Forward Genomics of Damage Control: An Undiscovered Class of Cancer Genes

描述 摘要 一类未被发现的癌症基因摘要该项目的中心假设是，存在一大类高度保守的基因/蛋白质，它们调节所有活细胞中自发的DNA损伤水平，以及基因组不稳定的近端上游效应/调节器。这些基因被提议包括许多高度保守的必需基因，在人类中，这些基因有望构成不同于(上游)两个主要公认类别的癌症基因：基因组看守基因和看门人基因。然而，由于两个限制，这些“损伤控制”基因/蛋白仍然没有被发现和识别。首先，没有技术可以直接在活细胞中检测自发的/内源性的DNA损伤，特别是DNA断裂。因此，影响内源性DNA损伤水平的因素大多没有被检测，也没有被考虑。其次，许多损伤控制基因可能对生物体的生存至关重要，而目前在模式生物中的正向遗传方法，本来可能会发现其中一些基因，但对必要基因是有偏见的。我们预计损伤控制基因至少包括以下内容：(1)正常代谢途径(碳代谢等)。不可避免地产生有毒副产物，与DNA发生反应，造成碱基/核苷酸损伤；(2)清除这些副产物的蛋白质/分子；(3)DNA复制组件。(DNA断裂通常是复制造成损伤的结果。)所有这些基因都被认为是非常保守的，因为它们是生命的基础，而且大多数被认为是必不可少的基因。这个项目的目标是：(1)发展一种新的正向基因组学方法论范式，能够快速识别生物学中任何问题感兴趣的基因，包括必需基因；(2)利用这一范式，在简单的模式生物大肠杆菌中寻找损伤控制基因，识别它们在人类中的对应物，然后

DESCRIPTION Abstract An Undiscovered Class of Cancer Genes ABSTRACT The central hypothesis of this project is that there exists a large, highly-conserved class of genes/proteins that regulate levels of spontaneous DNA damage in all living cells, and so are the proximal, upstream effectors/modulators of genome instability. These are proposed to include many highly conserved essential genes that, in humans, are expected to constitute a "new" class of cancer genes distinct from (upstream of) the two main recognized classes: genomic-caretaker and gatekeeper genes. However these "damage-control" genes/proteins have remained undiscovered and unrecognized because of two limitations. First, no technology existed to assay spontaneous/endogenous DNA damage, particularly DNA breakage, directly in living cells. Thus, factors that affect the levels of endogenous DNA damage have mostly not been assayed, and not considered. Second, many of the damage-control genes are likely to be essential for organism viability, and current forward-genetic approaches in model organisms, which might otherwise have found some of these genes, are biased against essential genes. We expect the damage-control genes to encompass at least the following: (1) normal metabolic pathways (carbon metabolism, etc.) that unavoidably produce toxic by-products that react with DNA causing base/nucleotide damage; (2) proteins/molecules that scavenge these by-products; (3) DNA replication components. (DNA breaks often result from replication into damage.) All of these are expected to be very highly conserved because they are so basic to life, and most are expected to be essential genes. The goals of this project are--(1) to develop a new methodological paradigm of forward genomics that will allow rapid identification of genes, including essential genes, of interest to any problem in biology; (2) using this paradigm, to find the damage-control genes in the simple model organism E. coli, identify their counterparts in human, then id