Structural Biochemistry/Three Domains of Life/Archaea/SAMPylation Protein in Archaea

General information
Post translational modifications of proteins were first found in eukaryotes, and recently, similar modifications were also found in some bacteria. Discovery of these proteins that have similar structure as that of ubiquitin can create polymeric chains and proteins that can result in covalent modification brings in new view to the three domains of life.

Ubiquitin are related modifiers
Some of the modifications of proteins are phosphorylation, acetylation, and glycosylation. Some of the eukaryotic proteins used to study these modifications include ubiquitin and ubiquitin-like derivatives. Ubiquitin is a somewhat small protein, which contains 76 amino acids. In the target protein, Gly at the C-terminus of ubiquitin often involves in conjugation with Lys residue. Through the use of ATP, Gly at the C-terminus is adenylated by an activated enzyme, and the adenylated Gly is then transported to a cysteine active site in the activated enzyme itself. Then, ubiquitin moves to a conjugating enzyme and the conjugated ubiquitin moves to a protein ligase. At the ligase, a bond forms and connects an isopeptide to the Lys residue on the target substrate. Further modification of ubiquitin can be carried out using excess ubiquitin in the N-terminus or Lys residue. A regulatory complex called the 26S proteasome recognizes proteins that need degradation. At the complex, ubiquitin is prepared for further ubiquitylation via the deubiquitylating protease (DUBs). There are several ubiquitin like proteins, containing the same β grasp fold as that of ubiquitin, found in eukaryotes. All sequence of the ubiquitin like proteins end in Gly-Gly. They are often used for changing the interaction between proteins, transferring target proteins to certain locations of the cell. Due to their functions, ubiquitin and ubiquitin like proteins play a significant role in eukaryotes.

A bacterial small protein modifier and Ubl proteins
In recent discovery, protein post translational modification is found in archaea and bacteria. Researchers are looking to understand the mechanism for targeted protein degradation. It was found that in mycobacteria a prokaryotic ubiquitin like protein (Pup) acts as the starting signal for proteasomal degradation. Different from the ubiquitin folding, Pup is a disordered protein, meaning that despite its ending sequence at the C-terminus is Gly-Gly, and it attaches to substrate through Glu rather than the usually used Gly. No polypupylation is observed, so it is assumed monopupylation may be sufficient for protein degradation. Only a few organisms contain Pup homologues whereas bacteria and archaea contain ubiquitin. For example, proteins like ThiS and MoaD have β grasp folding like ubiquitin, and they undergo similar reaction as that of ubiquitin. However, the difference is that ThiS and MoaD transfer sulfur instead of forming conjugation in proteins. Another protein called Urm 1, has similar structure as ThiS and Moad, carries sulfur in tRNA modification pathway. From these protein properties, one proposal is that bacterial protein that has similar structure as that of ubiquitin may covalently modify other proteins. An experiment was conducted to test the formation of conjugates in a halophilic archaeon. The criteria for the experiment were that the proteins used are small and those proteins must have an ending sequence of Gly-Gly. Out of the tested proteins, three out of five were in conjugate with the ubiquitin like protein, while the two remaining small proteins made conjugate with other proteins. From the obtained result, the two conjugated proteins are referred to as archaeal modifier protein. The factors that affect the modification properties are the growth conditions and the presence of proteasomal subunits. Result from the experiment suggested the archaeal modifier proteins may be involved in certain feedback inhibition if there is no full repertoire of proteasome function. Removal of the ending sequence Gly-Gly from the archaeal modifier proteins abolished SAMPlyation for the two proteins are each named SAMP1 and SAMP2. SAMP1 sites are revealed by the addition of Arg or Lys at the C-terminus of the protein. However, it seems that Lys is the target amino acid in the conjugation process, even though it might be the case that SAMP1 conjugates with other amino acids rather than Lys. Under high concentration of salt, the protein folding and protein activity are maximized. In contrast to SAMP1, SAMP2 conjugates with Lys58, a feature of polyubiquitylation. It remains unknown how many SAMP2 can fit into one chain of polymers for proteasomal degradation. Recent research suggests that phosphorylation is significant for target proteins in the process of proteasomal degradation since protein can regulate ubiquitylation in eukaryotic substrates.

SAMP enzymology
An isopeptide bond is formed between SAMP2 and MoeB, a homologue in the Urm 1 pathway, at Lys113. The formation of this bond suggested that the activity and stability of MoeB are regulated by SAMP2. The enzymes involved in forming conjugates might have similar structure as eukaryotic conjugating enzymes. The SAMPs proteins forms conjugates with other proteins via Gly rather than Glu. Furthermore, SAMPylation involves a homologue of the eukaryote. For the above two conditions, it suggested that the archaeal system has more similarities to the eukaryotic ubiquitin system and Pup system of bacterial has less similarities. The proteins that are involved in the deconjugation process of ubiquitin like proteins in eukaryotes have homologues in both bacteria and archaea.

Prospects
The newly discovered ubiquitin like proteins in archaeans gives new direction to the study of proteins targeting to a proteasome. There is no strong evidence to support that SAMPs are involved in the targeting protein to proteasome as in eukaryotic and bacterial species. To finding the function of proteasome having on SAMPylation, closely examine the transcriptional changes in the mutants of proteasome. The mutated proteasome function facilitates the translation of specific transcripts, thus leading to protein accumulation. One more finding is that all prokaryotes contain the ubiquitin like proteins, meaning that the ubiquitin like protein is not limited to be found in archaea. Despite that the post translational modifiers were thought to be found only in eukaryotic domain, the new discovery lead to new understanding that post translational modifiers are also found in every type of organisms.

Reference
K. Heran Darwin and Kay Hofmann. "SAMPyling proteins in archaea". http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2892244/pdf/nihms-188535.pdf