scholarly journals Switching Protein-DNA Recognition Specificity by Single-Amino-Acid Substitutions in the P1 par Family of Plasmid Partition Elements

2008 ◽  
Vol 191 (4) ◽  
pp. 1126-1131 ◽  
Author(s):  
Alena Dabrazhynetskaya ◽  
Therese Brendler ◽  
Xinhua Ji ◽  
Stuart Austin
Keyword(s):  
Amino Acid ◽  
Plasmid Dna ◽  
Dna Recognition ◽  
Species Specificity ◽  
Single Amino Acid ◽  
Binding Properties ◽  
Plasmid Partition ◽  
Daughter Cells ◽  
Recognition Specificity ◽  
Dna Binding Properties

ABSTRACT The P1, P7, and pMT1 par systems are members of the P1 par family of plasmid partition elements. Each has a ParA ATPase and a ParB protein that recognizes the parS partition site of its own plasmid type to promote the active segregation of the plasmid DNA to daughter cells. ParB contacts two parS motifs known as BoxA and BoxB, the latter of which determines species specificity. We found that the substitution of a single orthologous amino acid in ParB for that of a different species has major effects on the specificity of recognition. A single change in ParB can cause a complete switch in recognition specificity to that of another species or can abolish specificity. Specificity changes do not necessarily correlate with changes in the gross DNA binding properties of the protein. Molecular modeling suggests that species specificity is determined by the capacity to form a hydrogen bond between ParB residue 288 and the second base in the BoxB sequence. As changes in just one ParB residue and one BoxB base can alter species specificity, plasmids may use such simple changes to evolve new species rapidly.

Synthesis, characterization and DNA binding properties of oligopyridine-ruthenium(II)-amino acid conjugates

2007 ◽  
Vol 101 (10) ◽  
pp. 1483-1491 ◽  
Author(s):  
Konstantina Karidi ◽  
Jan Reedijk ◽  
Nick Hadjiliadis ◽  
Achilleas Garoufis
Keyword(s):  
Amino Acid ◽  
Dna Binding ◽  
Binding Properties ◽  
Amino Acid Conjugates ◽  
Dna Binding Properties

scholarly journals The DNA-binding specificity of the hepatocyte nuclear factor 3/forkhead domain is influenced by amino-acid residues adjacent to the recognition helix.

1994 ◽  
Vol 14 (4) ◽  
pp. 2755-2766 ◽  
Author(s):  
D G Overdier ◽  
A Porcella ◽  
R H Costa
Keyword(s):  
Amino Acid ◽  
Dna Binding ◽  
Hepatocyte Nuclear Factor ◽  
Binding Properties ◽  
Winged Helix ◽  
Amino Acid Region ◽  
Dna Binding Specificity ◽  
Recognition Helix ◽  
Dna Binding Properties ◽  
Acid Region

Three distinct hepatocyte nuclear factor 3 (HNF-3) proteins (HNF-3 alpha, -3 beta, and -3 gamma) are known to regulate the transcription of liver-specific genes. The HNF-3 proteins bind to DNA as a monomer through a modified helix-turn-helix, known as the winged helix motif, which is also utilized by a number of developmental regulators, including the Drosophila homeotic forkhead (fkh) protein. We have previously described the isolation, from rodent tissue, of an extensive family of tissue-specific HNF-3/fkh homolog (HFH) genes sharing homology in their winged helix motifs. In this report, we have determined the preferred DNA-binding consensus sequence for the HNF-3 beta protein as well as for two divergent family members, HFH-1 and HFH-2. We show that these HNF-3/fkh proteins bind to distinct DNA sites and that the specificity of protein recognition is dependent on subtle nucleotide alterations in the site. The HNF-3, HFH-1, and HFH-2 consensus binding sequences were also used to search DNA regulatory regions to identify potential target genes. Furthermore, an analysis of the DNA-binding properties of a series of HFH-1/HNF-3 beta protein chimeras has allowed us to identify a 20-amino-acid region, located adjacent to the DNA recognition helix, which contributes to DNA-binding specificity. These sequences are not involved in base-specific contacts and include residues which diverge within the HNF-3/fkh family. Replacement of this 20-amino-acid region in HNF-3 beta with corresponding residues from HFH-1 enabled the HNF-3 beta recognition helix to bind only HFH-1-specific DNA-binding sites. We propose a model in which this 20-amino-acid flanking region influences the DNA-binding properties of the recognition helix.

scholarly journals The −10 Region Is a Key Promoter Specificity Determinant for the Bacillus subtilis Extracytoplasmic-Function ς Factors ςX and ςW

2001 ◽  
Vol 183 (6) ◽  
pp. 1921-1927 ◽  
Author(s):  
Jian Qiu ◽  
John D. Helmann
Keyword(s):  
Bacillus Subtilis ◽  
Amino Acid ◽  
Rna Polymerase ◽  
Context Effects ◽  
Promoter Strength ◽  
Binding Properties ◽  
Promoter Specificity ◽  
Dna Binding Properties

ABSTRACT Transcriptional selectivity derives, in large part, from the sequence-specific DNA-binding properties of the ς subunit of RNA polymerase. There are 17 ς factors in Bacillus subtilis which, in general, recognize distinct sets of promoters. However, some ς factors have overlapping promoter selectivity. We hypothesize that the overlap between the regulons activated by the ςX and ςW factors can be explained by overlapping specificity for the −10 region: ςX recognizes −10 elements with the sequence CGAC and ςW recognizes CGTA, while both can potentially recognize CGTC. To test this model, we mutated the ςX-specific autoregulatory site (PX), containing the −10 element CGAC, to either CGTC or GCTA. Conversely, the ςW autoregulatory site (PW) was altered from CGTA to CGTC or CGAC. Transcriptional analyses, both in vitro and in vivo, indicate that changes to the −10 element are sufficient to switch a promoter from the ςX to the ςW regulon or, conversely, from the ςW to the ςX regulon, but context effects clearly play an important role in determining promoter strength. It seems likely that these subtle differences in promoter selectivity derive from amino acid differences in conserved region 2 of ς, which contacts the −10 element. However, we were unable to alter promoter selectivity by replacements of two candidate recognition residues in ςW.

Effect of single amino acid substitutions in the hemagglutinin on the receptor-binding properties of influenza B viruses

2015 ◽  
Vol 70 ◽  
pp. S29
Author(s):  
E. Sorokin ◽  
T. Tsareva ◽  
A. Sominina ◽  
M. Pisareva ◽  
A. Komissarov ◽  
...  
Keyword(s):  
Amino Acid ◽  
Receptor Binding ◽  
Single Amino Acid ◽  
Influenza B ◽  
Amino Acid Substitutions ◽  
Binding Properties

Engineering TaqII bifunctional endonuclease DNA recognition fidelity: the effect of a single amino acid substitution within the methyltransferase catalytic site

2016 ◽  
Vol 43 (4) ◽  
pp. 269-282 ◽  
Author(s):  
Agnieszka Zylicz-Stachula ◽  
Joanna Zebrowska ◽  
Edyta Czajkowska ◽  
Weronika Wrese ◽  
Ewa Sulecka ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Substitution ◽  
Dna Recognition ◽  
Catalytic Site ◽  
Single Amino Acid Substitution ◽  
Single Amino Acid
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