AHM1, a novel type of nuclear matrix-localized, MAR binding protein with a single AT hook and a J domain-homologous region

AT Hook-Like 10 phosphorylation determines ribosomal RNA processing 6-like 1 (RRP6L1) chromatin association and growth suppression during water stress

Phosphorylation of AT Hook-Like 10 (AHL10), one of the AT-hook family of plant-specific DNA binding proteins, is critical for growth suppression during moderate severity drought (low water potential, ψw ) stress. To understand how AHL10 phosphorylation determines drought response, we identified putative AHL10 interacting proteins and further characterized interaction with RRP6L1, a protein involved in epigenetic regulation. RRP6L1 and AHL10 mutants, as well as ahl10-1rrp6l1-2, had similar phenotypes of increased growth maintenance during low ψw . Chromatin precipitation demonstrated that RRP6L1 chromatin association increased during low ψw stress and was dependent upon AHL10 phosphorylation. Transcriptome analyses showed that AHL10 and RRP6L1 have concordant effects on expression of stress- and development-related genes. Together these results indicate that stress signalling can act via AHL10 phosphorylation to control the chromatin association of the key regulatory protein RRP6L1. AHL10 and RRP6L1 interaction in meristem cells is part of a mechanism to downregulate growth during low ψw stress. Interestingly, the loss of AHL13, which is homologous to AHL10 and phosphorylated at a similar C-terminal site, blocked the enhanced growth maintenance of ahl10-1. Thus, AHL10 and AHL13, despite their close homology, are not redundant but rather have distinct roles, likely related to the formation of AHL hetero-complexes.

Chemical Decorations of "MARs" Residents in Orchestrating Eukaryotic Gene Regulation

Genome organization plays a crucial role in gene regulation, orchestrating multiple cellular functions. A meshwork of proteins constituting a three-dimensional (3D) matrix helps in maintaining the genomic architecture. Sequences of DNA that are involved in tethering the chromatin to the matrix are called scaffold/matrix attachment regions (S/MARs), and the proteins that bind to these sequences and mediate tethering are termed S/MAR-binding proteins (S/MARBPs). The regulation of S/MARBPs is important for cellular functions and is altered under different conditions. Limited information is available presently to understand the structure–function relationship conclusively. Although all S/MARBPs bind to DNA, their context- and tissue-specific regulatory roles cannot be justified solely based on the available information on their structures. Conformational changes in a protein lead to changes in protein–protein interactions (PPIs) that essentially would regulate functional outcomes. A well-studied form of protein regulation is post-translational modification (PTM). It involves disulfide bond formation, cleavage of precursor proteins, and addition or removal of low-molecular-weight groups, leading to modifications like phosphorylation, methylation, SUMOylation, acetylation, PARylation, and ubiquitination. These chemical modifications lead to varied functional outcomes by mechanisms like modifying DNA–protein interactions and PPIs, altering protein function, stability, and crosstalk with other PTMs regulating subcellular localizations. S/MARBPs are reported to be regulated by PTMs, thereby contributing to gene regulation. In this review, we discuss the current understanding, scope, disease implications, and future perspectives of the diverse PTMs regulating functions of S/MARBPs.

Screening of a protein that interacts with the matrix attachment region-binding protein from Dunaliella salina

We isolated the matrix attachment region-binding protein (MBP) DMBP-1 from Dunaliella salina in our previous studies. MBPs are part of the cis-acting protein family cluster. The regulatory function possibly works through the interaction of the MBPs with each other. In the present study, DMBP-1 was used as the bait in screening the D. salina cDNA library for DMBP-1 interactors that could potentially mediate the DMBP-1-regulated functions. A novel MBP, namely, DMBP-2, was identified as a DMBP-1 binding partner. The cDNA of DMBP-1 was 823 bp long and contained a 573 bp open reading frame, which encoded a polypeptide of 191 amino acids. The interaction between DMBP-2 and DMBP-1 was further confirmed through glutathione S-transferase pull-down assays.

Upregulation of the AT-hook DNA binding gene BoMF2 in OguCMS anthers of Brassica oleracea suggests that it encodes a transcriptional regulatory factor for anther development

Ogura cytoplasmic male sterility (OguCMS) is the most important CMS system used for F1 hybrid cabbage production worldwide. The anther abortion and defective pollen development exhibited in OguCMS are coordinately regulated by the mitochondrial male sterile gene orf138 and many nuclear transcriptional regulatory factors. AT-hook DNA binding proteins regulate cell-specific gene expression. In this study, we cloned the gene encoding the AT-hook DNA binding protein BoMF2 using the cDNA-AFLP TDF sequence, which was upregulated in OguCMS cabbage flower buds, as a querying probe. BoMF2 contains a 783-nt continuous complete open reading frame encoding a 260 amino-acid polypeptide. In vivo transient expression assays using GFP fusions showed that BoMF2 protein was located in the nucleus. BoMF2 was preferentially expressed in cabbage stamens, with a short expression window at anther development stage 7-8. However, in OguCMS flowers, BoMF2 expression continued into the mature pollen stage and was concomitant with the continued proliferation of tapetum cells exhibited in this mutant. Arabidopsis plants overexpressing BoMF2 showed significantly shorter siliques than the wild type, as well as decrease of pollen viability. These results suggest that BoMF2, a transcriptional regulatory factor, might regulate tapetum proliferation during anther development.

In vivo mapping of arabidopsis scaffold/matrix attachment regions reveals link to nucleosome-disfavoring poly(dA:dT) tracts

Scaffold or matrix attachment regions (S/MARs) are found in all eukaryotes. The pattern of distribution and genomic context of S/MARs is thought to be important for processes such as chromatin organization and modulation of gene expression. Despite the importance of such processes, much is unknown about the large-scale distribution and sequence content of S/MARs in vivo. Here, we report the use of tiling microarrays to map 1358 S/MARs on Arabidopsis thaliana chromosome 4 (chr4). S/MARs occur throughout chr4, spaced much more closely than in the large plant and animal genomes that have been studied to date. Arabidopsis S/MARs can be divided into five clusters based on their association with other genomic features, suggesting a diversity of functions. While some Arabidopsis S/MARs may define structural domains, most occur near the transcription start sites of genes. Genes associated with these S/MARs have an increased probability of expression, which is particularly pronounced in the case of transcription factor genes. Analysis of sequence motifs and 6-mer enrichment patterns show that S/MARs are preferentially enriched in poly(dA:dT) tracts, sequences that resist nucleosome formation, and the majority of S/MARs contain at least one nucleosome-depleted region. This global view of S/MARs provides a framework to begin evaluating genome-scale models for S/MAR function.

The AT-hook/PPC domain protein TEK negatively regulates floral repressors including MAF4 and MAF5

Epigenetic regulations of transposable elements (TEs) and TE-like repeat sequences help to protect genomic integrity and control various developmental processes, including flowering time. This complex action of gene silencing requires the coordination of many key players including DNA methylases, histone deacetylases and histone methyltranferases. We have recently reported that an AT-hook DNA binding protein, TRANSPOSABLE ELEMENT SILENCING VIA AT-HOOK (TEK), participates in silencing TEs and TE-like sequence containing genes, such as Ler FLOWERING LOCUS C (FLC) and FWA. TEK knockdown in amiTEK plants causes increased histone acetylation, reduced H3K9me2 and DNA hypomethylation in the target loci, which ultimately leads to the upregulation of FLC and FWA as well as TE reactivation. In this report, we show that, besides FLC, other FLC-like genes MADS AFFECTING FLOWERING 4 (MAF4) and MAF5 are also upregulated in amiTEK. Here we discuss the role of the nuclear matrix protein TEK in the maintenance of genome integrity and in the control of flowering.

TM6, a novel nuclear matrix attachment region, enhances its flanking gene expression through influencing their chromatin structure

Nuclear matrix attachment regions (MARs) regulate the higher-order organization of chromatin and affect the expression of their flanking genes. In this study, a tobacco MAR, TM6, was isolated and demonstrated to remarkably increase the expression of four different promoters that drive gusA gene and adjacent nptII gene. In turn, this expression enhanced the transformation frequency of transgenic tobacco. Deletion analysis of topoisomerase II-binding site, AT-rich element, and MAR recognition signature (MRS) showed that MRS has the highest contribution (61.7%) to the TM6 sequence-mediated transcription activation. Micrococcal nuclease (MNase) accessibility assay showed that 35S and NOS promoter regions with TM6 are more sensitive than those without TM6. The analysis also revealed that TM6 reduces promoter DNA methylation which can affect the gusA expression. In addition, two tobacco chromatin-associated proteins, NtMBP1 and NtHMGB, isolated using a yeast one-hybrid system, specifically bound to the TM6II-1 region (761 bp to 870 bp) and to the MRS element in the TM6II-2 (934 bp to 1,021 bp) region, respectively. We thus suggested that TM6 mediated its chromatin opening and chromatin accessibility of its flanking promoters with consequent enhancement of transcription.

Cell-to-cell movement of two interacting AT-hook factors in Arabidopsis root vascular tissue patterning

The xylem and phloem, major conducting and supporting tissues in vascular plants, are established by cell division and cell-type specification in the procambium/cambium. The organization of the xylem, phloem, and procambium/cambium is tightly controlled. However, the underlying regulatory mechanisms remain largely unknown. In this study, we report the discovery of two transcription factors, AT-HOOK MOTIF NUCLEAR LOCALIZED PROTEIN 3 (AHL3) and AHL4, which regulate vascular tissue boundaries in Arabidopsis thaliana roots. In either of the knockout mutants of AHL3 and AHL4, encoding closely related AT-hook transcription factors, a misspecification of tissue boundaries between the xylem and procambium occurred and ectopic xylem developed in the procambium domain. In plants, specific types of transcription factors can serve as direct intercellular signals by moving from one cell to another, playing crucial roles in tissue patterning. Adding to this paradigm, AHL4 moves actively from the procambium to xylem in the root meristem to regulate the tissue boundaries. When the intercellular movement of AHL4 was impaired, AHL4 could not complement the xylem phenotype in the ahl4. Furthermore, AHL4 revealed unique characteristics in that it interacts with AHL3 in vivo and that this interaction facilitates their intercellular trafficking. Taken together, this study uncovered a novel mechanism in vascular tissue patterning that requires the intercellular trafficking of two interacting transcription factors.

Comprehensive analysis of AHL homologous genes encoding AT-hook motif nuclear localized protein in rice

The AT-hook motif is a small DNA-binding protein motif that has been found in the high mobility group of non-histone chromosomal proteins. The Arabidopsis genome contains 29 genes encoding the AT-hook motif DNA-binding protein (AHL). Recent studies of Arabidopsis genes (AtAHLs) have revealed that they might play diverse functional roles during plant growth and development. In this report, we mined 20 AHL genes (OsAHLs) from the rice genome database using AtAHL genes as queries and characterized their molecular features. A phylogenetic tree revealed that OsAHL proteins can be classified into 2 evolutionary clades. Tissue expression pattern analysis revealed that all of the OsAHL genes might be functionally expressed genes with 3 distinct expression patterns. Nuclear localization analysis using transgenic Arabidopsis showed that several OsAHL proteins are exclusively localized in the nucleus, indicating that they may act as architectural transcription factors to regulate expression of their target genes during plant growth and development.

The Arabidopsis thaliana DNA-binding protein AHL19 mediates verticillium wilt resistance

Verticillium spp. are destructive soilborne fungal pathogens that cause vascular wilt diseases in a wide range of plant species. Verticillium wilts are particularly notorious, and genetic resistance in crop plants is the most favorable means of disease control. In a gain-of-function screen using an activation-tagged Arabidopsis mutant collection, we identified four mutants, A1 to A4, which displayed enhanced resistance toward the vascular wilt species Verticillium dahliae, V. albo-atrum and V. longisporum but not to Fusarium oxysporum f. sp. raphani. Further testing revealed that mutant A2 displayed enhanced Ralstonia solanacearum resistance, while mutants A1 and A3 were more susceptible toward Pseudomonas syringae pv. tomato. Identification of the activation tag insertion site in the A1 mutant revealed an insertion in close proximity to the gene encoding AHL19, which was constitutively expressed in the mutant. AHL19 knock-out alleles were found to display enhanced Verticillium susceptibility whereas overexpression of AHL19 resulted in enhanced Verticillium resistance, showing that AHL19 acts as a positive regulator of plant defense.

BARREN STALK FASTIGIATE1 is an AT-hook protein required for the formation of maize ears

Ears are the seed-bearing inflorescences of maize (Zea mays) plants and represent a crucial component of maize yield. The first step in the formation of ears is the initiation of axillary meristems in the axils of developing leaves. In the classic maize mutant barren stalk fastigiate1 (baf1), first discovered in the 1950s, ears either do not form or, if they do, are partially fused to the main stalk. We positionally cloned Baf1 and found that it encodes a transcriptional regulator containing an AT-hook DNA binding motif. Single coorthologs of Baf1 are found in syntenic regions of brachypodium (Brachypodium distachyon), rice (Oryza sativa), and sorghum (Sorghum bicolor), suggesting that the gene is likely present in all cereal species. Protein-protein interaction assays suggest that BAF1 is capable of forming homodimers and heterodimers with other members of the AT-hook family. Another transcriptional regulator required for ear initiation is the basic helix-loop-helix protein BARREN STALK1 (BA1). Genetic and expression analyses suggest that Baf1 is required to reach a threshold level of Ba1 expression for the initiation of maize ears. We propose that Baf1 functions in the demarcation of a boundary region essential for the specification of a stem cell niche.

Characterization and heterologous expression of a new matrix attachment region binding protein from the unicellular green alga Dunaliella salina

Although interactions between the nuclear matrix and special regions of chromosomal DNA called matrix attachment regions (MARs) are implicated in various nuclear functions, the understanding of the regulatory mechanism of MARs is still poor. A few MAR-binding proteins (MARBP) have been isolated from some plants and animals, but not from the unicellular algae. Here, we identify a novel MAR-binding protein, namely DMBP-1, from the halotolerant alga Dunaliella salina. The cDNA of DMBP-1 is 2322-bp long and contains a 1626 bp of an open reading frame encoding a polypeptide of 542 amino acids (59 kDa). The DMBP-1 expressed in Escherichia coli specifically binds A/T-rich MAR DNA. The DMBP-1 fused to green fluorescent protein appears only inside the nuclei of Chinese hamster ovarian cells transfected with the pEGFP-MBP, indicating that the protein is located in the nuclei. The findings mentioned above may contribute to better understanding of the nuclear matrix-MAR interactions.

A mini review of MAR-binding proteins

Genomic DNA encompasses several levels of organization, the nuclear matrix mediates the formation of DNA loop domains that are anchored to matrix attachment regions (MARs). By means of specific interaction with MAR binding proteins (MARBPs), MAR plays an important regulation role in enhancing transgene expression, decreasing expression variation among individuals of different transformants and serving as the replication origin. Through these years, some MARBPs have been identified and characterized from humans, plants, animals and algae so far and the list is growing. Most of MARBPs exist in a co-repressor/co-activator complex and involve in chromosome folding, regulation of gene expression, influencing cell development and inducing cell apoptosis. This review covers recent advances that have contributed to our understanding of MARBPs.

AGAMOUS controls GIANT KILLER, a multifunctional chromatin modifier in reproductive organ patterning and differentiation

The floral, homeotic protein AGAMOUS coordinates multiple downstream genes through direct transcriptional regulation of the nuclear matrix attachment region binding protein GIANT KILLER.

The Arabidopsis homeotic protein AGAMOUS (AG), a MADS domain transcription factor, specifies reproductive organ identity during flower development. Using a binding assay and expression analysis, we identified a direct target of AG, GIANT KILLER (GIK), which fine-tunes the expression of multiple genes downstream of AG. The GIK protein contains an AT-hook DNA binding motif that is widely found in chromosomal proteins and that binds to nuclear matrix attachment regions of DNA elements. Overexpression and loss of function of GIK cause wide-ranging defects in patterning and differentiation of reproductive organs. GIK directly regulates the expression of several key transcriptional regulators, including ETTIN/AUXIN RESPONSE FACTOR 3 (ETT/ARF3) that patterns the gynoecium, by binding to the matrix attachment regions of target promoters. Overexpression of GIK causes a swift and dynamic change in repressive histone modification in the ETT promoter. We propose that GIK acts as a molecular node downstream of the homeotic protein AG, regulating patterning and differentiation of reproductive organs through chromatin organization.

Multicellular development depends on proper expression of thousands of genes. Master regulators, such as homeotic proteins, code for transcription factors in both plants and animals and are thought to act by regulating other genes. Recent genomic studies in the plant Arabidopsis have shown that over 1,000 genes are regulated by homeotic proteins that directly control various target genes, including different classes of transcriptional regulators. It is not known, however, how expression of so many genes is coordinated by a single homeotic gene to form functional organs and tissues. Here we identified a transcriptional target of the plant homeotic protein AGAMOUS using bioinformatics analysis and showed that AGAMOUS directly controls GIANT KILLER, a multifunctional chromatin modifier. GIANT KILLER then binds to the upstream regions of multiple genes involved in patterning and differentiation in the AGAMOUS pathway and fine-tunes the expression of these genes. These data therefore provide a possible mechanism by which a homeotic gene coordinates multiple downstream targets in plants.

Determination of the in vivo distribution of nuclear matrix attachment regions using a polymerase chain reaction-based assay in Arabidopsis thaliana

Matrix attachment regions (MARs) are the regions on genomic DNA that are attached to the nuclear matrix in eukaryotes. Previous in vitro and in silico MAR analyses have shown that MARs distribute at average intervals of about 5 kb on the Arabidopsis thaliana genome. However, the in vivo evidence for the distribution of MARs in A. thaliana is lacking. Therefore, we have used a polymerase chain reaction (PCR)-based method to investigate the in vivo locations of MARs across an 80 kb region of A. thaliana genome. This assay indicated that the average interval of MARs within this region is 4.7 kb (range 1 to 11 kb), well consistent with the previous in vitro and in silico MAR studies. This result suggests that average size of the chromatin loop in A. thaliana is smaller when compared with the other eukaryotes, in which the sizes are known to vary in the range from 9 to 100 kb. However, we found that the number of genes per chromatin loop (1-3 genes) in A. thaliana is similar to those found in other eukaryotes. Furthermore, as in animals' MARs, DNase I hypersensitive sites were also found in the MARs end-region in A. thaliana. Our results suggest that basic organization of chromatin loop in A. thaliana is similar to other eukaryotes in the view that it contains a few genes, and that the average size of chromatin loop in eukaryotes is possibly determined by genome structure, such as gene density and average gene size.

Expression-based discovery of candidate ovule development regulators through transcriptional profiling of ovule mutants

BACKGROUND

Arabidopsis ovules comprise four morphologically distinct parts: the nucellus, which contains the embryo sac, two integuments that become the seed coat, and the funiculus that anchors the ovule within the carpel. Analysis of developmental mutants has shown that ovule morphogenesis relies on tightly regulated genetic interactions that can serve as a model for developmental regulation. Redundancy, pleiotropic effects and subtle phenotypes may preclude identification of mutants affecting some processes in screens for phenotypic changes. Expression-based gene discovery can be used access such obscured genes.

RESULTS

Affymetrix microarrays were used for expression-based gene discovery to identify sets of genes expressed in either or both integuments. The genes were identified by comparison of pistil mRNA from wild type with mRNA from two mutants; inner no outer (ino, which lacks the outer integument), and aintegumenta (ant, which lacks both integuments). Pools of pistils representing early and late stages of ovule development were evaluated and data from the three genotypes were used to designate genes that were predominantly expressed in the integuments using pair-wise and cluster analyses. Approximately two hundred genes were found to have a high probability of preferential expression in these structures, and the predictive nature of the expression classes was confirmed with reverse transcriptase polymerase chain reaction and in situ hybridization.

CONCLUSION

The results showed that it was possible to use a mutant, ant, with broad effects on plant phenotype to identify genes expressed specifically in ovules, when coupled with predictions from known gene expression patterns, or in combination with a more specific mutant, ino. Robust microarray averaging (RMA) analysis of array data provided the most reliable comparisons, especially for weakly expressed genes. The studies yielded an over-abundance of transcriptional regulators in the identified genes, and these form a set of candidate genes for evaluation of roles in ovule development using reverse genetics.

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

SOB3, which encodes a plant-specific AT-hook motif containing protein, was identified from an activation-tagging screen for suppressors of the long-hypocotyl phenotype of a weak phyB allele, phyB-4. sob3-D (suppressor of phyB-4#3 dominant) overexpressing seedlings have shorter hypocotyls, and as adults develop larger flowers and leaves, and are delayed in senescence compared with wild-type plants. At the nucleotide level, SOB3 is closely related to ESCAROLA (ESC), which was identified in an independent activation-tagging screen. ESC overexpression also suppresses the phyB-4 long-hypocotyl phenotype, and confers an adult morphology similar to sob3-D, suggesting similar functions. Analysis of transgenic plants harboring SOB3:SOB3-GUS or ESC:ESC-GUS translational fusions, driven by their endogenous promoter regions, showed GUS activity in the hypocotyl and vasculature tissue in light- and dark-grown seedlings. A loss-of-function SOB3 allele (sob3-4) was generated through an ethyl methanesulfonate intragenic suppressor screen of sob3-D phyB-4 plants, and this allele was combined with a predicted null allele, disrupting ESC (esc-8), to examine potential genetic interactions. The sob3-4 esc-8 double mutant had a long hypocotyl in multiple fluence rates of continuous white, far-red, red and blue light. sob3-4 esc-8 phyB-9 and sob3-4 esc-8 cry-103 triple mutants also had longer hypocotyls than photoreceptor single mutants. In contrast, the sob3-4 esc-8 phyA-211 triple mutant was the same length as phyA-211 single mutants. Taken together, these data indicate that SOB3 and ESC act redundantly to modulate hypocotyl growth inhibition in response to light.

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

Leaf senescence is the final stage of leaf development and is finely regulated via a complex genetic regulatory network incorporating both developmental and environmental factors. In an effort to identify negative regulators of leaf senescence, we screened activation-tagged Arabidopsis lines for mutants that exhibit a delayed leaf senescence phenotype. One of the mutants (ore7-1D) showed a highly significant delay of leaf senescence in the heterozygous state, leading to at least a twofold increase in leaf longevity. The activated gene (ORE7/ESC) encoded a protein with an AT-hook DNA-binding motif; such proteins are known to co-regulate transcription of genes through modification of chromatin architecture. We showed that ORE7/ESC, in addition to binding to a plant AT-rich DNA fragment, could also modify the chromatin architecture, as illustrated by an altered distribution of a histone-GFP fusion protein in the nucleus of the mutant. Globally altered gene expression, shown by microarray analysis, also indicated that activation of ORE7/ESC results in a younger condition in the mutant leaves. We propose that ectopically expressed ORE7/ESC is negatively regulating leaf senescence and suggest that the resulting chromatin alteration may have a role in controlling leaf longevity. Interestingly, activation of ORE7/ESC also led to a highly extended post-harvest storage life.

AGF1, an AT-hook protein, is necessary for the negative feedback of AtGA3ox1 encoding GA 3-oxidase

Negative feedback is a fundamental mechanism of organisms to maintain the internal environment within tolerable limits. Gibberellins (GAs) are essential regulators of many aspects of plant development, including seed germination, stem elongation, and flowering. GA biosynthesis is regulated by the feedback mechanism in plants. GA 3-oxidase (GA3ox) catalyzes the final step of the biosynthetic pathway to produce the physiologically active GAs. Here, we found that only the AtGA3ox1 among the AtGA3ox family of Arabidopsis (Arabidopsis thaliana) is under the regulation of GA-negative feedback. We have identified a cis-acting sequence responsible for the GA-negative feedback of AtGA3ox1 using transgenic plants. Furthermore, we have identified an AT-hook protein, AGF1 (for the AT-hook protein of GA feedback regulation), as a DNA-binding protein for the cis-acting sequence of GA-negative feedback. The mutation in the cis-acting sequence abolished both GA-negative feedback and AGF1 binding. In addition, constitutive expression of AGF1 affected GA-negative feedback in Arabidopsis. Our results suggest that AGF1 plays a role in the homeostasis of GAs through binding to the cis-acting sequence of the GA-negative feedback of AtGA3ox1.

Functional isolation of novel nuclear proteins showing a variety of subnuclear localizations

Nuclear proteins play key roles in the fundamental regulation of genome instability, the phases of organ development, and physiological responsiveness through gene expression. Although nuclear proteins have been shown to account for approximately one-fourth of total proteins in yeast, no efficient method to identify novel nuclear proteins has been applied to plants. In this study, a trial to isolate nuclear proteins in rice was attempted, and several novel nuclear proteins showing a variety of subnuclear localizations were identified. The nuclear transportation trap (NTT) system, which is a modified two-hybrid system, isolated many nuclear proteins from rice (Oryza sativa) NTT cDNA libraries. Nuclear localization of the isolated proteins was confirmed by transient introduction of green fluorescent protein fusion constructs for a subset of protein genes into onion (Allium cepa) cells. The majority of these proteins, including novel proteins and proteins initially categorized as cytoplasmic proteins, were revealed to be localized in the nucleus. Detailed characterization of unknown proteins revealed various subnuclear localizations, indicating their possible association with chromatin and the nuclear matrix with a foci or speckle-like distribution. Some also showed dual distribution in the nucleus and cytoplasm. In the novel protein fraction, a protein was further identified for its chromatin-associated localization in a specific organ of rice by immunostaining. Thus, a variety of novel nuclear architectural proteins with chromatin or matrix associating abilities, which are important in nuclear organization by influencing certain organ developments or cell responsiveness, can be isolated using the NTT method. Because nuclear proteins other than transcription regulators have rarely been characterized in plants, such as matrix proteins and development-specific chromatin proteins, their identification and subsequent characterization could provide important information for genome-wide regulatory mechanisms controlled by nuclear organization.

Identification of a novel plant MAR DNA binding protein localized on chromosomal surfaces

We identified a novel nucleoplasm localized protein in Arabidopsis called AT-hook motif nuclear localized protein 1 (AHL1), which was isolated by visual screening of transformants using random GFP::cDNA fusions. AHL1 contains an AT-hook motif and unknown conserved PPC (plants and prokaryotes conserved) domain that includes a hydrophobic region. Approximately 30 paralogues were identified in the Arabidopsis genome. Proteins with PPC-like domains are found in Bacteria, Archaea and the plant kingdom, but in Bacteria and Archaea the PPC containing proteins of do not have an AT-hook motif. Thus, the PPC domain is evolutionary conserved and has a new function such as AT-rich DNA binding. AHL1 was mainly localized in the nucleoplasm, but little in the nucleolus and heterochromatic region, and was concentrated in the boundary region between euchromatin and heterochromatin. Biochemically, AHL1 was also found in the nuclear matrix fraction. In the M phase, AHL1 was localized on the chromosomal surface. The AT-hook motif was essential for matrix attachment region (MAR) binding, and the hydrophobic region of the PPC was indispensable for nuclear localization. Our results suggest that AHL1 is a novel plant MAR binding protein, which is related to the positioning of chromatin fibers in the nucleus by the presence of an AT-hook motif and PPC domain. In addition, AHL1 is located on the surface of chromosomes during mitosis.

The plant nuclear envelope: new prospects for a poorly understood structure

The nuclear envelope (NE) is one of the least characterized cellular structures in plant cells. In particular, knowledge of its dynamic behaviour during the cell cycle and of its protein composition is limited. This review summarizes current views on the plant NE and highlights fundamental differences with other organisms. We also introduce the power of new technology available to investigate the NE and how this has already begun to revolutionize our knowledge of the biology of the plant NE. Contents Summary 227 I. Introduction 227 II. The membranes of the nuclear envelope 228 III. Functions of the nuclear envelope 231 IV. Proteins associated with the nuclear envelope 236 V. New tools for studying the nuclear envelope 239 VI. Conclusions and future prospects 241 Acknowledgements 242 References 242.

Molecular properties of a matrix attachment region-binding protein located in the nucleoli of tobacco cells

We cloned a cDNA for matrix-attachment region (MAR)-binding protein from Nicotiana tabacum cells to elucidate the structure and function of the nuclear matrix. The cDNA encodes a protein of 555 amino acids (61,050 Da) with an isoelectric point of 9.4. We named the protein NtMARBP61. The sequence is 45% identical to yeast Nop58p, which is involved in rRNA processing. The C-terminal part is unique and rich in lysine residues. The recombinant C-terminal part had the ability to bind double-stranded DNAs of 12 tobacco MARs. The intracellular localization was determined to be in the nucleolus by fluorescent microscopy using the antibody to the recombinant NtMARBP61. The mRNA level was high in the lag and early-log phases of cultured cells but low in the stationary phase. The protein was accumulated only in the middle- and late-log phases, suggesting that NtMARBP61 is essential for growing cells. The results suggest at least the structural and regulatory function of NtMARBP61 in the nucleolus as a MAR-binding protein in a growth-stage specific manner.

The J-domain proteins of Arabidopsis thaliana: an unexpectedly large and diverse family of chaperones

A total of 89 J-domain proteins were identified in the genome of the model flowering plant Arabidopsis thaliana. The deduced amino acid sequences of the J-domain proteins were analyzed for an assortment of structural features and motifs. Based on the results of sequence comparisons and structure and function predictions, 51 distinct families were identified. The families ranged in size from 1 to 6 members. Subcellular localizations of the A thaliana J-domain proteins were predicted; species were found in both the soluble and membrane compartments of all cellular organelles. Based on digital Northern analysis, the J-domain proteins could be separated into groups of low, medium, and moderate expression levels. This genomics-based analysis of the A thaliana J-domain proteins establishes a framework for detailed studies of biological function and specificity. It additionally provides a comprehensive basis for evolutionary comparisons.