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Jinbiao Ma

Hehua Liu, Xiang Yu, Yiqing Chen, Jing Zhang, Baixing Wu, Lina Zheng, Phensinee Haruehanroengra, Rui Wang, Suhua Li, Jinzhong Lin, Jixi Li, Jia Sheng, Zhen Huang, Jinbiao Ma, Jianhua Gan
In addition to storage of genetic information, DNA can also catalyze various reactions. RNA-cleaving DNAzymes are the catalytic DNAs discovered the earliest, and they can cleave RNAs in a sequence-specific manner. Owing to their great potential in medical therapeutics, virus control, and gene silencing for disease treatments, RNA-cleaving DNAzymes have been extensively studied; however, the mechanistic understandings of their substrate recognition and catalysis remain elusive. Here, we report three catalytic form 8-17 DNAzyme crystal structures...
December 8, 2017: Nature Communications
Luqian Zheng, Elisabeth Mairhofer, Marianna Teplova, Ye Zhang, Jinbiao Ma, Dinshaw J Patel, Ronald Micura, Aiming Ren
Here we report on the crystal structure and cleavage assays of a four-way junctional twister-sister self-cleaving ribozyme. Notably, 11 conserved spatially separated loop nucleotides are brought into close proximity at the ribozyme core through long-range interactions mediated by hydrated Mg(2+) cations. The C62-A63 step at the cleavage site adopts a splayed-apart orientation, with flexible C62 directed outwards, whereas A63 is directed inwards and anchored by stacking and hydrogen-bonding interactions. Structure-guided studies of key base, sugar, and phosphate mutations in the twister-sister ribozyme, suggest contributions to the cleavage chemistry from interactions between a guanine at the active site and the non-bridging oxygen of the scissile phosphate, a feature found previously also for the related twister ribozyme...
October 30, 2017: Nature Communications
Mulugeta Seyoum Ademe, Shoupu He, Zhaoe Pan, Junling Sun, Qinglian Wang, Hongde Qin, Jinhai Liu, Hui Liu, Jun Yang, Dongyong Xu, Jinlong Yang, Zhiying Ma, Jinbiao Zhang, Zhikun Li, Zhongmin Cai, Xuelin Zhang, Xin Zhang, Aifen Huang, Xianda Yi, Guanyin Zhou, Lin Li, Haiyong Zhu, Baoyin Pang, Liru Wang, Yinhua Jia, Xiongming Du
Fiber yield and quality are the most important traits for Upland cotton (Gossypium hirsutum L.). Identifying high yield and good fiber quality genes are the prime concern of researchers in cotton breeding. Association mapping offers an alternative and powerful method for detecting those complex agronomic traits. In this study, 198 simple sequence repeats (SSRs) were used to screen markers associated with fiber yield and quality traits with 302 elite Upland cotton accessions that were evaluated in 12 locations representing the Yellow River and Yangtze River cotton growing regions of China...
December 2017: Molecular Genetics and Genomics: MGG
Baixing Wu, Jinhao Xu, Shichen Su, Hehua Liu, Jianhua Gan, Jinbiao Ma
Meiosis is one of the most dramatic differentiation programs accompanied by a striking change in gene expression profiles in fission yeast Schizosaccharomyces pombe. Whereas a number of meiosis-specific transcripts are expressed untimely in mitotic cells, and the entry of meiosis will be blocked as the accumulation of meiosis-specific mRNAs in the mitotic cells. A YTH domain containing protein Mmi1 was identified as a pivotal effector in a post-transcriptional event termed selective elimination of meiosis-specific mRNAs...
September 16, 2017: Biochemical and Biophysical Research Communications
Hehua Liu, Fusheng Shen, Phensinee Haruehanroengra, Qingqing Yao, Yunshan Cheng, Yiqing Chen, Chun Yang, Jing Zhang, Baixing Wu, Qiang Luo, Ruixue Cui, Jixi Li, Jinbiao Ma, Jia Sheng, Jianhua Gan
Metal-mediated base pairs have been extensively utilized in many research fields, including genetic-code extension, novel therapeutics development, and nanodevice design. Compared to other cations, Ag(I) is more flexible in pairing with natural base pairs. Herein, we present a DNA structure containing two C-Ag(I) -C pairs and the first reported G-Ag(I) -G pair in a short 8mer DNA strand. This structure not only provides detailed insight into these Ag(I) -mediated base-pairing patterns in DNA, but also represents the first nonhelical DNA structure driven by heavy-metal ions, thus further contributing to the structural diversity of DNA...
August 1, 2017: Angewandte Chemie
Baixing Wu, Li Li, Ying Huang, Jinbiao Ma, Jinrong Min
N(6)-methyladenosine (m(6)A) as the most prevalent internal modification in mammalian RNAs has been increasingly realized as an important reversible mark that participates in various biological processes and cancer pathogenesis. In this review, we discuss the catalytic mechanisms of MT-A70 domain family proteins for mediating adenosine N(6)-methylation, the removal of this RNA mark by members of ALKB homologue domain family proteins, and the recognition of these m(6)A-modified RNAs by YTH domain family proteins...
June 16, 2017: Current Opinion in Structural Biology
Chung-Nga Ko, Chao Yang, Sheng Lin, Shengnan Li, Zhenzhen Dong, Jinbiao Liu, Simon Ming-Yuen Lee, Chung-Hang Leung, Dik-Lung Ma
In this work, we report a novel iridium(III)-based luminescent switch on-off-on probe, for the in vitro and in vivo detection of sulfide ion. The mechanism of this platform is based on the effective charge transfer quenching of the iridium(III) complex 1 by Fe(3+), followed by the restoration of luminescence upon the addition of Na2S. The probe, hereinafter referred to as 1-Fe(3+), exhibited a linear range of detection for Na2S from 0.01 to 1.5mM, with a detection limit of 2.9μM at signal-to-noise ratio (S/N) of 3...
March 23, 2017: Biosensors & Bioelectronics
Xiang Yu, Xuhang Li, Lina Zheng, Jinbiao Ma, Jianhua Gan
RNaseIII proteins are dsRNA-specific endonucleases involved in many important biological processes, such as small RNA processing and maturation in eukaryotes. Various small RNAs have been identified in a protozoan parasite Entamoeba histolytica. EhRNaseIII is the only RNaseIII endonuclease domain (RIIID)-containing protein in E. histolytica. Here, we present three crystal structures that reveal several unique structural features of EhRNaseIII, especially the interactions between the two helixes (α1 and α7) flanking the RIIID core domain...
March 20, 2017: Scientific Reports
Yiqing Chen, Jing Zhang, Hehua Liu, Yanqing Gao, Xuhang Li, Lina Zheng, Ruixue Cui, Qingqing Yao, Liang Rong, Jixi Li, Zhen Huang, Jinbiao Ma, Jianhua Gan
African swine fever virus (ASFV) can cause highly lethal disease in pigs and is becoming a global threat. ASFV DNA Polymerase X (AsfvPolX) is the most distinctive DNA polymerase identified to date; it lacks two DNA-binding domains (the thumb domain and 8-KD domain) conserved in the homologous proteins. AsfvPolX catalyzes the gap-filling reaction during the DNA repair process of the ASFV virus genome; it is highly error prone and plays an important role during the strategic mutagenesis of the viral genome. The structural basis underlying the natural substrate binding and the most frequent dG:dGTP misincorporation of AsfvPolX remain poorly understood...
February 2017: PLoS Biology
Yu Yu, Lijuan Ji, Brandon H Le, Jixian Zhai, Jiayi Chen, Elizabeth Luscher, Lei Gao, Chunyan Liu, Xiaofeng Cao, Beixin Mo, Jinbiao Ma, Blake C Meyers, Xuemei Chen
The degradation of small RNAs in plants and animals is associated with small RNA 3' truncation and 3' uridylation and thus relies on exonucleases and nucleotidyl transferases. ARGONAUTE (AGO) proteins associate with small RNAs in vivo and are essential for not only the activities but also the stability of small RNAs. AGO1 is the microRNA (miRNA) effector in Arabidopsis, and its closest homolog, AGO10, maintains stem cell homeostasis in meristems by sequestration of miR165/6, a conserved miRNA acting through AGO1...
February 2017: PLoS Biology
Yan Zhu, Liang Rong, Qiang Luo, Baihui Wang, Nana Zhou, Yue Yang, Chi Zhang, Haiyang Feng, Lina Zheng, Wen-Hui Shen, Jinbiao Ma, Aiwu Dong
NUCLEOSOME ASSEMBLY PROTEIN1 (NAP1) defines an evolutionarily conserved family of histone chaperones and loss of function of the Arabidopsis thaliana NAP1 family genes NAP1-RELATED PROTEIN1 (NRP1) and NRP2 causes abnormal root hair formation. Yet, the underlying molecular mechanisms remain unclear. Here, we show that NRP1 interacts with the transcription factor WEREWOLF (WER) in vitro and in vivo and enriches at the GLABRA2 (GL2) promoter in a WER-dependent manner. Crystallographic analysis indicates that NRP1 forms a dimer via its N-terminal α-helix...
February 2017: Plant Cell
Hehua Liu, Chen Cai, Phensinee Haruehanroengra, Qingqing Yao, Yiqing Chen, Chun Yang, Qiang Luo, Baixing Wu, Jixi Li, Jinbiao Ma, Jia Sheng, Jianhua Gan
Owing to their great potentials in genetic code extension and the development of nucleic acid-based functional nanodevices, DNA duplexes containing HgII-mediated base pairs have been extensively studied during the past 60 years. However, structural basis underlying these base pairs remains poorly understood. Herein, we present five high-resolution crystal structures including one first-time reported C-HgII-T containing duplex, three T-HgII-T containing duplexes and one native duplex containing T-T pair without HgII...
March 17, 2017: Nucleic Acids Research
Zhifeng Mao, Jinbiao Liu, Tian-Shu Kang, Wanhe Wang, Quan-Bin Han, Chun-Ming Wang, Chung-Hang Leung, Dik-Lung Ma
In this study, we report the use of a cyclometalated luminescent iridium(III) complex for the visualization of thiols. The detection of glutathione (GSH) by complex 1 is achieved through the reduction of its phendione N^N donor, which influences the metal-to-ligand charge-transfer (MLCT) of the complex. Complex 1 produced a maximum threefold luminescence enhancement at 587 nm in response to GSH. The linear detection range of 1 for GSH is between 0.2 and 2 M equivalents of GSH, with a detection limit of 1.67 μM...
2016: Science and Technology of Advanced Materials
Jinbiao Liu, Qianhao Xiao, Runhong Zhou, Yong Wang, Qiaoyang Xian, Tongcui Ma, Ke Zhuang, Li Zhou, Deyin Guo, Xu Wang, Wen-Zhe Ho, Jieliang Li
Altered T-cell homeostasis, such as expansion of CD8(+) T cells to the secondary lymphatic compartments, has been suggested as a mechanism of HIV/simian immunodeficiency virus (SIV)-pathogenesis. However, the role of immune activation of CD8(+) T cells in the CD4/CD8 turnover and viral replication in these tissues is not completely understood. In this study, we compared the expression of immune activation markers (CD69 and HLA-DR) on CD8(+) T cells in the peripheral blood and lymph nodes (LNs) of SIV-infected/uninfected Chinese rhesus macaques...
2016: Frontiers in Immunology
Jing Zhang, Hehua Liu, Qingqing Yao, Xiang Yu, Yiqing Chen, Ruixue Cui, Baixing Wu, Lina Zheng, Junjun Zuo, Zhen Huang, Jinbiao Ma, Jianhua Gan
Translin and translin-associated factor-x are highly conserved in eukaroytes; they can form heteromeric complexes (known as C3POs) and participate in various nucleic acid metabolism pathways. In humans and Drosophila, C3POs cleave the fragmented siRNA passenger strands and facilitate the activation of RNA-induced silencing complex, the effector complex of RNA interference (RNAi). Here, we report three crystal structures of Nanoarchaeum equitans (Ne) C3PO. The apo-NeC3PO structure adopts an open form and unravels a potential substrates entryway for the first time...
November 2, 2016: Nucleic Acids Research
Hao Du, Ya Zhao, Jinqiu He, Yao Zhang, Hairui Xi, Mofang Liu, Jinbiao Ma, Ligang Wu
Methylation at the N6 position of adenosine (m(6)A) is the most abundant RNA modification within protein-coding and long noncoding RNAs in eukaryotes and is a reversible process with important biological functions. YT521-B homology domain family (YTHDF) proteins are the readers of m(6)A, the binding of which results in the alteration of the translation efficiency and stability of m(6)A-containing RNAs. However, the mechanism by which YTHDF proteins cause the degradation of m(6)A-containing RNAs is poorly understood...
August 25, 2016: Nature Communications
Xiangmin Miao, Wanhe Wang, Tianshu Kang, Jinbiao Liu, Kwok-Keung Shiu, Chung-Hang Leung, Dik-Lung Ma
The ultrasensitive electrochemical detection of miRNA-21 was realized by using a novel redox and catalytic "all-in-one" mechanism with an iridium(III) complex as a catalyst. To construct such a sensor, a capture probe (CP) was firstly immobilized onto the gold electrode surface. In the presence of miRNA-21, a sandwiched DNA complex could form between CP and a methylene blue (MB) labeled G-rich detection probe modified onto a gold nanoparticle (AuNP) surface (DP-AuNPs). Upon addition of K(+), the structure of DP changed to a G-quadruplex...
December 15, 2016: Biosensors & Bioelectronics
Jingru Zhao, Xiang Yu, Miao Zhu, Huaping Kang, Jinbiao Ma, Min Wu, Jianhua Gan, Xin Deng, Haihua Liang
Although quorum-sensing (QS) systems are important regulators of virulence gene expression in the opportunistic human pathogen Pseudomonas aeruginosa, their detailed regulatory mechanisms have not been fully characterized. Here, we show that deletion of PA2588 resulted in increased production of pyocyanin and biofilm, as well as enhanced pathogenicity in a mouse model. To gain insights into the function of PA2588, we performed a ChIP-seq assay and identified 28 targets of PA2588, including the intergenic region between PA2588 and pqsH, which encodes the key synthase of Pseudomonas quinolone signal (PQS)...
April 2016: PLoS Biology
Xia Cui, Falong Lu, Qi Qiu, Bing Zhou, Lianfeng Gu, Shuaibin Zhang, Yanyuan Kang, Xiekui Cui, Xuan Ma, Qingqing Yao, Jinbiao Ma, Xiaoyu Zhang, Xiaofeng Cao
RELATIVE OF EARLY FLOWERING 6 (REF6, also known as JMJ12) counteracts Polycomb-mediated gene silencing by removing methyl groups from trimethylated histone H3 lysine 27 (H3K27me3) in hundreds of genes in Arabidopsis thaliana. Here we show that REF6 function and genome-wide targeting require its four Cys2His2 zinc fingers, which directly recognize a CTCTGYTY motif. Motifs bound by REF6 tend to cluster and reside in loci with active chromatin states. Furthermore, REF6 targets CUP-SHAPED COTYLEDON 1 (CUC1), which harbors CTCTGYTY motifs, to modulate H3K27me3 levels and activate CUC1 expression...
June 2016: Nature Genetics
Zhifeng Mao, Modi Wang, Jinbiao Liu, Li-Juan Liu, Simon Ming-Yuen Lee, Chung-Hang Leung, Dik-Lung Ma
A long lifetime iridium(III) complex chemosensor 1 for cysteine detection has been synthesized. The luminescence signal of 1 could be recognized in strongly fluorescent media through time-resolved emission spectroscopy (TRES). The detection of cysteine in a living zebrafish was demonstrated.
March 25, 2016: Chemical Communications: Chem Comm
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