Crystal structure of <i>Pyrococcus horikoshii</i> PPC protein at 1.60 Å resolution

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

doi:10.1002/prot.21270

Cited by 11 publications

(10 citation statements)

References 13 publications

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“…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%

“…It is also predicted to adopt a similar tertiary structure as observed in the crystal structures of prokaryotic PPC/DUF296 proteins. The PPC/DUF296 proteins form a trimer, where the β-sheets mediate interactions among the three PPC monomers (14). This structure suggests that the PPC/DUF296 domains in Arabidopsis AHL proteins could associate with each other as their counterparts do in prokaryotes.…”

Section: Significancementioning

confidence: 96%

“…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%

“…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. The solved crystal structures suggest that the prokaryotic PPC/DUF296 proteins form a trimer (14). In land plants, the PPC/DUF296 domain is found in AHL proteins, where it is located at the carboxyl end relative to the AT-hook motif(s) (13).…”

mentioning

confidence: 99%

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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

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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

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Section: Discussionsupporting

confidence: 84%

Section: Significancementioning

confidence: 96%

mentioning

confidence: 99%

mentioning

confidence: 99%

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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

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“…JK974195, a putative DNA-binding protein, belongs to the DUF296 superfamily with unknown function. The AT-hook motif was found in JK974195, which suggested a role in DNA-binding for the protein as a whole [31] (Fig. S2B).…”

Section: Discussionmentioning

confidence: 98%

Profiling of Differentially Expressed Genes in Roots of Robinia pseudoacacia during Nodule Development Using Suppressive Subtractive Hybridization

et al. 2013

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BackgroundLegume-rhizobium symbiosis is a complex process that is regulated in the host plant cell through gene expression network. Many nodulin genes that are upregulated during different stages of nodulation have been identified in leguminous herbs. However, no nodulin genes in woody legume trees, such as black locust (Robinia pseudoacacia), have yet been reported.Methodology/Principal findingsTo identify the nodulin genes involved in R. pseudoacacia-Mesorhizobium amorphae CCNWGS0123 symbiosis, a suppressive subtractive hybridization approach was applied to reveal profiling of differentially expressed genes and two subtracted cDNA libraries each containing 600 clones were constructed. Then, 114 unigenes were identified from forward SSH library by differential screening and the putative functions of these translational products were classified into 13 categories. With a particular interest in regulatory genes, twenty-one upregulated genes encoding potential regulatory proteins were selected based on the result of reverse transcription-polymerase chain reaction (RT-PCR) analysis. They included nine putative transcription genes, eight putative post-translational regulator genes and four membrane protein genes. The expression patterns of these genes were further analyzed by quantitative RT-PCR at different stages of nodule development.ConclusionsThe data presented here offer the first insights into the molecular foundation underlying R. pseudoacacia–M. amorphae symbiosis. A number of regulatory genes screened in the present study revealed a high level of regulatory complexity (transcriptional, post-transcriptional, translational and post-translational) that is likely essential to develop symbiosis. In addition, the possible roles of these genes in black locust nodulation are discussed.

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Phylogenetic distribution and structural analyses of cyanobacterial glutaredoxins (Grxs)

Mondal

Kumar

Singh

2020

Computational Biology and Chemistry

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Crystal structure of Pyrococcus horikoshii PPC protein at 1.60 Å resolution

Cited by 11 publications

References 13 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

Profiling of Differentially Expressed Genes in Roots of Robinia pseudoacacia during Nodule Development Using Suppressive Subtractive Hybridization

Phylogenetic distribution and structural analyses of cyanobacterial glutaredoxins (Grxs)

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