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Oct and Sox
POU/HMG/DNA
complex


Ariel Bartholomew '13 and Kate Haller '13


Contents:


I. Introduction

The Oct and Sox transcription factors are present during early mammalian embryonic cell development and control specifically different aspects of neural development. Oct4 and Sox2 are two of the focused transcription factors whose combinations helped to established the first three lineages in the mammalian embryo. The interaction of these two play a key role in determining the many possible cell types in early embryogenesis. Low number of transcription factors are responsible for the development of the entire organism, forming multiprotein complexes on DNA. Thus establishing functional partnerships and transcriptional outcomes.

Very few transcription factors are responsible for developing entire organisms. Through the formation of multi-protein complexes on the DNA, different functional partnerships and transcriptional outcomes are established. The Oct and Sox transcription factors are present during early mammalian embryonic cell development and control specifically different aspects of neural development. Oct and Sox transcription factors are a part of the larger ternary POU/HMG/DNA complex. Oct proteins are transcription factors of the POU domain, while Sox proteins are transcription factors of the HMG domain. 


II. HMG

Sox2 induces a bend in the DNA of the ternary complex and binds in the minor groove of the DNA, forming a HMG/DNA interaction surface similar to the size of the POU/DNA interaction at about 1350 HMG bends the DNA 90 degrees towards the major groove. Hydrophopic side chains are inserted into the DNA, causing a bend of the DNA toward the major helix . Sox2 is sequence specific when binding to DNA,this binding is mediated by hydrogen bonds . The C-terminus of the HMG domain (residues 68-79) interacts with DNA and forms a protein-protein interface between helices 1 and 2 on Oct1 . Serine rich domain and the C-terminal end are necessary to enhance gene expression (amino acids 206-319) . Sox2 N-terminus region contains the DNA binding domain Sox2 1-180. Sox2 has lower affinity when binding DNA on its own rather than in a ternary complex . Sox2-HMG domain interacts with the compressed minor groove, suggesting its a factor in the complex formation Sox2-HMG domain will adopt an L-shape structure . The compressed minor groove is positioned by Tyr 72 and Pro 74 .

III. POU

The POU The POU binding domain is a highly charged region comprised of ~160 amino acids. The whole region is referred to as the POU domain, for the Pit-1, Oct-1 and Oct-2, and unc-86 region of sequence similarity. This domain’s sequence is similar to three mammalian transcription factors, Pit-1, Oct-1, and Oct-2. The POU domain consists of two subdomains, a C-terminal POU homeodomain (POUhd)  and an N-terminal POU-specific (POUs) domain . These two domains are connected by a flexible linker and interact with DNA in a two-way manner . The individual POU domains can bind DNA, but only very weakly. However, they have strong sequence-specific affinity when linked.

Oct-1 and Oct-2  recognize the same octameric sequence, ATGCAAAT. The POU domain is appropriate for sequence-specific binding. Both subdomain of POU contains a helix-turn-helix region important for DNA binding . The domain may also be involved in protein-protein interactions.

POUs forms protein-protein interactions as well as protein-DNA interactions in order to stabilize the POUs-DNA complex. Lys17 Thr26 Arg 20 are the 3 main residues involved in these interactions. The POUs domain is responsible for binding affinity as well as binding specificity through direct DNA contacts. Ser 48 and Arg 20 on POUs H-bond with a phosphate group on the DNA .

IV. General Structure

The Oct and Sox transcription factors interact with each other through their DNA binding domains in order to regulate transcription synergistically. Sox and POUs interact mostly through a hydrophobic boundary, surrounded by a ring of electrostatic interactions .However, a salt brigde between R75 on HMG and D29 of POU is the only sequence specific interaction between the POUs and HMG domains . This single sequence interaction could be the reason for the random formation of the POU/HMG/DNA complex.

Combinatorial control is a mechanism that integrates different signaling pathways in an ideal manner to provide a more complex regulatory network based on a finite number of transcription factors.  This mechanism is accomplished  through transcription factors with adaptable DNA and protein binding surfaces, which allows different combinations of these proteins to interact on specific promoter elements to drive synergistic transcription regulation. Both Oct3/4 and Oct1 can bind adjacently to Sox2 on the FGF4 and UTF1 promoter elements .FGF4 is able to made three additional base pairs between the Oct and Sox binding sites compared to UTF1.On FGF4, only 4 residues on POUs and 2 residues on Sox2 are involved in the protein-protein interface . The amount of cooperatively exerted by each protein is dependent of the amount of Oct4 and Sox2 present in the cell. 

Oct and Sox transcription factors regulate based on the standards of combinatorial control. The binding region of the Sox proteins, HMG, is a defined DNA binding region known as the HMG-box binding domain .   This binding domain recognizes variations of the sequence CTTTGTT.  Oct proteins bind though the POU domains, POUs and POUhd, and recognize the octamer sequence ATGCTAAT.

 Oct4 and Sox2 dimerize onto DNA in distinct conformational arrangements. Oct factors of the POU domain can homodimerize two distinct enhancers by separating the dimeriazion surface patches . interaction surfaces. One that interacts between the 3rd α-helix and POUs and one interaction on the C-terminus end interacting with the loop region on POUs between the 1st and 2nd helixes. Depending on which enhancer is present, will determine where POUs interacts on the Sox2 domain . The distance between the DNA motifs and the binding sites on each domain is essential to selecting which interface of Sox2 is selected. POU and SOX proteins interact selectively with other conserved domains POU and HMG all binding to DNA. DNA enhancer region of the target genes is responsible for the proper spacial arrangement of the glue-like interaction domains on their surface.   



VI. References

Grenfell, S.J., Latchman D.S., and Thomas N.S.B. 1996. CT-1 and Oct-2 DNA-binding site specificity is     regulated in vitro by different kinases. Biochem. J. 315: 889-893.

Herr W., Sturm, R.A., Clerc, R.G., Corcoran, L.M., Baltimore, D., Sharp, P.A., Ingraham, H.A., Rosenfeld,M.G., Finney, M., Ruvkun, G., and Horvitz, R.H. 2011. The POU domain: a large conserved region in the mammalian pit-1, oct-1, oct-2, and Caenorhabditis elegans unc-86 gene products. Genes & Development 2:1513-1516.

Nowling, T. K., L. R. Johnson, M. S. Wiebe, and A. Rizzino. 2000. Identification of the transactivation domain of the transcription factor Sox-2 and an associated co-activator. J. Biol. Chem. 275:3810-3818.

Remenyi, A., Lins, K., Nissen, L.J., Reinbold, R., Scholer, H.R., et al. Crystal structure of a POU/HMG/DNA ternary complex suggests differential assembly of Oct4 and Sox2 on two enhancers. Genes Dev. 2003;17:2048–2059.

Remenyi, A., Scholer, H.R., and Wilmanns M. 2004. Combinatorial Control of Gene Expression. Nature Structural & Molecular Biology.11: 812-815.

Sturm, R.A., and W. Herr.  1988. The POU domain is a bipartite DNA-binding structure. Nature 336:        601-604.

Williams, D.C., Cai, D.C., M., and G.M. Clore. Molecular basis for synergistic transcriptional activation by Oct1 and Sox2 revealed from the solution structure of the 42-kDa Oct1 center dot Sox2 center dot Hoxb1-DNA ternary transcription factor complex. J. Biol. Chem. 2004;279:1449-1457.

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