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Vinueza-Gavilanes R, Íñigo-Marco I, Larrea L, Lasa M, Carte B, Santamaría E, Fernández-Irigoyen J, Bugallo R, Aragón T, Aldabe R, Arrasate M. N-terminal acetylation mutants affect alpha-synuclein stability, protein levels and neuronal toxicity. Neurobiol Dis 2020; 137:104781. [PMID: 31991248 DOI: 10.1016/j.nbd.2020.104781] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 01/14/2020] [Accepted: 01/24/2020] [Indexed: 02/07/2023] Open
Abstract
Alpha-synuclein (aSyn) protein levels are sufficient to drive Parkinson's disease (PD) and other synucleinopathies. Despite the biomedical/therapeutic potential of aSyn protein regulation, little is known about mechanisms that limit/control aSyn levels. Here, we investigate the role of a post-translational modification, N-terminal acetylation, in aSyn neurotoxicity. N-terminal acetylation occurs in all aSyn molecules and has been proposed to determine its lipid binding and aggregation capacities; however, its effect in aSyn stability/neurotoxicity has not been evaluated. We generated N-terminal mutants that alter or block physiological aSyn N-terminal acetylation in wild-type or pathological mutant E46K aSyn versions and confirmed N-terminal acetylation status by mass spectrometry. By optical pulse-labeling in living primary neurons we documented a reduced half-life and accumulation of aSyn N-terminal mutants. To analyze the effect of N-terminal acetylation mutants in neuronal toxicity we took advantage of a neuronal model where aSyn toxicity was scored by longitudinal survival analysis. Salient features of aSyn neurotoxicity were previously investigated with this approach. aSyn-dependent neuronal death was recapitulated either by higher aSyn protein levels in the case of WT aSyn, or by the combined effect of protein levels and enhanced neurotoxicity conveyed by the E46K mutation. aSyn N-terminal mutations decreased E46K aSyn-dependent neuronal death both by reducing protein levels and, importantly, by reducing the intrinsic E46K aSyn toxicity, being the D2P mutant the least toxic. Together, our results illustrate that the N-terminus determines, most likely through its acetylation, aSyn protein levels and toxicity, identifying this modification as a potential therapeutic target.
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Affiliation(s)
- Rodrigo Vinueza-Gavilanes
- University of Navarra, Center for Applied Medical Research (CIMA), Neuroscience Program, Pamplona 31008, Spain; University of Navarra, School of Medicine, Graduate Program on Neuroscience and Cognition, Pamplona 31008, Spain.
| | - Ignacio Íñigo-Marco
- University of Navarra, Center for Applied Medical Research (CIMA), Neuroscience Program, Pamplona 31008, Spain.
| | - Laura Larrea
- University of Navarra, Center for Applied Medical Research (CIMA), Neuroscience Program, Pamplona 31008, Spain.
| | - Marta Lasa
- University of Navarra, Center for Applied Medical Research (CIMA), Hematology-Oncology Program, Pamplona 31008, Spain.
| | - Beatriz Carte
- University of Navarra, Center for Applied Medical Research (CIMA), Gene Therapy and Regulation of Gene Expression Program, Pamplona 31008, Spain; Digestive System and Metabolism Diseases Department, Navarra Institute for Health Research (IdiSNA), Pamplona 31008, Spain.
| | - Enrique Santamaría
- Proteored-Institute of Health Carlos III (ISCIII), Clinical Neuroproteomics Unit, Navarrabiomed, Navarra Health Department, Public University of Navarra, Navarra Institute for Health Research (IdiSNA), Pamplona 31008, Spain.
| | - Joaquín Fernández-Irigoyen
- Proteored-Institute of Health Carlos III (ISCIII), Clinical Neuroproteomics Unit, Navarrabiomed, Navarra Health Department, Public University of Navarra, Navarra Institute for Health Research (IdiSNA), Pamplona 31008, Spain.
| | - Ricardo Bugallo
- University of Navarra, Center for Applied Medical Research (CIMA), Neuroscience Program, Pamplona 31008, Spain; University of Navarra, School of Medicine, Graduate Program on Neuroscience and Cognition, Pamplona 31008, Spain.
| | - Tomás Aragón
- University of Navarra, Center for Applied Medical Research (CIMA), Gene Therapy and Regulation of Gene Expression Program, Pamplona 31008, Spain; Digestive System and Metabolism Diseases Department, Navarra Institute for Health Research (IdiSNA), Pamplona 31008, Spain.
| | - Rafael Aldabe
- University of Navarra, Center for Applied Medical Research (CIMA), Gene Therapy and Regulation of Gene Expression Program, Pamplona 31008, Spain; Digestive System and Metabolism Diseases Department, Navarra Institute for Health Research (IdiSNA), Pamplona 31008, Spain.
| | - Montserrat Arrasate
- University of Navarra, Center for Applied Medical Research (CIMA), Neuroscience Program, Pamplona 31008, Spain; University of Navarra, School of Medicine, Pamplona 31008, Spain; Neuroscience Department, Navarra Institute for Health Research (IdiSNA), Pamplona 31008, Spain.
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202
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Goodson-Gregg FJ, Rothbard B, Zhang A, Wright PW, Li H, Walker-Sperling VE, Carrington M, Anderson SK. Tuning of NK-Specific HLA-C Expression by Alternative mRNA Splicing. Front Immunol 2020; 10:3034. [PMID: 31998314 PMCID: PMC6966967 DOI: 10.3389/fimmu.2019.03034] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 12/11/2019] [Indexed: 01/05/2023] Open
Abstract
A complex system regulating HLA-C expression in NK cells, driven by an NK-specific promoter that produces alternatively spliced variants of the 5'-UTR has been recently identified. Exon content of the NK-specific 5'-UTR varies strikingly across HLA-C alleles, with some exons being allele specific. In order to investigate the possibility that allelic variation in the 5'-UTR modulates HLA-C expression levels, cDNAs containing several distinct classes of 5'-UTR were compared. Subtle changes in 5'-UTR content had a significant effect on the expression of HLA-C * 03 and HLA-C * 12 cDNA clones, suggesting that alternative splicing can fine-tune the level of protein expression. The HLA-C * 06 allele was found to be highly expressed in relation to the other alleles studied. However, its increased expression was primarily associated with differences in the peptide-binding groove. Although the impact of allele-specific alternative splicing of NK-Pro transcripts on protein levels can be modest when compared with the effect of changes in peptide-loading, alternative splicing may represent an additional regulatory mechanism to fine-tune HLA-C levels within NK cells in distinct tissue environments or at different stages of maturation in order to achieve optimal levels of missing-self recognition.
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Affiliation(s)
- Frederick J Goodson-Gregg
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States
| | - Brian Rothbard
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States
| | - Amy Zhang
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States
| | - Paul W Wright
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Hongchuan Li
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Victoria E Walker-Sperling
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States.,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, United States
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States.,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, United States
| | - Stephen K Anderson
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
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203
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Abstract
Viruses must co-opt the cellular translation machinery to produce progeny virions. Eukaryotic viruses have evolved a variety of ways to manipulate the cellular translation apparatus, in many cases using elegant RNA-centred strategies. Viral RNAs can alter or control every phase of protein synthesis and have diverse targets, mechanisms and structures. In addition, as cells attempt to limit infection by downregulating translation, some of these viral RNAs enable the virus to overcome this response or even take advantage of it to promote viral translation over cellular translation. In this Review, we present important examples of viral RNA-based strategies to exploit the cellular translation machinery. We describe what is understood of the structures and mechanisms of diverse viral RNA elements that alter or regulate translation, the advantages that are conferred to the virus and some of the major unknowns that provide motivation for further exploration. Eukaryotic viruses have evolved a variety of ways to manipulate the cellular translation apparatus. In this Review, Jaafar and Kieft present important examples of viral RNA-based strategies to exploit the cellular translation machinery.
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Affiliation(s)
- Zane A Jaafar
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO, USA
| | - Jeffrey S Kieft
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO, USA. .,RNA Bioscience Initiative, University of Colorado Denver School of Medicine, Aurora, CO, USA.
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204
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De Nijs Y, De Maeseneire SL, Soetaert WK. 5' untranslated regions: the next regulatory sequence in yeast synthetic biology. Biol Rev Camb Philos Soc 2019; 95:517-529. [PMID: 31863552 DOI: 10.1111/brv.12575] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 11/08/2019] [Accepted: 11/28/2019] [Indexed: 01/10/2023]
Abstract
When developing industrial biotechnology processes, Saccharomyces cerevisiae (baker's yeast or brewer's yeast) is a popular choice as a microbial host. Many tools have been developed in the fields of synthetic biology and metabolic engineering to introduce heterologous pathways and tune their expression in yeast. Such tools mainly focus on controlling transcription, whereas post-transcriptional regulation is often overlooked. Herein we discuss regulatory elements found in the 5' untranslated region (UTR) and their influence on protein synthesis. We provide not only an overall picture, but also a set of design rules on how to engineer a 5' UTR. The reader is also referred to currently available models that allow gene expression to be tuned predictably using different 5' UTRs.
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Affiliation(s)
- Yatti De Nijs
- Faculty of Bioscience Engineering, Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department Biotechnology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Sofie L De Maeseneire
- Faculty of Bioscience Engineering, Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department Biotechnology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Wim K Soetaert
- Faculty of Bioscience Engineering, Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department Biotechnology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
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205
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Baez WD, Roy B, McNutt ZA, Shatoff EA, Chen S, Bundschuh R, Fredrick K. Global analysis of protein synthesis in Flavobacterium johnsoniae reveals the use of Kozak-like sequences in diverse bacteria. Nucleic Acids Res 2019; 47:10477-10488. [PMID: 31602466 PMCID: PMC6847099 DOI: 10.1093/nar/gkz855] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/16/2019] [Accepted: 09/30/2019] [Indexed: 12/31/2022] Open
Abstract
In all cells, initiation of translation is tuned by intrinsic features of the mRNA. Here, we analyze translation in Flavobacterium johnsoniae, a representative of the Bacteroidetes. Members of this phylum naturally lack Shine-Dalgarno (SD) sequences in their mRNA, and yet their ribosomes retain the conserved anti-SD sequence. Translation initiation is tuned by mRNA secondary structure and by the identities of several key nucleotides upstream of the start codon. Positive determinants include adenine at position -3, reminiscent of the Kozak sequence of Eukarya. Comparative analysis of Escherichia coli reveals use of the same Kozak-like sequence to enhance initiation, suggesting an ancient and widespread mechanism. Elimination of contacts between A-3 and the conserved β-hairpin of ribosomal protein uS7 fails to diminish the contribution of A-3 to initiation, suggesting an indirect mode of recognition. Also, we find that, in the Bacteroidetes, the trinucleotide AUG is underrepresented in the vicinity of the start codon, which presumably helps compensate for the absence of SD sequences in these organisms.
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Affiliation(s)
- William D Baez
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Bappaditya Roy
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Zakkary A McNutt
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Elan A Shatoff
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Shicheng Chen
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Ralf Bundschuh
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Kurt Fredrick
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
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206
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Oleaga-Quintas C, Deswarte C, Moncada-Vélez M, Metin A, Krishna Rao I, Kanık-Yüksek S, Nieto-Patlán A, Guérin A, Gülhan B, Murthy S, Özkaya-Parlakay A, Abel L, Martínez-Barricarte R, Pérez de Diego R, Boisson-Dupuis S, Kong XF, Casanova JL, Bustamante J. A purely quantitative form of partial recessive IFN-γR2 deficiency caused by mutations of the initiation or second codon. Hum Mol Genet 2019; 27:3919-3935. [PMID: 31222290 DOI: 10.1093/hmg/ddy275] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 07/17/2018] [Accepted: 07/17/2018] [Indexed: 02/07/2023] Open
Abstract
Mendelian susceptibility to mycobacterial disease (MSMD) is characterized by clinical disease caused by weakly virulent mycobacteria, such as environmental mycobacteria and Bacillus Calmette-Guérin vaccines, in otherwise healthy individuals. All known genetic etiologies disrupt interferon (IFN)-γ immunity. Germline bi-allelic mutations of IFNGR2 can underlie partial or complete forms of IFN-γ receptor 2 (IFN-γR2) deficiency. Patients with partial IFN-γR2 deficiency express a dysfunctional molecule on the cell surface. We studied three patients with MSMD from two unrelated kindreds from Turkey (P1, P2) and India (P3), by whole-exome sequencing. P1 and P2 are homozygous for a mutation of the initiation codon(c.1A>G) of IFNGR2, whereas P3 is homozygous for a mutation of the second codon (c.4delC). Overexpressed mutant alleles produce small amounts of full-length IFN-γR2 resulting in an impaired, but not abolished, response to IFN-γ. Moreover, SV40-fibroblasts of P1 and P2 responded weakly to IFN-γ, and Epstein Barr virus-transformed B cells had a barely detectable response to IFN-γ. Studies in patients' primary T cells and monocyte-derived macrophages yielded similar results. The residual expression of IFN-γR2 protein of normal molecular weight and function is due to the initiation of translation between the second and ninth non-AUG codons. We thus describe mutations of the first and second codons of IFNGR2, which define a new form of partial recessive IFN-γR2 deficiency. Residual levels of IFN-γ signaling were very low, accounting for the more severe clinical phenotype of these patients with residual expression levels of normally functional surface receptors than of patients with partial recessive IFN-γR2 deficiency due to surface-expressed dysfunctional receptors, whose residual levels of IFN-γ signaling were higher.
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Affiliation(s)
- Carmen Oleaga-Quintas
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Imagine Institute, Necker Hospital for Sick Children, Paris, France.,Paris Descartes University, Paris, France.,Department of Immunology, School of Medicine, Complutense University, Madrid, Spain
| | - Caroline Deswarte
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Imagine Institute, Necker Hospital for Sick Children, Paris, France.,Paris Descartes University, Paris, France
| | - Marcela Moncada-Vélez
- Primary Immunodeficiencies Group, School of Medicine, University of Antioquia UdeA, Medellin, Colombia
| | - Ayse Metin
- Infectious Diseases Unit, Ankara Hematology Oncology Children's Training and Research Hospital, Ankara, Turkey
| | | | - Saliha Kanık-Yüksek
- Infectious Diseases Unit, Ankara Hematology Oncology Children's Training and Research Hospital, Ankara, Turkey
| | - Alejandro Nieto-Patlán
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Imagine Institute, Necker Hospital for Sick Children, Paris, France.,Paris Descartes University, Paris, France
| | - Antoine Guérin
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Imagine Institute, Necker Hospital for Sick Children, Paris, France.,Paris Descartes University, Paris, France
| | - Belgin Gülhan
- Infectious Diseases Unit, Ankara Hematology Oncology Children's Training and Research Hospital, Ankara, Turkey
| | - Savita Murthy
- Department of Pediatrics, St John's Medical College, Bangalore, India
| | - Aslınur Özkaya-Parlakay
- Infectious Diseases Unit, Ankara Hematology Oncology Children's Training and Research Hospital, Ankara, Turkey
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Imagine Institute, Necker Hospital for Sick Children, Paris, France.,Paris Descartes University, Paris, France.,St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, the Rockefeller University, New York, USA
| | - Rubén Martínez-Barricarte
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, the Rockefeller University, New York, USA
| | - Rebeca Pérez de Diego
- Laboratory of Immunogenetics of Human Diseases IdiPAZ Institute for Health Research, La Paz University Hospital, Madrid, Spain
| | - Stéphanie Boisson-Dupuis
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Imagine Institute, Necker Hospital for Sick Children, Paris, France.,Paris Descartes University, Paris, France.,St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, the Rockefeller University, New York, USA
| | - Xiao-Fei Kong
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, the Rockefeller University, New York, USA
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Imagine Institute, Necker Hospital for Sick Children, Paris, France.,Paris Descartes University, Paris, France.,St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, the Rockefeller University, New York, USA.,Howard Hughes Medical Institute, New York, USA.,Pediatric Hematology-Immunology Unit, AP-HP, Necker Hospital for Sick Children, Paris, France
| | - Jacinta Bustamante
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Imagine Institute, Necker Hospital for Sick Children, Paris, France.,Paris Descartes University, Paris, France.,St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, the Rockefeller University, New York, USA.,Center for the Study of Primary Immunodeficiencies, AP-HP, Necker Hospital for Sick Children, Paris, France
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207
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Fariña AE, Gorayeb ES, Camelo-García VM, Bonin J, Nagata T, Silva JMF, Bogo A, Rezende JAM, da Silva FN, Kitajima EW. Molecular and biological characterization of a putative new sobemovirus infecting Physalis peruviana. Arch Virol 2019; 164:2805-2810. [PMID: 31451963 DOI: 10.1007/s00705-019-04374-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 07/12/2019] [Indexed: 11/25/2022]
Abstract
Physalis peruviana is a perennial solanaceous plant that has recently been established as a commercial crop in Brazil. This work reports the near-complete genome sequence, particle morphology, and plant host responses to a putative new sobemovirus, named "physalis rugose mosaic virus". The virus, characterized by isometric particles of ca. 30 nm in diameter, causes foliar symptoms of mosaic, malformation and blistering, accompanied by stunting. The near-complete genome sequence comprises 4175 nucleotides and contains five open reading frames that are similar to those of other sobemoviruses. In addition to P. peruviana, the new virus systemically infected Capsicum annuum, Nicotiana tabacum and Solanum lycopersicum by mechanical inoculation. Thus, this virus may cause disease in these crops in the field.
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Affiliation(s)
- Arnaldo Esquivel Fariña
- Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Eduardo Silva Gorayeb
- Departamento de Agronomia, Fitopatologia, Universidade do Estado de Santa Catarina, Lages, SC, Brazil
| | - Viviana Marcela Camelo-García
- Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Jaíne Bonin
- Departamento de Agronomia, Fitopatologia, Universidade do Estado de Santa Catarina, Lages, SC, Brazil
| | - Tatsuya Nagata
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | - Joao Marcos F Silva
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | - Amauri Bogo
- Departamento de Agronomia, Fitopatologia, Universidade do Estado de Santa Catarina, Lages, SC, Brazil
| | - Jorge Alberto Marques Rezende
- Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP, Brazil.
| | - Fabio Nascimento da Silva
- Departamento de Agronomia, Fitopatologia, Universidade do Estado de Santa Catarina, Lages, SC, Brazil.
| | - Elliot W Kitajima
- Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP, Brazil
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208
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Lackie RE, Razzaq AR, Farhan SMK, Qiu LR, Moshitzky G, Beraldo FH, Lopes MH, Maciejewski A, Gros R, Fan J, Choy WY, Greenberg DS, Martins VR, Duennwald ML, Lerch JP, Soreq H, Prado VF, Prado MAM. Modulation of hippocampal neuronal resilience during aging by the Hsp70/Hsp90 co-chaperone STI1. J Neurochem 2019; 153:727-758. [PMID: 31562773 DOI: 10.1111/jnc.14882] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 08/22/2019] [Accepted: 09/25/2019] [Indexed: 12/18/2022]
Abstract
Chaperone networks are dysregulated with aging, but whether compromised Hsp70/Hsp90 chaperone function disturbs neuronal resilience is unknown. Stress-inducible phosphoprotein 1 (STI1; STIP1; HOP) is a co-chaperone that simultaneously interacts with Hsp70 and Hsp90, but whose function in vivo remains poorly understood. We combined in-depth analysis of chaperone genes in human datasets, analysis of a neuronal cell line lacking STI1 and of a mouse line with a hypomorphic Stip1 allele to investigate the requirement for STI1 in aging. Our experiments revealed that dysfunctional STI1 activity compromised Hsp70/Hsp90 chaperone network and neuronal resilience. The levels of a set of Hsp90 co-chaperones and client proteins were selectively affected by reduced levels of STI1, suggesting that their stability depends on functional Hsp70/Hsp90 machinery. Analysis of human databases revealed a subset of co-chaperones, including STI1, whose loss of function is incompatible with life in mammals, albeit they are not essential in yeast. Importantly, mice expressing a hypomorphic STI1 allele presented spontaneous age-dependent hippocampal neurodegeneration and reduced hippocampal volume, with consequent spatial memory deficit. We suggest that impaired STI1 function compromises Hsp70/Hsp90 chaperone activity in mammals and can by itself cause age-dependent hippocampal neurodegeneration in mice. Cover Image for this issue: doi: 10.1111/jnc.14749.
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Affiliation(s)
- Rachel E Lackie
- Robarts Research Institute, University of Western Ontario, London, Ontario, Canada.,Program in Neuroscience, University of Western Ontario, London, Ontario, Canada
| | - Abdul R Razzaq
- Robarts Research Institute, University of Western Ontario, London, Ontario, Canada.,Program in Neuroscience, University of Western Ontario, London, Ontario, Canada
| | - Sali M K Farhan
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, and The Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Boston, Massachusetts, USA
| | - Lily R Qiu
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Gilli Moshitzky
- Department of Biological Chemistry, The Edmond and Lily Safra Center for Brain Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Flavio H Beraldo
- Robarts Research Institute, University of Western Ontario, London, Ontario, Canada.,Department of Physiology and Pharmacology, University of Western Ontario, London, Ontario, Canada
| | - Marilene H Lopes
- Robarts Research Institute, University of Western Ontario, London, Ontario, Canada.,Laboratory of Neurobiology and Stem cells, Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Andrzej Maciejewski
- Department of Biochemistry, University of Western Ontario, London, Ontario, Canada
| | - Robert Gros
- Robarts Research Institute, University of Western Ontario, London, Ontario, Canada.,Department of Physiology and Pharmacology, University of Western Ontario, London, Ontario, Canada.,Department of Medicine, University of Western Ontario, London, Ontario, Canada
| | - Jue Fan
- Robarts Research Institute, University of Western Ontario, London, Ontario, Canada
| | - Wing-Yiu Choy
- Department of Biochemistry, University of Western Ontario, London, Ontario, Canada
| | - David S Greenberg
- Department of Biological Chemistry, The Edmond and Lily Safra Center for Brain Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Vilma R Martins
- International Research Center, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Martin L Duennwald
- Department of Anatomy & Cell Biology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada.,Department of Pathology and Laboratory Medicine, University of Western Ontario, London, Ontario, Canada
| | - Jason P Lerch
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Hermona Soreq
- Department of Biological Chemistry, The Edmond and Lily Safra Center for Brain Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Vania F Prado
- Robarts Research Institute, University of Western Ontario, London, Ontario, Canada.,Program in Neuroscience, University of Western Ontario, London, Ontario, Canada.,Department of Physiology and Pharmacology, University of Western Ontario, London, Ontario, Canada.,Department of Anatomy & Cell Biology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Marco A M Prado
- Robarts Research Institute, University of Western Ontario, London, Ontario, Canada.,Program in Neuroscience, University of Western Ontario, London, Ontario, Canada.,Department of Physiology and Pharmacology, University of Western Ontario, London, Ontario, Canada.,Department of Anatomy & Cell Biology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
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209
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Aliouat A, Hatin I, Bertin P, François P, Stierlé V, Namy O, Salhi S, Jean-Jean O. Divergent effects of translation termination factor eRF3A and nonsense-mediated mRNA decay factor UPF1 on the expression of uORF carrying mRNAs and ribosome protein genes. RNA Biol 2019; 17:227-239. [PMID: 31619139 PMCID: PMC6973328 DOI: 10.1080/15476286.2019.1674595] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In addition to its role in translation termination, eRF3A has been implicated in the nonsense-mediated mRNA decay (NMD) pathway through its interaction with UPF1. NMD is a RNA quality control mechanism, which detects and degrades aberrant mRNAs as well as some normal transcripts including those that harbour upstream open reading frames in their 5ʹ leader sequence. In this study, we used RNA-sequencing and ribosome profiling to perform a genome wide analysis of the effect of either eRF3A or UPF1 depletion in human cells. Our bioinformatics analyses allow to delineate the features of the transcripts controlled by eRF3A and UPF1 and to compare the effect of each of these factors on gene expression. We find that eRF3A and UPF1 have very different impacts on the human transcriptome, less than 250 transcripts being targeted by both factors. We show that eRF3A depletion globally derepresses the expression of mRNAs containing translated uORFs while UPF1 knockdown derepresses only the mRNAs harbouring uORFs with an AUG codon in an optimal context for translation initiation. Finally, we also find that eRF3A and UPF1 have opposite effects on ribosome protein gene expression. Together, our results provide important elements for understanding the impact of translation termination and NMD on the human transcriptome and reveal novel determinants of ribosome biogenesis regulation.
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Affiliation(s)
- Affaf Aliouat
- Sorbonne Université, CNRS, Biological Adaptation and Aging, B2A, 75005 Paris, France
| | - Isabelle Hatin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, Gif sur Yvette cedex, France
| | - Pierre Bertin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, Gif sur Yvette cedex, France
| | - Pauline François
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, Gif sur Yvette cedex, France
| | - Vérène Stierlé
- Sorbonne Université, CNRS, Biological Adaptation and Aging, B2A, 75005 Paris, France
| | - Olivier Namy
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, Gif sur Yvette cedex, France
| | - Samia Salhi
- Sorbonne Université, CNRS, Biological Adaptation and Aging, B2A, 75005 Paris, France
| | - Olivier Jean-Jean
- Sorbonne Université, CNRS, Biological Adaptation and Aging, B2A, 75005 Paris, France
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210
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Kawaguchi D, Shimizu S, Abe N, Hashiya F, Tomoike F, Kimura Y, Abe H. Translational control by secondary-structure formation in mRNA in a eukaryotic system. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2019; 39:195-203. [PMID: 31566082 DOI: 10.1080/15257770.2019.1671593] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Eukaryotic mRNA has a cap structure at the 5' end and a poly(A) tail at the 3' end. The cap and poly(A) tail form a complex with multiple translation factors, and mRNA forms a circularized structure called a closed-loop model. This circularized structure reportedly not only stabilizes mRNA but also promotes ribosome recycling during translation, which improves translation efficiency. We designed an artificial mRNA that forms a circularized structure without a cap structure and poly(A) tail and found that its translational efficiency was improved compared with that of a sequence without the circularized structure in a eukaryotic translation system.
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Affiliation(s)
| | - Saaya Shimizu
- Chemistry Department, Nagoya University, Nagoya, Japan
| | - Naoko Abe
- Research Center for Materials Science, Nagoya University, Nagoya, Japan
| | - Fumitaka Hashiya
- Research Center for Materials Science, Nagoya University, Nagoya, Japan
| | - Fumiaki Tomoike
- Research Center for Materials Science, Nagoya University, Nagoya, Japan
| | | | - Hiroshi Abe
- Chemistry Department, Nagoya University, Nagoya, Japan.,Research Center for Materials Science, Nagoya University, Nagoya, Japan.,CREST, Japan Science and Technology Agency, Tokyo, Japan
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211
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Tahmasebi S, Sonenberg N, Hershey JWB, Mathews MB. Protein Synthesis and Translational Control: A Historical Perspective. Cold Spring Harb Perspect Biol 2019; 11:cshperspect.a035584. [PMID: 30082466 DOI: 10.1101/cshperspect.a035584] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein synthesis and its regulation are central to all known forms of life and impinge on biological arenas as varied as agriculture, biotechnology, and medicine. Otherwise known as translation and translational control, these processes have been investigated with increasing intensity since the middle of the 20th century, and in increasing depth with advances in molecular and cell biology. We review the origins of the field, focusing on the underlying concepts and early studies of the cellular machinery and mechanisms involved. We highlight key discoveries and events on a timeline, consider areas where current research has engendered new ideas, and conclude with some speculation on future directions for the field.
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Affiliation(s)
- Soroush Tahmasebi
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montreal, QC H3A 1A3, Canada
| | - Nahum Sonenberg
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montreal, QC H3A 1A3, Canada
| | - John W B Hershey
- Department of Biochemistry and Molecular Medicine, University of California, School of Medicine, Davis, California 95616
| | - Michael B Mathews
- Department of Medicine, Rutgers New Jersey Medical School, Newark, New Jersey 07103
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212
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Weisser M, Ban N. Extensions, Extra Factors, and Extreme Complexity: Ribosomal Structures Provide Insights into Eukaryotic Translation. Cold Spring Harb Perspect Biol 2019; 11:11/9/a032367. [PMID: 31481454 DOI: 10.1101/cshperspect.a032367] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Although the basic aspects of protein synthesis are preserved in all kingdoms of life, there are many important structural and functional differences between bacterial and the more complex eukaryotic ribosomes. High-resolution cryo-electron microscopy (cryo-EM) and X-ray crystallography structures of eukaryotic ribosomes have revealed the complex architectures of eukaryotic ribosomes and species-specific variations in protein and ribosomal RNA (rRNA) extensions. They also enabled structural studies of a range of eukaryotic ribosomal complexes involved in translation initiation, elongation, and termination, revealing unique mechanistic features of the eukaryotic translation process, especially with respect to the identification and recognition of translation start and stop codons on messenger RNAs (mRNAs). Most recently, structural biology has provided insights into the eukaryotic ribosomal biogenesis pathway by visualizing several of its complex intermediates. This review highlights the past decade's structural work on eukaryotic ribosomes and its implications on our understanding of eukaryotic translation.
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Affiliation(s)
- Melanie Weisser
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Nenad Ban
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
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213
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Skittrall JP, Ingemarsdotter CK, Gog JR, Lever AML. A scale-free analysis of the HIV-1 genome demonstrates multiple conserved regions of structural and functional importance. PLoS Comput Biol 2019; 15:e1007345. [PMID: 31545786 PMCID: PMC6791557 DOI: 10.1371/journal.pcbi.1007345] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 10/14/2019] [Accepted: 08/19/2019] [Indexed: 12/22/2022] Open
Abstract
HIV-1 replicates via a low-fidelity polymerase with a high mutation rate; strong conservation of individual nucleotides is highly indicative of the presence of critical structural or functional properties. Identifying such conservation can reveal novel insights into viral behaviour. We analysed 3651 publicly available sequences for the presence of nucleic acid conservation beyond that required by amino acid constraints, using a novel scale-free method that identifies regions of outlying score together with a codon scoring algorithm. Sequences with outlying score were further analysed using an algorithm for producing local RNA folds whilst accounting for alignment properties. 11 different conserved regions were identified, some corresponding to well-known cis-acting functions of the HIV-1 genome but also others whose conservation has not previously been noted. We identify rational causes for many of these, including cis functions, possible additional reading frame usage, a plausible mechanism by which the central polypurine tract primes second-strand DNA synthesis and a conformational stabilising function of a region at the 5' end of env.
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Affiliation(s)
- Jordan P. Skittrall
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Carin K. Ingemarsdotter
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Julia R. Gog
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Centre for Mathematical Sciences, Cambridge, United Kingdom
| | - Andrew M. L. Lever
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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214
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Identification and characterization of the 285L and K145R proteins of African swine fever virus. J Gen Virol 2019; 100:1303-1314. [DOI: 10.1099/jgv.0.001306] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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215
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Ear J, Dunkel Y, Mittal Y, Lim BBC, Liu L, Holda MK, Nitsche U, Barbazán J, Goel A, Janssen KP, Aznar N, Ghosh P. Two Isoforms of the Guanine Nucleotide Exchange Factor, Daple/CCDC88C Cooperate as Tumor Suppressors. Sci Rep 2019; 9:12124. [PMID: 31431650 PMCID: PMC6702192 DOI: 10.1038/s41598-019-48420-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 08/01/2019] [Indexed: 01/27/2023] Open
Abstract
Previously, Aznar et al., showed that Daple/CCDC88C enables Wnt receptors to transactivate trimeric G-proteins during non-canonical Wnt signaling via a novel G-protein binding and activating (GBA) motif. By doing so, Daple serves two opposing roles; earlier during oncogenesis it suppresses neoplastic transformation and tumor growth, but later it triggers epithelial-to-mesenchymal-transition (EMT). We have identified and characterized two isoforms of the human Daple gene. While both isoforms cooperatively suppress tumor growth via their GBA motif, only the full-length transcript triggers EMT and invasion. Both isoforms are suppressed during colon cancer progression, and their reduced expression carries additive prognostic significance. These findings provide insights into the opposing roles of Daple during cancer progression and define the G-protein regulatory GBA motif as one of the minimal modules essential for Daple’s role as a tumor suppressor.
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Affiliation(s)
- Jason Ear
- Department of Medicine, University of California, San Diego, La Jolla, California, USA.,Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA
| | - Ying Dunkel
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Yash Mittal
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Blaze B C Lim
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Lawrence Liu
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Magda K Holda
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Ulrich Nitsche
- Department of Surgery, Klinikumrechts der Isar, TechnischeUniversitätMünchen, Munich, Germany
| | - Jorge Barbazán
- Translational Medical Oncology Laboratory, Health Research Institute of Santiago (IDIS), SERGAS., Santiago de Compostela, Spain
| | - Ajay Goel
- Division of Gastroenterology, Department of Internal Medicine and Charles A. Sammons Cancer Center and Baylor Research Institute, Baylor University Medical Center, Dallas, Texas, USA
| | - Klaus-Peter Janssen
- Department of Surgery, Klinikumrechts der Isar, TechnischeUniversitätMünchen, Munich, Germany
| | - Nicolas Aznar
- Department of Medicine, University of California, San Diego, La Jolla, California, USA. .,Cancer Research Center of Lyon, Centre Léon Bérard, Lyon, France.
| | - Pradipta Ghosh
- Department of Medicine, University of California, San Diego, La Jolla, California, USA. .,Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA. .,Moores Cancer Center, University of California, San Diego, La Jolla, California, USA.
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216
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Fesenko I, Kirov I, Kniazev A, Khazigaleeva R, Lazarev V, Kharlampieva D, Grafskaia E, Zgoda V, Butenko I, Arapidi G, Mamaeva A, Ivanov V, Govorun V. Distinct types of short open reading frames are translated in plant cells. Genome Res 2019; 29:1464-1477. [PMID: 31387879 PMCID: PMC6724668 DOI: 10.1101/gr.253302.119] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/01/2019] [Indexed: 02/07/2023]
Abstract
Genomes contain millions of short (<100 codons) open reading frames (sORFs), which are usually dismissed during gene annotation. Nevertheless, peptides encoded by such sORFs can play important biological roles, and their impact on cellular processes has long been underestimated. Here, we analyzed approximately 70,000 transcribed sORFs in the model plant Physcomitrella patens (moss). Several distinct classes of sORFs that differ in terms of their position on transcripts and the level of evolutionary conservation are present in the moss genome. Over 5000 sORFs were conserved in at least one of 10 plant species examined. Mass spectrometry analysis of proteomic and peptidomic data sets suggested that tens of sORFs located on distinct parts of mRNAs and long noncoding RNAs (lncRNAs) are translated, including conserved sORFs. Translational analysis of the sORFs and main ORFs at a single locus suggested the existence of genes that code for multiple proteins and peptides with tissue-specific expression. Functional analysis of four lncRNA-encoded peptides showed that sORFs-encoded peptides are involved in regulation of growth and differentiation in moss. Knocking out lncRNA-encoded peptides resulted in a decrease of moss growth. In contrast, the overexpression of these peptides resulted in a diverse range of phenotypic effects. Our results thus open new avenues for discovering novel, biologically active peptides in the plant kingdom.
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Affiliation(s)
- Igor Fesenko
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russian Federation
| | - Ilya Kirov
- Laboratory of marker-assisted and genomic selection of plants, All-Russian Research Institute of Agricultural Biotechnology, 127550 Moscow, Russian Federation
| | - Andrey Kniazev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russian Federation
| | - Regina Khazigaleeva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russian Federation
| | - Vassili Lazarev
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russian Federation.,Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Moscow Region, Russian Federation
| | - Daria Kharlampieva
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russian Federation
| | - Ekaterina Grafskaia
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russian Federation.,Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Moscow Region, Russian Federation
| | - Viktor Zgoda
- Laboratory of System Biology, Institute of Biomedical Chemistry, 119121 Moscow, Russian Federation
| | - Ivan Butenko
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russian Federation
| | - Georgy Arapidi
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russian Federation.,Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russian Federation
| | - Anna Mamaeva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russian Federation
| | - Vadim Ivanov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russian Federation
| | - Vadim Govorun
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russian Federation
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217
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Wang Y, Wang F, Xu S, Wang R, Chen W, Hou K, Tian C, Wang F, Zhao P, Xia Q. Optimization of a 2A self-cleaving peptide-based multigene expression system for efficient expression of upstream and downstream genes in silkworm. Mol Genet Genomics 2019; 294:849-859. [PMID: 30895377 DOI: 10.1007/s00438-019-01534-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 01/31/2019] [Indexed: 10/27/2022]
Abstract
The multigene expression system is highly attractive to co-express multiple genes or multi-subunit complex-based genes for their functional studies, and in gene therapy and visual tracking of expressed proteins. However, the current multiple gene co-expression strategies usually suffer from severe inefficiency and unbalanced expression of multiple genes. Here, we report on an improved 2A self-cleaving peptide (2A)-based multigene expression system (2A-MGES), by introducing an optimized Kozak region (Ck) and altering the gene arrangement, both of which contributed to the efficient expression of two fluorescent protein genes in silkworm. By co-expressing DsRed and EGFP genes in insect cells and silkworms, the potent Ck was first found to improve the translation efficiency of downstream genes, and the expression of the flanking genes of 2A were improved by altering the gene arrangement in 2A-MGES. Moreover, we showed that combining Ck and an optimized gene arrangement in 2A-MGES could synergistically improve the expression of genes in the cell. Further, these two flanking genes, regulated by modified 2A-MGES, were further co-expressed in the middle silk gland and secreted into the cocoon, and both achieved efficient expression in the transgenic silkworms and their cocoons. These results suggested that the modified Ck-2A-MGES will be a potent tool for multiple gene expression, for studies of their functions, and their applications in insect species.
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Affiliation(s)
- Yuancheng Wang
- Biological Science Research Center, Southwest University, Chongqing, 400715, People's Republic of China
- Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing, 400715, People's Republic of China
| | - Feng Wang
- Biological Science Research Center, Southwest University, Chongqing, 400715, People's Republic of China
- Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing, 400715, People's Republic of China
- Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing, 400715, People's Republic of China
| | - Sheng Xu
- Biological Science Research Center, Southwest University, Chongqing, 400715, People's Republic of China
- Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing, 400715, People's Republic of China
| | - Riyuan Wang
- Biological Science Research Center, Southwest University, Chongqing, 400715, People's Republic of China
- Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing, 400715, People's Republic of China
| | - Wenjing Chen
- Biological Science Research Center, Southwest University, Chongqing, 400715, People's Republic of China
- Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing, 400715, People's Republic of China
| | - Kai Hou
- Biological Science Research Center, Southwest University, Chongqing, 400715, People's Republic of China
- Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing, 400715, People's Republic of China
| | - Chi Tian
- Biological Science Research Center, Southwest University, Chongqing, 400715, People's Republic of China
- Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing, 400715, People's Republic of China
| | - Fan Wang
- Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing, 400715, People's Republic of China
| | - Ping Zhao
- Biological Science Research Center, Southwest University, Chongqing, 400715, People's Republic of China
- Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing, 400715, People's Republic of China
| | - Qingyou Xia
- Biological Science Research Center, Southwest University, Chongqing, 400715, People's Republic of China.
- Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing, 400715, People's Republic of China.
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218
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Nagayach A, Singh A, Geller AI. Separate Gene Transfers into Pre- and Postsynaptic Neocortical Neurons Connected by mGluR5-Containing Synapses. J Mol Neurosci 2019; 68:549-564. [PMID: 30972540 PMCID: PMC6615967 DOI: 10.1007/s12031-019-01317-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 03/28/2019] [Indexed: 11/25/2022]
Abstract
mGluR5-containing synapses have essential roles in synaptic plasticity, circuit physiology, and learning, and dysfunction at these synapses is implicated in specific neurological disorders. As mGluR5-containing synapses are embedded in large and complex distributed circuits containing many neuron and synapse types, it is challenging to elucidate the roles of these synapses and to develop treatments for the associated disorders. Thus, it would be advantageous to deliver different genes into pre- and postsynaptic neurons connected by a mGluR5-containing synapse. Here, we develop this capability: The first gene transfer, into the presynaptic neurons, uses standard techniques to deliver a vector that expresses a synthetic peptide neurotransmitter. This peptide neurotransmitter has three domains: a dense core vesicle sorting domain, a mGluR5-binding domain composed of a single-chain variable fragment anti-mGluR5, and the His tag. Upon release, this peptide neurotransmitter binds to mGluR5, predominately located on the postsynaptic neurons. Selective gene transfer into these neurons uses antibody-mediated, targeted gene transfer and anti-His tag antibodies, as the synthetic peptide neurotransmitter contains the His tag. For the model system, we studied the connection between neurons in two neocortical areas: postrhinal and perirhinal cortices. Targeted gene transfer was over 80% specific for mGluR5-containing synapses, but untargeted gene transfer was only ~ 15% specific for these synapses. This technology may enable studies on the roles of mGluR5-containing neurons and synapses in circuit physiology and learning and support gene therapy treatments for specific disorders that involve dysfunction at these synapses.
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Affiliation(s)
- Aarti Nagayach
- Department of Ophthalmology, Louisiana State University Health Sciences Center, New Orleans, USA
| | - Anshuman Singh
- Department of Ophthalmology, Louisiana State University Health Sciences Center, New Orleans, USA
| | - Alfred I Geller
- Department of Ophthalmology, Louisiana State University Health Sciences Center, New Orleans, USA.
- Department of Pharmacology, Louisiana State University Health Sciences Center, New Orleans, USA.
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219
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Han F, Li W, Liu X, Zhang D, Liu L, Wang Z. Rac1 GTPase is a critical factor in phagocytosis in the large yellow croaker Larimichthys crocea by interacting with tropomyosin. FISH & SHELLFISH IMMUNOLOGY 2019; 91:148-158. [PMID: 31082520 DOI: 10.1016/j.fsi.2019.04.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 04/03/2019] [Accepted: 04/22/2019] [Indexed: 06/09/2023]
Abstract
The Rho family GTPase Rac1 acts as a molecular switch for signal transduction to regulate various cellular functions. Here, a Rac1 homolog (LcRac1) was identified in large yellow croaker (Larimichthys crocea), one of the most economically important marine fishes. The LcRac1 protein was expressed in Escherichia coli and purified. Subsequently the specific antibody was raised using the purified fusion protein (GST-LcRac1). LcRac1 was ubiquitously expressed in all 12 tissues we examined, with the highest expression in heart and blood and the weakest expression in head-kidney and spleen. Moreover, time course analysis revealed that LcRac1 expression was obviously up-regulated in liver, spleen and head-kidney after immunization with Poly I:C, LPS and Vibrio parahemolyticus. On the other hand, on the basis of protein interaction, it was found that the LcRac1 interacted with Tropomyosin, a crucial protein in the process of phagocytosis. Furthermore, RNAi assays indicated that the phagocytic percentage and phagocytic index were significantly decreased when the LcRac1 gene was silenced by sequence-specific siRNA. Fluorescence microscopy assays revealed FITC-labeled V. parahemolyticus were remarkably decreased after LcRac1 was silenced by sequence-specific siRNA at 24 h. These findings implicate the vital role of LcRac1 in innate immunity in the large yellow croaker.
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Affiliation(s)
- Fang Han
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Yindou Road 43, Xiamen, 361021, China
| | - Wanbo Li
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Yindou Road 43, Xiamen, 361021, China
| | - Xiande Liu
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Yindou Road 43, Xiamen, 361021, China
| | - Dongling Zhang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Yindou Road 43, Xiamen, 361021, China
| | - Lanping Liu
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Yindou Road 43, Xiamen, 361021, China
| | - Zhiyong Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Yindou Road 43, Xiamen, 361021, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China.
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220
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Petersen SD, Zhang J, Lee JS, Jakociunas T, Grav LM, Kildegaard HF, Keasling JD, Jensen MK. Modular 5'-UTR hexamers for context-independent tuning of protein expression in eukaryotes. Nucleic Acids Res 2019; 46:e127. [PMID: 30124898 PMCID: PMC6265478 DOI: 10.1093/nar/gky734] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 08/01/2018] [Indexed: 11/25/2022] Open
Abstract
Functional characterization of regulatory DNA elements in broad genetic contexts is a prerequisite for forward engineering of biological systems. Translation initiation site (TIS) sequences are attractive to use for regulating gene activity and metabolic pathway fluxes because the genetic changes are minimal. However, limited knowledge is available on tuning gene outputs by varying TISs in different genetic and environmental contexts. Here, we created TIS hexamer libraries in baker’s yeast Saccharomyces cerevisiae directly 5′ end of a reporter gene in various promoter contexts and measured gene activity distributions for each library. Next, selected TIS sequences, resulted in almost 10-fold changes in reporter outputs, were experimentally characterized in various environmental and genetic contexts in both yeast and mammalian cells. From our analyses, we observed strong linear correlations (R2 = 0.75–0.98) between all pairwise combinations of TIS order and gene activity. Finally, our analysis enabled the identification of a TIS with almost 50% stronger output than a commonly used TIS for protein expression in mammalian cells, and selected TISs were also used to tune gene activities in yeast at a metabolic branch point in order to prototype fitness and carotenoid production landscapes. Taken together, the characterized TISs support reliable context-independent forward engineering of translation initiation in eukaryotes.
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Affiliation(s)
- Søren D Petersen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Jie Zhang
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Jae S Lee
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Tadas Jakociunas
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Lise M Grav
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Helene F Kildegaard
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Jay D Keasling
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.,Joint BioEnergy Institute, Emeryville, CA 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA.,Department of Bioengineering, University of California, Berkeley, CA 94720, USA.,Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes of Advanced Technologies, Shenzhen 518055, China
| | - Michael K Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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221
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Hernández G, Osnaya VG, Pérez-Martínez X. Conservation and Variability of the AUG Initiation Codon Context in Eukaryotes. Trends Biochem Sci 2019; 44:1009-1021. [PMID: 31353284 DOI: 10.1016/j.tibs.2019.07.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 06/22/2019] [Accepted: 07/02/2019] [Indexed: 01/30/2023]
Abstract
Selection of the translation initiation site (TIS) is a crucial step during translation. In the 1980s Marylin Kozak performed key studies on vertebrate mRNAs to characterize the optimal TIS consensus sequence, the Kozak motif. Within this motif, conservation of nucleotides in crucial positions, namely a purine at -3 and a G at +4 (where the A of the AUG is numbered +1), is essential for TIS recognition. Ever since its characterization the Kozak motif has been regarded as the optimal sequence to initiate translation in all eukaryotes. We revisit here published in silico data on TIS consensus sequences, as well as experimental studies from diverse eukaryotic lineages, and propose that, while the -3A/G position is universally conserved, the remaining variability of the consensus sequences enables their classification as optimal, strong, and moderate TIS sequences.
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Affiliation(s)
- Greco Hernández
- Translation and Cancer Laboratory, Unit of Biomedical Research on Cancer, National Institute of Cancer (Instituto Nacional de Cancerología, INCan), 22 San Fernando Avenue, Tlalpan, 14080 Mexico City, Mexico.
| | - Vincent G Osnaya
- Translation and Cancer Laboratory, Unit of Biomedical Research on Cancer, National Institute of Cancer (Instituto Nacional de Cancerología, INCan), 22 San Fernando Avenue, Tlalpan, 14080 Mexico City, Mexico
| | - Xochitl Pérez-Martínez
- Department of Molecular Genetics, Cell Physiology Institute (Instituto de Fisiología Celular), Universidad Nacional Autónoma de México (UNAM), 04510 Mexico City, Mexico
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222
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McGillivray P, Ault R, Pawashe M, Kitchen R, Balasubramanian S, Gerstein M. A comprehensive catalog of predicted functional upstream open reading frames in humans. Nucleic Acids Res 2019; 46:3326-3338. [PMID: 29562350 PMCID: PMC6283423 DOI: 10.1093/nar/gky188] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 03/14/2018] [Indexed: 01/09/2023] Open
Abstract
Upstream open reading frames (uORFs) latent in mRNA transcripts are thought to modify translation of coding sequences by altering ribosome activity. Not all uORFs are thought to be active in such a process. To estimate the impact of uORFs on the regulation of translation in humans, we first circumscribed the universe of all possible uORFs based on coding gene sequence motifs and identified 1.3 million unique uORFs. To determine which of these are likely to be biologically relevant, we built a simple Bayesian classifier using 89 attributes of uORFs labeled as active in ribosome profiling experiments. This allowed us to extrapolate to a comprehensive catalog of likely functional uORFs. We validated our predictions using in vivo protein levels and ribosome occupancy from 46 individuals. This is a substantially larger catalog of functional uORFs than has previously been reported. Our ranked list of likely active uORFs allows researchers to test their hypotheses regarding the role of uORFs in health and disease. We demonstrate several examples of biological interest through the application of our catalog to somatic mutations in cancer and disease-associated germline variants in humans.
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Affiliation(s)
- Patrick McGillivray
- Molecular Biophysics and Biochemistry Department, Yale University, New Haven, CT 06520, USA
| | - Russell Ault
- Molecular Biophysics and Biochemistry Department, Yale University, New Haven, CT 06520, USA
| | - Mayur Pawashe
- Molecular Biophysics and Biochemistry Department, Yale University, New Haven, CT 06520, USA
| | - Robert Kitchen
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - Suganthi Balasubramanian
- Molecular Biophysics and Biochemistry Department, Yale University, New Haven, CT 06520, USA.,Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - Mark Gerstein
- Molecular Biophysics and Biochemistry Department, Yale University, New Haven, CT 06520, USA.,Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.,Department of Computer Science, Yale University, New Haven, CT 06520 USA
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223
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Diaz de Arce AJ, Noderer WL, Wang CL. Complete motif analysis of sequence requirements for translation initiation at non-AUG start codons. Nucleic Acids Res 2019; 46:985-994. [PMID: 29228265 PMCID: PMC5778536 DOI: 10.1093/nar/gkx1114] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 12/06/2017] [Indexed: 01/23/2023] Open
Abstract
The initiation of mRNA translation from start codons other than AUG was previously believed to be rare and of relatively low impact. More recently, evidence has suggested that as much as half of all translation initiation utilizes non-AUG start codons, codons that deviate from AUG by a single base. Furthermore, non-AUG start codons have been shown to be involved in regulation of expression and disease etiology. Yet the ability to gauge expression based on the sequence of a translation initiation site (start codon and its flanking bases) has been limited. Here we have performed a comprehensive analysis of translation initiation sites that utilize non-AUG start codons. By combining genetic-reporter, cell-sorting, and high-throughput sequencing technologies, we have analyzed the expression associated with all possible variants of the -4 to +4 positions of non-AUG translation initiation site motifs. This complete motif analysis revealed that 1) with the right sequence context, certain non-AUG start codons can generate expression comparable to that of AUG start codons, 2) sequence context affects each non-AUG start codon differently, and 3) initiation at non-AUG start codons is highly sensitive to changes in the flanking sequences. Complete motif analysis has the potential to be a key tool for experimental and diagnostic genomics.
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Affiliation(s)
| | - William L Noderer
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Clifford L Wang
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
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224
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Ng XW, Sampath K, Wohland T. Fluorescence Correlation and Cross-Correlation Spectroscopy in Zebrafish. Methods Mol Biol 2019; 1863:67-105. [PMID: 30324593 DOI: 10.1007/978-1-4939-8772-6_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
There has been increasing interest in biophysical studies on live organisms to gain better insights into physiologically relevant biological events at the molecular level. Zebrafish (Danio rerio) is a viable vertebrate model to study such events due to its genetic and evolutionary similarities to humans, amenability to less invasive fluorescence techniques owing to its transparency and well-characterized genetic manipulation techniques. Fluorescence techniques used to probe biomolecular dynamics and interactions of molecules in live zebrafish embryos are therefore highly sought-after to bridge molecular and developmental events. Fluorescence correlation and cross-correlation spectroscopy (FCS and FCCS) are two robust techniques that provide molecular level information on dynamics and interactions respectively. Here, we detail the steps for applying confocal FCS and FCCS, in particular single-wavelength FCCS (SW-FCCS), in live zebrafish embryos, beginning with sample preparation, instrumentation, calibration, and measurements on the FCS/FCCS instrument and ending with data analysis.
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Affiliation(s)
- Xue Wen Ng
- Department of Chemistry and Centre for Bioimaging Sciences, National University of Singapore, Singapore, Singapore
| | - Karuna Sampath
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Thorsten Wohland
- Department of Chemistry and Centre for Bioimaging Sciences, National University of Singapore, Singapore, Singapore. .,Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
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225
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Malhotra D, Loganathan SK, Chiu AM, Lukowski CM, Casey JR. Human Corneal Expression of SLC4A11, a Gene Mutated in Endothelial Corneal Dystrophies. Sci Rep 2019; 9:9681. [PMID: 31273259 PMCID: PMC6609610 DOI: 10.1038/s41598-019-46094-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 06/21/2019] [Indexed: 12/21/2022] Open
Abstract
Two blinding corneal dystrophies, pediatric-onset congenital hereditary endothelial dystrophy (CHED) and some cases of late-onset Fuchs endothelial corneal dystrophy (FECD), are caused by SLC4A11 mutations. Three N-terminal SLC4A11 variants: v1, v2 and v3 are expressed in humans. We set out to determine which of these transcripts and what translated products, are present in corneal endothelium as these would be most relevant for CHED and FECD studies. Reverse transcription PCR (RT-PCR) and quantitative RT-PCR revealed only v2 and v3 mRNA in human cornea, but v2 was most abundant. Immunoblots probed with variant-specific antibodies revealed that v2 protein is about four times more abundant than v3 in human corneal endothelium. Bioinformatics and protein analysis using variant-specific antibodies revealed that second methionine in the open reading frame (M36) acts as translation initiation site on SLC4A11 v2 in human cornea. The v2 variants starting at M1 (v2-M1) and M36 (v2-M36) were indistinguishable in their cell surface trafficking and transport function (water flux). Structural homology models of v2-M36 and v3 suggest structural differences but their significance remains unclear. A combination of bioinformatics, RNA quantification and isoform-specific antibodies allows us to conclude that SLC4A11 variant 2 with start site M36 is predominant in corneal endothelium.
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Affiliation(s)
- Darpan Malhotra
- Department of Biochemistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
| | - Sampath K Loganathan
- Department of Biochemistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada.,Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, M5G 1X5, Canada
| | - Anthony M Chiu
- Department of Biochemistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
| | - Chris M Lukowski
- Department of Biochemistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
| | - Joseph R Casey
- Department of Biochemistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada.
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226
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Ferdinandusse S, Te Brinke H, Ruiter JPN, Haasjes J, Oostheim W, van Lenthe H, IJlst L, Ebberink MS, Wanders RJA, Vaz FM, Waterham HR. A mutation creating an upstream translation initiation codon in SLC22A5 5'UTR is a frequent cause of primary carnitine deficiency. Hum Mutat 2019; 40:1899-1904. [PMID: 31187905 PMCID: PMC6790604 DOI: 10.1002/humu.23839] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 05/28/2019] [Accepted: 06/05/2019] [Indexed: 12/31/2022]
Abstract
Primary carnitine deficiency is caused by a defect in the active cellular uptake of carnitine by Na+ -dependent organic cation transporter novel 2 (OCTN2). Genetic diagnostic yield for this metabolic disorder has been relatively low, suggesting that disease-causing variants are missed. We Sanger sequenced the 5' untranslated region (UTR) of SLC22A5 in individuals with possible primary carnitine deficiency in whom no or only one mutant allele had been found. We identified a novel 5'-UTR c.-149G>A variant which we characterized by expression studies with reporter constructs in HeLa cells and by carnitine-transport measurements in fibroblasts using a newly developed sensitive assay based on tandem mass spectrometry. This variant, which we identified in 57 of 236 individuals of our cohort, introduces a functional upstream out-of-frame translation initiation codon. We show that the codon suppresses translation from the wild-type ATG of SLC22A5, resulting in reduced OCTN2 protein levels and concomitantly lower transport activity. With an allele frequency of 24.2% the c.-149G>A variant is the most frequent cause of primary carnitine deficiency in our cohort and may explain other reported cases with an incomplete genetic diagnosis. Individuals carrying this variant should be clinically re-evaluated and monitored to determine if this variant has clinical consequences.
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Affiliation(s)
- Sacha Ferdinandusse
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology and Metabolism Research Institute, University of Amsterdam, Amsterdam, The Netherlands.,United for Metabolic Diseases, The Netherlands
| | - Heleen Te Brinke
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology and Metabolism Research Institute, University of Amsterdam, Amsterdam, The Netherlands
| | - Jos P N Ruiter
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology and Metabolism Research Institute, University of Amsterdam, Amsterdam, The Netherlands
| | - Janet Haasjes
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology and Metabolism Research Institute, University of Amsterdam, Amsterdam, The Netherlands
| | - Wendy Oostheim
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology and Metabolism Research Institute, University of Amsterdam, Amsterdam, The Netherlands
| | - Henk van Lenthe
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology and Metabolism Research Institute, University of Amsterdam, Amsterdam, The Netherlands
| | - Lodewijk IJlst
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology and Metabolism Research Institute, University of Amsterdam, Amsterdam, The Netherlands
| | - Merel S Ebberink
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology and Metabolism Research Institute, University of Amsterdam, Amsterdam, The Netherlands.,United for Metabolic Diseases, The Netherlands
| | - Ronald J A Wanders
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology and Metabolism Research Institute, University of Amsterdam, Amsterdam, The Netherlands.,United for Metabolic Diseases, The Netherlands
| | - Frédéric M Vaz
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology and Metabolism Research Institute, University of Amsterdam, Amsterdam, The Netherlands.,United for Metabolic Diseases, The Netherlands
| | - Hans R Waterham
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology and Metabolism Research Institute, University of Amsterdam, Amsterdam, The Netherlands.,United for Metabolic Diseases, The Netherlands
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227
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Hu X, Chen F, Zhu L, Yu L, Zhu M, Liang Z, Zhang X, Xue R, Cao G, Gong C. Bombyx mori cypovirus encoded small peptide inhibits viral multiplication. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2019; 96:51-57. [PMID: 30822453 DOI: 10.1016/j.dci.2019.02.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 02/23/2019] [Accepted: 02/24/2019] [Indexed: 06/09/2023]
Abstract
Bombyx mori cypovirus (BmCPV) is one of the most infectious pathogen in sericulture and a member of the family Reoviridae. It specifically infects the midgut of silkworm. The BmCPV genome consists of 10 dsRNAs segments (S1-S10), which have generally been assumed to be monocistronic. In this study, a small open reading frame encoding the peptide S5-sORF, containing 27 amino acid residues, was predicted in a region of the negative (-) strand of BmCPV segment S5. An immunofluorescence assay detected S5-sORF in the cytoplasm and nuclei of BmCPV-infected cells, and it was also detected in the virion with western blotting, suggesting that S5-sORF may be assembled into the BmCPV virion. Viral gene expression was inhibited by overexpressed S5-sORF, and viral multiplication was dose-dependently suppressed by the S5-sORF peptide. A viable recombinant virus, BmCPV-S5-sORFmut, in which the start codon (ATG) of S5-sORF was mutated to a stop codon (TGA), was generated with reverse genetics. The proliferation of BmCPV was increased by the abolition of S5-sORF expression. Furthermore, the RNA transcript of S5-sORF and small peptide of S5-sORF were involved in BmCPV replication. The expression of genes related to the innate immune pathways and apoptosis in the silkworm were not significantly affected by S5-sORF overexpression. Our results suggest that a viral nucleotide sequence is utilized by the host to generate an antiviral peptide, which may be a novel strategy protecting the host from viral infection.
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Affiliation(s)
- Xiaolong Hu
- School of Biology & Basic Medical Science, Soochow University, Suzhou, 215123, China; National Engineering Laboratory for Modern Silk, Soochow University, Suzhou, China
| | - Fei Chen
- School of Biology & Basic Medical Science, Soochow University, Suzhou, 215123, China; Agricultural Biotechnology Research Institute, Agricultural Biotechnology and Ecological Research Institute, Soochow University, Suzhou, 215123, China
| | - Liyuan Zhu
- School of Biology & Basic Medical Science, Soochow University, Suzhou, 215123, China; Agricultural Biotechnology Research Institute, Agricultural Biotechnology and Ecological Research Institute, Soochow University, Suzhou, 215123, China
| | - Lei Yu
- School of Biology & Basic Medical Science, Soochow University, Suzhou, 215123, China; Agricultural Biotechnology Research Institute, Agricultural Biotechnology and Ecological Research Institute, Soochow University, Suzhou, 215123, China
| | - Min Zhu
- School of Biology & Basic Medical Science, Soochow University, Suzhou, 215123, China; Agricultural Biotechnology Research Institute, Agricultural Biotechnology and Ecological Research Institute, Soochow University, Suzhou, 215123, China
| | - Zi Liang
- School of Biology & Basic Medical Science, Soochow University, Suzhou, 215123, China; Agricultural Biotechnology Research Institute, Agricultural Biotechnology and Ecological Research Institute, Soochow University, Suzhou, 215123, China
| | - Xing Zhang
- School of Biology & Basic Medical Science, Soochow University, Suzhou, 215123, China
| | - Renyu Xue
- School of Biology & Basic Medical Science, Soochow University, Suzhou, 215123, China; National Engineering Laboratory for Modern Silk, Soochow University, Suzhou, China
| | - Guangli Cao
- School of Biology & Basic Medical Science, Soochow University, Suzhou, 215123, China; National Engineering Laboratory for Modern Silk, Soochow University, Suzhou, China.
| | - Chengliang Gong
- School of Biology & Basic Medical Science, Soochow University, Suzhou, 215123, China; National Engineering Laboratory for Modern Silk, Soochow University, Suzhou, China; Agricultural Biotechnology Research Institute, Agricultural Biotechnology and Ecological Research Institute, Soochow University, Suzhou, 215123, China.
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228
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Sakai K, Yamamoto Y, Ikeuchi T. Vertebrates originally possess four functional subtypes of G protein-coupled melatonin receptor. Sci Rep 2019; 9:9465. [PMID: 31263128 PMCID: PMC6602942 DOI: 10.1038/s41598-019-45925-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 06/18/2019] [Indexed: 01/28/2023] Open
Abstract
Melatonin receptors (MTNRs) belonging to the G protein-coupled receptor family are considered to consist of three subtypes in vertebrates: MTNR1a, MTNR1b and MTNR1c. Additionally, MTNR1a-like genes have been identified in teleostean species as a fish-specific subtype of MTNR1a. However, similar molecules to this MTNR1a-like gene can be found in some reptiles upon searching the DNA database. We hypothesized that a vertebrate can essentially have four functional subtypes of MTNR as ohnologs. Thus, in the present study we examined the molecular phylogeny, expression patterns and pharmacological profile(s) using the teleost medaka (Oryzias latipes). The four conserved subtypes of MTNR (MTNR1a, MTNR1b, MTNR1c and MTNR1a-like) in vertebrates were classified based on synteny and phylogenetic analysis. The fourth MTNR, termed MTNR1a-like, could be classified as MTNR1d. It was observed by using RT-qPCR that expression patterns differed amongst these subtypes. Moreover, mtnr1a, mtnr1c and mtnr1a-like/mtnr1d expression was elevated during short days compared to long days in diencephalons. All the subtypes were activated by melatonin and transduced signals into the Gi pathway, to perform a cAMP-responsive reporter gene assay. It was shown that MTNR originally consisted of four subtypes: MTNR1a, MTNR1b, MTNR1c and MTNR1d. These subtypes were functional, at least in fish, although some organisms, including mammals, have lost one or two subtypes.
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Affiliation(s)
- Kotowa Sakai
- Graduate School of Biosciences, Nagahama Institute of Bio-Science and Technology, 1266, Tamura, Nagahama, Shiga, 526-0829, Japan
| | - Yuya Yamamoto
- Graduate School of Biosciences, Nagahama Institute of Bio-Science and Technology, 1266, Tamura, Nagahama, Shiga, 526-0829, Japan
| | - Toshitaka Ikeuchi
- Graduate School of Biosciences, Nagahama Institute of Bio-Science and Technology, 1266, Tamura, Nagahama, Shiga, 526-0829, Japan.
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229
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Sample PJ, Wang B, Reid DW, Presnyak V, McFadyen IJ, Morris DR, Seelig G. Human 5' UTR design and variant effect prediction from a massively parallel translation assay. Nat Biotechnol 2019; 37:803-809. [PMID: 31267113 PMCID: PMC7100133 DOI: 10.1038/s41587-019-0164-5] [Citation(s) in RCA: 177] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Accepted: 05/21/2019] [Indexed: 12/20/2022]
Abstract
The ability to predict the impact of cis-regulatory sequences on gene expression would facilitate discovery in fundamental and applied biology. Here we combine polysome profiling of a library of 280,000 randomized 5' untranslated regions (UTRs) with deep learning to build a predictive model that relates human 5' UTR sequence to translation. Together with a genetic algorithm, we use the model to engineer new 5' UTRs that accurately direct specified levels of ribosome loading, providing the ability to tune sequences for optimal protein expression. We show that the same approach can be extended to chemically modified RNA, an important feature for applications in mRNA therapeutics and synthetic biology. We test 35,212 truncated human 5' UTRs and 3,577 naturally occurring variants and show that the model predicts ribosome loading of these sequences. Finally, we provide evidence of 45 single-nucleotide variants (SNVs) associated with human diseases that substantially change ribosome loading and thus may represent a molecular basis for disease.
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Affiliation(s)
- Paul J Sample
- Department of Electrical Engineering, University of Washington, Seattle, WA, USA
| | - Ban Wang
- Department of Electrical Engineering, University of Washington, Seattle, WA, USA
| | | | | | | | - David R Morris
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Georg Seelig
- Department of Electrical Engineering, University of Washington, Seattle, WA, USA.
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA.
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230
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Chapman R, Rybicki EP. Use of a Novel Enhanced DNA Vaccine Vector for Preclinical Virus Vaccine Investigation. Vaccines (Basel) 2019; 7:vaccines7020050. [PMID: 31200559 PMCID: PMC6632145 DOI: 10.3390/vaccines7020050] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/07/2019] [Accepted: 06/11/2019] [Indexed: 12/14/2022] Open
Abstract
DNA vaccines are stable, safe, and cost effective to produce and relatively quick and easy to manufacture. However, to date, DNA vaccines have shown relatively poor immunogenicity in humans despite promising preclinical results. Consequently, a number of different approaches have been investigated to improve the immunogenicity of DNA vaccines. These include the use of improved delivery methods, adjuvants, stronger promoters and enhancer elements to increase antigen expression, and codon optimization of the gene of interest. This review describes the creation and use of a DNA vaccine vector containing a porcine circovirus (PCV-1) enhancer element that significantly increases recombinant antigen expression and immunogenicity and allows for dose sparing. A 172 bp region containing the PCV-1 capsid protein promoter (Pcap) and a smaller element (PC; 70 bp) within this were found to be equally effective. DNA vaccines containing the Pcap region expressing various HIV-1 antigens were found to be highly immunogenic in mice, rabbits, and macaques at 4-10-fold lower doses than normally used and to be highly effective in heterologous prime-boost regimens. By lowering the amount of DNA used for immunization, safety concerns over injecting large amounts of DNA into humans can be overcome.
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Affiliation(s)
- Rosamund Chapman
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town 7925, South Africa.
| | - Edward P Rybicki
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town 7925, South Africa.
- Biopharming Research Unit, Department of Molecular & Cell Biology, University of Cape Town, PB X3 Rondebosch, Cape Town 7701, South Africa.
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231
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Boersma S, Khuperkar D, Verhagen BMP, Sonneveld S, Grimm JB, Lavis LD, Tanenbaum ME. Multi-Color Single-Molecule Imaging Uncovers Extensive Heterogeneity in mRNA Decoding. Cell 2019; 178:458-472.e19. [PMID: 31178119 PMCID: PMC6630898 DOI: 10.1016/j.cell.2019.05.001] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 03/05/2019] [Accepted: 04/30/2019] [Indexed: 12/17/2022]
Abstract
mRNA translation is a key step in decoding genetic information. Genetic decoding is surprisingly heterogeneous because multiple distinct polypeptides can be synthesized from a single mRNA sequence. To study translational heterogeneity, we developed the MoonTag, a fluorescence labeling system to visualize translation of single mRNAs. When combined with the orthogonal SunTag system, the MoonTag enables dual readouts of translation, greatly expanding the possibilities to interrogate complex translational heterogeneity. By placing MoonTag and SunTag sequences in different translation reading frames, each driven by distinct translation start sites, start site selection of individual ribosomes can be visualized in real time. We find that start site selection is largely stochastic but that the probability of using a particular start site differs among mRNA molecules and can be dynamically regulated over time. This study provides key insights into translation start site selection heterogeneity and provides a powerful toolbox to visualize complex translation dynamics. Development of MoonTag, a fluorescence labeling system to visualize translation Combining MoonTag and SunTag enables visualization of translational heterogeneity mRNAs from a single gene vary in initiation frequency at different start sites Ribosomes take many different “paths” along the 5′ UTR of a single mRNA molecule
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Affiliation(s)
- Sanne Boersma
- Oncode Institute, Hubrecht Institute - KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Deepak Khuperkar
- Oncode Institute, Hubrecht Institute - KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Bram M P Verhagen
- Oncode Institute, Hubrecht Institute - KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Stijn Sonneveld
- Oncode Institute, Hubrecht Institute - KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jonathan B Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Marvin E Tanenbaum
- Oncode Institute, Hubrecht Institute - KNAW and University Medical Center Utrecht, Utrecht, the Netherlands.
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232
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Brunner E, Yagi R, Debrunner M, Beck-Schneider D, Burger A, Escher E, Mosimann C, Hausmann G, Basler K. CRISPR-induced double-strand breaks trigger recombination between homologous chromosome arms. Life Sci Alliance 2019; 2:e201800267. [PMID: 31196871 PMCID: PMC6587125 DOI: 10.26508/lsa.201800267] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 05/29/2019] [Accepted: 05/29/2019] [Indexed: 12/27/2022] Open
Abstract
CRISPR-Cas9-based genome editing has transformed the life sciences, enabling virtually unlimited genetic manipulation of genomes: The RNA-guided Cas9 endonuclease cuts DNA at a specific target sequence and the resulting double-strand breaks are mended by one of the intrinsic cellular repair pathways. Imprecise double-strand repair will introduce random mutations such as indels or point mutations, whereas precise editing will restore or specifically edit the locus as mandated by an endogenous or exogenously provided template. Recent studies indicate that CRISPR-induced DNA cuts may also result in the exchange of genetic information between homologous chromosome arms. However, conclusive data of such recombination events in higher eukaryotes are lacking. Here, we show that in Drosophila, the detected Cas9-mediated editing events frequently resulted in germline-transmitted exchange of chromosome arms-often without indels. These findings demonstrate the feasibility of using the system for generating recombinants and also highlight an unforeseen risk of using CRISPR-Cas9 for therapeutic intervention.
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Affiliation(s)
- Erich Brunner
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Ryohei Yagi
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zurich, Zurich, Switzerland
| | - Marc Debrunner
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | | | - Alexa Burger
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Eliane Escher
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Christian Mosimann
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - George Hausmann
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Konrad Basler
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
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Daverio MS, Anello M, Alcolea Ersinger V, Alvarez S, Frank E, Vidal-Rioja L, Di Rocco F. Identification of llama KRTAP7-1 and KRTAP8-1 fiber genes and polymorphism screening. Small Rumin Res 2019. [DOI: 10.1016/j.smallrumres.2019.04.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
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234
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Characterization of paralogous uncx transcription factor encoding genes in zebrafish. Gene X 2019; 721S:100011. [PMID: 31193955 PMCID: PMC6543554 DOI: 10.1016/j.gene.2019.100011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 02/12/2019] [Accepted: 02/15/2019] [Indexed: 12/23/2022] Open
Abstract
The paired-type homeodomain transcription factor Uncx is involved in multiple processes of embryogenesis in vertebrates. Reasoning that zebrafish genes uncx4.1 and uncx are orthologs of mouse Uncx, we studied their genomic environment and developmental expression. Evolutionary analyses indicate the zebrafish uncx genes as being paralogs deriving from teleost-specific whole-genome duplication. Whole-mount in situ mRNA hybridization of uncx transcripts in zebrafish embryos reveals novel expression domains, confirms those previously known, and suggests sub-functionalization of paralogs. Using genetic mutants and pharmacological inhibitors, we investigate the role of signaling pathways on the expression of zebrafish uncx genes in developing somites. In identifying putative functional role(s) of zebrafish uncx genes, we hypothesized that they encode transcription factors that coordinate growth and innervation of somitic muscles. The Uncx4.1 and Uncx genes derive from the teleost-specific whole-genome duplication. Uncx genes are expressed during embryogenesis in unique and overlapping domains. Uncx gene expression during somite differentiation is regulated by FGF signaling. Synteny and expression profiles correlate Uncx genes with axon guidance.
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Key Words
- AP, antero-posterior
- Ace, acerebellar
- CAMP, conserved ancestral microsyntenic pairs
- CNE, conserved non-coding elements
- CRM, cis-regulatory module
- CS, Corpuscle of Stannius
- CaP, caudal primary motor neuron axons
- Ce, cerebellum
- Development
- Di, diencephalon
- Elfn1, Extracellular Leucine Rich Repeat And Fibronectin Type III Domain Containing 1
- Ey, eye
- FB, forebrain
- FGF, fibroblast growth factor
- Flh, floating head
- HB, hindbrain
- HM, hybridization mix
- Hy, hypothalamus
- MO, morpholino
- Mical, molecule interacting with CasL
- No, notochord
- OP, olfactory placode
- OT, optic tectum
- PA, pharyngeal arches
- PSM, presomitic mesoderm
- SC, spinal cord
- Shh, sonic hedgehog
- Signaling pathway
- So, somites
- Synteny
- TSGD
- TSGD, teleost-specific genome duplication
- Te, telencephalon
- Th, thalamus
- Uncx
- VLP, ventro-lateral-posterior
- WIHC, whole-mount immunohistochemistry
- WISH, whole-mount in situ hybridization
- YE, yolk extension
- Yo, yolk
- Zebrafish
- cyc, cyclops
- fss, fused-somites
- hpf, hours post fertilization
- ptc, patched
- smu, slow-muscle-omitted
- syu, sonic-you
- yot, you-too
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235
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Nagayach A, Singh A, De Blas AL, Geller AI. Delivery of different genes into pre- and post-synaptic neocortical interneurons connected by GABAergic synapses. PLoS One 2019; 14:e0217094. [PMID: 31125364 PMCID: PMC6534327 DOI: 10.1371/journal.pone.0217094] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 05/03/2019] [Indexed: 12/13/2022] Open
Abstract
Local neocortical circuits play critical roles in information processing, including synaptic plasticity, circuit physiology, and learning, and GABAergic inhibitory interneurons have key roles in these circuits. Moreover, specific neurological disorders, including schizophrenia and autism, are associated with deficits in GABAergic transmission in these circuits. GABAergic synapses represent a small fraction of neocortical synapses, and are embedded in complex local circuits that contain many neuron and synapse types. Thus, it is challenging to study the physiological roles of GABAergic inhibitory interneurons and their synapses, and to develop treatments for the specific disorders caused by dysfunction at these GABAergic synapses. To these ends, we report a novel technology that can deliver different genes into pre- and post-synaptic neocortical interneurons connected by a GABAergic synapse: First, standard gene transfer into the presynaptic neurons delivers a synthetic peptide neurotransmitter, containing three domains, a dense core vesicle sorting domain, a GABAA receptor-binding domain, a single-chain variable fragment anti-GABAA ß2 or ß3, and the His tag. Second, upon release, this synthetic peptide neurotransmitter binds to GABAA receptors on the postsynaptic neurons. Third, as the synthetic peptide neurotransmitter contains the His tag, antibody-mediated, targeted gene transfer using anti-His tag antibodies is selective for these neurons. We established this technology by expressing the synthetic peptide neurotransmitter in GABAergic neurons in the middle layers of postrhinal cortex, and the delivering the postsynaptic vector into connected GABAergic neurons in the upper neocortical layers. Targeted gene transfer was 61% specific for the connected neurons, but untargeted gene transfer was only 21% specific for these neurons. This technology may support studies on the roles of GABAergic inhibitory interneurons in circuit physiology and learning, and support gene therapy treatments for specific disorders associated with deficits at GABAergic synapses.
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Affiliation(s)
- Aarti Nagayach
- Department of Ophthalmology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
| | - Anshuman Singh
- Department of Ophthalmology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
| | - Angel L. De Blas
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, Connecticut, United States of America
| | - Alfred I. Geller
- Department of Ophthalmology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
- Department of Pharmacology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
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236
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Liang XH, Shen W, Crooke ST. Specific Increase of Protein Levels by Enhancing Translation Using Antisense Oligonucleotides Targeting Upstream Open Frames. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019. [PMID: 28639196 DOI: 10.1007/978-981-10-4310-9_9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A number of diseases are caused by low levels of key proteins; therefore, increasing the amount of specific proteins in human bodies is of therapeutic interest. Protein expression is downregulated by some structural or sequence elements present in the 5' UTR of mRNAs, such as upstream open reading frames (uORF). Translation initiation from uORF(s) reduces translation from the downstream primary ORF encoding the main protein product in the same mRNA, leading to a less efficient protein expression. Therefore, it is possible to use antisense oligonucleotides (ASOs) to specifically inhibit translation of the uORF by base-pairing with the uAUG region of the mRNA, redirecting translation machinery to initiate from the primary AUG site. Here we review the recent findings that translation of specific mRNAs can be enhanced using ASOs targeting uORF regions. Appropriately designed and optimized ASOs are highly specific, and they act in a sequence- and position-dependent manner, with very minor off-target effects. Protein levels can be increased using this approach in different types of human and mouse cells, and, importantly, also in mice. Since uORFs are present in around half of human mRNAs, the uORF-targeting ASOs may thus have valuable potential as research tools and as therapeutics to increase the levels of proteins for a variety of genes.
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Affiliation(s)
- Xue-Hai Liang
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA, 92010, USA.
| | - Wen Shen
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA, 92010, USA
| | - Stanley T Crooke
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA, 92010, USA
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237
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Neininger K, Marschall T, Helms V. SNP and indel frequencies at transcription start sites and at canonical and alternative translation initiation sites in the human genome. PLoS One 2019; 14:e0214816. [PMID: 30978217 PMCID: PMC6461226 DOI: 10.1371/journal.pone.0214816] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 03/20/2019] [Indexed: 11/30/2022] Open
Abstract
Single-nucleotide polymorphisms (SNPs) are the most common form of genetic variation in humans and drive phenotypic variation. Due to evolutionary conservation, SNPs and indels (insertion and deletions) are depleted in functionally important sequence elements. Recently, population-scale sequencing efforts such as the 1000 Genomes Project and the Genome of the Netherlands Project have catalogued large numbers of sequence variants. Here, we present a systematic analysis of the polymorphisms reported by these two projects in different coding and non-coding genomic elements of the human genome (intergenic regions, CpG islands, promoters, 5’ UTRs, coding exons, 3’ UTRs, introns, and intragenic regions). Furthermore, we were especially interested in the distribution of SNPs and indels in direct vicinity to the transcription start site (TSS) and translation start site (CSS). Thereby, we discovered an enrichment of dinucleotides CpG and CpA and an accumulation of SNPs at base position −1 relative to the TSS that involved primarily CpG and CpA dinucleotides. Genes having a CpG dinucleotide at TSS position -1 were enriched in the functional GO terms “Phosphoprotein”, “Alternative splicing”, and “Protein binding”. Focusing on the CSS, we compared SNP patterns in the flanking regions of canonical and alternative AUG and near-cognate start sites where we considered alternative starts previously identified by experimental ribosome profiling. We observed similar conservation patterns of canonical and alternative translation start sites, which underlines the importance of alternative translation mechanisms for cellular function.
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Affiliation(s)
- Kerstin Neininger
- Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
- Graduate School of Computer Science, Saarland University, 66123 Saarbrücken, Germany
| | - Tobias Marschall
- Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
- Max Planck Institute for Informatics, 66123 Saarbrücken, Germany
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
- * E-mail:
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238
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Sivamani E, Nalapalli S, Prairie A, Bradley D, Richbourg L, Strebe T, Liebler T, Wang D, Que Q. A study on optimization of pat gene expression cassette for maize transformation. Mol Biol Rep 2019; 46:3009-3017. [PMID: 30859449 DOI: 10.1007/s11033-019-04737-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 02/28/2019] [Indexed: 11/30/2022]
Abstract
Phosphinothricin acetyltransferase gene (pat) is an important selectable marker and also a key herbicide trait gene in several commercial products. In maize, the transformation frequency (TF) using pat as a selectable marker is the lowest among the commonly used marker options including epsps, pmi or ppo. Low pat transformation efficiency can become a major bottleneck in our ability to efficiently produce large numbers of events, especially for large molecular stack vectors with multiple trait gene cassettes. The root cause of the lower efficiency of pat in maize is not well understood and it is possible that the causes are multifaceted, including maize genotype, pat marker cassette, trait gene combinations and selection system. In this work we have identified a new variant of pat gene through codon optimization that consistently produced a higher transformation frequency (> 2x) than an old version of the pat gene that has codons optimized for expression in dicot plants. The level of PAT protein in all 16 constructs was also found multifold higher (up to 40 fold) over that of the controls. All of the T0 low copy transgenic plants generated from the 16 different constructs showed excellent tolerance to ammonium glufosinate herbicide spray tests at 4x and 8x recommended field application rates (1x = 595 g active ingredient (ai)/hectare of ammonium glufosinate) in the greenhouse.
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Affiliation(s)
| | | | - Anna Prairie
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| | - David Bradley
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| | - Lee Richbourg
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| | - Tim Strebe
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| | - Tara Liebler
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| | - Daolong Wang
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| | - Qiudeng Que
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
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239
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Das BK, Roy P, Rout AK, Sahoo DR, Panda SP, Pattanaik S, Dehury B, Behera BK, Mishra SS. Molecular cloning, GTP recognition mechanism and tissue-specific expression profiling of myxovirus resistance (Mx) protein in Labeo rohita (Hamilton) after Poly I:C induction. Sci Rep 2019; 9:3956. [PMID: 30850653 PMCID: PMC6408538 DOI: 10.1038/s41598-019-40323-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 12/20/2018] [Indexed: 01/16/2023] Open
Abstract
The myxovirus resistance (Mx) proteins belong to interferon-induced dynamin GTPase and play pivotal role in the inhibition of replication of numerous viruses. These antiviral proteins are released in usual or diseased condition to prevent the viral attack and to carry regular cellular activities like endocytosis and trafficking of nucleoproteins into the nucleus. The invasion of virus up-regulates the expression of Mx transcripts and double-stranded RNA mimic like polyinosinic polycytidyilic acid (Poly I:C). To understand the tissue-specific expression profiling and mechanism of GTP recognition of Mx protein from Labeo rohita (rohu), the full-length gene was cloned, sequenced and characterized through various Bioinformatics tools for the first time. The Mx cDNA was comprised of 2297 bp, and the open reading frame of 1938 bp encodes polypeptide of 631 amino acids. The coding sequence of Mx protein possess the signature motif of dynamin superfamily, LPRG(S/K)GIVTR, the tripartite guanosine-5/triphosphate (GTP)-binding motif (GXXXSGKS/T, DXXG and T/NKXD) and the leucine zipper motifs at the C-terminal end, well conserved in all interferon-induced Mx protein in vertebrates. Western blotting confirmed the molecular weight of Mx protein to be 72 kDa. After the intraperitoneal challenge of L. rohita with a Poly I:C, up-regulation of Mx protein was observed in brain, spleen, liver, kidney, intestine, heart, muscle, and gill. Ontogeny study displayed pronounced expression of Mx protein in all stages of the developmental of Rohu after Poly I:C induction. However a persistent expression of Mx transcript was also observed in Rohu egg as well as milt without induction with Poly I:C. Higher expression of Mx gene was observed on 96 h where it was 6.4 folds higher than the control. The computational modelling of Mx protein portrayed the tripartite N-terminal G-domain that binds to GTP, the bundle-signaling element (BSE) which interconnects the G-domain to the elongated stalk domain and C-terminal helical stalk domain. In agreement with the experimental studies, a series of conserved residues viz., Gln52, Ser53, Ser54, Leu68, Pro69, Gly71, Gly73, Thr76, Asp151, Gly154, Thr220, Lys221, Val251, Cys253, Arg254, and Gly255 were computed to be indispensable for tight anchoring of GTP within binding cavity of G-domain. The binding free energy calculation study depicted that the van der Waals and electrostatic terms contributs significantly to molecular recognition of GTP. Collectively, our study provides mechanistic insights into the tissue-specific expression profiling and GTP binding mechanism of Mx protein from Labeo rohita, which is expected to drive further research on several cellular events including viral resistance and endocytosis in the near future.
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Affiliation(s)
- Basanta Kumar Das
- Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751012, India. .,Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700120, West Bengal, India.
| | - Pragyan Roy
- Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751012, India
| | - Ajaya Kumar Rout
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700120, West Bengal, India
| | - Deepak Ranjan Sahoo
- Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751012, India
| | - Soumya Prasad Panda
- Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751012, India
| | - Sushmita Pattanaik
- Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751012, India
| | - Budheswar Dehury
- Biomedical Informatics Centre, ICMR-Regional Medical Research Centre, Nalco Square, Chandrasekharpur, Bhubaneswar, 751023, Odisha, India.,Department of Chemistry, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark
| | - Bijay Kumar Behera
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700120, West Bengal, India
| | - Sudhansu Sekhar Mishra
- Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751012, India
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240
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Park SH, Hahn JS. Development of an efficient cytosolic isobutanol production pathway in Saccharomyces cerevisiae by optimizing copy numbers and expression of the pathway genes based on the toxic effect of α-acetolactate. Sci Rep 2019; 9:3996. [PMID: 30850698 PMCID: PMC6408573 DOI: 10.1038/s41598-019-40631-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 02/18/2019] [Indexed: 11/09/2022] Open
Abstract
Isobutanol production in Saccharomyces cerevisiae is limited by subcellular compartmentalization of the pathway enzymes. In this study, we improved isobutanol production in S. cerevisiae by constructing an artificial cytosolic isobutanol biosynthetic pathway consisting of AlsS, α-acetolactate synthase from Bacillus subtilis, and two endogenous mitochondrial enzymes, ketol-acid reductoisomerase (Ilv5) and dihydroxy-acid dehydratase (Ilv3), targeted to the cytosol. B. subtilis AlsS was more active than Ilv2ΔN54, an endogenous α-acetolactate synthase targeted to the cytosol. However, overexpression of alsS led to a growth inhibition, which was alleviated by overexpressing ILV5ΔN48 and ILV3ΔN19, encoding the downstream enzymes targeted to the cytosol. Therefore, accumulation of the intermediate α-acetolactate might be toxic to the cells. Based on these findings, we improved isobutanol production by expressing alsS under the control of a copper-inducible CUP1 promoter, and by increasing translational efficiency of the ILV5ΔN48 and ILV3ΔN19 genes by adding Kozak sequence. Furthermore, strains with multi-copy integration of alsS into the delta-sequences were screened based on growth inhibition upon copper-dependent induction of alsS. Next, the ILV5ΔN48 and ILV3ΔN19 genes were integrated into the rDNA sites of the alsS-integrated strain, and the strains with multi-copy integration were screened based on the growth recovery. After optimizing the induction conditions of alsS, the final engineered strain JHY43D24 produced 263.2 mg/L isobutanol, exhibiting about 3.3-fold increase in production compared to a control strain constitutively expressing ILV2ΔN54, ILV5ΔN48, and ILV3ΔN19 on plasmids.
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Affiliation(s)
- Seong-Hee Park
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Ji-Sook Hahn
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.
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241
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Hu L, Ma Y, Liu L, Kang L, Brito LF, Wang D, Wu H, Liu A, Wang Y, Xu Q. Detection of functional polymorphisms in the hsp70 gene and association with cold stress response in Inner-Mongolia Sanhe cattle. Cell Stress Chaperones 2019; 24:409-418. [PMID: 30838506 PMCID: PMC6439023 DOI: 10.1007/s12192-019-00973-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 01/18/2019] [Accepted: 01/22/2019] [Indexed: 10/27/2022] Open
Abstract
The genetic mechanisms underlying the cattle resilience to severe cold temperatures are still unknown. In this study, we observed that four blood biochemical parameters were significantly altered, i.e., blood adrenocorticotropic hormone (ACTH), triiodothyronine (T3), thyroxine (T4), and potassium (K+) after expose to - 32 °C for 3 h. This was observed using 105 healthy Sanhe heifers with similar weight (398.17 ± 34.06 kg) and age (19.30 ± 4.91 months). A total of 20 single nucleotide polymorphisms (SNPs) were identified in 5'-flanking region of the hsp70 gene in Sanhe cattle, while only 10 SNPs were segregating when comparing genetic variations between Sanhe cattle and 285 Chinese Holstein samples. Statistically significant associations between the genomic markers SNP-42-, SNP-105+, SNP-181+, and SNP-205+ with blood T3 and between SNP-105+ and blood T4 were observed by applying the general linear model procedure and Bonferroni t test. Furthermore, we demonstrated that the T alleles of SNP-42- and SNP-205+ in the GC box and Kozak sequence of the hsp70 gene, respectively, significantly decreased the green fluorescent proteins activity in vitro GFP reporter assays. These findings suggest that these two SNPs are causative polymorphisms involved in the regulation of hsp70 promoter activity and might contribute to the observed association between the hsp70 gene and T3 and T4 levels in Sanhe cattle. Thus, hsp70 gene is a promising candidate gene to be validated in independent cattle populations and functional studies related to cold stress resilience in cattle.
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Affiliation(s)
- Lirong Hu
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044 People’s Republic of China
| | - Yao Ma
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044 People’s Republic of China
| | - Lili Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 People’s Republic of China
| | - Ling Kang
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044 People’s Republic of China
| | - Luiz Fernando Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907 USA
| | - Dongsheng Wang
- Xiertala Cattle Breeding Farm, Hailaer Farm Buro, Hailaer, Inner Mongolia 021012 People’s Republic of China
| | - Hongjun Wu
- Xiertala Cattle Breeding Farm, Hailaer Farm Buro, Hailaer, Inner Mongolia 021012 People’s Republic of China
| | - Airong Liu
- Moguai Farm, Hailaer Farm Buro, Hailaer, Inner Mongolia 022150 People’s Republic of China
| | - Yachun Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 People’s Republic of China
| | - Qing Xu
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044 People’s Republic of China
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242
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Pierce BL, Tong L, Dean S, Argos M, Jasmine F, Rakibuz-Zaman M, Sarwar G, Islam MT, Shahriar H, Islam T, Rahman M, Yunus M, Lynch VJ, Oglesbee D, Graziano JH, Kibriya MG, Gamble MV, Ahsan H. A missense variant in FTCD is associated with arsenic metabolism and toxicity phenotypes in Bangladesh. PLoS Genet 2019; 15:e1007984. [PMID: 30893314 PMCID: PMC6443193 DOI: 10.1371/journal.pgen.1007984] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 04/01/2019] [Accepted: 01/23/2019] [Indexed: 12/02/2022] Open
Abstract
Inorganic arsenic (iAs) is a carcinogen, and exposure to iAs via food and water is a global public health problem. iAs-contaminated drinking water alone affects >100 million people worldwide, including ~50 million in Bangladesh. Once absorbed into the blood stream, most iAs is converted to mono-methylated (MMA) and then di-methylated (DMA) forms, facilitating excretion in urine. Arsenic metabolism efficiency varies among individuals, in part due to genetic variation near AS3MT (arsenite methyltransferase; 10q24.32). To identify additional arsenic metabolism loci, we measured protein-coding variants across the human exome for 1,660 Bangladeshi individuals participating in the Health Effects of Arsenic Longitudinal Study (HEALS). Among the 19,992 coding variants analyzed exome-wide, the minor allele (A) of rs61735836 (p.Val101Met) in exon 3 of FTCD (formiminotransferase cyclodeaminase) was associated with increased urinary iAs% (P = 8x10-13), increased MMA% (P = 2x10-16) and decreased DMA% (P = 6x10-23). Among 2,401 individuals with arsenic-induced skin lesions (an indicator of arsenic toxicity and cancer risk) and 2,472 controls, carrying the low-efficiency A allele (frequency = 7%) was associated with increased skin lesion risk (odds ratio = 1.35; P = 1x10-5). rs61735836 is in weak linkage disequilibrium with all nearby variants. The high-efficiency/major allele (G/Valine) is human-specific and eliminates a start codon at the first 5´-proximal Kozak sequence in FTCD, suggesting selection against an alternative translation start site. FTCD is critical for catabolism of histidine, a process that generates one-carbon units that can enter the one-carbon/folate cycle, which provides methyl groups for arsenic metabolism. In our study population, FTCD and AS3MT SNPs together explain ~10% of the variation in DMA% and support a causal effect of arsenic metabolism efficiency on arsenic toxicity (i.e., skin lesions). In summary, this work identifies a coding variant in FTCD associated with arsenic metabolism efficiency, providing new evidence supporting the established link between one-carbon/folate metabolism and arsenic toxicity.
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Affiliation(s)
- Brandon L. Pierce
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, United States of America
- Department of Human Genetics, The University of Chicago, Chicago, IL, United States of America
- Comprehensive Cancer Center, The University of Chicago, Chicago, IL United States of America
| | - Lin Tong
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, United States of America
| | - Samantha Dean
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, United States of America
| | - Maria Argos
- Division of Epidemiology and Biostatistics, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Farzana Jasmine
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, United States of America
| | | | - Golam Sarwar
- UChicago Research Bangladesh, Mohakhali, Dhaka, Bangladesh
| | | | - Hasan Shahriar
- UChicago Research Bangladesh, Mohakhali, Dhaka, Bangladesh
| | - Tariqul Islam
- UChicago Research Bangladesh, Mohakhali, Dhaka, Bangladesh
| | - Mahfuzar Rahman
- UChicago Research Bangladesh, Mohakhali, Dhaka, Bangladesh
- Research and Evaluation Division, BRAC, Dhaka, Bangladesh
| | - Md. Yunus
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Vincent J. Lynch
- Department of Human Genetics, The University of Chicago, Chicago, IL, United States of America
| | - Devin Oglesbee
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN, United States of America
| | - Joseph H. Graziano
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States of America
| | - Muhammad G. Kibriya
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, United States of America
| | - Mary V. Gamble
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States of America
| | - Habibul Ahsan
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, United States of America
- Department of Human Genetics, The University of Chicago, Chicago, IL, United States of America
- Comprehensive Cancer Center, The University of Chicago, Chicago, IL United States of America
- Department of Medicine, The University of Chicago, Chicago, IL, United States of America
- Institute for Population and Precision Health, The University of Chicago, Chicago, IL, United States of America
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243
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Cell Non-autonomous Function of daf-18/PTEN in the Somatic Gonad Coordinates Somatic Gonad and Germline Development in C. elegans Dauer Larvae. Curr Biol 2019; 29:1064-1072.e8. [PMID: 30827916 DOI: 10.1016/j.cub.2019.01.076] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/23/2019] [Accepted: 01/30/2019] [Indexed: 12/21/2022]
Abstract
C. elegans larvae integrate environmental information and developmental decisions [1-3]. In favorable conditions, worms develop rapidly and continuously through four larval stages into reproductive adulthood. However, if conditions are unfavorable through the second larval stage, worms enter dauer diapause, a state of global and reversible developmental arrest in which precursor cells remain quiescent and preserve developmental potential, anticipating developmental progression if conditions improve. Signaling from neurons, hypodermis, and intestine regulate the appearance and behavior of dauer larvae and many aspects of developmental arrest of the non-gonadal soma [1, 4, 5]. Here, we show that the decision of somatic gonad blast cells (SGBs) and germline stem cells (GSCs) to be quiescent or progress developmentally is regulated differently from the non-gonadal soma: daf-18/PTEN acts non-autonomously within the somatic gonad to maintain developmental quiescence of both SGBs and GSCs. Our analysis suggests that daf-18 acts in somatic gonad cells to produce a "pro-quiescence" signal (or signals) that acts inter se and between the somatic gonad and the germline. The inferred signal does not require DAF-2/insulin receptor or maintain quiescence of the nearby sex myoblasts, and developmental progression in daf-18(0) does not require dafachronic acids. Abrogating quiescence in dauer results in post-dauer sterility. Our results implicate the somatic gonad as an endocrine organ to synchronize somatic gonad and germline development during dauer diapause and recovery, and our finding that PTEN acts non-autonomously to control blast cell quiescence may be relevant to its function as a tumor suppressor in mammals and to combating parasitic nematodes.
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244
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Eraslan B, Wang D, Gusic M, Prokisch H, Hallström BM, Uhlén M, Asplund A, Pontén F, Wieland T, Hopf T, Hahne H, Kuster B, Gagneur J. Quantification and discovery of sequence determinants of protein-per-mRNA amount in 29 human tissues. Mol Syst Biol 2019; 15:e8513. [PMID: 30777893 PMCID: PMC6379048 DOI: 10.15252/msb.20188513] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 01/22/2019] [Accepted: 01/23/2019] [Indexed: 12/15/2022] Open
Abstract
Despite their importance in determining protein abundance, a comprehensive catalogue of sequence features controlling protein-to-mRNA (PTR) ratios and a quantification of their effects are still lacking. Here, we quantified PTR ratios for 11,575 proteins across 29 human tissues using matched transcriptomes and proteomes. We estimated by regression the contribution of known sequence determinants of protein synthesis and degradation in addition to 45 mRNA and 3 protein sequence motifs that we found by association testing. While PTR ratios span more than 2 orders of magnitude, our integrative model predicts PTR ratios at a median precision of 3.2-fold. A reporter assay provided functional support for two novel UTR motifs, and an immobilized mRNA affinity competition-binding assay identified motif-specific bound proteins for one motif. Moreover, our integrative model led to a new metric of codon optimality that captures the effects of codon frequency on protein synthesis and degradation. Altogether, this study shows that a large fraction of PTR ratio variation in human tissues can be predicted from sequence, and it identifies many new candidate post-transcriptional regulatory elements.
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Affiliation(s)
- Basak Eraslan
- Computational Biology, Department of Informatics, Technical University of Munich, Garching Munich, Germany
- Graduate School of Quantitative Biosciences (QBM), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Dongxue Wang
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Mirjana Gusic
- Institute of Human Genetics, Technical University of Munich, Munich, Germany
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Holger Prokisch
- Institute of Human Genetics, Technical University of Munich, Munich, Germany
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Björn M Hallström
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Anna Asplund
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Frederik Pontén
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Thomas Wieland
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Thomas Hopf
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | | | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
- Center For Integrated Protein Science Munich (CIPSM), Munich, Germany
| | - Julien Gagneur
- Computational Biology, Department of Informatics, Technical University of Munich, Garching Munich, Germany
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245
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Abstract
The eukaryotic translation pathway has been studied for more than four decades, but the molecular mechanisms that regulate each stage of the pathway are not completely defined. This is in part because we have very little understanding of the kinetic framework for the assembly and disassembly of pathway intermediates. Steps of the pathway are thought to occur in the subsecond to second time frame, but most assays to monitor these events require minutes to hours to complete. Understanding translational control in sufficient detail will therefore require the development of assays that can precisely monitor the kinetics of the translation pathway in real time. Here, we describe the translation pathway from the perspective of its kinetic parameters, discuss advances that are helping us move toward the goal of a rigorous kinetic understanding, and highlight some of the challenges that remain.
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246
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Buzzelli JN, O'Connor L, Scurr M, Chung Nien Chin S, Catubig A, Ng GZ, Oshima M, Oshima H, Giraud AS, Sutton P, Judd LM, Menheniott TR. Overexpression of IL-11 promotes premalignant gastric epithelial hyperplasia in isolation from germline gp130-JAK-STAT driver mutations. Am J Physiol Gastrointest Liver Physiol 2019; 316:G251-G262. [PMID: 30520693 DOI: 10.1152/ajpgi.00304.2018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Expression of the cytokine IL-11 is elevated in human Helicobacter pylori infection and progressively increases with worsening gastric pathology. Additionally, IL-11 is required for tumor development in STAT3-dependent murine models of gastric cancer (GC) and, when administered acutely, causes resolving atrophic gastritis. However, it is unclear whether locally elevated IL-11 ligand expression can, in isolation from oncogenic gp130-JAK-STAT pathway mutations, initiate GC pathogenesis. Here we developed a transgenic mouse model of stomach-specific (keratin 19 promoter) IL-11 ligand overexpression. Keratin 19 promoter-IL-11 transgenic ( K19-IL11Tg) mice showed specific IL-11 overexpression in gastric corpus and antrum but not elsewhere in the gastrointestinal tract or in other tissues. K19-IL11Tg mice developed spontaneous premalignant disease of the gastric epithelium, progressing from atrophic gastritis to TFF2-positive metaplasia and severe epithelial hyperplasia, including adenoma-like lesions in a subset of older (1 yr old) animals. Although locally advanced, the hyperplastic lesions remained noninvasive. H. pylori infection in K19-IL11Tg mice accelerated some aspects of the premalignant phenotype. Finally, K19-IL11Tg mice had splenomegaly in association with elevated serum IL-11, with spleens showing an expanded myeloid compartment. Our results provide direct in vivo functional evidence that stomach-specific overexpression of IL-11, in isolation from germline gp130-JAK-STAT3 genetic drivers, is sufficient for premalignant progression. These findings have important functional implications for human GC, in which frequent IL-11 overexpression occurs in the reported absence of somatic mutations in gp130 signaling components. NEW & NOTEWORTHY We provide direct in vivo functional evidence that stomach-specific overexpression of the cytokine IL-11, in isolation from gp130-JAK-STAT3 pathway mutations, can trigger spontaneous atrophic gastritis progressing to locally advanced epithelial hyperplasia (but not dysplasia or carcinoma), which does not require, but may be accelerated by, concomitant Helicobacter pylori infection.
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Affiliation(s)
- Jon N Buzzelli
- Murdoch Children's Research Institute, The Royal Children's Hospital , Parkville, Victoria , Australia
| | - Louise O'Connor
- Murdoch Children's Research Institute, The Royal Children's Hospital , Parkville, Victoria , Australia
| | - Michelle Scurr
- Murdoch Children's Research Institute, The Royal Children's Hospital , Parkville, Victoria , Australia
| | - Sharleen Chung Nien Chin
- Murdoch Children's Research Institute, The Royal Children's Hospital , Parkville, Victoria , Australia
| | - Angelique Catubig
- Murdoch Children's Research Institute, The Royal Children's Hospital , Parkville, Victoria , Australia
| | - Garrett Z Ng
- Murdoch Children's Research Institute, The Royal Children's Hospital , Parkville, Victoria , Australia
| | - Masanobu Oshima
- Division of Translational and Clinical Oncology, Cancer Research Institute, Kanazawa University , Kanazawa , Japan
| | - Hiroko Oshima
- Division of Translational and Clinical Oncology, Cancer Research Institute, Kanazawa University , Kanazawa , Japan
| | - Andrew S Giraud
- Murdoch Children's Research Institute, The Royal Children's Hospital , Parkville, Victoria , Australia.,Department of Paediatrics, University of Melbourne, The Royal Children's Hospital , Parkville, Victoria , Australia
| | - Philip Sutton
- Murdoch Children's Research Institute, The Royal Children's Hospital , Parkville, Victoria , Australia.,Department of Paediatrics, University of Melbourne, The Royal Children's Hospital , Parkville, Victoria , Australia.,Faculty of Veterinary and Agricultural Science, University of Melbourne , Parkville, Victoria , Australia
| | - Louise M Judd
- Murdoch Children's Research Institute, The Royal Children's Hospital , Parkville, Victoria , Australia.,Department of Paediatrics, University of Melbourne, The Royal Children's Hospital , Parkville, Victoria , Australia
| | - Trevelyan R Menheniott
- Murdoch Children's Research Institute, The Royal Children's Hospital , Parkville, Victoria , Australia.,Department of Paediatrics, University of Melbourne, The Royal Children's Hospital , Parkville, Victoria , Australia
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247
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Nagayach A, Singh A, Geller AI. Delivery of different genes into presynaptic and postsynaptic neocortical neurons connected by a BDNF-TrkB synapse. Brain Res 2019; 1712:16-24. [PMID: 30710509 DOI: 10.1016/j.brainres.2019.01.038] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 01/14/2019] [Accepted: 01/29/2019] [Indexed: 02/05/2023]
Abstract
Brain-Derived Neurotrophic Factor (BDNF) signaling through TrkB receptors has important roles in synapse formation, synaptic plasticity, learning, and specific diseases. However, it is challenging to relate BDNF-TrkB synapses to circuit physiology or learning, as BDNF-TrkB synapses are embedded in complex circuits that contain numerous neuron and synapse types. Thus, analyzing the physiology of neurons connected by BDNF-TrkB synapses would be advanced by a technology to deliver different genes into presynaptic and postsynaptic neurons, connected by a BDNF-TrkB synapse. Here, we report selective gene transfer across BDNF-TrkB synapses: The model system was the large projection from rat postrhinal to perirhinal cortex. The first gene transfer, into presynaptic neurons in postrhinal cortex, used a virus vector and standard gene transfer procedures. This vector expresses a synthetic peptide neurotransmitter composed of three domains, a dense core vesicle sorting domain, BDNF, and the His tag. Upon release, this peptide neurotransmitter binds to TrkB receptors on postsynaptic neurons. The second gene transfer, into connected postsynaptic neurons in perirhinal cortex, uses antibody-mediated, targeted gene transfer and an anti-His tag antibody, as the synthetic peptide neurotransmitter contains the His tag. Confocal microscope images showed that using untargeted gene transfer, only 10-15% of the transduced presynaptic axons were proximal to a transduced postsynaptic dendrite. But using targeted gene transfer, ∼70% of the transduced presynaptic axons were proximal to a transduced postsynaptic dendrite. This technology may support studies on the roles of neurons connected by BDNF-TrkB synapses in circuit physiology and learning.
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Affiliation(s)
- Aarti Nagayach
- Department of Ophthalmology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Anshuman Singh
- Department of Ophthalmology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Alfred I Geller
- Department of Ophthalmology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA; Department of Phamracology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA.
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248
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Wang J, Zhou H, Luo Y, Zhao M, Gong H, Hao Z, Hu J, Hickford JGH. Variation in the Caprine KAP24-1 Gene Affects Cashmere Fibre Diameter. Animals (Basel) 2019; 9:E15. [PMID: 30621287 PMCID: PMC6357099 DOI: 10.3390/ani9010015] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 12/10/2018] [Accepted: 12/29/2018] [Indexed: 01/02/2023] Open
Abstract
The keratin-associated proteins (KAPs) are structural components of cashmere fibres. The gene encoding the high-sulphur (HS)-KAP24-1 (KRTAP24-1) has been identified in humans and sheep, but it has not been described in goats. In this study, we report the identification of caprine KRTAP24-1, describe variation in this gene, and investigate the effect of this variation on cashmere traits. A search for sequences orthologous to the ovine gene in the goat genome revealed a 774 bp open reading frame on chromosome 1, which could encode an HS-KAP. Based on this goat genome sequence and comparison with ovine KRTAP24-1 sequences, polymerase chain reaction (PCR) primers were designed to amplify an 856 bp fragment that would contain the entire coding region of the putative caprine KRTAP24-1. Use of this PCR amplification with subsequent single-strand conformation polymorphism (SSCP) analysis of the amplicons identified four distinct patterns of DNA bands on gel electrophoresis, with these representing four different DNA sequences (A to D), in 340 Longdong cashmere goats reared in China. The variant sequences had the highest similarity to KRTAP24-1 sequences from sheep and humans, suggesting that they are variants of caprine KRTAP24-1. Nine single-nucleotide polymorphisms (SNPs) were detected in the gene, including four non-synonymous SNPs and an SNP in proximity to the ATG start codon. Of the three common genotypes (AA, AB, and BB) found in these Longdong cashmere goats, cashmere fibres from goats of genotype AA had lower mean fibre diameter (MFD) than did those of genotype AB, and cashmere fibres from goats of genotype AB had lower MFD than did those from goats of genotype BB.
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Affiliation(s)
- Jiqing Wang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Huitong Zhou
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
- Gene-Marker Laboratory, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand.
| | - Yuzhu Luo
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Mengli Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Hua Gong
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
- Gene-Marker Laboratory, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand.
| | - Zhiyun Hao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Jiang Hu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Jon G H Hickford
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
- Gene-Marker Laboratory, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand.
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249
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Machkovech HM, Bloom JD, Subramaniam AR. Comprehensive profiling of translation initiation in influenza virus infected cells. PLoS Pathog 2019; 15:e1007518. [PMID: 30673779 PMCID: PMC6361465 DOI: 10.1371/journal.ppat.1007518] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 02/04/2019] [Accepted: 12/10/2018] [Indexed: 12/11/2022] Open
Abstract
Translation can initiate at alternate, non-canonical start codons in response to stressful stimuli in mammalian cells. Recent studies suggest that viral infection and anti-viral responses alter sites of translation initiation, and in some cases, lead to production of novel immune epitopes. Here we systematically investigate the extent and impact of alternate translation initiation in cells infected with influenza virus. We perform evolutionary analyses that suggest selection against non-canonical initiation at CUG codons in influenza virus lineages that have adapted to mammalian hosts. We then use ribosome profiling with the initiation inhibitor lactimidomycin to experimentally delineate translation initiation sites in a human lung epithelial cell line infected with influenza virus. We identify several candidate sites of alternate initiation in influenza mRNAs, all of which occur at AUG codons that are downstream of canonical initiation codons. One of these candidate downstream start sites truncates 14 amino acids from the N-terminus of the N1 neuraminidase protein, resulting in loss of its cytoplasmic tail and a portion of the transmembrane domain. This truncated neuraminidase protein is expressed on the cell surface during influenza virus infection, is enzymatically active, and is conserved in most N1 viral lineages. We do not detect globally higher levels of alternate translation initiation on host transcripts upon influenza infection or during the anti-viral response, but the subset of host transcripts induced by the anti-viral response is enriched for alternate initiation sites. Together, our results systematically map the landscape of translation initiation during influenza virus infection, and shed light on the evolutionary forces shaping this landscape.
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Affiliation(s)
- Heather M. Machkovech
- Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Medical Scientist Training Program, University of Washington, Seattle, Washington, United States of America
| | - Jesse D. Bloom
- Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Arvind R. Subramaniam
- Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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250
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Silva J, Fernandes R, Romão L. Translational Regulation by Upstream Open Reading Frames and Human Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1157:99-116. [DOI: 10.1007/978-3-030-19966-1_5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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