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Pagani TD, Corrêa PR, Lima C, Gomes LHF, Schwarz MGA, Galvão TC, Degrave WM, Valadares NF, Mendonça-Lima L. Impact of Genomic Deletion RD16 on the Expression of the Mycobacterium bovis BCG Moreau VapBC47 Toxin-Antitoxin System. Curr Issues Mol Biol 2023; 45:6538-6549. [PMID: 37623231 PMCID: PMC10453824 DOI: 10.3390/cimb45080412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/23/2023] [Accepted: 05/27/2023] [Indexed: 08/26/2023] Open
Abstract
Mycobacterium bovis BCG is the only vaccine against tuberculosis. The variable forms of cultivation throughout the years, before seed-lots were developed, allowed in vitro evolution of the original strain, generating a family of vaccines with different phenotypic and genotypic characteristics. Molecular studies revealed regions of difference (RDs) in the genomes of the various BCG strains. This work aims to characterize the gene pair rv3407-rv3408 (vapB47-vapC47), coding for a toxin-antitoxin system of the VapBC family, and to evaluate possible transcriptional effects due to the adjacent BCG Moreau-specific genomic deletion RD16. We show that these genes are co-transcribed in BCG strains Moreau and Pasteur, and that the inactivation of an upstream transcriptional repressor (Rv3405c) due to RD16 has a polar effect, leading to increased vapBC47 expression. Furthermore, we detect VapB47 DNA binding in vitro, dependent on a 5' vapB47 sequence that contributes to a palindrome, spanning the promoter and coding region. Our data shed light on the regulation of VapBC systems and on the impact of the BCG Moreau RD16 deletion in the expression of adjacent genes, contributing to a better understanding of BCG Moreau physiology.
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Affiliation(s)
- Talita Duarte Pagani
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil; (T.D.P.); (P.R.C.); (C.L.); (L.H.F.G.); (M.G.A.S.); (W.M.D.)
| | - Paloma Rezende Corrêa
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil; (T.D.P.); (P.R.C.); (C.L.); (L.H.F.G.); (M.G.A.S.); (W.M.D.)
| | - Cristiane Lima
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil; (T.D.P.); (P.R.C.); (C.L.); (L.H.F.G.); (M.G.A.S.); (W.M.D.)
| | - Leonardo Henrique Ferreira Gomes
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil; (T.D.P.); (P.R.C.); (C.L.); (L.H.F.G.); (M.G.A.S.); (W.M.D.)
| | - Marcos Gustavo Araujo Schwarz
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil; (T.D.P.); (P.R.C.); (C.L.); (L.H.F.G.); (M.G.A.S.); (W.M.D.)
| | - Teca Calcagno Galvão
- Laboratório de Bacteriologia, Centro de Referência Prof. Hélio Fraga, Escola Nacional de Saúde Pública Sergio Arouca, Fiocruz, Rio de Janeiro 21041-210, RJ, Brazil;
| | - Wim Maurits Degrave
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil; (T.D.P.); (P.R.C.); (C.L.); (L.H.F.G.); (M.G.A.S.); (W.M.D.)
| | | | - Leila Mendonça-Lima
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil; (T.D.P.); (P.R.C.); (C.L.); (L.H.F.G.); (M.G.A.S.); (W.M.D.)
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Lu K, Fan Q, Zou X. Antisense oligonucleotide is a promising intervention for liver diseases. Front Pharmacol 2022; 13:1061842. [PMID: 36569303 PMCID: PMC9780395 DOI: 10.3389/fphar.2022.1061842] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022] Open
Abstract
As the body's critical metabolic organ, the liver plays an essential role in maintaining proper body homeostasis. However, as people's living standards have improved and the number of unhealthy lifestyles has increased, the liver has become overburdened. These have made liver disease one of the leading causes of death worldwide. Under the influence of adverse factors, liver disease progresses from simple steatosis to hepatitis, to liver fibrosis, and finally to cirrhosis and cancer, followed by increased mortality. Until now, there has been a lack of accepted effective treatments for liver disease. Based on current research, antisense oligonucleotide (ASO), as an alternative intervention for liver diseases, is expected to be an effective treatment due to its high efficiency, low toxicity, low dosage, strong specificity, and additional positive characteristics. In this review, we will first introduce the design, modification, delivery, and the mechanisms of ASO, and then summarize the application of ASO in liver disease treatment, including in non-alcoholic fatty liver disease (NAFLD), hepatitis, liver fibrosis, and liver cancer. Finally, we discuss challenges and perspectives on the transfer of ASO drugs into clinical use. This review provides a current and comprehensive understanding of the integrative and systematic functions of ASO for its use in liver disease.
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Affiliation(s)
- Kailing Lu
- College of Chinese Materia Medica and Yunnan Key Laboratory of Southern Medicinal Utilization, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Qijing Fan
- Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Xiaoju Zou
- College of Chinese Materia Medica and Yunnan Key Laboratory of Southern Medicinal Utilization, Yunnan University of Chinese Medicine, Kunming, Yunnan, China,*Correspondence: Xiaoju Zou,
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Szikszai M, Wise M, Datta A, Ward M, Mathews DH. Deep learning models for RNA secondary structure prediction (probably) do not generalize across families. Bioinformatics 2022; 38:3892-3899. [PMID: 35748706 PMCID: PMC9364374 DOI: 10.1093/bioinformatics/btac415] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/09/2022] [Accepted: 06/21/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION The secondary structure of RNA is of importance to its function. Over the last few years, several papers attempted to use machine learning to improve de novo RNA secondary structure prediction. Many of these papers report impressive results for intra-family predictions but seldom address the much more difficult (and practical) inter-family problem. RESULTS We demonstrate that it is nearly trivial with convolutional neural networks to generate pseudo-free energy changes, modelled after structure mapping data that improve the accuracy of structure prediction for intra-family cases. We propose a more rigorous method for inter-family cross-validation that can be used to assess the performance of learning-based models. Using this method, we further demonstrate that intra-family performance is insufficient proof of generalization despite the widespread assumption in the literature and provide strong evidence that many existing learning-based models have not generalized inter-family. AVAILABILITY AND IMPLEMENTATION Source code and data are available at https://github.com/marcellszi/dl-rna. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Marcell Szikszai
- Department of Computer Science & Software Engineering, The University of Western Australia, Perth, WA 6009, Australia
| | - Michael Wise
- Department of Computer Science & Software Engineering, The University of Western Australia, Perth, WA 6009, Australia
- The Marshall Centre for Infectious Diseases Research and Training, The University of Western Australia, Perth, WA 6009, Australia
| | - Amitava Datta
- Department of Computer Science & Software Engineering, The University of Western Australia, Perth, WA 6009, Australia
| | - Max Ward
- Department of Computer Science & Software Engineering, The University of Western Australia, Perth, WA 6009, Australia
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - David H Mathews
- Department of Biochemistry & Biophysics, Center for RNA Biology, and Department of Biostatistics & Computational Biology, University of Rochester, Rochester, NY 14642, USA
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He P, Zhang C, Ji Y, Ge MK, Yu Y, Zhang N, Yang S, Yu JX, Shen SM, Chen GQ. Epithelial cells-enriched lncRNA SNHG8 regulates chromatin condensation by binding to Histone H1s. Cell Death Differ 2022; 29:1569-1581. [PMID: 35140358 PMCID: PMC9345976 DOI: 10.1038/s41418-022-00944-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 01/17/2022] [Accepted: 01/17/2022] [Indexed: 12/12/2022] Open
Abstract
Linker histone H1 proteins contain many variants in mammalian and can stabilize the condensed state of chromatin by binding to nucleosomes and promoting a more inaccessible structure of DNA. However, it is poorly understood how the binding of histone H1s to chromatin DNA is regulated. Screened as one of a collection of epithelial cells-enriched long non-coding RNAs (lncRNAs), here we found that small nucleolar RNA host gene 8 (SNHG8) is a chromatin-localized lncRNA and presents strong interaction and phase separation with histone H1 variants. Moreover, SNHG8 presents stronger ability to bind H1s than linker DNA, and outcompetes linker DNA for H1 binding. Consequently, loss of SNHG8 increases the amount of H1s that bind to chromatin, promotes chromatin condensation, and induces an epithelial differentiation-associated gene expression pattern. Collectively, our results propose that the highly abundant SNHG8 in epithelial cells keeps histone H1 variants out of nucleosome and its loss contributes to epithelial cell differentiation.
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Affiliation(s)
- Ping He
- State Key Laboratory of Oncogenes and Related Genes, and Chinese Academy of Medical Sciences Research Unit (NO.2019RU043), Shanghai Cancer Institute, Renji hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, 200127, China
| | - Cheng Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, SJTU-SM, Shanghai, 200025, China
| | - Yan Ji
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Meng-Kai Ge
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, SJTU-SM, Shanghai, 200025, China
| | - Yun Yu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, SJTU-SM, Shanghai, 200025, China
| | - Na Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, SJTU-SM, Shanghai, 200025, China
| | - Shuo Yang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, SJTU-SM, Shanghai, 200025, China
| | - Jian-Xiu Yu
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, SJTU-SM, Shanghai, 200025, China
| | - Shao-Ming Shen
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, SJTU-SM, Shanghai, 200025, China.
| | - Guo-Qiang Chen
- State Key Laboratory of Oncogenes and Related Genes, and Chinese Academy of Medical Sciences Research Unit (NO.2019RU043), Shanghai Cancer Institute, Renji hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, 200127, China. .,Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, SJTU-SM, Shanghai, 200025, China.
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Wang N, Chen X, Hao Z, Yi H, Tang S. Association of ABCG2 polymorphisms with susceptibility to anti-tuberculosis drug-induced hepatotoxicity in the Chinese population. Xenobiotica 2022; 52:527-533. [PMID: 35735268 DOI: 10.1080/00498254.2022.2093685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Background The accumulation of endogenous hepatotoxin protoporphyrin IX (PPIX) in the liver was proposed to be a novel mechanism of anti-tuberculosis drug-induced hepatotoxicity (ATDH). ATP-binding cassette transporter G2 (ABCG2) plays an important role in modulating PPIX concentrations. This study aimed to explore the role of ABCG2 genetic polymorphisms in the risk of ATDH in Chinese patients.Methods A 1:4 matched case-control study was performed among 202 ATDH cases and 808 controls. Conditional logistic regression model was used to estimate the association between genotypes and the risk of ATDH by odds ratios (ORs) with 95% confidence intervals (CIs).Results Male patients with CC genotype of rs2622605 had an increased risk of ATDH (adjusted OR =1.615, 95% CI: 1.119-2.332, P = 0.011). The peak value of alkaline phosphatase was significantly higher in male patients with CC genotype of rs2622605 than in those with TT + TC genotype during antituberculosis treatment (102.0 U/L vs. 98.0 U/L, P = 0.029).Conclusions This is the first attempt to evaluate the association between ABCG2 genetic variants and the risk of ATDH. Based on the 1:4 matched case-control study, the polymorphism at rs2622605 in the ABCG2 gene may be associated with the susceptibility to ATDH in Chinese male patients.
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Affiliation(s)
- Nannan Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xinyu Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhuolu Hao
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Honggang Yi
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Shaowen Tang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
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D’Esposito RJ, Myers CA, Chen AA, Vangaveti S. Challenges with Simulating Modified RNA: Insights into Role and Reciprocity of Experimental and Computational Approaches. Genes (Basel) 2022; 13:genes13030540. [PMID: 35328093 PMCID: PMC8949676 DOI: 10.3390/genes13030540] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 01/12/2023] Open
Abstract
RNA is critical to a broad spectrum of biological and viral processes. This functional diversity is a result of their dynamic nature; the variety of three-dimensional structures that they can fold into; and a host of post-transcriptional chemical modifications. While there are many experimental techniques to study the structural dynamics of biomolecules, molecular dynamics simulations (MDS) play a significant role in complementing experimental data and providing mechanistic insights. The accuracy of the results obtained from MDS is determined by the underlying physical models i.e., the force-fields, that steer the simulations. Though RNA force-fields have received a lot of attention in the last decade, they still lag compared to their protein counterparts. The chemical diversity imparted by the RNA modifications adds another layer of complexity to an already challenging problem. Insight into the effect of RNA modifications upon RNA folding and dynamics is lacking due to the insufficiency or absence of relevant experimental data. This review provides an overview of the state of MDS of modified RNA, focusing on the challenges in parameterization of RNA modifications as well as insights into relevant reference experiments necessary for their calibration.
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Affiliation(s)
- Rebecca J. D’Esposito
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA; (R.J.D.); (A.A.C.)
| | - Christopher A. Myers
- Department of Physics, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA;
| | - Alan A. Chen
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA; (R.J.D.); (A.A.C.)
- The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Sweta Vangaveti
- The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
- Correspondence:
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Knezic B, Keyhani-Goldau S, Schwalbe H. Mapping the conformational landscape of the neutral network of RNA sequences that connect two functional distinctly different ribozymes. Chembiochem 2022; 23:e202200022. [PMID: 35112772 PMCID: PMC9305247 DOI: 10.1002/cbic.202200022] [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: 01/12/2022] [Revised: 02/02/2022] [Indexed: 11/08/2022]
Abstract
During evolution of an RNA world, the development of enzymatic function was essential. Such enzymatic function was linked to RNA sequences capable of adopting specific RNA folds that possess catalytic pockets to promote catalysis. Within this primordial RNA world, initially evolved self-replicating ribozymes presumably mutated to ribozymes with new functions. In 2000, Schultes and Bartel investigated such conversion from one ribozyme to a new ribozyme with distinctly different catalytic functions. Within a neutral network that linked these two prototype ribozymes, a single RNA chain could be identified that exhibited both enzymatic functions. This system serves as a paradigm for an evolutionary system that allows neutral drifts by stepwise mutation from one ribozyme into a different ribozyme without loss of intermittent function. Here, we investigated this complex functional diversification by analyzing several RNA sequences within this neutral network between two ribozymes with class III ligase activity and with self-cleavage reactivity. We utilized rapid RNA sample preparation for NMR spectroscopic studies together with SHAPE analysis and in-line probing to characterize secondary structure changes within the neutral network. Our investigations allowed delineation of the 2 nd structure space and by comparison with the previously determined catalytic function allowed correlation of the structure-function relation of ribozyme function in this neutral network.
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Affiliation(s)
- Bozana Knezic
- Goethe-Universitat Frankfurt am Main, Biochemistry, Chemistry, and Pharmacy, GERMANY
| | - Sara Keyhani-Goldau
- Goethe-Universitat Frankfurt am Main, Biochemistry, Chemistry, and Pharmacy, GERMANY
| | - Harald Schwalbe
- Goethe-Universitat Frankfurt am Main, Institut für Organische Chemie und Chemische Biologie, Max-von-Laue-Str. 7, 60438, Frankfurt, GERMANY
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8
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Identification of human microRNAs targeting Pseudomonas aeruginosa genes by an in silico hybridization method. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2022.101110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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9
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Steger G. Predicting the Structure of a Viroid : Structure, Structure Distribution, Consensus Structure, and Structure Drawing. Methods Mol Biol 2022; 2316:331-371. [PMID: 34845705 DOI: 10.1007/978-1-0716-1464-8_26] [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] [Indexed: 06/13/2023]
Abstract
Viroids are small non-coding RNAs that require a special sequence and structure to be replicated and transported by the host machinery. Many of these features can be predicted and later experimentally verified. Here, we will present workflows to predict viroid structures and draw the predicted structures in a pleasing and descriptive way using recently developed software.
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Affiliation(s)
- Gerhard Steger
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany.
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Gong J, Xu K, Ma Z, Lu ZJ, Zhang QC. A deep learning method for recovering missing signals in transcriptome-wide RNA structure profiles from probing experiments. NAT MACH INTELL 2021. [DOI: 10.1038/s42256-021-00412-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Alghoul F, Laure S, Eriani G, Martin F. Translation inhibitory elements from Hoxa3 and Hoxa11 mRNAs use uORFs for translation inhibition. eLife 2021; 10:e66369. [PMID: 34076576 PMCID: PMC8172242 DOI: 10.7554/elife.66369] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 05/20/2021] [Indexed: 01/20/2023] Open
Abstract
During embryogenesis, Hox mRNA translation is tightly regulated by a sophisticated molecular mechanism that combines two RNA regulons located in their 5'UTR. First, an internal ribosome entry site (IRES) enables cap-independent translation. The second regulon is a translation inhibitory element or TIE, which ensures concomitant cap-dependent translation inhibition. In this study, we deciphered the molecular mechanisms of mouse Hoxa3 and Hoxa11 TIEs. Both TIEs possess an upstream open reading frame (uORF) that is critical to inhibit cap-dependent translation. However, the molecular mechanisms used are different. In Hoxa3 TIE, we identify an uORF which inhibits cap-dependent translation and we show the requirement of the non-canonical initiation factor eIF2D for this process. The mode of action of Hoxa11 TIE is different, it also contains an uORF but it is a minimal uORF formed by an uAUG followed immediately by a stop codon, namely a 'start-stop'. The 'start-stop' sequence is species-specific and in mice, is located upstream of a highly stable stem loop structure which stalls the 80S ribosome and thereby inhibits cap-dependent translation of Hoxa11 main ORF.
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Affiliation(s)
- Fatima Alghoul
- Institut de Biologie Moléculaire et Cellulaire, “Architecture et Réactivité de l’ARN” CNRS UPR9002, Université de StrasbourgStrasbourgFrance
| | - Schaeffer Laure
- Institut de Biologie Moléculaire et Cellulaire, “Architecture et Réactivité de l’ARN” CNRS UPR9002, Université de StrasbourgStrasbourgFrance
| | - Gilbert Eriani
- Institut de Biologie Moléculaire et Cellulaire, “Architecture et Réactivité de l’ARN” CNRS UPR9002, Université de StrasbourgStrasbourgFrance
| | - Franck Martin
- Institut de Biologie Moléculaire et Cellulaire, “Architecture et Réactivité de l’ARN” CNRS UPR9002, Université de StrasbourgStrasbourgFrance
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Abdelsattar AS, Mansour Y, Aboul-Ela F. The Perturbed Free-Energy Landscape: Linking Ligand Binding to Biomolecular Folding. Chembiochem 2021; 22:1499-1516. [PMID: 33351206 DOI: 10.1002/cbic.202000695] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/19/2020] [Indexed: 12/24/2022]
Abstract
The effects of ligand binding on biomolecular conformation are crucial in drug design, enzyme mechanisms, the regulation of gene expression, and other biological processes. Descriptive models such as "lock and key", "induced fit", and "conformation selection" are common ways to interpret such interactions. Another historical model, linked equilibria, proposes that the free-energy landscape (FEL) is perturbed by the addition of ligand binding energy for the bound population of biomolecules. This principle leads to a unified, quantitative theory of ligand-induced conformation change, building upon the FEL concept. We call the map of binding free energy over biomolecular conformational space the "binding affinity landscape" (BAL). The perturbed FEL predicts/explains ligand-induced conformational changes conforming to all common descriptive models. We review recent experimental and computational studies that exemplify the perturbed FEL, with emphasis on RNA. This way of understanding ligand-induced conformation dynamics motivates new experimental and theoretical approaches to ligand design, structural biology and systems biology.
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Affiliation(s)
- Abdallah S Abdelsattar
- Center for X-Ray Determination of the Structure of Matter, Zewail City of Science and Technology, Ahmed Zewail Road, October Gardens, 12578, Giza, Egypt
| | - Youssef Mansour
- Center for X-Ray Determination of the Structure of Matter, Zewail City of Science and Technology, Ahmed Zewail Road, October Gardens, 12578, Giza, Egypt
| | - Fareed Aboul-Ela
- Center for X-Ray Determination of the Structure of Matter, Zewail City of Science and Technology, Ahmed Zewail Road, October Gardens, 12578, Giza, Egypt
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Gawroński P, Enroth C, Kindgren P, Marquardt S, Karpiński S, Leister D, Jensen PE, Vinther J, Scharff LB. Light-Dependent Translation Change of Arabidopsis psbA Correlates with RNA Structure Alterations at the Translation Initiation Region. Cells 2021; 10:322. [PMID: 33557293 PMCID: PMC7914831 DOI: 10.3390/cells10020322] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/26/2021] [Accepted: 01/29/2021] [Indexed: 01/21/2023] Open
Abstract
mRNA secondary structure influences translation. Proteins that modulate the mRNA secondary structure around the translation initiation region may regulate translation in plastids. To test this hypothesis, we exposed Arabidopsis thaliana to high light, which induces translation of psbA mRNA encoding the D1 subunit of photosystem II. We assayed translation by ribosome profiling and applied two complementary methods to analyze in vivo RNA secondary structure: DMS-MaPseq and SHAPE-seq. We detected increased accessibility of the translation initiation region of psbA after high light treatment, likely contributing to the observed increase in translation by facilitating translation initiation. Furthermore, we identified the footprint of a putative regulatory protein in the 5' UTR of psbA at a position where occlusion of the nucleotide sequence would cause the structure of the translation initiation region to open up, thereby facilitating ribosome access. Moreover, we show that other plastid genes with weak Shine-Dalgarno sequences (SD) are likely to exhibit psbA-like regulation, while those with strong SDs do not. This supports the idea that changes in mRNA secondary structure might represent a general mechanism for translational regulation of psbA and other plastid genes.
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Affiliation(s)
- Piotr Gawroński
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland; (P.G.); (S.K.)
| | - Christel Enroth
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 København N, Denmark; (C.E.); (J.V.)
| | - Peter Kindgren
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark; (P.K.); (S.M.)
| | - Sebastian Marquardt
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark; (P.K.); (S.M.)
| | - Stanisław Karpiński
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland; (P.G.); (S.K.)
| | - Dario Leister
- Plant Molecular Biology, Department Biology I, Ludwig-Maximilians-University Munich, Großhadernerstr. 2-4, 82152 Planegg-Martinsried, Germany;
| | - Poul Erik Jensen
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg C, Denmark;
| | - Jeppe Vinther
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 København N, Denmark; (C.E.); (J.V.)
| | - Lars B. Scharff
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark; (P.K.); (S.M.)
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14
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Advances in the Bioinformatics Knowledge of mRNA Polyadenylation in Baculovirus Genes. Viruses 2020; 12:v12121395. [PMID: 33291215 PMCID: PMC7762203 DOI: 10.3390/v12121395] [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: 10/24/2020] [Revised: 11/19/2020] [Accepted: 11/30/2020] [Indexed: 11/17/2022] Open
Abstract
Baculoviruses are a group of insect viruses with large circular dsDNA genomes exploited in numerous biotechnological applications, such as the biological control of agricultural pests, the expression of recombinant proteins or the gene delivery of therapeutic sequences in mammals, among others. Their genomes encode between 80 and 200 proteins, of which 38 are shared by all reported species. Thanks to multi-omic studies, there is remarkable information about the baculoviral proteome and the temporality in the virus gene expression. This allows some functional elements of the genome to be very well described, such as promoters and open reading frames. However, less information is available about the transcription termination signals and, consequently, there are still imprecisions about what are the limits of the transcriptional units present in the baculovirus genomes and how is the processing of the 3′ end of viral mRNA. Regarding to this, in this review we provide an update about the characteristics of DNA signals involved in this process and we contribute to their correct prediction through an exhaustive analysis that involves bibliography information, data mining, RNA structure and a comprehensive study of the core gene 3′ ends from 180 baculovirus genomes.
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15
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Simão M, Leite RB, Cancela ML. Expression of four new ferritins from grooved carpet shell clam Ruditapes decussatus challenged with Perkinsus olseni and metals (Cd, Cu and Zn). AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2020; 229:105675. [PMID: 33197689 DOI: 10.1016/j.aquatox.2020.105675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 10/30/2020] [Accepted: 10/31/2020] [Indexed: 06/11/2023]
Abstract
Iron has a fundamental role in life and in its biochemical reactions but, when in excess, it can promote the formation of free radicals which can lead to cell death. Therefore, managing the levels of iron is essential to regulate the production of oxidative stress related to iron, and ferritins are one of the main protein families involved in this process. Ferritins are ≈480 kDa multimeric proteins composed by 24 subunits, each with 19-26 kDa, which can accumulate up to 4500 iron atoms. Besides their role in managing iron bioavailability, they have also developed a role in organism immunity and defence present throughout evolution. In this work, we identified and characterized, for the first time, four different ferritin subunits in the clam Ruditapes decussatus, a bivalve commercially and ecologically important along the south Atlantic coast and in the Mediterranean basin, which is a major target of the parasitic protozoa Perkinsus olseni, considered one of the main causes of high levels of clam mortality. Following phylogenetic annotation, the four ferritins subunits identified were subdivided into two cytosolic and two secreted forms. All four subunits maintain the canonical ferritin structure with four main helices α (A-D) and a small helix (E), but the secreted ferritins present an additional helix in their N-terminal region (F), located after the signal peptide and with possible antimicrobial properties. Additionally, we identified in ferritin 4 an extra helix α (G) located between helices B and C. These alpha helix domains revealed high degree of similarity with antimicrobial peptides associated with antibacterial and antifungal activities. Analysis of the expression of these subunits showed that ferritins 1 and 2 are ubiquitously expressed while ferritins 3 and 4 are present mainly in visceral mass. Ferritin 1 lacked a putative functional iron response element (IRE) and appeared to be under a tight regulation. Ferritins 2 and 3 showed a strong response to infection by parasite Perkinsus olseni in contrast to ferritin 4, whose main response was related to exposure to a combination of metals. The synergistic effect between metals and infection promoted a general upregulation of the four ferritins. In conclusion, our results suggest that ferritins, besides their function in iron and metals detoxification, may play a determinant role in clam immune response.
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Affiliation(s)
- Márcio Simão
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Faro, Portugal; Department of Biomedical Sciences and Medicine (DCBM), Universidade do Algarve, Faro, Portugal.
| | - Ricardo B Leite
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Faro, Portugal
| | - M Leonor Cancela
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Faro, Portugal; Department of Biomedical Sciences and Medicine (DCBM), Universidade do Algarve, Faro, Portugal; Algarve Biomedical Center (ABC) and Center for Biomedical Research (CBMR), Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
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16
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Chandler-Bostock R, Mata CP, Bingham RJ, Dykeman EC, Meng B, Tuthill TJ, Rowlands DJ, Ranson NA, Twarock R, Stockley PG. Assembly of infectious enteroviruses depends on multiple, conserved genomic RNA-coat protein contacts. PLoS Pathog 2020; 16:e1009146. [PMID: 33370422 PMCID: PMC7793301 DOI: 10.1371/journal.ppat.1009146] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 01/08/2021] [Accepted: 11/11/2020] [Indexed: 02/04/2023] Open
Abstract
Picornaviruses are important viral pathogens, but despite extensive study, the assembly process of their infectious virions is still incompletely understood, preventing the development of anti-viral strategies targeting this essential part of the life cycle. We report the identification, via RNA SELEX and bioinformatics, of multiple RNA sites across the genome of a typical enterovirus, enterovirus-E (EV-E), that each have affinity for the cognate viral capsid protein (CP) capsomer. Many of these sites are evolutionarily conserved across known EV-E variants, suggesting they play essential functional roles. Cryo-electron microscopy was used to reconstruct the EV-E particle at ~2.2 Å resolution, revealing extensive density for the genomic RNA. Relaxing the imposed symmetry within the reconstructed particles reveals multiple RNA-CP contacts, a first for any picornavirus. Conservative mutagenesis of the individual RNA-contacting amino acid side chains in EV-E, many of which are conserved across the enterovirus family including poliovirus, is lethal but does not interfere with replication or translation. Anti-EV-E and anti-poliovirus aptamers share sequence similarities with sites distributed across the poliovirus genome. These data are consistent with the hypothesis that these RNA-CP contacts are RNA Packaging Signals (PSs) that play vital roles in assembly and suggest that the RNA PSs are evolutionarily conserved between pathogens within the family, augmenting the current protein-only assembly paradigm for this family of viruses.
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Affiliation(s)
- Rebecca Chandler-Bostock
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Carlos P. Mata
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Richard J. Bingham
- Department of Mathematics, University of York, York, United Kingdom
- Department of Biology, University of York, York, United Kingdom
- York Cross-disciplinary Centre for Systems Analysis, University of York, York, United Kingdom
| | - Eric C. Dykeman
- Department of Mathematics, University of York, York, United Kingdom
- York Cross-disciplinary Centre for Systems Analysis, University of York, York, United Kingdom
| | - Bo Meng
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Tobias J. Tuthill
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - David J. Rowlands
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- * E-mail: (DJR); (NAR); (RT); (PGS)
| | - Neil A. Ranson
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- * E-mail: (DJR); (NAR); (RT); (PGS)
| | - Reidun Twarock
- Department of Mathematics, University of York, York, United Kingdom
- Department of Biology, University of York, York, United Kingdom
- York Cross-disciplinary Centre for Systems Analysis, University of York, York, United Kingdom
- * E-mail: (DJR); (NAR); (RT); (PGS)
| | - Peter G. Stockley
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- * E-mail: (DJR); (NAR); (RT); (PGS)
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17
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Cuturello F, Tiana G, Bussi G. Assessing the accuracy of direct-coupling analysis for RNA contact prediction. RNA (NEW YORK, N.Y.) 2020; 26:637-647. [PMID: 32115426 PMCID: PMC7161351 DOI: 10.1261/rna.074179.119] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 02/26/2020] [Indexed: 05/31/2023]
Abstract
Many noncoding RNAs are known to play a role in the cell directly linked to their structure. Structure prediction based on the sole sequence is, however, a challenging task. On the other hand, thanks to the low cost of sequencing technologies, a very large number of homologous sequences are becoming available for many RNA families. In the protein community, the idea of exploiting the covariance of mutations within a family to predict the protein structure using the direct-coupling-analysis (DCA) method has emerged in the last decade. The application of DCA to RNA systems has been limited so far. We here perform an assessment of the DCA method on 17 riboswitch families, comparing it with the commonly used mutual information analysis and with state-of-the-art R-scape covariance method. We also compare different flavors of DCA, including mean-field, pseudolikelihood, and a proposed stochastic procedure (Boltzmann learning) for solving exactly the DCA inverse problem. Boltzmann learning outperforms the other methods in predicting contacts observed in high-resolution crystal structures.
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Affiliation(s)
- Francesca Cuturello
- Scuola Internazionale Superiore di Studi Avanzati, International School for Advanced Studies, 34136 Trieste, Italy
| | - Guido Tiana
- Center for Complexity and Biosystems and Department of Physics, Università degli Studi di Milano and INFN, 20133 Milano, Italy
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati, International School for Advanced Studies, 34136 Trieste, Italy
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18
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Gawroński P, Pałac A, Scharff LB. Secondary Structure of Chloroplast mRNAs In Vivo and In Vitro. PLANTS (BASEL, SWITZERLAND) 2020; 9:E323. [PMID: 32143324 PMCID: PMC7154907 DOI: 10.3390/plants9030323] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/25/2020] [Accepted: 02/28/2020] [Indexed: 01/09/2023]
Abstract
mRNA secondary structure can influence gene expression, e.g., by influencing translation initiation. The probing of in vivo mRNA secondary structures is therefore necessary to understand what determines the efficiency and regulation of gene expression. Here, in vivo mRNA secondary structure was analyzed using dimethyl sulfate (DMS)-MaPseq and compared to in vitro-folded RNA. We used an approach to analyze specific, full-length transcripts. To test this approach, we chose low, medium, and high abundant mRNAs. We included both monocistronic and multicistronic transcripts. Because of the slightly alkaline pH of the chloroplast stroma, we could probe all four nucleotides with DMS. The structural information gained was evaluated using the known structure of the plastid 16S rRNA. This demonstrated that the results obtained for adenosines and cytidines were more reliable than for guanosines and uridines. The majority of mRNAs analyzed were less structured in vivo than in vitro. The in vivo secondary structure of the translation initiation region of most tested genes appears to be optimized for high translation efficiency.
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Affiliation(s)
- Piotr Gawroński
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Aleksandra Pałac
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Lars B. Scharff
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, 1871 Frederiksberg C, Denmark
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19
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Sullivan NT, Dampier W, Chung CH, Allen AG, Atkins A, Pirrone V, Homan G, Passic S, Williams J, Zhong W, Kercher K, Desimone M, Li L, C Antell G, Mell JC, Ehrlich GD, Szep Z, Jacobson JM, Nonnemacher MR, Wigdahl B. Novel gRNA design pipeline to develop broad-spectrum CRISPR/Cas9 gRNAs for safe targeting of the HIV-1 quasispecies in patients. Sci Rep 2019; 9:17088. [PMID: 31745112 PMCID: PMC6864089 DOI: 10.1038/s41598-019-52353-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 10/16/2019] [Indexed: 12/20/2022] Open
Abstract
The CRISPR/Cas9 system has been proposed as a cure strategy for HIV. However, few published guide RNAs (gRNAs) are predicted to cleave the majority of HIV-1 viral quasispecies (vQS) observed within and among patients. We report the design of a novel pipeline to identify gRNAs that target HIV across a large number of infected individuals. Next generation sequencing (NGS) of LTRs from 269 HIV-1-infected samples in the Drexel CARES Cohort was used to select gRNAs with predicted broad-spectrum activity. In silico, D-LTR-P4-227913 (package of the top 4 gRNAs) accounted for all detectable genetic variation within the vQS of the 269 samples and the Los Alamos National Laboratory HIV database. In silico secondary structure analyses from NGS indicated extensive TAR stem-loop malformations predicted to inactivate proviral transcription, which was confirmed by reduced viral gene expression in TZM-bl or P4R5 cells. Similarly, a high sensitivity in vitro CRISPR/Cas9 cleavage assay showed that the top-ranked gRNA was the most effective at cleaving patient-derived HIV-1 LTRs from five patients. Furthermore, the D-LTR-P4-227913 was predicted to cleave a median of 96.1% of patient-derived sequences from other HIV subtypes. These results demonstrate that the gRNAs possess broad-spectrum cutting activity and could contribute to an HIV cure.
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Affiliation(s)
- Neil T Sullivan
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
| | - Will Dampier
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
- School of Biomedical Engineering and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Cheng-Han Chung
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
| | - Alexander G Allen
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
| | - Andrew Atkins
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
| | - Vanessa Pirrone
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
| | - Greg Homan
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
| | - Shendra Passic
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
| | - Jean Williams
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
| | - Wen Zhong
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
| | - Katherine Kercher
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
| | - Mathew Desimone
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
- School of Biomedical Engineering and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Luna Li
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
| | - Gregory C Antell
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
- School of Biomedical Engineering and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Joshua Chang Mell
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, 19102, Pennsylvania, USA
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, 19102, Pennsylvania, USA
| | - Garth D Ehrlich
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, 19102, Pennsylvania, USA
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, 19102, Pennsylvania, USA
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
- Department of Otolaryngology - Head and Neck Surgery, Drexel University College of Medicine, Philadelphia, 19102, PA, USA
| | - Zsofia Szep
- Center for Clinical and Translational Medicine, Institute for Molecular Medicine and Infectious Disease, Philadelphia, PA, USA
- Division of Infectious Disease and HIV Medicine, Department of Medicine, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
| | - Jeffrey M Jacobson
- Department of Neuroscience and Comprehensive NeuroAIDS Center, Lewis Katz School of Medicine, Temple University, Philadelphia, 19140, PA, USA
- Department of Medicine, Section of Infectious Disease, Lewis Katz School of Medicine, Temple University, Philadelphia, 19140, PA, USA
- Center for Translational AIDS Research, Lewis Katz School of Medicine, Temple University, Philadelphia, 19140, PA, USA
| | - Michael R Nonnemacher
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA.
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19102, USA.
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA.
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20
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Jiang G, Chen K, Sun J. Accurate prediction of secondary structure of tRNAs. Biochem Biophys Res Commun 2019; 509:64-68. [DOI: 10.1016/j.bbrc.2018.12.042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 12/05/2018] [Indexed: 11/28/2022]
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21
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Zhao Y, Wang J, Zeng C, Xiao Y. Evaluation of RNA secondary structure prediction for both base-pairing and topology. BIOPHYSICS REPORTS 2018. [DOI: 10.1007/s41048-018-0058-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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22
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Taylor AI, Holliger P. Selecting Fully-Modified XNA Aptamers Using Synthetic Genetics. ACTA ACUST UNITED AC 2018; 10:e44. [PMID: 29927117 DOI: 10.1002/cpch.44] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This unit describes the application of "synthetic genetics," i.e., the replication of xeno nucleic acids (XNAs), artificial analogs of DNA and RNA bearing alternative backbone or sugar congeners, to the directed evolution of synthetic oligonucleotide ligands (XNA aptamers) specific for target proteins or nucleic acid motifs, using a cross-chemistry selective exponential enrichment (X-SELEX) approach. Protocols are described for synthesis of diverse-sequence XNA repertoires (typically 1014 molecules) using DNA templates, isolation and panning for functional XNA sequences using targets immobilized on solid phase or gel shift induced by target binding in solution, and XNA reverse transcription to allow cDNA amplification or sequencing. The method may be generally applied to select fully-modified XNA aptamers specific for a wide range of target molecules. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Alexander I Taylor
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Philipp Holliger
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
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23
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Rife Magalis B, Kosakovsky Pond SL, Summers MF, Salemi M. Evaluation of global HIV/SIV envelope gp120 RNA structure and evolution within and among infected hosts. Virus Evol 2018; 4:vey018. [PMID: 29951250 PMCID: PMC6014367 DOI: 10.1093/ve/vey018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Lentiviral RNA genomes contain structural elements that play critical roles in viral replication. Although structural features of 5'-untranslated regions have been well characterized, attempts to identify important structures in other genomic regions by Selective 2'-Hydroxyl Acylation analyzed by Primer Extension (SHAPE) have led to conflicting structural and mechanistic conclusions. Previous approaches accounted neither for sequence heterogeneity that is ubiquitous in viral populations, nor for selective constraints operating at the protein level. We developed an approach that augments SHAPE with phylogenetic analyses and applied it to investigate structure in coding regions (cRNA) within the HIV and SIV envelope genes. Analysis of single-genome SHAPE data with phylogenetic information from diverse lentiviral sequences argues against the conservation of a putative global gp120 RNA structure but points to the existence of core RNA sub-structures. Our findings establish a framework for considering sequence heterogeneity and protein function in de novo RNA structure inference approaches.
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Affiliation(s)
- Brittany Rife Magalis
- Emerging Pathogens Institute and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
- Institute for Genomics and Evolutionary Medicine and Department of Biology, Temple University, Philadelphia, PA, USA
| | - Sergei L Kosakovsky Pond
- Institute for Genomics and Evolutionary Medicine and Department of Biology, Temple University, Philadelphia, PA, USA
| | - Michael F Summers
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Marco Salemi
- Emerging Pathogens Institute and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
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