Establishment of genomic library technology mediated by non-homologous end joining mechanism in Yarrowia lipolytica

Genomic variants libraries are conducive to obtain dominant strains with desirable phenotypic traits.The non-homologous end joining(NHEJ),which enables foreign DNA fragments to be randomly integrated into different chromosomal sites,shows prominent capability in genomic libraries construction.In this study,we established an efficient NHEJ-mediated genomic library technology in Yarrowia lipolytica through regulation of NHEJ repair process,employment of defective Ura marker and optimization of iterative transformations,which enhanced genes integration efficiency by 4.67,22.74 and 1.87 times,respectively.We further applied this technology to create high lycopene producing strains by multi-integration of heterologous genes of CrtE,CrtB and CrtI,with 23.8 times higher production than rDNA integration through homologous recombination(HR).The NHEJ-mediated genomic library technology also achieved random and scattered integration of loxP and vox sites,with the copy number up to 65 and 53,respectively,creating potential for further application of recombinase mediated genome rearrangement in Y.lipolytica.This work provides a high-efficient NHEJ-mediated genomic library technology,which enables random and scattered genomic integration of multiple heterologous fragments and rapid generation of diverse strains with superior phenotypes within 96 h.This novel technology also lays an excellent foundation for the development of other genetic technologies in Y.lipolytica.

Functional non-homologous end joining patterns triggered by CRISPR/Cas9 in human cells

CRISPR/Cas9-mediated genome engineering technologies are now widely applied in various organisms,including mouse and human cells（Cong et al.,2013;Mali et al.,2013;Yang et al.,2013;Hsu et al.,2014）.The most widely used customized CRISPR/Cas9（Sp Cas9）is derived from Streptococcus pyogenes（Cong et al.,2013）.

The phage T4 DNA ligase mediates bacterial chromosome DSBs repair as single component non-homologous end joining

DNA double-strand breaks(DSBs)are one of the most lethal forms of DNA damage that is not efficiently repaired in prokaryotes.Certain microorganisms can handle chromosomal DSBs using the error-prone non-homologous end joining(NHEJ)system and ultimately cause genome mutagenesis.Here,we demonstrated that Enterobacteria phage T4 DNA ligase alone is capable of mediating in vivo chromosome DSBs repair in Escherichia coli.The ligation efficiency of DSBs with T4 DNA ligase is one order of magnitude higher than the NHEJ system from Mycobacterium tuberculosis.This process introduces chromosome DNA excision with different sizes,which can be manipulated by regulating the activity of host-exonuclease RecBCD.The DNA deletion length reduced either by inactivating recB or expressing the RecBCD inhibitor Gam protein fromλphage.Furthermore,we also found single nucleotide substitutions at the DNA junction,suggesting that T4 DNA ligase,as a single component non-homologous end joining system,has great potential in genome mutagenesis,genome reduction and genome editing.

Flexibility in the order of action and in the enzymology of the nuclease, polymerases, and ligase of vertebrate non-homologous DNA end joining： relevance to cancer, aging, and the immune system

加入的 Nonhomologous 脱氧核糖核酸结束(NHEJ ) 是为在人的房间并且在多细胞的优核质的双海滨脱氧核糖核酸裂缝的修理的主要小径。双海滨裂缝的原因经常碎裂在损坏的地点的脱氧核糖核酸，导致在那里的信息的损失。NHEJ 不恢复失去的信息并且可以将切除另外的核苷酸在修理过程期间。修理大量 overhang 并且损坏配置的能力反映 NHEJ 的核酸酶，聚合酶，和连接酶的灵活性。单个部件的灵活性也解释 NHEJ 能在修理脱氧核糖核酸结束的任何给定的对的方法的大数字。局部地，在 NHEJ 的地点，修理可以贡献癌症和老化的信息的损失，而是由 NHEJ 的行动保证染色体的全部片断没被失去。

The endless tale of non-homologous end-joining

脱氧核糖核酸双海滨裂缝(DSB ) 被离子辐射和反应的氧种类在房间介绍。另外，他们通常在 V (D) J 再结合期间被产生，发展中的免疫系统的一个必要方面。有效地修理这些 DSB 的失败能在更高的脊椎动物的免疫系统导致染色体破裂，房间死亡，癌症的发作，和缺点。幸好，所有哺乳动物的房间拥有调停的二条酶的小径 DSB 的修理：相应再结合并且非相应加入结束(NHEJ ) 。NHEJ 过程利用捕获破脱氧核糖核酸分子的两结束，在 synaptic DNA 蛋白质建筑群一起带他们，并且最后修理脱氧核糖核酸裂缝的酶。在这评论，在 NHEJ 过程起一个作用的所有已知的酶被讨论，为这些酶的合作的一个工作模型在 DSB 修理期间被介绍。

利用非同源末端连接缺陷构建拟轮枝镰孢菌的高效基因敲除方法

拟轮枝镰孢菌(Fusarium verticillioides)是引起玉米茎基腐病和穗粒腐病的主要病原菌之一,严重威胁玉米的产量和品质。为了深入研究拟轮枝镰孢菌致病基因的功能,对该菌中非同源末端连接(non-homologous end joining,NHEJ)途径中的2个关键基因FvKu70和FvKu80分别进行了基因敲除以创制高效的基因敲除菌株,并比较了野生型菌株和突变体菌株在营养生长速率、菌落形态、产孢量、对玉米的致病力和基因敲除效率等方面的差异。研究结果表明,FvKu70和FvKu80的基因缺失突变体与野生型FvLNF15-11相比,在PDA平板上的形态特征(如菌丝形态、生长速率、菌落直径、产孢量)没有明显差异,对玉米茎秆的致病力也类似。此外,选择尿嘧啶生物合成相关基因FvpyrG作为敲除的靶基因,分析了FvKu70或FvKu80缺失突变体菌株的同源重组效率,结果显示突变体菌株均显著高于野生型,其中ΔFvKu70的同源重组效率最高。综上所述,FvKu70或FvKu80基因缺失突变体可以快速又高效地实现拟轮枝镰孢菌的基因敲除,为进一步研究该菌的功能基因提供了技术支持。

树的联的end-正则性

明确给出了具有正则自同态幺半群的两个树的联．

Enzalutamide and olaparib synergistically suppress castration-resistant prostate cancer progression by promoting apoptosis through inhibiting nonhomologous end joining pathway

Recent studies revealed the relationship among homologous recombination repair(HRR),androgen receptor(AR),and poly(adenosine diphosphate-ribose)polymerase(PARP);however,the synergy between anti-androgen enzalutamide(ENZ)and PARP inhibitor olaparib(OLA)remains unclear.Here,we showed that the synergistic effect of ENZ and OLA significantly reduced proliferation and induced apoptosis in AR-positive prostate cancer cell lines.Next-generation sequencing followed by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses revealed the significant effects of ENZ plus OLA on nonhomologous end joining(NHEJ)and apoptosis pathways.ENZ combined with OLA synergistically inhibited the NHEJ pathway by repressing DNA-dependent protein kinase catalytic subunit(DNA-PKcs)and X-ray repair cross complementing 4(XRCC4).Moreover,our data showed that ENZ could enhance the response of prostate cancer cells to the combination therapy by reversing the anti-apoptotic effect of OLA through the downregulation of anti-apoptotic gene insulin-like growth factor 1 receptor(IGF1R)and the upregulation of pro-apoptotic gene death-associated protein kinase 1(DAPK1).Collectively,our results suggested that ENZ combined with OLA can promote prostate cancer cell apoptosis by multiple pathways other than inducing HRR defects,providing evidence for the combined use of ENZ and OLA in prostate cancer regardless of HRR gene mutation status.

Expression of DNA-dependent protein kinase in human granulocytes

Human polymorphonuclear leukocytes (PMN) have been reported to completely lack of DNA-dependent protein kinase (DNA-PK) which is composed of Ku protein and the catalytic subunit DNA-PKcs, needed for nonhomologous end-joining (NHEJ) of DNA double-strand breaks. Promyelocytic HL-60 cells express a variant form of Ku resulting in enhanced radiation sensitivity. This raises the question if low efficiency of NHEJ, instrumental for the cellular repair of oxidative damage, is a normal characteristic of myeloid differentiation. Here we confirmed the complete lack of DNAPK in P MN protein extracts, and the expression of the truncated Ku86 variant form in HL-60. However, this degradation of DNA-PK was shown to be due to a DNA-PK-degrading protease in PMN and HL-60. In addition, by using a protease-resistant whole cell assay, both Ku86 and DNA-PKcs could be demonstrated in PMN, suggesting the previously reported absence in PMN of DNA-PK to be an artefact. The levels of Ku86 and DNA-PKcs were much reduced in PMN, as compared with that of the lymphocytes, whereas HL-60 displayed a markedly elevated DNA-PK concentration.In conclusion, our findings provide evidence of reduced, not depleted expression of DNA-PK during the mature stages of myeloid differentiation.

DNA end binding activity and Ku70/80 heterodimer expression in human colorectal tumor

AIM: To determine the DNA binding activity and protein levels of the Ku70/80 heterodimer, the functional mediator of the NHEJ activity, in human colorectal carcinogenesis.METHODS: The Ku70/80 DNA-binding activity was determined by electrophoretic mobility shift assays in 20 colon adenoma and 15 colorectal cancer samples as well as matched normal colonic tissues. Nuclear and cytoplasmic protein expression was determined by immunohistochemistry and Western blot analysis.RESULTS: A statistically significant difference was found in both adenomas and carcinomas as compared to matched normal colonic mucosa (P＜0.00). However,changes in binding activity were not homogenous with approximately 50% of the tumors showing a clear increase in the binding activity, 30% displaying a modest increase and 15% showing a decrease of the activity.Tumors, with increased DNA-binding activity, also showed a statistically significant increase in Ku70 and Ku86nuclear expression, as determined by Western blot and immunohistochemical analyses (P＜0.001). Cytoplasmic protein expression was found in pathological samples,but not in normal tissues either from tumor patients or from healthy subjects.CONCLUSION: Overall, our DNA-binding activity and protein level are consistent with a substantial activation of the NHEJ pathway in colorectal tumors. Since the NHEJ is an error prone mechanism, its abnormal activation can result in chromosomal instability and ultimately lead to tumorigenesis.

LC对非小细胞肺癌放疗增敏的作用及其机制研究

目的放疗是肺癌最常用的治疗手段之一,化疗药物可增强放疗敏感性,但相关毒副作用及耐药的产生严重影响放疗疗效,因此,寻找新型放疗增敏药物具有重要的现实意义。方法MTS法分析细梗香草总皂苷(LC)对肺癌细胞增殖的影响,集落形成实验、流式细胞术检测LC联合放疗后细胞集落形成率和凋亡的情况,Western blot和小干扰RNA探索其放疗增敏作用分子机制。结果MTS示LC对肺癌细胞株有增殖抑制作用,呈剂量和时间依赖性,同时其还增强放疗诱导的细胞增殖抑制和凋亡潜能。LC与放疗联合放射增敏比均>1.0,联合指数<1.0,表明二者具有协同作用。Western blot示LC调控非同源末端连接过程中相关蛋白的表达水平,小干扰RNA下调DNA-PKcs的表达后,LC的放疗增敏作用减弱。结论在非小细胞肺癌中LC通过抑制DNA损伤修复过程中的非同源末端连接而发挥放疗增敏作用。

DNA双链断裂修复缺陷在神经退行性疾病发生中的作用

DNA双链断裂修复(DNA Double-Strand Break Repair,DSBR)在保持神经元基因组稳定性和细胞存活方面发挥着重要作用。DSBR主要通过同源重组(Homologous Recombination,HR)及非同源末端连接(Non-Homologous End Joining,NHEJ)来完成,这两种修复途径对于维持神经元的正常生理功能至关重要。另外,DSBR异常在多种神经退行性疾病中扮演重要角色,因此,深入剖析DSBR机制对于理解神经退行性疾病的病理发生及研发有效治疗手段具有重要意义。本文综述了常见的DSBR途径,并概述了DSBR异常与几种常见神经退行性疾病发病机制的最新研究进展。

非同源末端连接中DNA连接酶Ⅳ抑制剂研究进展

DNA连接酶Ⅳ(LIG4)主要通过非同源末端连接(NHEJ)参与V(D)J重组和DNA双键断裂(DSB)修复,具有独特调控作用和广泛应用前景。研究发现,LIG4抑制剂在NHEJ中可作为增敏剂,与放化疗联合治疗肿瘤时具有较好的抗癌效果。此外,LIG4抑制剂还可作为一种有效的生化抑制剂介导CRISPR/Cas9基因编辑,有提高基因编辑效率的作用。近年来,许多研究基于此机制不断进行大规模药物筛选以发现新型抗癌药物,来为肿瘤治疗提供一种新思路。现对目前已报道的LIG4抑制剂及其衍生物的各种形式进行综述,并重点介绍目前应用较广的SCR7。

CRISPR-mediated host genomic DNA damage is efficiently repaired through microhomology-mediated end joining in Zymomonas mobilis

CRISPR-Cas systems provide bacteria and archaea with adaptive immunity against mobile genetic elements(MGEs)through uptake of invader-derived spacers.De novo adaptation samples spacers from both invaders and hosts,whereas primed adaptation shows higher specificity to sample spacers from invaders in many model systems as well as in the subtype I-F system of Zymomonas mobilis.Self-derived spacers will lead to CRISPR self-interference.However,our in vivo study demonstrated that this species used the microhomology-mediated end joining(MMEJ)pathway to efficiently repair subtype I-F CRISPR-Cas system-mediated DNA breaks guided by the self-targeting spacers.MMEJ repair of DNA breaks requires direct microhomologous sequences flanking the protospacers and leads to DNA deletions covering the protospacers.Importantly,CRISPR-mediated genomic DNA breaks failed to be repaired via MMEJ pathway in presence of higher copies of short homologous DNA.Moreover,CRISPR-cleaved exogenous plasmid DNA was failed to be repaired through MMEJ pathway,probably due to the inhibition of MMEJ by the presence of higher copies of the plasmid DNA in Z.mobilis.Our results infer that MMEJ pathway discriminates DNA damages between in the host chromosome versus mobile genetic element(MGE)DNA,and maintains genome stability post CRISPR immunity in Z.mobilis.

Genome engineering using the CRISPR/Cas system

Recently, an epoch-making genome engineering technology using clustered regularly at interspaced short palindromic repeats(CRISPR) and CRISPR associated(Cas) nucleases, was developed. Previous technologies for genome manipulation require the time-consuming design and construction of genome-engineered nucleases for each target and have, therefore, not been widely used in mouse research where standard techniques based on homologous recombination are commonly used. The CRISPR/Cas system only requires the design of sequences complementary to a target locus, making this technology fast and straightforward. In addition, CRISPR/Cas can be used to generate mice carrying mutations in multiple genes in a single step, an achievement not possible using other methods. Here, we review the uses of this technology in genetic analysis and manipulation, including achievements made possible to date and the prospects for future therapeutic applications.

DNA Double-Strand Breaks,Potential Targets for HBV Integration

Hepatitis B virus(HBV)-induced hepatocellular carcinoma(HCC) is one of the most fre-quently occurring cancers.Hepadnaviral DNA integrations are considered to be essential agents which can promote the process of the hepatocarcinogenesis.More and more researches were designed to find the relationship of the two.In this study,we investigated whether HBV DNA integration occurred at sites of DNA double-strand breaks(DSBs),one of the most detrimental DNA damage.An 18-bp I-SceI homing endonuclease recognition site was introduced into the DNA of HepG2 cell line by stable DNA transfection,then cells were incubated in patients’ serum with high HBV DNA copies and at the same time,DSBs were induced by transient expression of I-SceI after transfection of an I-SceI expression vector.By using nest PCR,the viral DNA was detected at the sites of the break.It appeared that integra-tion occurred between part of HBV x gene and the I-SceI induced breaks.The results suggested that DSBs,as the DNA damages,may serve as potential targets for hepadnaviral DNA insertion and the integrants would lead to widespread host genome changes necessarily.It provided a new site to investi-gate the integration.

DNA双链断裂损伤修复系统研究进展

多种内源或外源因素都能造成细胞基因组DNA损伤,细胞内建立了复杂的修复系统来应对不同形式的损伤。其中DNA双链断裂(DNA double-strand breaks,DSBs)作为最严重的损伤形式,主要激活同源重组修复(Homologous recombination repair)和非同源末端连接(Non-homologous end joining)通路。这两条通路都是由多个修复元件参与、经过多步反应的复杂过程。两者各具特点、协同作用,共同维护细胞基因组的稳定性。对其分子机制的阐明为肿瘤放化疗的辅助治疗提供了潜在的作用靶点。

宫颈癌组织LIG4、XRCC4、XRCC5、XRCC6、XRCC7的mRNA表达及与放疗敏感性的关系

目的研究DNA双链断裂非同源末端链接(NHEJ)修复通路中DNA连接酶IV(LIG4)、X射线修复交叉互补基因4、5、6、7(XRCC4、XRCC5、XRCC6、XRCC7)的mRNA表达水平与宫颈癌组织放射敏感性的关系。方法应用实时荧光定量RT-PCR技术检测61例宫颈癌组织中的LIG4、XRCC4、XRCC5、XRCC6和XRCC7的mRNA表达量,依据WHO实体瘤疗效评定标准,将放疗后的宫颈癌患者分为放疗高敏感组和放疗低敏感组,对比两组间以上基因表达水平的差异。结果 61例宫颈癌患者放疗后疗效评价为完全缓解(CR):60.7%(37/61),部分缓解及无变化(PR+NC):39.3%(24/61)。据此分为宫颈癌放疗高敏感组(CR)与放疗低敏感组(PR+NC)。放疗高敏感组LIG4mRNA、XRCC4mRNA、XRCC5mRNA、XRCC6mRNA、XRCC7mRNA在宫颈癌组织中的表达分别为0.84±0.60、1.46±0.58、2.07±1.09、0.54±0.23和0.60±0.34;放疗低敏感组为1.30±0.50、2.08±0.75、2.96±1.07、0.72±0.17和0.90±0.27,两组比较差异均有统计学意义(t=2.54、3.24、2.70、2.73、2.97,P=0.014、0.002、0.009、0.008、0.004)。结论患者宫颈癌组织中LIG4、XRCC4、XRCC5、XRCC6和XRCC7的mRNA高表达者,其对放疗抗拒,低表达则放疗高度敏感,上述基因可能成为预测宫颈癌放疗敏感性的指标和放疗增敏的分子靶点。

450t桥式起重机主梁焊接

介绍与奥地利合作生产制造的 45 0t桥式起重机偏轨箱形梁重要焊缝的工艺改进及质量控制。在生产制造过程中 ,根据实际情况采取了重要的工艺措施 。

通过缺失大丽轮枝菌Vdku80构建其高效基因敲除受体菌株

【目的】验证大丽轮枝菌(Verticillium dahliae)非同源末端连接途径关键基因Vdku80的功能,构建高效的大丽轮枝菌基因敲除受体菌株。【方法】利用常规基因敲除的方法,构建大丽轮枝菌Vdku80基因缺失的突变体菌株ΔVdku80。即将Vdku80的同源重组DNA片段(Vdku80的基因组上下游DNA片段之间连接潮霉素抗性基因)通过农杆菌介导的转化转入大丽轮枝菌,通过同源区段的重组,潮霉素抗性基因便会替换掉野生型Vdku80,从而获得突变体菌株ΔVdku80。对突变体菌株ΔVdku80的生物学表型,即生长速率、产孢量和对棉花的致病性进行测试。分别以大丽轮枝菌野生型菌株和ΔVdku80作为受体菌株,采用上述基因敲除方法测试2个几丁质合成酶编码基因ChsV和ChsVI的基因敲除效率。【结果】成功构建了Vdku80缺失突变体ΔVdku80。野生型和突变体菌株ΔVdku80在PDA培养基上的菌落形态相似,且培养8 d后菌落直径无明显差别。野生型和突变体菌株ΔVdku80产孢高峰均出现在摇瓶培养后第5天,且该时期产孢量亦无明显的变化。浓度为0.02%的MMS对野生型和突变体菌株ΔVdku80的生长均有明显的抑制作用,且抑制程度相同。接种野生型和突变体菌株ΔVdku80 4周后,棉株真叶均开始表现出萎蔫、褪绿等发病症状,野生型和突变体菌株ΔVdku80对棉花造成的病情指数分别为54.2±4.9和53.6±5.4,亦无明显变化。因此,突变体菌株ΔVdku80的生长速率、产孢量和致病性相对于野生型菌株均未发生明显变化。使用野生型菌株作为基因敲除的受体菌株,几丁质合成酶编码基因ChsV和ChsVI的基因敲除转化子在总转化子中的比例分别为44%和31%;而使用ΔVdku80作为基因敲除的受体菌株,几丁质合成酶编码基因ChsV和ChsVI基因敲除转化子在总转化子中的比例分别为94%和87%。【结论】Vdku80缺失的菌株ΔVdku80作为受体菌株可以提高其他基因的基因敲除效率,且Vdku80的缺失对大丽轮枝菌的生长速率、产孢量和致病性均无影响,因此不会干扰其他基因的敲除所带来的表型变化。Vdku80缺失的菌株ΔVdku80可作为高效的大丽轮枝菌基因敲除受体菌株。