Phospholipase D: molecular and cell biology of a novel gene family

Interaction of extracellular-signal molecules with cell-surface receptors often activates a phospholipase D (PLD)-mediated hydrolysis of phosphatidylcholine and other phospholipids, generating phosphatidic acid. The activation of PLD is believed to play an important role in the regulation of cell function and cell fate. Multiple PLD activities were characterized in eukaryotic cells, and, more recently, several PLD genes have been cloned. A PLD gene superfamily, defined by a number of structural domains and sequence motifs, also includes phosphatidyltransferases and certain phosphodiesterases. Among the eukaryotic PLD genes are those from mammals, nematodes, fungi and plants. The present review focuses on the structure, localization, regulation and possible functions of cloned mammalian and yeast PLDs. In addition, an overview of plant PLD genes, and of several distinct PLD activities that have not yet been cloned, is provided. Emerging evidence from recent work employing new molecular tools indicates that different PLD isoforms are localized in distinct cellular organelles, where they are likely to serve diverse functions in signal transduction, membrane vesicle trafficking and cytoskeletal dynamics.

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The Crk adapter protein is essential for Drosophila embryogenesis, where it regulates multiple actin-dependent morphogenic events

10.1101/654558 ◽

2019 ◽

Author(s):

Andrew J. Spracklen ◽

Emma M. Thornton-Kolbe ◽

Alison N. Bonner ◽

Alexandru Florea ◽

Peter J. Compton ◽

...

Keyword(s):

Cell Fate ◽

Neuronal Development ◽

Adapter Proteins ◽

Mitotic Spindles ◽

Fourth Chromosome ◽

Oncogenic Signaling ◽

Surface Receptors ◽

Downstream Signaling ◽

Cytoskeletal Dynamics ◽

And Behavior

AbstractSmall SH2/SH3 adapter proteins regulate cell fate and behavior by mediating interactions between cell surface receptors and downstream signaling effectors in many signal transduction pathways. The Crk family has tissue-specific roles in phagocytosis, cell migration and neuronal development, and mediates oncogenic signaling in pathways like that of Abelson kinase. However, redundancy among the two mammalian family members and the position of the Drosophila gene on the fourth chromosome precluded assessment of Crk’s full role in embryogenesis. We circumvented these limitations with shRNA and CRISPR technology to assess Crk’s function in Drosophila morphogenesis. We found Crk is essential beginning in the first few hours of development, where it ensures accurate mitosis by regulating orchestrated dynamics of the actin cytoskeleton to keep mitotic spindles in syncytial embryos from colliding. In this role, it positively regulates levels of the Arp2/3 complex, its regulator SCAR, and F-actin in actin caps and pseudocleavage furrows. Crk loss leads to loss of nuclei and formation of multinucleate cells. We also found roles for Crk in embryonic wound healing and in axon patterning in the nervous system, where it localizes to the axons and midline glia. Thus, Crk regulates diverse events in embryogenesis that require orchestrated cytoskeletal dynamics.

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Whole-genome-scale identification of novel non-protein-coding RNAs controlling cell proliferation and survival through a functional forward genetics strategy

Scientific Reports ◽

10.1038/s41598-021-03983-5 ◽

2022 ◽

Vol 12 (1) ◽

Author(s):

D. P. Tonge ◽

D. Darling ◽

F. Farzaneh ◽

G. T. Williams

Keyword(s):

Cell Proliferation ◽

Cell Fate ◽

Cell Biology ◽

Cell Function ◽

Forward Genetics ◽

Expression Library ◽

Protein Coding ◽

Sense Orientation ◽

Induced Apoptosis ◽

Genome Scale

AbstractIdentification of cell fate-controlling lncRNAs is essential to our understanding of molecular cell biology. Here we present a human genome-scale forward-genetics approach for the identification of lncRNAs based on gene function. This approach can identify genes that play a causal role, and immediately distinguish them from those that are differentially expressed but do not affect cell function. Our genome-scale library plus next-generation-sequencing and bioinformatic approach, radically upscales the breadth and rate of functional ncRNA discovery. Human gDNA was digested to produce a lentiviral expression library containing inserts in both sense and anti-sense orientation. The library was used to transduce human Jurkat T-leukaemic cells. Cell populations were selected using continuous culture ± anti-FAS IgM, and sequencing used to identify sequences controlling cell proliferation. This strategy resulted in the identification of thousands of new sequences based solely on their function including many ncRNAs previously identified as being able to modulate cell survival or to act as key cancer regulators such as AC084816.1*, AC097103.2, AC087473.1, CASC15*, DLEU1*, ENTPD1-AS1*, HULC*, MIRLET7BHG*, PCAT-1, SChLAP1, and TP53TG1. Independent validation confirmed 4 out of 5 sequences that were identified by this strategy, conferred a striking resistance to anti-FAS IgM-induced apoptosis.

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Receptor Tyrosine Kinases in Development: Insights from Drosophila

International Journal of Molecular Sciences ◽

10.3390/ijms21010188 ◽

2019 ◽

Vol 21 (1) ◽

pp. 188 ◽

Cited By ~ 1

Author(s):

Sarah Mele ◽

Travis K. Johnson

Keyword(s):

Cell Surface ◽

Cell Fate ◽

Tyrosine Kinases ◽

Cell Biology ◽

Receptor Tyrosine Kinases ◽

Cell Communication ◽

Model Organisms ◽

Cell Surface Receptors ◽

Surface Receptors ◽

Cell Fate Decisions

Cell-to-cell communication mediates a plethora of cellular decisions and behaviors that are crucial for the correct and robust development of multicellular organisms. Many of these signals are encoded in secreted hormones or growth factors that bind to and activate cell surface receptors, to transmit the cue intracellularly. One of the major superfamilies of cell surface receptors are the receptor tyrosine kinases (RTKs). For nearly half a century RTKs have been the focus of intensive study due to their ability to alter fundamental aspects of cell biology, such as cell proliferation, growth, and shape, and because of their central importance in diseases such as cancer. Studies in model organisms such a Drosophila melanogaster have proved invaluable for identifying new conserved RTK pathway components, delineating their contributions, and for the discovery of conserved mechanisms that control RTK-signaling events. Here we provide a brief overview of the RTK superfamily and the general mechanisms used in their regulation. We further highlight the functions of several RTKs that govern distinct cell-fate decisions in Drosophila and explore how their activities are developmentally controlled.

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The Crk adapter protein is essential for Drosophila embryogenesis, where it regulates multiple actin-dependent morphogenic events

Molecular Biology of the Cell ◽

10.1091/mbc.e19-05-0302 ◽

2019 ◽

Vol 30 (18) ◽

pp. 2399-2421 ◽

Cited By ~ 1

Author(s):

Andrew J. Spracklen ◽

Emma M. Thornton-Kolbe ◽

Alison N. Bonner ◽

Alexandru Florea ◽

Peter J. Compton ◽

...

Keyword(s):

Cell Fate ◽

Neuronal Development ◽

Adapter Proteins ◽

Filamentous Actin ◽

Fourth Chromosome ◽

Oncogenic Signaling ◽

Surface Receptors ◽

Downstream Signaling ◽

Cytoskeletal Dynamics ◽

Camp Receptor

Small Src homology domain 2 (SH2) and 3 (SH3) adapter proteins regulate cell fate and behavior by mediating interactions between cell surface receptors and downstream signaling effectors in many signal transduction pathways. The CT10 regulator of kinase (Crk) family has tissue-specific roles in phagocytosis, cell migration, and neuronal development and mediates oncogenic signaling in pathways like that of Abelson kinase. However, redundancy among the two mammalian family members and the position of the Drosophila gene on the fourth chromosome precluded assessment of Crk’s full role in embryogenesis. We circumvented these limitations with short hairpin RNA and CRISPR technology to assess Crk’s function in Drosophila morphogenesis. We found that Crk is essential beginning in the first few hours of development, where it ensures accurate mitosis by regulating orchestrated dynamics of the actin cytoskeleton to keep mitotic spindles in syncytial embryos from colliding. In this role, it positively regulates cortical localization of the actin-related protein 2/3 complex (Arp2/3), its regulator suppressor of cAMP receptor (SCAR), and filamentous actin to actin caps and pseudocleavage furrows. Crk loss leads to the loss of nuclei and formation of multinucleate cells. We also found roles for Crk in embryonic wound healing and in axon patterning in the nervous system, where it localizes to the axons and midline glia. Thus, Crk regulates diverse events in embryogenesis that require orchestrated cytoskeletal dynamics.

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The Cellular Senescence Stress Response in Post-Mitotic Brain Cells: Cell Survival at the Expense of Tissue Degeneration

Life ◽

10.3390/life11030229 ◽

2021 ◽

Vol 11 (3) ◽

pp. 229

Author(s):

Eric Sah ◽

Sudarshan Krishnamurthy ◽

Mohamed Y. Ahmidouch ◽

Gregory J. Gillispie ◽

Carol Milligan ◽

...

Keyword(s):

Stress Response ◽

Cell Fate ◽

Cellular Senescence ◽

Cell Biology ◽

Brain Aging ◽

Complex Stress ◽

Brain Cell ◽

Tissue Degeneration ◽

Cellular Dna

In 1960, Rita Levi-Montalcini and Barbara Booker made an observation that transformed neuroscience: as neurons mature, they become apoptosis resistant. The following year Leonard Hayflick and Paul Moorhead described a stable replicative arrest of cells in vitro, termed “senescence”. For nearly 60 years, the cell biology fields of neuroscience and senescence ran in parallel, each separately defining phenotypes and uncovering molecular mediators to explain the 1960s observations of their founding mothers and fathers, respectively. During this time neuroscientists have consistently observed the remarkable ability of neurons to survive. Despite residing in environments of chronic inflammation and degeneration, as occurs in numerous neurodegenerative diseases, often times the neurons with highest levels of pathology resist death. Similarly, cellular senescence (hereon referred to simply as “senescence”) now is recognized as a complex stress response that culminates with a change in cell fate. Instead of reacting to cellular/DNA damage by proliferation or apoptosis, senescent cells survive in a stable cell cycle arrest. Senescent cells simultaneously contribute to chronic tissue degeneration by secreting deleterious molecules that negatively impact surrounding cells. These fields have finally collided. Neuroscientists have begun applying concepts of senescence to the brain, including post-mitotic cells. This initially presented conceptual challenges to senescence cell biologists. Nonetheless, efforts to understand senescence in the context of brain aging and neurodegenerative disease and injury emerged and are advancing the field. The present review uses pre-defined criteria to evaluate evidence for post-mitotic brain cell senescence. A closer interaction between neuro and senescent cell biologists has potential to advance both disciplines and explain fundamental questions that have plagued their fields for decades.

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Conditionally immortalised leukaemia initiating cells co-expressing Hoxa9/Meis1 demonstrate microenvironmental adaptation properties ex vivo while maintaining myelomonocytic memory

Scientific Reports ◽

10.1038/s41598-021-84468-3 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Maike Stahlhut ◽

Teng Cheong Ha ◽

Ekaterina Takmakova ◽

Michael A. Morgan ◽

Adrian Schwarzer ◽

...

Keyword(s):

Stem Cell ◽

Cell Fate ◽

Cell Lines ◽

Cell Biology ◽

Ex Vivo ◽

Haematopoietic Stem Cell ◽

Transcriptional Dysregulation ◽

Conditional Gene Expression ◽

Exponential Expansion ◽

Drug Dependent

AbstractRegulation of haematopoietic stem cell fate through conditional gene expression could improve understanding of healthy haematopoietic and leukaemia initiating cell (LIC) biology. We established conditionally immortalised myeloid progenitor cell lines co-expressing constitutive Hoxa9.EGFP and inducible Meis1.dTomato (H9M-ciMP) to study growth behaviour, immunophenotype and morphology under different cytokine/microenvironmental conditions ex vivo upon doxycycline (DOX) induction or removal. The vector design and drug-dependent selection approach identified new retroviral insertion (RVI) sites that potentially collaborate with Meis1/Hoxa9 and define H9M-ciMP fate. For most cell lines, myelomonocytic conditions supported reversible H9M-ciMP differentiation into neutrophils and macrophages with DOX-dependent modulation of Hoxa9/Meis1 and CD11b/Gr-1 expression. Here, up-regulation of Meis1/Hoxa9 promoted reconstitution of exponential expansion of immature H9M-ciMPs after DOX reapplication. Stem cell maintaining conditions supported selective H9M-ciMP exponential growth. H9M-ciMPs that had Ninj2 RVI and were cultured under myelomonocytic or stem cell maintaining conditions revealed the development of DOX-dependent acute myeloid leukaemia in a murine transplantation model. Transcriptional dysregulation of Ninj2 and distal genes surrounding RVI (Rad52, Kdm5a) was detected. All studied H9M-ciMPs demonstrated adaptation to T-lymphoid microenvironmental conditions while maintaining immature myelomonocytic features. Thus, the established system is relevant to leukaemia and stem cell biology.

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Cyto-friendly polymerization at cell surfaces modulates cell fate by clustering cell-surface receptors

Chemical Science ◽

10.1039/c9sc06385d ◽

2020 ◽

Vol 11 (16) ◽

pp. 4221-4225 ◽

Cited By ~ 1

Author(s):

Jing Qi ◽

Weishuo Li ◽

Xiaoling Xu ◽

Feiyang Jin ◽

Di Liu ◽

...

Keyword(s):

Cell Surface ◽

Cell Fate ◽

Cell Surface Receptors ◽

Cell Surfaces ◽

Receptor Clustering ◽

Surface Polymerization ◽

Surface Receptors ◽

Anti Cd20 ◽

In Cells

Cell-surface polymerization of anti-CD20 aptamer modified macromer to induce CD20 receptor clustering, and effectively initiate the apoptotic signals in cells.

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II. One size fits all: nonclassical MHC molecules fulfill multiple roles in epithelial cell function

AJP Gastrointestinal and Liver Physiology ◽

10.1152/ajpgi.1998.274.2.g227 ◽

1998 ◽

Vol 274 (2) ◽

pp. G227-G231 ◽

Cited By ~ 3

Author(s):

Richard S. Blumberg

Keyword(s):

Epithelial Cell ◽

Mhc Class I ◽

Cell Biology ◽

Cell Function ◽

Surface Glycoprotein ◽

Class I ◽

Human Major Histocompatibility Complex ◽

Cell Surface Glycoprotein ◽

Mhc Molecules ◽

Nonclassical Mhc

The human major histocompatibility complex (MHC) on chromosome 6 encodes three classical class I genes: human leukocyte antigen-A (HLA-A), HLA-B, and HLA-C. These polymorphic genes encode a 43- to 45-kDa cell surface glycoprotein that, in association with the 12-kDa β2-microglobulin molecule, functions in the presentation of nine amino acid peptides to the T cell receptor of CD8-bearing T lymphocytes and killer inhibitory receptors on natural killer cells. In addition to these ubiquitously expressed polymorphic proteins, the human genome also encodes a number of nonclassical MHC class I-like, or class Ib, genes that in general encode nonpolymorphic molecules involved in a variety of specific immunologic functions. Many of these genes, including CD1, the neonatal Fc receptor for immunoglobulin G, HLA-G, the MHC class I chain-related gene A, and Hfe, are prominently displayed on epithelial cells, suggesting an important role in epithelial cell biology.

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COUP-TFII Regulates Human Endometrial Stromal Genes Involved in Inflammation

Molecular Endocrinology ◽

10.1210/me.2013-1191 ◽

2013 ◽

Vol 27 (12) ◽

pp. 2041-2054 ◽

Cited By ~ 32

Author(s):

Xilong Li ◽

Michael J. Large ◽

Chad J. Creighton ◽

Rainer B. Lanz ◽

Jae-Wook Jeong ◽

...

Keyword(s):

Cell Fate ◽

Cell Biology ◽

Embryo Implantation ◽

Orphan Nuclear Receptor ◽

Loss Of Function ◽

Mouse Uterus ◽

Endometrial Stromal Cells ◽

Endometrial Stroma ◽

Stroma Cell

Chicken ovalbumin upstream promoter-transcription factor II (COUP-TFII; NR2F2) is an orphan nuclear receptor involved in cell-fate specification, organogenesis, angiogenesis, and metabolism. Ablation of COUP-TFII in the mouse uterus causes infertility due to defects in embryo attachment and impaired uterine stromal cell decidualization. Although the function of COUP-TFII in uterine decidualization has been described in mice, its role in the human uterus remains unknown. We observed that, as in mice, COUP-TFII is robustly expressed in the endometrial stroma of healthy women, and its expression is reduced in the ectopic lesions of women with endometriosis. To interrogate the role of COUP-TFII in human endometrial function, we used a small interfering RNA-mediated loss of function approach in primary human endometrial stromal cells. Attenuation of COUP-TFII expression did not completely block decidualization; rather it had a selective effect on gene expression. To better elucidate the role of COUP-TFII in endometrial stroma cell biology, the COUP-TFII transcriptome was defined by pairing microarray comparison with chromatin immunoprecipitation followed by deep sequencing. Gene ontology analysis demonstrates that COUP-TFII regulates a subset of genes in endometrial stroma cell decidualization such as those involved in cell adhesion, angiogenesis, and inflammation. Importantly this analysis shows that COUP-TFII plays a role in controlling the expression of inflammatory cytokines. The determination that COUP-TFII plays a role in inflammation may add insight into the role of COUP-TFII in embryo implantation and in endometrial diseases such as endometriosis.

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Gene-free methodology for cell fate dynamics during development

eLife ◽

10.7554/elife.30743 ◽

2017 ◽

Vol 6 ◽

Cited By ~ 12

Author(s):

Francis Corson ◽

Eric D Siggia

Keyword(s):

Cell Fate ◽

Cell Function ◽

Geometric Model ◽

Model Fit ◽

Vulval Development ◽

Epistatic Interactions ◽

Compact Representations ◽

Special Points ◽

Unexpected Outcomes

Models of cell function that assign a variable to each gene frequently lead to systems of equations with many parameters whose behavior is obscure. Geometric models reduce dynamics to intuitive pictorial elements that provide compact representations for sparse in vivo data and transparent descriptions of developmental transitions. To illustrate, a geometric model fit to vulval development in Caenorhabditis elegans, implies a phase diagram where cell-fate choices are displayed in a plane defined by EGF and Notch signaling levels. This diagram defines allowable and forbidden cell-fate transitions as EGF or Notch levels change, and explains surprising observations previously attributed to context-dependent action of these signals. The diagram also reveals the existence of special points at which minor changes in signal levels lead to strong epistatic interactions between EGF and Notch. Our model correctly predicts experiments near these points and suggests specific timed perturbations in signals that can lead to additional unexpected outcomes.

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