Crystallization and preliminary X-ray crystallographic analysis of a conserved domain in plants and prokaryotes from<i>Pyrococcus horikoshii</i>OT3

Lin, Linyen; Nakano, Hiroaki; Uchiyama, Susumu; Fujimoto, Shinsaku; Matsunaga, Sachihiro; Nakamura, Shota; Kobayashi, Yuji; Ohkubo, Tadayasu; Fukui, Kiichi

doi:10.1107/s1744309105007815

Cited by 6 publications

(5 citation statements)

References 5 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…8). The predicted tertiary structure of the PPC/DUF296 domain of SOB3/AHL29 suggests trimeric oligomerization, which is similar to that observed in seven determined crystal structures of this domain from Bacteria and Archaea [Protein Data Bank (PDB) ID: 2H6L, 2DT4, 2HX0, 2NMU, 2P6Y, 3HTN, and 3HWU] (14,15). Trimer formation in a proposed AHL complex is also supported by the physical interactions observed among AHLs in this study (Figs.…”

Section: Discussionsupporting

confidence: 84%

See 1 more Smart Citation

Arabidopsis thaliana AHL family modulates hypocotyl growth redundantly by interacting with each other via the PPC/DUF296 domain

Zhao

Favero

Peng

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

113

256

View full text Add to dashboard Cite

The Arabidopsis thaliana genome encodes 29 AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED (AHL) genes, which evolved into two phylogenic clades. The AHL proteins contain one or two AT-hook motif(s) and one plant and prokaryote conserved (PPC)/domain of unknown function #296 (DUF296) domain. Seedlings lacking both SOB3/AHL29 and ESC/AHL27 confer a subtle long-hypocotyl phenotype compared with the WT or either single-null mutant. In contrast, the missense allele sob3-6 confers a dramatic long-hypocotyl phenotype in the light. In this study, we examined the dominant-negative feature of sob3-6 and found that it encodes a protein with a disrupted AT-hook motif that abolishes binding to AT-rich DNA. A loss-of-function approach demonstrated different, yet redundant, contributions of additional AHL genes in suppressing hypocotyl elongation in the light. We showed that AHL proteins interact with each other and themselves via the PPC/DUF296 domain. AHLs also share interactions with other nuclear proteins, such as transcription factors, suggesting that these interactions also contribute to the functional redundancy within this gene family. The coordinated action of AHLs requires an AT-hook motif capable of binding AT-rich DNA, as well as a PPC/DUF296 domain containing a conserved Gly-Arg-Phe-Glu-Ile-Leu region. Alteration of this region abolished SOB3/AHL29's physical interaction with transcription factors and resulted in a dominant-negative allele in planta that was phenotypically similar to sob3-6. We propose a molecular model where AHLs interact with each other and themselves, as well as other nuclear proteins, to form complexes which modulate plant growth and development.enhanceosome | seedling establishment

show abstract

Section: Discussionsupporting

confidence: 84%

“…Crystal structures of several bacterial and archaeal PPC/DUF296 proteins have been determined (14,15). All of the above prokaryotic PPC/DUF296 proteins share the same tertiary structure with five β-strands forming an antiparallel β-sheet, which partially surrounds a single α-helix.…”

mentioning

confidence: 99%

Arabidopsis thaliana AHL family modulates hypocotyl growth redundantly by interacting with each other via the PPC/DUF296 domain

Zhao

Favero

Peng

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

113

256

View full text Add to dashboard Cite

show abstract

“…Methods and the material for sample preparation, crystallization, and preliminary crystallographic analysis of Ph PPC have been reported 3. X‐ray diffraction data of native and Se‐Met‐substituted crystals were collected to a resolution of 1.6 and 2.6 Å, respectively, at BL41XU in SPring‐8 (Hyogo, Japan).…”

Section: Methodsmentioning

confidence: 99%

Crystal structure of Pyrococcus horikoshii PPC protein at 1.60 Å resolution

et al. 2007

Self Cite

View full text Add to dashboard Cite

“…The second functional unit of the AHL proteins is the PPC domain, which is approximately 120 amino acids in length and exists as a single protein in Bacteria and Archaea [ 32 ]. Crystal structures of several bacterial and archaeal PPC proteins suggested that the prokaryotic PPC proteins form a trimer [ 36 , 37 ]. In land plants, the PPC domain has been identified in AHL proteins where it is located at the carboxyl end relative to the AT-hook motif(s) [ 32 ].…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2014

View full text Add to dashboard Cite

BackgroundMembers 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.ResultsWe 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.ConclusionsOur 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-014-0266-7) contains supplementary material, which is available to authorized users.

show abstract

Crystallization and preliminary X-ray crystallographic analysis of a conserved domain in plants and prokaryotes fromPyrococcus horikoshiiOT3

Cited by 6 publications

References 5 publications

Arabidopsis thaliana AHL family modulates hypocotyl growth redundantly by interacting with each other via the PPC/DUF296 domain

Arabidopsis thaliana AHL family modulates hypocotyl growth redundantly by interacting with each other via the PPC/DUF296 domain

Crystal structure of Pyrococcus horikoshii PPC protein at 1.60 Å resolution

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

Contact Info

Product

Resources

About