scholarly journals HSP70 chaperones RNA-free TDP-43 into anisotropic intranuclear liquid spherical shells

Science ◽  
2020 ◽  
Vol 371 (6529) ◽  
pp. eabb4309 ◽  
Author(s):  
Haiyang Yu ◽  
Shan Lu ◽  
Kelsey Gasior ◽  
Digvijay Singh ◽  
Sonia Vazquez-Sanchez ◽  
...  
Keyword(s):  
Rna Binding ◽  
Solid Phase ◽  
Liquid Core ◽  
Proteasome Inhibition ◽  
Crystal Formation ◽  
Spherical Shells ◽  
Hsp70 Family ◽  
Age Related ◽  
Recognition Motifs

The RNA binding protein TDP-43 forms intranuclear or cytoplasmic aggregates in age-related neurodegenerative diseases. In this study, we found that RNA binding–deficient TDP-43 (produced by neurodegeneration-causing mutations or posttranslational acetylation in its RNA recognition motifs) drove TDP-43 demixing into intranuclear liquid spherical shells with liquid cores. These droplets, which we named “anisosomes”, have shells that exhibit birefringence, thus indicating liquid crystal formation. Guided by mathematical modeling, we identified the primary components of the liquid core to be HSP70 family chaperones, whose adenosine triphosphate (ATP)–dependent activity maintained the liquidity of shells and cores. In vivo proteasome inhibition within neurons, to mimic aging-related reduction of proteasome activity, induced TDP-43–containing anisosomes. These structures converted to aggregates when ATP levels were reduced. Thus, acetylation, HSP70, and proteasome activities regulate TDP-43 phase separation and conversion into a gel or solid phase.

scholarly journals TDP-43 and HSP70 phase separate into anisotropic, intranuclear liquid spherical annuli

2020 ◽  
Author(s):  
Haiyang Yu ◽  
Shan Lu ◽  
Kelsey Gasior ◽  
Digvijay Singh ◽  
Olga Tapia ◽  
...  
Keyword(s):  
Phase Separation ◽  
Rna Binding ◽  
Rna Binding Protein ◽  
Proteasome Inhibition ◽  
Chaperone Activity ◽  
Cell Nuclei ◽  
The Core ◽  
Hsp70 Family ◽  
Age Related ◽  
Annulus Formation

AbstractThe RNA binding protein TDP-43 naturally phase separates within cell nuclei and forms cytoplasmic aggregates in age-related neurodegenerative diseases. Here we show that acetylation-mediated inhibition of TDP-43 binding to RNA produces co-de-mixing of acetylated and unmodified TDP-43 into symmetrical, intranuclear spherical annuli whose shells and cores have liquid properties. Shells are anisotropic, like liquid crystals. Consistent with our modelling predictions that annulus formation is driven by components with strong self-interactions but weak interaction with TDP-43, the major components of annuli cores are identified to be HSP70 family proteins, whose chaperone activity is required to maintain liquidity of the core. Proteasome inhibition, mimicking reduction in proteasome activity during aging, induces TDP-43-containing annuli in neurons in rodents. Thus, we identify that TDP-43 phase separation is regulated by acetylation, proteolysis, and ATPase-dependent chaperone activity of HSP70.One Sentence SummaryAcetylation of TDP-43 drives its phase separation into spherical annuli that form a liquid-inside-a-liquid-inside-a-liquid.

Domain necessary for Drosophila ELAV nuclear localization: function requires nuclear ELAV

1999 ◽  
Vol 112 (24) ◽  
pp. 4501-4512 ◽  
Author(s):  
Y.M. Yannoni ◽  
K. White
Keyword(s):  
Nuclear Localization ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Nuclear Localization Sequence ◽  
Rna Recognition ◽  
Rna Recognition Motifs ◽  
Mutant Proteins ◽  
Localization Sequence ◽  
Recognition Motifs

The neuron specific Drosophila ELAV protein belongs to the ELAV family of RNA binding proteins which are characterized by three highly conserved RNA recognition motifs, an N-terminal domain, and a hinge region between the second and third RNA recognition motifs. Despite their highly conserved RNA recognition motifs the ELAV family members are a group of proteins with diverse posttranscriptional functions including splicing regulation, mRNA stability and translatability and have a variety of subcellular localizations. The role of the ELAV hinge in localization and function was examined using transgenes encoding ELAV hinge deletions, in vivo. Subcellular localization of the hinge mutant proteins revealed that residues between amino acids 333–374 are necessary for nuclear localization. This delineated sequence has no significant homology to classical nuclear localization sequences, but it is similar to the recently characterized nucleocytoplasmic shuttling sequence, the HNS, from a human ELAV family member, HuR. This defined sequence, however, was insufficient for nuclear localization as tested using hinge-GFP fusion proteins. Functional assays revealed that mutant proteins that fail to localize to the nucleus are unable to provide ELAV vital function, but their function is significantly restored when translocated into the nucleus by a heterologous nuclear localization sequence tag.

scholarly journals Target selection by natural and redesigned PUF proteins

2015 ◽  
Vol 112 (52) ◽  
pp. 15868-15873 ◽  
Author(s):  
Douglas F. Porter ◽  
Yvonne Y. Koh ◽  
Brett VanVeller ◽  
Ronald T. Raines ◽  
Marvin Wickens
Keyword(s):  
Rna Binding ◽  
Target Selection ◽  
Mutant Protein ◽  
Sequence Specificity ◽  
Wild Type ◽  
Rna Recognition Motifs ◽  
Puf Proteins ◽  
Binding Domains ◽  
Recognition Motifs

Pumilio/fem-3 mRNA binding factor (PUF) proteins bind RNA with sequence specificity and modularity, and have become exemplary scaffolds in the reengineering of new RNA specificities. Here, we report the in vivo RNA binding sites of wild-type (WT) and reengineered forms of the PUF protein Saccharomyces cerevisiae Puf2p across the transcriptome. Puf2p defines an ancient protein family present throughout fungi, with divergent and distinctive PUF RNA binding domains, RNA-recognition motifs (RRMs), and prion regions. We identify sites in RNA bound to Puf2p in vivo by using two forms of UV cross-linking followed by immunopurification. The protein specifically binds more than 1,000 mRNAs, which contain multiple iterations of UAAU-binding elements. Regions outside the PUF domain, including the RRM, enhance discrimination among targets. Compensatory mutants reveal that one Puf2p molecule binds one UAAU sequence, and align the protein with the RNA site. Based on this architecture, we redesign Puf2p to bind UAAG and identify the targets of this reengineered PUF in vivo. The mutant protein finds its target site in 1,800 RNAs and yields a novel RNA network with a dramatic redistribution of binding elements. The mutant protein exhibits even greater RNA specificity than wild type. The redesigned protein decreases the abundance of RNAs in its redesigned network. These results suggest that reengineering using the PUF scaffold redirects and can even enhance specificity in vivo.

scholarly journals Heat shock chaperone HSPB1 regulates cytoplasmic TDP-43 phase separation and liquid-to-gel transition

2021 ◽  
Author(s):  
Shan Lu ◽  
Jiaojiao Hu ◽  
Bankhole Aladesuyi ◽  
Alexander Goginashvili ◽  
Sonia Vazquez-Sanchez ◽  
...  
Keyword(s):  
Phase Separation ◽  
Heat Shock ◽  
Motor Neurons ◽  
Rna Binding ◽  
Isotope Labeling ◽  
Small Heat Shock Protein ◽  
Proteasome Inhibition ◽  
Low Complexity ◽  
Spinal Motor Neurons ◽  
Hsp70 Family

Abstract While the RNA binding protein TDP-43 reversibly phase separates within nuclei into complex droplets (anisosomes) with TDP-43-containing liquid outer shells and liquid centers of HSP70 family chaperones, cytoplasmic aggregates of TDP-43 are hallmarks of multiple neurodegenerative diseases, including ALS. Here we show that transient oxidative stress, proteasome inhibition, or inhibition of HSP70’s ATP-dependent chaperone activity provokes reversible cytoplasmic TDP-43 de-mixing and transition from liquid to gel/solid, independent of RNA binding or stress granules. Isotope labeling mass spectrometry is used to identify that phase separated cytoplasmic TDP-43 is primarily bound by the small heat shock protein HSPB1. Binding is direct, mediated through TDP-43’s RNA binding and low complexity domains. HSPB1 partitions into TDP-43 droplets, inhibits TDP-43 assembly into fibrils, and is essential for disassembly of stress-induced, TDP-43 droplets. Decrease of HSPB1 promotes cytoplasmic TDP-43 de-mixing and mislocalization. HSPB1 depletion is identified within ALS-patient spinal motor neurons containing aggregated TDP-43. These findings identify HSPB1 to be a regulator of cytoplasmic TDP-43 phase separation and aggregation.

scholarly journals Heat shock chaperone HSPB1 regulates cytoplasmic TDP-43 phase separation and liquid-to-gel transition

2021 ◽  
Author(s):  
Shan Lu ◽  
Jiaojiao Hu ◽  
Olubankole Aladesuyi Arogundade ◽  
Alexander Goginashvili ◽  
Sonia Vazquez-Sanchez ◽  
...  
Keyword(s):  
Phase Separation ◽  
Heat Shock ◽  
Motor Neurons ◽  
Rna Binding ◽  
Isotope Labeling ◽  
Small Heat Shock Protein ◽  
Proteasome Inhibition ◽  
Low Complexity ◽  
Spinal Motor Neurons ◽  
Hsp70 Family

While the RNA binding protein TDP-43 reversibly phase separates within nuclei into complex droplets (anisosomes) with TDP-43-containing liquid outer shells and liquid centers of HSP70 family chaperones, cytoplasmic aggregates of TDP-43 are hallmarks of multiple neurodegenerative diseases, including ALS. Here we show that transient oxidative stress, proteasome inhibition, or inhibition of HSP70's ATP-dependent chaperone activity provokes reversible cytoplasmic TDP-43 de-mixing and transition from liquid to gel/solid, independent of RNA binding or stress granules. Isotope labeling mass spectrometry is used to identify that phase separated cytoplasmic TDP-43 is primarily bound by the small heat shock protein HSPB1. Binding is direct, mediated through TDP-43's RNA binding and low complexity domains. HSPB1 partitions into TDP-43 droplets, inhibits TDP-43 assembly into fibrils, and is essential for disassembly of stress-induced, TDP-43 droplets. Decrease of HSPB1 promotes cytoplasmic TDP-43 de-mixing and mislocalization. HSPB1 depletion is identified within ALS-patient spinal motor neurons containing aggregated TDP-43. These findings identify HSPB1 to be a regulator of cytoplasmic TDP-43 phase separation and aggregation.

scholarly journals An essential RNA-binding lysine residue in the Nab3 RRM domain undergoes mono and trimethylation

2019 ◽  
Author(s):  
Kwan Yin Lee ◽  
Anand Chopra ◽  
Kyle Biggar ◽  
Marc D. Meneghini
Keyword(s):  
Rna Binding ◽  
Growth Defect ◽  
Rna Sequences ◽  
Rna Recognition Motifs ◽  
Rrm Domain ◽  
Lysine Residues ◽  
Recognition Motifs ◽  
Target Rna

AbstractThe Nrd1-Nab3-Sen1 (NNS) complex integrates molecular inputs to direct termination of noncoding transcription in budding yeast. NNS is positively regulated by methylation of histone H3 lysine-4 as well as through Nrd1 binding to the initiating form of RNA PolII. These cues collaborate with Nrd1 and Nab3 binding to target RNA sequences in nascent transcripts through their RRM RNA recognition motifs. In this study, we identify nine lysine residues distributed amongst Nrd1, Nab3, and Sen1 that are mono-, di-, or trimethylated, suggesting novel molecular inputs for NNS regulation. One of these methylated residues, Nab3 lysine-363 (K363), resides within its RRM, and is known to physically contact target RNA. Although mutation of Nab3-K363 to arginine (Nab3-K363R) causes a severe growth defect, it nevertheless produces a stable protein that is incorporated into the NNS complex, suggesting that RNA binding through Nab3-K363 is crucial for NNS function. Consistent with this hypothesis, K363R mutation decreases RNA binding of the Nab3 RRM in vitro and causes transcription termination defects in vivo. These findings reveal crucial roles for Nab3-K363 and suggest that methylation of this residue may modulate NNS activity through its impact on Nab3 RNA binding.

scholarly journals Function of RRM Domains of Drosophila melanogaster ELAV: RNP1 Mutations and RRM Domain Replacements With ELAV Family Proteins and SXL

Genetics ◽  
2000 ◽  
Vol 155 (4) ◽  
pp. 1789-1798 ◽  
Author(s):  
Michael J Lisbin ◽  
Marshall Gordon ◽  
Yvonne M Yannoni ◽  
Kalpana White
Keyword(s):  
Drosophila Melanogaster ◽  
Rna Binding ◽  
Sole Source ◽  
Complementation Test ◽  
Binding Property ◽  
Amino Acid Residues ◽  
Rna Recognition Motifs ◽  
Rrm Domain ◽  
Recognition Motifs

Abstract Members of the ELAV family of proteins contain three RNA recognition motifs (RRMs), which are highly conserved. ELAV, a Drosophila melanogaster member of this family, provides a vital function and exhibits a predominantly nuclear localization. To investigate if the RNA-binding property of each of the ELAV RRMs is required for ELAV's in vivo function, amino acid residues critical in RNA binding for each RRM were individually mutated. A stringent genetic complementation test revealed that when the mutant protein was the sole source of ELAV, RNA-binding ability of each RRM was essential to ELAV function. To assess the degree to which each domain was specific for ELAV function and which domains perhaps performed a function common to related ELAV proteins, we substituted an ELAV RRM with the corresponding RRM from RBP9, the D. melanogaster protein most homologous to ELAV; HuD, a human ELAV family protein; and SXL, which, although evolutionarily related, is not an ELAV family member. This analysis revealed that RRM3 replacements were fully functional, but RRM1 and RRM2 replacements were largely nonfunctional. Under less stringent conditions RRM1 and RRM2 replacements from SXL and RRM1 replacement from RBP9 were able to provide supplemental function in the presence of a mutant hypomorphic ELAV protein.

A Rapid and Sensitive Method for the Pharmacokinetic Study of Janumet (Sitagliptin and Metformin) Tablets by LC-MS/MS Coupled with Ion-Pair Solid Phase Extraction

2019 ◽  
Vol 15 (7) ◽  
pp. 776-784
Author(s):  
Xiaonian Han ◽  
Jing Wang ◽  
Jing Huang ◽  
Lirong Peng
Keyword(s):  
Solid Phase Extraction ◽  
Pharmacokinetic Study ◽  
Solid Phase ◽  
Multiple Reaction Monitoring ◽  
Ion Pair ◽  
Phase Extraction ◽  
Plasma Samples ◽  
Ionization Source ◽  
Tandem Mass Spectrometric

Background: As first-line treatments for diabetes, sitagliptin and metformin have been widely prescribed as a combination to enhance the therapeutic effect. Objective: To establish a methodology to simultaneously monitor the two drugs in vivo by a reversedphase Liquid Chromatography-Tandem Mass Spectrometric (LC-MS/MS) method. Methods: The two drugs were extracted from 50 μl human plasma by ion-pair solid phase extraction. The separation of the plasma samples was implemented on an Agilent Zorbax SB-CN column (150×4.6 mm, 5.0 µm). The mobile phase was the mixture (80:20, v/v) of methanol and 5.0 mM ammonium formate in water (pH 4.5). An ion trap spectrometer equipped with an electrospray ionization source was utilized to detect the elution in positive mode. Quantification of the analytes was achieved by Multiple Reaction Monitoring (MRM) using the transitions of m/z 408.3→235.1 for sitagliptin and m/z 130.1→ 60.2 for metformin. Results: Sitagliptin and metformin demonstrated good linearity among the range of 1.00-1000 ng/mL and 5.00-4000 ng/mL. The intra-day and inter-day investigations displayed precisions of ≤ 3.6% and an accuracy range of -7.5% to 6.0% for the two drugs. The mean recovery of the two drugs was 96.0% and 98.5%. Under mandatory storage conditions, both the drugs gave an acceptable stability. The throughput of the assay was found to be more than 100 plasma samples per day ascribed to the run time of 3.0 min for each sample. Conclusion: The developed method was successfully applied to a pharmacokinetic study for a fixeddose tablet formulation containing 50 mg sitagliptin and 500 mg metformin in 12 healthy volunteers.

68Ga-labeled HBED-CC Variant of uPAR Targeting Peptide AE105 Compared with 68Ga-NODAGA-AE105

2019 ◽  
Vol 18 (9) ◽  
pp. 1289-1294 ◽  
Author(s):  
Kusum Vats ◽  
Rohit Sharma ◽  
Haladhar D. Sarma ◽  
Drishty Satpati ◽  
Ashutosh Dash
Keyword(s):  
Solid Phase ◽  
Evaluation Studies ◽  
Radiochemical Yield ◽  
In Vivo Evaluation ◽  
Peptide Conjugates ◽  
Biodistribution Studies ◽  
Target Organs ◽  
U87mg Tumor

Aims: The urokinase Plasminogen Activator Receptors (uPAR) over-expressed on tumor cells and their invasive microenvironment are clinically significant molecular targets for cancer research. uPARexpressing cancerous lesions can be suitably identified and their progression can be monitored with radiolabeled uPAR targeted imaging probes. Hence this study aimed at preparing and evaluating two 68Ga-labeled AE105 peptide conjugates, 68Ga-NODAGA-AE105 and 68Ga-HBED-CC-AE105 as uPAR PET-probes. Method: The peptide conjugates, HBED-CC-AE105-NH2 and NODAGA-AE105-NH2 were manually synthesized by standard Fmoc solid phase strategy and subsequently radiolabeled with 68Ga eluted from a commercial 68Ge/68Ga generator. In vitro cell studies for the two radiotracers were performed with uPAR positive U87MG cells. Biodistribution studies were carried out in mouse xenografts with the subcutaneously induced U87MG tumor. Results: The two radiotracers, 68Ga-NODAGA-AE105 and 68Ga-HBED-CC-AE105 that were prepared in >95% radiochemical yield and >96% radiochemical purity, exhibited excellent in vitro stability. In vivo evaluation studies revealed higher uptake of 68Ga-HBED-CC-AE105 in U87MG tumor as compared to 68Ga-NODAGAAE105; however, increased lipophilicity of 68Ga-HBED-CC-AE105 resulted in slower clearance from blood and other non-target organs. The uPAR specificity of the two radiotracers was ascertained by significant (p<0.05) reduction in the tumor uptake with a co-injected blocking dose of unlabeled AE-105 peptide. Conclusion: Amongst the two radiotracers studied, the neutral 68Ga-NODAGA-AE105 with more hydrophilic chelator exhibited faster clearance from non-target organs. The conjugation of HBED-CC chelator (less hydrophilic) resulted in negatively charged 68Ga-HBED-CC-AE105 which was observed to have high retention in blood that decreased target to non-target ratios.

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