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Cell-free synthesis system-assisted pathway bottleneck diagnosis and engineering in Bacillus subtilis

Synthetic and Systems biotechnology 2020年第3期5卷 131-136页

作者： Rongzhen Tian Minghu Wang Jintian Shi Xiaolong Qin Haoyu Guo Xuanjie Jia Jianghua Li Long Liu Guocheng Du Jian Chen Yanfeng Liu Science Center for Future Foods Jiangnan UniversityWuxi214122China Key laboratory of Carbohydrate Chemistry and biotechnology Ministry of EducationJiangnan UniversityWuxi214122China National Engineering laboratory for Cereal Fermentation Technology Jiangnan UniversityWuxi214122China

Metabolic engineering is a key technology for cell factories construction by rewiring cellular resources to achieve efficient production of target ***,the existence of bottlenecks in synthetic pathway can seriously affect production efficiency,which is also one of the core issues for metabolic engineers to ***,developing an approach for diagnosing potential metabolic bottlenecks in a faster and simpler manner is of great significance to accelerate cell factories *** cell-free reaction system based on cell lysates can transfer metabolic reactions from in vivo to in vitro,providing a flexible access to directly change protein and metabolite variables,thus provides a potential solution for rapid identification of ***,bottleneck diagnosis of the N-acetylneuraminic acid(NeuAc)biosynthesis pathway in industrially important chassis microorganism Bacillus subtilis was performed using cell-free synthesis ***,a highly efficient *** cell-free system for NeuAc de novo synthesis was firstly constructed,which had a 305-fold NeuAc synthesis rate than that in vivo and enabled fast pathway dynamics ***,through the addition of all potential key intermediates in combination with substrate glucose respectively,it was found that insufficient phosphoenolpyruvate supply was one of the NeuAc pathway *** in vivo metabolic engineering of NeuAc-producing *** was further performed to eliminate the *** down-regulating the expression level of pyruvate kinase throughout the growth phase or only in the stationary phase using inhibitory Nterminal coding sequences(NCSs)and growth-dependent regulatory NCSs respectively,the maximal NeuAc titer increased *** study provides a rapid method for bottleneck diagnosis,which may help to accelerate the cycle of design,build,test and learn cycle for metabolic engineering.

关键词： Pathway bottleneck diagnosis Cell-free synthesis system Bacillus subtilis

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Functional analysis of the circadian clock gene timeless in Tribolium castaneum

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Insect Science 2018年第3期25卷 418-428页

作者： Cheng-Jun Li Xiao-Pei Yun Xiao-Juan Yu Bin Li Jiangsu Key laboratory for Biodiversity and biotechnology College of Life Sciences Nanjing Normal University Nanjing China Institute of Life Sciences School of Food and Biological Engineering Jiangsu University Zhenjiang Jiangsu Province China

Circadian rhythms are endogenous oscillations with a period of about 24 h driven by a circadian clock. So far, variable oscillators have been found in insects. To explore the circadian clock of Tribolium castaneum, we cloned the clock gene timeless （Tctimeless）. Its open reading frame is 3240 bp in length and consists of 10 exons. Tctimeless＇ is highly expressed in the late pupal stage. Tissue-specific expression analysis in late adult stages revealed high expression of Tctimeless in the head, epidermis, fat body and accessory glands. Silencing of Tctimeless by RNA interference （RNAi） at the late larval stages caused a failure to initiate eclosion. Tctimeless knockdown in late pupal stages led to a gender-independent decline in egg production and progeny survival. As a core clock gene, Tctimeless exhibited one expression peak in the middle of the circadian day. Knockdown of Tctimeless disrupted daily expression patterns of Tccycle, Tcclock, Tcperiod and itself, while Tctimeless and Tcperiod expression patterns over the circadian day were also perturbed when Tccycle or Tcclock is suppressed by RNAi. This study identified a complex transcriptional relationship among circadian clock genes in T. castaneum.

关键词： circadian rhythms clock cycle eclosion reproduction timeless

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Pentachlorophenol degradation by Pseudomonas stutzeri CL7 in the secondary sludge of pulp and paper mill

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Journal of Environmental Sciences 2010年第10期22卷 1608-1612页

作者： Santosh Kr.Karn S.K.Chakrabarty M.S.Reddy Department of biotechnology Thapar University Thapar Centre for Industrial Research and Development

A pentachlorophenol （PCP） mineralizing bacterium was isolated from the secondary sludge of pulp and paper mill and identified as Pseudomonas stutzeri strain CL7. This isolate used PCP as its sole source of carbon and energy and was capable of degrading this compound as indicated by stoichiometric release of chloride and biomass formation. P. stutzeri （CL7） was able to mineralize a high concentration of PCP （600 mg/L） than any previously reported Pseudomonad with PCP as sole carbon source. As the concentration of PCP increased from 50 to 600 mg/L, the reduction in the cell growth was observed and the PCP degradation was more than 90% in all studied concentrations. This isolate was able to remove 66.8% of PCP from the secondary sludge of pulp and paper mill when supplemented with 100 mg/L of PCP and grown for two weeks. This study showed that the removal efficiency of PCP by CL7 was found to be very effective and can be used in PCP remediation of pulp paper mill waste in the environment.

关键词： pentachlorophenol 16S rRNA secondary sludge bioremediation pulp and paper mill

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VitisGDB: The Multifunctional Database for grapevine Breeding and Genetics

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Molecular Plant 2020年第8期13卷 1098-1100页

作者： Xiao Dong Wei Chen Zhenchang Liang Xuzhen Li Peter Nick Shanshan Chen Yang Dong Shaohua Li Jun Sheng State Key laboratory for Conservation and Utilization of Bio-Resources in Yunnan Yunnan Agricultural UniversityKunming 650201China College of Agronomy and biotechnology Yunnan Agricultural UniversityKunming 650201China yunnan Research Institute for Local Plateau Agriculture and Industry Kunming 650201China Beijing Key laboratory of grape Sciences and Enology Laboratory of Plant ResourcesInstitute of BotanyChinese Academy of SciencesBeijing 100093China Sino-Africa Joint Research Center Chinese Academy of SciencesWuhan 430074China Faculty of Animal Science and Technology Yunnan Agricultural UniversityKunming 650201China Botanical Institute Karlsruhe Institute of TechnologyKarlsruhe 76128Germany BGI College Zhengzhou UniversityZhengzhou 450001China Key laboratory of Pu'er Tea Science Ministry of EducationYunnan Agricultural UniversityKunming 650201China

grapevine cultivation has been gaining commercial popularity in many parts of the world due to the high yield and versatility of this horticultural crop.A recent survey from the International Organization of Vine and Wine(OIV)estimated that the global area under vine cultivation in 2018 was about 7.4 million hectares and that the world production of grapes was about 77.8 million tons in total(OIV,2019).The majority of the global grape yield is used for producing wines,fresh fruit,and raisins,bringing in annual revenue of billions of US dollars(Alston and Sambucci,2019).In addition to its economic value,the grapevine is also a useful model for the study of the genetic basis of clonality,fruit development,sex determination,grafting,evolution,and domestication(This et al.,2006).Furthermore,for many countries in the world traditional viniculture and viticulture are important emblems of cultural *** these factors have made grapevine one of the most heavily invested plants in horticultural research.

关键词： invested culture bringing

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Molecular mechanisms underlying cell-in-cell formation:core machineries and beyond

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Journal of Molecular Cell Biology 2021年第5期13卷 329-334页

作者： Zubiao Niu Meifang He Qiang Sun laboratory of Cell Engineering Institute of BiotechnologyBeijing 100071China laboratory of General Surgery The First Affiliated HospitalSun Yat-sen UniversityGuangzhou 510080China Research Unit of Cell Death Mechanism Chinese Academy of Medical Sciences2020RU009Beijing 100071China

Although cell-in-cell structures(CICs),with one or more cells present inside another cell,had been identified for a century,it was not until recent years that scientists started to uncover their pivotal roles in multiple biological processes,primarily via mediating the death of internalized ***,considerable progresses were made on deciphering the mechanisms underlying their formation based on different *** was one of the best investigated CIC models,where cell internalization was coordinately driven by adherens junction and contractile ac-tomyosin,the two spatially polarized and complementary core elements that were coupled by mechanical ring,a recently identified core ***,an expanding group of factors were found capable of regulating CIC formation by targeting these core *** elucidation of the molecular machinery controlling CIC formation enables synthetic engineering of cells used for clinical and research purposes。

关键词： mechanisms beyond complementary

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The interaction between the membrane-proximal external region and the N-trimer region of HIV-1 gp41: Involvement in viral fusion

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Chinese Science Bulletin 2009年第10期54卷 1707-1712页

作者： LI Jing LU Lu WU Fan CHEN Xi NIU Ben JIANG ShiBo CHEN YingHua laboratory of Immunology Department of Biological Sciences and Biotechnology Tsinghua University Beijing 100084 China Beijing Key laboratory for Protein Therapeutics Beijing 100084 China laboratory of Viral Immunology Lindsley F. Kimball Research Institute New York Blood Center NY 10065 USA

The membrane proximal external region (MPER) of gp41 is extremely conserved among diverse HIV-1 variants, implying its important role in viral infection. Interestingly, two of the most broadly neutralizing antibodies, 2F5 and 4E10, specifically recognize this region. Our previous study demonstrated that the antigenicity and immunogenicity of 4E10 epitope are affected by remodeling gp41 fusion core, suggesting that the MPER may be associated with gp41 core and involved in gp41-mediated membrane fusion. Here we measured the binding activity of 4E10 epitope peptide (D4E10P) with various gp41 core-derived peptides and found that the N-trimer region in a construct designated N-trimer-6HB interacted significantly with D4E10P. Using N-trimer-6HB to screen a phage library, we identified a motif (WF) located in 4E10 epitope that may play a certain role in the interaction of gp41 MPER with the N-trimer in gp41 fusion core and, we thus speculated upon the potential involvement of MPER in the fusion process between viral envelope and target cell membrane.

关键词： gp41 病毒感染外部区域相互作用三聚体膜融合 HIV 抗原表位

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Polycomb Repressive Complex 2-Mediated H3K27 Trimethylation Is Required for Pathogenicity in Magnaporthe oryzae

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Rice science 2022年第4期29卷 363-374页

作者： WU Zhongling QIU Jiehua SHI Huanbin LIN Chuyu YUE Jiangnan LIU Zhiquan XIE Wei Naweed INAQVI KOU Yanjun TAO Zeng Ministry of Agriculture and Rural Affairs Key laboratory of Molecular Biology of Crop Pathogens and Insects Institute of BiotechnologyZhejiang UniversityHangzhou 310058China State Key laboratory of Rice Biology China National Rice Research InstituteHangzhou 311400China Temasek Life Sciences laboratory and Department of Biological Sciences 1 Research LinkNational University of SingaporeSingapore 117604Singapore

Polycomb repressive complex 2(PRC2)contributes to catalyze the methylation of histone H3 at lysine 27 and plays vital roles in transcriptional silencing and growth development in various *** Magnaporthe oryzae,histone H3K27 is found to associate with altered transcription of in planta induced ***,it is still unknown whether and how H3K27me3 modification is involved in pathogenicity to rice and stress *** this study,we found that core subunits of PRC2,Kmt6-Suz12-Eed,were required for fungal pathogenicity to rice in ***6-Suz12-Eed localized in the nuclei and was necessary for the establishment of H3K27me3 *** ChIP-seq analysis,9.0%of genome regions enriched with H3K27me3 occupancy,which corresponded to 1033 genes in ***,deletion of Kmt6,Suz12 or Eed altered genome-wide transcriptional expression,while the de-repression genes in theΔkmt6 strain were highly associated with H3K27me3 ***,plenty of genes which encode effectors and secreted enzymes,secondary metabolite synthesis genes,and cell wall stress-responsive genes were directly occupied with H3K27me3 modification and de-repression in theΔkmt6 *** results elaborately explained how PRC2 was required for pathogenicity,which is closely related to effector modulated host immunity and host environment adaption.

关键词： rice blast H3K27me3 transcriptional regulation pathogenicity Polycomb repressive complex 2

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Distribution of tetraether lipids in surface sediments of the northern South China Sea:Implications for TEX_(86) proxies

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Geoscience Frontiers 2013年第2期4卷 223-229页

作者： Huangmin Ge Chuanlun L.Zhang Hongyue Dang Chun Zhu Guodong Jia State Key laboratory of Marine Geology Tongji University Department of Marine Sciences University of Georgia State Key laboratory of Heavy Oil Processing & Centre for Bioengineering and biotechnology China University of Petroleum(East China) MARUM Center for Marine Environmental Sciences and Department of Geosciences University of Bremen CAS Key laboratory of Marginal Sea Geology Guangzhou Institute of GeochemistryChinese Academy of Sciences

Archaea have unique glycerol dialkyl glycerol tetraether（GDGT） lipids that can be used to develop paleotemperature proxies such as *** research is to validate proposed GDGT-proxies for paleotemperature determination in the South China Sea（SCS）.Samples were collected from core-top sediments （0-5 cm） in the northern *** lipids were extracted to obtain core GDGTs,which were identified and quantified using liquid chromatography-mass spectrometry（LC-MS）.The abundance of isoprenoidal GDGTs（/GDGTs） ranged from 271.5 ng/g dry sediment to 1266.3 ng/g dry sediment,whereas the branched GDGTs（bGDGTs）,supposedly derived from terrestrial sources,ranged from 22.2 ng/g dry sediment to 56.7 ng/g dry *** TEX_（86）-derived sea surface temperatures ranged from 20.9℃in the coast（water depth 〈 160 m） to 27.9℃offshore（water depth 〉 1000 m）.TEX86-derived temperatures near shore（〈 160 m water depth） averaged 23.1±2.5℃（n =4）,which were close to the satellite-derived winter mean sea surface temperature（average 22.6±1.0℃,n = 4）;whereas the TEX_（86）-derived temperatures offshore averaged 27.4±0.3℃（n = 7） and were consistent with the satellite mean annual sea surface temperature（average 26.8±0.4℃,n = 7）.These results suggest that TEX_（86） may record the sea surface mean annual temperature in the open ocean,while it likely records winter sea surface temperature in the shallower water.

关键词： Archaea GDGTs TEX86 Paleotemperature Northern South China Sea

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Clinical Significance of Apurinic/Apyrimidinic Endodeoxyribonuclease 1 and MicroRNA Axis in Hepatocellular Carcinoma

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Journal of Clinical and Translational Hepatology 2023年第6期11卷 1291-1307页

作者： Giovanna Mangiapane Devis Pascut Emiliano Dalla Giulia Antoniali Monica Degrassi Lory Saveria Crocè Veronica De Sanctis Silvano Piazza Giulia Canarutto Claudio Tiribelli Gianluca Tell laboratory of Molecular Biology and DNA Repair Department of MedicineUniversity of UdineUdineItaly Fondazione Italiana Fegato-ONLUS Liver Cancer UnitTriesteItaly Department of Medical Sciences University of TriesteTriesteItaly Clinica Patologie Fegato Azienda Sanitaria Universitaria Giuliano Isontina(ASUGI)TriesteItaly NGS core Facility Department CIBIOUniversity of TrentoTrentoItaly Computational Biology International Centre for Genetic Engineering and BiotechnologyICGEBTriesteItaly

Background and Aims:Identification of prognostic factors for hepatocellular carcinoma(HCC)opens new perspectives for *** and cellular onco-miRNAs are noncoding RNAs which can control the expression of genes involved in oncogenesis through post-transcriptional *** microRNAs(miRNAs)are considered novel prognostic and predictive factors in *** apurinic/apyrimidinic endodeoxyribonuclease 1(APE1)contributes to the quality control and processing of specific onco-miRNAs and is a negative prognostic factor in several *** present work aims to:a)define APE1 prognostic value in HCC;b)identify miRNAs regulated by APE1 and their relative target genes and c)study their prognostic ***:We used The Cancer Genome Atlas(commonly known as TCGA)data analysis to evaluate the expression of APE1 in *** identify differentially-expressed miRNAs(DEmiRNAs)upon APE1 depletion through specific small interfering RNA,we used NGS and nanostring approaches in the JHH-6 HCC tumor cell *** analyses were performed to identify signaling pathways involving APE1-regulated *** analysis was performed to identify miRNAs correlating with serum APE1 ***:APE1 is considerably overexpressed in HCC tissues compared to normal liver,according to the TCGA-liver HCC(known as LIHC)*** analyses showed that APE1-regulated miRNAs are implicated in signaling and metabolic pathways linked to cell proliferation,transformation,and angiogenesis,identifying Cyclin Dependent Kinase 6 and Lysosomal Associated Membrane Protein 2 as ***-33a-5p,miR-769,and miR-877 are related to lower overall survival in HCC *** array profiling,we identified eight circulating DE-miRNAs associated with APE1 overexpression.A training phase identified positive association between sAPE1 and miR-3180-3p and ***:APE1 regulates specific miRNAs having prognostic value in HCC.

关键词： APE1 miRNAs Prognostic factors Hepatocellular carcinoma

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Allele mining of wheat ABA receptor at Ta PYL4 suggests neo-functionalization among the wheat homoeologs

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Journal of Integrative Agriculture 2022年第8期21卷 2183-2196页

作者： WU Bang-bang SHI Meng-meng Mohammad POURKHEIRANDISH ZHAO Qi WANG Ying YANG Chen-kang QIAO Ling ZHAO Jia-jia YAN Su-xian ZHENG Xing-wei ZHENG Jun Institute of Wheat Research Shanxi Agricultural UniversityLinfen 041000P.R.China Plant Molecular Biology and biotechnology laboratory Faculty of Veterinary and Agricultural SciencesThe University of MelbourneParkvilleVictoria 3010Australia

ABA receptors(PYR/PYL/RCAR)play a central role in the water loss control of plants.A previous report indicated that TaPYL4 is a critical gene in wheat that improves grain production under drought conditions and increases water use *** this study,we analyzed the sequence polymorphisms and genetic effects of *** on isolated TaPYL4 genes from chromosomes 2A,2B and 2D,three haplotypes were detected in the promoter region of TaPYL4-2A,and two haplotypes were present in TaPYL4-2B and TaPYL4-2D,***/trait association analysis indicated that TaPYL4-2A was significantly associated with plant height in 262 Chinese wheat core collection accessions,as well as the drought tolerance coefficient(DTC)for plant height in 239 wheat varieties from Shanxi Province in multiple ***,the frequencies of favored drought-tolerant haplotype TaPYL4-2A-Hap2 were considerably low,accounting for only 10%,and lines with this certain Hap could be reserved in the breeding ***4-2B was significantly associated with grain number,and the favored haplotype TaPYL4-2B-Hap1 was the dominant allele of above 90% in the *** TaPYL4-2D,there were no significant differences in these traits between the two haplotypes in either of the two *** results indicate that variation might lead to functional differentiation among the homoeologs and the haplotypes had undergone artificial selection during *** molecular markers developed to distinguish these haplotypes could be used for breeding in water-limited regions.

关键词： TaPYL4 haplotypes neo-functionalization molecular markers

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