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how I can edit the different comparments of my PGDB

asked 2020-01-08 07:36:32 -0500

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Hello everybody! I am working with MetaFlux and my PGDB at Development Mode. I am trying to figure out which try-nutrient, try-biomass and try-secretion sets are more appropriate for my PGDB, and for each of them I have to indicate the comparment in which they are located. I have realized that my PGDB has the following compartments:

CCO45IN (CCO-IN) CCO45MIDDLE (CCO-MIDDLE) CCO45OUT (CCO-OUT) CCO45OUT45CCO45IN (CCO-OUT-CCO-IN) CCO45PM45BAC45NEG(CCO-PM-BAC-NEG) T (T) c (CCO-CYTOSOL)

Except the last one (c), I do not understant to what compartment they are referring to. Is there a way to remove or edit them? Is it possible to obtain a list of reactions located in each compartment of my PGDB? How many different compartment are there in MetaCyc? and how I can obtain the list of them?

Thank you so much

Best regards

Beatriz

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answered 2020-01-09 14:01:20 -0500

waikit gravatar image

Hi Beatriz,

What is the source of your SBML file? I'm not sure what you mean when you say the "compartments were assigned from reactions of MetaCyc".

After starting the SBML Import GUI, you probably created a new PGDB and entered the NCBI taxonomy ID for your organism. After the initial import (Import -> Import SBML File...) is completed, you have the option to fix any compartments that failed to map to a BioCyc CCO by selecting Fix SBML Compartment Mapping... before you continue the SBML import steps such as "Create SBML Species (Compound) and Reactions". There, you can select the correct compartment that corresponds to the compartment found in the SBML file.

You should be able to see the list of compartments defined in the SBML file if you search for listOfCompartments. If the SBML file contains compartments such as in, out, middle, then you would need to fix the SBML file. But I would be surprised if the SBML file contains such compartments. Was the SBML file exported from Pathway Tools?

As for MetaFlux, indeed the compartments are taken into account. I'm surprised you are not seeing the compartments CCO-PERI-BAC and CCO-EXTRACELLULAR assuming this is a gram-negative bacteria. Usually, biomass compounds are located in CCO-CYTOSOL, nutrients and secretions are located in CCO-EXTRACELLULAR. If you are still at an early stage of developing your PGDB for MetaFlux, you may try putting the nutrients and/or secretions in CCO-CYTOSOL to avoid dealing with transport reactions temporarily.

Hope that helps. If not, please describe how you created your PGDB in more detail.

Wai Kit

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Hello Wai Kit, Thank you so much for your explanation. I created the SBML File from Pathway Tools using the option Export -> Generate a SBML File for.... After that, I used the option Import -> Import SBML File. Because it was the way I found to known which compartments were present in my PGDB. After using the option of import, I did not see that there was the possibility of Fix SBML Compartment Mapping. I also do not understand why in my PGDB appear compartments such as CCO-IN, CCO-OUT and CCO-MIDDLE. Could you check my PGDB if something is wrong? I can not see neither of the compartments CCO-PERI-BAC and CCO-EXTRACELLULAR. The PGDB was created using PathoLogic and .fa and .gbk files as input files. And for MetaFlux, I am using the option you have mentioned, putting all nutrients and secretions in CCO-CYTOSOL Beatriz

bcamara gravatar imagebcamara ( 2020-01-10 00:37:52 -0500 )edit

Hi Beatriz, I do not understand why you would generate an SBML file for a PGDB within Pathway Tools (PT) and then re-import the SBML file back into PT. Could you elaborate on why you are doing this? What operating system are you using PT on? Are you saying that in the SBML Import GUI, under the Import menu, you see Import SBML File and Create SBML Species but not Fix SBML Compartment Mapping? Did you run transport inference parser after you created your PGDB using PathoLogic? Unfortunately, PathoLogic may not always succeed in trying to assign the right compartments for some types of reactions. There are some outstanding issues with this that we are still working to resolve, though I'm not sure if this applies in your case. For now, you would need to manually assign the correct compartments using the reaction editor. If you'd like, you ...(more)

waikit gravatar imagewaikit ( 2020-01-10 19:59:44 -0500 )edit

Hi Wai Kit, Thank you again for your message. I have already sent you my PGDB so you can check it. I am manually assignning comparments using the reaction editor, and it is starting to make sense.

bcamara gravatar imagebcamara ( 2020-01-23 01:22:19 -0500 )edit
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answered 2020-01-09 04:14:06 -0500

bcamara gravatar image

Hi Suzanne,

First of all, I would like to thank you for your prompt answer. Your message has definitely helped me to clarify these aspects related to the different compartments of my PGDB. I have checked the full CCO ontology to know all possible terms related to compartments in bacteria. And following your suggestions, I have also checked the Cellular Component Go Terms option in the Protein Editor, the Update Cellular Architecture and the Reaction Editor options. However, I can not see a direct correlation among some of the terms appearing in each of them.

In the case of the Reaction Editor, for Reaction location the options are: cytosol, extracellular, periplasm, in, out, middle, side 1 and side 2.

In the case of the Cellular Component Go Terms option, cytosol, extracellular and periplasm compartments are present but not the compartments in, out, middle, side 1 and side 2.

When the compartments, in, out, middle, side1 and side2 are used how I could know that they are referring to periplasm, cytosol or extracellular spaces.

I have obtained the list of compartments of my PGDB from the SBML file and subsequently importing it as database Except for the cytosol compartment, the remaining compartments were not recognized when mapping to BioCyc CCO as they are indicated as "unknown space". I do not understand why this is happening if this compartments were assigned from reactions of MetaCyc.

Maybe if I could know which reactions are occuring in which compartment, I could modify some of them to have something more consensual in terms of number of compartments.

In my opinion, the compartment information is highly relevant for MetaFlux. As I understand it, depending on where the nutrients and secretions are located the fluxes could be different. It would be helpful if you could ask another developer to weigh in on that subject.

Thank you so much for your help

Beatriz

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answered 2020-01-08 13:47:08 -0500

Suzanne Paley gravatar image

Hi Beatriz,

CCO-PM-BAC-NEG is the plasma membrane for a Gram-negative bacterium (if your organism is not a Gram-negative bacterium, you probably shouldn't have this compartment -- you should have the corresponding compartment for Gram-positive bacteria instead, but if you're seeing this as the location of a transport reaction, it probably means that the reaction was originally defined in MetaCyc for a Gram-negative bacterium and used the specific compartment instead of a generic one).

CCO-CYTOSOL is of course the cytosol.

CCO-IN, CCO-OUT and CCO-MIDDLE are generic compartments used to describe reactions that cross one or two unspecified membranes. In general, for a Gram-negative bacterium, CCO-IN and CCO-OUT will correspond to cytosol and periplasm respectively for reactions that cross the plasma membrane, and periplasm and extracellular respectively for reactions that cross the outer membrane, though they could also correspond to cytosol and extracellular, in which case CCO-MIDDLE would correspond to the periplasm.

There are a number of other compartments you haven't mentioned here (including CCO-EXTRACELLULAR), presumably because you haven't come across them.

CCO-OUT-CCO-IN and T are not actual valid compartments. I'm not entirely sure, but I assume T refers to a default of some kind (which will presumably map to cytosol), and CCO-OUT-CCO-IN is used for some transport reactions to refer to some unspecified membrane or set of membrane and spaces between the in and out compartments.

You can explore the full CCO ontology at http://brg.ai.sri.com/CCO/ (though I'm not sure how up-to-date it is). The vast majority of these terms are for eukaryotes, however, and will not be relevant for prokaryotes. If you invoke the protein editor for some protein in your PGDB, and click on the button to edit Cellular Component GO Terms, the left-hand pane of the resulting pop-up shows all the specific compartments (i.e. excluding CCO-IN, etc.) that are instantiated in your organism, and which GO terms they correspond to. The ids for most of these terms may differ from the ones you listed above -- if they start with CCI instead of CCO, then they are specific instances of the corresponding CCO class terms.

You do have some limited ability to update the set of compartments in your PGDB. If you open pathologic and invoke the command Refine -> Update Cellular Architecture, you can specify what structures are present/absent in your organism, but there is not necessarily a one-to-one correspondence between listed structures and CCO terms (in particular, a given organelle will have CCO terms for each of its membranes and spaces). I'm guessing you probably won't want to make any changes here, however, and regardless, I don't know that any changes you make would have any impact on MetaFlux. If you invoke the Reaction Editor on some reaction, you can assign compartments for the reaction substrates (either generic or specific but spaces only, not membranes) -- this may impact how the reaction is treated by MetaFlux, I'm not sure.

I personally do not know ... (more)

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Asked: 2020-01-08 07:36:32 -0500

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Last updated: Jan 09

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