Add pyrenoid parts (matrix, sheath, tubule lumen and membrane)

[cmungall]

Currently the representation of the pyrenoid (a structure found in
eukaryotic algae and moss for boosting efficiency of rubisco) is
incomplete and there is no strategy for population with gene products.

The components of the pyrenoid can be seen here

from Fig1 of New light on pyrenoid membrane tubules

I propose

Components:

• pyrenoid NTR: pyrenoid #10282
  • pyrenoid matrix NEW
  • pyrenoid tubule NTR: pyrenoid tubule #29280
    • pyrenoid tubule lumen NEW
    • pyrenoid tubule membrane NEW
  • pyrenoid starch sheath NEW

Add "depicted_by" annotations to Fig 1 above

Note that the matrix is considered a condensate, but we did not add a
term for this (#21881)

Processes:

• I also propose a new term "pyrenoid tubule morphogenesis"

Taxon constraints:

• only in euks (get rid of redundant negatives to bact/arch)
• exclude all vascular plants
• roll up choanos, metazoa, and fungi to opisthokontes
• consider more specific TCs for the parts, but lower priority

Gene Annotation strategy:

The key components of the matrix are rubisco and EPYC1 (LCI5). This
can be annotated for the model Chlamy species.

But I propose a more ambitious strategy - make a unirule to propagate
all rubisco complex annotations to the matrix, for all eukaryotic
algae (this could also be represented in the ontology as a taxon GCI, as we do for uberon).

For the morphogenesis of the tubules:
genes: SAGA1 and MITH1 IMP from https://www.nature.com/articles/s41477-024-01847-0

There is proteomics data linking 190 chlamy proteins to the pyrenoid, but it's not clear if all are active here and I think we need a separate discussion for integration of proteomics data for localization (PRIDE link: https://journals.plos.org/plosone/article/file?type=supplementary&id=10.1371/journal.pone.0185039.s003)

I will make a GO-CAM that represents the functioning of the pyrenoid in chlamy. It will look something like this (rough sketch):

• CAH1/2: [extracellular] carbonate dehydratase activity
• LCI1: inward CO2 faciliated diffusion
• LCIB: conversion of CO2 to bicarbonate (HCO3-)
• BST1-3: transport of bicarbonate (HCO3-) into lumen of thylakoid tubules
• CA3H: [lumen] pyrenoid converts NCO3- to CO2

Image annotation strategy:

coordinate with CZI CryoET group (cc @uermel)

[uermel]

Hi @cmungall, this is great. It's of course much better to have a comprehensive description of all parts of this structure than just the one part!

The context for the pyrenoid tubule term request is a new dataset of segmentations for Chlamydomonas tomograms. Eventually this will likely get as fine-grained as described above.

I'm wondering if there should be an extra term, child of pyrenoid tubule lumen, that describes the minitubules inside the membrane-bound pyrenoid tubules? As evidence see for instance Figure 9 in this publication or this tomogram, where they are visible (this is from a big set of Chlamy tomograms that to my knowledge is only published in conference abstracts, e.g. here ).

[uermel]

Chlamy experts from @CellArchLab could maybe also weigh in on this (@rdrighetto).

[rdrighetto]

Thanks for bringing this up @uermel, I will ask my colleagues (the true experts, I'm just the computer guy)