Student or educator? Sign up with your school email and get 6 months of Pro free.
CoChat
Sign Up
Cited by 15

The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.

Characterization of p53 Family Homologs in Evolutionary Remote Branches of Holozoa

Bartas, Martin, Brázda, Václav, Červeň, Jiří, Pečinka, Petr·2019·International Journal of Molecular Sciences
DOI 10.3390/ijms21010006
Open this paper in CoChat — free account

Abstract

The p53 family of transcription factors plays key roles in development, genome stability, senescence and tumor development, and p53 is the most important tumor suppressor protein in humans. Although intensively investigated for many years, its initial evolutionary history is not yet fully elucidated. Using bioinformatic and structure prediction methods on current databases containing newly-sequenced genomes and transcriptomes, we present a detailed characterization of p53 family homologs in remote members of the Holozoa group, in the unicellular clades Filasterea, Ichthyosporea and Corallochytrea. Moreover, we show that these newly characterized homologous sequences contain domains that can form structures with high similarity to the human p53 family DNA-binding domain, and some also show similarities to the oligomerization and SAM domains. The presence of these remote homologs demonstrates an ancient origin of the p53 protein family.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.3390/ijms21010006

Cites

6 of 6 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Show all 6 references

Research works printed but not linked: 64

  1. Hollstein, 1991, P53 Mutations in Human Cancers, Science, 253, 49, 10.1126/science.1905840 · DOI · Paper page
  2. Goh, 2011, The role of mutant p53 in human cancer, J. Pathol., 223, 116, 10.1002/path.2784 · DOI · Paper page
  3. Stiewe, 2018, How mutations shape p53 interactions with the genome to promote tumorigenesis and drug resistance, Drug Resist. Update, 38, 27, 10.1016/j.drup.2018.05.001 · DOI
  4. Joerger, 2016, The p53 pathway: Origins, inactivation in cancer, and emerging therapeutic approaches, Annu. Rev. Biochem., 85, 375, 10.1146/annurev-biochem-060815-014710 · DOI · Paper page
  5. Strano, 2001, From p63 to p53 across p73, FEBS Lett., 490, 163, 10.1016/S0014-5793(01)02119-6 · DOI
  6. Belyi, 2009, One billion years of p53/p63/p73 evolution, Proc. Natl. Acad. Sci. USA, 106, 17609, 10.1073/pnas.0910634106 · DOI
  7. Brazda, V., and Coufal, J. (2017). Recognition of Local DNA Structures by p53 Protein. Int. J. Mol. Sci., 18. · DOI · Paper page
  8. Vyas, 2017, Diverse p53/DNA binding modes expand the repertoire of p53 response elements, Proc. Natl. Acad. Sci. USA, 114, 10624, 10.1073/pnas.1618005114 · DOI
  9. Brázda, V., and Fojta, M. (2019). The Rich World of p53 DNA Binding Targets: The Role of DNA Structure. Int. J. Mol. Sci., 20. · DOI · Paper page
  10. Kern, 1992, Definition of a consensus binding site for p53, Nat. Genet., 1, 45, 10.1038/ng0492-45 · DOI · Paper page
  11. Battistin, 2017, The structure formed by inverted repeats in p53 response elements determines the transactivation activity of p53 protein, Biochem. Biophys. Res. Commun., 483, 516, 10.1016/j.bbrc.2016.12.113 · DOI
  12. Coufal, 2013, Preferential binding of p53 tumor suppressor to p21 promoter sites that contain inverted repeats capable of forming cruciform structure, Biochem. Biophys. Res. Commun., 441, 83, 10.1016/j.bbrc.2013.10.015 · DOI
  13. Dötsch, V., Bernassola, F., Coutandin, D., Candi, E., and Melino, G. (2010). p63 and p73, the Ancestors of p53. Cold Spring Harb. Perspect. Biol., 2. · DOI · Paper page
  14. Arrowsmith, 1999, Structure and function in the p53 family, Cell Death Differ., 6, 1169, 10.1038/sj.cdd.4400619 · DOI
  15. Joerger, 2009, Structural evolution of p53, p63, and p73: Implication for heterotetramer formation, Proc. Natl. Acad. Sci. USA, 106, 17705, 10.1073/pnas.0905867106 · DOI
  16. Pavletich, 1993, The DNA-binding domain of p53 contains the four conserved regions and the major mutation hot spots, Genes Dev., 7, 2556, 10.1101/gad.7.12b.2556 · DOI · Paper page
  17. Xue, 2013, Intrinsically disordered regions of p53 family are highly diversified in evolution, BBA Proteins Proteom., 1834, 725, 10.1016/j.bbapap.2013.01.012 · DOI
  18. Joerger, 2014, Tracing the Evolution of the p53 Tetramerization Domain, Structure, 22, 1301, 10.1016/j.str.2014.07.010 · DOI · Paper page
  19. Yang, 2002, On the shoulders of giants: p63, p73 and the rise of p53, Trends Genet., 18, 90, 10.1016/S0168-9525(02)02595-7 · DOI · Paper page
  20. Dos Santos, H.G., Nunez-Castilla, J., and Siltberg-Liberles, J. (2016). Functional diversification after gene duplication: Paralog specific regions of structural disorder and phosphorylation in p53, p63, and p73. PLoS ONE, 11. · DOI
  21. Laptenko, 2015, The p53 C terminus controls site-specific DNA binding and promotes structural changes within the central DNA binding domain, Mol. Cell, 57, 1034, 10.1016/j.molcel.2015.02.015 · DOI · Paper page
  22. Gu, 1997, Activation of p53 sequence-specific DNA binding by acetylation of the p53 C-terminal domain, Cell, 90, 595, 10.1016/S0092-8674(00)80521-8 · DOI · Paper page
  23. Luciani, 2004, Activation of the DNA-binding ability of latent p53 protein by protein kinase C is abolished by protein kinase CK2, Biochem. J., 378, 939, 10.1042/bj20030662 · DOI
  24. Ou, 2005, p53 C-terminal phosphorylation by CHK1 and CHK2 participates in the regulation of DNA-damage-induced C-terminal acetylation, Mol. Biol. Cell, 16, 1684, 10.1091/mbc.e04-08-0689 · DOI · Paper page
  25. Muller, 2018, Evidence for allosteric effects on p53 oligomerization induced by phosphorylation, Protein Sci., 27, 523, 10.1002/pro.3344 · DOI
  26. 2000, Specific modulation of p53 binding to consensus sequence within supercoiled DNA by monoclonal antibodies, Biochem. Biophys. Res. Commun., 267, 934, 10.1006/bbrc.1999.2056 · DOI
  27. Weinberg, 2004, Regulation of DNA binding of p53 by its C-terminal domain, J. Mol. Biol., 342, 801, 10.1016/j.jmb.2004.07.042 · DOI · Paper page
  28. Belyi, 2010, The origins and evolution of the p53 family of genes, Cold Spring Harb. Perspect. Biol., 2, a001198, 10.1101/cshperspect.a001198 · DOI · Paper page
  29. Nedelcu, 2007, Early diversification and complex evolutionary history of the p53 tumor suppressor gene family, Dev. Genes Evol., 217, 801, 10.1007/s00427-007-0185-9 · DOI
  30. Lang, 2011, Unexpected repertoire of metazoan transcription factors in the unicellular holozoan Capsaspora owczarzaki, Mol. Biol. Evol., 28, 1241, 10.1093/molbev/msq309 · DOI · Paper page
  31. Torruella, 2013, Transcription factor evolution in eukaryotes and the assembly of the regulatory toolkit in multicellular lineages, Proc. Natl. Acad. Sci. USA, 110, E4858
  32. 2016, High-throughput proteomics reveals the unicellular roots of animal phosphosignaling and cell differentiation, Dev. Cell, 39, 186, 10.1016/j.devcel.2016.09.019 · DOI
  33. Altschul, 1990, Basic local alignment search tool, J. Mol. Biol., 215, 403, 10.1016/S0022-2836(05)80360-2 · doi:10.1016/s0022-2836(05)80360-2 · Paper page
  34. Torruella, 2017, Dynamics of genomic innovation in the unicellular ancestry of animals, eLife, 6, e26036, 10.7554/eLife.26036 · DOI · Paper page
  35. Suga, 2015, Complex transcriptional regulation and independent evolution of fungal-like traits in a relative of animals, eLife, 4, e08904, 10.7554/eLife.08904 · DOI
  36. Chang, 2001, Various forms of mutant p53 confer sensitivity to cisplatin and doxorubicin in bladder cancer cells, J. Urol., 166, 304, 10.1016/S0022-5347(05)66150-2 · DOI
  37. Eldar, 2013, Structural studies of p53 inactivation by DNA-contact mutations and its rescue by suppressor mutations via alternative protein–DNA interactions, Nucleic Acids Res., 41, 8748, 10.1093/nar/gkt630 · DOI · Paper page
  38. Gomes, A.S., Trovão, F., Andrade Pinheiro, B., Freire, F., Gomes, S., Oliveira, C., Domingues, L., Romão, M.J., Saraiva, L., and Carvalho, A.L. (2018). The Crystal Structure of the R280K Mutant of Human p53 Explains the Loss of DNA Binding. Int. J. Mol. Sci., 19. · DOI
  39. Dittmer, 1993, Gain of function mutations in p53, Nat. Genet., 4, 42, 10.1038/ng0593-42 · DOI · Paper page
  40. Xu, 2012, Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field, Proteins Struct. Funct. Bioinform., 80, 1715, 10.1002/prot.24065 · DOI · Paper page
  41. Xu, 2013, Toward optimal fragment generations for ab initio protein structure assembly, Proteins Struct. Funct. Bioinform., 81, 229, 10.1002/prot.24179 · DOI
  42. Waterhouse, 2018, SWISS-MODEL: Homology modelling of protein structures and complexes, Nucleic Acids Res., 46, W296, 10.1093/nar/gky427 · DOI · Paper page
  43. Pettersen, 2004, UCSF Chimera—A visualization system for exploratory research and analysis, J. Comput. Chem., 25, 1605, 10.1002/jcc.20084 · DOI · Paper page
  44. Lion, M., Raimondi, I., Donati, S., Jousson, O., Ciribilli, Y., and Inga, A. (2015). Evolution of p53 Transactivation Specificity through the Lens of a Yeast-Based Functional Assay. PLoS ONE, 10. · DOI
  45. Jordan, 1998, Ribonucleotide Reductases, Annu. Rev. Biochem., 67, 71, 10.1146/annurev.biochem.67.1.71 · DOI · Paper page
  46. Åberg, E., Saccoccia, F., Grabherr, M., Ore, W.Y.J., Jemth, P., and Hultqvist, G. (2017). Evolution of the p53-MDM2 pathway. BMC Evol. Biol., 17. · DOI · Paper page
  47. Mendoza, 2003, Ehp53, an Entamoeba histolytica protein, ancestor of the mammalian tumour suppressor p53, Microbiology, 149, 885, 10.1099/mic.0.25892-0 · DOI
  48. Biscotti, 2019, The p53 gene family in vertebrates: Evolutionary considerations, J. Exp. Zool. Part B, 332, 171, 10.1002/jez.b.22856 · DOI
  49. Aravind, 2003, Evolutionary connections between bacterial and eukaryotic signaling systems: A genomic perspective, Curr. Opin. Microbiol., 6, 490, 10.1016/j.mib.2003.09.003 · DOI
  50. Okonechnikov, 2012, Unipro UGENE: A unified bioinformatics toolkit, Bioinformatics, 28, 1166, 10.1093/bioinformatics/bts091 · DOI · Paper page
  51. Kozlowski, 2016, IPC—Isoelectric Point Calculator, Biol. Direct, 11, 55, 10.1186/s13062-016-0159-9 · DOI · Paper page
  52. Derbyshire, 2015, CDD: NCBI’s conserved domain database, Nucleic Acids Res., 43, D222, 10.1093/nar/gku1221 · DOI · Paper page
  53. Kosugi, 2009, Systematic identification of cell cycle-dependent yeast nucleocytoplasmic shuttling proteins by prediction of composite motifs, Proc. Natl. Acad. Sci. USA, 106, 10171, 10.1073/pnas.0900604106 · DOI · Paper page
  54. Hedges, 2015, Tree of life reveals clock-like speciation and diversification, Mol. Biol. Evol., 32, 835, 10.1093/molbev/msv037 · DOI · Paper page
  55. Kumar, 2017, TimeTree: A resource for timelines, timetrees, and divergence times, Mol. Biol. Evol., 34, 1812, 10.1093/molbev/msx116 · DOI · Paper page
  56. Letunic, 2018, 20 years of the SMART protein domain annotation resource, Nucleic Acids Res., 46, D493, 10.1093/nar/gkx922 · DOI · Paper page
  57. Edgar, 2004, MUSCLE: Multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res., 32, 1792, 10.1093/nar/gkh340 · DOI · Paper page
  58. Jassem, 1997, TP53 mutational pattern in Spanish and Polish non-small cell lung cancer patients: Null mutations are associated with poor prognosis, Oncogene, 15, 2951, 10.1038/sj.onc.1201475 · doi:10.1038/sj.onc.1201475
  59. Huelsenbeck, 2001, MRBAYES: Bayesian inference of phylogenetic trees, Bioinformatics, 17, 754, 10.1093/bioinformatics/17.8.754 · DOI · Paper page
  60. Enthart, 2016, Solution structure and binding specificity of the p63 DNA binding domain, Sci. Rep., 6, 26707, 10.1038/srep26707 · DOI · Paper page
  61. Meng, E.C., Pettersen, E.F., Couch, G.S., Huang, C.C., and Ferrin, T.E. (2006). Tools for integrated sequence-structure analysis with UCSF Chimera. BMC Bioinform., 7. · DOI · Paper page
  62. Hu, 2015, GSDS 2.0: An upgraded gene feature visualization server, Bioinformatics, 31, 1296, 10.1093/bioinformatics/btu817 · DOI · Paper page
  63. Dereeper, 2008, Phylogeny. fr: Robust phylogenetic analysis for the non-specialist, Nucleic Acids Res., 36, W465, 10.1093/nar/gkn180 · DOI · Paper page
  64. Notredame, 2000, T-Coffee: A novel method for fast and accurate multiple sequence alignment, J. Mol. Biol., 302, 205, 10.1006/jmbi.2000.4042 · DOI · Paper page

Cited by

See all 15

Metadata

Authors
Bartas, M., Brázda, V., Červeň, J., & Pečinka, P.
Venue
International Journal of Molecular Sciences
Publisher
MDPI AG
Published
2019-12-18
Volume
21
Issue
1
Pages
6
ISSN
1422-0067
DOI
10.3390/ijms21010006
Cited by
15
References
6
Language
en
Licence
creativecommons.org/licenses/by/4.0/ (vor)
Funders
  • Ministry of Education, Youth and Sports of the Czech Republic in the “National Feasibility Program I” (project LO1208 TEWEP)
  • The Czech Science Foundation (18-15548S)
  • EU structural funding Operational Programme Research and Development for innovation (CZ.1.05/2.1.00/19.0388)
  • University of Ostrava (SGS/09/PrF/2019)

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

How to cite

Cite CoChat for the checks on this page, and the paper for its own findings.

This page
CoChat. (2026). Citation check: Characterization of p53 Family Homologs in Evolutionary Remote Branches of Holozoa. https://app.cochat.ai/papers/10.3390/ijms21010006
The paper
Bartas, M., Brázda, V., Červeň, J., & Pečinka, P. (2019). Characterization of p53 Family Homologs in Evolutionary Remote Branches of Holozoa. International Journal of Molecular Sciences. https://doi.org/10.3390/ijms21010006

Data sources

Bibliographic data: Semantic Scholar, OpenAlex, Crossref.

Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).

Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.