title: Investigating Evolutionary Dynamics of RHA1 Operons.
abstract: Grouping genes as operons is an important genomic feature of prokaryotic organisms. The comprehensive understanding of the operon organizations would be helpful to decipher transcriptional mechanisms, cellular pathways, and the evolutionary landscape of prokaryotic genomes. Although thousands of prokaryotes have been sequenced, genome-wide investigation of the evolutionary dynamics (division and recombination) of operons among these genomes remains unexplored. Here, we systematically analyzed the operon dynamics of Rhodococcus jostii RHA1 (RHA1), an oleaginous bacterium with high potential applications in biofuel, by comparing 340 prokaryotic genomes that were carefully selected from different genera. Interestingly, 99% of RHA1 operons were observed to exhibit evolutionary events of division and recombination among the 340 compared genomes. An operon that encodes all enzymes related to histidine biosynthesis in RHA1 (His-operon) was found to be segmented into smaller gene groups (sub-operons) in diverse genomes. These sub-operons were further reorganized with different functional genes as novel operons that are related to different biochemical processes. Comparatively, the operons involved in the functional categories of lipid transport and metabolism are relatively conserved among the 340 compared genomes. At the pathway level, RHA1 operons found to be significantly conserved were involved in ribosome synthesis, oxidative phosphorylation, and fatty acid synthesis. These analyses provide evolutionary insights of operon organization and the dynamic associations of various biochemical pathways in different prokaryotes.
authors.affiliation: National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.; Department of Biological Sciences, Center for Systems Biology, The University of Texas at Dallas, Richardson, TX, USA.
authors.forename: Yong
authors.initials: Y
authors.lastname: Chen
authors.affiliation: National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.; College of Computer and Information Engineering, Tianjin Normal University, Tianjin, China.
authors.forename: Dandan
authors.initials: D
authors.lastname: Geng
authors.affiliation: Department of Biological Sciences, Center for Systems Biology, The University of Texas at Dallas, Richardson, TX, USA.; Bioengineering Department, The University of Texas at Dallas, Richardson, TX, USA.
authors.forename: Kristina
authors.initials: K
authors.lastname: Ehrhardt
authors.affiliation: College of Computer and Information Engineering, Tianjin Normal University, Tianjin, China.
authors.forename: Shaoqiang
authors.initials: S
authors.lastname: Zhang
keywords: Rhodococcus jostii RHA1; evolutionary dynamics; operon; pathway