Pathogen-induced binding of the soybean zinc finger homeodomain proteins GmZF-HD1 and GmZF-HD2 to two repeats of ATTA homeodomain binding site in the calmodulin isoform 4 (GmCaM4) promoter

Calmodulin (CaM) is involved in defense responses in plants. In soybean (Glycine max), transcription of calmodulin isoform 4 (GmCaM4) is rapidly induced within 30 min after pathogen stimulation, but regulation of the GmCaM4 gene in response to pathogen is poorly understood. Here, we used the yeast one-hybrid system to isolate two cDNA clones encoding proteins that bind to a 30-nt A/T-rich sequence in the GmCaM4 promoter, a region that contains two repeats of a conserved homeodomain binding site, ATTA. The two proteins, GmZF-HD1 and GmZF-HD2, belong to the zinc finger homeodomain (ZF-HD) transcription factor family. Domain deletion analysis showed that a homeodomain motif can bind to the 30-nt GmCaM4 promoter sequence, whereas the two zinc finger domains cannot. Critically, the formation of super-shifted complexes by an anti-GmZF-HD1 antibody incubated with nuclear extracts from pathogen-treated cells suggests that the interaction between GmZF-HD1 and two homeodomain binding site repeats is regulated by pathogen stimulation. Finally, a transient expression assay with Arabidopsis protoplasts confirmed that GmZF-HD1 can activate the expression of GmCaM4 by specifically interacting with the two repeats. These results suggest that the GmZF-HD1 and –2 proteins function as ZF-HD transcription factors to activate GmCaM4 gene expression in response to pathogen

Molecular Modeling Study for Interaction between Bacillus subtilis Obg and Nucleotides

The bacterial Obg proteins (Spo0B-associated GTP-binding protein) belong to the subfamily of P-loop GTPase proteins that contain two equally and highly conserved domains, a C-terminal GTP binding domain and an N-terminal glycine-rich domain which is referred as the “Obg fold” and now it is considered as one of the new targets for antibacterial drug. When the Obg protein is associated with GTP, it becomes activated, because conformation of Obg fold changes due to the structural changes of GTPase switch elements in GTP binding site. In order to investigate the effects and structural changes in GTP bound to Obg and GTPase switch elements for activation, four different molecular dynamics (MD) simulations were performed with/without the three different nucleotides (GTP, GDP, and GDP + Pi) using the Bacillus subtilis Obg (BsObg) structure. The protein structures generated from the four different systems were compared using their representative structures. The pattern of Cα-Cα distance plot and angle between the two Obg fold domains of simulated apo form and each system (GTP, GDP, and GDP+Pi) were significantly different in the GTP-bound system from the others. The switch 2 element was significantly changed in GTP-bound system. Also root-mean-square fluctuation (RMSF) analysis revealed that the flexibility of the switch 2 element region was much higher than the others. This was caused by the characteristic binding mode of the nucleotides. When GTP was bound to Obg, its γ-phosphate oxygen was found to interact with the key residue (D212) of the switch 2 element, on the contrary there was no such interaction found in other systems. Based on the results, we were able to predict the possible binding conformation of the activated form of Obg with L13, which is essential for the assembly with ribosome

Identification of Six Single-Strand Initiation (ssi) Signals for Priming of DNA Replication in Various Plasmids

Using a mutant M13 phage derivative lacking a great part of the complementary strand synthesis origin, we identified six single-strand initiation (ssi) signals for DNA replication in pACYC184, pLG214, pGKV21, and pDPT270 plasmids, and named them tex:\small\textstyle$ssiA_{YC}$, tex:\small\textstyle$ssiA_{LG}$, tex:\small\textstyle$ssiB_{LG}$, tex:\small\textstyle$ssiA_{KV}$, tex:\small\textstyle$ssiA_{PT}$, and tex:\small\textstyle$ssiB_{PT}$, respectively. Two of them were from pDPT270, one from downstream the on of pACYC184, two from pLG214, one from upstream the plus origin of pGKV21. Introduction of these ssi signals into the deleted tex:\small\textstyle$ori_c$ site of a mutant filamentous M13 phage (tex:\small\textstyle$M13{\Delta}lac182$) resulted in the restoration of growth activity of this phage. These ssi signals were classified into a number of groups on the basis of sequence similarity. tex:\small\textstyle$ssiA_{YC}$ and tex:\small\textstyle$ssiA_{LG}$ show extensive sequence homology to the n'-site (primosome assembly sites) of ColE1, whereas tex:\small\textstyle$ssiB_{PT}$ is homologous to the n'-site of tex:\small\textstyle${\Phi}X174$. tex:\small\textstyle$ssiA_{PT}$ belongs to G4-type ssi signals which require only dnaG primase and SSB protein for the priming of replication. In addition, possible biological roles of these ssi signals are discussed.clos

Rheological characteristics of marine sediments from the Ulleung Basin, East Sea to estimate the mobility of submarine landslides

Special issue Geological implications for submarine geohazards, Ulleung Basin, East Sea.-- 17 pages, 12 figures, 1 tableIn estimating the geohazards posed by submarine landslides, the rheological properties of marine sediments are of significant importance for their postfailure dynamics. We report an experimental study of the rheological behavior of marine sediments taken from the Ulleung Basin, East Sea and their influence on numerical simulations of debris flow runout. Marine sediments exhibit a typical yield stress behavior, such as that of low-activity clays. For the materials examined, different yield stresses are observed depending on the shearing methods. Steady-state and oscillatory shear tests were conducted for different volumetric concentrations of sediment. According to the test results, the Bingham yield stresses under controlled shear stress and shear rate range from approximately 100 Pa to 1500 Pa, but the yield stresses under oscillatory shear loads range from approximately 25 Pa to 3500 Pa for a given sediment concentration. In the latter cases, the value obtained in the elastic region is approximately doubled. Experiments under steady-state and oscillatory shear loads can be helpful in determining the yield points in the elastic and viscous regions and in explaining changes in the structure of the soil sample due to shear. We apply the range of measured yield strength values to numerical simulations of debris flow runout using a Herschel-Bulkley model and find that only the lowest values of yield strength, despite the low sediment concentrations, could account for the observed runout and thickness distribution. We infer that significant wetting must occur during debris flow motion to attain the observed runoutThis research was supported by the KIGAM research project (21-3412-1; 21-9851). Special thanks for the research project entitled “Study on submarine active faults and evaluation of the possibility of submarine earthquakes in the southern part of the East Sea, Korea”. Many thanks for CSIC research funding. This work acknowledges the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)Peer reviewe

BIOCHEMICAL CHARACTERISTICS OF A RICE G PROTEIN ?? SUBUNIT EXPRESSED IN Escherichia coli

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Arabidopsis C-Terminal Domain Phosphatase-Like 1 Functions in miRNA Accumulation and DNA Methylation

<div><p>Arabidopsis CTD-PHOSPHATASE-LIKE 1 (CPL1) is a protein phosphatase that can dephosphorylate RNA polymerase II C-terminal domain (CTD). Unlike typical CTD-phosphatases, CPL1 contains a double-stranded (ds) RNA-binding motif (dsRBM) and has been implicated for gene regulation mediated by dsRNA-dependent pathways. We investigated the role of CPL1 and its dsRBMs in various gene silencing pathways. Genetic interaction analyses revealed that <i>cpl1</i> was able to partially suppress transcriptional gene silencing and DNA hypermethylation phenotype of <i>ros1</i> suggesting CPL1 is involved in the RNA-directed DNA methylation pathway without reducing siRNA production. By contrast, <i>cpl1</i> reduced some miRNA levels at the level of processing. Indeed, CPL1 protein interacted with proteins important for miRNA biogenesis, suggesting that CPL1 regulates miRNA processing. These results suggest that CPL1 regulates DNA methylation via a miRNA-dependent pathway.</p></div

Isolation and Characterization of STGA1, a Member of the TGA1 Family of bZIP Transcription Factors Soybean

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Characteristics and origins of long-runout submarine mass-transport deposits in the Ulleung Basin revealed from drilling and 2-D grid seismic reflection data

Korean Geological Society Conference, 26 October 2016, Pyeongchang, South KoreaPeer Reviewe