YKT6

A recent collaborative study has discovered rare variants in the YKT6 gene as the cause of a new neurological disorder characterized by developmental delays along with severe progressive liver disease and a potential risk for liver cancer. A recent collaborative study has discovered rare variants in the YKT6 gene as the cause of a new neurological disorder characterized by developmental delays along with severe progressive liver disease and a potential risk for liver cancer. The study, published in Genetics in Medicine, was led by Dr. Hugo Bellen, Distinguished Service Professor at Baylor College of Medicine and Principal Investigator at the Jan and Dan Duncan Neurological Research Institute (Duncan NRI) at Texas Children's Hospital, and Dr. Wendy Chung, the Chief of the Department of Pediatrics at Boston Children's Hospital. "It is known that the YKT6 gene plays important roles in many intracellular vesicular trafficking events in the cells but this is the first time it has been linked to a genetically inherited disorder," Dr. Bellen said. "This study, using patient samples and fruit flies, provides a solid experimental foundation for future studies to better understand this new disease and to develop therapies." YKT6 gene variants disrupt brain development and sometimes, liver function In collaboration with Dr. Mythily Ganapathi at Columbia University Irving Medical Center, Drs. Paula Hertel and Davut Pehlivan at Texas Children's Hospital and Dr. James Lupski at Baylor College of Medicine, and by using the GeneMatcher tool and Baylor Genetics clinical diagnostics laboratory, this team of researchers and clinicians found three unrelated individuals with missense (analogous to misspellings in a word) variants in both copies of the YKT6 gene. All three individuals had early onset of disease (four to six months of age) with failure to thrive. Two of them had an identical missense variant because of which the tyrosine amino acid at position 185 was changed to cysteine (Tyr185Cys). On the other hand, the third child carried a variant that caused the same amino acid change but in a different location (Tyr64Cys) of the YKT6 protein. Interestingly, in addition to developmental delays and neurological defects which were observed in all three children, only the two individuals with the Tyr185Cys variant had liver dysfunction and a potential risk for developing liver cancer. "Interestingly, both individuals with the Tyr185Cys variant belong to the Syrian/Saint Thomas Christians of Kerala, India, a group currently estimated to be comprised of about 5 million individuals worldwide," Dr. Mythily Ganapathi said. "Our genetic lineage analysis suggests this variant likely originated from a common ancestor before the community split." YKT6 gene variants impair autophagy To assess how YKT6 variants result in the observed disease pathologies, the Bellen team studied the fruit fly version of this gene which is quite similar to its human counterpart. "We found that the fly version of this protein is expressed in the fat body and brain which are analogous to the human liver and central nervous system respectively," Dr. Mengqi Ma, one of the first authors and a postdoctoral fellow in the Bellen lab, said. "Moreover, fly strains with loss of function mutations in this gene were lethal." Further, they observed that Ykt6 mutant flies expressing the normal fly version of the Ykt6 gene flies had an average lifespan. However, transgenic flies expressing the fly versions of the disease variants were less effective in restoring lifespan and other symptoms. While Ykt6 mutant flies expressing Tyr65Cys (equal to human Tyr64Cys) had normal lifespan and locomotion, those expressing Tyr186Cys (equal to human Tyr185Cys) had severely reduced lifespan and locomotor defects. "Our results showed that the fly Ykt6 Tyr186Cys cause more severe defects than Tyr65Cys," Dr. Ma added, "suggesting that the corresponding human YKT6 Tyr185Cys is a more severe variant than Tyr64Cys." To understand why these variants behaved differently, they delved deeper into their biology. YKT6 belongs to the SNARE family of proteins that regulate the flow of protein traffic to various compartments within the cell. In mammalian cells, YKT6 mediates the fusion of two cellular organelles -- the autophagosomes and lysosomes to form autolysosomes -- within which 'used' cellular proteins, lipids, and other molecules are degraded and recycled back for future use. This process called autophagy is critical for the proper function and health of the cells. The team found that the loss of fly Ykt6 led to an abnormal accumulation of proteins involved in autophagosome formation and autophagic cargo receptor, indicating a block in the autophagy pathway. Further studies revealed that just like lethality and other defects, fly Tyr186Cys (equal to human Tyr185Cys) was less efficient in reverting the symptoms compared to a normal copy of the Ykt6 gene. Furthermore, they observed that while autophagy initiation was normal, the steps involved in the breakdown of cellular waste were impaired in the absence of Ykt6. "Based on our findings, we recommend the YKT6 gene as a candidate for carrier screening in the Syrian/Saint Thomas Christian community of Kerala," Dr. Mythily Ganapathi said. "Our work suggests children diagnosed with YKT6 liver disease will also need to be screened for hepatocellular carcinoma," Dr. Paula Hertel said. "In summary, we have discovered YKT6 variants as the cause of a novel developmental disorder affecting brain function and in certain cases, also liver function, providing us valuable insights into a new genetic disease. However, additional studies with more patients will be needed to precisely understand the pathogenesis and to identify potential therapeutic targets for this condition," Dr. Bellen added. Others involved in the study and their institutional affiliations can be found here. This work was supported by the Huffington Foundation, the Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, the Office of Research Infrastructure Programs of the National Institutes of Health; the U.S. National Human Genome Research Institute (NHGRI) and the National Heart Lung and Blood Institute to the Baylor-Hopkins Center for Mendelian Genomics and Neurological Disorders and Stroke. Grant support was also received from the Rett Syndrome Research Trust, International Rett Syndrome Foundation, Doris Duke Charitable Foundation, and Neurological Disorders and Stroke. Confocal microscopy was performed in the BCM IDDRC Neurovisualization Core, supported by the National Institute of Child Health and Human Development.

蛋白酶高效和特异性切割蛋白质靶标的能力使其能够在生物学、生物技术和医学中发挥重要作用。虽然目前蛋白酶经过改造或进化可以提高稳定性、溶剂耐受性、抑制剂抗性、活性和改变的特异性，但成功改变底物特异性超过一级肽识别序列中单个氨基酸的报道很少见。如果通过重编程以选择性地切割不存在已知蛋白酶的新靶标的能力，蛋白酶的应用将大大扩展。近日，哈佛大学医学院的研究团队开发了一种针对蛋白酶的噬菌体辅助进化系统，首次实现了对肉毒杆菌神经毒素 (Botulinum neurotoxin，BoNT)底物特异性的改变，创造出的新肉毒素突变体可在神经细胞里特异性切割对神经再生起阻碍作用的重要药物靶点蛋白PTEN（Phosphatase and tensin homolog）。而且，它们不再有效切割神经元中肉毒素BoNT蛋白酶的原本天然底物。该研究首次建立了一套完整的蛋白酶定向进化方法，并为重编程蛋白酶建立了一个通用平台，可用于选择性地切割具有治疗意义的新靶标。该研究团队运用 PACE 正负选择系统，重新编程了BoNT LC 蛋白酶的底物特异性。他们发明的PACE系统的主体是一个生物反应器，其中有M13噬菌体和大肠杆菌作为噬菌体的宿主。M13噬菌体基因组中的gIII基因被需要进化的蛋白酶基因所取代；而gIII基因放入了辅助质粒（Assisitant plasmid, AP）中，辅助质粒编码一个活性被T7 溶菌酶抑制的T7 RNA聚合酶和一个T7 启动子控制的gIII，T7 RNA聚合酶和T7溶解酶之间由一段蛋白酶可以识别并切割的底物多肽连接；突变质粒（Mutated plasimid, MP）则用于提高进化速率。    当M13噬菌体感染大肠杆菌后，释放所编码的蛋白酶，切割了T3 RNA聚合酶和溶解酶之间的连接时，T3 RNA 聚合酶的活性得以释放，从而开始转录gIII，得到有侵染活性的噬菌体。反之则无法得到具有侵染活性的噬菌体。突变质粒则表达一些提高DNA复制时突变几率的蛋白，在噬菌体DNA复制时引入突变到蛋白酶的基因中，这样就完成了常规的提高蛋白酶活的正向筛选。    在这项研究中，最具创意的部分就是，为了可以降低进化的蛋白酶对原始识别序列的活性，研究人员在原先正向选择的系统上，逆向的添加了一个反向选择系统。反向选择质粒编码一个由蛋白酶原始的识别序列多肽连接的T7‘ RNA 聚合酶和T7 溶菌酶，和一个由T7启动子控制的显性失活gIII。当噬菌体所编码的蛋白酶既可以激活正向选择质粒gIII的表达和反向选择质粒的显性失活gIII表达时，产生的新的噬菌体不具备感染性。也就是说，只有进化活性而没有原始活性的蛋白酶将会拥有选择优势而被筛选出来。当正向选择和反向选择同时进行时，就可以同步完成活性和选择性的进化。    首先，为了验证系统的有效性，他们选择野生型的肉毒素X的轻链作为目标，利用PANCE系统将肉毒素X的偏好性向VAMP4和Ykt6进化。经过进化得到的突变体X(4130)B1和X(5010)B1分别对Ykt6和VAMP4的偏好性相对于VAMP1有了大幅提升。这两个肉毒素X轻链突变体也可以在全毒素的形式下被递送到体外培养的大鼠的神经元里切割其底物。进一步的，他们利用PACE的正向筛选逐渐将肉毒素F轻链进化为对VAMP7具有切割活性，这是一种已知肉毒素都不能切割的蛋白，但是它在蛋白的转运，分泌和细胞自噬中发挥重要作用。得到的突变体F(3041)B6虽然可以切割VAMP7，但是它还对保留有VAMP2的切割活性。又经过一系列的反向筛选，作者得到了另一个突变体F(3230)A3。这个突变体在体外酶活实验中展示了很高的VAMP7和极低的VAMP2切割活性，并在体内进行了验证。从晶体结构上来看，BoNT/X(4130)B1 的折叠与野生型 BoNT/X LC（PDB 6G47，rmsd=0.42 Å）相比基本没有变化。E166 突变将带负电荷的 Glu 侧链放置在从催化锌辅因子裂开的活性位点上。与 VAMP2 底物模拟物 结合的相关 BoNT/F 蛋白酶的结构表明 E166 可能与底物的 P3 残基相互作用。推测 A166E 突变静电排斥 VAMP1 中的阴离子 P3 残基 (D66)，同时耐受 Ykt6 中的中性 P3 氨基酸 (V171)，从而有助于 Ykt6 选择性。第三步，他们完成了从无到有的工作，创造了一个切割新蛋白的酶。先前的VAMP7毕竟与其他VAMP蛋白具有较高的同源性，同属于SNARE蛋白。而将肉毒素E轻链从切割SNAP-25进化为特异性地切割磷酸酯酶PTEN则完全创造了一个新的蛋白酶。PTEN是一个磷酸酶，将PI3P转化为PI2P，负性调控细胞膜上的PI3P水平，从而抑制PI3K/AKT/mTOR信号通路并抑制细胞增殖。突变导致PTEN功能缺陷是一些细胞癌变的重要原因，因此PTEN也被认为是一种抑癌蛋白。但是在神经元再生方面，PTEN却起到了抑制再生的作用。在受损的中枢神经元中敲除PTEN已经被证明可以极大地提高神经元的再生能力。    研究人员通过生物信息学比对选择了PTEN表面一段没有固定构像的肽段作为潜在的酶切靶点。这一段序列的20个氨基酸中仅有4个与SNAP-25 序列相同。经过一系列的双向筛选最终得到了突变体E(4130)A2。在体外酶活实验中，E(4130)A2对PTEN有较高的切割活性，而对SNAP-25的活性极低。但是当将E(4130)A2和PTEN共同表达在HEK293T细胞中时，并没有观察到明显的PTEN切割。他们分析也许由于PTEN在细胞膜上行使功能，而E(4130)A2主要在细胞质中，所以切割效率不如预期。当作者将定位在细胞膜上的PH结构域和E(4130)A2融合表达时，全长PTEN的水平显著下降。他们还通过病毒转染的方式在体外培养的大鼠皮质神经元中表达了PH-E(4130)A2，发现相对于对照组神经元中的PTEN水平有明显的下降，并且在神经细胞内部只有极低的SNAP-25切割活性。在E(4130)A2的基础上，作者根据肉毒素E识别SNAP-25蛋白结构方面的知识又加入了一个突变L167A，完全消除了对SNAP-25的切割活性。综上，本研究搭建的双向系统创造了从无到有的新蛋白酶，对进化不同蛋白都有良好的普适性。研究人员利用其完成了对肉毒素的重编程以识别一个全新的底物，创造了具有PTEN切割活性的锌蛋白酶PH-E(4130)A2以用于神经损伤后的再生。该技术也可以广泛应用于未来的蛋白酶和蛋白药物工程改造。参考文献Travis RB, Hao Liu, Michael SP, Xiaozhe Xiong, Pyung-Gang Lee, Sicai Zhang, Michelle Richter, George Minasov, Karla J F Satchell, Min Dong, David R Liu. Phage-assisted evolution of botulinum neurotoxin proteases with reprogrammed specificity. Science 2021, 371(6531):803-810.识别微信二维码，添加生物制品圈小编，符合条件者即可加入微信群！请注明：姓名+研究方向！版权声明本公众号所有转载文章系出于传递更多信息之目的，且明确注明来源和作者，不希望被转载的媒体或个人可与我们联系(cbplib@163.com)，我们将立即进行删除处理。所有文章仅代表作者观点，不代表本站立场。