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  3. AU="Schmidt, Monica A"
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  1. Article ; Online: ARVCF catenin controls force production during vertebrate convergent extension.

    Huebner, Robert J / Weng, Shinuo / Lee, Chanjae / Sarıkaya, Sena / Papoulas, Ophelia / Cox, Rachael M / Marcotte, Edward M / Wallingford, John B

    Developmental cell

    2022  Volume 57, Issue 9, Page(s) 1119–1131.e5

    Abstract: The design of an animal's body plan is encoded in the genome, and the execution of this program is a mechanical progression involving coordinated movement of proteins, cells, and whole tissues. Thus, a challenge to understanding morphogenesis is ... ...

    Abstract The design of an animal's body plan is encoded in the genome, and the execution of this program is a mechanical progression involving coordinated movement of proteins, cells, and whole tissues. Thus, a challenge to understanding morphogenesis is connecting events that occur across various length scales. Here, we describe how a poorly characterized adhesion effector, Arvcf catenin, controls Xenopus head-to-tail axis extension. We find that Arvcf is required for axis extension within the intact organism but not within isolated tissues. We show that the organism-scale phenotype results from a defect in tissue-scale force production. Finally, we determine that the force defect results from the dampening of the pulsatile recruitment of cell adhesion and cytoskeletal proteins to membranes. These results provide a comprehensive understanding of Arvcf function during axis extension and produce an insight into how a cellular-scale defect in adhesion results in an organism-scale failure of development.
    MeSH term(s) Animals ; Armadillo Domain Proteins/genetics ; Armadillo Domain Proteins/metabolism ; Cadherins/metabolism ; Catenins ; Cell Adhesion Molecules/metabolism ; Morphogenesis ; Phosphoproteins/metabolism ; Xenopus laevis/metabolism
    Chemical Substances Armadillo Domain Proteins ; Cadherins ; Catenins ; Cell Adhesion Molecules ; Phosphoproteins
    Language English
    Publishing date 2022-04-26
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2054967-2
    ISSN 1878-1551 ; 1534-5807
    ISSN (online) 1878-1551
    ISSN 1534-5807
    DOI 10.1016/j.devcel.2022.04.001
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  2. Article ; Online: Twinfilin1 controls lamellipodial protrusive activity and actin turnover during vertebrate gastrulation.

    Devitt, Caitlin C / Lee, Chanjae / Cox, Rachael M / Papoulas, Ophelia / Alvarado, José / Shekhar, Shashank / Marcotte, Edward M / Wallingford, John B

    Journal of cell science

    2021  Volume 134, Issue 14

    Abstract: The dynamic control of the actin cytoskeleton is a key aspect of essentially all animal cell movements. Experiments in single migrating cells and in vitro systems have provided an exceptionally deep understanding of actin dynamics. However, we still know ...

    Abstract The dynamic control of the actin cytoskeleton is a key aspect of essentially all animal cell movements. Experiments in single migrating cells and in vitro systems have provided an exceptionally deep understanding of actin dynamics. However, we still know relatively little of how these systems are tuned in cell-type-specific ways, for example in the context of collective cell movements that sculpt the early embryo. Here, we provide an analysis of the actin-severing and depolymerization machinery during vertebrate gastrulation, with a focus on Twinfilin1 (Twf1) in Xenopus. We find that Twf1 is essential for convergent extension, and loss of Twf1 results in a disruption of lamellipodial dynamics and polarity. Moreover, Twf1 loss results in a failure to assemble polarized cytoplasmic actin cables, which are essential for convergent extension. These data provide an in vivo complement to our more-extensive understanding of Twf1 action in vitro and provide new links between the core machinery of actin regulation and the specialized cell behaviors of embryonic morphogenesis.
    MeSH term(s) Actin Cytoskeleton ; Actins/genetics ; Animals ; Gastrulation ; Pseudopodia ; Xenopus laevis
    Chemical Substances Actins
    Language English
    Publishing date 2021-07-19
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2993-2
    ISSN 1477-9137 ; 0021-9533
    ISSN (online) 1477-9137
    ISSN 0021-9533
    DOI 10.1242/jcs.254011
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  3. Article: A systematic, label-free method for identifying RNA-associated proteins in vivo provides insights into vertebrate ciliary beating machinery

    Drew, Kevin / Lee, Chanjae / Cox, Rachael M / Dang, Vy / Devitt, Caitlin C / McWhite, Claire D / Papoulas, Ophelia / Huizar, Ryan L / Marcotte, Edward M / Wallingford, John B

    Developmental biology. 2020 Nov. 01, v. 467, no. 1-2

    2020  

    Abstract: Cell-type specific RNA-associated proteins are essential for development and homeostasis in animals. Despite a massive recent effort to systematically identify RNA-associated proteins, we currently have few comprehensive rosters of cell-type specific RNA- ...

    Abstract Cell-type specific RNA-associated proteins are essential for development and homeostasis in animals. Despite a massive recent effort to systematically identify RNA-associated proteins, we currently have few comprehensive rosters of cell-type specific RNA-associated proteins in vertebrate tissues. Here, we demonstrate the feasibility of determining the RNA-associated proteome of a defined vertebrate embryonic tissue using DIF-FRAC, a systematic and universal (i.e., label-free) method. Application of DIF-FRAC to cultured tissue explants of Xenopus mucociliary epithelium identified dozens of known RNA-associated proteins as expected, but also several novel RNA-associated proteins, including proteins related to assembly of the mitotic spindle and regulation of ciliary beating. In particular, we show that the inner dynein arm tether Cfap44 is an RNA-associated protein that localizes not only to axonemes, but also to liquid-like organelles in the cytoplasm called DynAPs. This result led us to discover that DynAPs are generally enriched for RNA. Together, these data provide a useful resource for a deeper understanding of mucociliary epithelia and demonstrate that DIF-FRAC will be broadly applicable for systematic identification of RNA-associated proteins from embryonic tissues.
    Keywords RNA ; Xenopus ; dynein ATPase ; epithelium ; homeostasis ; mitotic spindle apparatus ; proteome ; vertebrates
    Language English
    Dates of publication 2020-1101
    Size p. 108-117.
    Publishing place Elsevier Inc.
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 1114-9
    ISSN 1095-564X ; 0012-1606
    ISSN (online) 1095-564X
    ISSN 0012-1606
    DOI 10.1016/j.ydbio.2020.08.008
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  4. Article ; Online: Functional partitioning of a liquid-like organelle during assembly of axonemal dyneins.

    Lee, Chanjae / Cox, Rachael M / Papoulas, Ophelia / Horani, Amjad / Drew, Kevin / Devitt, Caitlin C / Brody, Steven L / Marcotte, Edward M / Wallingford, John B

    eLife

    2020  Volume 9

    Abstract: Ciliary motility is driven by axonemal dyneins that are assembled in the cytoplasm before deployment to cilia. Motile ciliopathy can result from defects in the dyneins themselves or from defects in factors required for their cytoplasmic pre-assembly. ... ...

    Abstract Ciliary motility is driven by axonemal dyneins that are assembled in the cytoplasm before deployment to cilia. Motile ciliopathy can result from defects in the dyneins themselves or from defects in factors required for their cytoplasmic pre-assembly. Recent work demonstrates that axonemal dyneins, their specific assembly factors, and broadly-acting chaperones are concentrated in liquid-like organelles in the cytoplasm called DynAPs (Dynein Axonemal Particles). Here, we use
    MeSH term(s) Animals ; Axonemal Dyneins/metabolism ; Cilia/metabolism ; Cytoplasm/metabolism ; Immunoprecipitation ; Mass Spectrometry ; Organelles/metabolism ; Tandem Affinity Purification ; Xenopus laevis/embryology
    Chemical Substances Axonemal Dyneins (EC 3.6.4.2)
    Language English
    Publishing date 2020-12-02
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.58662
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  5. Article ; Online: A systematic, label-free method for identifying RNA-associated proteins in vivo provides insights into vertebrate ciliary beating machinery.

    Drew, Kevin / Lee, Chanjae / Cox, Rachael M / Dang, Vy / Devitt, Caitlin C / McWhite, Claire D / Papoulas, Ophelia / Huizar, Ryan L / Marcotte, Edward M / Wallingford, John B

    Developmental biology

    2020  Volume 467, Issue 1-2, Page(s) 108–117

    Abstract: Cell-type specific RNA-associated proteins are essential for development and homeostasis in animals. Despite a massive recent effort to systematically identify RNA-associated proteins, we currently have few comprehensive rosters of cell-type specific RNA- ...

    Abstract Cell-type specific RNA-associated proteins are essential for development and homeostasis in animals. Despite a massive recent effort to systematically identify RNA-associated proteins, we currently have few comprehensive rosters of cell-type specific RNA-associated proteins in vertebrate tissues. Here, we demonstrate the feasibility of determining the RNA-associated proteome of a defined vertebrate embryonic tissue using DIF-FRAC, a systematic and universal (i.e., label-free) method. Application of DIF-FRAC to cultured tissue explants of Xenopus mucociliary epithelium identified dozens of known RNA-associated proteins as expected, but also several novel RNA-associated proteins, including proteins related to assembly of the mitotic spindle and regulation of ciliary beating. In particular, we show that the inner dynein arm tether Cfap44 is an RNA-associated protein that localizes not only to axonemes, but also to liquid-like organelles in the cytoplasm called DynAPs. This result led us to discover that DynAPs are generally enriched for RNA. Together, these data provide a useful resource for a deeper understanding of mucociliary epithelia and demonstrate that DIF-FRAC will be broadly applicable for systematic identification of RNA-associated proteins from embryonic tissues.
    MeSH term(s) Animals ; Cilia/metabolism ; Embryo, Nonmammalian/metabolism ; Epithelium/embryology ; RNA-Binding Proteins/metabolism ; Tissue Culture Techniques ; Xenopus ; Xenopus Proteins/metabolism
    Chemical Substances RNA-Binding Proteins ; Xenopus Proteins
    Language English
    Publishing date 2020-09-06
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1114-9
    ISSN 1095-564X ; 0012-1606
    ISSN (online) 1095-564X
    ISSN 0012-1606
    DOI 10.1016/j.ydbio.2020.08.008
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    Zs.B 508: Show issues Location:
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  6. Article: Fluorescent Probes for Tracking the Transfer of Iron–Sulfur Cluster and Other Metal Cofactors in Biosynthetic Reaction Pathways

    Vranish, James N / Barondeau David P / Cox Rachael M / Russell David H / Russell William K / Yu Lusa E

    Journal of the American Chemical Society. 2015 Jan. 14, v. 137, no. 1

    2015  

    Abstract: Iron–sulfur (Fe–S) clusters are protein cofactors that are constructed and delivered to target proteins by elaborate biosynthetic machinery. Mechanistic insights into these processes have been limited by the lack of sensitive probes for tracking Fe– ...

    Abstract Iron–sulfur (Fe–S) clusters are protein cofactors that are constructed and delivered to target proteins by elaborate biosynthetic machinery. Mechanistic insights into these processes have been limited by the lack of sensitive probes for tracking Fe–S cluster synthesis and transfer reactions. Here we present fusion protein- and intein-based fluorescent labeling strategies that can probe Fe–S cluster binding. The fluorescence is sensitive to different cluster types ([2Fe–2S] and [4Fe–4S] clusters), ligand environments ([2Fe–2S] clusters on Rieske, ferredoxin (Fdx), and glutaredoxin), and cluster oxidation states. The power of this approach is highlighted with an extreme example in which the kinetics of Fe–S cluster transfer reactions are monitored between two Fdx molecules that have identical Fe–S spectroscopic properties. This exchange reaction between labeled and unlabeled Fdx is catalyzed by dithiothreitol (DTT), a result that was confirmed by mass spectrometry. DTT likely functions in a ligand substitution reaction that generates a [2Fe–2S]–DTT species, which can transfer the cluster to either labeled or unlabeled Fdx. The ability to monitor this challenging cluster exchange reaction indicates that real-time Fe–S cluster incorporation can be tracked for a specific labeled protein in multicomponent assays that include several unlabeled Fe–S binding proteins or other chromophores. Such advanced kinetic experiments are required to untangle the intricate networks of transfer pathways and the factors affecting flux through branch points. High sensitivity and suitability with high-throughput methodology are additional benefits of this approach. We anticipate that this cluster detection methodology will transform the study of Fe–S cluster pathways and potentially other metal cofactor biosynthetic pathways.
    Keywords binding proteins ; biochemical pathways ; biosynthesis ; detection limit ; dithiothreitol ; fluorescent dyes ; fluorescent labeling ; iron ; ligands ; mass spectrometry ; mechanistic models ; oxidation ; reaction kinetics ; reaction mechanisms ; spectral analysis ; sulfur
    Language English
    Dates of publication 2015-0114
    Size p. 390-398.
    Publishing place American Chemical Society
    Document type Article
    ZDB-ID 3155-0
    ISSN 1520-5126 ; 0002-7863
    ISSN (online) 1520-5126
    ISSN 0002-7863
    DOI 10.1021%2Fja510998s
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  7. Article ; Online: A Pan-plant Protein Complex Map Reveals Deep Conservation and Novel Assemblies.

    McWhite, Claire D / Papoulas, Ophelia / Drew, Kevin / Cox, Rachael M / June, Viviana / Dong, Oliver Xiaoou / Kwon, Taejoon / Wan, Cuihong / Salmi, Mari L / Roux, Stanley J / Browning, Karen S / Chen, Z Jeffrey / Ronald, Pamela C / Marcotte, Edward M

    Cell

    2020  Volume 181, Issue 2, Page(s) 460–474.e14

    Abstract: Plants are foundational for global ecological and economic systems, but most plant proteins remain uncharacterized. Protein interaction networks often suggest protein functions and open new avenues to characterize genes and proteins. We therefore ... ...

    Abstract Plants are foundational for global ecological and economic systems, but most plant proteins remain uncharacterized. Protein interaction networks often suggest protein functions and open new avenues to characterize genes and proteins. We therefore systematically determined protein complexes from 13 plant species of scientific and agricultural importance, greatly expanding the known repertoire of stable protein complexes in plants. By using co-fractionation mass spectrometry, we recovered known complexes, confirmed complexes predicted to occur in plants, and identified previously unknown interactions conserved over 1.1 billion years of green plant evolution. Several novel complexes are involved in vernalization and pathogen defense, traits critical for agriculture. We also observed plant analogs of animal complexes with distinct molecular assemblies, including a megadalton-scale tRNA multi-synthetase complex. The resulting map offers a cross-species view of conserved, stable protein assemblies shared across plant cells and provides a mechanistic, biochemical framework for interpreting plant genetics and mutant phenotypes.
    MeSH term(s) Mass Spectrometry/methods ; Plant Proteins/genetics ; Plant Proteins/metabolism ; Plants/genetics ; Plants/metabolism ; Protein Interaction Mapping/methods ; Protein Interaction Maps/physiology ; Proteomics/methods
    Chemical Substances Plant Proteins
    Language English
    Publishing date 2020-03-18
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2020.02.049
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  8. Article ; Online: Fluorescent probes for tracking the transfer of iron-sulfur cluster and other metal cofactors in biosynthetic reaction pathways.

    Vranish, James N / Russell, William K / Yu, Lusa E / Cox, Rachael M / Russell, David H / Barondeau, David P

    Journal of the American Chemical Society

    2014  Volume 137, Issue 1, Page(s) 390–398

    Abstract: Iron-sulfur (Fe-S) clusters are protein cofactors that are constructed and delivered to target proteins by elaborate biosynthetic machinery. Mechanistic insights into these processes have been limited by the lack of sensitive probes for tracking Fe-S ... ...

    Abstract Iron-sulfur (Fe-S) clusters are protein cofactors that are constructed and delivered to target proteins by elaborate biosynthetic machinery. Mechanistic insights into these processes have been limited by the lack of sensitive probes for tracking Fe-S cluster synthesis and transfer reactions. Here we present fusion protein- and intein-based fluorescent labeling strategies that can probe Fe-S cluster binding. The fluorescence is sensitive to different cluster types ([2Fe-2S] and [4Fe-4S] clusters), ligand environments ([2Fe-2S] clusters on Rieske, ferredoxin (Fdx), and glutaredoxin), and cluster oxidation states. The power of this approach is highlighted with an extreme example in which the kinetics of Fe-S cluster transfer reactions are monitored between two Fdx molecules that have identical Fe-S spectroscopic properties. This exchange reaction between labeled and unlabeled Fdx is catalyzed by dithiothreitol (DTT), a result that was confirmed by mass spectrometry. DTT likely functions in a ligand substitution reaction that generates a [2Fe-2S]-DTT species, which can transfer the cluster to either labeled or unlabeled Fdx. The ability to monitor this challenging cluster exchange reaction indicates that real-time Fe-S cluster incorporation can be tracked for a specific labeled protein in multicomponent assays that include several unlabeled Fe-S binding proteins or other chromophores. Such advanced kinetic experiments are required to untangle the intricate networks of transfer pathways and the factors affecting flux through branch points. High sensitivity and suitability with high-throughput methodology are additional benefits of this approach. We anticipate that this cluster detection methodology will transform the study of Fe-S cluster pathways and potentially other metal cofactor biosynthetic pathways.
    MeSH term(s) Biosynthetic Pathways ; Catalysis ; Dithiothreitol/chemistry ; Dithiothreitol/metabolism ; Fluorescence ; Fluorescent Dyes/analysis ; Fluorescent Dyes/chemistry ; Iron-Sulfur Proteins/chemistry ; Iron-Sulfur Proteins/metabolism ; Kinetics
    Chemical Substances Fluorescent Dyes ; Iron-Sulfur Proteins ; Dithiothreitol (T8ID5YZU6Y)
    Language English
    Publishing date 2014-12-24
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 3155-0
    ISSN 1520-5126 ; 0002-7863
    ISSN (online) 1520-5126
    ISSN 0002-7863
    DOI 10.1021/ja510998s
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