1
|
Kubíková J, Reinig R, Salgania HK, Jeske M. LOTUS-domain proteins - developmental effectors from a molecular perspective. Biol Chem 2020; 402:7-23. [DOI: 10.1515/hsz-2020-0270] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 10/19/2020] [Indexed: 12/15/2022]
Abstract
Abstract
The LOTUS domain (also known as OST-HTH) is a highly conserved protein domain found in a variety of bacteria and eukaryotes. In animals, the LOTUS domain is present in the proteins Oskar, TDRD5/Tejas, TDRD7/TRAP/Tapas, and MARF1/Limkain B1, all of which play essential roles in animal development, in particular during oogenesis and/or spermatogenesis. This review summarizes the diverse biological as well as molecular functions of LOTUS-domain proteins and discusses their roles as helicase effectors, post-transcriptional regulators, and critical cofactors of piRNA-mediated transcript silencing.
Collapse
Affiliation(s)
- Jana Kubíková
- Heidelberg University Biochemistry Center , Im Neuenheimer Feld 328 , D-69120 Heidelberg , Germany
| | - Rebecca Reinig
- Heidelberg University Biochemistry Center , Im Neuenheimer Feld 328 , D-69120 Heidelberg , Germany
| | - Harpreet Kaur Salgania
- Heidelberg University Biochemistry Center , Im Neuenheimer Feld 328 , D-69120 Heidelberg , Germany
| | - Mandy Jeske
- Heidelberg University Biochemistry Center , Im Neuenheimer Feld 328 , D-69120 Heidelberg , Germany
| |
Collapse
|
2
|
Kaymak E, Farley BM, Hay SA, Li C, Ho S, Hartman DJ, Ryder SP. Efficient generation of transgenic reporter strains and analysis of expression patterns in Caenorhabditis elegans using library MosSCI. Dev Dyn 2016; 245:925-36. [PMID: 27294288 PMCID: PMC4981527 DOI: 10.1002/dvdy.24426] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 05/09/2016] [Accepted: 06/03/2016] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND In C. elegans, germline development and early embryogenesis rely on posttranscriptional regulation of maternally transcribed mRNAs. In many cases, the 3' untranslated region (UTR) is sufficient to govern the expression patterns of these transcripts. Several RNA-binding proteins are required to regulate maternal mRNAs through the 3'UTR. Despite intensive efforts to map RNA-binding protein-mRNA interactions in vivo, the biological impact of most binding events remains unknown. Reporter studies using single copy integrated transgenes are essential to evaluate the functional consequences of interactions between RNA-binding proteins and their associated mRNAs. RESULTS In this report, we present an efficient method of generating reporter strains with improved throughput by using a library variant of MosSCI transgenesis. Furthermore, using RNA interference, we identify the suite of RNA-binding proteins that control the expression pattern of five different maternal mRNAs. CONCLUSIONS The results provide a generalizable and efficient strategy to assess the functional relevance of protein-RNA interactions in vivo, and reveal new regulatory connections between key RNA-binding proteins and their maternal mRNA targets. Developmental Dynamics 245:925-936, 2016. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Ebru Kaymak
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Brian M. Farley
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
| | - Samantha A. Hay
- Virginia Commonwealth University School of Medicine, VA, USA
| | - Chihua Li
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Samantha Ho
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | | | - Sean P. Ryder
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| |
Collapse
|
3
|
Kim SY, Kim JY, Malik S, Son W, Kwon KS, Kim C. Negative regulation of EGFR/MAPK pathway by Pumilio in Drosophila melanogaster. PLoS One 2012; 7:e34016. [PMID: 22514614 PMCID: PMC3326002 DOI: 10.1371/journal.pone.0034016] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2011] [Accepted: 02/21/2012] [Indexed: 12/19/2022] Open
Abstract
In Drosophila melanogaster, specification of wing vein cells and sensory organ precursor (SOP) cells, which later give rise to a bristle, requires EGFR signaling. Here, we show that Pumilio (Pum), an RNA-binding translational repressor, negatively regulates EGFR signaling in wing vein and bristle development. We observed that loss of Pum function yielded extra wing veins and additional bristles. Conversely, overexpression of Pum eliminated wing veins and bristles. Heterozygotes for Pum produced no phenotype on their own, but greatly enhanced phenotypes caused by the enhancement of EGFR signaling. Conversely, over-expression of Pum suppressed the effects of ectopic EGFR signaling. Components of the EGFR signaling pathway are encoded by mRNAs that have Nanos Response Element (NRE)–like sequences in their 3’UTRs; NREs are known to bind Pum to confer regulation in other mRNAs. We show that these NRE-like sequences bind Pum and confer repression on a luciferase reporter in heterologous cells. Taken together, our evidence suggests that Pum functions as a negative regulator of EGFR signaling by directly targeting components of the pathway in Drosophila.
Collapse
Affiliation(s)
- Sung Yun Kim
- Hormone Research Center, School of Biological Sciences and Technology, Chonnam National University, Yongbong-Dong, Gwangju, South Korea
| | - Ji Young Kim
- Hormone Research Center, School of Biological Sciences and Technology, Chonnam National University, Yongbong-Dong, Gwangju, South Korea
- Aging Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, South Korea
| | - Sumira Malik
- Hormone Research Center, School of Biological Sciences and Technology, Chonnam National University, Yongbong-Dong, Gwangju, South Korea
| | - Wonseok Son
- Department of Biological Science, KAIST (Korea Advanced Institute of Science and Technology), Daejeon, South Korea
| | - Ki-Sun Kwon
- Aging Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, South Korea
| | - Changsoo Kim
- Hormone Research Center, School of Biological Sciences and Technology, Chonnam National University, Yongbong-Dong, Gwangju, South Korea
- * E-mail:
| |
Collapse
|
4
|
The SXL-UNR corepressor complex uses a PABP-mediated mechanism to inhibit ribosome recruitment to msl-2 mRNA. Mol Cell 2009; 36:571-82. [PMID: 19941818 DOI: 10.1016/j.molcel.2009.09.042] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Revised: 07/06/2009] [Accepted: 09/08/2009] [Indexed: 11/22/2022]
Abstract
Drosophila female viability requires translational repression of msl-2 mRNA by the SXL-UNR 3' UTR corepressor complex, which inhibits ribosome recruitment by an unknown mechanism. Here, we reveal a key role for the poly(A)-binding protein (PABP), a translational activator, in this inhibitory mechanism. Efficient msl-2 mRNA silencing via the 3' UTR requires both a poly(A) tail and PABP function, and we find that UNR directly interacts with PABP. To investigate how the repressor complex and PABP affect RNP composition during early steps in translation initiation, we established direct biochemical assays for synergistic recruitment of eIF4F and ribosomes by the cap and poly(A) tail. We find that the repressor complex targets ribosome binding after PABP-mediated recruitment of eIF4E/G. Our results uncover an important regulatory mechanism of Drosophila dosage compensation and provide insight into PABP-dependent translational control by 3' UTR-bound regulatory proteins.
Collapse
|
5
|
Jadhav S, Rana M, Subramaniam K. Multiple maternal proteins coordinate to restrict the translation of C. elegans nanos-2 to primordial germ cells. Development 2008; 135:1803-12. [PMID: 18417623 DOI: 10.1242/dev.013656] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Although germ cell formation has been relatively well understood in worms and insects, how germ cell-specific developmental programs are initiated is not clear. In Caenorhabditis elegans, translational activation of maternal nos-2 mRNA is the earliest known molecular event specific to the germline founder cell P(4). Cis-elements in nos-2 3'UTR have been shown to mediate translational control; however, the trans-acting proteins are not known. Here, we provide evidence that four maternal RNA-binding proteins, OMA-1, OMA-2, MEX-3 and SPN-4, bind nos-2 3'UTR to suppress its translation, and POS-1, another maternal RNA-binding protein, relieves this suppression in P(4). The POS-1: SPN-4 ratio in P(4) increases significantly over its precursor, P(3); and POS-1 competes with SPN-4 for binding to nos-2 RNA in vitro. We propose temporal changes in the relative concentrations of POS-1 and SPN-4, through their effect on the translational status of maternal mRNAs such as nos-2, initiate germ cell-specific developmental programs in C. elegans.
Collapse
Affiliation(s)
- Shreyas Jadhav
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | | | | |
Collapse
|
6
|
Vardy L, Orr-Weaver TL. The Drosophila PNG kinase complex regulates the translation of cyclin B. Dev Cell 2007; 12:157-66. [PMID: 17199048 DOI: 10.1016/j.devcel.2006.10.017] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2005] [Revised: 07/07/2006] [Accepted: 10/19/2006] [Indexed: 11/15/2022]
Abstract
The Drosophila PAN GU (PNG) kinase complex regulates the developmental translation of cyclin B. cyclin B mRNA becomes unmasked during oogenesis independent of PNG activity, but PNG is required for translation from egg activation. We find that although polyadenylation of cyclin B augments translation, it is not essential, and a fully elongated poly(A) is not required for translation to proceed. In fact, changes in poly(A) tail length are not sufficient to account for PNG-mediated control of cyclin B translation and of the early embryonic cell cycles. We present evidence that PNG functions instead as an antagonist of PUMILIO-dependent translational repression. Our data argue that changes in poly(A) tail length are not a universal mechanism governing embryonic cell cycles, and that PNG-mediated derepression of translation is an important alternative mechanism in Drosophila.
Collapse
Affiliation(s)
- Leah Vardy
- Whitehead Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | | |
Collapse
|
7
|
Abstract
Regulation of protein expression in neurons by controlling not only when, but where, mRNAs are translated is likely to play an important role in neuronal function. In this review I focus on the mRNA-binding proteins that control mRNA translation in neurons and how they may participate in local, synaptodendritic protein synthesis.
Collapse
Affiliation(s)
- David G Wells
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA.
| |
Collapse
|
8
|
Jeske M, Meyer S, Temme C, Freudenreich D, Wahle E. Rapid ATP-dependent deadenylation of nanos mRNA in a cell-free system from Drosophila embryos. J Biol Chem 2006; 281:25124-33. [PMID: 16793774 DOI: 10.1074/jbc.m604802200] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Shortening of the poly(A) tail (deadenylation) is the first and often rate-limiting step in the degradation pathway of most eukaryotic mRNAs and is also used as a means of translational repression, in particular in early embryonic development. The nanos mRNA is translationally repressed by the protein Smaug in Drosophila embryos. The RNA has a short poly(A) tail at steady state and decays gradually during the first 2-3 h of development. Smaug has recently also been implicated in mRNA deadenylation. To study the mechanism of sequence-dependent deadenylation, we have developed a cell-free system from Drosophila embryos that displays rapid deadenylation of nanos mRNA. The Smaug response elements contained in the nanos 3'-untranslated region are necessary and sufficient to induce deadenylation; thus, Smaug is likely to be involved. Unexpectedly, deadenylation requires the presence of an ATP regenerating system. The activity can be pelleted by ultracentrifugation, and both the Smaug protein and the CCR4.NOT complex, a known deadenylase, are enriched in the active fraction. The same extracts show pronounced translational repression mediated by the Smaug response elements. RNAs lacking a poly(A) tail are poorly translated in the extract; therefore, SRE-dependent deadenylation contributes to translational repression. However, repression is strong even with RNAs either bearing a poly(A) tract that cannot be removed or lacking poly(A) altogether; thus, an additional aspect of translational repression functions independently of deadenylation.
Collapse
Affiliation(s)
- Mandy Jeske
- Institute of Biochemistry, University of Halle, Kurt-Mothes-Strasse 3, 06120 Halle, Germany
| | | | | | | | | |
Collapse
|
9
|
Kang J, Lee MS, Watowich SJ, Gorenstein DG. Chemiluminescence-based electrophoretic mobility shift assay of RNA-protein interactions: application to binding of viral capsid proteins to RNA. J Virol Methods 2005; 131:155-9. [PMID: 16182384 DOI: 10.1016/j.jviromet.2005.08.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2005] [Accepted: 08/18/2005] [Indexed: 10/25/2022]
Abstract
A chemiluminescence electrophoretic mobility shift assay was introduced for the study of RNA-protein interactions that include association of genomic RNA and viral capsid proteins. Binding of the capsid protein of Venezuelan equine encephalitis virus (VEEV) to several types of RNA was used as a model system to test the application of the method. The effects of RNA secondary structures and the significance of electrostatic interaction on binding were identified. This method may have wide application to the study of RNA-protein interactions.
Collapse
Affiliation(s)
- Jonghoon Kang
- Sealy Center for Structural Biology and Department of Human Biological Chemistry and Genetics, The University of Texas Medical Branch, Galveston, TX 77555, USA
| | | | | | | |
Collapse
|
10
|
Soto M, Iborra S, Quijada L, Folgueira C, Alonso C, Requena JM. Cell-cycle-dependent translation of histone mRNAs is the key control point for regulation of histone biosynthesis in Leishmania infantum. Biochem J 2004; 379:617-25. [PMID: 14766017 PMCID: PMC1224130 DOI: 10.1042/bj20031522] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2003] [Revised: 02/02/2004] [Accepted: 02/09/2004] [Indexed: 11/17/2022]
Abstract
The cell-cycle-dependent expression of the four core histones (H2A, H2B, H3 and H4) has been studied in the protozoan parasite Leishmania infantum. For that purpose, the cell cycle was arrested by incubation of promastigotes with the DNA synthesis inhibitor hydroxyurea, which induced an accumulation of cells stalled in G1 phase. Hydroxyurea release resulted in a semi-synchronous entry into the cell cycle, as determined by flow cytometry. The steady-state levels of histone mRNAs in the G1, S and G2/M phases were found to be constant along the cell cycle. However, the levels of histone synthesis increased when parasites enter the S phase, in agreement with previous results showing that histone synthesis in Leishmania is tightly coupled with DNA replication. In addition, we analysed the distribution of histone mRNAs on polyribosomes at different stages of the cell cycle by separation of cytoplasmic RNAs in sucrose gradients. Remarkably, a drastic change in the polysome profiles of histone mRNAs was observed during the progression from G1 to S phase. Thus, in the S phase, histone mRNAs are present in ribosome-bound fractions, but in the G1 phase, the histone transcripts are exclusively found in the ribosome-free fractions. These results support a regulatory model in which the cell-cycle-regulated synthesis of histones in Leishmania is controlled through a reversible interaction between translational repressors and histone mRNAs.
Collapse
Affiliation(s)
- Manuel Soto
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | | | | | | | | | | |
Collapse
|
11
|
Liu N, Dansereau DA, Lasko P. Fat facets interacts with vasa in the Drosophila pole plasm and protects it from degradation. Curr Biol 2004; 13:1905-9. [PMID: 14588248 DOI: 10.1016/j.cub.2003.10.026] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Anterior-posterior patterning and germ cell specification in Drosophila requires the establishment, during oogenesis, of a specialized cytoplasmic region termed the pole plasm. Numerous RNAs and proteins accumulate to the pole plasm and assemble in polar granules. Translation of some of these RNAs is generally repressed and active only in pole plasm. Vasa (VAS) protein, an RNA helicase and a component of polar granules, is essential maternally for posterior patterning and germ cell specification, and VAS is a candidate translational activator in the pole plasm. VAS is stabilized within the pole plasm in that it is initially present throughout the entire embryo but strictly limited to the pole cells by the cellular blastoderm stage. hsp83 mRNA, which accumulates in the pole plasm through a stabilization-degradation mechanism, is another example. Here, we used a biochemical approach to identify proteins that copurify with VAS in crosslinked extracts. Prominent among these proteins was the ubiquitin-specific protease Fat facets (FAF), a pole plasm component [7], but one whose roles in posterior patterning and germ line specification have remained unclear. We present evidence that FAF interacts with VAS physically and reverses VAS ubiquitination, thereby stabilizing VAS in the pole plasm.
Collapse
Affiliation(s)
- Niankun Liu
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | | | | |
Collapse
|
12
|
Nicolaï M, Lasbleiz C, Dura JM. Gain-of-function screen identifies a role of theSrc64oncogene inDrosophilamushroom body development. ACTA ACUST UNITED AC 2003; 57:291-302. [PMID: 14608664 DOI: 10.1002/neu.10277] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Mushroom bodies (MB) are substructures in the Drosophila brain that are essential for memory. At present, MB anatomy is rather well described when compared to other brain areas, and elucidation of the genetic control of the development and projection patterns of MB neurons will be important to the understanding of their functions. We have performed a gain-of-function screen in order to identify genes that are involved in MB development. We drove expression of genes in MB neurons by crossing 2407 GAL4-driven UY element lines to lines containing an MB GAL4 source and UAS-GFP elements, and looked for defects in the MB structure. We have molecularly identified the genomic regions adjacent to the 26 positive UY insertions and found 18 potential genes that exhibit adult MB gain-of-function phenotypes. The proteins encoded by these candidate genes include, as well as genes with yet unknown function, transcription factors (e.g., tramtrack), nanos RNA-binding protein, microtubule-severing protein, vesicle trafficking proteins, axon guidance receptor, and the Src64 cytoplasmic protein tyrosine kinase. These genes are involved in key features of neuron cell biology. In three cases, tramtrack, nanos, and Src64, we show that the open reading frame located directly downstream of the UY P element is indeed the expressed target gene. Loss-of-function mutations of both ttk and Src64 lead to MB phenotypes proving that these genes are involved in the genetic control of MB development. Moreover, Src64 is shown here to act in a cell-autonomous fashion and is likely to interact with the previously-identified linotte/derailed receptor tyrosine kinase in MB development.
Collapse
Affiliation(s)
- Maryse Nicolaï
- Institut de Génétique Humaine, CNRS UPR1142, 141, rue de la cardonille, 34396 Montpellier Cedex, France
| | | | | |
Collapse
|
13
|
Abstract
Many crucial decisions, such as the location and timing of cell division, cell-fate determination, and embryonic axes establishment, are made in the early embryo, a time in development when there is often little or no transcription. For this reason, the control of variation in gene expression in the early embryo often relies on post-transcriptional control of maternal genes. Although the early embryo is rife with translational control, controlling mRNA activity is also important in other developmental processes, such as stem-cell proliferation, sex determination, neurogenesis and erythropoiesis.
Collapse
Affiliation(s)
- Scott Kuersten
- Laboratory of Genetics, University of Wisconsin-Madison, 445 Henry Mall, Madison, Wisconsin 53706, USA.
| | | |
Collapse
|