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Divergent evolution and purifying selection of the flaA gene sequences in Aeromonas.

Farfán M, Miñana-Galbis D, Fusté MC, Lorén JG - Biol. Direct (2009)

Bottom Line: The flagellum also provides a paradigm of how hierarchical gene regulation, intricate protein-protein interactions and controlled protein secretion can result in the assembly of a complex multi-protein structure tightly orchestrated in time and space.Ancestral reconstruction revealed that these 17 amino acids were among the amino acid changes detected in the ancestral sequence.This article was reviewed by Alexey Kondrashov, John Logsdon and Olivier Tenaillon (nominated by Laurence D Hurst).

View Article: PubMed Central - HTML - PubMed

Affiliation: Departament de Microbiologia i Parasitologia Sanitàries, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain. mfarfan@ub.edu

ABSTRACT

Background: The bacterial flagellum is the most important organelle of motility in bacteria and plays a key role in many bacterial lifestyles, including virulence. The flagellum also provides a paradigm of how hierarchical gene regulation, intricate protein-protein interactions and controlled protein secretion can result in the assembly of a complex multi-protein structure tightly orchestrated in time and space. As if to stress its importance, plants and animals produce receptors specifically dedicated to the recognition of flagella. Aside from motility, the flagellum also moonlights as an adhesion and has been adapted by humans as a tool for peptide display. Flagellar sequence variation constitutes a marker with widespread potential uses for studies of population genetics and phylogeny of bacterial species.

Results: We sequenced the complete flagellin gene (flaA) in 18 different species and subspecies of Aeromonas. Sequences ranged in size from 870 (A. allosaccharophila) to 921 nucleotides (A. popoffii). The multiple alignment displayed 924 sites, 66 of which presented alignment gaps. The phylogenetic tree revealed the existence of two groups of species exhibiting different FlaA flagellins (FlaA1 and FlaA2). Maximum likelihood models of codon substitution were used to analyze flaA sequences. Likelihood ratio tests suggested a low variation in selective pressure among lineages, with an omega ratio of less than 1 indicating the presence of purifying selection in almost all cases. Only one site under potential diversifying selection was identified (isoleucine in position 179). However, 17 amino acid positions were inferred as sites that are likely to be under positive selection using the branch-site model. Ancestral reconstruction revealed that these 17 amino acids were among the amino acid changes detected in the ancestral sequence.

Conclusion: The models applied to our set of sequences allowed us to determine the possible evolutionary pathway followed by the flaA gene in Aeromonas, suggesting that this gene have probably been evolving independently in the two groups of Aeromonas species since the divergence of a distant common ancestor after one or several episodes of positive selection.

Reviewers: This article was reviewed by Alexey Kondrashov, John Logsdon and Olivier Tenaillon (nominated by Laurence D Hurst).

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Related in: MedlinePlus

Distribution of the posterior means of the ω ratio. Posterior means of ω ratio under the M8 (beta & ω) model. In this model 10 equal-probability categories are used to approximate the beta distribution [27], giving 11 categories. The ordinate represents the average of ω over the 11 site classes, weighted by the posterior probabilities [30].
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Figure 5: Distribution of the posterior means of the ω ratio. Posterior means of ω ratio under the M8 (beta & ω) model. In this model 10 equal-probability categories are used to approximate the beta distribution [27], giving 11 categories. The ordinate represents the average of ω over the 11 site classes, weighted by the posterior probabilities [30].

Mentions: Even accepting M8 as the model that best fits our data, the parameter estimates showed that 99.6% of sites are under purifying selection and only one site (0.4%), the isoleucine in position 179, has an ω > 1 at a level of 95% (Table 2). Under this model, the ω average over the 285 codons was 0.073 with a variance of 0.024. Figure 5 shows the distribution of the posterior means of the ω ratio. The estimated distribution β (0.160, 1.976) has an extreme L shape, with an ω in the majority of sites close to 0. Assuming this model of ω distribution among sites, the ω mean would be 0.075 with a variance of 0.022, suggesting an extremely low probability that a site has an ω > 1. Estimates of the transition/transversion rate (κ) among the different models were very similar, with values ranging from 2.082 (M8 model) to 2.192 (M1a and M2a models) and a mean of 2.117 ± 0.02. These results confirm that purifying selection is the predominant force acting in the evolution of the flaA gene.


Divergent evolution and purifying selection of the flaA gene sequences in Aeromonas.

Farfán M, Miñana-Galbis D, Fusté MC, Lorén JG - Biol. Direct (2009)

Distribution of the posterior means of the ω ratio. Posterior means of ω ratio under the M8 (beta & ω) model. In this model 10 equal-probability categories are used to approximate the beta distribution [27], giving 11 categories. The ordinate represents the average of ω over the 11 site classes, weighted by the posterior probabilities [30].
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2724415&req=5

Figure 5: Distribution of the posterior means of the ω ratio. Posterior means of ω ratio under the M8 (beta & ω) model. In this model 10 equal-probability categories are used to approximate the beta distribution [27], giving 11 categories. The ordinate represents the average of ω over the 11 site classes, weighted by the posterior probabilities [30].
Mentions: Even accepting M8 as the model that best fits our data, the parameter estimates showed that 99.6% of sites are under purifying selection and only one site (0.4%), the isoleucine in position 179, has an ω > 1 at a level of 95% (Table 2). Under this model, the ω average over the 285 codons was 0.073 with a variance of 0.024. Figure 5 shows the distribution of the posterior means of the ω ratio. The estimated distribution β (0.160, 1.976) has an extreme L shape, with an ω in the majority of sites close to 0. Assuming this model of ω distribution among sites, the ω mean would be 0.075 with a variance of 0.022, suggesting an extremely low probability that a site has an ω > 1. Estimates of the transition/transversion rate (κ) among the different models were very similar, with values ranging from 2.082 (M8 model) to 2.192 (M1a and M2a models) and a mean of 2.117 ± 0.02. These results confirm that purifying selection is the predominant force acting in the evolution of the flaA gene.

Bottom Line: The flagellum also provides a paradigm of how hierarchical gene regulation, intricate protein-protein interactions and controlled protein secretion can result in the assembly of a complex multi-protein structure tightly orchestrated in time and space.Ancestral reconstruction revealed that these 17 amino acids were among the amino acid changes detected in the ancestral sequence.This article was reviewed by Alexey Kondrashov, John Logsdon and Olivier Tenaillon (nominated by Laurence D Hurst).

View Article: PubMed Central - HTML - PubMed

Affiliation: Departament de Microbiologia i Parasitologia Sanitàries, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain. mfarfan@ub.edu

ABSTRACT

Background: The bacterial flagellum is the most important organelle of motility in bacteria and plays a key role in many bacterial lifestyles, including virulence. The flagellum also provides a paradigm of how hierarchical gene regulation, intricate protein-protein interactions and controlled protein secretion can result in the assembly of a complex multi-protein structure tightly orchestrated in time and space. As if to stress its importance, plants and animals produce receptors specifically dedicated to the recognition of flagella. Aside from motility, the flagellum also moonlights as an adhesion and has been adapted by humans as a tool for peptide display. Flagellar sequence variation constitutes a marker with widespread potential uses for studies of population genetics and phylogeny of bacterial species.

Results: We sequenced the complete flagellin gene (flaA) in 18 different species and subspecies of Aeromonas. Sequences ranged in size from 870 (A. allosaccharophila) to 921 nucleotides (A. popoffii). The multiple alignment displayed 924 sites, 66 of which presented alignment gaps. The phylogenetic tree revealed the existence of two groups of species exhibiting different FlaA flagellins (FlaA1 and FlaA2). Maximum likelihood models of codon substitution were used to analyze flaA sequences. Likelihood ratio tests suggested a low variation in selective pressure among lineages, with an omega ratio of less than 1 indicating the presence of purifying selection in almost all cases. Only one site under potential diversifying selection was identified (isoleucine in position 179). However, 17 amino acid positions were inferred as sites that are likely to be under positive selection using the branch-site model. Ancestral reconstruction revealed that these 17 amino acids were among the amino acid changes detected in the ancestral sequence.

Conclusion: The models applied to our set of sequences allowed us to determine the possible evolutionary pathway followed by the flaA gene in Aeromonas, suggesting that this gene have probably been evolving independently in the two groups of Aeromonas species since the divergence of a distant common ancestor after one or several episodes of positive selection.

Reviewers: This article was reviewed by Alexey Kondrashov, John Logsdon and Olivier Tenaillon (nominated by Laurence D Hurst).

Show MeSH
Related in: MedlinePlus