RT Journal
A1 Chu, Stephanie W.
A1 Noyes, Marcus B.
A1 Christensen, Ryan G.
A1 Pierce, Brian G.
A1 Zhu, Lihua J.
A1 Weng, Zhiping
A1 Stormo, Gary D.
A1 Wolfe, Scot A.
T1 Exploring the DNA-recognition potential of homeodomains
JF Genome Research 
JO Genome Research 
YR 2012 
FD October 01 
VO 22 
IS 10 
SP 1889 
OP 1898 
DO 10.1101/gr.139014.112 
UL http://genome.cshlp.org/content/22/10/1889.abstract 
AB The recognition potential of most families of DNA-binding domains (DBDs) remains relatively unexplored. Homeodomains (HDs), like many other families of DBDs, display limited diversity in their preferred recognition sequences. To explore the recognition potential of HDs, we utilized a bacterial selection system to isolate HD variants, from a randomized library, that are compatible with each of the 64 possible 3′ triplet sites (i.e., TAANNN). The majority of these selections yielded sets of HDs with overrepresented residues at specific recognition positions, implying the selection of specific binders. The DNA-binding specificity of 151 representative HD variants was subsequently characterized, identifying HDs that preferentially recognize 44 of these target sites. Many of these variants contain novel combinations of specificity determinants that are uncommon or absent in extant HDs. These novel determinants, when grafted into different HD backbones, produce a corresponding alteration in specificity. This information was used to create more explicit HD recognition models, which can inform the prediction of transcriptional regulatory networks for extant HDs or the engineering of HDs with novel DNA-recognition potential. The diversity of recovered HD recognition sequences raises important questions about the fitness barrier that restricts the evolution of alternate recognition modalities in natural systems.