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Polyamines Disrupt the KaiABC Oscillator by Inducing Protein Denaturation

Jinkui Li, Lingya Zhang, Junwen Xiong, Xiyao Cheng, Yongqi Huang, Zhengding Su, Ming Yi, Sen Liu
2019 Molecules  
Polyamines are positively charged small molecules ubiquitously existing in all living organisms, and they are considered as one kind of the most ancient cellular components. The most common polyamines are spermidine, spermine, and their precursor putrescine generated from ornithine. Polyamines play critical roles in cells by stabilizing chromatin structure, regulating DNA replication, modulating gene expression, etc., and they also affect the structure and function of proteins. A few studies
more » ... e investigated the impact of polyamines on protein structure and function previously, but no reports have focused on a protein-based biological module with a dedicated function. In this report, we investigated the impact of polyamines (putrescine, spermidine, and spermine) on the cyanobacterial KaiABC circadian oscillator. Using an established in vitro reconstitution system, we noticed that polyamines could disrupt the robustness of the KaiABC oscillator by inducing the denaturation of the Kai proteins (KaiA, KaiB, and KaiC). Further experiments showed that the denaturation was likely due to the induced change of the thermal stability of the clock proteins. Our study revealed an intriguing role of polyamines as a component in complex cellular environments and would be of great importance for elucidating the biological function of polyamines in future.
doi:10.3390/molecules24183351 pmid:31540079 pmcid:PMC6767301 fatcat:n2f3gmwxwfdslfmsiozz3gpps4

CGAP: a new comprehensive platform for the comparative analysis of chloroplast genomes

Jinkui Cheng, Xu Zeng, Guomin Ren, Zhihua Liu
2013 BMC Bioinformatics  
Chloroplast is an essential organelle in plants which contains independent genome. Chloroplast genomes have been widely used for plant phylogenetic inference recently. The number of complete chloroplast genomes increases rapidly with the development of various genome sequencing projects. However, no comprehensive platform or tool has been developed for the comparative and phylogenetic analysis of chloroplast genomes. Thus, we constructed a comprehensive platform for the comparative and
more » ... tic analysis of complete chloroplast genomes which was named as chloroplast genome analysis platform (CGAP). Results: CGAP is an interactive web-based platform which was designed for the comparative analysis of complete chloroplast genomes. CGAP integrated genome collection, visualization, content comparison, phylogeny analysis and annotation functions together. CGAP implemented four web servers including creating complete and regional genome maps of high quality, comparing genome features, constructing phylogenetic trees using complete genome sequences, and annotating draft chloroplast genomes submitted by users. Conclusions: Both CGAP and source code are available at http://www.herbbol.org:8000/chloroplast. CGAP will facilitate the collection, visualization, comparison and annotation of complete chloroplast genomes. Users can customize the comparative and phylogenetic analysis using their own unpublished chloroplast genomes.
doi:10.1186/1471-2105-14-95 pmid:23496817 pmcid:PMC3636126 fatcat:jjjnpq4h35dnlirczdh4qc25oi

METHIONINE ADENOSYLTRANSFERASE4 Mediates DNA and Histone Methylation

Jingjing Meng, Lishuan Wang, Jingyi Wang, Xiaowen Zhao, Jinkui Cheng, Wenxiang Yu, Dan Jin, Qing Li, Zhizhong Gong
2018 Plant Physiology  
DNA and histone methylation coregulate heterochromatin formation and gene silencing in animals and plants. To identify factors involved in maintaining gene silencing, we conducted a forward genetic screen for mutants that release the silenced transgene Pro35S::NEOMYCIN PHOSPHOTRANSFERASE II in the transgenic Arabidopsis (Arabidopsis thaliana) line L119. We identified MAT4/SAMS3/MTO3/AT3G17390, which encodes methionine (Met) adenosyltransferase 4 (MAT4)/S-adenosyl-Met synthetase 3 that catalyzes
more » ... the synthesis of S-adenosyl-Met (SAM) in the one-carbon metabolism cycle. mat4 mostly decreases CHG and CHH DNA methylation and histone H3K9me2 and reactivates certain silenced transposons. The exogenous addition of SAM partially rescues the epigenetic defects of mat4. SAM content and DNA methylation were reduced more in mat4 than in three other mat mutants. MAT4 knockout mutations generated by CRISPR/Cas9 were lethal, indicating that MAT4 is an essential gene in Arabidopsis. MAT1, 2, and 4 proteins exhibited nearly equal activity in an in vitro assay, whereas MAT3 exhibited higher activity. The native MAT4 promoter driving MAT1, 2, and 3 cDNA complemented the mat4 mutant. However, most mat4 transgenic lines carrying native MAT1, 2, and 3 promoters driving MAT4 cDNA did not complement the mat4 mutant because of their lower expression in seedlings. Genetic analyses indicated that the mat1mat4 double mutant is dwarfed and the mat2mat4 double mutant was nonviable, while mat1mat2 showed normal growth and fertility. These results indicate that MAT4 plays a predominant role in SAM production, plant growth, and development. Our findings provide direct evidence of the cooperative actions between metabolism and epigenetic regulation.
doi:10.1104/pp.18.00183 pmid:29572390 pmcid:PMC6001336 fatcat:hdi6okjczjfxbpsobeuvep7vfy

Hairiness Gene Regulated Multicellular, Non-Glandular Trichome Formation in Pepper Species

Jinqiu Liu, Haoran Wang, Mengmeng Liu, Jinkui Liu, Sujun Liu, Qing Cheng, Huolin Shen
2021 Frontiers in Plant Science  
Trichomes are unicellular or multicellular epidermal structures that play a defensive role against environmental stresses. Although unicellular trichomes have been extensively studied as a mechanistic model, the genes involved in multicellular trichome formation are not well understood. In this study, we first classified the trichome morphology structures in Capsicum species using 280 diverse peppers. We cloned a key gene (Hairiness) on chromosome 10, which mainly controlled the formation of
more » ... ticellular non-glandular trichomes (types II, III, and V). Hairiness encodes a Cys2-His2 zinc-finger protein, and virus-induced gene silencing of the gene resulted in a hairless phenotype. Differential expression of Hairiness between the hairiness and hairless lines was due to variations in promoter sequences. Transgenic experiments verified the hypothesis that the promoter of Hairiness in the hairless line had extremely low activity causing a hairless phenotype. Hair controlled the formation of type I glandular trichomes in tomatoes, which was due to nucleotide differences. Taken together, our findings suggest that the regulation of multicellular trichome formation might have similar pathways, but the gene could perform slightly different functions in crops.
doi:10.3389/fpls.2021.784755 pmid:34975970 pmcid:PMC8716684 fatcat:24subqzis5hfzfo7xbkgpzn7bi

Chl1 coordinates with H3K9 methyltransferase Clr4 to reduce the accumulation of RNA-DNA hybrids and maintain genome stability

Deyun He, Yazhen Guo, Jinkui Cheng, Yu Wang
2022 iScience  
This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could
more » ... the content, and all legal disclaimers that apply to the journal pertain.
doi:10.1016/j.isci.2022.104313 fatcat:ststyc6g4ngyretoww25h4jvfu

Pyrazine-bridged Dy2 single-molecule magnet with a large anisotropic barrier

Yue Ma, Gong-Feng Xu, Xi Yang, Li-Cun Li, Jinkui Tang, Shi-Ping Yan, Peng Cheng, Dai-Zheng Liao
2010 Chemical Communications  
Synthesis of Dy 2 (hfac) 6 (H 2 O) 4 pz·2pz (1): Dy(hfac) 3 ·2H 2 O (0.1 mmol) was dissolved in boiling dry n-heptane (20 mL). After stirring for 2 hours, pyrazine (0.1 mmol) in CH 2 Cl 2 (5 mL) was added and refluxed for 30 minutes. Then the solution was cooled to room temperature, filtrated and the filtrate was stored in a refrigerator at 4ºC for a week to give pale-yellow crystals, which are suitable for X-ray analysis. Yield: 0.0095g, 5.1%. Elemental Analysis for C 42 H 26
doi:10.1039/c0cc01423k pmid:20927463 fatcat:ke5jhpbjvvfipknilfujy65pti

LINC00858 promotes retinoblastoma cell proliferation, migration and invasion by inhibiting miR‑3182

Qi Wang, Yanni Zhu, Guojin Zuo, Xiaoming Chen, Jinkui Cheng, Shu Zhang
2019 Experimental and Therapeutic Medicine  
The aim of the present study was to determine the role of long intergenic non-protein coding RNA 858 (LINC00858) in retinoblastoma (RB) and investigate the underlying molecular mechanisms. RB tissues and paracancerous tissues of 27 RB cases were obtained. RB cell lines (SO-RB50, Y79, HXO-RB44 and WERI-Rb1) and a normal retinal epithelial cell line (ARPE-19) were cultured for in vitro experiments. Batches of SO-RB50 and Y79 cells were assigned to groups transfected with small interfering RNA
more » ... eting LINC00858 (si-LINC00858 group), microRNA (miR)-3182 mimics or inhibitor, or the respective controls. A Cell Counting Kit-8 and Transwell assays were performed to assess the effect of the transfections on the proliferation, migration and invasion of SO-RB50 and Y79 cells. A luciferase reporter assay was performed using SO-RB50 cells to demonstrate the direct binding of LINC00858 and miR-3182. Reverse transcription-quantitative PCR was employed to detect LINC00858 and miR-3182 expression. Pearson correlation analysis was used to assess the correlation between the expression of LINC00858 and miR-3182. The results indicated that RB tissues and cells exhibited aberrantly elevated LINC00858 expression (P<0.05). Compared with those in the control-transfected group, SO-RB50 and Y79 cells of the si-LINC00858 group had a lower cell proliferation, as well as a lower number of migrated and invaded cells (all P<0.05). miR-3182 was proven to be a target gene of LINC00858, to be abnormally downregulated in RB tissues and cells (P<0.05) and to be negatively correlated with LINC00858 expression. Compared with those in the si-LINC00858 + inhibitor-negative control group, SO-RB50 and Y79 cells of the si-LINC00858 + miR-3182 inhibitor group exhibited a significantly higher relative proliferation, migration and invasion (all P<0.05). In conclusion, LINC00858 promoted RB cell proliferation, migration and invasion, at least partially by inhibiting miR-3182.
doi:10.3892/etm.2019.8294 pmid:32010262 pmcid:PMC6966175 fatcat:lbyyepp3rndqzlnu5756axrpvm

The second subunit of DNA-polymerase delta is required for genomic stability and epigenetic regulation

Jixiang Zhang, Shaojun Xie, Jinkui Cheng, Jinsheng Lai, Jian-Kang Zhu, Zhizhong Gong
2016 Plant Physiology  
ORCID IDs: 0000-0002-1641-8650 (J.Z.); 0000-0002-6719-9814 (S.X.); 0000-0001-5134-731X (J.-K.Z.). DNA polymerase d plays crucial roles in DNA repair and replication as well as maintaining genomic stability. However, the function of POLD2, the second small subunit of DNA polymerase d, has not been characterized yet in Arabidopsis (Arabidopsis thaliana). During a genetic screen for release of transcriptional gene silencing, we identified a mutation in POLD2. Whole-genome bisulfite sequencing
more » ... ated that POLD2 is not involved in the regulation of DNA methylation. POLD2 genetically interacts with Ataxia Telangiectasia-mutated and Rad3-related and DNA polymerase a. The pold2-1 mutant exhibits genomic instability with a high frequency of homologous recombination. It also exhibits hypersensitivity to DNA-damaging reagents and short telomere length. Whole-genome chromatin immunoprecipitation sequencing and RNA sequencing analyses suggest that pold2-1 changes H3K27me3 and H3K4me3 modifications, and these changes are correlated with the gene expression levels. Our study suggests that POLD2 is required for maintaining genome integrity and properly establishing the epigenetic markers during DNA replication to modulate gene expression. Figure 9 . IGV visualization of selected histone modification altered genes, and validation of ChIP-seq results. A, IGV views of reads density (RPKM) of H3K27me3 (K27me3), H3K4me3 (K4me3), H3, and Input from ChIP-seq data in the wild type (WT) and pold2-1 mutant. The data range of each modification was set to the same scale for the wild type and pold2-1 mutant. AT2G39250 and AT1G06360 are examples of genes with increased levels of H3K27me3 and decreased levels of H3K4me3. UBI is a positive control for H3K4me3 and a negative control for H3K27me3; the level of histone modification for UBI was similar for the wild type and the pold2-1 mutant. The other genes had decreased levels of H3K27me3 and increased levels of H3K4me3. The red bars on the top of each gene indicate the primer location used for validation. B to D, ChIP-qPCR verified the selected histone modification changed genes. The histone modification level of H3K27me3 (B), H3K4me3 (C), and total histone H3 (D) on each indicated gene
doi:10.1104/pp.15.01976 pmid:27208288 pmcid:PMC4902588 fatcat:yvoi2sfhe5ay3avdzxfkxo4awy

Coordination-perturbed single-molecule magnet behaviour of mononuclear dysprosium complexes

Gong-Jun Chen, Chun-Yan Gao, Jin-Lei Tian, Jinkui Tang, Wen Gu, Xin Liu, Shi-Ping Yan, Dai-Zheng Liao, Peng Cheng
2011 Dalton Transactions  
doi:10.1039/c1dt10050e pmid:21503303 fatcat:xpukcezyhzdtpj7l6blu2s4fii

Reversible structural transformation induced switchable single-molecule magnet behavior in lanthanide metal–organic frameworks

Mengmeng Wang, Xixi Meng, Fen Song, Yanfei He, Wei Shi, Hongling Gao, Jinkui Tang, Cheng Peng
2018 Chemical Communications  
The structural transformation between Ln-MOFs 1 and 2 and the corresponding switchable "on/off" single-molecule magnet behavior have been studied.
doi:10.1039/c8cc06058d pmid:30137097 fatcat:24jm5gx7xrgsbedeq32meouj5e

A promising new route towards single-molecule magnets based on the oxalate ligand

Gong-Feng Xu, Qing-Lun Wang, Patrick Gamez, Yue Ma, Rodolphe Clérac, Jinkui Tang, Shi-Ping Yan, Peng Cheng, Dai-Zheng Liao
2010 Chemical Communications  
An aqueous solution (20 mL) of K 2 ox·H 2 O (0.184 g, 1 mmol) and K(HBpz 3 ) (1.01 g, 4 mmol) was added to a stirred aqueous solution (20 mL) of DyCl 3 ·6H 2 O (0.754 g, 2 mmol,). The solution was stirred for 5 min, and then cooled in a refrigerator overnight. The resulting white precipitate was filtered off, washed three times with water, and dried under vacuum. The crude product was recrystallized from dichloromethane-acetonitrile several times (yield = 43%). Single crystals, suitable for
more » ... y diffraction analysis, were obtained by slow evaporation of the solvent from a solution of the compound in dichloromethane-acetonitrile.
doi:10.1039/b920215c pmid:20162163 fatcat:qkflvga6z5dyncbdqamv7k4t34

Degradation of the ABA co-receptor ABI1 by PUB12/13 U-box E3 ligases

Lingyao Kong, Jinkui Cheng, Yujuan Zhu, Yanglin Ding, Jingjing Meng, Zhizhong Chen, Qi Xie, Yan Guo, Jigang Li, Shuhua Yang, Zhizhong Gong
2015 Nature Communications  
Clade A protein phosphatase 2Cs (PP2Cs) are abscisic acid (ABA) co-receptors that block ABA signalling by inhibiting the downstream protein kinases. ABA signalling is activated after PP2Cs are inhibited by ABA-bound PYR/PYL/RCAR ABA receptors (PYLs) in Arabidopsis. However, whether these PP2Cs are regulated by other factors remains unknown. Here, we report that ABI1 (ABA-INSENSITIVE 1) can interact with the U-box E3 ligases PUB12 and PUB13, but is ubiquitinated only when it interacts with ABA
more » ... ceptors in an in vitro assay. A mutant form of ABI1-1 that is unable to interact with PYLs is more stable than the wild-type protein. Both ABI1 degradation and all tested ABA responses are reduced in pub12 pub13 mutants compared with the wild type. Introducing the abi1-3 loss-of-function mutation into pub12 pub13 mutant recovers the ABA-insensitive phenotypes of the pub12 pub13 mutant. We thus uncover an important regulatory mechanism for regulating ABI1 levels by PUB12 and PUB13. PUB12/13 mediate ABI1 ubiquitination in vitro. We then used an in vitro ubiquitination assay 29 to test whether PUB12 or PUB13 could ubiquitinate ABI1. All proteins including E1, E2, GST (glutathione S-transferase)-tagged PUB12 (PUB12-GST) or PUB13-GST, ABI1-His and PYR1-GST protein were purified from Escherichia coli, and Flag-tagged ubiquitin (Ub-Flag) is a commercial product. The abi1-1 mutation is hypermorphic, and abi1-1 mutant shows pleiotropic ABA-insensitive phenotypes in all tested ABA responses 4,5 . The mutation of G180 to D180 in abi1-1 blocks the interaction of ABI1 G180-D (ABI1-1) with PYL ABA receptors 6 . The mutated protein ABI1-1-His purified from E. coli was also included in the assays. Consistent with previous results 29 , both PUB12 and PUB13 possessed auto-ubiquitination activity when recombinant E1, E2, Ub-Flag and ATP were added (Fig. 3a,b) . Although ABI1-His was added to these two reactions ARTICLE NATURE COMMUNICATIONS |
doi:10.1038/ncomms9630 pmid:26482222 pmcid:PMC4667695 fatcat:sawztp4265gwppmvlarur2lgxu

Identification of the Regulatory Genes of UV-B-Induced Anthocyanin Biosynthesis in Pepper Fruit

Yihao Wang, Sujun Liu, Haoran Wang, Yingxue Zhang, Wenjie Li, Jinkui Liu, Qing Cheng, Liang Sun, Huolin Shen
2022 International Journal of Molecular Sciences  
Fruit peels of certain pepper (Capsicum annum L.) varieties accumulate a large amount of anthocyanins and exhibit purple color under medium-wave ultraviolet (UV-B) conditions, which severely impacts the commodity value of peppers. However, the regulatory mechanism of the above process has not been well studied so far. To explore which key genes are involved in this regulatory mechanism, pepper variety 19Q6100, the fruit peels of which turn purple under UV-B conditions, was investigated in this
more » ... tudy. Transcription factors with expression levels significantly impacted by UV-B were identified by RNA-seq. Those genes may be involved in the regulation of UV-B-induced anthocyanin biosynthesis. Yeast one-hybrid results revealed that seven transcription factors, CabHLH143, CaMYB113, CabHLH137, CaMYBG, CaWRKY41, CaWRKY44 and CaWRKY53 directly bound to the putative promotor regions of the structural genes in the anthocyanin biosynthesis pathway. CaMYB113 was found to interact with CabHLH143 and CaHY5 by yeast two-hybrid assay, and those three genes may participate collaboratively in UV-B-induced anthocyanin biosynthesis in pepper fruit. Virus-induced gene silencing (VIGS) indicated that fruit peels of CaMYB113-silenced plants were unable to turn purple under UV-B conditions. These findings could deepen our understanding of UV-B-induced anthocyanin biosynthesis in pepper.
doi:10.3390/ijms23041960 pmid:35216077 pmcid:PMC8879456 fatcat:c463aumh3jgvze76gnjrw7pivi

Detection of hepatocellular carcinoma in a population at risk: iodine-enhanced multidetector CT and/or gadoxetic acid-enhanced 3.0 T MRI

Lan Qiong, Zhao Jie, Zheng Zhong, Sheng Wen, Zhao Jun, Lu Liping, Cheng Jinkui
2022 BMJ Open  
ObjectiveTo evaluate the diagnostic performance of iodine-enhanced multidetector CT and gadoxetic acid-enhanced 3.0 Tesla (T) MRI for detection of hepatocellular carcinoma of patients.DesignRetrospective, multicentre cohort study.SettingThe Gong'an County People's Hospital, Gong'an County, China and the First People's Hospital of Jingzhou City, China.ParticipantsReports of CT, MRI and liver biopsies/histopathology data of a total of 815 patients who at risk were reviewed.Primary and secondary
more » ... tcome measuresThe lesions that possessed detection in the plain scan phase, enhanced arterial phase and/or enhanced portal phase of CT images and the lesions that possessed enhancements in the plain scan phase, enhanced arterial phase, enhanced portal phase and/or hepatobiliary phases of MRI were considered hepatocellular carcinoma. The decision of hepatocellular carcinoma was made based on the current Liver Imaging and Data Reporting System for diagnosing hepatocellular carcinoma.ResultsTrue positive hepatocellular carcinoma (563 vs 521, p=0.0314), true negative hepatocellular carcinoma (122 vs 91, p=0.0275), false positive hepatocellular carcinoma (88 vs 123, p=0.0121), false negative hepatocellular carcinoma (42 vs 80, p=0.0005), specificity (58.10 vs 42.52, p=0.0478) and negative clinical utility (0.1 vs 0.073, p=0.0386) were superior for gadoxetic acid-enhanced 3.0 T MRI than those of iodine-enhanced multidetector CT. Sensitivity and accuracy for gadoxetic acid-enhanced 3.0 T MRI were 93.06% and 77.40 %, respectively, and those for iodine-enhanced multidetector CT were 86.69% and 75.09 %, respectively. Likelihood to detect hepatocellular carcinoma for gadoxetic acid-enhanced 3.0 T MRI was 0–0.894 diagnostic confidence/lesion, and that for iodine-enhanced multidetector CT was 0–0.887 diagnostic confidence/lesion.ConclusionGadoxetic acid-enhanced 3.0 T MRI facilitates the confidence of initiation of treatment of hepatocellular carcinoma.Level of evidenceIII.Technical efficacy stage4.
doi:10.1136/bmjopen-2021-058461 pmid:35177466 pmcid:PMC8860074 fatcat:jtcqrjzoovgtrgo3dna4d3rlw4

No Consistent Evidence for Advancing or Delaying Trends in Spring Phenology on the Tibetan Plateau

Xufeng Wang, Jingfeng Xiao, Xin Li, Guodong Cheng, Mingguo Ma, Tao Che, Liyun Dai, Shaoying Wang, Jinkui Wu
2017 Journal of Geophysical Research - Biogeosciences  
Cheng, and M.G. Ma provided comments and suggestions on the manuscript.  ... 
doi:10.1002/2017jg003949 fatcat:faxvs2lubnaixbld3l4glmwoae
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