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Cell biology/Membrane Assembly: Signal Hypothesis

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• mutate sequences to find one (or more) regions of genes required for import.
• "isolate" signal protein-fuse it to a reporter protein (like GFP) to see if the signal is sufficient.
• This sequence has 5 basic charges in a row, which is common for a signal protein.
• Ribosomes require protein subunits to travel to the nucleus so they must have a nuclear localization signal (NLS) .
• In the nucleus, the protein subunits are assembled in complex with the ribosomal RNA.
• Finally, the ribosomes must have another signal, nuclear export signal (NES) to get out of the nucleus

Nucleocytoplasmic Exchange

Or Mechanism of Import and Export of Proteins Into/From the Nucleus.

• Involves a several carrier proteins and a GTP binding (regulatory) protein. The GTP protein must be bound to the cargo that is imported or exported out of the nucleus.
• The central feature of this regulatory pathway can be reduced to the conversion of protein, called Ran, from a guanosine diphosphate (GDP) bound state to a guanosine triphosphate (GTP) bound state (GDP or GDP are bound to Ran) or the reverse reaction.
• There are many small GDP/GTP binding proteins that regulate the traffic of proteins and cytoskeletal events throughout the cell.
• This small regulatory protein, Ran, is important because it controls the entry and exit of all proteins that must enter/exit the nucleus.
• Ran-GEF (always in the nucleus) binds in the nucleus to Ran-GDP and displaces the GDP allowing GTP to replaces it.
• Ran-GAP (always in the cytoplasm) binds Ran-GTP and stimulates GTP hydrolysis, so a phosphate group drops off, creating GDP.

What happens when a protein (cargo), in the cytoplasm wants to be imported into the nucleus?

See Diagram above.

• The cargo protein has an NLS (nuclear localization signal) and alpha importin binds to the NLS.
• Beta importin binds to the alpha importin.
• Beta importin is responsible for driving the protein complex just created through the pore. It makes contact with the inside of the pore complex (mildly hydrophobic), and binds and dissociates with protein sequences of the pore.
• Ran-GDP has already diffused in.
• Ran-GEF acts on (activates) Ran-GDP converting it to Ran-GTP.
• Ran-GTP binds with the alpha beta cargo complex and causes it to dissociate.
• The cargo molecule does whatever it was supposed to to (i.e. transcription or ribosome production).
• Ran-GTP binds to the beta importin (alpha importin follows) and the complex travels through the nuclear pore.
• On the cytoplasmic side the Ran-GAP pulls off a phosphate group, from Ran-GTP creating Ran-GDP
• Cells have lots of importin alphas which are devoted to importing a dozen (or two) cargo molecules.

What happens when a protein (cargo)wants to be exported from the nucleus?

• Exportin binds to NES (nuclear export signal) on the cargo protein.
• Exportin is responsible for interacting with the nuclear pore.
• When the complex exits the pore, Ran-GAP removes a phosphate group from Ran-GTP, creating Ran-GDP.
• Ran-GDP then detaches from the complex leaving the cargo protein in the cytoplasm along with exportin.
• Exportin must be transported back into the nucleus with Ran-GDP.

*Cells have lots of exportin alphas which are devoted to importing a dozen (or two) cargo molecules.

• Regulation of import/export of certain molecules is managed by regulating importin and exportin proteins.
• The NES or NLS is exposed late in the assembly of the desired protein/complex (ribosome) and so their is no attachment point for the transportation enzymes until the cargo molecules are ready for import/export.

Secretory or Membrane Protein Transport

Proteins that are transported to the into or out of cell membrane are very different from nucleocytoplasm transport. The pores that are on the cell membrane are quite small (diameter = 8 angstroms ) and only allow proteins to pass as they are being synthesized (compared to the nuclear membrane that allows all small proteins to pass and larger proteins to pass with Ran-GDP or Ran-GTP).

Enter the Endoplasmic Reticulum

The endoplasmic reticulum is a conveyor belt wrapped within the cell on which ribosomes are deposited. In pancreatic cells, 90% of the ribosomes are touching the cytoplasmic surface of the ER. Protected in the interior of the ER is a clear space called the lumen. The transfer of secretory proteins (as they are being made by the ribosomes) from the membrane to the lumen determines their future as a secretory protein. When the proteins complete production, the ER fuses with the cell membrane and releases the proteins to the outside of the cell.

• In the 1940s it first became possible to prepare cells and tissues to study with the electron microscope.

George Palade confirmed the function of the endoplasmic reticulum and Golgi Apparatus for producing secretory proteins. He also found that ribosomes are responsible for protein manufacturing. He studied the movement of proteins within the pancreas (90% of their energy is devoted to making secretory proteins and their endoplasmic reticulum (ER) has 25X the surface area of the plasma membrane).

• Palade performed an experiment where he homogenized pancreatic tissue and created vesicles that have ribosomes still bound (with their messenger RNA) and show that the ribosomes are caught in the act of translating a nascent polypeptide chain.
• He then took these vesicles and added translation factors, ATP, and GTP , transfer RNA and other materials necessary for protein synthesis. The vesicles would then create full proteins from their nascent state inside the vesicle.
• How do you prove that the proteins are discharged into the interior of the vesicle via vectorial translocation?

• Vectorial translocation is the name of transfer in a unidirectional manner.
• To prove this you can use an earlier study (protease protection). For this study, you would take the vesicles, ATP, GTP, transfer RNA and radiolabeled amino acids. Then treat one group with trypsin (protease) and another with trypsin and a detergent. This would show that trypsin can only act upon the amino acids when the detergent is used.
• From this we know that we can create a protein in a test tube.

How do these frequently polar molecules cross the lipid bilayer membrane?

• Cesar Milstein won the Nobel prize for monoclonal antibodies. But we are more interested in his work with the antibody light chain because he discovered the N-terminal extension on an immature protein, antibody light chain.
• Earlier work with SDS gels gave the mature light chain's structure and weight of 23.5kD.
• It is possible to get ribosomes and translation necessities, without a membrane, by breaking open reticulocytes.
• He found that the in vitro created protein, a precursor protein, had a weight of 25.5kD.
• So there are an extra 20 amino acids at the N-terminus of precursor secretory proteins that is later cleaved before the protein becomes fully developed.
• Günter Blobel (Palade's protege) also won the Nobel Prize.
• His study involved stripping ER vesicles of their ribosomes and adding mRNA and ribosomes to create fully formed proteins (without their N-terminus extension) inside of the ER vesicle.

To be continued in the next lecture.

Please feel free to add details or make changes where necessary. Contact me via email if you need help. Thanks, April

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Synthesis of Membrane Proteins and the "Signal Hypothesis"

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All of a cell’s proteins are synthesized by ribosomes, including, of course, those proteins that are destined for inclusion in the plasma membrane.

Cytoplasmic ri­bosomes in eukaryotic cells occur in two states: (1) “attached” (ribosomes associated with the mem­branes of the endoplasmic reticulum) and (2) “free” (ribosomes freely dispersed in the cytosol). Both attached and free ribosomes are be­lieved to contribute proteins to the plasma membrane.

Synthesis of Membrane Proteins and the “Signal Hypothesis”:

Principally as a result of the work of G. Blobel, D. D. Sabatini, C. M. Redman, C. Milstein, J. E. Rothman, J. Lenard, and H. F. Lodish, the mechanism that routes newly synthesized proteins to their proper des­tinations in the cell has gradually unfolded. A major contribution to this end has been the confirmation of the signal hypothesis proposed in the early 1970s by Blobel and Sabatini.

According to this hypothesis (Fig. 15-19), proteins that are to be either (a) secreted from the cell, (b) dispatched to lysosomes, or (c) incor­porated into the plasma membrane or membranes of the endoplasmic reticulum are encoded by mRNA molecules that contain a special nucleotide sequence called a “signal.”

The signal segment encodes a chain of about 16 to 26 amino acids that appears at or near the beginning of the polypeptide chain. Near its N- terminus, the signal sequence contains polar, basic residues, whereas the central domain is apolar. When a ribosome attaches to the mRNA in the cytosol and begins to translate the message, the signal sequence or signal peptide emerging from the ribosome is rec­ognized by a ribonucleoprotein complex in the cytosol called the signal recognition particle (i.e., SRP).

SRP, which consists of a 7 S cytoplasmic RNA mole­cule and six polypeptides, binds to the signal se­quence, bringing about a temporary halt to protein synthesis by that ribosome. Synthesis is resumed only if the SRP-ribosome complex attaches to the endo­plasmic reticulum; ribosomes synthesizing polypep­tides that lack a signal sequence do not interact with SRP and do not attach to the endoplasmic reticulum.

The amino acid sequences of a number of signal pep­tides have now been determined. Although they con­tain a specific distribution of hydrophobic and charged residues, no primary sequence homologies appear to exist. Consequently, it is be­lieved that SRP must recognize certain features con­tained in the signal peptide’s secondary and tertiary structure.

SRP-ribosome complexes attach to the endoplas­mic reticulum at specific sites occupied by SRP recep­tors (also called docking proteins). Once “docking” is completed, the SRP-ribosome-docking protein inter­action is replaced by a functional ribosome- membrane junction and the synthesis of the polypep­tide encoded by the mRNA is resumed. SRP returns to the cytosol where it can participate in another round of signal recognition and docking (i.e., the “SRP cycle” of Fig. 15-19a).

When protein synthesis is resumed by the docked ribosome, the elongating polypeptide chain passes through the ER membrane into the intracisternal space. This process, termed “translocation,” is presumed to involve active partici­pation of elements of the membrane. Translocation of the growing polypeptide into the intracisternal space is depicted in Figure 15-19 as taking place through a pore-like opening in the membrane solely to indicate that the membrane’s permeability barrier is tran­siently altered.

However, it is not known with cer­tainty whether translocation through the membrane takes place through such a proteinaceous water-filled channel or directly through the lipid bilayer. In most instances, the signal sequence is eventually cleaved from the remainder of the growing polypeptide by an extrinsic enzyme called signal peptidase attached to the lumenal surface of the ER.

If the protein being synthesized is destined for secretion from the cell, completion of synthesis is followed by the protein’s re­lease from the ribosome into the intracisternal space. The ribosome then detaches from the membrane and the mRNA and may participate in another round of protein synthesis. At the same time, the permeability barrier of the ER is restored.

Proteins discharged into the ER cisternae in this manner are ultimately con­veyed to the Golgi apparatus for chemical modifica­tion prior to secretion. In the case of pro­teins destined to be regular constituents of the endoplasmic reticulum or the plasma membrane, translocation into the intracisternal space is aborted before synthesis is finished so that the polypeptide is left anchored in the membrane (Fig. 15-19b). The in­formation halting the translocation is likely contained in the polypeptide itself and is recognized by the translocation apparatus.

For peripheral membrane proteins facing the exte­rior of the cell or the lumenal phase of the ER, the sig­nal sequence is followed by synthesis of the hydro- philic portion of the polypeptide. If an integral membrane protein is being synthesized, the hydro- philic portion is followed by a hydrophobic segment that remains anchored in the lipid bilayer. For pro­teins that span the membrane, synthesis is completed with the production of a final hydrophilic segment that faces the cytosol.

By comparing parts a and b of Figure 15-19, it is seen that the major distinction between the synthesis of secretory proteins and membrane proteins is that secretory proteins are released into the lumenal phase of the ER, whereas membrane proteins remain an­chored in the ER.

Addition of sugars to presumptive plasma membrane glycoproteins may occur soon after the hydrophilic portions of the molecules enter the ER cisternae. The membrane glycoprotein then migrates from the ER to the Golgi apparatus. Although the mechanism for this transfer is still uncertain, it is be­lieved to take place either by dispatchment of small vesicles from the ER, which then migrate to and fuse with the Golgi membranes, or by lat­eral “flow” along the ER membranes to the Golgi. Glycosylation of the membrane proteins is completed in the Golgi apparatus.

The Golgi apparatus dis­patches completed plasma membrane glycoproteins as small vesicles that migrate to and fuse with the plasma membrane. The overall process is summarized in Figure 15-20, which also shows that the intracellular/extracellular orientation of the mem­brane protein is maintained throughout its passage from the ER to the plasma membrane.

Some integral proteins have hydrophilic parts that face the interior of the cell and some peripheral proteins are associated only with the mem­brane’s cytoplasmic face. Although a similar mecha­nism is not precluded for the synthesis of these mem­brane proteins, they could be synthesized by free ribosomes.

Following release of these proteins in the cytosol they may diffuse to the plasma membrane. In­tegral proteins would be spontaneously inserted into the membrane by a hydrophobic segment (Fig. 15- 20), whereas peripheral proteins would attach to the membrane through polar interactions. Peripheral pro­teins reaching the plasma membrane in this manner could not pass through the membrane to the exterior surface because they could not traverse the hydropho­bic membrane core.

Prokaryotic cells do not contain an endoplasmic reticulum. Secretory proteins and new plasma membrane proteins are synthesized by ri­bosomes that attach to the inner surface of the plasma membrane. As in eukaryotic cells, ribosome attach­ment follows synthesis of a signal peptide encoded in the protein’s mRNA. The protein is then dispatched through the cell membrane and into the extracellular space.

Synthesis of Membrane Lipids:

In eukaryotic cells, phospholipid synthesis is associ­ated with the endoplasmic reticulum, whereas in pro­karyotic cells lipid synthesis is a property of the cyto­plasmic half of the plasma membrane. It is therefore likely that lipid synthesis in eukaryotic cells takes place in the cytoplasmic half of the ER membranes.

Following synthesis, the phospholipid becomes at least temporarily part of the interior monolayer but may ei­ther be enzymatically translocated to the outer layer or flip-flop between the two layers. In view of the fact that outer monolayer lipids are derived from the inner monolayer, an absolute asymmetry is precluded.

Because in prokaryotic cells lipid synthesis occurs in the plasma membrane, incorporation into the mem­brane’s structure is direct. In eukaryotic cells, how­ever, presumptive plasma membrane lipid must make its way from the ER to the plasma membrane.

This is believed to occur by one or both of two processes. Newly synthesized lipids inserted into ER membranes may make their way to the plasma membrane by the same mechanism that translocates ER membrane proteins (Fig. 15-20); that is both membrane proteins and lipids pass from the ER to the Golgi apparatus and are later dispatched to the plasma membrane via small vesicles.

The cytosol of eukaryotic cells contains a number of phospholipid transport proteins that function to transfer phospholipid molecules from one cellular membrane to another. These transport pro­teins might also play a major role in mediating the passage of phospholipids from the membranes of the ER to the plasma membrane.

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Signal hypothesis

The signal hypothesis relates to mechanisms such as the biological transport of proteins in cells to the appropriate organelles by insertion into the membranes or secreted outside the cell. Newly synthesized proteins are endowed with an intrinsic signal that must be deciphered at the target sites. Günter Blobel suggested, in 1975, that this signal determines their ability to go to and through the endoplasmic reticulum membrane, and he called this theory the signal hypothesis .

The signal consists of a hydrophobic peptide, the signal peptide , made up of about 20 amino acids in a particular order, which are the first to appear when the polypeptide chain is being synthesized. This peptide seems to signal to the cell that the protein to which it is bound must be transported, since when the peptide binds to a cytoplasmic protein this causes the protein to be secreted. It seems that the hydrophobicity of the signal peptide is one of the most important factors for protein transport to occur. The molecular principles described by Blobel that form the basis of this process are universal. signal peptides have a certain charge, since they have lys or arg in their coding sequences, the positive side, marked by these amino acids, always faces the cytosol. In addition, the translocation will be determined by this charge and the cost for the cell to carry out the translocation will also depend on it, since the charge must always be facing the cytosolic side, many times the protein chain is longer on the side where it is located. the negative charge of the signal peptide, which would imply a greater work to move this long chain through the translocon (membrane protein that fulfills the function of translocating the protein.

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• Published: 13 April 2011

Spatial expression of the genome: the signal hypothesis at forty

• Karl S. Matlin 1  

Nature Reviews Molecular Cell Biology volume  12 ,  pages 333–340 ( 2011 ) Cite this article

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The signal hypothesis, formulated by Günter Blobel and David Sabatini in 1971, and elaborated by Blobel and his colleagues between 1975 and 1980, fundamentally expanded our view of cells by introducing the concept of topogenic signals. Cells were no longer just morphological entities with compartmentalized biochemical functions; they were now active participants in the creation and perpetuation of their own form and identity, the decoders of linear genetic information into three dimensions.

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Acknowledgements

The author is grateful for support of this project from the US National Library of Medicine and the US National Institutes of Health (NIH), to W. Green, N. Matlin, A. Engelberg and J. Collier for review of the manuscript, and to members of the Committee on Conceptual and Historical Studies of Science at the University of Chicago, Illinois, USA, for stimulating discussions. Photographs in figure 2 were provided by the Laboratory of Molecular Biology at the University of Cambridge, UK, and by N. Dwyer, NIH, USA. The author thanks the many individuals who have provided information for this article through interviews.

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Karl S. Matlin is at Department of Surgery, The University of Chicago, 5841 South Maryland Avenue, MC 5032, SBRI J557, Chicago, Illinois 60637-1470, USA. [email protected],

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Matlin, K. Spatial expression of the genome: the signal hypothesis at forty. Nat Rev Mol Cell Biol 12 , 333–340 (2011). https://doi.org/10.1038/nrm3105

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Published : 13 April 2011

Issue Date : May 2011

DOI : https://doi.org/10.1038/nrm3105

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