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Zhang W, Zhao J, Deng L, Ishimwe N, Pauli J, Wu W, Shan S, Kempf W, Ballantyne MD, Kim D, Lyu Q, Bennett M, Rodor J, Turner AW, Lu YW, Gao P, Choi M, Warthi G, Kim HW, Barroso MM, Bryant WB, Miller CL, Weintraub NL, Maegdefessel L, Miano JM, Baker AH, Long X. INKILN is a Novel Long Noncoding RNA Promoting Vascular Smooth Muscle Inflammation via Scaffolding MKL1 and USP10. Circulation 2023. [PMID: 37199168 DOI: 10.1161/circulationaha.123.063760] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
BACKGROUND Activation of vascular smooth muscle cell (VSMC) inflammation is vital to initiate vascular disease. The role of human-specific long noncoding RNAs in VSMC inflammation is poorly understood. METHODS Bulk RNA sequencing in differentiated human VSMCs revealed a novel human-specific long noncoding RNA called inflammatory MKL1 (megakaryoblastic leukemia 1) interacting long noncoding RNA (INKILN). INKILN expression was assessed in multiple in vitro and ex vivo models of VSMC phenotypic modulation as well as human atherosclerosis and abdominal aortic aneurysm. The transcriptional regulation of INKILN was verified through luciferase reporter and chromatin immunoprecipitation assays. Loss-of-function and gain-of-function studies and multiple RNA-protein and protein-protein interaction assays were used to uncover a mechanistic role of INKILN in the VSMC proinflammatory gene program. Bacterial artificial chromosome transgenic mice were used to study INKILN expression and function in ligation injury-induced neointimal formation. RESULTS INKILN expression is downregulated in contractile VSMCs and induced in human atherosclerosis and abdominal aortic aneurysm. INKILN is transcriptionally activated by the p65 pathway, partially through a predicted NF-κB (nuclear factor kappa B) site within its proximal promoter. INKILN activates proinflammatory gene expression in cultured human VSMCs and ex vivo cultured vessels. INKILN physically interacts with and stabilizes MKL1, a key activator of VSMC inflammation through the p65/NF-κB pathway. INKILN depletion blocks interleukin-1β-induced nuclear localization of both p65 and MKL1. Knockdown of INKILN abolishes the physical interaction between p65 and MKL1 and the luciferase activity of an NF-κB reporter. Furthermore, INKILN knockdown enhances MKL1 ubiquitination through reduced physical interaction with the deubiquitinating enzyme USP10 (ubiquitin-specific peptidase 10). INKILN is induced in injured carotid arteries and exacerbates ligation injury-induced neointimal formation in bacterial artificial chromosome transgenic mice. CONCLUSIONS These findings elucidate an important pathway of VSMC inflammation involving an INKILN/MKL1/USP10 regulatory axis. Human bacterial artificial chromosome transgenic mice offer a novel and physiologically relevant approach for investigating human-specific long noncoding RNAs under vascular disease conditions.
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Affiliation(s)
- Wei Zhang
- Vascular Biology Center, Medical College of Georgia at Augusta University (W.Z., N.I., S.S., D.K., Q.L., G.W., H.W.K., W.B.B., N.L.W., J.M.M., X.L.)
| | - Jinjing Zhao
- Vascular Biology Center, Medical College of Georgia at Augusta University (W.Z., N.I., S.S., D.K., Q.L., G.W., H.W.K., W.B.B., N.L.W., J.M.M., X.L.)
- Department of Molecular and Cellular Physiology, Albany Medical College, NY (J.Z., W.W., Y.W.L., P.G., M.C., M.M.B., X.L.)
| | - Lin Deng
- Centre for Cardiovascular Science, University of Edinburgh, Scotland (L.D., M.D.B., M.B., J.R., A.H.B.)
| | - Nestor Ishimwe
- Vascular Biology Center, Medical College of Georgia at Augusta University (W.Z., N.I., S.S., D.K., Q.L., G.W., H.W.K., W.B.B., N.L.W., J.M.M., X.L.)
| | - Jessica Pauli
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, Germany (J.P., W.K., L.M.)
| | - Wen Wu
- Department of Molecular and Cellular Physiology, Albany Medical College, NY (J.Z., W.W., Y.W.L., P.G., M.C., M.M.B., X.L.)
| | - Shengshuai Shan
- Vascular Biology Center, Medical College of Georgia at Augusta University (W.Z., N.I., S.S., D.K., Q.L., G.W., H.W.K., W.B.B., N.L.W., J.M.M., X.L.)
| | - Wolfgang Kempf
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, Germany (J.P., W.K., L.M.)
| | - Margaret D Ballantyne
- Centre for Cardiovascular Science, University of Edinburgh, Scotland (L.D., M.D.B., M.B., J.R., A.H.B.)
| | - David Kim
- Vascular Biology Center, Medical College of Georgia at Augusta University (W.Z., N.I., S.S., D.K., Q.L., G.W., H.W.K., W.B.B., N.L.W., J.M.M., X.L.)
| | - Qing Lyu
- Vascular Biology Center, Medical College of Georgia at Augusta University (W.Z., N.I., S.S., D.K., Q.L., G.W., H.W.K., W.B.B., N.L.W., J.M.M., X.L.)
| | - Matthew Bennett
- Centre for Cardiovascular Science, University of Edinburgh, Scotland (L.D., M.D.B., M.B., J.R., A.H.B.)
| | - Julie Rodor
- Centre for Cardiovascular Science, University of Edinburgh, Scotland (L.D., M.D.B., M.B., J.R., A.H.B.)
| | - Adam W Turner
- Centre for Cardiovascular Science, University of Edinburgh, Scotland (L.D., M.D.B., M.B., J.R., A.H.B.)
- Center for Public Health Genomics, University of Virginia, Charlottesville. (A.W.T., C.L.M.)
| | - Yao Wei Lu
- Department of Molecular and Cellular Physiology, Albany Medical College, NY (J.Z., W.W., Y.W.L., P.G., M.C., M.M.B., X.L.)
| | - Ping Gao
- Department of Molecular and Cellular Physiology, Albany Medical College, NY (J.Z., W.W., Y.W.L., P.G., M.C., M.M.B., X.L.)
| | - Mihyun Choi
- Department of Molecular and Cellular Physiology, Albany Medical College, NY (J.Z., W.W., Y.W.L., P.G., M.C., M.M.B., X.L.)
| | - Ganesh Warthi
- Vascular Biology Center, Medical College of Georgia at Augusta University (W.Z., N.I., S.S., D.K., Q.L., G.W., H.W.K., W.B.B., N.L.W., J.M.M., X.L.)
| | - Ha Won Kim
- Vascular Biology Center, Medical College of Georgia at Augusta University (W.Z., N.I., S.S., D.K., Q.L., G.W., H.W.K., W.B.B., N.L.W., J.M.M., X.L.)
| | - Margarida M Barroso
- Department of Molecular and Cellular Physiology, Albany Medical College, NY (J.Z., W.W., Y.W.L., P.G., M.C., M.M.B., X.L.)
| | - William B Bryant
- Vascular Biology Center, Medical College of Georgia at Augusta University (W.Z., N.I., S.S., D.K., Q.L., G.W., H.W.K., W.B.B., N.L.W., J.M.M., X.L.)
| | - Clint L Miller
- Center for Public Health Genomics, University of Virginia, Charlottesville. (A.W.T., C.L.M.)
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville. (C.L.M.)
| | - Neal L Weintraub
- Vascular Biology Center, Medical College of Georgia at Augusta University (W.Z., N.I., S.S., D.K., Q.L., G.W., H.W.K., W.B.B., N.L.W., J.M.M., X.L.)
| | - Lars Maegdefessel
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, Germany (J.P., W.K., L.M.)
- German Center for Cardiovascular Research (DZHK, partner site Munich), Germany (L.M.)
- Department of Medicine, Karolinska Institute, Stockholm, Sweden (L.M.)
| | - Joseph M Miano
- Vascular Biology Center, Medical College of Georgia at Augusta University (W.Z., N.I., S.S., D.K., Q.L., G.W., H.W.K., W.B.B., N.L.W., J.M.M., X.L.)
| | - Andrew H Baker
- Centre for Cardiovascular Science, University of Edinburgh, Scotland (L.D., M.D.B., M.B., J.R., A.H.B.)
| | - Xiaochun Long
- Vascular Biology Center, Medical College of Georgia at Augusta University (W.Z., N.I., S.S., D.K., Q.L., G.W., H.W.K., W.B.B., N.L.W., J.M.M., X.L.)
- Department of Molecular and Cellular Physiology, Albany Medical College, NY (J.Z., W.W., Y.W.L., P.G., M.C., M.M.B., X.L.)
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Zhang W, Zhao J, Deng L, Ishimwe N, Pauli J, Wu W, Shan S, Kempf W, Ballantyne MD, Kim D, Lyu Q, Bennett M, Rodor J, Turner AW, Lu YW, Gao P, Choi M, Warthi G, Kim HW, Barroso MM, Bryant WB, Miller CL, Weintraub NL, Maegdefessel L, Miano JM, Baker AH, Long X. INKILN is a novel long noncoding RNA promoting vascular smooth muscle inflammation via scaffolding MKL1 and USP10. bioRxiv 2023:2023.01.07.522948. [PMID: 36711681 PMCID: PMC9881896 DOI: 10.1101/2023.01.07.522948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Background Activation of vascular smooth muscle cells (VSMCs) inflammation is vital to initiate vascular disease. However, the role of human-specific long noncoding RNAs (lncRNAs) in VSMC inflammation is poorly understood. Methods Bulk RNA-seq in differentiated human VSMCs revealed a novel human-specific lncRNA called IN flammatory M K L1 I nteracting L ong N oncoding RNA ( INKILN ). INKILN expression was assessed in multiple in vitro and ex vivo models of VSMC phenotypic modulation and human atherosclerosis and abdominal aortic aneurysm (AAA) samples. The transcriptional regulation of INKILN was determined through luciferase reporter system and chromatin immunoprecipitation assay. Both loss- and gain-of-function approaches and multiple RNA-protein and protein-protein interaction assays were utilized to uncover the role of INKILN in VSMC proinflammatory gene program and underlying mechanisms. Bacterial Artificial Chromosome (BAC) transgenic (Tg) mice were utilized to study INKLIN expression and function in ligation injury-induced neointimal formation. Results INKILN expression is downregulated in contractile VSMCs and induced by human atherosclerosis and abdominal aortic aneurysm. INKILN is transcriptionally activated by the p65 pathway, partially through a predicted NF-κB site within its proximal promoter. INKILN activates the proinflammatory gene expression in cultured human VSMCs and ex vivo cultured vessels. Mechanistically, INKILN physically interacts with and stabilizes MKL1, a key activator of VSMC inflammation through the p65/NF-κB pathway. INKILN depletion blocks ILIβ-induced nuclear localization of both p65 and MKL1. Knockdown of INKILN abolishes the physical interaction between p65 and MKL1, and the luciferase activity of an NF-κB reporter. Further, INKILN knockdown enhances MKL1 ubiquitination, likely through the reduced physical interaction with the deubiquitinating enzyme, USP10. INKILN is induced in injured carotid arteries and exacerbates ligation injury-induced neointimal formation in BAC Tg mice. Conclusions These findings elucidate an important pathway of VSMC inflammation involving an INKILN /MKL1/USP10 regulatory axis. Human BAC Tg mice offer a novel and physiologically relevant approach for investigating human-specific lncRNAs under vascular disease conditions.
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Warthi G, Faulkner JL, Doja J, Ghanam AR, Gao P, Yang AC, Slivano OJ, Barris CT, Kress TC, Zawieja SD, Griffin SH, Xie X, Ashworth A, Christie CK, Bryant WB, Kumar A, Davis MJ, Long X, Gan L, de Chantemèle EJB, Lyu Q, Miano JM. Generation and Comparative Analysis of an Itga8-CreER T2 Mouse with Preferential Activity in Vascular Smooth Muscle Cells. Nat Cardiovasc Res 2022; 1:1084-1100. [PMID: 36424917 PMCID: PMC9681021 DOI: 10.1038/s44161-022-00162-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 09/29/2022] [Indexed: 11/12/2022]
Abstract
All current smooth muscle cell (SMC) Cre mice similarly recombine floxed alleles in vascular and visceral SMCs. Here, we present an Itga8-CreER T2 knock-in mouse and compare its activity with a Myh11-CreER T2 mouse. Both Cre drivers demonstrate equivalent recombination in vascular SMCs. However, Myh11-CreER T2 mice, but not Itga8-CreER T2 mice, display high activity in visceral SMC-containing tissues such as intestine, show early tamoxifen-independent activity, and produce high levels of CreERT2 protein. Whereas Myh11-CreER T2 -mediated knockout of serum response factor (Srf) causes a lethal intestinal phenotype precluding analysis of the vasculature, loss of Srf with Itga8-CreER T2 (Srf Itga8 ) yields viable mice with no evidence of intestinal pathology. Male and female Srf Itga8 mice exhibit vascular contractile incompetence, and angiotensin II causes elevated blood pressure in wild type, but not Srf Itga8 , male mice. These findings establish the Itga8-CreER T2 mouse as an alternative to existing SMC Cre mice for unfettered phenotyping of vascular SMCs following selective gene loss.
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Affiliation(s)
- Ganesh Warthi
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | - Jessica L. Faulkner
- Department of Physiology, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | - Jaser Doja
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | - Amr R. Ghanam
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | - Pan Gao
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | - Allison C. Yang
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | - Orazio J. Slivano
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | - Candee T. Barris
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | - Taylor C. Kress
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | - Scott D. Zawieja
- Medical Pharmacology and Physiology, University of Missouri School of Medicine, Columbia, MO 65212
| | - Susan H. Griffin
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | - Xiaoling Xie
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, 94158
| | - Christine K. Christie
- Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642
| | - William B. Bryant
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | - Ajay Kumar
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | - Michael J. Davis
- Medical Pharmacology and Physiology, University of Missouri School of Medicine, Columbia, MO 65212
| | - Xiaochun Long
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | - Lin Gan
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | | | - Qing Lyu
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
- Biomedical and Health Institute, Chongqing Institute of Green and Intelligence Technology, Chongqing, China 400714
- Chongqing General Hospital, Chongqing, China 401147
| | - Joseph M. Miano
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
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Seligmann H, Warthi G. Natural pyrrolysine-biased translation of stop codons in mitochondrial peptides entirely coded by expanded codons. Biosystems 2020; 196:104180. [PMID: 32534170 DOI: 10.1016/j.biosystems.2020.104180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/02/2020] [Accepted: 06/02/2020] [Indexed: 12/31/2022]
Abstract
During the noncanonical deletion transcription, k nucleotides are systematically skipped/deleted after each transcribed trinucleotide producing deletion-RNAs (delRNAs). Peptides matching delRNAs either result from (a) canonical translation of delRNAs; or (b) noncanonical translation of regular transcripts along expanded codons. Only along frame "0" (start site) (a) and (b) produce identical peptides. Here, mitochondrial mass spectrometry data analyses assume expanded codon/del-transcription with 3 + k (k from 0 to 12) nucleotides. Detected peptides map preferentially on previously identified delRNAs. More peptides were detected for k (1-12) when del-transcriptional and expanded codon translations start sites coincide (i.e. the 0th frame) than for frames +1 or +2. Hence, both (a) and (b) produced peptides identified here. Biases for frame 0 decrease for k > 2, reflecting codon/anticodon expansion limits. Further analyses find preferential pyrrolysine insertion at stop codons, suggesting Pyl-specific mitochondrial suppressor tRNAs loaded by Pyl-specific tRNA synthetases with unknown origins. Pyl biases at stops are stronger for regular than expanded codons suggesting that Pyl-tRNAs are less competitive with near-cognate tRNAs in expanded codon contexts. Statistical biases for these findings exclude that detected peptides are experimental and/or bioinformatic artefacts implying both del-transcription and expanded codons translation occur in human mitochondria.
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Affiliation(s)
- Hervé Seligmann
- The National Natural History Collections, The Hebrew University of Jerusalem, 91404, Jerusalem, Israel; Université Grenoble Alpes, Faculty of Medicine, Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical, F-38700, La Tronche, France.
| | - Ganesh Warthi
- Aix-Marseille University, IRD, VITROME, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France.
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Warthi G, Fournier PE, Seligmann H. Systematic Nucleotide Exchange Analysis of ESTs From the Human Cancer Genome Project Report: Origins of 347 Unknown ESTs Indicate Putative Transcription of Non-Coding Genomic Regions. Front Genet 2020; 11:42. [PMID: 32117454 PMCID: PMC7027195 DOI: 10.3389/fgene.2020.00042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/15/2020] [Indexed: 12/16/2022] Open
Abstract
Expressed sequence tags (ESTs) provide an imprint of cellular RNA diversity irrespectively of sequence homology with template genomes. NCBI databases include many unknown RNAs from various normal and cancer cells. These are usually ignored assuming sequencing artefacts or contamination due to their lack of sequence homology with template DNA. Here, we report genomic origins of 347 ESTs previously assumed artefacts/unknown, from the FAPESP/LICR Human Cancer Genome Project. EST template detection uses systematic nucleotide exchange analyses called swinger transformations. Systematic nucleotide exchanges replace systematically particular nucleotides with different nucleotides. Among 347 unknown ESTs, 51 ESTs match mitogenome transcription, 17 and 2 ESTs are from nuclear chromosome non-coding regions, and uncharacterized nuclear genes. Identified ESTs mapped on 205 protein-coding genes, 10 genes had swinger RNAs in several biosamples. Whole cell transcriptome searches for 17 ESTs mapping on non-coding regions confirmed their transcription. The 10 swinger-transcribed genes identified more than once associate with cancer induction and progression, suggesting swinger transformation occurs mainly in highly transcribed genes. Swinger transformation is a unique method to identify noncanonical RNAs obtained from NGS, which identifies putative ncRNA transcribed regions. Results suggest that swinger transcription occurs in highly active genes in normal and genetically unstable cancer cells.
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Affiliation(s)
- Ganesh Warthi
- Aix Marseille Univ, IRD, APHM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Pierre-Edouard Fournier
- Aix Marseille Univ, IRD, APHM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Hervé Seligmann
- The National Natural History Collections, The Hebrew University of Jerusalem, Jerusalem, Israel.,Université Grenoble Alpes, Faculty of Medicine, Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecoms4Health, La Tronche, France
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Warthi G, Fournier PE, Seligmann H. Identification of Noncanonical Transcripts Produced by Systematic Nucleotide Exchanges in HIV-Associated Centroblastic Lymphoma. DNA Cell Biol 2019; 39:1444-1448. [PMID: 31750730 DOI: 10.1089/dna.2019.5066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Noncanonical transcriptions include transcriptions that systematically exchange nucleotides, also called bijective transformations or swinger transformations. Swinger transformation A↔T+C↔G recovers identities of 8 among 9 unknown RNAs differentially expressed in centroblastic lymphoma, a human immunodeficiency virus (HIV)-associated non-Hodgkin's lymphoma. The identified RNAs align with human genes with known anti-HIV1 or oncogenic activities. Function disruption through swinger-transformed transcription potentially enables avoiding antiviral responses and contributes to cancer induction.
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Affiliation(s)
- Ganesh Warthi
- IRD, APHM, Aix Marseille Univ, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Pierre-Edouard Fournier
- IRD, APHM, Aix Marseille Univ, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Hervé Seligmann
- The National Natural History Collections, The Hebrew University of Jerusalem, Jerusalem, Israel
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Seligmann H, Warthi G. Chimeric Translation for Mitochondrial Peptides: Regular and Expanded Codons. Comput Struct Biotechnol J 2019; 17:1195-1202. [PMID: 31534643 PMCID: PMC6742854 DOI: 10.1016/j.csbj.2019.08.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/19/2019] [Accepted: 08/21/2019] [Indexed: 02/07/2023] Open
Abstract
Frameshifting protein translation occasionally results from insertion of amino acids at isolated mono- or dinucleotide-expanded codons by tRNAs with expanded anticodons. Previous analyses of two different types of human mitochondrial MS proteomic data (Fisher and Waters technologies) detect peptides entirely corresponding to expanded codon translation. Here, these proteomic data are reanalyzed searching for peptides consisting of at least eight consecutive amino acids translated according to regular tricodons, and at least eight adjacent consecutive amino acids translated according to expanded codons. Both datasets include chimerically translated peptides (mono- and dinucleotide expansions, 42 and 37, respectively). The regular tricodon-encoded part of some chimeric peptides corresponds to standard human mitochondrial proteins (mono- and dinucleotide expansions, six (AT6, CytB, ND1, 2xND2, ND5) and one (ND1), respectively). Chimeric translation probably increases the diversity of mitogenome-encoded proteins, putatively producing functional proteins. These might result from translation by tRNAs with expanded anticodons, or from regular tricodon translation of RNAs where transcription/posttranscriptional edition systematically deleted mono- or dinucleotides after each trinucleotide. The pairwise matched combination of adjacent peptide parts translated from regular and expanded codons strengthens the hypothesis that translation of stretches of consecutive expanded codons occurs. Results indicate statistical translation producing distributions of alternative proteins. Genetic engineering should account for potential unexpected, unwanted secondary products.
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Affiliation(s)
- Hervé Seligmann
- The National Natural History Collections, The Hebrew University of Jerusalem, 91404 Jerusalem, Israel
| | - Ganesh Warthi
- Aix-Marseille University, IRD, VITROME, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
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Warthi G, Seligmann H. Transcripts with systematic nucleotide deletion of 1-12 nucleotide in human mitochondrion suggest potential non-canonical transcription. PLoS One 2019; 14:e0217356. [PMID: 31120958 PMCID: PMC6532905 DOI: 10.1371/journal.pone.0217356] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 05/09/2019] [Indexed: 11/22/2022] Open
Abstract
Raw transcriptomic data contain numerous RNA reads whose homology with template DNA doesn't match canonical transcription. Transcriptome analyses usually ignore such noncanonical RNA reads. Here, analyses search for noncanonical mitochondrial RNAs systematically deleting 1 to 12 nucleotides after each transcribed nucleotide triplet, producing deletion-RNAs (delRNAs). We detected delRNAs in the human whole cell and purified mitochondrial transcriptomes, and in Genbank's human EST database corresponding to systematic deletions of 1 to 12 nucleotides after each transcribed trinucleotide. DelRNAs detected in both transcriptomes mapped along with 55.63% of the EST delRNAs. A bias exists for delRNAs covering identical mitogenomic regions in both transcriptomic and EST datasets. Among 227 delRNAs detected in these 3 datasets, 81.1% and 8.4% of delRNAs were mapped on mitochondrial coding and hypervariable region 2 of dloop. Del-transcription analyses of GenBank's EST database confirm observations from whole cell and purified mitochondrial transcriptomes, eliminating the possibility that detected delRNAs are false positives matches, cytosolic DNA/RNA nuclear contamination or sequencing artefacts. These detected delRNAs are enriched in frameshift-inducing homopolymers and are poor in frameshift-preventing circular code codons (a set of 20 codons which regulate reading frame detection, over- and underrepresented in coding and other frames of genes, respectively) suggesting a motif-based regulation of non-canonical transcription. These findings show that rare non-canonical transcripts exist. Such non canonical del-transcription does increases mitochondrial coding potential and non-coding regulation of intracellular mechanisms, and could explain the dark DNA conundrum.
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Affiliation(s)
- Ganesh Warthi
- Aix-Marseille Université, IRD, VITROME, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Hervé Seligmann
- Aix-Marseille Université, IRD, MEPHI, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Marseille, France
- The National Natural History Collections, The Hebrew University of Jerusalem, Jerusalem, Israel
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Seligmann H, Warthi G. Genetic Code Optimization for Cotranslational Protein Folding: Codon Directional Asymmetry Correlates with Antiparallel Betasheets, tRNA Synthetase Classes. Comput Struct Biotechnol J 2017; 15:412-424. [PMID: 28924459 PMCID: PMC5591391 DOI: 10.1016/j.csbj.2017.08.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 07/20/2017] [Accepted: 08/05/2017] [Indexed: 12/14/2022] Open
Abstract
A new codon property, codon directional asymmetry in nucleotide content (CDA), reveals a biologically meaningful genetic code dimension: palindromic codons (first and last nucleotides identical, codon structure XZX) are symmetric (CDA = 0), codons with structures ZXX/XXZ are 5'/3' asymmetric (CDA = - 1/1; CDA = - 0.5/0.5 if Z and X are both purines or both pyrimidines, assigning negative/positive (-/+) signs is an arbitrary convention). Negative/positive CDAs associate with (a) Fujimoto's tetrahedral codon stereo-table; (b) tRNA synthetase class I/II (aminoacylate the 2'/3' hydroxyl group of the tRNA's last ribose, respectively); and (c) high/low antiparallel (not parallel) betasheet conformation parameters. Preliminary results suggest CDA-whole organism associations (body temperature, developmental stability, lifespan). Presumably, CDA impacts spatial kinetics of codon-anticodon interactions, affecting cotranslational protein folding. Some synonymous codons have opposite CDA sign (alanine, leucine, serine, and valine), putatively explaining how synonymous mutations sometimes affect protein function. Correlations between CDA and tRNA synthetase classes are weaker than between CDA and antiparallel betasheet conformation parameters. This effect is stronger for mitochondrial genetic codes, and potentially drives mitochondrial codon-amino acid reassignments. CDA reveals information ruling nucleotide-protein relations embedded in reversed (not reverse-complement) sequences (5'-ZXX-3'/5'-XXZ-3').
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Affiliation(s)
- Hervé Seligmann
- Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS UMR7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, Postal code 13385, France
- Dept. Ecol Evol Behav, Alexander Silberman Inst Life Sci, The Hebrew University of Jerusalem, IL-91904 Jerusalem, Israel
| | - Ganesh Warthi
- Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS UMR7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, Postal code 13385, France
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Kolte SW, Larcombe SD, Jadhao SG, Magar SP, Warthi G, Kurkure NV, Glass EJ, Shiels BR. PCR diagnosis of tick-borne pathogens in Maharashtra state, India indicates fitness cost associated with carrier infections is greater for crossbreed than native cattle breeds. PLoS One 2017; 12:e0174595. [PMID: 28358861 PMCID: PMC5373575 DOI: 10.1371/journal.pone.0174595] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 03/11/2017] [Indexed: 11/18/2022] Open
Abstract
Tick-borne pathogens (TBP) are responsible for significant economic losses to cattle production, globally. This is particularly true in countries like India where TBP constrain rearing of high yielding Bos taurus, as they show susceptibility to acute tick borne disease (TBD), most notably tropical theileriosis caused by Theileria annulata. This has led to a programme of cross breeding Bos taurus (Holstein-Friesian or Jersey) with native Bos indicus (numerous) breeds to generate cattle that are more resistant to disease. However, the cost to fitness of subclinical carrier infection in crossbreeds relative to native breeds is unknown, but could represent a significant hidden economic cost. In this study, a total of 1052 bovine blood samples, together with associated data on host type, sex and body score, were collected from apparently healthy animals in four different agro-climatic zones of Maharashtra state. Samples were screened by PCR for detection of five major TBPs: T. annulata, T. orientalis, B. bigemina, B. bovis and Anaplasma spp.. The results demonstrated that single and co-infection with TBP are common, and although differences in pathogen spp. prevalence across the climatic zones were detected, simplistic regression models predicted that host type, sex and location are all likely to impact on prevalence of TBP. In order to remove issues with autocorrelation between variables, a subset of the dataset was modelled to assess any impact of TBP infection on body score of crossbreed versus native breed cattle (breed type). The model showed significant association between infection with TBP (particularly apicomplexan parasites) and poorer body condition for crossbreed animals. These findings indicate potential cost of TBP carrier infection on crossbreed productivity. Thus, there is a case for development of strategies for targeted breeding to combine productivity traits with disease resistance, or to prevent transmission of TBP in India for economic benefit.
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Affiliation(s)
- Sunil W. Kolte
- Nagpur Veterinary College, Maharashtra Animal and Fishery Sciences, Nagpur, Maharashtra, India
| | - Stephen D. Larcombe
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
- * E-mail:
| | - Suresh G. Jadhao
- Nagpur Veterinary College, Maharashtra Animal and Fishery Sciences, Nagpur, Maharashtra, India
| | - Swapnil P. Magar
- Nagpur Veterinary College, Maharashtra Animal and Fishery Sciences, Nagpur, Maharashtra, India
| | - Ganesh Warthi
- Nagpur Veterinary College, Maharashtra Animal and Fishery Sciences, Nagpur, Maharashtra, India
| | - Nitin V. Kurkure
- Nagpur Veterinary College, Maharashtra Animal and Fishery Sciences, Nagpur, Maharashtra, India
| | - Elizabeth J. Glass
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Brian R. Shiels
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
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