Difference between revisions of "Electron Transport - Progress"

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We are going to start by aiming for low hanging fruit and we will see how far we get before it gets difficult and time-consuming.  
 
We are going to start by aiming for low hanging fruit and we will see how far we get before it gets difficult and time-consuming.  
  
==5th March==
+
==5th March 2008, 2pm GMT==
  
 
Participants: Jennifer Deegan, Pascale Gaudet.
 
Participants: Jennifer Deegan, Pascale Gaudet.

Revision as of 07:06, 5 March 2008

Beginning

  • 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.

Discussion Points

  • GO: 0006118 electron transport

and children

  • 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)

Emails

Hi Harold,

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

Thanks Pascale


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.


Harold


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,

Pascale


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

hjd


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.

David


Hi David,

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.

Jen

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.

Top Terms

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.

electron transport replacement terms

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.

Component Ontology

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.

[| go list response]

Branch File

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.


Action Items:

  • 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

child terms

Action item: obsolete GO:0006133 : 5,10-methylenetetrahydrofolate oxidation [0]
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 [1]
we looked at this and think its fine

O2 terms

merge
GO:0006138 : NADH-O2 electron transport [0]
GO:0006136 : succinate-O2 electron transport [0]
GO:0006137 : ubiquinone-8-O2 electron transport [0]
into aerobic electron transport

anaerobic/aerobic

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 [0]
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

Shuttle terms

GO:0006127 : glycerophosphate shuttle [5]
GO:0043490 : malate-aspartate shuttle [6]
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 [11]
obsolete
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:

Photosystems

  • Do we need to redefine the terms:
photosynthetic electron transport in photosystem I
photosynthetic electron transport in photosystem II
  • 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

  • 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 

MF-BP links

Is this a situation that would be simplified with MF-BP links?

For example,

photosynthetic electron transport in plastoquinone 
NADH dehydrogenase (plastoquinone) activity 

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 this be in process or function:
electron transport, cytochrome c to oxygen













19th February 2008 2.30pm GMT

Participants: Pascale Gaudet, Michelle Gwinn-Giglio, Jennifer Deegan.

We discussed the differences between terms like 'photosynthetic electron transport in photosystem I' and 'photosynthetic electron transport in cytochrome b6/f'. Pascale and Michelle agree that the cytochrome term and those others that cover electron transport to a single protein may be better placed as functions.

We also considered terms like 'mitochondrial electron transport, cytochrome c to oxygen' where there is location information included in the name.

  • We discussed the point that maybe such location information should only be included when the process occurs in a different way in different locations.
  • We looked at the ribosome terms to see how the situation had been handled where there is the same thing (ribosome) made of different parts in different places. We found that these were differentated and all implemented, rather than just having the term 'ribosome' to cover all ribosomes.
  • Michelle pointed out that we may be able to handle this by having just one generic term and then use the new column 16 in the gene association file to contain the component identifier for 'mitochondrion'. This would prevent the proliferation of terms that makes the ontology so unweildy for annotators but would still enable them to capture all the information.


19th February 2008 4pm GMT

Participants: Pascale Gaudet, Michelle Gwinn-Giglio, Jennifer Deegan, Jim Hu, Debby Siegele, Ingrid Keseler.

Since last meeting we discussed on email the problem the electron transport to some of the proteins in the photosynthetic electron transport chain are processes and some are really just functions. It seemed like we could waste a lot of time essentially splitting hairs trying to work out which were functions and which were processes, when currently so many are missing altogether.

It is hoped that very soon the GO will include links between the function and process ontologies, and this change would make it much easier to make a correct representation of this area of biology as the full set of terms would be linked together and visible as a group in a single window of the user interface.

This change to MF-BP links has not happened yet but is taking place as a pilot project. Therefore we discussed the idea of initially making a flat list of the functions and smaller processes that should come under respiratory electron transport chain and photosynthetic electron transport chain. We figure that having a flat list like this will make it much quicker to implement the whole area of biology once the technology to make MF-BP links comes along.

This idea has been discussed with David Hill and Midori Harris (the ontology development managers) and with Chris Mungall (who is figuring out the practicalities of making MF-BP links). They are very happy with this idea.

We discussed this further in this meeting, and the expert biologist participants are also keen to have a first go at making the list. All those concerned stated that while it is likely to be quite difficult, the results will be extremely useful.

As a first step Jim Hu suggested that we should take the full list of functions under 'electron carrier activity' and start with those. Therefore, I have extracted those terms and entered them as the left column in a google spreadsheet.

http://spreadsheets.google.com/
username: geneontology
password: goconsortium

As mentioned, the functions are listed in the left column.

We are going to try to make a start by making a list of:

  • where the given function *only* exists as part of a given process (which will be entered in the second column)
  • where there is a given process (entered in third column) that can *only* occur if the function mentioned is occurring as part of that process.
  • where the function mentioned is part of a named process (entered in fourth column) in some species but not in others. Further details also to be entered if available.
  • There is a comments column for where there is information on a possible connection, but where we can't be sure that an entry should be made in the more specific columns.

We are going to start by aiming for low hanging fruit and we will see how far we get before it gets difficult and time-consuming.

5th March 2008, 2pm GMT

Participants: Jennifer Deegan, Pascale Gaudet.

We had a chat on skype about what remains to be done. The interpro2go mapping needs updates and Jen followed up this meeting with a visit to Sandra Orchard to fill her in on what is happening.

We also discussed the cell location information and remaining function-type terms in process. However we decided it would be better to leave these until after we had committed the first batch of obsoletions so as not to overwhelm people.



Notes

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.