Targeted interactomics reveals a complex core cell cycle machinery in <i>Arabidopsis thaliana</i>

Leene, Jelle Van; Hollunder, Jens; Eeckhout, Dominique; Persiau, Geert; Slijke, Eveline Van De; Stals, Hilde; Isterdael, Gert Van; Verkest, Aurine; Neirynck, Sandy; Buffel, Yelle; Bodt, Stefanie De; Maere, Steven; Laukens, Kris; Pharazyn, Anne; Ferreira, Paulo Sérgio; Eloy, Núbia Barbosa; Rolny, Charlotte; Meyer, Christian; Faure, Jean‐Denis; Steinbrenner, Jens; Beynon, Jim; Larkin, John C.; Peer, Yves Van de; Hilson, Pierre; Kuiper, Martin; Veylder, Lieven De; Onckelen, Harry Van; Inzé, Dirk; Witters, Erwin; Jaeger, Geert De

doi:10.1038/msb.2010.53

Cited by 314 publications

(333 citation statements)

References 57 publications

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“…Putative false positive interactions were subtracted based on prior experience with c . 40 TAP experiments on wild‐type (WT) cultures and cultures expressing TAP‐tagged mock proteins GUS, RFP and GFP (Van Leene et al ., 2010). …”

Section: Methodsmentioning

confidence: 99%

Identification of factors required for m⁶A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI

et al. 2017

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Summary N6‐adenosine methylation (m6A) of mRNA is an essential process in most eukaryotes, but its role and the status of factors accompanying this modification are still poorly understood.Using combined methods of genetics, proteomics and RNA biochemistry, we identified a core set of mRNA m6A writer proteins in Arabidopsis thaliana.The components required for m6A in Arabidopsis included MTA, MTB, FIP37, VIRILIZER and the E3 ubiquitin ligase HAKAI. Downregulation of these proteins led to reduced relative m6A levels and shared pleiotropic phenotypes, which included aberrant vascular formation in the root, indicating that correct m6A methylation plays a role in developmental decisions during pattern formation.The conservation of these proteins amongst eukaryotes and the demonstration of a role in writing m6A for the E3 ubiquitin ligase HAKAI is likely to be of considerable relevance beyond the plant sciences.

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Section: Methodsmentioning

confidence: 99%

Identification of factors required for m⁶A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI

et al. 2017

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“…CDKD was previously shown to form a heterotrimeric CDK-activating kinase (CAK) complex with a regulatory CYCLIN H (CYCH) subunit and the assembly factor ''MENAGE A TROIS 1'' (MAT1) both in rice (Rohila et al 2006) and Arabidopsis (Van Leene et al 2010). In the same studies, the other sub-complex of the general transcription factor II H (TFIIH), i.e.…”

Section: Introductionmentioning

confidence: 95%

“…This increases the chance to obtain a protein fusion that is still capable of binding its interaction partners, improving the success rate of the purifications. We already knew in advance which fusions worked best in Arabidopsis thaliana for the baits we chose (Van Leene et al 2010) and therefore constructed only an N-terminal fusion for APC10 (LOC_Os05g50360, 81 % identity, 92 % similarity with Arabidopsis APC10) and a C-terminal fusion for CKS1 (LOC_Os03g05300, 97 % identity, 100 % similarity with Arabidopsis CKS1) and CDKD (LOC_Os05g32600, 70 % identity, 78 % similarity with Arabidopsis CDKD1;3).…”

Section: Construction Of Tap-fusion Cassettes For Use In Ricementioning

confidence: 99%

“…We first estimated the compatibility of a GS tag-based workflow (Van Leene et al 2010) in rice by comparing its performance to the current state-of-the-art in rice-a TAPi tag-based system (Rohila et al 2009). We purified complexes from GS and TAPi tag-fusions with the cell cycle protein CKS1 using rice callus cells (Table S1; Fig.…”

Section: Assessment Of the Transferability Of The Gs Tag To Ricementioning

confidence: 99%

“…In contrast to Y2H and PCA, AP-MS has been traditionally unable to detect transient interactions, which are often lost during the washing steps necessary to remove nonspecific binding. The technique already proved its merits though, in various plant species (Arabidopsis, rice, petunia, tomato, tobacco) for different cellular processes, including the cell cycle (Van Leene et al 2010), flowering (Smaczniak et al 2012), leaf development (Vercruyssen et al 2014) and endocytosis (Gadeyne et al 2014). …”

Section: Introductionmentioning

confidence: 99%

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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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The glycolytic enzymes glyceraldehyde‐3‐phosphate dehydrogenase and hexokinase interact with cell cycle proteins in maize

Vargas‐Cortez,

Guerrero‐Molina,

Axosco‐Marin

et al. 2023

FEBS Letters

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Cyclin/cyclin‐dependent kinase (CDK) heterodimers have multiple phosphorylation targets and may alter the activity of these targets. Proteins from different metabolic processes are among the phosphorylation targets, that is, enzymes of central carbon metabolism. This work explores the interaction of Cyc/CDK complex members with the glycolytic enzymes hexokinase 7 (HXK7) and glyceraldehyde‐3‐phosphate dehydrogenase (GAP). Both enzymes interacted steadily with CycD2;2, CycB2;1 and CDKA;1 but not with CDKB1;1. However, Cyc/CDKB1;1 complexes phosphorylated both enzymes, decreasing their activities. Treatment with a CDK‐specific inhibitor (RO‐3306) or with lambda phosphatase after kinase assay restored total HXK7 activity, but not GAP activity. In enzymatic assays, increasing concentrations of CDKB1;1, but not of CycD2;2, CycB2;1 or CycD2;2/CDKB1;1 complex, decreased GAP activity. Cell cycle regulators may modulate carbon channeling in glycolysis by two different mechanisms: Cyc/CDK‐mediated phosphorylation of targets (e.g., HXK7; canonical mechanism) or by direct and transient interaction of the metabolic enzyme (e.g., GAP) with CDKB1;1 without a Cyc partner (alternative mechanism).

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Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana

Cited by 314 publications

References 57 publications

Identification of factors required for m⁶A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI

Identification of factors required for m⁶A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI

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

The glycolytic enzymes glyceraldehyde‐3‐phosphate dehydrogenase and hexokinase interact with cell cycle proteins in maize

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Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana

Cited by 314 publications

References 57 publications

Identification of factors required for m6A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI

Identification of factors required for m6A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI

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

The glycolytic enzymes glyceraldehyde‐3‐phosphate dehydrogenase and hexokinase interact with cell cycle proteins in maize

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Identification of factors required for m⁶A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI

Identification of factors required for m⁶A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI