DNA Repair

DNA repair is a phenomenal multi-enzyme, multi-pathway system required to ensure the integrity of the cellular genome. Living organisms are constantly exposed to harmful metabolic by-products, environmental chemicals and radiation that damage their DNA, thus corrupting genetic information. In addition, normal cellular pH and temperature create conditions that are hostile to the integrity of DNA and its nucleotide components. DNA damage can also arise as a consequence of spontaneous errors during DNA replication. The DNA repair machinery continuously scans the genome and maintains genome integrity by removing or mending any detected damage.<p>Depending on the type of DNA damage and the cell cycle status, the DNA repair machinery utilizes several different pathways to restore the genome to its original state. When the damage and circumstances are such that the DNA cannot be repaired with absolute fidelity, the DNA repair machinery attempts to minimize the harm and patch the insulted genome well enough to ensure cell viability.<p>Accumulation of DNA alterations that are the result of cumulative DNA damage and utilization of "last resort" low fidelity DNA repair mechanisms is associated with cellular senescence, aging, and cancer. In addition, germline mutations in DNA repair genes are the underlying cause of many familial cancer syndromes, such as Fanconi anemia, xeroderma pigmentosum, Nijmegen breakage syndrome and Lynch syndrome, to name a few.<p> When the level of DNA damage exceeds the capacity of the DNA repair machinery, apoptotic cell death ensues. Actively dividing cells have a very limited time available for DNA repair and are therefore particularly sensitive to DNA damaging agents. This is the main rationale for using DNA damaging chemotherapeutic drugs to kill rapidly replicating cancer cells.<p>There are seven main pathways employed in human DNA repair: DNA damage bypass, DNA damage reversal, base excision repair, nucleotide excision repair, mismatch repair, repair of double strand breaks and repair of interstrand crosslinks (Fanconi anemia pathway). DNA repair pathways are intimately associated with other cellular processes such as DNA replication, DNA recombination, cell cycle checkpoint arrest and apoptosis.<p>The DNA damage bypass pathway does not remove the damage, but instead allows translesion DNA synthesis (TLS) using a damaged template strand. Translesion synthesis allows cells to complete DNA replication, postponing the repair until cell division is finished. DNA polymerases that participate in translesion synthesis are error-prone, frequently introducing base substitutions and/or small insertions and deletions.<p>The DNA damage reversal pathway acts on a very narrow spectrum of damaging base modifications to remove modifying groups and restore DNA bases to their original state.<p>The base excision repair (BER) pathway involves a number of DNA glycosylases that cleave a vast array of damaged bases from the DNA sugar-phosphate backbone. DNA glycosylases produce a DNA strand with an abasic site. The abasic site is processed by DNA endonucleases, DNA polymerases and DNA ligases, the choice of which depends on the cell cycle stage, the identity of the participating DNA glycosylase and the presence of any additional damage. Base excision repair yields error-free DNA molecules.<p>Mismatch repair (MMR) proteins recognize mismatched base pairs or small insertion or deletion loops during DNA replication and correct erroneous base pairing by excising mismatched nucleotides exclusively from the nascent DNA strand, leaving the template strand intact.<p>Nucleotide excision repair pathway is involved in removal of bulky lesions that cause distortion of the DNA double helix. NER proteins excise the oligonucleotide that contains the lesion from the affected DNA strand, which is followed by gap-filling DNA synthesis and ligation of the repaired DNA molecule. <p>Double strand breaks (DSBs) in the DNA can be repaired via a highly accurate homologous recombination repair (HRR) pathway, or through error-prone nonhomologous end joining (NHEJ), single strand annealing (SSA) and microhomology-mediated end joining (MMEJ) pathways. DSBs can be directly generated by some DNA damaging agents, such as X-rays and reactive oxygen species (ROS). DSBs can also be intermediates of the Fanconi anemia pathway.<p>Interstrand crosslinking (ICL) agents damage the DNA by introducing covalent bonds between two DNA strands, which disables progression of the replication fork. The Fanconi anemia proteins repair the ICLs by unhooking them from one DNA strand. TLS enables the replication fork to bypass the unhooked ICL, resulting in two replicated DNA molecules, one of which contains a DSB and triggers double strand break repair, while the sister DNA molecule contains a bulky unhooked ICL, which is removed through NER.<p>Single strand breaks (SSBs) in the DNA, generated either by DNA damaging agents or as intermediates of DNA repair pathways such as BER, are converted into DSBs if the repair is not complete prior to DNA replication. Simultaneous inhibition of DSB repair and BER through cancer mutations and anti-cancer drugs, respectively, is synthetic lethal in at least some cancer settings, and is a promising new therapeutic strategy.<p>For reviews of DNA repair pathways, please refer to Lindahl and Wood 1999 and Curtin 2012.<br>

DNA修复是一项卓越的多酶、多途径系统，其功能在于确保细胞基因组结构的完整性。生物体持续暴露于有害的代谢副产物、环境化学物质和辐射之中，这些因素会损害其DNA，从而破坏遗传信息。此外，正常的细胞pH值和温度也会形成对DNA及其核苷酸成分结构完整性的不利条件。DNA损伤也可能源于DNA复制过程中的自发错误。DNA修复机制持续扫描基因组，通过去除或修补任何检测到的损伤来维持基因组结构的完整性。<p>根据DNA损伤的类型和细胞周期状态，DNA修复机制利用多种不同的途径将基因组恢复至原始状态。当损伤和情况如此严重，以至于DNA无法以绝对忠实的方式得到修复时，DNA修复机制将尽力减轻损害，并尽可能好地修补受损的基因组，以确保细胞存活。<p>累积的DNA变异，其根源在于累积的DNA损伤和“最后手段”的低保真DNA修复机制的利用，与细胞衰老、衰老和癌症的发生密切相关。此外，DNA修复基因中的生殖细胞突变是许多家族性癌症综合征的根本原因，如范可尼贫血、着色性干皮病、尼姆根断裂综合征和林奇综合征等，仅举数例。<p>当DNA损伤水平超过DNA修复机制的处理能力时，细胞将引发凋亡性死亡。活跃分裂的细胞在DNA修复方面的时间非常有限，因此对DNA损伤剂特别敏感。这正是使用DNA损伤化疗药物杀死快速复制的癌细胞的主要理论依据。<p>人体DNA修复主要采用七种主要途径：DNA损伤绕过、DNA损伤逆转、碱基切除修复、核苷酸切除修复、错配修复、双链断裂修复和间链交联修复（范可尼贫血途径）。DNA修复途径与DNA复制、DNA重组、细胞周期检查点停滞和细胞凋亡等其他细胞过程密切相关。<p>DNA损伤绕过途径并非去除损伤，而是允许使用受损的模板链进行跨损伤DNA合成（TLS）。跨损伤合成允许细胞完成DNA复制，将修复推迟到细胞分裂完成。参与跨损伤合成的DNA聚合酶容易出错，经常引入碱基替换和/或小插入和小缺失。<p>DNA损伤逆转途径作用于损伤基团的非常狭窄的范围，以去除修饰基团并恢复DNA碱基至其原始状态。<p>碱基切除修复（BER）途径涉及多种DNA糖基化酶，这些酶从DNA糖-磷酸骨架中切割出大量的受损碱基。DNA糖基化酶产生一个带有无碱基位点的DNA单链。无碱基位点随后由DNA内切酶、DNA聚合酶和DNA连接酶处理，其选择取决于细胞周期阶段、参与DNA糖基化酶的身份以及是否存在任何额外的损伤。碱基切除修复产生无错误的DNA分子。<p>错配修复（MMR）蛋白在DNA复制过程中识别不匹配的碱基对或小插入或缺失环，通过仅从新生DNA链中切除不匹配的核苷酸来纠正错误的碱基配对，从而保持模板链的完整性。<p>核苷酸切除修复途径涉及移除引起DNA双螺旋结构扭曲的庞大损伤。NER蛋白从受影响的DNA链中切除含有损伤的寡核苷酸，随后进行缺失填补的DNA合成和修复DNA分子的连接。<p>DNA中的双链断裂（DSB）可以通过高度精确的同源重组修复（HRR）途径进行修复，也可以通过易错的非同源末端连接（NHEJ）、单链退火（SSA）和微同源末端连接（MMEJ）途径进行修复。某些DNA损伤剂，如X射线和活性氧（ROS），可以直接生成DSB。DSB也可以是范可尼贫血途径的中间体。<p>间链交联（ICL）剂通过在两条DNA链之间引入共价键来损害DNA，从而阻止复制叉的进展。范可尼贫血蛋白通过从一条DNA链上解开ICL来修复ICL。TLS使复制叉能够绕过未解开的ICL，从而产生两个复制的DNA分子，其中一个分子含有DSB并触发双链断裂修复，而另一个姐妹DNA分子含有庞大的未解开的ICL，通过NER将其去除。<p>DNA中的单链断裂（SSB）可能由DNA损伤剂或DNA修复途径（如BER）的中间体产生，如果修复在DNA复制之前未完成，SSB将被转化为DSB。通过癌症突变和抗癌药物分别抑制DSB修复和BER，在至少某些癌症环境中是合成致死性的，并且是一种有前景的新疗法。<p>有关DNA修复途径的综述，请参阅Lindahl和Wood 1999年及Curtin 2012年的著作。