Reitzer L, Schneider B L
Department of Molecular and Cell Biology, The University of Texas at Dallas, Richardson, TX 75083-0688, USA.
Microbiol Mol Biol Rev. 2001 Sep;65(3):422-44, table of contents. doi: 10.1128/MMBR.65.3.422-444.2001.
Sigma(54) has several features that distinguish it from other sigma factors in Escherichia coli: it is not homologous to other sigma subunits, sigma(54)-dependent expression absolutely requires an activator, and the activator binding sites can be far from the transcription start site. A rationale for these properties has not been readily apparent, in part because of an inability to assign a common physiological function for sigma(54)-dependent genes. Surveys of sigma(54)-dependent genes from a variety of organisms suggest that the products of these genes are often involved in nitrogen assimilation; however, many are not. Such broad surveys inevitably remove the sigma(54)-dependent genes from a potentially coherent metabolic context. To address this concern, we consider the function and metabolic context of sigma(54)-dependent genes primarily from a single organism, Escherichia coli, in which a reasonably complete list of sigma(54)-dependent genes has been identified by computer analysis combined with a DNA microarray analysis of nitrogen limitation-induced genes. E. coli appears to have approximately 30 sigma(54)-dependent operons, and about half are involved in nitrogen assimilation and metabolism. A possible physiological relationship between sigma(54)-dependent genes may be based on the fact that nitrogen assimilation consumes energy and intermediates of central metabolism. The products of the sigma(54)-dependent genes that are not involved in nitrogen metabolism may prevent depletion of metabolites and energy resources in certain environments or partially neutralize adverse conditions. Such a relationship may limit the number of physiological themes of sigma(54)-dependent genes within a single organism and may partially account for the unique features of sigma(54) and sigma(54)-dependent gene expression.
σ⁵⁴具有一些使其与大肠杆菌中的其他σ因子相区别的特征：它与其他σ亚基不同源，σ⁵⁴依赖性表达绝对需要一个激活因子，并且激活因子结合位点可能远离转录起始位点。这些特性的基本原理并不明显，部分原因是无法为σ⁵⁴依赖性基因赋予共同的生理功能。对来自多种生物体的σ⁵⁴依赖性基因的调查表明，这些基因的产物通常参与氮同化；然而，许多并非如此。这样广泛的调查不可避免地将σ⁵⁴依赖性基因从潜在连贯的代谢背景中移除。为了解决这个问题，我们主要从单一生物体大肠杆菌来考虑σ⁵⁴依赖性基因的功能和代谢背景，在大肠杆菌中，通过计算机分析结合对氮限制诱导基因的DNA微阵列分析，已经确定了一份相当完整的σ⁵⁴依赖性基因列表。大肠杆菌似乎有大约30个σ⁵⁴依赖性操纵子，其中约一半参与氮同化和代谢。σ⁵⁴依赖性基因之间可能的生理关系可能基于这样一个事实，即氮同化消耗能量和中心代谢的中间产物。不参与氮代谢的σ⁵⁴依赖性基因的产物可能在某些环境中防止代谢物和能量资源的消耗，或部分抵消不利条件。这种关系可能限制了单一生物体内σ⁵⁴依赖性基因的生理主题数量，并可能部分解释了σ⁵⁴和σ⁵⁴依赖性基因表达的独特特征。
