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Insights into the evolution and diversification of the AT-hook Motif Nuclear Localized gene family in land plants.

Zhao J, Favero DS, Qiu J, Roalson EH, Neff MM - BMC Plant Biol. (2014)

Bottom Line: This result suggests that the AHL genes from different land plant species may share conserved functions in regulating plant growth and development.Manipulating the AHL genes has been suggested to have tremendous effects in agriculture through increased seedling establishment, enhanced plant biomass and improved plant immunity.The information gleaned from this study, in turn, has the potential to be utilized to further improve crop production.

View Article: PubMed Central - PubMed

ABSTRACT

Background: Members of the ancient land-plant-specific transcription factor AT-Hook Motif Nuclear Localized (AHL) gene family regulate various biological processes. However, the relationships among the AHL genes, as well as their evolutionary history, still remain unexplored.

Results: We analyzed over 500 AHL genes from 19 land plant species, ranging from the early diverging Physcomitrella patens and Selaginella to a variety of monocot and dicot flowering plants. We classified the AHL proteins into three types (Type-I/-II/-III) based on the number and composition of their functional domains, the AT-hook motif(s) and PPC domain. We further inferred their phylogenies via Bayesian inference analysis and predicted gene gain/loss events throughout their diversification. Our analyses suggested that the AHL gene family emerged in embryophytes and further evolved into two distinct clades, with Type-I AHLs forming one clade (Clade-A), and the other two types together diversifying in another (Clade-B). The two AHL clades likely diverged before the separation of Physcomitrella patens from the vascular plant lineage. In angiosperms, Clade-A AHLs expanded into 5 subfamilies; while, the ones in Clade-B expanded into 4 subfamilies. Examination of their expression patterns suggests that the AHLs within each clade share similar expression patterns with each other; however, AHLs in one monophyletic clade exhibit distinct expression patterns from the ones in the other clade. Over-expression of a Glycine max AHL PPC domain in Arabidopsis thaliana recapitulates the phenotype observed when over-expressing its Arabidopsis thaliana counterpart. This result suggests that the AHL genes from different land plant species may share conserved functions in regulating plant growth and development. Our study further suggests that such functional conservation may be due to conserved physical interactions among the PPC domains of AHL proteins.

Conclusions: Our analyses reveal a possible evolutionary scenario for the AHL gene family in land plants, which will facilitate the design of new studies probing their biological functions. Manipulating the AHL genes has been suggested to have tremendous effects in agriculture through increased seedling establishment, enhanced plant biomass and improved plant immunity. The information gleaned from this study, in turn, has the potential to be utilized to further improve crop production.

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Phylogeny of the Clade-BAHLgene family in land plants using Bayesian analysis. Clade-B AHLs could be distinguished into 4 subfamilies (B1, B2, B3 and B4). Type-III AHLs that form sub-clades have been highlighted by gradient boxes (in Subfamilies B1 and B4) or pointed out by ③ if within Type-II AHL sub-clades. Type-II AHLs are pointed out by ② if within a Type-III AHL sub-clades (within Subfamily B4). Green boxes represent AHL genes from Poaceae, yellow boxes denote genes from Fabaceae, blue boxes denote genes from Rosaceae, orange boxes denote genes from Malpighiales, and red boxes denote genes from Brassicaceae. Numbers near branches indicate the Bayesian posterior probabilities for given clades. The red dots at internal nodes denote where gene duplication events have occurred.
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Fig7: Phylogeny of the Clade-BAHLgene family in land plants using Bayesian analysis. Clade-B AHLs could be distinguished into 4 subfamilies (B1, B2, B3 and B4). Type-III AHLs that form sub-clades have been highlighted by gradient boxes (in Subfamilies B1 and B4) or pointed out by ③ if within Type-II AHL sub-clades. Type-II AHLs are pointed out by ② if within a Type-III AHL sub-clades (within Subfamily B4). Green boxes represent AHL genes from Poaceae, yellow boxes denote genes from Fabaceae, blue boxes denote genes from Rosaceae, orange boxes denote genes from Malpighiales, and red boxes denote genes from Brassicaceae. Numbers near branches indicate the Bayesian posterior probabilities for given clades. The red dots at internal nodes denote where gene duplication events have occurred.

Mentions: Clade-B of the AHL gene family is comprised of Type-II and Type-III AHLs (Figures 6 and 7). The Type-II AHLs from the early diverging moss Physcomitrella patens and lycophyte Selaginella moellendorffii constitute a clade at the base of the phylogenetic tree (Figure 6). The angiosperm portion of Clade-B can be divided into four subfamilies (Subfamilies B1, B2, B3 and B4).Figure 6


Insights into the evolution and diversification of the AT-hook Motif Nuclear Localized gene family in land plants.

Zhao J, Favero DS, Qiu J, Roalson EH, Neff MM - BMC Plant Biol. (2014)

Phylogeny of the Clade-BAHLgene family in land plants using Bayesian analysis. Clade-B AHLs could be distinguished into 4 subfamilies (B1, B2, B3 and B4). Type-III AHLs that form sub-clades have been highlighted by gradient boxes (in Subfamilies B1 and B4) or pointed out by ③ if within Type-II AHL sub-clades. Type-II AHLs are pointed out by ② if within a Type-III AHL sub-clades (within Subfamily B4). Green boxes represent AHL genes from Poaceae, yellow boxes denote genes from Fabaceae, blue boxes denote genes from Rosaceae, orange boxes denote genes from Malpighiales, and red boxes denote genes from Brassicaceae. Numbers near branches indicate the Bayesian posterior probabilities for given clades. The red dots at internal nodes denote where gene duplication events have occurred.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4209074&req=5

Fig7: Phylogeny of the Clade-BAHLgene family in land plants using Bayesian analysis. Clade-B AHLs could be distinguished into 4 subfamilies (B1, B2, B3 and B4). Type-III AHLs that form sub-clades have been highlighted by gradient boxes (in Subfamilies B1 and B4) or pointed out by ③ if within Type-II AHL sub-clades. Type-II AHLs are pointed out by ② if within a Type-III AHL sub-clades (within Subfamily B4). Green boxes represent AHL genes from Poaceae, yellow boxes denote genes from Fabaceae, blue boxes denote genes from Rosaceae, orange boxes denote genes from Malpighiales, and red boxes denote genes from Brassicaceae. Numbers near branches indicate the Bayesian posterior probabilities for given clades. The red dots at internal nodes denote where gene duplication events have occurred.
Mentions: Clade-B of the AHL gene family is comprised of Type-II and Type-III AHLs (Figures 6 and 7). The Type-II AHLs from the early diverging moss Physcomitrella patens and lycophyte Selaginella moellendorffii constitute a clade at the base of the phylogenetic tree (Figure 6). The angiosperm portion of Clade-B can be divided into four subfamilies (Subfamilies B1, B2, B3 and B4).Figure 6

Bottom Line: This result suggests that the AHL genes from different land plant species may share conserved functions in regulating plant growth and development.Manipulating the AHL genes has been suggested to have tremendous effects in agriculture through increased seedling establishment, enhanced plant biomass and improved plant immunity.The information gleaned from this study, in turn, has the potential to be utilized to further improve crop production.

View Article: PubMed Central - PubMed

ABSTRACT

Background: Members of the ancient land-plant-specific transcription factor AT-Hook Motif Nuclear Localized (AHL) gene family regulate various biological processes. However, the relationships among the AHL genes, as well as their evolutionary history, still remain unexplored.

Results: We analyzed over 500 AHL genes from 19 land plant species, ranging from the early diverging Physcomitrella patens and Selaginella to a variety of monocot and dicot flowering plants. We classified the AHL proteins into three types (Type-I/-II/-III) based on the number and composition of their functional domains, the AT-hook motif(s) and PPC domain. We further inferred their phylogenies via Bayesian inference analysis and predicted gene gain/loss events throughout their diversification. Our analyses suggested that the AHL gene family emerged in embryophytes and further evolved into two distinct clades, with Type-I AHLs forming one clade (Clade-A), and the other two types together diversifying in another (Clade-B). The two AHL clades likely diverged before the separation of Physcomitrella patens from the vascular plant lineage. In angiosperms, Clade-A AHLs expanded into 5 subfamilies; while, the ones in Clade-B expanded into 4 subfamilies. Examination of their expression patterns suggests that the AHLs within each clade share similar expression patterns with each other; however, AHLs in one monophyletic clade exhibit distinct expression patterns from the ones in the other clade. Over-expression of a Glycine max AHL PPC domain in Arabidopsis thaliana recapitulates the phenotype observed when over-expressing its Arabidopsis thaliana counterpart. This result suggests that the AHL genes from different land plant species may share conserved functions in regulating plant growth and development. Our study further suggests that such functional conservation may be due to conserved physical interactions among the PPC domains of AHL proteins.

Conclusions: Our analyses reveal a possible evolutionary scenario for the AHL gene family in land plants, which will facilitate the design of new studies probing their biological functions. Manipulating the AHL genes has been suggested to have tremendous effects in agriculture through increased seedling establishment, enhanced plant biomass and improved plant immunity. The information gleaned from this study, in turn, has the potential to be utilized to further improve crop production.

Show MeSH
Related in: MedlinePlus