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Uncovering key salt-tolerant regulators through a combined eQTL and GWAS analysis using the super pan-genome in rice

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National Science Review 2024年第4期11卷 55-69页

作者： Hua Wei Xianmeng Wang Zhipeng Zhang Longbo Yang Qianqian Zhang Yilin Li Huiying He Dandan Chen Bin Zhang Chongke Zheng Yue Leng Xinglan Cao Yan Cui Chuanlin Shi Yifan Liu Yang Lv Jie Ma Wenchuang He Xiangpei Liu Qiang Xu Qiaoling Yuan Xiaoman Yu Tianyi Wang Hongge Qian Xiaoxia Li Bintao Zhang Hong Zhang Wu Chen Mingliang Guo Xiaofan Dai Yuexing Wang Xiaoming Zheng Longbiao Guo Xianzhi Xie Qian Qian Lianguang Shang Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural Sciences institute of Wetland Agriculture and Ecology Shandong Academy of Agricultural Sciences State Key Laboratory of Rice Biology China National Rice Research Institute National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop Science Chinese Academy of Agricultural Sciences Yazhouwan National Laboratory

For sessile plants, gene expression plays a pivotal role in responding to salinity stress by activating or suppressing specific genes. However, our knowledge of genetic variations governing gene expression in response to salt stress remains limited in natural germplasm. Through transcriptome analysis of the Global Mini-Core Rice Collection consisting of a panel of 202 accessions, we identified 22 345 and 27 610expression quantitative trait loci associated with the expression of 7787 and 9361 e Genes under normal and salt-stress conditions, respectively, leveraging the super pan-genome map. Notably, combined with genome-wide association studies, we swiftly pinpointed the potential candidate gene STG5—a major salt-tolerant locus known as q STS5. Intriguingly, STG5 is required for maintaining Na+/K+homeostasis by directly regulating the transcription of multiple members of the Os HKT gene family. Our study sheds light on how genetic variants influence the dynamic changes in gene expression responding to salinity stress and provides a valuable resource for the mining of salt-tolerant genes in the future.

关键词： super pan-genome expression quantitative trait loci GWAS salt tolerance rice

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Polysulfide modified PtCu intermetallic nanocatalyst with enrichment realizes efficient electrooxidation ethanol to CO_(2)

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Nano research 2024年第4期17卷 2320-2327页

作者： Shuanglong Zhou Zheng Lv Liang Zhao Dan Zhang Zuocao Wang Yu Dai Bin Li Olga Starostenko Jianping Lai Lei Wang Key Laboratory of Eco-chemical Engineering Ministry of EducationTaishan scholar advantage and characteristic discipline team of Eco-chemical process and technologyLaboratory of Inorganic Synthesis and Applied ChemistryCollege of Chemistry and Molecular EngineeringQingdao University of Science and TechnologyQingdao 266042China College of Foreign Languages Qingdao City UniversityQingdao 266106China College of Materials Science and Engineering Qingdao University of Science and TechnologyQingdao 266042China institute of Macromolecular Chemistry of the National Academy of Sciences of Ukraine Kyiv 02160Ukraine shandong Engineering research Center for Marine Environment Corrosion and Safety Protection College of Environment and Safety EngineeringQingdao University of Science and TechnologyQingdao 266042China

The main problem faced by ethanol oxidation reaction(EOR)includes low activity,poor selectivity,and *** the study,we found that polysulfide modified on the surface of PtCu intermetallic(IM)/C can simultaneously enrich hydroxyl and ethanol,which could effectively improve the catalytic activity,CO_(2) selectivity,and durability of *** mass activity and the specific activity of the product in 1 M KOH electrolyte reached 17.83 A·mgPt^(-1) and 24.67 mA·cm^(-2).The CO_(2) selectivity of polysulfide modified product achieved 93.5%,which was 30 folds higher than Pt/*** addition,the catalyst showed high catalytic *** mechanism study demonstrates that the surface modified polysulfide could significantly boost the enrichment effect of ethanol and hydroxyl species,accelerating C–C bond cleavage and CO oxidation.

关键词： Pt CO_(2) selectivity enrichment effect ethanol oxidation reaction(EOR) electrocatalyst

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Better use of experience from other reservoirs for accurate production forecasting by learn-to-learn method

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Petroleum Science 2024年第1期21卷 716-728页

作者： Hao-Chen Wang Kai Zhang Nancy Chen Wen-Sheng Zhou Chen Liu Ji-Fu Wang Li-Ming Zhang Zhi-Gang Yu Shi-Ti Cui Mei-Chun Yang China University of Petroleum(East China) 66 Changjiang West RoadQingdao West Coast New AreaQingdao266580ShandongChina University of Calgary 2500 University Dr NWCalgaryT2N 1N4AlbertaCanada Qingdao University of technology Qingdao266071ShandongChina State Key Laboratory of Offshore Oil Exploitation Beijing100028China CNOOC research institute Ltd. Beijing100028China CNPC Tarim Oilfield Branch Company Korla841000XinjiangChina National Engineering Laboratory for Exploration and Development of Low-Permeability Oil and Gas Fields Xi'an710000ShaanxiChina Sinopec Matrix Co. LTDQingdao266000ShandongChina

To assess whether a development strategy will be profitable enough,production forecasting is a crucial and difficult step in the *** development history of other reservoirs in the same class tends to be studied to make predictions ***,the permeability field,well patterns,and development regime must all be similar for two reservoirs to be considered in the same *** results in very few available experiences from other reservoirs even though there is a lot of historical information on numerous reservoirs because it is difficult to find such similar *** paper proposes a learn-to-learn method,which can better utilize a vast amount of historical data from various ***,the proposed method first learns how to learn samples before directly learning rules in ***,by utilizing gradients from networks with independent parameters and copied structure in each class of reservoirs,the proposed network obtains the optimal shared initial parameters which are regarded as transferable information across different *** on that,the network is able to predict future production indices for the target reservoir by only training with very limited samples collected from reservoirs in the same *** cases further demonstrate its superiority in accuracy to other widely-used network methods.

关键词： Production forecasting Multiple patterns Few-shot learning Transfer learning

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Tomato CYP94C1 inactivates bioactive JA-lle to attenuate jasmonate-mediated defense during fruit ripening

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Molecular Plant 2024年第4期17卷 509-512页

作者： Tianxia Yang Lei Deng Qinyang Wang Chuanlong Sun Muhammad Ali Fangming Wu Huawei Zhaj Qian Xu Peiyong Xin Shujing Cheng Jinfang Chu Tingting Huang Chang-Bao Li Chuanyou Li Key Laboratory of Seed innovation Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China College of Life Sciences Shandong Agricultural UniversityTai'an 271018China Taishan Academy of Tomato innovation Tai'an 271018China CAS Center for Excellence in Biotic Interactions University of Chinese Academy of SciencesBeijing 100049China College of Horticulture Science and Engineering Shandong Agricultural UniversityTaian 271018China institute of Vegetable Qingdao Academy of Agricultural SciencesQingdao 266100China Key Laboratory of Biology and Genetic Improvement of Horticultural Crops(North China) Ministry of AgricultureBeijing Vegetable Research CenterBeijing Academy of Agriculture and Forestry SciencesBejing 100097China Frontiers Science Center for Molecular Design Breeding(MOE) Department of Plant Genetics and BreedingChina Agricultural UniversityBeijing 100193China

Dear Editor,Fruit rot caused by necrotrophic pathogens results in substantial reductions in fruit yield and revenues worldwide(Petrasch et al.,2019).A widespread phenomenon in fleshy fruit species is the susceptibility of ripe fruits to necrotrophs(Silva et al.,2021),which facilitates seed dispersal(Forlani et al.,2019)but causes severe post-harvest losses in *** most of the nutritional and sensory qualities of fruits are elaborated at the ripening stage(Liu et al.,2015),balancing fruit ripening and pathogen resistance to maintain fruit quality has proven to be challenging.A deeper understanding of the mechanisms underlying the increased susceptibility of fruits to necrotrophs during ripening could lead to new strategies for producing necrotrophy-resistant fruits without compromising ripening-relatedquality.

关键词： susceptibility maintain fruit

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Knockout of miR396 genes increases seed size and yield in soybean

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Journal of Integrative Plant Biology 2024年第6期66卷 1148-1157页

作者： Hongtao Xie Fei Su Qingfeng Niu Leping Geng Xuesong Cao Minglei Song Jinsong Dong Zai Zheng Rui Guo Yang Zhang Yuanwei Deng Zhanbo Ji Kang Pang Jian‐Kang Zhu Jianhua Zhu School of Life Sciences Anhui Agricultural UniversityHefei 230036China research Center for Biological Breeding technology Research Institute of Frontier ScienceAnhui Agricultural UniversityHefei 230036China Bellagen Biotechnology Co.Ltd Jinan 250000China institute of Crop Sciences/National Nanfan research institute Chinese Academy of Agricultural SciencesKey Laboratory of Gene Editing Technologies(Hainan)Ministry of Agriculture and Rural AffairsSanya 572025China Southern University of Science and TechnologyShenzhen 518055China Hainan Yazhou Bay Seed Laboratory Sanya 572024China

Yield improvement has long been an important task for soybean breeding in the world in order to meet the increasing demand for food and animal *** R396 genes have been shown to negatively regulate grain size in rice,but whether mi R396 family members may function in a similar manner in soybean is ***,we generated eight soybean mutants harboring different combinations of homozygous mutations in the six soybean mi R396genes through genome editing with clustered regularly interspaced palindromic repeats(CRISPR)/CRISPR-associated nuclease(Cas)12SF01 in the elite soybean cultivar Zhonghuang 302(ZH302).Four triple mutants(mir396aci,mir396acd,mir396adf,and mir396cdf),two quadruple mutants(mir396-abcd and mir396acfi),and two quintuple mutants(mir396abcdf and mir396bcdfi)were *** found that plants of all the mir396 mutants produced larger seeds compared to ZH302 *** tests showed that mir396adf and mir396cdf plants have significantly increased yield in growth zones with relatively high latitude which are suited for ZH302 and moderately increased yield in lower *** contrast,mir396abcdf and mir396bcdfiplants have increased plant height and decreased yield in growth zones with relatively high latitude due to lodging issues,but they are suited for low latitude growth zones with increased yield without lodging *** together,our study demonstrated that loss-of-function of mi R396 genes leads to significantly enlarged seed size and increased yield in soybean,providing valuable germplasms for breeding high-yield soybean.

关键词： Cas12SF01 CRISPR/Cas miR396 seed size soybean yield

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Satellite-enabled enviromics to enhance crop improvement

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Molecular Plant 2024年第6期17卷 848-866页

作者： Rafael T.Resende Lee Hickey Cibele H.Amaral Lucas L.Peixoto Gustavo E.Marcatti Yunbi Xu Universidade Federal de Goia´s(UFG) Agronomy DepartmentPlant Breeding SectorGoiania(GO)74690-900Brazil TheCROP a Precision-Breeding Startup:EnviromicsPhenomicsand GenomicsNo Zip-codeOperating VirtuallyGoiania(GO)and Sete Lagoas(MG)Brazil Queensland Alliance for Agriculture and Food innovation The University of QueenslandBrisbaneQLDAustralia Earth Lab Cooperative Institute for Research in Environmental SciencesUniversity of Colorado BoulderBoulderCO 80303USA Environmental Data Science innovation&Inclusion Lab Cooperative Institute for Research in Environmental SciencesUniversity of Colorado BoulderBoulderCO 80303USA Universidade Federal de Sa˜o Joa˜o del-Rei Forest Engineering DepartmentCampus Sete LagoasSete Lagoas(MG)35701-970Brazil institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081China Peking University institute of Advanced Agricultural Sciences WeifangShandong 261325China BGI Bioverse Shenzhen 518083China

Enviromics refers to the characterization of micro-and macroenvironments based on large-scale environmental *** providing genotypic recommendations with predictive extrapolation at a site-specific level,enviromics could inform plant breeding decisions across varying conditions and anticipate productivity in a changing ***-based integration of statistics,envirotyping(i.e.,determining environmental factors),and remote sensing could help unravel the complex interplay of genetics,environment,and *** support this goal,exhaustive envirotyping to generate precise environmental profiles would significantly improve predictions of genotype performance and genetic gain in ***,informatics management platforms aggregate diverse environmental datasets obtained using optical,thermal,radar,and light detection and ranging(LiDAR)sensors that capture detailed information about vegetation,surface structure,and *** wealth of information,coupled with freely available climate data,fuels innovative enviromics *** enviromics holds immense potential for breeding,a few obstacles remain,such as the need for(1)integrative methodologies to systematically collect field data to scale and expand observations across the landscape with satellite data;(2)state-of-the-art AI models for data integration,simulation,and prediction;(3)cyberinfrastructure for processing big data across scales and providing seamless interfaces to deliver forecasts to stakeholders;and(4)collaboration and data sharing among farmers,breeders,physiologists,geoinformatics experts,and programmers across research *** these challenges is essential for leveraging the full potential of big data captured by satellites to transform 21st century agriculture and crop improvement through enviromics.

关键词： envirotyping precision breeding genotype-environment interactions remote sensing predictive models enviromic information

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Aging hallmarks of the primate ovary revealed by spatiotemporal transcriptomics

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Protein & Cell 2024年第5期15卷 364-384页

作者： Huifen Lu Ying Jing Chen Zhang Shuai Ma Weiqi Zhang Daoyuan Huang Bin Zhang Yuesheng Zuo Yingying Qin Guang-Hui Liu Yang Yu Jing Qu Si Wang Advanced innovation Center for Human Brain Protection National Clinical Research Center for Geriatric DisordersXuanwu Hospital Capital Medical UniversityBeijing 100053China State Key Laboratory of Stem Cell and Reproductive Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China Aging Translational Medicine Center International Center for Aging and CancerBeijing Municipal Geriatric Medical Research CenterXuanwu HospitalCapital Medical UniversityBeijing 100053China State Key Laboratory of Membrane Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Beijing institute for Stem Cell and Regenerative Medicine Beijing 100101China CAS Key Laboratory of Genomic and Precision Medicine Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China institute for Stem cell and Regeneration CASBeijing 100101China China National Center for Bioinformation Beijing 100101China The Fifth People’s Hospital of Chongqing Chongqing 400062China Sino-Danish College University of Chinese Academy of SciencesBeijing 101408China Sino-Danish Center for Education and research Beijing 101408China Department of Obstetrics and Gynecology Center for Reproductive MedicinePeking UniversityThird HospitalBeijing 100191China Clinical Stem Cell research Center Peking UniversityThird HospitalBeijing 100191China Center for Reproductive Medicine Cheeloo College of MedicineShandong UniversityJinan 250012China Key Laboratory of Reproductive Endocrinology of Ministry of Education National Research Center for Assisted Reproductive Technology and Reproductive GeneticsShandong Key Laboratory of Reproductive MedicineShandong Provincial Clinical Research Center for Reproductive HealthJinan 250012China Key Laboratory of Organ Regeneration and Reconstruction Institute of ZoologyChinese Academy of SciencesBeijing 100101China Aging Biomarker Consortium Beijing 100101China

The ovary is indispensable for female reproduction,and its age-dependent functional decline is the primary cause of ***,the molecular basis of ovarian aging in higher vertebrates remains poorly ***,we apply spatiotemporal transcriptomics to benchmark architecture organization as well as cellular and molecular determinants in young primate ovaries and compare these to aged primate *** a global view,somatic cells within the non-follicle region undergo more pronounced transcriptional fluctuation relative to those in the follicle region,likely constituting a hostile microenvironment that facilitates ovarian ***,we uncovered that inflammation,the senescent-associated secretory phenotype,senescence,and fibrosis are the likely primary contributors to ovarian aging(PCOA).Of note,we identified spatial co-localization between a PCOA-featured spot and an unappreciated MT2(Metallothionein 2)highly expressing spot(MT2^(high))characterized by high levels of inflammation,potentially serving as an aging hotspot in the primate ***,with advanced age,a subpopulation of MT2^(high)accumulates,likely disseminating and amplifying the senescent signal *** study establishes the first primate spatiotemporal transcriptomic atlas,advancing our understanding of mechanistic determinants underpinning primate ovarian aging and unraveling potential biomarkers and therapeutic targets for aging and age-associated human ovarian disorders.

关键词： spatial transcriptome primate ovary aging senescence inflammation

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The seismicity in the middle section of the Altyn Tagh Fault system revealed by a dense nodal seismic array

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Earthquake research Advances 2024年第3期4卷 7-15页

作者： Shi Yao Tao Xu Yingquan Sang Lingling Ye Tingwei Yang Chenglong Wu Minghui Zhang Key Laboratory of Mineral Resources Institute of Geology and GeophysicsChinese Academy of SciencesBeijing100029China Department of Earth and Space Sciences Southern University of Science and TechnologyShenzhen518055China innovation Academy for Earth Science Chinese Academy of SciencesBeijing100029China University of Chinese Academy of Sciences Beijing100049China School of Information Engineering Shandong University of AeronauticsBinzhou256603China

The left-lateral Altyn Tagh Fault(ATF) system is the northern boundary of the Qinghai-Xizang Plateau, separating the Tarim Basin and the Qaidam Basin. The middle section of ATF has not recorded any large earthquakes since1598 AD, so the potential seismic hazard is unclear. We develope an earthquake catalog using continuous waveform data recorded by the Tarim-Altyn-Qaidam dense nodal seismic array from September 17 to November23, 2021 in the middle section of ATF. With the machine learning-based picker, phase association, location, match and locate workflow, we detecte 233 earthquakes with M_L-1–3, far more than 6 earthquakes in the routine catalog. Combining with focal mechanism solutions and the local fault structure, we find that seismic events are clustered along the ATF with strike-slip focal mechanisms and on the southern secondary faults with thrusting focal mechanisms. This overall seismic activity in the middle section of the ATF might be due to the northeastward transpressional motion of the Qinghai-Xizang Plateau block at the western margin of the Qaidam Basin.

关键词： Altyn Tagh Fault Machine learning Seismicity Dense seismic array

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Phase reconfiguration of heterogeneous CoFeS/CoNiS nanoparticles for superior battery-type supercapacitors

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Journal of Energy Chemistry 2024年第9期96卷 217-225页

作者： Lina Ma Fan Li Min Zhou Jidong Dong Hao Luo Wei Zhang Wenchao Zhao Xinliang Li Zaixing Jiang Yudong Huang College of Chemistry and Chemical Engineering Qingdao UniversityQingdao 266071ShandongChina School of Materials Science and Engineering Xiamen University of TechnologyXiamen 361024FujianChina Co-innovation Center of Efficient Processing and Utilization of Forest Resources College of Materials Science and EngineeringNanjing Forestry UniversityNanjing 210037JiangusChina Key Laboratory of Material Physics Ministry of EducationSchool of Physics and MicroelectronicsZhengzhou UniversityZhengzhou 450052HenanChina MIIT Key Laboratory of Critical Materials technology for New Energy Conversion and Storage State Key Laboratory of Urban Water Resource and EnvironmentSchool of Chemistry and Chemical EngineeringHarbin Institute of TechnologyHarbin 150001HeilongjiangChina Material Science and Engineering College Northeast Forestry UniversityHarbin 150040HeilongjiangChina

Developing advanced battery-type materials with abundant active sites,high conductivity,versatile morphologies,and hierarchically porous structures is crucial for realizing high-quality hybrid ***,heterogeneous FeS@NiS is synthesized by cationic Co doping via surface-structure *** density functional theory(DFT)theoretical calculations are firstly performed to predict the advantages of Co dopant by improving the OH^(−)adsorption properties and adjusting electronic structure,benefiting ions/electron *** dynamic surface evolution is further explored which demonstrates that CoFeS@CoNiS could be quickly reconstructed to Ni(Co)Fe_(2)O_(4)during the charging process,while the unstable structure of the amorphous Ni(Co)Fe_(2)O_(4)results in partial conversion to Ni/Co/FeOOH at high potentials,which contributes to the more reactive active site and good structural ***,the free-standing electrode reveals excellent electrochemical performance with a superior capacity(335.6 mA h g^(−1),2684 F g^(−1))at 3 A g^(−1).Furthermore,the as-fabricated device shows a quality energy density of 78.1 W h kg^(−1)at a power density of 750 W kg^(−1)and excellent cycle life of 92.1%capacitance retention after 5000 *** work offers a facile strategy to construct versatile morphological structures using electrochemical activation and holds promising applications in energy-related fields.

关键词： In-situ reconfiguration Heterogeneous design Battery-type supercapacitors Superior performance Sulphide

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Efficient biosynthesis of creatine by whole-cell catalysis from guanidinoacetic acid in Corynebacterium glutamicum

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Synthetic and Systems Biotechnology 2024年第1期9卷 99-107页

作者： Chunjian Li Pengdong Sun Guoqing Wei Yuqi Zhu Jingyuan Li Yanfeng Liu Jian Chen Yang Deng College of Food Science and Engineering Qingdao Agricultural UniversityQingdao 266109China Key Laboratory of Special Food Processing(Co-construction by Ministry and Province) Ministry of Agriculture Rural AffairsQingdao Agricultural UniversityQingdao 266109China shandong technology innovation Center of Special Food Qingdao 266109China Qingdao Special Food research institute Qingdao 266109China Qingdao Nuoan Baite Biotechnology Co. Ltd.Qingdao 266109China Science Center for Future Foods Engineering Research Center of Ministry of Education on Food Synthetic Biotechnologyand Jiangsu Province Engineering Research Center of Food Synthetic BiotechnologyJiangnan UniversityWuxi 214122China Key Laboratory of Carbohydrate Chemistry and Biotechnology Ministry of EducationSchool of BiotechnologyJiangnan UniversityWuxi 214122China

Creatine is a naturally occurring derivative of an amino acid commonly utilized in functional foods and ***,the current industrial synthesis of creatine relies on chemical processes,which may hinder its utilization in certain ***,a biological approach was devised that employs whole-cell biocatalysis in the bacterium Corynebacterium glutamicum,which is considered safe for use in food production,to produce safe-for-consumption *** objective of this study was to identify a guanidinoacetate N-methyltransferase(GAMT)with superior catalytic activity for creatine *** employing whole-cell biocatalysis,a gamt gene from Mus caroli(Mcgamt)was cloned and expressed in *** ATCC 13032,resulting in a creatine titer of 3.37 g/***,the study employed a promoter screening strategy that utilized nine native strong promoters in *** to enhance the expression level of *** highest titer was achieved using the P1676 promoter,reaching 4.14 g/*** conditions of whole-cell biocatalysis were further optimized,resulting in a creatine titer of 5.42 g/*** is the first report of successful secretory creatine expression in ***,which provides a safer and eco-friendly approach for the industrial production of creatine.

关键词： Creatine Corynebacterium glutamicum Whole-cell biocatalysis Guanidinoacetate N-Methyltransferase Food additive

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