TAR DNA-binding protein (TDP-43) is an evolutionarily conserved heterogeneous nuclear ribonucleoprotein (hnRNP) involved in RNA processing, whose abnormal cellular distribution and post-translational modification are key markers of certain neurodegenerative diseases, such as amyotrophic lateral sclerosis and frontotemporal lobar degeneration. We generated human cell lines expressing tagged forms of wild-type and mutant TDP-43 and observed that TDP-43 controls its own expression through a negative feedback loop. The RNA-binding properties of TDP-43 are essential for the autoregulatory activity through binding to 3 0 UTR sequences in its own mRNA. Our analysis indicated that the C-terminal region of TDP-43, which mediates TDP-43-hnRNP interactions, is also required for self-regulation. TDP-43 binding to its 3 0 UTR does not significantly change the pre-mRNA splicing pattern but promotes RNA instability. Moreover, blocking exosome-mediated degradation partially recovers TDP-43 levels. Our findings demonstrate that cellular TDP-43 levels are under tight control and it is likely that disease-associated TDP-43 aggregates disrupt TDP-43 self-regulation, thus contributing to pathogenesis.

TDP-43 (also known as TARDBP) regulates different processes of gene expression, including transcription and splicing, through RNA and DNA binding. Moreover, recent reports have shown that the protein interacts with the 3′UTRs of specific mRNAs. The aberrant cellular distribution and aggregation of TDP-43 were recently reported in neurodegenerative diseases, namely frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). A detailed description of the determinants for cellular localization has yet to emerge, including information on how the known functions of TDP-43 and cellular targeting affect each other. We provide the first experimental evidence that TDP-43 continuously shuttles between nucleus and cytoplasm in a transcription-dependent manner. Furthermore, we investigate the role of the functional TDP-43 domains in determining cellular targeting through a combination of immunofluorescence and biochemical fractionation methods. Our analyses indicate that the C-terminus is essential for solubility and cellular localization, because its deletion results in the formation of large nuclear and cytoplasmic aggregates. Disruption of the RNA-recognition domain required for RNA and DNA binding, however, alters nuclear distribution by decreasing TDP-43 presence in the nucleoplasm. Our findings suggest that TDP-43 solubility and localization are particularly sensitive to disruptions that extend beyond the newly found nuclear localization signal and depend on a combination of factors that are closely connected to the functional properties of this protein.

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Thrombin is an allosteric serine protease existing in two forms, slow and fast, targeted toward anticoagulant and procoagulant activities. The slow 3 fast transition is induced by Na , and Lys 224 , and by three highly conserved water molecules in the D-Phe-Pro-Arg chloromethylketone thrombin. The sequence in the Na ؉ binding loop is highly conserved in thrombin from 11 different species and is homologous to that found in other serine proteases involved in blood coagulation. Mutation of two Asp residues flanking Arg 221a (D221A/D222K) almost abolishes the allosteric properties of thrombin and shows that the Na ؉ binding loop is also involved in direct recognition of protein C and antithrombin.

Nuclear factor TDP-43 has been reported to play multiple roles in transcription, pre-mRNA splicing, mRNA stability and mRNA transport. From a structural point of view, TDP-43 is a member of the hnRNP protein family whose structure includes two RRM domains flanked by the N-terminus and C-terminal regions. Like many members of this family, the C-terminal region can interact with cellular factors and thus serve to modulate its function. Previously, we have described that TDP-43 binds to several members of the hnRNP A/B family through this region. In this work, we set up a coupled minigene/siRNA cellular system that allows us to obtain in vivo data to address the functional significance of TDP-43-recruited hnRNP complex formation. Using this method, we have finely mapped the interaction between TDP-43 and the hnRNP A2 protein to the region comprised between amino acid residues 321 and 366. Our results provide novel details of protein–protein interactions in splicing regulation. In addition, we provide further insight on TDP-43 functional properties, particularly the lack of effects, as seen with our assays, of the disease-associated mutations that fall within the TDP-43 321-366 region: Q331K, M337V and G348C.

T DP-43 belongs to the family of heterogeneous nuclear ribonucleoproteins (hnRNPs) and binds single-stranded RNA via its N-terminal RNA recognition motif (1). Members of the hnRNP family serve multiple roles in the generation and processing of RNA, including transcription, splicing, transport, and stability. TDP-43 inhibits exon recognition during splicing upon recruitment to the 3Ј splice site of the cystic fibrosis transmembrane conductance regulator (CFTR) and apolipoprotein AII transcripts via a sequence of GU repeats (2-5). The binding affinity of the recombinant human, worm, and fly homologues for this target sequence is remarkably high, measured in the low nanomolar range (6). TDP-43 also has been implicated in the transcription regulation of HIV and the spermatid-specific gene SP-10 through promoter association (7,8). More recently, TDP-43 was identified as the main ubiquitinated component of cytoplasmic inclusions in neurodegenerative diseases, specifically frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS) (9, 10). Abnormal aggregation of TDP-43 in the cytoplasm now is thought to define a class of frontotemporal dementias termed TDP-43 proteinopathies. Mislocalization and the consequent loss of TDP-43 function in neuronal cells may represent a common event in FTLD pathogenesis. Despite the increasing awareness of processes involving TDP-43, the cellular role of the protein still is poorly defined.We depleted TDP-43 by RNA interference (RNAi) to identify TDP-43-regulated transcripts. Our results point to cyclindependent kinase 6 (Cdk6) as a unique target of TDP-43 regulation and suggest that TDP-43 inhibits Cdk6 expression through recruitment to the GU-rich transcript. Simultaneously, we found that TDP-43 silencing alters cell cycle distribution and induces apoptosis. Table 1 lists 16 of these proteins whose functions have been associated with retinoblastoma protein (pRb) activity. The tumor suppressor pRb is essential for the control of cell cycle progression, cellular differentiation, and maintenance of genome integrity. Inactivation of pRb occurs through its gradual phosphorylation by Cdks during the G 1 phase of the cell division cycle resulting in the activation of transcription factors that promote cell proliferation and enable transition on to the S phase (see ref. 11 for review). Our RNA microarray analyses showed altered levels of transcripts coding for proteins whose functions are related to the control of cell cycle progression (Cdk6, POLD4, cyclin B1, Cdk2, UBE2C, and SKP2). In addition, some of these factors are known to either directly interact with pRb (e.g., HDAC1, RBBP4, and CRI1), or act in response to pRb modulation (e.g., E2F8 and NAP1L1) (12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22).

TDP-43 is a highly conserved nuclear factor of yet unknown function that binds to ug-repeated sequences and is responsible for cystic fibrosis transmembrane conductance regulator exon 9 splicing inhibition. We have analyzed TDP-43 interactions with other splicing factors and identified the critical regions for the protein/protein recognition events that determine this biological function. We show here that the C-terminal region of TDP-43 is capable of binding directly to several proteins of the heterogeneous nuclear ribonucleoprotein (hnRNP) family with well known splicing inhibitory activity, in particular, hnRNP A2/B1 and hnRNP A1. Mutational analysis showed that TDP-43 proteins lacking the C-terminal region could not inhibit splicing probably because they were unable to form the hnRNP-rich complex involved in splicing inhibition. Finally, through splicing complex analysis, we show that splicing inhibition mediated by TDP-43 occurs at the earliest stages of spliceosomal assembly.In its most basic form, the splicing process has the task of removing from the primary RNA transcript all of those sequences (introns) that will not be present in the mature mRNA (1-3). Alternative splicing, i.e. the inclusion/exclusion of selected exonic sequences in particular tissues or developmental stages, has been heavily exploited by evolution to generate multiple mRNA transcripts from the same pre-mRNA sequence (4 -6). However, all of this flexibility also means that the splicing process is prone to mistakes following even minor changes (7), and alterations of splicing are being increasingly reported as the underlying cause of many genetic diseases (8 -12).At the molecular level, the removal of introns and the joining of exons are catalyzed by the spliceosome, which contains several hundred different proteins in addition to the five spliceosomal small nuclear RNAs (13,14). This complex arrangement of factors has two functions: first, to define the exact boundaries of an exon; and second, to catalyze the cut-and-paste generation of the mature mRNA. However, many external factors can also contribute to its workings, such as RNA secondary structure (15), transcription rates (16), the presence of splicing enhancer and silencer elements (17, 18), and even external stimuli (19,20). It is the combinatorial effect of all of these factors that will decide when, where, and to what degree a specific sequence will be included or not in the mature mRNA (17). Recently, the finding that at least 5% of all human alternative exons are derived from the highly repeated dimeric retrotransposons Alu elements has focused a lot of attention on the potential splicing modulatory ability of repeated nucleotide sequences (21).In previous works, we have focused our attention on clarifying the pathological role played by (ug)m-repeated sequences near the 3Ј-splice site of cystic fibrosis transmembrane conductance regulator (CFTR) 3 exon 9 (22-24), as they have been known to promote skipping and to correlate well with disease penetrance (25). In particular,...

The discovery of thrombin as a Na(+)-dependent allosteric enzyme has revealed a novel strategy for regulating protease activity and specificity. The alllosteric nature of this enzyme influences all its physiologically important interactions and rationalizes a large body of structural and functional information. For the first time, a coherent mechanistic framework is available for understanding how thrombin interacts with fibrinogen, thrombomodulin and protein C, and how Na+ binding influences the specificity sites of the enzyme. This information can be used for engineering thrombin mutants with selective specificity towards protein C and for the rational design of potent active site inhibitors. Thrombin also serves as a paradigm for allosteric proteases. Elucidation of the molecular basis of the Na(+)-dependent allosteric regulation of catalytic activity, based on the residue present at position 225, provides unprecedented insights into the function and evolution of serine proteases. This mechanism represents one of the simplest and most important structure-function correlations ever reported for enzymes in general. All vitamin K-dependent proteases and some complement factors are subject to the Na(+)-dependent regulation discovered for thrombin. Na+ is therefore a key factor in the activation of zymogens in the coagulation and complement systems.