scholarly journals Elucidating the evolutionary conserved DNA-binding specificities of WRKY transcription factors by molecular dynamics and in vitro binding assays

2013 ◽  
Vol 41 (21) ◽  
pp. 9764-9778 ◽  
Author(s):  
Luise H. Brand ◽  
Nina M. Fischer ◽  
Klaus Harter ◽  
Oliver Kohlbacher ◽  
Dierk Wanke
Keyword(s):  
Molecular Dynamics ◽  
Transcription Factors ◽  
Dna Binding ◽  
Binding Assays ◽  
Wrky Transcription Factors ◽  
In Vitro Binding ◽  
Vitro Binding

scholarly journals SKP1-like protein, CrSKP1-e, interacts with pollen-specific F-box proteins and assembles into SCF-type E3 complex in ‘Wuzishatangju’ (Citrus reticulata Blanco) pollen

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10578
Author(s):  
Yi Ren ◽  
Qingzhu Hua ◽  
Jiayan Pan ◽  
Zhike Zhang ◽  
Jietang Zhao ◽  
...  
Keyword(s):  
Ubiquitin Ligase ◽  
E3 Ubiquitin Ligase ◽  
Citrus Reticulata ◽  
S Locus ◽  
Binding Assays ◽  
In Vitro Binding ◽  
Genome Wide ◽  
Ubiquitin Ligase Complex ◽  
Vitro Binding

S-ribonuclease (S-RNase)-based self-incompatibility (SI) mechanisms have been extensively studied in Solanaceae, Rosaceae and Plantaginaceae. S-RNase-based SI is controlled by two closely related genes, S-RNase and S-locus F-box (SLF), located at a polymorphic S-locus. In the SI system, the SCF-type (SKP1-CUL1-F-box-RBX1) complex functions as an E3 ubiquitin ligase complex for ubiquitination of non-self S-RNase. Pummelo (Citrus grandis) and several mandarin cultivars are suggested to utilize an S-RNase-based SI system. However, the molecular mechanism of the non-S-factors involved in the SI reaction is not straightforward in Citrus. To investigate the SCF-type E3 complex responsible for the SI reaction in mandarin, SLF, SKP1-like and CUL1 candidates potentially involved in the SI reaction of ‘Wuzishatangju’ (Citrus reticulata Blanco) were identified based on the genome-wide identification and expression analyses. Sixteen pollen-specific F-box genes (CrFBX1-CrFBX16), one pollen-specific SKP1-like gene (CrSKP1-e) and two CUL1 genes (CrCUL1A and CrCUL1B) were identified and cloned from ‘Wuzishatangju’. Yeast two-hybrid (Y2H) and in vitro binding assays showed that five CrFBX proteins could bind to CrSKP1-e, which is an ortholog of SSK1 (SLF-interacting-SKP1-like), a non-S-factor responsible for the SI reaction. Luciferase complementation imaging (LCI) and in vitro binding assays also showed that CrSKP1-e interacts with the N-terminal region of both CrCUL1A and CrCUL1B. These results indicate that CrSKP1-e may serve as a functional member of the SCF-type E3 ubiquitin ligase complex in ‘Wuzishatangju’.

scholarly journals DNA Modeling Reveals an Extended Lac Repressor Conformation in Classic In Vitro Binding Assays

2011 ◽  
Vol 101 (3) ◽  
pp. 718-726 ◽  
Author(s):  
Andrew D. Hirsh ◽  
Todd D. Lillian ◽  
Troy A. Lionberger ◽  
N.C. Perkins
Keyword(s):  
Lac Repressor ◽  
Binding Assays ◽  
In Vitro Binding ◽  
Vitro Binding ◽  
Dna Modeling

scholarly journals Differences between MyoD DNA binding and activation site requirements revealed by functional random sequence selection.

1996 ◽  
Vol 16 (7) ◽  
pp. 3893-3900 ◽  
Author(s):  
J Huang ◽  
T K Blackwell ◽  
L Kedes ◽  
H Weintraub
Keyword(s):  
Dna Binding ◽  
Binding Site ◽  
Dna Sequences ◽  
Transcriptional Activation ◽  
Random Sequence ◽  
In Vitro Binding ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix ◽  
Vitro Binding

A method has been developed for selecting functional enhancer/promoter sites from random DNA sequences in higher eukaryotic cells. Of sequences that were thus selected for transcriptional activation by the muscle-specific basic helix-loop-helix protein MyoD, only a subset are similar to the preferred in vitro binding consensus, and in the same promoter context an optimal in vitro binding site was inactive. Other sequences with full transcriptional activity instead exhibit sequence preferences that, remarkably, are generally either identical or very similar to those found in naturally occurring muscle-specific promoters. This first systematic examination of the relation between DNA binding and transcriptional activation by basic helix-loop-helix proteins indicates that binding per se is necessary but not sufficient for transcriptional activation by MyoD and implies a requirement for other DNA sequence-dependent interactions or conformations at its binding site.

In vitro binding of aflatoxin B1 and 2-acetylaminofluorene to rat, mouse and human hepatocyte DNA: the relationship of DNA binding to carcinogenicity

1988 ◽  
Vol 9 (5) ◽  
pp. 711-716 ◽  
Author(s):  
Katharine E. Cole ◽  
Thomas W. Jones ◽  
Michael M. Lipsky ◽  
Benjamin F. Trump ◽  
Ih-Chang Hsu
Keyword(s):  
Dna Binding ◽  
Aflatoxin B1 ◽  
Human Hepatocyte ◽  
In Vitro Binding ◽  
Vitro Binding ◽  
Relationship Of ◽  
The Relationship
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