The N-terminus of TDP-43 promotes its oligomerization and enhances DNA binding affinity

Chang, Chung-ke; Wu, Tzong Huah; Wu, Chu Ya; Chiang, Ming Hui; Toh, Elsie Khai Woon; Hsu, Yin Chih; Lin, Ku Feng; Liao, Yu heng; Huang, Tai Huang; Huang, Joseph Jen‐Tse

doi:10.1016/j.bbrc.2012.07.071

Cited by 109 publications

(136 citation statements)

References 30 publications

Supporting

Mentioning

121

Contrasting

Order By: Relevance

“…As shown in Fig. 1B, similar to the previous report (16), the N-domain (1-102) has very unusual far-UV circular dichroism (CD) spectra with the maximal negative signal at 196 nm, an additional negative signal at 206 nm, and a positive signal at 232 nm but no positive signal below 200 nm, which are very similar in both salt-minimized aqueous solution (Milli-Q water, pH 4.0) and 1 mM phosphate buffer (pH 7.5). Most importantly, in Milli-Q water, we were able to acquire high-quality heteronuclear single quantum correlation (HSQC) spectra with protein concentrations up to 1 mM.…”

Section: Resultssupporting

confidence: 92%

“…Unfortunately, even at a molar ratio of 1:0.5 (protein:RNA), most HSQC peaks of the TDP-43 N-domain (1-102) disappeared, and visible aggregates formed. This result implies that RNA has a much higher capacity than ssDNA in inducing the specific oligomerization of the TDP-43 N terminus, which might be correlated to the higher binding affinity of the RNA/DNA to the TDP-43 N terminus (16).…”

Section: Resultsmentioning

confidence: 94%

“…Two TDP-43 RNA recognition motifs, RRM1 and RRM2, have been extensively demonstrated to primarily recognize single-stranded (TG)n/(UG)n repeats (8,16,33), and the TDP-43 N terminus might also be involved in the binding to nucleic acids (16). As such, we examined whether the TDP-43 N-domain (1-102) is able to bind the single-stranded (TG) 6 DNA.…”

Section: Resultsmentioning

confidence: 99%

“…In this regard, the elucidation of the structure of the TDP-43 N terminus would provide valuable insights into the molecular mechanism underlying this intriguing dichotomy. Unfortunately, despite intense efforts, high-quality NMR data could not be acquired for the TDP-43 N terminus due to its severe aggregation (16).…”

mentioning

confidence: 99%

See 3 more Smart Citations

TDP-43 N terminus encodes a novel ubiquitin-like fold and its unfolded form in equilibrium that can be shifted by binding to ssDNA

Qin¹,

Lim²,

Wei

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

133

213

View full text Add to dashboard Cite

Transactivation response element (TAR) DNA-binding protein 43 (TDP-43) is the principal component of ubiquitinated inclusions characteristic of most forms of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia-frontotemporal lobar degeneration with TDP-43-positive inclusions (FTLD-TDP), as well as an increasing spectrum of other neurodegenerative diseases. Previous structural and functional studies on TDP-43 have been mostly focused on its recognized domains. Very recently, however, its extreme N terminus was identified to be a double-edged sword indispensable for both physiology and proteinopathy, but thus far its structure remains unknown due to the severe aggregation. Here as facilitated by our previous discovery that protein aggregation can be significantly minimized by reducing salt concentrations, by circular dichroism and NMR spectroscopy we revealed that the TDP-43 N terminus encodes a well-folded structure in concentration-dependent equilibrium with its unfolded form. Despite previous failure in detecting any sequence homology to ubiquitin, the folded state was determined to adopt a novel ubiquitin-like fold by the CS-Rosetta program with NMR chemical shifts and 78 unambiguous longrange nuclear Overhauser effect (NOE) constraints. Remarkably, this ubiquitin-like fold could bind ssDNA, and the binding shifted the conformational equilibrium toward reducing the unfolded population. To the best of our knowledge, the TDP-43 N terminus represents the first ubiquitin-like fold capable of directly binding nucleic acid. Our results provide a molecular mechanism rationalizing the functional dichotomy of TDP-43 and might also shed light on the formation and dynamics of cellular ribonucleoprotein granules, which have been recently linked to ALS pathogenesis. As a consequence, one therapeutic strategy for TDP-43-causing diseases might be to stabilize its ubiquitin-like fold by ssDNA or designed molecules. 1, 2). Since then, numerous studies have confirmed that TDP43 protein is mechanistically linked to neurodegeneration (3, 4). TDP43 is a 414-residue protein that has been previously recognized to be composed of a nuclear localization signal (NLS), two RNA recognition motifs (RRM1 and RRM2) hosting a nuclear export signal (NES), and C-terminal glycine-rich prion-like domain (Fig. 1A). The NLS and NES regulate the shuttling of TDP-43 between the nucleus and the cytoplasm (5), whereas the RRM1 and RRM2 are responsible for binding to nucleic acids including single-or double-stranded DNA/RNA (5-8). The prion-like domain mediates protein-protein interactions between TDP-43 and other hnRNP members (9), which also hosts most known ALS-associated TDP-43 mutations.TDP43 is an aggregation-prone protein (1-4, 10-14), and its abnormal aggregation has been found in ∼97% ALS and ∼45% frontotemporal dementia (FTD) patients. Additionally, TDP-43 immunoreactive inclusions have also been observed in an increasing spectrum of other neurodegenerative disorders, which include ALS/parkinsonism-dementia complex of Guam, Alzhei...

show abstract

Section: Resultssupporting

confidence: 92%

Section: Resultsmentioning

confidence: 94%

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

See 2 more Smart Citations

TDP-43 N terminus encodes a novel ubiquitin-like fold and its unfolded form in equilibrium that can be shifted by binding to ssDNA

Qin¹,

Lim²,

Wei

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

133

213

View full text Add to dashboard Cite

show abstract

“…By staining the HEK 293T cells co-transfected with FLAG-tagged TDP-35 and HA-tagged TDP-43, we observed that TDP-43 co-localized with the cytoplasmic inclusions formed by TDP-35 (data not shown), as in the case of the previous observation [4]. As known, the N-terminal domain of TDP-43 may contribute to the dimerization or oligomerization of TDP-43 [27,28]. Because TDP-35 has this N-terminus deleted, it is unlikely that there exists direct proteinprotein interaction between TDP-35 and TDP-43.…”

Section: The Tdp-35 Inclusions Sequester Full-length Tdp-43 Through Rnasupporting

confidence: 67%

TDP‐35 sequesters TDP‐43 into cytoplasmic inclusions through binding with RNA

Xia

Jiang

et al. 2015

FEBS Letters

View full text Add to dashboard Cite

Edited by Barry HalliwellKeywords: TAR DNA binding protein of 43kDa C-terminal fragment of $35kDa Sequestration Cytoplasmic inclusion RNA recognition motif a b s t r a c t TDP-43 (TAR DNA binding protein of 43kDa) and its C-terminal fragments are thought to be linked to the pathologies of amyotrophic lateral sclerosis and frontotemporal lobar degeneration. Here, we demonstrate that the aggregates or inclusions formed by its 35-kDa fragment (namely TDP-35) sequester full-length TDP-43 into cytoplasmic inclusions; and this sequestration is mediated by binding with RNA that is enriched in the cytoplasmic inclusions. RNA recognition motif 1 (RRM1) of TDP-43/TDP-35 plays a dominant role in nucleic-acid binding; mutation in this moiety abrogates formation of the TDP-35 inclusions and its RNA-assisted association with TDP-43. Thus, TDP-35 is able to sequester TDP-43 from nuclear localization into cytoplasmic inclusions, and RNA binding plays an essential role in this process.

show abstract

TDP‐43 N‐terminal domain dimerisation or spatial separation by RNA binding decreases its propensity to aggregate

et al. 2023

View full text Add to dashboard Cite

Aggregation of the 43 kDa TAR DNA‐binding protein (TDP‐43) is a pathological hallmark of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). RNA binding and TDP‐43 N‐terminal domain dimerisation has been suggested to ameliorate TDP‐43 aggregation. However, the relationship between these factors and the solubility of TDP‐43 is largely unknown. Therefore, we developed new oligonucleotides that can recruit two TDP‐43 molecules and interfere with their intermolecular interactions via spatial separation. Using these oligonucleotides and TDP‐43‐preferable UG‐repeats, we uncovered two distinct mechanisms for modulating TDP‐43 solubility by RNA binding: One is N‐terminal domain dimerisation, and the other is the spatial separation of two TDP‐43 molecules. This study provides new molecular insights into the regulation of TDP‐43 solubility.

show abstract

The N-terminus of TDP-43 promotes its oligomerization and enhances DNA binding affinity

Cited by 109 publications

References 30 publications

TDP-43 N terminus encodes a novel ubiquitin-like fold and its unfolded form in equilibrium that can be shifted by binding to ssDNA

TDP-43 N terminus encodes a novel ubiquitin-like fold and its unfolded form in equilibrium that can be shifted by binding to ssDNA

TDP‐35 sequesters TDP‐43 into cytoplasmic inclusions through binding with RNA

TDP‐43 N‐terminal domain dimerisation or spatial separation by RNA binding decreases its propensity to aggregate

Contact Info

Product

Resources

About