Abstract
BackgroundOperon structures play an important role in transcriptional regulation in prokaryotes. However, there have been fewer studies on complicated operon structures in which the transcriptional units vary with changing environmental conditions. Information about such complicated operons is helpful for predicting and analyzing operon structures, as well as understanding gene functions and transcriptional regulation.ResultsWe systematically analyzed the experimentally verified transcriptional units (TUs) in Bacillus subtilis and Escherichia coli obtained from ODB and RegulonDB. To understand the relationships between TUs and operons, we defined a new classification system for adjacent gene pairs, divided into three groups according to the level of gene co-regulation: operon pairs (OP) belong to the same TU, sub-operon pairs (SOP) that are at the transcriptional boundaries within an operon, and non-operon pairs (NOP) belonging to different operons. Consequently, we found that the levels of gene co-regulation was correlated to intergenic distances and gene expression levels. Additional analysis revealed that they were also correlated to the levels of conservation across about 200 prokaryotic genomes. Most interestingly, we found that functional associations in SOPs were more observed in the environmental and genetic information processes.ConclusionComplicated operon strucutures were correlated with genome organization and gene expression profiles. Such intricately regulated operons allow functional differences depending on environmental conditions. These regulatory mechanisms are helpful in accommodating the variety of changes that happen around the cell. In addition, such differences may play an important role in the evolution of gene order across genomes.
Highlights
Operon structures play an important role in transcriptional regulation in prokaryotes
Classification of adjacent gene pairs based on operon structures We classified adjacent gene pairs located on the same strand into the following three groups (Figure 1): (i) operon pairs (OPs), (ii) sub-operon pairs (SOPs), and (iii) non-operon pairs (NOPs)
We defined a gene pair as a SOP when both genes belong to the same transcriptional units (TUs) and one of the two genes belongs to another TU
Summary
Operon structures play an important role in transcriptional regulation in prokaryotes. One of the reasons is that E. coli is a well-studied model organism and is characterized by abundant biological knowledge These predictions are not complete and problems still remain in our understanding of the complete details of operon organization. To understand such intricate gene transcriptional systems in prokaryotes, a database storing a large number of operons is needed. The combination of TUs in ODB and RegulonDB enables us to analyze more of the details of complex operon organization
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