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Harris SE, Alexis MS, Giri G, Cavazos FF, Murn J, Aleman MM, Burge CB, Dominguez D. Understanding species-specific and conserved RNA-protein interactions in vivo and in vitro. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.577729. [PMID: 38352439 PMCID: PMC10862761 DOI: 10.1101/2024.01.29.577729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
While evolution is often considered from a DNA- and protein-centric view, RNA-based regulation can also impact gene expression and protein sequences. Here we examined interspecies differences in RNA-protein interactions using the conserved neuronal RNA binding protein, Unkempt (UNK) as model. We find that roughly half of mRNAs bound in human are also bound in mouse. Unexpectedly, even when transcript-level binding was conserved across species differential motif usage was prevalent. To understand the biochemical basis of UNK-RNA interactions, we reconstituted the human and mouse UNK-RNA interactomes using a high-throughput biochemical assay. We uncover detailed features driving binding, show that in vivo patterns are captured in vitro, find that highly conserved sites are the strongest bound, and associate binding strength with downstream regulation. Furthermore, subtle sequence differences surrounding motifs are key determinants of species-specific binding. We highlight the complex features driving protein-RNA interactions and how these evolve to confer species-specific regulation.
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Affiliation(s)
- Sarah E. Harris
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC
| | - Maria S. Alexis
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA
- Current address: Remix Therapeutics, Cambridge, MA
| | - Gilbert Giri
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC
| | | | - Jernej Murn
- Department of Biochemistry, University of California, Riverside, CA
- Center for RNA Biology and Medicine, Riverside, CA
| | - Maria M. Aleman
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC
| | | | - Daniel Dominguez
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC
- RNA Discovery Center, University of North Carolina, Chapel Hill, NC
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2
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Jackson TC, Kochanek PM. RNA Binding Motif 5 (RBM5) in the CNS-Moving Beyond Cancer to Harness RNA Splicing to Mitigate the Consequences of Brain Injury. Front Mol Neurosci 2020; 13:126. [PMID: 32765218 PMCID: PMC7381114 DOI: 10.3389/fnmol.2020.00126] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 06/22/2020] [Indexed: 12/14/2022] Open
Abstract
Gene splicing modulates the potency of cell death effectors, alters neuropathological disease processes, influences neuronal recovery, but may also direct distinct mechanisms of secondary brain injury. Therapeutic targeting of RNA splicing is a promising avenue for next-generation CNS treatments. RNA-binding proteins (RBPs) regulate a variety of RNA species and are prime candidates in the hunt for druggable targets to manipulate and tailor gene-splicing responses in the brain. RBPs preferentially recognize unique consensus sequences in targeted mRNAs. Also, RBPs often contain multiple RNA-binding domains (RBDs)—each having a unique consensus sequence—suggesting the possibility that drugs could be developed to block individual functional domains, increasing the precision of RBP-targeting therapies. Empirical characterization of most RBPs is lacking and represents a major barrier to advance this emerging therapeutic area. There is a paucity of data on the role of RBPs in the brain including, identification of their unique mRNA targets, defining how CNS insults affect their levels and elucidating which RBPs (and individual domains within) to target to improve neurological outcomes. This review focuses on the state-of-the-art of the RBP tumor suppressor RNA binding motif 5 (RBM5) in the CNS. We discuss its potent pro-death roles in cancer, which motivated our interest to study it in the brain. We review recent studies showing that RBM5 levels are increased after CNS trauma and that it promotes neuronal death in vitro. Finally, we conclude with recent reports on the first set of RBM5 regulated genes identified in the intact brain, and discuss how those findings provide new clues germane to its potential function(s) in the CNS, and pose new questions on its therapeutic utility to mitigate CNS injury.
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Affiliation(s)
- Travis C Jackson
- Morsani College of Medicine, USF Health Heart Institute, University of South Florida, Tampa, FL, United States.,Morsani College of Medicine, Department of Molecular Pharmacology and Physiology, University of South Florida, Tampa, FL, United States
| | - Patrick M Kochanek
- Safar Center for Resuscitation Research, Department of Critical Care Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
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3
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Abstract
Cells respond to hypoxia by shifting cellular processes from general housekeeping functions to activating specialized hypoxia-response pathways. Oxygen plays an important role in generating ATP to maintain a productive rate of protein synthesis in normoxia. In hypoxia, the rate of the canonical protein synthesis pathway is significantly slowed and impaired due to limited ATP availability, necessitating an alternative mechanism to mediate protein synthesis and facilitate adaptation. Hypoxia adaptation is largely mediated by hypoxia-inducible factors (HIFs). While HIFs are well known for their transcriptional functions, they also play imperative roles in translation to mediate hypoxic protein synthesis. Such adaptations to hypoxia are often hyperactive in solid tumors, contributing to the expression of cancer hallmarks, including treatment resistance. The current literature on protein synthesis in hypoxia is reviewed here, inclusive of hypoxia-specific mRNA selection to translation termination. Current HIF targeting therapies are also discussed as are the opportunities involved with targeting hypoxia specific protein synthesis pathways.
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Affiliation(s)
- Nancy T Chee
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, 1501 NW 10th Avenue, Miami, FL, 33136, USA
| | - Ines Lohse
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, 1501 NW 10th Avenue, Miami, FL, 33136, USA
| | - Shaun P Brothers
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, 1501 NW 10th Avenue, Miami, FL, 33136, USA.
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Giuliani G, Giuliani F, Volk T, Rabouille C. The Drosophila RNA-binding protein HOW controls the stability of dgrasp mRNA in the follicular epithelium. Nucleic Acids Res 2014; 42:1970-86. [PMID: 24217913 PMCID: PMC3919595 DOI: 10.1093/nar/gkt1118] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 10/18/2013] [Accepted: 10/22/2013] [Indexed: 11/14/2022] Open
Abstract
Post-transcriptional regulation of RNA stability and localization underlies a wide array of developmental processes, such as axon guidance and epithelial morphogenesis. In Drosophila, ectopic expression of the classically Golgi peripheral protein dGRASP at the plasma membrane is achieved through its mRNA targeting at key developmental time-points, in a process critical to follicular epithelium integrity. However, the trans-acting factors that tightly regulate the spatio-temporal dynamics of dgrasp are unknown. Using an in silico approach, we identified two putative HOW Response Elements (HRE1 and HRE2) within the dgrasp open reading frame for binding to Held Out Wings (HOW), a member of the Signal Transduction and Activation of RNA family of RNA-binding proteins. Using RNA immunoprecipitations, we confirmed this by showing that the short cytoplasmic isoform of HOW binds directly to dgrasp HRE1. Furthermore, HOW loss of function in vivo leads to a significant decrease in dgrasp mRNA levels. We demonstrate that HRE1 protects dgrasp mRNA from cytoplasmic degradation, but does not mediate its targeting. We propose that this binding event promotes the formation of ribonucleoprotein particles that ensure dgrasp stability during transport to the basal plasma membrane, thus enabling the local translation of dgrasp for its roles at non-Golgi locations.
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Affiliation(s)
- Giuliano Giuliani
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands, Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel and The Department of Cell Biology, UMC Utrecht, The Netherlands
| | - Fabrizio Giuliani
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands, Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel and The Department of Cell Biology, UMC Utrecht, The Netherlands
| | - Talila Volk
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands, Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel and The Department of Cell Biology, UMC Utrecht, The Netherlands
| | - Catherine Rabouille
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands, Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel and The Department of Cell Biology, UMC Utrecht, The Netherlands
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5
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Evolutionary conservation and expression of human RNA-binding proteins and their role in human genetic disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 825:1-55. [PMID: 25201102 DOI: 10.1007/978-1-4939-1221-6_1] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RNA-binding proteins (RBPs) are effectors and regulators of posttranscriptional gene regulation (PTGR). RBPs regulate stability, maturation, and turnover of all RNAs, often binding thousands of targets at many sites. The importance of RBPs is underscored by their dysregulation or mutations causing a variety of developmental and neurological diseases. This chapter globally discusses human RBPs and provides a brief introduction to their identification and RNA targets. We review RBPs based on common structural RNA-binding domains, study their evolutionary conservation and expression, and summarize disease associations of different RBP classes.
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Blech-Hermoni Y, Ladd AN. RNA binding proteins in the regulation of heart development. Int J Biochem Cell Biol 2013; 45:2467-78. [PMID: 23973289 DOI: 10.1016/j.biocel.2013.08.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 08/09/2013] [Accepted: 08/13/2013] [Indexed: 11/28/2022]
Abstract
In vivo, RNA molecules are constantly accompanied by RNA binding proteins (RBPs), which are intimately involved in every step of RNA biology, including transcription, editing, splicing, transport and localization, stability, and translation. RBPs therefore have opportunities to shape gene expression at multiple levels. This capacity is particularly important during development, when dynamic chemical and physical changes give rise to complex organs and tissues. This review discusses RBPs in the context of heart development. Since the targets and functions of most RBPs--in the heart and at large--are not fully understood, this review focuses on the expression and roles of RBPs that have been implicated in specific stages of heart development or developmental pathology. RBPs are involved in nearly every stage of cardiogenesis, including the formation, morphogenesis, and maturation of the heart. A fuller understanding of the roles and substrates of these proteins could ultimately provide attractive targets for the design of therapies for congenital heart defects, cardiovascular disease, or cardiac tissue repair.
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Affiliation(s)
- Yotam Blech-Hermoni
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Program in Cell Biology, Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
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7
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The RNA-binding protein Whi3 is a key regulator of developmental signaling and ploidy in Saccharomyces cerevisiae. Genetics 2013; 195:73-86. [PMID: 23770701 DOI: 10.1534/genetics.113.153775] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
In Saccharomyces cerevisiae, the RNA-binding protein Whi3 controls cell cycle progression, biofilm formation, and stress response by post-transcriptional regulation of the Cdc28-Cln3 cyclin-dependent protein kinase and the dual-specificity protein kinase Yak1. Previous work has indicated that Whi3 might govern these processes by additional, yet unknown mechanisms. In this study, we have identified additional effectors of Whi3 that include the G1 cyclins Cln1/Cln2 and two known regulators of biofilm formation, the catalytic PKA subunit Tpk1 and the transcriptional activator Tec1. We also provide evidence that Whi3 regulates production of these factors by post-transcriptional control and might exert this function by affecting translational elongation. Unexpectedly, we also discovered that Whi3 is a key regulator of cellular ploidy, because haploid whi3Δ mutant strains exhibit a significant increase-in-ploidy phenotype that depends on environmental conditions. Our data further suggest that Whi3 might control stability of ploidy by affecting the expression of many key genes involved in sister chromatid cohesion and of NIP100 that encodes a component of the yeast dynactin complex for chromosome distribution. Finally, we show that absence of Whi3 induces a transcriptional stress response in haploid cells that is relieved by whole-genome duplication. In summary, our study suggests that the RNA-binding protein Whi3 acts as a central regulator of cell division and development by post-transcriptional control of key genes involved in chromosome distribution and cell signaling.
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Wu J, Campbell ZT, Menichelli E, Wickens M, Williamson JR. A protein.protein interaction platform involved in recruitment of GLD-3 to the FBF.fem-3 mRNA complex. J Mol Biol 2012; 425:738-54. [PMID: 23159559 DOI: 10.1016/j.jmb.2012.11.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 11/01/2012] [Accepted: 11/07/2012] [Indexed: 02/03/2023]
Abstract
The Pumilio and FBF (PUF) family of RNA-binding proteins interacts with protein partners to post-transcriptionally regulate mRNAs in eukaryotes. The interaction between PUF family member fem-3 binding factor (FBF) and germline development defective-3 (GLD-3) protein promotes spermatogenesis in Caenorhabditis elegans by increasing expression of the fem-3 mRNA. Defined here in these studies is the molecular basis for this critical interaction. A 10-amino-acid region within GLD-3 is required for FBF binding, while a 7-amino-acid loop in FBF between PUF repeats 7 and 8 is necessary for GLD-3 binding. These short sequences are conserved, as other FBF-binding proteins bear sequences similar to those in GLD-3 and other C. elegans PUF proteins contain sequences similar to those in FBF. The FBF-binding region of GLD-3 forms a ternary complex with FBF on the point mutation element (PME) in the fem-3 3' untranslated region, and formation of this GLD-3⋅FBF complex does not impact the RNA-binding activity of FBF. These data raise the possibility of alternative models involving the formation of a GLD-3⋅FBF⋅RNA complex in the regulation of germline mRNAs.
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Affiliation(s)
- Joann Wu
- Department of Molecular Biology, Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Jayasena CS, Bronner ME. Rbms3 functions in craniofacial development by posttranscriptionally modulating TGF-β signaling. ACTA ACUST UNITED AC 2012; 199:453-66. [PMID: 23091072 PMCID: PMC3483135 DOI: 10.1083/jcb.201204138] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Rbms3 regulates TGF-βr signaling, a critical pathway for chondrogenesis, by binding and stabilizing Smad2 transcripts. Cranial neural crest cells form much of the facial skeleton, and abnormalities in their development lead to severe birth defects. In a novel zebrafish protein trap screen, we identified an RNA-binding protein, Rbms3, that is transiently expressed in the cytoplasm of condensing neural crest cells within the pharyngeal arches. Morphants for rbms3 displayed reduced proliferation of prechondrogenic crest and significantly altered expression for chondrogenic/osteogenic lineage markers. This phenotype strongly resembles cartilage/crest defects observed in Tgf-βr2:Wnt1-Cre mutants, which suggests a possible link with TGF-β signaling. Consistent with this are the findings that: (a) Rbms3 stabilized a reporter transcript with smad2 3′ untranslated region, (b) RNA immunoprecipitation with full-length Rbms3 showed enrichment for smad2/3, and (c) pSmad2 levels were reduced in rbms3 morphants. Overall, these results suggest that Rbms3 posttranscriptionally regulates one of the major pathways that promotes chondrogenesis, the transforming growth factor β receptor (TGF-βr) pathway.
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Nir R, Grossman R, Paroush Z, Volk T. Phosphorylation of the Drosophila melanogaster RNA-binding protein HOW by MAPK/ERK enhances its dimerization and activity. PLoS Genet 2012; 8:e1002632. [PMID: 22479211 PMCID: PMC3315481 DOI: 10.1371/journal.pgen.1002632] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2011] [Accepted: 02/20/2012] [Indexed: 11/18/2022] Open
Abstract
Drosophila melanogaster Held Out Wings (HOW) is a conserved RNA-binding protein (RBP) belonging to the STAR family, whose closest mammalian ortholog Quaking (QKI) has been implicated in embryonic development and nervous system myelination. The HOW RBP modulates a variety of developmental processes by controlling mRNA levels and the splicing profile of multiple key regulatory genes; however, mechanisms regulating its activity in tissues have yet to be elucidated. Here, we link receptor tyrosine kinase (RTK) signaling to the regulation of QKI subfamily of STAR proteins, by showing that HOW undergoes phosphorylation by MAPK/ERK. Importantly, we show that this modification facilitates HOW dimerization and potentiates its ability to bind RNA and regulate its levels. Employing an antibody that specifically recognizes phosphorylated HOW, we show that HOW is phosphorylated in embryonic muscles and heart cardioblasts in vivo, thus documenting for the first time Serine/Threonine (Ser/Thr) phosphorylation of a STAR protein in the context of an intact organism. We also identify the sallimus/D-titin (sls) gene as a novel muscle target of HOW-mediated negative regulation and further show that this regulation is phosphorylation-dependent, underscoring the physiological relevance of this modification. Importantly, we demonstrate that HOW Thr phosphorylation is reduced following muscle-specific knock down of Drosophila MAPK rolled and that, correspondingly, Sls is elevated in these muscles, similarly to the HOW RNAi effect. Taken together, our results provide a coherent mechanism of differential HOW activation; MAPK/ERK-dependent phosphorylation of HOW promotes the formation of HOW dimers and thus enhances its activity in controlling mRNA levels of key muscle-specific genes. Hence, our findings bridge between MAPK/ERK signaling and RNA regulation in developing muscles.
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Affiliation(s)
- Ronit Nir
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Rona Grossman
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada (IMRIC), Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Ze'ev Paroush
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada (IMRIC), Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Talila Volk
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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Zhang JH, Seigneur EM, Pandey M, Loshakov A, Dagur PK, Connelly PS, Koo L, Panicker LM, Simonds WF. The EIF4EBP3 translational repressor is a marker of CDC73 tumor suppressor haploinsufficiency in a parathyroid cancer syndrome. Cell Death Dis 2012; 3:266. [PMID: 22297294 PMCID: PMC3288348 DOI: 10.1038/cddis.2012.6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Germline mutation of the tumor suppressor gene CDC73 confers susceptibility to the hyperparathyroidism-jaw tumor syndrome associated with a high risk of parathyroid malignancy. Inactivating CDC73 mutations have also been implicated in sporadic parathyroid cancer, but are rare in sporadic benign parathyroid tumors. The molecular pathways that distinguish malignant from benign parathyroid transformation remain elusive. We previously showed that a hypomorphic allele of hyrax (hyx), the Drosophila homolog of CDC73, rescues the loss-of-ventral-eye phenotype of lobe, encoding the fly homolog of Akt1s1/ PRAS40. We report now an interaction between hyx and Tor, a central regulator of cell growth and autophagy, and show that eukaryotic translation initiation factor 4E-binding protein (EIF4EBP), a translational repressor and effector of mammalian target of rapamycin (mTOR), is a conserved target of hyx/CDC73. Flies heterozygous for Tor and hyx, but not Mnn1, the homolog of the multiple endocrine neoplasia type 1 (MEN1) tumor suppressor associated with benign parathyroid tumors, are starvation resistant with reduced basal levels of Thor/4E-BP. Human peripheral blood cell levels of EIF4EBP3 were reduced in patients with CDC73, but not MEN1, heterozygosity. Chromatin immunoprecipitation demonstrated occupancy of EIF4EBP3 by endogenous parafibromin. These results show that EIF4EBP3 is a peripheral marker of CDC73 function distinct from MEN1-regulated pathways, and suggest a model whereby starvation resistance and/or translational de-repression contributes to parathyroid malignant transformation.
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Affiliation(s)
- J-H Zhang
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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Liu B, Lo SCL, Matton DP, Lang BF, Morse D. Daily changes in the phosphoproteome of the dinoflagellate Lingulodinium. Protist 2011; 163:746-54. [PMID: 22169124 DOI: 10.1016/j.protis.2011.11.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Revised: 11/01/2011] [Accepted: 11/02/2011] [Indexed: 11/26/2022]
Abstract
The dinoflagellate Lingulodinium has a large number of daily rhythms, many of which have no biochemical correlates. We examined the possibility that changes in protein phosphorylation may mediate some of the rhythmic changes by comparing proteins prepared from midday (LD6) and midnight (LD18) cultures. We used two different methods, one a 2D gel protocol in which phosphoproteins were identified after staining with ProQ Diamond, and the other an LC-MS/MS identification of tryptic phosphopeptides that had been purified by TiO(2) chromatography. Two differentially phosphorylated proteins, a light harvesting complex protein and Rad24, were identified using the 2D gel protocol. Six differentially phosphorylated proteins, a polyketide synthase, an uncharacterized transporter, a LIM (actin binding) domain and three RNA binding domain proteins, were identified using the phosphopeptide enrichment protocol. We conclude that changes in protein phosphorylation may underlie some of the rhythmic behavior of Lingulodinium.
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Affiliation(s)
- Bolin Liu
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Sherbrooke est, Montréal, Québec, Canada H1X 2B2
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Kerner P, Degnan SM, Marchand L, Degnan BM, Vervoort M. Evolution of RNA-binding proteins in animals: insights from genome-wide analysis in the sponge Amphimedon queenslandica. Mol Biol Evol 2011; 28:2289-303. [PMID: 21325094 DOI: 10.1093/molbev/msr046] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
RNA-binding proteins (RBPs) are key players in various biological processes, most notably regulation of gene expression at the posttranscriptional level. Although many RBPs have been carefully studied in model organisms, very few studies have addressed the evolution of these proteins at the scale of the animal kingdom. We identified a large set of putative RBPs encoded by the genome of the demosponge Amphimedon queenslandica, a species representing a basal animal lineage. We compared the Amphimedon RBPs with those encoded by the genomes of two bilaterians (human and Drosophila), representatives of two other basal metazoan lineages (a placozoan and a cnidarian), a choanoflagellate (probable sister group of animals), and two fungi. We established the evolutionary history of 32 families of RBPs and found that most of the diversity of RBPs present in contemporary metazoans, including humans, was already established in the last common ancestor (LCA) of animals. This includes RBPs known to be involved in key processes in bilaterians, such as development, stem and/or germ cells properties, and noncoding RNA pathways. From this analysis, we infer that a complex toolkit of RBPs was present in the LCA of animals and that it has been recruited to perform new functions during early animal evolution, in particular in relation to the acquisition of multicellularity.
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Affiliation(s)
- Pierre Kerner
- Development and Neurobiology Programme, Institut Jacques Monod, Centre national de la recherche scientifique/Université Paris Diderot-Paris 7, Paris cedex, France
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14
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Zhang JH, Panicker LM, Seigneur EM, Lin L, House CD, Morgan W, Chen WC, Mehta H, Haj-Ali M, Yu ZX, Simonds WF. Cytoplasmic polyadenylation element binding protein is a conserved target of tumor suppressor HRPT2/CDC73. Cell Death Differ 2010; 17:1551-65. [PMID: 20339377 PMCID: PMC3109426 DOI: 10.1038/cdd.2010.32] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Parafibromin, a tumor suppressor protein encoded by HRPT2/CDC73 and implicated in parathyroid cancer and the hyperparathyroidism-jaw tumor (HPT-JT) familial cancer syndrome, is part of the PAF1 transcriptional regulatory complex. Parafibromin has been implicated in apoptosis and growth arrest, but the mechanism by which its loss of function promotes neoplasia is poorly understood. In this study we report that a hypomorphic allele of hyrax (hyx), the Drosophila homolog of HRPT2/CDC73, rescues the loss-of-ventral-eye phenotype of lobe (Akt1s1). Such rescue is consistent with previous reports that hyx/parafibromin is required for the nuclear transduction of Wingless (Wg)/Wnt signals and that Wg signaling antagonizes lobe function. A screen using double hyx/lobe heterozygotes identified an additional interaction with orb and orb2, the homologs of mammalian cytoplasmic polyadenylation element binding protein (CPEB), a translational regulatory protein. Hyx and orb2 heterozygotes lived longer and were more resistant to starvation than controls. In mammalian cells, knockdown of parafibromin expression reduced levels of CPEB1. Chromatin immunoprecipitation (ChIP) showed occupancy of CPEB1 by endogenous parafibromin. Bioinformatic analysis revealed a significant overlap between human transcripts potentially regulated by parafibromin and CPEB. These results show that parafibromin may exert both transcriptional and, through CPEB, translational control over a subset of target genes and that loss of parafibromin (and CPEB) function may promote tumorigenesis in part by conferring resistance to nutritional stress.
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Affiliation(s)
- Jian-Hua Zhang
- Metabolic Diseases Branch, Bldg. 10/ Rm 8C-101, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892
| | - Leelamma M. Panicker
- Metabolic Diseases Branch, Bldg. 10/ Rm 8C-101, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892
| | - Erica M. Seigneur
- Metabolic Diseases Branch, Bldg. 10/ Rm 8C-101, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892
| | - Ling Lin
- Metabolic Diseases Branch, Bldg. 10/ Rm 8C-101, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892
| | - Carrie D. House
- Metabolic Diseases Branch, Bldg. 10/ Rm 8C-101, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892
| | - Wynne Morgan
- Metabolic Diseases Branch, Bldg. 10/ Rm 8C-101, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892
| | - Weiping C. Chen
- Genomics Core Laboratory, Bldg. 8/ Rm 1A-11, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892
| | - Hina Mehta
- Metabolic Diseases Branch, Bldg. 10/ Rm 8C-101, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892
| | - Mayce Haj-Ali
- Metabolic Diseases Branch, Bldg. 10/ Rm 8C-101, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892
| | - Zhu-Xi Yu
- Genetics & Development Biology Center, Bldg.14E/ Rm 107D, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - William F. Simonds
- Metabolic Diseases Branch, Bldg. 10/ Rm 8C-101, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892
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Andreassi C, Riccio A. To localize or not to localize: mRNA fate is in 3'UTR ends. Trends Cell Biol 2009; 19:465-74. [PMID: 19716303 DOI: 10.1016/j.tcb.2009.06.001] [Citation(s) in RCA: 257] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Revised: 06/17/2009] [Accepted: 06/18/2009] [Indexed: 01/30/2023]
Abstract
Translation of localized mRNA is a fast and efficient way of reacting to extracellular stimuli with the added benefit of providing spatial resolution to the cellular response. The efficacy of this adaptive response ultimately relies on the ability to express a particular protein at the right time and in the right place. Although mRNA localization is a mechanism shared by most organisms, it is especially relevant in highly polarized cells, such as differentiated neurons. 3'-Untranslated regions (3'UTRs) of mRNAs are critical both for the targeting of transcripts to specific subcellular compartments and for translational control. Here we review recent studies that indicate how, in response to extracellular cues, nuclear and cytoplasmic remodeling of the 3'UTR contributes to mRNA localization and local protein synthesis.
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Affiliation(s)
- Catia Andreassi
- MRC Laboratory for Molecular and Cell Biology, University College London, London WC1E 6BT, UK
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16
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Nicotine modulates the renin-angiotensin system of cultured neurons and glial cells from cardiovascular brain areas of Wistar Kyoto and spontaneously hypertensive rats. J Mol Neurosci 2007; 33:284-93. [PMID: 17952638 DOI: 10.1007/s12031-007-9006-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2007] [Accepted: 08/23/2007] [Indexed: 10/22/2022]
Abstract
Considering the importance of the renin-angiotensin system (RAS) for the central control of blood pressure and that nicotine increases the probability of development of hypertension associated to genetic predisposition, our aims are (1) to determine RAS in cultured neurons and glia from the brainstem and hypothalamus of spontaneously hypertensive (SHR) and Wistar Kyoto (WKY) rats; (2) to analyze the possibility of nicotine to interact with brain RAS; and (3) to hypothesize any contribution of nicotine and RAS to the development of neurogenic hypertension. This study demonstrated physiological differences in RAS between cultured neuronal and glial cells from the brainstem and hypothalamus of SHR and WKY neonate rats. Our study also featured evidences of direct modulation of the RAS by nicotine in neurons and glia of brainstem and hypothalamus, which seems to be differential between the two rat strains. Such modulation gives us a clue about the mechanisms possibly involved in the genesis of neurogenic hypertension in vivo, for example, increase in angiotensin II type 1 receptor binding and decrease in angiotensin-converting enzyme 2. In conclusion, we demonstrated that neuronal and glial RAS from the brainstem and hypothalamus of SHR differ from WKY rats and nicotine differentially modulates the brain RAS in SHR and WKY.
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Prinz S, Aldridge C, Ramsey SA, Taylor RJ, Galitski T. Control of signaling in a MAP-kinase pathway by an RNA-binding protein. PLoS One 2007; 2:e249. [PMID: 17327913 PMCID: PMC1803019 DOI: 10.1371/journal.pone.0000249] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2007] [Accepted: 02/02/2007] [Indexed: 11/25/2022] Open
Abstract
Signaling-protein mRNAs tend to have long untranslated regions (UTRs) containing binding sites for RNA-binding proteins regulating gene expression. Here we show that a PUF-family RNA-binding protein, Mpt5, represses the yeast MAP-kinase pathway controlling differentiation to the filamentous form. Mpt5 represses the protein levels of two pathway components, the Ste7 MAP-kinase kinase and the Tec1 transcriptional activator, and negatively regulates the kinase activity of the Kss1 MAP kinase. Moreover, Mpt5 specifically inhibits the output of the pathway in the absence of stimuli, and thereby prevents inappropriate cell differentiation. The results provide an example of what may be a genome-scale level of regulation at the interface of signaling networks and protein-RNA binding networks.
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Affiliation(s)
- Susanne Prinz
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Christine Aldridge
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Stephen A. Ramsey
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - R. James Taylor
- Institute for Systems Biology, Seattle, Washington, United States of America
- University of British Columbia, Vancouver, British Columbia, Canada
| | - Timothy Galitski
- Institute for Systems Biology, Seattle, Washington, United States of America
- University of British Columbia, Vancouver, British Columbia, Canada
- * To whom correspondence should be addressed. E-mail:
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18
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Fähling M, Steege A, Perlewitz A, Nafz B, Mrowka R, Persson PB, Thiele BJ. Role of nucleolin in posttranscriptional control of MMP-9 expression. BIOCHIMICA ET BIOPHYSICA ACTA 2005; 1731:32-40. [PMID: 16153722 DOI: 10.1016/j.bbaexp.2005.08.005] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2005] [Revised: 07/28/2005] [Accepted: 08/05/2005] [Indexed: 10/25/2022]
Abstract
Matrix-metalloproteinases (MMPs), which are able to degrade extra cellular matrix (ECM) components, are crucial in ECM-remodeling, under physiological (e.g., embryogenesis, wound healing, angiogenesis) or pathophysiological conditions (e.g., arthritis, cancer progression and metastasis, fibrosis). Treating HT1080 cells, a human fibrosarcoma cell line, with the iron chelator 2,2-Dipyridyl, which mimics certain aspects of hypoxia, leads to a 3-fold elevated Matrix-metalloproteinase-9 (MMP-9) protein level. This elevation occurs within 3 h, without any change of mRNA-concentration. The rapid increase in MMP-9 expression is caused by an enhancement of translational efficiency characterized by a recruitment of translationally inactive MMP-9 mRNP-complexes into the rough endoplasmatic reticulum (rER). Reporter gene assays, which depend on the untranslated regions (UTR) of MMP-9 mRNA, reveal that the posttranscriptional regulation is mainly attributed to the 3'UTR. RNA/protein interaction studies indicate that the elevated binding of nucleolin ( approximately 64 kDa form) to the 3'UTR may be of major importance for the increased efficiency of MMP-9 translation. The results show that MMP-9 expression can be regulated posttranscriptionally, affecting the efficiency of translation and localization of the mRNA.
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Affiliation(s)
- Michael Fähling
- Charité, Universitätsmedizin Berlin, Institut für Vegetative Physiologie, 10117 Berlin, Germany.
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McKee AE, Minet E, Stern C, Riahi S, Stiles CD, Silver PA. A genome-wide in situ hybridization map of RNA-binding proteins reveals anatomically restricted expression in the developing mouse brain. BMC DEVELOPMENTAL BIOLOGY 2005; 5:14. [PMID: 16033648 PMCID: PMC1199591 DOI: 10.1186/1471-213x-5-14] [Citation(s) in RCA: 129] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2005] [Accepted: 07/20/2005] [Indexed: 11/10/2022]
Abstract
Background In eukaryotic cells, RNA-binding proteins (RBPs) contribute to gene expression by regulating the form, abundance, and stability of both coding and non-coding RNA. In the vertebrate brain, RBPs account for many distinctive features of RNA processing such as activity-dependent transcript localization and localized protein synthesis. Several RBPs with activities that are important for the proper function of adult brain have been identified, but how many RBPs exist and where these genes are expressed in the developing brain is uncharacterized. Results Here we describe a comprehensive catalogue of the unique RBPs encoded in the mouse genome and provide an online database of RBP expression in developing brain. We identified 380 putative RBPs in the mouse genome. Using in situ hybridization, we visualized the expression of 323 of these RBP genes in the brains of developing mice at embryonic day 13.5, when critical fate choice decisions are made and at P0, when major structural components of the adult brain are apparent. We demonstrate i) that 16 of the 323 RBPs examined show neural-specific expression at the stages we examined, and ii) that a far larger subset (221) shows regionally restricted expression in the brain. Of the regionally restricted RBPs, we describe one group that is preferentially expressed in the E13.5 ventricular areas and a second group that shows spatially restricted expression in post-mitotic regions of the embryonic brain. Additionally, we find a subset of RBPs that share the same complex pattern of expression, in proliferating regions of the embryonic and postnatal NS and peripheral tissues. Conclusion Our data show that, in contrast to their proposed ubiquitous involvement in gene regulation, most RBPs are not uniformly expressed. Here we demonstrate the region-specific expression of RBPs in proliferating vs. post-mitotic brain regions as well as cell-type-specific RBP expression. We identify uncharacterized RBPs that exhibit neural-specific expression as well as novel RBPs that show expression in non-neural tissues. The data presented here and in an online database provide a visual filter for the functional analysis of individual RBPs.
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Affiliation(s)
- Adrienne E McKee
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115 USA
- Department of Cancer Biology, The Dana-Farber Cancer Institute, Boston, MA 02115 USA
| | - Emmanuel Minet
- Department of Cancer Biology, The Dana-Farber Cancer Institute, Boston, MA 02115 USA
- URBC-FUNDP, 61 rue de Bruxelles, 5000 Namur, Belgium
| | - Charlene Stern
- Department of Cancer Biology, The Dana-Farber Cancer Institute, Boston, MA 02115 USA
| | - Shervin Riahi
- Department of Cancer Biology, The Dana-Farber Cancer Institute, Boston, MA 02115 USA
| | - Charles D Stiles
- Department of Cancer Biology, The Dana-Farber Cancer Institute, Boston, MA 02115 USA
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115 USA
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115 USA
- Department of Cancer Biology, The Dana-Farber Cancer Institute, Boston, MA 02115 USA
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Gerber AP, Herschlag D, Brown PO. Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast. PLoS Biol 2004; 2:E79. [PMID: 15024427 PMCID: PMC368173 DOI: 10.1371/journal.pbio.0020079] [Citation(s) in RCA: 515] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2003] [Accepted: 01/09/2004] [Indexed: 11/19/2022] Open
Abstract
Genes encoding RNA-binding proteins are diverse and abundant in eukaryotic genomes. Although some have been shown to have roles in post-transcriptional regulation of the expression of specific genes, few of these proteins have been studied systematically. We have used an affinity tag to isolate each of the five members of the Puf family of RNA-binding proteins in Saccharomyces cerevisiae and DNA microarrays to comprehensively identify the associated mRNAs. Distinct groups of 40-220 different mRNAs with striking common themes in the functions and subcellular localization of the proteins they encode are associated with each of the five Puf proteins: Puf3p binds nearly exclusively to cytoplasmic mRNAs that encode mitochondrial proteins; Puf1p and Puf2p interact preferentially with mRNAs encoding membrane-associated proteins; Puf4p preferentially binds mRNAs encoding nucleolar ribosomal RNA-processing factors; and Puf5p is associated with mRNAs encoding chromatin modifiers and components of the spindle pole body. We identified distinct sequence motifs in the 3'-untranslated regions of the mRNAs bound by Puf3p, Puf4p, and Puf5p. Three-hybrid assays confirmed the role of these motifs in specific RNA-protein interactions in vivo. The results suggest that combinatorial tagging of transcripts by specific RNA-binding proteins may be a general mechanism for coordinated control of the localization, translation, and decay of mRNAs and thus an integral part of the global gene expression program.
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Affiliation(s)
- André P Gerber
- 1Department of Biochemistry, Stanford University School of MedicineStanford, CaliforniaUnited States of America
| | - Daniel Herschlag
- 1Department of Biochemistry, Stanford University School of MedicineStanford, CaliforniaUnited States of America
| | - Patrick O Brown
- 1Department of Biochemistry, Stanford University School of MedicineStanford, CaliforniaUnited States of America
- 2Howard Hughes Medical Institute, Stanford University School of MedicineStanford, CaliforniaUnited States of America
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