that all RuBisCOs should be changed to Rubisco - got a problem with that? Aaadddaaammm (talk) 15:00, 3 November 2008 (UTC)

I'd !vote for keeping it as is - it's more descriptive. -- MarcoTolo (talk) 17:00, 3 November 2008 (UTC)

It may be more descriptive, but it just looks so ugly to me. 141.14.217.217 (talk) 08:49, 5 November 2008 (UTC)

I agree it looks really bad in articles. I have certainly never written RuBisCO by hand and can't imagine many other people doing so. Smartse (talk) 23:49, 22 May 2009 (UTC)

As ugly as i think RuBisCO looks, it does appear to be the norm across the protein datbases i've looked at, so i figure i ought to stay as is :( Abergabe (talk) 16:17, 29 June 2010 (UTC)

reference check

I just took this out of the article:

In the initial reaction of RuBisCO in the light, the RuBP that was separated from RuBisCO binds with the carbamylated enzyme and after proton abstraction produces Enediol that can react with carbon dioxide. A limitation of either RuBisCO or RuBP at any stage will make the reaction insensitive to any other factor including carbon dioxide. For this reason, the leading C3 model that is based on a limitation of RuBisCO at low carbon dioxide levels such as compensation point is incorrect, since it cannot support life on the planet<ref>http://www.farazdaghi.com/</ref>. (added by Hfarazdaghi)

Can an expert verify the content and provide a citation to a specific published article rather than to this website? User Hfarazdaghi seems to run the cited website. --JWSchmidt (talk) 03:27, 14 June 2009 (UTC)

I suspect that edits from 99.231.80.189 such as this one are also from User:Hfarazdaghi. I think we need to remove all links to www.farazdaghi.com from the article. We need citations to peer-reviewed publications. --JWSchmidt (talk) 04:10, 14 June 2009 (UTC)

1) To satisfy yourself, Please check the latest volume of Advances in Photosynthesis and Respiration. Photosynthesis in Silico, A. Laisk, L. Nedbal and Govindjee (eds.), Photosynthesis in silico: Understanding Complexity from Molecules to Ecosystems, pp. 275–294.

c 2009 Springer Science+Business Media B.V.

Chapter 12: Modeling the Kinetics of Activation and Reaction of Rubisco from Gas Exchange Hadi Farazdaghi

2) Rubisco has been the origin of oxygenic life and is the main controller of CO2/O2 ratio on the planet. It is the only natural substance that can sequester CO2 and store it in vegetation.

3) Interested parties are welcome to comment directly on the site of www.farazdaghi.com —Preceding unsigned comment added by 99.231.80.189 (talk) 19:48, 12 July 2009 (UTC) The site also refers to other published articles. —Preceding unsigned comment added by 99.231.80.189 (talk) 20:46, 12 July 2009 (UTC)

Hi there, do you have any references to PubMed-listed journals that deal with this topic? This would deal with the problem easily, since we have no way of verifying if "www.farazdaghi.com" is run by an expert on Rubisco or accurately summarises the references that it cites. Tim Vickers (talk) 17:11, 20 July 2009 (UTC)

I removed the statement "However, authors of the same team [30] have been promoting the contradictory theory that photosynthesis is limited by RuBisCO at low CO2 concentration, which is in conflict with the existence of life on the planet.[18]" for a number of reasons.

1. The first part of the statement is not supported by the linked reference; 1 author of the team (Farquhar, GD) was part of the group that published the referenced finding (von Caemmerer S, Farquhar GD (1981). "Some relationships between the biochemistry of photosynthesis and the gas exchange of leaves". Planta 53: 376–87.), which is an article dated to 1981. Furthermore, the same authors (all of them) published a review of their work in 2001 ("Models of Photosynthesis, Plant Physiology, January 2001, Vol. 125, pp. 42-45) to provide a current context for the role of their original research. The cited research (from 1981) appears to represent part of an ongoing, long-term investigation by these authors, not a permanent contradiction to their later work.
2. The study by Tcherkez et al ("Despite slow catalysis...") is cited 16 times in the Pub-Med database.
3. As mentioned above, citation #18 appears to link to the editor's own website. Also, it isn't a primary source, while the article being refuted is a primary, peer-reviewed source.

Kinor sensase (talk) 17:38, 28 November 2010 (UTC)Kinor Sensase

Mechanism

Hi. A question came up on the reference desk Wikipedia:Reference_desk/Science#the organic chemistry of carbon dioxide fixation (i.e. mechanism of RuBisCO) about the mechanism of co2 capture, I found these [1] which is more detailed than the article about the active site in the enzyme - could this be incorporated into the article, or linked to? . maybe as further reading - thanks? I'm not a biochemist so I will leave it to whoever has got the article into it's present state - more expert than me.83.100.250.79 (talk) 15:13, 12 September 2009 (UTC)

See also the issue of the magazine "Nature" January 14, 2010 on Rubisco

See also the issue of the magazine "Nature" January 14, 2010 on Rubisco ("unintelligent design") —Preceding unsigned comment added by 83.77.248.104 (talk) 22:29, 14 January 2010 (UTC)

Thanks, I assume you are talking about this article. Smartse (talk) 21:10, 16 January 2010 (UTC)

Curious Referncing Style

Heya, i'm a bit confused by the referncing. Why is there information down there? Surely it should either be in the article or not at all? It almost reads a list of trivia. Abergabe (talk) 16:15, 29 June 2010 (UTC)

The references are in the article - they are completely conventional. There are two sets of references, those that are in-line, supporting statements made in the article, and others that dont fit in so well but are generally relevant. You can imagine that many thousands of articles have been written on this system.--Smokefoot (talk) 17:44, 28 November 2010 (UTC)

Edits of Oct, 2011

This protein is special so the article merits special attention. For this reason I wanted to explain my substantial revision of the lede. I just thought that people looking to understand how CO2 is fixed are not keen to read "shop talk" about the name RuBisCO coming from a geeky joke at a seminar. So I kept that bit but moved it to the deep south of the article. From the lede, I also removed mention of Calvin Cycle and the O2 pathway, the former being un-essential terminology if one wants a general understanding of this catalyst and the latter being a generally undesirable pathway that wrecks the enediol. But if there are worries about my edits, go ahead and revert them and we can discuss the options.--Smokefoot (talk) 02:18, 31 October 2011 (UTC)

Rubisco rate-limiting - NOT

Is someone going to edit the article to correct the assertion that Rubsio is rate limiting? I noticed that this has already been brought up on this talk page in 2006 and backed up with citations. Who ever manages this page, please update that section under Rate of enzymatic activity 20:40, 4 December 2015 (UTC) — Preceding unsigned comment added by Rhodydog (talk • contribs)

External links modified

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Net carbon dioxide fixation

From "Enzymatic activity", subsection "Products", paragraph 2: "At ambient levels of carbon dioxide and oxygen, the ratio of the reactions is about 4 to 1, which results in a net carbon dioxide fixation of only 3.5." What does the value of 3.5 represent? No reference is provided for the whole paragraph. Axl ¤ [Talk] 13:37, 13 March 2019 (UTC)

Errors/problems in structure section

AFAIK, the statement below is incorrect:

"In plants, algae, cyanobacteria, and phototrophic and chemoautotrophic proteobacteria, the enzyme usually consists of two types of protein subunit, called the large chain (L, about 55,000 Da) and the small chain (S, about 13,000 Da). The large-chain gene (rbcL) is encoded by the chloroplast DNA in plants.[4]"

Cyanobacteria is a prokaryote, which does not have a chloroplast. So the second sentence definitely does not apply to it. I'm not a rubisco expert, so I'm not sure if it exists in organisms that do not have chloroplasts. I would guess it does not. Also, the term "algae" is a bit informal, especially in comparison to proteobacteria. And if you're phototrophic, your're autotrophic, so probably the best edit would be to change the quoted text to:

"In plants, eukaryotic phytoplankton, and autotrophic proteobacteria, the enzyme usually ..."

I'm not a terrestrial ecologist, so I can't recommend an edit to "plants" to the correct scientific term.

briardew (talk) 17:47, 25 November 2019 (UTC)

Updating Expression in bacterial hosts

The statements in this section are no longer accurate. Rubisco has been expressed without chaperones in E. coli and has been used to form a fully autotrophic bacteria. https://www.cell.com/cell/pdf/S0092-8674(19)31230-9.pdf or https://www.nature.com/articles/d41586-019-03679-x

Ethan801 (talk) 23:03, 29 November 2020 (UTC)

Enzymatic Activity Reaction diagram

In the section "Enzymatic activity", the reaction diagram ("Two main reactions...") upper half, the left hand side of the reaction has a RuBP molecule with 11 oxygens, and a CO2 with two oxygens is added, so a total of 13 oxygens; on the RHS, the two resulting carboxylated molecules are identical, so unsurprisingly there are an even number, specifically 14, oxygen atoms. Thus the reaction is not balanced, and an oxygen is being imported in some unspecified way. Could a biochem wizard fix this? 2001:56A:F0E9:9B00:FCA0:3426:3FC5:CC7D (talk) 12:29, 30 August 2024 (UTC)JustSomeWikiReader