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Rice tissue-specific promoters and conditiondependent promoters for effective translational application

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Journal of Integrative Plant Biology 2015年第11期57卷 913-924页

作者： Hee-Jeong Jeong Ki-Hong Jung Department of Plant Molecular systems biotechnology and Crop Biotech Institute Kyung Hee University Graduate School of biotechnology Kyung Hee University

Rice （Oryza sativa） is one of the most important staple food crops for more than half of the world＇s population. The demand is increasing for food security because of population growth and environmental challenges triggered by climate changes. This scenario has led to more interest in developing crops with greater productivity and sustainability. The process of genetic transformation, a major tool for crop improvement, utilizes promoters as one of its key elements. Those promoters are generally divided into three types： constitutive, spatiotemporal, and condition-dependent. Tran- scriptional control of a constitutive promoter often leads to reduced plant growth, due to a negative effect of accumu- lated molecules during cellular functions or energy consump- tion. To maximize the effect of a transgene on transgenic plants, it is better to use condition-dependent or tissue- specific promoters. However, until now, those types have not been as widely applied in crop biotechnology. In this review, we introduce and discuss four groups of tissue-specific promoters （5o promoters in total） and six groups of condition-dependent promoters （27 promoters）. These pro- moters can be utilized to fine-tune desirable agronomic traits and develop crops with tolerance to various stresses, enhanced nutritional value, and advanced productivity.

关键词： Condition-dependent promoters crop biotechnologyapplication genetic transformation rice tissue-specific promoters

In-Depth Computational Analysis of Natural and Artificial Carbon Fixation Pathways

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BioDesign Research 2021年第1期2021卷 96-118页

作者： Hannes Löwe Andreas Kremling systems biotechnology Technical University of MunichGermany

In the recent years,engineering new-to-nature CO_(2)-and C1-fixing metabolic pathways made a leap ***,artificial pathways promise higher yields and activity than natural ones like the Calvin-Benson-Bassham(CBB)*** question remains how to best predict their in vivo performance and what actually makes one pathway“better”than *** this context,we explore aerobic carbon fixation pathways by a computational approach and compare them based on their specific activity and yield on methanol,formate,and CO_(2)/H_(2)considering the kinetics and thermodynamics of the *** pathways found in nature or implemented in the laboratory,this included two completely new cycles with favorable features:the reductive citramalyl-CoA cycle and the 2-hydroxyglutarate-reverse tricarboxylic acid cycle.A comprehensive kinetic data set was collected for all enzymes of all pathways,and missing kinetic data were sampled with the Parameter Balancing *** and thermodynamic data were fed to the Enzyme Cost Minimization algorithm to check for respective inconsistencies and calculate pathway-specific *** specific activities of the reductive glycine pathway,the CETCH cycle,and the new reductive citramalyl-CoA cycle were predicted to match the best natural cycles with superior productsubstrate ***,the CBB cycle performed better in terms of activity compared to the alternative pathways than previously *** make an argument that stoichiometric yield is likely not the most important design criterion of the CBB ***,alternative carbon fixation pathways were paretooptimal for specific activity and product-substrate yield in simulations with C1 substrates and CO_(2)/H_(2)and therefore hold great potential for future applications in Industrial biotechnology and Synthetic Biology.

关键词： argument kinetics thermodynamics

Proteomic dynamics revealed sex-biased responses to combined heat-drought stress in Marchantia

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Journal of Integrative Plant Biology 2024年第10期66卷 2226-2241页

作者： Sara Guerrero Víctor Roces Lara García-Campa Luis Valledor Mónica Meijón Department of Organisms and Systems BiologyFaculty of Biology/BiotechnologyInstitute of AsturiasUniversity of OviedoOviedoAsturias 33071Spain

Recent studies have documented plant responses to climate change extensively, particularly to single-stress exposures. However, critical factors for stress survival, such as sexual differentiation,are not often considered. The dioicous Marchantia polymorpha stands as an evolutionary milestone,potentially preserving ancestral traits from the early colonizers. In this study, we employed proteomic analyses complemented with physiological monitoring to investigate combined heat and drought responses in Tak-1(male) and Tak-2(female)accessions of this liverwort. Additionally, targeted transcriptomics was conducted using different natural populations from contrasting *** findings revealed sex-biased dynamics among natural accessions, particularly evident under control conditions and during early stress responses. Although Tak-2 exhibited greater diversity than Tak-1 under control conditions, male accession demonstrated distinct and more rapid stress sensing and signaling. These differences in stress response appeared to be strongly related to sex-specific plasticity influenced by geoclimatic origin. Furthermore, we established distinct protein gene ages and genomic distribution trends, underscoring the importance of protein diversification over time. This study provides an evolutionary perspective on sexual divergence and stress emergence employing a systems biology approach, which allowed for the establishment of global and sex-specific interaction networks in the stress response.

关键词： abiotic stress land adaptation liverwort sex-biased response systems biology

Development of a 16S r RNA gene-based microarray for the detection of marine bacterioplankton community

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Acta Oceanologica Sinica 2017年第10期36卷 106-114页

作者： ZHAO Wei WANG Jingjing LIANG Yajie HUANG Zhiyong Tianjin Key Laboratory of Industrial Biological systems and Process Engineering Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences

A better understanding of bacterioplankton community shifts following change in marine environments is critical to predict the marine ecosystem function. In order to get a snapshot of the microbial taxonomy profiling of a wide range marine area, a quick, convenient and low cost method would be favorable. In this study, we developed a 16S rRNA gene-based microarray using ARB software, which contained 447 probes targeting 160 families of marine bacteria. The specificity, sensitivity and quantitative capability of this microarray were assessed by single cloned16S rRNA genes. The reliability of this microarray was tested by eight environmental samples. The results showed that the microarray was specific, only 1.16% false results were detected in five single-clone hybridization tests. The microarray could detect DNA samples as few as 1 ng/μL and the signal intensity could reflect the relative abundance of the bacteria in the range of 1 ng/μL to 100 ng/μL of DNA concentration. Hybridization with environmental samples showed that it can discriminate bacterioplankton communities by sites and time. High throughput sequencing results from the eight samples confirmed the hybridization results. It indicated that this developed microarray could be used as a convenient tool to monitor the bacterioplankton community in marine environment.

关键词： microarray bacterioplankton community 16S rRNA gene marine environment

Rice Transcription Factor OsDOFll Modulates Sugar Transport by Promoting Expression of Sucrose Transporter and SWEET Genes

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Molecular Plant 2018年第6期11卷 833-845页

作者： Yunfei Wu Sang-Kyu Lee Youngchul Yoo Jinhuan Wei Suk-Yoon Kwon Sang-Won Lee Jong-Seong Jeon Gynheung An Crop Biotech Institute and Graduate School of biotechnology Kyung Hee University Yongin 17104 Korea Plant systems Engineering Research Center Korea Research Institute of Bioscience and Biotechnology Daejeon 34141 Korea

Sucrose is produced in mesophyll cells and transferred into phloem cells before it is delivered long- distance to sink tissues. However, little is known about how sucrose transport is regulated in plants. Here, we identified a T-DNA insertional mutant of Oryza sativa DNA BINDING WITH ONE FINGER 11 （OsDOF11）, which is expressed in the vascular cells of photosynthetic organs and in various sink tissues. The osdofll mutant plants are semi-dwarf and have fewer tillers and smaller panicles as compared with wild-type （WT） plants. Although sucrose enhanced root elongation in young WT seedlings, this enhance- ment did not occur in osdof11 seedlings due to reduced sucrose uptake. Sugar transport rate analyses revealed that less sugar was transported in osdofll plants than in the WT. Expression of four Sucrose Transporter （SUT） genes-OsSUT1, OsSUT3, OsSUT4, and OsSUT5-as well as two Sugars Will Eventually be Exported Transporters （SWEET） genes, OsSWEETll and OsSWEET14, was altered in various organs of the mutant, including the leaves. Chromatin immunoprecipitation assays showed that OsDOFll directly binds the promoter regions of SUT1, OsSWEETll, and OsSWEET14, indicating that the expression of these transporters responsible for sucrose transport via apopiastic loading is coordinately controlled by OsDOFll. We also observed that osdofll mutant plants were less susceptible to infection byXanthomonas oryzae pathovar oryzae, suggesting that OsDOFll participates in sugar distribution during pathogenic in- vasion. Collectively, these results suggest that OsDOFll modulates sugar transport by regulating the expression of both SUT and SWEET genes in rice.

关键词： OsDOF11 phloem loading rice SUT SWEET Xanthomonas oryzae

Study on the sensitivity to cadmium of marine fish Salaria basilisca(Pisces: Blennidae)

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Journal of Environmental Sciences 2009年第11期21卷 1620-1624页

作者： Imed Messaoudi Sana Barhoumi Khaled Sd Abdelhamid Kerken UR 09/30: Genetic and Biodiversity. Institute of biotechnology Trace Elements Free Radicals Antioxidant Systems and Environment and Humain Pathology

The present study tested the sensitivity of Salaria basilisca to water-cadmium （Cd） contamination. For this purpose, liver somatic index （LSI）, Cd concentrations and the activities of antioxidant enzymes such as catalase （CAT）, superoxide dismutase （SOD） and glutathione peroxidase （GSH-Px） were measured in the liver of S. basilisca exposed to Cd-contaminated water （2 mg Cd/L as CdCl2） for 14 and 28 d. The results showed that the LSI decreased significantly after 14 and 28 d of Cd-exposure. Cd bioaccumulation in the liver resulted in an increasing uptake up to 42 μg/g dry weight after 28 d of exposure. Activities of CAT and SOD were significantly increased with increasing exposure time. A significant increase in GSH-Px activity, under Cd influence, was observed during 14-day exposure period （p 〈 0.0001）. However, a significant decrease （p 〈 0.05） in this activity with respect to control fish was registered after 28 d of Cd-exposure. These results showed that Cd accumulation in the liver of S. basilisca could induce oxidative stress as demonstrated by changes in the antioxidant enzyme activities. Results also emphasized that S. basilisca may considered as a sensitive species to Cd exposure.

关键词： cadmium Salaria basilisca oxidative stress antioxidant enzymes

MicroRNA miR-252-5p regulates the Notch signaling pathway by targeting Rab6 in Drosophila wing development

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Insect Science 2023年第5期30卷 1431-1444页

作者： Do-Hwan Lim Min-Seok Choi Ji Won Jeon Young Sik Lee School of systems Biomedical Science Soongsil UniversitySeoulRepublic of Korea College of Life Sciences and biotechnology Korea UniversitySeoulRepublic of Korea Institute of Animal Molecular biotechnology Korea UniversitySeoulRepublic of Korea

The Notch signaling pathway plays a central role in the development of various ***,dysregulation of microRNAs(miRNAs),which are crucial regulators of gene expression,can disrupt signaling pathways at all stages of *** Notch signaling is involved in wing development in Drosophila,the mechanism underlying miRNA-based regulation of the Notch signaling pathway is ***,we report that loss of Drosophila miR-252 increases the size of adult wings,whereas the overexpression of miR-252 in specific compartments of larval wing discs leads to patterning defects in the adult *** miR-252 overexpression-induced wing phenotypes were caused by aberrant Notch signaling with intracellular accumulation of the full-length Notch receptor during development,which could be due to defects in intracellular Notch trafficking associated with its recycling to the plasma membrane and autophagy-mediated ***,we identified Rab6 as a direct target of miR-252-5p;Rab6 encodes a small Ras-like GTPase that regulates endosomal trafficking *** with this finding,RNAi-mediated downregulation of Rab6 led to similar defects in both wing patterning and Notch ***,co-overexpression of Rab6 completely rescued the wing phenotype associated with miR-252 overexpression,further supporting that Rab6 is a biologically relevant target of miR-252-5p in the context of wing ***,our data indicate that the miR-252-5p-Rab6 regulatory axis is involved in Drosophila wing development by controlling the Notch signaling pathway.

关键词： Drosophila miR-252-5p Notch signaling Rab6 wing development

The crossroads of receptor-mediated signaling and endocytosis in plants

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Journal of Integrative Plant Biology 2018年第9期60卷 827-840页

作者： Lucas Alves Neubus Claus Daniel V.Savatin Eugenia Russinova Department of Plant biotechnology and Bioinformatics Ghent University9052 GhentBelgium Center for Plant systems Biology VIB9052 GhentBelgium

Plants deploy numerous plasma membrane receptors to sense and rapidly react to environmental changes. Correct localization and adequate protein levels of the cell-surface receptors are critical for signaling activation and modulation of plant development and defense against pathogens. After ligand binding, receptors are internalized for degradation and signaling attenuation. However, one emerging notion is that the Iigand-induced endocytosis of reCeptor complexes is important for the signal duration, amplitude, and specificity. Recently, mutants of maior endocytosis players, including clathrin and dynamin, have been shown to display defects in activation of a subset of signal transduction pathways, implying that signaling in plants might not be solely restricted to the plasma membrane. Here, we summarize the up-to-date knowledge of receptor complex endocytosis and its effect on the signaling outcome, in the context of plant development and immunity.

关键词： The crossroads of receptor-mediated signaling and endocytosis in plants BRI PM

Construction and analysis of an integrated biological network of Escherichia coli

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systems Microbiology and Biomanufacturing 2022年第1期2卷 165-176页

作者： Zhitao Mao Teng Huang Qianqian Yuan Hongwu Ma Biodesign Center Key Laboratory of Systems Microbial BiotechnologyTianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjin 300308China University of Chinese Academy of Sciences Beijing 100049China

Escherichia coli is a model organism with a clear genetic background that is widely used in metabolic engineering and synthetic biology *** gain a complete picture of the complexly metabolic and regulatory interactions in ***,researchers often need to retrieve information from various databases which cover diferent types of interactions.A central one-stop service integrating various molecular interactions in *** would be helpful for the *** constructed a database called *** integrated network(EcoIN)by integrating known molecular interaction information from databases and *** contains nearly 160,000 pairs of interactions and users can easily search the diferent types of interacting partners for a metabolite,gene or protein,and thus gain access to a more comprehensive interaction map of *** illustrate the application of EcoIN,we used the full path algorithm to identify metabolic feedback/feedforward regulatory loops having at least two diferent types of regulatory *** this algorithm to analyze the regulatory loops for the amino acid biosynthetic pathways,we found some multi-step regulation loops which may afect the metabolic fux and are potential new engineering *** EcoIN database is freely accessible at http://***/and analysis codes are available at GitHub:https://***/maozhitao/EcoIN.

关键词： E.coli Integrated network Regulatory interactions Regulatory loops