Toshimasa Yamazaki

Identification of the DNA binding surface of H-NS protein from Escherichia coli by heteronuclear NMR spectroscopy.

The DNA binding domain of H‐NS protein was studied with various N‐terminal deletion mutant proteins and identified by gel retardation assay and heteronuclear 2D‐ and 3D‐NMR spectroscopies. It was shown from gel retardation assay that DNA binding affinity of the mutant proteins relative to that of native H‐NS falls in the range from 1/6 to 1/25 for H‐NS60–137, H‐NS70–137 and H‐NS80–137, whereas it was much weaker for H‐NS91–137. Thus, the DNA binding domain was defined to be the region from residue A80 to the C‐terminus. Sequential nuclear Overhauser effect (NOE) connectivities and those of medium ranges revealed that the region of residues Q60–R93 in mutant protein H‐NS60–137 forms a long stretch of disordered, flexible chain, and also showed that the structure of the C‐terminal region (residues A95–Q137) in mutant H‐NS60–137 was nearly identical to that of H‐NS91–137. 1H and 15N chemical shift perturbations induced by complex formation of H‐NS60–137 with an oligonucleotide duplex 14‐mer demonstrated that two loop regions, i.e. residues A80–K96 and T110–A117, play an essential role in DNA binding.

The Plant Zinc Finger Protein ZPT2–2 Has a Unique Mode of DNA Interaction

ZPT2–2 is a DNA-binding protein of petunia that contains two canonical TFIIIA-type zinc finger motifs separated by a long linker. We previously reported that ZPT2–2 bound to two separate AGT core sites, with each zinc finger making contact with each core site. Here we present our further characterization of ZPT2–2 by using selected and amplified binding sequence imprinting and surface plasmon resonance analyses; together, these assays revealed some unusual features of the interaction between ZPT2–2 and DNA. These experiments allowed us to conclude that 1) the optimal binding sequence for the N-terminal zinc finger is AGC(T), and that of the C-terminal one is CAGT; 2) multiple arrangements of the two core sites accommodate binding; and 3) the spacing between the two core sites affects the binding affinity. In light of these observations, we propose a new model for the DNA-ZPT2–2 interaction. Further, consistent with this model, a high affinity binding site for ZPT2–2 was found in the promoter region of theZPT2–2 gene. This site may serve as acis-element for the autoregulation of ZPT2–2gene expression.

NMR study of the structures of repeated sequences, GAGXGA (X = S, Y, V), in Bombyx mori liquid silk.

The silk fibroin stored in the silk gland of the Bombyx mori silkworm, called liquid silk, is spun out and converted into the silk fiber with extremely high strength and high toughness. Therefore it is important to determine the silk structure before spinning called Silk I at an atomic level to clarify the fiber formation mechanism. We proposed the repeated type II β-turn structure as Silk I in the solid state with the model peptide (AG)15 and several solid state NMR techniques previously. In this paper, the solution structure of native liquid silk was determined with solution NMR, especially for tandem repeated sequences with (GAGXGA)n (X = S, Y, V) and GAASGA motifs in the B. mori silk fibroin. The assignment of the (13)C, (15)N, and (1)H solution NMR spectra for the repetitive sequence motifs was achieved, and the chemical shifts were obtained. The program, TALOS-N, to predict the backbone torsion angles from the chemical shifts of proteins was applied to these motifs with (13)Cα, (13)Cβ, (13)CO, (1)Hα, (1)HN, and (15)N chemical shifts. The twenty-five best matches of torsion angles (ϕ, φ) were well populated and mainly fell into the regions for typical type II β-turn structures in the (ϕ, φ) map for the GAGXGA (X = S, Y, V) motifs. In contrast, (ϕ, φ) plots for motif GAASGA were scattered, indicating that the motif is in a disordered structure. Furthermore, inter-residue HN-Hα NOE cross peaks between i-th and (i+2)th residues in GAGXGA (X = S, Y, V) motifs were observed, supporting the repeated type II β-turn structure. Thus, we could show the presence of the repeated type II β-turn structure in liquid silk.

Solution structures and DNA binding properties of the N-terminal SAP domains of SUMO E3 ligases from Saccharomyces cerevisiae and Oryza sativa.

SUMO E3 ligase of the Siz/PIAS family that promotes sumoylation of target proteins contains SAP motif in its N‐terminal region. The SAP motif with a consensus sequence of 35 residues was first proposed to be as a new DNA binding motif found in diverse nuclear proteins involved in chromosomal organization. We have determined solution structures of the SAP domains of SUMO ligases Siz1 from yeast and rice by NMR spectroscopy, showing that the structure of the SAP domain (residues 2–105) of rice Siz1 is a four‐helix bundle with an up‐down‐extended loop‐down‐up topology, whereas the SAP domain (residues 1–111) of yeast Siz1 is comprised of five helices where the fifth helix α5 causes a significant change in the alignment of the four‐helix bundle characteristic to the SAP domains of the Siz/PIAS family. We have also demonstrated that both SAP domains have binding ability to an A/T‐rich DNA, but that binding affinity of yeast Siz1 SAP is at least by an order of magnitude higher than that of rice Siz1 SAP. Our NMR titration experiments clearly showed that yeast Siz1 SAP uses α2‐helix for DNA binding more effectively than rice Siz1 SAP, which would result from the dislocation of this helix due to the existence of the extra helix α5. In addition, based on the structures of the SAP domains determined here and registered in Protein Data Bank, general features of structures of the SAP domains are discussed in conjunction with equivocal nature of their DNA binding. Proteins 2009.

Deletion of the yhhP Gene Results in Filamentous Cell Morphology in Escherichia coli

The Escherichia coli yhhP gene was predicted to encode a small hypothetical protein of 81 amino acids, the cellular function of which is not known. To gain insight into the function of this uncharacterized YhhP protein, genetic and biochemical studies were done. We first tried to express and purify the YhhP protein to prepare an anti-YhhP antiserum. Western blotting showed that the hypothetical yhhP gene is indeed transcribed and translated as a minor cytoplasmic protein. YhhP-deficient (ΔyhhP) cells formed colonies poorly on a rich medium (e.g., Luria-Bertani medium) containing a relatively low concentration of NaCl, while they can grow normally either in LB containing 3% NaCl or in a synthetic medium (e.g., M9-glucose). During exponential growth in rich medium, an early step of cell division was inhibited in ΔyhhP cells, forming filaments. For the YhhP-deficient filamentous cells, the FtsZ-ring formation was analyzed with immunofluorescence microscopy. The FtsZ-ring formation did not occur normally in the ΔyhhP filaments, although the filamentous cells contained the FtsZ protein at a certain level comparable to that in the wild-type cells. The ftsZ gene was found to function as a multicopy suppressor of the ΔyhhP mutant. Another multicopy suppressor gene was identified as the dksA gene. Provided that either the ftsZ or dksA gene was introduced into the mutant cells with its multicopy state, the resulting transformants were capable of growing in rich medium, formed wild-type short rods. These results are discussed with regard to the presumed function of this ubiquitous protein.

Solution structure of an RNA fragment with the P7/P9.0 region and the 3'-terminal guanosine of the tetrahymena group I intron.

In the second step of the two consecutive transesterifications of the self-splicing reaction of the group I intron, the conserved guanosine at the 3 terminus of the intron (omegaG) binds to the guanosine-binding site (GBS) in the intron. In the present study, we designed a 22-nt model RNA (GBS/omegaG) including the GBS and omegaG from the Tetrahymena group I intron, and determined the solution structure by NMR methods. In this structure, omegaG is recognized by the formation of a base triple with the G264 x C311 base pair, and this recognition is stabilized by the stacking interaction between omegaG and C262. The bulged structure at A263 causes a large helical twist angle (40 +/- 80) between the G264 x C311 and C262 x G312 base pairs. We named this type of binding pocket with a bulge and a large twist, formed on the major groove, a Bulge-and-Twist (BT) pocket. With another twist angle between the C262 x G312 and G413 x C313 base pairs (45 +/- 100), the axis of GBS/omegaG is kinked at the GBS region. This kinked axis superimposes well on that of the corresponding region in the structure model built on a 5.0 A resolution electron density map (Golden et al., Science, 1998, 282:345-358). This compact structure of the GBS is also consistent with previous biochemical studies on group I introns. The BT pockets are also found in the arginine-binding site of the HIV-TAR RNA, and within the 16S rRNA and the 23S rRNA.

Hd18, Encoding Histone Acetylase Related to Arabidopsis FLOWERING LOCUS D, is Involved in the Control of Flowering Time in Rice

Flowering time is one of the most important agronomic traits in rice (Oryza sativa L.), because it defines harvest seasons and cultivation areas, and affects yields. We used a map-based strategy to clone Heading date 18 (Hd18). The difference in flowering time between the Japanese rice cultivars Koshihikari and Hayamasari was due to a single nucleotide polymorphism within the Hd18 gene, which encodes an amine oxidase domain-containing protein and is homologous to Arabidopsis FLOWERING LOCUS D (FLD). The Hayamasari Hd18 allele and knockdown of Hd18 gene expression delayed the flowering time of rice plants regardless of the day-length condition. Structural modeling of the Hd18 protein suggested that the non-synonymous substitution changed protein stability and function due to differences in interdomain hydrogen bond formation. Compared with those in Koshihikari, the expression levels of the flowering-time genes Early heading date 1 (Ehd1), Heading date 3a (Hd3a) and Rice flowering locus T1 (RFT1) were lower in a near-isogenic line with the Hayamasari Hd18 allele in a Koshihikari genetic background. We revealed that Hd18 acts as an accelerator in the rice flowering pathway under both short- and long-day conditions by elevating transcription levels of Ehd1 Gene expression analysis also suggested the involvement of MADS-box genes such as OsMADS50, OsMADS51 and OsMADS56 in the Hd18-associated regulation of Ehd1 These results suggest that, like FLD, its rice homolog accelerates flowering time but is involved in rice flowering pathways that differ from the autonomous pathways in Arabidopsis.

Comparison of Plant-Type Phosphoenolpyruvate Carboxylases from Rice: Identification of Two Plant-Specific Regulatory Regions of the Allosteric Enzyme

Phosphoenolpyruvate carboxylase (PEPC) is a key enzyme of primary metabolism in bacteria, algae and vascular plants, and it undergoes allosteric regulation by various metabolic effectors. Rice (Oryza sativa) has five plant-type PEPCs, four cytosolic and one chloroplastic. We investigated their kinetic properties using recombinant proteins and found that, like most plant-type PEPCs, rice cytosolic isozymes were activated by glucose 6-phosphate and by alkaline pH. In contrast, no such activation was observed for the chloroplastic isozyme, Osppc4. In addition, Osppc4 showed low affinity for the substrate phosphoenolpyruvate (PEP) and very low sensitivities to allosteric inhibitors aspartate and glutamate. By comparing the isozyme amino acid sequences and three-dimensional structures simulated on the basis of the reported crystal structures, we identified two regions where Osppc4 has unique features that can be expected to affect its kinetic properties. One is the N-terminal extension; replacement of the extension of Osppc2a (cytosolic) with that from Osppc4 reduced the aspartate and glutamate sensitivities to about one-tenth of the wild-type values but left the PEP affinity unaffected. The other is the N-terminal loop, in which a conserved lysine at the N-terminal end is replaced with a glutamate-alanine pair in Osppc4. Replacement of the lysine of Osppc2a with glutamate-alanine lowered the PEP affinity to a quarter of the wild-type level (down to the Osppc4 level), without affecting inhibitor sensitivity. Both the N-terminal extension and the N-terminal loop are specific to plant-type PEPCs, suggesting that plant-type isozymes acquired these regions so that their activity could be regulated properly at the sites where they function.

A Hox Gene, Antennapedia, Regulates Expression of Multiple Major Silk Protein Genes in the Silkworm Bombyx mori

Hox genes play a pivotal role in the determination of anteroposterior axis specificity during bilaterian animal development. They do so by acting as a master control and regulating the expression of genes important for development. Recently, however, we showed that Hox genes can also function in terminally differentiated tissue of the lepidopteran Bombyx mori. In this species, Antennapedia (Antp) regulates expression of sericin-1, a major silk protein gene, in the silk gland. Here, we investigated whether Antp can regulate expression of multiple genes in this tissue. By means of proteomic, RT-PCR, and in situ hybridization analyses, we demonstrate that misexpression of Antp in the posterior silk gland induced ectopic expression of major silk protein genes such as sericin-3, fhxh4, and fhxh5. These genes are normally expressed specifically in the middle silk gland as is Antp. Therefore, the evidence strongly suggests that Antp activates these silk protein genes in the middle silk gland. The putative sericin-1 activator complex (middle silk gland-intermolt-specific complex) can bind to the upstream regions of these genes, suggesting that Antp directly activates their expression. We also found that the pattern of gene expression was well conserved between B. mori and the wild species Bombyx mandarina, indicating that the gene regulation mechanism identified here is an evolutionarily conserved mechanism and not an artifact of the domestication of B. mori. We suggest that Hox genes have a role as a master control in terminally differentiated tissues, possibly acting as a primary regulator for a range of physiological processes.

Incoherent High-Resolution Z-Contrast Imaging of Silicon and Gallium Arsenide Using HAADF-STEM

The high-angle annular dark-field (HAADF) technique in a dedicated scanning transmission electron microscope (STEM) provides strong compositional sensitivity dependent on atomic number (Z-contrast image). Furthermore, a high spatial resolution image is comparable to that of conventional coherent imaging (HRTEM). However, it is difficult to obtain a clear atomic structure HAADF image using a hybrid TEM/STEM. In this work, HAADF images were obtained with a JEOL JEM-2010F (with a thermal-Schottky field-emission) gun in probe-forming mode at 200 kV. We performed experiments using Si and GaAs in the [110] orientation. The electron-optical conditions were optimized. As a result, the dumbbell structure was observed in an image of [110] Si. Intensity profiles for GaAs along [001] showed differences for the two atomic sites. The experimental images were analyzed and compared with the calculated atomic positions and intensities obtained from Bethes eigen-value method, which was modified to simulate HAADF-STEM based on Allen and Rossouws method for convergent-beam electron diffraction (CBED). The experimental results showed a good agreement with the simulation results.