Subcellular Protein Localization Event

A Subcellular Protein Localization Event is a biological event where a subcellular protein becomes localized in a subcellular component.

• AKA: SCL.
• Context:
  • It can (typically) be the conclusion of a Protein Localization Process.
  • It can be referenced by a Subcellular Protein Localization Event Referencer, such as a protein localization mention or a protein localization record (in an SCL database).
  • It can range from being a Prokaryotic SCL to being an Eukaryotic SCL.
• Example(s):
  • in Agrobacterium tumefaciens ... “virA encodes a membrane-bound sensor kinase protein and virG encodes a cytoplasmic regulator protein. ..." (Pan, Trevor et al., 1993).
  • …
• Counter-Example(s):
  • a Protein Secretion Event.
• See: PSORTdb, PPLRE Project, Extracellular Space.

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References

2014

• (Wikipedia, 2014) ⇒ http://en.wikipedia.org/wiki/Subcellular_localization Retrieved:2014-3-1.
  • The cells of eukaryotic organisms are elaborately subdivided into functionally distinct membrane bound compartments. Some major constituents of eukaryotic cells are: extracellular space, cytoplasm, nucleus, mitochondria, Golgi apparatus, endoplasmic reticulum (ER), peroxisome, vacuoles, cytoskeleton, nucleoplasm, nucleolus, nuclear matrix and ribosomes.

     Bacteria also have subcellular localizations that can be separated when the cell is fractionated. The most common localizations referred to include the cytoplasm, the cytoplasmic membrane (also referred to as the inner membrane in Gram-negative bacteria), the cell wall (which is usually thicker in Gram-positive bacteria) and the extracellular environment. Most Gram-negative bacteria also contain an outer membrane and periplasmic space. Unlike eukaryotes, most bacteria contain no membrane-bound organelles, however there are some exceptions (i.e. magnetosomes).

2010

• (Yu et al., 2010) ⇒ Nancy Y. Yu, James R. Wagner, Matthew R. Laird, Gabor Melli, Sébastien Rey, Raymond Lo, Phuong Dao, S. Cenk Sahinalp, Martin Ester, Leonard J. Foster, and Fiona S. L. Brinkman. (2010). “PSORTb 3.0: Improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes.” In: Bioinformatics, 26(13). doi:10.1093/bioinformatics/btq249
  • QUOTE: Computational prediction of bacterial protein subcellular localization (SCL) provides a quick and inexpensive means for gaining insight into protein function, verifying experimental results, annotating newly sequenced bacterial genomes, detecting potential cell surface/secreted drug targets, as well as identifying biomarkers for microbes. In recent years, this area of computational research has achieved an impressive level of precision (Gardy and Brinkman, 2006), allowing SCL prediction tools to be reliably integrated into automated proteome annotation pipelines and to complement analyses of high-throughput proteomics experiments.

2007

• (Melli et al., 2007) ⇒ Gabor Melli, Martin Ester, and Anoop Sarkar. (2007). “Recognition of Multi-sentence n-ary Subcellular Localization Mentions in Biomedical Abstracts.” In: Proceedings of LBM-2007. (presentation)

2003

• (Huh et al., 2003) ⇒ Won-Ki Huh, James V. Falvo, Luke C. Gerke, Adam S. Carroll, Russell W. Howson, Jonathan S. Weissman, and Erin K. O'Shea. (2003) "Global analysis of protein localization in budding yeast." Nature, 425(6959).
  • QUOTE: A fundamental goal of cell biology is to define the functions of proteins in the context of compartments that organize them in the cellular environment. Here we describe the construction and analysis of a collection of yeast strains expressing full-length, chromosomally tagged green fluorescent protein fusion proteins. We classify these proteins, representing 75% of the yeast proteome, into 22 distinct subcellular localization categories, and provide localization information for 70% of previously unlocalized proteins. Analysis of this high-resolution, high-coverage localization data set in the context of transcriptional, genetic, and protein–protein interaction data helps reveal the logic of transcriptional co-regulation, and provides a comprehensive view of interactions within and between organelles in eukaryotic cells.

     Eukaryotic cells are organized into a complex network of membranes and compartments, which are specialized for various biological functions. Comprehensive knowledge of the location of proteins within these cellular microenvironments is critical for understanding their functions and interactions; this requires assaying the cell’s full complement of [subcellular protein|protein]]s.

1993

• (Pan, Trevor et al., 1993) ⇒ Shen Q. Pan, Trevor Charles, Shouguang Jin, Zhi-Liang Wu, and Eugene W. Nester. (1993). “Preformed dimeric state of the sensor protein VirA is involved in plant--Agrobacterium signal transduction.” In: Proceedings of the National Academy of Sciences, 90(21).
  • ABSTRACT: Plant signal molecules such as acetosyringone and certain monosaccharides induce the expression of Agrobacterium tumefaciens virulence (vir) genes, which are required for the processing, transfer, and possibly integration of a piece of the bacterial plasmid DNA (T-DNA) into the plant genome. Two of the vir genes, virA and virG, belonging to the bacterial two-component regulatory system family, control the induction of vir genes by plant signals. virA encodes a membrane-bound sensor kinase protein and virG encodes a cytoplasmic regulator protein. Although it is well established from in vitro studies that the signal transduction process involves VirA autophosphorylation and subsequent phosphate transfer to VirG, the structural state of the VirA protein involved in signal transduction is not understood. In this communication, we describe an in vivo crosslinking approach which provides physical evidence that VirA exists as a homodimer in its native configuration. The dimerization of VirA neither requires nor is stimulated by the plant signal molecule acetosyringone. We also present genetic data which support the hypothesis that VirA exists as a homodimer which is the functional state transducing the plant signal in an intersubunit mechanism. To our knowledge, this report provides the first evidence that a bacterial membrane-bound sensor kinase exists and functions as a homodimer in vivo.

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