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Genes and proteins expressed at different life cycle stages in the model protist Euplotes vannus revealed by both transcriptomic and proteomic approaches

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Science China Life Sciences 2025年第1期68卷 232-248页

作者： Yaohan Jiang Xiao Chen Chundi Wang Liping Lyu Saleh A.Al-Farraj Naomi A.Stover Feng Gao key laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity Ocean University of China Marine College Shandong University Zoology Department College of ScienceKing Saud University Department of Biology Bradley University laboratory for Marine Biology and biotechnology Qingdao Marine Science and Technology Center

Sexual reproduction first appeared in unicellular protists and has continued to be an essential biological process in almost all *** protists, which contain both germline and somatic genomes within a single cell, have evolved a special form of sexual reproduction called conjugation that involves mitosis, meiosis, fertilization, nuclear differentiation, genome rearrangement, and the development of unique cellular structures. The molecular basis and mechanisms of conjugation vary dramatically among ciliates, and many details of the process and its regulation are still largely unknown. In order to better comprehend these processes and mechanisms from an evolutionary perspective, this study provides the first comprehensive overview of the transcriptome and proteome profiles during the entire life cycle of the newly-established marine model ciliate Euplotes vannus. Transcriptome analyses from 14 life cycle stages(three vegetative stages and 11 sexual stages) revealed over 26,000 genes that are specifically expressed at different stages, many of which are related to DNA replication,transcription, translation, mitosis, meiosis, nuclear differentiation, and/or genome rearrangement. Quantitative proteomic analyses identified 338 proteins with homologs associated with conjugation and/or somatic nuclear development in other ciliates, including dicer-like proteins, Hsp90 proteins, RNA polymerase Ⅱ and transcription elongation factors, ribosomal-associated proteins, and ubiquitin-related proteins. Four of these homologs belong to the PIWI family, each with different expression patterns identified and confirmed by RT-qPCR,which may function in small RNA-mediated genome rearrangement. Proteins involved in the nonhomologous end-joining pathway are induced early during meiosis and accumulate in the developing new somatic nucleus, where more than 80% of the germline sequences are eliminated from the somatic genome. A number of new candidate genes and proteins likely t

关键词： sexual reproduction transcriptomic proteomic genome rearrangement PIWI NHEJ

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Epigenetics in the modern era of crop improvements

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Science China Life Sciences 2025年

作者： Yan Xue Xiaofeng Cao Xiangsong Chen Xian Deng Xingwang Deng Yong Ding Aiwu Dong Chengguo Duan Xiaofeng Fang Lei Gong Zhizhong Gong Xiaofeng Gu Chongsheng He Hang He Shengbo He Xinjian He Yan He Yuehui He Guifang Jia Danhua Jiang Jianjun Jiang Jinsheng Lai Zhaobo Lang Chenlong Li Qing Li Xingwang Li Bao Liu Bing Liu Xiao Luo Yijun Qi Weiqiang Qian Guodong Ren Qingxin Song Xianwei Song Zhixi Tian Jiawei Wang Yuan Wang Liang Wu Zhe Wu Rui Xia Jun Xiao Lin Xu Zhengyi Xu Wenhao Yan Hongchun Yang Jixian Zhai Yijing Zhang Yusheng Zhao Xuehua Zhong Daoxiu Zhou Ming Zhou Yue Zhou Bo Zhu Jiankang Zhu Qikun Liu College of Life Sciences Institute of Life Science and Green Development Hebei University biotechnology Research Institute Chinese Academy of Agricultural Sciences College of Biology Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation Hunan Engineering and Technology Research Center of Hybrid Rapeseed Hunan University Institute of Advanced Agricultural Sciences School of Advanced Agricultural Sciences Peking University State key laboratory for Conservation and Utilization of Subtropical Agro-Bioresources Guangdong Laboratory for Lingnan Modern Agriculture South China Agricultural University National Institute of Biological Sciences key laboratory of Seed Innovation Institute of Genetics and Developmental Biology Chinese Academy of Sciences School of Advanced Agricultural Sciences Peking-Tsinghua Center for Life Sciences Peking University Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education College of Chemistry and Molecular Engineering Peking University key laboratory of Seed Innovation State Key Laboratory of Plant Genomics and National Center for Plant Gene Research Institute of Genetics and Developmental Biology Chinese Academy of Sciences State key laboratory of Wheat Improvement Peking University Institute of Advanced Agricultural Sciences Shandong Laboratory of Advanced Agricultural Sciences in Weifang State key laboratory of Crop Stress Adaptation and Improvement School of Life Sciences Henan University State key laboratory of Maize Bio-breeding National Maize Improvement Center Department of Plant Genetics and Breeding China Agricultural University Frontiers Science Center for Molecular Design Breeding China Agricultural University Center for Crop Functional Genomics and Molecular Breeding China Agricultural University Sanya Institute of China Agricultural University Hainan Yazhou Bay Seed laboratory Institute of Advan

Epigenetic mechanisms are integral to plant growth, development, and adaptation to environmental stimuli. Over the past two decades,our comprehension of these complex regulatory processes has expanded remarkably, producing a substantial body of knowledge on both locus-specific mechanisms and genome-wide regulatory patterns. Studies initially grounded in the model plant Arabidopsis have been broadened to encompass a diverse array of crop species, revealing the multifaceted roles of epigenetics in physiological and agronomic traits. With recent technological advancements, epigenetic regulations at the single-cell level and at the large-scale population level are emerging as new focuses. This review offers an in-depth synthesis of the diverse epigenetic regulations, detailing the catalytic machinery and regulatory functions. It delves into the intricate interplay among various epigenetic elements and their collective influence on the modulation of crop traits. Furthermore, it examines recent breakthroughs in technologies for epigenetic modifications and their integration into strategies for crop improvement. The review underscores the transformative potential of epigenetic strategies in bolstering crop performance, advocating for the development of efficient tools to fully exploit the agricultural benefits of epigenetic insights.

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Regulatory Function of Polyamine Oxidase-Generated Hydrogen Peroxide in Ethylene-Induced Stomatal Closure in Arabidopsis thaliana

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Journal of Integrative Agriculture 2013年第2期12卷 251-262页

作者： HOU Zhi-hui LIU Guo-hua HOU Li-xia WANG Lan-xiang LIU Xin College of Life Sciences Qingdao Agricultural University/University Key Laboratory of Plant Biotechnology in Shandong Province Universities of Shandong

Hydrogen peroxide （H2O2） is an important signaling molecule in ethylene-induced stomatal closure in Arabidopsis thaliana. Early studies on the sources of H2O2 mainly focused on NADPH oxidases and cell-wall peroxidases. Here, we report the involvement of polyamine oxidases （PAOs） in ethylene-induced H2O2 production in guard cells. In Arabidopsis epidermal peels, application of PAO inhibitors caused the failure of ethylene to induce H2O2 production and stomatal closure. Results of quantitative RT-PCR analysis and pharmacological experiments showed that AtPAO2 and AtPAO4 transcripts and activities of PAOs were both induced by ethylene. In transgenic Arabidopsis plants over-expressing AtPAO2 and AtPAO4, stomatal movement was more sensitive to ethylene treatment and H2O2 production was also significantly induced. The increased H2O2 production in the transgenic lines compared to the wild-type plants suggests that AtPAO2 and AtPAO4 probably are involved in ethylene-induced H2O2 production. Several factors which induce stomatal closure such as dehydration and high salinity all enhanced the expression of AtPAO2 and AtPAO4 to different degrees. Moreover, GFP- AtPAOs fusion protein localized in the nucleus, cytoplasm, and cell wall of the guard cells. Therefore, our results strongly indicated that PAO is a source of H2O2 generation in Arabidopsis guard cells and plays crucial roles in stomatal movement.

关键词： Arabidopsis thaliana ethylene guard cell hydrogen peroxide polyamine oxidase

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Hydrogen Sulfide Regulates Ethylene-induced Stomatal Closure in Arabidopsis thaliana

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Journal of Integrative plant Biology 2013年第3期55卷 277-289页

作者： Zhihui Hou Lanxiang Wang Jing Liu Lixia Hou Xin Liu College of Life Sciences Qingdao Agricultural UniversityUniversity Key Laboratory of Plant Biotechnology in Shandong Province

Hydrogen sulfide （H2S） is a newly-discovered signaling molecule in plants and has caused increasing attention in recent years, but its function in stomatal movement is unclear. In plants, H2S is synthesized via cysteine degradation catalyzed by D-/L-cysteine desulfhydrase （D-/L-CDes）. AtD-/L-CDes：：GUS transgenic Arabidopsis thaliana （L.） Heynh. plants were generated and used to investigate gene expression patterns, and results showed that AtD-/L-CDes can be expressed in guard cells. We also determined the subcellular localization of AtD-/L-CDes using transgenic plants of AtD-/L-CDes：：GFP, and the results showed that AtD-CDes and AtL-CDes are located in the chloroplast and in the cytoplasm, respectively. The transcript levels of AtD-CDes and AtL-CDes were affected by the chemicals that cause stomatal closure. Among these factors, ACC, a precursor of ethylene, has the most significant effect, which indicates that the H2S generated from D-/L-CDes may play an important role in ethylene-induced stomatal closure. Meanwhile, H2S synthetic inhibitors significantly inhibited ethylene-induced stomatal closure in Arabidopsis. Ethylene treatment caused an increase of H2S production and of AtD-/L-CDes activity in Arabidopsis leaves. AtD-/L-CDes over-expressing plants exhibited enhanced induction of stomatal closure compared to the wild-type after ethylene treatment; however, the effect was not observed in the Atd-cdes and Atl-cdes mutants. In conclusion, our results suggest that the D-/L-CDes-generated H2S is involved in the regulation of ethylene-induced stomatal closure in Arabidopsis thaliana.

关键词： Desulfhydrase D-/L-cysteine ethylene hydrogen sulfide stomatal closure.

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Hydrogen Sulfide May Function Downstream of Nitric Oxide in Ethylene-Induced Stomatal Closure in Vicia faba L.

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Journal of Integrative Agriculture 2012年第10期11卷 1644-1653页

作者： LIU Jing HOU Zhi-hui LIU Guo-hua HOU Li-xia LIU Xin key laboratory of plant biotechnology in Universities of shandong province/College of Life Science Qingdao Agricultural University

Pharmacological, laser scanning confocal microscopic （LSCM）, and spectrophotographic approaches were used to study the roles of hydrogen sulfide （H2S） and nitric oxide （NO） in signaling transduction of stomatal movement in response to ethylene in Viciafaba L. Ethylene treatment resulted in the dose-dependent stomatal closure under light, and this effect was blocked by the inhibitors of H2S biosynthesis in V. faba L. Additionally, ethylene induces H2S generation and increases L-/D-cysteine desulfhydrase （pyridoxalphosphate-dependent enzyme） activity in leaves of V. faba L. Inhibitors of H2S biosynthesis have no effect on the ethylene-induced stomatal closure, NO accumulation, and nitrate reductase （NR） activity in guard cells or leaves of II. faba L. Moreover, the ethylene-induced increase of H2S levels and L-/D- cysteine desulfhydrase activity declined when NO generation was inhibited. Therefore, we conclude that H2S and NO probably are involved in the signal transduction pathway of ethylene-induced stomatal closure. H2S may represent a novel component downstream of NO in the ethylene-induced stomatal movement in V. faba L.

关键词： hydrogen sulfide nitric oxide ethylene stomatal closure Vicia faba L.

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Comprehensive analyses of the proteome and ubiquitome revealed mechanism of high temperature accelerating petal abscission in tree peony

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Horticultural plant Journal 2024年第1期10卷 205-222页

作者： Chunying Liu Ziqi Liu Yanchao Yuan Yuxi Zhang Yifu Fang Junqiang Chen Shupeng Gai key laboratory of plant biotechnology in shandong province College of Life SciencesQingdao Agricultural UniversityQingdaoShandong 266109China shandong Academy of Forestry JinanShandong 250014China

Tree peony(Paeonia suffruticosa Andrews)is a well-known ornamental plant with high economic value,but the short fluorescence is a key obstacle to its ornamental value and industry *** temperature accelerates flower senescence and abscission,but the associated mechanisms are poorly *** this study,the tandem mass tag(TMT)proteome and label-free quantitative ubiquitome from tree peony cut flowers treated with 20℃for 0 h(RT0),20℃or 28℃for 60 h(RT60 or HT60)were examined based on morphological observation,***,6970 proteins and 1545 lysine ubiquitinated(Kub)sites in 844 proteins were *** residues(such as glutamate and aspartate)neighboring the Kub sites were in preference,and 36.01%of the Kub sites were located on the protein *** differentially expressed proteins(DEPs)and Kub-DEPs in HT60 vs RT60 were mainly enriched in ribosomal protein,protein biosynthesis,secondary metabolites biosynthesis,flavonoid metabolism,carbohydrate catabolism,and auxin biosynthesis and signaling revealed by GO and KEGG analysis,accompanying the increase of endogenous abscisic acid(ABA)accumulation and decrease of endogenous indoleacetic acid(IAA)***,the expression patterns of six enzymes(SAMS,ACO,YUC,CHS,ANS and PFK)putatively with Kub modifications were analyzed by proteome and real-time quantitative *** cell-free degradation assays showed PsSAMS and PsACO proteins could be degraded via the 26 S proteasome system in tree peony ***,a working model was proposed for the acceleration of flower senescence and abscission by high *** summary,all results contributed to understanding the mechanism of flower senescence induced by high temperature and prolonging fluorescence in tree peony.

关键词： Tree peony Proteome Ubiquitome High temperature Flower senescence

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Physiological and Biochemical Mechanisms of Exogenous Calcium Chloride on Alleviating Salt Stress in Two Tartary Buckwheat(Fagopyrum tataricum)Varieties Differing in Salinity Tolerance

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Phyton-International Journal of Experimental Botany 2022年第8期91卷 1643-1658页

作者： Tao Zhang Hongbing Yang key laboratory of plant biotechnology in Universities of shandong province College of Life ScienceQingdao Agricultural UniversityQingdao266109China

Salt stress is one of the most serious abiotic stresses limiting plant growth and *** as an essential nutrient element and important signaling molecule plays an important role in ameliorating the adverse effect of salinity on *** study aimed to investigate the impact of exogenous calcium on improving salt tolerance in Tartary buckwheat cultivars,***9920(salt-tolerant)and ***9909(salt-sensitive).Four-week-old Tartary buckwheat seedlings under 100 mM NaCl stress were treated with and without exogenous calcium chloride(CaCl_(2)),Ca^(2+)chelator ethylene glycol tetraacetic acid(EGTA)and Ca^(2+)-channel blocker lanthanum chloride(LaCl_(3))for 10 ***,some important physiological and biochemical indexes were *** results showed that salt stress significantly reduced seedling growth,decreased photosynthetic pigments,inhibited antioxidants and antioxidant enzyme ***,it increased the reactive oxygen species(ROS)levels in the two Tartary buckwheat *** 10 mM CaCl_(2)application on salt-stressed Tartary buckwheat seedlings obviously mitigated the negative effects of NaCl stress and partially restored seedlings ***^(2+)-treated salt-stressed seedlings diplayed a suppressed accumulation of ROS,increased the contents of total chlorophyll,soluble protein,proline and antioxidants,and elevated the activities of antioxidant enzymes compared with salt stress *** the contrary,the addition of 0.5 mM LaCl_(3)and 5 mM EGTA on salt-stressed Tartary buckwheat seedlings exhibited the opposite effects to those with CaCl_(2)*** results indicate that exogenous Ca^(2+)can enhance salt stress tolerance and Ca^(2+)supplementation may be an effective practice to cultivate Tartary buckwheat in saline soils.

关键词： Salt stress calcium antioxidant enzymes ROS scavenging osmoprotection tartary buckwheat

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Dual functions of PsmiR172b-PsTOE3 module in dormancy release and flowering in tree peony (Paeonia suffruticosa)

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Horticulture Research 2023年第4期10卷 174-186页

作者： Yuxi Zhang Linqiang Gao Yanyan Wang Demei Niu Yanchao Yuan Chunying Liu Xinmei Zhan Shupeng Gai College of Life Sciences Qingdao Agricultural UniversityQingdao266109China University key laboratory of plant biotechnology in shandong province Qingdao266109China

MicroRNAs(miRNAs)are non-coding RNAs that interact with target genes and are involved in many physiological processes in ***172-AP2 mainly plays a role in the regulation of f lowering time and floral organ *** dormancy release is necessary for forcing culture of tree peony in winter,but the mechanism of dormancy regulation is *** this study,we found that a miR172 family member,PsmiR172b,was downregulated during chilling-induced bud dormancy release in tree peony,exhibiting a trend opposite to that of *** ligase-mediated(RLM)5-RACE(rapid amplification of cDNA ends)confirmed that miR172b targeted PsTOE3,and the cleavage site was between bases 12(T)and 13(C)within the complementary site to *** functions of miR172b and PsTOE3 were detected by virus-induced gene silencing(VIGS)and their overexpression in tree peony ***172b negatively regulated bud dormancy release,but PsTOE3 promoted bud dormancy release,and the genes associated with bud dormancy release,including PsEBB1,PsEBB3,PsCYCD,and PsBG6,were *** analysis indicated that PsTOE3 directly regulated PsEBB1 by binding to its promoter,and the specific binding site was a C-repeat(ACCGAC).Ectopic expression in Arabidopsis revealed that the PsmiR172b-PsTOE3 module displayed conservative function in regulating f *** conclusion,our results provided a novel insight into the functions of PsmiR172-PsTOE3 and possible molecular mechanism underlying bud dormancy release in tree peony.

关键词： release functions bases

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PsRGL1 negatively regulates chilling- and gibberellin-induced dormancy release by PsF-box1-mediated targeting for proteolytic degradation in tree peony

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Horticulture Research 2023年第5期10卷 49-60页

作者： Linqiang Gao Demei Niu Tianyu Chi Yanchao Yuan Chunying Liu Shupeng Gai Yuxi Zhang College of Life Sciences Qingdao Agricultural UniversityQingdao 266109China University key laboratory of plant biotechnology in shandong province Qingdao 266109China

Tree peony bud endodormancy is a common survival strategy similar to many perennial woody plants in winter,and the activation of the GA signaling pathway is the key to breaking *** signal transduction is involved in many physiological *** the GA-GID1-DELLA regulatory module is conserved in many plants,it has a set of specific components that add complexity to the GA response *** proteins are key switches in GA ***,there is an urgent need to identify the key DELLA proteins involved in tree peony bud dormancy *** this study,the prolonged chilling increased the content of endogenously active ***1 among three DELLA proteins was significantly downregulated during chilling-and exogenous GA3-induced bud dormancy release by cell-free degradation assay,and a high level of polyubiquitination was *** PsRGL1 accelerated bud dormancy release by increasing the expression of the genes associated with dormancy release,including PsCYCD,PsEBB1,PsEBB3,PsBG6,and *** F-box protein family members responded to chilling and GA3 treatments,resulting in PsF-box1 *** two-hybrid and BiFC assays indicated that only PsF-box1 could bind to PsRGL1,and the binding site was in the C-terminal ***-box1 overexpression promoted dormancy release and upregulated the expression of the dormancy-related *** addition,yeast two-hybrid and pull-down assays showed that PsF-box1 also interacted with PsSKP1 to form an E3 ubiquitin *** findings enriched the molecular mechanism of the GA signaling pathway during dormancy release,and enhanced the understanding of tree peony bud endodormancy.

关键词： release tree breaking

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BnWRI1 coordinates fatty acid biosynthesis and photosynthesis pathways during oil accumulation in rapeseed

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Journal of Integrative plant Biology 2014年第6期56卷 582-593页

作者： Xue-Long Wu Zhi-Hong Liu Zhang-Hua Hu Rui-Zhi Huang Institute of Virology and biotechnology Zhejiang Academy of Agricultural Sciences Key Laboratory of Plant Metabolic Engineering of Zhejiang Province

Photosynthesis in“green”seeds, such as rapeseed, soybean, and Arabidopsis, plays a substantial role in the improved efficiency of oil accumulation. However, the molecular mecha-nism underpinning the coordinated expression of fatty acid （FA） biosynthesis-and photosynthesis-related genes in such develop-ing seeds remains to be elucidated. Here, we found that seed-specific overexpression of BnWRI1, a WRI1 homolog from rapeseed （Brassica napus cv. ZGY2）, results in enhanced chlorophyl content in developing seeds and increased oil content and seed mass in matured seeds. BnWRI1 was co-expressed with BnBCCP and BnCAB, two marker genes of FA biosynthesis and photosynthesis during seed development, respectively. Over-expression of BnWRI1 increased expression of both marker genes. Further, the nuclear-localized BnWRI1 protein was found to act as a transcription activator. It could bind to the GT1-element and/or GCC-box, which are widespread in the upstream regions of genes involved in FA biosynthesis and photosynthesis pathways. Accordingly, BnWRI1 could interact with promoters of BCCP2 and LHB1B2 in vivo. These results suggested that BnWRI1 may coordinate FA biosynthesis and photosynthesis pathways in developing seeds via directly stimulating expression of GT1-element and/or GCC-box containing genes.

关键词： BnWRI1 Brassica napus oil accumulation photosynthesis transcription factor

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