Special Issue "Protein-DNA Interactions"

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Molecular Genetics".

Deadline for manuscript submissions: closed (31 May 2017)

Special Issue Editors

Guest Editor
Prof. Dr. Linda Bloom

Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, USA
Website | E-Mail
Interests: Dynamic protein-DNA interactions; DNA replication; DNA repair
Guest Editor
Prof. Dr. Jörg Bungert

Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, USA
Website | E-Mail
Interests: Protein-DNA interactions; synthetic DNA-binding proteins; transcription

Special Issue Information

Dear Colleagues,

The binding of proteins to DNA is critical for maintaining and expressing genetic information. Protein-DNA interactions are involved in condensing chromosomes to fit into cells, regulating the expression of genetic information, duplicating the genome to pass copies to daughter cells, and preserving the structure and integrity of genomic DNA. Our understanding of protein-DNA interactions required for these critical functions has advanced on many levels. Structural approaches have elucidated mechanisms by which proteins physically interact with DNA to perform their functions. Biochemical studies have defined dynamic and transient protein-DNA interactions essential for enzyme transactions on DNA. Recently, exciting progress has been made in two areas: single molecule and in vivo studies of protein-DNA interactions. Single molecule approaches reveal the complex dynamics of molecular interactions between single protein molecules and DNA that are hidden by the ensemble averaging inherent in bulk methods. Observation of the behavior of individual molecules allows us to answer questions that are impossible to address by examining a large population of molecules where the dynamics are unsynchronized, and thus “blur” the picture that we get. Exciting progress has also been made in investigating protein-DNA interactions inside cells in the crowded and complex molecular environment where they naturally function. Researchers have been able to query unique loci to identify protein-DNA interactions that are required for a specific cellular process, and recent advances in DNA sequencing have permitted the development of approaches to map protein-DNA interactions across the genome and in a cell-type specific manner. These studies revealed that DNA shape and DNA motif environment contribute to efficient protein-DNA interactions. Articles in this special issue should provide insight into mechanisms of protein-DNA interactions, and papers using single-molecule approaches or investigating interactions in vivo would be of special interest.

Prof. Dr. Linda Bloom
Prof. Dr. Jörg Bungert
Guest Editors

Manuscript Submission Information

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Keywords

• protein-DNA interactions
• chromatin structure
• transcription
• DNA replication
• DNA repair
• DNA recombination

Published Papers (4 papers)

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Research

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Open AccessArticle Mutational and Kinetic Analysis of Lesion Recognition by Escherichia coli Endonuclease VIII
Genes 2017, 8(5), 140; doi:10.3390/genes8050140
Received: 27 February 2017 / Revised: 3 May 2017 / Accepted: 9 May 2017 / Published: 13 May 2017
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Abstract
Escherichia coli endonuclease VIII (Endo VIII) is a DNA glycosylase with substrate specificity for a wide range of oxidatively damaged pyrimidine bases. Endo VIII catalyzes hydrolysis of the N-glycosidic bond and β, δ-elimination of 3′- and 5′-phosphate groups of an apurinic/apyrimidinic site. Single
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Escherichia coli endonuclease VIII (Endo VIII) is a DNA glycosylase with substrate specificity for a wide range of oxidatively damaged pyrimidine bases. Endo VIII catalyzes hydrolysis of the N-glycosidic bond and β, δ-elimination of 3′- and 5′-phosphate groups of an apurinic/apyrimidinic site. Single mutants of Endo VIII L70S, L70W, Y71W, F121W, F230W, and P253W were analyzed here with the aim to elucidate the kinetic mechanism of protein conformational adjustment during damaged-nucleotide recognition and catalytic-complex formation. F121W substitution leads to a slight reduction of DNA binding and catalytic activity. F230W substitution slows the rate of the δ-elimination reaction indicating that interaction of Phe230 with a 5′-phosphate group proceeds in the latest catalytic step. P253W Endo VIII has the same activity as the wild type (WT) enzyme. Y71W substitution slightly reduces the catalytic activity due to the effect on the later steps of catalytic-complex formation. Both L70S and L70W substitutions significantly decrease the catalytic activity, indicating that Leu70 plays an important role in the course of enzyme-DNA catalytic complex formation. Our data suggest that Leu70 forms contacts with DNA earlier than Tyr71 does. Therefore, most likely, Leu70 plays the role of a DNA lesion “sensor”, which is used by Endo VIII for recognition of a DNA damage site. Full article
(This article belongs to the Special Issue Protein-DNA Interactions)
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Review

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Open AccessReview Acetylation- and Methylation-Related Epigenetic Proteins in the Context of Their Targets
Genes 2017, 8(8), 196; doi:10.3390/genes8080196
Received: 9 May 2017 / Revised: 19 July 2017 / Accepted: 31 July 2017 / Published: 7 August 2017
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Abstract
The nucleosome surface is covered with multiple modifications that are perpetuated by eight different classes of enzymes. These enzymes modify specific target sites both on DNA and histone proteins, and these modifications have been well identified and termed “epigenetics”. These modifications play critical
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The nucleosome surface is covered with multiple modifications that are perpetuated by eight different classes of enzymes. These enzymes modify specific target sites both on DNA and histone proteins, and these modifications have been well identified and termed “epigenetics”. These modifications play critical roles, either by affecting non-histone protein recruitment to chromatin or by disturbing chromatin contacts. Their presence dictates the condensed packaging of DNA and can coordinate the orderly recruitment of various enzyme complexes for DNA manipulation. This genetic modification machinery involves various writers, readers, and erasers that have unique structures, functions, and modes of action. Regarding human disease, studies have mainly focused on the genetic mechanisms; however, alteration in the balance of epigenetic networks can result in major pathologies including mental retardation, chromosome instability syndromes, and various types of cancers. Owing to its critical influence, great potential lies in developing epigenetic therapies. In this regard, this review has highlighted mechanistic and structural interactions of the main epigenetic families with their targets, which will help to identify more efficient and safe drugs against several diseases. Full article
(This article belongs to the Special Issue Protein-DNA Interactions)
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Open AccessReview Proteins Recognizing DNA: Structural Uniqueness and Versatility of DNA-Binding Domains in Stem Cell Transcription Factors
Genes 2017, 8(8), 192; doi:10.3390/genes8080192
Received: 10 May 2017 / Revised: 22 July 2017 / Accepted: 25 July 2017 / Published: 1 August 2017
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Abstract
Proteins in the form of transcription factors (TFs) bind to specific DNA sites that regulate cell growth, differentiation, and cell development. The interactions between proteins and DNA are important toward maintaining and expressing genetic information. Without knowing TFs structures and DNA-binding properties, it
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Proteins in the form of transcription factors (TFs) bind to specific DNA sites that regulate cell growth, differentiation, and cell development. The interactions between proteins and DNA are important toward maintaining and expressing genetic information. Without knowing TFs structures and DNA-binding properties, it is difficult to completely understand the mechanisms by which genetic information is transferred between DNA and proteins. The increasing availability of structural data on protein-DNA complexes and recognition mechanisms provides deeper insights into the nature of protein-DNA interactions and therefore, allows their manipulation. TFs utilize different mechanisms to recognize their cognate DNA (direct and indirect readouts). In this review, we focus on these recognition mechanisms as well as on the analysis of the DNA-binding domains of stem cell TFs, discussing the relative role of various amino acids toward facilitating such interactions. Unveiling such mechanisms will improve our understanding of the molecular pathways through which TFs are involved in repressing and activating gene expression. Full article
(This article belongs to the Special Issue Protein-DNA Interactions)
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Open AccessReview Eukaryotic Replicative Helicase Subunit Interaction with DNA and Its Role in DNA Replication
Genes 2017, 8(4), 117; doi:10.3390/genes8040117
Received: 17 February 2017 / Revised: 23 March 2017 / Accepted: 31 March 2017 / Published: 6 April 2017
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Abstract
The replicative helicase unwinds parental double-stranded DNA at a replication fork to provide single-stranded DNA templates for the replicative polymerases. In eukaryotes, the replicative helicase is composed of the Cdc45 protein, the heterohexameric ring-shaped Mcm2-7 complex, and the tetrameric GINS complex (CMG). The
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The replicative helicase unwinds parental double-stranded DNA at a replication fork to provide single-stranded DNA templates for the replicative polymerases. In eukaryotes, the replicative helicase is composed of the Cdc45 protein, the heterohexameric ring-shaped Mcm2-7 complex, and the tetrameric GINS complex (CMG). The CMG proteins bind directly to DNA, as demonstrated by experiments with purified proteins. The mechanism and function of these DNA-protein interactions are presently being investigated, and a number of important discoveries relating to how the helicase proteins interact with DNA have been reported recently. While some of the protein-DNA interactions directly relate to the unwinding function of the enzyme complex, other protein-DNA interactions may be important for minichromosome maintenance (MCM) loading, origin melting or replication stress. This review describes our current understanding of how the eukaryotic replicative helicase subunits interact with DNA structures in vitro, and proposed models for the in vivo functions of replicative helicase-DNA interactions are also described. Full article
(This article belongs to the Special Issue Protein-DNA Interactions)
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