Studholme David J, Dixon Ray
Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
FEMS Microbiol Lett. 2004 Jan 30;230(2):215-25. doi: 10.1016/S0378-1097(03)00897-8.
The planctomycetes are a phylogenetically distinct group of bacteria, widespread in aquatic and terrestrial environments. Their cell walls lack peptidoglycan and their compartmentalised cells undergo a yeast-like budding cell division process. Many bacteria regulate a subset of their genes by an enhancer-dependent mechanism involving the alternative sigma factor sigma54 (RpoN, sigmaN) in association with sigma54-dependent transcriptional activators known as enhancer-binding proteins (EBPs). The sigma54-dependent regulon has previously been studied in several groups of bacteria, but not in the planctomycetes. We wished to exploit the recently published complete genome sequence of Pirellula species strain 1 to predict and analyse the sigma54-dependent regulon in this interesting group of bacteria. The genome of Pirellula species strain 1 encodes one homologue of sigma54, and 16 sigma54-dependent EBPs, including 10 two-component response regulators and a homologue of Escherichia coli RtcR. Two EBPs contain forkhead-associated domains, representing a novel protein domain combination not previously observed in bacterial EBPs and suggesting a novel link between the enhancer-dependent regulon and 'eukaryotic-like' protein phosphorylation in bacterial signal transduction. We identified several potential sigma54-dependent promoters upstream of genes and operons including two homologues of csrA, which encodes the global regulator CsrA, and rtcBA, encoding a RNA 3'-terminal phosphate cyclase. Phylogenetic analysis of EBP sequences from a wide range of bacterial taxa suggested that planctomycete EBPs fall into several distinct clades. Also the phylogeny of the sigma54 factors is broadly consistent with that of the host organisms. These results are consistent with a very ancient origin of sigma54 within the bacterial lineage. The repertoire of functions predicted to be under the control of the sigma54-dependent regulon in Pirellula shares some similarities (e.g. rtcBA) as well as exhibiting differences with that in other taxonomic groups of bacteria, reinforcing the evolutionarily dynamic nature of this regulon.
浮霉菌是一类在系统发育上独特的细菌，广泛存在于水生和陆地环境中。它们的细胞壁缺乏肽聚糖，其具有分隔的细胞经历类似酵母的出芽细胞分裂过程。许多细菌通过一种依赖增强子的机制来调控其一部分基因，该机制涉及替代sigma因子sigma54（RpoN，sigmaN）以及与被称为增强子结合蛋白（EBP）的sigma54依赖性转录激活因子相关联。此前已在几组细菌中研究过sigma54依赖性调控子，但未在浮霉菌中进行研究。我们希望利用最近公布的皮氏菌属菌株1的完整基因组序列来预测和分析这一有趣细菌群体中的sigma54依赖性调控子。皮氏菌属菌株1的基因组编码一个sigma54的同源物和16个sigma54依赖性EBP，包括10个双组分响应调节因子和一个大肠杆菌RtcR的同源物。两个EBP含有叉头相关结构域，代表一种以前在细菌EBP中未观察到的新型蛋白质结构域组合，并暗示了增强子依赖性调控子与细菌信号转导中“类真核”蛋白质磷酸化之间的新联系。我们在基因和操纵子上游鉴定了几个潜在的sigma54依赖性启动子，包括编码全局调节因子CsrA的csrA的两个同源物以及编码RNA 3'-末端磷酸环化酶的rtcBA。对来自广泛细菌类群EBP序列的系统发育分析表明，浮霉菌EBP可分为几个不同的进化枝。此外，sigma54因子的系统发育与宿主生物的系统发育大致一致。这些结果与sigma54在细菌谱系中非常古老的起源一致。预测受皮氏菌中sigma54依赖性调控子控制的功能库与其他细菌分类群中的功能库有一些相似之处（例如rtcBA），也存在差异，这加强了该调控子进化上的动态性质。
