7 kDa DNA-binding protein
| 7kD DNA-binding domain | |||||||
|---|---|---|---|---|---|---|---|
| Identifiers | |||||||
| Symbol | 7kD_DNA_binding | ||||||
| Pfam | PF02294 | ||||||
| InterPro | IPR003212 | ||||||
| CATH | 1c8c | ||||||
| SCOP2 | 1c8c / SCOPe / SUPFAM | ||||||
| |||||||
The 7 kDa DNA-binding proteins are a family of DNA-binding proteins from Sulfolobales archaea. These proteins bind DNA in a mostly sequence-independent manner, with some preference for G/C rich regions and affinities that differ from each other. They serve a genome-packaing purpose analogous to histones. They are resistant to high temperatures as well as low and high pH.[1]
Biology
The 7kDa proteins are universally found in Sulfolobus, where two copies (Sul7d, Sul7e) are present as separate genes. The proteins are usually named after the species, e.g. Sso7d for the 7d of S. solfataricus and Sac7e for the 7e of S. acidocaldarius. Sul7a and Sul7b are truncated versions of 7d.[1] "Sso7c" does not appear to be a member of this family.[2] S. tokodaii is unusual in that the two copies only differ by one nucleotide and produce the same protein, so its version is simply called Sto7.[1]
Across Sulfolobales, Acidianus, Metallosphaera, and "Candidatus Aramenus" also encode a 7kDa DNA-binding protein, named according to the genus name or the species name in an analogous fashion. Each genome may carry anywhere from 1 to 3 versions of the protein.[1]
Biotechnology
The 7kDa proteins are valuable tools in biotechnology due to their ability to bind any dsDNA. When grafted onto a DNA polymerase, it greatly enhances the processivity of the enzyme by helping it stay bound to the DNA. Using such a modified enzyme allows a polymerase chain reaction to copy much longer pieces of DNA at a faster rate.[3] Such fusion polymerases are sold under various tradenames under premium prices since 2014,[4][5] but they can also be made and purified in a lab.[6] (The commercial versions include additional mutations for performance.)
The 7kDa protein scaffold is also a good starting point for artificial affinity proteins (affitins) that can be used to bind any molecule of interest.[1] Techniques such as phage display are used to screen a wide variety of mutants and select for the good binders. Compared to antibodies, they are much smaller and much stabler.[7]
References
- ^ a b c d e Kalichuk, V; Béhar, G; Renodon-Cornière, A; Danovski, G; Obal, G; Barbet, J; Mouratou, B; Pecorari, F (17 November 2016). "The archaeal "7 kDa DNA-binding" proteins: extended characterization of an old gifted family". Scientific Reports. 6 37274. Bibcode:2016NatSR...637274K. doi:10.1038/srep37274. PMC 5112516. PMID 27853299.
- ^ See https://www.uniprot.org/uniprotkb/P81551/entry, "Family and domain databases"
- ^ Ishino, S; Ishino, Y (2014). "DNA polymerases as useful reagents for biotechnology - the history of developmental research in the field". Frontiers in Microbiology. 5: 465. doi:10.3389/fmicb.2014.00465. PMC 4148896. PMID 25221550.
- ^ "The Power of Two—Fusion DNA polymerases".
- ^ Staff, Bioradiations (8 December 2015). "Sso7d Fusion Polymerase: A Review of What It Is and How It Helps PCR | Bio-Radiations".
- ^ Farooqui, AK; Ahmad, H; Rehmani, MU; Husain, A (August 2023). "Quick and easy method for extraction and purification of Pfu-Sso7d, a high processivity DNA polymerase". Protein Expression and Purification. 208–209 106276. doi:10.1016/j.pep.2023.106276. PMID 37156451.
- ^ Zhao, N; Schmitt, MA; Fisk, JD (April 2016). "Phage display selection of tight specific binding variants from a hyperthermostable Sso7d scaffold protein library". The FEBS Journal. 283 (7): 1351–67. doi:10.1111/febs.13674. PMID 26835881.