[보고서]바이오매스 생산 최적화를 위한 측근발달 유전자 조절 네트워크 시스템 연구

김정묵

보고서 정보

주관연구기관

전남대학교
Chonnam National University

연구책임자

김정묵

참여연구자

이보영 , 강나영 , Shashank Pandey , 전진 , 이미라 , 조철오 , 김민정 , 김미림 , 전은경 , 문선영

보고서유형

최종보고서

발행국가

대한민국

언어

한국어

발행년월

2018-02

과제시작연도

2017

주관부처

농촌진흥청
Rural Development Administration(RDA)

등록번호

TRKO201800043273

과제고유번호

1395049881

사업명

차세대바이오그린21

DB 구축일자

2018-12-15

키워드

옥신.뿌리체계.측근발달.애기장대.Auxin.LBD.Root architecture.Lateral root development.Arabidopsis.

DOI

https://doi.org/10.23000/TRKO201800043273

표 Analysis of LR formation of ProLBD18:LBD18:SRDX in wild-type and lbd18 mutant backgrounds. A. Seven-d-old seedlings of ProLBD18:LBD18:SRDX Arabidopsis and wild-type (Col-0). # indicates the line number of ProLBD18:LBD18:SRDX/Col-0 plants. B. Seven-d-old seedlings of ProLBD18:LBD18:SRDX/lbd18 plants and the lbd18 single mutant. # indicates the line number of ProLBD18:LBD18:SRDX/lbd18 plants. C. LR densities of Col-0, lbd18, ProLBD18:LBD18:SRDX/Col-0, and ProLBD18:LBD18:SRDX/lbd18 plants. n=20. Asterisks denote statistical significance at P < 0.01 (**) and P < 0.001 (***). D. Expression of EXP14 in wild-type (Col-0), lbd18, ProLBD18:LBD18:SRDX/Col-0 (line#), and ProLBD18:LBD18:SRDX/lbd18 plants. Seven-d-old seedlings were incubated with mock or 20 μM IAA for 6 h, and subjected to qRT-PCR for EXP14 expression. Relative transcript levels are plotted. Data are mean ± SE of three independent biological replications. Asterisks denote statistical significance at P < 0.05 (*). LBD18:SRDX/Col-0 = ProLBD18:LBD18:SRDX/Col-0 (line#2-5); LBD18:SRDX/lbd18 = ProLBD18:LBD18:SRDX/lbd18 (line#1-5)
표 GUS expression of Arabidopsis plants harboring the promoter of cell-cycle genes fused to GUS reporter and ProLBD16:LBD16:SRDX or ProLBD18:LBD18:SRDX in lbd18. A and B. GUS expression of CDKA1;1::GUS (A) or CDKB1;1::GUS (B) in Col-0, ProLBD16:LBD16:SRDX, and ProLBD18:LBD18:SRDX/lbd18 plants. C. GUS expression of CYCB1;1::GUS in Col-0 and ProLBD18:LBD18:SRDX/lbd18 plants. D. Time-course expression analysis of CDKA1;1, CDKB1;1, and CYCB1;1 genes following treatment with DEX in Pro35S:LBD18:GR plants. Seven-d-old Pro35S:LBD18:GR seedlings were incubated with 10 μM DEX for the indicated times, and subjected to qRT-PCR analysis for CDKA1;1, CDKB1;1, and CYCB1;1 gene expression; -12 h indicate samples incubated with mock for 12 h. E. Expression of CDKA1;1, CDKB1;1, and CYCB1;1 following treatment with DEX in ProLBD18:LBD18:GR plants. ProLBD18:LBD18:GR seedlings were grown for 7 d in the absence (filled squares) or presence (open squares) of DEX. Expression of CDKA1;1, CDKB1;1, and CYCB1;1 was then analyzed by qRT-PCR and plotted as relative expression levels
표 Structure prediction of zipper-like conformation of LBD16 and LBD18 dimer using the Phyre2 server. A. LBD18. a and b indicate the helices predicted from amino acids 111-150 of each monomer. B. LBD16. a and b indicate the helices predicted from amino acids 91-120 of each monomer
표 Scheme showing quadruple mutations in the coiled coil of LBD16 and LBD18
표 Analysis of the protein-protein interactions between LBD18 and LBD18Q. A. GST-pull-down assays. GST:LBD18 recombinant proteins were incubated with [35S]-LBD18 or [35S]-LBD18Q for pull-down assays. GST proteins were used as a control. B. Co-immunoprecipitation assays. Protoplasts isolated from 2-week-old Arabidopsis plants were transfected with YFPN:LBD18 and YFPC:LBD18 (lane 1) or with YFPN:LBD18 and YFPC:LBD18Q (lane 2) plasmid DNA. Samples prepared after incubation were precipitated with anti-c-Myc agarose, and immunoblot analysis was performed with monoclonal anti-HA or anti-c-Myc antibody
표 Western blot analysis of proteins isolated from Pro35S:HA:LBD16/lbd16 (A), Pro35S:HA:LBD16Q/lbd16 (B), Pro35S:HA:LBD18/lbd18 (C), and Pro35S:HA:LBD18Q/lbd18 (D) Arabidopsis transgenic lines. Total proteins from each transgenic line were subjected to immunoblot analysis with anti-HA antibody. The numbers within the bracket indicate relative fluorescence intensity of each band in the immunoblot. Fluorescence from each immunoblot band was quantified with the ImageJ. rbcL indicates Ponceau staining of the large subunit of ribulose 1,5-bisphosphate carboxylase/oxygenase used as a loading control
표 Analysis of the role of the dimerization of LBD16 or LBD18 mediated by the coiled-coil motif in lateral root formation in Arabidopsis. A and B, Complementation of lbd16 by LBD16:GR or LBD16Q:GR (A) and lbd18 by LBD18:GR or LBD18Q:GR (B). Plants were grown vertically for 7 days after germination in the absence or presence of 10 μM DEX and lateral root numbers per unit root length (cm) (lateral root density) measured were plotted. Data are mean ± SD values determined from three independent biological replicates. Asterisks denote statistical significance at P < 0.05 (*), P < 0.01 (**), P < 0.001 (***). C, Expression analysis of EXP14 in Pro35S:LBD18:GR/lbd18 and Pro35S:LBD18Q:GR/lbd18 plants. Seven-day-old seedlings were treated with or without 10 μM DEX for 4 h, and then roots were harvested for real-time RT-PCR analysis. Data are mean ± SE values determined from four independent biological replicates (each biological replicate was estimated as the average of two technical RT-PCR replicates). Asterisks denote statistical significance at P < 0.001 (***).
표 Transcriptional activities of LBD18 and LBD18Q via the EXP14 promoter in Arabidopsis mesophyll protoplasts. A, Schematic diagrams showing reporter plasmids and effector plasmids for transient gene expression assays. The effector plasmid consisted of the Gal4 DNA binding domain (GD) fused to the DNA sequences encoding the full-length of LBD18 or LBD18L120P,L127P,V131P,L138P under the control of the CaMV 35S promoter (Pro35S:Ω:LBD18 or Pro35S: Ω:LBD18L120P,L127P,V131P,L138P). The reporter construct consisted of three copies of the Gal4-DNA-binding domain elements fused to the LUC reporter gene (ProGal4(3X):LUC). The reporter construct consisting of LUC driven by the CaMV 35S promoter (Pro35S:GUS) was used for a transfection control. B, Transient gene expression assays. All the LUC activities are presented after normalizing to GUS activity. Data are mean ± SE values determined from three independent biological replicates. Asterisks denote statistical significance at P < 0.01 (*) and P < 0.001 (**)
표 Analysis of protein interaction domain of LBD18 using LCI assays. A, Diagram showing the polypeptide fragments of LBD18 used for LCI assays. The numbers on the LBD18 diagram and in the bracket indicate the positions of amino acids in the polypeptide and the fragments, respectively. B, The LUC images for homodimerization of various LBD18 polypeptide fragments. The numbers on top of the panel indicate the LBD18 polypeptide fragments as shown in Figure 1H. NLuc, N-terminal luciferase; Cluc, C-terminal luciferase. C, Quantification of LCI assays in (B). Data are mean ± SE values determined from three independent biological replicates. D, The LUC images for the protein-protein interactions between LBD18 and various LBD18 polypeptide fragments. E, Quantification of LCI assays in (D). Data are mean ± SE values determined from three independent biological replicates. Asterisks denote statistical significance at P < 0.05 (*) and P < 0.01 (**)
표 A schematic diagram for genome-wide analysis of genes directly or indirectly regulated by LBD18 using microarray analysis with Pro35S:LBR18:GR/lbd18 transgenic Arabidopsis
표 Summary of genes regulated downstream of LBD18 in Arabidopsis. Initiation, genes involved in lateral root initiation; emergence, genes involved in lateral root emergence
표 LBD18 and auxin additively induce ARF19 expression. Seven-day-old Pro35S:LBD18:GR seedlings were incubated with the indicated chemicals (20 μM IAA, 10 μM DEX, and/or 50 μM CHX) for 3 h then roots were harvested for real-time RT-PCR analysis. Mean ± SE values were determined from n = three biological replicates (each biological replicate was estimated as the average of two technical RT-qPCR replicates). Asterisks denote statistical significance at P < 0.01 (**) and P < 0.001 (***)
표 Expression Analysis of ARF19 Gene in ProLBD18:LBD18:GR. (A) Effect of cycloheximide (CHX) treatment on DEX-induced expression of ARF19 gene in ProLBD18:LBD18:GR roots. Seven-day-old seedlings were incubated with DEX and/or CHX for 2 hours and subjected to qRT-PCR analysis. (B) Expression of ARF19 gene in ProLBD18:LBD18:GR roots (8 DAG) treated with Mock, DEX, IAA and DEX+IAA for 2 hours. Mean ± SE values were determined from n = three biological replicates (each biological replicate was estimated as the average of two technical RT-qPCR replicates). Asterisks denote statistical significance at *P < 0.05, **P < 0.01 and ***P < 0.001
표 Expression Analysis of ARF19 in lbd18 Mutant and ProLBD18:LBD18:GR Overexpression Lines. (A) Expression of ARF19 in ProLBD18:LBD18:GR transgenic Arabidopsis grown with or without DEX. Plants were incubated in MS media supplemented with mock (□) or DEX (■) for 7 days, analyzed by qRT-PCR, and plotted as the relative expression level. (B) ARF19 gene expression in WT and lbd18 mutant in response to auxin. EXP14 and Ubiquitin-conjugating enzyme E2 (UBC) genes were used as positive and negative control, respectively. Seven days old seedlings were incubated with IAA (20 μM) or Mock (DMSO) for 3 hours and subjected to RT-qPCR analysis. Mean ± SE values were determined from n = three biological replicates (each biological replicate was estimated as the average of two technical RT-qPCR replicates). Asterisks denote statistical significance at P < 0.05 (*) and P < 0.01 (**)
표 GUS expression of ProARF19:GUS in LBD18 loss-of-function mutant and overexpression lines. Seven days-old light-grown seedlings were incubated with or without DEX (10 μM) for 16 hours and subjected to GUS staining .Scale bars: 50 μm
표 Protein-protein interactions between ARFs and LBD18. (A) BiFC assays for protein-protein interactions between LBD18 and ARFs in Arabidopsis protoplasts. Images represent epi(YFP), auto(chloroplast), and merged images. (B) Split-LUC assay for ARF7 and LBD18 protein interaction. (C) Quantification of Split-LUC assay for ARF7 and LBD18 protein interaction. Bars represent standard errors. Data are means ± standard errors of three independent experiments. (D) Domain structures of LBD18 and ARF7
표 LBD18 interacts with ARF7 through the domains III-IV of ARF7 in LCI assays. (A) Schematic diagram showing the conserved motifs and functional domains of LBD18 and ARF7. (B) The LCI assays in N. benthamiana. (C) Quantification of the LUC activities of LCI (B). Bars represent standard errors. Data are means ± standard errors of three independent experiments
표 Protein-Protein Interactions Between LBD18 and ARF7-III Domain. Full length LBD18 and C-terminal of ARF7-III (#aa811-1165) DNA was inserted into AD and BD vectors. Indicated constructs were transformed into yeast reporter strain Y190 and grown on -Trp/Leu/His media for 3 days. Filter lift assay was conducted for monitoring expression of LacZ reporter gene
표 Domain analysis of LBD18 that binds to ARF7-III/IV domain. (A) Schematic diagram showing the different domains of LBD18. (B) The LCI assays in N. benthamiana. (C) Quantification of the LUC activities of LCI (B). Bars represent standard errors. Data are means ± standard errors of three independent experiments
표 Effects of LBD18 or LB18:SRDX overexpression on the LUC reporter gene fused to the EXP14 promoter or the DR5 promoter in Arabidopsis protoplasts. Reporter constructs consisted of the promoter of EXP14 (ProExp14:LUC) or synthetic promoter DR5 (ProDR5(3X):LUC) fused to LUC. Protoplasts prepared from Arabidopsis mesophyll cells were transfected with the indicated reporters with (□) or without (■) Pro35S:Ω:LBD18 plasmid
표 GUS staining of ProDR5:GUS in wild-type and ProLBD18:LBD18:SRDX/lbd18 plants grown for 7days. Scale bars: 50 μm. WT, wild type
표 Adventitious root numbers of various mutants
표 Adventitious root numbers of arf7, arf19 single and arf7 arf19 double mutants
표 Expression of LBD16 and LBD18 in arf6 and arf8 mutants in response to auxin compared to wild type. Seven days old seedlings were treated with or without 20 μM IAA for indicated times, and then were harvested for RT-qPCR analysis. Mean ± SE values were determined from n = three biological replicates (each biological replicate was estimated as the average of two technical RT-qPCR replicates). WT, wild type
표 Expression of LBD16 and LBD18 in arf7, arf19, and arf7 arf19 mutants in response to auxin compared to wild type upon induction of adventitious root formation in the light for 0 (T0) and 72 h (T72L). (A) Expression of LBD16. (B) Expression of LBD18. Plates in which seeds were sterilized and sowed were incubated at 4℃ for 48 h for stratification and transferred to the light for 5 hours to induce germination. They were then wrapped with three layers of aluminum foil and kept in the dark until the seedling hypocotyls reached an average length of 6 mm (T0). Seedlings were then transferred to the light for induction of adventitious roots for 3 days (T72L) after to the light, and were subjected to RT-qPCR. Mean ± SE values were determined from n = three biological replicates (each biological replicate was estimated as the average of two technical RT-qPCR replicates)
표 Overalpping GUS expression patterns of ProLBD16:GUS and ProLBD18:GUS Arabidopsis during the formation of adventitious root primordium. (A) and (D) 72 h in the dark. (B) and (E) 72 h after transfer to the light. (C) and (F) 6 days after transfer to the light. Arrows indicate adventitious roots or primordia. B1, B2, C1, E1, and E2, magnified view of the square indicated by arrows in B, C, and E, respectively. Bar = 1 cm in (A-F) and 50 μm in (B1, B2, C1, E1, and E2)
표 Overalpping GUS expression patterns of ProARF7:GUS, ProARF19:GUS, and ProARF19:GUS Arabidopsis during the formation of adventitious root primordium. (A), (D) and (G) 72 h in the dark. (B), (E), and (H) 72 h after transfer to the light. (C), (F), and (I) 6 days after transfer to the light. Arrows indicate adventitious roots or primordia. B1, B2, C1, E1, E2, H1, and H2, magnified view of the square indicated by arrows in B, C, E, and H, respectively. Bar = 1 cm in (A-I) and 50 μm in (B1, B2, C1, E1, E2, H1, and H2)
표 Numbers of adventitious roots of lbd16, lbd18, and their complementation lines (ProLBD16:LBD16:myc/lbd16 and ProLBD16:LBD16:myc/lbd16). Plates in which seeds were sterilized and sowed were incubated at 4℃ for 48 h for stratification and transferred to the light for 5 hours to induce germination. They were then wrapped with three layers of aluminum foil and kept in the dark until the seedling hypocotyls reached an average length of 6 mm. Seedlings were then transferred to the light for induction of adventitious roots. Adventitious roots were counted, and the primary root length measured 7 d after transfer to the light. Mean ± SE values were determined from n = three biological replicates. Asterisks denote statistical significance at P < 0.05 (*), P < 0.01 (**), and P < 0.001 (***)
표 GUS expression of ProLBD14:GFP:GUS transgenic Arabidopsis. (A-C) GUS expression in 7-day-old light grown ProLBD14:GFP:GUS seedlings. GUS expression of whole seedling (A), primary and lateral roots (B), and LRP (C). Stages I–VII of primordia were based on the classification by Malamy and Benfey (1997). Scale bars = 50 ㎛
표 Analysis of subcellular localization and transcriptional activities of LBD14 in Arabidopsis mesophyll protoplasts. (A) Subcellular localization of EGFP fusion proteins of LBD14. Images represent epifluorescence (EGFP or RFP), merge, and black and white field images of mesophyll protoplasts transfected with the corresponding plasmid DNAs. Scale bar = 10 ㎛. (B) Transient gene expression assays with Arabidopsis mesophyll protoplasts. Schematic diagrams showing the effector and reporter plasmids. The DNA binding domain of Gal4 (Gal4BD) was fused to LBD14. VP16 was used as a positive control. Arabidopsis mesophyll protoplasts were transfected with the reporter plasmid, Gal4(3x):LUC and the effector plasmid along with 35S:GUS plasmid used as a transfection control. Values on the y-axis are derived from measurements of relative light units of LUC activity after normalizing to GUS activity from a minimum of triplicate experiments. The numbers below the column 1, 2, and 3 indicate the effector plasmids, Gal4BD, Gal4BD:VP16, and Gal4BD:LBD14, respectively. Asterisks denote statistical significance at p<0.05 (*). Bars indicate standard errors
표 Analysis of LR phenotype of DEX-inducible LBD14RNAi transgenic Arabidopsis in the absence or presence of DEX. (A) Quantitative RT-PCR analysis of the LBD13, LBD14, LBD15, LBD16, and LBD18 transcripts in wild-type and DEX-inducible LBD14RNAi transgenic plants. Total RNAs were isolated from 7-day-old seedlings and each RNA sample was subjected to qRT-PCR. Mean ± SE values were determined from n = three biological replicates (each biological replicate was estimated as the average of two technical RT-qPCR replicates). Asterisks denote statistical significance at p<0.01 (**), p<0.001 (***). (B) LR phenotypes of DEX-inducible LBD14RNAi transgenic plants. Seven-day-old seedlings of wild-type and DEX-inducible LBD14RNAi transgenic plants are shown. Scale bars = 1 cm. (C) Primary root lengths of DEX-inducible LBD14RNAi transgenic plants. Error bars indicate the SD (n = 20). (D) LR number of DEX-inducible LBD14RNAi transgenic plants. Error bars indicate the SD (n = 20). (E) LR densities of DEX-inducible LBD14RNAi transgenic plants. LR, densities, LR numbers per unit primary root lengths (cm) measured, were plotted. Error bars indicate the SD (n = 20)
표 Analysis of LR phenotype of Pro35S:LBD14transgenic Arabidopsis. (A) RT-PCR analysis of LBD14 from Pro35S:LBD14 transgenic plants compared with wild-type. Total RNAs were isolated from 7-day-old seedlings and each RNA sample was subjected to RT-PCR. Black triangles indicate transgenic lines used for phenotypic analysis. (B) Seven-day-old wild-type and Pro35S:LBD14 transgenic plants. Scale bars = 1 cm. (C) Primary root length of Pro35S:LBD14 transgenic plants compared with wild-type. (D) LR numbers of Pro35S:LBD14 transgenic plants compared with wild-type. (E) LR densities of Pro35S:LBD14 transgenic plants compared with wild-type. Error bars indicate the SD (n = 20). Asterisks denote statistical significance at p<0.05 (*), p<0.001 (***)
표 Analysis of GUS expression in ProLBD13:GUS transgenic Arabidopsis (A)and subcelluar localization of EGFP:LBD13 in tobacco (B)
표 Analysis of lateral root phenotypes of DEX-inducible LBD13RNAi lines with or without DEX
표 Analysis of lateral root phenotype of lbd36, lbd38, and lbd39 single, double, and triple mutants. (A) Lateral root phenotype. (B) Primary root length. (C) Number of emerged lateral roots per unit primary root length. (D) Number of lateral root primordia and emerged lateral roots. (E) Number of primordia at given primordium developmental stage. Plants were grown vertically for 7 days after germination and analyzed for lateral root number, primary root length, and lateral root primordium. Asterisks denote statistical significance at p<0.01 (**) and p<0.001 (***)
표 Analysis of lateral root length of lbd37, lbd38, and lbd39 mutants. A. Lateral root length of 7-d old light-grown seedlings. n =15. B. Rhizodermal cells on lateral root meristem of lbd37 lbd38 lbd39 comapred to wild type. Plants were vertically grown for 7 d on 0.5x MS agar plate, and photographed at 1000-fold magnification. n>10. C. Meristem cell number, cell size, and length. Asterisks denote statistical significance at p<0.001 (**). Scale bars = 2 μm. Bars indicate SE
표 GUS expression patterns of ProLBD37:GFP:GUS, ProLBD38:GFP:GUS, and ProLBD39:GFP:GUS plants in the root with or without 50 μM ABA
표 GUS expression patterns of ProLBD37:GFP:GUS, ProLBD38:GFP:GUS, and ProLBD39:GFP:GUS plants in in the roots with or without 1 μM epibrassinolide (A) or with or without 20 μM IAA (B)
표 Analysis of lateral root density of lbd37, lbd38, and lbd39 mutants with or without exogenous ABA. A. Number of primordia at given primordium developmental stage before emergence of lateral root. Plants were grown vertically for 3 d on 0.5x MS agar plate, then transferred to 0.5x MS agar plate containing 50 nM ABA, and vertically grown for additional 4 d. Number of lateral root primordium was then measured. n=20. Asterisks denote statistical significance at p<0.05 (*), p<0.01 (**). Bars indicate SE. B. Analysis of lateral root density with varying concentrations of ABA. C. Analysis of total lateral root length with or without ABA

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바이오매스 생산 최적화를 위한 측근발달 유전자 조절 네트워크 시스템 연구
System analysis of gene regulatory network for lateral root development for optimizing plant biomass yield 원문보기

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