Database : MEDLINE
Search on : MADS and Domain and Proteins [Words]
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  1 / 1937 MEDLINE  
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[PMID]: 29474620
[Au] Autor:Rümpler F; Theißen G; Melzer R
[Ad] Address:Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, Jena, Germany.
[Ti] Title:A conserved leucine zipper-like motif accounts for strong tetramerization capabilities of SEPALLATA-like MADS-domain transcription factors.
[So] Source:J Exp Bot;, 2018 Feb 21.
[Is] ISSN:1460-2431
[Cp] Country of publication:England
[La] Language:eng
[Ab] Abstract:The development of angiosperm flowers is regulated by homeotic MIKC-type MADS-domain transcription factors that activate or repress target genes via the formation of DNA-bound, organ specific tetrameric complexes. The protein-protein interaction (PPI) capabilities differ considerably between different MIKC-type proteins. The floral homeotic protein SEPALLATA3 (SEP3) acts as a hub that incorporates numerous other MADS-domain proteins into tetrameric complexes that would otherwise not form. However, the molecular mechanisms that underlie these promiscuous interactions remain largely unknown. In this study we created a collection of amino acid substitution mutants of SEP3 to quantify the contribution of individual residues on protein tetramerization during DNA-binding, employing methods of molecular biophysics. We show that leucine residues at certain key positions form a leucine zipper structure that is essential for tetramerization of SEP3, whereas the introduction of physicochemically very similar residues at respective sites impedes the formation of DNA-bound tetramers. Comprehensive molecular evolutionary analyses of MADS-domain proteins from a diverse set of flowering plants revealed exceedingly high conservation of the identified leucine residues within SEP3-subfamily proteins throughout angiosperm evolution. In contrast, MADS-domain proteins that are unable to tetramerize among themselves exhibit preferences for other amino acids at homologous sites. Our findings indicate that the subfamily-specific conservation of amino acid residues at just a few key positions account for subfamily-specific interaction capabilities of MADS-domain transcription factors and shaped the present-day structure of the PPI network controlling flower development.
[Pt] Publication type:JOURNAL ARTICLE
[Em] Entry month:1802
[Cu] Class update date: 180223
[Lr] Last revision date:180223
[St] Status:Publisher
[do] DOI:10.1093/jxb/ery063

  2 / 1937 MEDLINE  
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[PMID]: 29298836
[Au] Autor:Bollier N; Sicard A; Leblond J; Latrasse D; Gonzalez N; Gévaudant F; Benhamed M; Raynaud C; Lenhard M; Chevalier C; Hernould M; Delmas F
[Ad] Address:UMR1332 BFP, INRA, Université de Bordeaux, 33882 Villenave d'Ornon Cedex, France.
[Ti] Title:At-MINI ZINC FINGER2 and Sl-INHIBITOR OF MERISTEM ACTIVITY, a Conserved Missing Link in the Regulation of Floral Meristem Termination in Arabidopsis and Tomato.
[So] Source:Plant Cell;30(1):83-100, 2018 Jan.
[Is] ISSN:1532-298X
[Cp] Country of publication:United States
[La] Language:eng
[Ab] Abstract:In angiosperms, the gynoecium is the last structure to develop within the flower due to the determinate fate of floral meristem (FM) stem cells. The maintenance of stem cell activity before its arrest at the stage called FM termination affects the number of carpels that develop. The necessary inhibition at this stage of ( ), which is responsible for stem cell maintenance, involves a two-step mechanism. Direct repression mediated by the MADS domain transcription factor AGAMOUS (AG), followed by indirect repression requiring the C2H2 zinc-finger protein KNUCKLES (KNU), allow for the complete termination of floral stem cell activity. Here, we show that MINI ZINC FINGER2 (AtMIF2) and its homolog in tomato ( ), INHIBITOR OF MERISTEM ACTIVITY (SlIMA), participate in the FM termination process by functioning as adaptor proteins. AtMIF2 and SlIMA recruit AtKNU and SlKNU, respectively, to form a transcriptional repressor complex together with TOPLESS and HISTONE DEACETYLASE19. AtMIF2 and SlIMA bind to the and loci in the respective plants, leading to their repression. These results provide important insights into the molecular mechanisms governing (FM) termination and highlight the essential role of AtMIF2/SlIMA during this developmental step, which determines carpel number and therefore fruit size.
[Pt] Publication type:JOURNAL ARTICLE
[Em] Entry month:1801
[Cu] Class update date: 180223
[Lr] Last revision date:180223
[St] Status:In-Data-Review
[do] DOI:10.1105/tpc.17.00653

  3 / 1937 MEDLINE  
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[PMID]: 29222401
[Ti] Title:Genetics of Floral Development (By Christine Fleet).
[So] Source:Plant Cell;29(11), 2017 Nov.
[Is] ISSN:1532-298X
[Cp] Country of publication:United States
[La] Language:eng
[Ab] Abstract:Summaryplantcell;29/11/tpc.117.tt1117/FIG1F1fig1A basic model for floral organ identity has been developed using model systems such as , snapdragon ( ), and petunia ( ). In this model, different combinations of proteins known as ABCDE proteins, mostly MADS-domain transcription factors, activate the transcription of target genes to specify the identity of each whorl of floral organs. Changes in the regulation or activation of these target genes contribute to the wide variety of floral forms that we see within and across species. In addition, duplications and divergence of these genes in different groups of flowering plants have resulted in differences in gene function and expression patterns, contributing to differences in flower form across species. Posted December 8, 2017.Click HERE to access Teaching Tool Components.
[Pt] Publication type:JOURNAL ARTICLE
[Em] Entry month:1712
[Cu] Class update date: 171220
[Lr] Last revision date:171220
[St] Status:In-Process

  4 / 1937 MEDLINE  
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[PMID]: 28950098
[Au] Autor:Sharif J; Koseki H
[Ad] Address:Developmental Genetics Group, Center for Integrative Medical Sciences (IMS), RIKEN, 1-7-22 Suehiuro-cho, Tsurumi-ku, Yokohama-shi, Kanagawa-ken 230-0045, Japan. Electronic address: jafar.sharif@riken.jp.
[Ti] Title:No Winter Lasts Forever: Polycomb Complexes Convert Epigenetic Memory of Cold into Flowering.
[So] Source:Dev Cell;42(6):563-564, 2017 09 25.
[Is] ISSN:1878-1551
[Cp] Country of publication:United States
[La] Language:eng
[Ab] Abstract:Two recent papers in Science (Jiang and Berger, 2017 and Yang et al., 2017) reveal that an epigenetic mechanism, mediated by polycomb repressor complex 2 (PRC2), induces flowering after prolonged cold. This repression is biphasic, requiring nucleation and propagation; and, strikingly, appears to be intrinsically linked with DNA replication.
[Mh] MeSH terms primary: Arabidopsis Proteins/genetics
MADS Domain Proteins/genetics
[Mh] MeSH terms secundary: Arabidopsis/genetics
Flowers/genetics
Gene Expression Regulation, Plant
Polycomb-Group Proteins/genetics
Repressor Proteins/genetics
[Pt] Publication type:JOURNAL ARTICLE; COMMENT
[Nm] Name of substance:0 (Arabidopsis Proteins); 0 (MADS Domain Proteins); 0 (Polycomb-Group Proteins); 0 (Repressor Proteins)
[Em] Entry month:1710
[Cu] Class update date: 171030
[Lr] Last revision date:171030
[Js] Journal subset:IM
[Da] Date of entry for processing:170927
[St] Status:MEDLINE

  5 / 1937 MEDLINE  
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[PMID]: 28759577
[Au] Autor:Kim DH; Xi Y; Sung S
[Ad] Address:Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, the University of Texas at Austin, TX, United States of America.
[Ti] Title:Modular function of long noncoding RNA, COLDAIR, in the vernalization response.
[So] Source:PLoS Genet;13(7):e1006939, 2017 Jul.
[Is] ISSN:1553-7404
[Cp] Country of publication:United States
[La] Language:eng
[Ab] Abstract:The long noncoding RNA COLDAIR is necessary for the repression of a floral repressor FLOWERING LOCUS C (FLC) during vernalization in Arabidopsis thaliana. The repression of FLC is mediated by increased enrichment of Polycomb Repressive Complex 2 (PRC2) and subsequent trimethylation of Histone H3 Lysine 27 (H3K27me3) at FLC chromatin. In this study we found that the association of COLDAIR with chromatin occurs only at the FLC locus and that the central region of the COLDAIR transcript is critical for this interaction. A modular motif in COLDAIR is responsible for the association with PRC2 in vitro, and the mutations within the motif that reduced the association of COLDAIR with PRC2 resulted in vernalization insensitivity. The vernalization insensitivity caused by mutant COLDAIR was rescued by the ectopic expression of the wild-type COLDAIR. Our study reveals the molecular framework in which COLDAIR lncRNA mediates the PRC2-mediated repression of FLC during vernalization.
[Mh] MeSH terms primary: Arabidopsis Proteins/genetics
Epigenesis, Genetic
MADS Domain Proteins/genetics
RNA, Long Noncoding/genetics
Repressor Proteins/genetics
[Mh] MeSH terms secundary: Arabidopsis/genetics
Arabidopsis/growth & development
Chromatin/genetics
Flowers/genetics
Flowers/growth & development
Gene Expression Regulation, Plant
Mutation
Nucleotide Motifs/genetics
Plants, Genetically Modified/genetics
Plants, Genetically Modified/growth & development
RNA-Binding Proteins/genetics
[Pt] Publication type:JOURNAL ARTICLE
[Nm] Name of substance:0 (Arabidopsis Proteins); 0 (COLDWRAP long noncoding RNA, Arabidopsis); 0 (Chromatin); 0 (FLF protein, Arabidopsis); 0 (MADS Domain Proteins); 0 (PRC2 protein, Arabidopsis); 0 (RNA, Long Noncoding); 0 (RNA-Binding Proteins); 0 (Repressor Proteins)
[Em] Entry month:1708
[Cu] Class update date: 170827
[Lr] Last revision date:170827
[Js] Journal subset:IM
[Da] Date of entry for processing:170801
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pgen.1006939

  6 / 1937 MEDLINE  
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[PMID]: 28733422
[Au] Autor:Smaczniak C; Muiño JM; Chen D; Angenent GC; Kaufmann K
[Ad] Address:Laboratory of Molecular Biology, Wageningen University, Wageningen 6708PB, The Netherlands.
[Ti] Title:Differences in DNA Binding Specificity of Floral Homeotic Protein Complexes Predict Organ-Specific Target Genes.
[So] Source:Plant Cell;29(8):1822-1835, 2017 Aug.
[Is] ISSN:1532-298X
[Cp] Country of publication:United States
[La] Language:eng
[Ab] Abstract:Floral organ identities in plants are specified by the combinatorial action of homeotic master regulatory transcription factors. However, how these factors achieve their regulatory specificities is still largely unclear. Genome-wide in vivo DNA binding data show that homeotic MADS domain proteins recognize partly distinct genomic regions, suggesting that DNA binding specificity contributes to functional differences of homeotic protein complexes. We used in vitro systematic evolution of ligands by exponential enrichment followed by high-throughput DNA sequencing (SELEX-seq) on several floral MADS domain protein homo- and heterodimers to measure their DNA binding specificities. We show that specification of reproductive organs is associated with distinct binding preferences of a complex formed by SEPALLATA3 and AGAMOUS. Binding specificity is further modulated by different binding site spacing preferences. Combination of SELEX-seq and genome-wide DNA binding data allows differentiation between targets in specification of reproductive versus perianth organs in the flower. We validate the importance of DNA binding specificity for organ-specific gene regulation by modulating promoter activity through targeted mutagenesis. Our study shows that intrafamily protein interactions affect DNA binding specificity of floral MADS domain proteins. Differential DNA binding of MADS domain protein complexes plays a role in the specificity of target gene regulation.
[Pt] Publication type:JOURNAL ARTICLE
[Em] Entry month:1707
[Cu] Class update date: 170926
[Lr] Last revision date:170926
[St] Status:In-Process
[do] DOI:10.1105/tpc.17.00145

  7 / 1937 MEDLINE  
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[PMID]: 28726092
[Au] Autor:Slugina MA; Kochieva EZ; Skryabin KG; Shchennikova AV
[Ad] Address:Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia. machinmail@mail.ru.
[Ti] Title:Homeotic MADS-box genes encoding LeMADS-MC orthologues in wild tomato species (genus Solanum).
[So] Source:Dokl Biochem Biophys;474(1):224-227, 2017 May.
[Is] ISSN:1608-3091
[Cp] Country of publication:Russia (Federation)
[La] Language:eng
[Ab] Abstract:New full-length genes encoding the LeMADS-MC transcription factor orthologues were identified and functionally characterized in wild tomato species S. cheesmaniae and S. habrochaites. A comparative analysis of the encoded proteins and LeMADS-MC of the cultivated tomato species S. lycopersicum revealed two major amino acid residues substitutions: V155E in the K-domain of ShaMADS-MC (S. habrochaites) and S80L in the I-region of SchMADS-MC (S. cheesmaniae). Structural differences of the C-terminal regions of MC and the canonical euAP1 proteins indicate possible chromosomal rearrangements in the Solanoideae subfamily, which, however, did not change the main known conserved euAP1 functions.
[Mh] MeSH terms primary: Plant Proteins/genetics
Sequence Homology, Nucleic Acid
Solanum/genetics
[Mh] MeSH terms secundary: Amino Acid Sequence
Gene Expression Regulation, Plant
Plant Proteins/chemistry
Plant Proteins/metabolism
Solanum/metabolism
[Pt] Publication type:JOURNAL ARTICLE
[Nm] Name of substance:0 (Plant Proteins)
[Em] Entry month:1709
[Cu] Class update date: 170906
[Lr] Last revision date:170906
[Js] Journal subset:IM
[Da] Date of entry for processing:170721
[St] Status:MEDLINE
[do] DOI:10.1134/S1607672917030206

  8 / 1937 MEDLINE  
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[PMID]: 28623580
[Au] Autor:Smaczniak C; Angenent GC; Kaufmann K
[Ad] Address:Laboratory of Molecular Biology, Wageningen University, Wageningen, The Netherlands.
[Ti] Title:SELEX-Seq: A Method to Determine DNA Binding Specificities of Plant Transcription Factors.
[So] Source:Methods Mol Biol;1629:67-82, 2017.
[Is] ISSN:1940-6029
[Cp] Country of publication:United States
[La] Language:eng
[Ab] Abstract:Systematic evolution of ligands by exponential enrichment (SELEX) is a method that allows isolating specific nucleotide sequences that interact with a DNA binding protein of choice. By using a transcription factor (TF) and a randomized pool of double-stranded DNA, this technique can be used to characterize TF DNA binding specificities and affinities. The method is based on protein-DNA complex immunoprecipitation with protein-specific antibodies and subsequent DNA selection and amplification. Application of massively parallel sequencing (-seq) at each cycle of SELEX allows determining the relative affinities to any DNA sequence for any transcription factor or TF complex. The resulting TF DNA binding motifs can be used to predict potential DNA binding sites in genomes and thereby direct target genes of TFs.
[Pt] Publication type:JOURNAL ARTICLE
[Em] Entry month:1706
[Cu] Class update date: 170617
[Lr] Last revision date:170617
[St] Status:In-Process
[do] DOI:10.1007/978-1-4939-7125-1_6

  9 / 1937 MEDLINE  
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[PMID]: 28562649
[Au] Autor:Jin Y; Wang Y; Zhang D; Shen X; Liu W; Chen F
[Ad] Address:Biotechnology Research Center, China Three Gorges University, Yichang, Hubei Province, P. R. China.
[Ti] Title:Floral organ MADS-box genes in Cercidiphyllum japonicum (Cercidiphyllaceae): Implications for systematic evolution and bracts definition.
[So] Source:PLoS One;12(5):e0178382, 2017.
[Is] ISSN:1932-6203
[Cp] Country of publication:United States
[La] Language:eng
[Ab] Abstract:The dioecious relic Cercidiphyllum japonicum is one of two species of the sole genus Cercidiphyllum, with a tight inflorescence lacking an apparent perianth structure. In addition, its systematic place has been much debated and, so far researches have mainly focused on its morphology and chloroplast genes. In our investigation, we identified 10 floral organ identity genes, including four A-class, three B-class, two C-class and one D-class. Phylogenetic analyses showed that all ten genes are grouped with Saxifragales plants, which confirmed the phylogenetic place of C. japonicum. Expression patterns of those genes were examined by quantitative reverse transcriptase PCR, with some variations that did not completely coincide with the ABCDE model, suggesting some subfunctionalization. As well, our research supported the idea that thebract actually is perianth according to our morphological and molecular analyses in Cercidiphyllum japonicum.
[Mh] MeSH terms primary: Evolution, Molecular
Genes, Plant
MADS Domain Proteins/physiology
Saxifragaceae/genetics
[Mh] MeSH terms secundary: MADS Domain Proteins/genetics
Phylogeny
Saxifragaceae/classification
[Pt] Publication type:JOURNAL ARTICLE
[Nm] Name of substance:0 (MADS Domain Proteins)
[Em] Entry month:1709
[Cu] Class update date: 170921
[Lr] Last revision date:170921
[Js] Journal subset:IM
[Da] Date of entry for processing:170601
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0178382

  10 / 1937 MEDLINE  
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[PMID]: 28528644
[Au] Autor:Soyk S; Lemmon ZH; Oved M; Fisher J; Liberatore KL; Park SJ; Goren A; Jiang K; Ramos A; van der Knaap E; Van Eck J; Zamir D; Eshed Y; Lippman ZB
[Ad] Address:Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
[Ti] Title:Bypassing Negative Epistasis on Yield in Tomato Imposed by a Domestication Gene.
[So] Source:Cell;169(6):1142-1155.e12, 2017 Jun 01.
[Is] ISSN:1097-4172
[Cp] Country of publication:United States
[La] Language:eng
[Ab] Abstract:Selection for inflorescence architecture with improved flower production and yield is common to many domesticated crops. However, tomato inflorescences resemble wild ancestors, and breeders avoided excessive branching because of low fertility. We found branched variants carry mutations in two related transcription factors that were selected independently. One founder mutation enlarged the leaf-like organs on fruits and was selected as fruit size increased during domestication. The other mutation eliminated the flower abscission zone, providing "jointless" fruit stems that reduced fruit dropping and facilitated mechanical harvesting. Stacking both beneficial traits caused undesirable branching and sterility due to epistasis, which breeders overcame with suppressors. However, this suppression restricted the opportunity for productivity gains from weak branching. Exploiting natural and engineered alleles for multiple family members, we achieved a continuum of inflorescence complexity that allowed breeding of higher-yielding hybrids. Characterizing and neutralizing similar cases of negative epistasis could improve productivity in many agricultural organisms. VIDEO ABSTRACT.
[Mh] MeSH terms primary: Epistasis, Genetic
Lycopersicon esculentum/genetics
MADS Domain Proteins/genetics
Plant Proteins/genetics
[Mh] MeSH terms secundary: Amino Acid Sequence
Domestication
Inflorescence/metabolism
Lycopersicon esculentum/growth & development
Lycopersicon esculentum/physiology
MADS Domain Proteins/chemistry
MADS Domain Proteins/metabolism
Meristem/metabolism
Plant Breeding
Plant Proteins/metabolism
Sequence Alignment
[Pt] Publication type:JOURNAL ARTICLE
[Nm] Name of substance:0 (MADS Domain Proteins); 0 (Plant Proteins)
[Em] Entry month:1707
[Cu] Class update date: 170907
[Lr] Last revision date:170907
[Js] Journal subset:IM
[Da] Date of entry for processing:170523
[St] Status:MEDLINE


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