Discrepancy between mRNA and protein abundance: insight from information retrieval process in computers.
Discrepancy between mRNA and protein abundance: insight from information retrieval process in computers.
复制标题
DOI：
10.1016/j.compbiolchem.2008.07.014
复制
发表时间：
2008-12
影响因子：
3.1
通讯作者：
Wang, Degeng
中科院分区：
文献类型：
--
作者：
Wang, Degeng
关键词：
经常观察到同源蛋白质和 RNA 分子的丰度之间的差异。对这种差异的理论上的理解仍然难以捉摸，并且在文献中经常将其描述为令人惊讶和/或技术困难。蛋白质和RNA代表多步骤细胞遗传信息流过程的不同步骤，其中它们是动态产生和降解的。本文探讨了与计算机中类似过程的比较——从存储层到执行层的多步骤信息流。检索过程的几乎每个方面都可以找到功能上的相似性。首先，共享通用架构，因为核糖体（RNA 空间）和蛋白质组（蛋白质空间）在功能上分别类似于计算机主存储器和计算机高速缓存。其次，在这两个系统中，检索过程的功能是支持动态网络的运行——细胞中的生化调节网络，以及计算机中CPU在执行计算机程序时所经过的虚拟网络（CPU指令）。此外，在信息检索过程的每个步骤中，许多调节技术都在计算机中实现，目的是优化系统性能。通过这些调控技术可以轻松识别细胞对应物。换句话说，这项比较研究试图利用计算机系统设计原理的理论见解作为催化，勾画出基因表达过程的综合视图，即它如何发挥作用以确保整个细胞调控网络的有效运行。在这种鸟瞰图的背景下，蛋白质和 RNA 丰度之间的差异成为人们所期望的合乎逻辑的观察结果。有人建议，当在系统操作的背景下解释时，这种差异可以作为破译生化网络操作下的监管逻辑的潜在信息源。
Discrepancy between the abundance of cognate protein and RNA molecules is frequently observed. A theoretical understanding of this discrepancy remains elusive, and it is frequently described as surprises and/or technical difficulties in the literature. Protein and RNA represent different steps of the multi-stepped cellular genetic information flow process, in which they are dynamically produced and degraded. This paper explores a comparison with a similar process in computers - multi-step information flow from storage level to the execution level. Functional similarities can be found in almost every facet of the retrieval process. Firstly, common architecture is shared, as the ribonome (RNA space) and the proteome (protein space) are functionally similar to the computer primary memory and the computer cache memory respectively. Secondly, the retrieval process functions, in both systems, to support the operation of dynamic networks – biochemical regulatory networks in cells and, in computers, the virtual networks (of CPU instructions) that the CPU travels through while executing computer programs. Moreover, many regulatory techniques are implemented in computers at each step of the information retrieval process, with a goal of optimizing system performance. Cellular counterparts can be easily identified for these regulatory techniques. In other words, this comparative study attempted to utilize theoretical insight from computer system design principles as catalysis to sketch an integrative view of the gene expression process, that is, how it functions to ensure efficient operation of the overall cellular regulatory network. In context of this bird’s-eye view, discrepancy between protein and RNA abundance became a logical observation one would expect. It was suggested that this discrepancy, when interpreted in the context of system operation, serves as a potential source of information to decipher regulatory logics underneath biochemical network operation.
登录
查看更多内容
影响因子：
1.6
作者：
Ji, S
通讯作者：
Ji, S
影响因子：
3.9
作者：
Wang, DG;Gribskov, M
通讯作者：
Gribskov, M
影响因子：
7
作者：
Griffin, TJ;Gygi, SP;Aebersold, R
通讯作者：
Aebersold, R
DOI：
10.1073/pnas.95.26.15293
发表时间：
1998-12-22
影响因子：
11.1
作者：
Fan, XHC;Steitz, JA
通讯作者：
Steitz, JA
影响因子：
3.4
作者：
Flory, Mark R.;Lee, Hookeun;Aebersold, Ruedi
通讯作者：
Aebersold, Ruedi