Conservation of the Nucleotide Excision Repair Pathway: Characterization of Hydra Xeroderma Pigmentosum Group F Homolog

Abstract

Hydra, one of the earliest metazoans with tissue grade organization and nervous system, is an animal with a remarkable regeneration capacity and shows no signs of organismal aging. We have for the first time identified genes of the nucleotide excision repair (NER) pathway from hydra. Here we report cloning and characterization of hydra homolog of xeroderma pigmentosum group F (XPF) gene that encodes a structure-specific 5′ endonuclease which is a crucial component of NER. In silico analysis shows that hydra XPF amino acid sequence is very similar to its counterparts from other animals, especially vertebrates, and shows all features essential for its function. By in situ hybridization, we show that hydra XPF is expressed prominently in the multipotent stem cell niche in the central region of the body column. Ectoderm of the diploblastic hydra was shown to express higher levels of XPF as compared to the endoderm by semi-quantitative RT-PCR. Semi-quantitative RT-PCR analysis also demonstrated that interstitial cells, a multipotent and rapidly cycling stem cell lineage of hydra, express higher levels of XPF mRNA than other cell types. Our data show that XPF and by extension, the NER pathway is highly conserved during evolution. The prominent expression of an NER gene in interstitial cells may have implications for the lack of senescence in hydra.

Structural and Sequence Similarities of Hydra Xeroderma Pigmentosum A Protein to Human Homolog Suggest Early Evolution and Conservation

“…The closest matches were found to be with homologs from many mammals like human, mouse, rat, dog, elephant, macaque, cattle, chimpanzee, and so forth, and other vertebrates like Anolis , Xenopus , Danio, and Gallus . This corroborates our earlier observations that hydra protein sequences often show greater similarity with their vertebrate homologs [23, 41]. The findings support the hypothesis of Kortschak et al [42] that cnidarian genes are often more similar to vertebrate counterparts than to those in model invertebrates like Drosophila , indicating high complexity of cnidarian genomes and gene loss in model invertebrates.…”

“…Hydra XPA is closely related to echinoderm XPA and groups with the deuterostomes rather than protostomes. This matches with our observations regarding another NER gene, XPF , where the cluster of early metazoan XPFs consistently grouped with the chordate-echinoderm cluster [23]. Since XPA sequences from other early metazoan members are not available at present, conclusions drawn on the basis of hydra XPA show that the observations of Kortschak et al [42] and Chapman et al [40] regarding the similarity between cnidarian and bilaterian lineages despite early divergence hold true for XPA as well.…”

“…We have recently identified and cloned parts of all seven XP genes from hydra for the first time. The complete CDS of hydra XPF , which encodes the 5′ endonuclease of NER, has been partially characterized [23]. Here, we report identification and cloning of the XPA homolog from Hydra vulgaris Ind-Pune [24].…”

Hydra , a Model System for Deciphering the Mechanisms of Aging and Resistance to Aging

“…The Hydra Xeroderma Pigmentosum group A ortholog (XPA) is highly similar to human XPA, encoding the ERCC1 helix-hairpin-helix motif and a nuclear localization signal (58). Similarly the function of Xeroderma Pigmentosum group F (XPF), which encodes an ERCC4 endonuclease domain and is predominantly expressed in ISCs, is likely conserved in Hydra (59). Concerning the BER pathway, genes encoding the Flap endonuclease 1 (Fen1), XRCC1, Polymerase-β (Polb) and Ligase3 were identified in genomic and transcriptomic analyses in Hydra (11,13) as well as in the jellyfish Aurelia aurita (60).…”

Hydra, a model system for deciphering the mechanisms of aging and resistance to aging

“…The Hydra Xeroderma Pigmentosum group A ortholog (XPA) is highly similar to human XPA, encoding the ERCC1 helix-hairpin-helix motif and a nuclear localization signal (58). Similarly the function of Xeroderma Pigmentosum group F (XPF), which encodes an ERCC4 endonuclease domain and is predominantly expressed in ISCs, is likely conserved in Hydra (59). Concerning the BER pathway, genes encoding the Flap endonuclease 1 (Fen1), XRCC1, Polymerase-β (Polβ) and Ligase3 were identified in genomic and transcriptomic analyses in Hydra (11,13) as well as in the jellyfish Aurelia aurita (60).…”