Automatic protein structure prediction system enabling rapid and accurate model building for enzyme screening

Protein structure prediction has great potential of understanding the function of proteins at the molecular level and designing novel protein functions. Here, we report rapid and accurate structure prediction system running in an automated manner. Since fold recognition of the target protein to be modeled is the starting point of the template-guided model building process, various approaches – such as profile analysis, threading, and SCOP fold classification – have been applied to generate the template library and to select the best template structure. After the best template was determined, fold consistency within the template candidates was considered using TM-score and SCOP database to select additional template structures among the template library. To generate a total of 100 decoy sets, MODELLER was used with the selected template structure. The predicted decoys were clustered with the RMSD deviation criterion of 3 Å to obtain centroids from each cluster. Finally, the selected centroids were subject to side-chain rearrangement using SCWRL module. Our fully automated structure prediction system was examined with sample test sets consisting of recently released 80 PDB chains. Judged by the TM-score (≥0.4), we concluded that 60 cases (75%) showed similar structures of statistical significance. This prediction system provides the users with simple and reliable models within hours of query submission, so that it is quite simply used for high throughput enzyme screening.     

Overexpression of CaDSR6 increases tolerance to drought and salt stresses in transgenic Arabidopsis plants

The partial CaDSR6 (Capsicum annuum Drought Stress Responsive 6) cDNA was previously identified as a drought-induced gene in hot pepper root tissues. However, the cellular role of CaDSR6 with regard to drought stress tolerance was unknown. In this report, full-length CaDSR6 cDNA was isolated. The deduced CaDSR6 protein was composed of 234 amino acids and contained an approximately 30 amino acid-long Asp-rich domain in its central region. This Asp-rich domain was highly conserved in all plant DSR6 homologs identified and shared a sequence identity with the N-terminal regions of yeast p23^fyp and human hTCTP, which contain Rab protein binding sites. Transgenic Arabidopsis plants overexpressing CaDSR6 (35S:CaDSR6-sGFP) were tolerant to high salinity, as identified by more vigorous root growth and higher levels of total chlorophyll than wild type plants. CaDSR6-overexpressors were also more tolerant to drought stress compared to wild type plants. The 35S:CaDSR6-sGFP leaves retained their water content and chlorophyll more efficiently than wild type leaves in response to dehydration stress. The expression of drought-induced marker genes, such as RD20, RD22, RD26, RD29A, RD29B, RAB18, KIN2, ABF3, and ABI5, was markedly increased in CaDSR6-overexpressing plants relative to wild type plants under both normal and drought conditions. These results suggest that overexpression of CaDSR6 is associated with increased levels of stress-induced genes, which, in turn, conferred a drought tolerant phenotype in transgenic Arabidopsis plants. Overall, our data suggest that CaDSR6 plays a positive role in the response to drought and salt stresses.     

Over-expression of Roquin aggravates T cell mediated hepatitis in transgenic mice using T cell specific promoter

Chronic hepatitis is a major cause of liver cancer, so earlier treatment of hepatitis might be reducing liver cancer incidence. Hepatitis can be induced in mice by treatment with Concanavalin A (Con A); the resulting liver injury causes significant CD4⁺ T cell activation and infiltration. In these T cells, Roquin, a ring-type E3 ubiquitin ligase, is activated. To investigate the role of Roquin, we examined Con A-induced liver injury and T cell infiltration in transgenic (Tg) mice overexpressing Roquin specifically in T cells. In Roquin Tg mice, Con A treatment caused greater increases in both the levels of liver injury enzymes and liver tissue apoptosis, as revealed by TUNEL and H&E staining, than wild type (WT) mice. Further, Roquin Tg mice respond to Con A treatment with greater increases in the T cell population, particularly Th17 cells, though Treg cell counts are lower. Roquin overexpression also enhances increases in pro-inflammatory cytokines, including IFN-γ, TNF-α and IL-6, upon liver injury. Furthermore, Roquin regulates the immune response and apoptosis in Con A induced hepatitis via STATs, Bax and Bcl2. These findings suggest that over-expression of Roquin exacerbates T-cell mediated hepatitis.     

Mechanisms governing the accumulation of estrogen receptor alpha in MCF-7 breast cancer cells treated with hydroxytamoxifen and related antiestrogens

This study aimed at a better understanding of estrogen receptor alpha (ER) up regulation induced by partial estrogen antagonists. Effect of treatment with hydroxytamoxifen (OH-Tam) on ER level in MCF-7 cells was investigated by an approach combining ER measurement (enzyme immunoassay) and morphological demonstration (immunofluorescence). Furthermore, the influence of drug exposure on the rates of ER synthesis and degradation was assessed by determining [35S]methionine incorporated into the receptor in different experimental conditions (measurement of synthesis or pulse-chase experiments). ER up regulation was already induced by a 1-h pulse treatment with OH-Tam, thus a continuous exposure was not required. This process appeared reversible (i.e. ER accumulation due to OH-Tam rapidly vanished upon subsequent exposure to 17beta-estradiol (E2) or the pure antiestrogen RU 58668). While OH-Tam did not affect the rate of [35S]methionine incorporation into ER, it clearly caused an impairment of ER degradation (pulse-chase experiments) indicating that up regulation results from a stabilization of the receptor associated with the maintenance of its synthesis. Various tamoxifen derivatives, as well as a few related partial antiestrogens, were compared on the basis of binding ability and propensity to induce ER up regulation. A close relationship was found between both properties. Structure-activity analysis revealed that the capacity of these compounds to induce ER up regulation is associated with characteristics of their aminoalkyle side-chain, similar to those required for antiestrogenicity.     

Candidate target genes for the Saccharomyces cerevisiae transcription factor, Yap2

In Saccharomyces cerevisiae, the Yap family of basic leucine zipper (bZip) proteins contains eight members. The Yap family proteins are implicated in a variety of stress responses; among these proteins, Yap1 acts as a major regulator of oxidative stress responses. However, the functional roles of the remaining Yap family members are poorly understood. To elucidate the function of Yap2, we mined candidate target genes of Yap2 by proteomic analysis. Among the identified genes, FRM2 was previously identified as a target gene of Yap2, which confirmed the validity of our screening method. YNL134C and YDL124W were also identified as candidate Yap2 target genes. These genes were upregulated in strains overexpressing Yap2 and possess Yap2 target sequences in their promoter regions. Furthermore, chromatin immunoprecipitation assays showed that YNL134C and YDL124W have Yap2 binding motif. These data will help to elucidate the functional role of Yap2.     

Scl1-dependent internalization of group A Streptococcus via direct interactions with the alpha2beta(1) integrin enhances pathogen survival and re-emergence

The molecular pathogenesis of infections caused by group A Streptococcus (GAS) is not fully understood. We recently reported that a recombinant protein derived from the collagen-like surface protein, Scl1, bound to the human collagen receptor, integrin α₂β₁. Here, we investigate whether the same Scl1 variant expressed by GAS cells interacts with the integrin α₂β₁ and affects the biological outcome of host–pathogen interactions. We demonstrate that GAS adherence and internalization involve direct interactions between surface expressed Scl1 and the α₂β₁ integrin, because (i) both adherence and internalization of the scl1- inactivated mutant were significantly decreased, and were restored by in-trans complementation of Scl1 expression, (ii) GAS internalization was reduced by pre-treatment of HEp-2 cells with anti-α₂ integrin-subunit antibody and type I collagen, (iii) recombinant α₂-I domain bound the wild-type GAS cells and (iv) internalization of wild-type cells was significantly increased in C2C12 cells expressing the α₂β₁ integrin as the only collagen-binding integrin. Next, we determined that internalized GAS re-emerges from epithelial cells into the extracellular environment. Taken together, our data describe a new molecular mechanism used by GAS involving the direct interaction between Scl1 and integrins, which increases the overall capability of the pathogen to survive and re-emerge.     

Effectiveness of rehabilitation treatments on a slowly revegetating hillslope in a recently burned coastal forest,Republic of Korea

In April 2000, a large forest fire burned through the largest mountain range in the eastern coastal area of the Republic of Korea. Although various measures are applied to restore vegetation cover and minimize surface soil erosion after forest fires, few studies have quantified their effectiveness in the Republic of Korea. The goal of this study was to evaluate the effectiveness of rehabilitation treatments on a slowly revegetating hillslope after burning. In 2002, we installed six treatments (ground seeding, hydroseeding, tree planting, sodding, vegetation sacks, log erosion barriers), examined the vegetation coverage and sediment yield in these treated sites, and compared these results to those in an untreated site. The results showed that our study hillslope, which features a high-severity fire regime, erodible silty sands, steep slopes, and frequent high-intensity rainfall, required at least 4 years to achieve surface soil stability through the recovery of native plant species. However, the rehabilitation treatments achieved surface soil stability more quickly. In particular, despite frequent high-intensity rainfall, the hydroseeding and vegetation sack treatments were highly effective in early recovery because they provided seed stability and a high growth rate. The log erosion barrier treatment was critically effective in reducing the sediment yield because it provided storage spaces.     

Jabuticaba‐Inspired Hybrid Carbon Filler/Polymer Electrode for Use in Highly Stretchable Aqueous Li‐Ion Batteries

Stretchable electronics are considered as next‐generation devices; however, to realize stretchable electronics, it is first necessary to develop a deformable energy device. Of the various components in energy devices, the fabrication of stretchable current collectors is crucial because they must be mechanically robust and have high electrical conductivity under deformation. In this study, the authors present a conductive polymer composite composed of Jabuticaba‐like hybrid carbon fillers containing carbon nanotubes and carbon black in a simple solution process. The hybrid carbon/polymer (HCP) composite is found to effectively retain its electrical conductivity, even when under high strain of ≈200%. To understand the behavior of conductive fillers in the polymer matrix when under mechanical strain, the authors investigate the microstructure of the composite using an in situ small‐angle X‐ray scattering analysis. The authors observe that the HCP produces efficient electrical pathways for filler interconnections upon stretching. The authors develop a stretchable aqueous rechargeable lithium‐ion battery (ARLB) that utilizes this HCP composite as a stretchable current collector. The ARLB exhibits excellent rate capability (≈90 mA h g^?1 at a rate of 20 C) and outstanding capacity retention of 93% after 500 cycles. Moreover, the stretchable ARLB is able to efficiently deliver power even when under 100% strain.