Cellular Model of TAR DNA-binding Protein 43 (TDP-43) Aggregation Based on Its C-terminal Gln/Asn-rich Region

Budini, Mauricio; Buratti, Emanuele; Stuani, Cristiana; Guarnaccia, Corrado; Romanò, Valentina; Conti, Laura De; Baralle, Francisco E.

doi:10.1074/jbc.m111.288720

Cited by 108 publications

(128 citation statements)

References 84 publications

Supporting

Mentioning

119

Contrasting

Order By: Relevance

“…These values are in excellent agreement with the theoretical mass of 9927 Da calculated for the sequence of this construct: M-11R-10G-9SHHH-5HHHG-1 S0M1SEYI5RVTED10ENDEP15I EIPS20EDDGT25VLLST30VTAQF35PGACG40LRY RN45PVSQC50MRGVR55LVEGI60LHAPD65AGW GN70LVYVV75NY77, for which the His-tag is shown in italics. The 13 C, 15 N protein shows a mass peak at 10 424.8 Da, which is slightly lower than the calculated mass of 10 480.9 Da for the 13 C, 15 N-labeled protein. Based on this difference, the overall incorporation of 13 C and 15 N is calculated to be 89.9%.…”

Section: Mass Spectracontrasting

confidence: 59%

“…The b-strands, a-helix, and three of four turns are generally rigid, although the loop formed by residues 47-53 is mobile, as determined by model-free analysis of the 15 transport were identified in 2001 [2] and have been reviewed recently [3]. Nine years ago, TDP-43 was found to form aberrant polyubiquitinated, hyperphosphorylated cytosolic aggregates that have been causatively linked to amyotrophic lateral sclerosis/ frontotemporal lobar degeneration (ALS/FTLD) [4,5] and, more recently, to Alzheimer's disease [6].…”

mentioning

confidence: 99%

See 1 more Smart Citation

The TDP‐43 N‐terminal domain structure at high resolution

et al. 2016

Self Cite

View full text Add to dashboard Cite

Transactive response DNA-binding protein 43 kDa (TDP-43) is an RNA transporting and processing protein whose aberrant aggregates are implicated in neurodegenerative diseases. The C-terminal domain of this protein plays a key role in mediating this process. However, the N-terminal domain (residues 1-77) is needed to effectively recruit TDP-43 monomers into this aggregate. In the present study, we report, for the first time, the essentially complete 1 H, 15N and 13C NMR assignments and the structure of the N-terminal domain determined on the basis of 26 hydrogen-bond, 60 torsion angle and 1058 unambiguous NOE structural restraints. The structure consists of an a-helix and six b-strands. Two b-strands form a b-hairpin not seen in the ubiquitin fold. All Pro residues are in the trans conformer and the two Cys are reduced and distantly separated on the surface of the protein. The domain has a well defined hydrophobic core composed of F35, Y43, W68, Y73 and 17 aliphatic side chains. The fold is topologically similar to the reported structure of axin 1. The protein is stable and no denatured species are observed at pH 4 and 25°C. At 4 kcalÁmol À1 , the conformational stability of the domain, as measured by hydrogen/deuterium exchange, is comparable to ubiquitin (6 kcalÁmol À1 ).The b-strands, a-helix, and three of four turns are generally rigid, although the loop formed by residues 47-53 is mobile, as determined by model-free analysis of the 15 N{ 1 H}NOE, as well as the translational and transversal relaxation rates.

show abstract

Section: Mass Spectracontrasting

confidence: 59%

mentioning

confidence: 99%

The TDP‐43 N‐terminal domain structure at high resolution

et al. 2016

Self Cite

View full text Add to dashboard Cite

show abstract

“…Several of the 74 genes are implicated in disorders of the human nervous system, including childhood neurodevelopmental disorders, such as Autism spectrum disorders (ASD), syndromic and nonsyndromic mental retardation (MR), and late-onset neurodegenerative processes, including frontotemporal lobar degeneration (FTLD), amyotrophic lateral sclerosis (ALS), and Huntington and Parkinson diseases (Table S4). Several genes within this group, including TARDBP, TIAL1, SIRT1, and PQBP1, which have recently been implicated in neurodegenerative diseases (ALS/FTLD spectrum, SMA, Lewy Body Dementia, Parkinson disease, MR, respectively), are involved in mRNA trafficking, stability, and microRNA biogenesis, associated with various types of RNA granules or involved in protein misfolding (25,26). Silencing of additional genes within these pathways (e.g., G3BP1, TAF15, and SNRPB2) in our shRNA screen displayed different PSA-NCAM phenotypes (Table S5), in line with the interaction and differential regulation of RNA granule components (27).…”

Section: Resultsmentioning

confidence: 99%

Functional genomic screen of human stem cell differentiation reveals pathways involved in neurodevelopment and neurodegeneration

Zhang

Schulz

Reed³

et al. 2013

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

View full text Add to dashboard Cite

Human embryonic stem cells (hESCs) can be induced and differentiated to form a relatively homogeneous population of neuronal precursors in vitro. We have used this system to screen for genes necessary for neural lineage development by using a pooled human short hairpin RNA (shRNA) library screen and massively parallel sequencing. We confirmed known genes and identified several unpredicted genes with interrelated functions that were specifically required for the formation or survival of neuronal progenitor cells without interfering with the self-renewal capacity of undifferentiated hESCs. Among these are several genes that have been implicated in various neurodevelopmental disorders (i.e., brain malformations, mental retardation, and autism). Unexpectedly, a set of genes mutated in late-onset neurodegenerative disorders and with roles in the formation of RNA granules were also found to interfere with neuronal progenitor cell formation, suggesting their functional relevance in early neurogenesis. This study advances the feasibility and utility of using pooled shRNA libraries in combination with next-generation sequencing for a high-throughput, unbiased functional genomic screen. Our approach can also be used with patient-specific human-induced pluripotent stem cell-derived neural models to obtain unparalleled insights into developmental and degenerative processes in neurological or neuropsychiatric disorders with monogenic or complex inheritance. O ur general aim is to identify genes and pathways of early neural differentiation that are relevant for the development and function of the human nervous system. In vitro differentiation of human embryonic stem cells (hESCs) yielding developmentally competent neuronal progenitors is an attractive model for these studies and several approaches for this have been developed, including those by our group (1).Large-scale loss-of-function analysis by RNA interference (RNAi) using small hairpin (shRNA) or small interfering RNA (siRNA) -mediated knockdown of genes is a powerful screening approach in mammalian cells (2-7). ShRNAs provide the opportunity for long-term silencing by stable infection of cells maintained under selection pressure. Furthermore, pooled libraries of shRNAs can be efficiently used instead of arrayed individual clones. Screening experiments can be designed for detection of shRNAs that produce a desired effect in a cell (positive screens) or for the depletion of shRNA species that silence a necessary gene (dropout screens). The abundance of shRNAs has been measured by using barcodes and array hybridization (8, 9), but this procedure is subject to cross-hybridization and nonlinear responses. Most positive screens have been limited to studies of cellular proliferation or survival because it is easier to analyze the recovered enriched shRNAs (10). For dropout screens it is critical to accurately measure the abundance of shRNAs that are retained in cells at the end of the experiment to determine which shRNAs were depleted (8). In part because of this challenge, ...

show abstract

“…Missense mutations in the TDP-43 gene cluster in exon 6, which encodes the C-terminal GRR (14 -19), aggravate cytotoxicity (20 -23). A wealth of studies have suggested that the C-terminal region of TDP-43 is aggregation-or inclusionprone (24 -27), whereas a Gln/Asn-rich domain in the C terminus was also proposed to have a strong tendency for self-aggregation (21,28,29). The C-terminal GRR domain is composed of ϳ150 amino acid residues (positions 262-414) and is critical not only for cytoplasmic deposition (30,31) but also for seeding full-length TDP-43 in vitro or in cells (32,33).…”

Section: Tdp-43 (Tar Dna-binding Protein Of 43 Kda) Is a Majormentioning

confidence: 99%

Structural Transformation of the Amyloidogenic Core Region of TDP-43 Protein Initiates Its Aggregation and Cytoplasmic Inclusion

Jiang

Xia

Zhao

et al. 2013

Journal of Biological Chemistry

138

190

View full text Add to dashboard Cite

Background:The highly flexible C-terminal region of TDP-43 is implicated in disease pathology. Results: An amyloidogenic core was identified to be critical for TDP-43 aggregation. Conclusion: Helix-to-sheet structural transformation of the amyloidogenic core initiates TDP-43 aggregation and cytoplasmic inclusion formation. Significance: This is a potential therapeutic target for mitigating the TDP-43 proteinopathies.

show abstract

Cellular Model of TAR DNA-binding Protein 43 (TDP-43) Aggregation Based on Its C-terminal Gln/Asn-rich Region

Cited by 108 publications

References 84 publications

The TDP‐43 N‐terminal domain structure at high resolution

The TDP‐43 N‐terminal domain structure at high resolution

Functional genomic screen of human stem cell differentiation reveals pathways involved in neurodevelopment and neurodegeneration

Structural Transformation of the Amyloidogenic Core Region of TDP-43 Protein Initiates Its Aggregation and Cytoplasmic Inclusion

Contact Info

Product

Resources

About