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 constructed based on ACC deaminase and related PLP enzymes protein sequences.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 99 aminoacid sequences and 570 patterns were found (out of a total of 594 sites). Sequences used for the construction of this phylogram are described in Table S6.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0099168-g005: Phylogram constructed based on ACC deaminase and related PLP enzymes protein sequences.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 99 aminoacid sequences and 570 patterns were found (out of a total of 594 sites). Sequences used for the construction of this phylogram are described in Table S6.

Mentions: To gain additional knowledge regarding the origin and evolution of ACC deaminase multiple searches of the database were conducted; sequences showing a high similarity to different deaminases were obtained and a phylogram was constructed (Fig. 5). In this instance it was observed that ACC deaminase forms a distinct and unique group, where ACC deaminases from different organisms like Bacteria and Fungi cluster together. This is also observed with D-cysteine desulfhydrase, however only a few representatives of the considered “true” D-cysteine desulfhydrases (E.coli D-cysteine desulfhydrase) were obtained. When searching in the database, it was observed that D-cysteine desulfhydrase is an enzyme whose distribution is not widespread and it may also be not nearly as conserved as ACC deaminase. Its presence has been verified mainly in γ-Proteobacteria. Other proteins showing some homology were found in Firmicutes and other α-Proteobacteria, but in those instances showing low identity scores (39%).


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 constructed based on ACC deaminase and related PLP enzymes protein sequences.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 99 aminoacid sequences and 570 patterns were found (out of a total of 594 sites). Sequences used for the construction of this phylogram are described in Table S6.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0099168-g005: Phylogram constructed based on ACC deaminase and related PLP enzymes protein sequences.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 99 aminoacid sequences and 570 patterns were found (out of a total of 594 sites). Sequences used for the construction of this phylogram are described in Table S6.
Mentions: To gain additional knowledge regarding the origin and evolution of ACC deaminase multiple searches of the database were conducted; sequences showing a high similarity to different deaminases were obtained and a phylogram was constructed (Fig. 5). In this instance it was observed that ACC deaminase forms a distinct and unique group, where ACC deaminases from different organisms like Bacteria and Fungi cluster together. This is also observed with D-cysteine desulfhydrase, however only a few representatives of the considered “true” D-cysteine desulfhydrases (E.coli D-cysteine desulfhydrase) were obtained. When searching in the database, it was observed that D-cysteine desulfhydrase is an enzyme whose distribution is not widespread and it may also be not nearly as conserved as ACC deaminase. Its presence has been verified mainly in γ-Proteobacteria. Other proteins showing some homology were found in Firmicutes and other α-Proteobacteria, but in those instances showing low identity scores (39%).

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