Cell's sense of starvation stress, triggers TDP-43 misfolding

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It’s unknown why misfolded aggregates appear in cells cytosol during neurodegenerative diseases. If the forming mechanism was elucidated it would enable designing new and efficient therapies. One of those protein aggregates is composed of misfolded TDP-43. Aggregates hyper-phosphorylated, ubiquitinated and cleaved form of TDP-43 are found in frontotemporal dementia, in amyotrophic lateral sclerosis and in some cases of Alzheimer and Parkinson.

My feeling is that scientists, from Academy of Scientific and Innovative Research (AcSIR) in India, achieved one of the most important milestone since 2006, when Virginia Lee provided evidence of involvement of TDP-43 in ALS.

For the proper functioning of the cells, neutral pH is required. However during normal metabolism, all foods create waste products which are acidic. Accumulated waste and toxins ages the cell, sometimes causes it to change to a sick or abnormal cell. For example the cytosol of yeast cells acidifies during aging.

Cells experience a variety of stress-like conditions, in particular, nutrient starvation stress acidifies the cytosol and increases the cytosolic proton ion concentration due to the reduced efficiency of ATP proton pump.

In chemistry, protonation describes the addition of a proton to a molecule, forming an acid. Some proteins or protein domains inside the cells can function as biosensors. It has been proposed that cells sense starvation stress at the molecular level by protonating the side chains of biosensor protein molecules.

The scientists Divya Patni  and  Santosh Kumar Jha observed in a previous study that two domains of TDP-43 (tRRM) could function as a biosensor and sense pH stress. They shown that under low-pH conditions, mimicking starvation stress, TDP-43tRRM undergoes a conformational change named "L structure". enter image description here The L form structure is held by weak interactions and eventually fully misfolds and oligomerizes to form a β-sheet rich "β form". The unstructured regions of the protein gain structure during L ⇌ β conversion.

TDP-43 consists of 4 domains:

  • An N-terminal domain
  • Two RNA recognition motifs RRM1 and RRM2 working as a tandem (tRMM)
  • An unstructured C-terminal domain.

In this paper, Patni  and  Jha showed that the monomeric N form of TDP-43tRRM forms a misfolded amyloid-like protein assembly, β form, in a pH-dependent manner.

The side chains of the ionizable amino acid residues buried inside the protein structure can protonate or deprotonate only upon partial or complete unfolding.

They are promising candidates to function as gatekeeper residues for protein aggregation as it often begins with partial unfolding of the protein.

The scientists from the Academy of Scientific and Innovative Research in Ghaziabad India, hypothesized that ionization of a protein side-chain buried in the protein structure might be coupled to the formation of the misfolded β form.

An examination of the protein structure revealed that out of all of the amino acid residues whose side chain could titrate in the acidic pH range, only D105, H166, and H256 are almost completely buried in the protein structure. They systematically mutated these residues to neutral amino acids whose side chains cannot undergo protonation-deprotonation reaction ( D105A, H166Q and H256Q).

Patni  and  Jha observed that D105A and H256Q behaved like TDP-43tRRM in their pH-dependent misfolding behavior. However, H166Q retained the N-like secondary structure under low-pH conditions and did not show pH-dependent misfolding to the β form.

These results indicate that H166 is the critical side-chain residue whose protonation triggers the misfolding of TDP-43tRRM.

These results indicate also that the protonation of H166 functions as a critical trigger switch that controls the amyloid-like misfolding of TDP-43tRRM upon pH stress sensing. It appears that the protonation of H166 results in proximal or distal conformational changes that initiate the misfolding of the protein.

It’s suspected since a long time that the RNA-Recognition motifs of TDP-43 may play a role in the aberrant self-assembly of the protein. Now a clear mechanism of action had been described, while it may not be the only one, hopefully it will enable the design of new therapies.

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