Protein Degradation

Protein Degradation in Laboratories
a literature review paper on a topic relevant to the material
(3-6) current papers on a single topic (from a one or a few labs) with background papers (10-20) as needed to establish
relevance and significance.
Proteasome/ Ubiquitin pathway
The proteasome section in the interior cellular machinery is involved in the breakdown of particular cellular proteins. Ubiquitin is a protein which attaches itself to other proteins and assigns them for degradation through helping the proteins to stick to proteasomes. The pathway is associated with extremely crucial role- sanitation. The pathway disposes unneeded and damaged proteins. An additional role is surveillance. For instance, some proteins meant for secretion are at times misrouted to the inside of a cell, where they make the cell function abnormally. According to Hochstrasser (1995), the proteasome/ubiquitin pathway gets rid of errant proteins.
Enzymes, which assist in the proteasome/ ubiquitin pathway, were described nearly two decades ago. However, their exact role in the cells was unclear until few years ago. Currently, people are aware that the process is vital in various situations- from oncogenesis to apoptosis. In his study, Hochstrasser discusses his proteasome/ ubiquitin pathway literature’ interpretation as idiosyncratic. He argues that his is a genetic perspective as opposed to the majority of enzymologists who initiated the field long ago (Bennett & Mayor, 2012). According to Hochstrasser, the system is controlled at various steps than the investigators focused their attention. Majority of them concentrated on the protein’s role that places ubiquitin on the protein for degradation. They thought that after the protein is attached to ubiquitin, it dies. Hochstrasser asserts that the system is controlled at different levels past this step.
Hochstrasser focuses on the degradation of specific regulatory proteins which govern differentiation and cell production. This work implicates on immunology, cell cycling, cancer biology and signal transduction. For instance, his laboratory has discovered an oncogene product which is an enzyme defective form that eliminates ubiquitin from proteins (Hwang, Saffert & Kalejta, 2011).
Lysosomal Proteolysis
Lysosomal proteolysis refers to protein degradation within eukaryotic cells and involves protein uptake by lysosomes (Hwang, Winkler & Kalejta, 2011).  Lysosomes are organelles that are enclosed with a membrane and contain various digestive enzymes which include proteases. Lysosomes have various functions in cell metabolism. This includes extracellular proteins’ digestion which is incorporated trough endocytosis. Another role is the steady turnover of cytosolic proteins and cytoplasmic organelles.
The presence of proteases as well as other digestive enzymes in lysosomes curbs uncontrolled degradation of the cell’s contents. Hence, to enhance cellular proteins degradation by lysosomal proteolysis, they have to be first taken up by lysosomes. Hwang and Kalejta (2007) assert that autophagy is one of the cellular protein uptake pathways. In involves vesicles formation (autophagosomes) whereby small cytoplasmic organelles or cytoplasm areas are bounded in membranes created from endoplasmic reticulum. The vesicles consequently fuse with lysosomes. Then, degradative lysosomal enzymes have their contents digested. Proteins uptake into autophagosomes is nonselective. Therefore, it eventually results to slow degradation of cytoplasmic proteins, which are long- lived (Cooper, 2000).
It is worth noting that not all lysosomes’ protein uptake is nonselective. For instance, lysosomes have the ability to take up and then degrade some cytosolic proteins selectively as a cellular starvation response. Under these conditions, proteins broken down by lysosomal proteases have amino acids sequences that are the same as the wide consensus sequence Lys-Phe-Glu-Arg-Gln.
In conclusion, protein breakdown is a process that uses a lot of energy. The mechanisms involved in lysosome degradation are direct translocation from the cytosol, microautophagy, macroautophagy, crinophagy and endocytosis. Ubiquitination is a three step enzymatic process that is regulated tightly. These processes are ubiquitin activation, conjugation to E2, and ubiquitin transfer and substrate recognition.
References
Bennett, E. J. andMayor, T. (2012).Proteomics propels protein degradation studies in San             Diego. Retrieved on 25th September, 2012 from            http://www.mcponline.org/content/early/2012/07/12/mcp.O112.020008.abstract

Cooper, G. M. (2000). Protein Degradation. Retrieved on 25th September, 2012 from             http://www.ncbi.nlm.nih.gov/books/NBK9957/

Hochstrasser,M. (1995). “Ubiquitin, proteasomes, and the regulation of intracellular protein             degradation.” Current Opinion in Cell Biology, 7, 215-23.

Hwang, J. and Kalejta, R.F. (2007). “Proteasome-dependent, ubiquitin-independent degradation     of Daxx by the viral pp71 protein in human cytomegalovirus-infected cells.”  Virology,        367, 334-338.

Hwang, J., Saffert, R. T., and Kalejta, R. F. (2011).“Elongin B-mediated epigenetic alteration of    viral chromatin correlates with efficient human cytomegalovirus gene expression and            replication.”mBio, 2(2), 1-22.
Hwang, J., Winkler, L., and Kalejta, R.F.  (2011).“Ubiquitin-independent proteasomal             degradation during oncogenic viral infections.  Biochim. Biophys. Acta, 1816 (2), 147-     157.
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