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Molecular and Cellular Biology, May 2006, p. 3935-3941, Vol. 26, No. 10
0270-7306/06/$08.00+0 doi:10.1128/MCB.26.10.3935-3941.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
Department of Immunology, The University of Texas M. D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030,1 The CBR Institute for Biomedical Research, Howard Hughes Medical Institute, Children's Hospital, and Harvard Medical School, Boston, Massachusetts 021152
Received 6 December 2005/ Returned for modification 21 December 2005/ Accepted 2 March 2006
| ABSTRACT |
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| INTRODUCTION |
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DNA ligase III is found in two isoforms, ligase III
and ligase IIIß, produced by alternative pre-mRNA splicing (7, 18, 52). The two spliced variants of ligase III differ at their C termini (31). DNA ligase III
contains a unique BRCT motif, whereas DNA ligase IIIß is a shorter polypeptide that lacks a BRCT motif. DNA ligase III
is ubiquitously expressed, suggesting a role in broader DNA repair processes, while ligase IIIß is expressed uniquely in pachytene spermatocytes and haploid spermatids of the testes, implying a specific role in meiotic recombination (31). Both forms of DNA ligase III have a putative zinc finger near the N terminus. Similar structures have been found in other proteins such as poly(ADP-ribose) polymerase (PARP), which is known as a sensor for DNA nicks (39). Several studies have demonstrated the interaction between DNA ligase III and PARP1 and PARP2 (3, 24, 35), thus suggesting a role for DNA ligase III in SSB repair (19, 30, 38, 39). DNA ligase III also contains mitochondrion-targeting sequences. By initiating translation at two different AUG codons, DNA ligase III can be targeted to either the nucleus or the mitochondria (22, 23, 34). Therefore, DNA ligase III may also function in the replication and repair of mitochondrial DNA.
A recent study showed DNA ligase III directly interacts with tyrosyl phosphodiesterase 1 in the SSB repair complex, which is important for maintaining the genomic integrity of developing neurons (9). Furthermore, DNA ligase III may act as a backup ligase in the repair of DNA double-stranded breaks (50), especially when the main ligase for the nonhomologous end-joining pathways, ligase IV, is deficient. Also, the LIG3 gene likely encodes DNA ligase II, a proteolytic product derived from DNA ligase III, found to be active in the liver (18, 42, 51).
All DNA ligases function together with its "partner" protein: ligase I associates with replication factor proliferating cell nuclear antigen (PCNA) (25, 45), and ligase IV associates with XRCC4 (13-15, 37). Ligase III
associates with DNA repair protein XRCC1 (4, 5, 33) via BRCT motifs (20, 56). A study showed that a mutation in the BRCT motif of XRCC1 abolishes the SSB DNA repair activity of the protein, specifically at the G1 phase of the cell cycle (38). XRCC1-deficient cells have a decreased level of DNA ligase III compared to normal cells and are hypersensitive to many DNA-damaging agents, particularly alkylating agents. XRCC1 mutant cells also show an increased level of sister chromatid exchanges (SCE), which demonstrate a general status of DNA instability, and are defective in joining SSBs (5, 6, 27, 43). All these results strongly suggest the DNA ligase III and XRCC1 complex plays an important role in the repair of SSBs.
Besides its association with DNA ligase III, XRCC1 is able to interact with many additional proteins, such as DNA polymerase ß (pol ß), PARP1, PARP2, polynucleotide kinase (3, 16, 21, 53), PCNA (10), and major apyrimidinic endonuclease (APE) (49). This indicates XRCC1 is the centerpiece for holding together protein complexes in SSB repair (2) or for assembling multiple complexes and therefore functioning independently of DNA ligase III.
Currently, LIG3-deficient mice or cells have not yet been described, but it has been shown that deficiency of XRCC1 leads to early embryonic lethality at 6.5 days postcoitum (dpc) through 7.5 dpc (40, 41). One can predict that LIG3-deficient mice have a similar phenotype. Here, we report the first mutation of the LIG3 gene by gene targeting. We found mutant mice homozygous for LIG3 inactivation are indeed early embryonic lethal but survive slightly longer than XRCC1-deficient embryos.
| MATERIALS AND METHODS |
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Southern blotting, Western blotting, and PCR genotyping. DNA samples from ES cells or mouse tails were digested with EcoRV, and Southern blot analyses were performed with 5', 3', and neo probes (Fig. 1B). Western blot analysis was performed in extracts obtained from 8.5-dpc mutant, heterozygous, and wild-type embryos with primary antibodies against ligase III (Transduction Labs, San Jose, CA) and XRCC1 (Bethyl Laboratories, Montgomery, TX). For PCR genotyping, primers 5' and 3' to the replaced regions together with primers from the neo-resistant gene region were used to detect targeted mutations. PCR primers within the replaced region were used to detect the wild-type allele (Fig. 1C). Primer sequences were as follows: neo-resistant primer CZ43, CGCAGCGCATCGCCTTCTATCGC; 5' primer CZ58, CGGCTGATCAAACATGATCTGAAGATG; 5' replaced primer CZ94, CAGGCGTCATCAGTGAGG CCTGGAC.
RNA interference. A pair of complementary 56-mer oligonucleotides were synthesized, annealed, and ligated into pSuppressor-Neo vector (Imgenex, San Diego, CA). This small interfering RNA system is able to produce a small hairpin RNA with an 8-nucleotide loop and a 19-nucleotide double-stranded region matching the human DNA ligase III gene near the 5' end. Small interfering RNA vector DNA with or without inserts was introduced into HeLa cells by electroporation. The cells were selected in G418, and the knockdown cells were screened by Western blotting. The sense strand of oligonucleotide (CZ125) sequence is 5'-TCGAGTCCTAGCTACAACACGAAGGAGTACTGCTTCGTGTTGTAGCTAGGATTTTT.
Histological analysis. After dissection, mutant and wild-type embryos were fixed in paraformaldehyde and embedded in paraffin. Samples were then sectioned, mounted onto positively charged glass slides, and stained with hematoxylin and eosin.
TUNEL assays. Terminal deoxynucleotidyltransferase-mediated dUTP-biotin nick end labeling (TUNEL; Promega, Madison, WI) was performed on embryonic tissue, including a DNase-treated positive control. Briefly, tissue sections were pretreated with proteinase K and DNA strand breaks were labeled with fluorescein-12-dUTP. The green fluorescence of apoptotic cells in a red background (propidium iodide) was detected by fluorescence microscopy.
SCE assay. Embryos (8.5 dpc) from heterozygous breeding were cultured in the presence of bromodeoxyuridine (BrdU) for 48 h. After 2 h of Colcemid (Gibco BRL) incubation, the embryos were placed in hypotonic solution, fixed, and spread onto slides. The slides were stained with Hoechst 33258 and exposed to UV light. The slides were stained with Giemsa, mounted with antifading agent and 4',6'-diamidino-2-phenylindole (DAPI; Vector), and analyzed using fluorescence microscopy. The average SCE per chromosome was determined as a ratio of the number of SCEs to the total number of chromosomes.
| RESULTS |
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Western blotting analysis was performed to determine that the targeted disruption of LIG3 generates a null mutation. As demonstrated in Fig. 2A, anti-DNA ligase III antibody clearly detected DNA ligase III from HeLa cells as well as wild-type and LIG3+/ embryos, but DNA ligase III was undetectable in LIG3/ embryos, indicating that indeed the targeted inactivation of LIG3 generates a null mutation.
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Inactivation of the DNA ligase III gene and resultant early embryonic lethality. Mice heterozygous for the LIG3 mutation were fertile and did not display phenotypic abnormalities. Additionally, no evidence of early susceptibility to cancer or any other disease was observed in these mice within the first 20 months of life. Our attempts to breed heterozygous mice to generate homozygous LIG3 mutant mice yielded no viable LIG3/ pups (Table 1) in nearly 800 young mice genotyped by Southern blotting or PCR. These results clearly demonstrate DNA ligase III is essential for mouse embryonic development and survival.
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| DISCUSSION |
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Some DNA repair activities, such as BER, are essential for the early development of the embryo and its subsequent survival. Base excision repair is the major pathway for the repair of DNA base damage caused by genotoxins, such as alkylating and oxidizing agents. This pathway is initiated by the removal of damaged bases by DNA glycosylase, followed by the generation of SSB by APE1, and finally repaired by the SSB repair machinery, which includes XRCC1, PARP-1, pol ß, and DNA ligase III (2). In addition, oxidative agents may also damage deoxyribose, which will lead to SSBs. Targeted inactivation of key components of BER, such as XRCC1, APE1, or pol ß, results in early embryonic mortality from 5.5 to 7.5 dpc (17, 28, 40, 55), suggesting that embryonic cells suffering from DNA damage during normal development can only be repaired by BER. Other DNA repair genes associated with early embryonic mortality due to deficiency include XPD and the homologous recombination factors Rad51, Brca1, and Brca2 (8, 26, 29). Together, these findings imply that base modification and strand breaks occur frequently during early embryonic development. The most probable source of this DNA damage is oxidizing agents, which are produced by normal metabolic processes and are known to be able to modify bases as well as attack deoxyribose, both of which will lead to SSBs. Deficiency in DNA repair leads to the accumulation of DNA damage, activating cellular responses resulting in DNA repair and cellular survival.
Remarkably, other DNA repair pathways are not as critical for embryonic development in the early stages. Such pathways include nucleotide excision repair, DNA mismatch repair, and nonhomologous end joining, all of which are important for late embryonic development and survival. This indicates either certain types of DNA damage occur more frequently during early stages of development or redundant repair pathways exist for certain types of damage.
Our findings suggest that a deficiency in BER activity allows the accumulation of damaged cells to reach a critical level, thus halting embryonic development and leading to the death of the embryo. As we observed, LIG3-deficient embryos die approximately at 8.5 dpc, which is a later stage than XRCC1-deficient embryos, most likely due to DNA ligase functioning in the last step of the repair process. Therefore, the initial responses to DNA damage, such as the activation of the protein XRCC1 and other early factors, may still be intact and able to initiate repair of damaged DNA. This may also delay cell death, while normal embryonic development continues to a limited extent. It is further of note that all embryonic development stops at 8.5 dpc in all LIG3/ embryos, indicating this critical developmental stage is absolutely sensitive to the accumulation of DNA damage in cells.
In addition to the aforementioned role in the maintenance of nuclear genomic integrity by repairing damaged DNA, the ligases possess the ability to maintain the mitochondrial genome. The mitochondrial form of DNA ligase is generated by alternative initiation of translation to the product that carries mitochondrial targeting sequences. Examples include the yeast CDC9 gene, which is a DNA ligase I homolog (54), and the LIG3 gene in mice and humans (22). Antisense-RNA experiments have shown ligase III as an important factor in repairing DNA breaks and in maintaining DNA content in mitochondria (22, 23). These studies suggest ligase III-deficient cells lack the ability for repairing DNA and thus have unstable mitochondria. It may also explain the early embryonic mortality of LIG3/ embryos and the inability to establish a ligase III-deficient cell line (LIG3/ cells). However, our results show it is unlikely DNA ligase III is required for cell viability, despite failure to generate null ES cells screened by high G418 selection or second-allele targeting (results not shown) and/or by growing mutant mouse blastocysts from heterozygous crossbreeding (data not shown). We did not observe 8.5-dpc LIG3/ embryos displaying elevated levels of apoptosis (data not shown) but found embryos showing increased levels of apoptosis at 9.5 through 10.5 dpc, thus suggesting embryonic development continues until 8.5 dpc. We argue that LIG3/ embryos failing to develop beyond 8.5 dpc might be due to accumulation of unrepaired DNA damage rather than due to unstable mitochondrial DNA. Abnormal SCE observed in LIG3-deficient cells supports this notion. Taken together, our results demonstrate for the first time that the targeted inactivation of DNA ligase III leads to early embryonic mortality.
| ACKNOWLEDGMENTS |
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This work was partially supported by a Cancer Research Institution fellowship, an institutional grant from The University of Texas M. D. Anderson Cancer Center, and a grant from the Leukemia Research Foundation (to C.Z.). F.W.A. is a Howard Hughes Medical Institute Investigator. This work is partially supported by NIH grant AI35714 (to F.W.A.).
| FOOTNOTES |
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Supplemental material for this article may be found at http://mcb.asm.org/. ![]()
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