Amyloid-like aggregation and fibril core determination of TDP-43 C-terminal domain

Chang, Ziwei; Deng, Jing; Zhao, Wenxue; Yang, Jun

doi:10.1016/j.bbrc.2020.08.096

Cited by 13 publications

(22 citation statements)

References 33 publications

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“…residues 306–343 and 362–397). 42 However, our result is quite distinct from that work. First, our samples were purified under conditions that completely solubilized the inclusion body fraction of the E. coli .…”

Section: Discussioncontrasting

confidence: 99%

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Identification of the Rigid Core for Aged Liquid Droplets of the TDP-43 Low Complexity Domain

Bd¹,

Km²,

Nr³

et al. 2021

Preprint

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The biomolecular condensation of proteins with low complexity sequences plays a functional role in RNA metabolism and a pathogenic role in neurodegenerative diseases. The formation of dynamic liquid droplets brings biomolecules together to achieve complex cellular functions. The rigidification of liquid droplets into β-strand-rich hydrogel structures composed of protein fibrils is thought to be purely pathological in nature. However, low complexity sequences often harbor multiple fibril-prone regions with delicately balanced functional and pathological interactions. Here, we investigate the maturation of liquid droplets formed by the low complexity domain of the TAR DNA-binding protein 43 (TDP-43). Solid state nuclear magnetic resonance measurements on the aged liquid droplets identify a structured core region distinct from the region thought to be most important for pathological fibril formation and aggregation. The results of this study show that multiple segments of this low complexity domain are prone to form fibrils, and that stabilization of β-strand-rich structure in one segment precludes the other region from adopting rigid fibril structure.

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Section: Discussioncontrasting

confidence: 99%

“…The stars indicate the Ala peaks that are present in the spectra of the full-length TDP-43 fibrils from reference 19 . In panel (d) the X-marks indicate the assigned Ala signals from the E. coli inclusion body seeded residue 274–414 fibrils from reference 42 .…”

Section: Discussionmentioning

confidence: 99%

Identification of the Rigid Core for Aged Liquid Droplets of the TDP-43 Low Complexity Domain

Bd¹,

Km²,

Nr³

et al. 2021

Preprint

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“…Second, the overwhelming majority of disease-related mutations on the TDP-43 gene ( TARDBP ) are missense mutations in the CTD (Figure a) . Finally, N-terminally truncated TDP-43 containing the full CTD is heavily enriched in ALS-related aggregates. , To date, most research on the TDP-43 CTD aggregation in vitro has focused on small peptide fragments from the CTD. ,− A few groups have studied the aggregation of the whole CTD, though its high aggregation propensity has generally led to the use of a His-tagged protein to enhance solubility. − ,− Furthermore, different experimental conditions have been used to facilitate these studies such as reduced temperature (≤25 °C), ,− acidic pH, , presence of urea as a chemical denaturant, , and slow dilution by dialysis. , While in vitro amyloid formation of TDP-43 CTD has been reported, ,, this observation has been contested . Although very recently, cryo-electron microscopy (cryo-EM) results strongly support the ability of TDP-43 CTD to form amyloid fibrils …”

Section: Introductionmentioning

confidence: 99%

“…15,22−26 A few groups have studied the aggregation of the whole CTD, though its high aggregation propensity has generally led to the use of a His-tagged protein to enhance solubility. 17−19,27−29 Furthermore, different experimental conditions have been used to facilitate these studies such as reduced temperature (≤25 °C), 17,27−29 acidic pH, 18,30 presence of urea as a chemical denaturant, 29,31 and slow dilution by dialysis. 19,28 While in vitro amyloid formation of TDP-43 CTD has been reported, 27,29,31 this observation has been contested.…”

Section: ■ Introductionmentioning

confidence: 99%

Tryptophan Probes of TDP-43 C-Terminal Domain Amyloid Formation

Shuster

Lee

2021

J. Phys. Chem. B

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Aggregated TAR DNA-binding protein 43 (TDP-43) forms the cytoplasmic hallmarks associated with patients suffering from amyotrophic lateral sclerosis and frontotemporal lobar degeneration with ubiquitin. Under normal conditions, TDP-43 is a 414-amino acid protein; however, aggregates are enriched with N-terminal truncations which contain residues 267–414, known as the C-terminal domain of TDP-43 (TDP-43CTD). To gain residue-specific information on the aggregation process of TDP-43CTD, we created three single-Trp containing mutants (W385F/W412F, W334F/W412F, and W334F/W385F) by substituting two of the three native Trp residues with Phe, yielding fluorescent probes at W334, W385, and W412, respectively. Aggregation kinetics, secondary structure, and fibril morphology were compared to the wild-type protein using thioflavin-T fluorescence, Raman spectroscopy, and transmission electron microscopy, respectively. While only W334 is determined to be in the proteinase-K resistant core, all three sites are sensitive reporters of aggregation, revealing site-specific differences. Interestingly, W334 exhibited unusual multistep Trp kinetics, pinpointing a distinctive role for W334 and its nearby region during aggregation. This behavior is retained even upon seeding, suggesting the observed spectral change is related to fibril growth. This work provides new insights into the aggregation mechanism of TDP-43CTD and exemplifies the advantages of Trp as a site-specific environmentally sensitive fluorescent probe.

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“…In 2021, Fonda et al evidenced that the LCD formed amyloid fibrils with a β-strand signature and indicated TDP-43 365–400 was involved in formation of both liquid droplets and amyloid fibrils ( Figure 4 ) [ 37 ]. Shenoy et al and Chang et al also reported the structure of the LCD fibrils determined by NMR [ 116 , 117 ], and pointed out that the TDP-43 368–414 fragment was crucial for the formation of the LCD fibrils. ( Figure 4 ) Furthermore, the atomic structures of the fragments and the entire length of the LCD was solved by cryo-EM recently, which provided structural insights for further pathological investigations ( Figure 2 ) [ 34 , 105 , 118 ].…”

Section: The Introduction Of Tdp-43 Lcdmentioning

confidence: 99%

The Different Faces of the TDP-43 Low-Complexity Domain: The Formation of Liquid Droplets and Amyloid Fibrils

Chien

Lee

Huang

2021

IJMS

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Transactive response DNA-binding protein 43 (TDP-43) is a nucleic acid-binding protein that is involved in transcription and translation regulation, non-coding RNA processing, and stress granule assembly. Aside from its multiple functions, it is also known as the signature protein in the hallmark inclusions of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) patients. TDP-43 is built of four domains, but its low-complexity domain (LCD) has become an intense research focus that brings to light its possible role in TDP-43 functions and involvement in the pathogenesis of these neurodegenerative diseases. Recent endeavors have further uncovered the distinct biophysical properties of TDP-43 under various circumstances. In this review, we summarize the multiple structural and biochemical properties of LCD in either promoting the liquid droplets or inducing fibrillar aggregates. We also revisit the roles of the LCD in paraspeckles, stress granules, and cytoplasmic inclusions to date.

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Amyloid-like aggregation and fibril core determination of TDP-43 C-terminal domain

Cited by 13 publications

References 33 publications

Identification of the Rigid Core for Aged Liquid Droplets of the TDP-43 Low Complexity Domain

Identification of the Rigid Core for Aged Liquid Droplets of the TDP-43 Low Complexity Domain

Tryptophan Probes of TDP-43 C-Terminal Domain Amyloid Formation

The Different Faces of the TDP-43 Low-Complexity Domain: The Formation of Liquid Droplets and Amyloid Fibrils

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