Update on Plant HMG-Box Proteins Plant Proteins Containing High Mobility Group Box DNA-Binding Domains Modulate Different Nuclear Processes1[W]

The HMG-box is an approximately 75-amino acid residue protein domain that occurs in all eukaryotic organisms and was first identified as a characteristic feature of the chromosomal high mobility group (HMG) proteins of the HMGB type. Structural studies have demonstrated that the L-shaped fold of the domain formed by three a-helices is conserved to a greater extent than expected from amino acid sequence similarity between different HMG-boxes. The long arm consists of helix III and the N-terminal extended strand, whereas the short arm of the L-shape is composed of helices I and II forming an angle of approximately 80° between the arms (Thomas and Travers, 2001; Stros et al., 2007). The HMG-box domain mediates DNA binding primarily through the minor groove of DNA. Hydrophobic residues of the concave face of the L-shaped molecule partially intercalate between the DNA bases, thereby widening the minor groove, which results in unwinding and remarkable bending of the DNA helix. Thus, the HMG-box domain binds the outside of the DNA bend, compressing the major groove (Thomas and Travers, 2001; Stros, 2010). Some HMG-box proteins can interact with DNA sequence specifically (e.g. mammalian transcription factors such as SEX DETERMINING REGION OF Y [SRY] and LYMPHOID ENHANCHER-BINDING FACTOR1 [LEF-1]), whereas other HMG-box proteins bind DNA sequence independently (e.g. chromosomal HMGB proteins and Structure-Specific Recognition Protein1 [SSRP1]). A typical feature of both types of HMGbox domains is their selective binding to certain DNA structures, including four-way junctions and DNA minicircles (Bustin, 1999; Thomas and Travers, 2001; Stros et al., 2007; Wegner, 2010). Because HMG-box proteins induce DNA bending upon binding to linear DNA, they often act as architectural facilitators in the assembly of nucleoprotein complexes involved in transcription, recombination, or other DNA-dependent processes (Bustin, 1999; Thomas and Travers, 2001; Stros et al., 2007). HMG-box domains are found in a variety of proteins that interact with DNA. In these proteins, the HMGbox domain(s) occurs in combination with various other protein domains of different function. Accordingly, because of this structural variability and their interaction with various other proteins, HMG-box proteins are involved in different nuclear functions. There are HMG-box proteins, for instance, that act as architectural chromosomal proteins (HMGB proteins), whereas others are transcription factors or subunits of chromatin-remodeling complexes, or they modulate DNA recombination/repair (Bustin, 1999; Stros et al., 2007). In addition to the cell nucleus, HMG-box proteins are found in mitochondria of animals and yeast, where they serve as transcriptional regulators and contribute to the organization of the mitochondrial DNA (Bonawitz et al., 2006; Kucej and Butow, 2007). Currently, there is no evidence for the occurrence of HMG-box proteins in plant mitochondria. However, an unusual HMG-box protein from Physcomitrella localizes to plastids in tobacco (Nicotiana tabacum) BY-2 cell protoplasts (Kiilerich et al., 2008), but no higher plant HMG-box protein has been reported to occur in plastids. Various plant genomes were found to encode HMGbox proteins, suggesting that they commonly occur in plants (Riechmann et al., 2000; Stros et al., 2007). Higher plant genomes encode 10 to 15 different HMGbox proteins that range from approximately 13 to 72 kD. When compared with the human genome, which encodes 47 HMG-box proteins ranging from approximately 15 to 193 kD, HMG-box proteins are less diversified in plants (Stros et al., 2007). Whereas in humans, HMG-box-containing transcription factors represent the largest subgroup (Stros et al., 2007; Wegner, 2010), to date, it is unclear whether any of the plant HMG-box proteins act as transcription factors. No sequence-specific DNA interactions have been reported for any of the plant HMG-box proteins. In plants, the family of small chromosomal HMGB proteins represents the most diversified subgroup of HMG-box proteins (Stros et al., 2007). We have searched various databases, including the Plant Chromatin Database (www.chromdb.org/) and that of MIPS (database from the Munich Information 1 This work was supported by the German Research Foundation and the Danish Research Council (grants to K.D.G.). * Corresponding author; e-mail [email protected]. [W] The online version of this article contains Web-only data. www.plantphysiol.org/cgi/doi/10.1104/pp.112.198283