Identification of Dynamin as an Interactor of Rice GIGANTEA by Tandem Affinity Purification (TAP)

Abe, Makoto; Fujiwara, Masayuki; Kurotani, Ken-ichi; Yokoi, Shuji; Shimamoto, Ko

doi:10.1093/pcp/pcn019

Cited by 34 publications

(28 citation statements)

References 72 publications

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“…Consistent with this, no morphological or developmental defects were observed in single homozygous drp2a or drp2b mutants. By contrast, Abe et al (2008) reported an aerial rosette phenotype in 50 to 90% of plants from homozygous drp2a (drp2a-1, drp2a-2, and drp2a-3) and drp2b (drp2b-2 and drp2b-3) single mutant lines compared with only in 10% of wild-type plants. We did not observe aerial rosettes in either wild-type or any drp2a or drp2b mutant plants analyzed in this study, suggesting that different growth conditions may be required for the manifestation of this phenotype.…”

Section: Drp2a and Drp2b Play Functionally Redundant Roles In Plant Dmentioning

confidence: 90%

TheArabidopsisDynamin-Related Protein2 Family Is Essential for Gametophyte Development

et al. 2010

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Clathrin-mediated membrane trafficking is critical for multiple stages of plant growth and development. One key component of clathrin-mediated trafficking in animals is dynamin, a polymerizing GTPase that plays both regulatory and mechanical roles. Other eukaryotes use various dynamin-related proteins (DRP) in clathrin-mediated trafficking. Plants are unique in the apparent involvement of both a family of classical dynamins (DRP2) and a family of dynamin-related proteins (DRP1) in clathrin-mediated membrane trafficking. Our analysis of drp2 insertional mutants demonstrates that, similar to the DRP1 family, the DRP2 family is essential for Arabidopsis thaliana development. Gametophytes lacking both DRP2A and DRP2B were inviable, arresting prior to the first mitotic division in both male and female gametogenesis. Mutant pollen displayed a variety of defects, including branched or irregular cell plates, altered Golgi morphology and ectopic callose deposition. Ectopic callose deposition was also visible in the pollen-lethal drp1c-1 mutant and appears to be a specific feature of pollen-defective mutants with impaired membrane trafficking. However, drp2ab pollen arrested at earlier stages in development than drp1c-1 pollen and did not accumulate excess plasma membrane or display other gross defects in plasma membrane morphology. Therefore, the DRP2 family, but not DRP1C, is necessary for cell cycle progression during early gametophyte development. This suggests a possible role for DRP2-dependent clathrin-mediated trafficking in the transduction of developmental signals in the gametophyte.

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Section: Drp2a and Drp2b Play Functionally Redundant Roles In Plant Dmentioning

confidence: 90%

TheArabidopsisDynamin-Related Protein2 Family Is Essential for Gametophyte Development

et al. 2010

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“…The former two certainly have shown their merits in the identification of binary interactions; AP-MS is complementary to Y2H and PCA, since it isolates and identifies protein complexes rather than binary interactions. Several studies reported the development of an AP-MS approach in rice, two based on purification from cultured cells (Zhong et al 2003;Abe et al 2008), and three based on experiments on 6-8-week-old seedlings (Rohila et al 2006(Rohila et al , 2009Dong et al 2013). However, the majority only purified one complex, which makes it difficult to evaluate these individual platforms.…”

Section: Discussionmentioning

confidence: 99%

“…In that frame, five AP-MS approaches have so far been presented using rice for screening PPIs. Three used cultured cells, and their performance has been proven with the isolation of interaction partners of the TATA-BINDING PROTEIN (Zhong et al 2003), GIGANTEA (Abe et al 2008) or the FERTI-LILZATION-INSENSITIVE ENDOSPERM 2-polycomb protein complex (Nallamilli et al 2013). The fourth approach reported the purification of VIRESCENT YEL-LOW LEAF associated proteins from shoots of 6-8-weekold seedlings (Dong et al 2013).…”

Section: Introductionmentioning

confidence: 99%

Transferring an optimized TAP-toolbox for the isolation of protein complexes to a portfolio of rice tissues

et al. 2016

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Proteins are the cell's functional entities. Rather than operating independently, they interact with other proteins. Capturing in vivo protein complexes is therefore crucial to gain understanding of the function of a protein in a cellular context. Affinity purification coupled to mass spectrometry has proven to yield a wealth of information about protein complex constitutions for a broad range of organisms. For Oryza sativa, the technique has been initiated in callus and shoots, but has not been optimized ever since. We translated an optimized tandem affinity purification (TAP) approach from Arabidopsis thaliana toward Oryza sativa, and demonstrate its applicability in a variety of rice tissues. A list of non-specific and false positive interactors is presented, based on reoccurrence over more than 170 independent experiments, to filter bona fide interactors. We demonstrate the sensitivity of our approach by isolating the complexes for the rice ANAPHASE PROMOTING COMPLEX SUB-UNIT 10 (APC10) and CYCLIN-DEPENDENT KINASE D (CDKD) proteins from the proliferation zone of the emerging fourth leaf. Next to APC10 and CDKD, we tested several additional baits in the different rice tissues and reproducibly retrieved at least one interactor for 81.4 % of the baits screened for in callus tissue and T1 seedlings. By transferring an optimized TAP tag combined with state-ofthe-art mass spectrometry, our TAP protocol enables the discovery of interactors for low abundance proteins in rice and opens the possibility to capture complex dynamics by comparing tissues at different stages of a developing rice organ.

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“…LINKING THE PROTEOME & organisms, through varying the nature of the two tags to maximize complex recovery (Burckstummer et al, 2006). TAP protocols were thus designed for insect cells (Forler et al, 2003), mammalian cells or transgenic organisms (Bouwmeester et al, 2004;Angrand et al, 2006;Jeronimo et al, 2007), and plants (Rohila et al, 2004;Abe et al, 2008). Among recent improved versions of TAP, Glatter et al (2009) optimized a whole workflow integrating MS analysis, to get efficient and robust protein complex identification from human cells.…”

Section: Short Overview Of Affinity Purification Strategiesmentioning

confidence: 99%

Linking the proteins—Elucidation of proteome‐scale networks using mass spectrometry

Pflieger

Gonnet

Bentem

et al. 2011

Mass Spectrometry Reviews

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Proteomes are intricate. Typically, thousands of proteins interact through physical association and post‐translational modifications (PTMs) to give rise to the emergent functions of cells. Understanding these functions requires one to study proteomes as “systems” rather than collections of individual protein molecules. The abstraction of the interacting proteome to “protein networks” has recently gained much attention, as networks are effective representations, that lose specific molecular details, but provide the ability to see the proteome as a whole. Mostly two aspects of the proteome have been represented by network models: proteome‐wide physical protein–protein‐binding interactions organized into Protein Interaction Networks (PINs), and proteome‐wide PTM relations organized into Protein Signaling Networks (PSNs). Mass spectrometry (MS) techniques have been shown to be essential to reveal both of these aspects on a proteome‐wide scale. Techniques such as affinity purification followed by MS have been used to elucidate protein–protein interactions, and MS‐based quantitative phosphoproteomics is critical to understand the structure and dynamics of signaling through the proteome. We here review the current state‐of‐the‐art MS‐based analytical pipelines for the purpose to characterize proteome‐scale networks. © 2010 Wiley Periodicals, Inc., Mass Spec Rev 30:268–297, 2011

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Identification of Dynamin as an Interactor of Rice GIGANTEA by Tandem Affinity Purification (TAP)

Cited by 34 publications

References 72 publications

TheArabidopsisDynamin-Related Protein2 Family Is Essential for Gametophyte Development

TheArabidopsisDynamin-Related Protein2 Family Is Essential for Gametophyte Development

Transferring an optimized TAP-toolbox for the isolation of protein complexes to a portfolio of rice tissues

Linking the proteins—Elucidation of proteome‐scale networks using mass spectrometry

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