-
Science (New York, N.Y.) Aug 2023Cells use ubiquitin to mark proteins for proteasomal degradation. Although the proteasome also eliminates proteins that are not ubiquitinated, how this occurs...
Cells use ubiquitin to mark proteins for proteasomal degradation. Although the proteasome also eliminates proteins that are not ubiquitinated, how this occurs mechanistically is unclear. Here, we found that midnolin promoted the destruction of many nuclear proteins, including transcription factors encoded by the immediate-early genes. Diverse stimuli induced midnolin, and its overexpression was sufficient to cause the degradation of its targets by a mechanism that did not require ubiquitination. Instead, midnolin associated with the proteasome via an α helix, used its Catch domain to bind a region within substrates that can form a β strand, and used a ubiquitin-like domain to promote substrate destruction. Thus, midnolin contains three regions that function in concert to target a large set of nuclear proteins to the proteasome for degradation.
Topics: Nuclear Proteins; Proteasome Endopeptidase Complex; Ubiquitin; Ubiquitination; Proteolysis; Genes, Immediate-Early; HEK293 Cells; NIH 3T3 Cells; Transcription, Genetic
PubMed: 37616343
DOI: 10.1126/science.adh5021 -
Current Opinion in Structural Biology Feb 2011Chromatin plays a fundamental role in eukaryotic genomic regulation, and the increasing awareness of the importance of epigenetic processes in human health and disease... (Review)
Review
Chromatin plays a fundamental role in eukaryotic genomic regulation, and the increasing awareness of the importance of epigenetic processes in human health and disease emphasizes the need for understanding the structure and function of the nucleosome. Recent advances in chromatin structural studies, including the first structures of nucleosomes containing the Widom 601 sequence and the structure of a chromatin protein-nucleosome assembly, have provided new insight into stretching of nucleosomal DNA, nucleosome positioning, binding of metal ions, drugs and therapeutic candidates to nucleosomes, and nucleosome recognition by nuclear proteins. These discoveries ensure promising future prospects for unravelling structural attributes of chromatin.
Topics: Animals; DNA; Humans; Nuclear Proteins; Nucleosomes; Protein Binding
PubMed: 21176878
DOI: 10.1016/j.sbi.2010.11.006 -
Cells Dec 2022Almost a half century ago, a group of nuclear proteins were co-purified with histones from calf thymus and termed as "high mobility group" (HMG) proteins because of...
Almost a half century ago, a group of nuclear proteins were co-purified with histones from calf thymus and termed as "high mobility group" (HMG) proteins because of their relative rapid mobility on SDS-PAGE gels [...].
Topics: HMGB1 Protein; Histones; High Mobility Group Proteins; Nuclear Proteins; Thymus Gland
PubMed: 36611839
DOI: 10.3390/cells12010046 -
RNA Biology 2015Initially identified as a marker of coiled bodies (now Cajal bodies or CBs), the protein coilin was discovered a quarter of century ago. Coilin is now known to scaffold... (Review)
Review
Initially identified as a marker of coiled bodies (now Cajal bodies or CBs), the protein coilin was discovered a quarter of century ago. Coilin is now known to scaffold the CB, but its structure and function are poorly understood. Nearly devoid of predicted structural motifs, coilin has numerous reported molecular interactions that must underlie its role in the formation and function of CBs. In this review, we summarize what we have learned in the past 25 years about coilin's structure, post-transcriptional modifications, and interactions with RNA and proteins. We show that genes with homology to human coilin are found in primitive metazoans and comment on differences among model organisms. Coilin's function in Cajal body formation and RNP metabolism will be discussed in the light of these developments.
Topics: Animals; Coiled Bodies; History, 20th Century; History, 21st Century; Humans; Nuclear Proteins; Protein Processing, Post-Translational
PubMed: 25970135
DOI: 10.1080/15476286.2015.1034923 -
Removal of nonspecific binding proteins is required in co-immunoprecipitation with nuclear proteins.BioTechniques Dec 2022Whether protein samples should be pretreated to remove nonspecific binding proteins in co-immunoprecipitation (CO-IP) is controversial. In this work, nonspecific binding...
Whether protein samples should be pretreated to remove nonspecific binding proteins in co-immunoprecipitation (CO-IP) is controversial. In this work, nonspecific binding of proteins to agarose beads was found to be greater than that to magnetic beads. The nonspecific binding was increased with the decrease of ion concentrations but reduced by Nonidet P40. Western blot indicated that p65 and β-actin were present as nonspecifically bound protein to the beads. p53 and β-actin were present in the CO-IP precipitates of nuclear proteins but pretreatment cleared the nonspecifically pulled down p53 and β-actin. These data suggest that magnetic beads are better for CO-IP, but preclearing is necessary to minimize false positive regardless of which bead is used, particularly for nuclear proteins.
Topics: Actins; Carrier Proteins; Nuclear Proteins; Tumor Suppressor Protein p53; Immunoprecipitation; Protein Binding
PubMed: 36401550
DOI: 10.2144/btn-2022-0048 -
Current Biology : CB Jun 2011
Review
Topics: Amino Acid Sequence; Animals; Conserved Sequence; Cytoskeleton; Humans; Membrane Proteins; Mice; Models, Biological; Nuclear Proteins; Protein Structure, Tertiary; Protein Transport
PubMed: 21640895
DOI: 10.1016/j.cub.2011.04.022 -
Journal of Lipid Research Apr 2009The lipin protein family, consisting of three members, was first identified early this century. In the last few years, the lipin proteins have been shown to have... (Review)
Review
The lipin protein family, consisting of three members, was first identified early this century. In the last few years, the lipin proteins have been shown to have important roles in glycerolipid biosynthesis and gene regulation, and mutations in the corresponding genes cause lipodystrophy, myoglobinuria, and inflammatory disorders. Here, we review some of the progress toward elucidating the molecular and physiological functions of the lipin proteins.
Topics: Adipogenesis; Animals; Homeostasis; Humans; Insulin; Lipoproteins; Nuclear Proteins; Substrate Specificity
PubMed: 18941140
DOI: 10.1194/jlr.R800052-JLR200 -
Biomolecules Jul 2014In their natural environment, cells are regularly exposed to various stress conditions that may lead to protein misfolding, but also in the absence of stress, misfolded... (Review)
Review
In their natural environment, cells are regularly exposed to various stress conditions that may lead to protein misfolding, but also in the absence of stress, misfolded proteins occur as the result of mutations or failures during protein synthesis. Since such partially denatured proteins are prone to aggregate, cells have evolved several elaborate quality control systems to deal with these potentially toxic proteins. First, various molecular chaperones will seize the misfolded protein and either attempt to refold the protein or target it for degradation via the ubiquitin-proteasome system. The degradation of misfolded proteins is clearly compartmentalized, so unique degradation pathways exist for misfolded proteins depending on whether their subcellular localization is ER/secretory, mitochondrial, cytosolic or nuclear. Recent studies, mainly in yeast, have shown that the nucleus appears to be particularly active in protein quality control. Thus, specific ubiquitin-protein ligases located in the nucleus, target not only misfolded nuclear proteins, but also various misfolded cytosolic proteins which are transported to the nucleus prior to their degradation. In comparison, much less is known about these mechanisms in mammalian cells. Here we highlight recent advances in our understanding of nuclear protein quality control, in particular regarding substrate recognition and proteasomal degradation.
Topics: Active Transport, Cell Nucleus; Animals; Cell Nucleus; Humans; Nuclear Proteins; Protein Folding
PubMed: 25010148
DOI: 10.3390/biom4030646 -
Journal of Molecular Cell Biology Feb 2017Mouse double minute (Mdm) genes span an evolutionary timeframe from the ancient eukaryotic placozoa Trichoplax adhaerens to Homo sapiens, implying a significant and... (Review)
Review
Mouse double minute (Mdm) genes span an evolutionary timeframe from the ancient eukaryotic placozoa Trichoplax adhaerens to Homo sapiens, implying a significant and possibly conserved cellular role throughout history. Maintenance of DNA integrity and response to DNA damage involve many key regulatory pathways, including precise control over the tumour suppressor protein p53. In most vertebrates, degradation of p53 through proteasomal targeting is primarily mediated by heterodimers of Mdm2 and the Mdm2-related protein Mdm4 (also known as MdmX). Both Mdm2 and Mdm4 have p53-binding regions, acidic domains, zinc fingers, and C-terminal RING domains that are conserved throughout evolution. Vertebrates typically have both Mdm2 and Mdm4 genes, while analyses of sequenced genomes of invertebrate species have identified single Mdm genes, suggesting that a duplication event occurred prior to emergence of jawless vertebrates about 550-440 million years ago. The functional relationship between Mdm and p53 in T. adhaerens, an organism that has existed for 1 billion years, implies that these two proteins have evolved together to maintain a conserved and regulated function.
Topics: Amino Acid Sequence; Animals; Biological Evolution; Humans; Models, Animal; Nuclear Proteins; Protein Domains; Proto-Oncogene Proteins c-mdm2; Viruses
PubMed: 28077607
DOI: 10.1093/jmcb/mjx002 -
Nucleus (Austin, Tex.) 2014Current anti-cancer therapies have a great deal of undesirable side effects; therefore, there is a need to develop efficient and cancer cell-specific new drugs without... (Review)
Review
Current anti-cancer therapies have a great deal of undesirable side effects; therefore, there is a need to develop efficient and cancer cell-specific new drugs without strong dose-limiting side effects. In my opinion, mechanisms of nuclear assembly and organization represent a novel platform for drug targets, which might fulfill these criteria. The nuclear stiffness and organization of some cancer types are often compromised, making them more vulnerable for further targeting the mechanisms of nuclear integrity than their normal counterparts. Here I will discuss the nuclear organization of normal cells and cancer cells, the molecular mechanisms that govern nuclear assembly with emphasis on those that, in my view, might be considered as targets for future anti-cancer therapies.
Topics: Animals; Antineoplastic Agents; Cell Line, Tumor; Drug Delivery Systems; Gene Targeting; Humans; Mitosis; Neoplasms; Nuclear Proteins; Xenograft Model Antitumor Assays
PubMed: 24637400
DOI: 10.4161/nucl.27928