1
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Bin-Jumah MN. Do functional traits and biochemical biomarkers of the nematode Oncholaimus campylocercoides De Coninck and Schuurmans Stekhoven, 1933 affected by fluoranthene and polystyrene microplastics? Results from a microcosm bioassay and molecular modeling. MARINE POLLUTION BULLETIN 2023; 194:115294. [PMID: 37506479 DOI: 10.1016/j.marpolbul.2023.115294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023]
Abstract
The current experiment measured the multifaceted effects of polystyrene and fluoranthene, acting alone or in a mixture, on the meiobenthic nematode species Oncholaimus campylocercoides. This Oncholaimid was first experimentally selected from an entire nematode assemblage taken from the Jeddah coasts (Saudi Arabia). Several discernible changes were found in morphometry and functional traits after exposure to single and combined treatments. An increase in the activity of the biochemical biomarkers catalase and glutathione S-transferase was also observed following the exposure of males and gravid females of O. campylocercoides to 37.5 ng fluoranthene·g-1 dry weight (DW) and 62.5 mg polystyrene·kg-1 DW paralleled by a higher vulnerability of females. Moreover, the reproduction and feeding of this species were impaired, starting from 37.5 ng fluoranthene·g-1 and 62.5 mg polystyrene·kg-1, respectively. These results have been confirmed by good binding affinities and molecular interactions of fluoranthene and polystyrene with both GLD-3 and SDP receptors.
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Affiliation(s)
- May Nasser Bin-Jumah
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia.
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2
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Suskiewicz MJ, Munnur D, Strømland Ø, Yang JC, Easton L, Chatrin C, Zhu K, Baretić D, Goffinont S, Schuller M, Wu WF, Elkins J, Ahel D, Sanyal S, Neuhaus D, Ahel I. Updated protein domain annotation of the PARP protein family sheds new light on biological function. Nucleic Acids Res 2023; 51:8217-8236. [PMID: 37326024 PMCID: PMC10450202 DOI: 10.1093/nar/gkad514] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/09/2023] [Accepted: 06/03/2023] [Indexed: 06/17/2023] Open
Abstract
AlphaFold2 and related computational tools have greatly aided studies of structural biology through their ability to accurately predict protein structures. In the present work, we explored AF2 structural models of the 17 canonical members of the human PARP protein family and supplemented this analysis with new experiments and an overview of recent published data. PARP proteins are typically involved in the modification of proteins and nucleic acids through mono or poly(ADP-ribosyl)ation, but this function can be modulated by the presence of various auxiliary protein domains. Our analysis provides a comprehensive view of the structured domains and long intrinsically disordered regions within human PARPs, offering a revised basis for understanding the function of these proteins. Among other functional insights, the study provides a model of PARP1 domain dynamics in the DNA-free and DNA-bound states and enhances the connection between ADP-ribosylation and RNA biology and between ADP-ribosylation and ubiquitin-like modifications by predicting putative RNA-binding domains and E2-related RWD domains in certain PARPs. In line with the bioinformatic analysis, we demonstrate for the first time PARP14's RNA-binding capability and RNA ADP-ribosylation activity in vitro. While our insights align with existing experimental data and are probably accurate, they need further validation through experiments.
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Affiliation(s)
| | - Deeksha Munnur
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Øyvind Strømland
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Ji-Chun Yang
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Laura E Easton
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Chatrin Chatrin
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Kang Zhu
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Domagoj Baretić
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | | | - Marion Schuller
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Wing-Fung Wu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jonathan M Elkins
- Centre for Medicines Discovery, University of Oxford, Oxford OX3 7DQ, UK
| | - Dragana Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Sumana Sanyal
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - David Neuhaus
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
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3
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Badraoui R, Allouche M, El Ouaer D, Siddiqui AJ, Ishak S, Hedfi A, Beyrem H, Pacioglu O, Rudayni HA, Boufahja F. Ecotoxicity of chrysene and phenanthrene on meiobenthic nematodes with a case study of Terschellingia longicaudata: Taxonomics, toxicokinetics, and molecular interactions modelling. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 316:120459. [PMID: 36273696 DOI: 10.1016/j.envpol.2022.120459] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 06/16/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are toxic for humans and marine fauna alike. The current study assessed the impact of PAHs on the migratory behaviour of meiobenthic nematodes collected from the Bizerte lagoon, Tunisia. The experiment lasted for 15 days and was carried in open microcosms, which comprised a lower, contaminated and an upper, uncontaminated compartment. Three treatments were used, for each of them an untreated control was set up: sediment contaminated with chrysene (116 ng g-1 dry weight (DW), with phenanthrene (116 ng g-1 DW) and a mixture of both. The results showed a significant decrease in diversty and abundance in the lower, contaminated compartments compared to the upper zones. The results also highlighted that under an increased stress some species progressively increased in number, these were considered PAH-tolerant species such as Odontophora villoti, some others had an occasionally increased in number were considered as opportunistic species, such as Paracomesoma dubium and the species that showed a progressive decreased in number, such as Metoncholaimus pristiurus and Steineria sp., Terschellingia. longicaudata, and Oncholaimellus sp. were classified as PAH-sensitive. Moreover, an increase in the activity of biochemical biomarkers was observed following the exposure of males and gravid females of T. longicaudata to 29, 58 and 87 ng g-1 DW of chrysene and phenanthrene paralleled by a higher vulnerability of the latter demographic category. Besides, a significant decrease in fertility of females and an increase in pharyngeal sucking power were observed for both types of PAHs considered. The sex ratio was also significantly imbalanced in the favor of males, which suggest that chrysene and phenanthrene affect also the hormone system of T. longicaudata. The high affinities of these PAHs and their molecular interactions with both germ line development protein 3 (GLD-3) and sex-determining protein (SDP) may justify these results and explain the toxicokinetic attributes.
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Affiliation(s)
- Riadh Badraoui
- Department of Biology, Laboratory of General Biology, College of Science, University of Ha'il, Ha'il, 81451, Saudi Arabia; Section of Histology-Cytology, Medicine Faculty of Tunis, University of Tunis El Manar, 1007 La Rabta, Tunis, Tunisia
| | - Mohamed Allouche
- University of Carthage, Faculty of Sciences of Bizerte, Laboratory of Environment Biomonitoring, Coastal Ecology and Ecotoxicology Unit, 7021, Zarzouna, Tunisia
| | - Dhia El Ouaer
- University of Carthage, Faculty of Sciences of Bizerte, Laboratory of Environment Biomonitoring, Coastal Ecology and Ecotoxicology Unit, 7021, Zarzouna, Tunisia
| | - Arif J Siddiqui
- Department of Biology, Laboratory of General Biology, College of Science, University of Ha'il, Ha'il, 81451, Saudi Arabia
| | - Sahar Ishak
- University of Carthage, Faculty of Sciences of Bizerte, Laboratory of Environment Biomonitoring, Coastal Ecology and Ecotoxicology Unit, 7021, Zarzouna, Tunisia
| | - Amor Hedfi
- Department of Biology, College of Sciences, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia
| | - Hamouda Beyrem
- University of Carthage, Faculty of Sciences of Bizerte, Laboratory of Environment Biomonitoring, Coastal Ecology and Ecotoxicology Unit, 7021, Zarzouna, Tunisia
| | - Octavian Pacioglu
- National Institute of Research and Development for Biological Sciences, Bucharest, Romania
| | - Hassan A Rudayni
- Biology Department, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, 11623, Saudi Arabia
| | - Fehmi Boufahja
- Biology Department, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, 11623, Saudi Arabia.
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4
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Hedfi A, Ben Ali M, Korkobi M, Allouche M, Harrath AH, Beyrem H, Pacioglu O, Badraoui R, Boufahja F. The exposure to polyvinyl chloride microplastics and chrysene induces multiple changes in the structure and functionality of marine meiobenthic communities. JOURNAL OF HAZARDOUS MATERIALS 2022; 436:129161. [PMID: 35739702 DOI: 10.1016/j.jhazmat.2022.129161] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/11/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
The effects of microplastics and sorbed polycyclic aromatic hydrocarbons at community levels were rarely assessed in laboratory experiments, despite their obvious advantage in reflecting better the natural conditions compared to traditionally single species-focused toxicological experiments. In the current study, the multifaceted effects of polyvinyl chloride and chrysene, acting alone or combined, on general marine meiobenthos, but with a special focus on free-living marine nematode communities were tested in a laboratory experiment carried in microcosms. The meiobenthos was exposed to two polyvinyl chloride (5 and 10 mg.kg-1 Dry Weight 'DW') and chrysene (37.5 and 75 ng.g-1 DW) concentrations, respectively, as well as to a mixture of both compounds, for 30 days. The results highlighted a significant decrease in the abundance of all meiobenthic generic groups, including nematodes, directly with increasing dosages of these compounds when added alone. The addition of chrysene adheres to microplastics, making the sediment matrix glueyer, hence inducing greater mortality among generic meiobenthic groups. Moreover, the nematofauna went through a strong restructuring phase following the exposure to both compounds when added alone, leading to the disappearance of sensitive nematodes and their replacement with tolerant taxa. However, the similarity in nematofauna composition between control and polyvinyl chloride and chrysene mixtures suggests that the toxicity of the latter could be attenuated by its physical bonding to the former pollutant. Other changes in the functional traits within the nematode communities were a decline in the fertility of females and an increase of the pharyngeal pumping power following exposure to both pollutants for the dominant species. The latter results were also supported by additional toxicokinetics analyses and in silico modeling.
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Affiliation(s)
- Amor Hedfi
- University of Carthage, Faculty of Sciences of Bizerte, LR01ES14 Laboratory of Environment Biomonitoring, Coastal Ecology and Ecotoxicology Unit, 7021 Zarzouna, Tunisia
| | - Manel Ben Ali
- University of Carthage, Faculty of Sciences of Bizerte, LR01ES14 Laboratory of Environment Biomonitoring, Coastal Ecology and Ecotoxicology Unit, 7021 Zarzouna, Tunisia
| | - Marwa Korkobi
- University of Carthage, Faculty of Sciences of Bizerte, LR01ES14 Laboratory of Environment Biomonitoring, Coastal Ecology and Ecotoxicology Unit, 7021 Zarzouna, Tunisia
| | - Mohamed Allouche
- University of Carthage, Faculty of Sciences of Bizerte, LR01ES14 Laboratory of Environment Biomonitoring, Coastal Ecology and Ecotoxicology Unit, 7021 Zarzouna, Tunisia
| | - Abdel Halim Harrath
- King Saud University, Zoology Department, College of Science, Box 2455, Riyadh 11451, Saudi Arabia
| | - Hamouda Beyrem
- University of Carthage, Faculty of Sciences of Bizerte, LR01ES14 Laboratory of Environment Biomonitoring, Coastal Ecology and Ecotoxicology Unit, 7021 Zarzouna, Tunisia
| | - Octavian Pacioglu
- National Institute of Research and Development for Biological Sciences, Bucharest, Romania
| | - Riadh Badraoui
- Section of Histology-Cytology, Medicine Faculty of Tunis, University of Tunis El Manar, 1007 La Rabta-Tunis, Tunisia
| | - Fehmi Boufahja
- University of Carthage, Faculty of Sciences of Bizerte, LR01ES14 Laboratory of Environment Biomonitoring, Coastal Ecology and Ecotoxicology Unit, 7021 Zarzouna, Tunisia.
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5
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Allouche M, Ishak S, Ben Ali M, Hedfi A, Almalki M, Karachle PK, Harrath AH, Abu-Zied RH, Badraoui R, Boufahja F. Molecular interactions of polyvinyl chloride microplastics and beta-blockers (Diltiazem and Bisoprolol) and their effects on marine meiofauna: Combined in vivo and modeling study. JOURNAL OF HAZARDOUS MATERIALS 2022; 431:128609. [PMID: 35278946 DOI: 10.1016/j.jhazmat.2022.128609] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 02/20/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
The ecotoxicological effects of beta-blockers (i.e. Diltiazem and Bisoprolol) and their interactions with the microplastic polyvinyl chloride on marine meiofauna were tested in laboratory microcosms. An experimental factorial design was applied, using meiobenthic fauna collected from the Old Harbor of Bizerte (NE Tunisia), but with a main focus on the nematode communities. The meiobenthic invertebrates were exposed to two concentrations of Diltiazem and Bisoprolol, of 1.8 µg.L-1 and 1.8 mg.L-1, respectively, and one concentration of polyvinyl chloride (i.e. 20 mg.kg-1), separately and mixed. The overall meiofauna abundance was significantly reduced in all treatments, mainly that of polychaetes and amphipods. Moreover, the juveniles-gravid female ratios of the nematode communities were the lowest in the 1.8 µg.L-1 Bisoprolol treatment and for the 1.8 mg.L-1 mixture of Diltiazem and microplastics, suggesting that different dosages influence the maturity status of the examined species. The demographic results were also supported by in silico approach. The simulation of molecular interactions revealed acceptable binding affinities (up to -8.1 kcal/mol) and interactions with key residues in the germ line development protein 3 and sex-determining protein from Coenorhabditis elegans. Overall, the experimental outcome strongly indicates synergistic interactions among the beta-blockers Diltiazem and Bisoprolol and the microplastic polyvinyl chloride on marine nematode communities.
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Affiliation(s)
- Mohamed Allouche
- University of Carthage, Faculty of Sciences of Bizerte, LR01ES14 Laboratory of Environment Biomonitoring, Coastal Ecology and Ecotoxicology Unit, 7021 Zarzouna, Tunisia
| | - Sahar Ishak
- University of Carthage, Faculty of Sciences of Bizerte, LR01ES14 Laboratory of Environment Biomonitoring, Coastal Ecology and Ecotoxicology Unit, 7021 Zarzouna, Tunisia
| | - Manel Ben Ali
- University of Carthage, Faculty of Sciences of Bizerte, LR01ES14 Laboratory of Environment Biomonitoring, Coastal Ecology and Ecotoxicology Unit, 7021 Zarzouna, Tunisia
| | - Amor Hedfi
- University of Carthage, Faculty of Sciences of Bizerte, LR01ES14 Laboratory of Environment Biomonitoring, Coastal Ecology and Ecotoxicology Unit, 7021 Zarzouna, Tunisia
| | - Mohammed Almalki
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Paraskevi K Karachle
- Hellenic Centre for Marine Research, Institute of Marine Biological Resources and Inland Waters, 46.7 Athens-Sounio Ave., P.O. Box 712, 19013 Anavyssos, Attika, Greece
| | - Abdel Halim Harrath
- King Saud University, Zoology Department, College of Science, Box 2455, Riyadh 11451, Saudi Arabia
| | - Ramadan H Abu-Zied
- Geology department, Faculty of Science, Mansoura University, El-Mansoura 35516, Egypt
| | - Riadh Badraoui
- Section of Histology-Cytology, Medicine Faculty of Tunis, University of Tunis El Manar, 1007 La Rabta-Tunis, Tunisia
| | - Fehmi Boufahja
- University of Carthage, Faculty of Sciences of Bizerte, LR01ES14 Laboratory of Environment Biomonitoring, Coastal Ecology and Ecotoxicology Unit, 7021 Zarzouna, Tunisia.
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6
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Minegishi K, Rothé B, Komatsu KR, Ono H, Ikawa Y, Nishimura H, Katoh TA, Kajikawa E, Sai X, Miyashita E, Takaoka K, Bando K, Kiyonari H, Yamamoto T, Saito H, Constam DB, Hamada H. Fluid flow-induced left-right asymmetric decay of Dand5 mRNA in the mouse embryo requires a Bicc1-Ccr4 RNA degradation complex. Nat Commun 2021; 12:4071. [PMID: 34210974 PMCID: PMC8249388 DOI: 10.1038/s41467-021-24295-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 06/09/2021] [Indexed: 12/02/2022] Open
Abstract
Molecular left-right (L-R) asymmetry is established at the node of the mouse embryo as a result of the sensing of a leftward fluid flow by immotile cilia of perinodal crown cells and the consequent degradation of Dand5 mRNA on the left side. We here examined how the fluid flow induces Dand5 mRNA decay. We found that the first 200 nucleotides in the 3' untranslated region (3'-UTR) of Dand5 mRNA are necessary and sufficient for the left-sided decay and to mediate the response of a 3'-UTR reporter transgene to Ca2+, the cation channel Pkd2, the RNA-binding protein Bicc1 and their regulation by the flow direction. We show that Bicc1 preferentially recognizes GACR and YGAC sequences, which can explain the specific binding to a conserved GACGUGAC motif located in the proximal Dand5 3'-UTR. The Cnot3 component of the Ccr4-Not deadenylase complex interacts with Bicc1 and is also required for Dand5 mRNA decay at the node. These results suggest that Ca2+ currents induced by leftward fluid flow stimulate Bicc1 and Ccr4-Not to mediate Dand5 mRNA degradation specifically on the left side of the node.
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Affiliation(s)
- Katsura Minegishi
- Laboratory for Organismal Patterning, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan
| | - Benjamin Rothé
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, Lausanne, Switzerland
| | - Kaoru R Komatsu
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Hiroki Ono
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Yayoi Ikawa
- Laboratory for Organismal Patterning, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan
| | - Hiromi Nishimura
- Laboratory for Organismal Patterning, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan
| | - Takanobu A Katoh
- Laboratory for Organismal Patterning, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan
| | - Eriko Kajikawa
- Laboratory for Organismal Patterning, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan
| | - Xiaorei Sai
- Laboratory for Organismal Patterning, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan
| | - Emi Miyashita
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Katsuyoshi Takaoka
- Laboratory for Organismal Patterning, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan
| | - Kana Bando
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan
| | - Hiroshi Kiyonari
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan
| | - Tadashi Yamamoto
- Laboratory for Immunogenetics, Center for Integrative Medical Sciences, Suehiro-cho, Yokohama, Japan
- Cell Signal Unit, Okinawa Institute of Science and Technology, Kunigami-gun, Okinawa, Japan
| | - Hirohide Saito
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan.
| | - Daniel B Constam
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, Lausanne, Switzerland.
| | - Hiroshi Hamada
- Laboratory for Organismal Patterning, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan.
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7
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Yadav M, Singh RS, Hogan D, Vidhyasagar V, Yang S, Chung IYW, Kusalik A, Dmitriev OY, Cygler M, Wu Y. The KH domain facilitates the substrate specificity and unwinding processivity of DDX43 helicase. J Biol Chem 2021; 296:100085. [PMID: 33199368 PMCID: PMC7949032 DOI: 10.1074/jbc.ra120.015824] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/03/2020] [Accepted: 11/16/2020] [Indexed: 01/21/2023] Open
Abstract
The K-homology (KH) domain is a nucleic acid-binding domain present in many proteins. Recently, we found that the DEAD-box helicase DDX43 contains a KH domain in its N-terminus; however, its function remains unknown. Here, we purified recombinant DDX43 KH domain protein and found that it prefers binding ssDNA and ssRNA. Electrophoretic mobility shift assay and NMR revealed that the KH domain favors pyrimidines over purines. Mutational analysis showed that the GXXG loop in the KH domain is involved in pyrimidine binding. Moreover, we found that an alanine residue adjacent to the GXXG loop is critical for binding. Systematic evolution of ligands by exponential enrichment, chromatin immunoprecipitation-seq, and cross-linking immunoprecipitation-seq showed that the KH domain binds C-/T-rich DNA and U-rich RNA. Bioinformatics analysis suggested that the KH domain prefers to bind promoters. Using 15N-heteronuclear single quantum coherence NMR, the optimal binding sequence was identified as TTGT. Finally, we found that the full-length DDX43 helicase prefers DNA or RNA substrates with TTGT or UUGU single-stranded tails and that the KH domain is critically important for sequence specificity and unwinding processivity. Collectively, our results demonstrated that the KH domain facilitates the substrate specificity and processivity of the DDX43 helicase.
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Affiliation(s)
- Manisha Yadav
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Ravi Shankar Singh
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Daniel Hogan
- Department of Computer Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | | | - Shizhuo Yang
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Ivy Yeuk Wah Chung
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Anthony Kusalik
- Department of Computer Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Oleg Y Dmitriev
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Miroslaw Cygler
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Yuliang Wu
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.
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8
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Rothé B, Gagnieux C, Leal-Esteban LC, Constam DB. Role of the RNA-binding protein Bicaudal-C1 and interacting factors in cystic kidney diseases. Cell Signal 2019; 68:109499. [PMID: 31838063 DOI: 10.1016/j.cellsig.2019.109499] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 01/03/2023]
Abstract
Polycystic kidneys frequently associate with mutations in individual components of cilia, basal bodies or centriolar satellites that perturb complex protein networks. In this review, we focus on the RNA-binding protein Bicaudal-C1 (BICC1) which was found mutated in renal cystic dysplasia, and on its interactions with the ankyrin repeat and sterile α motif (SAM)-containing proteins ANKS3 and ANKS6 and associated kinases and their partially overlapping ciliopathy phenotypes. After reviewing BICC1 homologs in model organisms and their functions in mRNA and cell metabolism during development and in renal tubules, we discuss recent insights from cell-based assays and from structure analysis of the SAM domains, and how SAM domain oligomerization might influence multivalent higher order complexes that are implicated in ciliary signal transduction.
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Affiliation(s)
- Benjamin Rothé
- Ecole Polytechnique Fédérale de Lausanne (EPFL) SV ISREC, Station 19, CH-1015 Lausanne, Switzerland
| | - Céline Gagnieux
- Ecole Polytechnique Fédérale de Lausanne (EPFL) SV ISREC, Station 19, CH-1015 Lausanne, Switzerland
| | - Lucia Carolina Leal-Esteban
- Ecole Polytechnique Fédérale de Lausanne (EPFL) SV ISREC, Station 19, CH-1015 Lausanne, Switzerland; Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Daniel B Constam
- Ecole Polytechnique Fédérale de Lausanne (EPFL) SV ISREC, Station 19, CH-1015 Lausanne, Switzerland.
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9
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Ishii T, Sekiguchi M. Two ways of escaping from oxidative RNA damage: Selective degradation and cell death. DNA Repair (Amst) 2019; 81:102666. [PMID: 31326364 DOI: 10.1016/j.dnarep.2019.102666] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Reactive oxygen species (ROS) are produced during normal cellular metabolism, and various oxidized compounds are formed by the ROS attack. Among oxidized bases, 8-oxo-7,8-dihydroguanine (8-oxoG) is most abundant and seems important with respect to the maintenance and transfer of genetic information. The accumulation of 8-oxoG in messenger RNA may cause errors during codon-anticodon pairing in the translation process, which may result in the synthesis of abnormal proteins. Organisms that use oxygen as the source of energy production must therefore have some mechanisms to eliminate the deleterious effects of RNA oxidation. Recently, we found two protein factors, AUF1 and PCBP1, which each have a different binding capacity to oxidized RNA. Evidence demonstrated that AUF1 is involved in the specific degradation of oxidized RNA, and that PCBP1 has a function of inducing cell death to eliminate severely damaged RNA.
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Affiliation(s)
- Takashi Ishii
- Department of Biochemistry, Fukuoka Dental College, Fukuoka 814-0193, Japan.
| | - Mutsuo Sekiguchi
- Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
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10
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Controlling the Messenger: Regulated Translation of Maternal mRNAs in Xenopus laevis Development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 953:49-82. [PMID: 27975270 DOI: 10.1007/978-3-319-46095-6_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The selective translation of maternal mRNAs encoding cell-fate determinants drives the earliest decisions of embryogenesis that establish the vertebrate body plan. This chapter will discuss studies in Xenopus laevis that provide insights into mechanisms underlying this translational control. Xenopus has been a powerful model organism for many discoveries relevant to the translational control of maternal mRNAs because of the large size of its oocytes and eggs that allow for microinjection of molecules and the relative ease of manipulating the oocyte to egg transition (maturation) and fertilization in culture. Consequently, many key studies have focused on the expression of maternal mRNAs during the oocyte to egg transition (the meiotic cell cycle) and the rapid cell divisions immediately following fertilization. This research has made seminal contributions to our understanding of translational regulatory mechanisms, but while some of the mRNAs under consideration at these stages encode cell-fate determinants, many encode cell cycle regulatory proteins that drive these early cell cycles. In contrast, while maternal mRNAs encoding key developmental (i.e., cell-fate) regulators that function after the first cleavage stages may exploit aspects of these foundational mechanisms, studies reveal that these mRNAs must also rely on distinct and, as of yet, incompletely understood mechanisms. These findings are logical because the functions of such developmental regulatory proteins have requirements distinct from cell cycle regulators, including becoming relevant only after fertilization and then only in specific cells of the embryo. Indeed, key maternal cell-fate determinants must be made available in exquisitely precise amounts (usually low), only at specific times and in specific cells during embryogenesis. To provide an appreciation for the regulation of maternal cell-fate determinant expression, an overview of the maternal phase of Xenopus embryogenesis will be presented. This section will be followed by a review of translational mechanisms operating in oocytes, eggs, and early cleavage-stage embryos and conclude with a discussion of how the regulation of key maternal cell-fate determinants at the level of translation functions in Xenopus embryogenesis. A key theme is that the molecular asymmetries critical for forming the body axes are established and further elaborated upon by the selective temporal and spatial regulation of maternal mRNA translation.
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Nakel K, Bonneau F, Basquin C, Habermann B, Eckmann CR, Conti E. Structural basis for the antagonistic roles of RNP-8 and GLD-3 in GLD-2 poly(A)-polymerase activity. RNA (NEW YORK, N.Y.) 2016; 22:1139-1145. [PMID: 27288313 PMCID: PMC4931106 DOI: 10.1261/rna.056598.116] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 04/28/2016] [Indexed: 06/06/2023]
Abstract
Cytoplasmic polyadenylation drives the translational activation of specific mRNAs in early metazoan development and is performed by distinct complexes that share the same catalytic poly(A)-polymerase subunit, GLD-2. The activity and specificity of GLD-2 depend on its binding partners. In Caenorhabditis elegans, GLD-2 promotes spermatogenesis when bound to GLD-3 and oogenesis when bound to RNP-8. GLD-3 and RNP-8 antagonize each other and compete for GLD-2 binding. Following up on our previous mechanistic studies of GLD-2-GLD-3, we report here the 2.5 Å resolution structure and biochemical characterization of a GLD-2-RNP-8 core complex. In the structure, RNP-8 embraces the poly(A)-polymerase, docking onto several conserved hydrophobic hotspots present on the GLD-2 surface. RNP-8 stabilizes GLD-2 and indirectly stimulates polyadenylation. RNP-8 has a different amino-acid sequence and structure as compared to GLD-3. Yet, it binds the same surfaces of GLD-2 by forming alternative interactions, rationalizing the remarkable versatility of GLD-2 complexes.
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Affiliation(s)
- Katharina Nakel
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, D-82152 Martinsried, Germany
| | - Fabien Bonneau
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, D-82152 Martinsried, Germany
| | - Claire Basquin
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, D-82152 Martinsried, Germany
| | - Bianca Habermann
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, D-82152 Martinsried, Germany
| | - Christian R Eckmann
- Department of Genetics, Martin-Luther-University of Halle-Wittenberg, Institute of Biology, 06120 Halle (Saale), Germany
| | - Elena Conti
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, D-82152 Martinsried, Germany
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Abstract
Loss of the RNA-binding protein Bicaudal-C (Bicc1) provokes renal and pancreatic cysts as well as ectopic Wnt/β-catenin signaling during visceral left-right patterning. Renal cysts are linked to defective silencing of Bicc1 target mRNAs, including adenylate cyclase 6 (AC6). RNA binding of Bicc1 is mediated by N-terminal KH domains, whereas a C-terminal sterile alpha motif (SAM) self-polymerizes in vitro and localizes Bicc1 in cytoplasmic foci in vivo. To assess a role for multimerization in silencing, we conducted structure modeling and then mutated the SAM domain residues which in this model were predicted to polymerize Bicc1 in a left-handed helix. We show that a SAM-SAM interface concentrates Bicc1 in cytoplasmic clusters to specifically localize and silence bound mRNA. In addition, defective polymerization decreases Bicc1 stability and thus indirectly attenuates inhibition of Dishevelled 2 in the Wnt/β-catenin pathway. Importantly, aberrant C-terminal extension of the SAM domain in bpk mutant Bicc1 phenocopied these defects. We conclude that polymerization is a novel disease-relevant mechanism both to stabilize Bicc1 and to present associated mRNAs in specific silencing platforms.
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13
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Structural basis for the activation of the C. elegans noncanonical cytoplasmic poly(A)-polymerase GLD-2 by GLD-3. Proc Natl Acad Sci U S A 2015; 112:8614-9. [PMID: 26124149 DOI: 10.1073/pnas.1504648112] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Caenorhabditis elegans germ-line development defective (GLD)-2-GLD-3 complex up-regulates the expression of genes required for meiotic progression. GLD-2-GLD-3 acts by extending the short poly(A) tail of germ-line-specific mRNAs, switching them from a dormant state into a translationally active state. GLD-2 is a cytoplasmic noncanonical poly(A) polymerase that lacks the RNA-binding domain typical of the canonical nuclear poly(A)-polymerase Pap1. The activity of C. elegans GLD-2 in vivo and in vitro depends on its association with the multi-K homology (KH) domain-containing protein, GLD-3, a homolog of Bicaudal-C. We have identified a minimal polyadenylation complex that includes the conserved nucleotidyl-transferase core of GLD-2 and the N-terminal domain of GLD-3, and determined its structure at 2.3-Å resolution. The structure shows that the N-terminal domain of GLD-3 does not fold into the predicted KH domain but wraps around the catalytic domain of GLD-2. The picture that emerges from the structural and biochemical data are that GLD-3 activates GLD-2 both indirectly by stabilizing the enzyme and directly by contributing positively charged residues near the RNA-binding cleft. The RNA-binding cleft of GLD-2 has distinct structural features compared with the poly(A)-polymerases Pap1 and Trf4. Consistently, GLD-2 has distinct biochemical properties: It displays unusual specificity in vitro for single-stranded RNAs with at least one adenosine at the 3' end. GLD-2 thus appears to have evolved specialized nucleotidyl-transferase properties that match the 3' end features of dormant cytoplasmic mRNAs.
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Elewa A, Shirayama M, Kaymak E, Harrison PF, Powell DR, Du Z, Chute CD, Woolf H, Yi D, Ishidate T, Srinivasan J, Bao Z, Beilharz TH, Ryder SP, Mello CC. POS-1 Promotes Endo-mesoderm Development by Inhibiting the Cytoplasmic Polyadenylation of neg-1 mRNA. Dev Cell 2015; 34:108-18. [PMID: 26096734 DOI: 10.1016/j.devcel.2015.05.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 04/17/2015] [Accepted: 05/27/2015] [Indexed: 12/01/2022]
Abstract
The regulation of mRNA translation is of fundamental importance in biological mechanisms ranging from embryonic axis specification to the formation of long-term memory. POS-1 is one of several CCCH zinc-finger RNA-binding proteins that regulate cell fate specification during C. elegans embryogenesis. Paradoxically, pos-1 mutants exhibit striking defects in endo-mesoderm development but have wild-type distributions of SKN-1, a key determinant of endo-mesoderm fates. RNAi screens for pos-1 suppressors identified genes encoding the cytoplasmic poly(A)-polymerase homolog GLD-2, the Bicaudal-C homolog GLD-3, and the protein NEG-1. We show that NEG-1 localizes in anterior nuclei, where it negatively regulates endo-mesoderm fates. In posterior cells, POS-1 binds the neg-1 3' UTR to oppose GLD-2 and GLD-3 activities that promote NEG-1 expression and cytoplasmic lengthening of the neg-1 mRNA poly(A) tail. Our findings uncover an intricate series of post-transcriptional regulatory interactions that, together, achieve precise spatial expression of endo-mesoderm fates in C. elegans embryos.
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Affiliation(s)
- Ahmed Elewa
- Program in Molecular Medicine, RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Masaki Shirayama
- Program in Molecular Medicine, RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Ebru Kaymak
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Paul F Harrison
- Victorian Bioinformatics Consortium, Monash University, Clayton, Victoria 3800, Australia; Life Sciences Computation Centre, Victorian Life Sciences Computation Initiative, Carlton, Victoria 3053, Australia
| | - David R Powell
- Victorian Bioinformatics Consortium, Monash University, Clayton, Victoria 3800, Australia; Life Sciences Computation Centre, Victorian Life Sciences Computation Initiative, Carlton, Victoria 3053, Australia
| | - Zhuo Du
- Developmental Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
| | - Christopher D Chute
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Life Science and Bioengineering Center, Gateway Park, 60 Prescott Street, Worcester, MA 01605, USA
| | - Hannah Woolf
- Program in Molecular Medicine, RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Dongni Yi
- Program in Molecular Medicine, RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Takao Ishidate
- Program in Molecular Medicine, RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Jagan Srinivasan
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Life Science and Bioengineering Center, Gateway Park, 60 Prescott Street, Worcester, MA 01605, USA
| | - Zhirong Bao
- Developmental Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
| | - Traude H Beilharz
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Sean P Ryder
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Craig C Mello
- Program in Molecular Medicine, RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
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15
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Nicastro G, Taylor IA, Ramos A. KH-RNA interactions: back in the groove. Curr Opin Struct Biol 2015; 30:63-70. [PMID: 25625331 DOI: 10.1016/j.sbi.2015.01.002] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 12/20/2014] [Accepted: 01/08/2015] [Indexed: 12/30/2022]
Abstract
The hnRNP K-homology (KH) domain is a single stranded nucleic acid binding domain that mediates RNA target recognition by a large group of gene regulators. The structure of the KH fold is well characterised and some initial rules for KH-RNA recognition have been drafted. However, recent findings have shown that these rules need to be revisited and have now provided a better understanding of how the domain can recognise a sequence landscape larger than previously thought as well as revealing the diversity of structural expansions to the KH domain. Finally, novel structural and functional data show how multiple KH domains act in a combinatorial fashion to both allow recognition of longer RNA motifs and remodelling of the RNA structure. These advances set the scene for a detailed molecular understanding of KH selection of the cellular targets.
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Affiliation(s)
- Giuseppe Nicastro
- Division of Molecular Structure, MRC National Institute for Medical Research, London, UK
| | - Ian A Taylor
- Division of Molecular Structure, MRC National Institute for Medical Research, London, UK
| | - Andres Ramos
- Research Department of Structural and Molecular Biology, University College London, London, UK; Division of Molecular Structure, MRC National Institute for Medical Research, London, UK.
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16
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Zhang Y, Park S, Blaser S, Sheets MD. Determinants of RNA binding and translational repression by the Bicaudal-C regulatory protein. J Biol Chem 2014; 289:7497-504. [PMID: 24478311 DOI: 10.1074/jbc.m113.526426] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bicaudal-C (Bic-C) RNA binding proteins function as important translational repressors in multiple biological contexts within metazoans. However, their RNA binding sites are unknown. We recently demonstrated that Bic-C functions in spatially regulated translational repression of the xCR1 mRNA during Xenopus development. This repression contributes to normal development by confining the xCR1 protein, a regulator of key signaling pathways, to specific cells of the embryo. In this report, we combined biochemical approaches with in vivo mRNA reporter assays to define the minimal Bic-C target site within the xCR1 mRNA. This 32-nucleotide Bic-C target site is predicted to fold into a stem-loop secondary structure. Mutational analyses provided evidence that this stem-loop structure is important for Bic-C binding. The Bic-C target site was sufficient for Bic-C mediated repression in vivo. Thus, we describe the first RNA binding site for a Bic-C protein. This identification provides an important step toward understanding the mechanisms by which evolutionarily conserved Bic-C proteins control cellular function in metazoans.
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Affiliation(s)
- Yan Zhang
- From the Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53706
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17
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Charlesworth A, Meijer HA, de Moor CH. Specificity factors in cytoplasmic polyadenylation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 4:437-61. [PMID: 23776146 PMCID: PMC3736149 DOI: 10.1002/wrna.1171] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 04/08/2013] [Accepted: 04/09/2013] [Indexed: 12/12/2022]
Abstract
Poly(A) tail elongation after export of an messenger RNA (mRNA) to the cytoplasm is called cytoplasmic polyadenylation. It was first discovered in oocytes and embryos, where it has roles in meiosis and development. In recent years, however, has been implicated in many other processes, including synaptic plasticity and mitosis. This review aims to introduce cytoplasmic polyadenylation with an emphasis on the factors and elements mediating this process for different mRNAs and in different animal species. We will discuss the RNA sequence elements mediating cytoplasmic polyadenylation in the 3' untranslated regions of mRNAs, including the CPE, MBE, TCS, eCPE, and C-CPE. In addition to describing the role of general polyadenylation factors, we discuss the specific RNA binding protein families associated with cytoplasmic polyadenylation elements, including CPEB (CPEB1, CPEB2, CPEB3, and CPEB4), Pumilio (PUM2), Musashi (MSI1, MSI2), zygote arrest (ZAR2), ELAV like proteins (ELAVL1, HuR), poly(C) binding proteins (PCBP2, αCP2, hnRNP-E2), and Bicaudal C (BICC1). Some emerging themes in cytoplasmic polyadenylation will be highlighted. To facilitate understanding for those working in different organisms and fields, particularly those who are analyzing high throughput data, HUGO gene nomenclature for the human orthologs is used throughout. Where human orthologs have not been clearly identified, reference is made to protein families identified in man.
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Affiliation(s)
- Amanda Charlesworth
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, USA
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18
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Chen T, Cui P, Chen H, Ali S, Zhang S, Xiong L. A KH-domain RNA-binding protein interacts with FIERY2/CTD phosphatase-like 1 and splicing factors and is important for pre-mRNA splicing in Arabidopsis. PLoS Genet 2013; 9:e1003875. [PMID: 24146632 PMCID: PMC3798263 DOI: 10.1371/journal.pgen.1003875] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 08/28/2013] [Indexed: 11/19/2022] Open
Abstract
Eukaryotic genomes encode hundreds of RNA-binding proteins, yet the functions of most of these proteins are unknown. In a genetic study of stress signal transduction in Arabidopsis, we identified a K homology (KH)-domain RNA-binding protein, HOS5 (High Osmotic Stress Gene Expression 5), as required for stress gene regulation and stress tolerance. HOS5 was found to interact with FIERY2/RNA polymerase II (RNAP II) carboxyl terminal domain (CTD) phosphatase-like 1 (FRY2/CPL1) both in vitro and in vivo. This interaction is mediated by the first double-stranded RNA-binding domain of FRY2/CPL1 and the KH domains of HOS5. Interestingly, both HOS5 and FRY2/CPL1 also interact with two novel serine-arginine (SR)-rich splicing factors, RS40 and RS41, in nuclear speckles. Importantly, FRY2/CPL1 is required for the recruitment of HOS5. In fry2 mutants, HOS5 failed to be localized in nuclear speckles but was found mainly in the nucleoplasm. hos5 mutants were impaired in mRNA export and accumulated a significant amount of mRNA in the nuclei, particularly under salt stress conditions. Arabidopsis mutants of all these genes exhibit similar stress-sensitive phenotypes. RNA-seq analyses of these mutants detected significant intron retention in many stress-related genes under salt stress but not under normal conditions. Our study not only identified several novel regulators of pre-mRNA processing as important for plant stress response but also suggested that, in addition to RNAP II CTD that is a well-recognized platform for the recruitment of mRNA processing factors, FRY2/CPL1 may also recruit specific factors to regulate the co-transcriptional processing of certain transcripts to deal with environmental challenges. Pre-mRNA processing, including 5′ capping, splicing, and 3′ polyadenylation, is critical for gene expression and is closely coupled with transcription. Phosphorylated carboxyl terminal domain (CTD) of RNA Polymerase II (RNAP II) serves as a platform for the recruitment of pre-mRNA processing factors, yet other components involved in the recruitment are less known. In a genetic study of stress signal transduction in Arabidopsis, we isolated a KH-domain RNA-binding protein HOS5 that plays important roles in stress gene regulation and stress tolerance. We found that HOS5 interacts with FIERY2/CTD phosphatase-like 1 (FRY2/CPL1) and they both also interact with two novel splicing factors, RS40 and RS41, in nuclear speckles. In fry2 mutants, HOS5 was unable to be recruited to nuclear speckles but rather was mainly localized in the nucleoplasm. Mutants in these genes have similar stress-sensitive phenotypes. Transcriptome analyses identified significant intron retention in many stress-related genes in these mutants under salt stress conditions. Our study reveals that, in addition to RNAP II, the CTD phosphatase may also recruit specific splicing factors and RNA binding proteins to regulate the co-transcriptional processing of certain transcripts to deal with environmental stresses.
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Affiliation(s)
- Tao Chen
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Peng Cui
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Hao Chen
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Shahjahan Ali
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Shoudong Zhang
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Liming Xiong
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- * E-mail:
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S1 and KH domains of polynucleotide phosphorylase determine the efficiency of RNA binding and autoregulation. J Bacteriol 2013; 195:2021-31. [PMID: 23457244 DOI: 10.1128/jb.00062-13] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To better understand the roles of the KH and S1 domains in RNA binding and polynucleotide phosphorylase (PNPase) autoregulation, we have identified and investigated key residues in these domains. A convenient pnp::lacZ fusion reporter strain was used to assess autoregulation by mutant PNPase proteins lacking the KH and/or S1 domains or containing point mutations in those domains. Mutant enzymes were purified and studied by using in vitro band shift and phosphorolysis assays to gauge binding and enzymatic activity. We show that reductions in substrate affinity accompany impairment of PNPase autoregulation. A remarkably strong correlation was observed between β-galactosidase levels reflecting autoregulation and apparent KD values for the binding of a model RNA substrate. These data show that both the KH and S1 domains of PNPase play critical roles in substrate binding and autoregulation. The findings are discussed in the context of the structure, binding sites, and function of PNPase.
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Translational control in the Caenorhabditis elegans germ line. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 757:205-47. [PMID: 22872479 DOI: 10.1007/978-1-4614-4015-4_8] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Translational control is a prevalent form of gene expression regulation in the Caenorhabditis elegans germ line. Linking the amount of protein synthesis to mRNA quantity and translational accessibility in the cell cytoplasm provides unique advantages over DNA-based controls for developing germ cells. This mode of gene expression is especially exploited in germ cell fate decisions and during oogenesis, when the developing oocytes stockpile hundreds of different mRNAs required for early embryogenesis. Consequently, a dense web of RNA regulators, consisting of diverse RNA-binding proteins and RNA-modifying enzymes, control the translatability of entire mRNA expression programs. These RNA regulatory networks are tightly coupled to germ cell developmental progression and are themselves under translational control. The underlying molecular mechanisms and RNA codes embedded in the mRNA molecules are beginning to be understood. Hence, the C. elegans germ line offers fertile grounds for discovering post-transcriptional mRNA regulatory mechanisms and emerges as great model for a systems level understanding of translational control during development.
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Hollingworth D, Candel AM, Nicastro G, Martin SR, Briata P, Gherzi R, Ramos A. KH domains with impaired nucleic acid binding as a tool for functional analysis. Nucleic Acids Res 2012; 40:6873-86. [PMID: 22547390 PMCID: PMC3413153 DOI: 10.1093/nar/gks368] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Revised: 04/05/2012] [Accepted: 04/11/2012] [Indexed: 02/07/2023] Open
Abstract
In eukaryotes, RNA-binding proteins that contain multiple K homology (KH) domains play a key role in coordinating the different steps of RNA synthesis, metabolism and localization. Understanding how the different KH modules participate in the recognition of the RNA targets is necessary to dissect the way these proteins operate. We have designed a KH mutant with impaired RNA-binding capability for general use in exploring the role of individual KH domains in the combinatorial functional recognition of RNA targets. A double mutation in the hallmark GxxG loop (GxxG-to-GDDG) impairs nucleic acid binding without compromising the stability of the domain. We analysed the impact of the GDDG mutations in individual KH domains on the functional properties of KSRP as a prototype of multiple KH domain-containing proteins. We show how the GDDG mutant can be used to directly link biophysical information on the sequence specificity of the different KH domains of KSRP and their role in mRNA recognition and decay. This work defines a general molecular biology tool for the investigation of the function of individual KH domains in nucleic acid binding proteins.
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Affiliation(s)
- David Hollingworth
- Molecular Structure Division, Physical Biochemistry Division, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK and Gene Expression Regulation Laboratory, IRCCS AOU San Martino – IST, Largo R. Benzi 10, Genova, Italy
| | - Adela M. Candel
- Molecular Structure Division, Physical Biochemistry Division, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK and Gene Expression Regulation Laboratory, IRCCS AOU San Martino – IST, Largo R. Benzi 10, Genova, Italy
| | - Giuseppe Nicastro
- Molecular Structure Division, Physical Biochemistry Division, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK and Gene Expression Regulation Laboratory, IRCCS AOU San Martino – IST, Largo R. Benzi 10, Genova, Italy
| | - Stephen R. Martin
- Molecular Structure Division, Physical Biochemistry Division, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK and Gene Expression Regulation Laboratory, IRCCS AOU San Martino – IST, Largo R. Benzi 10, Genova, Italy
| | - Paola Briata
- Molecular Structure Division, Physical Biochemistry Division, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK and Gene Expression Regulation Laboratory, IRCCS AOU San Martino – IST, Largo R. Benzi 10, Genova, Italy
| | - Roberto Gherzi
- Molecular Structure Division, Physical Biochemistry Division, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK and Gene Expression Regulation Laboratory, IRCCS AOU San Martino – IST, Largo R. Benzi 10, Genova, Italy
| | - Andres Ramos
- Molecular Structure Division, Physical Biochemistry Division, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK and Gene Expression Regulation Laboratory, IRCCS AOU San Martino – IST, Largo R. Benzi 10, Genova, Italy
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22
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The Bic-C family of developmental translational regulators. Comp Funct Genomics 2012; 2012:141386. [PMID: 22611335 PMCID: PMC3352585 DOI: 10.1155/2012/141386] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Accepted: 02/18/2012] [Indexed: 12/14/2022] Open
Abstract
Regulation of mRNA translation is especially important during cellular and developmental processes. Many evolutionarily conserved proteins act in the context of multiprotein complexes and modulate protein translation both at the spatial and the temporal levels. Among these, Bicaudal C constitutes a family of RNA binding proteins whose founding member was first identified in Drosophila and contains orthologs in vertebrates. We discuss recent advances towards understanding the functions of these proteins in the context of the cellular and developmental biology of many model organisms and their connection to human disease.
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Minasaki R, Eckmann CR. Subcellular specialization of multifaceted 3'end modifying nucleotidyltransferases. Curr Opin Cell Biol 2012; 24:314-22. [PMID: 22551970 DOI: 10.1016/j.ceb.2012.03.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Revised: 03/24/2012] [Accepted: 03/29/2012] [Indexed: 10/28/2022]
Abstract
While canonical 3'end modifications of mRNAs or tRNAs are well established, recent technological advances in RNA analysis have given us a glimpse of how widespread other types of distinctive 3'end modifications appear to be. Next to alternative nuclear or cytoplasmic polyadenylation mechanisms, evidence accumulated for a variety of 3'end mono-nucleotide and oligo-nucleotide additions of primarily adenosines or uracils on a variety of RNA species. Enzymes responsible for such non-templated additions are non-canonical RNA nucleotidyltransferases, which possess surprising flexibility in RNA substrate selection and enzymatic activity. We will highlight recent findings supporting the view that RNA nucleotidyltransferase activity, RNA target selection and sub-compartimentalization are spatially, temporally and physiologically regulated by dedicated co-factors. Along with the diversification of non-coding RNA classes, the evolutionary conservation of these multifaceted RNA modifiers underscores the prevalence and importance of diverse 3'end formation mechanisms.
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Affiliation(s)
- Ryuji Minasaki
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
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Kraus MRC, Clauin S, Pfister Y, Di Maïo M, Ulinski T, Constam D, Bellanné-Chantelot C, Grapin-Botton A. Two mutations in human BICC1 resulting in Wnt pathway hyperactivity associated with cystic renal dysplasia. Hum Mutat 2011; 33:86-90. [PMID: 21922595 DOI: 10.1002/humu.21610] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Accepted: 08/29/2011] [Indexed: 01/22/2023]
Abstract
Bicaudal C homologue 1 (Bicc1) knockout in mice causes polycystic kidney disease and pancreas development defects, including a reduction in insulin-producing β-cells and ensuing diabetes. We therefore screened 137 patients with renal abnormalities or association of early-onset diabetes and renal disease for genetic alterations in BICC1. We identified two heterozygous mutations, one nonsense in the first K Homology (KH) domain and one missense in the sterile alpha motif (SAM) domain. In mice, Bicc1 blocks canonical Wnt signaling, mostly via its SAM domain. We show that the human BICC1, similar to its mouse counterpart, blocks canonical Wnt signaling. The nonsense mutation identified results in a complete loss of Wnt inhibitory activity. The point mutation in the SAM domain has a similar effect to a complete SAM domain deletion, resulting in a 22% loss of activity.
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Affiliation(s)
- Marine R-C Kraus
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Station 19, Lausanne, Switzerland
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