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Sejour R, Leatherwood J, Yurovsky A, Futcher B. Enrichment of rare codons at 5' ends of genes is a spandrel caused by evolutionary sequence turnover and does not improve translation. eLife 2024; 12:RP89656. [PMID: 39008347 PMCID: PMC11249729 DOI: 10.7554/elife.89656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/16/2024] Open
Abstract
Previously, Tuller et al. found that the first 30-50 codons of the genes of yeast and other eukaryotes are slightly enriched for rare codons. They argued that this slowed translation, and was adaptive because it queued ribosomes to prevent collisions. Today, the translational speeds of different codons are known, and indeed rare codons are translated slowly. We re-examined this 5' slow translation 'ramp.' We confirm that 5' regions are slightly enriched for rare codons; in addition, they are depleted for downstream Start codons (which are fast), with both effects contributing to slow 5' translation. However, we also find that the 5' (and 3') ends of yeast genes are poorly conserved in evolution, suggesting that they are unstable and turnover relatively rapidly. When a new 5' end forms de novo, it is likely to include codons that would otherwise be rare. Because evolution has had a relatively short time to select against these codons, 5' ends are typically slightly enriched for rare, slow codons. Opposite to the expectation of Tuller et al., we show by direct experiment that genes with slowly translated codons at the 5' end are expressed relatively poorly, and that substituting faster synonymous codons improves expression. Direct experiment shows that slow codons do not prevent downstream ribosome collisions. Further informatic studies suggest that for natural genes, slow 5' ends are correlated with poor gene expression, opposite to the expectation of Tuller et al. Thus, we conclude that slow 5' translation is a 'spandrel'--a non-adaptive consequence of something else, in this case, the turnover of 5' ends in evolution, and it does not improve translation.
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Affiliation(s)
- Richard Sejour
- Department of Pharmacological Sciences, Stony Brook UniversityStony BrookUnited States
| | - Janet Leatherwood
- Department of Microbiology and Immunology, Stony Brook UniversityStony BrookUnited States
| | - Alisa Yurovsky
- Department of Biomedical Informatics, Stony Brook UniversityStony BrookUnited States
| | - Bruce Futcher
- Department of Microbiology and Immunology, Stony Brook UniversityStony BrookUnited States
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2
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Higdon AL, Won NH, Brar GA. Truncated protein isoforms generate diversity of protein localization and function in yeast. Cell Syst 2024; 15:388-408.e4. [PMID: 38636458 PMCID: PMC11075746 DOI: 10.1016/j.cels.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 01/21/2024] [Accepted: 03/20/2024] [Indexed: 04/20/2024]
Abstract
Genome-wide measurement of ribosome occupancy on mRNAs has enabled empirical identification of translated regions, but high-confidence detection of coding regions that overlap annotated coding regions has remained challenging. Here, we report a sensitive and robust algorithm that revealed the translation of 388 N-terminally truncated proteins in budding yeast-more than 30-fold more than previously known. We extensively experimentally validated them and defined two classes. The first class lacks large portions of the annotated protein and tends to be produced from a truncated transcript. We show that two such cases, Yap5truncation and Pus1truncation, have condition-specific regulation and distinct functions from their respective annotated isoforms. The second class of truncated protein isoforms lacks only a small region of the annotated protein and is less likely to be produced from an alternative transcript isoform. Many display different subcellular localizations than their annotated counterpart, representing a common strategy for dual localization of otherwise functionally identical proteins. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Andrea L Higdon
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Nathan H Won
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Gloria A Brar
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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Hannon Bozorgmehr J. Four classic "de novo" genes all have plausible homologs and likely evolved from retro-duplicated or pseudogenic sequences. Mol Genet Genomics 2024; 299:6. [PMID: 38315248 DOI: 10.1007/s00438-023-02090-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 10/15/2023] [Indexed: 02/07/2024]
Abstract
Despite being previously regarded as extremely unlikely, the idea that entirely novel protein-coding genes can emerge from non-coding sequences has gradually become accepted over the past two decades. Examples of "de novo origination", resulting in lineage-specific "orphan" genes, lacking coding orthologs, are now produced every year. However, many are likely cases of duplicates that are difficult to recognize. Here, I re-examine the claims and show that four very well-known examples of genes alleged to have emerged completely "from scratch"- FLJ33706 in humans, Goddard in fruit flies, BSC4 in baker's yeast and AFGP2 in codfish-may have plausible evolutionary ancestors in pre-existing genes. The first two are likely highly diverged retrogenes coding for regulatory proteins that have been misidentified as orphans. The antifreeze glycoprotein, moreover, may not have evolved from repetitive non-genic sequences but, as in several other related cases, from an apolipoprotein that could have become pseudogenized before later being reactivated. These findings detract from various claims made about de novo gene birth and show there has been a tendency not to invest the necessary effort in searching for homologs outside of a very limited syntenic or phylostratigraphic methodology. A robust approach is used for improving detection that draws upon similarities, not just in terms of statistical sequence analysis, but also relating to biochemistry and function, to obviate notable failures to identify homologs.
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Higdon AL, Won NH, Brar GA. Truncated protein isoforms generate diversity of protein localization and function in yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.13.548938. [PMID: 37503254 PMCID: PMC10369987 DOI: 10.1101/2023.07.13.548938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Genome-wide measurements of ribosome occupancy on mRNA transcripts have enabled global empirical identification of translated regions. These approaches have revealed an unexpected diversity of protein products, but high-confidence identification of new coding regions that entirely overlap annotated coding regions - including those that encode truncated protein isoforms - has remained challenging. Here, we develop a sensitive and robust algorithm focused on identifying N-terminally truncated proteins genome-wide, identifying 388 truncated protein isoforms, a more than 30-fold increase in the number known in budding yeast. We perform extensive experimental validation of these truncated proteins and define two general classes. The first set lack large portions of the annotated protein sequence and tend to be produced from a truncated transcript. We show two such cases, Yap5 truncation and Pus1 truncation , to have condition-specific regulation and functions that appear distinct from their respective annotated isoforms. The second set of N-terminally truncated proteins lack only a small region of the annotated protein and are less likely to be regulated by an alternative transcript isoform. Many localize to different subcellular compartments than their annotated counterpart, representing a common strategy for achieving dual localization of otherwise functionally identical proteins.
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Ordon J, Kiel N, Becker D, Kretschmer C, Schulze-Lefert P, Stuttmann J. Targeted gene deletion with SpCas9 and multiple guide RNAs in Arabidopsis thaliana: four are better than two. PLANT METHODS 2023; 19:30. [PMID: 36978193 PMCID: PMC10053088 DOI: 10.1186/s13007-023-01010-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/21/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND In plant genome editing, RNA-guided nucleases such as Cas9 from Streptococcus pyogenes (SpCas9) predominantly induce small insertions or deletions at target sites. This can be used for inactivation of protein-coding genes by frame shift mutations. However, in some cases, it may be advantageous to delete larger chromosomal segments. This is achieved by simultaneously inducing double strand breaks upstream and downstream of the segment to be deleted. Experimental approaches for the deletion of larger chromosomal segments have not been systematically evaluated. RESULTS We designed three pairs of guide RNAs for deletion of a ~ 2.2 kb chromosomal segment containing the Arabidopsis WRKY30 locus. We tested how the combination of guide RNA pairs and co-expression of the exonuclease TREX2 affect the frequency of wrky30 deletions in editing experiments. Our data demonstrate that compared to one pair of guide RNAs, two pairs increase the frequency of chromosomal deletions. The exonuclease TREX2 enhanced mutation frequency at individual target sites and shifted the mutation profile towards larger deletions. However, TREX2 did not elevate the frequency of chromosomal segment deletions. CONCLUSIONS Multiplex editing with at least two pairs of guide RNAs (four guide RNAs in total) elevates the frequency of chromosomal segment deletions at least at the AtWRKY30 locus, and thus simplifies the selection of corresponding mutants. Co-expression of the TREX2 exonuclease can be used as a general strategy to increase editing efficiency in Arabidopsis without obvious negative effects.
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Affiliation(s)
- Jana Ordon
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, D50829, Cologne, Germany
| | - Niklas Kiel
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, D50829, Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Dieter Becker
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, D50829, Cologne, Germany
| | - Carola Kretschmer
- Institute for Biology, Department of Plant Genetics, Martin Luther University Halle-Wittenberg, D06120, Halle, Germany
| | - Paul Schulze-Lefert
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, D50829, Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Johannes Stuttmann
- Institute for Biosafety in Plant Biotechnology, Federal Research Centre for Cultivated Plants, Julius Kühn-Institute (JKI), 06484, Quedlinburg, Germany.
- CEA, CNRS, BIAM, UMR7265, LEMiRE (Rhizosphère et Interactions sol-plante-microbiote), Aix Marseille University, 13115, Saint-Paul lez Durance, France.
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6
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Rozenberg I, Moses E, Harel I. CRISPR-Cas9 Genome Editing in Nothobranchius furzeri for Gene Knockout and Knock-In. Cold Spring Harb Protoc 2023; 2023:90-99. [PMID: 36223984 DOI: 10.1101/pdb.prot107742] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The African turquoise killifish Nothobranchius furzeri has recently gained interest as an emerging vertebrate model system for the study of aging, owing to its naturally short life span and generation time. Here, we provide a step-by-step guide for effective genome engineering using the CRISPR-Cas9 system to generate loss-of-function (i.e., knockout) alleles and for precise editing (i.e., knock-in) of short sequences into the genome. Using this approach, a new stable line can be created within several months. The killifish's tough chorion, rapid growth, and short life span are considered in this protocol and account for the key deviations from similar protocols in other fish models.
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Affiliation(s)
- Itai Rozenberg
- Department of Genetics, the Silberman Institute, the Hebrew University of Jerusalem, Givat Ram, Jerusalem, 91904 Israel
| | - Eitan Moses
- Department of Genetics, the Silberman Institute, the Hebrew University of Jerusalem, Givat Ram, Jerusalem, 91904 Israel
| | - Itamar Harel
- Department of Genetics, the Silberman Institute, the Hebrew University of Jerusalem, Givat Ram, Jerusalem, 91904 Israel
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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] [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.
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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
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Luo X, Maciaszek JL, Thompson BA, Leong HS, Dixon K, Sousa S, Anderson M, Roberts ME, Lee K, Spurdle AB, Mensenkamp AR, Brannan T, Pardo C, Zhang L, Pesaran T, Wei S, Fasaye GA, Kesserwan C, Shirts BH, Davis JL, Oliveira C, Plon SE, Schrader KA, Karam R. Optimising clinical care through CDH1-specific germline variant curation: improvement of clinical assertions and updated curation guidelines. J Med Genet 2022; 60:568-575. [PMID: 36600593 DOI: 10.1136/jmg-2022-108807] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 10/10/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND Germline pathogenic variants in CDH1 are associated with increased risk of diffuse gastric cancer and lobular breast cancer. Risk reduction strategies include consideration of prophylactic surgery, thereby making accurate interpretation of germline CDH1 variants critical for physicians deciding on these procedures. The Clinical Genome Resource (ClinGen) CDH1 Variant Curation Expert Panel (VCEP) developed specifications for CDH1 variant curation with a goal to resolve variants of uncertain significance (VUS) and with ClinVar conflicting interpretations and continues to update these specifications. METHODS CDH1 variant classification specifications were modified based on updated genetic testing clinical criteria, new recommendations from ClinGen and expert knowledge from ongoing CDH1 variant curations. The CDH1 VCEP reviewed 273 variants using updated CDH1 specifications and incorporated published and unpublished data provided by diagnostic laboratories. RESULTS Updated CDH1-specific interpretation guidelines include 11 major modifications since the initial specifications from 2018. Using the refined guidelines, 97% (36 of 37) of variants with ClinVar conflicting interpretations were resolved to benign, likely benign, likely pathogenic or pathogenic, and 35% (15 of 43) of VUS were resolved to benign or likely benign. Overall, 88% (239 of 273) of curated variants had non-VUS classifications. To date, variants classified as pathogenic are either nonsense, frameshift, splicing, or affecting the translation initiation codon, and the only missense variants classified as pathogenic or likely pathogenic have been shown to affect splicing. CONCLUSIONS The development and evolution of CDH1-specific criteria by the expert panel resulted in decreased uncertain and conflicting interpretations of variants in this clinically actionable gene, which can ultimately lead to more effective clinical management recommendations.
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Affiliation(s)
- Xi Luo
- Department of Pediatrics/Hematology-Oncology, Baylor College of Medicine, Houston, Texas, USA
| | - Jamie L Maciaszek
- Department of Pathology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Bryony A Thompson
- Department of Pathology, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Huei San Leong
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Katherine Dixon
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Sónia Sousa
- Instituto de Investigação e Inovação em Saúde - (i3S), University of Porto, Porto, Portugal.,Institute of Molecular Pathology and Immunology - (IPATIMUP), University of Porto, Porto, Portugal
| | | | | | - Kristy Lee
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Amanda B Spurdle
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Arjen R Mensenkamp
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | | | - Liying Zhang
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California, USA
| | | | - Sainan Wei
- Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, Kentucky, USA
| | - Grace-Ann Fasaye
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Brian H Shirts
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Jeremy L Davis
- Surgical Oncology Program, National Cancer Institute, Bethesda, Maryland, USA
| | - Carla Oliveira
- Instituto de Investigação e Inovação em Saúde - (i3S), University of Porto, Porto, Portugal.,Institute of Molecular Pathology and Immunology - (IPATIMUP), University of Porto, Porto, Portugal.,Department of Pathology, University of Porto, Porto, Portugal
| | - Sharon E Plon
- Department of Pediatrics/Hematology-Oncology, Baylor College of Medicine, Houston, Texas, USA
| | - Kasmintan A Schrader
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada.,Hereditary Cancer Program, BC Cancer, Vancouver, British Columbia, Canada
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9
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Maddi AMA, Kavousi K, Arabfard M, Ohadi H, Ohadi M. Tandem repeats ubiquitously flank and contribute to translation initiation sites. BMC Genom Data 2022; 23:59. [PMID: 35896982 PMCID: PMC9331589 DOI: 10.1186/s12863-022-01075-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 07/18/2022] [Indexed: 12/31/2022] Open
Abstract
Background While the evolutionary divergence of cis-regulatory sequences impacts translation initiation sites (TISs), the implication of tandem repeats (TRs) in TIS selection remains largely elusive. Here, we employed the TIS homology concept to study a possible link between TRs of all core lengths and repeats with TISs. Methods Human, as reference sequence, and 83 other species were selected, and data was extracted on the entire protein-coding genes (n = 1,611,368) and transcripts (n = 2,730,515) annotated for those species from Ensembl 102. Following TIS identification, two different weighing vectors were employed to assign TIS homology, and the co-occurrence pattern of TISs with the upstream flanking TRs was studied in the selected species. The results were assessed in 10-fold cross-validation. Results On average, every TIS was flanked by 1.19 TRs of various categories within its 120 bp upstream sequence, per species. We detected statistically significant enrichment of non-homologous human TISs co-occurring with human-specific TRs. On the contrary, homologous human TISs co-occurred significantly with non-human-specific TRs. 2991 human genes had at least one transcript, TIS of which was flanked by a human-specific TR. Text mining of a number of the identified genes, such as CACNA1A, EIF5AL1, FOXK1, GABRB2, MYH2, SLC6A8, and TTN, yielded predominant expression and functions in the human brain and/or skeletal muscle. Conclusion We conclude that TRs ubiquitously flank and contribute to TIS selection at the trans-species level. Future functional analyses, such as a combination of genome editing strategies and in vitro protein synthesis may be employed to further investigate the impact of TRs on TIS selection. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-022-01075-5.
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Wang Y, Chen P, Zhao M, Cao H, Zhao Y, Ji M, Hou P, Chen M. EGFL7 drives the evolution of resistance to EGFR inhibitors in lung cancer by activating NOTCH signaling. Cell Death Dis 2022; 13:910. [PMID: 36309484 PMCID: PMC9617940 DOI: 10.1038/s41419-022-05354-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 10/15/2022] [Accepted: 10/17/2022] [Indexed: 11/07/2022]
Abstract
Accumulating evidence supports evolutionary trait of drug resistance. Like resilience in other systems, most tumor cells experience drug-tolerant state before full resistance acquired. However, the underlying mechanism is still poorly understood. Here, we identify that EGF like domain multiple 7 (EGFL7) is a responsive gene to epidermal growth factor receptor (EGFR) kinase inhibition during a period when tumors are decimated. Moreover, our data reveal that the adaptive increase of EGFL7 during this process is controlled by the depression of nonsense-mediated mRNA decay (NMD) pathway. Upregulation of EGFL7 activates NOTCH signaling in lung cancer cells, which slows down the decrease of c-Myc caused by EGFR inhibition, thereby helping the survival of cancer cells. Our data, taken together, demonstrate that EGFL7 is a driver gene for resistance to EGFR kinase inhibition, and suggest that targeting EGFL7/NOTCH signaling may improve the clinical benefits of EGFR inhibitors in patients with EGFR mutant tumors.
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Affiliation(s)
- Yubo Wang
- grid.452438.c0000 0004 1760 8119Department of Respiratory Medicine, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061 Shaanxi PR China ,grid.452438.c0000 0004 1760 8119Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061 PR China
| | - Pu Chen
- grid.452438.c0000 0004 1760 8119Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061 PR China ,grid.452438.c0000 0004 1760 8119Department of Endocrinology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061 Shaanxi PR China
| | - Man Zhao
- grid.452438.c0000 0004 1760 8119Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061 PR China ,grid.452438.c0000 0004 1760 8119Department of Endocrinology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061 Shaanxi PR China
| | - Hongxin Cao
- grid.452438.c0000 0004 1760 8119Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061 PR China ,grid.452438.c0000 0004 1760 8119Department of Endocrinology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061 Shaanxi PR China
| | - Yuelei Zhao
- grid.452438.c0000 0004 1760 8119Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061 PR China ,grid.452438.c0000 0004 1760 8119Department of Endocrinology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061 Shaanxi PR China
| | - Meiju Ji
- grid.452438.c0000 0004 1760 8119Center for Translational Medicine, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061 Shaanxi PR China
| | - Peng Hou
- grid.452438.c0000 0004 1760 8119Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061 PR China ,grid.452438.c0000 0004 1760 8119Department of Endocrinology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061 Shaanxi PR China
| | - Mingwei Chen
- grid.452438.c0000 0004 1760 8119Department of Respiratory Medicine, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061 Shaanxi PR China
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11
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A previously unknown Argonaute 2 variant positively modulates the viability of melanoma cells. Cell Mol Life Sci 2022; 79:475. [PMID: 35943635 PMCID: PMC9363364 DOI: 10.1007/s00018-022-04496-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 07/13/2022] [Accepted: 07/18/2022] [Indexed: 11/28/2022]
Abstract
In malignant melanoma, a highly aggressive form of skin cancer, many microRNAs are aberrantly expressed contributing to tumorigenesis and progression. Further, deregulation of microRNA processing enzymes, like the miRNA-binding protein Argonaute 2, significantly impacts microRNA function. This study characterizes a novel splice variant of Argonaut 2, AGO2-ex1/3. AGO2-ex1/3 is substantially expressed in different melanoma cell lines and patient-derived tissue samples. It is a mature mRNA, which is translated into an N-terminally truncated Argonaute 2 protein form. Molecular dynamics simulations show that the PAZ, MID, and PIWI domain largely retain their structure in AGO2-ex1/3 and that the truncation of the N-terminus leads to an increased interdomain flexibility. Expression of AGO2-ex1/3 provides a survival advantage for melanoma cells while the knockdown causes significantly reduced proliferation and increases apoptosis. RNA-sequencing revealed that in cells lacking AGO2-ex1/3 expression many miRNA target genes are deregulated, implicating a considerable role of AGO2-ex1/3 for miRNA function. This study inaugurates insights into an important role of a so far unknown splice variant of Argonaute 2 for the miRNA pathway as well as the mechanisms which drive growth and survival of melanoma cells. This knowledge provides the basis for potential new promising therapeutic targets focusing on small RNA-mediated gene regulation in melanoma.
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Curson JE, Luo L, Liu L, Burgess BJ, Bokil NJ, Wall AA, Brdicka T, Kapetanovic R, Stow JL, Sweet MJ. An alternative downstream translation start site in the non-TIR adaptor Scimp enables selective amplification of CpG DNA responses in mouse macrophages. Immunol Cell Biol 2022; 100:267-284. [PMID: 35201640 PMCID: PMC9544816 DOI: 10.1111/imcb.12540] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 02/17/2022] [Accepted: 02/22/2022] [Indexed: 01/01/2023]
Abstract
Toll-like receptor (TLR) signaling relies on Toll/interleukin-1 receptor homology (TIR) domain-containing adaptor proteins that recruit downstream signaling molecules to generate tailored immune responses. In addition, the palmitoylated transmembrane adaptor protein family member Scimp acts as a non-TIR-containing adaptor protein in macrophages, scaffolding the Src family kinase Lyn to enable TLR phosphorylation and proinflammatory signaling responses. Here we report the existence of a smaller, naturally occurring translational variant of Scimp (Scimp TV1), which is generated through leaky scanning and translation at a downstream methionine. Scimp TV1 also scaffolds Lyn, but in contrast to full-length Scimp, it is basally rather than lipopolysaccharide (LPS)-inducibly phosphorylated. Macrophages from mice that selectively express Scimp TV1, but not full-length Scimp, have impaired sustained LPS-inducible cytokine responses. Furthermore, in granulocyte macrophage colony-stimulating factor-derived myeloid cells that express high levels of Scimp, selective overexpression of Scimp TV1 enhances CpG DNA-inducible cytokine production. Unlike full-length Scimp that localizes to the cell surface and filopodia, Scimp TV1 accumulates in intracellular compartments, particularly the Golgi. Moreover, this variant of Scimp is not inducibly phosphorylated in response to CpG DNA, suggesting that it may act via an indirect mechanism to enhance TLR9 responses. Our findings thus reveal the use of alternative translation start sites as a previously unrecognized mechanism for diversifying TLR responses in the innate immune system.
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Affiliation(s)
- James Eb Curson
- Institute for Molecular Bioscience (IMB), IMB Centre for Inflammation and Disease Research, and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Lin Luo
- Institute for Molecular Bioscience (IMB), IMB Centre for Inflammation and Disease Research, and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Liping Liu
- Institute for Molecular Bioscience (IMB), IMB Centre for Inflammation and Disease Research, and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Belinda J Burgess
- Institute for Molecular Bioscience (IMB), IMB Centre for Inflammation and Disease Research, and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Nilesh J Bokil
- Institute for Molecular Bioscience (IMB), IMB Centre for Inflammation and Disease Research, and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Adam A Wall
- Institute for Molecular Bioscience (IMB), IMB Centre for Inflammation and Disease Research, and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Tomas Brdicka
- Laboratory of Leukocyte Signaling, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Ronan Kapetanovic
- Institute for Molecular Bioscience (IMB), IMB Centre for Inflammation and Disease Research, and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia.,Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Jennifer L Stow
- Institute for Molecular Bioscience (IMB), IMB Centre for Inflammation and Disease Research, and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Matthew J Sweet
- Institute for Molecular Bioscience (IMB), IMB Centre for Inflammation and Disease Research, and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
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13
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Beaudoin CA, Bartas M, Volná A, Pečinka P, Blundell TL. Are There Hidden Genes in DNA/RNA Vaccines? Front Immunol 2022; 13:801915. [PMID: 35211117 PMCID: PMC8860813 DOI: 10.3389/fimmu.2022.801915] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/14/2022] [Indexed: 02/02/2023] Open
Abstract
Due to the fast global spreading of the Severe Acute Respiratory Syndrome Coronavirus - 2 (SARS-CoV-2), prevention and treatment options are direly needed in order to control infection-related morbidity, mortality, and economic losses. Although drug and inactivated and attenuated virus vaccine development can require significant amounts of time and resources, DNA and RNA vaccines offer a quick, simple, and cheap treatment alternative, even when produced on a large scale. The spike protein, which has been shown as the most antigenic SARS-CoV-2 protein, has been widely selected as the target of choice for DNA/RNA vaccines. Vaccination campaigns have reported high vaccination rates and protection, but numerous unintended effects, ranging from muscle pain to death, have led to concerns about the safety of RNA/DNA vaccines. In parallel to these studies, several open reading frames (ORFs) have been found to be overlapping SARS-CoV-2 accessory genes, two of which, ORF2b and ORF-Sh, overlap the spike protein sequence. Thus, the presence of these, and potentially other ORFs on SARS-CoV-2 DNA/RNA vaccines, could lead to the translation of undesired proteins during vaccination. Herein, we discuss the translation of overlapping genes in connection with DNA/RNA vaccines. Two mRNA vaccine spike protein sequences, which have been made publicly-available, were compared to the wild-type sequence in order to uncover possible differences in putative overlapping ORFs. Notably, the Moderna mRNA-1273 vaccine sequence is predicted to contain no frameshifted ORFs on the positive sense strand, which highlights the utility of codon optimization in DNA/RNA vaccine design to remove undesired overlapping ORFs. Since little information is available on ORF2b or ORF-Sh, we use structural bioinformatics techniques to investigate the structure-function relationship of these proteins. The presence of putative ORFs on DNA/RNA vaccine candidates implies that overlapping genes may contribute to the translation of smaller peptides, potentially leading to unintended clinical outcomes, and that the protein-coding potential of DNA/RNA vaccines should be rigorously examined prior to administration.
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Affiliation(s)
- Christopher A. Beaudoin
- Department of Biochemistry, Sanger Building, University of Cambridge, Cambridge, United Kingdom
| | - Martin Bartas
- Department of Biology and Ecology, University of Ostrava, Ostrava, Czechia
| | - Adriana Volná
- Department of Physics, University of Ostrava, Ostrava, Czechia
| | - Petr Pečinka
- Department of Biology and Ecology, University of Ostrava, Ostrava, Czechia
| | - Tom L. Blundell
- Department of Biochemistry, Sanger Building, University of Cambridge, Cambridge, United Kingdom
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14
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Willems P, Ndah E, Jonckheere V, Van Breusegem F, Van Damme P. To New Beginnings: Riboproteogenomics Discovery of N-Terminal Proteoforms in Arabidopsis Thaliana. FRONTIERS IN PLANT SCIENCE 2022; 12:778804. [PMID: 35069635 PMCID: PMC8770321 DOI: 10.3389/fpls.2021.778804] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/18/2021] [Indexed: 06/14/2023]
Abstract
Alternative translation initiation is a widespread event in biology that can shape multiple protein forms or proteoforms from a single gene. However, the respective contribution of alternative translation to protein complexity remains largely enigmatic. By complementary ribosome profiling and N-terminal proteomics (i.e., riboproteogenomics), we provide clear-cut evidence for ~90 N-terminal proteoform pairs shaped by (alternative) translation initiation in Arabidopsis thaliana. Next to several cases additionally confirmed by directed mutagenesis, identified alternative protein N-termini follow the enzymatic rules of co-translational N-terminal protein acetylation and initiator methionine removal. In contrast to other eukaryotic models, N-terminal acetylation in plants cannot generally be considered as a proxy of translation initiation because of its posttranslational occurrence on mature proteolytic neo-termini (N-termini) localized in the chloroplast stroma. Quantification of N-terminal acetylation revealed differing co- vs. posttranslational N-terminal acetylation patterns. Intriguingly, our data additionally hints to alternative translation initiation serving as a common mechanism to supply protein copies in multiple cellular compartments, as alternative translation sites are often in close proximity to cleavage sites of N-terminal transit sequences of nuclear-encoded chloroplastic and mitochondrial proteins. Overall, riboproteogenomics screening enables the identification of (differential localized) N-terminal proteoforms raised upon alternative translation.
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Affiliation(s)
- Patrick Willems
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Vlaams Instituut voor Biotechnologie (VIB)-Center for Plant Systems Biology, Ghent, Belgium
| | - Elvis Ndah
- integrative Riboproteogenomics, Interactomics and Proteomics Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Veronique Jonckheere
- integrative Riboproteogenomics, Interactomics and Proteomics Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Vlaams Instituut voor Biotechnologie (VIB)-Center for Plant Systems Biology, Ghent, Belgium
| | - Petra Van Damme
- integrative Riboproteogenomics, Interactomics and Proteomics Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
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15
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Xu C, Zhang J. Mammalian Alternative Translation Initiation Is Mostly Nonadaptive. Mol Biol Evol 2021; 37:2015-2028. [PMID: 32145028 DOI: 10.1093/molbev/msaa063] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Alternative translation initiation (ATLI) refers to the existence of multiple translation initiation sites per gene and is a widespread phenomenon in eukaryotes. ATLI is commonly assumed to be advantageous through creating proteome diversity or regulating protein synthesis. We here propose an alternative hypothesis that ATLI arises primarily from nonadaptive initiation errors presumably due to the limited ability of ribosomes to distinguish sequence motifs truly signaling translation initiation from similar sequences. Our hypothesis, but not the adaptive hypothesis, predicts a series of global patterns of ATLI, all of which are confirmed at the genomic scale by quantitative translation initiation sequencing in multiple human and mouse cell lines and tissues. Similarly, although many codons differing from AUG by one nucleotide can serve as start codons, our analysis suggests that using non-AUG start codons is mostly disadvantageous. These and other findings strongly suggest that ATLI predominantly results from molecular error, requiring a major revision of our understanding of the precision and regulation of translation initiation.
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Affiliation(s)
- Chuan Xu
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
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16
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Solaguren-Beascoa M, Bujakowska KM, Méjécase C, Emmenegger L, Orhan E, Neuillé M, Mohand-Saïd S, Condroyer C, Lancelot ME, Michiels C, Demontant V, Antonio A, Letexier M, Saraiva JP, Lonjou C, Carpentier W, Léveillard T, Pierce EA, Dollfus H, Sahel JA, Bhattacharya SS, Audo I, Zeitz C. WDR34, a candidate gene for non-syndromic rod-cone dystrophy. Clin Genet 2020; 99:298-302. [PMID: 33124039 DOI: 10.1111/cge.13872] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 09/01/2020] [Accepted: 10/26/2020] [Indexed: 01/30/2023]
Abstract
Rod-cone dystrophy (RCD), also called retinitis pigmentosa, is characterized by rod followed by cone photoreceptor degeneration, leading to gradual visual loss. Mutations in over 65 genes have been associated with non-syndromic RCD explaining 60% to 70% of cases, with novel gene defects possibly accounting for the unsolved cases. Homozygosity mapping and whole-exome sequencing applied to a case of autosomal recessive non-syndromic RCD from a consanguineous union identified a homozygous variant in WDR34. Mutations in WDR34 have been previously associated with severe ciliopathy syndromes possibly associated with a retinal dystrophy. This is the first report of a homozygous mutation in WDR34 associated with non-syndromic RCD.
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Affiliation(s)
- Maria Solaguren-Beascoa
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Kinga M Bujakowska
- Department of Ophthalmology, Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, USA
| | - Cécile Méjécase
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Lisa Emmenegger
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Elise Orhan
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Marion Neuillé
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Saddek Mohand-Saïd
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, INSERM-DGOS, CIC 1423, Paris, France
| | - Christel Condroyer
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Marie-Elise Lancelot
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Christelle Michiels
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Vanessa Demontant
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Aline Antonio
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | | | | | - Christine Lonjou
- Plateforme Post-Génomique P3S, Hôpital Pitié Salpêtrière, Paris, France
| | - Wassila Carpentier
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,Plateforme Post-Génomique P3S, Hôpital Pitié Salpêtrière, Paris, France
| | - Thierry Léveillard
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Eric A Pierce
- Department of Ophthalmology, Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, USA
| | - Hélène Dollfus
- Centre de Référence Pour les Affections Rares en Génétique Ophtalmologique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.,Laboratoire UMRS_1112, Institut de Génétique Médicale d'Alsace, Université de Strasbourg, Strasbourg, France
| | - José-Alain Sahel
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, INSERM-DGOS, CIC 1423, Paris, France.,Fondation Ophtalmologique Adolphe de Rothschild, Paris, France.,Department of Ophthalmology, The University of Pittsburgh School of Medicine University, Pittsburgh, USA.,Académie des Sciences-Institut de France, Paris, France
| | - Shomi S Bhattacharya
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,UCL-Institute of Ophthalmology, London, UK.,Department of Cellular Therapy and Regenerative Medicine, Andalusian Centre for Molecular Biology and Regenerative Medicine (CABIMER), Seville, Spain
| | - Isabelle Audo
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, INSERM-DGOS, CIC 1423, Paris, France.,UCL-Institute of Ophthalmology, London, UK
| | - Christina Zeitz
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
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17
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Identification and characterization of a new isoform of small GTPase RhoE. Commun Biol 2020; 3:572. [PMID: 33060740 PMCID: PMC7562701 DOI: 10.1038/s42003-020-01295-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 09/04/2020] [Indexed: 11/09/2022] Open
Abstract
The Rho family of GTPases consists of 20 members including RhoE. Here, we discover the existence of a short isoform of RhoE designated as RhoEα, the first Rho GTPase isoform generated from alternative translation. Translation of this new isoform is initiated from an alternative start site downstream of and in-frame with the coding region of the canonical RhoE. RhoEα exhibits a similar subcellular distribution while its protein stability is higher than RhoE. RhoEα contains binding capability to RhoE effectors ROCK1, p190RhoGAP and Syx. The distinct transcriptomes of cells with the expression of RhoE and RhoEα, respectively, are demonstrated. The data propose distinctive and overlapping biological functions of RhoEα compared to RhoE. In conclusion, this study reveals a new Rho GTPase isoform generated from alternative translation. The discovery provides a new scope of understanding the versatile functions of small GTPases and underlines the complexity and diverse roles of small GTPases. Dai et al. report the identification and characterization of a new isoform of RhoE (RhoEα), a member of the Rho GTPase family, which is generated from the same gene by alternative translation initiation at the downstream ATG codon 46. Compared to RhoE, RhoEα does not differ in the subcellular localization but has increased protein stability and distinct molecular signalling profile.
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18
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Translation initiation downstream from annotated start codons in human mRNAs coevolves with the Kozak context. Genome Res 2020; 30:974-984. [PMID: 32669370 PMCID: PMC7397870 DOI: 10.1101/gr.257352.119] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 06/25/2020] [Indexed: 12/13/2022]
Abstract
Eukaryotic translation initiation involves preinitiation ribosomal complex 5′-to-3′ directional probing of mRNA for codons suitable for starting protein synthesis. The recognition of codons as starts depends on the codon identity and on its immediate nucleotide context known as Kozak context. When the context is weak (i.e., nonoptimal), leaky scanning takes place during which a fraction of ribosomes continues the mRNA probing. We explored the relationship between the context of AUG codons annotated as starts of protein-coding sequences and the next AUG codon occurrence. We found that AUG codons downstream from weak starts occur in the same frame more frequently than downstream from strong starts. We suggest that evolutionary selection on in-frame AUGs downstream from weak start codons is driven by the advantage of the reduction of wasteful out-of-frame product synthesis and also by the advantage of producing multiple proteoforms from certain mRNAs. We confirmed translation initiation downstream from weak start codons using ribosome profiling data. We also tested translation of alternative start codons in 10 specific human genes using reporter constructs. In all tested cases, initiation at downstream start codons was more productive than at the annotated ones. In most cases, optimization of Kozak context did not completely abolish downstream initiation, and in the specific example of CMPK1 mRNA, the optimized start remained unproductive. Collectively, our work reveals previously uncharacterized forces shaping the evolution of protein-coding genes and points to the plurality of translation initiation and the existence of sequence features influencing start codon selection, other than Kozak context.
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19
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Bogaert A, Fernandez E, Gevaert K. N-Terminal Proteoforms in Human Disease. Trends Biochem Sci 2020; 45:308-320. [PMID: 32001092 DOI: 10.1016/j.tibs.2019.12.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 12/06/2019] [Accepted: 12/31/2019] [Indexed: 12/20/2022]
Abstract
The collection of chemically different protein variants, or proteoforms, by far exceeds the number of protein-coding genes in the human genome. Major contributors are alternative splicing and protein modifications. In this review, we focus on those proteoforms that differ at their N termini with a molecular link to disease. We describe the main underlying mechanisms that give rise to such N-terminal proteoforms, these being splicing, initiation of protein translation, and protein modifications. Given their role in several human diseases, it is becoming increasingly clear that several of these N-terminal proteoforms may have potential as therapeutic interventions and/or for diagnosing and prognosing their associated disease.
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Affiliation(s)
- Annelies Bogaert
- VIB Center for Medical Biotechnology, VIB, B-9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium
| | - Esperanza Fernandez
- VIB Center for Medical Biotechnology, VIB, B-9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology, VIB, B-9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.
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20
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Verma M, Choi J, Cottrell KA, Lavagnino Z, Thomas EN, Pavlovic-Djuranovic S, Szczesny P, Piston DW, Zaher HS, Puglisi JD, Djuranovic S. A short translational ramp determines the efficiency of protein synthesis. Nat Commun 2019; 10:5774. [PMID: 31852903 PMCID: PMC6920384 DOI: 10.1038/s41467-019-13810-1] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 11/25/2019] [Indexed: 01/26/2023] Open
Abstract
Translation initiation is a major rate-limiting step for protein synthesis. However, recent studies strongly suggest that the efficiency of protein synthesis is additionally regulated by multiple factors that impact the elongation phase. To assess the influence of early elongation on protein synthesis, we employed a library of more than 250,000 reporters combined with in vitro and in vivo protein expression assays. Here we report that the identity of the amino acids encoded by codons 3 to 5 impact protein yield. This effect is independent of tRNA abundance, translation initiation efficiency, or overall mRNA structure. Single-molecule measurements of translation kinetics revealed pausing of the ribosome and aborted protein synthesis on codons 4 and 5 of distinct amino acid and nucleotide compositions. Finally, introduction of preferred sequence motifs only at specific codon positions improves protein synthesis efficiency for recombinant proteins. Collectively, our data underscore the critical role of early elongation events in translational control of gene expression. Several factors contribute to the efficiency of protein expression. Here the authors show that the identity of amino acids encoded by codons at position 3–5 significantly impact translation efficiency and protein expression levels.
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Affiliation(s)
- Manasvi Verma
- Department of Cell Biology and Physiology, Washington University School of Medicine, 600 South Euclid Avenue, Campus Box 8228, St. Louis, MO, 63110, USA
| | - Junhong Choi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305-5126, USA.,Department of Applied Physics, Stanford University, Stanford, CA, 94305-5126, USA.,Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Kyle A Cottrell
- Department of Cell Biology and Physiology, Washington University School of Medicine, 600 South Euclid Avenue, Campus Box 8228, St. Louis, MO, 63110, USA
| | - Zeno Lavagnino
- Department of Cell Biology and Physiology, Washington University School of Medicine, 600 South Euclid Avenue, Campus Box 8228, St. Louis, MO, 63110, USA.,Experimental Imaging Center, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Erica N Thomas
- Department of Biology, Washington University, St Louis, MO, 63105, USA
| | - Slavica Pavlovic-Djuranovic
- Department of Cell Biology and Physiology, Washington University School of Medicine, 600 South Euclid Avenue, Campus Box 8228, St. Louis, MO, 63110, USA
| | - Pawel Szczesny
- Department of Bioinformatics, Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland
| | - David W Piston
- Department of Cell Biology and Physiology, Washington University School of Medicine, 600 South Euclid Avenue, Campus Box 8228, St. Louis, MO, 63110, USA
| | - Hani S Zaher
- Department of Biology, Washington University, St Louis, MO, 63105, USA
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305-5126, USA
| | - Sergej Djuranovic
- Department of Cell Biology and Physiology, Washington University School of Medicine, 600 South Euclid Avenue, Campus Box 8228, St. Louis, MO, 63110, USA.
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21
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Kulkarni SD, Zhou F, Sen ND, Zhang H, Hinnebusch AG, Lorsch JR. Temperature-dependent regulation of upstream open reading frame translation in S. cerevisiae. BMC Biol 2019; 17:101. [PMID: 31810458 PMCID: PMC6898956 DOI: 10.1186/s12915-019-0718-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 11/01/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Translation of an mRNA in eukaryotes starts at an AUG codon in most cases, but near-cognate codons (NCCs) such as UUG, ACG, and AUU can also be used as start sites at low levels in Saccharomyces cerevisiae. Initiation from NCCs or AUGs in the 5'-untranslated regions (UTRs) of mRNAs can lead to translation of upstream open reading frames (uORFs) that might regulate expression of the main ORF (mORF). Although there is some circumstantial evidence that the translation of uORFs can be affected by environmental conditions, little is known about how it is affected by changes in growth temperature. RESULTS Using reporter assays, we found that changes in growth temperature can affect translation from NCC start sites in yeast cells, suggesting the possibility that gene expression could be regulated by temperature by altering use of different uORF start codons. Using ribosome profiling, we provide evidence that growth temperature regulates the efficiency of translation of nearly 200 uORFs in S. cerevisiae. Of these uORFs, most that start with an AUG codon have increased translational efficiency at 37 °C relative to 30 °C and decreased efficiency at 20 °C. For translationally regulated uORFs starting with NCCs, we did not observe a general trend for the direction of regulation as a function of temperature, suggesting mRNA-specific features can determine the mode of temperature-dependent regulation. Consistent with this conclusion, the position of the uORFs in the 5'-leader relative to the 5'-cap and the start codon of the main ORF correlates with the direction of temperature-dependent regulation of uORF translation. We have identified several novel cases in which changes in uORF translation are inversely correlated with changes in the translational efficiency of the downstream main ORF. Our data suggest that translation of these mRNAs is subject to temperature-dependent, uORF-mediated regulation. CONCLUSIONS Our data suggest that alterations in the translation of specific uORFs by temperature can regulate gene expression in S. cerevisiae.
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Affiliation(s)
- Shardul D Kulkarni
- Laboratory on the Mechanism and Regulation of Protein Synthesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Fujun Zhou
- Laboratory on the Mechanism and Regulation of Protein Synthesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Neelam Dabas Sen
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
- Present Address: School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Hongen Zhang
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Alan G Hinnebusch
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
| | - Jon R Lorsch
- Laboratory on the Mechanism and Regulation of Protein Synthesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
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22
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David G, Fogeron ML, Montserret R, Lecoq L, Page A, Delolme F, Nassal M, Böckmann A. Phosphorylation and Alternative Translation on Wheat Germ Cell-Free Protein Synthesis of the DHBV Large Envelope Protein. Front Mol Biosci 2019; 6:138. [PMID: 31850370 PMCID: PMC6902406 DOI: 10.3389/fmolb.2019.00138] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/18/2019] [Indexed: 12/13/2022] Open
Abstract
Wheat-germ cell-free protein synthesis (WG-CFPS) is a potent platform for the high-yield production of proteins. It is especially of interest for difficult-to-express eukaryotic proteins, such as toxic and transmembrane proteins, and presents an important tool in high-throughput protein screening. Until recently, an assumed drawback of WG-CFPS was a reduced capacity for post-translational modifications. Meanwhile, phosphorylation has been observed in WG-CFPS; yet, authenticity of the respective phosphorylation sites remained unclear. Here we show that a viral membrane protein, the duck hepatitis B virus (DHBV) large envelope protein (DHBs L), produced by WG-CFPS, is phosphorylated upon translation at the same sites as DHBs L produced during DHBV infection of primary hepatocytes. Furthermore, we show that alternative translation initiation of the L protein, previously identified in virus-producing hepatic cells, occurs on WG-CFPS as well. Together, these findings further strengthen the high potential of WG-CFPS to include the reproduction of specific modifications proteins experience in vivo.
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Affiliation(s)
- Guillaume David
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, Lyon, France
| | - Marie-Laure Fogeron
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, Lyon, France
| | - Roland Montserret
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, Lyon, France
| | - Lauriane Lecoq
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, Lyon, France
| | - Adeline Page
- Protein Science Facility, SFR BioSciences CNRS UMS3444, Inserm US8, UCBL, ENS de Lyon, Lyon, France
| | - Frédéric Delolme
- Protein Science Facility, SFR BioSciences CNRS UMS3444, Inserm US8, UCBL, ENS de Lyon, Lyon, France
| | - Michael Nassal
- Internal Medicine II/Molecular Biology, University Hospital Freiburg, Freiburg, Germany
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, Lyon, France
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23
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Klepsch O, Namer LS, Köhler N, Kaempfer R, Dittrich A, Schaper F. Intragenic regulation of SOCS3 isoforms. Cell Commun Signal 2019; 17:70. [PMID: 31238931 PMCID: PMC6593527 DOI: 10.1186/s12964-019-0379-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 05/01/2019] [Indexed: 11/13/2022] Open
Abstract
Background Inflammatory reactions are commonly affected by stress responses. Interleukin-6 signalling is part of the inflammatory response and is stringently regulated by the feedback inhibitor SOCS3 expressed in a short and long isoform. Here, we studied the inhibitory potential of the two SOCS3 isoforms. Furthermore, we analysed the regulation of SOCS3 isoform expression and the role of PKR stress kinase signalling in SOCS3 protein expression. Methods We performed Western blotting, reporter assays, genetic analyses and manipulations for studying SOCS3 isoform expression and activation of signalling components involved in interleukin-6-induced and PKR-dependent signalling. Results Interleukin-6-induced endogenous expression of both SOCS3 isoforms was found in distinct cell types. Forced expression of either the long or short SOCS3 isoform demonstrated equal inhibitory activity of each isoform and confirmed longer half-life of the short isoform. Study of intragenic regulation of SOCS3 isoform expression revealed that (i) the 5′-UTR of SOCS3 mRNA restrains specifically expression of the long SOCS3 isoform, (ii) expression of the long isoform restrains expression of the short isoform, and (iii) signalling through the stress kinase PKR does not impact on SOCS3 isoform ratio. Conclusions Both SOCS3 isoforms show a similar potential for inhibiting interleukin-6 signalling but differ in their half-lives. Relative expression of the isoforms depends on intragenic elements yet is independent of PKR signalling. Graphic abstract ![]()
Electronic supplementary material The online version of this article (10.1186/s12964-019-0379-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Oliver Klepsch
- Department of Systems Biology, Institute of Biology, Otto-von-Guericke University Magdeburg, Universitätsplatz 2, 39106, Magdeburg, Germany
| | - Lise Sarah Namer
- Department of Biochemistry and Molecular Biology, Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, 9112102, Jerusalem, Israel
| | - Nadine Köhler
- Department of Systems Biology, Institute of Biology, Otto-von-Guericke University Magdeburg, Universitätsplatz 2, 39106, Magdeburg, Germany
| | - Raymond Kaempfer
- Department of Biochemistry and Molecular Biology, Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, 9112102, Jerusalem, Israel
| | - Anna Dittrich
- Department of Systems Biology, Institute of Biology, Otto-von-Guericke University Magdeburg, Universitätsplatz 2, 39106, Magdeburg, Germany.
| | - Fred Schaper
- Department of Systems Biology, Institute of Biology, Otto-von-Guericke University Magdeburg, Universitätsplatz 2, 39106, Magdeburg, Germany.
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24
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Lu Z, Lin Z. Pervasive and dynamic transcription initiation in Saccharomyces cerevisiae. Genome Res 2019; 29:1198-1210. [PMID: 31076411 PMCID: PMC6633255 DOI: 10.1101/gr.245456.118] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 05/07/2019] [Indexed: 12/15/2022]
Abstract
Transcription initiation is finely regulated to ensure proper expression and function of genes. The regulated transcription initiation in response to various environmental stimuli in a classic model organism Saccharomyces cerevisiae has not been systematically investigated. In this study, we generated quantitative maps of transcription start sites (TSSs) at a single-nucleotide resolution for S. cerevisiae grown in nine different conditions using no-amplification nontagging Cap analysis of gene expression (nAnT-iCAGE) sequencing. We mapped ∼1 million well-supported TSSs, suggesting highly pervasive transcription initiation in the compact genome of the budding yeast. The comprehensive TSS maps allowed us to identify core promoters for ∼96% verified protein-coding genes. We corrected misannotation of translation start codon for 122 genes and suggested an alternative start codon for 57 genes. We found that 56% of yeast genes are controlled by multiple core promoters, and alternative core promoter usage by a gene is widespread in response to changing environments. Most core promoter shifts are coupled with altered gene expression, indicating that alternative core promoter usage might play an important role in controlling gene transcriptional activities. Based on their activities in responding to environmental cues, we divided core promoters into constitutive class (55%) and inducible class (45%). The two classes of core promoters display distinctive patterns in transcriptional abundance, chromatin structure, promoter shape, and sequence context. In summary, our study improved the annotation of the yeast genome and demonstrated a much more pervasive and dynamic nature of transcription initiation in yeast than previously recognized.
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Affiliation(s)
- Zhaolian Lu
- Department of Biology, Saint Louis University, St. Louis, Missouri 63104, USA
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, St. Louis, Missouri 63104, USA
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25
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Sapkota D, Lake AM, Yang W, Yang C, Wesseling H, Guise A, Uncu C, Dalal JS, Kraft AW, Lee JM, Sands MS, Steen JA, Dougherty JD. Cell-Type-Specific Profiling of Alternative Translation Identifies Regulated Protein Isoform Variation in the Mouse Brain. Cell Rep 2019; 26:594-607.e7. [PMID: 30650354 PMCID: PMC6392083 DOI: 10.1016/j.celrep.2018.12.077] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 10/23/2018] [Accepted: 12/18/2018] [Indexed: 12/27/2022] Open
Abstract
Alternative translation initiation and stop codon readthrough in a few well-studied cases have been shown to allow the same transcript to generate multiple protein variants. Because the brain shows a particularly abundant use of alternative splicing, we sought to study alternative translation in CNS cells. We show that alternative translation is widespread and regulated across brain transcripts. In neural cultures, we identify alternative initiation on hundreds of transcripts, confirm several N-terminal protein variants, and show the modulation of the phenomenon by KCl stimulation. We also detect readthrough in cultures and show differential levels of normal and readthrough versions of AQP4 in gliotic diseases. Finally, we couple translating ribosome affinity purification to ribosome footprinting (TRAP-RF) for cell-type-specific analysis of neuronal and astrocytic translational readthrough in the mouse brain. We demonstrate that this unappreciated mechanism generates numerous and diverse protein isoforms in a cell-type-specific manner in the brain.
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Affiliation(s)
- Darshan Sapkota
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Allison M Lake
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Wei Yang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chengran Yang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hendrik Wesseling
- Boston Children's Hospital, F.M. Kirby Center for Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Amanda Guise
- Boston Children's Hospital, F.M. Kirby Center for Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Ceren Uncu
- Boston Children's Hospital, F.M. Kirby Center for Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Jasbir S Dalal
- Boston Children's Hospital, F.M. Kirby Center for Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Andrew W Kraft
- Departments of Neurology, Radiology, and Biomedical Engineering, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jin-Moo Lee
- Departments of Neurology, Radiology, and Biomedical Engineering, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Mark S Sands
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Deparment of Medicine, Washington University School of Medicine, St. Louis, MO 63112, USA
| | - Judith A Steen
- Boston Children's Hospital, F.M. Kirby Center for Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Joseph D Dougherty
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA.
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26
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Arabfard M, Kavousi K, Delbari A, Ohadi M. Link between short tandem repeats and translation initiation site selection. Hum Genomics 2018; 12:47. [PMID: 30373661 PMCID: PMC6206671 DOI: 10.1186/s40246-018-0181-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 10/10/2018] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Despite their vast biological implication, the relevance of short tandem repeats (STRs)/microsatellites to the protein-coding gene translation initiation sites (TISs) remains largely unknown. METHODS We performed an Ensembl-based comparative genomics study of all annotated orthologous TIS-flanking sequences in human and 46 other species across vertebrates, on the genomic DNA and cDNA platforms (755,956 TISs), aimed at identifying human-specific STRs in this interval. The collected data were used to examine the hypothesis of a link between STRs and TISs. BLAST was used to compare the initial five amino acids (excluding the initial methionine), codons of which were flanked by STRs in human, with the initial five amino acids of all annotated proteins for the orthologous genes in other vertebrates (total of 5,314,979 pair-wise TIS comparisons on the genomic DNA and cDNA platforms) in order to compare the number of events in which human-specific and non-specific STRs occurred with homologous and non-homologous TISs (i.e., ≥ 50% and < 50% similarity of the five amino acids). RESULTS We detected differential distribution of the human-specific STRs in comparison to the overall distribution of STRs on the genomic DNA and cDNA platforms (Mann Whitney U test p = 1.4 × 10-11 and p < 7.9 × 10-11, respectively). We also found excess occurrence of non-homologous TISs with human-specific STRs and excess occurrence of homologous TISs with non-specific STRs on both platforms (p < 0.00001). CONCLUSION We propose a link between STRs and TIS selection, based on the differential co-occurrence rate of human-specific STRs with non-homologous TISs and non-specific STRs with homologous TISs.
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Affiliation(s)
- Masoud Arabfard
- Department of Bioinformatics, Kish International Campus University of Tehran, Kish, Iran
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Kaveh Kavousi
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Ahmad Delbari
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Mina Ohadi
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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27
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Krivtsova O, Makarova A, Lazarevich N. Aberrant expression of alternative isoforms of transcription factors in hepatocellular carcinoma. World J Hepatol 2018; 10:645-661. [PMID: 30386458 PMCID: PMC6206146 DOI: 10.4254/wjh.v10.i10.645] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/08/2018] [Accepted: 06/28/2018] [Indexed: 02/06/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most prevalent malignancies worldwide and the second leading cause of death among all cancer types. Deregulation of the networks of tissue-specific transcription factors (TFs) observed in HCC leads to profound changes in the hepatic transcriptional program that facilitates tumor progression. In addition, recent reports suggest that substantial aberrations in the production of TF isoforms occur in HCC. In vitro experiments have identified distinct isoform-specific regulatory functions and related biological effects of liver-specific TFs that are implicated in carcinogenesis, which may be relevant for tumor progression and clinical outcome. This study reviews available data on the expression of isoforms of liver-specific and ubiquitous TFs in the liver and HCC and their effects, including HNF4α, C/EBPs, p73 and TCF7L2, and indicates that assessment of the ratio of isoforms and targeting specific TF variants may be beneficial for the prognosis and treatment of HCC.
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Affiliation(s)
- Olga Krivtsova
- Federal State Budgetary Institution, “N. N. Blokhin Medical Research Center of Oncology” of the Ministry of Health of the Russian Federation, Moscow 115478, Russian
- M. V. Lomonosov Moscow State University, Moscow 119991, Russian
| | - Anna Makarova
- Federal State Budgetary Institution, “N. N. Blokhin Medical Research Center of Oncology” of the Ministry of Health of the Russian Federation, Moscow 115478, Russian
| | - Natalia Lazarevich
- Federal State Budgetary Institution, “N. N. Blokhin Medical Research Center of Oncology” of the Ministry of Health of the Russian Federation, Moscow 115478, Russian
- M. V. Lomonosov Moscow State University, Moscow 119991, Russian
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28
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Abou Tayoun AN, Pesaran T, DiStefano MT, Oza A, Rehm HL, Biesecker LG, Harrison SM. Recommendations for interpreting the loss of function PVS1 ACMG/AMP variant criterion. Hum Mutat 2018; 39:1517-1524. [PMID: 30192042 DOI: 10.1002/humu.23626] [Citation(s) in RCA: 478] [Impact Index Per Article: 79.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 07/15/2018] [Accepted: 08/23/2018] [Indexed: 12/24/2022]
Abstract
The 2015 ACMG/AMP sequence variant interpretation guideline provided a framework for classifying variants based on several benign and pathogenic evidence criteria, including a pathogenic criterion (PVS1) for predicted loss of function variants. However, the guideline did not elaborate on specific considerations for the different types of loss of function variants, nor did it provide decision-making pathways assimilating information about variant type, its location, or any additional evidence for the likelihood of a true null effect. Furthermore, this guideline did not take into account the relative strengths for each evidence type and the final outcome of their combinations with respect to PVS1 strength. Finally, criteria specifying the genes for which PVS1 can be applied are still missing. Here, as part of the ClinGen Sequence Variant Interpretation (SVI) Workgroup's goal of refining ACMG/AMP criteria, we provide recommendations for applying the PVS1 criterion using detailed guidance addressing the above-mentioned gaps. Evaluation of the refined criterion by seven disease-specific groups using heterogeneous types of loss of function variants (n = 56) showed 89% agreement with the new recommendation, while discrepancies in six variants (11%) were appropriately due to disease-specific refinements. Our recommendations will facilitate consistent and accurate interpretation of predicted loss of function variants.
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Affiliation(s)
- Ahmad N Abou Tayoun
- The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,The University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | | | - Marina T DiStefano
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Andrea Oza
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Heidi L Rehm
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Leslie G Biesecker
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Steven M Harrison
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
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29
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Lia D, Reyes A, de Melo Campos JTA, Piolot T, Baijer J, Radicella JP, Campalans A. Mitochondrial maintenance under oxidative stress depends on mitochondrially localised α-OGG1. J Cell Sci 2018; 131:jcs.213538. [PMID: 29848661 DOI: 10.1242/jcs.213538] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 05/21/2018] [Indexed: 12/18/2022] Open
Abstract
Accumulation of 8-oxoguanine (8-oxoG) in mitochondrial DNA and mitochondrial dysfunction have been observed in cells deficient for the DNA glycosylase OGG1 when exposed to oxidative stress. In human cells, up to eight mRNAs for OGG1 can be generated by alternative splicing and it is still unclear which of them codes for the protein that ensures the repair of 8-oxoG in mitochondria. Here, we show that the α-OGG1 isoform, considered up to now to be exclusively nuclear, has a functional mitochondrial-targeting sequence and is imported into mitochondria. We analyse the sub-mitochondrial localisation of α-OGG1 with unprecedented resolution and show that this DNA glycosylase is associated with DNA in mitochondrial nucleoids. We show that the presence of α-OGG1 inside mitochondria and its enzymatic activity are required to preserve the mitochondrial network in cells exposed to oxidative stress. Altogether, these results unveil a new role of α-OGG1 in the mitochondria and indicate that the same isoform ensures the repair of 8-oxoG in both nuclear and mitochondrial genomes. The activity of α-OGG1 in mitochondria is sufficient for the recovery of organelle function after oxidative stress.
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Affiliation(s)
- Debora Lia
- Institut de Biologie François Jacob (IBFJ), Institute of Cellular and Molecular Radiobiology, CEA, UMR967 INSERM, 96265 Fontenay aux Roses, France.,Université Paris Diderot/Université Paris-Sud, 96265 Fontenay aux Roses, France
| | - Aurelio Reyes
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Julliane Tamara Araújo de Melo Campos
- Institut de Biologie François Jacob (IBFJ), Institute of Cellular and Molecular Radiobiology, CEA, UMR967 INSERM, 96265 Fontenay aux Roses, France.,Laboratório de Biologia Molecular e Genômica, Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN 59072-970, Brazil
| | - Tristan Piolot
- Institut Curie, CNRS UMR3215, INSERM U934, 75248 Paris, France
| | - Jan Baijer
- Institut de Biologie François Jacob (IBFJ), Institute of Cellular and Molecular Radiobiology, CEA, UMR967 INSERM, 96265 Fontenay aux Roses, France.,Université Paris Diderot/Université Paris-Sud, 96265 Fontenay aux Roses, France
| | - J Pablo Radicella
- Institut de Biologie François Jacob (IBFJ), Institute of Cellular and Molecular Radiobiology, CEA, UMR967 INSERM, 96265 Fontenay aux Roses, France.,Université Paris Diderot/Université Paris-Sud, 96265 Fontenay aux Roses, France
| | - Anna Campalans
- Institut de Biologie François Jacob (IBFJ), Institute of Cellular and Molecular Radiobiology, CEA, UMR967 INSERM, 96265 Fontenay aux Roses, France .,Université Paris Diderot/Université Paris-Sud, 96265 Fontenay aux Roses, France
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30
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Karagyaur MN, Rubtsov YP, Vasiliev PA, Tkachuk VA. Practical Recommendations for Improving Efficiency and Accuracy of the CRISPR/Cas9 Genome Editing System. BIOCHEMISTRY. BIOKHIMIIA 2018; 83:629-642. [PMID: 30195321 DOI: 10.1134/s0006297918060020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Indexed: 12/26/2022]
Abstract
CRISPR/Cas9 genome-editing system is a powerful, fairly accurate, and efficient tool for modifying genomic DNA. Despite obvious advantages, it is not devoid of certain drawbacks, such as propensity for introduction of additional nonspecific DNA breaks, insufficient activity against aneuploid genomes, and relative difficulty in delivering its components to cells. In this review, we focus on the difficulties that can limit the use of CRISPR/Cas9 and suggest a number of practical recommendations and information sources that will make it easier for the beginners to work with this outstanding technological achievement of the XXI century.
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Affiliation(s)
- M N Karagyaur
- Lomonosov Moscow State University, Institute of Regenerative Medicine, Moscow, 119192, Russia.
- Lomonosov Moscow State University, Faculty of Fundamental Medicine, Moscow, 119192, Russia
| | - Y P Rubtsov
- Lomonosov Moscow State University, Faculty of Fundamental Medicine, Moscow, 119192, Russia
| | - P A Vasiliev
- Research Center of Medical Genetics, Russian Academy of Medical Sciences, Moscow, 115478, Russia
| | - V A Tkachuk
- Lomonosov Moscow State University, Institute of Regenerative Medicine, Moscow, 119192, Russia
- Lomonosov Moscow State University, Faculty of Fundamental Medicine, Moscow, 119192, Russia
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31
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Medeiros AC, Soares CS, Coelho PO, Vieira NA, Baqui MMA, Teixeira FR, Gomes MD. DNA damage response signaling does not trigger redistribution of SAMHD1 to nuclear foci. Biochem Biophys Res Commun 2018; 499:790-796. [PMID: 29614270 DOI: 10.1016/j.bbrc.2018.03.225] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 03/30/2018] [Indexed: 11/16/2022]
Abstract
SAMHD1 (Sterile alpha motif and histidine-aspartic acid (HD) domain containing protein 1) is a deoxyribonucleoside triphosphate (dNTP) triphosphohydrolase (dNTPase) that restricts viral replication in infected cells. This protein is also involved in DNA repair by assisting in DNA end resection by homologous recombination (HR) after DNA double-strand break (DSB) induction with camptothecin (CPT) or etoposide (ETO). We showed that a monoclonal anti-SAMHD1 antibody produced against the full-length protein detected an unspecific 50 kDa protein that colocalized with dot-like structures after CPT treatment in HeLa cells. In contrast, a polyclonal anti-SAMHD1 antibody raised against the N-terminus of this protein specifically detected SAMHD1, as shown in Jurkat, HAP1KO and HEK293T SAMHD1-siRNA cell lysates compared with their respective controls. Our findings showed that SAMHD1 is not localized in dot-like structures under DSB induction in HeLa cells.
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Affiliation(s)
- Ana Carla Medeiros
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Brazil
| | - Claudia S Soares
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Brazil
| | - Priscila O Coelho
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Brazil
| | - Nichelle A Vieira
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Brazil
| | - Munira M A Baqui
- Department of Cell Biology, Ribeirão Preto Medical School, University of São Paulo, Brazil
| | - Felipe R Teixeira
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Brazil; Ribeirao Preto Medical School, University of São Paulo, and Department of Genetics and Evolution, Federal University of Sao Carlos, Brazil.
| | - Marcelo D Gomes
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Brazil.
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32
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van Zeijl A, Wardhani TAK, Seifi Kalhor M, Rutten L, Bu F, Hartog M, Linders S, Fedorova EE, Bisseling T, Kohlen W, Geurts R. CRISPR/Cas9-Mediated Mutagenesis of Four Putative Symbiosis Genes of the Tropical Tree Parasponia andersonii Reveals Novel Phenotypes. FRONTIERS IN PLANT SCIENCE 2018; 9:284. [PMID: 29559988 PMCID: PMC5845686 DOI: 10.3389/fpls.2018.00284] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 02/19/2018] [Indexed: 05/18/2023]
Abstract
Parasponia represents five fast-growing tropical tree species in the Cannabaceae and is the only plant lineage besides legumes that can establish nitrogen-fixing nodules with rhizobium. Comparative analyses between legumes and Parasponia allows identification of conserved genetic networks controlling this symbiosis. However, such studies are hampered due to the absence of powerful reverse genetic tools for Parasponia. Here, we present a fast and efficient protocol for Agrobacterium tumefaciens-mediated transformation and CRISPR/Cas9 mutagenesis of Parasponia andersonii. Using this protocol, knockout mutants are obtained within 3 months. Due to efficient micro-propagation, bi-allelic mutants can be studied in the T0 generation, allowing phenotypic evaluation within 6 months after transformation. We mutated four genes - PanHK4, PanEIN2, PanNSP1, and PanNSP2 - that control cytokinin, ethylene, or strigolactone hormonal networks and that in legumes commit essential symbiotic functions. Knockout mutants in Panhk4 and Panein2 displayed developmental phenotypes, namely reduced procambium activity in Panhk4 and disturbed sex differentiation in Panein2 mutants. The symbiotic phenotypes of Panhk4 and Panein2 mutant lines differ from those in legumes. In contrast, PanNSP1 and PanNSP2 are essential for nodule formation, a phenotype similar as reported for legumes. This indicates a conserved role for these GRAS-type transcriptional regulators in rhizobium symbiosis, illustrating the value of Parasponia trees as a research model for reverse genetic studies.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Rene Geurts
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University & Research, Wageningen, Netherlands
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33
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Loughran G, Firth AE, Atkins JF, Ivanov IP. Translational autoregulation of BZW1 and BZW2 expression by modulating the stringency of start codon selection. PLoS One 2018; 13:e0192648. [PMID: 29470543 PMCID: PMC5823381 DOI: 10.1371/journal.pone.0192648] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 01/26/2018] [Indexed: 01/20/2023] Open
Abstract
The efficiency of start codon selection during ribosomal scanning in eukaryotic translation initiation is influenced by the context or flanking nucleotides surrounding the AUG codon. The levels of eukaryotic translation initiation factors 1 (eIF1) and 5 (eIF5) play critical roles in controlling the stringency of translation start site selection. The basic leucine zipper and W2 domain-containing proteins 1 and 2 (BZW1 and BZW2), also known as eIF5-mimic proteins, are paralogous human proteins containing C-terminal HEAT domains that resemble the HEAT domain of eIF5. We show that translation of mRNAs encoding BZW1 and BZW2 homologs in fungi, plants and metazoans is initiated by AUG codons in conserved unfavorable initiation contexts. This conservation is reminiscent of the conserved unfavorable initiation context that enables autoregulation of EIF1. We show that overexpression of BZW1 and BZW2 proteins enhances the stringency of start site selection, and that their poor initiation codons confer autoregulation on BZW1 and BZW2 mRNA translation. We also show that overexpression of these two proteins significantly diminishes the effect of overexpressing eIF5 on stringency of start codon selection, suggesting they antagonize this function of eIF5. These results reveal a surprising role for BZW1 and BZW2 in maintaining homeostatic stringency of start codon selection, and taking into account recent biochemical, genetic and structural insights into eukaryotic initiation, suggest a model for BZW1 and BZW2 function.
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Affiliation(s)
- Gary Loughran
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Andrew E. Firth
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - John F. Atkins
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Ivaylo P. Ivanov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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34
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Fu Y, Zhang SS, Xiao S, Basheer WA, Baum R, Epifantseva I, Hong T, Shaw RM. Cx43 Isoform GJA1-20k Promotes Microtubule Dependent Mitochondrial Transport. Front Physiol 2017; 8:905. [PMID: 29163229 PMCID: PMC5682029 DOI: 10.3389/fphys.2017.00905] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 10/25/2017] [Indexed: 01/26/2023] Open
Abstract
Connexin 43 (Cx43, encoded by GJA1) is a cell-cell communication gap junction protein expressed in all organ systems. It was recently found that GJA1 mRNA undergoes alternative translation to generate N-terminal truncated isoforms, of which GJA1-20k is the most abundant. Here we report a surprising finding that, unlike full length GJA1-43k, GJA1-20k has a strong tropism for mitochondria. Exploring function, we found that GJA1-20k appears to be an organelle chaperone and that overexpression of GJA1-20k is sufficient to rescue mitochondrial localization to the cell periphery upon exposure to hydrogen peroxide, which effectively limits the network fragmentation that occurs with oxidative stress. By high-resolution fluorescent imaging and electron microscopy, we determined that GJA1-20k is enriched at the interface between mitochondria and microtubules, appearing to load organelles for transport. Mutagenesis experiments revealed that although the microtubule-binding domain (MTBD) in GJA1-20k is not necessary for protein localization to mitochondria, the MTBD is essential for GJA1-20k to facilitate mitochondrial transport and maintain mitochondrial localization at the periphery. These results reveal an unexpected role for the alternatively translated isoform of the Cx43 gap junction protein, GJA1-20k, which is to facilitate microtubule-based mitochondrial transport and to maintain mitochondrial network integrity during cellular stress.
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Affiliation(s)
- Ying Fu
- Cedars-Sinai Medical Center, Cedars-Sinai Heart Institute, Los Angeles, CA, United States
| | - Shan-Shan Zhang
- Cedars-Sinai Medical Center, Cedars-Sinai Heart Institute, Los Angeles, CA, United States
| | - Shaohua Xiao
- Cedars-Sinai Medical Center, Cedars-Sinai Heart Institute, Los Angeles, CA, United States
| | - Wassim A Basheer
- Cedars-Sinai Medical Center, Cedars-Sinai Heart Institute, Los Angeles, CA, United States
| | - Rachel Baum
- Cedars-Sinai Medical Center, Cedars-Sinai Heart Institute, Los Angeles, CA, United States
| | - Irina Epifantseva
- Cedars-Sinai Medical Center, Cedars-Sinai Heart Institute, Los Angeles, CA, United States
| | - TingTing Hong
- Cedars-Sinai Medical Center, Cedars-Sinai Heart Institute, Los Angeles, CA, United States.,Department of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Robin M Shaw
- Cedars-Sinai Medical Center, Cedars-Sinai Heart Institute, Los Angeles, CA, United States.,Department of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
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35
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Hossain MA, Claggett JM, Edwards SR, Shi A, Pennebaker SL, Cheng MY, Hasty J, Johnson TL. Posttranscriptional Regulation of Gcr1 Expression and Activity Is Crucial for Metabolic Adjustment in Response to Glucose Availability. Mol Cell 2017; 62:346-358. [PMID: 27153533 DOI: 10.1016/j.molcel.2016.04.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 03/03/2016] [Accepted: 04/11/2016] [Indexed: 12/20/2022]
Abstract
The transcription factor Gcr1 controls expression of over 75% of the genes in actively growing yeast. Yet despite its widespread effects, regulation of Gcr1 itself remains poorly understood. Here, we show that posttranscriptional Gcr1 regulation is nutrient dependent. Moreover, GCR1 RNA contains a long, highly conserved intron, which allows the cell to generate multiple RNA and protein isoforms whose levels change upon glucose depletion. Intriguingly, an isoform generated by intron retention is exported from the nucleus, and its translation is initiated from a conserved, intronic translation start site. Expression of gene products from both the spliced and unspliced RNAs is essential, as cells expressing only one isoform cannot adjust their metabolic program in response to environmental changes. Finally, we show that the Gcr1 proteins form dimers, providing an elegant mechanism by which this one gene, through its regulation, can perform the repertoire of transcriptional activities necessary for fine-tuned environmental response.
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Affiliation(s)
- Munshi Azad Hossain
- Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Julia M Claggett
- Molecular Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Samantha R Edwards
- Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Aishan Shi
- Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Sara L Pennebaker
- Molecular Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Melodyanne Y Cheng
- Molecular Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jeff Hasty
- Molecular Biology Section, Division of Biological Sciences, San Diego Center for Systems Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Tracy L Johnson
- Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
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36
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Abstract
The two main mechanisms that expand the proteomic output of eukaryotic genes are alternative splicing and alternative translation initiation signals. Despite being essential to generate isoforms of gene products that create functional diversity during development, the impact of these mechanisms on fine-tuning regulatory gene networks is still underappreciated. In this review, we use the Grainyhead-like (Grhl) family as a case study to illustrate the importance of isoforms when investigating transcription factor family function during development and disease, and highlight the potential for differential modulation of downstream target genes. We provide insights into the importance of considering alternative gene products when designing, undertaking, and analysing primary research, and the effect that isoforms may have on development. This review also covers known mutations in Grhl family members, and postulates how genetic changes may dictate transcriptional specificity between the Grhl family members. It also contrasts and compares the available literature on the function and importance of the Grhl isoforms, and highlights current gaps in our understanding of their regulatory gene networks in development and disease.
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Affiliation(s)
- Lee B Miles
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Sebastian Dworkin
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Charbel Darido
- Division of Cancer Research, Peter MacCallum Cancer Centre, Grattan Street, Parkville, VIC 3052, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, VIC 3052, Australia.
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37
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Ashley SN, Somanathan S, Hinderer C, Arias M, McMenamin D, Draper C, Wilson JM. Alternative Start Sites Downstream of Non-Sense Mutations Drive Antigen Presentation and Tolerance Induction to C-Terminal Epitopes. THE JOURNAL OF IMMUNOLOGY 2017; 198:4581-4587. [PMID: 28500077 DOI: 10.4049/jimmunol.1601131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 04/15/2017] [Indexed: 11/19/2022]
Abstract
CTL responses to the transgene product remain an active area of concern for the gene therapy field. A patient's underlying genetic mutation may influence the qualitative nature of these potentially destructive T cell responses. Individuals with a mutation that introduces a premature termination codon (PTC) that prevents synthesis of the full-length peptide are considered more likely to mount a transgene-specific T cell response because of a lack of immune tolerance to C-terminal epitopes as a consequence of absent endogenous Ag presentation. In this article, we demonstrate that a human ornithine transcarbamylase gene containing various PTC-inducing non-sense mutations is able to generate and present epitopes downstream of the termination codon. Generation of these epitopes occurs primarily from alternative translation start sites downstream of the stop codon. Furthermore, we show that expression of these genes from adeno-associated virus vectors in C57BL/6 mice is able to induce peripheral tolerance to epitopes downstream of the PTC. These results suggest that, despite the lack of full-length endogenous protein, patients with PTC-inducing non-sense mutations may still present T cell epitopes downstream of the premature termination site that may render the subject tolerant to wild-type transgene products.
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Affiliation(s)
- Scott N Ashley
- Gene Therapy Program, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104
| | - Suryanarayan Somanathan
- Gene Therapy Program, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104
| | - Christian Hinderer
- Gene Therapy Program, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104
| | - Maxwell Arias
- Gene Therapy Program, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104
| | - Deirdre McMenamin
- Gene Therapy Program, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104
| | - Christine Draper
- Gene Therapy Program, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104
| | - James M Wilson
- Gene Therapy Program, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104
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38
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Willems P, Ndah E, Jonckheere V, Stael S, Sticker A, Martens L, Van Breusegem F, Gevaert K, Van Damme P. N-terminal Proteomics Assisted Profiling of the Unexplored Translation Initiation Landscape in Arabidopsis thaliana. Mol Cell Proteomics 2017; 16:1064-1080. [PMID: 28432195 PMCID: PMC5461538 DOI: 10.1074/mcp.m116.066662] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 04/11/2017] [Indexed: 01/05/2023] Open
Abstract
Proteogenomics is an emerging research field yet lacking a uniform method of analysis. Proteogenomic studies in which N-terminal proteomics and ribosome profiling are combined, suggest that a high number of protein start sites are currently missing in genome annotations. We constructed a proteogenomic pipeline specific for the analysis of N-terminal proteomics data, with the aim of discovering novel translational start sites outside annotated protein coding regions. In summary, unidentified MS/MS spectra were matched to a specific N-terminal peptide library encompassing protein N termini encoded in the Arabidopsis thaliana genome. After a stringent false discovery rate filtering, 117 protein N termini compliant with N-terminal methionine excision specificity and indicative of translation initiation were found. These include N-terminal protein extensions and translation from transposable elements and pseudogenes. Gene prediction provided supporting protein-coding models for approximately half of the protein N termini. Besides the prediction of functional domains (partially) contained within the newly predicted ORFs, further supporting evidence of translation was found in the recently released Araport11 genome re-annotation of Arabidopsis and computational translations of sequences stored in public repositories. Most interestingly, complementary evidence by ribosome profiling was found for 23 protein N termini. Finally, by analyzing protein N-terminal peptides, an in silico analysis demonstrates the applicability of our N-terminal proteogenomics strategy in revealing protein-coding potential in species with well- and poorly-annotated genomes.
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Affiliation(s)
- Patrick Willems
- From the ‡VIB/UGent Center for Plant Systems Biology, 9052 Ghent, Belgium.,§Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent.,¶VIB/UGent Center for Medical Biotechnology, 9000 Ghent, Belgium.,‖Ghent University, Department of Biochemistry, 9000 Ghent, Belgium
| | - Elvis Ndah
- ¶VIB/UGent Center for Medical Biotechnology, 9000 Ghent, Belgium.,‖Ghent University, Department of Biochemistry, 9000 Ghent, Belgium.,**Ghent University, Department of Mathematical Modeling, Statistics and Bioinformatics, 9000 Ghent, Belgium
| | - Veronique Jonckheere
- ¶VIB/UGent Center for Medical Biotechnology, 9000 Ghent, Belgium.,‖Ghent University, Department of Biochemistry, 9000 Ghent, Belgium
| | - Simon Stael
- From the ‡VIB/UGent Center for Plant Systems Biology, 9052 Ghent, Belgium.,§Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent.,¶VIB/UGent Center for Medical Biotechnology, 9000 Ghent, Belgium.,‖Ghent University, Department of Biochemistry, 9000 Ghent, Belgium
| | - Adriaan Sticker
- ¶VIB/UGent Center for Medical Biotechnology, 9000 Ghent, Belgium.,‖Ghent University, Department of Biochemistry, 9000 Ghent, Belgium.,**Ghent University, Department of Mathematical Modeling, Statistics and Bioinformatics, 9000 Ghent, Belgium
| | - Lennart Martens
- ¶VIB/UGent Center for Medical Biotechnology, 9000 Ghent, Belgium.,‖Ghent University, Department of Biochemistry, 9000 Ghent, Belgium.,**Ghent University, Department of Mathematical Modeling, Statistics and Bioinformatics, 9000 Ghent, Belgium
| | - Frank Van Breusegem
- From the ‡VIB/UGent Center for Plant Systems Biology, 9052 Ghent, Belgium.,§Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent
| | - Kris Gevaert
- ¶VIB/UGent Center for Medical Biotechnology, 9000 Ghent, Belgium.,‖Ghent University, Department of Biochemistry, 9000 Ghent, Belgium
| | - Petra Van Damme
- ¶VIB/UGent Center for Medical Biotechnology, 9000 Ghent, Belgium; .,‖Ghent University, Department of Biochemistry, 9000 Ghent, Belgium
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39
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Ben-Nissan G, Belov ME, Morgenstern D, Levin Y, Dym O, Arkind G, Lipson C, Makarov AA, Sharon M. Triple-Stage Mass Spectrometry Unravels the Heterogeneity of an Endogenous Protein Complex. Anal Chem 2017; 89:4708-4715. [PMID: 28345864 DOI: 10.1021/acs.analchem.7b00518] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Protein complexes often represent an ensemble of different assemblies with distinct functions and regulation. This increased complexity is enabled by the variety of protein diversification mechanisms that exist at every step of the protein biosynthesis pathway, such as alternative splicing and post transcriptional and translational modifications. The resulting variation in subunits can generate compositionally distinct protein assemblies. These different forms of a single protein complex may comprise functional variances that enable response and adaptation to varying cellular conditions. Despite the biological importance of this layer of complexity, relatively little is known about the compositional heterogeneity of protein complexes, mostly due to technical barriers of studying such closely related species. Here, we show that native mass spectrometry (MS) offers a way to unravel this inherent heterogeneity of protein assemblies. Our approach relies on the advanced Orbitrap mass spectrometer capable of multistage MS analysis across all levels of protein organization. Specifically, we have implemented a two-step fragmentation process in the inject flatapole device, which was converted to a linear ion trap, and can now probe the intact protein complex assembly, through its constituent subunits, to the primary sequence of each protein. We demonstrate our approach on the yeast homotetrameric FBP1 complex, the rate-limiting enzyme in gluconeogenesis. We show that the complex responds differently to changes in growth conditions by tuning phosphorylation dynamics. Our methodology deciphers, on a single instrument and in a single measurement, the stoichiometry, kinetics, and exact position of modifications, contributing to the exposure of the multilevel diversity of protein complexes.
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Affiliation(s)
- Gili Ben-Nissan
- Department of Biomolecular Sciences, Weizmann Institute of Science , Rehovot 7610001, Israel
| | | | - David Morgenstern
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science , Rehovot 7610001, Israel
| | - Yishai Levin
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science , Rehovot 7610001, Israel
| | - Orly Dym
- Israel Structural Proteomics Center, Weizmann Institute of Science , Rehovot 7610001, Israel
| | - Galina Arkind
- Department of Biomolecular Sciences, Weizmann Institute of Science , Rehovot 7610001, Israel
| | - Carni Lipson
- Department of Biomolecular Sciences, Weizmann Institute of Science , Rehovot 7610001, Israel
| | | | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science , Rehovot 7610001, Israel
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40
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Vitale L, Caracausi M, Casadei R, Pelleri MC, Piovesan A. Difficulty in obtaining the complete mRNA coding sequence at 5' region (5' end mRNA artifact): Causes, consequences in biology and medicine and possible solutions for obtaining the actual amino acid sequence of proteins (Review). Int J Mol Med 2017; 39:1063-1071. [PMID: 28393177 DOI: 10.3892/ijmm.2017.2942] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 03/16/2017] [Indexed: 11/06/2022] Open
Abstract
The known difficulty in obtaining the actual full length, complete sequence of a messenger RNA (mRNA) may lead to the erroneous determination of its coding sequence at the 5' region (5' end mRNA artifact), and consequently to the wrong assignment of the translation start codon, leading to the inaccurate prediction of the encoded polypeptide at its amino terminus. Among the known human genes whose study was affected by this artifact, we can include disco interacting protein 2 homolog A (DIP2A; KIAA0184), Down syndrome critical region 1 (DSCR1), SON DNA binding protein (SON), trefoil factor 3 (TFF3) and URB1 ribosome biogenesis 1 homolog (URB1; KIAA0539) on chromosome 21, as well as receptor for activated C kinase 1 (RACK1, also known as GNB2L1), glutaminyl‑tRNA synthetase (QARS) and tyrosyl-DNA phosphodiesterase 2 (TDP2) along with another 474 loci, including interleukin 16 (IL16). In this review, we discuss the causes of this issue, its quantitative incidence in biomedical research, the consequences in biology and medicine, and the possible solutions for obtaining the actual amino acid sequence of proteins in the post-genomics era.
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Affiliation(s)
- Lorenza Vitale
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, I‑40126 Bologna, Italy
| | - Maria Caracausi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, I‑40126 Bologna, Italy
| | - Raffaella Casadei
- Department for Life Quality Studies, University of Bologna, I‑47921 Rimini, Italy
| | - Maria Chiara Pelleri
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, I‑40126 Bologna, Italy
| | - Allison Piovesan
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, I‑40126 Bologna, Italy
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41
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Prykhozhij SV, Steele SL, Razaghi B, Berman JN. A rapid and effective method for screening, sequencing and reporter verification of engineered frameshift mutations in zebrafish. Dis Model Mech 2017; 10:811-822. [PMID: 28280001 PMCID: PMC5483001 DOI: 10.1242/dmm.026765] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 03/03/2017] [Indexed: 12/30/2022] Open
Abstract
Clustered regularly interspaced palindromic repeats (CRISPR)/Cas-based adaptive immunity against pathogens in bacteria has been adapted for genome editing and applied in zebrafish (Danio rerio) to generate frameshift mutations in protein-coding genes. Although there are methods to detect, quantify and sequence CRISPR/Cas9-induced mutations, identifying mutations in F1 heterozygous fish remains challenging. Additionally, sequencing a mutation and assuming that it causes a frameshift does not prove causality because of possible alternative translation start sites and potential effects of mutations on splicing. This problem is compounded by the relatively few antibodies available for zebrafish proteins, limiting validation at the protein level. To address these issues, we developed a detailed protocol to screen F1 mutation carriers, and clone and sequence identified mutations. In order to verify that mutations actually cause frameshifts, we created a fluorescent reporter system that can detect frameshift efficiency based on the cloning of wild-type and mutant cDNA fragments and their expression levels. As proof of principle, we applied this strategy to three CRISPR/Cas9-induced mutations in pycr1a, chd7 and hace1 genes. An insertion of seven nucleotides in pycr1a resulted in the first reported observation of exon skipping by CRISPR/Cas9-induced mutations in zebrafish. However, of these three mutant genes, the fluorescent reporter revealed effective frameshifting exclusively in the case of a two-nucleotide deletion in chd7, suggesting activity of alternative translation sites in the other two mutants even though pycr1a exon-skipping deletion is likely to be deleterious. This article provides a protocol for characterizing frameshift mutations in zebrafish, and highlights the importance of checking mutations at the mRNA level and verifying their effects on translation by fluorescent reporters when antibody detection of protein loss is not possible.
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Affiliation(s)
| | - Shelby L Steele
- Department of Pediatrics, Dalhousie University, Halifax, NS, Canada B3K 6R8
| | - Babak Razaghi
- Department of Pediatrics, Dalhousie University, Halifax, NS, Canada B3K 6R8
| | - Jason N Berman
- Department of Pediatrics, Dalhousie University, Halifax, NS, Canada B3K 6R8 .,Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada B3H 4R2.,Department of Pathology, Dalhousie University, Halifax, NS, Canada B3H4R2
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42
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Pancsa R, Tompa P. Coding Regions of Intrinsic Disorder Accommodate Parallel Functions. Trends Biochem Sci 2016; 41:898-906. [DOI: 10.1016/j.tibs.2016.08.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 08/16/2016] [Accepted: 08/19/2016] [Indexed: 02/01/2023]
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43
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Abstract
Translational readthrough (TR) has come into renewed focus because systems biology approaches have identified the first human genes undergoing functional translational readthrough (FTR). FTR creates functional extensions to proteins by continuing translation of the mRNA downstream of the stop codon. Here we review recent developments in TR research with a focus on the identification of FTR in humans and the systems biology methods that have spurred these discoveries.
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Affiliation(s)
- Fabian Schueren
- University Medical Center, Department of Child and Adolescent Health, University of Göttingen, Göttingen, Germany
| | - Sven Thoms
- University Medical Center, Department of Child and Adolescent Health, University of Göttingen, Göttingen, Germany
- * E-mail:
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44
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Valli M, Tatto NE, Peymann A, Gruber C, Landes N, Ekker H, Thallinger GG, Mattanovich D, Gasser B, Graf AB. Curation of the genome annotation ofPichia pastoris(Komagataella phaffii) CBS7435 from gene level to protein function. FEMS Yeast Res 2016; 16:fow051. [DOI: 10.1093/femsyr/fow051] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2016] [Indexed: 11/14/2022] Open
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45
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Chi G, Rohde PR, Ridone P, Hankamer B, Martinac B, Landsberg MJ. Functional similarities between heterogeneously and homogenously expressed MscL constructs. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2015; 44:589-98. [PMID: 26233759 DOI: 10.1007/s00249-015-1062-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 06/29/2015] [Accepted: 07/14/2015] [Indexed: 11/30/2022]
Abstract
The mechanosensitive channel of large conductance MscL is a well-characterized mechanically gated non-selective ion channel, which often serves as a prototype mechanosensitive channel for mechanotransduction studies. However, there are some discrepancies between MscL constructs used in these studies, most notably unintended heterogeneous expression from some MscL expression constructs. In this study we investigate the possible cause of this expression pattern, and compare the original non-homogenously expressing constructs with our new homogeneously expressing one to confirm that there is little functional difference between them. In addition, a new MscL construct has been developed with an improved molar extinction coefficient at 280 nm, enabling more accurate protein quantification.
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Affiliation(s)
- Gamma Chi
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia
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46
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Chorev DS, Ben-Nissan G, Sharon M. Exposing the subunit diversity and modularity of protein complexes by structural mass spectrometry approaches. Proteomics 2015; 15:2777-91. [PMID: 25727951 DOI: 10.1002/pmic.201400517] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 01/08/2015] [Accepted: 02/24/2015] [Indexed: 12/11/2022]
Abstract
Although the number of protein-encoding genes in the human genome is only about 20 000 not far from the amount found in the nematode worm genome, the number of proteins that are translated from these sequences is larger by several orders of magnitude. A number of mechanisms have evolved to enable this diversity. For example, genes can be alternatively spliced to create multiple transcripts; they may also be translated from different alternative initiation sites. After translation, hundreds of chemical modifications can be introduced in proteins, altering their chemical properties, folding, stability, and activity. The complexity is then further enhanced by the various combinations that are generated from the assembly of different subunit variants into protein complexes. This, in turn, confers structural and functional flexibility, and endows the cell with the ability to adapt to various environmental conditions. Therefore, exposing the variability of protein complexes is an important step toward understanding their biological functions. Revealing this enormous diversity, however, is not a simple task. In this review, we will focus on the array of MS-based strategies that are capable of performing this mission. We will also discuss the challenges that lie ahead, and the future directions toward which the field might be heading.
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Affiliation(s)
- Dror S Chorev
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Gili Ben-Nissan
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Sharon
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
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47
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Goodswen SJ, Barratt JLN, Kennedy PJ, Ellis JT. Improving the gene structure annotation of the apicomplexan parasite Neospora caninum fulfils a vital requirement towards an in silico-derived vaccine. Int J Parasitol 2015; 45:305-18. [PMID: 25747726 DOI: 10.1016/j.ijpara.2015.01.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 01/12/2015] [Accepted: 01/12/2015] [Indexed: 12/16/2022]
Abstract
Neospora caninum is an apicomplexan parasite which can cause abortion in cattle, instigating major economic burden. Vaccination has been proposed as the most cost-effective control measure to alleviate this burden. Consequently the overriding aspiration for N. caninum research is the identification and subsequent evaluation of vaccine candidates in animal models. To save time, cost and effort, it is now feasible to use an in silico approach for vaccine candidate prediction. Precise protein sequences, derived from the correct open reading frame, are paramount and arguably the most important factor determining the success or failure of this approach. The challenge is that publicly available N. caninum sequences are mostly derived from gene predictions. Annotated inaccuracies can lead to erroneously predicted vaccine candidates by bioinformatics programs. This study evaluates the current N. caninum annotation for potential inaccuracies. Comparisons with annotation from a closely related pathogen, Toxoplasma gondii, are also made to distinguish patterns of inconsistency. More importantly, a mRNA sequencing (RNA-Seq) experiment is used to validate the annotation. Potential discrepancies originating from a questionable start codon context and exon boundaries were identified in 1943 protein coding sequences. We conclude, where experimental data were available, that the majority of N. caninum gene sequences were reliably predicted. Nevertheless, almost 28% of genes were identified as questionable. Given the limitations of RNA-Seq, the intention of this study was not to replace the existing annotation but to support or oppose particular aspects of it. Ideally, many studies aimed at improving the annotation are required to build a consensus. We believe this study, in providing a new resource on gene structure and annotation, is a worthy contributor to this endeavour.
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Affiliation(s)
- Stephen J Goodswen
- School of Medical and Molecular Sciences, University of Technology Sydney (UTS), 15 Broadway, Ultimo, NSW 2007, Australia.
| | - Joel L N Barratt
- School of Medical and Molecular Sciences, University of Technology Sydney (UTS), 15 Broadway, Ultimo, NSW 2007, Australia
| | - Paul J Kennedy
- School of Software, Faculty of Engineering and Information Technology and the Centre for Quantum Computation and Intelligent Systems at the University of Technology Sydney (UTS), 15 Broadway, Ultimo, NSW 2007, Australia
| | - John T Ellis
- School of Medical and Molecular Sciences, University of Technology Sydney (UTS), 15 Broadway, Ultimo, NSW 2007, Australia
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48
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Gawron D, Gevaert K, Van Damme P. The proteome under translational control. Proteomics 2014; 14:2647-62. [PMID: 25263132 DOI: 10.1002/pmic.201400165] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 08/21/2014] [Accepted: 09/23/2014] [Indexed: 02/02/2023]
Abstract
A single eukaryotic gene can give rise to a variety of protein forms (proteoforms) as a result of genetic variation and multilevel regulation of gene expression. In addition to alternative splicing, an increasing line of evidence shows that alternative translation contributes to the overall complexity of proteomes. Identifying the repertoire of proteins and micropeptides expressed by alternative selection of (near-)cognate translation initiation sites and different reading frames however remains challenging with contemporary proteomics. MS-enabled identification of proteoforms is expected to benefit from transcriptome and translatome data by the creation of customized and sample-specific protein sequence databases. Here, we focus on contemporary integrative omics approaches that complement proteomics with DNA- and/or RNA-oriented technologies to elucidate the mechanisms of translational control. Together, these technologies enable to map the translation (initiation) landscape and more comprehensively define the inventory of proteoforms raised upon alternative translation, thus assisting in the (re-)annotation of genomes.
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Affiliation(s)
- Daria Gawron
- Department of Medical Protein Research, VIB, Ghent, Belgium; Department of Biochemistry, Ghent University, Ghent, Belgium
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49
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Justa-Schuch D, Möller U, Geiss-Friedlander R. The amino terminus extension in the long dipeptidyl peptidase 9 isoform contains a nuclear localization signal targeting the active peptidase to the nucleus. Cell Mol Life Sci 2014; 71:3611-26. [PMID: 24562348 PMCID: PMC11113674 DOI: 10.1007/s00018-014-1591-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 02/11/2014] [Accepted: 02/13/2014] [Indexed: 12/25/2022]
Abstract
The intracellular prolyl peptidase DPP9 is implied to be involved in various cellular pathways including amino acid recycling, antigen maturation, cellular homeostasis, and viability. Interestingly, the major RNA transcript of DPP9 contains two possible translation initiation sites, which could potentially generate a longer (892 aa) and a shorter version (863 aa) of DPP9. Although the endogenous expression of the shorter DPP9 form has been previously verified, it is unknown whether the longer version is expressed, and what is its biological significance. By developing specific antibodies against the amino-terminal extension of the putative DPP9-long form, we demonstrate for the first time the endogenous expression of this longer isoform within cells. Furthermore, we show that DPP9-long represents a significant fraction of total DPP9 in cells, under steady-state conditions. Using biochemical cell fractionation assays in combination with immunofluorescence studies, we find the two isoforms localize to separate subcellular compartments. Whereas DPP9-short is present in the cytosol, DPP9-long localizes preferentially to the nucleus. This differential localization is attributed to a classical monopartite nuclear localization signal (K(K/R)X(K/R)) in the N-terminal extension of DPP9-long. Furthermore, we detect prolyl peptidase activity in nuclear fractions, which can be inhibited by specific DPP8/9 inhibitors. In conclusion, a considerable fraction of DPP9, which was previously considered as a purely cytosolic peptidase, localizes to the nucleus and is active there, raising the intriguing possibility that the longer DPP9 isoform may regulate the activity or stability of nuclear proteins, such as transcription factors.
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Affiliation(s)
- Daniela Justa-Schuch
- Department of Molecular Biology, Faculty of Medicine, Georg-August-University of Goettingen, Humboldtallee 23, 37073 Goettingen, Germany
| | - Ulrike Möller
- Department of Molecular Biology, Faculty of Medicine, Georg-August-University of Goettingen, Humboldtallee 23, 37073 Goettingen, Germany
| | - Ruth Geiss-Friedlander
- Department of Molecular Biology, Faculty of Medicine, Georg-August-University of Goettingen, Humboldtallee 23, 37073 Goettingen, Germany
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50
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Noderer WL, Flockhart RJ, Bhaduri A, Diaz de Arce AJ, Zhang J, Khavari PA, Wang CL. Quantitative analysis of mammalian translation initiation sites by FACS-seq. Mol Syst Biol 2014; 10:748. [PMID: 25170020 PMCID: PMC4299517 DOI: 10.15252/msb.20145136] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
An approach combining fluorescence-activated cell sorting and high-throughput DNA sequencing
(FACS-seq) was employed to determine the efficiency of start codon recognition for all possible
translation initiation sites (TIS) utilizing AUG start codons. Using FACS-seq, we measured
translation from a genetic reporter library representing all 65,536 possible TIS sequences spanning
the −6 to +5 positions. We found that the motif RYMRMVAUGGC enhanced start codon
recognition and translation efficiency. However, dinucleotide interactions, which cannot be conveyed
by a single motif, were also important for modeling TIS efficiency. Our dataset combined with
modeling allowed us to predict genome-wide translation initiation efficiency for all mRNA
transcripts. Additionally, we screened somatic TIS mutations associated with tumorigenesis to
identify candidate driver mutations consistent with known tumor expression patterns. Finally, we
implemented a quantitative leaky scanning model to predict alternative initiation sites that produce
truncated protein isoforms and compared predictions with ribosome footprint profiling data. The
comprehensive analysis of the TIS sequence space enables quantitative predictions of translation
initiation based on genome sequence.
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Affiliation(s)
- William L Noderer
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
| | - Ross J Flockhart
- The Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Aparna Bhaduri
- The Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA The Program in Cancer Biology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Jiajing Zhang
- The Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Paul A Khavari
- The Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA
| | - Clifford L Wang
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
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