Uncharacterized conserved motifs outside the HD-Zip domain in HD-Zip subfamily I transcription factors; a potential source of functional diversity

Abstract

BackgroundPlant HD-Zip transcription factors are modular proteins in which a homeodomain is associated to a leucine zipper. Of the four subfamilies in which they are divided, the tested members from subfamily I bind in vitro the same pseudopalindromic sequence CAAT(A/T)ATTG and among them, several exhibit similar expression patterns. However, most experiments in which HD-Zip I proteins were over or ectopically expressed under the control of the constitutive promoter 35S CaMV resulted in transgenic plants with clearly different phenotypes. Aiming to elucidate the structural mechanisms underlying such observation and taking advantage of the increasing information in databases of sequences from diverse plant species, an in silico analysis was performed. In addition, some of the results were also experimentally supported.ResultsA phylogenetic tree of 178 HD-Zip I proteins together with the sequence conservation presented outside the HD-Zip domains allowed the distinction of six groups of proteins. A motif-discovery approach enabled the recognition of an activation domain in the carboxy-terminal regions (CTRs) and some putative regulatory mechanisms acting in the amino-terminal regions (NTRs) and CTRs involving sumoylation and phosphorylation. A yeast one-hybrid experiment demonstrated that the activation activity of ATHB1, a member of one of the groups, is located in its CTR. Chimerical constructs were performed combining the HD-Zip domain of one member with the CTR of another and transgenic plants were obtained with these constructs. The phenotype of the chimerical transgenic plants was similar to the observed in transgenic plants bearing the CTR of the donor protein, revealing the importance of this module inside the whole protein.ConclusionsThe bioinformatical results and the experiments conducted in yeast and transgenic plants strongly suggest that the previously poorly analyzed NTRs and CTRs of HD-Zip I proteins play an important role in their function, hence potentially constituting a major source of functional diversity among members of this subfamily.

A genome-wide survey of homeodomain-leucine zipper genes and analysis of cold-responsive HD-Zip I members’ expression in tomato

“…Arce et al have described six motifs associated with the CTRs of HD-Zip I subfamily in signal transduction pathways of different species, which were always ignored in the past. 10) But in this study, the 10 nonidentified motifs were not found to match Arce's results. Therefore, we concluded that the 10 non-identified motifs could have special functions, and this need to be further verified.…”

“…42) ATHB54 is a atypical HD-Zip I protein with an extremely long CTR (325aa) which a RNA recognition motif can be identified in. 10) In class II, HD-Zip genes of three species were divided into several subclasses as reported in Arabidopsis.…”

“…Meanwhile, they are distinctive in different subclasses. For instance, all class II HD domains contain Arg 13 , Lys 10 , Glu, 18 or Asp 18 . And all class I HD domains contain Val 3 or Ile, 13 and Gln 41 .…”

“…By analyzing motifs of 178 HD-Zip I proteins from different species, the results revealed that an AHA motif in CTR could perform the activation role at the molecular level as that in HSFs. 10) HD-Zip proteins exist in all tissues and organs of higher plants. They mainly participated in plants growth, development, morphological formation, regulation of biotic and abiotic stress responses.…”

Rice HOX12 Regulates Panicle Exsertion by Directly Modulating the Expression of ELONGATED UPPERMOST INTERNODE1

“…HD-ZIP genes play diverse functions in plant development and plant adaptation to environmental stresses (Arce et al, 2011;Brandt et al, 2014). A common feature of HD-ZIP transcription factors is the presence of a leucine zipper (ZIP) domain adjacent to the homeodomain (HD); the HD domain is responsible for the specificity of protein-DNA interactions, and the ZIP domain is important for homo-and heterodimerization.…”