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Relationship between operon preference and functional properties of persistent genes in bacterial genomes.

Bratlie MS, Johansen J, Drabløs F - BMC Genomics (2010)

Bottom Line: This indicates that there are opposing effects influencing the tendency for operon formation, and these effects may be reflected in properties like evolutionary rate, complex formation, metabolic pathways and gene fusion.Genes with a weak tendency for operon participation tend to produce proteins with more interaction partners, but possibly in more dynamic complexes and convergent pathways.Genes that are not regulated through operons are therefore more evolutionary constrained than the corresponding operon-associated genes and will on average evolve more slowly.

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Affiliation: Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, N-7006 Trondheim, Norway.

ABSTRACT

Background: Genes in bacteria may be organised into operons, leading to strict co-expression of the genes that participate in the same operon. However, comparisons between different bacterial genomes have shown that much of the operon structure is dynamic on an evolutionary time scale. This indicates that there are opposing effects influencing the tendency for operon formation, and these effects may be reflected in properties like evolutionary rate, complex formation, metabolic pathways and gene fusion.

Results: We have used multi-species protein-protein comparisons to generate a high-quality set of genes that are persistent in bacterial genomes (i.e. they have close to universal distribution). We have analysed these genes with respect to operon participation and important functional properties, including evolutionary rate and protein-protein interactions.

Conclusions: Genes for ribosomal proteins show a very slow rate of evolution. This is consistent with a strong tendency for the genes to participate in operons and for their proteins to be involved in essential and well defined complexes. Persistent genes for non-ribosomal proteins can be separated into two classes according to tendency to participate in operons. Those with a strong tendency for operon participation make proteins with fewer interaction partners that seem to participate in relatively static complexes and possibly linear pathways. Genes with a weak tendency for operon participation tend to produce proteins with more interaction partners, but possibly in more dynamic complexes and convergent pathways. Genes that are not regulated through operons are therefore more evolutionary constrained than the corresponding operon-associated genes and will on average evolve more slowly.

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Average protein bit score for strong and weak operon gene clusters. A box plot showing the different gene clusters ranked according to average pair-wise bit score of the protein sequences (BitScore) normalised against alignment length (AliLen). The legend text shows the median score of each group (weak operon 0.79 bits, strong operon 0.65 bits). Ribosomal genes are not included. When they are included the numbers are 0.81 and 0.75, respectively.
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Figure 9: Average protein bit score for strong and weak operon gene clusters. A box plot showing the different gene clusters ranked according to average pair-wise bit score of the protein sequences (BitScore) normalised against alignment length (AliLen). The legend text shows the median score of each group (weak operon 0.79 bits, strong operon 0.65 bits). Ribosomal genes are not included. When they are included the numbers are 0.81 and 0.75, respectively.

Mentions: We then performed the same analyses as described above, but comparing strong and weak operon proteins. The ribosomal and the fused/mixed proteins were left out of the analysis. The result is shown in Figure 9. The median of average bit scores for strong and weak operon proteins is 0.65 and 0.79 respectively, thus indicating that the strong operon genes evolve faster than the weak operon genes (p-value 3.527 × 10-5). As already mentioned the r-proteins have a median of average bit scores of 0.97. There is also a difference regarding protein length for strong and weak operon proteins. The proteins from weak operon genes (Figure 10) have an average length of 497.31 amino acids compared to 335.06 amino acids for proteins from strong operon genes (p-value 1.361 × 10-5).


Relationship between operon preference and functional properties of persistent genes in bacterial genomes.

Bratlie MS, Johansen J, Drabløs F - BMC Genomics (2010)

Average protein bit score for strong and weak operon gene clusters. A box plot showing the different gene clusters ranked according to average pair-wise bit score of the protein sequences (BitScore) normalised against alignment length (AliLen). The legend text shows the median score of each group (weak operon 0.79 bits, strong operon 0.65 bits). Ribosomal genes are not included. When they are included the numbers are 0.81 and 0.75, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2837039&req=5

Figure 9: Average protein bit score for strong and weak operon gene clusters. A box plot showing the different gene clusters ranked according to average pair-wise bit score of the protein sequences (BitScore) normalised against alignment length (AliLen). The legend text shows the median score of each group (weak operon 0.79 bits, strong operon 0.65 bits). Ribosomal genes are not included. When they are included the numbers are 0.81 and 0.75, respectively.
Mentions: We then performed the same analyses as described above, but comparing strong and weak operon proteins. The ribosomal and the fused/mixed proteins were left out of the analysis. The result is shown in Figure 9. The median of average bit scores for strong and weak operon proteins is 0.65 and 0.79 respectively, thus indicating that the strong operon genes evolve faster than the weak operon genes (p-value 3.527 × 10-5). As already mentioned the r-proteins have a median of average bit scores of 0.97. There is also a difference regarding protein length for strong and weak operon proteins. The proteins from weak operon genes (Figure 10) have an average length of 497.31 amino acids compared to 335.06 amino acids for proteins from strong operon genes (p-value 1.361 × 10-5).

Bottom Line: This indicates that there are opposing effects influencing the tendency for operon formation, and these effects may be reflected in properties like evolutionary rate, complex formation, metabolic pathways and gene fusion.Genes with a weak tendency for operon participation tend to produce proteins with more interaction partners, but possibly in more dynamic complexes and convergent pathways.Genes that are not regulated through operons are therefore more evolutionary constrained than the corresponding operon-associated genes and will on average evolve more slowly.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, N-7006 Trondheim, Norway.

ABSTRACT

Background: Genes in bacteria may be organised into operons, leading to strict co-expression of the genes that participate in the same operon. However, comparisons between different bacterial genomes have shown that much of the operon structure is dynamic on an evolutionary time scale. This indicates that there are opposing effects influencing the tendency for operon formation, and these effects may be reflected in properties like evolutionary rate, complex formation, metabolic pathways and gene fusion.

Results: We have used multi-species protein-protein comparisons to generate a high-quality set of genes that are persistent in bacterial genomes (i.e. they have close to universal distribution). We have analysed these genes with respect to operon participation and important functional properties, including evolutionary rate and protein-protein interactions.

Conclusions: Genes for ribosomal proteins show a very slow rate of evolution. This is consistent with a strong tendency for the genes to participate in operons and for their proteins to be involved in essential and well defined complexes. Persistent genes for non-ribosomal proteins can be separated into two classes according to tendency to participate in operons. Those with a strong tendency for operon participation make proteins with fewer interaction partners that seem to participate in relatively static complexes and possibly linear pathways. Genes with a weak tendency for operon participation tend to produce proteins with more interaction partners, but possibly in more dynamic complexes and convergent pathways. Genes that are not regulated through operons are therefore more evolutionary constrained than the corresponding operon-associated genes and will on average evolve more slowly.

Show MeSH