scholarly journals The mapping of nucleosomes and regulatory protein binding sites at the Saccharomyces cerevisiae MFA2 gene: a high resolution approach

2001 ◽  
Vol 29 (13) ◽  
pp. 64e-64 ◽  
Author(s):  
Y. Teng
Keyword(s):  
Saccharomyces Cerevisiae ◽  
High Resolution ◽  
Protein Binding ◽  
Binding Sites ◽  
Regulatory Protein ◽  
Protein Binding Sites

scholarly journals Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae

2013 ◽  
Vol 14 (2) ◽  
pp. R13 ◽  
Author(s):  
Mallory A Freeberg ◽  
Ting Han ◽  
James J Moresco ◽  
Andy Kong ◽  
Yu-Cheng Yang ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Protein Binding ◽  
Binding Sites ◽  
Protein Binding Sites ◽  
Mrna Transcriptome

Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governing conservation and change

Development ◽  
1998 ◽  
Vol 125 (5) ◽  
pp. 949-958 ◽  
Author(s):  
M.Z. Ludwig ◽  
N.H. Patel ◽  
M. Kreitman
Keyword(s):  
Protein Binding ◽  
Reporter Gene ◽  
Dna Sequences ◽  
Binding Sites ◽  
Regulatory Protein ◽  
P Element ◽  
Systematic Change ◽  
Stabilizing Selection ◽  
Protein Binding Sites ◽  
Adaptive Mutations

Experimental investigations of eukaryotic enhancers suggest that multiple binding sites and trans-acting regulatory factors are often required for wild-type enhancer function. Genetic analysis of the stripe 2 enhancer of even-skipped (eve), an important developmental gene in Drosophila, provides support for this view. Given the importance of even-skipped expression in early Drosophila development, it might be predicted that many structural features of the stripe 2 enhancer will be evolutionarily conserved, including the DNA sequences of protein binding sites and the spacing between them. To test this hypothesis, we compared sequences of the stripe 2 enhancer between four species of Drosophila: D. melanogaster, D. yakuba, D. erecta and D. pseudoobscura. Our analysis revealed a large number of nucleotide substitutions in regulatory protein binding sites for bicoid, hunchback, Kruppel and giant, as well as a systematic change in the size of the enhancer. Some of the binding sites in D. melanogaster are either absent or modified in other species. One functionally important bicoid-binding site in D. melanogaster appears to be recently evolved. We, therefore, investigated possible functional consequences of sequence differences among these stripe 2 enhancers by P-element-mediated transformation. This analysis revealed that the eve stripe 2 enhancer from each of the four species drove reporter gene expression at the identical time and location in D. melanogaster embryos. Double staining of native eve protein and transgene mRNA in early embryos showed that the reporter gene mimicked native eve expression and, in every case, produced sharply defined stripes at the blastoderm stage that were coincident with eve stripe 2 protein. We argue that stripe 2 eve expression in Drosophila evolution can be viewed as being under constant stabilizing selection with respect to the location of the anterior and posterior borders of the stripe. We further hypothesize that the stripe 2 enhancer is functionally robust, so that its evolution may be governed by the fixation of both slightly deleterious and adaptive mutations in regulatory protein binding sites as well as in the spacing between binding sites. This view allows for a slow but continual turnover of functionally important changes in the stripe 2 enhancer.

scholarly journals Selective high-resolution DNP-enhanced NMR of biomolecular binding sites

2019 ◽  
Vol 10 (11) ◽  
pp. 3366-3374 ◽  
Author(s):  
Ildefonso Marin-Montesinos ◽  
David Goyard ◽  
Emilie Gillon ◽  
Olivier Renaudet ◽  
Anne Imberty ◽  
...  
Keyword(s):  
High Resolution ◽  
Protein Binding ◽  
Binding Sites ◽  
Selective Recovery ◽  
Protein Binding Sites ◽  
Biomolecular Binding

Sel-DNP allows selective recovery of high-resolution information from protein binding sites by DNP-enhanced NMR.

Roles of ABF1, NPL3, and YCL54 in silencing in Saccharomyces cerevisiae.

Genetics ◽  
1995 ◽  
Vol 141 (3) ◽  
pp. 889-902 ◽  
Author(s):  
S Loo ◽  
P Laurenson ◽  
M Foss ◽  
A Dillin ◽  
J Rine
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Protein Binding ◽  
Binding Sites ◽  
Genetic Screen ◽  
Essential Genes ◽  
Temperature Sensitive ◽  
Protein Binding Sites ◽  
Temperature Sensitive Mutation

Abstract A sensitized genetic screen was carried out to identify essential genes involved in silencing in Saccharomyces cerevisiae. This screen identified temperature-sensitive alleles of ORC2 and ORC5, as described elsewhere, and ABF1, NPL3, and YCL54, as described here. Alleles of ABF1 that caused silencing defects provided the genetic proof of Abflp's role in silencing. The roles of Npl3p and Ycl54p are less clear. These proteins did not act exclusively through any one of the three protein binding sites of the HMR-E silencer. Unlike the orc2, orc5, and abf1 mutations that were isolated in the same (or a similar) screen for silencing mutants, neither temperature-sensitive mutation in NPL3 or YCL54 caused overt replication defects.

scholarly journals PredictRegulon: a web server for the prediction of the regulatory protein binding sites and operons in prokaryote genomes

2004 ◽  
Vol 32 (Web Server) ◽  
pp. W318-W320 ◽  
Author(s):  
S. Yellaboina ◽  
J. Seshadri ◽  
M. S. Kumar ◽  
A. Ranjan
Keyword(s):  
Protein Binding ◽  
Binding Sites ◽  
Regulatory Protein ◽  
Web Server ◽  
Protein Binding Sites

EVALUATION OF TISSUE STEROID BINDING IN VITRO

1971 ◽  
Vol 68 (1_Suppl) ◽  
pp. S223-S246 ◽  
Author(s):  
C. R. Wira ◽  
H. Rochefort ◽  
E. E. Baulieu
Keyword(s):  
Protein Binding ◽  
Binding Sites ◽  
Experimental System ◽  
Specific Protein ◽  
Coupling Mechanism ◽  
Target Tissue ◽  
Protein Binding Sites ◽  
Definition Of ◽  
Hormone Specificity

ABSTRACT The definition of a RECEPTOR* in terms of a receptive site, an executive site and a coupling mechanism, is followed by a general consideration of four binding criteria, which include hormone specificity, tissue specificity, high affinity and saturation, essential for distinguishing between specific and nonspecific binding. Experimental approaches are proposed for choosing an experimental system (either organized or soluble) and detecting the presence of protein binding sites. Techniques are then presented for evaluating the specific protein binding sites (receptors) in terms of the four criteria. This is followed by a brief consideration of how receptors may be located in cells and characterized when extracted. Finally various examples of oestrogen, androgen, progestagen, glucocorticoid and mineralocorticoid binding to their respective target tissues are presented, to illustrate how researchers have identified specific corticoid and mineralocorticoid binding in their respective target tissue receptors.

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