scholarly journals Phage lambda Cro protein and cI repressor use two different patterns of specific protein-DNA interactions to achieve sequence specificity in vivo.

Genetics ◽  
1989 ◽  
Vol 121 (1) ◽  
pp. 5-12
Author(s):  
N Benson ◽  
P Youderian
Keyword(s):  
Specific Protein ◽  
Specific Interactions ◽  
Sequence Specificity ◽  
Base Pairs ◽  
Lambda Repressor ◽  
Protein Dna Interactions ◽  
Cro Protein ◽  
Data Call ◽  
Half Site

Abstract By assaying the binding of wild-type Cro to a set of 40 mutant lambda operators in vivo, we have determined that the 14 outermost base pairs of the 17 base pair, consensus lambda operator are critical for Cro binding. Cro protein recognizes 4 base pairs in a lambda operator half-site in different ways than cI repressor. The sequence determinants of Cro binding at these critical positions in vivo are nearly perfectly consistent with the model proposed by W. F. ANDERSON, D. H. OHLENDORF, Y. TAKEDA and B. W. MATTHEWS and modified by Y. TAKEDA, A. SARAI and V. M. RIVERA for the specific interactions between Cro and its operator, and explain the relative order of affinities of the six natural lambda operators for Cro. Our data call into question the idea that lambda repressor and Cro protein recognize the consensus lambda operator by nearly identical patterns of specific interactions.

scholarly journals DNA sequence determinants of lambda repressor binding in vivo.

Genetics ◽  
1988 ◽  
Vol 118 (1) ◽  
pp. 21-29
Author(s):  
N Benson ◽  
P Sugiono ◽  
P Youderian
Keyword(s):  
Dna Sequence ◽  
Base Pair ◽  
Operator Function ◽  
Wild Type ◽  
Base Pairs ◽  
Lambda Repressor ◽  
Half Site ◽  
Better Than

Abstract The critical operator determinants for lambda repressor recognition have been defined by analyzing the binding of wild-type repressor to a set of mutant operators in vivo. Base pair substitutions at six positions within the lambda operator half-site impair binding severely, and define these base pairs as critical for operator function. One mutant operator binds repressor better than the consensus operator, and is a superoperator. The model proposed by M. Lewis in 1983 for the binding of lambda repressor to its operator accurately predicts the observed operator requirements for binding in vivo, with several minor exceptions. The order of affinities of the six natural lambda operators has also been determined.

scholarly journals Facilitation of DNA loop formation by protein–DNA non-specific interactions

Soft Matter ◽  
2019 ◽  
Vol 15 (26) ◽  
pp. 5255-5263 ◽  
Author(s):  
Jaeoh Shin ◽  
Anatoly B. Kolomeisky
Keyword(s):  
Specific Protein ◽  
Dna Looping ◽  
Specific Interactions ◽  
Loop Formation ◽  
Dna Interactions ◽  
Dna Loop ◽  
Protein Dna Interactions

DNA looping is facilitated by non-specific protein–DNA interactions.

Tissue specific expression of avian vitellogenin gene is correlated with DNA hypomethylation and in vivo specific protein-DNA interactions

1990 ◽  
Vol 326 (1235) ◽  
pp. 231-240 ◽  
Keyword(s):  
Promoter Region ◽  
Gene Activation ◽  
Specific Protein ◽  
Egg Laying ◽  
Dna Hypomethylation ◽  
Dna Interactions ◽  
Specific Expression ◽  
Protein Dna Interactions ◽  
Vitellogenin Gene

The avian vitellogenin gene is expressed only in the liver of egg-laying hens. It can, however, be activated in immature chicks or roosters by oestradiol. Parallel to the onset of transcription, there is a demethylation of specific mCpGs in the promoter region and in the oestrogen response element (ERE). The methylation pattern in the promoter region is hormone and expression specific, whereas in the ERE it is only hormone and not organ specific. The demethylation occurring in the promoter region is correlated with the appearance of DNase I hypersensitivity sites and changes in the specific protein-DNA interactions. In vivo genomic footprinting of the ERE with varying concentrations of dimethylsulphate revealed, upon gene activation, only minor changes in the protein-DNA interaction. We present evidence that there is another protein that binds with high affinity to the ERE, besides the oestrogen receptor.

scholarly journals In Vivo Analysis of Developmentally and Evolutionarily Dynamic Protein-DNA Interactions Regulating Transcription of the Pgk2 Gene during Mammalian Spermatogenesis

2007 ◽  
Vol 27 (22) ◽  
pp. 7871-7885 ◽  
Author(s):  
Hirotaka Yoshioka ◽  
Christopher B. Geyer ◽  
Jacey L. Hornecker ◽  
Krishan T. Patel ◽  
John R. McCarrey
Keyword(s):  
Phosphoglycerate Kinase ◽  
Gene Promoter ◽  
Specific Protein ◽  
Dna Interactions ◽  
Tissue Specific ◽  
Rate Limiting Step ◽  
Protein Dna Interactions ◽  
Genes Encoding ◽  
Specific Regulation

ABSTRACT Transcription of the testis-specific Pgk2 gene is selectively activated in primary spermatocytes to provide a source of phosphoglycerate kinase that is critical to normal motility and fertility of mammalian spermatozoa. We examined dynamic changes in protein-DNA interactions at the Pgk2 gene promoter during murine spermatogenesis in vivo by performing genomic footprinting and chromatin immunoprecipitation assays with enriched populations of murine spermatogenic cells at stages prior to, during, and following transcription of this gene. We found that genes encoding the testis-specific homeodomain factor PBX4 and its coactivator, PREP1, are expressed in patterns that mirror expression of the Pgk2 gene and that these factors become bound to the Pgk2 enhancer in cells in which this gene is actively expressed. We therefore suggest that these factors, along with CREM and SP3, direct stage- and cell type-specific transcription of the Pgk2 gene during spermatogenesis. We propose that binding of PBX4, plus its coactivator PREP1, is a rate-limiting step leading to the initiation of tissue-specific transcription of the Pgk2 gene. This study provides insight into the developmentally dynamic establishment of tissue-specific protein-DNA interactions in vivo. It also allows us to speculate about the events that led to tissue-specific regulation of the Pgk2 gene during mammalian evolution.

scholarly journals Lambda repressor recognizes the approximately 2-fold symmetric half-operator sequences asymmetrically

1989 ◽  
Vol 86 (17) ◽  
pp. 6513-6517 ◽  
Author(s):  
A Sarai ◽  
Y Takeda
Keyword(s):  
Amino Acids ◽  
Symmetric Operator ◽  
Dna Bases ◽  
Base Substitution ◽  
Base Pairs ◽  
Lambda Repressor ◽  
Base Substitutions ◽  
Protein Dna Interactions ◽  
Operator Sequence ◽  
Recognition Code

Results of systematic base-substitution experiments suggest that the lambda repressor dimer, made of identical subunits, recognizes the "pseudo(2-fold)symmetric" operator sequence asymmetrically. Base substitutions within the consensus half of the operator affect binding more than base substitutions within the nonconsensus half of the operator. Furthermore, changing the nonconsensus base pairs to the consensus base pairs does not increase, but decreases, binding. Evidently, the two subunits of the lambda repressor dimer bind to the two halves of the operator differently. This is consistent with the recently determined crystal structure of the complex, which shows that the relative positioning of the amino acids to the DNA bases are slightly different in the two halves of the operator. The sequence-specific interactions indicated by the systematic base-substitution experiments correlate well with the locations of the specific contacts found in the complex. Thus, the amino acids of lambda repressor, mainly of alpha 3-helix and the N-terminus arm, seem to directly read-out the DNA sequence by forming specific hydrogen bonds and hydrophobic contacts to the DNA bases. The observed asymmetric recognition suggests that no recognition code governs amino acids and DNA bases in protein-DNA interactions.

Specific Labeling of Protein Domains with Antibody Fragments

1981 ◽  
Vol 39 ◽  
pp. 416-417
Author(s):  
U. Aebi ◽  
L.E. Buhle ◽  
W.E. Fowler
Keyword(s):  
Image Processing ◽  
Specific Protein ◽  
Antibody Fragments ◽  
Supramolecular Organization ◽  
Two Dimensional ◽  
Ordered Structures ◽  
Virus Capsids ◽  
Processing Techniques

Many important supramolecular structures such as filaments, microtubules, virus capsids and certain membrane proteins and bacterial cell walls exist as ordered polymers or two-dimensional crystalline arrays in vivo. In several instances it has been possible to induce soluble proteins to form ordered polymers or two-dimensional crystalline arrays in vitro. In both cases a combination of electron microscopy of negatively stained specimens with analog or digital image processing techniques has proven extremely useful for elucidating the molecular and supramolecular organization of the constituent proteins. However from the reconstructed stain exclusion patterns it is often difficult to identify distinct stain excluding regions with specific protein subunits. To this end it has been demonstrated that in some cases this ambiguity can be resolved by a combination of stoichiometric labeling of the ordered structures with subunit-specific antibody fragments (e.g. Fab) and image processing of the electron micrographs recorded from labeled and unlabeled structures.

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