Electron Transport - Progress
- 1 Beginning
- 2 First Meeting Jan 2008
- 3 16th Jan 2008
- 4 Action Items:
- 5 23rd Jan 2008
- 6 6th February 2008
- 7 Notes
- Jen is contacting Jim Hu to try to arrange a skype call to clear up some relationship problems under electron transport. 12/12/07
- Meeting will be on Tuesday Dec 18, 9 AM Central Time.
- GO: 0006118 electron transport
- GO:0006133 : 5,10-methylenetetrahydrofolate oxidation
- GO:0019646 : aerobic electron transport
- GO:0019645 : anaerobic electron transport
- GO:0000044 : ascorbate stabilization
- GO:0042773 : ATP synthesis coupled electron transport
- GO:0010478 : chlororespiration
- GO:0006127 : glycerophosphate shuttle
- GO:0043490 : malate-aspartate shuttle
- GO:0006123 : mitochondrial electron transport, cytochrome c to oxygen (ok?)
- GO:0006120 : mitochondrial electron transport, NADH to ubiquinone (ok?)
- GO:0006121 : mitochondrial electron transport, succinate to ubiquinone (ok?)
- GO:0006122 : mitochondrial electron transport, ubiquinol to cytochrome c (ok?)
- GO:0006138 : NADH-O2 electron transport(ok?)
- GO:0009767 : photosynthetic electron transport (ok?)
- GO:0030965 : plasma membrane electron transport, NADH to quinone
- GO:0009766 : primary charge separation
- GO:0006136 : succinate-O2 electron transport
- GO:0006125 : thioredoxin pathway
- GO:0006137 : ubiquinone-8-O2 electron transport(ok?)
while we're at it:
- NADH dehydrogenase complex (plastoquinone) (sensu Cyanobacteria)
- NADH dehydrogenase complex (quinone) (sensu Bacteria)
- NADH dehydrogenase complex (ubiquinone) (sensu Bacteria)
Do you know if all cytochrome P450 proteins are involved in electron transport?
I wonder if those mappings are always correct: http://www.ebi.ac.uk/interpro/IEntry?ac=IPR001128
In I nutshell, and based on our def, yes.
Cytochome P450s are a large group of monooxygenase enzymes that metabolize of toxic hydrocarbons. They use NADPH coenzyme. Oxygen is a substrate. Some are enzymes are located in the endoplasmic reticulum as well as in the the mitochondrial membrane. So the ones in the mitochondria might be considered to be involved in THE electron transport if you are referring to the one that makes ATP. So, unless the definition of electron transport is really broad, I wonder if it would not be fair to classify all of them as being invovled in that process. SO, notice that our def is very broad: :*GO:0006118: **The transport of electrons from an electron donor to an electron acceptor.
- It has a child,
GO term: *NADH-O2 electron transport* GO id: *GO:0006138*
SO I would say any CYP450 is involved in GO:0006138.
But, remember how we've have been trying to clean that up?
see http://sourceforge.net/tracker/index.php?func=detail&aid=1226172&group_id=36855&atid=440764 there was also this really fun item: http://sourceforge.net/tracker/index.php?func=detail&aid=1332197&group_id=36855&atid=440764 but that was rather for function.
The problem is that this used to cover all electron transfer reactions, including all oxidoreductases. I just wonder if that's the case for some cytochrome P450s. Also, electron transport is a child of 'generation of precursor metabolites and energy'. It's possible that many children of 'electron transport' dont belong there. If that parent is correct, then 'electron transport' as you describe it above should not be a child. Also, GO:6120 to 6023 should be children of 'ATP synthesis coupled electron transport'??
Seems like some work is needed here... Should I open a SF item?
Thanks for your input,
Yes, most definitely, tt seems obvious that the standing definition of "electron transport" is too broad. The Oxford Dictionary of Biochemistry (aka, the bible), has this for an entry
Electron transport: 1. respiratory electron transport: the process by which pairs of electrons derived from intermediates of the tricarboxcylic acid cycle and other substraes flows down the respiratory chain to dioxygen, the ultimate electron acceptor in respiration. 2. photosynthetic elecron transport: the process by which pairs of electrons are trasported from water to NADP+ in the light phase of photosynthesis during noncyclic photophosphorylation.
Also, I still object to the actual term "electron transport", since it is not has if the same electron is passed down the chain. However, the term is historical in context, so we need to keep the convention.
So, some CYP450's could be annotated using def. 1; not all
It is clear that electron transport uses oxidation/reduction at each of it's steps. The way ET is defined in the GO now is almost meaningless
A definite SF item
Hi Jen and Pascale,
Is this really transport? According to Harold it's not. The electrons don't really get transported anywhere. People just call it that.
Transport for me is transmembrane transport, which this isn't. But this also happens in membranes, and I know a fair bit about both, so I'd be happy to take the ball, quietly rename it, and then run with it.
First Meeting Jan 2008
Participants: Debby Siegele, Jim Hu, Jennifer Deegan, David Hill, Michelle Gwinn-Giglio, Pascale Gaudet.
In our fist meeting we figured out that there are quite a lot of changes needed in this area of the ontology and that we should start by properly defining the top term 'electron transport'. We were also not sure whether photosynthetic eletron transport was a type of respiratory electron transport so we went away to figure this out for the next meeting.
16th Jan 2008
Participants: Jennifer Deegan, Pascale Gaudet, Michelle Gwinn-Gigio, Jim Hu, Debby Siegele.
We examined the very top terms in great detail.
GO:0006118 name: electron transport Def: The transport of electrons from an electron donor to an electron acceptor.
was redefined to:
id: GO:0006118 name: respiratory electron transport chain namespace: biological_process def: "A process whereby a series of electron carriers operate together to transfer electrons from donors such as NADH and FADH2 to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient." [GOC:mtg_electron_transport, http://cancerweb.ncl.ac.uk/] subset: goslim_candida subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok synonym: "6-phosphofructokinase reduction" RELATED  synonym: "dihydrobiopterin reduction" RELATED  synonym: "dihydrolipoamide reduction" RELATED  synonym: "dihydrolipoylprotein reduction" RELATED  synonym: "dihydropteridine reduction" RELATED  synonym: "electron transfer" EXACT  synonym: "other pathways of electron transport" RELATED  synonym: "oxidized glutathione reduction" RELATED  synonym: "protein-disulfide reduction" RELATED  is_a: GO:0022900 ! electron transport chain
though via email right after the meeting someone pointed out that we should have obsoleted.
Action item: Jen to obsolete GO:0006118 ; electron transport and make the above term as a new term.
We made a new grouping term as below:
[Term] id: GO:0022900 name: electron transport chain namespace: biological_process def: "A process whereby a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient." [GOC:mtg_electron_transport] is_a: GO:0006091 ! generation of precursor metabolites and energy
There was some discussion of whether photosynthetic electron transport chain was a type of respiratory electron transport chain:
[i]respiratory electron transport chain ---[i]photosynthetic electron transport chain
but in the end we decided to make these to terms siblings under a new grouping term (above) which is GO:0022900 ; electron transport chain:
[i]electron transport chain ---[i]respiratory electron transport chain ---[i]photosynthetic electron transport chain
The three terms were carefully redefined.
During our edits we also discovered a term in the component ontology that should be obsoleted:
GO:0009502 photosynthetic electron transport chain def: A series of membrane-linked oxidation-reduction reactions in which electrons are transferred from an initial electron donor through a series of intermediates to a final electron acceptor (usually oxygen).
Action item: Jen to obsolete this term.
The edits were made in a branch file that was checked out at about 2.30 pm GMT on 16th Jan 2008 and the file was committed to go/scratch as electron_transport.obo
The number range being used is 0022900 - 0023000.
- obsolete: GO:0009502 ; photosynthetic electron transport chain : obsoleted in branch, but mail not yet sent.
- obsolete: GO:0006118 ; name: electron transport : obsoleted in branch, but mail not yet sent.
Question for group
- In this obsoletion: GO:0006118 ; name: electron transport, I put 'consider' for oxidoreductase activity ; GO:0016491 and respiratory electron transport chain ; GO:0022904.
However there were lots of old obsolete terms that had consider GO:0006118 and I have changed them to consider GO:0022900 ; electron transport chain. Which is correct?
- Can we have some examples of the kind of wrong annotations to this term so I can make it clear in the annotation email why it needs to go?
23rd Jan 2008
Obsoleting electron trasnport
We will put comment on obsoletion of old electron transport to consider new election transport chain and children and also oxidoreductase - we will also add info in the comment about why we did this and about the kinds of errors that were present and why it is important to fix them
Action item: obsolete GO:0006133 : 5,10-methylenetetrahydrofolate oxidation 
no annotations no def
will tell people to consider these function terms:
methylenetetrahydrofolate dehydrogenase (NAD+) activity ; GO:0004487
methylenetetrahydrofolate dehydrogenase (NADP+) activity ; GO:0004488
methylenetetrahydrofolate reductase (ferredoxin) activity ; GO:0033738
methylenetetrahydrofolate reductase (NADPH) activity ; GO:0004489
GO:0010478 : chlororespiration 
we looked at this and think its fine
GO:0006138 : NADH-O2 electron transport 
GO:0006136 : succinate-O2 electron transport 
GO:0006137 : ubiquinone-8-O2 electron transport 
into aerobic electron transport
updated defs of anaerobic and aerobic to be parent def plus qualification of oxygen or not - -also updated term names to include "chain"
GO nuts wiki
Jim suggests putting commentary on this site
GO:0000044 : ascorbate stabilization 
ascorbate stabilization discussion - can't quite figure out if it is a process or a function - should we obsolete it or merge it to a metabolic parent?
decided to obsolete it - no annotations and functiony def
GO:0006127 : glycerophosphate shuttle 
GO:0043490 : malate-aspartate shuttle 
these feed electrons into electron transport from cytosolic NADH produced by glycolysis
Leaving these here but changing relationships to part of.
Need to find isa parents for these
GO:0006125 : thioredoxin pathway 
and tell people to consider cell redox homeostasis
suggested expert: Rob Gunsalus
6th February 2008
Participants: Jim Hu, Debby Siegele, Ingrid Keseler, Jennifer Deegan, David Hill.
We changed photoinhibition to a part_of child of photosynthetic electron transport chain.
We considered a few questions:
1) Do we need to redefine the photosynthetic electron transport in photosystem I photosynthetic electron transport in photosystem II terms? Are there processes? We think they are fine as processes as photosystems have so many parts that there must be many steps.
other membrane proteins
2) For the sibling terms covering transport in single proteins: photosynthetic electron transport in plastocyanin photosynthetic electron transport in plastoquinone Do we need process terms for these? If they are single proteins, then does transport of electrons in them need a process term or should this be a function?
Should we really have these or would the gene products just be annotated to the component? The experts present were not experienced enough in annotation or in these processes to know what to do. These terms were undefined and had no annotations. Action: Ask TAIR or photsynthetic bacteria people.
These are the relevant terms: photosynthetic electron transport in cytochrome b6/f photosynthetic electron transport in plastocyanin photosynthetic electron transport in plastoquinone
Is this a situation that would be simplified with MF-BP links?
For example, photosynthetic electron transport in plastoquinone (- NADH dehydrogenase (plastoquinone) activity MF BP link maybe?)
Names ending in 'chain'
Is this name processy enough? 'photosynthetic electron transport chain'
Concurrent annotations to cellular component?
Should we have the word 'mitochondrial' in terms like mitochondrial electron transport, cytochrome c to oxygen or should this be done with concurrent annotation to 'mitochondrion' and 'electron transport, cytochrome c to oxygen'.
Should 'electron transport, cytochrome c to oxygen' be in process or function?
I have obsoleted all terms requested up to 4th February and sent all required obsoletion warnings. I am putting a date of 4th April on the obsoletion warnings.