These are my notes from week 12 of MIT course 7.88j: Protein Folding and Human Disease, held by Dr. Jonathan King on April 30, 2015.
Today was the first week of student final project presentations. Truc Do presented on trigger factor. I presented on SOD1.
Protein folding machinery and the protein quality control network are highly conserved across many domains of life [Doyle 2013]. E. coli have a protein quality control network fairly analogous to that in eukaryotes. Nascent polypeptides coming from ribosomes can get help folding from DnaK/JE and GroEL/ES. Proteins from stalled ribosomes get tagged with ssrA for degradation.
In eubacteria there is a protein called trigger factor (TF) that is the first point of contact for many new polypeptides coming off the ribosome. It holds the polypeptide in a state that allows folding. This is an alternate folding pathway for proteins that do not use DnaK/JE or GroEL/ES.
The discovery of trigger factor [Crooke & Wickner 1987] arose from a search for chaperones that allow proteins to insert into the membrane. They used an inverted membrane system wherein only membrane-bound proteins would be spared from protease digestion, and they found that a protein called pro-OmpA had to be co-incubated with trigger factor prior to exposure to membranes in order to insert correctly. They therefore thought trigger factor acted specifically to help with membrane insertion. However, they later found that depletion of trigger factor causes defects in cell division (the bacteria undergo filamentation) but does not prevent export of proteins [Guthrie & Wickner 1990]. This forced a re-thinking of trigger factor’s role.
It eventually turned out that trigger factor is a prolyl isomerase [Stoller 1995, Hesterkamp 1996], meaning that it controls whether prolines in nascent polypeptides end up in a cis or trans configuration, which would be critical for correct folding. It does also, however, have the activity of holding onto proteins while they fold [Scholz 1997]. Evidently it has two separate domains responsible for the “holding” function and the prolyl isomerase function, and you can mutagenize one domain while leaving the other’s activity intact [Li 2001]. It is now understood that trigger factor is a multi-domain protein that essentially covers the ribosome exit site and “cradles” the nascent polypeptide [Ferbitz 2004].
Trigger factor binds to folding intermediates, not finished proteins. One study introduced new disulfide bonds into lactalbumin to create conformations resembling intermediates thought to be present its folding process, and found that trigger factor only bound to the early, “pre-molten globule” intermediates [Huang 2000].
It turns out that the first 118 N-terminal amino acids contain the entire domain responsible for binding new polypeptides coming off the ribosome [Hesterkamp 1997]. This was later narrowed down to a smaller substring of amino acids, and the site on the ribosome that they associate with was identified [Kramer 2002].
Deletion of trigger factor (Δtig) gives no growth phenotype and appears to be compensated by a heat shock response, but in combination with DnaK deletion it is synthetic lethal [reviewed in Hoffmann 2010]. Indeed, it has been recognized for some time that trigger factor and DnaK cooperate in protein-folding [Deuerling 1999]. DnaK is inessential for bacterial growth at 37°C but is essential at lower or higher temperatures. Some of the same proteins rely on both trigger factor and DnaK for their folding [Deuerling 2003].
Q. What about signal peptides?
A. Those are handled by the SecB chaperone, which as far as we know does not interact at all with trigger factor. So if trigger factor is bound to the ribosome and it sees a signal peptide emerge from the exit channel, it must let go.
I basically just presented the stuff I wrote in today’s blog post.