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Conservation and Diversification of the SHR-SCR- SCL23 Regulatory Network in the Development of the Functional Endodermis in Arabidopsis Shoots

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Molecular Plant 2016年第8期9卷 1197-1209页

作者： Eun Kyung Yoon Souvik Dhar Mi-Hyun Lee Jae Hyo Song Shin Ae Lee Gyuree Kim Sejeong Jang Ji Won Choi Jeong-Eun Choe Jeong Hoe Kim Myeong Min Lee Jun Lim Department of systems biotechnology Konkuk University Seoul 05029 Korea Department of systems Biology Yonsei University Seoul 03722 Korea Department of Biology Kyungpook National University Daegu 41566 Korea 4TheSe tlRors cotribCited equally/to ttats article Present address: Department of Agricultural biotechnology National Institute of Agricultural Sciences Jeonju 54874 Korea Present address: Department of Agricultural Biology National Institute of Agricultural Sciences Wanju 55365 Korea

Development of the functional endodermis of Arabidopsis thaliana roots is controlled, in part, by GRAS transcription factors, namely SHORT-ROOT （SHR）, SCARECROW （SCR）, and SCARECROW-LIKE 23 （SCL23）. Recently, it has been shown that the SHR-SCR-SCL23 regulatory module is also essential for spec- ification of the endodermis （known as the bundle sheath） in leaves. Nevertheless, compared with what is known about the role of the SHR-SCR-SCL23 regulatory network in roots, the molecular interactions of SHR, SCR, and SCL23 are much less understood in shoots. Here, we show that SHR forms protein com- plexes with SCL23 to regulate transcription of SCL23 in shoots, similar to the regulation mode of SCR expression. Our results indicate that SHR acts as master regulator to directly activate the expression of SCR and SCL23. In the SHR-SCR-SCL23 network, we found a previously uncharacterized negative feed- back loop whereby SCL23 modulates SHR levels. Through molecular, genetic, physiological, and morpho- logical analyses, we also reveal that the SHR-SCR-SCL23 module plays a key role in the formation of the endodermis （known as the starch sheath） in hypocotyls. Taken together, our results provide new insights into the regulatory role of the SHR-SCR-SCL23 network in the endodermis development in both roots and shoots.

关键词： endodermis gene regulatory network SHORT-ROOT SCARECROW SCARECROW-LIKE 23,transcription factor

Soil carbon storage and stratification under different tillage/residue-management practices in double rice cropping system

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Journal of Integrative Agriculture 2015年第8期14卷 1551-1560页

作者： CHEN Zhong-du ZHANG Hai-lin S Batsile Dikgwatlhe XUE Jian-fu QIU Kang-cheng TANG Hai-ming CHEN fu College of Agronomy and biotechnology China Agricultural University/Key Laboratory of Farming System Ministry of Agriculture Limpopo Department of Agriculture Research Services (Plant Production Systems Division) Hunan Soil and Fertilizer Institute

The importance of soil organic carbon（SOC） sequestration in agricultural soils as climate-change-mitigating strategy has become an area of focus by the scientific community in relation to soil *** study was conducted to determine the temporal effect of different tillage systems and residue management on distribution, storage and stratification of SOC, and the yield of rice under double rice（Oryza sativa L.） cropping system in the southern China.A tillage experiment was conducted in the southern China during 2005–2011, including plow tillage with residue removed（PT0）, plow tillage with residue retention（PT）, rotary tillage with residue retention（RT）, and no-till with residue retention on the surface（NT）.The soil samples were obtained at the harvesting of late rice in October of 2005, 2007 and ***-year residue return application significantly increased rice yields for the two rice-cropping systems; yields of early and late rice were higher under RT than those under other tillage systems in both years in *** with PT0, SOC stocks were increased in soil under NT at 0–5, 5–10, 10–20, and 20–30 cm depths by 33.8, 4.1, 6.6, and 53.3%, respectively, in *** stocks under RT were higher than these under other tillage treatments at 0–30 cm *** stocks in soil under PT were higher than those under PT0 in the 0–5 and 20–30 cm soil ***, crop residues played an important role in SOC management, and improvement of soil *** the 0–20 cm layer, the stratification ratio（SR） of SOC followed the order NT〉RT〉PT〉PT0; when the 0–30 cm layer was considered, NT also had the highest SR of SOC, but the SR of SOC under PT was higher than that under RT with a multiple-year tillage ***, the notion that conservation tillage lead to higher SOC stocks and soil quality than plowed systems requires cautious ***, some benefits associated with RT system present a greater potential for its adoption in view of the

关键词： soil organic carbon carbon stocks conservation tillage stratification ratio rice yield paddy soil southern China

MINI-EX:Integrative inference of single-cell gene regulatory networks in plants

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Molecular Plant 2022年第11期15卷 1807-1824页

作者： Camilla Ferrari Nicolás Manosalva Pérez Klaas Vandepoele Department of Plant biotechnology and Bioinformatics Ghent University9052 GhentBelgium Center for Plant systems Biology VIB9052 GhentBelgium Bioinformatics Institute Ghent Ghent University9052 GhentBelgium

Multicellular organisms,such as plants,are characterized by highly specialized and tightly regulated cell populations,establishing specific morphological structures and executing distinct *** regulatory networks(GRNs)describe condition-specific interactions of transcription factors(TFs)regulating the expression of target genes,underpinning these specific *** efficient and validated methods to identify cell-type-specific GRNs from single-cell data in plants are lacking,limiting our understanding of the organization of specific cell types in both model species and crops,we developed MINI-EX(Motif-Informed Network Inference based on single-cell EXpression data),an integrative approach to infer cell-type-specific networks in ***-EX uses single-cell transcriptomic data to define expression-based networks and integrates TF motif information to filter the inferred regulons,resulting in networks with increased ***,regulons are assigned to different cell types,leveraging cell-specific expression,and candidate regulators are prioritized using network centrality measures,functional annotations,and expression *** embedded prioritization strategy offers a unique and efficient means to unravel signaling cascades in specific cell types controlling a biological process of *** demonstrate the stability of MINI-EX toward input data sets with low number of cells and its robustness toward missing data,and show that it infers state-of-the-art networks with a better performance compared with other related single-cell network ***-EX successfully identifies key regulators controlling root development in Arabidopsis and rice,leaf development in Arabidopsis,and ear development in maize,enhancing our understanding of cell-type-specific regulation and unraveling the roles of different regulators controlling the development of specific cell types in plants.

关键词： single-cell RNA-seq gene regulatory network transcription factors systems biology

Nucleotide Recognition by a Guanidinocalixarene Receptor in Aqueous Solution

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Chemical Research in Chinese Universities 2023年第1期39卷 144-150页

作者： GENG Wenchao ZHENG Zhe JIANG Huifeng GUO Dongsheng Key Laboratory of systems Microbial biotechnology Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjin300308P.R.China College of Chemistry Key Laboratory of Functional Polymer Materials of Ministry of EducationState Key Laboratory of Elemento-Organic ChemistryNankai UniversityTianjin300071P.R.China

Nucleotides participate in various physiological processes through their supramolecular interactions with ***,the molecular recognition of nucleotides became an important topic in supramolecular chemistry and exhibited many biomedical *** showed very strong binding affinities towards nucleotides,even reaching the nanomolar *** this work,we systematically determined the binding constants between a typical guanidinocalixarene(guanidinium-modified calix[5]arene,GC5A)and various nucleotides and revealed the driving forces behind the molecular recognition using theoretical *** electrostatic interactions and hydrogen bonding provided by the phosphate groups of the nucleotides dominated the binding between the nucleotides and *** lower rim alkyl chains and the skeleton of GC5A provide preorganized cavity and upper guanidinium *** difference in the type of nucleobase is also attributed to the different binding *** work provides insight into the molecular recognition of nucleotides and facilitates the development of new supramolecular hosts for nucleotides and related biological applications.

关键词： Calixarene Nucleotide Molecular recognition Indicator displacement assay Theoretical calculation

Efect of the Gad system on Actinobacillus succinogenes during acid stress

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systems Microbiology and Biomanufacturing 2022年第1期2卷 177-185页

作者： Chunmei Chen Qun Zhang Junzhu Qian Dan Wu Pengcheng Chen Pu Zheng The Key Laboratory of Industrial biotechnology Ministry of EducationSchool of BiotechnologyJiangnan UniversityWuxi 214122China

The glutamate decarboxylase(Gad)system is an important amino acid-dependent acid resistance system commonly found in *** succinogenes is one of the best natural producers of succinic acid(SA)but lacks glutamate *** study assessed the efects of Gad system introduction into *** recombinant strains gadB-SW and gadBC-SW were constructed by heterologous expression of gadB alone,or gadB together with gadC,*** 1.0 and 1.5 h of acid stress at pH 4.6,cell survival of gadBC-SW was greater than *** growth of gadB-SW and gadBC-SW was both afected by the expression of heterologous proteins and byγ-aminobutyric acid,with gadBC-SW growth reduced at a neutral *** production in acidic conditions was evaluated by a shake fask and by 3-L bioreactor *** results showed gadBC-SW to increase SA production by 8.4%in shake fask compared to the parent strain,*** a 3-L bioreactor batch fermentation under acidic environment,the highest conversion rate of sugar to SA was observed for gadBC-SW,reaching 96%.However,SA concentration by gadBC-SW was only 47 g/L and 31 g/L at pH 6.5 and pH 6.0,*** summary,the introduction of heterologous gadB and gadC into *** not only improved acid tolerance but also infuenced the synthesis of SA and added a metabolic burden.

关键词： Actinobacillus succinogenes Acid stress Glutamate decarboxylase Succinic acid Glutamate

Methanol tolerance upgrading of Proteus mirabilis lipase by machine learning‑assisted directed evolution

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systems Microbiology and Biomanufacturing 2023年第3期3卷 427-439页

作者： Rui Ma Yingnan Li Meng Zhang Fei Xu Ministry of Education Key Laboratory of Industrial biotechnology School of BiotechnologyJiangnan UniversityWuxi 214122China

For many crucial industrial applications,enzyme-catalyzed processes take place in harsh organic solvent ***,it remains a challenging problem to improve enzyme stability in organic *** study utilized the MLDE(machine learning-assisted directed evolution)protocol to improve the methanol tolerance of Proteus mirabilis lipase(PML).The machine learning(ML)models were trained based on 266 combinatorial *** top 3 in 22 regression models based on evaluation of tenfold cross-validation,the fitness landscape of the 8000 full-space combinatorial mutants was *** mutants in the restricted library showed higher methanol tolerance,among which the methanol tolerance of G202N/K208G/G266S(NGS)was up to 13-fold compared with the *** dynamics(MD)simulation showed that reconstructing of critical hydrogen bond network in the mutant region of NGS provides a more stable local *** compact structure may improve the methanol tolerance by preventing organic solvent molecules into the activity site and resisting structural *** work provides a successful case of evolution guided by ML for higher organic solvent tolerance of enzyme,and may also be a reference for broad enzyme modifications.

关键词： Organic solvent tolerance Enzyme engineering Fitness prediction Site striation mutagenesis Molecular dynamics

Enhanced thermostability and catalytic efciency of glucose oxidase in Pichia Pastoris

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systems Microbiology and Biomanufacturing 2022年第2期2卷 296-304页

作者： Hanlei Zhou Pu Zheng Pengcheng Chen Xiaowei Yu Dan Wu The Key Laboratory of Industrial biotechnology Ministry of EducationSchool of BiotechnologyJiangnan UniversityWuxi 214122China

Glucose oxidase(GOD)has many practical applications,but its poor thermostability limits its broader *** this research,three primary mutants of wild-type GOD were designed using rational mutagenesis,and the GODm mutant was constructed by combinatorial *** expression,purifcation,and enzymatic properties of the mutants were *** specifc enzyme activity of GODm was 2.10-fold higher than that of wild type,and the(k_(cat)/K_(m))value was increased by *** treatment at 55℃for 3 h,GODm retained 37.5%of its enzymatic activity,and the half-life(t_(1/2))of GODm at 55℃and 65℃was 2.28-fold and 3.36-fold higher than that of wild type,*** analyzing the three-dimensional structure of wild type and the GODm mutant,it was found that T30V formed a new hydrogen bond with FAD and strengthened the hydrophobic interaction,D315K optimized the surface electrostatic interaction,and A162T improved the efciency of the electron ***,a novel mutant with improved thermostability and catalytic efciency was obtained in this research.

关键词： Glucose oxidase Pichia pastoris Thermostability Catalytic efciency Rational mutagenesis

Observation of mitochondrial activity based on temporal and spatial pH variations measured by near-field fluorescent ratiometry

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Science China(Physics,Mechanics & Astronomy) 2011年第12期54卷 2225-2229页

作者： LI YongBo SHIONHARA Ryosuke IWAMI Kentaro OHTA Yoshihiro UMEDA Norihiro Department of Mechanical systems Engineering Tokyo University of Agriculture and Technology Tokyo 184-8588 Japan Department of biotechnology and Life Science Tokyo University of Agriculture and Technology Tokyo 184-8588 Japan

A novel method combining dual wavelength fluorescent ratiometry with scanning near-field optical microscopy (SNOM) is proposed and developed to measure the concentration and distribution of protons in the vicinity of biological samples. This method involves immersing mitochondria in a pH-sensitive fluorescent dye solution instead of injecting the dye into the surface of the mitochondrial membrane. It uses a dual emission pH-sensitive dye and SNOM with a thermally pulled and metal-coated optical fiber probe to improve the spatial resolution. The time dependence of the fluorescence intensity ratio (FIR) under acid addition and the response of mitochondria to nutritional supplementation were studied by using this method. Activation of mitochondria and a distance-dependent delay in the FIR response were observed. The results confirmed that mitochondrial activity could be observed by using this method.

关键词： local pH pH measurement SNOM proton concentration mitochondrial membrane ATP synthesis

Identification of neutral genome integration sites with high expression and high integration efficiency in Fusarium venenatum TB01

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Synthetic and systems biotechnology 2023年第1期8卷 141-147页

作者： Sheng Tong Kexin An Wuxi Chen Mengdan Chai Yuanxia Sun Qinhong Wang Demao Li Tianjin Key Laboratory for Industrial Biological systems and Bioprocessing Engineering Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjin300308China National Innovation Centre for Synthetic Biology Tianjin300308China

CRISPR/Cas9-mediated homology-directed recombination is an efficient method to express target *** on the above method,providing ideal neutral integration sites can ensure the reliable,stable,and high expression of target *** this study,we obtained a fluorescent transformant with neutral integration and high expression of the GFP expression cassette from the constructed GFP expression library and named strain *** integration site mapped at 4886 bp upstream of the gene FVRRES_00686 was identified in strain FS based on a Y-shaped adaptor-dependent extension,and the sequence containing 600 bp upstream and downstream of this site was selected as the candidate region for designing sgRNAs(Sites)for CRISPR/Cas9-mediated homology-directed *** analysis showed that the integration efficiency of CRISPR/Cas9-mediated integration of target genes in designed sites reached 100%.Further expression stability and applicability analysis revealed that the integration of the target gene into the above designed sites can be stably inherited and expressed and has no negative effect on the growth of *** *** results indicate the above designed neutral sites have the potential to accelerate the development of *** TB01 through overexpression of target genes in metabolic engineering.

关键词： GFP expression library Neutral integration site Y-shaped adaptor-dependent extension CRISPR/Cas9 Fusarium venenatum