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Characterization of relationships between transcriptional units and operon structures in Bacillus subtilis and Escherichia coli.

Okuda S, Kawashima S, Kobayashi K, Ogasawara N, Kanehisa M, Goto S - BMC Genomics (2007)

Bottom Line: Consequently, we found that the levels of gene co-regulation was correlated to intergenic distances and gene expression levels.Most interestingly, we found that functional associations in SOPs were more observed in the environmental and genetic information processes.In addition, such differences may play an important role in the evolution of gene order across genomes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan. okuda@kuicr.kyoto-u.ac.jp <okuda@kuicr.kyoto-u.ac.jp>

ABSTRACT

Background: Operon 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.

Results: We 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.

Conclusion: Complicated operon structures 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.

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Related in: MedlinePlus

Conservation of adajcent gene pairs across genomes. The left figure indicates the conservation ratio based on the gene pairs from B. subtilis, and the right figure is from E. coli. The ratios of adjacently conserved gene pairs for OPs, SOPs and NOPs are shown in blue, red and green, respectively.
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Figure 3: Conservation of adajcent gene pairs across genomes. The left figure indicates the conservation ratio based on the gene pairs from B. subtilis, and the right figure is from E. coli. The ratios of adjacently conserved gene pairs for OPs, SOPs and NOPs are shown in blue, red and green, respectively.

Mentions: To investigate the relationships between the levels of gene co-regulation in OPs, SOPs and NOPs, and their evolution, we surveyed the conservation of the three groups of adjacent gene pairs among 185 prokaryotic genomes (Fig. 3). We counted the ratio of the gene pairs in B. subtilis and E. coli that are conserved adjacently in other genomes. The conservation ratio for a gene pair represents the fraction of genomes considered in which the adjacency of the gene pair is conserved. Figure 3 shows the conservation ratio of the gene pairs, where the x axis indicates the ratio and y axis indicates the frequency. When the adjacently located ortholog pairs are conserved across many genomes, the conservation ratio is close to one. Therefore, OPs in both B. subtilis and E. coli were well-conserved across many genomes, compared to the others. In contrast, conservation of NOPs drastically decreased along with the increasing conservation ratio. SOPs appear to be intermediate between OPs and NOPs. All the pairs of them were significantly different by a chi-squred test (p < 0.01). These results indicate that gene order is often corrupted at the regulatory boundary and corruption can occur even within an operon if some different TUs overlap.


Characterization of relationships between transcriptional units and operon structures in Bacillus subtilis and Escherichia coli.

Okuda S, Kawashima S, Kobayashi K, Ogasawara N, Kanehisa M, Goto S - BMC Genomics (2007)

Conservation of adajcent gene pairs across genomes. The left figure indicates the conservation ratio based on the gene pairs from B. subtilis, and the right figure is from E. coli. The ratios of adjacently conserved gene pairs for OPs, SOPs and NOPs are shown in blue, red and green, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1808063&req=5

Figure 3: Conservation of adajcent gene pairs across genomes. The left figure indicates the conservation ratio based on the gene pairs from B. subtilis, and the right figure is from E. coli. The ratios of adjacently conserved gene pairs for OPs, SOPs and NOPs are shown in blue, red and green, respectively.
Mentions: To investigate the relationships between the levels of gene co-regulation in OPs, SOPs and NOPs, and their evolution, we surveyed the conservation of the three groups of adjacent gene pairs among 185 prokaryotic genomes (Fig. 3). We counted the ratio of the gene pairs in B. subtilis and E. coli that are conserved adjacently in other genomes. The conservation ratio for a gene pair represents the fraction of genomes considered in which the adjacency of the gene pair is conserved. Figure 3 shows the conservation ratio of the gene pairs, where the x axis indicates the ratio and y axis indicates the frequency. When the adjacently located ortholog pairs are conserved across many genomes, the conservation ratio is close to one. Therefore, OPs in both B. subtilis and E. coli were well-conserved across many genomes, compared to the others. In contrast, conservation of NOPs drastically decreased along with the increasing conservation ratio. SOPs appear to be intermediate between OPs and NOPs. All the pairs of them were significantly different by a chi-squred test (p < 0.01). These results indicate that gene order is often corrupted at the regulatory boundary and corruption can occur even within an operon if some different TUs overlap.

Bottom Line: Consequently, we found that the levels of gene co-regulation was correlated to intergenic distances and gene expression levels.Most interestingly, we found that functional associations in SOPs were more observed in the environmental and genetic information processes.In addition, such differences may play an important role in the evolution of gene order across genomes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan. okuda@kuicr.kyoto-u.ac.jp <okuda@kuicr.kyoto-u.ac.jp>

ABSTRACT

Background: Operon 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.

Results: We 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.

Conclusion: Complicated operon structures 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.

Show MeSH
Related in: MedlinePlus