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Nuclear Protein Sorting01:34

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Nuclear protein sorting is the selective trafficking of histones, polymerases, gene regulatory proteins into the nucleus and exporting RNAs and ribosomes to the cytosol. It is a tightly controlled process that regulates gene expression within a cell.
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Nuclear protein sorting regulates nucleus composition and gene expression, crucial for determining the fate of a eukaryotic cell. Hence, the entry and exit of molecules across the nuclear envelope is a tightly controlled process. Nuclear protein sorting can be inhibited by one of the following ways: 1) masking cargo signal sequences, 2) modifying the nuclear receptor's affinity for cargo, 3) controlling the nuclear pore size, 4) retaining the cargo during its transit to the cytosol or the...
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Proteins targeted to the nucleus carry short stretches of amino acid sequences called the nuclear localization signal or NLS. Classical nuclear localization signals are of two types: monopartite and bipartite NLS. Monopartite classical NLS (cNLS) consists of a single cluster of 4-8 amino acids. Bipartite cNLS consists of two clusters of  2-3 amino acids and a 9-12 residue long proline-rich linker bridging the two clusters. Signal clusters are rich in positively charged amino acids such as...
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Before mRNAs are exported to the cytoplasm, it is crucial to check each mRNA for structural and functional integrity. Eukaryotic cells use several different mechanisms, collectively known as mRNA surveillance, to look for irregularities in mRNAs. Irregular or aberrant mRNA are rapidly degraded by various enzymes. If a defective mRNA escapes the surveillance, it would be translated into a protein which would either be non-functional or not function properly. One of the primary irregularities in...
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Nuclear Export01:42

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The nucleus restricts several proteins within and allows others to pass. The restricted proteins possess a nuclear retention sequence or NRS, anchoring them to the nuclear lamins and preventing their transport to the cytosol. The non-restricted proteins, after their synthesis, are transported to their site of action, such as the cytosol or other organelles, with the help of nuclear export signals or NES.
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Ras-related nuclear protein or Ran is a small G protein that cycles between its GTP and GDP bound states. Ran specific regulators, a Ran GTPase Activating Protein or RanGAP present in the cytosol and a Ran guanine nucleotide exchange factor or RanGEF present inside the nucleus regulate GTP/GDP exchange. A high concentration of GTP inside the cells, in addition to this asymmetric distribution of  Ran-specific regulators, leads to a higher RanGTP concentration inside the nucleus. This...
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In Vivo Proximity Biotinylation for Protein Interaction Studies in Paramecium tetraurelia
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Probing nuclear pore complex architecture with proximity-dependent biotinylation.

Dae In Kim1, K C Birendra1, Wenhong Zhu2

  • 1Sanford Children's Health Research Center, Sanford Research, Sioux Falls, SD 57104;

Proceedings of the National Academy of Sciences of the United States of America
|June 14, 2014
PubMed
Summary

Proximity-dependent biotin identification (BioID) reveals distinct protein associations within the human nuclear pore complex (NPC). This method helps map the organization of large protein assemblies like the NPC in living cells.

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Area of Science:

  • Cell Biology
  • Molecular Biology
  • Biochemistry

Background:

  • The human nuclear pore complex (NPC) is a large macromolecular assembly essential for nucleocytoplasmic transport.
  • Understanding NPC organization is crucial for comprehending cellular function and dysfunction.
  • Proximity-dependent biotin identification (BioID) is an in vivo technique for mapping protein interactions.

Purpose of the Study:

  • To investigate the protein associations within the human nuclear pore complex (NPC) using BioID.
  • To explore the organization of conserved NPC subcomplexes, specifically the Nup107-160 and Nup93 complexes.
  • To define the labeling radius of BioID using the stable Nup107-160 subcomplex structure.

Main Methods:

  • Application of BioID by fusing promiscuous biotin ligase to NPC constituents.
  • Analysis of protein interactomes generated by BioID fusions at different NPC locations.
  • Utilizing the Nup107-160 subcomplex structure as a molecular ruler to calibrate BioID.

Main Results:

  • BioID identified distinct sets of NPC constituents based on the fusion protein's location within the NPC.
  • Refined understanding of the Nup107-160 subcomplex, including a direct interaction between Nup43 and Nup85.
  • Established the practical labeling radius of BioID for studying large protein assemblies.

Conclusions:

  • BioID is effective for exploring the constituency and organization of large protein assemblies in living cells.
  • The study provides insights into the structural organization of the human nuclear pore complex.
  • BioID serves as a valuable tool for mapping protein interactions in complex cellular structures.