1
|
Yu L, Majerciak V, Zheng ZM. HPV16 and HPV18 Genome Structure, Expression, and Post-Transcriptional Regulation. Int J Mol Sci 2022; 23:ijms23094943. [PMID: 35563334 PMCID: PMC9105396 DOI: 10.3390/ijms23094943] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 12/18/2022] Open
Abstract
Human papillomaviruses (HPV) are a group of small non-enveloped DNA viruses whose infection causes benign tumors or cancers. HPV16 and HPV18, the two most common high-risk HPVs, are responsible for ~70% of all HPV-related cervical cancers and head and neck cancers. The expression of the HPV genome is highly dependent on cell differentiation and is strictly regulated at the transcriptional and post-transcriptional levels. Both HPV early and late transcripts differentially expressed in the infected cells are intron-containing bicistronic or polycistronic RNAs bearing more than one open reading frame (ORF), because of usage of alternative viral promoters and two alternative viral RNA polyadenylation signals. Papillomaviruses proficiently engage alternative RNA splicing to express individual ORFs from the bicistronic or polycistronic RNA transcripts. In this review, we discuss the genome structures and the updated transcription maps of HPV16 and HPV18, and the latest research advances in understanding RNA cis-elements, intron branch point sequences, and RNA-binding proteins in the regulation of viral RNA processing. Moreover, we briefly discuss the epigenetic modifications, including DNA methylation and possible APOBEC-mediated genome editing in HPV infections and carcinogenesis.
Collapse
|
2
|
Billey E, Hafidh S, Cruz-Gallardo I, Litholdo CG, Jean V, Carpentier MC, Picart C, Kumar V, Kulichova K, Maréchal E, Honys D, Conte MR, Deragon JM, Bousquet-Antonelli C. LARP6C orchestrates posttranscriptional reprogramming of gene expression during hydration to promote pollen tube guidance. THE PLANT CELL 2021; 33:2637-2661. [PMID: 34124761 DOI: 10.1101/2020.11.27.401307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 05/06/2021] [Indexed: 05/19/2023]
Abstract
Increasing evidence suggests that posttranscriptional regulation is a key player in the transition between mature pollen and the progamic phase (from pollination to fertilization). Nonetheless, the actors in this messenger RNA (mRNA)-based gene expression reprogramming are poorly understood. We demonstrate that the evolutionarily conserved RNA-binding protein LARP6C is necessary for the transition from dry pollen to pollen tubes and the guided growth of pollen tubes towards the ovule in Arabidopsis thaliana. In dry pollen, LARP6C binds to transcripts encoding proteins that function in lipid synthesis and homeostasis, vesicular trafficking, and polarized cell growth. LARP6C also forms cytoplasmic granules that contain the poly(A) binding protein and possibly represent storage sites for translationally silent mRNAs. In pollen tubes, the loss of LARP6C negatively affects the quantities and distribution of storage lipids, as well as vesicular trafficking. In Nicotiana benthamiana leaf cells and in planta, analysis of reporter mRNAs designed from the LARP6C target MGD2 provided evidence that LARP6C can shift from a repressor to an activator of translation when the pollen grain enters the progamic phase. We propose that LARP6C orchestrates the timely posttranscriptional regulation of a subset of mRNAs in pollen during the transition from the quiescent to active state and along the progamic phase to promote male fertilization in plants.
Collapse
Affiliation(s)
- Elodie Billey
- Laboratoire Génome et Développement des Plantes, UMR5096, CNRS, 66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Said Hafidh
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, 16502 Prague 6, Czech Republic
| | - Isabel Cruz-Gallardo
- Randall Centre for Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK
| | - Celso G Litholdo
- Laboratoire Génome et Développement des Plantes, UMR5096, CNRS, 66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Viviane Jean
- Laboratoire Génome et Développement des Plantes, UMR5096, CNRS, 66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Marie-Christine Carpentier
- Laboratoire Génome et Développement des Plantes, UMR5096, CNRS, 66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Claire Picart
- Laboratoire Génome et Développement des Plantes, UMR5096, CNRS, 66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Vinod Kumar
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, 16502 Prague 6, Czech Republic
| | - Katarina Kulichova
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, 16502 Prague 6, Czech Republic
| | - Eric Maréchal
- Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168 CNRS, CEA, INRAE, Université Grenoble Alpes, IRIG, CEA Grenoble, 38054 Grenoble, France
| | - David Honys
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, 16502 Prague 6, Czech Republic
| | - Maria R Conte
- Randall Centre for Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK
| | - Jean-Marc Deragon
- Laboratoire Génome et Développement des Plantes, UMR5096, CNRS, 66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
- Institut Universitaire de France, 75231 Paris Cedex 5, France
| | - Cécile Bousquet-Antonelli
- Laboratoire Génome et Développement des Plantes, UMR5096, CNRS, 66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| |
Collapse
|
3
|
Náprstková A, Malínská K, Záveská Drábková L, Billey E, Náprstková D, Sýkorová E, Bousquet-Antonelli C, Honys D. Characterization of ALBA Family Expression and Localization in Arabidopsis thaliana Generative Organs. Int J Mol Sci 2021; 22:1652. [PMID: 33562109 PMCID: PMC7914821 DOI: 10.3390/ijms22041652] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 01/31/2021] [Accepted: 02/03/2021] [Indexed: 12/21/2022] Open
Abstract
ALBA DNA/RNA-binding proteins form an ancient family, which in eukaryotes diversified into two Rpp25-like and Rpp20-like subfamilies. In most studied model organisms, their function remains unclear, but they are usually associated with RNA metabolism, mRNA translatability and stress response. In plants, the enriched number of ALBA family members remains poorly understood. Here, we studied ALBA dynamics during reproductive development in Arabidopsis at the levels of gene expression and protein localization, both under standard conditions and following heat stress. In generative tissues, ALBA proteins showed the strongest signal in mature pollen where they localized predominantly in cytoplasmic foci, particularly in regions surrounding the vegetative nucleus and sperm cells. Finally, we demonstrated the involvement of two Rpp25-like subfamily members ALBA4 and ALBA6 in RNA metabolism in mature pollen supported by their co-localization with poly(A)-binding protein 3 (PABP3). Collectively, we demonstrated the engagement of ALBA proteins in male reproductive development and the heat stress response, highlighting the involvement of ALBA4 and ALBA6 in RNA metabolism, storage and/or translational control in pollen upon heat stress. Such dynamic re-localization of ALBA proteins in a controlled, developmentally and environmentally regulated manner, likely reflects not only their redundancy but also their possible functional diversification in plants.
Collapse
Affiliation(s)
- Alena Náprstková
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic; (A.N.); (L.Z.D.); (D.N.)
| | - Kateřina Malínská
- Imaging Facility, Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic;
| | - Lenka Záveská Drábková
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic; (A.N.); (L.Z.D.); (D.N.)
| | - Elodie Billey
- CNRS LGDP-UMR5096, 58 Av. Paul Alduy, 66860 Perpignan, France; (E.B.); (C.B.-A.)
- LGDP-UMR5096, Université de Perpignan via Domitia, 58 Av. Paul Alduy, 66860 Perpignan, France
| | - Dagmar Náprstková
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic; (A.N.); (L.Z.D.); (D.N.)
| | - Eva Sýkorová
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská, 612 00 Brno, Czech Republic;
| | - Cécile Bousquet-Antonelli
- CNRS LGDP-UMR5096, 58 Av. Paul Alduy, 66860 Perpignan, France; (E.B.); (C.B.-A.)
- LGDP-UMR5096, Université de Perpignan via Domitia, 58 Av. Paul Alduy, 66860 Perpignan, France
| | - David Honys
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic; (A.N.); (L.Z.D.); (D.N.)
| |
Collapse
|
4
|
Brambilla M, Martani F, Bertacchi S, Vitangeli I, Branduardi P. The Saccharomyces cerevisiae
poly (A) binding protein (Pab1): Master regulator of mRNA metabolism and cell physiology. Yeast 2018; 36:23-34. [DOI: 10.1002/yea.3347] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 06/26/2018] [Accepted: 07/06/2018] [Indexed: 12/15/2022] Open
Affiliation(s)
- Marco Brambilla
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 20126 Milan Italy
| | - Francesca Martani
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 20126 Milan Italy
| | - Stefano Bertacchi
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 20126 Milan Italy
| | - Ilaria Vitangeli
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 20126 Milan Italy
| | - Paola Branduardi
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 20126 Milan Italy
| |
Collapse
|
5
|
The Evolutionarily-conserved Polyadenosine RNA Binding Protein, Nab2, Cooperates with Splicing Machinery to Regulate the Fate of pre-mRNA. Mol Cell Biol 2016; 36:2697-2714. [PMID: 27528618 PMCID: PMC5064217 DOI: 10.1128/mcb.00402-16] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Numerous RNA binding proteins are deposited onto an mRNA transcript to modulate post-transcriptional processing events ensuring proper mRNA maturation. Defining the interplay between RNA binding proteins that couple mRNA biogenesis events is crucial for understanding how gene expression is regulated. To explore how RNA binding proteins control mRNA processing, we investigated a role for the evolutionarily conserved polyadenosine RNA binding protein, Nab2, in mRNA maturation within the nucleus. This work reveals that nab2 mutant cells accumulate intron-containing pre-mRNA in vivo We extend this analysis to identify genetic interactions between mutant alleles of nab2 and genes encoding the splicing factor, MUD2, and the RNA exosome, RRP6, with in vivo consequences of altered pre-mRNA splicing and poly(A) tail length control. As further evidence linking Nab2 proteins to splicing, an unbiased proteomic analysis of vertebrate Nab2, ZC3H14, identifies physical interactions with numerous components of the spliceosome. We validated the interaction between ZC3H14 and U2AF2/U2AF65 Taking all the findings into consideration, we present a model where Nab2/ZC3H14 interacts with spliceosome components to allow proper coupling of splicing with subsequent mRNA processing steps contributing to a kinetic proofreading step that allows properly processed mRNA to exit the nucleus and escape Rrp6-dependent degradation.
Collapse
|
6
|
Mu X, Su M, Gui L, Liang X, Zhang P, Hu P, Liu Z, Zhang J. Comparative renal gene expression in response to abrupt hypoosmotic shock in spotted scat (Scatophagus argus). Gen Comp Endocrinol 2015; 215:25-35. [PMID: 25304824 DOI: 10.1016/j.ygcen.2014.09.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 09/17/2014] [Accepted: 09/20/2014] [Indexed: 11/18/2022]
Abstract
Scatophagus argus, a euryhaline fish, is notable for its ability to tolerate a wide range of environmental salinities and especially for its tolerance to a rapid, marked reduction in salinity. Therefore, S. argus is a good model for studying the molecular mechanisms mediating abrupt hyperosmoregulation. The serum osmotic pressure decreased steeply within one hour after transferring S. argus from seawater (SW) to freshwater (FW) and remained at new balance throughout the duration of one week. To explain this phenomenon and understand the molecular responses to an abrupt hypoosmotic shock, hypoosmotic stress responsive genes were identified by constructing two suppression subtractive hybridization (SSH) cDNA libraries from the kidneys of S. argus that had been transferred from SW to FW. After trimming and blasting, 52 ESTs were picked out from the subtractive library. Among them, 11 genes were significantly up-regulated (p < 0.05). The kinetics studies of gene expression levels were conducted for 1 week after the transfer using quantitative real-time PCR. A significant variation in the expression of these genes occurred within 12h after the hypoosmotic shock, except for growth hormone (GH) and polyadenylate binding protein 1 (PBP1), which were significantly up-regulated 2 days post-transfer. Our results suggest different functional roles for these genes in response to hypoosmotic stress during the stress response phase (1 hpt-12 hpt) and stable phase (12 hpt-7 dpt). Furthermore, the plasma growth hormone level was detected to be significantly elevated at 1 hpt and 24 hpt following abrupt hypoosmotic shock. Meanwhile, several hematological parameters, hemoglobin (HGB), red blood cell (RBC) and mean cellular hemoglobin concentration (MCHC), were observed to be significantly increased at 12 hpt and 2 dpt compared with that of control group. Our results provide a solid basis from which to conduct future studies on the osmoregulatory mechanisms in the euryhaline fish.
Collapse
Affiliation(s)
- Xingjiang Mu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Maoliang Su
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Lang Gui
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Xuemei Liang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Peipei Zhang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Pan Hu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Zhenhao Liu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Junbin Zhang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China.
| |
Collapse
|
7
|
Guerra-Pérez N, Ramos E, García-Hernández M, Pinto C, Soto M, Martín ME, González VM. Molecular and Functional Characterization of ssDNA Aptamers that Specifically Bind Leishmania infantum PABP. PLoS One 2015; 10:e0140048. [PMID: 26457419 PMCID: PMC4601788 DOI: 10.1371/journal.pone.0140048] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 09/21/2015] [Indexed: 02/05/2023] Open
Abstract
SUMMARY A poly (A)-binding protein from Leishmania infantum (LiPABP) has been recently cloned and characterized in our laboratory. Although this protein shows a very high homology with PABPs from other eukaryotic organisms including mammals and other parasites, exist divergences along the sequence that convert them in potential diagnostic markers and/or therapeutics targets. Aptamers are oligonucleotide ligands that are selected in vitro by their affinity and specificity for the target as a consequence of the particular tertiary structure that they are able to acquire depending on their sequence. Development of high-affinity molecules with the ability to recognize specifically Leishmania proteins is essential for the progress of this kind of study. RESULTS We have selected a ssDNA aptamer population against a recombinant 6xHIS-LiPABP protein (rLiPABP) that is able to recognize the target with a low Kd. Cloning, sequencing and in silico analysis of the aptamers obtained from the population yielded three aptamers (ApPABP#3, ApPABP#7 and ApPABP#11) that significantly bound to PABP with higher affinity than the naïve population. These aptamers were analyzed by ELONA and slot blot to establish affinity and specificity for rLiPABP. Results demonstrated that the three aptamers have high affinity and specificity for the target and that they are able to detect an endogenous LiPABP (eLiPABP) protein amount corresponding to 2500 L. infantum promastigotes in a significant manner. The functional analysis of the aptamers also revealed that ApPABP#11 disrupts the binding of both Myc-LiPABP and eLiPABP to poly (A) in vitro. On the other hand, these aptamers are able to bind and purify LiPABP from complex mixes. CONCLUSION Results presented here demonstrate that aptamers represent new reagents for characterization of LiPABP and that they can affect LiPABP activity. At this respect, the use of these aptamers as therapeutic tool affecting the physiological role of PABP has to be analyzed.
Collapse
Affiliation(s)
- Natalia Guerra-Pérez
- Laboratory of aptamers, Servicio de Bioquímica-Investigación, IRYCIS-Hospital Ramón y Cajal, Madrid, Spain
| | - Edurne Ramos
- Laboratory of aptamers, Servicio de Bioquímica-Investigación, IRYCIS-Hospital Ramón y Cajal, Madrid, Spain
| | | | - Celia Pinto
- Laboratory of aptamers, Servicio de Bioquímica-Investigación, IRYCIS-Hospital Ramón y Cajal, Madrid, Spain
| | - Manuel Soto
- Departamento de Biología Molecular, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - M. Elena Martín
- Laboratory of aptamers, Servicio de Bioquímica-Investigación, IRYCIS-Hospital Ramón y Cajal, Madrid, Spain
| | - Víctor M. González
- Laboratory of aptamers, Servicio de Bioquímica-Investigación, IRYCIS-Hospital Ramón y Cajal, Madrid, Spain
- * E-mail:
| |
Collapse
|
8
|
Gallie DR, Liu R. Phylogenetic analysis reveals dynamic evolution of the poly(A)-binding protein gene family in plants. BMC Evol Biol 2014; 14:238. [PMID: 25421536 PMCID: PMC4252990 DOI: 10.1186/s12862-014-0238-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 11/07/2014] [Indexed: 01/05/2023] Open
Abstract
Background The poly(A)-binding protein (PABP) binds the poly(A) tail of eukaryotic mRNAs and functions to maintain the integrity of the mRNA while promoting protein synthesis through its interaction with eukaryotic translation initiation factor (eIF) 4G and eIF4B. PABP is encoded by a single gene in yeast and marine algae but during plant evolution the PABP gene family expanded substantially, underwent sequence divergence into three subclasses, and acquired tissue-specificity in gene family member expression. Although such changes suggest functional specialization, the size of the family and its sequence divergence have complicated an understanding of which gene family members may be foundational and which may represent more recent expansions of the family to meet the specific needs of speciation. Here, we examine the evolution of the plant PABP gene family to provide insight into these aspects of the family that may yield clues into the function of individual family members. Results The PABP gene family had expanded to two members by the appearance of fresh water algae and four members in non-vascular plants. In lycophytes, the first sequence divergence yielding a specific class member occurs. The earliest members of the gene family share greatest similarity to those modern members whose expression is confined to reproductive tissues, suggesting that supporting reproductive-associated gene expression is the most conserved function of this family. A family member sharing similarity to modern vegetative-associated members first appears in gymnosperms. Further elaboration of the reproductive-associated and vegetative-associated members occurred during the evolution of flowering plants. Conclusions Expansion of the plant PABP gene family began prior to the colonization of land. By the evolution of lycophytes, the first class member whose expression is confined to reproductive tissues in higher plants had appeared. A second class member whose expression is vegetative-associated appeared in gymnosperms and all three modern classes had fully evolved by the appearance of the first known basal angiosperm. The size of each PABP class underwent further expansion during subsequent evolution, especially in the Brassicaceae, suggesting that the family is undergoing dynamic evolution. Electronic supplementary material The online version of this article (doi:10.1186/s12862-014-0238-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Daniel R Gallie
- Department of Biochemistry, University of California, Riverside, CA, 92521-0129, USA.
| | - Renyi Liu
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521-0129, USA.
| |
Collapse
|
9
|
Eliseeva IA, Lyabin DN, Ovchinnikov LP. Poly(A)-binding proteins: structure, domain organization, and activity regulation. BIOCHEMISTRY (MOSCOW) 2014; 78:1377-91. [PMID: 24490729 DOI: 10.1134/s0006297913130014] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
RNA-binding proteins are of vital importance for mRNA functioning. Among these, poly(A)-binding proteins (PABPs) are of special interest due to their participation in virtually all mRNA-dependent events that is caused by their high affinity for A-rich mRNA sequences. Apart from mRNAs, PABPs interact with many proteins, thus promoting their involvement in cellular events. In the nucleus, PABPs play a role in polyadenylation, determine the length of the poly(A) tail, and may be involved in mRNA export. In the cytoplasm, they participate in regulation of translation initiation and either protect mRNAs from decay through binding to their poly(A) tails or stimulate this decay by promoting mRNA interactions with deadenylase complex proteins. This review presents modern notions of the role of PABPs in mRNA-dependent events; peculiarities of regulation of PABP amount in the cell and activities are also discussed.
Collapse
Affiliation(s)
- I A Eliseeva
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
| | | | | |
Collapse
|
10
|
Datu AK, Bag J. Enhanced translation of mRNAs encoding proteins involved in mRNA translation during recovery from heat shock. PLoS One 2013; 8:e64171. [PMID: 23696868 PMCID: PMC3655933 DOI: 10.1371/journal.pone.0064171] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 04/12/2013] [Indexed: 01/03/2023] Open
Abstract
The mRNAs encoding poly (A) binding protein (PABP1), eukaryotic elongation factor 1A (eEF1A) and ribosomal protein S6 (RPS6) belong to the family of terminal oligo pyrimidine tract (TOP) containing mRNAs. Translation of the TOP mRNAs is regulated by growth signals and usually codes for proteins involved in mRNA translation. Previous studies from our laboratory showed that translation of PABP1 mRNA was preferentially enhanced during recovery of HeLa cells from heat shock. Presence of the 5′ TOP cis element was required for the observed increase of PABP1 mRNA translation. In the studies reported here we showed that translation of two additional TOP mRNAs such as, eEF1A and RPS6 was similarly enhanced during recovery. In addition, we showed by in vivo cross-linking experiments that the cellular nucleic acid binding protein ZNF9 binds to all three TOP mRNAs examined in these studies as well as to the β-actin mRNA that lacks a TOP cis element. Binding of ZNF9 to mRNAs was observed in both heat-shocked and non heat- shocked cells. However, depletion of ZNF9 by siRNA prevented the preferred stimulation of PABP1, eEF1A and RPS6 expression during recovery from heat shock. There was no detectable effect of ZNF9 depletion on the basal level of expression of either β-actin or PABP1, eEF1A and RPS6 in HeLa cells following recovery from heat shock. Conclusion Although the presence of ZNF9 was required for the translational stimulation of PABP1, eEF1A and RPS6 mRNAs, the mechanistic details of this process are still unclear. Since ZNF9 was shown to bind both TOP and non-TOP mRNAs, it is uncertain whether ZNF9 exerts its stimulatory effect on TOP mRNA translation following recovery from heat shock through the TOP cis-element. Perhaps additional factors or post-translational modification(s) of ZNF9 following heat shock are necessary for the preferred increase of TOP mRNA translation.
Collapse
Affiliation(s)
- Andrea-Kaye Datu
- University of Guelph, Department of Molecular & Cellular Biology, Guelph, Ontario, Canada
| | - Jnanankur Bag
- University of Guelph, Department of Molecular & Cellular Biology, Guelph, Ontario, Canada
- * E-mail:
| |
Collapse
|
11
|
Abstract
Shortening of the poly(A) tail is the first and often rate-limiting step in mRNA degradation. Three poly(A)-specific 3' exonucleases have been described that can carry out this reaction: PAN, composed of two subunits; PARN, a homodimer; and the CCR4-NOT complex, a heterooligomer that contains two catalytic subunits and may have additional functions in the cell. Current evidence indicates that all three enzymes use a two-metal ion mechanism to release nucleoside monophosphates in a hydrolytic reaction. The CCR4-NOT is the main deadenylase in all organisms examined, and mutations affecting the complex can be lethal. The contribution of PAN, apparently an initial deadenylation preceding the activity of CCR4-NOT, is less important, whereas the activity of PARN seems to be restricted to specific substrates or circumstances, for example, stress conditions. Rapid deadenylation and decay of specific mRNAs can be caused by recruitment of both PAN and the CCR4-NOT complex. This function can be carried out by RNA-binding proteins, for example, members of the PUF family. Alternatively, miRNAs can recruit the deadenylase complexes with the help of their associated GW182 proteins.
Collapse
Affiliation(s)
- Christiane Harnisch
- Martin-Luther-University of Halle-Wittenberg, Institute of Biochemistry and Biotechnology, Kurt-Mothes-Strasse 3, Halle, Germany
| | - Bodo Moritz
- Martin-Luther-University of Halle-Wittenberg, Institute of Biochemistry and Biotechnology, Kurt-Mothes-Strasse 3, Halle, Germany
| | - Christiane Rammelt
- Martin-Luther-University of Halle-Wittenberg, Institute of Biochemistry and Biotechnology, Kurt-Mothes-Strasse 3, Halle, Germany
| | - Claudia Temme
- Martin-Luther-University of Halle-Wittenberg, Institute of Biochemistry and Biotechnology, Kurt-Mothes-Strasse 3, Halle, Germany
| | - Elmar Wahle
- Martin-Luther-University of Halle-Wittenberg, Institute of Biochemistry and Biotechnology, Kurt-Mothes-Strasse 3, Halle, Germany.
| |
Collapse
|
12
|
Soucek S, Corbett AH, Fasken MB. The long and the short of it: the role of the zinc finger polyadenosine RNA binding protein, Nab2, in control of poly(A) tail length. BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1819:546-54. [PMID: 22484098 PMCID: PMC3345082 DOI: 10.1016/j.bbagrm.2012.03.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 03/01/2012] [Accepted: 03/02/2012] [Indexed: 11/23/2022]
Abstract
In eukaryotic cells, addition of poly(A) tails to transcripts by 3'-end processing/polyadenylation machinery is a critical step in gene expression. The length of the poly(A) tail influences the stability, nuclear export and translation of mRNA transcripts. Control of poly(A) tail length is thus an important mechanism to regulate the abundance and ultimate translation of transcripts. Understanding the global regulation of poly(A) tail length will require dissecting the contributions of enzymes, regulatory factors, and poly(A) binding proteins (Pabs) that all cooperate to regulate polyadenylation. A recent addition to the Pab family is the CCCH-type zinc finger class of Pabs that includes S. cerevisiae Nab2 and its human counterpart, ZC3H14. In S. cerevisiae, Nab2 is an essential nuclear Pab implicated in both poly(A) RNA export from the nucleus and control of poly(A) tail length. Consistent with an important role in regulation of poly(A) tail length, depletion of Nab2 from yeast cells results in hyperadenylation of poly(A) RNA. In this review, we focus on the role of Nab2 in poly(A) tail length control and speculate on potential mechanisms by which Nab2 could regulate poly(A) tail length based on reported physical and genetic interactions. We present models, illustrating how Nab2 could regulate poly(A) tail length by limiting polyadenylation and/or enhancing trimming. Given that mutation of the gene encoding the human Nab2 homologue, ZC3H14, causes a form of autosomal recessive intellectual disability, we also speculate on how mutations in a gene encoding a ubiquitously expressed Pab lead specifically to neurological defects. This article is part of a Special Issue entitled: Nuclear Transport and RNA Processing.
Collapse
Affiliation(s)
- Sharon Soucek
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Anita H. Corbett
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Milo B. Fasken
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| |
Collapse
|
13
|
Brockmann C, Soucek S, Kuhlmann SI, Mills-Lujan K, Kelly SM, Yang JC, Iglesias N, Stutz F, Corbett AH, Neuhaus D, Stewart M. Structural basis for polyadenosine-RNA binding by Nab2 Zn fingers and its function in mRNA nuclear export. Structure 2012; 20:1007-18. [PMID: 22560733 PMCID: PMC3384006 DOI: 10.1016/j.str.2012.03.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Revised: 03/19/2012] [Accepted: 03/26/2012] [Indexed: 01/19/2023]
Abstract
Polyadenylation regulation and efficient nuclear export of mature mRNPs both require the polyadenosine-RNA-binding protein, Nab2, which contains seven CCCH Zn fingers. We describe here the solution structure of fingers 5-7, which are necessary and sufficient for high-affinity polyadenosine-RNA binding, and identify key residues involved. These Zn fingers form a single structural unit. Structural coherence is lost in the RNA-binding compromised Nab2-C437S mutant, which also suppresses the rat8-2 allele of RNA helicase Dbp5. Structure-guided Nab2 variants indicate that dbp5(rat8-2) suppression is more closely linked to hyperadenylation and suppression of mutant alleles of the nuclear RNA export adaptor, Yra1, than to affinity for polyadenosine-RNA. These results indicate that, in addition to modulating polyA tail length, Nab2 has an unanticipated function associated with generating export-competent mRNPs, and that changes within fingers 5-7 lead to suboptimal assembly of mRNP export complexes that are more easily disassembled by Dbp5 upon reaching the cytoplasm.
Collapse
Affiliation(s)
- Christoph Brockmann
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
mRNA 3' end processing factors: a phylogenetic comparison. Comp Funct Genomics 2012; 2012:876893. [PMID: 22400011 PMCID: PMC3287031 DOI: 10.1155/2012/876893] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Revised: 09/22/2011] [Accepted: 10/11/2011] [Indexed: 01/23/2023] Open
Abstract
Almost all eukaryotic mRNAs possess 3′ ends with a polyadenylate (poly(A)) tail. This poly(A) tail is not encoded in the genome but is added by the process of polyadenylation. Polyadenylation is a two-step process, and this process is accomplished by multisubunit protein factors. Here, we comprehensively compare the protein machinery responsible for polyadenylation of mRNAs across many evolutionary divergent species, and we have found these protein factors to be remarkably conserved in nature. These data suggest that polyadenylation of mRNAs is an ancient process.
Collapse
|
15
|
Meier I. mRNA export and sumoylation-Lessons from plants. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:531-7. [PMID: 22306659 DOI: 10.1016/j.bbagrm.2012.01.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 01/15/2012] [Accepted: 01/19/2012] [Indexed: 01/22/2023]
Abstract
SUMO is a small ubiquitin-related protein modifier that is involved in a number of biological processes, including transcription, DNA repair, genome stability, and chromatin organization. Its potential role in mRNA biogenesis is less well investigated. The biogenesis of mRNA is closely coupled to transcription as well as mRNA nuclear export and several of the involved proteins have dual roles and appear in several complexes. Recently, SUMO-proteome analyses have discovered a number of these proteins as putative targets of SUMO regulation. In the model plant Arabidopsis thaliana, several mutants as well as environmental conditions have been identified that show a close correlation between over- and under-sumoylation of nuclear proteins and mRNA export retention. Three new plant SUMO-proteome studies add to the list of potentially sumoylated RNA-related proteins. Here, the emerging connection between SUMO and mRNA export is compared across kingdoms and its potential mechanistic role is discussed. This article is part of a Special Issue entitled: Nuclear Transport and RNA Processing.
Collapse
Affiliation(s)
- Iris Meier
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA.
| |
Collapse
|
16
|
Borah S, Darricarrère N, Darnell A, Myoung J, Steitz JA. A viral nuclear noncoding RNA binds re-localized poly(A) binding protein and is required for late KSHV gene expression. PLoS Pathog 2011; 7:e1002300. [PMID: 22022268 PMCID: PMC3192849 DOI: 10.1371/journal.ppat.1002300] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2011] [Accepted: 08/19/2011] [Indexed: 01/01/2023] Open
Abstract
During the lytic phase of infection, the gamma herpesvirus Kaposi's Sarcoma-Associated Herpesvirus (KSHV) expresses a highly abundant, 1.1 kb nuclear noncoding RNA of unknown function. We observe that this polyadenylated nuclear (PAN) RNA avidly binds host poly(A)-binding protein C1 (PABPC1), which normally functions in the cytoplasm to bind the poly(A) tails of mRNAs, regulating mRNA stability and translation efficiency. During the lytic phase of KSHV infection, PABPC1 is re-localized to the nucleus as a consequence of expression of the viral shutoff exonuclease (SOX) protein; SOX also mediates the host shutoff effect in which host mRNAs are downregulated while viral mRNAs are selectively expressed. We show that whereas PAN RNA is not required for the host shutoff effect or for PABPC1 re-localization, SOX strongly upregulates the levels of PAN RNA in transient transfection experiments. This upregulation is destroyed by the same SOX mutation that ablates the host shutoff effect and PABPC1 nuclear re-localization or by removal of the poly(A) tail of PAN. In cells induced into the KSHV lytic phase, depletion of PAN RNA using RNase H-targeting antisense oligonucleotides reveals that it is necessary for the production of late viral proteins from mRNAs that are themselves polyadenylated. Our results add to the repertoire of functions ascribed to long noncoding RNAs and suggest a mechanism of action for nuclear noncoding RNAs in gamma herpesvirus infection. Almost all eukaryotic messenger RNAs (mRNAs) have a string of 150–200 adenylates at the 3′ end. This poly(A) tail has been implicated as important for regulating mRNA translation, stability and export. During the lytic phase of infection of Kaposi's Sarcoma-Associated Herpesvirus (KSHV), a noncoding viral RNA is synthesized that resembles an mRNA in that it is transcribed by RNA polymerase II, is methyl-G capped at the 5′ end, and is polyadenylated at the 3′ end; yet this RNA is never exported to the cytoplasm for translation. Rather, it builds up in the nucleus to exceedingly high levels. We present evidence that the function of this abundant, polyadenylated nuclear (PAN) RNA is to bind poly(A) binding protein, which normally binds poly(A) tails of mRNAs in the cytoplasm but is re-localized into the nucleus during lytic KSHV infection. The interaction between PAN RNA and re-localized poly(A) binding protein is important for formation of new virus, in particular for the synthesis of proteins made late in infection. Our study provides new insight into the function of this noncoding RNA during KSHV infection and expands recent discoveries regarding re-localization of poly(A) binding protein during many viral infections.
Collapse
Affiliation(s)
- Sumit Borah
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, United States of America
| | - Nicole Darricarrère
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Alicia Darnell
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, United States of America
| | - Jinjong Myoung
- Department of Microbiology and Immunology, Howard Hughes Medical Institute, University of California, San Francisco, California, United States of America
| | - Joan A. Steitz
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, United States of America
- * E-mail:
| |
Collapse
|
17
|
Alves MS, Reis PAB, Dadalto SP, Faria JAQA, Fontes EPB, Fietto LG. A novel transcription factor, ERD15 (Early Responsive to Dehydration 15), connects endoplasmic reticulum stress with an osmotic stress-induced cell death signal. J Biol Chem 2011; 286:20020-30. [PMID: 21482825 PMCID: PMC3103375 DOI: 10.1074/jbc.m111.233494] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Revised: 04/07/2011] [Indexed: 11/06/2022] Open
Abstract
As in all other eukaryotic organisms, endoplasmic reticulum (ER) stress triggers the evolutionarily conserved unfolded protein response in soybean, but it also communicates with other adaptive signaling responses, such as osmotic stress-induced and ER stress-induced programmed cell death. These two signaling pathways converge at the level of gene transcription to activate an integrated cascade that is mediated by N-rich proteins (NRPs). Here, we describe a novel transcription factor, GmERD15 (Glycine max Early Responsive to Dehydration 15), which is induced by ER stress and osmotic stress to activate the expression of NRP genes. GmERD15 was isolated because of its capacity to stably associate with the NRP-B promoter in yeast. It specifically binds to a 187-bp fragment of the NRP-B promoter in vitro and activates the transcription of a reporter gene in yeast. Furthermore, GmERD15 was found in both the cytoplasm and the nucleus, and a ChIP assay revealed that it binds to the NRP-B promoter in vivo. Expression of GmERD15 in soybean protoplasts activated the NRP-B promoter and induced expression of the NRP-B gene. Collectively, these results support the interpretation that GmERD15 functions as an upstream component of stress-induced NRP-B-mediated signaling to connect stress in the ER to an osmotic stress-induced cell death signal.
Collapse
Affiliation(s)
- Murilo S. Alves
- From the Departamento de Bioquímica e Biologia Molecular, BIOAGRO and
- National Institute of Science and Technology in Plant-Pest Interactions,Universidade Federal de Viçosa, 36571.000 Viçosa, MG, Brazil
| | - Pedro A. B. Reis
- From the Departamento de Bioquímica e Biologia Molecular, BIOAGRO and
- National Institute of Science and Technology in Plant-Pest Interactions,Universidade Federal de Viçosa, 36571.000 Viçosa, MG, Brazil
| | | | | | - Elizabeth P. B. Fontes
- From the Departamento de Bioquímica e Biologia Molecular, BIOAGRO and
- National Institute of Science and Technology in Plant-Pest Interactions,Universidade Federal de Viçosa, 36571.000 Viçosa, MG, Brazil
| | - Luciano G. Fietto
- From the Departamento de Bioquímica e Biologia Molecular, BIOAGRO and
- National Institute of Science and Technology in Plant-Pest Interactions,Universidade Federal de Viçosa, 36571.000 Viçosa, MG, Brazil
| |
Collapse
|
18
|
Li H, Yuan Z, Vizcay-Barrena G, Yang C, Liang W, Zong J, Wilson ZA, Zhang D. PERSISTENT TAPETAL CELL1 encodes a PHD-finger protein that is required for tapetal cell death and pollen development in rice. PLANT PHYSIOLOGY 2011; 156:615-30. [PMID: 21515697 PMCID: PMC3177263 DOI: 10.1104/pp.111.175760] [Citation(s) in RCA: 207] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
In higher plants, timely degradation of tapetal cells, the innermost sporophytic cells of the anther wall layer, is a prerequisite for the development of viable pollen grains. However, relatively little is known about the mechanism underlying programmed tapetal cell development and degradation. Here, we report a key regulator in monocot rice (Oryza sativa), PERSISTANT TAPETAL CELL1 (PTC1), which controls programmed tapetal development and functional pollen formation. The evolutionary significance of PTC1 was revealed by partial genetic complementation of the homologous mutation MALE STERILITY1 (MS1) in the dicot Arabidopsis (Arabidopsis thaliana). PTC1 encodes a PHD-finger (for plant homeodomain) protein, which is expressed specifically in tapetal cells and microspores during anther development in stages 8 and 9, when the wild-type tapetal cells initiate a typical apoptosis-like cell death. Even though ptc1 mutants show phenotypic similarity to ms1 in a lack of tapetal DNA fragmentation, delayed tapetal degeneration, as well as abnormal pollen wall formation and aborted microspore development, the ptc1 mutant displays a previously unreported phenotype of uncontrolled tapetal proliferation and subsequent commencement of necrosis-like tapetal death. Microarray analysis indicated that 2,417 tapetum- and microspore-expressed genes, which are principally associated with tapetal development, degeneration, and pollen wall formation, had changed expression in ptc1 anthers. Moreover, the regulatory role of PTC1 in anther development was revealed by comparison with MS1 and other rice anther developmental regulators. These findings suggest a diversified and conserved switch of PTC1/MS1 in regulating programmed male reproductive development in both dicots and monocots, which provides new insights in plant anther development.
Collapse
|
19
|
Merkle T. Nucleo-cytoplasmic transport of proteins and RNA in plants. PLANT CELL REPORTS 2011; 30:153-76. [PMID: 20960203 PMCID: PMC3020307 DOI: 10.1007/s00299-010-0928-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Accepted: 09/30/2010] [Indexed: 05/19/2023]
Abstract
Transport of macromolecules between the nucleus and the cytoplasm is an essential necessity in eukaryotic cells, since the nuclear envelope separates transcription from translation. In the past few years, an increasing number of components of the plant nuclear transport machinery have been characterised. This progress, although far from being completed, confirmed that the general characteristics of nuclear transport are conserved between plants and other organisms. However, plant-specific components were also identified. Interestingly, several mutants in genes encoding components of the plant nuclear transport machinery were investigated, revealing differential sensitivity of plant-specific pathways to impaired nuclear transport. These findings attracted attention towards plant-specific cargoes that are transported over the nuclear envelope, unravelling connections between nuclear transport and components of signalling and developmental pathways. The current state of research in plants is summarised in comparison to yeast and vertebrate systems, and special emphasis is given to plant nuclear transport mutants.
Collapse
Affiliation(s)
- Thomas Merkle
- Faculty of Biology, Institute for Genome Research and Systems Biology, University of Bielefeld, 33594 Bielefeld, Germany.
| |
Collapse
|
20
|
Guerra N, Vega-Sendino M, Pérez-Morgado MI, Ramos E, Soto M, Gonzalez VM, Martín ME. Identification and functional characterization of a poly(A)-binding protein from Leishmania infantum (LiPABP). FEBS Lett 2011; 585:193-8. [PMID: 21115009 DOI: 10.1016/j.febslet.2010.11.042] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 11/22/2010] [Accepted: 11/23/2010] [Indexed: 02/05/2023]
Abstract
Gene expression regulation in Leishmania has been related to post-transcriptional events involving mainly sequences present in the 5' and 3' untranslated regions. PABPs are high-affinity poly(A)-binding proteins that are implicated in the regulation of translation initiation, RNA stability and other important biological processes. We describe a PABP from Leishmania infantum (LiPABP) that shows a very high homology with PABPs from other eukaryotic organisms, including mammals and other parasites. LiPABP conserves the main domains present in other PABPs, maintains poly(A)-binding properties and is phosphorylated by p38 mitogen-activated protein kinase. Using the sera from dogs infected with L. infantum, we demonstrate that LiPABP is expressed in L. infantum promastigotes.
Collapse
Affiliation(s)
- Natalia Guerra
- Servicio de Bioquímica-Investigación, Hospital Ramón y Cajal, IRyCIS, Madrid, Spain
| | | | | | | | | | | | | |
Collapse
|
21
|
da Costa Lima TD, Moura DMN, Reis CRS, Vasconcelos JRC, Ellis L, Carrington M, Figueiredo RCBQ, de Melo Neto OP. Functional characterization of three leishmania poly(a) binding protein homologues with distinct binding properties to RNA and protein partners. EUKARYOTIC CELL 2010; 9:1484-94. [PMID: 20675580 PMCID: PMC2950419 DOI: 10.1128/ec.00148-10] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Accepted: 07/19/2010] [Indexed: 11/20/2022]
Abstract
Trypanosomatid protozoans are reliant on posttranscriptional processes to control gene expression. Regulation occurs at the levels of mRNA processing, stability, and translation, events that may require the participation of the poly(A) binding protein (PABP). Here, we have undertaken a functional study of the three distinct Leishmania major PABP (LmPABP) homologues: the previously described LmPABP1; LmPABP2, orthologous to the PABP described from Trypanosoma species; and LmPABP3, unique to Leishmania. Sequence identity between the three PABPs is no greater than 40%. In assays measuring binding to A-rich sequences, LmPABP1 binding was poly(A) sensitive but heparin insensitive; LmPABP2 binding was heparin sensitive and less sensitive to poly(A), compatible with unique substitutions observed in residues implicated in poly(A) binding; and LmPABP3 displayed intermediate properties. All three homologues are simultaneously expressed as abundant cytoplasmic proteins in L. major promastigotes, but only LmPABP1 is present as multiple isoforms. Upon transcription inhibition, LmPABP2 and -3 migrated to the nucleus, while LmPABP1 remained predominantly cytoplasmic. Immunoprecipitation assays showed an association between LmPABP2 and -3. Although the three proteins bound to a Leishmania homologue of the translation initiation factor eukaryotic initiation factor 4G (eIF4G) (LmEIF4G3) in vitro, LmPABP1 was the only one to copurify with native LmEIF4G3 from cytoplasmic extracts. Functionality was tested using RNA interference (RNAi) in Trypanosoma brucei, where both orthologues to LmPABP1 and -2 are required for cellular viability. Our results indicate that these homologues have evolved divergent functions, some of which may be unique to the trypanosomatids, and reinforces a role for LmPABP1 in translation through its interaction with the eIF4G homologue.
Collapse
Affiliation(s)
- Tamara D. da Costa Lima
- Departamento de Microbiologia, Centro de Pesquisas Aggeu Magalhães/Fiocruz, Av. Moraes Rego s/n, Campus UFPE, Recife, PE 50670-420, Brazil
| | - Danielle M. N. Moura
- Departamento de Microbiologia, Centro de Pesquisas Aggeu Magalhães/Fiocruz, Av. Moraes Rego s/n, Campus UFPE, Recife, PE 50670-420, Brazil
| | - Christian R. S. Reis
- Departamento de Microbiologia, Centro de Pesquisas Aggeu Magalhães/Fiocruz, Av. Moraes Rego s/n, Campus UFPE, Recife, PE 50670-420, Brazil
| | - J. Ronnie C. Vasconcelos
- Departamento de Microbiologia, Centro de Pesquisas Aggeu Magalhães/Fiocruz, Av. Moraes Rego s/n, Campus UFPE, Recife, PE 50670-420, Brazil
| | - Louise Ellis
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Mark Carrington
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Regina C. B. Q. Figueiredo
- Departamento de Microbiologia, Centro de Pesquisas Aggeu Magalhães/Fiocruz, Av. Moraes Rego s/n, Campus UFPE, Recife, PE 50670-420, Brazil
| | - Osvaldo P. de Melo Neto
- Departamento de Microbiologia, Centro de Pesquisas Aggeu Magalhães/Fiocruz, Av. Moraes Rego s/n, Campus UFPE, Recife, PE 50670-420, Brazil
| |
Collapse
|
22
|
Kelly SM, Leung SW, Apponi LH, Bramley AM, Tran EJ, Chekanova JA, Wente SR, Corbett AH. Recognition of polyadenosine RNA by the zinc finger domain of nuclear poly(A) RNA-binding protein 2 (Nab2) is required for correct mRNA 3'-end formation. J Biol Chem 2010; 285:26022-32. [PMID: 20554526 PMCID: PMC2924000 DOI: 10.1074/jbc.m110.141127] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Proteins bound to the poly(A) tail of mRNA transcripts, called poly(A)-binding proteins (Pabs), play critical roles in regulating RNA stability, translation, and nuclear export. Like many mRNA-binding proteins that modulate post-transcriptional processing events, assigning specific functions to Pabs is challenging because these processing events are tightly coupled to one another. To investigate the role that a novel class of zinc finger-containing Pabs plays in these coupled processes, we defined the mode of polyadenosine RNA recognition for the conserved Saccharomyces cerevisiae Nab2 protein and assessed in vivo consequences caused by disruption of RNA binding. The polyadenosine RNA recognition domain of Nab2 consists of three tandem Cys-Cys-Cys-His (CCCH) zinc fingers. Cells expressing mutant Nab2 proteins with decreased binding to polyadenosine RNA show growth defects as well as defects in poly(A) tail length but do not accumulate poly(A) RNA in the nucleus. We also demonstrate genetic interactions between mutant nab2 alleles and mutant alleles of the mRNA 3'-end processing machinery. Together, these data provide strong evidence that Nab2 binding to RNA is critical for proper control of poly(A) tail length.
Collapse
Affiliation(s)
- Seth M Kelly
- Departments of Biochemistry, Emory University School ofMedicine, Atlanta, Georgia 30322, USA
| | | | | | | | | | | | | | | |
Collapse
|
23
|
Meier I, Brkljacic J. The Arabidopsis nuclear pore and nuclear envelope. THE ARABIDOPSIS BOOK 2010; 8:e0139. [PMID: 22303264 PMCID: PMC3244964 DOI: 10.1199/tab.0139] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The nuclear envelope is a double membrane structure that separates the eukaryotic cytoplasm from the nucleoplasm. The nuclear pores embedded in the nuclear envelope are the sole gateways for macromolecular trafficking in and out of the nucleus. The nuclear pore complexes assembled at the nuclear pores are large protein conglomerates composed of multiple units of about 30 different nucleoporins. Proteins and RNAs traffic through the nuclear pore complexes, enabled by the interacting activities of nuclear transport receptors, nucleoporins, and elements of the Ran GTPase cycle. In addition to directional and possibly selective protein and RNA nuclear import and export, the nuclear pore gains increasing prominence as a spatial organizer of cellular processes, such as sumoylation and desumoylation. Individual nucleoporins and whole nuclear pore subcomplexes traffic to specific mitotic locations and have mitotic functions, for example at the kinetochores, in spindle assembly, and in conjunction with the checkpoints. Mutants of nucleoporin genes and genes of nuclear transport components lead to a wide array of defects from human diseases to compromised plant defense responses. The nuclear envelope acts as a repository of calcium, and its inner membrane is populated by functionally unique proteins connected to both chromatin and-through the nuclear envelope lumen-the cytoplasmic cytoskeleton. Plant nuclear pore and nuclear envelope research-predominantly focusing on Arabidopsis as a model-is discovering both similarities and surprisingly unique aspects compared to the more mature model systems. This chapter gives an overview of our current knowledge in the field and of exciting areas awaiting further exploration.
Collapse
Affiliation(s)
- Iris Meier
- Department of Plant Cellular and Molecular Biology and Plant Biotechnology Center, The Ohio State University, 520 Aronoff Laboratory, 318 W 12th Avenue, Columbus, OH 43210
- Address correspondence to
| | - Jelena Brkljacic
- Department of Plant Cellular and Molecular Biology and Plant Biotechnology Center, The Ohio State University, 520 Aronoff Laboratory, 318 W 12th Avenue, Columbus, OH 43210
| |
Collapse
|
24
|
Lemieux C, Bachand F. Cotranscriptional recruitment of the nuclear poly(A)-binding protein Pab2 to nascent transcripts and association with translating mRNPs. Nucleic Acids Res 2009; 37:3418-30. [PMID: 19336419 PMCID: PMC2691841 DOI: 10.1093/nar/gkp207] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Synthesis of the pre-mRNA poly(A) tail in the nucleus has important consequences on the translational activity of the mature mRNA in the cytoplasm. In most eukaryotes, nuclear polyadenylation of pre-mRNAs is thought to require the nuclear poly(A)-binding protein (PABP2/PABPN1) for poly(A) tail synthesis and ultimate length control. As yet, however, the extent of the association between PABP2 and the exported mRNA remains poorly understood. Here, we used chromatin immunoprecipitation (ChIP) assays to show that the fission yeast ortholog of mammalian PABP2 (Pab2) is cotranscriptionally recruited to active genes. Notably, the association of Pab2 to genes precedes that of a typical 3'-processing/polyadenylation factor, suggesting that Pab2 recruitment during the transcription cycle precedes polyadenylation. The inclusion of an RNase step in our ChIP and immunoprecipitation assays suggests that Pab2 is cotranscriptionally recruited via nascent mRNA ribonucleoprotein (mRNPs). Tandem affinity purification coupled with mass spectrometry also revealed that Pab2 associates with several ribosomal proteins as well as general translation factors. Importantly, whereas previous results suggest that the nuclear poly(A)-binding protein is not present on cytoplasmic mRNAs, we show that fission yeast Pab2 is associated with polysomes. Our findings suggest that Pab2 is recruited to nascent mRNPs during transcription and remains associated with translated mRNPs after nuclear export.
Collapse
Affiliation(s)
- Caroline Lemieux
- RNA Group, Department of Biochemistry, Université de Sherbrooke, Québec, Canada
| | | |
Collapse
|
25
|
Jia R, Zheng ZM. Regulation of bovine papillomavirus type 1 gene expression by RNA processing. Front Biosci (Landmark Ed) 2009; 14:1270-82. [PMID: 19273129 DOI: 10.2741/3307] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Bovine papillomavirus type 1 (BPV-1) has served as a prototype for studying the molecular biology and pathogenesis of papillomaviruses. The expression of BPV-1 early and late genes is highly regulated at both transcription and post-transcriptional levels and strictly tied to the differentiation of keratinocytes. BPV-1 infects keratinocytes in the basal layer of the skin and replicates in the nucleus of infected cells in a differentiation-dependent manner. Although viral early genes begin to be expressed from the infected, undifferentiated basal cells, viral late genes are not expressed until the infected cells enter the terminal differentiation stage. Both BPV-1 early and late transcripts are intron-containing bicistronic or polycistronic RNAs, bearing more than one open reading frame and are polyadenylated at either an early or late poly (A) site. Nuclear RNA processing of these transcripts by RNA splicing and poly (A) site selection has been extensively analyzed in the past decade and various viral cis-elements and cellular factors involved in regulation of viral RNA processing were discovered, leading to our better understanding of the gene expression and biology of human papillomaviruses.
Collapse
Affiliation(s)
- Rong Jia
- HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | |
Collapse
|
26
|
|
27
|
Nuclear localization of cytoplasmic poly(A)-binding protein upon rotavirus infection involves the interaction of NSP3 with eIF4G and RoXaN. J Virol 2008; 82:11283-93. [PMID: 18799579 DOI: 10.1128/jvi.00872-08] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Rotavirus nonstructural protein NSP3 interacts specifically with the 3' end of viral mRNAs, with the eukaryotic translation initiation factor eIF4G, and with RoXaN, a cellular protein of yet-unknown function. By evicting cytoplasmic poly(A) binding protein (PABP-C1) from translation initiation complexes, NSP3 shuts off the translation of cellular polyadenylated mRNAs. We show here that PABP-C1 evicted from eIF4G by NSP3 accumulates in the nucleus of rotavirus-infected cells. Through modeling of the NSP3-RoXaN complex, we have identified mutations in NSP3 predicted to interrupt its interaction with RoXaN without disturbing the NSP3 interaction with eIF4G. Using these NSP3 mutants and a deletion mutant unable to associate with eIF4G, we show that the nuclear localization of PABP-C1 not only is dependent on the capacity of NSP3 to interact with eIF4G but also requires the interaction of NSP3 with a specific region in RoXaN, the leucine- and aspartic acid-rich (LD) domain. Furthermore, we show that the RoXaN LD domain functions as a nuclear export signal and that RoXaN tethers PABP-C1 with RNA. This work identifies RoXaN as a cellular partner of NSP3 involved in the nucleocytoplasmic localization of PABP-C1.
Collapse
|
28
|
Nagaike T, Suzuki T, Ueda T. Polyadenylation in mammalian mitochondria: insights from recent studies. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2008; 1779:266-9. [PMID: 18312863 DOI: 10.1016/j.bbagrm.2008.02.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2007] [Revised: 01/27/2008] [Accepted: 02/04/2008] [Indexed: 10/22/2022]
Abstract
Polyadenylation in animal mitochondria is very unique. Unlike other systems, polyadenylation is needed to generate UAA stop codons that are not encoded in mitochondrial (mt) DNA. In some cases, polyadenylation is required for the mt tRNA maturation by editing of its 3' termini. Furthermore, recent studies on human mt poly(A) polymerase (PAP) and PNPase provide new insights and questions for the regulatory mechanism and functional role of polyadenylation in human mitochondria.
Collapse
Affiliation(s)
- Takashi Nagaike
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | | | | |
Collapse
|
29
|
Abstract
Human mitochondria contain a genome encoding 13 proteins, all of which are components of respiratory chain complexes. Mutations in human mitochondrial DNA often have pathological consequences. Although 12 of the mitochondrial mRNAs are generated from the same polycistronic transcript, the steady-state level of each mRNA differs. The stability of each mitochondrial mRNA is post-transcriptionally controlled by polyadenylation and deadenylation. However, the molecular mechanism by which each mRNA attains a unique stability is not fully understood. In this report, we describe a practical method for measuring the half-lives of human mitochondrial mRNAs using quantitative real-time reverse transcription PCR.
Collapse
Affiliation(s)
- Asuteka Nagao
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
| | | | | |
Collapse
|
30
|
|
31
|
Abstract
Different RNA species are rigorously discriminated and exported by distinct export factors, but this discrimination mechanism remains largely unknown. We previously showed, by RNA microinjection experiments, that intronless mRNAs are discriminated from U snRNAs based on their difference in RNA length. However, it was unclear how they are discriminated in the natural situation in which their nascent transcripts emerge progressively during transcription. We hypothesized that transcription from the corresponding promoters is important for this discrimination. Here we show that contrary to our hypothesis, the discrimination process was not significantly influenced by whether transcription occurred from an mRNA- versus a U snRNA-type promoter. Rather, the features of transcribed RNAs determined the RNA identity, consistent with our previous results of RNA microinjection. Moreover, we found that the poly (A) tail can function as an identity element for mRNA export. The presence of a poly (A) tail of an appropriate length committed otherwise short Pol II transcripts to the mRNA export pathway in a dominant manner, indicating that the poly (A) tail either contributes to increasing the RNA length or functions as a platform to recruit mRNA export factors. Our results reveal a novel function of the poly (A) tail in mRNA export.
Collapse
Affiliation(s)
- Hiroyuki Fuke
- Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan
| | | |
Collapse
|
32
|
Dresios J, Panopoulos P, Synetos D. Eukaryotic ribosomal proteins lacking a eubacterial counterpart: important players in ribosomal function. Mol Microbiol 2006; 59:1651-63. [PMID: 16553873 DOI: 10.1111/j.1365-2958.2006.05054.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The ribosome is a macromolecular machine responsible for protein synthesis in all organisms. Despite the enormous progress in studies on the structure and function of prokaryotic ribosomes, the respective molecular details of the mechanism by which the eukaryotic ribosome and associated factors construct a polypeptide accurately and rapidly still remain largely unexplored. Eukaryotic ribosomes possess more RNA and a higher number of proteins than eubacterial ribosomes. As the tertiary structure and basic function of the ribosomes are conserved, what is the contribution of these additional elements? Elucidation of the role of these components should provide clues to the mechanisms of translation in eukaryotes and help unravel the molecular mechanisms underlying the differences between eukaryotic and eubacterial ribosomes. This article focuses on a class of eukaryotic ribosomal proteins that do not have a eubacterial homologue. These proteins play substantial roles in ribosomal structure and function, and in mRNA binding and nascent peptide folding. The role of these proteins in human diseases and viral expression, as well as their potential use as targets for antiviral agents is discussed.
Collapse
Affiliation(s)
- John Dresios
- Department of Neurobiology, Scripps Research Institute, La Jolla, CA 92037, USA
| | | | | |
Collapse
|
33
|
Chen IH, Chou WJ, Lee PY, Hsu YH, Tsai CH. The AAUAAA motif of bamboo mosaic virus RNA is involved in minus-strand RNA synthesis and plus-strand RNA polyadenylation. J Virol 2006; 79:14555-61. [PMID: 16282455 PMCID: PMC1287560 DOI: 10.1128/jvi.79.23.14555-14561.2005] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bamboo mosaic virus (BaMV) has a single-stranded positive-sense RNA genome with a 5'-cap structure and a 3' poly(A) tail. Deleting the internal loop that contains the putative polyadenylation signal (AAUAAA) in the 3' untranslated region (UTR) of BaMV genomic RNA appeared to diminish coat protein accumulation to 2% (C. P. Cheng and C. H. Tsai, J. Mol. Biol. 288:555-565, 1999). To investigate the function of the AAUAAA motif, mutations were introduced into an infectious BaMV cDNA at each residue except the first nucleotide. After transfection of Nicotiana benthamiana protoplasts with RNA transcript, the accumulations of viral coat protein and RNAs were determined. Based on the results, three different categories could be deduced for the mutants. Category 1 includes two mutants expressing levels of the viral products similar to those of the wild-type virus. Six mutations in category 2 led to decreased to similar levels of both minus-strand and genomic RNAs. Category 3 includes the remaining seven mutations that also bring about decreases in both minus- and plus-strand RNA levels, with more significant effects on genomic RNA accumulation. Mutant transcripts from each category were used to infect N. benthamiana plants, from which viral particles were isolated. The genomic RNAs of mutants in category 3 were found to have shorter poly(A) tails. Taken together, the results suggest that the AAUAAA motif in the 3' UTR of BaMV genomic RNA is involved not only in the formation of the poly(A) tail of the plus-strand RNA, but also in minus-strand RNA synthesis.
Collapse
Affiliation(s)
- I-Hsuan Chen
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | | | | | | | | |
Collapse
|
34
|
Belostotsky DA, Rose AB. Plant gene expression in the age of systems biology: integrating transcriptional and post-transcriptional events. TRENDS IN PLANT SCIENCE 2005; 10:347-53. [PMID: 15951220 DOI: 10.1016/j.tplants.2005.05.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2005] [Revised: 04/20/2005] [Accepted: 05/26/2005] [Indexed: 05/02/2023]
Abstract
The extensive mechanistic and regulatory interconnections between the various events of mRNA biogenesis are now recognized as a fundamental principle of eukaryotic gene expression, yet the specific details of the coupling between the various steps of mRNA biogenesis do differ, and sometimes dramatically, between the different kingdoms. In this review, we emphasize examples where plants must differ in this respect from other eukaryotes, and highlight a recurring trend of recruiting the conserved, versatile functional modules, which have evolved to support the general mRNA biogenesis reactions, for plant-specific functions. We also argue that elucidating the inner workings of the plant 'mRNA factory' is essential for accomplishing the ambitious goal of building the 'virtual plant'.
Collapse
Affiliation(s)
- Dmitry A Belostotsky
- Department of Biological Sciences, State University of New York at Albany, 1400 Washington Ave, Albany, NY 12222, USA.
| | | |
Collapse
|
35
|
Nagaike T, Suzuki T, Katoh T, Ueda T. Human mitochondrial mRNAs are stabilized with polyadenylation regulated by mitochondria-specific poly(A) polymerase and polynucleotide phosphorylase. J Biol Chem 2005; 280:19721-7. [PMID: 15769737 DOI: 10.1074/jbc.m500804200] [Citation(s) in RCA: 157] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mammalian mitochondrial (mt) mRNAs have short poly(A) tails at their 3' termini that are post-transcriptionally synthesized by mt poly(A) polymerase (PAP). The polyadenylation of mt mRNAs is known to be a key process needed to create UAA stop codons that are not encoded in mtDNA. In some cases, polyadenylation is required for the tRNA maturation by editing of its 3' terminus. However, little is known about the functional roles the poly(A) tail of mt mRNAs plays in mt translation and RNA turnover. Here we show human mt PAP (hmtPAP) and human polynucleotide phosphorylase (hPNPase) control poly(A) synthesis in human mitochondria. Partial inactivation of hmtPAP by RNA interference using small interfering RNA in HeLa cells resulted in shortened poly(A) tails and decreased steady state levels of some mt mRNAs as well as their translational products. Moreover, knocking down hmtPAP generated markedly defective mt membrane potentials and reduced oxygen consumption. In contrast, knocking down hPNPase showed significantly extended poly(A) tails of mt mRNAs. These results demonstrate that the poly(A) length of human mt mRNAs is controlled by polyadenylation by hmtPAP and deadenylation by hPNPase, and polyadenylation is required for the stability of mt mRNAs.
Collapse
Affiliation(s)
- Takashi Nagaike
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba Prefecture, Japan
| | | | | | | |
Collapse
|
36
|
Mustafa F, Phillip PS, Jayanth P, Ghazawi A, Lew KA, Schmidt RD, Rizvi TA. Close proximity of the MPMV CTE to the polyadenylation sequences is important for efficient function in the subgenomic context. Virus Res 2005; 105:209-18. [PMID: 15351494 DOI: 10.1016/j.virusres.2004.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2004] [Revised: 06/29/2004] [Accepted: 06/30/2004] [Indexed: 10/26/2022]
Abstract
The constitutive transport element (CTE) of Mason-Pfizer monkey virus (MPMV) is a short cis-acting sequence element critical for virus gene expression. Analogous to the Rev/Rev Responsive Element (RRE) of primate lentiviruses, CTE allows the nucleocytoplasmic transport of unspliced viral mRNAs. In fact, CTE can functionally replace Rev/RRE in the genomic context and has been used successfully in the expression of viral and cellular genes from expression vectors as well. However, unlike RRE, CTE accomplishes this by interacting with cellular factors, making CTE function independent of co-expressed trans factors. Thus, CTE has proven to be a valuable tool in the expression of heterologous genes. Our previous studies have shown that close proximity of CTE to the polyadenylation sequences is important for CTE function in the genomic context. However, it is controversial whether CTE needs to be located spatially close to the polyadenylation sequences in the subgenomic context. Since CTE is being frequently used in expression vectors, we investigated the position dependency of CTE in the heterologous, subgenomic background using both genetic and structural analyses. Our results reveal that similar to the genomic situation, close proximity of CTE to the polyadenylation sequences is important for its function in the heterologous subgenomic context.
Collapse
MESH Headings
- Active Transport, Cell Nucleus
- Animals
- Base Sequence
- Gene Expression Regulation, Viral
- Genes, env
- Genes, rev
- Mason-Pfizer monkey virus/genetics
- Mason-Pfizer monkey virus/physiology
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- RNA, Messenger/genetics
- RNA, Messenger/physiology
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Regulatory Sequences, Ribonucleic Acid
Collapse
Affiliation(s)
- Farah Mustafa
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, The United Arab Emirates University, Al Ain, UAE
| | | | | | | | | | | | | |
Collapse
|
37
|
Bravo J, Aguilar-Henonin L, Olmedo G, Guzmán P. Four distinct classes of proteins as interaction partners of the PABC domain of Arabidopsis thaliana Poly(A)-binding proteins. Mol Genet Genomics 2005; 272:651-65. [PMID: 15650869 DOI: 10.1007/s00438-004-1090-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2004] [Accepted: 11/11/2004] [Indexed: 10/25/2022]
Abstract
Poly(A)-binding proteins (PABPs) play an important role in the regulation of translation and the control of mRNA stability in eukaryotes, and their functions are known to be essential in many organisms. PABPs contain a highly conserved C-terminal segment termed the PABC domain. The PABC domain from human PABP interacts with the proteins PAIP1, PAIP2 and RF3 via its PAM2 motifs. These interactions are important for modulating translation. Arabidopsis has eight PABPs, an unexpectedly large number in comparison to other eukaryotes whose genomes have been sequenced. Six of the Arabidopsis PABPs contain the conserved PABC domain. In this work, we have identified PABC-interacting proteins in Arabidopsis. Two proteins, which we named CID1 and CID7, were initially isolated in a two-hybrid screen, and eleven more were predicted to be present in the Arabidopsis proteome and eleven in the rice proteome. Among the 24 PAM2-containing proteins in this set, we observed a diversity of modules of intriguing function, ranging from acidic regions similar to the PAM1 motif found in human PAIP1 and PAIP2, to domains such as the small MutS-related domain, the Lsm domains of Ataxin-2, and RNA recognition motifs (RRMs). We suggest that the large number of PABPs and PAM2-containing proteins may have evolved to provide plants with greater flexibility in modulating the metabolism of specific transcripts. We also found that two PABP genes, PAB2 (ubiquitously expressed) and PAB5 (expressed in reproductive tissues), are essential for viability, suggesting that each has a vital and specific function.
Collapse
Affiliation(s)
- Jaime Bravo
- Departamento de Ingeniería Genética de Plantas, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Apartado Postal 629, Irapuato, Gto., 36500, México
| | | | | | | |
Collapse
|
38
|
Dower K, Kuperwasser N, Merrikh H, Rosbash M. A synthetic A tail rescues yeast nuclear accumulation of a ribozyme-terminated transcript. RNA (NEW YORK, N.Y.) 2004; 10:1888-99. [PMID: 15547135 PMCID: PMC1370677 DOI: 10.1261/rna.7166704] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
To investigate the role of 3' end formation in yeast mRNA export, we replaced the mRNA cleavage and polyadenylation signal with a self-cleaving hammerhead ribozyme element. The resulting RNA is unadenylated and accumulates near its site of synthesis. Nonetheless, a significant fraction of this RNA reaches the cytoplasm. Nuclear accumulation was relieved by insertion of a stretch of DNA-encoded adenosine residues immediately upstream of the ribozyme element (a synthetic A tail). This indicates that a 3' stretch of adenosines can promote export, independently of cleavage and polyadenylation. We further show that a synthetic A tail-containing RNA is unaffected in 3' end formation mutant strains, in which a normally cleaved and polyadenylated RNA accumulates within nuclei. Our results support a model in which a polyA tail contributes to efficient mRNA progression away from the gene, most likely through the action of the yeast polyA-tail binding protein Pab1p.
Collapse
MESH Headings
- Base Sequence
- Cell Nucleus/metabolism
- Green Fluorescent Proteins/genetics
- Green Fluorescent Proteins/metabolism
- In Situ Hybridization, Fluorescence
- Models, Biological
- Mutation
- Poly A/chemistry
- Poly A/genetics
- Poly A/metabolism
- Poly(A)-Binding Proteins/genetics
- Poly(A)-Binding Proteins/metabolism
- RNA, Catalytic/metabolism
- RNA, Fungal/chemistry
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Transcription, Genetic
Collapse
Affiliation(s)
- Ken Dower
- Howard Hughes Medical Institute, Department of Biology, Brandeis University, 415 South Street, Waltham, MA 02454, USA
| | | | | | | |
Collapse
|
39
|
Kühn U, Wahle E. Structure and function of poly(A) binding proteins. ACTA ACUST UNITED AC 2004; 1678:67-84. [PMID: 15157733 DOI: 10.1016/j.bbaexp.2004.03.008] [Citation(s) in RCA: 246] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2004] [Revised: 03/30/2004] [Accepted: 03/31/2004] [Indexed: 01/01/2023]
Abstract
Poly (A) tails are found at the 3' ends of almost all eukaryotic mRNAs. They are bound by two different poly (A) binding proteins, PABPC in the cytoplasm and PABPN1 in the nucleus. PABPC functions in the initiation of translation and in the regulation of mRNA decay. In both functions, an interaction with the m7G cap at the 5' end of the message plays an important role. PABPN1 is involved in the synthesis of poly (A) tails, increasing the processivity of poly (A) polymerase and contributing to defining the length of a newly synthesized poly (A) tail.
Collapse
Affiliation(s)
- Uwe Kühn
- Institut für Biochemie, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes-Stasse. 3, D-06120 Halle, Germany
| | | |
Collapse
|
40
|
Albrecht M, Lengauer T. Survey on the PABC recognition motif PAM2. Biochem Biophys Res Commun 2004; 316:129-38. [PMID: 15003521 DOI: 10.1016/j.bbrc.2004.02.024] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2004] [Indexed: 10/26/2022]
Abstract
The PABP-interacting motif PAM2 has been identified in various eukaryotic proteins as an important binding site for the PABC domain. This domain is contained in homologs of the poly(A)-binding protein PABP and the ubiquitin-protein ligase HYD. Despite the importance of the PAM2 motif, a comprehensive analysis of its occurrence in different proteins has been missing. Using iterated sequence profile searches, we obtained an extensive list of proteins carrying the PAM2 motif. We discuss their functional context and domain architecture, which often consists of RNA-binding domains. Our list of PAM2 motif proteins includes eukaryotic homologs of eRF3/GSPT1/2, PAIP1/2, Tob1/2, Ataxin-2, RBP37, RBP1, Blackjack, HELZ, TPRD, USP10, ERD15, C1D4.14, and the viral protease P29. The identification of the PAM2 motif in as yet uncharacterized proteins can give valuable hints with respect to their cellular function and potential interaction partners and suggests further experimentation. It is also striking that the PAM2 motif appears to occur solely outside globular protein domains.
Collapse
Affiliation(s)
- Mario Albrecht
- Max-Planck-Institute for Informatics, Stuhlsatzenhausweg 85, Saarbrücken 66123, Germany.
| | | |
Collapse
|