PPLRE Domain Description

This page describes the PPLRE Project's Domain of interest.

Overview

The physical domain of interest to this project is the movement of proteins within the sub-cellular structures of Prokaryote cells. Below are some relevant points.

• The process is referred to as Protein Sorting (thus PSORT), or also Protein Targeting and Protein Transport.
• The underlying physical process can be understood as a set of three binary relationships:
  • An Organism contains Genes G(1..g),
  • A Gene can produce a Protein P(1..g)
  • A Protein can Localize in one or more Cellular Locations L(1..l).
• A Localization can occur on either side of a Cell Membrane, or in the membrane itself.
• Most Proteins are localized in a single region, but some proteins, especially large proteins, can be localized in more than one region.
• A protein is a complex organic molecule made up of a sequence of amino acids. This sequence determines its shape, function, and in part the localization target.

Gram Positive vs. Gram Negative Bacteria Cells

• When experimental extraction is performed, everything in between the outer membrane and the cytoplasmic membrane (including cell wall) tends to be considered as part of the periplasmic fraction. So it might be hard to find "Gram Negative cell wall proteins" from literature. I'm guessing biologically it is less important to identify Gram -ve cell wall proteins because the wall is thin and assumed not to have many proteins anchored to it, and also less of a translocation barrier than the two membranes in general.

http://koch.pathogenomics.ca/pplre/images/GramPosNegBacteria.gif

Figure 1 -Illustration of the cellular structures of Gram-positive and Gram-negative Bacteria cells. [Z. Lu, 2004]

Proteins Near/In Membranes

Figure 2 -(source: http://www.geneontology.org/images/diag-membrane.gif)

The Flagellum

Below are two conceptual pictures of the flagellum. Notice that the whole flagellum apparatus traverses multiple locations, from within the cytoplasm to outside the cell. The first diagram illustrates how individual proteins are localized to one or more locations (as defined by current PSORTb). So from a prediction point of view, a flagellar protein that is localized to a membrane, or periplasm etc will shared sequence/feature similarity with other proteins localized to the same cellular components. However, from a database point of view, we would still like to label these proteins as "flagellar". To accomplish this we may need an extra field in the database representing "secondary location"…

http://koch.pathogenomics.ca/pplre/images/flagellum_diagram1.jpg

Figure 3 -PMID: 15817382 - Pallen MJ et al. Trends in Microbiology 2005 Apr;13(4):143-9. Derived from http://www.genome.jp/kegg/pathway/eco/eco02040.html

http://koch.pathogenomics.ca/pplre/images/flagellum_diagram2.gif

Figure 4 - Molecular Biology of the Cell, 4th edition, Figure 15-67 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=books&doptcmdl=GenBookHL&term=flagella%5BAll+Fields%5D+AND+mboc4%5Bbook%5D+AND+373902%5Buid%5D&rid=mboc4.figgrp.2879