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The protein-protein interaction landscape of Transcription factors during gynoecium development in Arabidopsis

Molecular Plant 2023年第1期16卷 260-278页

作者： Humberto Herrera-Ubaldo Sergio E.Campos Pablo López-Gómez Valentín Luna-García Víctor M.Zúñiga-Mayo Gerardo E.Armas-Caballero Karla L.González-Aguilera Alexander DeLuna Nayelli Marsch-Martínez Carlos Espinosa-Soto Stefan de Folter Unidad de Genómica Avanzada(UGA-LANGEBIO) Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional(CINVESTAV-IPN)IrapuatoGuanajuato 36824México Departamento de Biotecnología y Bioquímica Unidad IrapuatoCINVESTAV-IPNIrapuatoGuanajuato 36824México Instituto de Física Universidad de San Luis PotosíSan Luis PotosíSLP 78290México Present address:Department of Plant Sciences University of CambridgeCambridgeUK Present address:Department of Molecular and Cellular Biology University of California DavisDavisCAUSA Present address:CONACYT Instituto de FitosanidadColegio de PostgraduadosCampus MontecilloTexcocoMéxico

Flowers are composed of organs whose identity is defined by the combinatorial activity of Transcription factors(TFs).The interactions between MADS-box TFs and protein complex formation have been schematized in the floral quartet model of flower development.The gynoecium is the flower’s female reproductive part,crucial for fruit and seed production and,hence,for reproductive success.After the establishment of carpel identity,many tissues arise to form a mature gynoecium.TFs have been described as regulators of gynoecium development,and some interactions and complexes have been identified.However,broad knowledge about the interactions among these TFs and their participation during development remains scarce.In this study,we used a systems biology approach to understand the formation of a complex reproductive unit—as the gynoecium—by mapping binary interactions between well-characterized TFs.We analyzed almost 4500 combinations and detected more than 250 protein-protein interactions(PPIs),resulting in a process-specific interaction map.Topological analyses suggest hidden functions and novel roles for many TFs.In addition,we observed a close relationship between TFs involved in auxin and cytokinin-signaling pathways and other TFs.Furthermore,we analyzed the network by combining PPI data,expression,and genetic data,which helped us to dissect it into several dynamic spatio-temporal subnetworks related to gynoecium development processes.Finally,we generated an extended PPI network that predicts new players in gynoecium development.Taken together,all these results serve as a valuable resource for the plant community.

关键词： interactome networks Transcription factors gynoecium development

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Three Transcription factors and the way immune cells affected by different plasma change in opposite ways in the development of the syndrome of pre-eclampsia

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Chinese Medical Journal 2014年第12期127卷 2252-2258页

作者： Liang Zhou Zhu Jing Wang Yunfei Wang You Zhang Yu Lin Jianhua Di Wen Department of Obstetrics and Gynecology Ren Ji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai 200127China Shanghai Key Laboratory of Gynecologic Oncology Shanghai 200127China

Background How the transcriptional factors regulated the innate and adaptive immune system in pregnancy and preeclampsia are less understood.Nevertheless,what the plasma work in the development of this disease was not sure.The present study was design to evaluate what the transcriptional factors change in innate and adaptive immune system and what the plasma do in this filed.Methods Peripheral blood mononuclear cells （PBMC） from non-pregnant women （n=18）,women with clinically normal pregnancies （n=23） and women with pre-eclampsia （n=20） were separated from peripheral blood to isolate monocytes and T cells.The purity of monocytes and T cells were analysed by flow cytometry.Monocytes and T cells were stimulated in either lipopolysaccharides （LPS） or phorbol-myristate-acetate （PMA）,respectively.transcription Factor Arrays were used to screen the Transcription factors of interest in comparing of different groups.PBMC were isolated from another 8 nonpregnant samples were co-incubated with different groups of plasma.Polymerase chain reaction （PCR） was performed using whole cell extractions of the samples.Results Nuclear factor of activated T-cells-1 （NFAT-1）,signal transducers and activators of transcription-1 （STAT-1） and activator protein-1 （AP-1） are up-regulated in monocytes in pregnancy and more so in pre-eclampsia.On the the contrary,NFAT-1,STAT-1 and AP-1 are down-regulated in T cells in pregnancy and more so in pre-eclampsia.A reduction was observed in interferon （IFN）-y,interleukin （IL）-12 and IL-4 expression in T cells incubated with pre-eclamptic plasma.An elevation was observed in tumor necrosis factor （TNF）-α,IL-1 and IL-12 expression in monocytes incubated with preeclamptic plasma.Conclusions Innate immunity is over activated and adaptive immunity is over suppressed in the development of preeclampsia.NFAT-1,STAT-1 and AP-1 might be the central Transcription factors in the pathogenesis of pre-eclampsia.They induced some changes in plasma and ＂educate＂ the monocytes and T cells for relevant cytokine product

关键词： pre-eclampsia monocytes T cells Transcription factors

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Identification of Target Genes and Transcription factors Implicated in Translation-Dependent Retrograde Sig- naling in Arabidopsis

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Molecular Plant 2014年第7期7卷 1228-1247页

作者： Dario Leister Isidora Romani Lukas Mittermayr Francesca Paieri Elena Fenino Tatjana Kleine Plant Molecular Biology (Botany) Department Biology I Ludwig-Maximilians-University Munich Gro0haderner Str. 2 D-82152Martinsried Germany

Changes in organellar gene expression （OGE） trigger retrograde signaling. The molecular dissection of OGE-dependent retrograde signaling based on analyses of mutants with altered OGE is complicated by compensatory responses that mask the primary signaling defect and by secondary effects that influence other retrograde signaling pathways. Therefore, to identify the earliest effects of altered OGE on nuclear transcript accumulation, we have induced OGE defects in adult plants by ethanol-dependent repression of PRORS1, which encodes a prolyl-tRNA synthetase located in chloroplasts and mitochondria. After 32 h of PRORS1 repression, the translational capacity of chloroplasts was reduced, and this effect subsequently intensified, while basic photosynthetic parameters were still unchanged at 51 h. Analysis of changes in whole-genome transcriptomes during exposure to ethanol revealed that induced PRORS1 silencing affects the expression of 1020 genes in all. Some of these encode photosynthesis-related proteins, including several down-regulated light-harvesting chlorophyll a/b binding （LHC） proteins. Interestingly, genes for presumptive endoplasmic reticulum pro- teins are transiently up-regulated. Furthermore, several NAC-domain-containing proteins are among the Transcription factors regulated. Candidate cis-acting elements which may coordinate the transcriptional co-regulation of genes sets include both G-box variants and sequence motifs with no similarity to known plant c/s-elements.

关键词： Arabidopsis chloroplast mitochondrion retrograde signaling target genes Transcription factors cis-elements.

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Molecular mechanisms of the suppression of axon regeneration by KLF Transcription factors

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Neural Regeneration Research 2014年第15期9卷 1418-1421页

作者： Akintomide Apara Jeffrey L.Goldberg University of Miami Miller School of Medicine MiamiFL USA Shiley Eye CenterUniversity of California San Diego La JollaCA USA

Molecular mechanisms of the Kruppel-like family of Transcription factors （KLFs） have been studied more in proliferating cells than in post-mitotic cells such as neurons. We recently found that KLFs regulate intrinsic axon growth ability in central nervous system （CNS） neurons in- cluding retinal ganglion cells, and hippocampal and cortical neurons. With at least 15 of 17 KLF family members expressed in neurons and at least 5 structurally unique subfamilies, it is import- ant to determine how this complex family functions in neurons to regulate the intricate genetic programs of axon growth and regeneration. By characterizing the molecular mechanisms of the KLF family in the nervous system, including binding partners and gene targets, and comparing them to defined mechanisms defined outside the nervous system, we may better understand how KLFs regulate neurite growth and axon regeneration.

关键词： optic nerve regeneration axon growth retina retinal ganglion cells spinal cord Transcription factors

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Culture conditions for equine bone marrow mesenchymal stem cells and expression of key Transcription factors during their differentiation into osteoblasts

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Journal of Animal Science and Biotechnology 2014年第2期5卷 163-172页

作者： Elizabeth R A Glynn Alfredo Sanchez Londono Steven A Zinn Thomas A Hoagl Kristen E Govoni Department of Animal Science University of Connecticut3636 Horsebarn Road Ext.Unit 4040StorrsCT 06269-4040USA Department of Environmental and Population Health Tufts University North GraftonMA 01536USA

Background： The use of equine bone marrow mesenchymal stem cells （BMSC） is a novel method to improve fracture healing in horses. However, additional research is needed to identify optimal culture conditions and to determine the mechanisms involved in regulating BMSC differentiation into osteoblasts. The objectives of the experiments were to determine： 1） if autologous or commercial serum is better for proliferation and differentiation of equine BMSC into osteoblasts, and 2） the expression of key Transcription factors during the differentiation of equine BMSC into osteoblasts. Equine BMSC were isolated from the sterna of 3 horses, treated with purchased fetal bovine serum （FBS） or autologous horse serum （HS）, and cell proliferation determined. To induce osteoblast differentiation, cells were incubated with L-ascorbic acid-2-phosphate and glycerol-2-phosphate in the presence or absence of human bone morphogenetic protein2 （BMP2）, dexamethasone （DEX）, or combination of the two. Alkaline phosphatase （ALP） activity, a marker of osteoblast differentiation, was determined by ELISA. Total RNA was isolated from differentiating BMSC between d 0 to 18 to determine expression of runt-reloted tronscrJption foctor2 （Runx2）, osterix （Osx）, and T-box3 （Tbx3）. Data were analyzed by ANOVA. Results： Relative to control, FBS and HS increased cell number （133 ± 5 and 116 ± 5%, respectively; P 〈 0.001） and 5-bromo- 2＇-deoxyuridine （BrdU） incorporation （167 ± 6 and 120 ± 6%, respectively; P 〈 0.001）. Treatment with DEX increased ALP activity compared with control （1,638 ± 38%; P 〈 0.001）. In the absence and presence of Dex, BMP-2 did not alter ALP activity （P 〉 0.8）. Runt-reloted transcription foctor2 expression increased 3-fold （P 〈 0.001） by d 6 of culture. Osterix expression increased 94old （P 〈 0.05） by d 18 of culture. Expression of Tbx3 increased 1.8-fold at d 3 （P 〈 0.01）; however expression was reduced 4-fold at d 18 （P 〈 0.01）. Conclusions： Dexamethasone, but not BMP-2, is required for differentiation of equine BMSC into osteo

关键词： Bone marrow mesenchymal stem cells Cell culture Equine Osteoblasts Transcription factors

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Genome-wide Expansion and Expression Divergence of the Basic Leucine Zipper Transcription factors in Higher Plants with an Emphasis on Sorghum

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Journal of Integrative Plant Biology 2011年第3期53卷 212-231页

作者： Jizhou Wang Junxia Zhou Baolan Zhang Jeevanandam Vanitha Srinivasan Ramachandran Shu-Ye Jiang Institute of Botany and Temasek Life Sciences Laboratory Joint Research & Development Laboratory Institute of Botany the Chinese Academy of Sciences Beijing 100093 China Temasek Life Sciences Laboratory 1 Research Link the National University of Singapore Singapore 117604 Singapore

Plant bZIP Transcription factors play crucial roles in multiple biological processes. However, little is known about the sorghum bZIP gene family although the sorghum genome has been completely sequenced. In this study, we have carried out a genome-wide identification and characterization of this gene family in sorghum. Our data show that the genome encodes at least 92 bZIP Transcription factors. These bZIP genes have been expanded mainly by segmental duplication. Such an expansion mechanism has also been observed in rice, arabidopsis and many other plant organisms, suggesting a common expansion mode of this gene family in plants. Further investigation shows that most of the bZIP members have been present in the most recent common ancestor of sorghum and rice and the major expansion would occur before the sorghum-rice split era. Although these bZlP genes have been duplicated with a long history, they exhibited limited functional divergence as shown by nonsynonymous substitutions （Ka）lsynonymous substitutions （Ks） analyses. Their retention was mainly due to the high percentages of expression divergence. Our data also showed that this gene family might play a role in multiple developmental stages and tissues and might be regarded as important regulators of various abiotic stresses and sugar signaling.

关键词： Transcription factors transcription Plants Planting Families Genes Sorghum Genomes Stress Data

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A High-Throughput Screening System for Arabidopsis Transcription factors and Its Application to Med25-Dependent transcriptional Regulation

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Molecular Plant 2011年第3期4卷 546-555页

作者： Bin Oua Kang-Quan Yin Sai-Nan Liu Yan Yang Tren Gu Jennifer Man Wing Hui Li Zhang Jin Miao Youichi Kondou Minami Matsui Hong-Ya Gu Li-Jia Qu National Laboratory for Protein Engineering and Plant Genetic Engineering College of Life Sciences Peking University Beijing 100871 People's Republic ofChina Plant Science Center RIKEN Yokohama Institute 1-7-22 Suehiro-cho Tsurumi-ku Yokohama City Kanagawa 230-0045 Japan The National Plant Gene Research Center (Beijing) Beijing 100101 People's Republic of China

The activities of Transcription factors （TFs） require interactions with specific DNA sequences and other reg- ulatory proteins. To detect such interactions in Arabidopsis, we developed a high-throughput screening system with a Gateway-compatible Gal4-AD-TF library of 1589 Arabidopsis TFs, which can be easily screened by mating-based yeast-one-hybrid （YIH） and yeast-two-hybrid （Y2H） methods. The efficiency of the system was validated by examining two well-characterized TF-DNA and TF-protein interactions： the CHE-CCA1 promoter interaction by YIH and NPR1-TGAs interactions by Y2H. We used this system to identify eight TFs that interact with a Mediator subunit, Med25, a key reg- ulator in JA signaling. We identified five TFs that interacted with the GCC-box cis-element in the promoter of PDF1.2, a downstream gene of Med25. We found that three of these TFs, all from the AP2-EREBP family, interact directly both with Med25 and the GCC-box of PDF1.2, suggesting that Med25 regulates PDF1.2 expression through these three TFs. These results demonstrate that this high-throughput Y1H/Y2H screening system is an efficient tool for studying transcrip- tional regulation networks in Arabidopsis. This system will be available for other Arabidopsis researchers, and thus it provides a vital resource for the Arabidopsis community.

关键词： Transcription factors Arabidopsis yeast-one-hybrid yeast-two-hybrid Med25.

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SQUAMOSA Promoter-Binding Protein-Like Transcription factors:Star Players for Plant Growth and Development

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Journal of Integrative Plant Biology 2010年第11期52卷 946-951页

作者： Xiaobo Chen Zenglin Zhang Danmei Liu Kai Zhang Aili Li Long Mao National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) MOA Key Laboratory of Crop Germplasm & BiotechnologyInstitute of Crop ScienceChinese Academy of Agricultural Sciences (CAAS)Beijing 100081China

SQUAMOSA Promoter-Binding Protein-Like （SPL） genes encode plantspecific Transcription factors that play important roles in plant phase transition,flower and fruit development,plant architecture,gibberellins signaling,sporogenesis,and response to copper and fungal toxins.In Arabidopsis,many SPL genes are post-transcriptionally regulated by the microRNA （miRNA） miR156,among which AtSPL9 in turn positively regulates the expression of the second miRNA miR172.This miR156AtSPL9-miR172 regulatory pathway plays critical roles during juvenile to adult leaf development and the miR156-SPLs feedback interaction persists all through the plant development,which may be conserved in other plants.In the present paper,we provide a concise review on the most recent progress in the regulatory mechanisms associated with plant SPL Transcription factors,especially in relation to miRNAs.The potential application of these discoveries in agriculture is briefly discussed.

关键词： Transcription factors transcription Plants Planting Genes Regulations

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Transcription factors specificity protein and nuclear receptor 4A1 in pancreatic cancer

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World Journal of Gastroenterology 2021年第38期27卷 6387-6398页

作者： Stephen Safe Rupesh Shrestha Kumaravel Mohankumar Marcell Howard Erik Hedrick Maen Abdelrahim Department of Veterinary Physiology and Pharmacology Texas A&M UniversityCollege StationTX 77845United States Department of Biochemistry and Biophysics Texas A&M UniversityCollege StationTX 77845United States Cancer Institute Cleveland ClinicClevelandOH 44195United States Department of Medical Oncology Houston Methodist Hospital Cancer CenterHoustonTX 77030United States

Specificity protein(Sp)Transcription factors(TFs)Sp1,Sp3 and Sp4,and the orphan nuclear receptor 4A1(NR4A1)are highly expressed in pancreatic tumors and Sp1 is a negative prognostic factor for pancreatic cancer patient survival.Results of knockdown and overexpression of Sp1,Sp3 and Sp4 in pancreatic and other cancer lines show that these TFs are individually pro-oncogenic factors and loss of one Sp TF is not compensated by other members.NR4A1 is also a prooncogenic factor and both NR4A1 and Sp TFs exhibit similar functions in pancreatic cancer cells and regulate cell growth,survival,migration and invasion.There is also evidence that Sp TFs and NR4A1 regulate some of the same genes including survivin,epidermal growth factor receptor,PAX3-FOXO1,α5-andα6-integrins,β1-,β3-andβ4-integrins;this is due to NR4A1 acting as a cofactor and mediating NR4A1/Sp1/4-regulated gene expression through GC-rich gene promoter sites.Several studies show that drugs targeting Sp downregulation or NR4A1 antagonists are highly effective inhibitors of Sp/NR4A1-regulated pathways and genes in pancreatic and other cancer cells,and the triterpenoid celastrol is a novel dual-acting agent that targets both Sp TFs and NR4A1.

关键词： Specificity protein Nuclear receptor 4A1 Pancreatic cancer Transcription factors Ligand inhibitors Nuclear receptor 4A antagonists

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Oocyte-associated Transcription factors in reprogramming after somatic cell nuclear transfer:a review

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Frontiers of Agricultural Science and Engineering 2014年第2期1卷 104-113页

作者： Fengxia YIN Hui LIU Shorgan BOU Guangpeng LI The Key Laboratory of National Education Ministry for Mammalian Reproductive Biology and Biotechnology the College of Life SciencesInner Mongolia UniversityHohhot 010070China

Oocytes are unique cells with the inherent capability to reprogram nuclei.The reprogramming of the somatic nucleus from its original cellular state to a totipotent state is essential for term development after somatic cell nuclear transfer.The nuclear-associated factors contained within oocytes are critical for normal fertilization by sperm or for somatic cell nuclear reprogramming.The chromatin of somatic nuclei can be reprogrammed by factors in the egg cytoplasm whose natural function is to reprogram sperm chromatin.The oocyte first obtains its reprogramming capability in the early fetal follicle,and then its capacity is enriched in the late growth phase and reaches its highest capability for reprogramming as fully-grown germinal vesicle oocytes.The cytoplasmic milieu most likely contains all of the specific transcription and/or reprogramming factors necessary for cellular reprogramming.Certain Transcription factors in the cytoplast may be critical as has been demonstrated for induced pluripotent stem cells.The maternal pronucleus exerts a predominant,transcriptiondependent effect on embryo cytofragmentation,with a lesser effect imposed by the ooplasm and the paternal pronucleus.With deep analysis of transcriptomics in oocytes and early developmental stage embryos more maternal Transcription factors inducing cellular reprogramming will be identified.

关键词： nuclear reprogramming somatic cell Transcription factors transcriptomics

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