Limits...
New insights into 1-aminocyclopropane-1-carboxylate (ACC) deaminase phylogeny, evolution and ecological significance.

Nascimento FX, Rossi MJ, Soares CR, McConkey BJ, Glick BR - PLoS ONE (2014)

Bottom Line: Still, results suggest a considerable degree of horizontal gene transfer events, including interkingdom transfer events.In this study we provide a more complete view of the role for ACC deaminase than was previously available.The results show that ACC deaminase may not only be related to plant growth promotion abilities, but may also play multiple roles in microorganism's developmental processes.

View Article: PubMed Central - PubMed

Affiliation: Universidade Federal de Santa Catarina, Departamento de Microbiologia, Laboratório de Microbiologia do Solo, Florianópolis SC, Brazil.

ABSTRACT
The main objective of this work is the study of the phylogeny, evolution and ecological importance of the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase, the activity of which represents one of the most important and studied mechanisms used by plant growth-promoting microorganisms. The ACC deaminase gene and its regulatory elements presence in completely sequenced organisms was verified by multiple searches in diverse databases, and based on the data obtained a comprehensive analysis was conducted. Strain habitat, origin and ACC deaminase activity were taken into account when analyzing the results. In order to unveil ACC deaminase origin, evolution and relationships with other closely related pyridoxal phosphate (PLP) dependent enzymes a phylogenetic analysis was also performed. The data obtained show that ACC deaminase is mostly prevalent in some Bacteria, Fungi and members of Stramenopiles. Contrary to previous reports, we show that ACC deaminase genes are predominantly vertically inherited in various bacterial and fungal classes. Still, results suggest a considerable degree of horizontal gene transfer events, including interkingdom transfer events. A model for ACC deaminase origin and evolution is also proposed. This study also confirms the previous reports suggesting that the Lrp-like regulatory protein AcdR is a common mechanism regulating ACC deaminase expression in Proteobacteria, however, we also show that other regulatory mechanisms may be present in some Proteobacteria and other bacterial phyla. In this study we provide a more complete view of the role for ACC deaminase than was previously available. The results show that ACC deaminase may not only be related to plant growth promotion abilities, but may also play multiple roles in microorganism's developmental processes. Hence, exploring the origin and functioning of this enzyme may be the key in a variety of important agricultural and biotechnological applications.

Show MeSH

Related in: MedlinePlus

Phylogram based on AcdS protein.The evolutionary history was inferred by using the Maximum Likelihood method based on the WAG model. A discrete Gamma distribution was used to model evolutionary rate differences among sites (4 categories). Branch support was evaluated using both aLRT (SH like) and bootstrap analysis (100 replicates). Bootstrap values above 0.75 (75%) are displayed in the phylograms shown next to the branches as *. The analysis involved 431 amino acid sequences and 386 patterns were found (out of a total of 421 sites). Functional ACC deaminases are shown in bold.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4048297&req=5

pone-0099168-g003: Phylogram based on AcdS protein.The evolutionary history was inferred by using the Maximum Likelihood method based on the WAG model. A discrete Gamma distribution was used to model evolutionary rate differences among sites (4 categories). Branch support was evaluated using both aLRT (SH like) and bootstrap analysis (100 replicates). Bootstrap values above 0.75 (75%) are displayed in the phylograms shown next to the branches as *. The analysis involved 431 amino acid sequences and 386 patterns were found (out of a total of 421 sites). Functional ACC deaminases are shown in bold.

Mentions: Interestingly, the Pseudomonas sp. ACP AcdS sequence shares higher identity (96.7%) with Burkholderia xenovorans LB400 functional ACC deaminase than with Pseudomonas sp. UW4 AcdS (85.3%). This is also observed in the AcdS phylogram, where Pseudomonas sp. ACP groups closer to Burkholderia xenovorans LB400 (Fig. 3). While, Honma and Shimomura [1] tentatively identified Pseudomonas sp. ACP bacterium by phenotypic methods, it is conceivable that Pseudomonas sp. ACP is in fact a Burkholderia strain [64]. If this is in fact the case, then previous studies regarding the phylogeny of acdS may also have been influenced by the confusing relationship between Pseudomonas and Burkholderia. Furthermore, due to the recent divergent evolution and close relationship between γ and β-Proteobacteria, it is very difficult to prove acdS HGT in these classes.


New insights into 1-aminocyclopropane-1-carboxylate (ACC) deaminase phylogeny, evolution and ecological significance.

Nascimento FX, Rossi MJ, Soares CR, McConkey BJ, Glick BR - PLoS ONE (2014)

Phylogram based on AcdS protein.The evolutionary history was inferred by using the Maximum Likelihood method based on the WAG model. A discrete Gamma distribution was used to model evolutionary rate differences among sites (4 categories). Branch support was evaluated using both aLRT (SH like) and bootstrap analysis (100 replicates). Bootstrap values above 0.75 (75%) are displayed in the phylograms shown next to the branches as *. The analysis involved 431 amino acid sequences and 386 patterns were found (out of a total of 421 sites). Functional ACC deaminases are shown in bold.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4048297&req=5

pone-0099168-g003: Phylogram based on AcdS protein.The evolutionary history was inferred by using the Maximum Likelihood method based on the WAG model. A discrete Gamma distribution was used to model evolutionary rate differences among sites (4 categories). Branch support was evaluated using both aLRT (SH like) and bootstrap analysis (100 replicates). Bootstrap values above 0.75 (75%) are displayed in the phylograms shown next to the branches as *. The analysis involved 431 amino acid sequences and 386 patterns were found (out of a total of 421 sites). Functional ACC deaminases are shown in bold.
Mentions: Interestingly, the Pseudomonas sp. ACP AcdS sequence shares higher identity (96.7%) with Burkholderia xenovorans LB400 functional ACC deaminase than with Pseudomonas sp. UW4 AcdS (85.3%). This is also observed in the AcdS phylogram, where Pseudomonas sp. ACP groups closer to Burkholderia xenovorans LB400 (Fig. 3). While, Honma and Shimomura [1] tentatively identified Pseudomonas sp. ACP bacterium by phenotypic methods, it is conceivable that Pseudomonas sp. ACP is in fact a Burkholderia strain [64]. If this is in fact the case, then previous studies regarding the phylogeny of acdS may also have been influenced by the confusing relationship between Pseudomonas and Burkholderia. Furthermore, due to the recent divergent evolution and close relationship between γ and β-Proteobacteria, it is very difficult to prove acdS HGT in these classes.

Bottom Line: Still, results suggest a considerable degree of horizontal gene transfer events, including interkingdom transfer events.In this study we provide a more complete view of the role for ACC deaminase than was previously available.The results show that ACC deaminase may not only be related to plant growth promotion abilities, but may also play multiple roles in microorganism's developmental processes.

View Article: PubMed Central - PubMed

Affiliation: Universidade Federal de Santa Catarina, Departamento de Microbiologia, Laboratório de Microbiologia do Solo, Florianópolis SC, Brazil.

ABSTRACT
The main objective of this work is the study of the phylogeny, evolution and ecological importance of the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase, the activity of which represents one of the most important and studied mechanisms used by plant growth-promoting microorganisms. The ACC deaminase gene and its regulatory elements presence in completely sequenced organisms was verified by multiple searches in diverse databases, and based on the data obtained a comprehensive analysis was conducted. Strain habitat, origin and ACC deaminase activity were taken into account when analyzing the results. In order to unveil ACC deaminase origin, evolution and relationships with other closely related pyridoxal phosphate (PLP) dependent enzymes a phylogenetic analysis was also performed. The data obtained show that ACC deaminase is mostly prevalent in some Bacteria, Fungi and members of Stramenopiles. Contrary to previous reports, we show that ACC deaminase genes are predominantly vertically inherited in various bacterial and fungal classes. Still, results suggest a considerable degree of horizontal gene transfer events, including interkingdom transfer events. A model for ACC deaminase origin and evolution is also proposed. This study also confirms the previous reports suggesting that the Lrp-like regulatory protein AcdR is a common mechanism regulating ACC deaminase expression in Proteobacteria, however, we also show that other regulatory mechanisms may be present in some Proteobacteria and other bacterial phyla. In this study we provide a more complete view of the role for ACC deaminase than was previously available. The results show that ACC deaminase may not only be related to plant growth promotion abilities, but may also play multiple roles in microorganism's developmental processes. Hence, exploring the origin and functioning of this enzyme may be the key in a variety of important agricultural and biotechnological applications.

Show MeSH
Related in: MedlinePlus