AHM1, a Novel Type of Nuclear Matrix–Localized, MAR Binding Protein with a Single AT Hook and a J Domain–Homologous Region

Abstract

Interactions between the nuclear matrix and special regions of chromosomal DNA called matrix attachment regions (MARs) have been implicated in various nuclear functions. We have identified a novel protein from wheat, AT hookcontaining MAR binding protein1 (AHM1), that binds preferentially to MARs. A multidomain protein, AHM1 has the special combination of a J domain-homologous region and a Zn finger-like motif (a J-Z array) and an AT hook. For MAR binding, the AT hook at the C terminus was essential, and an internal portion containing the Zn finger-like motif was additionally required in vivo. AHM1 was found in the nuclear matrix fraction and was localized in the nucleoplasm. AHM1 fused to green fluorescent protein had a speckled distribution pattern inside the nucleus. AHM1 is most likely a nuclear matrix component that functions between intranuclear framework and MARs. J-Z arrays can be found in a group of (hypothetical) proteins in plants, which may share some functions, presumably to recruit specific Hsp70 partners as co-chaperones. INTRODUCTIONThe nuclear matrix, operationally defined, is the dynamic fibrogranular structure forming the skeletal framework that surrounds and penetrates the interphase nucleus; it has been implicated in most nuclear functions, including replication, repair, transcription, RNA processing, and RNA transport (Berezney and Jeon, 1995). The chromosomal DNAs are known to be associated with the nuclear matrix at specific regions called matrix attachment regions (MARs) and are thereby thought to be organized into topologically constrained loops, each of which represents a sort of functional or structural domain (or both) (Laemmli et al., 1992;Bode et al., 1996). In animals, interactions between the nuclear matrix and MARs have also been shown to be involved in DNA replication and repair and in various aspects of gene regulation, thus playing a key role in the essential functions of the nucleus (Boulikas, 1995;Bode et al., 1996).MARs consist of AT-rich sequences extending over at least a few hundred base pairs and containing various ATrich motifs as well as structural motifs such as base-unpairing regions and intrinsically curved portions (Boulikas, 1995). In animals, MAR binding activity has been found in a wide range of structurally and functionally diverse proteins (listed in Boulikas, 1995). These include topoisomerase II (Adachi et al., 1989); filament proteins such as lamins and NuMA (Ludérus et al., 1992(Ludérus et al., , 1994; ARBP, identical to a methylated CpG binding protein (von Kries et al., 1991;Weitzel et al., 1997); hnRNP-U/SAF1, an RNA binding protein involved in RNA processing (Fackelmayer et al., 1994;von Kries et al., 1994); SATB1, a tissue-specific transcription factor with high affinity for base-unpairing regions (Dickinson et al., 1992; de Belle et al., 1998); and architectural chromatin proteins such as histone H1 and HMG-I/Y (Zhao et al., 1993).In plants, MARs have been found in intergenic regions, often in or close to the regulatory regions of genes, and clo...

The AT‐hook‐containing proteins SOB3/AHL29 and ESC/AHL27 are negative modulators of hypocotyl growth in Arabidopsis

“…Single AT‐hook domain containing proteins such as SOB3 and ESC are hypothesized to bind DNA, and associate with the nuclear matrix (Fujimoto et al. , 2004; Morisawa et al. , 2000).…”

“…The rice HMGA protein, PF1, is able to bind and enhance the activity of the rice PHYA promoter, suggesting a gene regulatory role for AT-hook proteins in photomorphogenesis (Martinez-Garcia and Quail, 1999). Single AT-hook domain containing proteins such as SOB3 and ESC are hypothesized to bind DNA, and associate with the nuclear matrix (Fujimoto et al, 2004;Morisawa et al, 2000). A SOB3/ ESC family member, AHL1, is suggested to encode a nuclear localized matrix attachment region (MAR) protein (Fujimoto et al, 2004).…”

Overexpression of a chromatin architecture‐controlling AT‐hook protein extends leaf longevity and increases the post‐harvest storage life of plants

“…Furthermore, it can affect transcription of a large number of genes, as we demonstrated by microarray analysis. Studies on AT‐hook proteins in wheat ( Triticum aestivum ) ( AHM1 , Morisawa et al. , 2000) and Arabidopsis ( AHL1 , Fujimoto et al.…”

“…Furthermore, it can affect transcription of a large number of genes, as we demonstrated by microarray analysis. Studies on AT-hook proteins in wheat (Triticum aestivum) (AHM1, Morisawa et al, 2000) and Arabidopsis (AHL1, Fujimoto et al, 2004) have revealed that they can bind to the matrix attachment region (MAR) and are localized to the nuclear matrix, suggesting that they can function as a nuclear matrix component. ORE7/ESC appears to be paralogous to AHL1 with a similarity in sequence and protein size.…”

TM6, a Novel Nuclear Matrix Attachment Region, Enhances Its Flanking Gene Expression through Influencing Their Chromatin Structure

“…AHM1 and AHL1 are two other nuclear matrix-localized and MAR-binding proteins that contain a single AT hook and a J domain-homologous region or plant and prokaryote conserved (PPC) domain. These proteins function between the intranuclear framework and MARs by recruiting specific partners as co-chaperones (Fujimoto et al, 2004;Morisawa et al, 2000). Other MAR-binding proteins, such as MARBP-1 and MARBP-2, may have multifunctional roles in chromatin organization and ribosome biogenesis (Hatton and Gray, 1999).…”