作者：
Ke Liu;Jin Zhang;Yuqing Xiao;Ally Yang;Xiaosheng Song;...
期刊：
Journal of Biological Chemistry,2023年299(6):104734 ISSN：0021-9258
通讯作者：
Ke Liu<&wdkj&>Jinrong Min
作者机构：
[Ke Liu; Jin Zhang; Yuqing Xiao; Yunxia Chen] Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, PR China;[Ally Yang; Timothy R. Hughes] Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada;[Xiaosheng Song; Yanjun Li] Structural Genomics Consortium and Department of Physiology, University of Toronto, Toronto, Ontario, Canada;[Jinrong Min] Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, PR China<&wdkj&>Structural Genomics Consortium and Department of Physiology, University of Toronto, Toronto, Ontario, Canada
通讯机构：
[Ke Liu; Jinrong Min] H;Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, PR China<&wdkj&>Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, PR China<&wdkj&>Structural Genomics Consortium and Department of Physiology, University of Toronto, Toronto, Ontario, Canada
关键词：
BEN domain;BANP;BEND6;DNA methylation;X-ray crystallography
摘要：
The BEN domain-containing transcription factors regulate transcription by recruiting chromatin-modifying factors to specific chromatin regions via their DNA-binding BEN domains. The BEN domain of BANP has been shown to bind to a CGCG DNA sequence or an AAA-containing matrix attachment regions DNA sequence. Consistent with these in vivo observations, we identified an optimal DNA-binding sequence of AAATCTCG by protein binding microarray, which was also confirmed by our isothermal titration calorimetry and mutagenesis results. We then determined crystal structures of the BANP BEN domain in apo form and in complex with a CGCG-containing DNA, respectively, which revealed that the BANP BEN domain mainly used the electrostatic interactions to bind DNA with some base-specific interactions with the TC motifs. Our isothermal titration calorimetry results also showed that BANP bound to unmethylated and methylated DNAs with comparable binding affinities. Our complex structure of BANP-mCGCG revealed that the BANP BEN domain bound to the unmethylated and methylated DNAs in a similar mode and cytosine methylation did not get involved in binding, which is also consistent with our observations from the complex structures of the BEND6 BEN domain with the CGCG or CGmCG DNAs. Taken together, our results further elucidate the elements important for DNA recognition and transcriptional regulation by the BANP BEN domain-containing transcription factor.
期刊：
Journal of Phycology,2023年59(2):370-382 ISSN：0022-3646
通讯作者：
Renhui Li<&wdkj&>Bao-Sheng Qiu
作者机构：
[Zhang, Lu-Dan; Shen, Li-Qin; Huang, Li; Qiu, Bao-Sheng; Zhang, Zhong-Chun] Cent China Normal Univ, Sch Life Sci, Wuhan, Hubei, Peoples R China.;[Zhang, Lu-Dan; Shen, Li-Qin; Huang, Li; Qiu, Bao-Sheng; Zhang, Zhong-Chun] Cent China Normal Univ, Hubei Key Lab Genet Regulat & Integrat Biol, Wuhan, Hubei, Peoples R China.;[Yu, Gongliang] Chinese Acad Sci, Inst Hydrobiol, Key Lab Algal Biol, Wuhan, Hubei, Peoples R China.;[Chen, Min] Univ Sydney, Sch Life & Environm Sci, Sydney, NSW, Australia.;[Li, Renhui] Wenzhou Univ, Coll Life & Environm Sci, Zhejiang, Peoples R China.
通讯机构：
[Renhui Li] C;[Bao-Sheng Qiu] S;School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, China<&wdkj&>College of Life and Environmental Sciences, Wenzhou University, Zhejiang, China
摘要：
Chlorophyll (Chl) f was recently identified in a few cyanobacteria as the fifth chlorophyll of oxygenic organisms. In this study, two Leptolyngbya-like strains of CCNU0012 and CCNU0013 were isolated from a dry ditch in Chongqing city and a brick wall in Mount Emei Scenic Area in China, respectively. These two strains were described as new species: Elainella chongqingensis sp. nov. (Oculatellaceae, Synechococcales) and Pegethrix sichuanica sp. nov. (Oculatellaceae, Synechococcales) by the polyphasic approach based on morphological features, phylogenetic analysis of 16S rRNA gene and secondary structure comparison of 16S-23S internal transcribed spacer domains. Both strains produced Chl a under white light (WL) but additionally induced Chl f synthesis under far-red light (FRL). Unexpectedly, the content of Chl f in P. sichuanica was nearly half that in most Chl f-producing cyanobacteria. Red-shifted phycobiliproteins were also induced in both strains under FRL conditions. Subsequently, additional absorption peak beyond 700 nm in the FRL spectral region appeared in these two strains. This is the first report of Chl f production induced by FRL in the family Oculatellaceae. This study not only extended the diversity of Chl f-producing cyanobacteria, but also provided precious samples to elucidate the essential binding sites of Chl f within cyanobacterial photosystems.
关键词：
E. coli;E. coli arrays;IgA;IgG;alcoholic hepatitis;autoantibodies;human;immunology;inflammation
摘要：
The pathogenesis of antibodies in severe alcoholic hepatitis (SAH) remains unknown. We analyzed immunoglobulins (Ig) in explanted livers from SAH patients (n=45) undergoing liver transplantation and tissues from corresponding healthy donors (HD, n=10) and found massive deposition of IgG and IgA isotype antibodies associated with complement fragment C3d and C4d staining in ballooned hepatocytes in SAH livers. Ig extracted from SAH livers, but not patient serum exhibited hepatocyte killing efficacy. Employing human and Escherichia coli K12 proteome arrays, we profiled the antibodies extracted from explanted SAH, livers with other diseases, and HD livers. Compared with their counterparts extracted from livers with other diseases and HD, antibodies of IgG and IgA isotypes were highly accumulated in SAH and recognized a unique set of human proteins and E. coli antigens. Further, both Ig- and E. coli-captured Ig from SAH livers recognized common autoantigens enriched in several cellular components including cytosol and cytoplasm (IgG and IgA), nucleus, mitochondrion, and focal adhesion (IgG). Except IgM from primary biliary cholangitis livers, no common autoantigen was recognized by Ig- and E. coli-captured Ig from livers with other diseases. These findings demonstrate the presence of cross-reacting anti-bacterial IgG and IgA autoantibodies in SAH livers.
作者机构：
[Han, Fei; Dai, Xiongfeng; Wang, Yanling; Dai, XF; Zhu, Manlu; Wang, Qian; Mu, Haoyan] Cent China Normal Univ, Sch Life Sci, Hubei Key Lab Genet Regulat & Integrat Biol, Wuhan, Hubei, Peoples R China.
通讯机构：
[Dai, XF ] C;Cent China Normal Univ, Sch Life Sci, Hubei Key Lab Genet Regulat & Integrat Biol, Wuhan, Hubei, Peoples R China.
摘要：
Growth and survival are key determinants of bacterial fitness. However, how resource allocation of bacteria could reconcile these two traits to maximize fitness remains poorly understood. Here, we find that the resource allocation strategy of Bacillus subtilis does not lead to growth maximization on various carbon sources. Survival-related pathways impose strong proteome constraints on B. subtilis. Knockout of a master regulator gene, spo0A, triggers a global resource reallocation from survival-related pathways to biosynthesis pathways, further strongly stimulating the growth of B. subtilis. However, the fitness of spo0A-null strain is severely compromised because of various disadvantageous phenotypes (e.g., abolished sporulation and enhanced cell lysis). In particular, it also exhibits a strong defect in peptide utilization, being unable to efficiently recycle nutrients from the lysed cell debris to maintain long-term viability. Our work uncovers a fitness trade-off between growth and survival that governed by Spo0A-mediated proteome allocation constraints in B. subtilis, further shedding light on the fundamental design principle of bacteria.
摘要：
INTRODUCTION: Aging is characterized by progressive metabolic dyshomeostasis that increases morbidity and mortality. Solutions for optimizing healthy aging are challenged by lacking appropriate biomarkers. Moreover, druggable targets to rejuvenate the aging-associated metabolic phenotypes remain unavailable. METHODS: Proteomics analysis was performed in a cohort of young and elderly adults. Circulating levels of insulin-like growth factor 1 (IGF-1) and fatty acid binding protein 4 (FABP4) were evaluated by ELISA. FABP4 was silenced in elderly mice by adeno-associated virus. Metabolic activities were measured by metabolic cages. Cognitive function was evaluated by Morris water maze. Glucose and lipid metabolism were evaluated by biochemistry assays with blood samples. RNA-seq in mouse liver was performed for transcriptome analysis. RESULTS: Among 9 aging-sensitive proteins shared by both male and female, FABP4 was identified as a reliable aging biomarker in both human and mouse. Silencing FABP4 in elderly mice significantly rejuvenated the aging-associated decline in metabolic activities. FABP4 knockdown reversed the aging-associated metabolic disorders by promoting degradation of cholesterol and fatty acids, while suppressing gluconeogenesis. Transcriptome analysis revealed a restoration of the pro-aging gene reprogramming towards inflammation and metabolic disorders in the liver after FABP4 knockdown. FABP4 overexpression promoted human LO2 cell senescence. Moreover, administration of an FABP4 inhibitor BMS309403 delivered metabolic benefits in elderly mice. CONCLUSION: Our findings demonstrate FABP4 as a reliable aging biomarker as well as a practicable target to improve healthy aging in the elderly.
作者机构：
[Sun, Qian; Wang, Dong; Wang, D; Xu, Xiaodong] Cent China Normal Univ, Sch Life Sci, Wuhan 430079, Hubei, Peoples R China.;[Wang, Dong; Wang, D] Shaanxi Univ Technol, Bioresources key Lab Shaanxi Prov, Hanzhong 723001, Shaanxi, Peoples R China.;[Li, Niya] Wuhan Sinoeco Ecol Sci & Technol Co Ltd, Wuhan 430000, Hubei, Peoples R China.;[Wang, Liang] Lanzhou Univ, Sch Ecol, Lanzhou, Gansu, Peoples R China.;[Wang, Liang] Adm Gansu Anxi Extraarid Desert Natl Nat Reserve, Guazhou, Gansu, Peoples R China.
通讯机构：
[Wang, D ] C;Cent China Normal Univ, Sch Life Sci, Wuhan 430079, Hubei, Peoples R China.;Shaanxi Univ Technol, Bioresources key Lab Shaanxi Prov, Hanzhong 723001, Shaanxi, Peoples R China.
摘要：
Corydalis mianxianensis, a new species of C. sect. Cheilanthifoliae Liden (Papaveracae), is described from Qinling-Daba mountains and adjacent Minshan mountains, central China. It is similar to C. moupinensis Franch., but it differs from the latter in racemes with 30-50(-70) flowers, spur being much shorter than limb of upper petal, and arcuate to strongly contorted fruits. These two species are also much different in stigma and ecology as well. In addition, we confirmed that the record of C. saxicola G.S.Bunting in Shaanxi Province as documented in the Chinese floras was a misidentification of this new species.
作者机构：
[Peng, Yan; Peng, Jie; Xiao, Yutao; Shan, Yinxue; Jin, Minghui] Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Shenzhen Branch,Minist Agr & Rural Affairs, Guangdong Lab Lingnan Modern Agr,Key Lab Gene Edit, Shenzhen, Peoples R China.;[Peng, Yan; Peng, Jie] Huazhong Agr Univ, Coll Plant Sci & Technol, Wuhan, Peoples R China.;[Zhang, Huihui; Liu, Kaiyu] Cent China Normal Univ, Inst Entomol, Sch Life Sci, Wuhan, Peoples R China.
通讯机构：
[Xiao, YT ] C;Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Shenzhen Branch,Minist Agr & Rural Affairs, Guangdong Lab Lingnan Modern Agr,Key Lab Gene Edit, Shenzhen, Peoples R China.
摘要：
The rapid evolution of resistance in agricultural pest poses a serious threat to global food security. However, the mechanisms of resistance through metabolic regulation are largely unknown. Here, we found that a GST gene cluster was strongly selected in North China (NTC) population, and it was significantly genetically-linked to lambda-cyhalothrin resistance. Knockout of the GST cluster using CRISPR/Cas9 significantly increased the sensitivity of the knockout strain to lambda-cyhalothrin. Haplotype analysis revealed no non-synonymous mutations or structural variations in the GST cluster, whereas GST_119 and GST_121 were significantly overexpressed in the NTC population. Silencing of GST_119 or co-silencing of GST_119 and GST_121 with RNAi significantly increased larval sensitivity to lambda-cyhalothrin. We also identified additional GATAe transcription factor binding sites in the promoter of NTC_GST_119. Transient expression of GATAe in Hi5 cells activated NTC_GST_119 and Xinjiang (XJ)_GST_119 transcription, but the transcriptional activity of NTC_GST_119 was significantly higher than that of XJ_GST_119. These results demonstrate that variations in the regulatory region result in complex expression changes in the GST cluster, which enhances lambda-cyhalothrin resistance in field-populations. This study deepens our knowledge of the evolutionary mechanism of pest adaptation under environmental stress and provides potential targets for monitoring pest resistance and integrated management. A glutathione S-transferase gene cluster in the cotton bollworm, Helicoverpa armigera, contributes to natural insecticide resistance in this agricultural pest.
摘要：
The successful establishment of seedlings is very important for plant regeneration, but it is vulnerable to many factors at this stage. Cotyledon damage will directly affect the health of seedlings, thus affecting the regeneration of the plant population. However, little is known about the effects of different cotyledon loss degrees of large and small seeds on seedling growth. We investigated the effects of 1/4 (light excision), 1/2 (moderate excision), and complete excision of cotyledons (heavy excision) on the growth characteristics of seedlings germinating from different sizes of seeds. The results showed that (1) shoot height, basal stem diameter, number of leaves, leaf area per plant, specific leaf area, and biomass were significantly higher in large-seeded seedlings than in small-seeded seedlings; (2) slight cotyledon excision had no effect on the biomass of large-seeded seedlings but significantly reduced the biomass of small-seeded seedlings. Our study highlights that large-seeded seedlings are more tolerant than small-seeded seedlings in the early seedling recruitment, suggesting that large-seeded seedlings have a strong fitness for recruitment in young populations of Q. wutaishanica.
作者机构：
[Yang, Lijian; Zhan, Xuan; Jia, Ya; Yu, Dong] Cent China Normal Univ, Dept Phys, Wuhan 430079, Peoples R China.;[Fu, Ziying] Cent China Normal Univ, Sch Life Sci, Wuhan 430079, Peoples R China.
通讯机构：
[Ya Jia] D;Department of Physics, Central China Normal University, Wuhan, China
关键词：
Logical stochastic resonance;Ionic energy consumption;Ion channel noise;Stochastic Hodgkin–Huxley neuron
摘要：
In this work, we reported a new way to design logic circuits. The output of a stochastic Hodgkin-Huxley (HH) neuron system can be continuously mapped to a specific logic gate operation, logical stochastic resonance occurs. The energy consumption of neurons was estimated by the equivalent circuit of the HH model. It is found that reliable logic operations can be obtained with low energy consumption in the neuronal system, the HH neurons are excellent building blocks for logic circuits. The underlying mechanisms are intuitively interpreted using bifurcation and phase plane diagrams. The reliability of logic gates is based on the transition between the two steady states (resting and spiking) of the neuron. According to this mechanism, methods to improve the reliability of logical operations can be obtained. In this paper, a neuronal network is constructed to obtain more reliable logic operations. Synaptic currents modulate the logical operational performance of neuronal networks by regulating the mean switching time between steady states. Finally, we discuss the possible schemes for enhancing the reliability of logic gates. The obtained findings may provide a novel perspective for the design of new logic devices.
作者机构：
[Zhang, Jian-Feng; Chu, Hui-Hui; Liao, Dan; Tong, Yi-Kai; Liu, Ying-Ying; Ren, Feng] Cent China Normal Univ, Sch Life Sci, Hubei Key Lab Genet Regulat & Integrat Biol, Wuhan 430079, Peoples R China.;[Ma, Guang-Jing] Chinese Acad Sci, Innovat Acad Seed Design, Wuhan Bot Garden, CAS Key Lab Plant Germplasm Enhancement & Specialt, Wuhan 430074, Peoples R China.;[Li, Jun] Chinese Acad Agr Sci, Minist Agr, Key Lab Biol & Genet Improvement Oil Crops, Oil Crops Res Inst, Wuhan, Peoples R China.
通讯机构：
[Feng Ren] H;Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
摘要：
The members of PHOSPHATE 1 (PHO1) family play important roles in plant phosphate (Pi) transport and adaptation to Pi deficiency. The functions of PHO1 family proteins have been reported in several plant species, with the exception of Brassica species. Here, we identified 23, 23, and 44 putative PHO1 family genes in Brassica rapa, Brassica oleracea, and Brassica napus by whole genome analysis, respectively. The phylogenetic analysis divided PHO1 family proteins into eight groups, which represented the orthologous relationships among PHO1 members. The gene structure and the conserved motif analysis indicated that the most PHO1 family genes had similar gene structures and the PHO1 proteins shared mutual conserved motifs. The chromosome distribution analysis showed that the majority of BnPHO1 family genes distributed analogously at chromosomes with BrPHO1 and BoPHO1 family genes. The data showed that PHO1 family genes were highly conserved during evolution from diploid to tetraploid. Furthermore, the expression analysis showed that PHO1 family genes had different expression patterns in plant tissues, suggesting the diversity of gene functions in Brassica species. Meanwhile, the expression analysis also revealed that some PHO1 family genes were significantly responsive to Pi deficiency, suggesting that PHO1 family genes play critical roles in Pi uptake and homeostasis under low Pi stress. Altogether, the characteristics of PHO1 family genes provide a reliable groundwork for further dissecting their functions in Brassica species.
摘要：
Dibutyl phthalate (DBP), used as a plasticizer, is of wide concern as an environmental pollutant since it has certain immunotoxicity. Although there is growing evidence supporting a link between DBP exposure and allergic airway inflammation, there is less information concerned with whether the ferroptosis pathway is involved in DBP-aggravated allergic asthma in ovalbumin (OVA)-sensitized mice. This study aimed to investigate the role and underlying mechanisms of ferroptosis in DBP-exposed allergic asthmatic mice. Balb/c mice were orally exposed to 40mg/kg(-1) DBP for 28 days, followed by sensitization with OVA and seven consecutive challenges with nebulized OVA. We analyzed airway hyperresponsiveness (AHR), immunoglobulins, inflammation and pulmonary histopathology, to investigate whether DBP exacerbates allergic asthma in OVA-induced mice. We also measured the biomarkers of ferroptosis (Fe(2+), GPX4, PTGS2), proteins related to the ferroptosis pathway (VEGF, IL-33, HMGB1, SLC7A11, ALOX15, PEBP1), and indices of lipid peroxidation (ROS, Lipid ROS, GSH, MDA, 4-HNE), to explore the role of ferroptosis in DBP+OVA mice. Finally, we used ferrostatin-1 (Fer-1) as an antagonist against the harmful effects of DBP. The results showed that, DBP+OVA mice had a significant increase in AHR, airway wall remodeling and airway inflammation. Further, we showed that DBP aggravated allergic asthma via ferroptosis and lipid peroxidation, and that Fer-1 inhibited ferroptosis and alleviated the pulmonary toxicity of DBP. These results suggest that ferroptosis participates in the exacerbation of allergic asthma resulting from oral exposure to DBP, highlighting a novel pathway for the connection between DBP and allergic asthma.
