Week 2 HW: DNA Design
Before diving into this week’s homework…
To achieve what I was imaging in homework 1, I can break the material down into two main components: a substrate made out of biosilica, and living pigments. After a discussion with ChatGPT about the expression host, I decided to narrow down, to first focus on the biosilica component from diatoms.
This still gives me a couple of different options for what I want to biomanufacture:
- Replicating diatom biomineralisation, silica precipitation in vitro
- Putting the genes that are responsible for the processes into a bacteria such as E.coli, to see if E.coli is capable of producing similar peptides that are responsible for silica precipitation in diatoms.
- Identifying and manipulating individual genes that influence frustule morphology.
A little bit about diatom biomineralisation
Diatoms build their cell walls in intricate porous structures with hydrated amorphous silica (SiO2). Their silica cell walls can also be referred to as frustules.
In nature, silicon is present in water, dissolved as orthosilicic acid, Si(OH)4, and diatoms use this silicic acid to make silica.
Membrane proteins called silicic acid transporters (SITs), facilitate the transportation of silicic acid from outside of their shells into cytoplasm and silica deposition vesicles.
Silica deposition vesicles (SDVs) is a specific intercellular compartment for where this silicon gets converted into solid biosilicon. It is membrane bound, so silica does not float around in the cytoplasm.
The name of my repository and folder: Xiaomeng-HTBAA-2026 / xiaomeng-project
The expression target
There are many different proteins responsible for silica biomineralisation in diatoms, depending on the species of the diatoms. Silaffins and silacidins in the lumen of SDVs, the acidic inner spaces. There are also proteins responsible for the process, found in the membrane of SDVs, such as Silicanin-1 (Sin1), or the protein family SAPs (Silicalemma-Associated Proteins), that has more to do with the structure, or morphology of the silica.
Possible proteins to look in to:
- Silaffin-1 (SIL1), 265 amino acids
- maybe silaffin and silacidins are good because they are found in acidic environments
- one of the SAPs in Thalassiosira pseudonana?
- or Sin1? (that was expressed in E.coli in a research paper), 426 amino acids
(in the process of deciding, leaning towards silaffin and silacidins, one that is well studied)