潘学文博士《自然》子刊技术性文章

　　生物通报道：来自贝勒医学院Verna与Marrs McLean生物化学与分子生物学系（Verna and Marrs McLean Department of Biochemistry and Molecular Biology），约翰霍普金斯医学院高通量生物学中心的研究人员报道了一种用以分析酵母中非缺失等位基因（non-deletion alleles，生物通注）的简单plasmid-chromosome穿梭技术方法，对于研究必需基因功能，以及蛋白结构功能相互作用的全基因组检测意义重大。这一研究成果公布在《Nature Methods》杂志上。 文章的通讯作者之一是华裔科学家潘学文博士（Xuewen Pan，生物通音译），其早年毕业于华中农业大学，2001年获得杜克大学医学中心的博士学位，之后赴约翰霍普金斯医学院进行博士后研究，目前任贝勒医学院生化与分子生物学，分子与人类遗传学系的副教授。 在之前的一篇《Cell》文章中，Pan等人在利用一种整体性的SFL（synthetic fitness or lethality defect）相互作用遗传分析方法在单细胞酵母中确定出了一个掌控DNA完整性的网络。 在这个新确定的网络中，研究人员在整体SFL相互作用分析的基础上确定出了16种功能模块或称微途径（minipathway）。他们确定出与DNA复制、DNA复制检测点（DRC）和氧化压力反应有关的模块或基因是抵抗致死性自发DNA损伤、有效修复DNA损伤的主要保卫者。此外，研究人员还确定出了这种整个基因组范围的基因相互作用网络的新成分——DIA2、NPT1、HST3、HST4和CSM1模块。这些成分可能有助于有丝分裂期间DNA复制和基因组稳定性。这个网络将有助于研究人员发现酵母和其他生物通体中掌控DNA完整性机制的更详细的特征。 这个研究团队不是个别地研究蛋白质以及基因的行为，而是通过对各自的相互关系及相互作用整体的研究去理解生命现象，这即是所谓”系统生物学”，长期以来，生物学研究是在规模较小的实验室进行的，系统生物学将在更大范围和更高层次进行学科交叉和国际合作，如人类基因组计划、人类单体型图谱计划、人类表观基因组学计划等。 Pan等人利用Saccharomyces cerevisiae酿酒酵母这种模式生物进行系统生物学的研究，他们发展了一种称为dSLAM（heterozygous diploid-based Synthetic Lethality Analysis on Microarrays）的方法对不同类型的全基因组遗传相互作用进行分析，其中也包括合成致死性和遗传抑制，并且利用酵母敲除（yeast knockout，YKO）突变进行高通量分析。 这篇文章则是这一研究团队在原有实验的基础上发展而来的新方法，能在酿酒酵母中获得并分析非缺失等位基因，其优点主要是利用全基因组范围内单倍体变化（haploid-convertible）异质双倍体酵母敲除突变，因此能在研究必需基因功能，以及蛋白结构功能相互作用的全基因组检测方面发挥作用。 （生物通：张迪） 原文摘要： Nature Methods - 5, 167 - 169 (2008) Published online: 13 January 2008; | doi:10.1038/nmeth.1173 Plasmid-chromosome shuffling for non-deletion alleles in yeast 『Abstract』 附： Xuewen Pan, Ph.D. Assistant Professor, Biochemistry & Molecular Biology and Molecular & Human Genetics [e-mail] Education and Awards B.S., Huazhong Agricultural University, Wuhan, P. R. China, 1993 Ph.D., Duke University Medical Center, North Carolina, 2001 Postdoctoral Training, Johns Hopkins University School of Medicine, Maryland, 2006 Genetic Networking Emerging evidence suggests that most biological functions are carried out by pathways consisting of multiple components rather than by single gene products alone. These pathways further interconnect to form a robust biological network that defines life. In this post genome era, a daunting task is, in addition to understand the functions of each gene product, to identify the pathway structures and network connectivity among the thousands of gene products encoded by a genome. We address these questions using the baker's yeast Saccharomyces cerevisiae as a model system. We have developed a methodology called dSLAM (heterozygous diploid-based Synthetic Lethality Analysis on Microarrays) for studying various types of genome-wide genetic interactions, including both synthetic lethality and genetic suppression, in a high throughput manner by using the yeast knockout (YKO) mutants. These genetic interactions could be effectively used to assign genes into the same or functionally compensatory pathways. This technology has been used to dissect the genetic network and pathway topologies governing DNA integrity in yeast. Currently, we are vigorously characterizing this network in greater detail with a combination of functional genomics, proteomics, and traditional molecular biology approaches. In addition, we are applying the dSLAM technology to study pathways involved in other biological processes. Chemical Genomics Technologies profiling the YKO mutants such as dSLAM could be effectively exploited to investigate the mechanisms of actions of anti-proliferation small molecules and to identify the genetic determinants that dictates individual's susceptibility to therapeutic drugs and environmentally hazardous compounds. Comparing to other methodologies, dSLAM has the added advantage of studying these problems in a network context. We have used this technology to study the effects of several poorly characterized anti-cancer and anti-malaria drugs on yeast and gained interesting insight into both their mechanisms of actions and the genetic networks involving the drug targets. A short-term goal of ours is to identify as many as possible the targets of existing poorly characterized therapeutic compounds and health-threatening environmental contaminants with yeast as a platform. Our long-term goal is to search for novel bioactive chemicals as potential therapeutic compounds or biological probes. Technology Development Another active area of our research is to continue developing cutting edge functional genomics tools for studying both genetic networks and chemical genomics.