51
|
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: 43] [Impact Index Per Article: 3.9] [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.
Collapse
Affiliation(s)
- Guoning Liao
- Center for Cell Biology and Cancer Research, Albany Medical College, Albany, NY, USA
| | | | | | | |
Collapse
|
52
|
Carlile TM, Rojas-Duran MF, Zinshteyn B, Shin H, Bartoli KM, Gilbert WV. Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells. Nature 2014; 515:143-6. [PMID: 25192136 PMCID: PMC4224642 DOI: 10.1038/nature13802] [Citation(s) in RCA: 773] [Impact Index Per Article: 70.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 08/27/2014] [Indexed: 01/14/2023]
Abstract
Post-transcriptional modification of RNA nucleosides occurs in all living organisms. Pseudouridine, the most abundant modified nucleoside in non-coding RNAs1, enhances the function of transfer RNA and ribosomal RNA by stabilizing RNA structure2–8. mRNAs were not known to contain pseudouridine, but artificial pseudouridylation dramatically affects mRNA function – it changes the genetic code by facilitating non-canonical base pairing in the ribosome decoding center9,10. However, without evidence of naturally occurring mRNA pseudouridylation, its physiological was unclear. Here we present a comprehensive analysis of pseudouridylation in yeast and human RNAs using Pseudo-seq, a genome-wide, single-nucleotide-resolution method for pseudouridine identification. Pseudo-seq accurately identifies known modification sites as well as 100 novel sites in non-coding RNAs, and reveals hundreds of pseudouridylated sites in mRNAs. Genetic analysis allowed us to assign most of the new modification sites to one of seven conserved pseudouridine synthases, Pus1–4, 6, 7 and 9. Notably, the majority of pseudouridines in mRNA are regulated in response to environmental signals, such as nutrient deprivation in yeast and serum starvation in human cells. These results suggest a mechanism for the rapid and regulated rewiring of the genetic code through inducible mRNA modifications. Our findings reveal unanticipated roles for pseudouridylation and provide a resource for identifying the targets of pseudouridine synthases implicated in human disease11–13.
Collapse
Affiliation(s)
- Thomas M Carlile
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Maria F Rojas-Duran
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Boris Zinshteyn
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Hakyung Shin
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Kristen M Bartoli
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Wendy V Gilbert
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| |
Collapse
|
53
|
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: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 04/17/2014] [Indexed: 10/25/2022]
|
54
|
Shan X, Williams WP. Toward elucidation of genetic and functional genetic mechanisms in corn host resistance to Aspergillus flavus infection and aflatoxin contamination. Front Microbiol 2014; 5:364. [PMID: 25101068 PMCID: PMC4104783 DOI: 10.3389/fmicb.2014.00364] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 06/29/2014] [Indexed: 12/29/2022] Open
Abstract
Aflatoxins are carcinogenic mycotoxins produced by some species in the Aspergillus genus, such as A. flavus and A. parasiticus. Contamination of aflatoxins in corn profusely happens at pre-harvest stage when heat and drought field conditions favor A. flavus colonization. Commercial corn hybrids are generally susceptible to A. flavus infection. An ideal strategy for preventing aflatoxin contamination is through the enhancement of corn host resistance to Aspergillus infection and aflatoxin production. Constant efforts have been made by corn breeders to develop resistant corn genotypes. Significantly low levels of aflatoxin accumulation have been determined in certain resistant corn inbred lines. A number of reports of quantitative trait loci have provided compelling evidence supporting the quantitative trait genetic basis of corn host resistance to aflatoxin accumulation. Important findings have also been obtained from the investigation on candidate resistance genes through transcriptomics approach. Elucidation of molecular mechanisms will provide in-depth understanding of the host-pathogen interactions and hence facilitate the breeding of corn with resistance to A. flavus infection and aflatoxin accumulation.
Collapse
Affiliation(s)
- Xueyan Shan
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State UniversityMississippi, MS, USA
| | - W. Paul Williams
- Agricultural Research Service, United States Department of Agriculture, Corn Host Plant Resistance Research UnitMississippi, MS, USA
| |
Collapse
|
55
|
Doroshenk KA, Tian L, Crofts AJ, Kumamaru T, Okita TW. Characterization of RNA binding protein RBP-P reveals a possible role in rice glutelin gene expression and RNA localization. PLANT MOLECULAR BIOLOGY 2014; 85:381-394. [PMID: 24682961 DOI: 10.1007/s11103-014-0191-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 03/22/2014] [Indexed: 06/03/2023]
Abstract
RNA binding proteins (RBPs) play an important role in mRNA metabolism including synthesis, maturation, transport, localization, and stability. In developing rice seeds, RNAs that code for the major storage proteins are transported to specific domains of the cortical endoplasmic reticulum (ER) by a regulated mechanism requiring RNA cis-localization elements, or zipcodes. Putative trans-acting RBPs that recognize prolamine RNA zipcodes required for restricted localization to protein body-ER have previously been identified. Here, we describe the identification of RBP-P using a Northwestern blot approach as an RBP that recognizes and binds to glutelin zipcode RNA, which is required for proper RNA localization to cisternal-ER. RBP-P protein expression coincides with that of glutelin during seed maturation and is localized to both the nucleus and cytosol. RNA-immunoprecipitation and subsequent RT-PCR analysis further demonstrated that RBP-P interacts with glutelin RNAs. In vitro RNA-protein UV-crosslinking assays showed that recombinant RBP-P binds strongly to glutelin mRNA, and in particular, 3' UTR and zipcode RNA. RBP-P also exhibited strong binding activity to a glutelin intron sequence, suggesting that RBP-P might participate in mRNA splicing. Overall, these results support a multifunctional role for RBP-P in glutelin mRNA metabolism, perhaps in nuclear pre-mRNA splicing and cytosolic localization to the cisternal-ER.
Collapse
Affiliation(s)
- Kelly A Doroshenk
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164-6340, USA
| | | | | | | | | |
Collapse
|
56
|
Abstract
A comprehensive understanding of RNA structure will provide fundamental insights into the cellular function of both coding and non-coding RNAs. Although many RNA structures have been analysed by traditional biophysical and biochemical methods, the low-throughput nature of these approaches has prevented investigation of the vast majority of cellular transcripts. Triggered by advances in sequencing technology, genome-wide approaches for probing the transcriptome are beginning to reveal how RNA structure affects each step of protein expression and RNA stability. In this Review, we discuss the emerging relationships between RNA structure and the regulation of gene expression.
Collapse
|
57
|
Asters MC, Williams WP, Perkins AD, Mylroie JE, Windham GL, Shan X. Relating significance and relations of differentially expressed genes in response to Aspergillus flavus infection in maize. Sci Rep 2014; 4:4815. [PMID: 24770700 PMCID: PMC4001098 DOI: 10.1038/srep04815] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 04/08/2014] [Indexed: 12/21/2022] Open
Abstract
Aspergillus flavus is a pathogenic fungus infecting maize and producing aflatoxins that are health hazards to humans and animals. Characterizing host defense mechanism and prioritizing candidate resistance genes are important to the development of resistant maize germplasm. We investigated methods amenable for the analysis of the significance and relations among maize candidate genes based on the empirical gene expression data obtained by RT-qPCR technique from maize inbred lines. We optimized a pipeline of analysis tools chosen from various programs to provide rigorous statistical analysis and state of the art data visualization. A network-based method was also explored to construct the empirical gene expression relational structures. Maize genes at the centers in the network were considered as important candidate genes for maize DNA marker studies. The methods in this research can be used to analyze large RT-qPCR datasets and establish complex empirical gene relational structures across multiple experimental conditions.
Collapse
Affiliation(s)
- Matthew C. Asters
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, Mississippi, USA
| | - W. Paul Williams
- Agricultural Research Service, United States Department of Agriculture, Corn Host Plant Resistance Research Unit, Mississippi State, Mississippi, USA
| | - Andy D. Perkins
- Department of Computer Science and Engineering, Mississippi State University, Mississippi State, Mississippi, USA
| | - J. Erik Mylroie
- Agricultural Research Service, United States Department of Agriculture, Corn Host Plant Resistance Research Unit, Mississippi State, Mississippi, USA
| | - Gary L. Windham
- Agricultural Research Service, United States Department of Agriculture, Corn Host Plant Resistance Research Unit, Mississippi State, Mississippi, USA
| | - Xueyan Shan
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, Mississippi, USA
| |
Collapse
|
58
|
Di Liegro CM, Schiera G, Di Liegro I. Regulation of mRNA transport, localization and translation in the nervous system of mammals (Review). Int J Mol Med 2014; 33:747-62. [PMID: 24452120 PMCID: PMC3976132 DOI: 10.3892/ijmm.2014.1629] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 12/09/2013] [Indexed: 12/13/2022] Open
Abstract
Post-transcriptional control of mRNA trafficking and metabolism plays a critical role in the actualization and fine tuning of the genetic program of cells, both in development and in differentiated tissues. Cis-acting signals, responsible for post-transcriptional regulation, reside in the RNA message itself, usually in untranslated regions, 5′ or 3′ to the coding sequence, and are recognized by trans-acting factors: RNA-binding proteins (RBPs) and/or non-coding RNAs (ncRNAs). ncRNAs bind short mRNA sequences usually present in the 3′-untranslated (3′-UTR) region of their target messages. RBPs recognize specific nucleotide sequences and/or secondary/tertiary structures. Most RBPs assemble on mRNA at the moment of transcription and shepherd it to its destination, somehow determining its final fate. Regulation of mRNA localization and metabolism has a particularly important role in the nervous system where local translation of pre-localized mRNAs has been implicated in developing axon and dendrite pathfinding, and in synapse formation. Moreover, activity-dependent mRNA trafficking and local translation may underlie long-lasting changes in synaptic efficacy, responsible for learning and memory. This review focuses on the role of RBPs in neuronal development and plasticity, as well as possible connections between ncRNAs and RBPs.
Collapse
Affiliation(s)
- Carlo Maria Di Liegro
- Department of Biological Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), I-90128 Palermo, Italy
| | - Gabriella Schiera
- Department of Biological Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), I-90128 Palermo, Italy
| | - Italia Di Liegro
- Department of Experimental Biomedicine and Clinical Neurosciences (BIONEC), University of Palermo, I-90127 Palermo, Italy
| |
Collapse
|
59
|
Sabarinathan R, Wenzel A, Novotny P, Tang X, Kalari KR, Gorodkin J. Transcriptome-wide analysis of UTRs in non-small cell lung cancer reveals cancer-related genes with SNV-induced changes on RNA secondary structure and miRNA target sites. PLoS One 2014; 9:e82699. [PMID: 24416147 PMCID: PMC3885406 DOI: 10.1371/journal.pone.0082699] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 10/26/2013] [Indexed: 01/08/2023] Open
Abstract
Traditional mutation assessment methods generally focus on predicting disruptive changes in protein-coding regions rather than non-coding regulatory regions like untranslated regions (UTRs) of mRNAs. The UTRs, however, are known to have many sequence and structural motifs that can regulate translational and transcriptional efficiency and stability of mRNAs through interaction with RNA-binding proteins and other non-coding RNAs like microRNAs (miRNAs). In a recent study, transcriptomes of tumor cells harboring mutant and wild-type KRAS (V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog) genes in patients with non-small cell lung cancer (NSCLC) have been sequenced to identify single nucleotide variations (SNVs). About 40% of the total SNVs (73,717) identified were mapped to UTRs, but omitted in the previous analysis. To meet this obvious demand for analysis of the UTRs, we designed a comprehensive pipeline to predict the effect of SNVs on two major regulatory elements, secondary structure and miRNA target sites. Out of 29,290 SNVs in 6462 genes, we predict 472 SNVs (in 408 genes) affecting local RNA secondary structure, 490 SNVs (in 447 genes) affecting miRNA target sites and 48 that do both. Together these disruptive SNVs were present in 803 different genes, out of which 188 (23.4%) were previously known to be cancer-associated. Notably, this ratio is significantly higher (one-sided Fisher's exact test p-value = 0.032) than the ratio (20.8%) of known cancer-associated genes (n = 1347) in our initial data set (n = 6462). Network analysis shows that the genes harboring disruptive SNVs were involved in molecular mechanisms of cancer, and the signaling pathways of LPS-stimulated MAPK, IL-6, iNOS, EIF2 and mTOR. In conclusion, we have found hundreds of SNVs which are highly disruptive with respect to changes in the secondary structure and miRNA target sites within UTRs. These changes hold the potential to alter the expression of known cancer genes or genes linked to cancer-associated pathways.
Collapse
Affiliation(s)
- Radhakrishnan Sabarinathan
- Center for non-coding RNA in Technology and Health, Section for Animal Genetics, Bioinformatics and Breeding, IKVH, University of Copenhagen, Frederiksberg, Denmark
| | - Anne Wenzel
- Center for non-coding RNA in Technology and Health, Section for Animal Genetics, Bioinformatics and Breeding, IKVH, University of Copenhagen, Frederiksberg, Denmark
| | - Peter Novotny
- Bioinformatics Centre, Department of Biology and Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Xiaojia Tang
- Division of Biostatistics and Bioinformatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Krishna R. Kalari
- Division of Biostatistics and Bioinformatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida, United States of America
| | - Jan Gorodkin
- Center for non-coding RNA in Technology and Health, Section for Animal Genetics, Bioinformatics and Breeding, IKVH, University of Copenhagen, Frederiksberg, Denmark
- * E-mail:
| |
Collapse
|
60
|
The functions and regulatory principles of mRNA intracellular trafficking. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 825:57-96. [PMID: 25201103 DOI: 10.1007/978-1-4939-1221-6_2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The subcellular localization of RNA molecules is a key step in the control of gene expression that impacts a broad array of biological processes in different organisms and cell types. Like other aspects of posttranscriptional gene regulation discussed in this collection of reviews, the intracellular trafficking of mRNAs is modulated by a complex regulatory code implicating specific cis-regulatory elements, RNA-binding proteins, and cofactors that function combinatorially to dictate precise localization mechanisms. In this review, we first discuss the functional benefits of transcript localization, the regulatory principles involved, and specific molecular mechanisms that have been described for a few well-characterized mRNAs. We also overview some of the emerging genomic and imaging technologies that have provided significant insights into this layer of gene regulation. Finally, we highlight examples of human diseases where defective transcript localization has been documented.
Collapse
|
61
|
Alves LR, Guerra-Slompo EP, de Oliveira AV, Malgarin JS, Goldenberg S, Dallagiovanna B. mRNA localization mechanisms in Trypanosoma cruzi. PLoS One 2013; 8:e81375. [PMID: 24324687 PMCID: PMC3852752 DOI: 10.1371/journal.pone.0081375] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 10/13/2013] [Indexed: 01/06/2023] Open
Abstract
Asymmetric mRNA localization is a sophisticated tool for regulating and optimizing protein synthesis and maintaining cell polarity. Molecular mechanisms involved in the regulated localization of transcripts are widespread in higher eukaryotes and fungi, but not in protozoa. Trypanosomes are ancient eukaryotes that branched off early in eukaryote evolution. We hypothesized that these organisms would have basic mechanisms of mRNA localization. FISH assays with probes against transcripts coding for proteins with restricted distributions showed a discrete localization of the mRNAs in the cytoplasm. Moreover, cruzipain mRNA was found inside reservosomes suggesting new unexpected functions for this vacuolar organelle. Individual mRNAs were also mobilized to RNA granules in response to nutritional stress. The cytoplasmic distribution of these transcripts changed with cell differentiation, suggesting that localization mechanisms might be involved in the regulation of stage-specific protein expression. Transfection assays with reporter genes showed that, as in higher eukaryotes, 3'UTRs were responsible for guiding mRNAs to their final location. Our results strongly suggest that Trypanosoma cruzi have a core, basic mechanism of mRNA localization. This kind of controlled mRNA transport is ancient, dating back to early eukaryote evolution.
Collapse
Affiliation(s)
- Lysangela R. Alves
- Laboratório de Regulação da Expressão Gênica, Instituto Carlos Chagas, Fiocruz-Paraná. Curitiba, Paraná, Brasil
| | - Eloise P. Guerra-Slompo
- Laboratório de Regulação da Expressão Gênica, Instituto Carlos Chagas, Fiocruz-Paraná. Curitiba, Paraná, Brasil
| | - Arthur V. de Oliveira
- Laboratório de Regulação da Expressão Gênica, Instituto Carlos Chagas, Fiocruz-Paraná. Curitiba, Paraná, Brasil
| | - Juliane S. Malgarin
- Laboratório de Regulação da Expressão Gênica, Instituto Carlos Chagas, Fiocruz-Paraná. Curitiba, Paraná, Brasil
| | - Samuel Goldenberg
- Laboratório de Regulação da Expressão Gênica, Instituto Carlos Chagas, Fiocruz-Paraná. Curitiba, Paraná, Brasil
| | - Bruno Dallagiovanna
- Laboratório de Regulação da Expressão Gênica, Instituto Carlos Chagas, Fiocruz-Paraná. Curitiba, Paraná, Brasil
- * E-mail:
| |
Collapse
|
62
|
Khudayberdiev SA, Zampa F, Rajman M, Schratt G. A comprehensive characterization of the nuclear microRNA repertoire of post-mitotic neurons. Front Mol Neurosci 2013; 6:43. [PMID: 24324399 PMCID: PMC3840315 DOI: 10.3389/fnmol.2013.00043] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 11/07/2013] [Indexed: 11/17/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs with important functions in the development and plasticity of post-mitotic neurons. In addition to the well-described cytoplasmic function of miRNAs in post-transcriptional gene regulation, recent studies suggested that miRNAs could also be involved in transcriptional and post-transcriptional regulatory processes in the nuclei of proliferating cells. However, whether miRNAs localize to and function within the nucleus of post-mitotic neurons is unknown. Using a combination of microarray hybridization and small RNA deep sequencing, we identified a specific subset of miRNAs which are enriched in the nuclei of neurons. Nuclear enrichment of specific candidate miRNAs (miR-25 and miR-92a) could be independently validated by Northern blot, quantitative real-time PCR (qRT-PCR) and fluorescence in situ hybridization (FISH). By cross-comparison to published reports, we found that nuclear accumulation of miRNAs might be linked to a down-regulation of miRNA expression during in vitro development of cortical neurons. Importantly, by generating a comprehensive isomiR profile of the nuclear and cytoplasmic compartments, we found a significant overrepresentation of guanine nucleotides (nt) at the 3′-terminus of nuclear-enriched isomiRs, suggesting the presence of neuron-specific mechanisms involved in miRNA nuclear localization. In conclusion, our results provide a starting point for future studies addressing the nuclear function of specific miRNAs and the detailed mechanisms underlying subcellular localization of miRNAs in neurons and possibly other polarized cell types.
Collapse
Affiliation(s)
- Sharof A Khudayberdiev
- Biochemisch-Pharmakologisches Centrum, Institut für Physiologische Chemie, Philipps-Universität Marburg Marburg, Germany
| | | | | | | |
Collapse
|
63
|
Characterization of mRNA-cytoskeleton interactions in situ using FMTRIP and proximity ligation. PLoS One 2013; 8:e74598. [PMID: 24040294 PMCID: PMC3770708 DOI: 10.1371/journal.pone.0074598] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 08/04/2013] [Indexed: 12/23/2022] Open
Abstract
Many studies have demonstrated an association between the cytoskeleton and mRNA, as well as the asymmetric distribution of mRNA granules within the cell in response to various signaling events. It is likely that the extensive cytoskeletal network directs mRNA transport and localization, with different cytoskeletal elements having their own specific roles. In order to understand the spatiotemporal changes in the interactions between the mRNA and the cytoskeleton as a response to a stimulus, a technique that can visualize and quantify these changes across a population of cells while capturing cell-to-cell variations is required. Here, we demonstrate a method for imaging and quantifying mRNA-cytoskeleton interactions on a per cell basis with single-interaction sensitivity. Using a proximity ligation assay with flag-tagged multiply-labeled tetravalent RNA imaging probes (FMTRIP), we quantified interactions between mRNAs and β-tubulin, vimentin, or filamentous actin (F-actin) for two different mRNAs, poly(A) + and β-actin mRNA, in two different cell types, A549 cells and human dermal fibroblasts (HDF). We found that the mRNAs interacted predominantly with F-actin (>50% in HDF, >20% in A549 cells), compared to β-tubulin (<5%) and vimentin (11-13%). This likely reflects differences in mRNA management by the two cell types. We then quantified changes in these interactions in response to two perturbations, F-actin depolymerization and arsenite-induced oxidative stress, both of which alter either the cytoskeleton itself and mRNA localization. Both perturbations led to a decrease in poly(A) + mRNA interactions with F-actin and an increase in the interactions with microtubules, in a time dependent manner.
Collapse
|
64
|
Moving RNA moves RNA forward. SCIENCE CHINA-LIFE SCIENCES 2013; 56:914-20. [DOI: 10.1007/s11427-013-4545-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 08/23/2013] [Indexed: 12/11/2022]
|
65
|
Kraut-Cohen J, Afanasieva E, Haim-Vilmovsky L, Slobodin B, Yosef I, Bibi E, Gerst JE. Translation- and SRP-independent mRNA targeting to the endoplasmic reticulum in the yeast Saccharomyces cerevisiae. Mol Biol Cell 2013; 24:3069-84. [PMID: 23904265 PMCID: PMC3784381 DOI: 10.1091/mbc.e13-01-0038] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Although mRNAs encoding secreted and membrane proteins are believed to associate with the ER only upon translation, they access the membrane independently of both translational control and the signal recognition particle. Thus, alternate paths exist for RNA delivery to and retention at the ER. mRNAs encoding secreted/membrane proteins (mSMPs) are believed to reach the endoplasmic reticulum (ER) in a translation-dependent manner to confer protein translocation. Evidence exists, however, for translation- and signal recognition particle (SRP)–independent mRNA localization to the ER, suggesting that there are alternate paths for RNA delivery. We localized endogenously expressed mSMPs in yeast using an aptamer-based RNA-tagging procedure and fluorescence microscopy. Unlike mRNAs encoding polarity and secretion factors that colocalize with cortical ER at the bud tip, mSMPs and mRNAs encoding soluble, nonsecreted, nonpolarized proteins localized mainly to ER peripheral to the nucleus (nER). Synthetic nontranslatable uracil-rich mRNAs were also demonstrated to colocalize with nER in yeast. This mRNA–ER association was verified by subcellular fractionation and reverse transcription-PCR, single-molecule fluorescence in situ hybridization, and was not inhibited upon SRP inactivation. To better understand mSMP targeting, we examined aptamer-tagged USE1, which encodes a tail-anchored membrane protein, and SUC2, which encodes a soluble secreted enzyme. USE1 and SUC2 mRNA targeting was not abolished by the inhibition of translation or removal of elements involved in translational control. Overall we show that mSMP targeting to the ER is both translation- and SRP-independent, and regulated by cis elements contained within the message and trans-acting RNA-binding proteins (e.g., She2, Puf2).
Collapse
Affiliation(s)
- Judith Kraut-Cohen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | | | | | | | | | | |
Collapse
|
66
|
Single-molecule reconstitution of mRNA transport by a class V myosin. Nat Struct Mol Biol 2013; 20:952-7. [PMID: 23812374 PMCID: PMC3735863 DOI: 10.1038/nsmb.2614] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 05/14/2013] [Indexed: 12/27/2022]
Abstract
Molecular motors are instrumental in mRNA localization, which provides spatial and temporal control of protein expression and function. To obtain mechanistic insight into how a class V myosin transports mRNA, we performed single-molecule in vitro assays on messenger ribonucleoprotein (mRNP) complexes reconstituted from purified proteins and a localizing mRNA found in budding yeast. mRNA is required to form a stable, processive transport complex on actin--an elegant mechanism to ensure that only cargo-bound motors are motile. Increasing the number of localizing elements ('zip codes') on the mRNA, or configuring the track to resemble actin cables, enhanced run length and event frequency. In multi-zip-code mRNPs, motor separation distance varied during a run, thus showing the dynamic nature of the transport complex. Building the complexity of single-molecule in vitro assays is necessary to understand how these complexes function within cells.
Collapse
|
67
|
Eliscovich C, Buxbaum AR, Katz ZB, Singer RH. mRNA on the move: the road to its biological destiny. J Biol Chem 2013; 288:20361-8. [PMID: 23720759 DOI: 10.1074/jbc.r113.452094] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cells have evolved to regulate the asymmetric distribution of specific mRNA targets to institute spatial and temporal control over gene expression. Over the last few decades, evidence has mounted as to the importance of localization elements in the mRNA sequence and their respective RNA-binding proteins. Live imaging methodologies have shown mechanistic details of this phenomenon. In this minireview, we focus on the advanced biochemical and cell imaging techniques used to tweeze out the finer aspects of mechanisms of mRNA movement.
Collapse
Affiliation(s)
- Carolina Eliscovich
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461, USA
| | | | | | | |
Collapse
|
68
|
Weis BL, Schleiff E, Zerges W. Protein targeting to subcellular organelles via MRNA localization. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1833:260-73. [PMID: 23457718 DOI: 10.1016/j.bbamcr.2012.04.004] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Cells have complex membranous organelles for the compartmentalization and the regulation of most intracellular processes. Organelle biogenesis and maintenance requires newly synthesized proteins, each of which needs to go from the ribosome translating its mRNA to the correct membrane for insertion or transclocation to an a organellar subcompartment. Decades of research have revealed how proteins are targeted to the correct organelle and translocated across one or more organelle membranes ro the compartment where they function. The paradigm examples involve interactions between a peptide sequence in the protein, localization factors, and various membrane embedded translocation machineries. Membrane translocation is either cotranslational or posttranslational depending on the protein and target organelle. Meanwhile research in embryos, neurons and yeast revealed an alternative targeting mechanism in which the mRNA is localized and only then translated to synthesize the protein in the correct location. In these cases, the targeting information is coded by the cis-acting sequences in the mRNA ("Zipcodes") that interact with localization factors and, in many cases, are transported by the molecular motors on the cytoskeletal filaments. Recently, evidence has been found for this "mRNA based" mechanism in organelle protein targeting to endoplasmic reticulum, mitochondria, and the photosynthetic membranes within chloroplasts. Here we review known and potential roles of mRNA localization in protein targeting to and within organelles. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.
Collapse
Affiliation(s)
- Benjamin L Weis
- Goether University, Cluster of Excellence Macromolecular Complexes, Institute for Molecular Biosciences, Max-von-Laue Str. 9, D-60438 Frankfort, Germany
| | | | | |
Collapse
|
69
|
Cody NA, Iampietro C, Lécuyer E. The many functions of mRNA localization during normal development and disease: from pillar to post. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2013; 2:781-96. [DOI: 10.1002/wdev.113] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
70
|
Skamagki M, Wicher KB, Jedrusik A, Ganguly S, Zernicka-Goetz M. Asymmetric localization of Cdx2 mRNA during the first cell-fate decision in early mouse development. Cell Rep 2013; 3:442-57. [PMID: 23375373 PMCID: PMC3607255 DOI: 10.1016/j.celrep.2013.01.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2012] [Revised: 06/01/2012] [Accepted: 01/07/2013] [Indexed: 11/08/2022] Open
Abstract
A longstanding question in mammalian development is whether the divisions that segregate pluripotent progenitor cells for the future embryo from cells that differentiate into extraembryonic structures are asymmetric in cell-fate instructions. The transcription factor Cdx2 plays a key role in the first cell-fate decision. Here, using live-embryo imaging, we show that localization of Cdx2 transcripts becomes asymmetric during development, preceding cell lineage segregation. Cdx2 transcripts preferentially localize apically at the late eight-cell stage and become inherited asymmetrically during divisions that set apart pluripotent and differentiating cells. Asymmetric localization depends on a cis element within the coding region of Cdx2 and requires cell polarization as well as intact microtubule and actin cytoskeletons. Failure to enrich Cdx2 transcripts apically results in a significant decrease in the number of pluripotent cells. We discuss how the asymmetric localization and segregation of Cdx2 transcripts could contribute to multiple mechanisms that establish different cell fates in the mouse embryo.
Collapse
Affiliation(s)
- Maria Skamagki
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, United Kingdom
| | | | | | | | | |
Collapse
|
71
|
Blower MD. Molecular insights into intracellular RNA localization. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2013; 302:1-39. [PMID: 23351709 DOI: 10.1016/b978-0-12-407699-0.00001-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Localization of mRNAs to specific destinations within a cell or an embryo is important for local control of protein synthesis. mRNA localization is well known to function in very large and polarized cells such as neurons, and to facilitate embryonic patterning during early development. However, recent genome-wide studies have revealed that mRNA localization is more widely utilized than previously thought to control gene expression. Not only can transcripts be localized asymmetrically within the cytoplasm, they are often also localized to symmetrically distributed organelles. Recent genetic, cytological, and biochemical studies have begun to provide molecular insight into how cells select RNAs for transport, move them to specific destinations, and control their translation. This chapter will summarize recent insights into the mechanisms and function of RNA localization with a specific emphasis on molecular insights into each step in the mRNA localization process.
Collapse
Affiliation(s)
- Michael D Blower
- Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
72
|
Xing L, Bassell GJ. mRNA localization: an orchestration of assembly, traffic and synthesis. Traffic 2012; 14:2-14. [PMID: 22913533 DOI: 10.1111/tra.12004] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Revised: 08/20/2012] [Accepted: 08/22/2012] [Indexed: 12/14/2022]
Abstract
Asymmetrical mRNA localization and subsequent local translation provide efficient mechanisms for protein sorting in polarized cells. Defects in mRNA localization have been linked to developmental abnormalities and neurological diseases. Thus, it is critical to understand the machineries mediating and mechanisms underlying the asymmetrical distribution of mRNA and its regulation. The goal of this review is to summarize recent advances in the understanding of mRNA transport and localization, including the assembly and sorting of transport messenger ribonucleic protein (mRNP) granules, molecular mechanisms of active mRNP transport, cytoskeletal interactions and regulation of these events by extracellular signals.
Collapse
Affiliation(s)
- Lei Xing
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | | |
Collapse
|
73
|
Farooq M, Choi J, Seoane AI, Lleras RA, Tran HV, Mandal SA, Nelson CL, Soto JG. Identification of 3'UTR sequence elements and a teloplasm localization motif sufficient for the localization of Hro-twist mRNA to the zygotic animal and vegetal poles. Dev Growth Differ 2012; 54:519-34. [PMID: 22587329 DOI: 10.1111/j.1440-169x.2012.01352.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The early localization of mRNA transcripts is critical in sorting cell fate determinants in the developing embryo. In the glossiphoniid leech, Helobdella robusta, maternal mRNAs, such as Hro-twist, localize to the zygotic teloplasm. Ten seven nucleotide repeat elements (AAUAAUA) called ARE2 and a predicted secondary structural motif, called teloplasm localization motif (TLM), are present in the 3'UTR of Hro-twist mRNA. We used site-directed mutagenesis, deletions, and microinjection of labeled, exogenous transcripts to determine if ARE2 elements, and the TLM, play a role in Hro-twist mRNA localization. Deleting the poly-A tail and the cytoplasmic polyadenylation element (CPE) had no effect on Hro-twist mRNA localization. Site-directed mutagenesis of nucleotides that altered ARE2 element sequences or the TLM suggest that the ARE2 elements and the TLM are important for Hro-twist mRNA localization to the teloplasm of pre-cleavage zygotes. Hro-Twist protein expression data suggest that the localization of Hro-twist transcripts in zygotes and stage two embryos is not involved in ensuring mesoderm specification, as Hro-Twist protein is expressed uniformly in most cells before gastrulation. Our data may support a shared molecular mechanism for leech transcripts that localize to the teloplasm.
Collapse
Affiliation(s)
- Mehrin Farooq
- Biological Sciences Department, San Jose State University, San Jose, CA 95192-0100, USA
| | | | | | | | | | | | | | | |
Collapse
|
74
|
Jansen RP, Niessing D. Assembly of mRNA-protein complexes for directional mRNA transport in eukaryotes--an overview. Curr Protein Pept Sci 2012; 13:284-93. [PMID: 22708485 PMCID: PMC3474952 DOI: 10.2174/138920312801619493] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 01/10/2012] [Accepted: 01/20/2012] [Indexed: 12/11/2022]
Abstract
At all steps from transcription to translation, RNA-binding proteins play important roles in determining mRNA function. Initially it was believed that for the vast majority of transcripts the role of RNA-binding proteins is limited to general functions such as splicing and translation. However, work from recent years showed that members of this class of proteins also recognize several mRNAs via cis-acting elements for their incorporation into large motor-containing particles. These particles are transported to distant subcellular sites, where they become subsequently translated. This process, called mRNA localization, occurs along microtubules or actin filaments, and involves kinesins, dyneins, as well as myosins. Although mRNA localization has been detected in a large number of organisms from fungi to humans, the underlying molecular machineries are not well understood. In this review we will outline general principles of mRNA localization and highlight three examples, for which a comparably large body of information is available. The first example is She2p/She3p-dependent localization of ASH1 mRNA in budding yeast. It is particularly well suited to highlight the interdependence between different steps of mRNA localization. The second example is Staufen-dependent localization of oskar mRNA in the Drosophila embryo, for which the importance of nuclear events for cytoplasmic localization and translational control has been clearly demonstrated. The third example summarizes Egalitarian/Bicaudal D-dependent mRNA transport events in the oocyte and embryo of Drosophila. We will highlight general themes and differences, point to similarities in other model systems, and raise open questions that might be answered in the coming years.
Collapse
Affiliation(s)
- Ralf-Peter Jansen
- Interfaculty Institute for Biochemistry, University of Tübingen, Tübingen, Germany
| | - Dierk Niessing
- Institute of Structural Biology, Helmholtz Zentrum München–German Research Center for Environmental Health, München, Germany
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-University, München, Germany
| |
Collapse
|
75
|
Washida H, Sugino A, Doroshenk KA, Satoh-Cruz M, Nagamine A, Katsube-Tanaka T, Ogawa M, Kumamaru T, Satoh H, Okita TW. RNA targeting to a specific ER sub-domain is required for efficient transport and packaging of α-globulins to the protein storage vacuole in developing rice endosperm. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 70:471-9. [PMID: 22168839 DOI: 10.1111/j.1365-313x.2011.04880.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Studies focusing on the targeting of RNAs that encode rice storage proteins, prolamines and glutelins to specific sub-domains of the endoplasmic reticulum (ER), as well as mis-localization studies of other storage protein RNAs, indicate a close relationship between the ER site of RNA translation and the final site of protein deposition in the endomembrane system in developing rice endosperm. In addition to prolamine and glutelin, rice accumulates smaller amounts of α-globulins, which are deposited together with glutelin in the protein storage vacuole (PSV). In situ RT-PCR analysis revealed that α-globulin RNAs are not distributed to the cisternal ER as expected for a PSV-localized protein, but instead are targeted to the protein body-ER (PB-ER) by a regulated process requiring cis-sorting sequences. Sequence alignments with putative maize δ-zein cis-localization elements identified several candidate regulatory sequences that may be responsible for PB-ER targeting. Immunocytochemical analysis confirmed the presence of α-globulin on the periphery of the prolamine protein bodies and packaging in Golgi-associated dense vesicles, as well as deposition and storage within peripheral regions of the PSV. Mis-targeting of α-globulin RNAs to the cisternal ER dramatically alters the spatial arrangement of α-globulin and glutelin within the PSV, with the accompanying presence of numerous small α-globulin particles in the cytoplasm. These results indicate that α-globulin RNA targeting to the PB-ER sub-domain is essential for efficient transport of α-globulins to the PSV and its spatial arrangement in the PSV. Such RNA localization prevents potential deleterious protein-protein interactions, in addition to performing a role in protein targeting.
Collapse
Affiliation(s)
- Haruhiko Washida
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
76
|
Control of RNP motility and localization by a splicing-dependent structure in oskar mRNA. Nat Struct Mol Biol 2012; 19:441-9. [PMID: 22426546 DOI: 10.1038/nsmb.2257] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Accepted: 01/07/2012] [Indexed: 11/08/2022]
Abstract
oskar RNA localization to the posterior pole of the Drosophila melanogaster oocyte requires splicing of the first intron and the exon junction complex (EJC) core proteins. The functional link between splicing, EJC deposition and oskar localization has been unclear. Here we demonstrate that the EJC associates with oskar mRNA upon splicing in vitro and that Drosophila EJC deposition is constitutive and conserved. Our in vivo analysis reveals that splicing creates the spliced oskar localization element (SOLE), whose structural integrity is crucial for ribonucleoprotein motility and localization in the oocyte. Splicing thus has a dual role in oskar mRNA localization: assembling the SOLE and depositing the EJC required for mRNA transport. The SOLE complements the EJC in formation of a functional unit that, together with the oskar 3' UTR, maintains proper kinesin-based motility of oskar mRNPs and posterior mRNA targeting.
Collapse
|
77
|
CodingMotif: exact determination of overrepresented nucleotide motifs in coding sequences. BMC Bioinformatics 2012; 13:32. [PMID: 22333114 PMCID: PMC3298695 DOI: 10.1186/1471-2105-13-32] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Accepted: 02/14/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND It has been increasingly appreciated that coding sequences harbor regulatory sequence motifs in addition to encoding for protein. These sequence motifs are expected to be overrepresented in nucleotide sequences bound by a common protein or small RNA. However, detecting overrepresented motifs has been difficult because of interference by constraints at the protein level. Sampling-based approaches to solve this problem based on codon-shuffling have been limited to exploring only an infinitesimal fraction of the sequence space and by their use of parametric approximations. RESULTS We present a novel O(N(log N)2)-time algorithm, CodingMotif, to identify nucleotide-level motifs of unusual copy number in protein-coding regions. Using a new dynamic programming algorithm we are able to exhaustively calculate the distribution of the number of occurrences of a motif over all possible coding sequences that encode the same amino acid sequence, given a background model for codon usage and dinucleotide biases. Our method takes advantage of the sparseness of loci where a given motif can occur, greatly speeding up the required convolution calculations. Knowledge of the distribution allows one to assess the exact non-parametric p-value of whether a given motif is over- or under- represented. We demonstrate that our method identifies known functional motifs more accurately than sampling and parametric-based approaches in a variety of coding datasets of various size, including ChIP-seq data for the transcription factors NRSF and GABP. CONCLUSIONS CodingMotif provides a theoretically and empirically-demonstrated advance for the detection of motifs overrepresented in coding sequences. We expect CodingMotif to be useful for identifying motifs in functional genomic datasets such as DNA-protein binding, RNA-protein binding, or microRNA-RNA binding within coding regions. A software implementation is available at http://bioinformatics.bc.edu/chuanglab/codingmotif.tar.
Collapse
|
78
|
Shahbabian K, Chartrand P. Control of cytoplasmic mRNA localization. Cell Mol Life Sci 2012; 69:535-52. [PMID: 21984598 PMCID: PMC11115051 DOI: 10.1007/s00018-011-0814-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Revised: 08/09/2011] [Accepted: 09/01/2011] [Indexed: 12/17/2022]
Abstract
mRNA localization is a mechanism used by various organisms to control the spatial and temporal production of proteins. This process is a highly regulated event that requires multiple cis- and trans-acting elements that mediate the accurate localization of target mRNAs. The intrinsic nature of localization elements, together with their interaction with different RNA-binding proteins, establishes control mechanisms that can oversee the transcript from its birth in the nucleus to its specific final destination. In this review, we aim to summarize the different mechanisms of mRNA localization, with a particular focus on the various control mechanisms that affect the localization of mRNAs in the cytoplasm.
Collapse
Affiliation(s)
- Karen Shahbabian
- Department of Biochemistry, Université de Montréal, 2900 Edouard-Montpetit, Montréal, Qc Canada
| | - Pascal Chartrand
- Department of Biochemistry, Université de Montréal, 2900 Edouard-Montpetit, Montréal, Qc Canada
| |
Collapse
|
79
|
An intracellular transmission control protocol: assembly and transport of ribonucleoprotein complexes. Curr Opin Cell Biol 2012; 24:202-10. [PMID: 22278045 DOI: 10.1016/j.ceb.2011.12.014] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Revised: 12/21/2011] [Accepted: 12/27/2011] [Indexed: 12/31/2022]
Abstract
Initially assumed to be a special feature of highly polarized eukaryotic cells, recent evidence suggests that mRNA localization coupled with local translation is a widespread strategy for spatial restriction of protein synthesis within cells. Genome-wide analyses and live imaging approaches have shed new light on the prevalence and the mechanistic details of this phenomenon. Here we review some of the recent findings that have emerged from research from the RNA localization field, from the birth of mRNAs in the nucleus, to their delivery at specific sites within the cytoplasm.
Collapse
|
80
|
Santangelo PJ, Alonas E, Jung J, Lifland AW, Zurla C. Probes for intracellular RNA imaging in live cells. Methods Enzymol 2012; 505:383-99. [PMID: 22289464 DOI: 10.1016/b978-0-12-388448-0.00028-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
RNA localization, dynamics, and regulation are becoming increasingly important to our basic understanding of gene expression and RNA virus pathogenesis. An improved understanding of these processes will be necessary in order to identify new drug targets, as well as to create models of gene expression networks. Much of this new understanding will likely come from imaging studies of RNA, which can generate the spatiotemporal information necessary to characterize RNA within the cellular milieu. Ideally, this would be performed imaging native, nonengineered RNAs, but the approaches for performing these experiments are still evolving. In order for them to reach their potential, it is critical that they have characteristics that allow for the tracking of RNA throughout their life cycle. This chapter presents an overview of RNA imaging methodologies, and focuses on a single RNA sensitive method, employing exogenous probes, for imaging, native, nonengineered RNA in live cells.
Collapse
Affiliation(s)
- Philip J Santangelo
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, USA
| | | | | | | | | |
Collapse
|
81
|
Xu Z, Almudevar A, Mathews DH. Statistical evaluation of improvement in RNA secondary structure prediction. Nucleic Acids Res 2011; 40:e26. [PMID: 22139940 PMCID: PMC3287165 DOI: 10.1093/nar/gkr1081] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
With discovery of diverse roles for RNA, its centrality in cellular functions has become increasingly apparent. A number of algorithms have been developed to predict RNA secondary structure. Their performance has been benchmarked by comparing structure predictions to reference secondary structures. Generally, algorithms are compared against each other and one is selected as best without statistical testing to determine whether the improvement is significant. In this work, it is demonstrated that the prediction accuracies of methods correlate with each other over sets of sequences. One possible reason for this correlation is that many algorithms use the same underlying principles. A set of benchmarks published previously for programs that predict a structure common to three or more sequences is statistically analyzed as an example to show that it can be rigorously evaluated using paired two-sample t-tests. Finally, a pipeline of statistical analyses is proposed to guide the choice of data set size and performance assessment for benchmarks of structure prediction. The pipeline is applied using 5S rRNA sequences as an example.
Collapse
Affiliation(s)
- Zhenjiang Xu
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, USA
| | | | | |
Collapse
|
82
|
Batagov AO, Kuznetsov VA, Kurochkin IV. Identification of nucleotide patterns enriched in secreted RNAs as putative cis-acting elements targeting them to exosome nano-vesicles. BMC Genomics 2011; 12 Suppl 3:S18. [PMID: 22369587 PMCID: PMC3333177 DOI: 10.1186/1471-2164-12-s3-s18] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background Exosomes are nanoscale membrane vesicles released by most cells. They are postulated to be involved in cell–cell communication and genetic reprogramming of their target cells. In addition to proteins and lipids, they release RNA molecules many of which are not present in the donor cells implying a highly selective mode of their packaging into these vesicles. Sequence motifs targeting RNA to the vesicles are currently unknown. Results Ab initio approach was applied for computational identification of potential RNA secretory motifs in the primary sequences of exosome-enriched RNAs (eRNAs). Exhaustive motif analysis for the first time revealed unique sequence features of eRNAs. We discovered multiple linear motifs specifically enriched in secreted RNAs. Their potential function as cis-acting elements targeting RNAs to exosomes is proposed. The motifs co-localized in the same transcripts suggesting combinatorial organization of these secretory signals. We investigated associations of the discovered motifs with other RNA parameters. Secreted RNAs were found to have almost twice shorter half-life times on average, in comparison with cytoplasmic RNAs, and the occurrence of some eRNA-specific motifs significantly correlated with this eRNA feature. Also, we found that eRNAs are highly enriched in long noncoding RNAs. Conclusions Secreted RNAs share specific sequence motifs that may potentially function as cis-acting elements targeting RNAs to exosomes. Discovery of these motifs will be useful for our understanding the roles of eRNAs in cell-cell communication and genetic reprogramming of the target cells. It will also facilitate nano-scale vesicle engineering and selective targeting of RNAs of interest to these vesicles for gene therapy purposes.
Collapse
Affiliation(s)
- Arsen O Batagov
- Department of Genome and Gene Expression Data Analysis, Bioinformatics Institute, 30 Biopolis str #07-01, Singapore, 138671.
| | | | | |
Collapse
|
83
|
Muslimov IA, Patel MV, Rose A, Tiedge H. Spatial code recognition in neuronal RNA targeting: role of RNA-hnRNP A2 interactions. ACTA ACUST UNITED AC 2011; 194:441-57. [PMID: 21807882 PMCID: PMC3153643 DOI: 10.1083/jcb.201010027] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Recognition of non-canonical purine•purine RNA motifs by hnRNP A2 mediates targeted delivery of neuronal RNAs to dendrites. In neurons, regulation of gene expression occurs in part through translational control at the synapse. A fundamental requirement for such local control is the targeted delivery of select neuronal mRNAs and regulatory RNAs to distal dendritic sites. The nature of spatial RNA destination codes, and the mechanism by which they are interpreted for dendritic delivery, remain poorly understood. We find here that in a key dendritic RNA transport pathway (exemplified by BC1 RNA, a dendritic regulatory RNA, and protein kinase M ζ [PKMζ] mRNA, a dendritic mRNA), noncanonical purine•purine nucleotide interactions are functional determinants of RNA targeting motifs. These motifs are specifically recognized by heterogeneous nuclear ribonucleoprotein A2 (hnRNP A2), a trans-acting factor required for dendritic delivery. Binding to hnRNP A2 and ensuing dendritic delivery are effectively competed by RNAs with CGG triplet repeat expansions. CGG repeats, when expanded in the 5′ untranslated region of fragile X mental retardation 1 (FMR1) mRNA, cause fragile X–associated tremor/ataxia syndrome. The data suggest that cellular dysregulation observed in the presence of CGG repeat RNA may result from molecular competition in neuronal RNA transport pathways.
Collapse
Affiliation(s)
- Ilham A Muslimov
- The Robert F. Furchgott Center for Neural and Behavioral Science, Department of Physiology and Pharmacology, State University of New York, Health Science Center at Brooklyn, USA
| | | | | | | |
Collapse
|
84
|
Kilchert C, Spang A. Cotranslational transport of ABP140 mRNA to the distal pole of S. cerevisiae. EMBO J 2011; 30:3567-80. [PMID: 21792172 DOI: 10.1038/emboj.2011.247] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Accepted: 06/24/2011] [Indexed: 11/09/2022] Open
Abstract
In budding yeast, several mRNAs are selectively transported into the daughter cell in an actin-dependent manner by a specialized myosin system, the SHE machinery. With ABP140 mRNA, we now describe the first mRNA that is transported in the opposite direction and localizes to the distal pole of the mother cell, independent of the SHE machinery. Distal pole localization is not observed in mutants devoid of actin cables and can be disrupted by latrunculin A. Furthermore, localization of ABP140 mRNA requires the N-terminal actin-binding domain of Abp140p to be expressed. By replacing the N-terminal localization motif, ABP140 mRNA can be retargeted to different subcellular structures. In addition, accumulation of the mRNA at the distal pole can be prevented by disruption of polysomes. Using the MS2 system, the mRNA was found to associate with actin cables and to follow actin cable dynamics. We therefore propose a model of translational coupling, in which ABP140 mRNA is tethered to actin cables via its nascent protein product and is transported to the distal pole by actin retrograde flow.
Collapse
|
85
|
Abstract
mRNA transport is a widely used method to achieve the asymmetric distribution of proteins within a cell or organism. In order to understand how RNA is transported, it is essential to utilize a system that can readily detect RNA movement in live cells. The tagged RNA system has recently emerged as a feasible non-invasive solution for such purpose. In this chapter, we describe in detail the U1A-based tagged RNA system. This system coexpresses U1Ap-GFP with the RNA of interest tagged with U1A aptamers, and has been proven to effectively track RNA in vivo. In addition, we provide further applications of the system for ribonucleoprotein complex purification by TAP-tagging the U1Ap-GFP construct.
Collapse
|
86
|
VerMilyea MD, Maneck M, Yoshida N, Blochberger I, Suzuki E, Suzuki T, Spang R, Klein CA, Perry ACF. Transcriptome asymmetry within mouse zygotes but not between early embryonic sister blastomeres. EMBO J 2011; 30:1841-51. [PMID: 21468028 PMCID: PMC3101998 DOI: 10.1038/emboj.2011.92] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Accepted: 03/03/2011] [Indexed: 11/09/2022] Open
Abstract
Transcriptome regionalization is an essential polarity determinant among metazoans, directing embryonic axis formation during normal development. Although conservation of this principle in mammals is assumed, recent evidence is conflicting and it is not known whether transcriptome asymmetries exist within unfertilized mammalian eggs or between the respective cleavage products of early embryonic divisions. We here address this by comparing transcriptome profiles of paired single cells and sub-cellular structures obtained microsurgically from mouse oocytes and totipotent embryos. Paired microsurgical spindle and remnant samples from unfertilized metaphase II oocytes possessed distinguishable profiles. Fertilization produces a totipotent 1-cell embryo (zygote) and associated spindle-enriched second polar body whose paired profiles also differed, reflecting spindle transcript enrichment. However, there was no programmed transcriptome asymmetry between sister cells within 2- or 3-cell embryos. Accordingly, there is transcriptome asymmetry within mouse oocytes, but not between the sister blastomeres of early embryos. This work places constraints on pre-patterning in mammals and provides documentation correlating potency changes and transcriptome partitioning at the single-cell level.
Collapse
Affiliation(s)
- Matthew D VerMilyea
- Laboratory of Mammalian Molecular Embryology, RIKEN Center for Developmental Biology, Kobe, Japan
| | - Matthias Maneck
- Department of Pathology, University of Regensburg, Regensburg, Germany
- Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Naoko Yoshida
- Laboratory of Mammalian Molecular Embryology, RIKEN Center for Developmental Biology, Kobe, Japan
- Department of Biomedical Sciences, Ritsumeikan University, Shiga, Japan
| | | | - Emi Suzuki
- Laboratory of Mammalian Molecular Embryology, RIKEN Center for Developmental Biology, Kobe, Japan
| | - Toru Suzuki
- Laboratory of Mammalian Molecular Embryology, RIKEN Center for Developmental Biology, Kobe, Japan
- Department of Biology and Biochemistry, Laboratory of Mammalian Molecular Embryology, and Bath Centre for Regenerative Medicine, University of Bath, Bath, UK
| | - Rainer Spang
- Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Christoph A Klein
- Department of Pathology, University of Regensburg, Regensburg, Germany
| | - Anthony C F Perry
- Laboratory of Mammalian Molecular Embryology, RIKEN Center for Developmental Biology, Kobe, Japan
- Department of Biology and Biochemistry, Laboratory of Mammalian Molecular Embryology, and Bath Centre for Regenerative Medicine, University of Bath, Bath, UK
| |
Collapse
|
87
|
Raju CS, Fukuda N, López-Iglesias C, Göritz C, Visa N, Percipalle P. In neurons, activity-dependent association of dendritically transported mRNA transcripts with the transacting factor CBF-A is mediated by A2RE/RTS elements. Mol Biol Cell 2011; 22:1864-77. [PMID: 21471000 PMCID: PMC3103402 DOI: 10.1091/mbc.e10-11-0904] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We report that the transacting factor CArG Box binding Factor A (CBF-A) binds the RNA trafficking sequences found in activity-regulated cytoskeleton-associated protein, calmodulin-dependent protein kinase II, and brain-derived neurotrophic factor mRNAs in an activity-dependent manner and accompanies the transcripts from gene to dendrites. CBF-A gene silencing impaired dendritic mRNA localization. We propose that CBF-A is important for trafficking of RNA trafficking sequence–containing neuronal mRNAs. In neurons certain mRNA transcripts are transported to synapses through mechanisms that are not fully understood. Here we report that the heterogeneous nuclear ribonucleoprotein CBF-A (CArG Box binding Factor A) facilitates dendritic transport and localization of activity-regulated cytoskeleton-associated protein (Arc), brain-derived neurotrophic factor (BDNF), and calmodulin-dependent protein kinase II (CaMKIIα) mRNAs. We discovered that, in the adult mouse brain, CBF-A has a broad distribution. In the nucleus, CBF-A was found at active transcription sites and interchromosomal spaces and close to nuclear pores. In the cytoplasm, CBF-A localized to dendrites as well as pre- and postsynaptic sites. CBF-A was found in synaptosomal fractions, associated with Arc, BDNF, and CaMKIIα mRNAs. Electrophoretic mobility shift assays demonstrated a direct interaction mediated via their hnRNP A2 response element (A2RE)/RNA trafficking sequence (RTS) elements located in the 3′ untranslated regions. In situ hybridization and microscopy on live hippocampal neurons showed that CBF-A is in dynamic granules containing Arc, BDNF, and CaMKIIα mRNAs. N-methyl-d-aspartate (NMDA) and α-amino-3-hydroxyl-5-methyl-4-isoxazole-propionate (AMPA) postsynaptic receptor stimulation led to CBF-A accumulation in dendrites; increased Arc, BDNF, and CaMKIIα mRNA levels; and increased amounts of transcripts coprecipitating with CBF-A. Finally, CBF-A gene knockdown led to decreased mRNA levels. We propose that CBF-A cotranscriptionally binds RTSs in Arc, BDNF, and CaMKIIα mRNAs and follows the transcripts from genes to dendrites, promoting activity-dependent nuclear sorting of transport-competent mRNAs.
Collapse
Affiliation(s)
- Chandrasekhar S Raju
- Department of Cell and Molecular Biology, Karolinska Institutet, S-171 77 Stockholm, Sweden
| | | | | | | | | | | |
Collapse
|
88
|
Jo A, Nam YJ, Oh JY, Cheon HS, Jeromin A, Lee JA, Kim HK. Dendritic localization and a cis-acting dendritic targeting element of Kv4.2 mRNA. BMB Rep 2011; 43:677-82. [PMID: 21034530 DOI: 10.5483/bmbrep.2010.43.10.677] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Kv4.2, a pore-forming α-subunit of voltage-gated A-type potassium channels, is expressed abundantly in the soma and dendrites of hippocampal neurons, and is responsible for somatodendritic I(A) current. Recent studies have suggested that changes in the surface levels of Kv4.2 potassium channels might be relevant to synaptic plasticity. Although the function and expression of Kv4.2 protein have been extensively studied, the dendritic localization of Kv4.2 mRNA is not well described. In this study, Kv4.2 mRNAs were shown to be localized in the dendrites near postsynaptic regions. The dendritic transport of Kv4.2 mRNAs were mediated by microtubule- based movement. The 500 nucleotides of specific regions within the 3'-untranslated region of Kv4.2 mRNA were found to be necessary and sufficient for its dendritic localization. Collectively, these results suggest that the dendritic localization of Kv4.2 mRNAs might regulate the dendritic surface level of Kv4.2 channels and synaptic plasticity.
Collapse
Affiliation(s)
- Anna Jo
- Department of Medicine and Microbiology, College of Medicine, Signaling Disorder Research Center, Chungbuk National University, Cheongju 361-763, Korea
| | | | | | | | | | | | | |
Collapse
|
89
|
Abstract
Interest in the mechanisms of subcellular localization of mRNAs and the effects of localized translation has increased over the last decade. Polarized eukaryotic cells transport mRNA-protein complexes to subcellular sites, where translation of the mRNAs can be regulated by physiological stimuli. The long distances separating distal neuronal processes from their cell body have made neurons a useful model system for dissecting mechanisms of mRNA trafficking. Both the dendritic and axonal processes of neurons have been shown to have protein synthetic capacity and the diversity of mRNAs discovered in these processes continues to increase. Localized translation of mRNAs requires a co-ordinated effort by the cell body to target both mRNAs and necessary translational machinery into distal sites, as well as temporal control of individual mRNA translation. In addition to altering protein composition locally at the site of translation, some of the proteins generated in injured nerves retrogradely signal to the cell body, providing both temporal and spatial information on events occurring at distant subcellular sites.
Collapse
Affiliation(s)
| | - Mike Fainzilber
- Department of Biological Chemistry, Weizmann Institute, Rehovot, Israel
| | - Jeffery L. Twiss
- Department of Biological Science, University of Delaware, Newark, Delaware USA
- Department of Biology, Drexel University, Philadelphia, Pennsylvania USA
| |
Collapse
|
90
|
Kraut-Cohen J, Gerst JE. Addressing mRNAs to the ER: cis sequences act up! Trends Biochem Sci 2010; 35:459-69. [DOI: 10.1016/j.tibs.2010.02.006] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Revised: 02/15/2010] [Accepted: 02/18/2010] [Indexed: 12/26/2022]
|
91
|
Chung S, Takizawa PA. Multiple Myo4 motors enhance ASH1 mRNA transport in Saccharomyces cerevisiae. J Cell Biol 2010; 189:755-67. [PMID: 20457760 PMCID: PMC2872910 DOI: 10.1083/jcb.200912011] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Accepted: 04/15/2010] [Indexed: 11/22/2022] Open
Abstract
In Saccharomyces cerevisiae, ASH1 mRNA is transported to the bud tip by the class V myosin Myo4. In vivo, Myo4 moves RNA in a rapid and continuous fashion, but in vitro Myo4 is a nonprocessive, monomeric motor that forms a complex with She3. To understand how nonprocessive motors generate continuous transport, we used a novel purification method to show that Myo4, She3, and the RNA-binding protein She2 are the sole major components of an active ribonucleoprotein transport unit. We demonstrate that a single localization element contains multiple copies of Myo4 and a tetramer of She2, which suggests that She2 may recruit multiple motors to an RNA. Furthermore, we show that increasing the number of Myo4-She3 molecules bound to ASH1 RNA in the absence of She2 increases the efficiency of RNA transport to the bud. Our data suggest that multiple, nonprocessive Myo4 motors can generate continuous transport of mRNA to the bud tip.
Collapse
Affiliation(s)
- Sunglan Chung
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA
| | | |
Collapse
|
92
|
Crofts AJ, Crofts N, Whitelegge JP, Okita TW. Isolation and identification of cytoskeleton-associated prolamine mRNA binding proteins from developing rice seeds. PLANTA 2010; 231:1261-76. [PMID: 20217123 DOI: 10.1007/s00425-010-1125-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Accepted: 02/10/2010] [Indexed: 05/08/2023]
Abstract
The messenger RNA of the rice seed storage protein prolamine is targeted to the endoplasmic reticulum (ER) membranes surrounding prolamine protein bodies via a mechanism, which is dependent upon both RNA sorting signals and the actin cytoskeleton. In this study we have used an RNA bait corresponding to the previously characterized 5'CDS prolamine cis-localization sequence for the capture of RNA binding proteins (RBPs) from cytoskeleton-enriched fractions of developing rice seed. In comparison to a control RNA, the cis-localization RNA bait sequence led to the capture of a much larger number of proteins, 18 of which have been identified by tandem mass spectrometry. Western blots demonstrate that several of the candidate proteins analyzed to date show good to excellent specificity for binding to cis-localization sequences over the control RNA bait. Temporal expression studies showed that steady state protein levels for one RNA binding protein, RBP-A, paralleled prolamine gene expression. Immunoprecipitation studies showed that RBP-A is bound to prolamine and glutelin RNAs in vivo, supporting a direct role in storage protein gene expression. Using confocal immunofluorescence microscopy, RBP-A was found to be distributed to multiple compartments in the cell. In addition to the nucleus, RBP-A co-localizes with microtubules and is associated with cortical ER membranes. Collectively, these results indicate that employing a combination of in vitro binding and in vivo binding and localization studies is a valid strategy for the identification of putative prolamine mRNA binding proteins, such as RBP-A, which play a role in controlling expression of storage protein mRNAs in the cytoplasm.
Collapse
Affiliation(s)
- Andrew J Crofts
- Institute of Biological Chemistry, Washington State University, Clark Hall, Room #299, 100 Dairy Road, Pullman, WA 99164-6340, USA.
| | | | | | | |
Collapse
|
93
|
Yoo S, van Niekerk EA, Merianda TT, Twiss JL. Dynamics of axonal mRNA transport and implications for peripheral nerve regeneration. Exp Neurol 2010; 223:19-27. [PMID: 19699200 PMCID: PMC2849851 DOI: 10.1016/j.expneurol.2009.08.011] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Revised: 08/05/2009] [Accepted: 08/08/2009] [Indexed: 12/12/2022]
Abstract
Locally generating new proteins in subcellular regions provide means to spatially and temporally modify protein content in polarized cells. Recent years have seen resurgence of the concept that axonal processes of neurons can locally synthesize proteins. Experiments from a number of groups have now shown that axonal protein synthesis helps to initiate growth, provides a means to respond to guidance cues, and generates retrograde signaling complexes. Additionally, there is increasing evidence that locally synthesized proteins provide functions beyond injury responses and growth in the mature peripheral nervous system. A key regulatory event in this translational regulation is moving the mRNA templates into the axonal compartment. Transport of mRNAs into axons is a highly regulated and specific process that requires interaction of RNA binding proteins with specific cis-elements or structures within the mRNAs. mRNAs are transported in ribonucleoprotein particles that interact with microtubule motor proteins for long-range axonal transport and likely use microfilaments for short-range movement in the axons. The mature axon is able to recruit mRNAs into translation with injury and possibly other stimuli, suggesting that mRNAs can be stored in a dormant state in the distal axon until needed. Axotomy triggers a shift in the populations of mRNAs localized to axons, indicating a dynamic regulation of the specificity of the axonal transport machinery. In this review, we discuss how axonal mRNA transport and localization are regulated to achieve specific changes in axonal RNA content in response to axonal stimuli.
Collapse
Affiliation(s)
- Soonmoon Yoo
- Nemours Biomedical Research, Alfred I. DuPont Hospital for Children, Wilmington, Delaware 19803
| | - Erna A. van Niekerk
- Department of Neurosciences, University of California, San Diego, La Jolla, California 92093
| | - Tanuja T. Merianda
- Nemours Biomedical Research, Alfred I. DuPont Hospital for Children, Wilmington, Delaware 19803
| | - Jeffery L. Twiss
- Nemours Biomedical Research, Alfred I. DuPont Hospital for Children, Wilmington, Delaware 19803
- Department of Biological Sciences, University of Delaware, Newark, Delaware 19716
| |
Collapse
|
94
|
Aschrafi A, Natera-Naranjo O, Gioio AE, Kaplan BB. Regulation of axonal trafficking of cytochrome c oxidase IV mRNA. Mol Cell Neurosci 2010; 43:422-30. [PMID: 20144716 PMCID: PMC2845174 DOI: 10.1016/j.mcn.2010.01.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Revised: 01/20/2010] [Accepted: 01/26/2010] [Indexed: 01/10/2023] Open
Abstract
Trafficking and local translation of axonal mRNAs play a critical role in the development and function of this neuronal subcellular structural domain. In this report, we studied cytochrome c oxidase subunit IV (COXIV) mRNA trafficking into distal axons of primary superior cervical ganglia (SCG) neurons, and provided evidence that axonal trafficking and mitochondrial association of the mRNA are mediated by an element located in a 38bp-long, hairpin-loop forming region within the 3'UTR of the transcript. Our results also suggest that suppression of local translation of COXIV mRNA results in significant attenuation of axonal elongation. Taken together, the results provide the first evidence for the existence of a cis-acting axonal transport element within a nuclear-encoding mitochondrial gene, and demonstrate the importance of the axonal trafficking and local translation of nuclear-encoded mitochondrial mRNAs in axonal growth.
Collapse
Affiliation(s)
- Armaz Aschrafi
- Laboratory of Molecular Biology, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892-1381, USA
| | - Orlangie Natera-Naranjo
- Laboratory of Molecular Biology, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892-1381, USA
| | - Anthony E. Gioio
- Laboratory of Molecular Biology, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892-1381, USA
| | - Barry B. Kaplan
- Laboratory of Molecular Biology, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892-1381, USA
| |
Collapse
|
95
|
Vuppalanchi D, Coleman J, Yoo S, Merianda TT, Yadhati AG, Hossain J, Blesch A, Willis DE, Twiss JL. Conserved 3'-untranslated region sequences direct subcellular localization of chaperone protein mRNAs in neurons. J Biol Chem 2010; 285:18025-38. [PMID: 20308067 DOI: 10.1074/jbc.m109.061333] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
mRNA localization provides polarized cells with a locally renewable source of proteins. In neurons, mRNA translation can occur at millimeters to centimeters from the cell body, giving the dendritic and axonal processes a means to autonomously respond to their environment. Despite that hundreds of mRNAs have been detected in neuronal processes, there are no reliable means to predict mRNA localization elements. Here, we have asked what RNA elements are needed for localization of transcripts encoding endoplasmic reticulum chaperone proteins in neurons. The 3'-untranslated regions (UTRs) of calreticulin and Grp78/BiP mRNAs show no homology to one another, but each shows extensive regions of high sequence identity to their 3'UTRs in mammalian orthologs. These conserved regions are sufficient for subcellular localization of reporter mRNAs in neurons. The 3'UTR of calreticulin has two conserved regions, and either of these is sufficient for axonal and dendritic targeting. However, only nucleotides 1315-1412 show ligand responsiveness to neurotrophin 3 (NT3) and myelin-associated glycoprotein (MAG). This NT3- and MAG-dependent axonal mRNA transport requires activation of JNK, both for calreticulin mRNA and for other mRNAs whose axonal levels are commonly regulated by NT3 and MAG.
Collapse
Affiliation(s)
- Deepika Vuppalanchi
- Department of Biological Sciences, University of Delaware, Newark, Delaware 19716, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
96
|
Claussen M, Pieler T. Identification of vegetal RNA-localization elements in Xenopus oocytes. Methods 2010; 51:146-51. [PMID: 20178845 DOI: 10.1016/j.ymeth.2010.02.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Revised: 02/15/2010] [Accepted: 02/16/2010] [Indexed: 11/17/2022] Open
Abstract
Localized mRNAs have been identified in a large variety of cell types where they contribute to the establishment of cell asymmetries and can function as cell fate determinants. In Xenopus, RNAs that localize to the vegetal cortex during oogenesis function in early embryonic patterning as well as in the development of primordial germ cells. Based on their temporal and spatial localization patterns, vegetally localizing RNAs are referred to as either early-pathway RNAs which transiently localize in the mitochondrial cloud, or as late-pathway RNAs. Vegetal RNA-localization is driven by cis-acting signal sequences that, in most cases, were found to reside in the 3'-UTRs and which are recognized by trans-acting localization factors. Here we describe the methods of how vegetal RNA-localization elements can be identified by injection of fluorescently-labeled or tagged RNAs.
Collapse
Affiliation(s)
- Maike Claussen
- Department of Developmental Biochemistry, Göttingen Center for Molecular Biosciences, Justus-von-Liebig-Weg 11, Göttingen, Germany
| | | |
Collapse
|
97
|
Abstract
Subcellular localization of messenger RNAs (mRNAs) can give precise control over where protein products are synthesized and operate. However, just 10 years ago many in the broader cell biology community would have considered this a specialized mechanism restricted to a very small fraction of transcripts. Since then, it has become clear that subcellular targeting of mRNAs is prevalent, and there is mounting evidence for central roles for this process in many cellular events. Here, we review current knowledge of the mechanisms and functions of mRNA localization in animal cells.
Collapse
Affiliation(s)
- Christine E. Holt
- Department of Physiology, Development, and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - Simon L. Bullock
- Cell Biology Division, Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| |
Collapse
|
98
|
Kural D, Ding Y, Wu J, Korpi AM, Chuang JH. COMIT: identification of noncoding motifs under selection in coding sequences. Genome Biol 2009; 10:R133. [PMID: 19930548 PMCID: PMC3091326 DOI: 10.1186/gb-2009-10-11-r133] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Revised: 09/18/2009] [Accepted: 11/20/2009] [Indexed: 11/16/2022] Open
Abstract
COMIT is presented; an algorithm for detecting functional non-coding motifs in coding regions, separating nucleotide and amino acid effects. Coding nucleotide sequences contain myriad functions independent of their encoded protein sequences. We present the COMIT algorithm to detect functional noncoding motifs in coding regions using sequence conservation, explicitly separating nucleotide from amino acid effects. COMIT concurs with diverse experimental datasets, including splicing enhancers, silencers, replication motifs, and microRNA targets, and predicts many novel functional motifs. Intriguingly, COMIT scores are well-correlated to scores uncalibrated for amino acids, suggesting that nucleotide motifs often override peptide-level constraints.
Collapse
Affiliation(s)
- Deniz Kural
- Department of Biology, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA.
| | | | | | | | | |
Collapse
|
99
|
Washida H, Sugino A, Kaneko S, Crofts N, Sakulsingharoj C, Kim D, Choi SB, Hamada S, Ogawa M, Wang C, Esen A, Higgins TJV, Okita TW. Identification of cis-localization elements of the maize 10-kDa delta-zein and their use in targeting RNAs to specific cortical endoplasmic reticulum subdomains. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 60:146-155. [PMID: 19508424 DOI: 10.1111/j.1365-313x.2009.03944.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The RNAs for the storage proteins of rice (Oryza sativa), prolamines and glutelins, which are stored as inclusions in the lumen of the endoplasmic reticulum (ER) and storage vacuoles, respectively, are targeted by specific cis-localization elements to distinct subdomains of the cortical ER. Glutelin RNA has one or more cis-localization elements (zip codes) at the 3' end of the RNA, whereas prolamine has two cis-elements; one located in the 5' end of the coding sequence and a second residing in the 3'-untranslated region (UTR). We had earlier demonstrated that the RNAs for the maize zeins ('prolamine' class) are localized to the spherical protein body ER (PB-ER) in developing maize endosperm. As the PB-ER localization of the 10-kDa delta-zein RNA is maintained in developing rice seeds, we determined the number and proximate location of their cis-localization elements by expressing GFP fusions containing various zein RNA sequences in transgenic rice and analyzing their spatial distribution on the cortical ER by in situ RT-PCR and confocal microscopy. Four putative cis-localization elements were identified; three in the coding sequences and one in the 3'-UTR. Two of these zip codes are required for restricted localization to the PB-ER. Using RNA targeting determinants we show, by mis-targeting the storage protein RNAs from their normal destination on the cortical ER, that the coded proteins are redirected from their normal site of deposition. Targeting of RNA to distinct cortical ER subdomains may be the underlying basis for the variable use of the ER lumen or storage vacuole as the final storage deposition site of storage proteins among flowering plant species.
Collapse
Affiliation(s)
- Haruhiko Washida
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
100
|
Santangelo PJ. Molecular beacons and related probes for intracellular RNA imaging. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2009; 2:11-9. [DOI: 10.1002/wnan.52] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
|