Simonis Nicolas, Gonze Didier, Orsi Chris, van Helden Jacques, Wodak Shoshana J
Service de Conformation des Macromolécules Biologiques, Centre de Biologie Structurale et Bioinformatique, CP 263, Université Libre de Bruxelles, Bld. du Triomphe B-1050 Bruxelles, Belgium.
J Mol Biol. 2006 Oct 20;363(2):589-610. doi: 10.1016/j.jmb.2006.06.024. Epub 2006 Jul 3.
A comprehensive study is performed on the condition-dependent expression of genes coding for the components of hand curated multi-protein complexes of the yeast Saccharomyces cerevisiae, in order to identify coherent transcriptional modules within these complexes. Such modules are defined as groups of genes within complexes whose expression profiles under a common set of experimental conditions allow us to discriminate them from random sets of genes. Our analysis reveals that complexes such as the cytoplasmic ribosome, the proteasome and the respiration chain complexes previously characterized as "stable" or "permanent" represent transcriptional modules that are coherently up or down-regulated in many different conditions. Overall however, some level of coherent expression is detected only in 71 out of the total of 113 complexes with at least five different protein components that could be reliably analyzed. Of these, 26 behave as coherently expressed transcriptional modules encompassing all the components of the complex. In another 15, at least half of the components make up such modules and in ten, few or no modules are detected. In an additional 20 complexes coherent expression is detected, but in too few conditions to enable reliable module detection. Interestingly, the transcriptional modules, when detected, often correspond to one or more known sub-complexes with specific functions. Furthermore, detected modules are generally consistent with transcriptional modules identified on the basis of predicted cis-regulatory sequence motifs. Also, groups of genes shared between complexes that carry out related functions tend to be part of overlapping transcriptional modules identified in these complexes. Together these findings suggest that transcriptional modules may represent basic functional and evolutionary building blocs of protein complexes.
对酿酒酵母手工挑选的多蛋白复合物组分的编码基因的条件依赖性表达进行了全面研究，以识别这些复合物中的连贯转录模块。此类模块被定义为复合物中的基因组，其在一组共同实验条件下的表达谱使我们能够将它们与随机基因集区分开来。我们的分析表明，诸如细胞质核糖体、蛋白酶体和呼吸链复合物等先前被表征为“稳定”或“永久”的复合物代表了在许多不同条件下被连贯上调或下调的转录模块。然而总体而言，在总共113个具有至少五个可可靠分析的不同蛋白质组分的复合物中，仅在71个复合物中检测到了一定程度的连贯表达。其中，26个表现为包含复合物所有组分的连贯表达转录模块。在另外15个复合物中，至少一半的组分构成此类模块，而在10个复合物中，检测到很少或没有模块。在另外20个复合物中检测到了连贯表达，但条件太少以至于无法进行可靠的模块检测。有趣的是，转录模块一旦被检测到，通常对应于一个或多个具有特定功能的已知亚复合物。此外，检测到的模块通常与基于预测的顺式调控序列基序鉴定的转录模块一致。而且，执行相关功能的复合物之间共享的基因组往往是在这些复合物中鉴定出的重叠转录模块的一部分。这些发现共同表明，转录模块可能代表了蛋白质复合物的基本功能和进化构建单元。
