Here are some more upgrade proposals, this time focused on prokaryotic parts. Again, most of these aren’t my “new ideas”; they’re just a more finalized list of upgrades with a few newer ideas.
Metabolosomes
Environmental
Increased Cold Tolerance – Metabolosomes generate excess heat at the cost of total energy produced and heat tolerance.
Toxicity
Increased Toxin Resistance – Metabolosomes will assist in breaking down toxins at a cost of energy production.
Rusticyanin
Structural
Anaerobic Photolithotrophy (V) – The breakdown of iron is now based on sunlight instead of oxygen, resulting in more ATP generation. However, your species becomes much less tolerant to oxygen. Releases oxygen as a byproduct, so can require oxygen tolerance if your species has a significant impact on the environment.
Thermosynthase
Environmental
Hyperthermophilic Enzymes (M) - Insulation from heat, but less tolerance towards cold and normal conditions.
Chemosynthesizing Proteins
Structural
Photolithotrophy (V) – Your cell will breakdown hydrogen sulfide with the availability of sunlight instead of just carbon dioxide, producing more glucose. However, your species becomes less tolerant to oxygen and will become dependent on sunlight.
Environmental
Hyperthermophilic Enzymes (M) – Insulation from heat, but less tolerance towards cold and normal conditions.
Thylakoids
Structural
Red-Pigmented Thylakoids (V) – Increases photosynthetic efficiency in lower-lit environments, but decreases photosynthetic efficiency in higher-lit environments.
Environmental
Brown Pigments (M) – Greater protection from the cold, but less tolerance towards heat.
Cytoplasm
Structural
Storage Capacity v. Glycolysis (M) – Choose between either better storage capacity or better glycolysis.
Nitrogenase
Unsure. Perhaps something reflective of the nitrogen cycle.