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Child JR, Hofler AC, Chen Q, Yang BH, Kristofich J, Zheng T, Hannigan MM, Elles AL, Reid DW, Nicchitta CV. Examining SRP pathway function in mRNA localization to the endoplasmic reticulum. RNA (NEW YORK, N.Y.) 2023; 29:1703-1724. [PMID: 37643813 PMCID: PMC10578483 DOI: 10.1261/rna.079643.123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 07/17/2023] [Indexed: 08/31/2023]
Abstract
Signal recognition particle (SRP) pathway function in protein translocation across the endoplasmic reticulum (ER) is well established; its role in RNA localization to the ER remains, however, unclear. In current models, mRNAs undergo translation- and SRP-dependent trafficking to the ER, with ER localization mediated via interactions between SRP-bound translating ribosomes and the ER-resident SRP receptor (SR), a heterodimeric complex comprising SRA, the SRP-binding subunit, and SRB, an integral membrane ER protein. To study SRP pathway function in RNA localization, SR knockout (KO) mammalian cell lines were generated and the consequences of SR KO on steady-state and dynamic mRNA localization examined. CRISPR/Cas9-mediated SRPRB KO resulted in profound destabilization of SRA. Pairing siRNA silencing of SRPRA in SRPRB KO cells yielded viable SR KO cells. Steady-state mRNA compositions and ER-localization patterns in parental and SR KO cells were determined by cell fractionation and deep sequencing. Notably, steady-state cytosol and ER mRNA compositions and partitioning patterns were largely unaltered by loss of SR expression. To examine SRP pathway function in RNA localization dynamics, the subcellular trafficking itineraries of newly exported mRNAs were determined by 4-thiouridine (4SU) pulse-labeling/4SU-seq/cell fractionation. Newly exported mRNAs were distinguished by high ER enrichment, with ER localization being SR-independent. Intriguingly, under conditions of translation initiation inhibition, the ER was the default localization site for all newly exported mRNAs. These data demonstrate that mRNA localization to the ER can be uncoupled from the SRP pathway function and reopen questions regarding the mechanism of RNA localization to the ER.
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Affiliation(s)
- Jessica R Child
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Alex C Hofler
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Qiang Chen
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Brenda H Yang
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - JohnCarlo Kristofich
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Tianli Zheng
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Molly M Hannigan
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Andrew L Elles
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - David W Reid
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Christopher V Nicchitta
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, USA
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2
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Packard M, Gilbert MC, Tetrault E, Albertson RC. Zebrafish crocc2 mutants exhibit divergent craniofacial shape, misregulated variability, and aberrant cartilage morphogenesis. Dev Dyn 2023; 252:1026-1045. [PMID: 37032317 PMCID: PMC10524572 DOI: 10.1002/dvdy.591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 03/21/2023] [Accepted: 03/29/2023] [Indexed: 04/11/2023] Open
Abstract
BACKGROUND Phenotypic variation is of paramount importance in development, evolution, and human health; however, the molecular mechanisms that influence organ shape and shape variability are not well understood. During craniofacial development, the behavior of skeletal precursors is regulated by both biochemical and environmental inputs, and the primary cilia play critical roles in transducing both types of signals. Here, we examine a gene that encodes a key constituent of the ciliary rootlets, crocc2, and its role in cartilage morphogenesis in larval zebrafish. RESULTS Geometric morphometric analysis of crocc2 mutants revealed altered craniofacial shapes and expanded variation. At the cellular level, we observed altered chondrocyte shapes and planar cell polarity across multiple stages in crocc2 mutants. Notably, cellular defects were specific to areas that experience direct mechanical input. Cartilage cell number, apoptosis, and bone patterning were not affected in crocc2 mutants. CONCLUSIONS Whereas "regulatory" genes are widely implicated in patterning the craniofacial skeleton, genes that encode "structural" aspects of the cell are increasingly implicated in shaping the face. Our results add crocc2 to this list, and demonstrate that it affects craniofacial geometry and canalizes phenotypic variation. We propose that it does so via mechanosensing, possibly through the ciliary rootlet. If true, this would implicate a new organelle in skeletal development and evolution.
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Affiliation(s)
- Mary Packard
- Department of Biology, University of Massachusetts, Amherst, MA 01003, U.S.A
| | - Michelle C. Gilbert
- Organismic and Evolutionary Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, U.S.A
- Current address, Department of Biology, Penn State University, University Park, PA 16802, U.S.A
| | - Emily Tetrault
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, U.S.A
| | - R. Craig Albertson
- Department of Biology, University of Massachusetts, Amherst, MA 01003, U.S.A
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3
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Gyanani V, Goswami R. Key Design Features of Lipid Nanoparticles and Electrostatic Charge-Based Lipid Nanoparticle Targeting. Pharmaceutics 2023; 15:pharmaceutics15041184. [PMID: 37111668 PMCID: PMC10144967 DOI: 10.3390/pharmaceutics15041184] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 04/02/2023] [Accepted: 04/03/2023] [Indexed: 04/29/2023] Open
Abstract
Lipid nanoparticles (LNP) have gained much attention after the approval of mRNA COVID-19 vaccines. The considerable number of currently ongoing clinical studies are testament to this fact. These efforts towards the development of LNPs warrant an insight into the fundamental developmental aspects of such systems. In this review, we discuss the key design aspects that confer efficacy to a LNP delivery system, i.e., potency, biodegradability, and immunogenicity. We also cover the underlying considerations regarding the route of administration and targeting of LNPs to hepatic and non-hepatic targets. Furthermore, since LNP efficacy is also a function of drug/nucleic acid release within endosomes, we take a holistic view of charged-based targeting approaches of LNPs not only in the context of endosomal escape but also in relation to other comparable target cell internalization strategies. Electrostatic charge-based interactions have been used in the past as a potential strategy to enhance the drug release from pH-sensitive liposomes. In this review, we cover such strategies around endosomal escape and cell internalization in low pH tumor micro-environments.
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Affiliation(s)
- Vijay Gyanani
- T.J.L. School of Pharmacy, University of the Pacific, Stockton, CA 95211, USA
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4
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Kumar A, Schrader AW, Boroojeny AE, Asadian M, Lee J, Song YJ, Zhao SD, Han HS, Sinha S. Intracellular Spatial Transcriptomic Analysis Toolkit (InSTAnT). RESEARCH SQUARE 2023:rs.3.rs-2481749. [PMID: 36747718 PMCID: PMC9901031 DOI: 10.21203/rs.3.rs-2481749/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Imaging-based spatial transcriptomics technologies such as MERFISH offer snapshots of cellular processes in unprecedented detail, but new analytic tools are needed to realize their full potential. We present InSTAnT, a computational toolkit for extracting molecular relationships from spatial transcriptomics data at the intra-cellular resolution. InSTAnT detects gene pairs and modules with interesting patterns of mutual co-localization within and across cells, using specialized statistical tests and graph mining. We showcase the toolkit on datasets profiling a human cancer cell line and hypothalamic preoptic region of mouse brain. We performed rigorous statistical assessment of discovered co-localization patterns, found supporting evidence from databases and RNA interactions, and identified subcellular domains associated with RNA-colocalization. We identified several novel cell type-specific gene co-localizations in the brain. Intra-cellular spatial patterns discovered by InSTAnT mirror diverse molecular relationships, including RNA interactions and shared sub-cellular localization or function, providing a rich compendium of testable hypotheses regarding molecular functions.
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Affiliation(s)
- Anurendra Kumar
- College of Computing, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Alex W. Schrader
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | | | - Marisa Asadian
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Juyeon Lee
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - You Jin Song
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Sihai Dave Zhao
- Department of Statistics, University of Illinois Urbana-Champaign, Urbana, IL, 61820, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Hee-Sun Han
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Saurabh Sinha
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- H. Milton Stewart School of Industrial & Systems Engineering, Georgia Institute of Technology, Atlanta, GA, 30318, USA
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5
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Yanagisawa M, Watanabe C, Yoshinaga N, Fujiwara K. Cell-Size Space Regulates the Behavior of Confined Polymers: From Nano- and Micromaterials Science to Biology. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:11811-11827. [PMID: 36125172 DOI: 10.1021/acs.langmuir.2c01397] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Polymer micromaterials in a liquid or gel phase covered with a surfactant membrane are widely used materials in pharmaceuticals, cosmetics, and foods. In particular, cell-sized micromaterials of biopolymer solutions covered with a lipid membrane have been studied as artificial cells to understand cells from a physicochemical perspective. The characteristics and phase transitions of polymers confined to a microscopic space often differ from those in bulk systems. The effect that causes this difference is referred to as the cell-size space effect (CSE), but the specific physicochemical factors remain unclear. This study introduces the analysis of CSE on molecular diffusion, nanostructure transition, and phase separation and presents their main factors, i.e., short- and long-range interactions with the membrane surface and small volume (finite element nature). This serves as a guide for determining the dominant factors of CSE. Furthermore, we also introduce other factors of CSE such as spatial closure and the relationships among space size, the characteristic length of periodicity, the structure size, and many others produced by biomolecular assemblies through the analysis of protein reaction-diffusion systems and biochemical reactions.
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Affiliation(s)
- Miho Yanagisawa
- Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo, Tokyo 113-0033, Japan
| | - Chiho Watanabe
- School of Integrated Arts and Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-7-1, Higashi-Hiroshima 739-8521, Japan
| | - Natsuhiko Yoshinaga
- Mathematical Science Group, WPI Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, Katahira 2-1-1, Aoba-Ku, Sendai 9808577, Japan
- MathAM-OIL, National Institute of Advanced Industrial Science and Technology, Sendai 980-8577, Japan
| | - Kei Fujiwara
- Department of Biosciences & Informatics, Keio University, Yokohama 223-8522, Japan
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6
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Angert I, Karuka SR, Mansky LM, Mueller JD. Partitioning of ribonucleoprotein complexes from the cellular actin cortex. SCIENCE ADVANCES 2022; 8:eabj3236. [PMID: 35984883 PMCID: PMC9390997 DOI: 10.1126/sciadv.abj3236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
The cell cortex plays a crucial role in cell mechanics, signaling, and development. However, little is known about the influence of the cortical meshwork on the spatial distribution of cytoplasmic biomolecules. Here, we describe a fluorescence microscopy method with the capacity to infer the intracellular distribution of labeled biomolecules with subresolution accuracy. Unexpectedly, we find that RNA binding proteins are partially excluded from the cytoplasmic volume adjacent to the plasma membrane that corresponds to the actin cortex. Complementary diffusion measurements of RNA-protein complexes suggest that a rudimentary model based on excluded volume interactions can explain this partitioning effect. Our results suggest the actin cortex meshwork may play a role in regulating the biomolecular content of the volume immediately adjacent to the plasma membrane.
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Affiliation(s)
- Isaac Angert
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, USA
- Institute of Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
- Division of Basic Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Siddarth Reddy Karuka
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Louis M. Mansky
- Institute of Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
- Division of Basic Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Joachim D. Mueller
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, USA
- Institute of Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
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7
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Nadkarni AV, Heald R. Reconstitution of muscle cell microtubule organization in vitro. Cytoskeleton (Hoboken) 2022; 78:492-502. [PMID: 35666041 DOI: 10.1002/cm.21710] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 05/31/2022] [Accepted: 06/01/2022] [Indexed: 11/06/2022]
Abstract
Skeletal muscle differentiation occurs as muscle precursor cells (myoblasts) elongate and fuse to form multinucleated syncytial myotubes in which the highly-organized actomyosin sarcomeres of muscle fibers assemble. Although less well characterized, the microtubule cytoskeleton also undergoes dramatic rearrangement during myogenesis. The centrosome-nucleated microtubule array found in myoblasts is lost as the nuclear membrane acquires microtubule nucleating activity and microtubules emerge from multiple sites in the cell, eventually rearranging into a grid-like pattern in myotubes. In order to characterize perinuclear microtubule organization using a biochemically tractable system, we isolated nuclei from mouse C2C12 skeletal muscle cells during the course of differentiation and incubated them in cytoplasmic extracts prepared from eggs of the frog Xenopus laevis. Whereas centrosomes associated with myoblast nuclei gave rise to radial microtubule arrays in extracts, myotube nuclei produced a sun-like pattern with microtubules transiently nucleating from the entire nuclear envelope. Perinuclear microtubule growth was suppressed by inhibition of Aurora A kinase or by degradation of RNA, treatments that also inhibited microtubule growth from sperm centrosomes. Myotube nuclei displayed microtubule motor-based movements leading to their separation, as occurs in myotubes. This in vitro assay therefore recapitulates key features of microtubule organization and nuclear movement observed during muscle cell differentiation. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Ambika V Nadkarni
- Department of Molecular & Cell Biology, University of California, Berkeley, CA, USA
| | - Rebecca Heald
- Department of Molecular & Cell Biology, University of California, Berkeley, CA, USA
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8
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Liedmann S, Liu X, Guy CS, Crawford JC, Rodriguez DA, Kuzuoğlu-Öztürk D, Guo A, Verbist KC, Temirov J, Chen MJ, Ruggero D, Zhang H, Thomas PG, Green DR. Localization of a TORC1-eIF4F translation complex during CD8 + T cell activation drives divergent cell fate. Mol Cell 2022; 82:2401-2414.e9. [PMID: 35597236 DOI: 10.1016/j.molcel.2022.04.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 02/22/2022] [Accepted: 04/12/2022] [Indexed: 11/30/2022]
Abstract
Activated CD8+ T lymphocytes differentiate into heterogeneous subsets. Using super-resolution imaging, we found that prior to the first division, dynein-dependent vesicular transport polarized active TORC1 toward the microtubule-organizing center (MTOC) at the proximal pole. This active TORC1 was physically associated with active eIF4F, required for the translation of c-myc mRNA. As a consequence, c-myc-translating polysomes polarized toward the cellular pole proximal to the immune synapse, resulting in localized c-myc translation. Upon division, the TORC1-eIF4A complex preferentially sorted to the proximal daughter cell, facilitating asymmetric c-Myc synthesis. Transient disruption of eIF4A activity at first division skewed long-term cell fate trajectories to memory-like function. Using a genetic barcoding approach, we found that first-division sister cells often displayed differences in transcriptional profiles that largely correlated with c-Myc and TORC1 target genes. Our findings provide mechanistic insights as to how distinct T cell fate trajectories can be established during the first division.
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Affiliation(s)
- Swantje Liedmann
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| | - Xueyan Liu
- Department of Mathematics, University of New Orleans, New Orleans, LA 70148, USA
| | - Clifford S Guy
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jeremy Chase Crawford
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Diego A Rodriguez
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Duygu Kuzuoğlu-Öztürk
- Department of Urology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ao Guo
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Katherine C Verbist
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jamshid Temirov
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Mark J Chen
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Davide Ruggero
- Department of Urology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Hui Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Douglas R Green
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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9
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What defines the maternal transcriptome? Biochem Soc Trans 2021; 49:2051-2062. [PMID: 34415300 PMCID: PMC8589422 DOI: 10.1042/bst20201125] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/05/2021] [Accepted: 07/19/2021] [Indexed: 01/09/2023]
Abstract
In somatic cells, RNA polymerase II (Pol II) transcription initiation starts by the binding of the general transcription factor TFIID, containing the TATA-binding protein (TBP) and 13 TBP-associated factors (TAFs), to core promoters. However, in growing oocytes active Pol II transcription is TFIID/TBP-independent, as during oocyte growth TBP is replaced by its vertebrate-specific paralog TBPL2. TBPL2 does not interact with TAFs, but stably associates with TFIIA. The maternal transcriptome is the population of mRNAs produced and stored in the cytoplasm of growing oocytes. After fertilization, maternal mRNAs are inherited by the zygote from the oocyte. As transcription becomes silent after oocyte growth, these mRNAs are the sole source for active protein translation. They will participate to complete the protein pool required for oocyte terminal differentiation, fertilization and initiation of early development, until reactivation of transcription in the embryo, called zygotic genome activation (ZGA). All these events are controlled by an important reshaping of the maternal transcriptome. This procedure combines cytoplasmic readenylation of stored transcripts, allowing their translation, and different waves of mRNA degradation by deadenylation coupled to decapping, to eliminate transcripts coding for proteins that are no longer required. The reshaping ends after ZGA with an almost total clearance of the maternal transcripts. In the past, the murine maternal transcriptome has received little attention but recent progresses have brought new insights into the regulation of maternal mRNA dynamics in the mouse. This review will address past and recent data on the mechanisms associated with maternal transcriptome dynamic in the mouse.
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10
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Child JR, Chen Q, Reid DW, Jagannathan S, Nicchitta CV. Recruitment of endoplasmic reticulum-targeted and cytosolic mRNAs into membrane-associated stress granules. RNA (NEW YORK, N.Y.) 2021; 27:1241-1256. [PMID: 34244458 PMCID: PMC8456999 DOI: 10.1261/rna.078858.121] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 07/03/2021] [Indexed: 06/13/2023]
Abstract
Stress granules (SGs) are membraneless organelles composed of mRNAs and RNA binding proteins which undergo assembly in response to stress-induced inactivation of translation initiation. In general, SG recruitment is limited to a subpopulation of a given mRNA species and RNA-seq analyses of purified SGs revealed that signal sequence-encoding (i.e., endoplasmic reticulum [ER]-targeted) transcripts are significantly underrepresented, consistent with prior reports that ER localization can protect mRNAs from SG recruitment. Using translational profiling, cell fractionation, and single molecule mRNA imaging, we examined SG biogenesis following activation of the unfolded protein response (UPR) by 1,4-dithiothreitol (DTT) and report that gene-specific subsets of cytosolic and ER-targeted mRNAs can be recruited into SGs. Furthermore, we demonstrate that SGs form in close proximity to or directly associated with the ER membrane. ER-associated SG assembly was also observed during arsenite stress, suggesting broad roles for the ER in SG biogenesis. Recruitment of a given mRNA into SGs required stress-induced translational repression, though translational inhibition was not solely predictive of an mRNA's propensity for SG recruitment. SG formation was prevented by the transcriptional inhibitors actinomycin D or triptolide, suggesting a functional link between gene transcriptional state and SG biogenesis. Collectively these data demonstrate that ER-targeted and cytosolic mRNAs can be recruited into ER-associated SGs and this recruitment is sensitive to transcriptional inhibition. We propose that newly transcribed mRNAs exported under conditions of suppressed translation initiation are primary SG substrates, with the ER serving as the central subcellular site of SG formation.
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Affiliation(s)
- Jessica R Child
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Qiang Chen
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - David W Reid
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Sujatha Jagannathan
- Department of Biochemistry and Molecular Genetics, University of Colorado, Anschutz Medical Campus, Denver, Colorado 80045, USA
- RNA Bioscience Initiative, University of Colorado, Anschutz Medical Campus, Denver, Colorado 80045, USA
| | - Christopher V Nicchitta
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
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11
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Ulrychová L, Ostašov P, Chanová M, Mareš M, Horn M, Dvořák J. Spatial expression pattern of serine proteases in the blood fluke Schistosoma mansoni determined by fluorescence RNA in situ hybridization. Parasit Vectors 2021; 14:274. [PMID: 34022917 PMCID: PMC8140508 DOI: 10.1186/s13071-021-04773-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 05/03/2021] [Indexed: 11/24/2022] Open
Abstract
Background The blood flukes of genus Schistosoma are the causative agent of schistosomiasis, a parasitic disease that infects more than 200 million people worldwide. Proteases of schistosomes are involved in critical steps of host–parasite interactions and are promising therapeutic targets. We recently identified and characterized a group of S1 family Schistosoma mansoni serine proteases, including SmSP1 to SmSP5. Expression levels of some SmSPs in S. mansoni are low, and by standard genome sequencing technologies they are marginally detectable at the method threshold levels. Here, we report their spatial gene expression patterns in adult S. mansoni by the high-sensitivity localization assay. Methodology Highly sensitive fluorescence in situ RNA hybridization (FISH) was modified and used for the localization of mRNAs encoding individual SmSP proteases (including low-expressed SmSPs) in tissues of adult worms. High sensitivity was obtained due to specifically prepared tissue and probes in combination with the employment of a signal amplification approach. The assay method was validated by detecting the expression patterns of a set of relevant reference genes including SmCB1, SmPOP, SmTSP-2, and Sm29 with localization formerly determined by other techniques. Results FISH analysis revealed interesting expression patterns of SmSPs distributed in multiple tissues of S. mansoni adults. The expression patterns of individual SmSPs were distinct but in part overlapping and were consistent with existing transcriptome sequencing data. The exception were genes with significantly low expression, which were also localized in tissues where they had not previously been detected by RNA sequencing methods. In general, SmSPs were found in various tissues including reproductive organs, parenchymal cells, esophagus, and the tegumental surface. Conclusions The FISH-based assay provided spatial information about the expression of five SmSPs in adult S. mansoni females and males. This highly sensitive method allowed visualization of low-abundantly expressed genes that are below the detection limits of standard in situ hybridization or by RNA sequencing. Thus, this technical approach turned out to be suitable for sensitive localization studies and may also be applicable for other trematodes. The results suggest that SmSPs may play roles in diverse processes of the parasite. Certain SmSPs expressed at the surface may be involved in host–parasite interactions. Graphic abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-021-04773-8.
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Affiliation(s)
- Lenka Ulrychová
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo n. 2, 16610, Prague, Czech Republic.,Department of Parasitology, Faculty of Science, Charles University, Viničná 7, 12844, Prague 2, Czech Republic
| | - Pavel Ostašov
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/76, 32300, Pilsen, Czech Republic
| | - Marta Chanová
- Institute of Immunology and Microbiology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studničkova 2028/7, 12800, Prague, Czech Republic
| | - Michael Mareš
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo n. 2, 16610, Prague, Czech Republic
| | - Martin Horn
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo n. 2, 16610, Prague, Czech Republic.
| | - Jan Dvořák
- Department of Zoology and Fisheries, Centre of Infectious Animal Diseases, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences in Prague, Kamýcká 129, 16500, Prague 6, Czech Republic.
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12
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Forlani G, Di Ventura B. A light way for nuclear cell biologists. J Biochem 2021; 169:273-286. [PMID: 33245128 PMCID: PMC8053400 DOI: 10.1093/jb/mvaa139] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 11/12/2020] [Indexed: 12/11/2022] Open
Abstract
The nucleus is a very complex organelle present in eukaryotic cells. Having the crucial task to safeguard, organize and manage the genetic information, it must tightly control its molecular constituents, its shape and its internal architecture at any given time. Despite our vast knowledge of nuclear cell biology, much is yet to be unravelled. For instance, only recently we came to appreciate the existence of a dynamic nuclear cytoskeleton made of actin filaments that regulates processes such as gene expression, DNA repair and nuclear expansion. This suggests further exciting discoveries ahead of us. Modern cell biologists embrace a new methodology relying on precise perturbations of cellular processes that require a reversible, highly spatially confinable, rapid, inexpensive and tunEable external stimulus: light. In this review, we discuss how optogenetics, the state-of-the-art technology that uses genetically encoded light-sensitive proteins to steer biological processes, can be adopted to specifically investigate nuclear cell biology.
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Affiliation(s)
- Giada Forlani
- Spemann Graduate School of Biology and Medicine (SGBM)
- Centers for Biological Signalling Studies BIOSS and CIBSS
- Faculty of Biology, Institute of Biology II, Albert Ludwigs University of Freiburg, Freiburg, Germany
| | - Barbara Di Ventura
- Centers for Biological Signalling Studies BIOSS and CIBSS
- Faculty of Biology, Institute of Biology II, Albert Ludwigs University of Freiburg, Freiburg, Germany
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13
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Wozniak AL, Adams A, King KE, Dunn W, Christenson LK, Hung WT, Weinman SA. The RNA binding protein FMR1 controls selective exosomal miRNA cargo loading during inflammation. J Cell Biol 2021; 219:152116. [PMID: 32970791 PMCID: PMC7659717 DOI: 10.1083/jcb.201912074] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 04/22/2020] [Accepted: 07/09/2020] [Indexed: 12/16/2022] Open
Abstract
Cells respond to inflammatory disease states by releasing exosomes containing highly specific protein and RNA cargos, but how inflammation alters cargo specificity and secretion of exosomes is unknown. We show that increases in exosome secretion induced by either viral infection or LPS/ATP exposure result from inflammasome activation and subsequent caspase-1–dependent cleavage of the trafficking adaptor protein RILP. This cleaved form of RILP promotes the movement of multivesicular bodies toward the cell periphery and induces selective exosomal miRNA cargo loading. We have identified a common short sequence motif present in miRNAs that are selectively loaded into exosomes after RILP cleavage. This motif binds the RNA binding protein FMR1 and directs miRNA loading into exosomes via interaction with components of the ESCRT (endosomal sorting complex required for transport) pathway. These results indicate that inflammasome-mediated RILP cleavage, and sequence-specific interactions between miRNAs and FMR1, play a significant role in exosome cargo loading and enhanced secretion during cellular inflammatory responses.
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Affiliation(s)
- Ann L Wozniak
- Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS.,Liver Center, University of Kansas Medical Center, Kansas City KS
| | - Abby Adams
- Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS.,Liver Center, University of Kansas Medical Center, Kansas City KS
| | - Kayla E King
- Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS.,Liver Center, University of Kansas Medical Center, Kansas City KS
| | - Winston Dunn
- Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS.,Liver Center, University of Kansas Medical Center, Kansas City KS
| | - Lane K Christenson
- Department of Molecular & Integrative Physiology, University of Kansas Medical Center, Kansas City KS
| | - Wei-Ting Hung
- Department of Molecular & Integrative Physiology, University of Kansas Medical Center, Kansas City KS.,Center for Systems Biology, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Steven A Weinman
- Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS.,Liver Center, University of Kansas Medical Center, Kansas City KS
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14
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Mitochondrial biogenesis in organismal senescence and neurodegeneration. Mech Ageing Dev 2020; 191:111345. [DOI: 10.1016/j.mad.2020.111345] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/17/2020] [Accepted: 08/27/2020] [Indexed: 12/19/2022]
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15
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A Dual Protein-mRNA Localization Screen Reveals Compartmentalized Translation and Widespread Co-translational RNA Targeting. Dev Cell 2020; 54:773-791.e5. [PMID: 32783880 DOI: 10.1016/j.devcel.2020.07.010] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 06/01/2020] [Accepted: 07/14/2020] [Indexed: 12/21/2022]
Abstract
Local translation allows spatial control of gene expression. Here, we performed a dual protein-mRNA localization screen, using smFISH on 523 human cell lines expressing GFP-tagged genes. 32 mRNAs displayed specific cytoplasmic localizations with local translation at unexpected locations, including cytoplasmic protrusions, cell edges, endosomes, Golgi, the nuclear envelope, and centrosomes, the latter being cell-cycle-dependent. Automated classification of mRNA localization patterns revealed a high degree of intercellular heterogeneity. Surprisingly, mRNA localization frequently required ongoing translation, indicating widespread co-translational RNA targeting. Interestingly, while P-body accumulation was frequent (15 mRNAs), four mRNAs accumulated in foci that were distinct structures. These foci lacked the mature protein, but nascent polypeptide imaging showed that they were specialized translation factories. For β-catenin, foci formation was regulated by Wnt, relied on APC-dependent polysome aggregation, and led to nascent protein degradation. Thus, translation factories uniquely regulate nascent protein metabolism and create a fine granular compartmentalization of translation.
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16
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Tian L, Doroshenk KA, Zhang L, Fukuda M, Washida H, Kumamaru T, Okita T. Zipcode RNA-Binding Proteins and Membrane Trafficking Proteins Cooperate to Transport Glutelin mRNAs in Rice Endosperm. THE PLANT CELL 2020; 32:2566-2581. [PMID: 32471860 PMCID: PMC7401010 DOI: 10.1105/tpc.20.00111] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 05/12/2020] [Accepted: 05/24/2020] [Indexed: 05/04/2023]
Abstract
In rice (Oryza sativa) endosperm cells, mRNAs encoding glutelin and prolamine are translated on distinct cortical-endoplasmic reticulum (ER) subdomains (the cisternal-ER and protein body-ER), a process that facilitates targeting of their proteins to different endomembrane compartments. Although the cis- and trans-factors responsible for mRNA localization have been defined over the years, how these mRNAs are transported to the cortical ER has yet to be resolved. Here, we show that the two interacting glutelin zipcode RNA binding proteins (RBPs), RBP-P and RBP-L, form a quaternary complex with the membrane fusion factors n-ethylmaleimide-sensitive factor (NSF) and the small GTPase Rab5a, enabling mRNA transport on endosomes. Direct interaction of RBP-L with Rab5a, between NSF and RBP-P, and between NSF and Rab5a, were established. Biochemical and microscopic analyses confirmed the co-localization of these RBPs with NSF on Rab5a-positive endosomes that carry glutelin mRNAs. Analysis of a loss-of-function rab5a mutant showed that glutelin mRNA and the quaternary complex were mis-targeted to the extracellular paramural body structure formed by aborted endosomal trafficking, further confirming the involvement of endosomal trafficking in glutelin mRNA transport. Overall, these findings demonstrate that mRNA localization in plants co-opts membrane trafficking via the acquisition of new functional binding properties between RBPs and two essential membrane trafficking factors, thus defining an endosomal anchoring mechanism in mRNA localization.
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Affiliation(s)
- Li Tian
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340
| | - Kelly A Doroshenk
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340
| | - Laining Zhang
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340
| | - Masako Fukuda
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340
- Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Haruhiko Washida
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340
| | | | - Thomas Okita
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340
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17
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Wu KE, Fazal FM, Parker KR, Zou J, Chang HY. RNA-GPS Predicts SARS-CoV-2 RNA Residency to Host Mitochondria and Nucleolus. Cell Syst 2020; 11:102-108.e3. [PMID: 32673562 PMCID: PMC7305881 DOI: 10.1016/j.cels.2020.06.008] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/20/2020] [Accepted: 06/17/2020] [Indexed: 02/06/2023]
Abstract
SARS-CoV-2 genomic and subgenomic RNA (sgRNA) transcripts hijack the host cell's machinery. Subcellular localization of its viral RNA could, thus, play important roles in viral replication and host antiviral immune response. We perform computational modeling of SARS-CoV-2 viral RNA subcellular residency across eight subcellular neighborhoods. We compare hundreds of SARS-CoV-2 genomes with the human transcriptome and other coronaviruses. We predict the SARS-CoV-2 RNA genome and sgRNAs to be enriched toward the host mitochondrial matrix and nucleolus, and that the 5' and 3' viral untranslated regions contain the strongest, most distinct localization signals. We interpret the mitochondrial residency signal as an indicator of intracellular RNA trafficking with respect to double-membrane vesicles, a critical stage in the coronavirus life cycle. Our computational analysis serves as a hypothesis generation tool to suggest models for SARS-CoV-2 biology and inform experimental efforts to combat the virus. A record of this paper's Transparent Peer Review process is included in the Supplemental Information.
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Affiliation(s)
- Kevin E Wu
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Personal and Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Furqan M Fazal
- Center for Personal and Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kevin R Parker
- Center for Personal and Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - James Zou
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Howard Y Chang
- Center for Personal and Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
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18
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Hossain E, Habiba U, Yanagawa-Matsuda A, Alam A, Ahmed I, Towfik Alam M, Yasuda M, Higashino F. Advantages of Using Paclitaxel in Combination with Oncolytic Adenovirus Utilizing RNA Destabilization Mechanism. Cancers (Basel) 2020; 12:cancers12051210. [PMID: 32408515 PMCID: PMC7281177 DOI: 10.3390/cancers12051210] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 04/29/2020] [Accepted: 05/07/2020] [Indexed: 12/17/2022] Open
Abstract
Oncolytic virotherapy is a novel approach to cancer therapy. Ad-fosARE is a conditionally replicative adenovirus engineered by inserting AU-rich elements (ARE) in the 3'-untranslated region of the E1A gene. In this study, we examined the oncolytic activity of Ad-fosARE and used it in a synergistic combination with the chemotherapeutic agent paclitaxel (PTX) for treating cancer cells. The expression of E1A was high in cancer cells due to stabilized E1A-ARE mRNA. As a result, the efficiency of its replication and cytolytic activity in cancer cells was higher than in normal cells. PTX treatment increased the cytoplasmic HuR relocalization in cancer cells, enhanced viral replication through elevated E1A expression, and upregulated CAR (Coxsackie-adenovirus receptor) required for viral uptake. Furthermore, PTX altered the instability of microtubules by acetylation and detyrosination, which is essential for viral internalization and trafficking to the nucleus. These results indicate that PTX can provide multiple advantages to the efficacy of Ad-fosARE both in vitro and in vivo, and provides a basis for designing novel clinical trials. Thus, this virus has a lot of benefits that are not found in other oncolytic viruses. The virus also has the potential for treating PXT-resistant cancers.
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Affiliation(s)
- Elora Hossain
- Department of Molecular Oncology, Faculty of Dental Medicine and Graduate School of Biomedical Science and Engineering, Hokkaido University, Sapporo 060-8638, Japan; (E.H.); (I.A.)
| | - Umma Habiba
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo 060-8638, Japan;
| | - Aya Yanagawa-Matsuda
- Department of Vascular Biology and Molecular Pathology, Faculty of Dental Medicine and Graduate School of Dental Medicine, Hokkaido University, Sapporo 060-8586, Japan; (A.Y.-M.); (M.T.A.)
| | - Arefin Alam
- Department of Restorative Dentistry, Faculty of Dental Medicine and Graduate School of Dental Medicine, Hokkaido University, Sapporo 060-8586, Japan;
| | - Ishraque Ahmed
- Department of Molecular Oncology, Faculty of Dental Medicine and Graduate School of Biomedical Science and Engineering, Hokkaido University, Sapporo 060-8638, Japan; (E.H.); (I.A.)
| | - Mohammad Towfik Alam
- Department of Vascular Biology and Molecular Pathology, Faculty of Dental Medicine and Graduate School of Dental Medicine, Hokkaido University, Sapporo 060-8586, Japan; (A.Y.-M.); (M.T.A.)
| | - Motoaki Yasuda
- Department of Oral Molecular Microbiology, Faculty of Dental Medicine and Graduate School of Dental Medicine, Hokkaido University, Sapporo 060-8586, Japan;
| | - Fumihiro Higashino
- Department of Molecular Oncology, Faculty of Dental Medicine and Graduate School of Biomedical Science and Engineering, Hokkaido University, Sapporo 060-8638, Japan; (E.H.); (I.A.)
- Department of Vascular Biology and Molecular Pathology, Faculty of Dental Medicine and Graduate School of Dental Medicine, Hokkaido University, Sapporo 060-8586, Japan; (A.Y.-M.); (M.T.A.)
- Correspondence: ; Tel.: +81-(0)11-706-4237
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19
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Abstract
RNA localization is a key biological strategy for organizing the cytoplasm and generating both cellular and developmental polarity. During RNA localization, RNAs are targeted asymmetrically to specific subcellular destinations, resulting in spatially and temporally restricted gene expression through local protein synthesis. First discovered in oocytes and embryos, RNA localization is now recognized as a significant regulatory strategy for diverse RNAs, both coding and non-coding, in a wide range of cell types. Yet, the highly polarized cytoplasm of the oocyte remains a leading model to understand not only the principles and mechanisms underlying RNA localization, but also links to the formation of biomolecular condensates through phase separation. Here, we discuss both RNA localization and biomolecular condensates in oocytes with a particular focus on the oocyte of the frog, Xenopus laevis.
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Affiliation(s)
- Sarah E Cabral
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, United States
| | - Kimberly L Mowry
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, United States.
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20
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Wu H, Zhou J, Zhu T, Cohen I, Dictenberg J. A kinesin adapter directly mediates dendritic mRNA localization during neural development in mice. J Biol Chem 2020; 295:6605-6628. [PMID: 32111743 DOI: 10.1074/jbc.ra118.005616] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 08/19/2019] [Indexed: 11/06/2022] Open
Abstract
Motor protein-based active transport is essential for mRNA localization and local translation in animal cells, yet how mRNA granules interact with motor proteins remains poorly understood. Using an unbiased yeast two-hybrid screen for interactions between murine RNA-binding proteins (RBPs) and motor proteins, here we identified protein interaction with APP tail-1 (PAT1) as a potential direct adapter between zipcode-binding protein 1 (ZBP1, a β-actin RBP) and the kinesin-I motor complex. The amino acid sequence of mouse PAT1 is similar to that of the kinesin light chain (KLC), and we found that PAT1 binds to KLC directly. Studying PAT1 in mouse primary hippocampal neuronal cultures from both sexes and using structured illumination microscopic imaging of these neurons, we observed that brain-derived neurotrophic factor (BDNF) enhances co-localization of dendritic ZBP1 and PAT1 within granules that also contain kinesin-I. PAT1 is essential for BDNF-stimulated neuronal growth cone development and dendritic protrusion formation, and we noted that ZBP1 and PAT1 co-locate along with β-actin mRNA in actively transported granules in living neurons. Acute disruption of the PAT1-ZBP1 interaction in neurons with PAT1 siRNA or a dominant-negative ZBP1 construct diminished localization of β-actin mRNA but not of Ca2+/calmodulin-dependent protein kinase IIα (CaMKIIα) mRNA in dendrites. The aberrant β-actin mRNA localization resulted in abnormal dendritic protrusions and growth cone dynamics. These results suggest a critical role for PAT1 in BDNF-induced β-actin mRNA transport during postnatal development and reveal a new molecular mechanism for mRNA localization in vertebrates.
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Affiliation(s)
- Hao Wu
- Department of Biological Sciences, Hunter College, City University of New York, New York, New York 10065 .,Biology Program, Graduate School and University Center, City University of New York, New York, New York 10016
| | - Jing Zhou
- Biology Program, Graduate School and University Center, City University of New York, New York, New York 10016.,Biology Department, Lehman College, City University of New York, Bronx, New York 10468
| | - Tianhui Zhu
- Department of Biological Sciences, Hunter College, City University of New York, New York, New York 10065.,Biology Program, Graduate School and University Center, City University of New York, New York, New York 10016
| | - Ivan Cohen
- Department of Biological Sciences, Hunter College, City University of New York, New York, New York 10065
| | - Jason Dictenberg
- Cell Biology, State University of New York Downstate, Brooklyn, New York 11226 .,Biotechnology Incubator, AccelBio, Brooklyn, New York 11226
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21
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Chou HL, Tian L, Washida H, Fukuda M, Kumamaru T, Okita TW. The rice storage protein mRNAs as a model system for RNA localization in higher plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 284:203-211. [PMID: 31084873 DOI: 10.1016/j.plantsci.2019.04.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 04/09/2019] [Accepted: 04/15/2019] [Indexed: 06/09/2023]
Abstract
The transport and targeting of mRNAs to specific intracellular locations is a ubiquitous process in prokaryotic and eukaryotic organisms. Despite the prevalent nature of RNA localization in guiding development, differentiation, cellular movement and intracellular organization of biochemical activities, only a few examples exist in higher plants. Here, we summarize past studies on mRNA-based protein targeting to specific subdomains of the cortical endoplasmic reticulum (ER) using the rice storage protein mRNAs as a model. Such studies have demonstrated that there are multiple pathways of RNA localization to the cortical ER that are controlled by cis-determinants (zipcodes) on the mRNA. These zipcode sequences are recognized by specific RNA binding proteins organized into multi-protein complexes. The available evidence suggests mRNAs are transported to their destination sites by co-opting membrane trafficking factors. Lastly, we discuss the major gaps in our knowledge on RNA localization and how information on the targeting of storage protein mRNAs can be used to further our understanding on how plant mRNAs are organized into regulons to facilitate protein localization and formation of multi-protein complexes.
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Affiliation(s)
- Hong-Li Chou
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164-6340, United States
| | - Li Tian
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164-6340, United States
| | - Haruhiko Washida
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164-6340, United States
| | - Masako Fukuda
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164-6340, United States; Faculty of Agriculture, Kyushu University, 744 Motooka Nishi-ku, Fukuoka, 819-0395, Japan
| | - Toshihiro Kumamaru
- Faculty of Agriculture, Kyushu University, 744 Motooka Nishi-ku, Fukuoka, 819-0395, Japan
| | - Thomas W Okita
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164-6340, United States.
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22
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Heber S, Gáspár I, Tants JN, Günther J, Moya SMF, Janowski R, Ephrussi A, Sattler M, Niessing D. Staufen2-mediated RNA recognition and localization requires combinatorial action of multiple domains. Nat Commun 2019; 10:1659. [PMID: 30971701 PMCID: PMC6477676 DOI: 10.1038/s41467-019-09655-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 03/20/2019] [Indexed: 11/08/2022] Open
Abstract
Throughout metazoans, Staufen (Stau) proteins are core factors of mRNA localization particles. They consist of three to four double-stranded RNA binding domains (dsRBDs) and a C-terminal dsRBD-like domain. Mouse Staufen2 (mStau2)-like Drosophila Stau (dmStau) contains four dsRBDs. Existing data suggest that only dsRBDs 3-4 are necessary and sufficient for mRNA binding. Here, we show that dsRBDs 1 and 2 of mStau2 bind RNA with similar affinities and kinetics as dsRBDs 3 and 4. While RNA binding by these tandem domains is transient, all four dsRBDs recognize their target RNAs with high stability. Rescue experiments in Drosophila oocytes demonstrate that mStau2 partially rescues dmStau-dependent mRNA localization. In contrast, a rescue with mStau2 bearing RNA-binding mutations in dsRBD1-2 fails, confirming the physiological relevance of our findings. In summary, our data show that the dsRBDs 1-2 play essential roles in the mRNA recognition and function of Stau-family proteins of different species.
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Affiliation(s)
- Simone Heber
- Institute of Pharmaceutical Biotechnology, 89081 Ulm University, Ulm, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Imre Gáspár
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
- Institute of Molecular Biotechnology, 1030, Vienna, Austria
| | - Jan-Niklas Tants
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR Spectroscopy, Department Chemistry, Technische Universität München, 85747, Garching, Germany
| | - Johannes Günther
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR Spectroscopy, Department Chemistry, Technische Universität München, 85747, Garching, Germany
| | - Sandra M Fernandez Moya
- Biomedical Center Munich, Department of Cell Biology, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany
| | - Robert Janowski
- Institute of Structural Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Anne Ephrussi
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR Spectroscopy, Department Chemistry, Technische Universität München, 85747, Garching, Germany
| | - Dierk Niessing
- Institute of Pharmaceutical Biotechnology, 89081 Ulm University, Ulm, Germany.
- Institute of Structural Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany.
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23
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Tian L, Chou HL, Zhang L, Okita TW. Targeted Endoplasmic Reticulum Localization of Storage Protein mRNAs Requires the RNA-Binding Protein RBP-L. PLANT PHYSIOLOGY 2019; 179:1111-1131. [PMID: 30659066 PMCID: PMC6393789 DOI: 10.1104/pp.18.01434] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 01/11/2019] [Indexed: 05/18/2023]
Abstract
The transport and targeting of glutelin and prolamine mRNAs to distinct subdomains of the cortical endoplasmic reticulum is a model for mRNA localization in plants. This process requires a number of RNA-binding proteins (RBPs) that recognize and bind to mRNA cis-localization (zipcode) elements to form messenger ribonucleoprotein complexes, which then transport the RNAs to their destination sites at the cortical endoplasmic reticulum. Here, we present evidence that the rice (Oryza sativa) RNA-binding protein, RBP-L, like its interacting RBP-P partner, specifically binds to glutelin and prolamine zipcode RNA sequences and is required for proper mRNA localization in rice endosperm cells. A transfer DNA insertion in the 3' untranslated region resulted in reduced expression of the RBP-L gene to 10% to 25% of that in the wild-type. Reduced amounts of RBP-L caused partial mislocalization of glutelin and prolamine RNAs and conferred other general growth defects, including dwarfism, late flowering, and smaller seeds. Transcriptome analysis showed that RBP-L knockdown greatly affected the expression of prolamine family genes and several classes of transcription factors. Collectively, these results indicate that RBP-L, like RBP-P, is a key RBP involved in mRNA localization in rice endosperm cells. Moreover, distinct from RBP-P, RBP-L exhibits additional regulatory roles in development, either directly through its binding to corresponding RNAs or indirectly through its effect on transcription factors.
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Affiliation(s)
- Li Tian
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340
| | - Hong-Li Chou
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340
| | - Laining Zhang
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340
| | - Thomas W Okita
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340
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24
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Quantum mechanical investigation of the nature of nucleobase-urea stacking interaction, a crucial driving force in RNA unfolding in aqueous urea. J CHEM SCI 2018. [DOI: 10.1007/s12039-018-1563-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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25
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Tian L, Chou HL, Zhang L, Hwang SK, Starkenburg SR, Doroshenk KA, Kumamaru T, Okita TW. RNA-Binding Protein RBP-P Is Required for Glutelin and Prolamine mRNA Localization in Rice Endosperm Cells. THE PLANT CELL 2018; 30:2529-2552. [PMID: 30190374 PMCID: PMC6241268 DOI: 10.1105/tpc.18.00321] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 08/08/2018] [Accepted: 08/31/2018] [Indexed: 05/18/2023]
Abstract
In developing rice (Oryza sativa) endosperm, mRNAs of the major storage proteins, glutelin and prolamine, are transported and anchored to distinct subdomains of the cortical endoplasmic reticulum. RNA binding protein RBP-P binds to both glutelin and prolamine mRNAs, suggesting a role in some aspect of their RNA metabolism. Here, we show that rice lines expressing mutant RBP-P mislocalize both glutelin and prolamine mRNAs. Different mutant RBP-P proteins exhibited varying degrees of reduced RNA binding and/or protein-protein interaction properties, which may account for the mislocalization of storage protein RNAs. In addition, partial loss of RBP-P function conferred a broad phenotypic variation ranging from dwarfism, chlorophyll deficiency, and sterility to late flowering and low spikelet fertility. Transcriptome analysis highlighted the essential role of RBP-P in regulating storage protein genes and several essential biological processes during grain development. Overall, our data demonstrate the significant roles of RBP-P in glutelin and prolamine mRNA localization and in the regulation of genes important for plant growth and development through its RNA binding activity and cooperative regulation with interacting proteins.
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Affiliation(s)
- Li Tian
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340
| | - Hong-Li Chou
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Laining Zhang
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340
| | - Seon-Kap Hwang
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340
| | | | - Kelly A Doroshenk
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340
| | | | - Thomas W Okita
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340
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26
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Protein phosphorylation and its role in the regulation of Annexin A2 function. Biochim Biophys Acta Gen Subj 2017; 1861:2515-2529. [PMID: 28867585 DOI: 10.1016/j.bbagen.2017.08.024] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 08/17/2017] [Accepted: 08/30/2017] [Indexed: 02/08/2023]
Abstract
BACKGROUND Annexin A2 (AnxA2) is a multifunctional protein involved in endocytosis, exocytosis, membrane domain organisation, actin remodelling, signal transduction, protein assembly, transcription and mRNA transport, as well as DNA replication and repair. SCOPE OF REVIEW The current knowledge of the role of phosphorylation in the functional regulation of AnxA2 is reviewed. To provide a more comprehensive treatment of this topic, we also address in depth the phosphorylation process in general and discuss its possible conformational effects. Furthermore, we discuss the apparent limitations of the methods used to investigate phosphoproteins, as exemplified by the study of AnxA2. MAJOR CONCLUSIONS AnxA2 is subjected to complex regulation by post-translational modifications affecting its cellular functions, with Ser11, Ser25 and Tyr23 representing important phosphorylation sites. Thus, Ser phosphorylation of AnxA2 is involved in the recruitment and docking of secretory granules, the regulation of its association with S100A10, and sequestration of perinuclear, translationally inactive mRNP complexes. By contrast, Tyr phosphorylation of AnxA2 regulates its role in actin dynamics and increases its association with endosomal compartments. Modification of its three main phosphorylation sites is not sufficient to discriminate between its numerous functions. Thus, fine-tuning of AnxA2 function is mediated by the joint action of several post-translational modifications. GENERAL SIGNIFICANCE AnxA2 participates in malignant cell transformation, and its overexpression and/or phosphorylation is associated with cancer progression and metastasis. Thus, tight regulation of AnxA2 function is an integral aspect of cellular homeostasis. The presence of AnxA2 in cancer cell-derived exosomes, as well as the potential regulation of exosomal AnxA2 by phosphorylation or other PTMs, are topics of great interest.
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27
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Fukuda M, Kawagoe Y, Murakami T, Washida H, Sugino A, Nagamine A, Okita TW, Ogawa M, Kumamaru T. The Dual Roles of the Golgi Transport 1 (GOT1B): RNA Localization to the Cortical Endoplasmic Reticulum and the Export of Proglutelin and α-Globulin from the Cortical ER to the Golgi. PLANT & CELL PHYSIOLOGY 2016; 57:2380-2391. [PMID: 27565205 DOI: 10.1093/pcp/pcw154] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 08/23/2016] [Indexed: 06/06/2023]
Abstract
The rice glup2 lines are characterized by their abnormally high levels of endosperm 57 kDa proglutelins and of the luminal chaperone binding protein (BiP), features characteristic of a defect within the endoplasmic reticulum (ER). To elucidate the underlying genetic basis, the glup2 locus was identified by map based cloning. DNA sequencing of the genomes of three glup2 alleles and wild type demonstrated that the underlying genetic basis was mutations in the Golgi transport 1 (GOT1B) coding sequence. This conclusion was further validated by restoration of normal proglutelin levels in a glup2 line complemented by a GOT1B gene. Microscopic analyses indicated the presence of proglutelin-α-globulin-containing intracisternal granules surrounded by prolamine inclusions within the ER lumen. As assessed by in situ reverse transcriptase polymerase chain reaction (RT-PCR) analysis of developing endosperm sections, prolamine and α-globulin RNAs were found to be mis-targeted from their usual sites on the protein body ER to the cisternal ER, the normal sites of proglutelin synthesis. Our results indicate that GLUP2/GOT1B has a dual role during rice endosperm development. It is required for localization of prolamine and α-globulin RNAs to the protein body ER and for efficient export of proglutelin and α-globulin proteins from the ER to the Golgi apparatus.
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Affiliation(s)
- Masako Fukuda
- Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan
| | - Yasushi Kawagoe
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
- Deceased
| | | | - Haruhiko Washida
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340, USA
- Present address: U-TEC Corporation, 648-1 Matsukasa, Yamatokoriyama, Nara 639-1124, Japan
| | - Aya Sugino
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340, USA
| | - Ai Nagamine
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340, USA
| | - Thomas W Okita
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340, USA
| | - Masahiro Ogawa
- Department of General Education, Yamaguchi Prefectural University, Yamaguchi 753-8502, Japan
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28
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Heuer-Jungemann A, El-Sagheer AH, Lackie PM, Brown T, Kanaras AG. Selective killing of cells triggered by their mRNA signature in the presence of smart nanoparticles. NANOSCALE 2016; 8:16857-16861. [PMID: 27714148 DOI: 10.1039/c6nr06154k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The design of nanoparticles that can selectively perform multiple roles is of utmost importance for the development of the next generation of nanoparticulate drug delivery systems. So far most research studies are focused on the customization of nanoparticulate carriers to maximize their drug loading, enhance their optical signature for tracking in cells or provide photo-responsive effects for therapeutic purposes. However, a vital requirement of the new generation of drug carriers must be the ability to deliver their payload selectively only to cells of interest rather than the majority of various cells in the vicinity. Here we show for the first time a new design of nanoparticulate drug carriers that can specifically distinguish different cell types based on their mRNA signature. These nanoparticles sense and efficiently kill model tumour cells by the delivery of an anti-cancer drug but retain their payload in cells lacking the specific mRNA target.
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Affiliation(s)
| | - Afaf H El-Sagheer
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK and Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez 43721, Egypt
| | - Peter M Lackie
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
| | - Tom Brown
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Antonios G Kanaras
- Physics and Astronomy, Faculty of Physical Sciences and Engineering, UK and Institute for Life Sciences, University of Southampton, Southampton, SO171BJ, UK.
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29
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Eberhardt W, Badawi A, Biyanee A, Pfeilschifter J. Cytoskeleton-Dependent Transport as a Potential Target for Interfering with Post-transcriptional HuR mRNA Regulons. Front Pharmacol 2016; 7:251. [PMID: 27582706 PMCID: PMC4987335 DOI: 10.3389/fphar.2016.00251] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 08/02/2016] [Indexed: 01/04/2023] Open
Abstract
The ubiquitous mRNA binding protein human antigen R (HuR), a member of the embryonal lethal abnormal vision protein family has a critical impact on the post-transcriptional control of AU-rich element bearing mRNA regulons implied in inflammation, senescence, and carcinogenesis. HuR in addition to mRNA stability can affect many other aspects of mRNA processing including splicing, polyadenylation, translation, modulation of miRNA repression, and intracellular mRNA trafficking. Since many of the identified HuR mRNA targets ("HuR mRNA regulons") encode tumor-related proteins, HuR is not only discussed as an useful biomarker but also as promising therapeutic target for treatment of various human cancers. HuR which is most abundantly localized in the nucleus is translocated to the cytoplasm which is fundamental for most of the described HuR functions on target mRNAs. Accordingly, an elevation in cytoplasmic HuR was found in many tumors and correlated with a high grade of malignancy and a poor prognosis of patients. Therefore, direct interference with the intracellular trafficking of HuR offers an attractive approach to intervene with pathologically deregulated HuR functions. Data from several laboratories implicate that the integrity of the cytoskeleton is critical for HuR-mediated intracellular mRNA localization and translation. This review will particularly focus on drugs which have proven a direct inhibitory effect on HuR translocation. Based on the results from those studies, we will also discuss on the principle value of targeting cytoskeleton-dependent transport of HuR by natural or synthetic inhibitors as a potential therapeutic avenue for interfering with dysregulated post-transcriptional HuR mRNA regulons and related tumor cell functions. In spite of that, interfering with cytoplasmic HuR transport could highlight a so far underestimated action of microtubule inhibitors clinically used for cancer chemotherapy.
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Affiliation(s)
- Wolfgang Eberhardt
- Pharmazentrum Frankfurt/ZAFES, Klinikum der Johann Wolfgang Goethe-Universität Frankfurt am Main, Germany
| | - Amel Badawi
- Pharmazentrum Frankfurt/ZAFES, Klinikum der Johann Wolfgang Goethe-Universität Frankfurt am Main, Germany
| | - Abhiruchi Biyanee
- Pharmazentrum Frankfurt/ZAFES, Klinikum der Johann Wolfgang Goethe-Universität Frankfurt am Main, Germany
| | - Josef Pfeilschifter
- Pharmazentrum Frankfurt/ZAFES, Klinikum der Johann Wolfgang Goethe-Universität Frankfurt am Main, Germany
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30
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Varela N, Aranguiz A, Lizama C, Sepulveda H, Antonelli M, Thaler R, Moreno RD, Montecino M, Stein GS, van Wijnen AJ, Galindo M. Mitotic Inheritance of mRNA Facilitates Translational Activation of the Osteogenic-Lineage Commitment Factor Runx2 in Progeny of Osteoblastic Cells. J Cell Physiol 2016; 231:1001-14. [PMID: 26381402 PMCID: PMC5812339 DOI: 10.1002/jcp.25188] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 09/03/2015] [Indexed: 12/24/2022]
Abstract
Epigenetic mechanisms mediate the acquisition of specialized cellular phenotypes during tissue development, maintenance and repair. When phenotype-committed cells transit through mitosis, chromosomal condensation counteracts epigenetic activation of gene expression. Subsequent post-mitotic re-activation of transcription depends on epigenetic DNA and histone modifications, as well as other architecturally bound proteins that "bookmark" the genome. Osteogenic lineage commitment, differentiation and progenitor proliferation require the bone-related runt-related transcription factor Runx2. Here, we characterized a non-genomic mRNA mediated mechanism by which osteoblast precursors retain their phenotype during self-renewal. We show that osteoblasts produce maximal levels of Runx2 mRNA, but not protein, prior to mitotic cell division. Runx2 mRNA partitions symmetrically between daughter cells in a non-chromosomal tubulin-containing compartment. Subsequently, transcription-independent de novo synthesis of Runx2 protein in early G1 phase results in increased functional interactions of Runx2 with a representative osteoblast-specific target gene (osteocalcin/BGLAP2) in chromatin. Somatic transmission of Runx2 mRNAs in osteoblasts and osteosarcoma cells represents a versatile mechanism for translational rather than transcriptional induction of this principal gene regulator to maintain osteoblast phenotype identity after mitosis.
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Affiliation(s)
- Nelson Varela
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences (ICBM), Faculty of Medicine, University of Chile, Santiago, Chile
- Department of Medical Technology, Faculty of Medicine, University of Chile, Santiago, Chile
- Millennium Institute on Immunology and Immunotherapy, University of Chile, Santiago, Chile
| | - Alejandra Aranguiz
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences (ICBM), Faculty of Medicine, University of Chile, Santiago, Chile
- Millennium Institute on Immunology and Immunotherapy, University of Chile, Santiago, Chile
| | - Carlos Lizama
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Hugo Sepulveda
- Center for Biomedical Research and FONDAP Center for Genome Regulation, Faculty of Biological Sciences and Faculty of Medicine, Universidad Andres Bello, Santiago, Chile
| | - Marcelo Antonelli
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences (ICBM), Faculty of Medicine, University of Chile, Santiago, Chile
| | - Roman Thaler
- Departments of Orthopedic Surgery & Biochemistry and Molecular Biology, Mayo Clinic, 200 First Street S.W., MSB 3-69, Rochester, MN 55905
| | - Ricardo D. Moreno
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Martin Montecino
- Center for Biomedical Research and FONDAP Center for Genome Regulation, Faculty of Biological Sciences and Faculty of Medicine, Universidad Andres Bello, Santiago, Chile
| | - Gary S. Stein
- Department of Biochemistry, HSRF 326, Vermont Cancer Center for Basic and Translational Research, University of Vermont Medical School, Burlington, VT
| | - Andre J. van Wijnen
- Departments of Orthopedic Surgery & Biochemistry and Molecular Biology, Mayo Clinic, 200 First Street S.W., MSB 3-69, Rochester, MN 55905
| | - Mario Galindo
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences (ICBM), Faculty of Medicine, University of Chile, Santiago, Chile
- Millennium Institute on Immunology and Immunotherapy, University of Chile, Santiago, Chile
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31
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Kubota M, Tran C, Spitale RC. Progress and challenges for chemical probing of RNA structure inside living cells. Nat Chem Biol 2015; 11:933-41. [PMID: 26575240 PMCID: PMC5068366 DOI: 10.1038/nchembio.1958] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 10/14/2015] [Indexed: 01/18/2023]
Abstract
Proper gene expression is essential for the survival of every cell. Once thought to be a passive transporter of genetic information, RNA has recently emerged as a key player in nearly every pathway in the cell. A full description of its structure is critical to understanding RNA function. Decades of research have focused on utilizing chemical tools to interrogate the structures of RNAs, with recent focus shifting to performing experiments inside living cells. This Review will detail the design and utility of chemical reagents used in RNA structure probing. We also outline how these reagents have been used to gain a deeper understanding of RNA structure in vivo. We review the recent merger of chemical probing with deep sequencing. Finally, we outline some of the hurdles that remain in fully characterizing the structure of RNA inside living cells, and how chemical biology can uniquely tackle such challenges.
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Affiliation(s)
- Miles Kubota
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California, USA
| | - Catherine Tran
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California, USA
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California, USA
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32
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Yeast mRNA localization: protein asymmetry, organelle localization and response to stress. Biochem Soc Trans 2015; 42:1256-60. [PMID: 25110034 DOI: 10.1042/bst20140086] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The localization of mRNA forms a key facet of the post-transcriptional control of gene expression and recent evidence suggests that it may be considerably more widespread than previously anticipated. For example, defined mRNA-containing granules can be associated with translational repression or activation. Furthermore, mRNA P-bodies (processing bodies) harbour much of the mRNA decay machinery and stress granules are thought to play a role in mRNA storage. In the present review, we explore the process of mRNA localization in the yeast Saccharomyces cerevisiae, examining connections between organellar mRNA localization and the response to stress. We also review recent data suggesting that even where there is a global relocalization of mRNA, the specificity and kinetics of this process can be regulated.
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33
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Tian L, Okita TW. mRNA-based protein targeting to the endoplasmic reticulum and chloroplasts in plant cells. CURRENT OPINION IN PLANT BIOLOGY 2014; 22:77-85. [PMID: 25282588 DOI: 10.1016/j.pbi.2014.09.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 08/06/2014] [Accepted: 09/15/2014] [Indexed: 05/12/2023]
Abstract
The targeting of proteins to subcellular organelles is specified by the presence of signal/leader peptide sequences normally located on the N-terminus. In the past two decades, messenger RNA (mRNA) localization, a pathway driven by cis-acting localization elements within the RNA sequence, has emerged as an alternative mechanism for protein targeting to specific locations in the cytoplasm, on the endoplasmic reticulum or to mitochondria and chloroplasts. In this review, we will summarize studies on mRNA-based protein targeting to the endoplasmic reticulum and chloroplast within plant cells.
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Affiliation(s)
- Li Tian
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
| | - Thomas W Okita
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA.
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34
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Reid DW, Chen Q, Tay ASL, Shenolikar S, Nicchitta CV. The unfolded protein response triggers selective mRNA release from the endoplasmic reticulum. Cell 2014; 158:1362-1374. [PMID: 25215492 DOI: 10.1016/j.cell.2014.08.012] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 05/16/2014] [Accepted: 07/22/2014] [Indexed: 01/23/2023]
Abstract
The unfolded protein response (UPR) is a stress response program that reprograms cellular translation and gene expression in response to proteotoxic stress in the endoplasmic reticulum (ER). One of the primary means by which the UPR alleviates this stress is by reducing protein flux into the ER via a general suppression of protein synthesis and ER-specific mRNA degradation. We report here an additional UPR-induced mechanism for the reduction of protein flux into the ER, where mRNAs that encode signal sequences are released from the ER to the cytosol. By removing mRNAs from the site of translocation, this mechanism may serve as a potent means to transiently reduce ER protein folding load and restore proteostasis. These findings identify the dynamic subcellular localization of mRNAs and translation as a selective and rapid regulatory feature of the cellular response to protein folding stress.
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Affiliation(s)
- David W Reid
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Qiang Chen
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Angeline S-L Tay
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Graduate Medical School, Singapore 169857, Singapore
| | - Shirish Shenolikar
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Graduate Medical School, Singapore 169857, Singapore; Program in Neuroscience and Behavioral Disorders, Duke-National University of Singapore Graduate Medical School, Singapore 169857, Singapore
| | - Christopher V Nicchitta
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA; Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA.
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35
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Liao G, Mingle L, Van De Water L, Liu G. Control of cell migration through mRNA localization and local translation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 6:1-15. [PMID: 25264217 DOI: 10.1002/wrna.1265] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 06/13/2014] [Accepted: 07/31/2014] [Indexed: 02/06/2023]
Abstract
Cell migration plays an important role in many normal and pathological functions such as development, wound healing, immune defense, and tumor metastasis. Polarized migrating cells exhibit asymmetric distribution of many cytoskeletal proteins, which is believed to be critical for establishing and maintaining cell polarity and directional cell migration. To target these proteins to the site of function, cells use a variety of mechanisms such as protein transport and messenger RNA (mRNA) localization-mediated local protein synthesis. In contrast to the former which is intensively investigated and relatively well understood, the latter has been understudied and relatively poorly understood. However, recent advances in the study of mRNA localization and local translation have demonstrated that mRNA localization and local translation are specific and effective ways for protein localization and are crucial for embryo development, neuronal function, and many other cellular processes. There are excellent reviews on mRNA localization, transport, and translation during development and other cellular processes. This review will focus on mRNA localization-mediated local protein biogenesis and its impact on somatic cell migration.
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Affiliation(s)
- Guoning Liao
- Center for Cell Biology and Cancer Research, Albany Medical College, Albany, NY, USA
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36
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Czaplinski K. Understanding mRNA trafficking: Are we there yet? Semin Cell Dev Biol 2014; 32:63-70. [DOI: 10.1016/j.semcdb.2014.04.025] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 04/17/2014] [Indexed: 10/25/2022]
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37
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Jagannathan S, Hsu JCC, Reid DW, Chen Q, Thompson WJ, Moseley AM, Nicchitta CV. Multifunctional roles for the protein translocation machinery in RNA anchoring to the endoplasmic reticulum. J Biol Chem 2014; 289:25907-24. [PMID: 25063809 DOI: 10.1074/jbc.m114.580688] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Signal sequence-encoding mRNAs undergo translation-dependent localization to the endoplasmic reticulum (ER) and at the ER are anchored via translation on Sec61-bound ribosomes. Recent investigations into the composition and membrane association characteristics of ER-associated mRNAs have, however, revealed both ribosome-dependent (indirect) and ribosome-independent (direct) modes of mRNA association with the ER. These findings raise important questions regarding our understanding of how mRNAs are selected, localized, and anchored to the ER. Using semi-intact tissue culture cells, we performed a polysome solubilization screen and identified conditions that distinguish polysomes engaged in the translation of distinct cohorts of mRNAs. To gain insight into the molecular basis of direct mRNA anchoring to the ER, we performed RNA-protein UV photocross-linking studies in rough microsomes and demonstrate that numerous ER integral membrane proteins display RNA binding activity. Quantitative proteomic analyses of HeLa cytosolic and ER-bound polysome fractions identified translocon components as selective polysome-interacting proteins. Notably, the Sec61 complex was highly enriched in polysomes engaged in the translation of endomembrane organelle proteins, whereas translocon accessory proteins, such as ribophorin I, were present in all subpopulations of ER-associated polysomes. Analyses of the protein composition of oligo(dT)-selected UV photocross-linked ER protein-RNA adducts identified Sec61α,β and ribophorin I as ER-poly(A) mRNA-binding proteins, suggesting unexpected roles for the protein translocation and modification machinery in mRNA anchoring to the ER. In summary, we propose that multiple mechanisms of mRNA and ribosome association with ER operate to enable an mRNA transcriptome-wide function for the ER in protein synthesis.
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Affiliation(s)
| | | | | | - Qiang Chen
- From the Departments of Cell Biology and
| | - Will J Thompson
- the Duke Proteomics Core Facility, Duke University Medical Center, Durham, North Carolina 27710
| | - Arthur M Moseley
- the Duke Proteomics Core Facility, Duke University Medical Center, Durham, North Carolina 27710
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38
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Polyansky AA, Hlevnjak M, Zagrovic B. Analogue encoding of physicochemical properties of proteins in their cognate messenger RNAs. Nat Commun 2014; 4:2784. [PMID: 24253588 PMCID: PMC3868254 DOI: 10.1038/ncomms3784] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 10/16/2013] [Indexed: 12/21/2022] Open
Abstract
Being related by the genetic code, mRNAs and their cognate proteins exhibit mutually interdependent compositions, which implies the possibility of a direct connection between their general physicochemical properties. Here we probe the general potential of the cell to encode information about proteins in the average characteristics of their cognate mRNAs and decode it in a ribosome-independent manner. We show that average protein hydrophobicity, calculated from either sequences or 3D structures, can be encoded in an analogue fashion by many different average mRNA sequence properties with the only constraint being that pyrimidine and purine bases be clearly distinguishable on average. Moreover, average characteristics of mRNA sequences enable discrimination between cytosolic and membrane proteins even in the absence of topogenic signal-based mechanisms. Our results suggest that protein and mRNA localization may be partly determined by basic physicochemical rationales and interdependencies between the two biomolecules. mRNA transport contributes to the proper localization of its cognate proteins. Here the authors report a correlation between the physicochemical properties of mRNAs and their cognate proteins, suggesting that these properties of mRNAs can predict the subcellular localization of their cognate proteins.
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Affiliation(s)
- Anton A Polyansky
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
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39
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Abstract
Myosin 4 protein (Myo4p), one of five distinct myosins of yeast, is dedicated to cytoplasmic transport of two types of cargos, zipcoded messenger ribonucleoprotein particles (mRNPs) and tubular endoplasmic reticulum (tER). Neither cargo binds directly to Myo4p. Instead, swi5p-dependent HO expression 3 protein (She3p) serves as an "adaptor" that contains three binding modules, one for Myo4p and one each for zipcoded mRNP and tER. The assembly of a transport-competent motor complex is poorly understood. Here, we report that Myo4p•She3p forms a stable 1:2 heterotrimer in solution. In the Myo4p•She3p crystal structure, Myo4p's C-terminal domain (CTD) assumes a lobster claw-shaped form, the minor prong of which adheres to a pseudocoiled-coil region of She3p. The extensive Myo4p•She3p interactome buries 3,812 Å(2) surface area and is primarily hydrophobic. Because the Myo4p•She3p heterotrimer contains only one myosin molecule, it is not transport-competent. By stepwise reconstitution, we found a single molecule of synthetic oligonucleotide (representing the mRNA zipcode element) bound to a single tetramer of zipcode binding protein She2p to be sufficient for Myo4p•She3p dimerization. Therefore, cargo initiates cross-linking of two Myo4p•She3p heterotrimers to an ensemble that contains two myosin molecules obligatory for movement. An additional crystal structure comprising an overlapping upstream portion of She3p showed continuation of the pseudocoiled-coil structure and revealed another highly conserved surface region. We suggest this region as a candidate binding site for a yet unidentified tER ligand. We propose a model whereby zipcoded mRNP and/or tER ligands couple two Myo4p•She3p heterotrimers and thereby generate a transport-competent motor complex either for separate transport or cotransport of these two cargos.
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