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Related Concept Videos

Regulation of Nuclear Protein Sorting01:45

Regulation of Nuclear Protein Sorting

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...
Nuclear Protein Sorting01:34

Nuclear Protein Sorting

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...
Nuclear Localization Signals and Import01:46

Nuclear Localization Signals and Import

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...
Nuclear Export01:42

Nuclear Export

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.
NES are of three types- the canonical 10-residue long leucine-rich signal and other...
Nucleoid01:24

Nucleoid

The nucleoid represents a structurally and functionally distinct region within prokaryotic cells, where the cell's DNA and associated proteins are housed. Unlike eukaryotic cells, prokaryotes lack a membrane-bound nucleus, and the nucleoid facilitates the organization and accessibility of the genetic material within this constraint. The DNA in most bacteria and archaea exists as a single, circular, double-stranded molecule that is highly compacted through supercoiling and interactions with...
Nuclear Export of mRNA02:31

Nuclear Export of mRNA

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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Related Experiment Video

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Identification of Nucleolar Factors During HIV-1 Replication Through Rev Immunoprecipitation and Mass Spectrometry
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Published on: June 26, 2019

A putative nuclear growth factor-like globular nematode specific protein.

Ranil Samantha Dassanayake1, Witharanage Wasana Prasadini Rodrigo, Eric Hamilton Karunanayake

  • 1Department of Chemistry, University of Colombo, Colombo 3, Sri Lanka. rsdassan@webmail.cmb.ac.lk

Bioinformation
|September 18, 2009
PubMed
Summary

This study characterizes novel uncharacterized proteins (UPs) in nematodes. These growth factor-like proteins are found in all life cycle stages, are nucleus-localized, and possess beta-pleated structures.

Keywords:
Setaria digitatabioinformaticsnematodesservers

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08:56

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Published on: May 5, 2020

Area of Science:

  • * Bioinformatics
  • * Molecular Biology
  • * Parasitology

Background:

  • * Expressed sequence tags (ESTs) aid in discovering novel genes.
  • * A specific uncharacterized protein (UP) from Setaria digitata lacked functional annotation in public databases.
  • * This study focuses on the bioinformatic characterization of this UP and its homologs.

Purpose of the Study:

  • * To extensively characterize the uncharacterized protein (UP) from Setaria digitata using bioinformatic approaches.
  • * To identify and analyze homologous proteins across various nematode species and related organisms.
  • * To predict the function, localization, and structural properties of these UP proteins.

Main Methods:

  • * Bioinformatic analysis of approximately 250 ESTs from Setaria digitata.
  • * Database searches (NCBI, NEMBASE3, PGD) for homologous sequences.
  • * Phylogenetic analysis, secondary structure prediction (Jpred), transmembrane/globular protein prediction (TMMHH, beta barrel finder).
  • * Motif discovery (MEME), subcellular localization prediction (Signal IP, TargetP, Psort), and phosphorylation site analysis (ScanProsite).
  • * Putative functional analysis (ProtFun 2.1 Server).

Main Results:

  • * Identified an uncharacterized protein (SDUP) in S. digitata with 204 amino acids (22.8 KDa, pI 9.94).
  • * Homologs found in human (Wuchereria bancrofti, Brugia malayi, Onchocerca volvulus), mouse (Litomosoides sigmodontis), swine (Ascaris suum), plant (Meloidogyne hapla), and free-living nematodes (Caenorhabditis elegans, C. briggsae).
  • * UPs exhibit divergent evolution, are expressed in all Brugia malayi stages, possess beta-pleated structures, are globular, and contain novel motifs.
  • * Predicted to be nucleus-localized, lacking signal peptides or mitochondrial targeting, with potential phosphorylation sites.
  • * Functionally predicted as nonenzymatic, growth factor-like proteins.

Conclusions:

  • * Uncharacterized proteins (UPs) in nematodes are likely specific, growth factor-like proteins.
  • * These UPs are expressed throughout the nematode life cycle and localized to the nucleus.
  • * Structural analysis reveals a high content of beta-pleated strands.
  • * Phosphorylation regulates UP activity, suggesting a role in cellular signaling.
  • * Further research is warranted to elucidate the precise functions of these nematode-specific proteins.