Adam D. Hoppe

South Dakota State University

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Jason G. Kerkvliet

South Dakota State University

Brandon L. Scott

South Dakota School of Mines and Technology

Joel A. Swanson

University of Michigan–Ann Arbor

Elizabeth M. Bailey

South Dakota State University

R. Blachnik

Osnabrück University

Natalie W. Thiex

South Dakota State University

Lu Huang

University of Arkansas for Medical Sciences

R. B. Anderson

South Dakota School of Mines and Technology

Harika Vuppula

South Dakota State University

Steven J. Smith

Joint Global Change Research Institute

Cooperative Institutions

South Dakota State University

University of Michigan–Ann Arbor

Yale University

Michigan United

South Dakota School of Mines and Technology

National Institutes of Health

University of South Dakota

University of Nebraska Medical Center

Harvard University

Centre National de la Recherche Scientifique

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Prediction of regulatory motifs from human Chip-sequencing data using a deep learning framework

Nucleic Acids Research (2019)

Jinyu Yang Anjun Ma Adam D. Hoppe Cankun Wang Yang Li

Abstract The identification of transcription factor binding sites and cis-regulatory motifs is a frontier whereupon the rules governing protein–DNA binding are being revealed. Here, we developed a new method (DEep Sequence and Shape mOtif or DESSO) for cis-regulatory motif prediction using deep neural networks and the binomial distribution model. DESSO outperformed existing tools, including DeepBind, in predicting motifs in 690 human ENCODE ChIP-sequencing datasets. Furthermore, the deep-learning framework of DESSO expanded motif discovery beyond the state-of-the-art by allowing the identification of known and new protein–protein–DNA tethering interactions in human transcription factors (TFs). Specifically, 61 putative tethering interactions were identified among the 100 TFs expressed in the K562 cell line. In this work, the power of DESSO was further expanded by integrating the detection of DNA shape features. We found that shape information has strong predictive power for TF–DNA binding and provides new putative shape motif information for human TFs. Thus, DESSO improves in the identification and structural analysis of TF binding sites, by integrating the complexities of DNA binding into a deep-learning framework.

ENCODE

Sequence motif

DNA binding site

Motif (music)

10.1093/nar/gkz672

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Citations (67)

SlyD: A novel epitope-presenting thermostable scaffold for the development of highly specific IGF-1/-2 antibodies

Clinica Chimica Acta (2019)

Carmen Peeß D. Casagolda Vallribera Michael Gerg Frank Kowalewsky C. Scholz

10.1016/j.cca.2019.03.737

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The coordination of signaling during Fc receptor-mediated phagocytosis

Journal of Leukocyte Biology (2004)

Joel A. Swanson Adam D. Hoppe

Abstract Phagocytosis by macrophages can be initiated by Fcγ receptors (FcR) in membranes that bind to Fc regions of immunoglobulin G (IgG). Activated FcR transduce signals to cytoplasm, which regulate the internalization of IgG-coated particles into plasma membrane-derived vacuoles, phagosomes. Particles internalized by phagocytosis are much larger than FcR, which prompts questions of if and how the receptors are coordinated with each other. FcR-mediated signal transduction entails recruitment of proteins from cytoplasm to the receptor, largely via protein phosphorylation. These FcR signaling complexes then activate proteins that regulate actin, myosin, membrane fusion, and the production of reactive oxygen intermediates. Recent fluorescence microscopic studies of phagocytosis in macrophages indicate that signaling by FcR occurs as a sequence of distinct stages, evident in the spatial and temporal patterns of phosphoinositides, protein kinase C, and Rho-family GTPase activation on forming phagosomes. The coordination of these stages may be regulated by lipids or lipid-anchored proteins, which diffuse away from FcR complexes. Lateral diffusion of FcR-derived signals could integrate FcR-dependent responses over large areas of membrane in the forming phagosome.

Internalization

Fc receptor

10.1189/jlb.0804439

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Citations (321)

Delivery of the CSF-1R to the lumen of macropinosomes promotes its destruction in macrophages

Journal of Cell Science (2014)

Jieqiong Lou Shalini T. Low-Nam Jason G. Kerkvliet Adam D. Hoppe

Activation of the macrophage Colony Stimulating Factor-1 Receptor (CSF-1R) by CSF-1 stimulates pronounced macropinocytosis and drives proliferation of macrophages. While the role of macropinocytosis in CSF-1R signaling remains unknown, we show that despite internalizing large quantities of plasma membrane, macropinosomes contribute little to the internalization of the CSF-1/CSF-1R complex. Rather, internalization of the CSF-1R in small, endocytic vesicles, sensitive to clathrin disruption, out-compete macropinosomes for CSF-1R endocytosis. Following internalization, small vesicles carrying the CSF-1R underwent homotypic fusion and then trafficked to newly formed macropinosomes bearing Rab5. As these macropinosomes matured, acquiring Rab7, the CSF-1R was transported into their lumen, and degraded. Inhibition of macropinocytosis delayed receptor degradation despite no disruption of CSF-1R endocytosis. These data indicate that CSF-1-stimulated macropinosomes are sites of multivesicular body formation and accelerate CSF-1R degradation. Further, we demonstrate that macropinocytosis and cell growth have a matching dose dependence on CSF-1, suggesting that macropinosomes may be a central mechanism coupling CSF-1R signaling and macrophage growth.

Pinocytosis

Internalization

10.1242/jcs.154393

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Citations (32)

Gga/Clathrin‐Dependent Transport from the TGN to the Late Endosome/Prevacuolar Compartment

The FASEB Journal (2008)

Robert S. Fuller Mohamed E. Abazeed Adam D. Hoppe Xuefeng Zhang Anuj Kumar

Localization of membrane proteins (Kex2p, Vps10p) to the trans Golgi network (TGN) in yeast requires vesicular transport between the TGN and endosomes. While Vps10p follows a direct pathway between the TGN and the late endosome/prevacuolar compartment (PVC), Kex2p partitions between this pathway and an indirect pathway through the early endosome. Using cell‐free reconstitution of TGN‐PVC transport [Abazeed, M.E., et al. (2005) J. Biol. Chem., 280:4442–50], we now find that the direct pathway requires the Gga1/2 clathrin adapators, in addition to clathrin, the dynamin homolog Vps1p, the Vps21p GTPase, the SM protein Vps45p and the PVC syntaxin Pep12p, but is independent of AP‐1 2‐hybrid analysis identifies sites in the Kex2p and Vps10p C‐tails that bind the Gga2p VHS domain. Mutation of the Gga binding site in Kex2p alters Kex2p localization as judged by a sensitive mating assay. To study TGN‐PVC transport in vivo, we are employing quantitative fluorescence resonance energy transfer (FRET) microscopy using donor and acceptor C‐terminal fluorescent protein fusions created in haploids by integrative recombination of Venus YFP and mCherry RFP. Microscopic analysis utilizes “Fast 4D” FRET stoichiometry combined with algorithms for mathematical elimination of autofluorescence. Using this method we have visualized the real‐time interaction between Gga2p and the Arf1 GTPase. Support was from NIH RO1 GM50957.

Transport protein

Yellow fluorescent protein

10.1096/fasebj.22.1_supplement.628.6

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Bulletin of the American Physical Society (2017)

Steve Smith Amy Hor Anh Luu Lin Kang Brandon L. Scott

Source

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Ezrin drives adaptation of monocytes to the inflamed lung microenvironment

Cell Death and Disease (2024)

Ravindra Gudneppanavar Caterina Di Pietro Hasan Halit Öz Ping-Xia Zhang Ee-chun Cheng

Abstract Ezrin, an actin-binding protein, orchestrates the organization of the cortical cytoskeleton and plasma membrane during cell migration, adhesion, and proliferation. Its role in monocytes/macrophages (MΦs) is less understood. Here, we used a monocyte/MΦ-specific ezrin knock-out mouse model to investigate the contribution of ezrin to monocyte recruitment and adaptation to the lung extracellular matrix (ECM) in response to lipopolysaccharide (LPS). Our study revealed that LPS induces ezrin expression in monocytes/MΦs and is essential for monocytes to adhere to lung ECM, proliferate, and differentiate into tissue-resident interstitial MΦs. Mechanistically, the loss of ezrin in monocytes disrupts activation of focal adhesion kinase and AKT serine-threonine protein kinase signaling, essential for lung-recruited monocytes and monocyte-derived MΦs to adhere to the ECM, proliferate, and survive. In summary, our data show that ezrin plays a role beyond structural cellular support, influencing diverse monocytes/MΦ processes and signaling pathways during inflammation, facilitating their differentiation into tissue-resident macrophages.

Monocyte

10.1038/s41419-024-07255-8

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Cdc42, Rac1, and Rac2 Display Distinct Patterns of Activation during Phagocytosis

Molecular Biology of the Cell (2004)

Adam D. Hoppe Joel A. Swanson

The small G proteins Cdc42, Rac1, and Rac2 regulate the rearrangements of actin and membrane necessary for Fcgamma receptor-mediated phagocytosis by macrophages. Activated, GTP-bound Cdc42, Rac1, and Rac2 bind to the p21-binding domain (PBD) of PAK1, and this interaction provided a basis for microscopic methods to localize activation of these G proteins inside cells. Fluorescence resonance energy transfer-based stoichiometry of fluorescent chimeras of actin, PBD, Cdc42, Rac1, and Rac2 was used to quantify G protein activation relative to actin movements during phagocytosis of IgG-opsonized erythrocytes. The activation dynamics of endogenous G proteins, localized using yellow fluorescent protein-labeled PBD, was restricted to phagocytic cups, with a prominent spike of activation over an actin-poor region at the base of the cup. Refinements of fluorescence resonance energy transfer stoichiometry allowed calculation of the fractions of activated GTPases in forming phagosomes. Cdc42 activation was restricted to the leading margin of the cell, whereas Rac1 was active throughout the phagocytic cup. During phagosome closure, activation of Rac1 and Rac2 increased uniformly and transiently in the actin-poor region of phagosomal membrane. These distinct roles for Cdc42, Rac1, and Rac2 in the component activities of phagocytosis indicate mechanisms by which their differential regulation coordinates rearrangements of actin and membranes.

Rac GTP-Binding Proteins

CDC42

10.1091/mbc.e03-11-0847

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Citations (344)

Self-growth suppression in Bradyrhizobium diazoefficiens is caused by a diffusible antagonist

bioRxiv (Cold Spring Harbor Laboratory) (2024)

Armaan Kaur Sandhu Brady R. Fischer Senthil Subramanian Adam D. Hoppe Volker S. Brözel

Abstract Microbes in soil navigate interactions by recognizing kin, forming social groups, exhibiting antagonistic behavior, and engaging in competitive kin rivalry. Here, we investigated a novel phenomenon of self-growth suppression (sibling rivalry) observed in Bradyrhizobium diazoefficiens USDA 110. Swimming colonies of USDA 110 developed a distinct demarcation line and inter-colony zone when inoculated adjacent to each other. In addition to self, USDA 110 suppressed growth of other Bradyrhizobium strains and several other soil bacteria. We demonstrated that the phenomenon of sibling rivalry is due to growth suppression but not cell death. The cells in the inter-colony zone were culturable but have reduced respiratory activity, ATP levels and motility. The observed growth suppression was due to the presence of a diffusible effector compound. This effector was labile, preventing extraction, and identification, but it is unlikely a protein or a strong acid or base. This counterintuitive phenomenon of self-growth suppression suggests a strategic adaptation for conserving energy and resources in competitive soil environments. Bradyrhizobium’s utilization of antagonism including self-growth suppression likely provides a competitive advantage for long-term success in soil ecosystems.

10.1101/2024.06.01.596975

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CSF-1 receptor signalling is governed by pre-requisite EHD1 mediated receptor display on the macrophage cell surface

Cellular Signalling (2016)

Luke R. Cypher Timothy A. Bielecki Lu Huang Wei An Fany Iseka

10.1016/j.cellsig.2016.05.013

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Citations (13)