1
|
Hikage R, Sekiya Y, Sawasato K, Nishiyama KI. CdsA, a CDP-diacylglycerol synthase involved in phospholipid and glycolipid MPIase biosynthesis, possesses multiple initiation codons. Genes Cells 2024; 29:347-355. [PMID: 38351722 DOI: 10.1111/gtc.13104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 01/25/2024] [Accepted: 02/01/2024] [Indexed: 04/04/2024]
Abstract
CdsA is a CDP-diacylglycerol synthase essential for phospholipid and glycolipid MPIase biosynthesis, and therefore for growth. The initiation codon of CdsA has been assigned as "TTG," while methionine at the 37th codon was reported to be an initiation codon in the original report. Since a vector containing the open reading frame starting with "TTG" under a controllable promoter complemented the cdsA knockout, "TTG" could function as an initiation codon. However, no evidence supporting that this "TTG" is the sole initiation codon has been reported. We determined the initiation codon by examining the ability of mutants around the N-terminal region to complement cdsA mutants. Even if the "TTG" was substituted with a stop codon, the clear complementation was observed. Moreover, the clones with multiple mutations of stop codons complemented the cdsA mutant up to the 37th codon, indicating that cdsA possesses multiple codons that can function as initiation codons. We constructed an experimental system in which the chromosomal expression of cdsA can be analyzed. By means of this system, we found that the cdsA mutant with substitution of "TTG" with a stop codon is fully functional. Thus, we concluded that CdsA contains multiple initiation codons.
Collapse
Affiliation(s)
- Runa Hikage
- Department of Applied Biological Chemistry, Faculty of Agriculture, Iwate University, Morioka, Japan
| | - Yusei Sekiya
- Department of Applied Biological Chemistry, Faculty of Agriculture, Iwate University, Morioka, Japan
| | - Katsuhiro Sawasato
- Department of Applied Biological Chemistry, Faculty of Agriculture, Iwate University, Morioka, Japan
| | - Ken-Ichi Nishiyama
- Department of Applied Biological Chemistry, Faculty of Agriculture, Iwate University, Morioka, Japan
| |
Collapse
|
2
|
González-Sánchez AM, Castellanos-Silva EA, Díaz-Figueroa G, Cate JHD. JUN mRNA translation regulation is mediated by multiple 5' UTR and start codon features. PLoS One 2024; 19:e0299779. [PMID: 38483896 PMCID: PMC10939236 DOI: 10.1371/journal.pone.0299779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/14/2024] [Indexed: 03/17/2024] Open
Abstract
Regulation of mRNA translation by eukaryotic initiation factors (eIFs) is crucial for cell survival. In humans, eIF3 stimulates translation of the JUN mRNA which encodes the transcription factor JUN, an oncogenic transcription factor involved in cell cycle progression, apoptosis, and cell proliferation. Previous studies revealed that eIF3 activates translation of the JUN mRNA by interacting with a stem loop in the 5' untranslated region (5' UTR) and with the 5' -7-methylguanosine cap structure. In addition to its interaction site with eIF3, the JUN 5' UTR is nearly one kilobase in length, and has a high degree of secondary structure, high GC content, and an upstream start codon (uAUG). This motivated us to explore the complexity of JUN mRNA translation regulation in human cells. Here we find that JUN translation is regulated in a sequence and structure-dependent manner in regions adjacent to the eIF3-interacting site in the JUN 5' UTR. Furthermore, we identify contributions of an additional initiation factor, eIF4A, in JUN regulation. We show that enhancing the interaction of eIF4A with JUN by using the compound Rocaglamide A (RocA) represses JUN translation. We also find that both the upstream AUG (uAUG) and the main AUG (mAUG) contribute to JUN translation and that they are conserved throughout vertebrates. Our results reveal additional layers of regulation for JUN translation and show the potential of JUN as a model transcript for understanding multiple interacting modes of translation regulation.
Collapse
Affiliation(s)
- Angélica M. González-Sánchez
- Comparative Biochemistry Graduate Program, University of California, Berkeley, Berkeley, CA, United States of America
| | - Eimy A. Castellanos-Silva
- Department of Biochemistry and Molecular Biology, University of California, Davis, Davis, CA, United States of America
| | - Gabriela Díaz-Figueroa
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America
| | - Jamie H. D. Cate
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America
| |
Collapse
|
3
|
Brito Querido J, Díaz-López I, Ramakrishnan V. The molecular basis of translation initiation and its regulation in eukaryotes. Nat Rev Mol Cell Biol 2024; 25:168-186. [PMID: 38052923 DOI: 10.1038/s41580-023-00624-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2023] [Indexed: 12/07/2023]
Abstract
The regulation of gene expression is fundamental for life. Whereas the role of transcriptional regulation of gene expression has been studied for several decades, it has been clear over the past two decades that post-transcriptional regulation of gene expression, of which translation regulation is a major part, can be equally important. Translation can be divided into four main stages: initiation, elongation, termination and ribosome recycling. Translation is controlled mainly during its initiation, a process which culminates in a ribosome positioned with an initiator tRNA over the start codon and, thus, ready to begin elongation of the protein chain. mRNA translation has emerged as a powerful tool for the development of innovative therapies, yet the detailed mechanisms underlying the complex process of initiation remain unclear. Recent studies in yeast and mammals have started to shed light on some previously unclear aspects of this process. In this Review, we discuss the current state of knowledge on eukaryotic translation initiation and its regulation in health and disease. Specifically, we focus on recent advances in understanding the processes involved in assembling the 43S pre-initiation complex and its recruitment by the cap-binding complex eukaryotic translation initiation factor 4F (eIF4F) at the 5' end of mRNA. In addition, we discuss recent insights into ribosome scanning along the 5' untranslated region of mRNA and selection of the start codon, which culminates in joining of the 60S large subunit and formation of the 80S initiation complex.
Collapse
Affiliation(s)
- Jailson Brito Querido
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Irene Díaz-López
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - V Ramakrishnan
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.
| |
Collapse
|
4
|
Hernández G, García A, Weingarten-Gabbay S, Mishra R, Hussain T, Amiri M, Moreno-Hagelsieb G, Montiel-Dávalos A, Lasko P, Sonenberg N. Functional analysis of the AUG initiator codon context reveals novel conserved sequences that disfavor mRNA translation in eukaryotes. Nucleic Acids Res 2024; 52:1064-1079. [PMID: 38038264 PMCID: PMC10853783 DOI: 10.1093/nar/gkad1152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 12/02/2023] Open
Abstract
mRNA translation is a fundamental process for life. Selection of the translation initiation site (TIS) is crucial, as it establishes the correct open reading frame for mRNA decoding. Studies in vertebrate mRNAs discovered that a purine at -3 and a G at +4 (where A of the AUG initiator codon is numbered + 1), promote TIS recognition. However, the TIS context in other eukaryotes has been poorly experimentally analyzed. We analyzed in vitro the influence of the -3, -2, -1 and + 4 positions of the TIS context in rabbit, Drosophila, wheat, and yeast. We observed that -3A conferred the best translational efficiency across these species. However, we found variability at the + 4 position for optimal translation. In addition, the Kozak motif that was defined from mammalian cells was only weakly predictive for wheat and essentially non-predictive for yeast. We discovered eight conserved sequences that significantly disfavored translation. Due to the big differences in translational efficiency observed among weak TIS context sequences, we define a novel category that we termed 'barren AUG context sequences (BACS)', which represent sequences disfavoring translation. Analysis of mRNA-ribosomal complexes structures provided insights into the function of BACS. The gene ontology of the BACS-containing mRNAs is presented.
Collapse
Affiliation(s)
- Greco Hernández
- mRNA and Cancer Laboratory, Unit of Biomedical Research on Cancer, National Institute of Cancer (INCan), Mexico City 14080, Mexico
| | - Alejandra García
- mRNA and Cancer Laboratory, Unit of Biomedical Research on Cancer, National Institute of Cancer (INCan), Mexico City 14080, Mexico
| | - Shira Weingarten-Gabbay
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Rishi Kumar Mishra
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru-560012, India
| | - Tanweer Hussain
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru-560012, India
| | - Mehdi Amiri
- Department of Biochemistry and Goodman Cancer Institute. McGill University., Montreal, QC H3A 1A3, Canada
| | - Gabriel Moreno-Hagelsieb
- Department of Biology, Wilfrid Laurier University. 75 University Ave. W, Waterloo, ON N2L 3C5, Canada
| | - Angélica Montiel-Dávalos
- mRNA and Cancer Laboratory, Unit of Biomedical Research on Cancer, National Institute of Cancer (INCan), Mexico City 14080, Mexico
| | - Paul Lasko
- Department of Biology, McGill University. Montreal, QC H3G 0B1, Canada
| | - Nahum Sonenberg
- Department of Biochemistry and Goodman Cancer Institute. McGill University., Montreal, QC H3A 1A3, Canada
| |
Collapse
|
5
|
Tidu A, Martin F. The interplay between cis- and trans-acting factors drives selective mRNA translation initiation in eukaryotes. Biochimie 2024; 217:20-30. [PMID: 37741547 DOI: 10.1016/j.biochi.2023.09.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/20/2023] [Accepted: 09/14/2023] [Indexed: 09/25/2023]
Abstract
Translation initiation consists in the assembly of the small and large ribosomal subunits on the start codon. This important step directly modulates the general proteome in living cells. Recently, genome wide studies revealed unexpected translation initiation events from unsuspected novel open reading frames resulting in the synthesis of a so-called 'dark proteome'. Indeed, the identification of the start codon by the translation machinery is a critical step that defines the translational landscape of the cell. Therefore, translation initiation is a highly regulated process in all organisms. In this review, we focus on the various cis- and trans-acting factors that rule the regulation of translation initiation in eukaryotes. Recent discoveries have shown that the guidance of the translation machinery for the choice of the start codon require sophisticated molecular mechanisms. In particular, the 5'UTR and the coding sequences contain cis-acting elements that trigger the use of AUG codons but also non-AUG codons to initiate protein synthesis. The use of these alternative start codons is also largely influenced by numerous trans-acting elements that drive selective mRNA translation in response to environmental changes.
Collapse
Affiliation(s)
- Antonin Tidu
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, Architecture et Réactivité de l'ARN, CNRS UPR9002, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Franck Martin
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, Architecture et Réactivité de l'ARN, CNRS UPR9002, 2, allée Konrad Roentgen, F-67084 Strasbourg, France.
| |
Collapse
|
6
|
Guca E, Alarcon R, Palo MZ, Santos L, Alonso-Gil S, Davyt M, de Lima LHF, Boissier F, Das S, Zagrovic B, Puglisi JD, Hashem Y, Ignatova Z. N 6-methyladenosine in 5' UTR does not promote translation initiation. Mol Cell 2024; 84:584-595.e6. [PMID: 38244546 PMCID: PMC10909339 DOI: 10.1016/j.molcel.2023.12.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 10/19/2023] [Accepted: 12/16/2023] [Indexed: 01/22/2024]
Abstract
The most abundant N6-methyladenosine (m6A) modification on mRNAs is installed non-stoichiometrically across transcripts, with 5' untranslated regions (5' UTRs) being the least conductive. 5' UTRs are essential for translation initiation, yet the molecular mechanisms orchestrated by m6A remain poorly understood. Here, we combined structural, biochemical, and single-molecule approaches and show that at the most common position, a single m6A does not affect translation yields, the kinetics of translation initiation complex assembly, or start codon recognition both under permissive growth and following exposure to oxidative stress. Cryoelectron microscopy (cryo-EM) structures of the late preinitiation complex reveal that m6A purine ring established stacking interactions with an arginine side chain of the initiation factor eIF2α, although with only a marginal energy contribution, as estimated computationally. These findings provide molecular insights into m6A interactions with the initiation complex and suggest that the subtle stabilization is unlikely to affect the translation dynamics under homeostatic conditions or stress.
Collapse
Affiliation(s)
- Ewelina Guca
- INSERM U1212 Acides nucléiques: Régulations Naturelle et Artificielle (ARNA), Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac 33607, France
| | - Rodrigo Alarcon
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany
| | - Michael Z Palo
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Leonardo Santos
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany
| | - Santiago Alonso-Gil
- Department of Structural and Computational Biology, Center for Molecular Biology, University of Vienna, 1030, Vienna, Austria; Max Perutz Labs, Vienna Biocenter Campus (VBC), 1030, Vienna, Austria
| | - Marcos Davyt
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany
| | - Leonardo H F de Lima
- INSERM U1212 Acides nucléiques: Régulations Naturelle et Artificielle (ARNA), Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac 33607, France; Department of Exact and Biological Sciences, Federal University of São João Del Rei, Sete Lagoas Campus, Sete Lagoas 35701-970, Minas Gerais, Brazil
| | - Fanny Boissier
- INSERM U1212 Acides nucléiques: Régulations Naturelle et Artificielle (ARNA), Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac 33607, France
| | - Sarada Das
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany
| | - Bojan Zagrovic
- Department of Structural and Computational Biology, Center for Molecular Biology, University of Vienna, 1030, Vienna, Austria; Max Perutz Labs, Vienna Biocenter Campus (VBC), 1030, Vienna, Austria
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Yaser Hashem
- INSERM U1212 Acides nucléiques: Régulations Naturelle et Artificielle (ARNA), Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac 33607, France.
| | - Zoya Ignatova
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany.
| |
Collapse
|
7
|
Gaikwad S, Ghobakhlou F, Zhang H, Hinnebusch AG. Yeast eIF2A has a minimal role in translation initiation and uORF-mediated translational control in vivo. eLife 2024; 12:RP92916. [PMID: 38266075 PMCID: PMC10945734 DOI: 10.7554/elife.92916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024] Open
Abstract
Initiating translation of most eukaryotic mRNAs depends on recruitment of methionyl initiator tRNA (Met-tRNAi) in a ternary complex (TC) with GTP-bound eukaryotic initiation factor 2 (eIF2) to the small (40S) ribosomal subunit, forming a 43S preinitiation complex (PIC) that attaches to the mRNA and scans the 5'-untranslated region (5' UTR) for an AUG start codon. Previous studies have implicated mammalian eIF2A in GTP-independent binding of Met-tRNAi to the 40S subunit and its recruitment to specialized mRNAs that do not require scanning, and in initiation at non-AUG start codons, when eIF2 function is attenuated by phosphorylation of its α-subunit during stress. The role of eIF2A in translation in vivo is poorly understood however, and it was unknown whether the conserved ortholog in budding yeast can functionally substitute for eIF2. We performed ribosome profiling of a yeast deletion mutant lacking eIF2A and isogenic wild-type (WT) cells in the presence or absence of eIF2α phosphorylation induced by starvation for amino acids isoleucine and valine. Whereas starvation of WT confers changes in translational efficiencies (TEs) of hundreds of mRNAs, the eIF2AΔ mutation conferred no significant TE reductions for any mRNAs in non-starved cells, and it reduced the TEs of only a small number of transcripts in starved cells containing phosphorylated eIF2α. We found no evidence that eliminating eIF2A altered the translation of mRNAs containing putative internal ribosome entry site (IRES) elements, or harboring uORFs initiated by AUG or near-cognate start codons, in non-starved or starved cells. Thus, very few mRNAs (possibly only one) appear to employ eIF2A for Met-tRNAi recruitment in yeast cells, even when eIF2 function is attenuated by stress.
Collapse
Affiliation(s)
- Swati Gaikwad
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
| | - Fardin Ghobakhlou
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
| | - Hongen Zhang
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
| | - Alan G Hinnebusch
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
| |
Collapse
|
8
|
Estrada K, Garciarrubio A, Merino E. Unraveling the plasticity of translation initiation in prokaryotes: Beyond the invariant Shine-Dalgarno sequence. PLoS One 2024; 19:e0289914. [PMID: 38206950 PMCID: PMC10783764 DOI: 10.1371/journal.pone.0289914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 07/28/2023] [Indexed: 01/13/2024] Open
Abstract
Translation initiation in prokaryotes is mainly defined, although not exclusively, by the interaction between the anti-Shine-Dalgarno sequence (antiSD), located at the 3'-terminus of the 16S ribosomal RNA, and a complementary sequence, the ribosome binding site, or Shine-Dalgarno (SD), located upstream of the start codon in prokaryotic mRNAs. The antiSD has a conserved 5'-CCUCC-3' core, but inter-species variations have been found regarding the participation of flanking bases in binding. These variations have been described for certain bacteria and, to a lesser extent, for some archaea. To further analyze these variations, we conducted binding-energy prediction analyses on over 6,400 genomic sequences from both domains. We identified 15 groups of antiSD variants that could be associated with the organisms' phylogenetic origin. Additionally, our findings revealed that certain organisms exhibit variations in the core itself. Importantly, an unaltered core is not necessarily required for the interaction between the 3'-terminus of the rRNA and the region preceding the AUG of the mRNA. In our study, we classified organisms into four distinct categories: i) those possessing a conserved core and demonstrating binding; ii) those with a conserved core but lacking evidence of binding; iii) those exhibiting binding in the absence of a conserved core; and iv) those lacking both a conserved core and evidence of binding. Our results demonstrate the flexibility of organisms in evolving different sequences involved in translation initiation beyond the traditional Shine-Dalgarno sequence. These findings are discussed in terms of the evolution of translation initiation in prokaryotic organisms.
Collapse
Affiliation(s)
- Karel Estrada
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos (UAEM), Cuernavaca, Morelos, México
- Massive Sequencing and Bioinformatics Unit, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Alejandro Garciarrubio
- Department of Cell Engineering and Biocatalysis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Enrique Merino
- Department of Molecular Microbiology, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| |
Collapse
|
9
|
Schwarz MGA, Correa PR, Almeida PSL, Mendonça-Lima L. Mycobacterium bovis BCG dodecin gene codes a functional protein despite of a start codon mutation. Tuberculosis (Edinb) 2023; 143:102400. [PMID: 37672955 DOI: 10.1016/j.tube.2023.102400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 08/14/2023] [Accepted: 08/30/2023] [Indexed: 09/08/2023]
Abstract
Dodecin is a dodecamer involved in flavin homeostasis, with interesting temperature and osmolarity endurance features in Mycobacterium tuberculosis. A single nucleotide polymorphism in the gene's start codon in BCG, converting ATG to ACG, is predicted to generate a N-terminal shorter isoform, lacking the first 7 amino acids. We previously reported that the shortened recombinant protein has reduced extremophilic features. Here we investigate if within the mycobacterial context dodecin can be produced from both alleles, carrying ATG and ACG start codons. Reporter gene assays using mcherry cloned downstream and in phase to both M.tb and BCG "upstream" regions confirms production of functional proteins. Complementation with both dod alleles similarly enhances M. smegmatis growth after entry into logarithmic phase and exposure to hydrogen peroxide, possibly implicating this protein in oxidative stress response mechanisms. Altogether these data indicate that BCG dodecin is indeed produced, notwithstanding in lower levels compared to M.tb, conferring similar phenotypes, even with the SNP altering the M.tb ATG start codon to the BCG ACG. This protein might be an interesting drug target for the development of new therapeutics against tuberculosis.
Collapse
Affiliation(s)
| | - Paloma Rezende Correa
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil.
| | - Paula Silva Lacerda Almeida
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil.
| | - Leila Mendonça-Lima
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil.
| |
Collapse
|
10
|
Mao Y, Jia L, Dong L, Shu XE, Qian SB. Start codon-associated ribosomal frameshifting mediates nutrient stress adaptation. Nat Struct Mol Biol 2023; 30:1816-1825. [PMID: 37957305 DOI: 10.1038/s41594-023-01119-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 09/07/2023] [Indexed: 11/15/2023]
Abstract
A translating ribosome is typically thought to follow the reading frame defined by the selected start codon. Using super-resolution ribosome profiling, here we report pervasive out-of-frame translation immediately from the start codon. Start codon-associated ribosomal frameshifting (SCARF) stems from the slippage of ribosomes during the transition from initiation to elongation. Using a massively paralleled reporter assay, we uncovered sequence elements acting as SCARF enhancers or repressors, implying that start codon recognition is coupled with reading frame fidelity. This finding explains thousands of mass spectrometry spectra that are unannotated in the human proteome. Mechanistically, we find that the eukaryotic initiation factor 5B (eIF5B) maintains the reading frame fidelity by stabilizing initiating ribosomes. Intriguingly, amino acid starvation induces SCARF by proteasomal degradation of eIF5B. The stress-induced SCARF protects cells from starvation by enabling amino acid recycling and selective mRNA translation. Our findings illustrate a beneficial effect of translational 'noise' in nutrient stress adaptation.
Collapse
Affiliation(s)
- Yuanhui Mao
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Longfei Jia
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
| | - Leiming Dong
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
| | - Xin Erica Shu
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
| | - Shu-Bing Qian
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA.
| |
Collapse
|
11
|
Katsuma S, Matsuda-Imai N. A seamless connection from the burst sequence to the start codon is essential for polyhedrin hyperexpression in alphabaculoviruses. Biochem Biophys Res Commun 2023; 679:1-5. [PMID: 37651871 DOI: 10.1016/j.bbrc.2023.08.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 08/21/2023] [Indexed: 09/02/2023]
Abstract
Alphabaculoviruses produce a large number of occlusion bodies (OBs) in host cells during the late stage of infection. OBs are mainly composed of polyhedrin (POLH), and high-level transcription of the polh gene has been exploited to express foreign proteins in insect cells. While making Bombyx mori nucleopolyhedrovirus (BmNPV) polh mutants using a conventional transfer vector-based method, we noticed that a virus with a short sequence insertion just before the polh start codon produces fewer very small OBs. Detailed analysis of several BmNPV mutants revealed that insertions between the burst sequence and start codon markedly decrease POLH accumulation and polh transcription. We further confirmed this decrease using recombinant viruses expressing a reporter gene driven by the polh promoter. These findings underscore the critical importance of a seamless connection from the burst sequence to the start codon for baculovirus polh hyperexpression.
Collapse
Affiliation(s)
- Susumu Katsuma
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan.
| | - Noriko Matsuda-Imai
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| |
Collapse
|
12
|
Xie J, Zhuang Z, Gou S, Zhang Q, Wang X, Lan T, Lian M, Li N, Liang Y, Ouyang Z, Ye Y, Wu H, Lai L, Wang K. Precise genome editing of the Kozak sequence enables bidirectional and quantitative modulation of protein translation to anticipated levels without affecting transcription. Nucleic Acids Res 2023; 51:10075-10093. [PMID: 37650635 PMCID: PMC10570039 DOI: 10.1093/nar/gkad687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 07/31/2023] [Accepted: 08/10/2023] [Indexed: 09/01/2023] Open
Abstract
None of the existing approaches for regulating gene expression can bidirectionally and quantitatively fine-tune gene expression to desired levels. Here, on the basis of precise manipulations of the Kozak sequence, which has a remarkable influence on translation initiation, we proposed and validated a novel strategy to directly modify the upstream nucleotides of the translation initiation codon of a given gene to flexibly alter the gene translation level by using base editors and prime editors. When the three nucleotides upstream of the translation initiation codon (named KZ3, part of the Kozak sequence), which exhibits the most significant base preference of the Kozak sequence, were selected as the editing region to alter the translation levels of proteins, we confirmed that each of the 64 KZ3 variants had a different translation efficiency, but all had similar transcription levels. Using the ranked KZ3 variants with different translation efficiencies as predictors, base editor- and prime editor-mediated mutations of KZ3 in the local genome could bidirectionally and quantitatively fine-tune gene translation to the anticipated levels without affecting transcription in vitro and in vivo. Notably, this strategy can be extended to the whole Kozak sequence and applied to all protein-coding genes in all eukaryotes.
Collapse
Affiliation(s)
- Jingke Xie
- China–New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China
- Guangdong Provincial Key Laboratory of Large Animal models for Biomedicine, Wuyi University, Jiangmen 529020, China
| | - Zhenpeng Zhuang
- China–New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shixue Gou
- China–New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China
| | - Quanjun Zhang
- China–New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou 510530, China
| | - Xia Wang
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
| | - Ting Lan
- China–New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meng Lian
- China–New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou 510530, China
| | - Nan Li
- China–New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China
- Guangdong Provincial Key Laboratory of Large Animal models for Biomedicine, Wuyi University, Jiangmen 529020, China
| | - Yanhui Liang
- China–New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China
| | - Zhen Ouyang
- China–New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China
- Guangdong Provincial Key Laboratory of Large Animal models for Biomedicine, Wuyi University, Jiangmen 529020, China
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou 510530, China
| | - Yinghua Ye
- China–New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou 510530, China
| | - Han Wu
- China–New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou 510530, China
| | - Liangxue Lai
- China–New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China
- Guangdong Provincial Key Laboratory of Large Animal models for Biomedicine, Wuyi University, Jiangmen 529020, China
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou 510530, China
| | - Kepin Wang
- China–New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China
- Guangdong Provincial Key Laboratory of Large Animal models for Biomedicine, Wuyi University, Jiangmen 529020, China
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou 510530, China
| |
Collapse
|
13
|
Hedaya OM, Venkata Subbaiah KC, Jiang F, Xie LH, Wu J, Khor ES, Zhu M, Mathews DH, Proschel C, Yao P. Secondary structures that regulate mRNA translation provide insights for ASO-mediated modulation of cardiac hypertrophy. Nat Commun 2023; 14:6166. [PMID: 37789015 PMCID: PMC10547706 DOI: 10.1038/s41467-023-41799-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 09/19/2023] [Indexed: 10/05/2023] Open
Abstract
Translation of upstream open reading frames (uORFs) typically abrogates translation of main (m)ORFs. The molecular mechanism of uORF regulation in cells is not well understood. Here, we data-mined human and mouse heart ribosome profiling analyses and identified a double-stranded RNA (dsRNA) structure within the GATA4 uORF that cooperates with the start codon to augment uORF translation and inhibits mORF translation. A trans-acting RNA helicase DDX3X inhibits the GATA4 uORF-dsRNA activity and modulates the translational balance of uORF and mORF. Antisense oligonucleotides (ASOs) that disrupt this dsRNA structure promote mORF translation, while ASOs that base-pair immediately downstream (i.e., forming a bimolecular double-stranded region) of either the uORF or mORF start codon enhance uORF or mORF translation, respectively. Human cardiomyocytes and mice treated with a uORF-enhancing ASO showed reduced cardiac GATA4 protein levels and increased resistance to cardiomyocyte hypertrophy. We further show the broad utility of uORF-dsRNA- or mORF-targeting ASO to regulate mORF translation for other mRNAs. This work demonstrates that the uORF-dsRNA element regulates the translation of multiple mRNAs as a generalizable translational control mechanism. Moreover, we develop a valuable strategy to alter protein expression and cellular phenotypes by targeting or generating dsRNA downstream of a uORF or mORF start codon.
Collapse
Affiliation(s)
- Omar M Hedaya
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
| | - Kadiam C Venkata Subbaiah
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
| | - Feng Jiang
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
| | - Li Huitong Xie
- Department of Biomedical Genetics, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
| | - Jiangbin Wu
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
| | - Eng-Soon Khor
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
| | - Mingyi Zhu
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
- The Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
| | - David H Mathews
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
- The Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
- The Center for Biomedical Informatics, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
| | - Chris Proschel
- Department of Biomedical Genetics, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
| | - Peng Yao
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA.
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA.
- The Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA.
- The Center for Biomedical Informatics, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA.
| |
Collapse
|
14
|
Kaufmann L, Pilic J, Auinger L, Mayer AL, Blatterer J, Semmler-Bruckner J, Abbas S, Rehman K, Ayaz M, Graier WF, Malli R, Petek E, Wagner K, Al Kaissi A, Khan MA, Windpassinger C. Analysis of a non-lethal biallelic frameshift mutation in ZMPSTE24 reveals utilization of alternative translation initiation codons. Clin Genet 2023; 104:491-496. [PMID: 37270786 DOI: 10.1111/cge.14381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/12/2023] [Accepted: 05/23/2023] [Indexed: 06/06/2023]
Abstract
Restrictive dermopathy (RD) is a lethal condition caused by biallelic loss-of-function mutations in ZMPSTE24, whereas mutations preserving residual enzymatic activity of the ZMPSTE24 protein lead to the milder mandibuloacral dysplasia with type B lipodystrophy (MADB) phenotype. Remarkably, we identified a homozygous, presumably loss-of-function mutation in ZMPSTE24 [c.28_29insA, p.(Leu10Tyrfs*37)] in two consanguineous Pakistani families segregating MADB. To clarify how lethal consequences are prevented in affected individuals, functional analysis was performed. Expression experiments supported utilization of two alternative translation initiation sites, preventing complete loss of protein function consistent with the relatively mild phenotypic outcome in affected patients. One of these alternative start codons is newly formed at the insertion site. Our findings indicate that the creation of new potential start codons through N-terminal mutations in other disease-associated genes should generally be taken into consideration in the variant interpretation process.
Collapse
Affiliation(s)
- Lukas Kaufmann
- Diagnostic and Research Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Johannes Pilic
- Gottfried Schatz Research Center, Department of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Lisa Auinger
- Division of Haematology, Medical University of Graz, Graz, Austria
| | - Anna-Lena Mayer
- Diagnostic and Research Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Jasmin Blatterer
- Diagnostic and Research Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Johann Semmler-Bruckner
- Neurogenetics Laboratory, Department of Neurology, Medical University of Graz, Graz, Austria
| | - Safdar Abbas
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Pakistan
| | - Khurram Rehman
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gomal University, Dera Ismail Khan, Pakistan
| | - Muhammad Ayaz
- Department of Biological Sciences, Gomal University, Dera Ismail Khan, Pakistan
| | - Wolfgang F Graier
- Gottfried Schatz Research Center, Department of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
| | - Roland Malli
- Gottfried Schatz Research Center, Department of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
| | - Erwin Petek
- Diagnostic and Research Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Klaus Wagner
- Diagnostic and Research Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Ali Al Kaissi
- Pediatric Orthopedic Department, Speising Hospital, Vienna, Austria
| | - Muzammil Ahmad Khan
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Pakistan
| | - Christian Windpassinger
- Diagnostic and Research Institute of Human Genetics, Medical University of Graz, Graz, Austria
- Neurogenetics Laboratory, Department of Neurology, Medical University of Graz, Graz, Austria
| |
Collapse
|
15
|
Palacıoğlu G, Alkan M, Derviş S, Bayraktar H, Özer G. Molecular phylogeny of plant pathogenic fungi based on start codon targeted (SCoT) polymorphism. Mol Biol Rep 2023; 50:8271-8279. [PMID: 37578578 DOI: 10.1007/s11033-023-08735-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/02/2023] [Indexed: 08/15/2023]
Abstract
BACKGROUND A number of molecular marker systems have been developed to assess genetic diversity, carry out phylogenetic analysis, and diagnose and discriminate plant pathogenic fungi. The start codon targeted (SCoT) markers system is a novel approach used here to investigate intra and interspecific polymorphisms of phytopathogenic fungi. MATERIALS AND METHODS This study assessed genetic variability between and within 96 isolates of ten fungal species associated with a variety of plant species using 36 SCoT primers. RESULTS The six primers generated 331 distinct and reproducible banding patterns, of which 322 were polymorphic (97.28%), resulting in 53.67 polymorphic bands per primer. All primers produced informative amplification profiles that distinguished all fungal species. With a resolving power of 10.65, SCoT primer 12 showed the highest polymorphism among species, followed by primer 33 and primer 29. Polymorphic loci (PPL), Nei's diversity index (h), and Shannon index (I) percentages were 6.25, 0.018, and 0.028, respectively. UPGMA analysis separated all isolates based on morphological classification and revealed significant genetic variation among fungal isolates at the intraspecific level. PCoA analysis strongly supported fungal species discrimination and genetic variation. The other parameters of evaluation proved that SCoT markers are at least as effective as other DNA markers. CONCLUSIONS SCoT markers were effective in identifying plant pathogenic fungi and were a powerful tool for estimating genetic variation and population structure of different fungi species.
Collapse
Affiliation(s)
- Gülsüm Palacıoğlu
- Department of Plant Protection, Faculty of Agriculture, Şırnak University, Şırnak, Turkey
| | - Mehtap Alkan
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Turkey
| | - Sibel Derviş
- Department of Plant and Animal Production, Vocational School of Kızıltepe, Mardin Artuklu University, Mardin, Turkey
| | - Harun Bayraktar
- Department of Plant Protection, Faculty of Agriculture, Ankara University, Ankara, Turkey.
| | - Göksel Özer
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Turkey
| |
Collapse
|
16
|
Fang JC, Liu MJ. Translation initiation at AUG and non-AUG triplets in plants. Plant Sci 2023; 335:111822. [PMID: 37574140 DOI: 10.1016/j.plantsci.2023.111822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 07/22/2023] [Accepted: 08/07/2023] [Indexed: 08/15/2023]
Abstract
In plants and other eukaryotes, precise selection of translation initiation site (TIS) on mRNAs shapes the proteome in response to cellular events or environmental cues. The canonical translation of mRNAs initiates at a 5' proximal AUG codon in a favorable context. However, the coding and non-coding regions of plant genomes contain numerous unannotated alternative AUG and non-AUG TISs. Determining how and why these unexpected and prevalent TISs are activated in plants has emerged as an exciting research area. In this review, we focus on the selection of plant TISs and highlight studies that revealed previously unannotated TISs used in vivo via comparative genomics and genome-wide profiling of ribosome positioning and protein N-terminal ends. The biological signatures of non-AUG TIS-initiated open reading frames (ORFs) in plants are also discussed. We describe what is understood about cis-regulatory RNA elements and trans-acting eukaryotic initiation factors (eIFs) in the site selection for translation initiation by featuring the findings in plants along with supporting findings in non-plant species. The prevalent, unannotated TISs provide a hidden reservoir of ORFs that likely help reshape plant proteomes in response to developmental or environmental cues. These findings underscore the importance of understanding the mechanistic basis of TIS selection to functionally annotate plant genomes, especially for crops with large genomes.
Collapse
Affiliation(s)
- Jhen-Cheng Fang
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 711, Taiwan
| | - Ming-Jung Liu
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 711, Taiwan; Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan.
| |
Collapse
|
17
|
Sonobe Y, Lee S, Krishnan G, Gu Y, Kwon DY, Gao FB, Roos RP, Kratsios P. Translation of dipeptide repeat proteins in C9ORF72 ALS/FTD through unique and redundant AUG initiation codons. eLife 2023; 12:e83189. [PMID: 37675986 PMCID: PMC10541178 DOI: 10.7554/elife.83189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 09/06/2023] [Indexed: 09/08/2023] Open
Abstract
A hexanucleotide repeat expansion in C9ORF72 is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). A hallmark of ALS/FTD pathology is the presence of dipeptide repeat (DPR) proteins, produced from both sense GGGGCC (poly-GA, poly-GP, poly-GR) and antisense CCCCGG (poly-PR, poly-PG, poly-PA) transcripts. Translation of sense DPRs, such as poly-GA and poly-GR, depends on non-canonical (non-AUG) initiation codons. Here, we provide evidence for canonical AUG-dependent translation of two antisense DPRs, poly-PR and poly-PG. A single AUG is required for synthesis of poly-PR, one of the most toxic DPRs. Unexpectedly, we found redundancy between three AUG codons necessary for poly-PG translation. Further, the eukaryotic translation initiation factor 2D (EIF2D), which was previously implicated in sense DPR synthesis, is not required for AUG-dependent poly-PR or poly-PG translation, suggesting that distinct translation initiation factors control DPR synthesis from sense and antisense transcripts. Our findings on DPR synthesis from the C9ORF72 locus may be broadly applicable to many other nucleotide repeat expansion disorders.
Collapse
Affiliation(s)
- Yoshifumi Sonobe
- University of Chicago Medical CenterChicagoUnited States
- Department of Neurology, University of Chicago Medical CenterChicagoUnited States
- Neuroscience Institute, University of ChicagoChicagoUnited States
| | - Soojin Lee
- RNA Therapeutics Institute, University of Massachusetts Chan Medical SchoolWorcesterUnited States
- Department of Neurology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Gopinath Krishnan
- RNA Therapeutics Institute, University of Massachusetts Chan Medical SchoolWorcesterUnited States
- Department of Neurology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Yuanzheng Gu
- Neuromuscular & Movement Disorders, BiogenCambridgeUnited States
| | - Deborah Y Kwon
- Neuromuscular & Movement Disorders, BiogenCambridgeUnited States
| | - Fen-Biao Gao
- RNA Therapeutics Institute, University of Massachusetts Chan Medical SchoolWorcesterUnited States
- Department of Neurology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Raymond P Roos
- University of Chicago Medical CenterChicagoUnited States
- Department of Neurology, University of Chicago Medical CenterChicagoUnited States
- Neuroscience Institute, University of ChicagoChicagoUnited States
| | - Paschalis Kratsios
- Neuroscience Institute, University of ChicagoChicagoUnited States
- Department of Neurobiology, University of ChicagoChicagoUnited States
| |
Collapse
|
18
|
Xiang Y, Huang W, Tan L, Chen T, He Y, Irving PS, Weeks KM, Zhang QC, Dong X. Pervasive downstream RNA hairpins dynamically dictate start-codon selection. Nature 2023; 621:423-430. [PMID: 37674078 PMCID: PMC10499604 DOI: 10.1038/s41586-023-06500-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 07/31/2023] [Indexed: 09/08/2023]
Abstract
Translational reprogramming allows organisms to adapt to changing conditions. Upstream start codons (uAUGs), which are prevalently present in mRNAs, have crucial roles in regulating translation by providing alternative translation start sites1-4. However, what determines this selective initiation of translation between conditions remains unclear. Here, by integrating transcriptome-wide translational and structural analyses during pattern-triggered immunity in Arabidopsis, we found that transcripts with immune-induced translation are enriched with upstream open reading frames (uORFs). Without infection, these uORFs are selectively translated owing to hairpins immediately downstream of uAUGs, presumably by slowing and engaging the scanning preinitiation complex. Modelling using deep learning provides unbiased support for these recognizable double-stranded RNA structures downstream of uAUGs (which we term uAUG-ds) being responsible for the selective translation of uAUGs, and allows the prediction and rational design of translating uAUG-ds. We found that uAUG-ds-mediated regulation can be generalized to human cells. Moreover, uAUG-ds-mediated start-codon selection is dynamically regulated. After immune challenge in plants, induced RNA helicases that are homologous to Ded1p in yeast and DDX3X in humans resolve these structures, allowing ribosomes to bypass uAUGs to translate downstream defence proteins. This study shows that mRNA structures dynamically regulate start-codon selection. The prevalence of this RNA structural feature and the conservation of RNA helicases across kingdoms suggest that mRNA structural remodelling is a general feature of translational reprogramming.
Collapse
Affiliation(s)
- Yezi Xiang
- Department of Biology, Duke University, Durham, NC, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC, USA
| | - Wenze Huang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Beijing Frontier Research Center for Biological Structures, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Lianmei Tan
- Department of Pharmacology and Cancer Biology, Duke Medical Center, Duke University, Durham, NC, USA
| | - Tianyuan Chen
- Department of Biology, Duke University, Durham, NC, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC, USA
| | - Yang He
- Department of Biology, Duke University, Durham, NC, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC, USA
| | - Patrick S Irving
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Beijing Frontier Research Center for Biological Structures, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Xinnian Dong
- Department of Biology, Duke University, Durham, NC, USA.
- Howard Hughes Medical Institute, Duke University, Durham, NC, USA.
| |
Collapse
|
19
|
Buscà R, Onesto C, Egensperger M, Pouysségur J, Pagès G, Lenormand P. N-terminal alanine-rich (NTAR) sequences drive precise start codon selection resulting in elevated translation of multiple proteins including ERK1/2. Nucleic Acids Res 2023; 51:7714-7735. [PMID: 37414542 PMCID: PMC10450180 DOI: 10.1093/nar/gkad528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 06/12/2023] [Indexed: 07/08/2023] Open
Abstract
We report the discovery of N-terminal alanine-rich sequences, which we term NTARs, that act in concert with their native 5'-untranslated regions to promote selection of the proper start codon. NTARs also facilitate efficient translation initiation while limiting the production of non-functional polypeptides through leaky scanning. We first identified NTARs in the ERK1/2 kinases, which are among the most important signaling molecules in mammals. Analysis of the human proteome reveals that hundreds of proteins possess NTARs, with housekeeping proteins showing a particularly high prevalence. Our data indicate that several of these NTARs act in a manner similar to those found in the ERKs and suggest a mechanism involving some or all of the following features: alanine richness, codon rarity, a repeated amino acid stretch and a nearby second AUG. These features may help slow down the leading ribosome, causing trailing pre-initiation complexes (PICs) to pause near the native AUG, thereby facilitating accurate translation initiation. Amplification of erk genes is frequently observed in cancer, and we show that NTAR-dependent ERK protein levels are a rate-limiting step for signal output. Thus, NTAR-mediated control of translation may reflect a cellular need to precisely control translation of key transcripts such as potential oncogenes. By preventing translation in alternative reading frames, NTAR sequences may be useful in synthetic biology applications, e.g. translation from RNA vaccines.
Collapse
Affiliation(s)
- Roser Buscà
- Université Côte d’Azur (UCA), CNRS UMR 7284 and INSERM U 1081, Institute for Research on Cancer and Aging Nice (IRCAN), 28 Avenue de Valombrose, 06107 Nice, France
- Centre Antoine Lacassagne, Nice, France
| | - Cercina Onesto
- Université Côte d’Azur (UCA), CNRS UMR 7284 and INSERM U 1081, Institute for Research on Cancer and Aging Nice (IRCAN), 28 Avenue de Valombrose, 06107 Nice, France
- Centre Antoine Lacassagne, Nice, France
- Polytech’Nice Sophia, Bioengineering Department, Sophia-Antipolis, France
| | - Mylène Egensperger
- Université Côte d’Azur (UCA), CNRS UMR 7284 and INSERM U 1081, Institute for Research on Cancer and Aging Nice (IRCAN), 28 Avenue de Valombrose, 06107 Nice, France
- Centre Antoine Lacassagne, Nice, France
| | - Jacques Pouysségur
- Université Côte d’Azur (UCA), CNRS UMR 7284 and INSERM U 1081, Institute for Research on Cancer and Aging Nice (IRCAN), 28 Avenue de Valombrose, 06107 Nice, France
- Centre Antoine Lacassagne, Nice, France
- Centre Scientifique de Monaco, Biomedical Department, Principality of Monaco
| | - Gilles Pagès
- Université Côte d’Azur (UCA), CNRS UMR 7284 and INSERM U 1081, Institute for Research on Cancer and Aging Nice (IRCAN), 28 Avenue de Valombrose, 06107 Nice, France
- Centre Antoine Lacassagne, Nice, France
- Centre Scientifique de Monaco, Biomedical Department, Principality of Monaco
| | - Philippe Lenormand
- Université Côte d’Azur (UCA), CNRS UMR 7284 and INSERM U 1081, Institute for Research on Cancer and Aging Nice (IRCAN), 28 Avenue de Valombrose, 06107 Nice, France
- Centre Antoine Lacassagne, Nice, France
| |
Collapse
|
20
|
Aburayyan A, Carlson RJ, Rabie GN, Lee MK, Gulsuner S, Walsh T, Avraham KB, Kanaan MN, King MC. A paradoxical genotype-phenotype relationship: Low level of GOSR2 translation from a non-AUG start codon in a family with profound hearing loss. Hum Mol Genet 2023; 32:2265-2268. [PMID: 37074134 PMCID: PMC10321379 DOI: 10.1093/hmg/ddad066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 03/25/2023] [Accepted: 04/10/2023] [Indexed: 04/20/2023] Open
Affiliation(s)
- Amal Aburayyan
- Department of Genome Sciences and Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- Hereditary Research Laboratory, Department of Biology, Bethlehem University, Bethlehem, Palestine
| | - Ryan J Carlson
- Department of Genome Sciences and Department of Medicine, University of Washington, Seattle, WA, USA
| | - Grace N Rabie
- Hereditary Research Laboratory, Department of Biology, Bethlehem University, Bethlehem, Palestine
| | - Ming K Lee
- Department of Genome Sciences and Department of Medicine, University of Washington, Seattle, WA, USA
| | - Suleyman Gulsuner
- Department of Genome Sciences and Department of Medicine, University of Washington, Seattle, WA, USA
| | - Tom Walsh
- Department of Genome Sciences and Department of Medicine, University of Washington, Seattle, WA, USA
| | - Karen B Avraham
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Moien N Kanaan
- Hereditary Research Laboratory, Department of Biology, Bethlehem University, Bethlehem, Palestine
| | - Mary-Claire King
- Department of Genome Sciences and Department of Medicine, University of Washington, Seattle, WA, USA
| |
Collapse
|
21
|
Shamoon R, Yassin A, Charkaneh A. Detection of a Rare Mutation in the Initiation Codon of the β-Globin Gene ( HBB:C.2T > C; P.Met1Thr). Hemoglobin 2023; 47:118-121. [PMID: 37503544 DOI: 10.1080/03630269.2023.2240708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/14/2023] [Accepted: 07/19/2023] [Indexed: 07/29/2023]
Abstract
β-thalassemia is one of the most common inherited autosomal disorders in the northern Iraqi Kurdistan region. This study reports a rare mutation in the initiation codon of the β-globin gene (HBB: c.2T > C; p.Met1Thr) in an 11-year-old male with severe transfusion-dependent β-thalassemia. Molecular testing to uncover the mutations of the β-globin gene in the proband and his parents was performed by amplification and reverse hybridization. Sanger sequencing was conducted for further identification. A severe β-globin gene mutation in codon 8/9 [+G] was initially identified in the proband and his mother's DNA samples. However, the detection of only one β-globin gene mutation was not enough to elucidate the patient's severe phenotype. Thus, a rare mutation in the initiation codon was identified later in the proband and his father by Sanger sequencing. In thalassemias, the presence of a rare mutation should be suspected when the patient's genotype does not correlate with the phenotype.
Collapse
Affiliation(s)
- Rawand Shamoon
- Department of Pathology, College of Medicine, Hawler Medical University, Erbil, Iraq
- Department of Hematology, Nanakali Hospital of Blood Diseases and Cancer, Erbil, Iraq
- Department of Hematology, Thalassemia Care Center, Erbil, Iraq
- Department of Laboratory Medical Sciences, College of Health Sciences, Catholic University in Erbil, Erbil, Iraq
- Genetics Unit, Laboratory Division, PAR Private Hospital, Erbil, Iraq
| | - Ahmed Yassin
- Department of Internal Medicine, College of Medicine, Hawler Medical University, Erbil, Iraq
- Department of Clinical Hematology, Nanakali Hospital of Blood Diseases and Cancer, Erbil, Iraq
| | - Amir Charkaneh
- Genetics Unit, Laboratory Division, PAR Private Hospital, Erbil, Iraq
- Department of Biology, University of Guilan, Rasht, Iran
| |
Collapse
|
22
|
Rai MK. Start codon targeted (SCoT) polymorphism marker in plant genome analysis: current status and prospects. Planta 2023; 257:34. [PMID: 36622439 DOI: 10.1007/s00425-023-04067-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
The present review illustrates a comprehensive overview of the start codon targeted (SCoT) polymorphism marker and their utilization in various applications related to genetic and genomic studies. Start codon targeted (SCoT) polymorphism marker, a targeted fingerprinting marker technique, has gained considerable importance in plant genetics, genomics, and molecular breeding due to its many desirable features. SCoT marker targets the region flanking the start codon, a highly conserved region in plant genes. Therefore, it can distinguish genetic variations in a specific gene that link to a specific trait. It is a simple, novel, cost-effective, highly polymorphic, and reproducible molecular marker for which there is no need for prior sequence information. In the recent past, SCoT markers have been employed in many commercially important and underutilized plant species for a variety of applications, including genetic diversity analysis, interspecific/generic genetic relationships, cultivar/hybrid/species identification, sex determination, construction of linkage map, association mapping/analysis, differential gene expression, and genetic fidelity analysis of tissue culture-raised plants. The main aim of this review is to provide up-to-date information on SCoT markers and their application in many commercially important and underutilized plant species, mainly progress made in the last 8-10 years.
Collapse
Affiliation(s)
- Manoj K Rai
- Department of Environmental Science, Indira Gandhi National Tribal University, Amarkantak, MP, 484887, India.
| |
Collapse
|
23
|
Hiragori Y, Takahashi H, Karino T, Kaido A, Hayashi N, Sasaki S, Nakao K, Motomura T, Yamashita Y, Naito S, Onouchi H. Genome-wide identification of Arabidopsis non-AUG-initiated upstream ORFs with evolutionarily conserved regulatory sequences that control protein expression levels. Plant Mol Biol 2023; 111:37-55. [PMID: 36044152 DOI: 10.1007/s11103-022-01309-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
This study identified four novel regulatory non-AUG-initiated upstream ORFs (uORFs) with evolutionarily conserved sequences in Arabidopsis and elucidated the mechanism by which a non-AUG-initiated uORF promotes main ORF translation. Upstream open reading frames (uORFs) are short ORFs found in the 5'-untranslated regions (5'-UTRs) of eukaryotic transcripts and can influence the translation of protein-coding main ORFs (mORFs). Recent genome-wide ribosome profiling studies have revealed that hundreds or thousands of uORFs initiate translation at non-AUG start codons. However, the physiological significance of these non-AUG uORFs has so far been demonstrated for only a few of them. In this study, to identify physiologically important regulatory non-AUG uORFs in Arabidopsis, we took an approach that combined bioinformatics and experimental analysis. Since physiologically important non-AUG uORFs are likely to be conserved across species, we first searched the Arabidopsis genome for non-AUG-initiated uORFs with evolutionarily conserved sequences. Then, we examined the effects of the conserved non-AUG uORFs on the expression of the downstream mORFs using transient expression assays. As a result, three inhibitory and one promotive non-AUG uORFs were identified. Among the inhibitory non-AUG uORFs, two exerted repressive effects on mORF expression in an amino acid sequence-dependent manner. These two non-AUG uORFs are likely to encode regulatory peptides that cause ribosome stalling, thereby enhancing their repressive effects. In contrast, one of the identified regulatory non-AUG uORFs promoted mORF expression by alleviating the inhibitory effect of a downstream AUG-initiated uORF. These findings provide insights into the mechanisms that enable non-AUG uORFs to play regulatory roles despite their low translation initiation efficiencies.
Collapse
Affiliation(s)
- Yuta Hiragori
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Hiro Takahashi
- Graduate School of Medical Sciences, Kanazawa University, Kanazawa, 920-1192, Japan
- Graduate School of Horticulture, Chiba University, Matsudo, 271-8510, Japan
| | - Taihei Karino
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Atsushi Kaido
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Noriya Hayashi
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Shun Sasaki
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Kodai Nakao
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Taichiro Motomura
- Graduate School of Medical Sciences, Kanazawa University, Kanazawa, 920-1192, Japan
| | - Yui Yamashita
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Satoshi Naito
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Hitoshi Onouchi
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan.
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan.
| |
Collapse
|
24
|
López-Iniesta MJ, Parkar SN, Ramalho AC, Lacerda R, Costa IF, Zhao J, Romão L, Candeias MM. Conserved Double Translation Initiation Site for Δ160p53 Protein Hints at Isoform's Key Role in Mammalian Physiology. Int J Mol Sci 2022; 23:ijms232415844. [PMID: 36555484 PMCID: PMC9779343 DOI: 10.3390/ijms232415844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
p53 is the most commonly mutated gene in human cancers. Two fundamental reasons for this are its long protein isoforms protect from cancer, while its shorter C-terminal isoforms can support cancer and metastasis. Previously, we have shown that the Δ160p53 protein isoform enhances survival and the invasive character of cancer cells. Here, we identified a translation initiation site nine codons downstream of codon 160-the known initiation codon for the translation of Δ160p53-that is recognized by the translation machinery. When translation failed to initiate from AUG160 due to mutation, it initiated from AUG169 instead, producing similar levels of a similar protein, Δ169p53, which promoted cell survival as efficiently as Δ160p53 following DNA damage. Interestingly, almost all mammalian species with an orthologue to human AUG160 also possess one for AUG169, while none of the non-mammalian species lacking AUG160 have AUG169, even if that region of the p53 gene is well conserved. In view of our findings, we do not believe that Δ169p53 acts as a different p53 protein isoform; instead, we propose that the double translation initiation site strengthens the translation of these products with a critical role in cell homeostasis. Future studies will help verify if this is a more general mechanism for the expression of essential proteins in mammals.
Collapse
Affiliation(s)
- Maria José López-Iniesta
- MaRCU—Molecular and RNA Cancer Unit, Kyoto 606-8501, Japan
- Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Shrutee N. Parkar
- MaRCU—Molecular and RNA Cancer Unit, Kyoto 606-8501, Japan
- Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Ana Catarina Ramalho
- MaRCU—Molecular and RNA Cancer Unit, Kyoto 606-8501, Japan
- Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, 1649-016 Lisbon, Portugal
- BioISI–Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
- Laboratory of Cancer cell Biology, Graduate School of Biostudies, Kyoto University, 606-8501 Kyoto, Japan
| | - Rafaela Lacerda
- MaRCU—Molecular and RNA Cancer Unit, Kyoto 606-8501, Japan
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, 1649-016 Lisbon, Portugal
- BioISI–Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Inês F. Costa
- MaRCU—Molecular and RNA Cancer Unit, Kyoto 606-8501, Japan
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, 1649-016 Lisbon, Portugal
- BioISI–Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Jingyuan Zhao
- MaRCU—Molecular and RNA Cancer Unit, Kyoto 606-8501, Japan
- Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Luísa Romão
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, 1649-016 Lisbon, Portugal
- BioISI–Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Marco M. Candeias
- MaRCU—Molecular and RNA Cancer Unit, Kyoto 606-8501, Japan
- Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, 1649-016 Lisbon, Portugal
- BioISI–Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
- Correspondence: ; Tel.: +81-(0)75-753-9297
| |
Collapse
|
25
|
Gleason AC, Ghadge G, Sonobe Y, Roos RP. Kozak Similarity Score Algorithm Identifies Alternative Translation Initiation Codons Implicated in Cancers. Int J Mol Sci 2022; 23:ijms231810564. [PMID: 36142475 PMCID: PMC9506484 DOI: 10.3390/ijms231810564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/05/2022] [Accepted: 09/08/2022] [Indexed: 11/16/2022] Open
Abstract
Ribosome profiling and mass spectroscopy have identified canonical and noncanonical translation initiation codons (TICs) that are upstream of the main translation initiation site and used to translate oncogenic proteins. There have previously been conflicting reports about the patterns of nucleotides that surround noncanonical TICs. Here, we use a Kozak Similarity Score algorithm to find that nearly all of these TICs have flanking nucleotides closely matching the Kozak sequence. Remarkably, the nucleotides flanking alternative noncanonical TICs are frequently closer to the Kozak sequence than the nucleotides flanking TICs used to translate the gene’s main protein. Of note, the 5′ untranslated region (5‘UTR) of cancer-associated genes with an upstream TIC tend to be significantly longer than the same region in genes not associated with cancer. The presence of a longer-than-typical 5′UTR increases the likelihood of ribosome binding to upstream noncanonical TICs, and may be a distinguishing feature of a number of genes overexpressed in cancer. Noncanonical TICs that are located in the 5′UTR, although thought by some to be disadvantageous and suppressed by evolution, may translate oncogenic proteins because of their flanking nucleotides.
Collapse
|
26
|
Shi JJ, Cao Y, Lang QH, Dong Y, Huang LY, Yang LJ, Li JJ, Zhang XX, Wang DY. The effect of the nucleotides immediately upstream of the AUG start codon on the efficiency of translation initiation in sperm cells. Plant Reprod 2022; 35:221-231. [PMID: 35674836 DOI: 10.1007/s00497-022-00442-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
It is widely known that an optimal nucleotide sequence context immediately upstream of the AUG start codon greatly improves the efficiency of translation initiation of mRNA in mammalian and plant somatic cells, which in turn increases protein levels. However, it is still unclear whether a similar regulatory mechanism is also present in highly differentiated cells. Here, we surveyed this issue in Arabidopsis thaliana sperm cells and found that the sequence context-mediated regulation of translation initiation in sperm cells is generally similar to that in somatic cells. A simple motif of four adenine nucleotides at positions - 1 to - 4 greatly improved the efficiency of translation initiation, and when the motif was present there, translation was even initiated at some non-AUG codons in sperm cells. However, unlike that in mammalian cells, a mainly effective nucleotide site to regulate the efficiency of translation initiation was not present at positions - 1 to - 4 in sperm cells. Meanwhile, different from somatic cells, sperm cells did not use eukaryotic translation initiation factor 1 to regulate the efficiency in a poor context consisting of the lowest frequency nucleotides. All these results contribute to our understanding of the cytoplasmic event of translation initiation in highly differentiated sperm cells.
Collapse
Affiliation(s)
- Jiao-Jiao Shi
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, 710069, China
| | - Yuan Cao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, 710069, China
| | - Qiu-Hua Lang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, 710069, China
| | - Yao Dong
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, 710069, China
| | - Liu-Yuan Huang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, 710069, China
| | - Liu-Jie Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, 710069, China
| | - Jing-Jing Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, 710069, China
| | - Xue-Xin Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, 710069, China
| | - Dan-Yang Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, 710069, China.
| |
Collapse
|
27
|
Yeken MZ, Emiralioğlu O, Çiftçi V, Bayraktar H, Palacioğlu G, Özer G. Analysis of genetic diversity among common bean germplasm by start codon targeted (SCoT) markers. Mol Biol Rep 2022; 49:3839-3847. [PMID: 35301653 DOI: 10.1007/s11033-022-07229-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/01/2022] [Accepted: 02/03/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Breeding strategies to improve modern varieties having high yield, high nutritional value and resistance to biotic and abiotic stress, etc. is very important to make up for the food deficiencies. Molecular studies as a tool in breeding programs for the characterization of germplasm have been performed with several DNA marker systems. MATERIALS AND METHODS In the present study, the genetic diversity of 53 common bean landraces and 22 registered varieties from Turkey, and 12 genotypes from USDA was investigated using start codon targeted (SCoT) markers for the first time worldwide. The 8 primers having stronger and more polymorphic bands were used for PCR amplification. RESULTS The mean polymorphic band of all primers was found as 13.13. The average of polymorphic information content and resolving power values was 0.34 and 7.55, respectively. Analysis of molecular variance (AMOVA) explored the existence of higher genetic diversity within populations accounting for 92% compared to among populations variations. According to cluster analysis (UPGMA) and genetic structure based on SCoT data, accessions were separated into Andean (PopA) and Mesoamerican PopB) gene pools. Moreover, accessions were mostly placed in the same groups/subgroups according to their geographical origin. CONCLUSIONS A high level of genetic diversity was observed between the investigated accessions in this work. The findings will help to plant breeders to characterize common bean accessions.
Collapse
Affiliation(s)
- Mehmet Zahit Yeken
- Department of Field Crops, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Turkey
| | - Orkun Emiralioğlu
- Department of Field Crops, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Turkey
| | - Vahdettin Çiftçi
- Department of Field Crops, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Turkey
| | - Harun Bayraktar
- Department of Plant Protection, Faculty of Agriculture, Ankara University, Ankara, Turkey
| | - Gülsüm Palacioğlu
- Department of Plant Protection, Faculty of Agriculture, Ankara University, Ankara, Turkey
| | - Göksel Özer
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Turkey.
| |
Collapse
|
28
|
Licata NV, Cristofani R, Salomonsson S, Wilson KM, Kempthorne L, Vaizoglu D, D’Agostino VG, Pollini D, Loffredo R, Pancher M, Adami V, Bellosta P, Ratti A, Viero G, Quattrone A, Isaacs AM, Poletti A, Provenzani A. C9orf72 ALS/FTD dipeptide repeat protein levels are reduced by small molecules that inhibit PKA or enhance protein degradation. EMBO J 2022; 41:e105026. [PMID: 34791698 PMCID: PMC8724771 DOI: 10.15252/embj.2020105026] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 09/21/2021] [Accepted: 10/12/2021] [Indexed: 11/09/2022] Open
Abstract
Intronic GGGGCC (G4C2) hexanucleotide repeat expansion within the human C9orf72 gene represents the most common cause of familial forms of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) (C9ALS/FTD). Repeat-associated non-AUG (RAN) translation of repeat-containing C9orf72 RNA results in the production of neurotoxic dipeptide-repeat proteins (DPRs). Here, we developed a high-throughput drug screen for the identification of positive and negative modulators of DPR levels. We found that HSP90 inhibitor geldanamycin and aldosterone antagonist spironolactone reduced DPR levels by promoting protein degradation via the proteasome and autophagy pathways respectively. Surprisingly, cAMP-elevating compounds boosting protein kinase A (PKA) activity increased DPR levels. Inhibition of PKA activity, by both pharmacological and genetic approaches, reduced DPR levels in cells and rescued pathological phenotypes in a Drosophila model of C9ALS/FTD. Moreover, knockdown of PKA-catalytic subunits correlated with reduced translation efficiency of DPRs, while the PKA inhibitor H89 reduced endogenous DPR levels in C9ALS/FTD patient-derived iPSC motor neurons. Together, our results suggest new and druggable pathways modulating DPR levels in C9ALS/FTD.
Collapse
Affiliation(s)
- Nausicaa V Licata
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Riccardo Cristofani
- Dipartimento di Scienze Farmacologiche e BiomolecolariUniversità degli Studi di MilanoMilanItaly
| | - Sally Salomonsson
- Department of Neurodegenerative DiseaseUCL Queen Square Institute of NeurologyLondonUK
- UK Dementia Research Institute at UCLUCL Queen Square Institute of NeurologyLondonUK
| | - Katherine M Wilson
- Department of Neurodegenerative DiseaseUCL Queen Square Institute of NeurologyLondonUK
- UK Dementia Research Institute at UCLUCL Queen Square Institute of NeurologyLondonUK
| | - Liam Kempthorne
- Department of Neurodegenerative DiseaseUCL Queen Square Institute of NeurologyLondonUK
- UK Dementia Research Institute at UCLUCL Queen Square Institute of NeurologyLondonUK
| | - Deniz Vaizoglu
- Department of Neurodegenerative DiseaseUCL Queen Square Institute of NeurologyLondonUK
- UK Dementia Research Institute at UCLUCL Queen Square Institute of NeurologyLondonUK
| | - Vito G D’Agostino
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Daniele Pollini
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Rosa Loffredo
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Michael Pancher
- HTS Core Facility, Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Valentina Adami
- HTS Core Facility, Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Paola Bellosta
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
- Department of MedicineNYU at Grossman School of MedicineNYUSA
| | - Antonia Ratti
- Department of NeurologyStroke Unit and Laboratory of NeuroscienceIstituto Auxologico Italiano, IRCCSMilanItaly
- Dipartimento di Biotecnologie Mediche e Medicina TraslazionaleUniversità degli Studi di MilanoMilanItaly
| | | | - Alessandro Quattrone
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Adrian M Isaacs
- Department of Neurodegenerative DiseaseUCL Queen Square Institute of NeurologyLondonUK
- UK Dementia Research Institute at UCLUCL Queen Square Institute of NeurologyLondonUK
| | - Angelo Poletti
- Dipartimento di Scienze Farmacologiche e BiomolecolariUniversità degli Studi di MilanoMilanItaly
| | - Alessandro Provenzani
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| |
Collapse
|
29
|
Bhandari BK, Lim CS, Remus DM, Chen A, van Dolleweerd C, Gardner PP. Analysis of 11,430 recombinant protein production experiments reveals that protein yield is tunable by synonymous codon changes of translation initiation sites. PLoS Comput Biol 2021; 17:e1009461. [PMID: 34610008 PMCID: PMC8519471 DOI: 10.1371/journal.pcbi.1009461] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 10/15/2021] [Accepted: 09/19/2021] [Indexed: 12/16/2022] Open
Abstract
Recombinant protein production is a key process in generating proteins of interest in the pharmaceutical industry and biomedical research. However, about 50% of recombinant proteins fail to be expressed in a variety of host cells. Here we show that the accessibility of translation initiation sites modelled using the mRNA base-unpairing across the Boltzmann's ensemble significantly outperforms alternative features. This approach accurately predicts the successes or failures of expression experiments, which utilised Escherichia coli cells to express 11,430 recombinant proteins from over 189 diverse species. On this basis, we develop TIsigner that uses simulated annealing to modify up to the first nine codons of mRNAs with synonymous substitutions. We show that accessibility captures the key propensity beyond the target region (initiation sites in this case), as a modest number of synonymous changes is sufficient to tune the recombinant protein expression levels. We build a stochastic simulation model and show that higher accessibility leads to higher protein production and slower cell growth, supporting the idea of protein cost, where cell growth is constrained by protein circuits during overexpression.
Collapse
Affiliation(s)
- Bikash K. Bhandari
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Chun Shen Lim
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Daniela M. Remus
- Callaghan Innovation Protein Science and Engineering, University of Canterbury, Christchurch, New Zealand
| | - Augustine Chen
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Craig van Dolleweerd
- Biomolecular Interaction Center, University of Canterbury, Christchurch, New Zealand
| | - Paul P. Gardner
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
- Biomolecular Interaction Center, University of Canterbury, Christchurch, New Zealand
| |
Collapse
|
30
|
Kameda T, Asano K, Togashi Y. Free energy landscape of RNA binding dynamics in start codon recognition by eukaryotic ribosomal pre-initiation complex. PLoS Comput Biol 2021; 17:e1009068. [PMID: 34125830 PMCID: PMC8224888 DOI: 10.1371/journal.pcbi.1009068] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 06/24/2021] [Accepted: 05/12/2021] [Indexed: 12/25/2022] Open
Abstract
Specific interaction between the start codon, 5’-AUG-3’, and the anticodon, 5’-CAU-3’, ensures accurate initiation of translation. Recent studies show that several near-cognate start codons (e.g. GUG and CUG) can play a role in initiating translation in eukaryotes. However, the mechanism allowing initiation through mismatched base-pairs at the ribosomal decoding site is still unclear at an atomic level. In this work, we propose an extended simulation-based method to evaluate free energy profiles, through computing the distance between each base-pair of the triplet interactions involved in recognition of start codons in eukaryotic translation pre-initiation complex. Our method provides not only the free energy penalty for mismatched start codons relative to the AUG start codon, but also the preferred pathways of transitions between bound and unbound states, which has not been described by previous studies. To verify the method, the binding dynamics of cognate (AUG) and near-cognate start codons (CUG and GUG) were simulated. Evaluated free energy profiles agree with experimentally observed changes in initiation frequencies from respective codons. This work proposes for the first time how a G:U mismatch at the first position of codon (GUG)-anticodon base-pairs destabilizes the accommodation in the initiating eukaryotic ribosome and how initiation at a CUG codon is nearly as strong as, or sometimes stronger than, that at a GUG codon. Our method is expected to be applied to study the affinity changes for various mismatched base-pairs. Ribosomes synthesize proteins according to the sequence of nucleotides (A, U, G, and C) in mRNA, translating three nucleotides (codon) into an amino acid. If the reading frame is shifted, the resulting amino-acid sequence will be totally different. Hence, the translation should start at an exactly determined position of mRNA. This position is usually indicated by “AUG” (start codon), which is recognized by “CAU” anticodon in tRNA and then translated into methionine. However, translation sometimes initiates at another codon such as “GUG” or “CUG”, and its frequency varies depending on the codon. Then, what regulates the possibility of translation-initiation at such a mismatched codon? To answer the question, we employed computer simulation for the structural changes of RNAs and proteins involved in the process. Through the numerical analysis, we estimated how strongly the mRNA (codon) and the tRNA (anticodon) bind to each other and also inferred how they approach. The binding-strength correlates with the initiation frequency observed in experiments, and the approaching pathway could explain the difference. Our result shows the underlying mechanism for the fidelity of translation-initiation, and our method will be applied to the prediction and design of RNA-RNA interactions.
Collapse
Affiliation(s)
- Takeru Kameda
- Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
- RIKEN Center for Biosystems Dynamics Research (BDR), Wako, Saitama, Japan
| | - Katsura Asano
- Molecular Cellular and Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, Kansas, United States of America
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
- Hiroshima Research Center for Healthy Aging (HiHA), Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
- * E-mail: (KA); (YT)
| | - Yuichi Togashi
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
- Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
- RIKEN Center for Biosystems Dynamics Research (BDR), Higashi-Hiroshima, Hiroshima, Japan
- * E-mail: (KA); (YT)
| |
Collapse
|
31
|
Uehara H, Zhang X, Pereira F, Narendran S, Choi S, Bhuvanagiri S, Liu J, Ravi Kumar S, Bohner A, Carroll L, Archer B, Zhang Y, Liu W, Gao G, Ambati J, Jun AS, Ambati BK. Start codon disruption with CRISPR/Cas9 prevents murine Fuchs' endothelial corneal dystrophy. eLife 2021; 10:e55637. [PMID: 34100716 PMCID: PMC8216720 DOI: 10.7554/elife.55637] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 06/07/2021] [Indexed: 12/17/2022] Open
Abstract
A missense mutation of collagen type VIII alpha 2 chain (COL8A2) gene leads to early-onset Fuchs' endothelial corneal dystrophy (FECD), which progressively impairs vision through the loss of corneal endothelial cells. We demonstrate that CRISPR/Cas9-based postnatal gene editing achieves structural and functional rescue in a mouse model of FECD. A single intraocular injection of an adenovirus encoding both the Cas9 gene and guide RNA (Ad-Cas9-Col8a2gRNA) efficiently knocked down mutant COL8A2 expression in corneal endothelial cells, prevented endothelial cell loss, and rescued corneal endothelium pumping function in adult Col8a2 mutant mice. There were no adverse sequelae on histology or electroretinography. Col8a2 start codon disruption represents a non-surgical strategy to prevent vision loss in early-onset FECD. As this demonstrates the ability of Ad-Cas9-gRNA to restore the phenotype in adult post-mitotic cells, this method may be widely applicable to adult-onset diseases, even in tissues affected with disorders of non-reproducing cells.
Collapse
Affiliation(s)
- Hironori Uehara
- Phil and Penny Knight Campus for Accelerating Scientific Impact, University of OregonEugene, ORUnited States
| | - Xiaohui Zhang
- Phil and Penny Knight Campus for Accelerating Scientific Impact, University of OregonEugene, ORUnited States
| | - Felipe Pereira
- Department of Ophthalmology, University of VirginiaCharlottesvilleUnited States
| | - Siddharth Narendran
- Department of Ophthalmology, University of VirginiaCharlottesvilleUnited States
| | - Susie Choi
- Moran Eye Center, Department of Ophthalmology and Visual Sciences, University of UtahSalt Lake CityUnited States
| | - Sai Bhuvanagiri
- Moran Eye Center, Department of Ophthalmology and Visual Sciences, University of UtahSalt Lake CityUnited States
| | - Jinlu Liu
- Moran Eye Center, Department of Ophthalmology and Visual Sciences, University of UtahSalt Lake CityUnited States
| | - Sangeetha Ravi Kumar
- Phil and Penny Knight Campus for Accelerating Scientific Impact, University of OregonEugene, ORUnited States
| | - Austin Bohner
- Moran Eye Center, Department of Ophthalmology and Visual Sciences, University of UtahSalt Lake CityUnited States
| | - Lara Carroll
- Moran Eye Center, Department of Ophthalmology and Visual Sciences, University of UtahSalt Lake CityUnited States
| | - Bonnie Archer
- Phil and Penny Knight Campus for Accelerating Scientific Impact, University of OregonEugene, ORUnited States
| | - Yue Zhang
- Division of Epidemiology, Department of Internal Medicine, University of UtahSalt Lake CityUnited States
| | - Wei Liu
- Division of Epidemiology, Department of Internal Medicine, University of UtahSalt Lake CityUnited States
| | - Guangping Gao
- Gene Therapy Center, Department of Microbiology and Physiological Science Systems, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Jayakrishna Ambati
- Department of Ophthalmology, University of VirginiaCharlottesvilleUnited States
| | - Albert S Jun
- Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - Balamurali K Ambati
- Phil and Penny Knight Campus for Accelerating Scientific Impact, University of OregonEugene, ORUnited States
| |
Collapse
|
32
|
Auth M, Nyikó T, Auber A, Silhavy D. The role of RST1 and RIPR proteins in plant RNA quality control systems. Plant Mol Biol 2021; 106:271-284. [PMID: 33864582 PMCID: PMC8116306 DOI: 10.1007/s11103-021-01145-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 03/22/2021] [Indexed: 05/03/2023]
Abstract
To keep mRNA homeostasis, the RNA degradation, quality control and silencing systems should act in balance in plants. Degradation of normal mRNA starts with deadenylation, then deadenylated transcripts are degraded by the SKI-exosome 3'-5' and/or XRN4 5'-3' exonucleases. RNA quality control systems identify and decay different aberrant transcripts. RNA silencing degrades double-stranded transcripts and homologous mRNAs. It also targets aberrant and silencing prone transcripts. The SKI-exosome is essential for mRNA homeostasis, it functions in normal mRNA degradation and different RNA quality control systems, and in its absence silencing targets normal transcripts. It is highly conserved in eukaryotes, thus recent reports that the plant SKI-exosome is associated with RST1 and RIPR proteins and that, they are required for SKI-exosome-mediated decay of silencing prone transcripts were unexpected. To clarify whether RST1 and RIPR are essential for all SKI-exosome functions or only for the elimination of silencing prone transcripts, degradation of different reporter transcripts was studied in RST1 and RIPR inactivated Nicotiana benthamiana plants. As RST1 and RIPR, like the SKI-exosome, were essential for Non-stop and No-go decay quality control systems, and for RNA silencing- and minimum ORF-mediated decay, we propose that RST1 and RIPR are essential components of plant SKI-exosome supercomplex.
Collapse
Affiliation(s)
- Mariann Auth
- Biological Research Centre, Institute of Plant Biology, ELKH, Temesvári krt 62, 6726, Szeged, Hungary
- Agricultural Biotechnology Institute, Department of Genetics, NARIC, Gödöllő, Hungary
| | - Tünde Nyikó
- Agricultural Biotechnology Institute, Department of Genetics, NARIC, Gödöllő, Hungary
| | - Andor Auber
- Agricultural Biotechnology Institute, Department of Genetics, NARIC, Gödöllő, Hungary
| | - Dániel Silhavy
- Biological Research Centre, Institute of Plant Biology, ELKH, Temesvári krt 62, 6726, Szeged, Hungary.
- Agricultural Biotechnology Institute, Department of Genetics, NARIC, Gödöllő, Hungary.
| |
Collapse
|
33
|
Wang B, Wang Z, Pan N, Huang J, Wan C. Improved Identification of Small Open Reading Frames Encoded Peptides by Top-Down Proteomic Approaches and De Novo Sequencing. Int J Mol Sci 2021; 22:ijms22115476. [PMID: 34067398 PMCID: PMC8197016 DOI: 10.3390/ijms22115476] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/14/2021] [Accepted: 05/18/2021] [Indexed: 12/20/2022] Open
Abstract
Small open reading frames (sORFs) have translational potential to produce peptides that play essential roles in various biological processes. Nevertheless, many sORF-encoded peptides (SEPs) are still on the prediction level. Here, we construct a strategy to analyze SEPs by combining top-down and de novo sequencing to improve SEP identification and sequence coverage. With de novo sequencing, we identified 1682 peptides mapping to 2544 human sORFs, which were all first characterized in this work. Two-thirds of these new sORFs have reading frame shifts and use a non-ATG start codon. The top-down approach identified 241 human SEPs, with high sequence coverage. The average length of the peptides from the bottom-up database search was 19 amino acids (AA); from de novo sequencing, it was 9 AA; and from the top-down approach, it was 25 AA. The longer peptide positively boosts the sequence coverage, more efficiently distinguishing SEPs from the known gene coding sequence. Top-down has the advantage of identifying peptides with sequential K/R or high K/R content, which is unfavorable in the bottom-up approach. Our method can explore new coding sORFs and obtain highly accurate sequences of their SEPs, which can also benefit future function research.
Collapse
|
34
|
Abstract
Upstream open reading frames (uORFs) play widespread regulatory functions in modulating mRNA translation in eukaryotes, but the principles underlying the genomic distribution and evolution of uORFs remain poorly understood. Here, we analyze ~17 million putative canonical uORFs in 478 eukaryotic species that span most of the extant taxa of eukaryotes. We demonstrate how positive and purifying selection, coupled with differences in effective population size (Ne), has shaped the contents of uORFs in eukaryotes. Besides, gene expression level is important in influencing uORF occurrences across genes in a species. Our analyses suggest that most uORFs might play regulatory roles rather than encode functional peptides. We also show that the Kozak sequence context of uORFs has evolved across eukaryotic clades, and that noncanonical uORFs tend to have weaker suppressive effects than canonical uORFs in translation regulation. This study provides insights into the driving forces underlying uORF evolution in eukaryotes.
Collapse
Affiliation(s)
- Hong Zhang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
| | - Yirong Wang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
- College of Biology, Hunan University, Changsha, China
| | - Xinkai Wu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
| | - Xiaolu Tang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
| | - Changcheng Wu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China.
| |
Collapse
|
35
|
Despons L, Martin F. How Many Messenger RNAs Can Be Translated by the START Mechanism? Int J Mol Sci 2020; 21:ijms21218373. [PMID: 33171614 PMCID: PMC7664666 DOI: 10.3390/ijms21218373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/29/2020] [Accepted: 11/05/2020] [Indexed: 11/22/2022] Open
Abstract
Translation initiation is a key step in the protein synthesis stage of the gene expression pathway of all living cells. In this important process, ribosomes have to accurately find the AUG start codon in order to ensure the integrity of the proteome. “Structure Assisted RNA Translation”, or “START”, has been proposed to use stable secondary structures located in the coding sequence to augment start site selection by steric hindrance of the progression of pre-initiation complex on messenger RNA. This implies that such structures have to be located downstream and at on optimal distance from the AUG start codon (i.e., downstream nucleotide +16). In order to assess the importance of the START mechanism in the overall mRNA translation process, we developed a bioinformatic tool to screen coding sequences for such stable structures in a 50 nucleotide-long window spanning the nucleotides from +16 to +65. We screened eight bacterial genomes and six eukaryotic genomes. We found stable structures in 0.6–2.5% of eukaryotic coding sequences. Among these, approximately half of them were structures predicted to form G-quadruplex structures. In humans, we selected 747 structures. In bacteria, the coding sequences from Gram-positive bacteria contained 2.6–4.2% stable structures, whereas the structures were less abundant in Gram-negative bacteria (0.2–2.7%). In contrast to eukaryotes, putative G-quadruplex structures are very rare in the coding sequence of bacteria. Altogether, our study reveals that the START mechanism seems to be an ancient strategy to facilitate the start codon recognition that is used in different kingdoms of life.
Collapse
|
36
|
Simonetti A, Guca E, Bochler A, Kuhn L, Hashem Y. Structural Insights into the Mammalian Late-Stage Initiation Complexes. Cell Rep 2020; 31:107497. [PMID: 32268096 PMCID: PMC7166083 DOI: 10.1016/j.celrep.2020.03.061] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/17/2020] [Accepted: 03/18/2020] [Indexed: 12/12/2022] Open
Abstract
In higher eukaryotes, the mRNA sequence in the direct vicinity of the start codon, called the Kozak sequence (CRCCaugG, where R is a purine), is known to influence the rate of the initiation process. However, the molecular basis underlying its role remains poorly understood. Here, we present the cryoelectron microscopy (cryo-EM) structures of mammalian late-stage 48S initiation complexes (LS48S ICs) in the presence of two different native mRNA sequences, β-globin and histone 4, at overall resolution of 3 and 3.5 Å, respectively. Our high-resolution structures unravel key interactions from the mRNA to eukaryotic initiation factors (eIFs): 1A, 2, 3, 18S rRNA, and several 40S ribosomal proteins. In addition, we are able to study the structural role of ABCE1 in the formation of native 48S ICs. Our results reveal a comprehensive map of ribosome/eIF-mRNA and ribosome/eIF-tRNA interactions and suggest the impact of mRNA sequence on the structure of the LS48S IC.
Collapse
MESH Headings
- ATP-Binding Cassette Transporters/genetics
- ATP-Binding Cassette Transporters/metabolism
- Animals
- Codon, Initiator/genetics
- Codon, Initiator/ultrastructure
- Cryoelectron Microscopy/methods
- Enhancer Elements, Genetic/genetics
- Eukaryotic Initiation Factor-1/genetics
- Eukaryotic Initiation Factor-1/metabolism
- Eukaryotic Initiation Factor-2/genetics
- Eukaryotic Initiation Factor-2/metabolism
- Eukaryotic Initiation Factor-3/genetics
- Eukaryotic Initiation Factor-3/metabolism
- Eukaryotic Initiation Factors/metabolism
- Eukaryotic Initiation Factors/ultrastructure
- Humans
- Mice
- Peptide Chain Initiation, Translational
- Protein Biosynthesis
- RNA, Messenger/metabolism
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 18S/metabolism
- RNA, Transfer/metabolism
- Ribosomal Proteins/metabolism
- Ribosomes/metabolism
- Transcription Initiation, Genetic/physiology
- beta-Globins/genetics
- beta-Globins/ultrastructure
Collapse
Affiliation(s)
- Angelita Simonetti
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg 67000, France
| | - Ewelina Guca
- INSERM U1212 Acides nucléiques: Régulations Naturelle et Artificielle (ARNA), Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac 33607, France
| | - Anthony Bochler
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg 67000, France; INSERM U1212 Acides nucléiques: Régulations Naturelle et Artificielle (ARNA), Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac 33607, France
| | - Lauriane Kuhn
- Proteomic Platform Strasbourg - Esplanade, Institut de Biologie Moléculaire et Cellulaire, CNRS, Université de Strasbourg, Strasbourg 67000, France
| | - Yaser Hashem
- INSERM U1212 Acides nucléiques: Régulations Naturelle et Artificielle (ARNA), Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac 33607, France.
| |
Collapse
|
37
|
Khan YA, Jungreis I, Wright JC, Mudge JM, Choudhary JS, Firth AE, Kellis M. Evidence for a novel overlapping coding sequence in POLG initiated at a CUG start codon. BMC Genet 2020; 21:25. [PMID: 32138667 PMCID: PMC7059407 DOI: 10.1186/s12863-020-0828-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 02/19/2020] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND POLG, located on nuclear chromosome 15, encodes the DNA polymerase γ(Pol γ). Pol γ is responsible for the replication and repair of mitochondrial DNA (mtDNA). Pol γ is the only DNA polymerase found in mitochondria for most animal cells. Mutations in POLG are the most common single-gene cause of diseases of mitochondria and have been mapped over the coding region of the POLG ORF. RESULTS Using PhyloCSF to survey alternative reading frames, we found a conserved coding signature in an alternative frame in exons 2 and 3 of POLG, herein referred to as ORF-Y that arose de novo in placental mammals. Using the synplot2 program, synonymous site conservation was found among mammals in the region of the POLG ORF that is overlapped by ORF-Y. Ribosome profiling data revealed that ORF-Y is translated and that initiation likely occurs at a CUG codon. Inspection of an alignment of mammalian sequences containing ORF-Y revealed that the CUG codon has a strong initiation context and that a well-conserved predicted RNA stem-loop begins 14 nucleotides downstream. Such features are associated with enhanced initiation at near-cognate non-AUG codons. Reanalysis of the Kim et al. (2014) draft human proteome dataset yielded two unique peptides that map unambiguously to ORF-Y. An additional conserved uORF, herein referred to as ORF-Z, was also found in exon 2 of POLG. Lastly, we surveyed Clinvar variants that are synonymous with respect to the POLG ORF and found that most of these variants cause amino acid changes in ORF-Y or ORF-Z. CONCLUSIONS We provide evidence for a novel coding sequence, ORF-Y, that overlaps the POLG ORF. Ribosome profiling and mass spectrometry data show that ORF-Y is expressed. PhyloCSF and synplot2 analysis show that ORF-Y is subject to strong purifying selection. An abundance of disease-correlated mutations that map to exons 2 and 3 of POLG but also affect ORF-Y provides potential clinical significance to this finding.
Collapse
Affiliation(s)
- Yousuf A Khan
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK.
| | - Irwin Jungreis
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | - James C Wright
- Functional Proteomics, Division of Cancer Biology, Institute of Cancer Research, 123 Old Brompton Road, London, SW7 3RP, UK
| | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | | | - Andrew E Firth
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| |
Collapse
|
38
|
Manjunath H, Zhang H, Rehfeld F, Han J, Chang TC, Mendell JT. Suppression of Ribosomal Pausing by eIF5A Is Necessary to Maintain the Fidelity of Start Codon Selection. Cell Rep 2019; 29:3134-3146.e6. [PMID: 31801078 PMCID: PMC6917043 DOI: 10.1016/j.celrep.2019.10.129] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 10/19/2019] [Accepted: 10/30/2019] [Indexed: 12/12/2022] Open
Abstract
Sequences within 5' UTRs dictate the site and efficiency of translation initiation. In this study, an unbiased screen designed to interrogate the 5' UTR-mediated regulation of the growth-promoting gene MYC unexpectedly revealed the ribosomal pause relief factor eIF5A as a regulator of translation initiation codon selection. Depletion of eIF5A enhances upstream translation within 5' UTRs across yeast and human transcriptomes, including on the MYC transcript, where this results in increased production of an N-terminally extended protein. Furthermore, ribosome profiling experiments established that the function of eIF5A as a suppressor of ribosomal pausing at sites of suboptimal peptide bond formation is conserved in human cells. We present evidence that proximal ribosomal pausing on a transcript triggers enhanced use of upstream suboptimal or non-canonical initiation codons. Thus, we propose that eIF5A functions not only to maintain efficient translation elongation in eukaryotic cells but also to maintain the fidelity of translation initiation.
Collapse
Affiliation(s)
- Hema Manjunath
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - He Zhang
- Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390-8821, USA; Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390-8821, USA
| | - Frederick Rehfeld
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Jaeil Han
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Tsung-Cheng Chang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Joshua T Mendell
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| |
Collapse
|
39
|
Pons J, Bover P, Bidegaray-Batista L, Arnedo MA. Arm-less mitochondrial tRNAs conserved for over 30 millions of years in spiders. BMC Genomics 2019; 20:665. [PMID: 31438844 PMCID: PMC6706885 DOI: 10.1186/s12864-019-6026-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 08/12/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND In recent years, Next Generation Sequencing (NGS) has accelerated the generation of full mitogenomes, providing abundant material for studying different aspects of molecular evolution. Some mitogenomes have been observed to harbor atypical sequences with bizarre secondary structures, which origins and significance could only be fully understood in an evolutionary framework. RESULTS Here we report and analyze the mitochondrial sequences and gene arrangements of six closely related spiders in the sister genera Parachtes and Harpactocrates, which belong to the nocturnal, ground dwelling family Dysderidae. Species of both genera have compacted mitogenomes with many overlapping genes and strikingly reduced tRNAs that are among the shortest described within metazoans. Thanks to the conservation of the gene order and the nucleotide identity across close relatives, we were able to predict the secondary structures even on arm-less tRNAs, which would be otherwise unattainable for a single species. They exhibit aberrant secondary structures with the lack of either DHU or TΨC arms and many miss-pairings in the acceptor arm but this degeneracy trend goes even further since at least four tRNAs are arm-less in the six spider species studied. CONCLUSIONS The conservation of at least four arm-less tRNA genes in two sister spider genera for about 30 myr suggest that these genes are still encoding fully functional tRNAs though they may be post-transcriptionally edited to be fully functional as previously described in other species. We suggest that the presence of overlapping and truncated tRNA genes may be related and explains why spider mitogenomes are smaller than those of other invertebrates.
Collapse
Affiliation(s)
- Joan Pons
- Departamento de Biodiversidad y Conservación, Instituto Mediterráneo de Estudios Avanzados (CSIC-UIB), Miquel Marquès, 21, 07190 Esporles, Illes Balears Spain
| | - Pere Bover
- ARAID Foundation – IUCA Grupo-Aragosaurus, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12 -, 50009 Zaragoza, Spain
| | - Leticia Bidegaray-Batista
- Departamento de Biodiversidad y Genética, Instituto de Investigaciones Biológicas Clemente Estable, Avenida Italia 3318, 11600 Montevideo, CP Uruguay
| | - Miquel A. Arnedo
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals & Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Av. Diagonal 643, E-8028 Barcelona, Catalonia Spain
| |
Collapse
|
40
|
Pavel-Dinu M, Wiebking V, Dejene BT, Srifa W, Mantri S, Nicolas CE, Lee C, Bao G, Kildebeck EJ, Punjya N, Sindhu C, Inlay MA, Saxena N, DeRavin SS, Malech H, Roncarolo MG, Weinberg KI, Porteus MH. Gene correction for SCID-X1 in long-term hematopoietic stem cells. Nat Commun 2019; 10:1634. [PMID: 30967552 PMCID: PMC6456568 DOI: 10.1038/s41467-019-09614-y] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 03/12/2019] [Indexed: 12/28/2022] Open
Abstract
Gene correction in human long-term hematopoietic stem cells (LT-HSCs) could be an effective therapy for monogenic diseases of the blood and immune system. Here we describe an approach for X-linked sSevere cCombined iImmunodeficiency (SCID-X1) using targeted integration of a cDNA into the endogenous start codon to functionally correct disease-causing mutations throughout the gene. Using a CRISPR-Cas9/AAV6 based strategy, we achieve up to 20% targeted integration frequencies in LT-HSCs. As measures of the lack of toxicity we observe no evidence of abnormal hematopoiesis following transplantation and no evidence of off-target mutations using a high-fidelity Cas9 as a ribonucleoprotein complex. We achieve high levels of targeting frequencies (median 45%) in CD34+ HSPCs from six SCID-X1 patients and demonstrate rescue of lymphopoietic defect in a patient derived HSPC population in vitro and in vivo. In sum, our study provides specificity, toxicity and efficacy data supportive of clinical development of genome editing to treat SCID-Xl.
Collapse
Affiliation(s)
- Mara Pavel-Dinu
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Volker Wiebking
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Beruh T Dejene
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Waracharee Srifa
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Sruthi Mantri
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Carmencita E Nicolas
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Ciaran Lee
- Department of Bioengineering, Rice University, Houston, TX, 77030, USA
| | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX, 77030, USA
| | - Eric J Kildebeck
- Center for Engineering Innovation, University of Texas at Dallas, Richardson, TX, 75080, USA
| | - Niraj Punjya
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
- University of California Davis, School of Medicine, Sacramento, CA, 95817, USA
| | - Camille Sindhu
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Matthew A Inlay
- Department of Cellular and Molecular Biosciences, University of California Irvine, Irvine, CA, 92697, USA
| | - Nivedita Saxena
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Suk See DeRavin
- Laboratory of Host Defenses, National Institutes of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, 20892, USA
| | - Harry Malech
- Laboratory of Host Defenses, National Institutes of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, 20892, USA
| | - Maria Grazia Roncarolo
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Kenneth I Weinberg
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Matthew H Porteus
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA.
| |
Collapse
|
41
|
Sanz MA, Almela EG, García-Moreno M, Marina AI, Carrasco L. A viral RNA motif involved in signaling the initiation of translation on non-AUG codons. RNA 2019; 25:431-452. [PMID: 30659060 PMCID: PMC6426287 DOI: 10.1261/rna.068858.118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 01/11/2019] [Indexed: 06/09/2023]
Abstract
Noncanonical translation, and particularly initiation on non-AUG codons, are frequently used by viral and cellular mRNAs during virus infection and disease. The Sindbis virus (SINV) subgenomic mRNA (sgRNA) constitutes a unique model system to analyze the translation of a capped viral mRNA without the participation of several initiation factors. Moreover, sgRNA can initiate translation even when the AUG initiation codon is replaced by other codons. Using SINV replicons, we examined the efficacy of different codons in place of AUG to direct the synthesis of the SINV capsid protein. The substitution of AUG by CUG was particularly efficient in promoting the incorporation of leucine or methionine in similar percentages at the amino terminus of the capsid protein. Additionally, valine could initiate translation when the AUG is replaced by GUG. The ability of sgRNA to initiate translation on non-AUG codons was dependent on the integrity of a downstream stable hairpin (DSH) structure located in the coding region. The structural requirements of this hairpin to signal the initiation site on the sgRNA were examined in detail. Of interest, a virus bearing CUG in place of AUG in the sgRNA was able to infect cells and synthesize significant amounts of capsid protein. This virus infects the human haploid cell line HAP1 and the double knockout variant that lacks eIF2A and eIF2D. Collectively, these findings indicate that leucine-tRNA or valine-tRNA can participate in the initiation of translation of sgRNA by a mechanism dependent on the DSH. This mechanism does not involve the action of eIF2, eIF2A, or eIF2D.
Collapse
MESH Headings
- Capsid Proteins/biosynthesis
- Capsid Proteins/genetics
- Cell Line, Tumor
- Codon, Initiator/genetics
- Codon, Initiator/metabolism
- Eukaryotic Initiation Factor-2/deficiency
- Eukaryotic Initiation Factor-2/genetics
- Fibroblasts/metabolism
- Fibroblasts/virology
- Gene Expression Regulation
- Haploidy
- Host-Pathogen Interactions/genetics
- Humans
- Inverted Repeat Sequences
- Leucine/genetics
- Leucine/metabolism
- Methionine/genetics
- Methionine/metabolism
- Nucleic Acid Conformation
- Protein Biosynthesis
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Transfer, Leu/genetics
- RNA, Transfer, Leu/metabolism
- RNA, Transfer, Val/genetics
- RNA, Transfer, Val/metabolism
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Replicon
- Signal Transduction/genetics
- Sindbis Virus/genetics
- Sindbis Virus/metabolism
- Valine/genetics
- Valine/metabolism
Collapse
Affiliation(s)
- Miguel Angel Sanz
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco 28049 Madrid, Spain
| | - Esther González Almela
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco 28049 Madrid, Spain
| | - Manuel García-Moreno
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco 28049 Madrid, Spain
| | - Ana Isabel Marina
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco 28049 Madrid, Spain
| | - Luis Carrasco
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco 28049 Madrid, Spain
| |
Collapse
|
42
|
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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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.
Collapse
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
| |
Collapse
|
43
|
Gao F, Alekhina OM, Vassilenko KS, Simon AE. Unusual dicistronic expression from closely spaced initiation codons in an umbravirus subgenomic RNA. Nucleic Acids Res 2018; 46:11726-11742. [PMID: 30272199 PMCID: PMC6294492 DOI: 10.1093/nar/gky871] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 08/24/2018] [Accepted: 09/19/2018] [Indexed: 12/16/2022] Open
Abstract
Translation commencing at closely spaced initiation codons is common in RNA viruses with limited genome space. In the subgenomic RNA (sgRNA) of Pea enation mosaic virus 2, two closely spaced, out-of-frame start codons direct synthesis of movement/stability proteins p26 and p27. Efficient translation from AUG26/AUG27 is dependent on three 3'-proximal cap-independent translation enhancers (3'CITEs), whereas translation of the genomic (gRNA) requires only two. Contrary to strictly scanning-dependent initiation at the gRNA, sequence context of AUG26/AUG27 does not conform with Kozak requirements and insertion of efficient upstream AUGs had pronounced effects for AUG26 but only moderate effects for AUG27. Insertion of a hairpin within an extended 5' UTR did not significantly impact translation from AUG26/AUG27. Furthermore, AUG27 repressed translation from upstream AUG26 and this effect was mitigated when inter-codon spacing was reduced. Addition of a stable hairpin to the very 5' end of the sgRNA severely restricted translation, testifying that this 3'CITE-driven initiation is 5' end-dependent. Similar to gRNA, sgRNA reporter transcripts were nearly exclusively associated with light polysomes and 3'CITE-promoted long-distance interaction connecting the sgRNA ends affected the number of templates translated and not the initiation rate. We propose a non-canonical, 3'CITE-driven mechanism for efficient dicistronic expression from umbravirus sgRNAs.
Collapse
Affiliation(s)
- Feng Gao
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Olga M Alekhina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow 119435, Russia
| | - Konstantin S Vassilenko
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Anne E Simon
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| |
Collapse
|
44
|
Llácer JL, Hussain T, Saini AK, Nanda JS, Kaur S, Gordiyenko Y, Kumar R, Hinnebusch AG, Lorsch JR, Ramakrishnan V. Translational initiation factor eIF5 replaces eIF1 on the 40S ribosomal subunit to promote start-codon recognition. eLife 2018; 7:e39273. [PMID: 30475211 PMCID: PMC6298780 DOI: 10.7554/elife.39273] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 11/21/2018] [Indexed: 12/22/2022] Open
Abstract
In eukaryotic translation initiation, AUG recognition of the mRNA requires accommodation of Met-tRNAi in a 'PIN' state, which is antagonized by the factor eIF1. eIF5 is a GTPase activating protein (GAP) of eIF2 that additionally promotes stringent AUG selection, but the molecular basis of its dual function was unknown. We present a cryo-electron microscopy (cryo-EM) reconstruction of a yeast 48S pre-initiation complex (PIC), at an overall resolution of 3.0 Å, featuring the N-terminal domain (NTD) of eIF5 bound to the 40S subunit at the location vacated by eIF1. eIF5 interacts with and allows a more accommodated orientation of Met-tRNAi. Substitutions of eIF5 residues involved in the eIF5-NTD/tRNAi interaction influenced initiation at near-cognate UUG codonsin vivo, and the closed/open PIC conformation in vitro, consistent with direct stabilization of the codon:anticodon duplex by the wild-type eIF5-NTD. The present structure reveals the basis for a key role of eIF5 in start-codon selection.
Collapse
Affiliation(s)
- Jose Luis Llácer
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
- Instituto de Biomedicina de Valencia (IBV-CSIC)ValenciaSpain
| | - Tanweer Hussain
- Department of Molecular Reproduction, Development and GeneticsIndian Institute of ScienceBangaloreIndia
| | - Adesh K Saini
- Shoolini University of Biotechnology and Management SciencesHimachal PradeshIndia
| | - Jagpreet Singh Nanda
- Laboratory on the Mechanism and Regulation of Protein SynthesisEunice K Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
| | - Sukhvir Kaur
- Shoolini University of Biotechnology and Management SciencesHimachal PradeshIndia
| | | | - Rakesh Kumar
- Shoolini University of Biotechnology and Management SciencesHimachal PradeshIndia
| | - Alan G Hinnebusch
- Laboratory of Gene Regulation and DevelopmentEunice K Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
| | - Jon R Lorsch
- Laboratory on the Mechanism and Regulation of Protein SynthesisEunice K Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
| | - V Ramakrishnan
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| |
Collapse
|
45
|
Ma S, Viola R, Sui L, Cherubini V, Barbetti F, Egli D. β Cell Replacement after Gene Editing of a Neonatal Diabetes-Causing Mutation at the Insulin Locus. Stem Cell Reports 2018; 11:1407-1415. [PMID: 30503261 PMCID: PMC6294262 DOI: 10.1016/j.stemcr.2018.11.006] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 11/02/2018] [Accepted: 11/05/2018] [Indexed: 01/29/2023] Open
Abstract
Permanent neonatal diabetes mellitus (PNDM) can be caused by insulin mutations. We generated induced pluripotent stem cells from fibroblasts of a patient with PNDM and undetectable insulin at birth due to a homozygous mutation in the translation start site of the insulin gene. Differentiation of mutant cells resulted in insulin-negative endocrine stem cells expressing MAFA, NKX6.1, and chromogranin A. Correction of the mutation in stem cells and differentiation to pancreatic endocrine cells restored insulin production and insulin secretion to levels comparable to those of wild-type cells. Grafting of corrected cells into mice, followed by ablating mouse β cells using streptozotocin, resulted in normal glucose homeostasis, including at night, and the stem cell-derived grafts adapted insulin secretion to metabolic changes. Our study provides proof of principle for the generation of genetically corrected cells autologous to a patient with non-autoimmune insulin-dependent diabetes. These cases should be readily amenable to autologous cell therapy.
Collapse
Affiliation(s)
- Shuangyu Ma
- Naomi Berrie Diabetes Center & Department of Pediatrics, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY 10032, USA
| | - Ryan Viola
- Naomi Berrie Diabetes Center & Department of Pediatrics, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY 10032, USA
| | - Lina Sui
- Naomi Berrie Diabetes Center & Department of Pediatrics, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY 10032, USA
| | | | | | - Dieter Egli
- Naomi Berrie Diabetes Center & Department of Pediatrics, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY 10032, USA.
| |
Collapse
|
46
|
Sakuragi S, Shioda T, Sakuragi JI. Relationship between genome packaging and Gag translation/AUG of primate lentiviruses. Microbes Infect 2018; 21:119-123. [PMID: 30292880 DOI: 10.1016/j.micinf.2018.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 09/25/2018] [Accepted: 09/26/2018] [Indexed: 11/30/2022]
Abstract
About the relationship between retroviral genome packaging and translation, three possible modes (random-, trans-, and cis-) of packaging process could be assumed. In this report, we developed an assay system based on the RT-qPCR to measure the packaging efficiency of primate lentiviruses. With this system, we analyzed the genome packaging modes of primate lentiviruses such as HIV-1, 2, SIVmac and SIVagm. The data suggested that the modes of all viruses analyzed were very similar. In addition, we observed that the Gag-AUG sequences of them played important roles for maintaining efficient packaging, other than the initiation of translation.
Collapse
Affiliation(s)
- Sayuri Sakuragi
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Tatsuo Shioda
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Jun-Ichi Sakuragi
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan.
| |
Collapse
|
47
|
Abstract
Annotated sequence data are instrumental in nearly all realms of biology. However, the advent of next-generation sequencing has rapidly facilitated an imbalance between accurate sequence data and accurate annotation data. To increase the annotation accuracy of the Caulobacter vibrioides CB13b1a (CB13) genome, we compared the PGAP and RAST annotations of the CB13 genome. A total of 64 unique genes were identified in the PGAP annotation that were either completely or partially absent in the RAST annotation, and a total of 16 genes were identified in the RAST annotation that were not included in the PGAP annotation. Moreover, PGAP identified 73 frameshifted genes and 22 genes with an internal stop. In contrast, RAST annotated the larger segment of these frameshifted genes without indicating a change in reading frame may have occurred. The RAST annotation did not include any genes with internal stop codons, since it chose start codons that were after the internal stop. To confirm the discrepancies between the two annotations and verify the accuracy of the CB13 genome sequence data, we re-sequenced and re-annotated the entire genome and obtained an identical sequence, except in a small number of homopolymer regions. A genome sequence comparison between the two versions allowed us to determine the correct number of bases in each homopolymer region, which eliminated frameshifts for 31 genes annotated as frameshifted genes and removed 24 pseudogenes from the PGAP annotation. Both annotation systems correctly identified genes that were missed by the other system. In addition, PGAP identified conserved gene fragments that represented the beginning of genes, but it employed no corrective method to adjust the reading frame of frameshifted genes or the start sites of genes harboring an internal stop codon. In doing so, the PGAP annotation identified a large number of pseudogenes, which may reflect evolutionary history but likely do not produce gene products. These results demonstrate that re-sequencing and annotation comparisons can be used to increase the accuracy of genomic data and the corresponding gene annotation.
Collapse
Affiliation(s)
- Louis Berrios
- Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208, USA
| | - Bert Ely
- Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208, USA.
| |
Collapse
|
48
|
Wang YJ, Vaidyanathan PP, Rojas-Duran MF, Udeshi ND, Bartoli KM, Carr SA, Gilbert WV. Lso2 is a conserved ribosome-bound protein required for translational recovery in yeast. PLoS Biol 2018; 16:e2005903. [PMID: 30208026 PMCID: PMC6135351 DOI: 10.1371/journal.pbio.2005903] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 08/09/2018] [Indexed: 02/05/2023] Open
Abstract
Ribosome-binding proteins function broadly in protein synthesis, gene regulation, and cellular homeostasis, but the complete complement of functional ribosome-bound proteins remains unknown. Using quantitative mass spectrometry, we identified late-annotated short open reading frame 2 (Lso2) as a ribosome-associated protein that is broadly conserved in eukaryotes. Genome-wide crosslinking and immunoprecipitation of Lso2 and its human ortholog coiled-coil domain containing 124 (CCDC124) recovered 25S ribosomal RNA in a region near the A site that overlaps the GTPase activation center. Consistent with this location, Lso2 also crosslinked to most tRNAs. Ribosome profiling of yeast lacking LSO2 (lso2Δ) revealed global translation defects during recovery from stationary phase with translation of most genes reduced more than 4-fold. Ribosomes accumulated at start codons, were depleted from stop codons, and showed codon-specific changes in occupancy in lso2Δ. These defects, and the conservation of the specific ribosome-binding activity of Lso2/CCDC124, indicate broadly important functions in translation and physiology. Translation, or the production of protein from messenger RNA (mRNA), is catalyzed by a universally conserved macromolecular machine known as the ribosome. Ribosome-binding factors are also required for all substeps of translation, from initial recruitment of mRNA to peptide chain elongation to release of the mature polypeptide. However, many ribosome interactors have been identified whose effects on translation and physiology are unknown. Here, we show that the uncharacterized yeast protein late-annotated short open reading frame 2 (Lso2) crosslinks to a region of the ribosome that underlies accurate progression through all substeps of translation, the GTPase activation center. This specific binding activity is conserved in the human ortholog of Lso2, coiled-coil domain containing 124 (CCDC124). Null mutants of lso2 also show severe translation defects during recovery from extended starvation, including failure to initiate on most mRNAs and a general block to peptide chain elongation. We propose that these defects could arise from a function for Lso2 in modulating the activity or integrity of the ribosome GTPase activation center during challenging growth regimes.
Collapse
Affiliation(s)
- Yinuo J. Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | | | - Maria F. Rojas-Duran
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Namrata D. Udeshi
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Kristen M. Bartoli
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Steven A. Carr
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Wendy V. Gilbert
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
49
|
Charles Antony A, Alone PV. Fidelity of HIS4 start codon selection influences 3-amino-1,2,4-triazole sensitivity in GTPase activating protein function defective eIF5. J Genet 2018; 97:953-964. [PMID: 30262708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The eIF5 protein plays an important role in the fidelity of AUG start codon selection. However, the hyper GTPase eIF5G31R mutation in yeast causes preferential utilization of UUG as initiation codon and is termed as suppressor of initiation codon (Sui-) phenotype. The eIF5G31R mutant recognizes upUUG initiation codon from the 5' regulatory leader region of GCN4 transcript and dominantly represses GCN4 expression thereby conferring sensitivity to 3-amino-1,2,4-triazole (3AT)-induced starvation. The 3AT sensitivity was rescued by supplementing HIS4UUG allele. The eIF5G31R mutant has a better efficiency of UUG codon recognition from the HIS4UUG allele under starvation conditions. Moreover, the expression of HIS4UUG allele was significantly lower than the critical level causing additional derepression of GCN4 expression in eIF5G31R mutant to rescue its 3AT sensitivity. The overexpression of eIF1 improved expression of HIS4AUG allele and GCN4 transcript causing 3AT resistance, whereas overexpression of eIF1 resulted in diminished UUG codon recognition of HIS4UUG allele causing 3AT sensitivity, despite having higher GCN4 expression. This paper reports the critical role of HIS4 expression necessary in response to 3AT-induced starvation in the eIF5G31R mutant which is ostensibly not a direct target of 3AT inhibition.
Collapse
Affiliation(s)
- A Charles Antony
- School of Biological Sciences, National Institute of Science Education and Research, P.O. Jatni, Bhubaneswar, Khurda 752 050, India.
| | | |
Collapse
|
50
|
Rafizadeh A, Koohi-Dehkordi M, Sorkheh K. Molecular insights of genetic variation in milk thistle (Silybum marianum [L.] Gaertn.) populations collected from southwest Iran. Mol Biol Rep 2018; 45:601-609. [PMID: 29882084 DOI: 10.1007/s11033-018-4198-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 05/24/2018] [Indexed: 10/14/2022]
Abstract
Milk thistle (Silybum marianum) is among the world's popular medicinal plants. Start Codon Targeted (SCoT) marker system was utilized to investigate the genetic variability of 80 S. marianum genotypes from eight populations in Iran. SCoT marker produced 255 amplicons and 84.03% polymorphism was generated. The SCoT marker system's polymorphism information content value was 0.43. The primers' resolving power values were between 4.18 and 7.84. The percentage of polymorphic bands was between 33.3 and 100%. The Nei's gene diversity (h) was 0.19-1.30 with an average 0.72. The Shannon's index (I) ranged from 0.29 to 1.38 with an average value of 0.83. The average gene flow (0.37) demonstrated a high genetic variation among the studied populations. The variation of 42% was displayed by the molecular variance analysis among the populations while a recorded variation of 58% was made within the populations. Current investigation suggested that SCoT marker system could effectively evaluate milk thistle genotypes genetic diversity.
Collapse
Affiliation(s)
- Azam Rafizadeh
- Department of Agricultural Science, Payame-Noor University, P. O. Box 19395-3697, Tehran, Iran
| | - Mehrana Koohi-Dehkordi
- Department of Agricultural Science, Payame-Noor University, P. O. Box 19395-3697, Tehran, Iran.
| | - Karim Sorkheh
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahid Chamran University of Ahvaz, P. O. Box 61355/144, Ahvaz, Iran
| |
Collapse
|