nuclear proteins
Recently Published Documents


TOTAL DOCUMENTS

1341
(FIVE YEARS 70)

H-INDEX

85
(FIVE YEARS 5)

Biomolecules ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 1656
Author(s):  
Vladimir I. Muronetz ◽  
Maria V. Medvedeva ◽  
Irina A. Sevostyanova ◽  
Elena V. Schmalhausen

This review focuses on the consequences of GAPDH S-nitrosylation at the catalytic cysteine residue. The widespread hypothesis according to which S-nitrosylation causes a change in GAPDH structure and its subsequent binding to the Siah1 protein is considered in detail. It is assumed that the GAPDH complex with Siah1 is transported to the nucleus by carrier proteins, interacts with nuclear proteins, and induces apoptosis. However, there are several conflicting and unproven elements in this hypothesis. In particular, there is no direct confirmation of the interaction between the tetrameric GAPDH and Siah1 caused by S-nitrosylation of GAPDH. The question remains as to whether the translocation of GAPDH into the nucleus is caused by S-nitrosylation or by some other modification of the catalytic cysteine residue. The hypothesis of the induction of apoptosis by oxidation of GAPDH is considered. This oxidation leads to a release of the coenzyme NAD+ from the active center of GAPDH, followed by the dissociation of the tetramer into subunits, which move to the nucleus due to passive transport and induce apoptosis. In conclusion, the main tasks are summarized, the solutions to which will make it possible to more definitively establish the role of nitric oxide in the induction of apoptosis.


2021 ◽  
Author(s):  
Thao Nguyen ◽  
Eli Costa ◽  
Tim Deibert ◽  
Jose Reyes ◽  
Felix Keber ◽  
...  

The development of a fertilized egg to an embryo requires the proper temporal control of gene expression. During cell differentiation, timing is often controlled via cascades of transcription factors (TFs). However, in early development, transcription is often inactive, and many TF levels are constant, suggesting that unknown mechanisms govern the observed rapid and ordered onset of gene expression. Here, we find that in early embryonic development, access of maternally deposited nuclear proteins to the genome is temporally ordered via importin affinities, thereby timing the expression of downstream targets. We quantify changes in the nuclear proteome during early development and find that nuclear proteins, such as TFs and RNA polymerases, enter nuclei sequentially. Moreover, we find that the timing of the access of nuclear proteins to the genome corresponds to the timing of downstream gene activation. We show that the affinity of proteins to importin is a major determinant in the timing of protein entry into embryonic nuclei. Thus, we propose a mechanism by which embryos encode the timing of gene expression in early development via biochemical affinities. This process could be critical for embryos to organize themselves before deploying the regulatory cascades that control cell identities.


2021 ◽  
Author(s):  
Ido Lavi ◽  
Supriya Bhattacharya ◽  
Ola Orgil ◽  
Nir Avital ◽  
Guy Journo ◽  
...  

AbstractDirectional recruitment of protein complexes is critical for proper function of many nuclear processes. Here we present CRISPR-PITA (Protein Interaction and Telomere Recruitment Assay), an assay that determines the ability of a given protein to recruit any other nuclear factor. The protein of interest is directed via CRISPR/dCas9, a dead Cas9 that does not cut DNA, to a repeat sequence, such as telomeres, to obtain dots that are easily detectable by microscopy. The recruitment of endogenous nuclear proteins to these dots can then be visualized using specific antibodies. We determined recruitment abilities in CRISPR-PITA to methyl-CpG binding protein MeCP2, histone deacetylase 1 (HDAC1), heterochromatin protein 1 (HP1α), and the latency-associated nuclear antigen (LANA) encoded by Kaposi’s sarcoma associated herpesvirus (KSHV, HHV-8). LANA was able to recruit its known interactors ORC2 and SIN3A to LANA-telomere dots. In contrast, LANA was unable to recruit MeCP2 whereas MeCP2 was able to recruit LANA. Similarly, HDAC1 that interacts with MeCP2 through the transcriptional-repression domain (TRD) same as LANA, was unable to recruit MeCP2, but MeCP2 recruited HDAC1. One important function of LANA is to tether the viral episomal genomes to the cellular chromosomes during cell division. The unidirectional recruitment of LANA by MeCP2, makes MeCP2 a candidate anchor for KSHV genome tethering by LANA. We found that cells derived from Rett syndrome and express a mutant MeCP2 (T158M), impaired in DNA binding, cannot support KSHV genome maintenance. In summary, we describe a broadly applicable protein recruitment assay based on CRISPR/dCas9.Significance StatementCRISPR/Cas9 is a revolutionary system that has profoundly impacted biology research. Here we present another application for CRISPR/Cas9, in evaluating recruitment relations between nuclear proteins. A protein of interest is directed to a repeat sequence via the catalytically inactive Cas9 (dCas9) to generate easily detectable dots. Then, the recruitment of other nuclear proteins to these dots can be evaluated. Using this assay, we show that some interacting proteins have a unidirectional recruitment property, where only one of the proteins can recruit its partner. We propose that available interacting domains can force this unidirectional recruitment. Using this recruitment assay, we found unidirectional recruitment of the KSHV encoded LANA and HDAC1 by MeCP2. Furthermore, this unidirectional recruitment is critical for viral latency, since LANA fails to maintain the viral genomes in MeCP2 mutant cells.


2021 ◽  
Vol 18 (10) ◽  
pp. 1204-1212
Author(s):  
Hattie Chung ◽  
Christopher N. Parkhurst ◽  
Emma M. Magee ◽  
Devan Phillips ◽  
Ehsan Habibi ◽  
...  
Keyword(s):  

2021 ◽  
Vol 22 (16) ◽  
pp. 8853
Author(s):  
Chiara Rossi ◽  
Anna Fernàndez ◽  
Pascual Torres ◽  
Omar Ramirez-Nuñez ◽  
Ana Belén Granado-Serrano ◽  
...  

Previous evidence links the formation of extranuclear inclusions of transcription factors, such as ERK, Jun, TDP-43, and REST, with oxidative, endoplasmic-reticulum, proteasomal, and osmotic stress. To further characterize its extranuclear location, we performed a high-content screening based on confocal microscopy and automatized image analyses of an epithelial cell culture treated with hydrogen peroxide, thapsigargin, epoxomicin, or sorbitol at different concentrations and times to recreate the stresses mentioned above. We also performed a subcellular fractionation of the brain from transgenic mice overexpressing the Q331K-mutated TARDBP, and we analyzed the REST-regulated mRNAs. The results show that these nuclear proteins exhibit a mitochondrial location, together with significant nuclear/extranuclear ratio changes, in a protein and stress-specific manner. The presence of these proteins in enriched mitochondrial fractions in vivo confirmed the results of the image analyses. TDP-43 aggregation was associated with alterations in the mRNA levels of the REST target genes involved in calcium homeostasis, apoptosis, and metabolism. In conclusion, cell stress increased the mitochondrial translocation of nuclear proteins, increasing the chance of proteostasis alterations. Furthermore, TDP-43 aggregation impacts REST target genes, disclosing an exciting interaction between these two transcription factors in neurodegenerative processes.


2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Kazuhiro Fukumura ◽  
Rei Yoshimoto ◽  
Luca Sperotto ◽  
Hyun-Seo Kang ◽  
Tetsuro Hirose ◽  
...  

AbstractHuman pre-mRNA introns vary in size from under fifty to over a million nucleotides. We searched for essential factors involved in the splicing of human short introns by screening siRNAs against 154 human nuclear proteins. The splicing activity was assayed with a model HNRNPH1 pre-mRNA containing short 56-nucleotide intron. We identify a known alternative splicing regulator SPF45 (RBM17) as a constitutive splicing factor that is required to splice out this 56-nt intron. Whole-transcriptome sequencing of SPF45-deficient cells reveals that SPF45 is essential in the efficient splicing of many short introns. To initiate the spliceosome assembly on a short intron with the truncated poly-pyrimidine tract, the U2AF-homology motif (UHM) of SPF45 competes out that of U2AF65 (U2AF2) for binding to the UHM-ligand motif (ULM) of the U2 snRNP protein SF3b155 (SF3B1). We propose that splicing in a distinct subset of human short introns depends on SPF45 but not U2AF heterodimer.


Author(s):  
Anna C. Kögler ◽  
Yacine Kherdjemil ◽  
Katharina Bender ◽  
Adam Rabinowitz ◽  
Raquel Marco-Ferreres ◽  
...  
Keyword(s):  

Cells ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1755
Author(s):  
Bela Vasileva ◽  
Dessislava Staneva ◽  
Natalia Krasteva ◽  
George Miloshev ◽  
Milena Georgieva

Complex interactions among DNA and nuclear proteins maintain genome organization and stability. The nuclear proteins, particularly the histones, organize, compact, and preserve the stability of DNA, but also allow its dynamic reorganization whenever the nuclear processes require access to it. Five histone classes exist and they are evolutionarily conserved among eukaryotes. The linker histones are the fifth class and over time, their role in chromatin has been neglected. Linker histones interact with DNA and the other histones and thus sustain genome stability and nuclear organization. Saccharomyces cerevisiae is a brilliant model for studying linker histones as the gene for it is a single-copy and is non-essential. We, therefore, created a linker histone-free yeast strain using a knockout of the relevant gene and traced the way cells age chronologically. Here we present our results demonstrating that the altered chromatin dynamics during the chronological lifespan of the yeast cells with a mutation in ARP4 (the actin-related protein 4) and without the gene HHO1 for the linker histone leads to strong alterations in the gene expression profiles of a subset of genes involved in DNA repair and autophagy. The obtained results further prove that the yeast mutants have reduced survival upon UVA/B irradiation possibly due to the accelerated decompaction of chromatin and impaired proliferation. Our hypothesis posits that the higher-order chromatin structure and the interactions among chromatin proteins are crucial for the maintenance of chromatin organization during chronological aging under optimal and UVA-B stress conditions.


Sign in / Sign up

Export Citation Format

Share Document