Generating table for linkers/osmolytes

This notebook describes the steps to generate the

import pandas as pd

linkers_dict = {}

Add the amino acids as linker reactions in the vacuole of both the guard cell and mesophyll cell. They have an osmotic effect in the guard cell but not the mesophyll

amino_acid_list = [
    '4_AMINO_BUTYRATE',
    'LEU',
    'GLY',
    'VAL',
    'L_ALPHA_ALANINE',
    'ASN',
    'MET',
    'LYS',
    'THR',
    'ILE',
    'SER',
    'GLT',
    'TRP',
    'GLN',
    'TYR',
    'L_ASPARTATE',
    'PRO',
    'PHE',
    'HIS',
    'bHIS',
    'CYS',
    'ARG',
]

for cell, osmolarity in zip(["me", "gc"], [0, 1]):
    for amino_acid in amino_acid_list:
        linkers_dict[f"{amino_acid}_v_{cell}"] = osmolarity

Use vacuolar linkers from previous diel paper for mesophyll non-osmotic linkers

me_linkers = [
    "MAL",
    "aMAL",
    "SUCROSE",
    "CIT",
    "aCIT",
]

for me_linker in me_linkers:
    linkers_dict[f"{me_linker}_v_me"] = 0

Add non-osmotic apoplastic linkers based on what has been found to be present in the apoplast of guard cells

a_linkers = [
    'Cl',
    'FRU',
    'GLC',
    'K',
    'MAL',
    'NITRATE',
    'SUCROSE',
    'aMAL',
]

for a_linker in a_linkers:
    linkers_dict[f"{a_linker}_a"] = 0

Add osmotic linkers to cytoplasm and vacuole of GC based on what has been hypothesised to accumulate

gc_c_linkers = [
    'CIT',
    'Cl',
    'FRU',
    'GLC',
    'K',
    'MAL',
    'NITRATE',
    'SUCROSE',
]

for gc_c_linker in gc_c_linkers:
    linkers_dict[f"{gc_c_linker}_c_gc"] = 1

gc_v_linkers = [
    'CIT',
    'Cl',
    'FRU',
    'GLC',
    'K',
    'MAL',
    'NITRATE',
    'SUCROSE',
    'aCIT',
    'aMAL',
]

for gc_v_linker in gc_v_linkers:
    linkers_dict[f"{gc_v_linker}_v_gc"] = 1

Add starch as a non-osmotic linker reaction in both the gc and me plastid

linkers_dict[f"STARCH_p_gc"] = 0
linkers_dict["STARCH_p_me"] = 0

Add palmitate fatty acid as a linker reaction to the GC cytoplasm

Palmitate is the only fatty acid in the model. Adding other FAs and formation of lipids only makes a minor difference to energy costs involved (Unpublished work), so this is sufficient. Palmitate will not have an osmotic contribution because we assume it is stored in lipid droplets.

linkers_dict[f"PALMITATE_c_gc"] = 0

Add maltose as a linker reaction to the cytoplasm of GC (not ME)

Maltose contributes to osmotic pressure with osmotic coefficient of 1 in GC.

#linkers_dict[f"MALTOSE_c_me"] = 0
linkers_dict[f"MALTOSE_c_gc"] = 1

Save as .csv file

osmolytes_df = pd.DataFrame.from_dict(linkers_dict, orient="Index", columns=["Osmotic Coefficient"])
osmolytes_df.index.name = "Linker"
osmolytes_df.to_csv("../inputs/osmolytes.csv")

Generate a prettier DF for investigating here if wanted

def get_compartment_cell(linker):

    split_name = linker.split("_")
    cell = split_name[-1]
    if cell != "a":
        compartment = split_name[-2]
        metabolite = split_name[:-2]
    else:
        compartment = "NA"
        metabolite = split_name[:-1]

    if type(metabolite) == list:
        metabolite = "_".join(metabolite)

    return metabolite, compartment, cell

osmolytes_df_prettyindex = pd.MultiIndex.from_tuples([get_compartment_cell(i) for i in osmolytes_df.index], names=[
                                                     "Metabolite", "Compartment", "Cell"])
osmolytes_df.index = osmolytes_df_prettyindex
osmolytes_df = osmolytes_df.sort_index()
osmolytes_df

			Osmotic Coefficient
Metabolite	Compartment	Cell
4_AMINO_BUTYRATE	v	gc	1
4_AMINO_BUTYRATE	v	me	0
ARG	v	gc	1
ARG	v	me	0
ASN	v	gc	1
...	...	...	...
aMAL	NA	a	0
	v	gc	1
	v	me	0
bHIS	v	gc	1
bHIS	v	me	0

79 rows × 1 columns

def return_list_of_items(groupobject):
    return ", ".join(list(groupobject.values.astype("str")))

linkers_met_dict = {
    "SUCROSE": "Sucrose",
    "GLC": "Glucose",
    "FRU": "Fructose",
    "MAL": "Malate",
    "CIT": "Citrate",
    "Cl": "Cl",
    "K": "K",
    "NITRATE": "Nitrate",
    "aMAL": "aMalate",
    "STARCH": "Starch",
    "aCIT": "aCitrate",
    "bHIS": "bHis",
}

osmolytes_tidy = osmolytes_df.reset_index().set_index(["Osmotic Coefficient", "Cell", "Compartment"]).sort_index()

leftovers = set(osmolytes_tidy.Metabolite) - set(linkers_met_dict.keys())

for l in leftovers:
    linkers_met_dict[l] = l.capitalize()

osmolytes_tidy.Metabolite = osmolytes_tidy.Metabolite.map(lambda x: linkers_met_dict[x])
osmolytes_tidy = osmolytes_tidy.groupby(["Osmotic Coefficient", "Cell", "Compartment"]).agg(return_list_of_items)
osmolytes_tidy.to_csv("../plant_cell_paper/supplemental_table_1.csv")
osmolytes_tidy

			Metabolite
Osmotic Coefficient	Cell	Compartment
0	a	NA	Cl, Fructose, Glucose, K, Malate, Nitrate, Suc...
	gc	c	Palmitate
	gc	p	Starch
	me	p	Starch
	me	v	4_amino_butyrate, Arg, Asn, Citrate, Cys, Gln,...
1	gc	c	Citrate, Cl, Fructose, Glucose, K, Malate, Mal...
1	gc	v	4_amino_butyrate, Arg, Asn, Citrate, Cys, Cl, ...