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Related Concept Videos

Nuclear Localization Signals and Import01:46

Nuclear Localization Signals and Import

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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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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.
Proteins targeted to the nucleus carry nuclear localization signals or NLS recognized by import receptors in the cytosol. Similarly, proteins with nuclear export signals are recognized by export receptors. Import and export receptors are...
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Proteomics01:33

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A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
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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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Related Experiment Video

Updated: May 10, 2025

Using Caenorhabditis elegans as a Model System to Study Protein Homeostasis in a Multicellular Organism
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Localizatome: a database for stress-dependent subcellular localization changes in proteins.

Takahide Matsushima1, Yuki Naito1, Tomoki Chiba1

  • 1Department of Systems BioMedicine, Graduate School of Medical and Dental Sciences, Institute of Science Tokyo, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan.

Database : the Journal of Biological Databases and Curation
|April 21, 2025
PubMed
Summary
This summary is machine-generated.

The Localizatome database maps how human proteins move within cells during oxidative stress. This resource reveals dynamic protein localization changes critical for understanding cellular stress responses and diseases.

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Area of Science:

  • Cell Biology
  • Molecular Biology
  • Bioinformatics

Background:

  • Protein subcellular localization is key to cellular function and disease.
  • Existing databases lack data on dynamic, stress-induced protein localization changes.
  • Understanding these dynamics is vital for disease mechanism elucidation.

Purpose of the Study:

  • To create a comprehensive database of stress-induced protein localization dynamics.
  • To analyze protein localization changes in human cells under oxidative stress.
  • To provide open access to data on cellular stress responses.

Main Methods:

  • Developed a high-throughput microscopy system.
  • Applied machine learning algorithms to analyze protein localization.
  • Studied 10,287 fluorescent protein-fused human proteins in HeLa cells before and after oxidative stress.

Main Results:

  • Identified 1910 proteins with oxidative stress-dependent localization changes, often forming distinct foci.
  • Found stress granule assembly factors, autophagy proteins, and signaling pathway components among these proteins.
  • Identified specific amino acid motifs and intrinsically disordered regions linked to stress-induced protein redistribution.

Conclusions:

  • The Localizatome database captures critical stress-induced protein localization dynamics.
  • Data supports studies on cellular stress response and disease mechanisms.
  • Provides a valuable resource for researchers investigating cellular dynamics under stress.