Evaluating ribosomal frameshifting in CCR5 mRNA decoding
PCR with reverse transcription (RT-PCR) of reporter RNAs showed that for cells transfected with the CCRS reporters, there was substantially less full-length cDNA and a simultaneous appearance of smaller molecular mass products (Fig. 1g). [...]the claim that the frameshift site is highly conserved am...
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| Published in | Nature (London) Vol. 604; no. 7906; pp. E16 - E23 |
|---|---|
| Main Authors | , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
London
Nature Publishing Group UK
21.04.2022
Nature Publishing Group |
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| Online Access | Get full text |
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| Abstract | PCR with reverse transcription (RT-PCR) of reporter RNAs showed that for cells transfected with the CCRS reporters, there was substantially less full-length cDNA and a simultaneous appearance of smaller molecular mass products (Fig. 1g). [...]the claim that the frameshift site is highly conserved among higher primates does not indicate that the (putative) frameshift signal is subject to purifying selection. [...]a rabbit reticulocyte lysate in vitro translation system was programmed with capped RNAs (Fig. 2j). Methods Alignment of CCR5 slippery sites The NCBI RefSeq database was searched with tblastn using the human CCR5 amino acid sequence derived from mRNA accession NM_000579.3 as query on 4 December 2018 using default parameters, with the number of hits expanded from 100 to 500. |
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| AbstractList | PCR with reverse transcription (RT-PCR) of reporter RNAs showed that for cells transfected with the CCRS reporters, there was substantially less full-length cDNA and a simultaneous appearance of smaller molecular mass products (Fig. 1g). [...]the claim that the frameshift site is highly conserved among higher primates does not indicate that the (putative) frameshift signal is subject to purifying selection. [...]a rabbit reticulocyte lysate in vitro translation system was programmed with capped RNAs (Fig. 2j). Methods Alignment of CCR5 slippery sites The NCBI RefSeq database was searched with tblastn using the human CCR5 amino acid sequence derived from mRNA accession NM_000579.3 as query on 4 December 2018 using default parameters, with the number of hits expanded from 100 to 500. |
| Author | Stewart, Hazel Kiniry, Stephen J. Loughran, Gary Khan, Yousuf A. Baranov, Pavel V. Atkins, John F. Steckelberg, Anna-Lena Kieft, Jeffrey S. Brown, Katherine Firth, Andrew E. |
| AuthorAffiliation | 1 Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK 6 Department of Human Genetics, University of Utah, Salt Lake City, UT 84112 7 These authors contributed equally to this work 5 Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia 3 School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland 8 Present address: Department of Biochemistry and Molecular Biophysics, Columbia University, NY 10032. USA 4 Department of Biochemistry and Molecular Genetics, Denver School of Medicine, Mail Stop 8101, Aurora, CO 80045. USA 2 Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States |
| AuthorAffiliation_xml | – name: 2 Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States – name: 1 Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK – name: 6 Department of Human Genetics, University of Utah, Salt Lake City, UT 84112 – name: 5 Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia – name: 3 School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland – name: 7 These authors contributed equally to this work – name: 4 Department of Biochemistry and Molecular Genetics, Denver School of Medicine, Mail Stop 8101, Aurora, CO 80045. USA – name: 8 Present address: Department of Biochemistry and Molecular Biophysics, Columbia University, NY 10032. USA |
| Author_xml | – sequence: 1 givenname: Yousuf A. orcidid: 0000-0003-0201-2796 surname: Khan fullname: Khan, Yousuf A. organization: Division of Virology, Department of Pathology, University of Cambridge, Department of Molecular and Cellular Physiology, Stanford University – sequence: 2 givenname: Gary surname: Loughran fullname: Loughran, Gary organization: School of Biochemistry and Cell Biology, University College Cork – sequence: 3 givenname: Anna-Lena surname: Steckelberg fullname: Steckelberg, Anna-Lena organization: Department of Biochemistry and Molecular Genetics, Denver School of Medicine, Department of Biochemistry and Molecular Biophysics, Columbia University – sequence: 4 givenname: Katherine surname: Brown fullname: Brown, Katherine organization: Division of Virology, Department of Pathology, University of Cambridge – sequence: 5 givenname: Stephen J. surname: Kiniry fullname: Kiniry, Stephen J. organization: School of Biochemistry and Cell Biology, University College Cork – sequence: 6 givenname: Hazel orcidid: 0000-0003-1438-1089 surname: Stewart fullname: Stewart, Hazel organization: Division of Virology, Department of Pathology, University of Cambridge – sequence: 7 givenname: Pavel V. orcidid: 0000-0001-9017-0270 surname: Baranov fullname: Baranov, Pavel V. organization: School of Biochemistry and Cell Biology, University College Cork – sequence: 8 givenname: Jeffrey S. orcidid: 0000-0002-3718-1891 surname: Kieft fullname: Kieft, Jeffrey S. email: jeffrey.kieft@cuanschutz.edu organization: Department of Biochemistry and Molecular Genetics, Denver School of Medicine – sequence: 9 givenname: Andrew E. orcidid: 0000-0002-7986-9520 surname: Firth fullname: Firth, Andrew E. email: aef24@cam.ac.uk organization: Division of Virology, Department of Pathology, University of Cambridge – sequence: 10 givenname: John F. orcidid: 0000-0001-7933-0165 surname: Atkins fullname: Atkins, John F. email: j.atkins@ucc.ie organization: School of Biochemistry and Cell Biology, University College Cork, Department of Human Genetics, University of Utah |
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| CitedBy_id | crossref_primary_10_1002_pro_4397 crossref_primary_10_1038_s41594_025_01492_x crossref_primary_10_1073_pnas_2317453121 crossref_primary_10_1093_nar_gkac626 crossref_primary_10_1016_j_jbc_2022_102592 crossref_primary_10_1016_j_tig_2022_05_009 crossref_primary_10_1016_j_molcel_2022_08_025 crossref_primary_10_1016_j_molcel_2022_08_024 crossref_primary_10_3390_ijms25031766 crossref_primary_10_3390_v13071251 crossref_primary_10_1073_pnas_2221683120 crossref_primary_10_1109_TCBB_2024_3362308 crossref_primary_10_1093_nar_gkae1248 crossref_primary_10_1128_mbio_02468_21 crossref_primary_10_1073_pnas_2414768121 crossref_primary_10_1016_j_celrep_2023_112076 crossref_primary_10_1146_annurev_biophys_101922_072452 crossref_primary_10_1093_molbev_msae154 crossref_primary_10_3390_v15122296 crossref_primary_10_1093_nar_gkae035 crossref_primary_10_1093_nar_gkac1180 crossref_primary_10_1016_j_isci_2023_108492 crossref_primary_10_1093_nar_gkae121 |
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| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 ObjectType-Article-2 ObjectType-Correspondence-1 content type line 23 Author contribution statement: The splicing work, which was initiated in 2016, was performed by A-L.S and J.S.K.; two teams, one involving G.L. and J.F.A, and the other involving Y.A.K., K.B., H.S. and A.E.F. semi-independently performed the frameshifting analysis; S.J.K. and P.V.B., with input from A.E.F. performed the ribosome profiling analysis. After initial independent work of the teams involved, Y.A.K. and J.F.A. coordinated their combination. Y.A.K. and G.L. had major roles in preparing the manuscript with contributions and refinements from all other authors. |
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| Snippet | PCR with reverse transcription (RT-PCR) of reporter RNAs showed that for cells transfected with the CCRS reporters, there was substantially less full-length... |
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| SubjectTerms | 38/39 631/337/574/1789 631/45/500 Amino acid sequence Amino acids CCR5 protein Complementary DNA Efficiency Frameshifting, Ribosomal - genetics Gene expression Humanities and Social Sciences Laboratories Matters Arising multidisciplinary Nucleic Acid Conformation Polymerase chain reaction Proteins Reticulocytes Reverse transcription Ribosomes - genetics Ribosomes - metabolism RNA polymerase RNA, Messenger - genetics RNA, Messenger - metabolism Science Science (multidisciplinary) |
| Title | Evaluating ribosomal frameshifting in CCR5 mRNA decoding |
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