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Fazel F, Doost JS, Raj S, Boodhoo N, Karimi K, Sharif S. The mRNA vaccine platform for veterinary species. Vet Immunol Immunopathol 2024; 274:110803. [PMID: 39003921 DOI: 10.1016/j.vetimm.2024.110803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 06/27/2024] [Indexed: 07/16/2024]
Abstract
Vaccination has proven to be an effective means of controlling pathogens in animals. Since the introduction of veterinary vaccines in the 19th century, several generations of vaccines have been introduced. These vaccines have had a positive impact on global animal health and production. Despite, the success of veterinary vaccines, there are still some pathogens for which there are no effective vaccines available, such as African swine fever. Further, animal health is under the constant threat of emerging and re-emerging pathogens, some of which are zoonotic and can pose a threat to human health. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has highlighted the need for new vaccine platforms that are safe and efficacious, but also importantly, are adaptable and can be modified rapidly to match the circulating pathogens. mRNA vaccines have been shown to be an effective vaccine platform against various viral and bacterial pathogens. This review will cover some of the recent advances in the field of mRNA vaccines for veterinary species. Moreover, various mRNA vaccines and their delivery methods, as well as their reported efficacy, will be discussed. Current limitations and future prospects of this vaccine platform in veterinary medicine will also be discussed.
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Affiliation(s)
- Fatemeh Fazel
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Janan Shoja Doost
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Sugandha Raj
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Nitish Boodhoo
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Khalil Karimi
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Shayan Sharif
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
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2
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Sarkar P, Gopi P, Pandya P, Paria S, Hossain M, Siddiqui MH, Alamri S, Bhadra K. Insights on the comparative affinity of ribonucleic acids with plant-based beta carboline alkaloid, harmine: Spectroscopic, calorimetric and computational evaluation. Heliyon 2024; 10:e34183. [PMID: 39100473 PMCID: PMC11295990 DOI: 10.1016/j.heliyon.2024.e34183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 07/04/2024] [Accepted: 07/04/2024] [Indexed: 08/06/2024] Open
Abstract
Small molecules as ligands target multifunctional ribonucleic acids (RNA) for therapeutic engagement. This study explores how the anticancer DNA intercalator harmine interacts various motifs of RNAs, including the single-stranded A-form poly (rA), the clover leaf tRNAphe, and the double-stranded A-form poly (rC)-poly (rG). Harmine showed the affinity to the polynucleotides in the order, poly (rA) > tRNAphe > poly (rC)·poly (rG). While no induced circular dichroism change was detected with poly (rC)poly (rG), significant structural alterations of poly (rA) followed by tRNAphe and occurrence of concurrent initiation of optical activity in the attached achiral molecule of alkaloid was reported. At 25 °C, the affinity further showed exothermic and entropy-driven binding. The interaction also highlighted heat capacity (ΔC o p ) and Gibbs energy contribution from the hydrophobic transfer (ΔG hyd) of binding with harmine. Molecular docking calculations indicated that harmine exhibits higher affinity for poly (rA) compared to tRNAphe and poly (rC)·poly (rG). Subsequent molecular dynamics simulations were conducted to investigate the binding mode and stability of harmine with poly(A), tRNAphe, and poly (rC)·poly (rG). The results revealed that harmine adopts a partial intercalative binding with poly (rA) and tRNAphe, characterized by pronounced stacking forces and stronger binding free energy observed with poly (rA), while a comparatively weaker binding free energy was observed with tRNAphe. In contrast, the stacking forces with poly (rC)·poly (rG) were comparatively less pronounced and adopts a groove binding mode. It was also supported by ferrocyanide quenching analysis. All these findings univocally provide detailed insight into the binding specificity of harmine, to single stranded poly (rA) over other RNA motifs, probably suggesting a self-structure formation in poly (rA) with harmine and its potential as a lead compound for RNA based drug targeting.
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Affiliation(s)
- Paromita Sarkar
- University of Kalyani, Department of Zoology, Nadia, W. Bengal, 741235, India
| | - Priyanka Gopi
- Amity Institute of Forensic Sciences, Amity University, Noida, Uttar Pradesh, India
| | - Prateek Pandya
- Amity Institute of Forensic Sciences, Amity University, Noida, Uttar Pradesh, India
| | - Samaresh Paria
- Vidyasagar University, Department of Chemistry, Midnapore 721 102, West Bengal, India
| | - Maidul Hossain
- Vidyasagar University, Department of Chemistry, Midnapore 721 102, West Bengal, India
| | - Manzer H. Siddiqui
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Saud Alamri
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Kakali Bhadra
- University of Kalyani, Department of Zoology, Nadia, W. Bengal, 741235, India
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3
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Li X, Che Y, Wang X, Zhu Y. A pan-cancer analysis of the core pre-mRNA 3' end processing factors, and their association with prognosis, tumor microenvironment, and potential targets. Sci Rep 2024; 14:17428. [PMID: 39075070 PMCID: PMC11286879 DOI: 10.1038/s41598-024-57402-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 03/18/2024] [Indexed: 07/31/2024] Open
Abstract
Alternative polyadenylation (APA) is a crucial mechanism for regulating gene expression during pre-mRNA 3' processing. Pre-mRNA 3' end processing factors is the main factor involved in this process. However, pre-mRNA 3' end processing factors in different cancer expression profiles and the relationship between pre-mRNA 3' end processing factors and tumor microenvironment and the prognosis of the same patient is still unclear. In this study, we conducted a comprehensive exploration of the core pre-mRNA 3' end processing factors across various cancer types by utilizing common cancer database, and revealing a robust correlation between the expression of these core factors and tumor characteristics. Leveraging advanced bioinformatics databases, we evaluated the expression levels and prognostic relevance of pre-mRNA 3' end processing factors across pan-cancer tissues. Our extensive pan-cancer analysis revealed unique expression patterns of pre-mRNA 3' end processing factors in both tumor and adjacent non-tumorous tissues. Notably, we found a significant correlation between the expression levels of pre-mRNA 3' end processing factors and patient prognosis. Furthermore, we identified strong associations between pre-mRNA 3' end processing factors expression and various factors, such as stromal, immune, RNA stemness, and DNA stemness scores across pan-cancer tissues. Our data also highlighted a link between the expression of pre-mRNA 3' end processing factors and sensitivity to specific drugs, including pyrazoloacndine, amonaflide, and chelerythrinede, among others. We found four key pre-mRNA 3' end processing factors that play a crucial role in mRNA preprocessing. Our study illuminates the potential promotion and inhibition role of pre-mRNA 3' end processing regulators in the progression of cancer, CPSF2, CPSF3, CSTF2, SYMPK offering valuable insights for future research investigations on these regulators as diagnostic markers and therapeutic targets across pan-cancer.
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Affiliation(s)
- Xiangyu Li
- College of Basic Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Yu Che
- College of Basic Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Xiaoyan Wang
- Chongqing Medical and Pharmaceutical College, Chongqing, 401331, China.
| | - Yong Zhu
- College of Basic Medicine, Chongqing Medical University, Chongqing, 400016, China.
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Chen Q, Malki S, Xu X, Bennett B, Lackford BL, Kirsanov O, Geyer CB, Hu G. Cnot3 is required for male germ cell development and spermatogonial stem cell maintenance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.13.562256. [PMID: 37873304 PMCID: PMC10592795 DOI: 10.1101/2023.10.13.562256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The foundation of spermatogenesis and lifelong fertility is provided by spermatogonial stem cells (SSCs). SSCs divide asymmetrically to either replenish their numbers (self-renewal) or produce undifferentiated progenitors that proliferate before committing to differentiation. However, regulatory mechanisms governing SSC maintenance are poorly understood. Here, we show that the CCR4-NOT mRNA deadenylase complex subunit CNOT3 plays a critical role in maintaining spermatogonial populations in mice. Cnot3 is highly expressed in undifferentiated spermatogonia, and its deletion in spermatogonia resulted in germ cell loss and infertility. Single cell analyses revealed that Cnot3 deletion led to the de-repression of transcripts encoding factors involved in spermatogonial differentiation, including those in the glutathione redox pathway that are critical for SSC maintenance. Together, our study reveals that CNOT3 - likely via the CCR4-NOT complex - actively degrades transcripts encoding differentiation factors to sustain the spermatogonial pool and ensure the progression of spermatogenesis, highlighting the importance of CCR4-NOT-mediated post-transcriptional gene regulation during male germ cell development.
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Affiliation(s)
- Qing Chen
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
- Present address: Clinical Microbiome Unit (CMU), Laboratory of Host Immunity and Microbiome (LHIM), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Safia Malki
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Xiaojiang Xu
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
- Present address: Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA 70112
| | - Brian Bennett
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Brad L. Lackford
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Oleksandr Kirsanov
- Department of Anatomy & Cell Biology, Brody School of Medicine at East Carolina University, Greenville, NC, USA
| | - Christopher B. Geyer
- Department of Anatomy & Cell Biology, Brody School of Medicine at East Carolina University, Greenville, NC, USA
- East Carolina Diabetes and Obesity Institute East Carolina University, Greenville, NC, USA
| | - Guang Hu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
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5
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Brooks EG, Elorriaga E, Liu Y, Duduit JR, Yuan G, Tsai CJ, Tuskan GA, Ranney TG, Yang X, Liu W. Plant Promoters and Terminators for High-Precision Bioengineering. BIODESIGN RESEARCH 2023; 5:0013. [PMID: 37849460 PMCID: PMC10328392 DOI: 10.34133/bdr.0013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 06/12/2023] [Indexed: 10/19/2023] Open
Abstract
High-precision bioengineering and synthetic biology require fine-tuning gene expression at both transcriptional and posttranscriptional levels. Gene transcription is tightly regulated by promoters and terminators. Promoters determine the timing, tissues and cells, and levels of the expression of genes. Terminators mediate transcription termination of genes and affect mRNA levels posttranscriptionally, e.g., the 3'-end processing, stability, translation efficiency, and nuclear to cytoplasmic export of mRNAs. The promoter and terminator combination affects gene expression. In the present article, we review the function and features of plant core promoters, proximal and distal promoters, and terminators, and their effects on and benchmarking strategies for regulating gene expression.
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Affiliation(s)
- Emily G. Brooks
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
| | - Estefania Elorriaga
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
| | - Yang Liu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - James R. Duduit
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Chung-Jui Tsai
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Warnell School of Forestry and Natural Resource, University of Georgia, Athens, GA 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Thomas G. Ranney
- Mountain Crop Improvement Lab, Department of Horticultural Science, Mountain Horticultural Crops Research and Extension Center, North Carolina State University, Mills River, NC 28759, USA
| | - Xiaohan Yang
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Warnell School of Forestry and Natural Resource, University of Georgia, Athens, GA 30602, USA
| | - Wusheng Liu
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
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Rouhana L, Edgar A, Hugosson F, Dountcheva V, Martindale MQ, Ryan JF. Cytoplasmic Polyadenylation Is an Ancestral Hallmark of Early Development in Animals. Mol Biol Evol 2023; 40:msad137. [PMID: 37288606 PMCID: PMC10284499 DOI: 10.1093/molbev/msad137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 04/18/2023] [Accepted: 06/05/2023] [Indexed: 06/09/2023] Open
Abstract
Differential regulation of gene expression has produced the astonishing diversity of life on Earth. Understanding the origin and evolution of mechanistic innovations for control of gene expression is therefore integral to evolutionary and developmental biology. Cytoplasmic polyadenylation is the biochemical extension of polyadenosine at the 3'-end of cytoplasmic mRNAs. This process regulates the translation of specific maternal transcripts and is mediated by the Cytoplasmic Polyadenylation Element-Binding Protein family (CPEBs). Genes that code for CPEBs are amongst a very few that are present in animals but missing in nonanimal lineages. Whether cytoplasmic polyadenylation is present in non-bilaterian animals (i.e., sponges, ctenophores, placozoans, and cnidarians) remains unknown. We have conducted phylogenetic analyses of CPEBs, and our results show that CPEB1 and CPEB2 subfamilies originated in the animal stem lineage. Our assessment of expression in the sea anemone, Nematostella vectensis (Cnidaria), and the comb jelly, Mnemiopsis leidyi (Ctenophora), demonstrates that maternal expression of CPEB1 and the catalytic subunit of the cytoplasmic polyadenylation machinery (GLD2) is an ancient feature that is conserved across animals. Furthermore, our measurements of poly(A)-tail elongation reveal that key targets of cytoplasmic polyadenylation are shared between vertebrates, cnidarians, and ctenophores, indicating that this mechanism orchestrates a regulatory network that is conserved throughout animal evolution. We postulate that cytoplasmic polyadenylation through CPEBs was a fundamental innovation that contributed to animal evolution from unicellular life.
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Affiliation(s)
- Labib Rouhana
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA
| | - Allison Edgar
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
| | - Fredrik Hugosson
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
| | - Valeria Dountcheva
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA
| | - Mark Q Martindale
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
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7
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Ramming A, Kappel C, Kanaoka MM, Higashiyama T, Lenhard M. Poly(A) polymerase 1 contributes to competence acquisition of pollen tubes growing through the style in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:651-667. [PMID: 36811355 DOI: 10.1111/tpj.16162] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 02/16/2023] [Indexed: 05/10/2023]
Abstract
Polyadenylation of mRNAs is critical for their export from the nucleus, stability, and efficient translation. The Arabidopsis thaliana genome encodes three isoforms of canonical nuclear poly(A) polymerase (PAPS) that redundantly polyadenylate the bulk of pre-mRNAs. However, previous studies have indicated that subsets of pre-mRNAs are preferentially polyadenylated by either PAPS1 or the other two isoforms. Such functional specialization raises the possibility of an additional level of gene-expression control in plants. Here we test this notion by studying the function of PAPS1 in pollen-tube growth and guidance. Pollen tubes growing through female tissue acquire the competence to find ovules efficiently and upregulate PAPS1 expression at the transcriptional, but not detectably at the protein level compared with in vitro grown pollen tubes. Using the temperature-sensitive paps1-1 allele we show that PAPS1 activity during pollen-tube growth is required for full acquisition of competence, resulting in inefficient fertilization by paps1-1 mutant pollen tubes. While these mutant pollen tubes grow almost at the wild-type rate, they are compromised in locating the micropyles of ovules. Previously identified competence-associated genes are less expressed in paps1-1 mutant than in wild-type pollen tubes. Estimating the poly(A) tail lengths of transcripts suggests that polyadenylation by PAPS1 is associated with reduced transcript abundance. Our results therefore suggest that PAPS1 plays a key role in the acquisition of competence and underline the importance of functional specialization between PAPS isoforms throughout different developmental stages.
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Affiliation(s)
- Anna Ramming
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam-Golm, Germany
| | - Christian Kappel
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam-Golm, Germany
| | - Masahiro M Kanaoka
- Prefectural University of Hiroshima, Faculty of Life and Environmental Sciences, Faculty of Bioresource Sciences, Shobara, Hiroshima, Japan
| | - Tetsuya Higashiyama
- The University of Tokyo Graduate School of Science, Faculty of Science, Bunkyo-ku, Tokyo, Japan
| | - Michael Lenhard
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam-Golm, Germany
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8
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Lopes M, Louzada S, Ferreira D, Veríssimo G, Eleutério D, Gama-Carvalho M, Chaves R. Human Satellite 1A analysis provides evidence of pericentromeric transcription. BMC Biol 2023; 21:28. [PMID: 36755311 PMCID: PMC9909926 DOI: 10.1186/s12915-023-01521-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/19/2023] [Indexed: 02/10/2023] Open
Abstract
BACKGROUND Pericentromeric regions of human chromosomes are composed of tandem-repeated and highly organized sequences named satellite DNAs. Human classical satellite DNAs are classified into three families named HSat1, HSat2, and HSat3, which have historically posed a challenge for the assembly of the human reference genome where they are misrepresented due to their repetitive nature. Although being known for a long time as the most AT-rich fraction of the human genome, classical satellite HSat1A has been disregarded in genomic and transcriptional studies, falling behind other human satellites in terms of functional knowledge. Here, we aim to characterize and provide an understanding on the biological relevance of HSat1A. RESULTS The path followed herein trails with HSat1A isolation and cloning, followed by in silico analysis. Monomer copy number and expression data was obtained in a wide variety of human cell lines, with greatly varying profiles in tumoral/non-tumoral samples. HSat1A was mapped in human chromosomes and applied in in situ transcriptional assays. Additionally, it was possible to observe the nuclear organization of HSat1A transcripts and further characterize them by 3' RACE-Seq. Size-varying polyadenylated HSat1A transcripts were detected, which possibly accounts for the intricate regulation of alternative polyadenylation. CONCLUSION As far as we know, this work pioneers HSat1A transcription studies. With the emergence of new human genome assemblies, acrocentric pericentromeres are becoming relevant characters in disease and other biological contexts. HSat1A sequences and associated noncoding RNAs will most certainly prove significant in the future of HSat research.
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Affiliation(s)
- Mariana Lopes
- grid.12341.350000000121821287CytoGenomics Lab, Department of Genetics and Biotechnology (DGB), University of Trás-Os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal ,grid.9983.b0000 0001 2181 4263BioISI – Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal
| | - Sandra Louzada
- grid.12341.350000000121821287CytoGenomics Lab, Department of Genetics and Biotechnology (DGB), University of Trás-Os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal ,grid.9983.b0000 0001 2181 4263BioISI – Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal
| | - Daniela Ferreira
- grid.12341.350000000121821287CytoGenomics Lab, Department of Genetics and Biotechnology (DGB), University of Trás-Os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal ,grid.9983.b0000 0001 2181 4263BioISI – Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal
| | - Gabriela Veríssimo
- grid.12341.350000000121821287CytoGenomics Lab, Department of Genetics and Biotechnology (DGB), University of Trás-Os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal ,grid.9983.b0000 0001 2181 4263BioISI – Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal
| | - Daniel Eleutério
- grid.9983.b0000 0001 2181 4263BioISI – Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal
| | - Margarida Gama-Carvalho
- grid.9983.b0000 0001 2181 4263BioISI – Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal
| | - Raquel Chaves
- CytoGenomics Lab, Department of Genetics and Biotechnology (DGB), University of Trás-Os-Montes and Alto Douro (UTAD), 5000-801, Vila Real, Portugal. .,BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016, Lisbon, Portugal.
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9
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Karim ME, Haque ST, Al-Busaidi H, Bakhtiar A, Tha KK, Holl MMB, Chowdhury EH. Scope and challenges of nanoparticle-based mRNA delivery in cancer treatment. Arch Pharm Res 2022; 45:865-893. [DOI: 10.1007/s12272-022-01418-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 11/15/2022] [Indexed: 11/27/2022]
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10
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Kim B, Park Y, Hwang HJ, Chang J, Kim YK, Lee JB. Single polysome analysis of mRNP. Biochem Biophys Res Commun 2022; 618:73-78. [PMID: 35716598 DOI: 10.1016/j.bbrc.2022.06.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 06/06/2022] [Indexed: 11/17/2022]
Abstract
Eukaryotic translation is a complex process that involves the interplay of various translation factors to convert genetic information into a specific amino acid chain. According to an elegant model of eukaryotic translation initiation, the 3' poly(A) tail of an mRNA, which is occupied by poly(A)-binding proteins (PABPs), communicates with the 5'-cap bound by eIF4E to enhance translation. Although the circularization of mRNA resulting from the communication is widely understood, it has yet to be directly observed. To explore mRNA circularization in translation, we analyzed the level of colocalization of eIF4E, eIF4G, and PABP on individual mRNAs in polysomal and subpolysomal fractions using single polysome analysis. Our results show that the three tested proteins barely coexist in mRNA in either polysomal or subpolysomal fractions, implying that the closed-loop structure generated by the communication between eIF4E, eIF4G, and PAPB may be transient during translation.
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Affiliation(s)
- Byungju Kim
- Department of Physics, Pohang University of Science & Technology (POSTECH), Pohang, 37673, South Korea
| | - Yeonkyoung Park
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul, 02841, South Korea; School of Life Sciences, Korea University, Seoul, 02841, South Korea
| | - Hyun Jung Hwang
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul, 02841, South Korea; School of Life Sciences, Korea University, Seoul, 02841, South Korea
| | - Jeeyoon Chang
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul, 02841, South Korea; School of Life Sciences, Korea University, Seoul, 02841, South Korea
| | - Yoon Ki Kim
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul, 02841, South Korea; School of Life Sciences, Korea University, Seoul, 02841, South Korea.
| | - Jong-Bong Lee
- Department of Physics, Pohang University of Science & Technology (POSTECH), Pohang, 37673, South Korea; School of Interdisciplinary Bioscience & Bioengineering, POSTECH, Pohang, 37673, South Korea.
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11
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Hassan A, Khalaily N, Kilav-Levin R, Nechama M, Volovelsky O, Silver J, Naveh-Many T. Molecular Mechanisms of Parathyroid Disorders in Chronic Kidney Disease. Metabolites 2022; 12:metabo12020111. [PMID: 35208186 PMCID: PMC8878033 DOI: 10.3390/metabo12020111] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/17/2022] [Accepted: 01/20/2022] [Indexed: 01/27/2023] Open
Abstract
Secondary hyperparathyroidism (SHP) is a common complication of chronic kidney disease (CKD) that induces morbidity and mortality in patients. How CKD stimulates the parathyroid to increase parathyroid hormone (PTH) secretion, gene expression and cell proliferation remains an open question. In experimental SHP, the increased PTH gene expression is post-transcriptional and mediated by PTH mRNA–protein interactions that promote PTH mRNA stability. These interactions are orchestrated by the isomerase Pin1. Pin1 participates in conformational change-based regulation of target proteins, including mRNA-binding proteins. In SHP, Pin1 isomerase activity is decreased, and thus, the Pin1 target and PTH mRNA destabilizing protein KSRP fails to bind PTH mRNA, increasing PTH mRNA stability and levels. An additional level of post-transcriptional regulation is mediated by microRNA (miRNA). Mice with parathyroid-specific knockout of Dicer, which facilitates the final step in miRNA maturation, lack parathyroid miRNAs but have normal PTH and calcium levels. Surprisingly, these mice fail to increase serum PTH in response to hypocalcemia or uremia, indicating a role for miRNAs in parathyroid stimulation. SHP often leads to parathyroid hyperplasia. Reduced expressions of parathyroid regulating receptors, activation of transforming growth factor α-epidermal growth factor receptor, cyclooxygenase 2-prostaglandin E2 and mTOR signaling all contribute to the enhanced parathyroid cell proliferation. Inhibition of mTOR by rapamycin prevents and corrects the increased parathyroid cell proliferation of SHP. This review summarizes the current knowledge on the mechanisms that stimulate the parathyroid cell at multiple levels in SHP.
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Affiliation(s)
- Alia Hassan
- Minerva Center for Bone and Mineral Research, Nephrology Services, Hadassah—Hebrew University Medical Center, Jerusalem 91120, Israel; (A.H.); (N.K.); (R.K.-L.); (J.S.)
| | - Nareman Khalaily
- Minerva Center for Bone and Mineral Research, Nephrology Services, Hadassah—Hebrew University Medical Center, Jerusalem 91120, Israel; (A.H.); (N.K.); (R.K.-L.); (J.S.)
| | - Rachel Kilav-Levin
- Minerva Center for Bone and Mineral Research, Nephrology Services, Hadassah—Hebrew University Medical Center, Jerusalem 91120, Israel; (A.H.); (N.K.); (R.K.-L.); (J.S.)
- Nursing, Jerusalem College of Technology, Jerusalem 91160, Israel
| | - Morris Nechama
- Pediatric Nephrology, Hadassah—Hebrew University Medical Center, Jerusalem 91120, Israel; (M.N.); (O.V.)
- The Wohl Institute for Translational Medicine, Hadassah—Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Oded Volovelsky
- Pediatric Nephrology, Hadassah—Hebrew University Medical Center, Jerusalem 91120, Israel; (M.N.); (O.V.)
- The Wohl Institute for Translational Medicine, Hadassah—Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Justin Silver
- Minerva Center for Bone and Mineral Research, Nephrology Services, Hadassah—Hebrew University Medical Center, Jerusalem 91120, Israel; (A.H.); (N.K.); (R.K.-L.); (J.S.)
| | - Tally Naveh-Many
- Minerva Center for Bone and Mineral Research, Nephrology Services, Hadassah—Hebrew University Medical Center, Jerusalem 91120, Israel; (A.H.); (N.K.); (R.K.-L.); (J.S.)
- The Wohl Institute for Translational Medicine, Hadassah—Hebrew University Medical Center, Jerusalem 91120, Israel
- Correspondence:
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12
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Architectural and functional details of CF IA proteins involved in yeast 3'-end pre-mRNA processing and its significance for eukaryotes: A concise review. Int J Biol Macromol 2021; 193:387-400. [PMID: 34699898 DOI: 10.1016/j.ijbiomac.2021.10.129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/04/2021] [Accepted: 10/18/2021] [Indexed: 11/22/2022]
Abstract
In eukaryotes, maturation of pre-mRNA relies on its precise 3'-end processing. This processing involves co-transcriptional steps regulated by sequence elements and other proteins. Although, it holds tremendous importance, defect in the processing machinery will result in erroneous pre-mRNA maturation leading to defective translation. Remarkably, more than 20 proteins in humans and yeast share homology and execute this processing. The defects in this processing are associated with various diseases in humans. We shed light on the CF IA subunit of yeast Saccharomyces cerevisiae that contains four proteins (Pcf11, Clp1, Rna14 and Rna15) involved in this processing. Structural details of various domains of CF IA and their roles during 3'-end processing, like cleavage and polyadenylation at 3'-UTR of pre-mRNA and other cellular events are explained. Further, the chronological development and important discoveries associated with 3'-end processing are summarized. Moreover, the mammalian homologues of yeast CF IA proteins, along with their key roles are described. This knowledge would be helpful for better comprehension of the mechanism associated with this marvel; thus opening up vast avenues in this area.
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13
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Shah A, Mittleman BE, Gilad Y, Li YI. Benchmarking sequencing methods and tools that facilitate the study of alternative polyadenylation. Genome Biol 2021; 22:291. [PMID: 34649612 PMCID: PMC8518154 DOI: 10.1186/s13059-021-02502-z] [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: 02/05/2021] [Accepted: 09/16/2021] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Alternative cleavage and polyadenylation (APA), an RNA processing event, occurs in over 70% of human protein-coding genes. APA results in mRNA transcripts with distinct 3' ends. Most APA occurs within 3' UTRs, which harbor regulatory elements that can impact mRNA stability, translation, and localization. RESULTS APA can be profiled using a number of established computational tools that infer polyadenylation sites from standard, short-read RNA-seq datasets. Here, we benchmarked a number of such tools-TAPAS, QAPA, DaPars2, GETUTR, and APATrap- against 3'-Seq, a specialized RNA-seq protocol that enriches for reads at the 3' ends of genes, and Iso-Seq, a Pacific Biosciences (PacBio) single-molecule full-length RNA-seq method in their ability to identify polyadenylation sites and quantify polyadenylation site usage. We demonstrate that 3'-Seq and Iso-Seq are able to identify and quantify the usage of polyadenylation sites more reliably than computational tools that take short-read RNA-seq as input. However, we find that running one such tool, QAPA, with a set of polyadenylation site annotations derived from small quantities of 3'-Seq or Iso-Seq can reliably quantify variation in APA across conditions, such asacross genotypes, as demonstrated by the successful mapping of alternative polyadenylation quantitative trait loci (apaQTL). CONCLUSIONS We envisage that our analyses will shed light on the advantages of studying APA with more specialized sequencing protocols, such as 3'-Seq or Iso-Seq, and the limitations of studying APA with short-read RNA-seq. We provide a computational pipeline to aid in the identification of polyadenylation sites and quantification of polyadenylation site usages using Iso-Seq data as input.
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Affiliation(s)
- Ankeeta Shah
- Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Briana E Mittleman
- Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Yoav Gilad
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Yang I Li
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA.
- Department of Human Genetics, University of Chicago, Chicago, IL, USA.
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The pentatricopeptide repeat protein Rmd9 recognizes the dodecameric element in the 3'-UTRs of yeast mitochondrial mRNAs. Proc Natl Acad Sci U S A 2021; 118:2009329118. [PMID: 33876744 DOI: 10.1073/pnas.2009329118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Stabilization of messenger RNA is an important step in posttranscriptional gene regulation. In the nucleus and cytoplasm of eukaryotic cells it is generally achieved by 5' capping and 3' polyadenylation, whereas additional mechanisms exist in bacteria and organelles. The mitochondrial mRNAs in the yeast Saccharomyces cerevisiae comprise a dodecamer sequence element that confers RNA stability and 3'-end processing via an unknown mechanism. Here, we isolated the protein that binds the dodecamer and identified it as Rmd9, a factor that is known to stabilize yeast mitochondrial RNA. We show that Rmd9 associates with mRNA around dodecamer elements in vivo and that recombinant Rmd9 specifically binds the element in vitro. The crystal structure of Rmd9 bound to its dodecamer target reveals that Rmd9 belongs to the family of pentatricopeptide (PPR) proteins and uses a previously unobserved mode of specific RNA recognition. Rmd9 protects RNA from degradation by the mitochondrial 3'-exoribonuclease complex mtEXO in vitro, indicating that recognition and binding of the dodecamer element by Rmd9 confers stability to yeast mitochondrial mRNAs.
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15
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Translational regulation of Chk1 expression by eIF3a via interaction with the RNA-binding protein HuR. Biochem J 2020; 477:1939-1950. [PMID: 32391557 DOI: 10.1042/bcj20200025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 05/04/2020] [Accepted: 05/07/2020] [Indexed: 01/10/2023]
Abstract
eIF3a is a putative subunit of the eukaryotic translation initiation factor 3 complex. Accumulating evidence suggests that eIF3a may have a translational regulatory function by suppressing translation of a subset of mRNAs while accelerating that of other mRNAs. Albeit the suppression of mRNA translation may derive from eIF3a binding to the 5'-UTRs of target mRNAs, how eIF3a may accelerate mRNA translation remains unknown. In this study, we show that eIF3a up-regulates translation of Chk1 but not Chk2 mRNA by interacting with HuR, which binds directly to the 3'-UTR of Chk1 mRNA. The interaction between eIF3a and HuR occurs at the 10-amino-acid repeat domain of eIF3a and the RNA recognition motif domain of HuR. This interaction may effectively circularize Chk1 mRNA to form an end-to-end complex that has recently been suggested to accelerate mRNA translation. Together with previous findings, we conclude that eIF3a may regulate mRNA translation by directly binding to the 5'-UTR to suppress or by interacting with RNA-binding proteins at 3'-UTRs to accelerate mRNA translation.
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Poly(A)-DG: A deep-learning-based domain generalization method to identify cross-species Poly(A) signal without prior knowledge from target species. PLoS Comput Biol 2020; 16:e1008297. [PMID: 33151940 PMCID: PMC7671507 DOI: 10.1371/journal.pcbi.1008297] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 11/17/2020] [Accepted: 08/30/2020] [Indexed: 11/19/2022] Open
Abstract
In eukaryotes, polyadenylation (poly(A)) is an essential process during mRNA maturation. Identifying the cis-determinants of poly(A) signal (PAS) on the DNA sequence is the key to understand the mechanism of translation regulation and mRNA metabolism. Although machine learning methods were widely used in computationally identifying PAS, the need for tremendous amounts of annotation data hinder applications of existing methods in species without experimental data on PAS. Therefore, cross-species PAS identification, which enables the possibility to predict PAS from untrained species, naturally becomes a promising direction. In our works, we propose a novel deep learning method named Poly(A)-DG for cross-species PAS identification. Poly(A)-DG consists of a Convolution Neural Network-Multilayer Perceptron (CNN-MLP) network and a domain generalization technique. It learns PAS patterns from the training species and identifies PAS in target species without re-training. To test our method, we use four species and build cross-species training sets with two of them and evaluate the performance of the remaining ones. Moreover, we test our method against insufficient data and imbalanced data issues and demonstrate that Poly(A)-DG not only outperforms state-of-the-art methods but also maintains relatively high accuracy when it comes to a smaller or imbalanced training set.
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17
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Ni WJ, Xie F, Leng XM. Terminus-Associated Non-coding RNAs: Trash or Treasure? Front Genet 2020; 11:552444. [PMID: 33101379 PMCID: PMC7522407 DOI: 10.3389/fgene.2020.552444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 08/25/2020] [Indexed: 12/13/2022] Open
Abstract
3′ untranslated regions (3′ UTRs) of protein-coding genes are well known for their important roles in determining the fate of mRNAs in diverse processes, including trafficking, stabilization, translation, and RNA–protein interactions. However, non-coding RNAs (ncRNAs) scattered around 3′ termini of the protein-coding genes, here referred to as terminus-associated non-coding RNAs (TANRs), have not attracted wide attention in RNA research. Indeed, whether TANRs are transcriptional noise, degraded mRNA products, alternative 3′ UTRs, or functional molecules has remained unclear for a long time. As a new category of ncRNAs, TANRs are widespread, abundant, and conserved in diverse eukaryotes. The biogenesis of TANRs mainly follows the same promoter model, the RNA-dependent RNA polymerase activity-dependent model, or the independent promoter model. Functional studies of TANRs suggested that they are significantly involved in the versatile regulation of gene expression. For instance, at the transcriptional level, they can lead to transcriptional interference, induce the formation of gene loops, and participate in transcriptional termination. Furthermore, at the posttranscriptional level, they can act as microRNA sponges, and guide cleavage or modification of target RNAs. Here, we review current knowledge of the potential role of TANRs in the modulation of gene expression. In this review, we comprehensively summarize the current state of knowledge about TANRs, and discuss TANR nomenclature, relation to ncRNAs, cross-talk biogenesis pathways and potential functions. We further outline directions of future studies of TANRs, to promote investigations of this emerging and enigmatic category of RNA.
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Affiliation(s)
- Wen-Juan Ni
- School of Basic Medicine, Gannan Medical University, Ganzhou, China
| | - Fuhua Xie
- School of Basic Medicine, Gannan Medical University, Ganzhou, China
| | - Xiao-Min Leng
- School of Basic Medicine, Gannan Medical University, Ganzhou, China
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18
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Kilav-Levin R, Hassan A, Nechama M, Shilo V, Silver J, Ben-Dov IZ, Naveh-Many T. Post-transcriptional mechanisms regulating parathyroid hormone gene expression in secondary hyperparathyroidism. FEBS J 2020; 287:2903-2913. [PMID: 32191397 DOI: 10.1111/febs.15300] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 12/10/2019] [Accepted: 03/17/2020] [Indexed: 12/11/2022]
Abstract
Parathyroid hormone (PTH) regulates serum calcium levels and bone strength. Secondary hyperparathyroidism (SHP) is a common complication of chronic kidney disease (CKD) that correlates with morbidity and mortality. In experimental SHP, the increased PTH gene expression is due to increased PTH mRNA stability and is mediated by protein-PTH mRNA interactions. Adenosine-uridine-rich binding factor 1 (AUF1) stabilizes and K-homology splicing regulatory protein (KSRP) destabilizes PTH mRNA. The peptidyl-prolyl cis/trans isomerase Pin1 acts on target proteins, including mRNA-binding proteins. Pin1 leads to KSRP dephosphorylation, but in SHP, parathyroid Pin1 activity is decreased and phosphorylated KSRP fails to bind PTH mRNA, leading to increased PTH mRNA stability and levels. A further level of post-transcriptional regulation occurs through microRNA (miRNA). Dicer mediates the final step of miRNA maturation. Parathyroid-specific Dicer knockout mice that lack miRNAs in the parathyroid develop normally. Surprisingly, these mice fail to increase serum PTH in response to both hypocalcemia and CKD, indicating that parathyroid Dicer and miRNAs are essential for stimulation of the parathyroid. Human and rodent parathyroids share similar miRNA profiles that are altered in hyperparathyroidism. The evolutionary conservation of abundant miRNAs and their regulation in hyperparathyroidism indicate their significance in parathyroid physiology and pathophysiology. let-7 and miR-148 antagonism modifies PTH secretion in vivo and in vitro, suggesting roles for specific miRNAs in parathyroid function. This review summarizes the current knowledge on the post-transcriptional mechanisms of PTH gene expression in SHP and the central contribution of miRNAs to the high serum PTH levels of both primary hyperparathyroidism and SHP.
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Affiliation(s)
- Rachel Kilav-Levin
- Minerva Center for Bone and Mineral Research, Nephrology Services, Hadassah - Hebrew University Medical Center, Jerusalem, Israel.,Nursing, Jerusalem College of Technology, Israel
| | - Alia Hassan
- Minerva Center for Bone and Mineral Research, Nephrology Services, Hadassah - Hebrew University Medical Center, Jerusalem, Israel
| | - Morris Nechama
- Minerva Center for Bone and Mineral Research, Nephrology Services, Hadassah - Hebrew University Medical Center, Jerusalem, Israel.,Pediatric Nephrology, Hadassah - Hebrew University Medical Center, Jerusalem, Israel.,The Wohl Institute for Translational Medicine, Hadassah - Hebrew University Medical Center, Jerusalem, Israel
| | - Vitali Shilo
- Minerva Center for Bone and Mineral Research, Nephrology Services, Hadassah - Hebrew University Medical Center, Jerusalem, Israel
| | - Justin Silver
- Minerva Center for Bone and Mineral Research, Nephrology Services, Hadassah - Hebrew University Medical Center, Jerusalem, Israel
| | - Iddo Z Ben-Dov
- Laboratory of Medical Transcriptomics, Nephrology Services, Hadassah - Hebrew University Medical Center, Jerusalem, Israel
| | - Tally Naveh-Many
- Minerva Center for Bone and Mineral Research, Nephrology Services, Hadassah - Hebrew University Medical Center, Jerusalem, Israel.,The Wohl Institute for Translational Medicine, Hadassah - Hebrew University Medical Center, Jerusalem, Israel
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19
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Kim P, Yang M, Yiya K, Zhao W, Zhou X. ExonSkipDB: functional annotation of exon skipping event in human. Nucleic Acids Res 2020; 48:D896-D907. [PMID: 31642488 PMCID: PMC7145592 DOI: 10.1093/nar/gkz917] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/21/2019] [Accepted: 10/03/2019] [Indexed: 12/20/2022] Open
Abstract
Exon skipping (ES) is reported to be the most common alternative splicing event due to loss of functional domains/sites or shifting of the open reading frame (ORF), leading to a variety of human diseases and considered therapeutic targets. To date, systematic and intensive annotations of ES events based on the skipped exon units in cancer and normal tissues are not available. Here, we built ExonSkipDB, the ES annotation database available at https://ccsm.uth.edu/ExonSkipDB/, aiming to provide a resource and reference for functional annotation of ES events in multiple cancer and tissues to identify therapeutically targetable genes in individual exon units. We collected 14 272 genes that have 90 616 and 89 845 ES events across 33 cancer types and 31 normal tissues from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx). For the ES events, we performed multiple functional annotations. These include ORF assignment of exon skipped transcript, studies of lost protein functional features due to ES events, and studies of exon skipping events associated with mutations and methylations based on multi-omics evidence. ExonSkipDB will be a unique resource for cancer and drug research communities to identify therapeutically targetable exon skipping events.
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Affiliation(s)
- Pora Kim
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Mengyuan Yang
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Ke Yiya
- College of Electronics and Information Engineering, Tongji University, Shanghai, China
| | - Weiling Zhao
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Xiaobo Zhou
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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20
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Woo YM, Kwak Y, Namkoong S, Kristjánsdóttir K, Lee SH, Lee JH, Kwak H. TED-Seq Identifies the Dynamics of Poly(A) Length during ER Stress. Cell Rep 2019; 24:3630-3641.e7. [PMID: 30257221 DOI: 10.1016/j.celrep.2018.08.084] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 07/02/2018] [Accepted: 08/28/2018] [Indexed: 12/31/2022] Open
Abstract
Post-transcriptional RNA processing is a core mechanism of gene expression control in cell stress response. The poly(A) tail influences mRNA translation and stability, but it is unclear whether there are global roles of poly(A)-tail lengths in cell stress. To address this, we developed tail-end displacement sequencing (TED-seq) for an efficient transcriptome-wide profiling of poly(A) lengths and applied it to endoplasmic reticulum (ER) stress in human cells. ER stress induced increases in the poly(A) lengths of certain mRNAs, including known ER stress regulators, XBP1, DDIT3, and HSPA5. Importantly, the mRNAs with increased poly(A) lengths are both translationally de-repressed and stabilized. Furthermore, mRNAs in stress-induced RNA granules have shorter poly(A) tails than in the cytoplasm, supporting the view that RNA processing is compartmentalized. In conclusion, TED-seq reveals that poly(A) length is dynamically regulated upon ER stress, with potential consequences for both translation and mRNA turnover.
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Affiliation(s)
- Yu Mi Woo
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Yeonui Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Sim Namkoong
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Katla Kristjánsdóttir
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Seung Ha Lee
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jun Hee Lee
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
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21
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Jafari Najaf Abadi MH, Shafabakhsh R, Asemi Z, Mirzaei HR, Sahebnasagh R, Mirzaei H, Hamblin MR. CFIm25 and alternative polyadenylation: Conflicting roles in cancer. Cancer Lett 2019; 459:112-121. [PMID: 31181319 DOI: 10.1016/j.canlet.2019.114430] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 06/01/2019] [Accepted: 06/04/2019] [Indexed: 12/11/2022]
Abstract
Alternative polyadenylation (APA) is now widely recognized to regulate gene expression. APA is an RNA-processing mechanism that generates distinct 3' termini on mRNAs, producing mRNA isoforms. Different factors influence the initiation and development of this process. CFIm25 (among others) is a cleavage and polyadenylation factor that plays a key role in the regulation of APA. Shortening of the 3'UTRs on mRNAs leads to enhanced cellular proliferation and tumorigenicity. One reason may be the up-regulation of growth promoting factors, such as Cyclin D1. Different studies have reported a dual role of CFIm25 in cancer (both oncogenic and tumor suppressor). microRNAs (miRNAs) may be involved in CFIm25 function as well as competing endogenous RNAs (ceRNAs). The present review focuses on the role of CFIm25 in cancer, cancer treatment, and possible involvement in other human diseases. We highlight the involvement of miRNAs and ceRNAs in the function of CFIm25 to affect gene expression. The lack of understanding of the mechanisms and regulation of CFIm25 and APA has underscored the need for further research regarding their role in cancer and other diseases.
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Affiliation(s)
| | - Rana Shafabakhsh
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, Iran.
| | - Zatollah Asemi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, Iran.
| | - Hamid Reza Mirzaei
- Department of Medical Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
| | - Roxana Sahebnasagh
- Department of Molecular Medicine, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran.
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, Iran.
| | - Michael R Hamblin
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, 40 Blossom Street, Boston, MA, 02114, USA.
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22
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Miyamoto T, Shin T, Iijima M, Minase G, Okada H, Saijo Y, Sengoku K. The poly(A) polymerase beta gene may not be associated with azoospermia caused by Sertoli-cell-only syndrome in Japanese patients by comparing patients and normal controls. J OBSTET GYNAECOL 2019; 39:434-436. [DOI: 10.1080/01443615.2018.1504205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- T. Miyamoto
- Department of Obstetrics and Gynecology, Asahikawa Medical University, Asahikawa, Japan
| | - T. Shin
- Department of Urology, Dokkyo Medical University Koshigaya Hospital, Koshigaya, Japan
| | - M. Iijima
- Department of Urology, Kanazawa University Graduate School of Medical Science, Kanazawa, Japan
| | - G. Minase
- Department of Obstetrics and Gynecology, Asahikawa Medical University, Asahikawa, Japan
| | - H. Okada
- Department of Urology, Dokkyo Medical University Koshigaya Hospital, Koshigaya, Japan
| | - Y. Saijo
- Department of Social Medicine, Division of Public Health and Epidemiology, Asahikawa Medical University, Asahikawa, Japan
| | - K. Sengoku
- Department of Obstetrics and Gynecology, Asahikawa Medical University, Asahikawa, Japan
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23
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Hunter M, Yuan P, Vavilala D, Fox M. Optimization of Protein Expression in Mammalian Cells. ACTA ACUST UNITED AC 2018; 95:e77. [DOI: 10.1002/cpps.77] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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24
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Ospina-Villa JD, García-Contreras J, Rosas-Trigueros JL, Ramírez-Moreno E, López-Camarillo C, Zamora-López B, Marchat LA, Zamorano-Carrillo A. Importance of amino acids Leu135 and Tyr236 for the interaction between EhCFIm25 and RNA: a molecular dynamics simulation study. J Mol Model 2018; 24:202. [PMID: 30003410 DOI: 10.1007/s00894-018-3729-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 06/19/2018] [Indexed: 11/28/2022]
Abstract
The CFIm25 subunit of the heterotetrameric cleavage factor Im (CFIm) is a critical factor in the formation of the poly(A) tail at mRNA 3' end, regulating the recruitment of polyadenylation factors, poly(A) site selection, and cleavage/polyadenylation reactions. We previously reported the homologous protein (EhCFIm25) in Entamoeba histolytica, the protozoan causing human amoebiasis, and showed the relevance of conserved Leu135 and Tyr236 residues for RNA binding. We also identified the GUUG sequence as the recognition site of EhCFIm25. To understand the interactions network that allows the EhCFIm25 to maintain its three-dimensional structure and function, here we performed molecular dynamics simulations of wild-type (WT) and mutant proteins, alone or interacting with the GUUG molecule. Our results indicated that in the presence of the GUUG sequence, WT converged more quickly to lower RMSD values in comparison with mutant proteins. However, RMSF values showed that movements of amino acids of WT and EhCFIm25*L135 T were almost identical, interacting or not with the GUUG molecule. Interestingly, EhCFIm25*L135 T, which is the only mutant with a slight RNA binding activity experimentally, presents the same stabilization of bend structures and alpha helices as WT, notably in the C-terminus. Moreover, WT and EhCFIm25*L135 T presented almost the same number of contacts that mainly involve lysine residues interacting with the G4 nucleotide. Overall, our data proposed a clear description of the structural and mechanistic data that govern the RNA binding capacity of EhCFIm25.
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Affiliation(s)
- Juan David Ospina-Villa
- Programa Institucional de Biomedicina Molecular, Programa de Doctorado en Ciencias en Biotecnología, ENMH, Instituto Politécnico Nacional, Guillermo Massieu Helguera 239, Fracc. La Escalera, Ticomán, Del. Gustavo A. Madero, CP 07320, Ciudad de México, Mexico
| | - Juan García-Contreras
- Programa Institucional de Biomedicina Molecular, Programa de Doctorado en Ciencias en Biotecnología, ENMH, Instituto Politécnico Nacional, Guillermo Massieu Helguera 239, Fracc. La Escalera, Ticomán, Del. Gustavo A. Madero, CP 07320, Ciudad de México, Mexico
| | - Jorge Luis Rosas-Trigueros
- Laboratorio Transdisciplinario de Investigación en Sistemas Evolutivos, ESCOM, Instituto Politécnico Nacional, Av. Juan de Dios Bátiz esq. Miguel Othón de Mendizábal, Col. Lindavista, Del. Gustavo A. Madero, CP 07738, Ciudad de México, Mexico
| | - Esther Ramírez-Moreno
- Programa Institucional de Biomedicina Molecular, Programa de Doctorado en Ciencias en Biotecnología, ENMH, Instituto Politécnico Nacional, Guillermo Massieu Helguera 239, Fracc. La Escalera, Ticomán, Del. Gustavo A. Madero, CP 07320, Ciudad de México, Mexico
| | - César López-Camarillo
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, San Lorenzo 290, Colonia del Valle, CP 03100, Ciudad de México, Mexico
| | - Beatriz Zamora-López
- Departamento de Psiquiatría y Salud Mental, Facultad de Medicina, UNAM, Circuito Interior y Cerro del Agua, CP 04510, Ciudad de México, Mexico
| | - Laurence A Marchat
- Programa Institucional de Biomedicina Molecular, Programa de Doctorado en Ciencias en Biotecnología, ENMH, Instituto Politécnico Nacional, Guillermo Massieu Helguera 239, Fracc. La Escalera, Ticomán, Del. Gustavo A. Madero, CP 07320, Ciudad de México, Mexico
| | - Absalom Zamorano-Carrillo
- Programa Institucional de Biomedicina Molecular, Programa de Doctorado en Ciencias en Biotecnología, ENMH, Instituto Politécnico Nacional, Guillermo Massieu Helguera 239, Fracc. La Escalera, Ticomán, Del. Gustavo A. Madero, CP 07320, Ciudad de México, Mexico.
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de Castro Barbosa T, Salgueiro RB, Serrano-Nascimento C, Amaral FG, Cipolla-Neto J, Nunes MT. Molecular basis of growth hormone daily mRNA and protein synthesis in rats. Life Sci 2018; 207:36-41. [PMID: 29842863 DOI: 10.1016/j.lfs.2018.05.043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 05/09/2018] [Accepted: 05/25/2018] [Indexed: 10/16/2022]
Abstract
AIMS Daily and seasonal rhythms coordinate the endocrine and metabolic functions. The pituitary gland is the master regulator of several endocrine activities, and its function is classically regulated by endocrine signals from its target glands as well as from the hypothalamus. The growth hormone (GH) produced and secreted by the anterior pituitary presents a pulsatile secretion throughout the 24-hour cycle. However, the molecular mechanisms regulating the daily pattern of GH secretion are still unclear. Herein we investigated whether circadian GH mRNA and protein synthesis is modulated by acute adjustments in the stability and expression of GH mRNA. MAIN METHODS GH mRNA and protein content were evaluated by real-time PCR and Western blotting, respectively, in pituitary gland of rats euthanized every 3 h during a 24-h period at the Zeitgeber times (ZT3 to ZT24). The GH mRNA poly(A) tail length was determined by RACE-PAT assay. KEY FINDINGS We identified two main peaks of GH mRNA level in the pituitary gland of rats; one in the middle of the light-cycle and another in the middle of the dark-cycle. The latter was associated with an increase in pituitary GH protein content. Interestingly, an increment in the poly(A) tail length of the GH transcript was observed in association to reduced migration rate of the GH transcript and increased mRNA content in the dark-cycle period. SIGNIFICANCE Our findings provide evidence that changes in the GH mRNA poly(A) length may underlie the circadian pattern of GH mRNA and protein levels in the pituitary gland of rats.
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Affiliation(s)
- T de Castro Barbosa
- Karolinska Institutet, Department of Medicine H7, Huddinge, Sweden; University of Sao Paulo, Department of Physiology and Biophysics, Sao Paulo, Brazil.
| | - R B Salgueiro
- University of Sao Paulo, Department of Physiology and Biophysics, Sao Paulo, Brazil
| | - C Serrano-Nascimento
- University of Sao Paulo, Department of Physiology and Biophysics, Sao Paulo, Brazil; Hospital Israelita Albert Einstein, Sao Paulo, Brazil
| | - F G Amaral
- University of Sao Paulo, Department of Physiology and Biophysics, Sao Paulo, Brazil; Federal University of Sao Paulo, Department of Physiology, Sao Paulo, Brazil
| | - J Cipolla-Neto
- University of Sao Paulo, Department of Physiology and Biophysics, Sao Paulo, Brazil
| | - M T Nunes
- University of Sao Paulo, Department of Physiology and Biophysics, Sao Paulo, Brazil
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Chatterjee S, Suresh Kumar G. Small molecule induced poly(A) single strand to self-structure conformational switching: evidence for the prominent role of H-bonding interactions. MOLECULAR BIOSYSTEMS 2018; 13:1000-1009. [PMID: 28405661 DOI: 10.1039/c7mb00031f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
All messenger RNAs (mRNAs) have a polyadenylic acid tail that is added during post transcriptional RNA processing. Investigation of the structure-function and interactions of polyadenylic acid is an important area to target for cancer and related diseases. Jatrorrhizine and coptisine are two important isoquinoline alkaloids that are structurally very similar, differing only in the substituents on the isoquinoline chromophore. Here we demonstrate that these alkaloids differentially induce a self-structure in single stranded poly(A) using absorbance, thermal melting and differential scanning calorimetry experiments. Jatrorrhizine was found to be more effective than coptisine in binding to poly(A) from spectroscopy and calorimetry data. Molecular modeling results suggested the involvement of more H-bonds in the complexation of the former with poly(A). It appears that the presence of substituents on the alkaloid that can form H-bonding interactions with the adenine nucleotides may play a critical role in the binding and structural rearrangement of poly(A) into the self-structure. The atomic force microscopy data directly visualized the poly(A) self-structured network. We propose a plausible mechanism of the small molecule induced self-structure formation in poly(A). The results presented here may help in the design of effective poly(A) targeted molecules for therapeutic use.
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Affiliation(s)
- Sabyasachi Chatterjee
- Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India.
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Riedlinger T, Dommerholt MB, Wijshake T, Kruit JK, Huijkman N, Dekker D, Koster M, Kloosterhuis N, Koonen DP, de Bruin A, Baker D, Hofker MH, van Deursen J, Jonker JW, Schmitz ML, van de Sluis B. NF-κB p65 serine 467 phosphorylation sensitizes mice to weight gain and TNFα-or diet-induced inflammation. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:1785-1798. [DOI: 10.1016/j.bbamcr.2017.07.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 06/23/2017] [Accepted: 07/14/2017] [Indexed: 01/04/2023]
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28
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Verbeeren J, Verma B, Niemelä EH, Yap K, Makeyev EV, Frilander MJ. Alternative exon definition events control the choice between nuclear retention and cytoplasmic export of U11/U12-65K mRNA. PLoS Genet 2017; 13:e1006824. [PMID: 28549066 PMCID: PMC5473595 DOI: 10.1371/journal.pgen.1006824] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 06/16/2017] [Accepted: 05/16/2017] [Indexed: 12/20/2022] Open
Abstract
Cellular homeostasis of the minor spliceosome is regulated by a negative feed-back loop that targets U11-48K and U11/U12-65K mRNAs encoding essential components of the U12-type intron-specific U11/U12 di-snRNP. This involves interaction of the U11 snRNP with an evolutionarily conserved splicing enhancer giving rise to unproductive mRNA isoforms. In the case of U11/U12-65K, this mechanism controls the length of the 3′ untranslated region (3′UTR). We show that this process is dynamically regulated in developing neurons and some other cell types, and involves a binary switch between translation-competent mRNAs with a short 3′UTR to non-productive isoforms with a long 3′UTR that are retained in the nucleus or/and spliced to the downstream amylase locus. Importantly, the choice between these alternatives is determined by alternative terminal exon definition events regulated by conserved U12- and U2-type 5′ splice sites as well as sequence signals used for pre-mRNA cleavage and polyadenylation. We additionally show that U11 snRNP binding to the U11/U12-65K mRNA species with a long 3′UTR is required for their nuclear retention. Together, our studies uncover an intricate molecular circuitry regulating the abundance of a key spliceosomal protein and shed new light on the mechanisms limiting the export of non-productively spliced mRNAs from the nucleus to the cytoplasm. The cellular homeostasis of many components of the eukaryotic RNA processing machinery is regulated via negative feed-back pathways that result in the formation of both productive and non-productive mRNA species. Typically, the formation of non-productive mRNAs species results from changes in alternative splicing that disrupt the reading frame of the protein coding region and leads to destabilization of the mRNA. Here, we have investigated the homeostasis regulation of the U11/U12-65K mRNA that encodes an essential protein component of the minor (U12-dependent) spliceosome intron recognition complex. We show that homeostasis is regulated at the level of nuclear mRNA export and mRNA 3′-end formation, and that it can be further regulated during neuronal differentiation. We describe a multilayered regulatory system utilizing alternative exon definition interactions that use the input from both spliceosomes and the polyadenylation machinery to decide between productive and non-productive mRNA formation. Because the 65K protein is an essential component of the minor spliceosome, this regulatory pathway can potentially affect the expression of ~700 genes containing U12-type introns.
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Affiliation(s)
- Jens Verbeeren
- Institute of Biotechnology, FI-00014 University of Helsinki, Helsinki, Finland
| | - Bhupendra Verma
- Institute of Biotechnology, FI-00014 University of Helsinki, Helsinki, Finland
| | - Elina H. Niemelä
- Institute of Biotechnology, FI-00014 University of Helsinki, Helsinki, Finland
| | - Karen Yap
- Centre for Developmental Neurobiology, King’s College London, London, United Kingdom
| | - Eugene V. Makeyev
- Centre for Developmental Neurobiology, King’s College London, London, United Kingdom
| | - Mikko J. Frilander
- Institute of Biotechnology, FI-00014 University of Helsinki, Helsinki, Finland
- * E-mail:
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29
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Wang X, Milne M, Martínez F, Scholl TJ, Hudson RHE. Synthesis of a poly(Gd( iii)-DOTA)–PNA conjugate as a potential MRI contrast agent via post-synthetic click chemistry functionalization. RSC Adv 2017. [DOI: 10.1039/c7ra09040d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
An operationally easy method provides poly(Gd3+chelate) PNA conjugates that form comb-like complexes with poly(rA) and demonstrate increased relaxivity.
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Affiliation(s)
- Xiaoxiao Wang
- Department of Chemistry
- The University of Western Ontario
- London
- Canada
| | - Mark Milne
- Department of Chemistry
- The University of Western Ontario
- London
- Canada
| | - Francisco Martínez
- Department of Medical Biophysics
- The Robarts Research Institute
- The University of Western Ontario
- London
- Canada
| | - Timothy J. Scholl
- Department of Medical Biophysics
- The Robarts Research Institute
- The University of Western Ontario
- London
- Canada
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30
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Pradhan AB, Bhuiya S, Haque L, Das S. Spectroscopic study on the binding of chelerythrine with duplex poly (rA): A model of RNA intercalation. Int J Biol Macromol 2016; 95:340-347. [PMID: 27884672 DOI: 10.1016/j.ijbiomac.2016.11.073] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 11/16/2016] [Accepted: 11/17/2016] [Indexed: 10/20/2022]
Abstract
Here we have reported a detail study on the interaction of the benzophenanthridine alkaloid chelerythrine (CHL) with double stranded polyriboadenylic acid [ds poly (rA)] by exploiting various spectroscopic techniques. The alkaloid shows high binding affinity (binding constant is 1.10×105M-1) towards the double stranded RNA as revealed from Scatchard plot. The binding was confirmed by hypochromic effect in the UV-vis spectrum of CHL, increase in fluorescence intensity of CHL and perturbations of the circular dichroism (CD) spectrum of ds poly (rA). Later fluorescence quenching, cooperative CD melting transition, viscometric and molecular modeling studies establish the fact that the alkaloid binds to the ds poly (rA) by the mechanism of intercalation. Thermodynamic parameters obtained from the isothermal titration calorimetric (ITC) study show that the binding is favoured by negative enthalpy and small positive entropy changes. This report may be a model for intercalation of small molecule like CHL to the double stranded RNA.
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Affiliation(s)
- Ankur Bikash Pradhan
- Department of Chemistry, Jadavpur University, Raja S.C. Mullick Road, Jadavpur, Kolkata 700 032, India.
| | - Sutanwi Bhuiya
- Department of Chemistry, Jadavpur University, Raja S.C. Mullick Road, Jadavpur, Kolkata 700 032, India.
| | - Lucy Haque
- Department of Chemistry, Jadavpur University, Raja S.C. Mullick Road, Jadavpur, Kolkata 700 032, India.
| | - Suman Das
- Department of Chemistry, Jadavpur University, Raja S.C. Mullick Road, Jadavpur, Kolkata 700 032, India.
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Dutta DJ, Raj H, Dev AH. Polyadenylated tail length variation pattern in ultra-rapid vitrified bovine oocytes. Vet World 2016; 9:1070-1074. [PMID: 27847415 PMCID: PMC5104714 DOI: 10.14202/vetworld.2016.1070-1074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 08/28/2016] [Indexed: 11/16/2022] Open
Abstract
Aim: Thecurrent study aims at investigating the polyadenylated (poly[A]) tail length of morphologically high and low competent oocytes at different developmental stages. Furthermore, effect of ultra-rapid vitrification on the poly(A) tail length was studied. Materials and Methods: Fresh bovine cumulus oocyte complexes from abattoir originated ovaries were graded based on morphological characters and matured in vitro. Cryopreservation was done by ultra-rapid vitrification method. mRNA was isolated from different categories of oocyte and subjected to ligation-mediated poly(A) test followed by polymerase chain reaction for determining the poly(A) tail length of β actin, gap junction protein alpha 1 (GJA1), poly(A) polymerase alpha (PAPOLA), and heat shock 70 kDa protein (HSP70) transcripts. Results: GJA1, PAPOLA, and HSP70 showed significantly higher poly(A) in immature oocytes of higher competence irrespective of vitrification effects as compared to mature oocytes of higher competence. Conclusion: mRNA poly(A) tail size increases in developmentally high competent immature bovine oocytes. There was limited effect of ultra-rapid vitrification of bovine oocytes on poly(A).
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Affiliation(s)
- D J Dutta
- Department of Veterinary Physiology, Faculty of Veterinary Science, Assam Agricultural University, Khanapara, Guwahati - 781 022, Assam, India
| | - Himangshu Raj
- Department of Veterinary Physiology, Faculty of Veterinary Science, Assam Agricultural University, Khanapara, Guwahati - 781 022, Assam, India
| | - And Hiramoni Dev
- Department of Veterinary Physiology, Faculty of Veterinary Science, Assam Agricultural University, Khanapara, Guwahati - 781 022, Assam, India
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32
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Wang H, Li R, Zhou X, Xue L, Xu X, Liu B. Genome-Wide Analysis and Functional Characterization of the Polyadenylation Site in Pigs Using RNAseq Data. Sci Rep 2016; 6:36388. [PMID: 27812017 PMCID: PMC5095665 DOI: 10.1038/srep36388] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 10/14/2016] [Indexed: 12/05/2022] Open
Abstract
Polyadenylation, a critical step in the production of mature mRNA for translation in most eukaryotes, involves cleavage and poly(A) tail addition at the 3′ end of mRNAs at the polyadenylation site (PAS). Sometimes, one gene can have more than one PAS, which can produce the alternative polyadenylation (APA) phenomenon and affect the stability, localization and translation of the mRNA. In this study, we discovered 28,363 PASs using pig RNAseq data, with 13,033 located in 7,403 genes. Among the genes, 41% were identified to have more than one PAS. PAS distribution analysis indicated that the PAS position was highly variable in genes. Additionally, the analysis of RNAseq data from the liver and testis showed a difference in their PAS number and usage. RT-PCR and qRT-PCR were performed to confirm our findings by detecting the expression of 3′UTR isoforms for five candidate genes. The analysis of RNAseq data under a different androstenone level and salmonella inoculation indicated that the functional usage of PAS might participate in the immune response and may be related to the androstenone level in pigs. This study provides new insights into pig PAS and facilitates further functional research of PAS.
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Affiliation(s)
- Hongyang Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education &Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture; Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Rui Li
- Department of Animal Sciences, Washington State University, Pullman, WA, United States
| | - Xiang Zhou
- Department of Animal Sciences, Washington State University, Pullman, WA, United States
| | - Liyao Xue
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education &Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture; Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Xuewen Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education &Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture; Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Bang Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education &Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture; Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
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Kashiwabara SI, Tsuruta S, Okada K, Yamaoka Y, Baba T. Adenylation by testis-specific cytoplasmic poly(A) polymerase, PAPOLB/TPAP, is essential for spermatogenesis. J Reprod Dev 2016; 62:607-614. [PMID: 27647534 PMCID: PMC5177979 DOI: 10.1262/jrd.2016-116] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The testis-specific cytoplasmic poly(A) polymerase PAPOLB/TPAP is essential for spermatogenesis. Although this enzyme is responsible for poly(A) tail
extension of a subset of mRNAs in round spermatids, the stability and translational efficiency of these mRNAs are unaffected by the absence of PAPOLB. To
clarify the functional importance of this enzyme’s adenylation activity, we produced PAPOLB-null mice expressing a polyadenylation-defective PAPOLB mutant
(PAPOLBD114A), in which the catalytic Asp at residue 114 was mutated to Ala. Introducing PAPOLBD114A failed to rescue PAPOLB-null
phenotypes, such as reduced expression of haploid-specific mRNAs, spermiogenesis arrest, and male infertility. These results suggest that PAPOLB regulates
spermatogenesis through its adenylation activity.
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Affiliation(s)
- Shin-Ichi Kashiwabara
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki 305-8572, Japan
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34
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Zhu ZJ, Huang P, Chong YX, Kang LX, Huang X, Zhu ZX, Nie L. MicroRNA-181a promotes proliferation and inhibits apoptosis by suppressing CFIm25 in osteosarcoma. Mol Med Rep 2016; 14:4271-4278. [DOI: 10.3892/mmr.2016.5741] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Accepted: 08/22/2016] [Indexed: 11/05/2022] Open
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Schupp AK, Trilling M, Rattay S, Le-Trilling VTK, Haselow K, Stindt J, Zimmermann A, Häussinger D, Hengel H, Graf D. Bile Acids Act as Soluble Host Restriction Factors Limiting Cytomegalovirus Replication in Hepatocytes. J Virol 2016; 90:6686-6698. [PMID: 27170759 PMCID: PMC4944301 DOI: 10.1128/jvi.00299-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 05/06/2016] [Indexed: 02/06/2023] Open
Abstract
UNLABELLED The liver constitutes a prime site of cytomegalovirus (CMV) replication and latency. Hepatocytes produce, secrete, and recycle a chemically diverse set of bile acids, with the result that interactions between bile acids and cytomegalovirus inevitably occur. Here we determined the impact of naturally occurring bile acids on mouse CMV (MCMV) replication. In primary mouse hepatocytes, physiological concentrations of taurochenodeoxycholic acid (TCDC), glycochenodeoxycholic acid, and to a lesser extent taurocholic acid significantly reduced MCMV-induced gene expression and diminished the generation of virus progeny, while several other bile acids did not exert antiviral effects. The anticytomegalovirus activity required active import of bile acids via the sodium-taurocholate-cotransporting polypeptide (NTCP) and was consistently observed in hepatocytes but not in fibroblasts. Under conditions in which alpha interferon (IFN-α) lacks antiviral activity, physiological TCDC concentrations were similarly effective as IFN-γ. A detailed investigation of distinct steps of the viral life cycle revealed that TCDC deregulates viral transcription and diminishes global translation in infected cells. IMPORTANCE Cytomegaloviruses are members of the Betaherpesvirinae subfamily. Primary infection leads to latency, from which cytomegaloviruses can reactivate under immunocompromised conditions and cause severe disease manifestations, including hepatitis. The present study describes an unanticipated antiviral activity of conjugated bile acids on MCMV replication in hepatocytes. Bile acids negatively influence viral transcription and exhibit a global effect on translation. Our data identify bile acids as site-specific soluble host restriction factors against MCMV, which may allow rational design of anticytomegalovirus drugs using bile acids as lead compounds.
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Affiliation(s)
- Anna-Kathrin Schupp
- Department of Gastroenterology, Hepatology and Infectious Diseases, Heinrich-Heine-University, Düsseldorf, Germany
| | - Mirko Trilling
- Institute for Virology, Heinrich-Heine-University, Düsseldorf, Germany
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Stephanie Rattay
- Institute for Virology, Heinrich-Heine-University, Düsseldorf, Germany
| | - Vu Thuy Khanh Le-Trilling
- Institute for Virology, Heinrich-Heine-University, Düsseldorf, Germany
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Katrin Haselow
- Department of Gastroenterology, Hepatology and Infectious Diseases, Heinrich-Heine-University, Düsseldorf, Germany
| | - Jan Stindt
- Department of Gastroenterology, Hepatology and Infectious Diseases, Heinrich-Heine-University, Düsseldorf, Germany
| | - Albert Zimmermann
- Institute for Virology, Heinrich-Heine-University, Düsseldorf, Germany
| | - Dieter Häussinger
- Department of Gastroenterology, Hepatology and Infectious Diseases, Heinrich-Heine-University, Düsseldorf, Germany
| | - Hartmut Hengel
- Institute for Virology, Heinrich-Heine-University, Düsseldorf, Germany
- Department for Medical Microbiology and Hygiene, Institute of Virology, Albert-Ludwigs-University, Freiburg, Germany
| | - Dirk Graf
- Department of Gastroenterology, Hepatology and Infectious Diseases, Heinrich-Heine-University, Düsseldorf, Germany
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Ospina-Villa JD, Zamorano-Carrillo A, Lopez-Camarillo C, Castañon-Sanchez CA, Soto-Sanchez J, Ramirez-Moreno E, Marchat LA. Amino acid residues Leu135 and Tyr236 are required for RNA binding activity of CFIm25 in Entamoeba histolytica. Biochimie 2015; 115:44-51. [PMID: 25941172 DOI: 10.1016/j.biochi.2015.04.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 04/22/2015] [Indexed: 11/29/2022]
Abstract
Pre-mRNA 3' end processing in the nucleus is essential for mRNA stability, efficient nuclear transport, and translation in eukaryotic cells. In Human, the cleavage/polyadenylation machinery contains the 25 kDa subunit of the Cleavage Factor Im (CFIm25), which specifically recognizes two UGUA elements and regulates the assembly of polyadenylation factors, poly(A) site selection and polyadenylation. In Entamoeba histolytica, the protozoan parasite responsible for human amoebiasis, EhCFIm25 has been reported as a RNA binding protein that interacts with the Poly(A) Polymerase. Here, we follow-up with the study of EhCFIm25 to characterize its interaction with RNA. Using in silico strategy, we identified Leu135 and Tyr236 in EhCFIm25 as conserved amino acids among CFIm25 homologues. We therefore generated mutant EhCFIm25 proteins to investigate the role of these residues for RNA interaction. Results showed that RNA binding activity was totally abrogated when Leu135 and Tyr236 were replaced with Ala residue, and Tyr236 was changed for Phe. In contrast, RNA binding activity was less affected when Leu135 was substituted by Thr. Our data revealed for the first time -until we know-the functional relevance of the conserved Leu135 and Tyr236 in EhCFIm25 for RNA binding activity. They also gave some insights about the possible chemical groups that could be interacting with the RNA molecule.
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Affiliation(s)
| | - Absalom Zamorano-Carrillo
- Biotechnology Program, ENMH-IPN, Mexico City, Mexico; Molecular Biomedicine Program, ENMH-IPN, Mexico City, Mexico
| | | | - Carlos A Castañon-Sanchez
- Subdirección de Enseñanza e Investigación, Hospital Regional de Alta Especialidad de Oaxaca, Oaxaca, Mexico
| | | | - Esther Ramirez-Moreno
- Biotechnology Program, ENMH-IPN, Mexico City, Mexico; Molecular Biomedicine Program, ENMH-IPN, Mexico City, Mexico
| | - Laurence A Marchat
- Biotechnology Program, ENMH-IPN, Mexico City, Mexico; Molecular Biomedicine Program, ENMH-IPN, Mexico City, Mexico.
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37
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Transcriptional profile of processing machinery of 3′ end of mRNA in Trichomonas vaginalis. Genes Genomics 2015. [DOI: 10.1007/s13258-015-0268-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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38
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Nie Q, Yue X, Liu B. Development of Vibrio spp. infection resistance related SNP markers using multiplex SNaPshot genotyping method in the clam Meretrix meretrix. FISH & SHELLFISH IMMUNOLOGY 2015; 43:469-476. [PMID: 25655323 DOI: 10.1016/j.fsi.2015.01.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 01/22/2015] [Accepted: 01/26/2015] [Indexed: 06/04/2023]
Abstract
The clam Meretrix meretrix is a commercially important mollusc species in the coastal areas of South and Southeast Asia. In the present study, large-scale SNPs were genotyped by the Multiplex SNaPshot genotyping method among the stocks of M. meretrix with different Vibrio spp. infection resistance profile. Firstly, the AUTOSNP software was applied to mine SNPs from M. meretrix transcriptome, and 323 SNP loci (including 120 indels) located on 64 contigs were selected based on Uniprot-GO associations. Then, 38 polymorphic SNP loci located on 15 contigs were genotyped successfully in the clam stocks with different resistance to Vibrio parahaemolyticus infection (11-R and 11-S groups). Pearson's Chi-square test was applied to compare the allele and genotype frequency distributions of the SNPs between the different stocks, and seven SNP markers located on three contigs were found to be associated with V. parahaemolyticus infection resistance trait. Haplotype-association analysis showed that six haplotypes had significantly different frequency distributions in 11-S and 11-R (P < 0.05). With selective genotyping between 09-R and 09-C populations, which had different resistance to Vibrio harveyi infection, four out of the seven selected SNPs had significantly different distributions (P < 0.05) and therefore they were considered to be associated with Vibrio spp. infection resistance. Sequence alignments and annotations indicated that the contigs containing the associated SNPs had high similarity to the immune related genes. All these results would be useful for the future marker-assisted selection of M. meretrix strains with high Vibrio spp. infection resistance.
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Affiliation(s)
- Qing Nie
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Xin Yue
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Baozhong Liu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
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39
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Lai DP, Tan S, Kang YN, Wu J, Ooi HS, Chen J, Shen TT, Qi Y, Zhang X, Guo Y, Zhu T, Liu B, Shao Z, Zhao X. Genome-wide profiling of polyadenylation sites reveals a link between selective polyadenylation and cancer metastasis. Hum Mol Genet 2015; 24:3410-7. [DOI: 10.1093/hmg/ddv089] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 03/06/2015] [Indexed: 01/10/2023] Open
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40
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Abstract
The binding of small molecules to non-canonical nucleic acid structures has been a major focus of rational drug design. Among the non-canonical nucleic acid structures, targeting poly(A) using small molecules has attracted a special interest due to the cellular functions of poly(A) tails. Here, the methods for determining the binding of a small molecule to poly(A) using UV-visible(UV-Vis) and Circular Dichroism (CD) Spectroscopy are described. Experiments used in determining the melting temperature, binding stoichiometry and dissociation constant of poly(A)-small molecule systems are depicted.
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41
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Van Lint S, Renmans D, Broos K, Dewitte H, Lentacker I, Heirman C, Breckpot K, Thielemans K. The ReNAissanCe of mRNA-based cancer therapy. Expert Rev Vaccines 2014; 14:235-51. [PMID: 25263094 DOI: 10.1586/14760584.2015.957685] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
About 25 years ago, mRNA became a tool of interest in anticancer vaccination approaches. However, due to its rapid degradation in situ, direct application of mRNA was confronted with considerable skepticism during its early use. Consequently, mRNA was for a long time mainly used for the ex vivo transfection of dendritic cells, professional antigen-presenting cells known to stimulate immunity. The interest in direct application of mRNA experienced a revival, as researchers became aware of the many advantages mRNA offers. Today, mRNA is considered to be an ideal vehicle for the induction of strong immune responses against cancer. The growing numbers of preclinical trials and as a consequence the increasing clinical application of mRNA as an off-the-shelf anticancer vaccine signifies a renaissance for transcript-based antitumor therapy. In this review, we highlight this renaissance using a timeline providing all milestones in the application of mRNA for anticancer vaccination.
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Affiliation(s)
- Sandra Van Lint
- Laboratory of Molecular and Cellular Therapy, Department of Biomedical Sciences, Medical School of the Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, B-1090 Jette, Belgium
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Lutz CS, Cornett AL. Regulation of genes in the arachidonic acid metabolic pathway by RNA processing and RNA-mediated mechanisms. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 4:593-605. [PMID: 23956046 DOI: 10.1002/wrna.1183] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 05/28/2013] [Accepted: 05/29/2013] [Indexed: 01/22/2023]
Abstract
Arachidonic acid (AA) is converted by enzymes in an important metabolic pathway to produce molecules known collectively as eicosanoids, 20 carbon molecules with significant physiological and pathological functions in the human body. Cyclooxygenase (COX) enzymes work in one arm of the pathway to produce prostaglandins (PGs) and thromboxanes (TXs), while the actions of 5-lipoxygenase (ALOX5 or 5LO) and its associated protein (ALOX5AP or FLAP) work in the other arm of the metabolic pathway to produce leukotrienes (LTs). The expression of the COX and ALOX5 enzymes that convert AA to eicosanoids is highly regulated at the post- or co-transcriptional level by alternative mRNA splicing, alternative mRNA polyadenylation, mRNA stability, and microRNA (miRNA) regulation. This review article will highlight these mechanisms of mRNA modulation.
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Affiliation(s)
- Carol S Lutz
- Department of Biochemistry and Molecular Biology, New Jersey Medical School and the Graduate School of Biomedical Sciences, Rutgers, NJ, USA.
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43
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Fluorescence detection of polyadenylation reaction through the coordination of adenosine₂-coralyne-adenosine₂. Methods Mol Biol 2014. [PMID: 24590781 DOI: 10.1007/978-1-62703-971-0_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
A simple, sensitive, and selective-detection system for polyadenylation reaction was developed based on the fact that coralyne induces conformational change of polyadenosine [poly(A)] oligonucleotide through adenosine2-coralyne-adenosine2 coordination. Double-strand chelating dye SYBR Green I fluoresces weakly in the presence of random coil of poly(A). Coralyne enables poly(A) to change its conformation from a random coil to a folded structure, which leads to an increased fluorescence of SYBR Green I. When the 3' end of RNA is polyadenylated with poly(A) polymerase, coralyne-induced fluorescence enhancement of the poly(A)-SYBR Green I complex is well suited for monitoring polyadenylation reaction.
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Zhou J, Sayre DA, Zheng Y, Szmacinski H, Sintim HO. Unexpected complex formation between coralyne and cyclic diadenosine monophosphate providing a simple fluorescent turn-on assay to detect this bacterial second messenger. Anal Chem 2014; 86:2412-20. [PMID: 24494631 PMCID: PMC3983017 DOI: 10.1021/ac403203x] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
![]()
Cyclic
diadenosine monophosphate (c-di-AMP) has emerged as an important
dinucleotide that is involved in several processes in bacteria, including
cell wall remodeling (and therefore resistance to antibiotics that
target bacterial cell wall). Small molecules that target c-di-AMP
metabolism enzymes have the potential to be used as antibiotics. Coralyne
is known to form strong complexes with polyadenine containing eight
or more adenine stretches but not with short polyadenine oligonucleotides.
Using a panel of techniques (UV, both steady state fluorescence and
fluorescence lifetime measurements, circular dichroism (CD), NMR,
and Job plots), we demonstrate that c-di-AMP, which contains only
two adenine bases is an exception to this rule and that it can form
complexes with coralyne, even at low micromolar concentrations. Interestingly,
pApA (the linear analog of c-di-AMP that also contains two adenines)
or cyclic diguanylate (c-di-GMP, another nucleotide second messenger
in bacteria) did not form any complex with coralyne. Unlike polyadenine,
which forms a 2:1 complex with coralyne, c-di-AMP forms a higher order
complex with coralyne (≥6:1). Additionally, whereas polyadenine
reduces the fluorescence of coralyne when bound, c-di-AMP enhances
the fluorescence of coralyne. We use the quenching property of halides
to selectively quench the fluorescence of unbound coralyne but not
that of coralyne bound to c-di-AMP. Using this simple selective quenching
strategy, the assay could be used to monitor the synthesis of c-di-AMP
by DisA or the degradation of c-di-AMP by YybT. Apart from the practical
utility of this assay for c-di-AMP research, this work also demonstrates
that, when administered to cells, intercalators might not only associate
with polynucleotides, such as DNA or RNA, but also could associate
with cyclic dinucleotides to disrupt or modulate signal transduction
processes mediated by these nucleotides.
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Affiliation(s)
- Jie Zhou
- Department of Chemistry and Biochemistry, University of Maryland , College Park, Maryland 20742, United States
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Yan YB. Deadenylation: enzymes, regulation, and functional implications. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 5:421-43. [PMID: 24523229 DOI: 10.1002/wrna.1221] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 12/20/2013] [Accepted: 12/21/2013] [Indexed: 12/27/2022]
Abstract
Lengths of the eukaryotic messenger RNA (mRNA) poly(A) tails are dynamically changed by the opposing effects of poly(A) polymerases and deadenylases. Modulating poly(A) tail length provides a highly regulated means to control almost every stage of mRNA lifecycle including transcription, processing, quality control, transport, translation, silence, and decay. The existence of diverse deadenylases with distinct properties highlights the importance of regulating poly(A) tail length in cellular functions. The deadenylation activity can be modulated by subcellular locations of the deadenylases, cis-acting elements in the target mRNAs, trans-acting RNA-binding proteins, posttranslational modifications of deadenylase and associated factors, as well as transcriptional and posttranscriptional regulation of the deadenylase genes. Among these regulators, the physiological functions of deadenylases are largely dependent on the interactions with the trans-acting RNA-binding proteins, which recruit deadenylases to the target mRNAs. The task of these RNA-binding proteins is to find and mark the target mRNAs based on their sequence features. Regulation of the regulators can switch on or switch off deadenylation and thereby destabilize or stabilize the targeted mRNAs, respectively. The distinct domain compositions and cofactors provide various deadenylases the structural basis for the recruitments by distinct RNA-binding protein subsets to meet dissimilar cellular demands. The diverse deadenylases, the numerous types of regulators, and the reversible posttranslational modifications together make up a complicated network to precisely regulate intracellular mRNA homeostasis. This review will focus on the diverse regulators of various deadenylases and will discuss their functional implications, remaining problems, and future challenges.
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Affiliation(s)
- Yong-Bin Yan
- State Key Laboratory of Biomembrane and Membrane Biotechnology, School of Life Sciences, Tsinghua University, Beijing, China
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46
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Pradhan AB, Haque L, Roy S, Das S. Binding of phenazinium dye safranin T to polyriboadenylic acid: spectroscopic and thermodynamic study. PLoS One 2014; 9:e87992. [PMID: 24498422 PMCID: PMC3912202 DOI: 10.1371/journal.pone.0087992] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 01/02/2014] [Indexed: 11/18/2022] Open
Abstract
Here, we report results from experiments designed to explore the association of the phenazinium dye safranin T (ST, 3,7-diamino-2,8-dimethyl-5-phenylphenazinium chloride) with single and double stranded form of polyriboadenylic acid (hereafter poly-A) using several spectroscopic techniques. We demonstrate that the dye binds to single stranded polyriboadenylic acid (hereafter ss poly-A) with high affinity while it does not interact at all with the double stranded (ds) form of the polynucleotide. Fluorescence and absorption spectral studies reveal the molecular aspects of binding of ST to single stranded form of the polynucleotide. This observation is also supported by the circular dichroism study. Thermodynamic data obtained from temperature dependence of binding constant reveals that association is driven by negative enthalpy change and opposed by negative entropy change. Ferrocyanide quenching studies have shown intercalative binding of ST to ss poly-A. Experiments on viscosity measurements confirm the binding mode of the dye to be intercalative. The effect of [Na⁺] ion concentration on the binding process suggests the role of electrostatic forces in the complexation. Present studies reveal the utility of the dye in probing nucleic acid structure.
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Affiliation(s)
| | - Lucy Haque
- Department of Chemistry, Jadavpur University, Jadavpur, Kolkata, India
| | - Snigdha Roy
- Department of Chemistry, Jadavpur University, Jadavpur, Kolkata, India
| | - Suman Das
- Department of Chemistry, Jadavpur University, Jadavpur, Kolkata, India
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Das S, Parveen S, Pradhan AB. An insight into the interaction of phenanthridine dyes with polyriboadenylic acid: spectroscopic and thermodynamic approach. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 118:356-366. [PMID: 24060481 DOI: 10.1016/j.saa.2013.08.106] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 08/17/2013] [Accepted: 08/23/2013] [Indexed: 06/02/2023]
Abstract
Interaction of two phenanthridine dyes, namely ethidium bromide (EB) and propidium iodide (PI) with polyriboadenylic acid was investigated using various spectroscopic techniques. They were found to bind only with the single stranded form of the polymer, while no affinity was observed for the double stranded form. Enhanced binding observed for PI compared to EB may be attributed to the presence of external alkyl chain in PI. Thermodynamic studies showed negative enthalpy and negative entropy changes for the binding of both the dyes. Salt dependent studies revealed a lesser electrolytic contribution compared to the nonelectrolytic contribution to the total Gibbs free energy change in each case. This indicated importance of hydrophobic and van der Waal's interaction for the binding process. Overall, the binding data and detail energetics of interaction presented here would be helpful in the design of phenanthridine based molecules that interact with specific RNA structure.
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Affiliation(s)
- Suman Das
- Department of Chemistry, Jadavpur University, Raja S.C. Mullick Road, Jadavpur, Kolkata 700 032, India.
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48
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Pradhan AB, Haque L, Bhuiya S, Das S. Induction of self-structure in polyriboadenylic acid by the benzophenanthridine plant alkaloid chelerythrine: a spectroscopic approach. RSC Adv 2014. [DOI: 10.1039/c4ra07075e] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Induction of self-structure in polyriboadenylic acid by chelerythrine.
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Affiliation(s)
| | - Lucy Haque
- Department of Chemistry
- Jadavpur University
- Kolkata 700 032, India
| | - Sutanwi Bhuiya
- Department of Chemistry
- Jadavpur University
- Kolkata 700 032, India
| | - Suman Das
- Department of Chemistry
- Jadavpur University
- Kolkata 700 032, India
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Majerciak V, Ni T, Yang W, Meng B, Zhu J, Zheng ZM. A viral genome landscape of RNA polyadenylation from KSHV latent to lytic infection. PLoS Pathog 2013; 9:e1003749. [PMID: 24244170 PMCID: PMC3828183 DOI: 10.1371/journal.ppat.1003749] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 09/20/2013] [Indexed: 11/30/2022] Open
Abstract
RNA polyadenylation (pA) is one of the major steps in regulation of gene expression at the posttranscriptional level. In this report, a genome landscape of pA sites of viral transcripts in B lymphocytes with Kaposi sarcoma-associated herpesvirus (KSHV) infection was constructed using a modified PA-seq strategy. We identified 67 unique pA sites, of which 55 could be assigned for expression of annotated ∼90 KSHV genes. Among the assigned pA sites, twenty are for expression of individual single genes and the rest for multiple genes (average 2.7 genes per pA site) in cluster-gene loci of the genome. A few novel viral pA sites that could not be assigned to any known KSHV genes are often positioned in the antisense strand to ORF8, ORF21, ORF34, K8 and ORF50, and their associated antisense mRNAs to ORF21, ORF34 and K8 could be verified by 3′RACE. The usage of each mapped pA site correlates to its peak size, the larger (broad and wide) peak size, the more usage and thus, the higher expression of the pA site-associated gene(s). Similar to mammalian transcripts, KSHV RNA polyadenylation employs two major poly(A) signals, AAUAAA and AUUAAA, and is regulated by conservation of cis-elements flanking the mapped pA sites. Moreover, we found two or more alternative pA sites downstream of ORF54, K2 (vIL6), K9 (vIRF1), K10.5 (vIRF3), K11 (vIRF2), K12 (Kaposin A), T1.5, and PAN genes and experimentally validated the alternative polyadenylation for the expression of KSHV ORF54, K11, and T1.5 transcripts. Together, our data provide not only a comprehensive pA site landscape for understanding KSHV genome structure and gene expression, but also the first evidence of alternative polyadenylation as another layer of posttranscriptional regulation in viral gene expression. A genome-wide polyadenylation landscape in the expression of human herpesviruses has not been reported. In this study, we provide the first genome landscape of viral RNA polyadenylation sites in B cells from KSHV latent to lytic infection by using a modified PA-seq protocol and selectively validated by 3′ RACE. We found that KSHV genome contains 67 active pA sites for the expression of its ∼90 genes and a few antisense transcripts. Among the mapped pA sites, a large fraction of them are for the expression of cluster genes and the production of bicistronic or polycistronic transcripts from KSHV genome and only one-third are used for the expression of single genes. We found that the size of individual PA peaks is positively correlated with the usage of corresponding pA site, which is determined by the number of reads within the PA peak from latent to lytic KSHV infection, and the strength of cis-elements surrounding KSHV pA site determines the expression level of viral genes. Lastly, we identified and experimentally validated alternative polyadenylation of KSHV ORF54, T1.5, and K11 during viral lytic infection. To our knowledge, this is the first report on alternative polyadenylation events in KSHV infection.
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Affiliation(s)
- Vladimir Majerciak
- Tumor Virus RNA Biology Section, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ting Ni
- DNA Sequencing and Genomics Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Wenjing Yang
- DNA Sequencing and Genomics Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Bowen Meng
- Tumor Virus RNA Biology Section, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jun Zhu
- DNA Sequencing and Genomics Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (JZ); (ZMZ)
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (JZ); (ZMZ)
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50
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Biochemical and biophysical characterization of the deadenylase CrCaf1 from Chlamydomonas reinhardtii. PLoS One 2013; 8:e69582. [PMID: 23936053 PMCID: PMC3720613 DOI: 10.1371/journal.pone.0069582] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 06/14/2013] [Indexed: 01/02/2023] Open
Abstract
The modulation of mRNA turnover has been increasingly recognized as a hotpoint for gene expression regulation at the post-transcriptional level. In eukaryotic cells, most mRNAs are degraded via the deadenylation-dependent pathway, in which the removal of the poly(A) tail is the initial and rate-limiting step. Caf1, a deadenylase specifically degrades poly(A) from the 3′-end, is highly conserved from yeast to mammalians. Caf1s in higher plants have been shown to be involved in plant development and stress response. However, little is known about the biochemical and biophysical properties of Caf1s in plants. In this research, we cloned the crcaf1 gene from Chlamydomonas reinhardtii and studied the properties of the recombinant proteins. The results showed that CrCaf1 was a deadenylase with conserved sequence motifs, structural features, and catalytic properties of the Caf1 family. CrCaf1 degraded poly(A) in a distributive mode with the optimal reacting conditions at pH 7 and 35°C. CrCaf1 had similar activity when coordinated with Mg2+ and Mn2+, while the enzyme bound to Ca2+ or Zn2+ was almost inactivated. Zn2+ could induce CrCaf1 aggregation with the disruption of the native structure, while Mg2+, Mn2+ and Ca2+ could stabilize CrCaf1 against thermal denaturation by reducing protein aggregation. Among the various metal ions, Mn2+ showed the strongest protective effect on CrCaf1 stability, implying that Mn2+ might play a role in regulating CrCaf1 stability in the C. reinhardtii cells under some stressed conditions. These findings provide a starting point for further investigation of the physiological functions of CrCaf1 in C. reinhardtii.
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