A central characteristic of life is the response to molecules of the extracellular environment. These responses are mediated by signal transduction cascades, which mostly start with an extracellular signaling molecule and end with an
activated transcription factor. Transcription factors are central to these pathways, as they are activated through different mechanisms of their translocation from the cytoplasm to the nucleus. The activation cascade of a transcription factor can be considered as a module in a biological network. Delineating the topology and dynamics of such a transcription factor network helps to understand, how these networks originate and how they enable the cell to respond to environmental signals, such as dietary molecules, growth signals or stress derived from infections and inflammation.
A central transcription factor network is that of cellular differentiation from omnipotent embryonic stem cells to terminally differentiated cells. Accute inflammation is the response of cells to stress derived from microbial infection. The inflammatory gene expression program is critically controlled by three classes of transcription factors, including NFKB, ATF3 and CEBPD. In contrast, other forms of cellular stress, such as DNA damage, are sensed via the activation of p53. This transcription factor is encoded by a tumor suppressor gene and regulates cell-cycle arrest, senescence and apoptosis. We will formalize the action of these transcription factors in respective biological networks.
Activation of transcription factors by membrane receptor signaling pathways.
There are two major pathways, how activated membrane receptors can activate transcription factors: either they stimulate kinase signaling cascades, which result in phosphorylation of various different transcription factors ( left), or they induce the translocation of latent transcription factor from the cytoplasm to the nucleus ( right). More details in the text
Many proteins function in the cytoplasm where they are produced. These proteins probably need little information targeting them to specific locations. But a large number of proteins must arrive at specific destinations within or outside of the cell in order to function. For example, some proteins are designated to function within the membrane of the endoplasmic reticulum of the cell. Others must be secreted to the outside of the cell, or perhaps in the outer or inner membrane of the mitochondrion , the intramembranous space, or into the mitochondrial matrix. Correct targeting of the protein to each of these different space areas requires explicit instructions within the targeted protein.
In the case of the mitochondrion, an organelle of the cell responsible for converting stored energy into ATP, there are four distinct target areas. Although the mitochondrion has its own DNA and protein synthesizing equipment, most of the mitochondrial proteins are made from DNA contained in the nucleus of the cell. These proteins are produced in the cytoplasm, and must navigate from there into the correct compartment of the mitochondrion .
The mitochondrion contains four different target areas that must be separately coded in the protein. The matrix is the site of most of the metabolic activity, and of most of the proteins of the mitochondrion. Both inner and outer membranes are separately targeted by a variety of other proteins, and the intermembrane space is the site for several of the cytochromes..
The targeting processes are complex, and some of the details are still being elaborated, but many of the features are well understood.
Each compartment of the mitochondrion is handled by a different set of signals and signal receptors, with the result that each protein arrives at the correct destination.
how did these signal receptors evolve ?
Some proteins must remain within the membrane, either the endoplasmic reticulum, or the outer cell membrane, or in some other cellular membrane. Such proteins play a vital role in regulating the passage of materials through the membrane, and in other vital cellular processes. In order for the protein to be produced in this configuration, the gene for its production must contain, in addition to the usual information on how to build an active functional protein, a variety of instructions informing the cell as to what destination and pathway the protein must follow.
how did these instructions evolve ?
One of the possible destinations for a protein is the outer cellular membrane. Proteins destined for this fate begin with a special set of instructions termed a signal. This system of signals are recognized by a special cytoplasmic body called the signal recognition particle (SRP)
The Signal-Recognition Particle (SRP) is part of a complex of proteins responsible for targeting proteins to specific compartments of the cell. The mechanisms, components and the targeting information appear to be universal, being recognized in plant, animal, and even yeast cells. Proteins destined for targets outside of the cytoplasm (either in membrane-bound compartments, or in the membranes themselves, or for secretion outside the cell), are designated by specific sequences of amino acids in the leader region of the protein. The particle responsible for identifying these specific sequences, called signal peptides in nascent (growing) proteins, is the SRP. This complex consists of a chain of 300 specific bases of RNA and six proteins, identified by their respective molecular weights (in kilodaltons): P9, P14, P54, P68 and P72. It is known that the P54 protein is responsible for reading and interacting with the signal peptide, the two small proteins interact with the ribosome, and the large P68/P72 proteins are involved in the movement of the nascent peptide chain. The SRP will stop protein synthesis after about 70 amino acid residues, in the absence of suitable membrane interactions, preventing the synthesis of proteins in inappropriate environments.
This particle identifies a coded message in the first 50 or so amino acids of non-cytoplasmic proteins as they are being produced by the ribosome, and binds to this leader sequence, referred to as the "signal peptide".
1. The Signal Receptor Particle (SRP)recognizes and binds to the emerging signal anchor sequence (red) of the nascent (growing) protein and integrates into the ribosome.
2. The integrated SRP engages a complex SRP receptor (alpha and beta proteins) in the membrane of the endoplasmic reticulum.
3. When thus anchored, the hydrolysis of GTP (Guanosine triphosphate) triggers the release of the SRP and the SRP receptor from the ribosome, opens the gate blocking the translocon, and inserts the nascent protein chain into the translocon. The translocon is a membrane complex made up of three or four sec61 complexes, each composed of three proteins (sec61 alpha, beta and gamma) The alpha protein is a membrane-spanning protein, making ten membrane crossings. Another major component of the translocon is the TRAM protein, which crosses the membrane at least eight times.
4. The ribosome is now anchored to the translocon by the growing peptide. As the peptide elongates, the helical signal-anchor sequence (red) extends through the membrane to the inner lumen.
5. When a second helical series of amino acids, the Stop-Transfer Membrane-Anchor Sequence (blue) is encountered, the movement of the growing peptide chain into the translocon ceases.
Molecules such as the voltage-gated sodium channel protein discussed below must have encoded within them all of the information for their functional and structural attributes, as well as information for acquiring their active domains, distributed throughout the entire length of the molecule.
This signaling mechanism is universal, since the processes operate in the same way in virtually all eukaryotic cells, including yeast, plant and animal cells. Further, the proteins comprising the translocon and the SRP receptor, that are responsible for the insertion of membrane-targeted proteins into the membrane are also multipass membrane-bound proteins. This means that they also must be inserted into the membrane by a similar mechanism. The universality means the proteins and the mechanism for their acquisition by membranes were already present in the first metazoans of record, and in the ancestral eukaryotc cell, as well.