2014 Vol. 5, No. 5

Characterization of poplar GrxS14 in different structural forms
Lei Wang, Yifei Li, Jean-Pierre Jacquot, Nicolas Rouhier, Bin Xia
2014, 5(5): 329-333. doi: 10.1007/s13238-014-0042-3
Distance measurement between two flexible sites in proteins in high viscosity medium at physiological temperature using continuous wave EPR
Lu Yu, Wei Wang, Shenglong Ling, Yao He, Liang Xiao, Kaiqi Wu, Longhua Zhang, Changlin Tian
2014, 5(5): 334-337. doi: 10.1007/s13238-014-0040-5
Efficient generation of mouse ESCs-like pig induced pluripotent stem cells
Qi Gu, Jie Hao, Tang Hai, Jianyu Wang, Yundan Jia, Qingran Kong, Juan Wang, Chunjing Feng, Binghua Xue, Bingteng Xie, Shichao Liu, Jinyu Li, Yilong He, Jialu Sun, Lei Liu, Liu Wang, Zhonghua Liu, Qi Zhou
2014, 5(5): 338-342. doi: 10.1007/s13238-014-0043-2
The crystal structure of fibroblast growth factor 18 (FGF18)
Alan Brown, Lucy E. Adam, Tom L. Blundell
2014, 5(5): 343-347. doi: 10.1007/s13238-014-0033-4
Competitive virus and host RNAs: the interplay of a hidden virus and host interaction
Changfei Li, Jun Hu, Junli Hao, Bao Zhao, Bo Wu, Lu Sun, Shanxin Peng, George F. Gao, Songdong Meng
2014, 5(5): 348-356. doi: 10.1007/s13238-014-0039-y
During virus infection, viral RNAs and mRNAs function as blueprints for viral protein synthesis and possibly as pathogen-associated molecular patterns (PAMPs) in innate immunity. Here, considering recent research progress in microRNAs (miRNAs) and competitive endogenous RNAs (ceRNAs), we speculate that viral RNAs act as sponges and can sequester endogenous miRNAs within infected cells, thus cross-regulating the stability and translational efficiency of host mRNAs with shared miRNA response elements. This cross-talk and these reciprocal interactions between viral RNAs and host mRNAs are termed "competitive viral and host RNAs" (cvhRNAs). We further provide recent experimental evidence for the existence of cvhRNAs networks in hepatitis B virus (HBV), as well as Herpesvirus saimiri (HVS), lytic murine cytomegalovirus (MCMV) and human cytomegalovirus (HCMV) infections. In addition, the cvhRNA hypothesis also predicts possible cross-regulation between host and other viruses, such as hepatitis C virus (HCV), HIV, influenza virus, human papillomaviruses (HPV). Since the interaction between miRNAs and viral RNAs also inevitably leads to repression of viral RNA function, we speculate that virus may evolve either to employ cvhRNA networks or to avoid miRNA targeting for optimal fitness within the host. CvhRNA networks may therefore play a fundamental role in the regulation of viral replication, infection establishment, and viral pathogenesis.
Research articles
Elimination of inter-domain interactions increases the cleavage fidelity of the restriction endonuclease DraIII
Wei Zhuo, Xuhui Lai, Liqing Zhang, Siu-Hong Chan, Fengjuan Li, Zhenyu Zhu, Maojun Yang, Dapeng Sun
2014, 5(5): 357-368. doi: 10.1007/s13238-014-0038-z
DraⅢ is a type ⅡP restriction endonucleases (REases) that recognizes and creates a double strand break within the gapped palindromic sequence CAC↑NNN↓GTG of double-stranded DNA (↑ indicates nicking on the bottom strand; ↓ indicates nicking on the top strand). However, wild type DraⅢ shows significant star activity. In this study, it was found that the prominent star site is CAT↑GTT↓GTG, consisting of a star 5' half (CAT) and a canonical 3' half (GTG). DraⅢ nicks the 3' canonical half site at a faster rate than the 5' star half site, in contrast to the similar rate with the canonical full site. The crystal structure of the DraⅢ protein was solved. It indicated, as supported by mutagenesis, that DraⅢ possesses a ββα-metal HNH active site. The structure revealed extensive intra-molecular interactions between the N-terminal domain and the C-terminal domain containing the HNH active site. Disruptions of these interactions through sitedirected mutagenesis drastically increased cleavage fidelity. The understanding of fidelity mechanisms will enable generation of high fidelity REases.
SARS coronavirus papain-like protease inhibits the type I interferon signaling pathway through interaction with the STING-TRAF3-TBK1 complex
Xiaojuan Chen, Xingxing Yang, Yang Zheng, Yudong Yang, Yaling Xing, Zhongbin Chen
2014, 5(5): 369-381. doi: 10.1007/s13238-014-0026-3
SARS coronavirus (SARS-CoV) develops an antagonistic mechanism by which to evade the antiviral activities of interferon (IFN). Previous studies suggested that SARS-CoV papain-like protease (PLpro) inhibits activation of the IRF3 pathway, which would normally elicit a robust IFN response, but the mechanism(s) used by SARS PLpro to inhibit activation of the IRF3 pathway is not fully known. In this study, we uncovered a novel mechanism that may explain how SARS PLpro efficiently inhibits activation of the IRF3 pathway. We found that expression of the membrane-anchored PLpro domain (PLpro-TM) from SARS-CoV inhibits STING/TBK1/IKKε-mediated activation of type I IFNs and disrupts the phosphorylation and dimerization of IRF3, which are activated by STING and TBK1. Meanwhile, we showed that PLpro-TM physically interacts with TRAF3, TBK1, IKKε, STING, and IRF3, the key components that assemble the STING-TRAF3-TBK1 complex for activation of IFN expression. However, the interaction between the components in STING-TRAF3-TBK1 complex is disrupted by PLpro-TM. Furthermore, SARS PLpro-TM reduces the levels of ubiquitinated forms of RIG-I, STING, TRAF3, TBK1, and IRF3 in the STING-TRAF3-TBK1 complex. These results collectively point to a new mechanism used by SARS-CoV through which PLpro negatively regulates IRF3 activation by interaction with STING-TRAF3-TBK1 complex, yielding a SARS-CoV countermeasure against host innate immunity.
Epigenetic reprogramming, gene expression and in vitro development of porcine SCNT embryos are significantly improved by a histone deacetylase inhibitor-m-carboxycinnamic acid bishydroxamide (CBHA)
Yuran Song, Tang Hai, Ying Wang, Runfa Guo, Wei Li, Liu Wang, Qi Zhou
2014, 5(5): 382-393. doi: 10.1007/s13238-014-0034-3
Insufficient epigenetic reprogramming of donor nuclei is believed to be one of the most important causes of low development efficiency of mammalian somatic cell nuclear transfer (SCNT). Previous studies have shown that both the in vitro and in vivo development of mouse SCNT embryos could be increased significantly by treatment with various histone deacetylase inhibitors (HDACi), including Trichostatin A, Scriptaid, and m-carboxycinnamic acid bishydroxamide (CBHA), in which only the effect of CBHA has not yet been tested in other species. In this paper we examine the effect of CBHA treatment on the development of porcine SCNT embryos. We have discovered the optimum dosage and time for CBHA treatment:incubating SCNT embryos with 2 μmol/L CBHA for 24 h after activation could increase the blastocyst rate from 12.7% to 26.5%. Immunofluorescence results showed that the level of acetylation at histone 3 lysine 9 (AcH3K9), acetylation at histone 3 lysine 18 (AcH3K18), and acetylation at histone 4 lysine 16 (AcH4K16) was raised after CBHA treatment. Meanwhile, CBHA treatment improved the expression of development relating genes such as pou5f1, cdx2, and the imprinted genes like igf2. Despite these promising in vitro results and histone reprogramming, the full term development was not significantly increased after treatment. In conclusion, CBHA improves the in vitro development of pig SCNT embryos, increases the global histone acetylation and corrects the expression of some developmentally important genes at early stages. As in mouse SCNT, we have shown that nuclear epigenetic reprogramming in pig early SCNTembryos can be modified by CBHA treatment.
Structural insights into the assembly of the 30S ribosomal subunit in vivo: functional role of S5 and location of the 17S rRNA precursor sequence
Zhixiu Yang, Qiang Guo, Simon Goto, Yuling Chen, Ningning Li, Kaige Yan, Yixiao Zhang, Akira Muto, Haiteng Deng, Hyouta Himeno, Jianlin Lei, Ning Gao
2014, 5(5): 394-407. doi: 10.1007/s13238-014-0044-1
The in vivo assembly of ribosomal subunits is a highly complex process, with a tight coordination between protein assembly and rRNA maturation events, such as folding and processing of rRNA precursors, as well as modifications of selected bases. In the cell, a large number of factors are required to ensure the efficiency and fidelity of subunit production. Here we characterize the immature 30S subunits accumulated in a factor-null Escherichia coli strain (ΔrsgAΔrbfA). The immature 30S subunits isolated with varying salt concentrations in the buffer system show interesting differences on both protein composition and structure. Specifically, intermediates derived under the two contrasting salt conditions (high and low) likely reflect two distinctive assembly stages, the relatively early and late stages of the 3' domain assembly, respectively. Detailed structural analysis demonstrates a mechanistic coupling between the maturation of the 5' end of the 17S rRNA and the assembly of the 30S head domain, and attributes a unique role of S5 in coordinating these two events. Furthermore, our structural results likely reveal the location of the unprocessed terminal sequences of the 17S rRNA, and suggest that the maturation events of the 17S rRNA could be employed as quality control mechanisms on subunit production and protein translation.