Biology Department, Siena College, Loudonville, NY, USA.
Biology Department, Regis University, Denver, CO, USA.
BMC Genomics. 2021 Nov 1;22(1):784. doi: 10.1186/s12864-021-08051-w.
The Myxococcales are well known for their predatory and developmental social processes, and for the molecular complexity of regulation of these processes. Many species within this order have unusually large genomes compared to other bacteria, and their genomes have many genes that are unique to one specific sequenced species or strain. Here, we describe RNAseq based transcriptome analysis of the FruA regulon of Myxococcus xanthus and a comparative RNAseq analysis of two Myxococcus species, M. xanthus and Myxococcus stipitatus, as they respond to starvation and begin forming fruiting bodies.
We show that both species have large numbers of genes that are developmentally regulated, with over half the genome showing statistically significant changes in expression during development in each species. We also included a non-fruiting mutant of M. xanthus that is missing the transcriptional regulator FruA to identify the direct and indirect FruA regulon and to identify transcriptional changes that are specific to fruiting and not just the starvation response. We then identified Interpro gene ontologies and COG annotations that are significantly up- or down-regulated during development in each species. Our analyses support previous data for M. xanthus showing developmental upregulation of signal transduction genes, and downregulation of genes related to cell-cycle, translation, metabolism, and in some cases, DNA replication. Gene expression in M. stipitatus follows similar trends. Although not all specific genes show similar regulation patterns in both species, many critical developmental genes in M. xanthus have conserved expression patterns in M. stipitatus, and some groups of otherwise unstudied orthologous genes share expression patterns.
By identifying the FruA regulon and identifying genes that are similarly and uniquely regulated in two different species, this work provides a more complete picture of transcription during Myxococcus development. We also provide an R script to allow other scientists to mine our data for genes whose expression patterns match a user-selected gene of interest.
粘球菌目以其掠夺性和发育性社会过程以及这些过程的分子调控复杂性而闻名。与其他细菌相比，该目中的许多物种具有异常大的基因组，并且它们的基因组中有许多基因是特定于一个特定测序物种或菌株的。在这里，我们描述了粘球菌黄单胞菌 FruA 调控子的 RNAseq 转录组分析，以及两种粘球菌物种，粘球菌黄单胞菌和粘球菌 stipitatus 的比较 RNAseq 分析，因为它们对饥饿做出反应并开始形成子实体。
我们表明，这两个物种都有大量发育调控的基因，超过一半的基因组在每个物种的发育过程中表达都有统计学意义的变化。我们还包括了一个缺失转录调节剂 FruA 的粘球菌黄单胞菌非产孢突变体，以鉴定直接和间接的 FruA 调控子，并鉴定与产孢特异性相关的转录变化，而不仅仅是对饥饿的反应。然后，我们确定了在每个物种的发育过程中显著上调或下调的 Interpro 基因本体和 COG 注释。我们的分析支持以前粘球菌黄单胞菌的数据，表明信号转导基因在发育过程中上调，以及与细胞周期、翻译、代谢相关的基因下调，在某些情况下，DNA 复制也下调。粘球菌 stipitatus 的基因表达遵循类似的趋势。尽管并非所有特定基因在两个物种中都表现出相似的调控模式，但粘球菌黄单胞菌中的许多关键发育基因在粘球菌 stipitatus 中具有保守的表达模式，并且一些其他未研究的直系同源基因组也具有相似的表达模式。
通过鉴定 FruA 调控子和鉴定在两个不同物种中相似和独特调节的基因，这项工作提供了粘球菌发育过程中转录的更完整图景。我们还提供了一个 R 脚本，允许其他科学家挖掘我们的数据，以寻找表达模式与用户选择的感兴趣基因匹配的基因。
