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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

Distributions of frequency of intergenic distances between adjacent genes. The upper figures are the distributions of intergenic distances (bp) between adjacent genes at 20 bp intervals in B. subtilis (A) and in E. coli (C), and the bottom figures are their box plots (B and D). The leftmost, rightmost and middle vertical lines of the boxes represent the first and third quartiles and median value, respectively. The intergenic distances more than 1000 bps are not shown. Blue, red and green lines indicate OPs, SOPs and NOPs, respectively.
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Figure 2: Distributions of frequency of intergenic distances between adjacent genes. The upper figures are the distributions of intergenic distances (bp) between adjacent genes at 20 bp intervals in B. subtilis (A) and in E. coli (C), and the bottom figures are their box plots (B and D). The leftmost, rightmost and middle vertical lines of the boxes represent the first and third quartiles and median value, respectively. The intergenic distances more than 1000 bps are not shown. Blue, red and green lines indicate OPs, SOPs and NOPs, respectively.

Mentions: It is already known that the intergenic regions between genes within an operon are smaller than those in different operons in the E. coli genome [6]. The B. subtilis genome also has a similar distribution of intergenic distances [11]. Figure 2 shows the distribution of intergenic distances (bp) and box plots for the three groups of adjacent gene pairs in B. subtilis and E. coli; negative distances mean that the gene pairs partially overlap. It is clear that the distances in both species show a similar distribution pattern. The distances of almost all OPs and SOPs are short. On the other hand, NOPs have larger intergenic distances (p < 1E-14 for OP-NOP and SOP-NOP, chi-squared test). This result is in agreement with past results that showed that gene pairs within an operon and those between operons are clearly different in E. coli [6].


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)

Distributions of frequency of intergenic distances between adjacent genes. The upper figures are the distributions of intergenic distances (bp) between adjacent genes at 20 bp intervals in B. subtilis (A) and in E. coli (C), and the bottom figures are their box plots (B and D). The leftmost, rightmost and middle vertical lines of the boxes represent the first and third quartiles and median value, respectively. The intergenic distances more than 1000 bps are not shown. Blue, red and green lines indicate OPs, SOPs and NOPs, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Distributions of frequency of intergenic distances between adjacent genes. The upper figures are the distributions of intergenic distances (bp) between adjacent genes at 20 bp intervals in B. subtilis (A) and in E. coli (C), and the bottom figures are their box plots (B and D). The leftmost, rightmost and middle vertical lines of the boxes represent the first and third quartiles and median value, respectively. The intergenic distances more than 1000 bps are not shown. Blue, red and green lines indicate OPs, SOPs and NOPs, respectively.
Mentions: It is already known that the intergenic regions between genes within an operon are smaller than those in different operons in the E. coli genome [6]. The B. subtilis genome also has a similar distribution of intergenic distances [11]. Figure 2 shows the distribution of intergenic distances (bp) and box plots for the three groups of adjacent gene pairs in B. subtilis and E. coli; negative distances mean that the gene pairs partially overlap. It is clear that the distances in both species show a similar distribution pattern. The distances of almost all OPs and SOPs are short. On the other hand, NOPs have larger intergenic distances (p < 1E-14 for OP-NOP and SOP-NOP, chi-squared test). This result is in agreement with past results that showed that gene pairs within an operon and those between operons are clearly different in E. coli [6].

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