- About this Journal
- Abstracting and Indexing
- Aims and Scope
- Annual Issues
- Article Processing Charges
- Articles in Press
- Author Guidelines
- Bibliographic Information
- Citations to this Journal
- Contact Information
- Editorial Board
- Editorial Workflow
- Free eTOC Alerts
- Publication Ethics
- Reviewers Acknowledgment
- Submit a Manuscript
- Subscription Information
- Table of Contents
BioMed Research International
Volume 2013 (2013), Article ID 854745, 9 pages
Structural and Sequence Similarities of Hydra Xeroderma Pigmentosum A Protein to Human Homolog Suggest Early Evolution and Conservation
1Division of Animal Sciences, Agharkar Research Institute, G. G. Agarkar Road, Pune 411 004, India
2Department of Zoology, University of Pune, Ganeshkhind, Pune 411 007, India
Received 15 April 2013; Accepted 31 July 2013
Academic Editor: Sanford I. Bernstein
Copyright © 2013 Apurva Barve et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- R. Hakem, “DNA-damage repair; the good, the bad, and the ugly,” The EMBO Journal, vol. 27, no. 4, pp. 589–605, 2008.
- O. D. Schärer, “A molecular basis for damage recognition in eukaryotic nucleotide excision repair,” ChemBioChem, vol. 9, no. 1, pp. 21–23, 2008.
- L. C. J. Gillet and O. D. Schärer, “Molecular mechanisms of mammalian global genome nucleotide excision repair,” Chemical Reviews, vol. 106, no. 2, pp. 253–276, 2006.
- A. Aboussekhra, M. Biggerstaff, M. K. K. Shivji et al., “Mammalian DNA nucleotide excision repair reconstituted with purified protein components,” Cell, vol. 80, no. 6, pp. 859–868, 1995.
- T. Kobayashi, S. Takeuchi, M. Saijo et al., “Mutational analysis of a function of xeroderma pigmentosum group A (XPA) protein in strand-specific DNA repair,” Nucleic Acids Research, vol. 26, no. 20, pp. 4662–4668, 1998.
- L. Li, X. Lu, C. A. Peterson, and R. J. Legerski, “An interaction between the DNA repair factor XPA and replication protein A appears essential for nucleotide excision repair,” Molecular and Cellular Biology, vol. 15, no. 10, pp. 5396–5402, 1995.
- J. E. Cleaver and J. C. States, “The DNA damage-recognition problem in human and other eukaryotic cells: the XPA damage binding protein,” Biochemical Journal, vol. 328, no. 1, pp. 1–12, 1997.
- P. Robins, C. J. Jones, M. Biggerstaff, T. Lindahl, and R. D. Wood, “Complementation of DNA repair in xeroderma pigmentosum group A cell extracts by a protein with affinity for damaged DNA,” The EMBO Journal, vol. 10, no. 12, pp. 3913–3921, 1991.
- B. S. Thoma and K. M. Vasquez, “Critical DNA damage recognition functions of XPC-hHR23B and XPA-RPA in nucleotide excision repair,” Molecular Carcinogenesis, vol. 38, no. 1, pp. 1–13, 2003.
- L. Li, S. J. Elledge, C. A. Peterson, E. S. Bales, and R. J. Legerski, “Specific association between the human DNA repair proteins XPA and ERCC1,” Proceedings of the National Academy of Sciences of the United States of America, vol. 91, no. 11, pp. 5012–5016, 1994.
- C. Park and A. Sancar, “Formation of a ternary complex by human XPA, ERCC1, and ERCC4(XPF) excision repair proteins,” Proceedings of the National Academy of Sciences of the United States of America, vol. 91, no. 11, pp. 5017–5021, 1994.
- T. Kang, J. T. Reardon, and A. Sancar, “Regulation of nucleotide excision repair activity by transcriptional and post-transcriptional control of the XPA protein,” Nucleic Acids Research, vol. 39, no. 8, pp. 3176–3187, 2011.
- T. Kang, L. A. Lindsey-Boltz, J. T. Reardon, and A. Sancar, “Circadian control of XPA and excision repair of cisplatin-DNA damage by cryptochrome and HERC2 ubiquitin ligase,” Proceedings of the National Academy of Sciences of the United States of America, vol. 107, no. 11, pp. 4890–4895, 2010.
- M. F. White, “Archaeal DNA repair: Paradigms and puzzles,” Biochemical Society Transactions, vol. 31, no. 3, pp. 690–693, 2003.
- O. V. Tsodikov, D. Ivanov, B. Orelli et al., “Structural basis for the recruitment of ERCC1-XPF to nucleotide excision repair complexes by XPA,” The EMBO Journal, vol. 26, no. 22, pp. 4768–4776, 2007.
- L. J. Hoeijmakers, “How relevant is the Escherichia coli UvrABC model for excision repair in eukaryotes?” Journal of Cell Science, vol. 100, no. 4, pp. 687–691, 1991.
- J. H. J. Hoeijmakers, “Nucleotide excision repair II: From yeast to mammals,” Trends in Genetics, vol. 9, no. 6, pp. 211–217, 1993.
- T. Shimamoto, T. Tanimura, Y. Yoneda et al., “Expression and functional analyses of the Dxpa gene, the Drosophila homolog of the human excision repair gene XPA,” The Journal of Biological Chemistry, vol. 270, no. 38, pp. 22452–22459, 1995.
- B. Galliot and V. Schmid, “Cnidarians as a model system for understanding evolution and regeneration,” International Journal of Developmental Biology, vol. 46, no. 1, pp. 39–48, 2002.
- T. C. G. Bosch, “Stem cells in immortal hydra,” in Stem Cells: From Hydra to Man, T. C. G. Bosch, Ed., pp. 27–57, Springer, Amsterdam, The Netherlands, 2008.
- H. R. Bode, “The interstitial cell lineage of hydra: a stem cell system that arose early in evolution,” Journal of Cell Science, vol. 109, no. 6, pp. 1155–1164, 1996.
- D. E. Martínez, “Mortality patterns suggest lack of senescence in hydra,” Experimental Gerontology, vol. 33, no. 3, pp. 217–225, 1998.
- A. Barve, S. Ghaskadbi, and S. Ghaskadbi, “Conservation of the nucleotide excision repair pathway: characterization of hydra xeroderma pigmentosumgroup F homolog,” PLoS ONE, vol. 8, no. 4, Article ID e61062, 2013.
- P. Chandramouli Reddy, A. Barve, and S. Ghaskadbi, “Description and phylogenetic characterization of common hydra from India,” Current Science, vol. 101, no. 6, pp. 736–738, 2011.
- S. F. Altschul, T. L. Madden, A. A. Schäffer et al., “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs,” Nucleic Acids Research, vol. 25, no. 17, pp. 3389–3402, 1997.
- S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, “Basic local alignment search tool,” Journal of Molecular Biology, vol. 215, no. 3, pp. 403–410, 1990.
- E. Gasteiger, A. Gattiker, C. Hoogland, I. Ivanyi, R. D. Appel, and A. Bairoch, “ExPASy: The proteomics server for in-depth protein knowledge and analysis,” Nucleic Acids Research, vol. 31, no. 13, pp. 3784–3788, 2003.
- J. Schultz, F. Milpetz, P. Bork, and C. P. Ponting, “SMART, a simple modular architecture research tool: identification of signaling domains,” Proceedings of the National Academy of Sciences of the United States of America, vol. 95, no. 11, pp. 5857–5864, 1998.
- I. Letunic, T. Doerks, and P. Bork, “SMART 6: recent updates and new developments,” Nucleic Acids Research, vol. 37, no. 1, pp. D229–D232, 2009.
- M. A. Larkin, G. Blackshields, N. P. Brown et al., “Clustal W and Clustal X version 2.0,” Bioinformatics, vol. 23, no. 21, pp. 2947–2948, 2007.
- M. Goujon, H. McWilliam, W. Li et al., “A new bioinformatics analysis tools framework at EMBL-EBI,” Nucleic Acids Research, vol. 38, no. 2, Article ID gkq313, pp. W695–W699, 2010.
- T. Schwede, J. Kopp, N. Guex, and M. C. Peitsch, “SWISS-MODEL: an automated protein homology-modeling server,” Nucleic Acids Research, vol. 31, no. 13, pp. 3381–3385, 2003.
- K. Arnold, L. Bordoli, J. Kopp, and T. Schwede, “The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling,” Bioinformatics, vol. 22, no. 2, pp. 195–201, 2006.
- N. Guex and M. C. Peitsch, “SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling,” Electrophoresis, vol. 18, no. 15, pp. 2714–2723, 1997.
- K. Tamura, D. Peterson, N. Peterson, G. Stecher, M. Nei, and S. Kumar, “MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods,” Molecular Biology and Evolution, vol. 28, no. 10, pp. 2731–2739, 2011.
- M. Nei and S. Kumar, Molecular Evolution and Phylogenetics, Oxford University Press, New York, NY, USA, 2000.
- D. T. Jones, W. R. Taylor, and J. M. Thornton, “The rapid generation of mutation data matrices from protein sequences,” Computer Applications in the Biosciences, vol. 8, no. 3, pp. 275–282, 1992.
- A. Rzhetsky and M. Nei, “A simple method for estimating and testing minimum-evolution trees,” Molecular Biology and Evolution, vol. 9, no. 5, pp. 945–967, 1992.
- J. Felsenstein, “Confidence limits on phylogenies: an approach using the bootstrap,” Evolution, vol. 39, pp. 783–791, 1985.
- J. A. Chapman, E. F. Kirkness, O. Simakov, et al., “The dynamic genome of Hydra,” Nature, vol. 464, pp. 592–596, 2010.
- P. Reddy, S. S. Bidaye, and S. Ghaskadbi, “Genome-wide screening reveals the emergence and divergence of RTK homologues in basal Metazoan Hydra magnipapillata,” Journal of Biosciences, vol. 36, no. 2, pp. 289–296, 2011.
- R. D. Kortschak, G. Samuel, R. Saint, and D. J. Miller, “EST analysis of the cnidarian Acropora millepora reveals extensive gene loss and rapid sequence divergence in the model invertebrates,” Current Biology, vol. 13, no. 24, pp. 2190–2195, 2003.
- I. G. Macara, “Transport into and out of the nucleus,” Microbiology and Molecular Biology Reviews, vol. 65, no. 4, pp. 570–594, 2001.
- I. Miyamoto, N. Miura, H. Niwa, J. Miyazaki, and K. Tanaka, “Mutational analysis of the structure and function of the xeroderma pigmentosum group A complementing protein. Identification of essential domains for nuclear localization and DNA excision repair,” The Journal of Biological Chemistry, vol. 267, no. 17, pp. 12182–12187, 1992.
- J. Robbins, S. M. Dilworth, R. A. Laskey, and C. Dingwall, “Two interdependent basic domains in nucleoplasmin nuclear targeting sequence: identification of a class of bipartite nuclear targeting sequence,” Cell, vol. 64, no. 3, pp. 615–623, 1991.
- K. Tanaka, N. Miura, I. Satokata et al., “Analysis of a human DNA excision repair gene involved in group A xeroderma pigmentosum and containing a zinc-finger domain,” Nature, vol. 348, no. 6296, pp. 73–76, 1990.
- M. K. Kenny, U. Schlegel, H. Furneaux, and J. Hurwitz, “The role of human single-stranded DNA binding protein and its individual subunits in simian virus 40 DNA replication,” The Journal of Biological Chemistry, vol. 265, no. 13, pp. 7693–7700, 1990.
- L. Li, C. A. Peterson, X. Lu, and R. J. Legerski, “Mutations in XPA that prevent association with ERCC1 are defective in nucleotide excision repair,” Molecular and Cellular Biology, vol. 15, no. 4, pp. 1993–1998, 1995.
- K. Tripsianes, G. E. Folkers, C. Zheng et al., “Analysis of the XPA and ssDNA-binding surfaces on the central domain of human ERCC1 reveals evidence for subfunctionalization,” Nucleic Acids Research, vol. 35, no. 17, pp. 5789–5798, 2007.
- C.-H. Park, D. Mu, J. T. Reardon, and A. Sancar, “The general transcription-repair factor TFIIH is recruited to the excision repair complex by the XPA protein independent of the TFIIE transcription factor,” The Journal of Biological Chemistry, vol. 270, no. 9, pp. 4896–4902, 1995.
- T. Ikegami, I. Kuraoka, M. Saijo et al., “Solution structure of the DNA- and RPA-binding domain of the human repair factor XPA,” Nature Structural Biology, vol. 5, no. 8, pp. 701–706, 1998.
- G. W. Buchko, G. W. Daughdrill, R. De Lorimier et al., “Interactions of human nucleotide excision repair protein XPA with DNA and RPA70ΔC327: chemical shift mapping and 15-N NMR relaxation studies,” Biochemistry, vol. 38, no. 46, pp. 15116–15128, 1999.
- S. Kuru, M. Yasuma, M. Sakai, M. Konagaya, and S. Moriwaki, “Siblings with xeroderma pigmentosum group A showing mild cutaneous and various neurological manifestations,” Clinical Neurology, vol. 46, no. 2, pp. 134–139, 2006.
- A. Anttinen, L. Koulu, E. Nikoskelainen et al., “Neurological symptoms and natural course of xeroderma pigmentosum,” Brain, vol. 131, no. 8, pp. 1979–1989, 2008.
- J. E. Cleaver, E. T. Lam, and I. Revet, “Disorders of nucleotide excision repair: the genetic and molecular basis of heterogeneity,” Nature Reviews Genetics, vol. 10, no. 11, pp. 756–768, 2009.