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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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Related in: MedlinePlus

Type of AHL proteins and their AT-hook motifs in land plants. Ice-Logo analysis of the Type-I AT-hook motifs (a) and Type-II AT-hook motifs (b) in land-plant AHL proteins. The star symbol denotes the core sequence of the AT-hook motif. The conserved sequence downstream of the core sequences in Type-I and Type-II AT-hook motifs were pointed out by the triangle and diamond symbols accordingly. (c) Topology of three types of AHL proteins identified in land plants based on the combination of AT-hook motifs and PPC domain.
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Fig3: Type of AHL proteins and their AT-hook motifs in land plants. Ice-Logo analysis of the Type-I AT-hook motifs (a) and Type-II AT-hook motifs (b) in land-plant AHL proteins. The star symbol denotes the core sequence of the AT-hook motif. The conserved sequence downstream of the core sequences in Type-I and Type-II AT-hook motifs were pointed out by the triangle and diamond symbols accordingly. (c) Topology of three types of AHL proteins identified in land plants based on the combination of AT-hook motifs and PPC domain.

Mentions: Two types of AT-hook motifs (Type-I and -II) are found in the AHL proteins (FigureĀ 3a,b; Additional file 7) [33,34]. Both types of AT-hook motifs in the AHL proteins share the same conserved Arg-Gly-Arg core and use this conserved palindromic core to bind the minor groove of AT-rich B-form DNA [35]. Clade-A AHLs contain only one copy of the Type-I AT-hook motifs; while, in Clade-B, some of the AHLs contain only one copy of the Type-II AT-hook motifs and the rest contain both types of AT-hook motifs.Figure 3


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)

Type of AHL proteins and their AT-hook motifs in land plants. Ice-Logo analysis of the Type-I AT-hook motifs (a) and Type-II AT-hook motifs (b) in land-plant AHL proteins. The star symbol denotes the core sequence of the AT-hook motif. The conserved sequence downstream of the core sequences in Type-I and Type-II AT-hook motifs were pointed out by the triangle and diamond symbols accordingly. (c) Topology of three types of AHL proteins identified in land plants based on the combination of AT-hook motifs and PPC domain.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig3: Type of AHL proteins and their AT-hook motifs in land plants. Ice-Logo analysis of the Type-I AT-hook motifs (a) and Type-II AT-hook motifs (b) in land-plant AHL proteins. The star symbol denotes the core sequence of the AT-hook motif. The conserved sequence downstream of the core sequences in Type-I and Type-II AT-hook motifs were pointed out by the triangle and diamond symbols accordingly. (c) Topology of three types of AHL proteins identified in land plants based on the combination of AT-hook motifs and PPC domain.
Mentions: Two types of AT-hook motifs (Type-I and -II) are found in the AHL proteins (FigureĀ 3a,b; Additional file 7) [33,34]. Both types of AT-hook motifs in the AHL proteins share the same conserved Arg-Gly-Arg core and use this conserved palindromic core to bind the minor groove of AT-rich B-form DNA [35]. Clade-A AHLs contain only one copy of the Type-I AT-hook motifs; while, in Clade-B, some of the AHLs contain only one copy of the Type-II AT-hook motifs and the rest contain both types of AT-hook motifs.Figure 3

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