Clarifying functions of the p53 protein is a crucial aspect of cancer research. We analyzed the binding sites of p53 wild-type (WT) protein and its oncologically significant mutants and evaluated their transactivation properties using a functional yeast assay. Unlike the binding sites as determined in myeloid leukemia cell lines by chromatin immunoprecipitation of p53-R175H, p53-Y220C, p53-M237I, p53-R248Q, and p53-R273H mutants, the target sites of p53-WT and p53-R282W were significantly associated with putative G-quadruplex sequences (PQSs). Guanine-quadruplex (G-quadruplex or G4) formation in these sequences was evaluated by using a set of biophysical methods. G4s can modulate gene expression induced by p53. At low p53 expression level, PQS upstream of the p53-response element (RE) leads to greater gene expression induced by p53-R282W compared to that for the RE without PQS. Meanwhile, p53-WT protein expression is decreased by the PQS presence. At a high p53 expression level, the presence of PQS leads to a decreased expression of the reporter regardless of the distance and localization of the G4 from the RE.

• Publication type
• Journal Article MeSH

P53, P63, and P73 proteins belong to the P53 family of transcription factors, sharing a common gene organization that, from the P1 and P2 promoters, produces two groups of mRNAs encoding proteins with different N-terminal regions; moreover, alternative splicing events at C-terminus further contribute to the generation of multiple isoforms. P53 family proteins can influence a plethora of cellular pathways mainly through the direct binding to specific DNA sequences known as response elements (REs), and the transactivation of the corresponding target genes. However, the transcriptional activation by P53 family members can be regulated at multiple levels, including the DNA topology at responsive promoters. Here, by using a yeast-based functional assay, we evaluated the influence that a G-quadruplex (G4) prone sequence adjacent to the p53 RE derived from the apoptotic PUMA target gene can exert on the transactivation potential of full-length and N-terminal truncated P53 family α isoforms (wild-type and mutant). Our results show that the presence of a G4 prone sequence upstream or downstream of the P53 RE leads to significant changes in the relative activity of P53 family proteins, emphasizing the potential role of structural DNA features as modifiers of P53 family functions at target promoter sites.

• Keywords
• G-quadruplex (G4) prone sequence, P53 family, transactivation potential, wild-type and mutant P53/P63 proteins, yeast,
• MeSH
• Apoptosis genetics   MeSH
• DNA genetics   ultrastructure   MeSH
• G-Quadruplexes * MeSH
• Nucleic Acid Conformation MeSH
• Humans MeSH
• Membrane Proteins genetics   ultrastructure   MeSH
• Tumor Suppressor Protein p53 genetics   ultrastructure   MeSH
• Promoter Regions, Genetic genetics   MeSH
• Tumor Protein p73 genetics   ultrastructure   MeSH
• Apoptosis Regulatory Proteins genetics   MeSH
• Proto-Oncogene Proteins genetics   MeSH
• Response Elements genetics   MeSH
• Saccharomyces cerevisiae genetics   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• BBC3 protein, human MeSH Browser
• CKAP4 protein, human MeSH Browser
• DNA MeSH
• Membrane Proteins MeSH
• Tumor Suppressor Protein p53 MeSH
• Tumor Protein p73 MeSH
• Apoptosis Regulatory Proteins MeSH
• Proto-Oncogene Proteins MeSH
• TP73 protein, human MeSH Browser

Nucleic acid-binding proteins are traditionally divided into two categories: With the ability to bind DNA or RNA. In the light of new knowledge, such categorizing should be overcome because a large proportion of proteins can bind both DNA and RNA. Another even more important features of nucleic acid-binding proteins are so-called sequence or structure specificities. Proteins able to bind nucleic acids in a sequence-specific manner usually contain one or more of the well-defined structural motifs (zinc-fingers, leucine zipper, helix-turn-helix, or helix-loop-helix). In contrast, many proteins do not recognize nucleic acid sequence but rather local DNA or RNA structures (G-quadruplexes, i-motifs, triplexes, cruciforms, left-handed DNA/RNA form, and others). Finally, there are also proteins recognizing both sequence and local structural properties of nucleic acids (e.g., famous tumor suppressor p53). In this mini-review, we aim to summarize current knowledge about the amino acid composition of various types of nucleic acid-binding proteins with a special focus on significant enrichment and/or depletion in each category.

• Keywords
• DNA, G-quadruplex, RNA, Z-DNA, Z-RNA, amino acid composition, cruciform, i-motif, protein binding, triplex,
• MeSH
• DNA-Binding Proteins genetics   MeSH
• DNA genetics   ultrastructure   MeSH
• G-Quadruplexes MeSH
• Nucleic Acid Conformation * MeSH
• Leucine Zippers genetics   MeSH
• Humans MeSH
• Nucleoproteins genetics   ultrastructure   MeSH
• RNA chemistry   ultrastructure   MeSH
• Amino Acid Sequence genetics   MeSH
• Carrier Proteins genetics   ultrastructure   MeSH
• DNA, Z-Form MeSH
• Zinc Fingers genetics   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Review MeSH
• Names of Substances
• DNA-Binding Proteins MeSH
• DNA MeSH
• Nucleoproteins MeSH
• RNA MeSH
• Carrier Proteins MeSH
• DNA, Z-Form MeSH

p53 is one of the most studied tumor suppressor proteins that plays an important role in basic biological processes including cell cycle, DNA damage response, apoptosis, and senescence. The human TP53 gene contains alternative promoters that produce N-terminally truncated proteins and can produce several isoforms due to alternative splicing. p53 function is realized by binding to a specific DNA response element (RE), resulting in the transactivation of target genes. Here, we evaluated the influence of quadruplex DNA structure on the transactivation potential of full-length and N-terminal truncated p53α isoforms in a panel of S. cerevisiae luciferase reporter strains. Our results show that a G-quadruplex prone sequence is not sufficient for transcription activation by p53α isoforms, but the presence of this feature in proximity to a p53 RE leads to a significant reduction of transcriptional activity and changes the dynamics between co-expressed p53α isoforms.

• Keywords
• p53 protein, protein-DNA interaction, transactivation potential,
• MeSH
• G-Quadruplexes * MeSH
• Humans MeSH
• Tumor Suppressor Protein p53 genetics   metabolism   MeSH
• Promoter Regions, Genetic genetics   MeSH
• Protein Isoforms genetics   metabolism   MeSH
• Apoptosis Regulatory Proteins genetics   metabolism   MeSH
• Proto-Oncogene Proteins genetics   metabolism   MeSH
• Response Elements genetics   MeSH
• Protein Binding MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• BBC3 protein, human MeSH Browser
• Tumor Suppressor Protein p53 MeSH
• Protein Isoforms MeSH
• Apoptosis Regulatory Proteins MeSH
• Proto-Oncogene Proteins MeSH

The tumor suppressor functions of p53 and its roles in regulating the cell cycle, apoptosis, senescence, and metabolism are accomplished mainly by its interactions with DNA. p53 works as a transcription factor for a significant number of genes. Most p53 target genes contain so-called p53 response elements in their promoters, consisting of 20 bp long canonical consensus sequences. Compared to other transcription factors, which usually bind to one concrete and clearly defined DNA target, the p53 consensus sequence is not strict, but contains two repeats of a 5'RRRCWWGYYY3' sequence; therefore it varies remarkably among target genes. Moreover, p53 binds also to DNA fragments that at least partially and often completely lack this consensus sequence. p53 also binds with high affinity to a variety of non-B DNA structures including Holliday junctions, cruciform structures, quadruplex DNA, triplex DNA, DNA loops, bulged DNA, and hemicatenane DNA. In this review, we summarize information of the interactions of p53 with various DNA targets and discuss the functional consequences of the rich world of p53 DNA binding targets for its complex regulatory functions.

• Keywords
• consensus sequence, cruciform, local DNA structures, p53, protein-DNA interactions,
• MeSH
• DNA chemistry   metabolism   MeSH
• Nucleic Acid Conformation MeSH
• Protein Conformation MeSH
• Consensus Sequence MeSH
• Humans MeSH
• Models, Molecular MeSH
• Tumor Suppressor Protein p53 chemistry   metabolism   MeSH
• Amino Acid Sequence MeSH
• Protein Binding MeSH
• Binding Sites MeSH
• Animals MeSH
• Check Tag
• Humans MeSH
• Animals MeSH
• Publication type
• Journal Article MeSH
• Review MeSH
• Names of Substances
• DNA MeSH
• Tumor Suppressor Protein p53 MeSH

Expansions of trinucleotide repeats (TNRs) are associated with genetic disorders such as Friedreich's ataxia. The tumor suppressor p53 is a central regulator of cell fate in response to different types of insults. Sequence and structure-selective modes of DNA recognition are among the main attributes of p53 protein. The focus of this work was analysis of the p53 structure-selective recognition of TNRs associated with human neurodegenerative diseases. Here, we studied binding of full length p53 and several deletion variants to TNRs folded into DNA hairpins or loops. We demonstrate that p53 binds to all studied non-B DNA structures, with a preference for non-B DNA structures formed by pyrimidine (Py) rich strands. Using deletion mutants, we determined the C-terminal DNA binding domain of p53 to be crucial for recognition of such non-B DNA structures. We also observed that p53 in vitro prefers binding to the Py-rich strand over the purine (Pu) rich strand in non-B DNA substrates formed by sequence derived from the first intron of the frataxin gene. The binding of p53 to this region was confirmed using chromatin immunoprecipitation in human Friedreich's ataxia fibroblast and adenocarcinoma cells. Altogether these observations provide further evidence that p53 binds to TNRs' non-B DNA structures.

• Keywords
• DNA hairpin, DNA–protein, frataxin, non-B DNA, p53, trinucleotide repeat,
• MeSH
• DNA chemistry   metabolism   MeSH
• Trinucleotide Repeat Expansion * MeSH
• Gene Expression MeSH
• Friedreich Ataxia genetics   metabolism   MeSH
• Protein Interaction Domains and Motifs MeSH
• Nucleic Acid Conformation * MeSH
• Humans MeSH
• Tumor Suppressor Protein p53 chemistry   metabolism   MeSH
• Pyrimidines MeSH
• Recombinant Proteins MeSH
• Trinucleotide Repeats * MeSH
• Protein Binding MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• DNA MeSH
• Tumor Suppressor Protein p53 MeSH
• Pyrimidines MeSH
• Recombinant Proteins MeSH
• TP53 protein, human MeSH Browser

p53 plays critical roles in regulating cell cycle, apoptosis, senescence and metabolism and is commonly mutated in human cancer. These roles are achieved by interaction with other proteins, but particularly by interaction with DNA. As a transcription factor, p53 is well known to bind consensus target sequences in linear B-DNA. Recent findings indicate that p53 binds with higher affinity to target sequences that form cruciform DNA structure. Moreover, p53 binds very tightly to non-B DNA structures and local DNA structures are increasingly recognized to influence the activity of wild-type and mutant p53. Apart from cruciform structures, p53 binds to quadruplex DNA, triplex DNA, DNA loops, bulged DNA and hemicatenane DNA. In this review, we describe local DNA structures and summarize information about interactions of p53 with these structural DNA motifs. These recent data provide important insights into the complexity of the p53 pathway and the functional consequences of wild-type and mutant p53 activation in normal and tumor cells.

• Keywords
• local DNA structures, p53 protein, protein-DNA interactions,
• MeSH
• DNA, B-Form MeSH
• DNA chemistry   genetics   metabolism   MeSH
• Nucleic Acid Conformation * MeSH
• Humans MeSH
• Tumor Suppressor Protein p53 chemistry   metabolism   MeSH
• Protein Binding MeSH
• Binding Sites MeSH
• Structure-Activity Relationship MeSH
• Animals MeSH
• Check Tag
• Humans MeSH
• Animals MeSH
• Publication type
• Journal Article MeSH
• Review MeSH
• Names of Substances
• DNA, B-Form MeSH
• DNA MeSH
• Tumor Suppressor Protein p53 MeSH
• triplex DNA MeSH Browser

Triplex DNA is implicated in a wide range of biological activities, including regulation of gene expression and genomic instability leading to cancer. The tumor suppressor p53 is a central regulator of cell fate in response to different type of insults. Sequence and structure specific modes of DNA recognition are core attributes of the p53 protein. The focus of this work is the structure-specific binding of p53 to DNA containing triplex-forming sequences in vitro and in cells and the effect on p53-driven transcription. This is the first DNA binding study of full-length p53 and its deletion variants to both intermolecular and intramolecular T.A.T triplexes. We demonstrate that the interaction of p53 with intermolecular T.A.T triplex is comparable to the recognition of CTG-hairpin non-B DNA structure. Using deletion mutants we determined the C-terminal DNA binding domain of p53 to be crucial for triplex recognition. Furthermore, strong p53 recognition of intramolecular T.A.T triplexes (H-DNA), stabilized by negative superhelicity in plasmid DNA, was detected by competition and immunoprecipitation experiments, and visualized by AFM. Moreover, chromatin immunoprecipitation revealed p53 binding T.A.T forming sequence in vivo. Enhanced reporter transactivation by p53 on insertion of triplex forming sequence into plasmid with p53 consensus sequence was observed by luciferase reporter assays. In-silico scan of human regulatory regions for the simultaneous presence of both consensus sequence and T.A.T motifs identified a set of candidate p53 target genes and p53-dependent activation of several of them (ABCG5, ENOX1, INSR, MCC, NFAT5) was confirmed by RT-qPCR. Our results show that T.A.T triplex comprises a new class of p53 binding sites targeted by p53 in a DNA structure-dependent mode in vitro and in cells. The contribution of p53 DNA structure-dependent binding to the regulation of transcription is discussed.

• MeSH
• Transcriptional Activation genetics   MeSH
• DNA-Binding Proteins chemistry   genetics   MeSH
• DNA chemistry   genetics   MeSH
• Nucleic Acid Conformation MeSH
• Humans MeSH
• Tumor Suppressor Protein p53 chemistry   genetics   MeSH
• Nucleotide Motifs genetics   MeSH
• Plasmids genetics   MeSH
• Promoter Regions, Genetic MeSH
• Regulatory Sequences, Nucleic Acid genetics   MeSH
• Sequence Deletion genetics   MeSH
• Binding Sites MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• DNA-Binding Proteins MeSH
• DNA MeSH
• Tumor Suppressor Protein p53 MeSH
• TP53 protein, human MeSH Browser
• triplex DNA MeSH Browser