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. The cytoplasm, the cytoplasmic membrane and the cell wall are subcellular localizations, whereas the extracellular environment is clearly not. 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).
Protein Subcellular Location Databases
Curated protein subcellular locations can be searched in UniProtKB. There are several computationally predicted protein subcellular location databases, constructed by Dr. Min's group at Youngstown State University, including the fungal secretome knowledgebase (FunSecKB), the fungal secretome and subcellular proteome knowledgebase - version 2 (FunSecKB2), the plant secretome and subcellular proteome knowledgebase (PlantSecKB), MetazSecKB for human and animals, and ProtSecKB for protists. And there are also a few others, such as the lactic acid bacterial secretome database. Though there are some inaccuracies in the computational prediction, these databases provide useful resources for further characterizing the protein subcellular locations.
- Schuler D. (2004). Molecular analysis of a subcellular compartment: the magnetosome membrane in Magnetospirillum gryphiswaldense. Arch Microbiol. 181:1-7