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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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Akirtava C, May G, McManus CJ. Deciphering the cis-regulatory landscape of natural yeast Transcript Leaders. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.03.601937. [PMID: 39005336 PMCID: PMC11245039 DOI: 10.1101/2024.07.03.601937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Protein synthesis is a vital process that is highly regulated at the initiation step of translation. Eukaryotic 5' transcript leaders (TLs) contain a variety of cis-regulatory features that influence translation and mRNA stability. However, the relative influences of these features in natural TLs are poorly characterized. To address this, we used massively parallel reporter assays (MPRAs) to quantify RNA levels, ribosome loading, and protein levels from 11,027 natural yeast TLs in vivo and systematically compared the relative impacts of their sequence features on gene expression. We found that yeast TLs influence gene expression over two orders of magnitude. While a leaky scanning model using Kozak contexts and uAUGs explained half of the variance in expression across transcript leaders, the addition of other features explained ~70% of gene expression variation. Our analyses detected key cis-acting sequence features, quantified their effects in vivo, and compared their roles to motifs reported from an in vitro study of ribosome recruitment. In addition, our work quantitated the effects of alternative transcription start site usage on gene expression in yeast. Thus, our study provides new quantitative insights into the roles of TL cis-acting sequences in regulating gene expression.
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Affiliation(s)
- Christina Akirtava
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
- RNA Bioscience Initiative, University of Colorado - Anshutz, Aurora, CO, 80045, USA
| | - Gemma May
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - C Joel McManus
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
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Parag RR, Yamamoto T, Saito K, Zhu D, Yang L, Van Meir EG. Novel Isoforms of Adhesion G Protein-Coupled Receptor B1 (ADGRB1/BAI1) Generated from an Alternative Promoter in Intron 17. Mol Neurobiol 2024:10.1007/s12035-024-04293-3. [PMID: 38941066 DOI: 10.1007/s12035-024-04293-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 06/06/2024] [Indexed: 06/29/2024]
Abstract
Brain-specific angiogenesis inhibitor 1 (BAI1) belongs to the adhesion G-protein-coupled receptors, which exhibit large multi-domain extracellular N termini that mediate cell-cell and cell-matrix interactions. To explore the existence of BAI1 isoforms, we queried genomic datasets for markers of active chromatin and new transcript variants in the ADGRB1 (adhesion G-protein-coupled receptor B1) gene. Two major types of mRNAs were identified in human/mouse brain, those with a start codon in exon 2 encoding a full-length protein of a predicted size of 173.5/173.3 kDa and shorter transcripts starting from alternative exons at the intron 17/exon 18 boundary with new or exon 19 start codons, predicting two shorter isoforms of 76.9/76.4 and 70.8/70.5 kDa, respectively. Immunoblots on wild-type and Adgrb1 exon 2-deleted mice, reverse transcription PCR, and promoter-luciferase reporter assay confirmed that the shorter isoforms originate from an alternative promoter in intron 17. The shorter BAI1 isoforms lack most of the N terminus and are very close in structure to the truncated BAI1 isoform generated through GPS processing from the full-length receptor. The cleaved BAI1 isoform has a 19 amino acid extracellular stalk that may serve as a receptor agonist, while the alternative transcripts generate BAI1 isoforms with extracellular N termini of 5 or 60 amino acids. Further studies are warranted to compare the functions of these isoforms and examine the distinct roles they play in different tissues and cell types.
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Affiliation(s)
- Rashed Rezwan Parag
- Laboratory of Molecular Neuro-Oncology, Department of Neurosurgery, Heersink School of Medicine, University of Alabama at Birmingham (UAB), WTI 520E, 1824 6th Avenue South, Birmingham, AL, 35233, USA
- Graduate Biomedical Sciences, University of Alabama at Birmingham (UAB), Birmingham, AL, USA
| | - Takahiro Yamamoto
- Laboratory of Molecular Neuro-Oncology, Department of Neurosurgery, Heersink School of Medicine, University of Alabama at Birmingham (UAB), WTI 520E, 1824 6th Avenue South, Birmingham, AL, 35233, USA
- Department of Neurosurgery, Kumamoto University, Kumamoto, Japan
| | - Kiyotaka Saito
- Laboratory of Molecular Neuro-Oncology, Department of Neurosurgery, Heersink School of Medicine, University of Alabama at Birmingham (UAB), WTI 520E, 1824 6th Avenue South, Birmingham, AL, 35233, USA
| | - Dan Zhu
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA, USA
| | - Liquan Yang
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA, USA
| | - Erwin G Van Meir
- Laboratory of Molecular Neuro-Oncology, Department of Neurosurgery, Heersink School of Medicine, University of Alabama at Birmingham (UAB), WTI 520E, 1824 6th Avenue South, Birmingham, AL, 35233, USA.
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA, USA.
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham (UAB), Birmingham, AL, USA.
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Rein HL, Bernstein KA. Variants in the first methionine of RAD51C are homologous recombination proficient due to an alternative start site. DNA Repair (Amst) 2024; 135:103644. [PMID: 38330859 PMCID: PMC10923178 DOI: 10.1016/j.dnarep.2024.103644] [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: 09/08/2023] [Revised: 11/26/2023] [Accepted: 01/25/2024] [Indexed: 02/10/2024]
Abstract
In the 20+ years since the discovery of RAD51C, scientists have been perplexed as to how missense variants in this tumor suppressor gene impacts its function and pathogenicity. With a strong connection to breast and ovarian cancer, classifying these variants as pathogenic or benign aids in the diagnosis and treatment of patients with RAD51C variants. In particular, variants at translational starts sites are disruptive as they prevent protein expression. These variants are often classified as pathogenic, unless an alternative translational start is shown to produce a functional isoform to rescue protein expression. In this study, we utilized the ribosome profiling database GWIPS-VIZ to identify two active translational start sites in human RAD51C at methionine one and methionine ten. This second translational start at methionine ten is both conserved in 97 % of mammals and is the sole translational start in 80 % of mammals. Missense variants at either methionine have been identified in 47 individuals, preventing expression from one of these two start sites. Therefore, we stably expressed both wildtype isoforms, as well as the RAD51C M1 and M10 variants in a RAD51C CRISPR/Cas9 knockout U2OS cell and compared their homologous recombination function. Surprisingly, we find that expression of human RAD51C from either start site can equivalently rescue homologous recombination of RAD51C CRISPR/Cas9 knockout U2OS cells through a sister chromatid recombination assay. Similarly, each of our RAD51C CRISPR/Cas9 KO cells stably complemented with RAD51C missense variants at either M1 or M10 are homologous recombination proficient. Together, our data demonstrate that RAD51C has two translational start sites and that variants in either methionine result in homologous recombination proficiency. With this critical discovery, individuals with variants at M1 will be more accurately informed of their cancer risk upon reclassification of these variants.
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Affiliation(s)
- Hayley L Rein
- University of Pittsburgh, School of Medicine, Department of Pharmacology and Chemical Biology, Pittsburgh, PA, USA
| | - Kara A Bernstein
- University of Pennsylvania School of Medicine, Department of Biochemistry and Biophysics, 421 Curie Boulevard, Philadelphia, PA, USA.
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Zhao C, Ding Y, Zhang Y, Chu M, Ning X, Ji J, Wang T, Zhang G, Yin S, Zhang K. Integrated analysis of transcriptome, translatome and proteome reveals insights into yellow catfish (Pelteobagrus fulvidraco) brain in response to hypoxia. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2024; 266:106801. [PMID: 38096642 DOI: 10.1016/j.aquatox.2023.106801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 11/11/2023] [Accepted: 12/10/2023] [Indexed: 01/02/2024]
Abstract
Brain plays a central role in adapting to environmental changes and is highly sensitive to the oxygen level. Although previous studies investigated the molecular response of brain exposure to acute hypoxia in fish, the lack of studies at the translational level hinders further understanding of the regulatory mechanism response to hypoxia from multi-omics levels. Yellow catfish (Pelteobagrus fulvidraco) is an important freshwater aquaculture species; however, hypoxia severely restricts the sustainable development of its breeding industry. In the present study, the transcriptome, translatome, and proteome were integrated to study the global landscapes of yellow catfish brain response to hypoxia. The evidently increased amount of cerebral cortical cells with oedema and pyknotic nuclei has been observed in hypoxia group of yellow catfish. A total of 2750 genes were significantly changed at the translational level. Comparative transcriptional and translational analysis suggested the HIF-1 signaling pathway, autophagy and glycolysis/gluconeogenesis were up-regulated after hypoxia exposure. KEGG enrichment of translational efficiency (TE) differential genes suggested that the lysosome and autophagy were highly enriched. Our result showed that yellow catfish tends to inhibit the TE of genes by increasing the translation of uORFs to adapt to hypoxia. Correlation analysis showed that transcriptome and translatome exhibit higher correlation. In summary, this study demonstrated that hypoxia dysregulated the cerebral function of yellow catfish at the transcriptome, translatome, and proteome, which provides a better understanding of hypoxia adaptation in teleost.
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Affiliation(s)
- Cheng Zhao
- College of Marine Science and Engineering, Nanjing Normal University, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing 210023, China; Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang 222005, Jiangsu, China
| | - Yubing Ding
- College of Marine Science and Engineering, Nanjing Normal University, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing 210023, China
| | - Yufei Zhang
- College of Marine Science and Engineering, Nanjing Normal University, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing 210023, China
| | - Mingxu Chu
- College of Marine Science and Engineering, Nanjing Normal University, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing 210023, China
| | - Xianhui Ning
- College of Marine Science and Engineering, Nanjing Normal University, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing 210023, China; Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang 222005, Jiangsu, China
| | - Jie Ji
- College of Marine Science and Engineering, Nanjing Normal University, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing 210023, China; Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang 222005, Jiangsu, China
| | - Tao Wang
- College of Marine Science and Engineering, Nanjing Normal University, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing 210023, China; Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang 222005, Jiangsu, China
| | - Guosong Zhang
- Key Laboratory for Physiology Biochemistry and Application, Heze University, Heze 274015, China
| | - Shaowu Yin
- College of Marine Science and Engineering, Nanjing Normal University, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing 210023, China; Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang 222005, Jiangsu, China
| | - Kai Zhang
- College of Marine Science and Engineering, Nanjing Normal University, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing 210023, China; Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang 222005, Jiangsu, China.
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Zhang D, Lin R, Yamamoto N, Wang Z, Lin H, Okada K, Liu Y, Xiang X, Zheng T, Zheng H, Yi X, Noutoshi Y, Zheng A. Mitochondrial-targeting effector RsIA_CtaG/Cox11 in Rhizoctonia solani AG-1 IA has two functions: plant immunity suppression and cell death induction mediated by a rice cytochrome c oxidase subunit. MOLECULAR PLANT PATHOLOGY 2024; 25:e13397. [PMID: 37902589 PMCID: PMC10799210 DOI: 10.1111/mpp.13397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 09/24/2023] [Accepted: 09/29/2023] [Indexed: 10/31/2023]
Abstract
Rhizoctonia solani AG-1 IA causes a necrotrophic rice disease and is a serious threat to rice production. To date, only a few effectors have been characterized in AG-1 IA. We previously identified RsIA_CtaG/Cox11 and showed that infiltration of the recombinant protein into rice leaves caused disease-like symptoms. In the present study, we further characterized the functionality of RsIA_CtaG/Cox11. RsIA_CtaG/Cox11 is an alternative transcript of cytochrome c oxidase copper chaperone Cox11 that starts from the second AUG codon, but contains a functional secretion signal peptide. RNA interference with RsIA_CtaG/Cox11 reduced the pathogenicity of AG-1 IA towards rice and Nicotiana benthamiana without affecting its fitness or mycelial morphology. Transient expression of the RsIA_CtaG/Cox11-GFP fusion protein demonstrated the localization of RsIA_CtaG/Cox11 to mitochondria. Agro-infiltration of RsIA_CtaG/Cox11 into N. benthamiana leaves inhibited cell death by BAX and INF1. In contrast to rice, agro-infiltration of RsIA_CtaG/Cox11 did not induce cell death in N. benthamiana. However, cell death was observed when it was coinfiltrated with Os_CoxVIIa, which encodes a subunit of cytochrome c oxidase. Os_CoxVIIa appeared to interact with RsIA_CtaG/Cox11. The cell death triggered by coexpression of RsIA_CtaG/Cox11 and Os_CoxVIIa is independent of the leucine-rich repeat receptor kinases BAK1/SOBIR1 and enhanced the susceptibility of N. benthamiana to AG-1 IA. Two of the three evolutionarily conserved cysteine residues at positions 25 and 126 of RsIA_CtaG/Cox11 were essential for its immunosuppressive activity, but not for cell death induction. This report suggests that RsIA_CtaG/Cox11 appears to have a dual role in immunosuppression and cell death induction during pathogenesis.
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Affiliation(s)
- Danhua Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaChengduChina
- School of AgronomySichuan Agricultural UniversityChengduChina
| | - Runmao Lin
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests Ministry of EducationHainan UniversityHaikouChina
| | - Naoki Yamamoto
- School of AgronomySichuan Agricultural UniversityChengduChina
| | - Zhaoyilin Wang
- Rice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Hui Lin
- School of AgronomySichuan Agricultural UniversityChengduChina
| | - Kazunori Okada
- Agro‐Biotechnology Research CenterThe University of TokyoTokyoJapan
| | - Yao Liu
- Key Laboratory of Sichuan Province, Crop Research InstituteSichuan Academy of Agricultural SciencesChengduChina
| | - Xing Xiang
- School of AgronomySichuan Agricultural UniversityChengduChina
| | - Tengda Zheng
- School of AgronomySichuan Agricultural UniversityChengduChina
| | | | - Xiaoqun Yi
- School of AgronomySichuan Agricultural UniversityChengduChina
| | - Yoshiteru Noutoshi
- Graduate School of Environmental, Life, and Natural Science and TechnologyOkayama UniversityOkayamaJapan
| | - Aiping Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaChengduChina
- School of AgronomySichuan Agricultural UniversityChengduChina
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7
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Jian H, Wen S, Liu R, Zhang W, Li Z, Chen W, Zhou Y, Khassanov V, Mahmoud AMA, Wang J, Lyu D. Dynamic Translational Landscape Revealed by Genome-Wide Ribosome Profiling under Drought and Heat Stress in Potato. PLANTS (BASEL, SWITZERLAND) 2023; 12:2232. [PMID: 37375858 DOI: 10.3390/plants12122232] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/02/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023]
Abstract
The yield and quality of potatoes, an important staple crop, are seriously threatened by high temperature and drought stress. In order to deal with this adverse environment, plants have evolved a series of response mechanisms. However, the molecular mechanism of potato's response to environmental changes at the translational level is still unclear. In this study, we performed transcriptome- and ribosome-profiling assays with potato seedlings growing under normal, drought, and high-temperature conditions to reveal the dynamic translational landscapes for the first time. The translational efficiency was significantly affected by drought and heat stress in potato. A relatively high correlation (0.88 and 0.82 for drought and heat stress, respectively) of the fold changes of gene expression was observed between the transcriptional level and translational level globally based on the ribosome-profiling and RNA-seq data. However, only 41.58% and 27.69% of the different expressed genes were shared by transcription and translation in drought and heat stress, respectively, suggesting that the transcription or translation process can be changed independently. In total, the translational efficiency of 151 (83 and 68 for drought and heat, respectively) genes was significantly changed. In addition, sequence features, including GC content, sequence length, and normalized minimal free energy, significantly affected the translational efficiencies of genes. In addition, 28,490 upstream open reading frames (uORFs) were detected on 6463 genes, with an average of 4.4 uORFs per gene and a median length of 100 bp. These uORFs significantly affected the translational efficiency of downstream major open reading frames (mORFs). These results provide new information and directions for analyzing the molecular regulatory network of potato seedlings in response to drought and heat stress.
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Affiliation(s)
- Hongju Jian
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Chongqing 400715, China
| | - Shiqi Wen
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Rongrong Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Wenzhe Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Ziyan Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Weixi Chen
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Yonghong Zhou
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Chongqing 400715, China
| | - Vadim Khassanov
- Department of Plant Protection and Quarantine, Faculty of Agronomy, S. Seifullin Kazakh Agrotechnical University, Zhenis Avenue, 010011 Astana, Kazakhstan
| | - Ahmed M A Mahmoud
- Department of Vegetable Crops, Faculty of Agriculture, Cairo University, Giza 12613, Egypt
| | - Jichun Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Chongqing 400715, China
| | - Dianqiu Lyu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Chongqing 400715, China
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Tsang MJ, Cheeseman IM. Alternative CDC20 translational isoforms tune mitotic arrest duration. Nature 2023; 617:154-161. [PMID: 37100900 PMCID: PMC10461078 DOI: 10.1038/s41586-023-05943-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 03/13/2023] [Indexed: 04/28/2023]
Abstract
Mitotic defects activate the spindle-assembly checkpoint, which inhibits the anaphase-promoting complex co-activator CDC20 to induce a prolonged cell cycle arrest1,2. Once errors are corrected, the spindle-assembly checkpoint is silenced, allowing anaphase onset to occur. However, in the presence of persistent unresolvable errors, cells can undergo 'mitotic slippage', exiting mitosis into a tetraploid G1 state and escaping the cell death that results from a prolonged arrest. The molecular logic that enables cells to balance these duelling mitotic arrest and slippage behaviours remains unclear. Here we demonstrate that human cells modulate the duration of their mitotic arrest through the presence of conserved, alternative CDC20 translational isoforms. Downstream translation initiation results in a truncated CDC20 isoform that is resistant to spindle-assembly-checkpoint-mediated inhibition and promotes mitotic exit even in the presence of mitotic perturbations. Our study supports a model in which the relative levels of CDC20 translational isoforms control the duration of mitotic arrest. During a prolonged mitotic arrest, new protein synthesis and differential CDC20 isoform turnover create a timer, with mitotic exit occurring once the truncated Met43 isoform achieves sufficient levels. Targeted molecular changes or naturally occurring cancer mutations that alter CDC20 isoform ratios or its translational control modulate mitotic arrest duration and anti-mitotic drug sensitivity, with potential implications for the diagnosis and treatment of human cancers.
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Affiliation(s)
- Mary-Jane Tsang
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Iain M Cheeseman
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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Maslakova AA, Golyshev SA, Potashnikova DM, Moisenovich AM, Orlovsky IV, Smirnova OV, Rubtsov MA. SERPINA1 long transcripts produce non-secretory alpha1-antitrypsin isoform: In vitro translation in living cells. Int J Biol Macromol 2023; 241:124433. [PMID: 37086761 DOI: 10.1016/j.ijbiomac.2023.124433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 04/24/2023]
Abstract
SERPINA1 is a well-studied serpin gene due to its dramatic impact on human health. Translation initiation at the main SERPINA1 start codon produces the only known alpha1-antitrypsin (AAT) isoform intended for secretion. AAT performs essential functions by inhibiting proteases and modulating immunity. However, SERPINA1 expression at the level of translation is not sufficiently studied. Here we hypothesize that the main SERPINA1 ORF can be alternatively translated, producing a non-secretory AAT isoform by either masking or excluding a signal peptide. We defined SERPINA1 long mRNA isoforms specific for prostate (DU145) and liver (HepG2) cell lines and studied their individual expression by in vitro assay. We found that all long transcripts produce both glycosylated secretory AAT-eGFP fusion protein and non-glycosylated intracellular AAT-eGFP (initiated from an alternative AUG-2 start codon), with the proportion regulated by the SERPINA1 5'-UTR. Both fusion proteins localize to distinct cellular compartments: in contrast to a fusion with the secretory AAT accumulating in the ER, the intracellular one exhibits nuclear-cytoplasmic shuttling. We detected putative endogenous AAT isoform enriching the nuclear speckles. CONCLUSION: Alternative translation initiation might be a mechanism through which SERPINA1 expands the biological diversity of its protein products. Our findings open up new prospects for the study of SERPINA1 gene expression.
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Affiliation(s)
- A A Maslakova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia.
| | - S A Golyshev
- A.N. Belozersky Institute of Physical and Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119992, Russia
| | - D M Potashnikova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
| | - A M Moisenovich
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
| | - I V Orlovsky
- Research Institute of Molecular and Cellular Medicine, Рeoples' Friendship University of Russia (RUDN University), Miklukho-Maklaya, Moscow 117198, Russia
| | - O V Smirnova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
| | - M A Rubtsov
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia; Center for Industrial Technologies and Entrepreneurship, I.M. Sechenov First Moscow State Medical University (Sechenov University), Trubetskaya, Moscow 119991, Russia
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10
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Ma Q, Wang Y, Li S, Wen J, Zhu L, Yan K, Du Y, Li S, Yan L, Xie Z, Lyu Y, Shen F, Li Q. Ribosome footprint profiling enables elucidating the systemic regulation of fatty acid accumulation in Acer truncatum. BMC Biol 2023; 21:68. [PMID: 37013569 PMCID: PMC10071632 DOI: 10.1186/s12915-023-01564-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/14/2023] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND The accumulation of fatty acids in plants covers a wide range of functions in plant physiology and thereby affects adaptations and characteristics of species. As the famous woody oilseed crop, Acer truncatum accumulates unsaturated fatty acids and could serve as the model to understand the regulation and trait formation in oil-accumulation crops. Here, we performed Ribosome footprint profiling combing with a multi-omics strategy towards vital time points during seed development, and finally constructed systematic profiling from transcription to proteomes. Additionally, we characterized the small open reading frames (ORFs) and revealed that the translational efficiencies of focused genes were highly influenced by their sequence features. RESULTS The comprehensive multi-omics analysis of lipid metabolism was conducted in A. truncatum. We applied the Ribo-seq and RNA-seq techniques, and the analyses of transcriptional and translational profiles of seeds collected at 85 and 115 DAF were compared. Key members of biosynthesis-related structural genes (LACS, FAD2, FAD3, and KCS) were characterized fully. More meaningfully, the regulators (MYB, ABI, bZIP, and Dof) were identified and revealed to affect lipid biosynthesis via post-translational regulations. The translational features results showed that translation efficiency tended to be lower for the genes with a translated uORF than for the genes with a non-translated uORF. They provide new insights into the global mechanisms underlying the developmental regulation of lipid metabolism. CONCLUSIONS We performed Ribosome footprint profiling combing with a multi-omics strategy in A. truncatum seed development, which provides an example of the use of Ribosome footprint profiling in deciphering the complex regulation network and will be useful for elucidating the metabolism of A. truncatum seed oil and the regulatory mechanisms.
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Affiliation(s)
- Qiuyue Ma
- Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement Nanjing, Nanjing, 210014, China
| | - Yuxiao Wang
- Nanjing Forestry University, Nanjing, 210037, China
| | - Shushun Li
- Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement Nanjing, Nanjing, 210014, China
| | - Jing Wen
- Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement Nanjing, Nanjing, 210014, China
| | - Lu Zhu
- Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement Nanjing, Nanjing, 210014, China
| | - Kunyuan Yan
- Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement Nanjing, Nanjing, 210014, China
| | - Yiming Du
- Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement Nanjing, Nanjing, 210014, China
| | - Shuxian Li
- Nanjing Forestry University, Nanjing, 210037, China
| | - Liping Yan
- Shandong Academy of Forestry Sciences, Jinan, 250014, China
| | - Zhijun Xie
- Xiangyang Forestry Science and Technology Extension Station, Xiangyang, 441000, China
| | - Yunzhou Lyu
- Jiangsu Academy of Forestry, Nanjing, 211153, China.
| | - Fei Shen
- Institute of Biology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100197, China.
| | - Qianzhong Li
- Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement Nanjing, Nanjing, 210014, China.
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11
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Kremlitzka M, Colineau L, Nowacka AA, Mohlin FC, Wozniak K, Blom AM, King BC. Alternative translation and retrotranslocation of cytosolic C3 that detects cytoinvasive bacteria. Cell Mol Life Sci 2022; 79:291. [PMID: 35546365 PMCID: PMC9095555 DOI: 10.1007/s00018-022-04308-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/29/2022] [Accepted: 04/12/2022] [Indexed: 01/05/2023]
Abstract
Complement C3 was originally regarded as a serum effector protein, although recent data has emerged suggesting that intracellular C3 can also regulate basic cellular processes. Despite the growing interest in intracellular C3 functions, the mechanism behind its generation has not been demonstrated. In this study we show that C3 can be expressed from an alternative translational start site, resulting in C3 lacking the signal peptide, which is therefore translated in the cytosol. In contrast to the secreted form, alternatively translated cytosolic C3 is not glycosylated, is present mainly in a reduced state, and is turned over by the ubiquitin–proteasome system. C3 can also be retrotranslocated from the endoplasmic reticulum into the cytosol, structurally resembling secreted C3. Finally, we demonstrate that intracellular cytosolic C3 can opsonize invasive Staphylococcus aureus within epithelial cell, slowing vacuolar escape as well as impacting bacterial survival on subsequent exposure to phagocytes. Our work therefore reveals the existence and origin of intracellular, cytosolic C3, and demonstrates functions for cytosolic C3 in intracellular detection of cytoinvasive pathogens.
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Affiliation(s)
- Mariann Kremlitzka
- Division of Medical Protein Chemistry, Department of Translational Medicine, Lund University, Malmö, Sweden.,Department of Immunology, Eötvös Loránd University, Budapest, Hungary
| | - Lucie Colineau
- Division of Medical Protein Chemistry, Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Alicja A Nowacka
- Division of Medical Protein Chemistry, Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Frida C Mohlin
- Division of Medical Protein Chemistry, Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Katarzyna Wozniak
- Division of Medical Protein Chemistry, Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Anna M Blom
- Division of Medical Protein Chemistry, Department of Translational Medicine, Lund University, Malmö, Sweden.
| | - Ben C King
- Division of Medical Protein Chemistry, Department of Translational Medicine, Lund University, Malmö, Sweden
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12
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Wang H, Zhang Y, Norris A, Jiang CZ. S1-bZIP Transcription Factors Play Important Roles in the Regulation of Fruit Quality and Stress Response. FRONTIERS IN PLANT SCIENCE 2022; 12:802802. [PMID: 35095974 PMCID: PMC8795868 DOI: 10.3389/fpls.2021.802802] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
Sugar metabolism not only determines fruit sweetness and quality but also acts as signaling molecules to substantially connect with other primary metabolic processes and, therefore, modulates plant growth and development, fruit ripening, and stress response. The basic region/leucine zipper motif (bZIP) transcription factor family is ubiquitous in eukaryotes and plays a diverse array of biological functions in plants. Among the bZIP family members, the smallest bZIP subgroup, S1-bZIP, is a unique one, due to the conserved upstream open reading frames (uORFs) in the 5' leader region of their mRNA. The translated small peptides from these uORFs are suggested to mediate Sucrose-Induced Repression of Translation (SIRT), an important mechanism to maintain sucrose homeostasis in plants. Here, we review recent research on the evolution, sequence features, and biological functions of this bZIP subgroup. S1-bZIPs play important roles in fruit quality, abiotic and biotic stress responses, plant growth and development, and other metabolite biosynthesis by acting as signaling hubs through dimerization with the subgroup C-bZIPs and other cofactors like SnRK1 to coordinate the expression of downstream genes. Direction for further research and genetic engineering of S1-bZIPs in plants is suggested for the improvement of quality and safety traits of fruit.
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Affiliation(s)
- Hong Wang
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Department of Plant Sciences, University of California at Davis, Davis, CA, United States
| | - Yunting Zhang
- Department of Plant Sciences, University of California at Davis, Davis, CA, United States
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Ayla Norris
- Crops Pathology and Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service, Davis, CA, United States
| | - Cai-Zhong Jiang
- Department of Plant Sciences, University of California at Davis, Davis, CA, United States
- Crops Pathology and Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service, Davis, CA, United States
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13
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Reixachs-Solé M, Eyras E. Uncovering the impacts of alternative splicing on the proteome with current omics techniques. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1707. [PMID: 34979593 PMCID: PMC9542554 DOI: 10.1002/wrna.1707] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 11/27/2021] [Accepted: 11/29/2021] [Indexed: 12/15/2022]
Abstract
The high‐throughput sequencing of cellular RNAs has underscored a broad effect of isoform diversification through alternative splicing on the transcriptome. Moreover, the differential production of transcript isoforms from gene loci has been recognized as a critical mechanism in cell differentiation, organismal development, and disease. Yet, the extent of the impact of alternative splicing on protein production and cellular function remains a matter of debate. Multiple experimental and computational approaches have been developed in recent years to address this question. These studies have unveiled how molecular changes at different steps in the RNA processing pathway can lead to differences in protein production and have functional effects. New and emerging experimental technologies open exciting new opportunities to develop new methods to fully establish the connection between messenger RNA expression and protein production and to further investigate how RNA variation impacts the proteome and cell function. This article is categorized under:RNA Processing > Splicing Regulation/Alternative Splicing Translation > Regulation RNA Evolution and Genomics > Computational Analyses of RNA
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Affiliation(s)
- Marina Reixachs-Solé
- The John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia.,EMBL Australia Partner Laboratory Network and the Australian National University, Canberra, Australian Capital Territory, Australia
| | - Eduardo Eyras
- The John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia.,EMBL Australia Partner Laboratory Network and the Australian National University, Canberra, Australian Capital Territory, Australia.,Catalan Institution for Research and Advanced Studies, Barcelona, Spain.,Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
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14
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Translational and post-translational regulation of polyamine metabolic enzymes in plants. J Biotechnol 2021; 344:1-10. [PMID: 34915092 DOI: 10.1016/j.jbiotec.2021.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 09/19/2021] [Accepted: 12/03/2021] [Indexed: 10/19/2022]
Abstract
Polyamines are small organic and basic polycations that perform essential regulatory functions in all living organisms. Fluctuations in polyamine content have been observed to occur during growth, development and under stress conditions, implying that polyamines play pivotal roles in diverse cellular and physiological processes. To achieve polyamine homeostasis, the entire metabolic pathway is subjected to a fine-tuned regulation of its biosynthetic and catabolic genes and enzymes. In this review, we describe and discuss the most important mechanisms implicated in the translational and post-translational regulation of polyamine metabolic enzymes in plants. At the translational level, we emphasize the role of polyamines in the modulation of upstream open reading frame (uORF) activities that control the translation of polyamine biosynthetic and catabolic mRNAs. At the post-translational level, different aspects of the regulation of polyamine metabolic proteins are depicted, such as the proteolytic activation of enzyme precursors, the importance of dimerization in protein stability as well as in protein intracellular localization.
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15
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Canonical and Divergent N-Terminal HBx Isoform Proteins Unveiled: Characteristics and Roles during HBV Replication. Biomedicines 2021; 9:biomedicines9111701. [PMID: 34829930 PMCID: PMC8616016 DOI: 10.3390/biomedicines9111701] [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: 10/21/2021] [Revised: 11/11/2021] [Accepted: 11/11/2021] [Indexed: 11/16/2022] Open
Abstract
Hepatitis B virus (HBV) X protein (HBx) is a viral regulatory and multifunctional protein. It is well-known that the canonical HBx reading frame bears two phylogenetically conserved internal in-frame translational initiation codons at Met2 and Met3, thus possibly generating divergent N-terminal smaller isoforms during translation. Here, we demonstrate that the three distinct HBx isoforms are generated from the ectopically expressed HBV HBx gene, named XF (full-length), XM (medium-length), and XS (short-length); they display different subcellular localizations when expressed individually in cultured hepatoma cells. Particularly, the smallest HBx isoform, XS, displayed a predominantly cytoplasmic localization. To study HBx proteins during viral replication, we performed site-directed mutagenesis to target the individual or combinatorial expression of the HBx isoforms within the HBV viral backbone (full viral genome). Our results indicate that of all HBx isoforms, only the smallest HBx isoform, XS, can restore WT levels of HBV replication, and bind to the viral mini chromosome, thereby establishing an active chromatin state, highlighting its crucial activities during HBV replication. Intriguingly, we found that sequences of HBV HBx genotype H are devoid of the conserved Met3 position, and therefore HBV genotype H infection is naturally silent for the expression of the HBx XS isoform. Finally, we found that the HBx XM (medium-length) isoform shares significant sequence similarity with the N-terminus domain of the COMMD8 protein, a member of the copper metabolism MURR1 domain-containing (COMMD) protein family. This novel finding might facilitate studies on the phylogenetic origin of the HBV X protein. The identification and functional characterization of its isoforms will shift the paradigm by changing the concept of HBx from being a unique, canonical, and multifunctional protein toward the occurrence of different HBx isoforms, carrying out different overlapping functions at different subcellular localizations during HBV genome replication. Significantly, our current work unveils new crucial HBV targets to study for potential antiviral research, and human virus pathogenesis.
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16
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Palma MB, Tronik-Le Roux D, Amín G, Castañeda S, Möbbs AM, Scarafia MA, La Greca A, Daouya M, Poras I, Inda AM, Moro LN, Carosella ED, García MN, Miriuka SG. HLA-G gene editing in tumor cell lines as a novel alternative in cancer immunotherapy. Sci Rep 2021; 11:22158. [PMID: 34773056 PMCID: PMC8589947 DOI: 10.1038/s41598-021-01572-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 10/22/2021] [Indexed: 11/08/2022] Open
Abstract
Cancer immunotherapies based mainly on the blockade of immune-checkpoint (IC) molecules by anti-IC antibodies offer new alternatives for treatment in oncological diseases. However, a considerable proportion of patients remain unresponsive to them. Hence, the development of novel clinical immunotherapeutic approaches and/or targets are crucial.W In this context, targeting the immune-checkpoint HLA-G/ILT2/ILT4 has caused great interest since it is abnormally expressed in several malignancies generating a tolerogenic microenvironment. Here, we used CRISPR/Cas9 gene editing to block the HLA-G expression in two tumor cell lines expressing HLA-G, including a renal cell carcinoma (RCC7) and a choriocarcinoma (JEG-3). Different sgRNA/Cas9 plasmids targeting HLA-G exon 1 and 2 were transfected in both cell lines. Downregulation of HLA-G was reached to different degrees, including complete silencing. Most importantly, HLA-G - cells triggered a higher in vitro response of immune cells with respect to HLA-G + wild type cells. Altogether, we demonstrated for the first time the HLA-G downregulation through gene editing. We propose this approach as a first step to develop novel clinical immunotherapeutic approaches in cancer.
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Affiliation(s)
- María Belén Palma
- Cátedra de Citología, Histología y Embriología, Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata, Argentina
- LIAN-CONICET, Fundación FLENI, Buenos Aires, Argentina
| | - Diana Tronik-Le Roux
- Atomic Energy and Alternative Energies Agency (CEA), Hematology and Immunology Research Division, Saint-Louis Hospital, Paris, France
- U976 HIPI Unit, University of Paris, Paris, France
| | | | | | - Alan M Möbbs
- LIAN-CONICET, Fundación FLENI, Buenos Aires, Argentina
| | | | | | - Marina Daouya
- Atomic Energy and Alternative Energies Agency (CEA), Hematology and Immunology Research Division, Saint-Louis Hospital, Paris, France
- U976 HIPI Unit, University of Paris, Paris, France
| | - Isabelle Poras
- Atomic Energy and Alternative Energies Agency (CEA), Hematology and Immunology Research Division, Saint-Louis Hospital, Paris, France
- U976 HIPI Unit, University of Paris, Paris, France
| | - Ana María Inda
- Cátedra de Citología, Histología y Embriología, Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata, Argentina
- Comisión de Investigaciones Científicas (CIC), Buenos Aires, Argentina
| | - Lucía N Moro
- LIAN-CONICET, Fundación FLENI, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Edgardo D Carosella
- Atomic Energy and Alternative Energies Agency (CEA), Hematology and Immunology Research Division, Saint-Louis Hospital, Paris, France
- U976 HIPI Unit, University of Paris, Paris, France
| | - Marcela N García
- Cátedra de Citología, Histología y Embriología, Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata, Argentina.
| | - Santiago G Miriuka
- LIAN-CONICET, Fundación FLENI, Buenos Aires, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
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17
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Congenital disorder of glycosylation caused by starting site-specific variant in syntaxin-5. Nat Commun 2021; 12:6227. [PMID: 34711829 PMCID: PMC8553859 DOI: 10.1038/s41467-021-26534-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 10/05/2021] [Indexed: 12/26/2022] Open
Abstract
The SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) protein syntaxin-5 (Stx5) is essential for Golgi transport. In humans, the STX5 mRNA encodes two protein isoforms, Stx5 Long (Stx5L) from the first starting methionine and Stx5 Short (Stx5S) from an alternative starting methionine at position 55. In this study, we identify a human disorder caused by a single missense substitution in the second starting methionine (p.M55V), resulting in complete loss of the short isoform. Patients suffer from an early fatal multisystem disease, including severe liver disease, skeletal abnormalities and abnormal glycosylation. Primary human dermal fibroblasts isolated from these patients show defective glycosylation, altered Golgi morphology as measured by electron microscopy, mislocalization of glycosyltransferases, and compromised ER-Golgi trafficking. Measurements of cognate binding SNAREs, based on biotin-synchronizable forms of Stx5 (the RUSH system) and Förster resonance energy transfer (FRET), revealed that the short isoform of Stx5 is essential for intra-Golgi transport. Alternative starting codons of Stx5 are thus linked to human disease, demonstrating that the site of translation initiation is an important new layer of regulating protein trafficking.
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18
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Shang P, Stepicheva N, Teel K, McCauley A, Fitting CS, Hose S, Grebe R, Yazdankhah M, Ghosh S, Liu H, Strizhakova A, Weiss J, Bhutto IA, Lutty GA, Jayagopal A, Qian J, Sahel JA, Samuel Zigler J, Handa JT, Sergeev Y, Rajala RVS, Watkins S, Sinha D. βA3/A1-crystallin regulates apical polarity and EGFR endocytosis in retinal pigmented epithelial cells. Commun Biol 2021; 4:850. [PMID: 34239035 PMCID: PMC8266859 DOI: 10.1038/s42003-021-02386-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 06/24/2021] [Indexed: 12/20/2022] Open
Abstract
The retinal pigmented epithelium (RPE) is a monolayer of multifunctional cells located at the back of the eye. High membrane turnover and polarization, including formation of actin-based apical microvilli, are essential for RPE function and retinal health. Herein, we demonstrate an important role for βA3/A1-crystallin in RPE. βA3/A1-crystallin deficiency leads to clathrin-mediated epidermal growth factor receptor (EGFR) endocytosis abnormalities and actin network disruption at the apical side that result in RPE polarity disruption and degeneration. We found that βA3/A1-crystallin binds to phosphatidylinositol transfer protein (PITPβ) and that βA3/A1-crystallin deficiency diminishes phosphatidylinositol 4,5-biphosphate (PI(4,5)P2), thus probably decreasing ezrin phosphorylation, EGFR activation, internalization, and degradation. We propose that βA3/A1-crystallin acquired its RPE function before evolving as a structural element in the lens, and that in the RPE, it modulates the PI(4,5)P2 pool through PITPβ/PLC signaling axis, coordinates EGFR activation, regulates ezrin phosphorylation and ultimately the cell polarity.
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Affiliation(s)
- Peng Shang
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Nadezda Stepicheva
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kenneth Teel
- Dean McGee Eye Institute, University of Oklahoma Health Science Center, Oklahoma City, OK, USA
| | - Austin McCauley
- Dean McGee Eye Institute, University of Oklahoma Health Science Center, Oklahoma City, OK, USA
| | | | - Stacey Hose
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Rhonda Grebe
- Wilmer Eye Institute, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Meysam Yazdankhah
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Sayan Ghosh
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Haitao Liu
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Anastasia Strizhakova
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Joseph Weiss
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Imran A Bhutto
- Wilmer Eye Institute, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Gerard A Lutty
- Wilmer Eye Institute, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Jiang Qian
- Wilmer Eye Institute, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - José-Alain Sahel
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Institut de la Vision, INSERM, CNRS, Sorbonne Université, Paris, France
| | - J Samuel Zigler
- Wilmer Eye Institute, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - James T Handa
- Wilmer Eye Institute, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yuri Sergeev
- National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Raju V S Rajala
- Dean McGee Eye Institute, University of Oklahoma Health Science Center, Oklahoma City, OK, USA
| | - Simon Watkins
- Department of Cell Biology and Center for Biologic Imaging, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Debasish Sinha
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Wilmer Eye Institute, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Cell Biology and Center for Biologic Imaging, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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19
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Guerra-Almeida D, Tschoeke DA, da-Fonseca RN. Understanding small ORF diversity through a comprehensive transcription feature classification. DNA Res 2021; 28:6317669. [PMID: 34240112 PMCID: PMC8435553 DOI: 10.1093/dnares/dsab007] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Indexed: 11/13/2022] Open
Abstract
Small open reading frames (small ORFs/sORFs/smORFs) are potentially coding sequences smaller than 100 codons that have historically been considered junk DNA by gene prediction software and in annotation screening; however, the advent of next-generation sequencing has contributed to the deeper investigation of junk DNA regions and their transcription products, resulting in the emergence of smORFs as a new focus of interest in systems biology. Several smORF peptides were recently reported in noncanonical mRNAs as new players in numerous biological contexts; however, their relevance is still overlooked in coding potential analysis. Hence, this review proposes a smORF classification based on transcriptional features, discussing the most promising approaches to investigate smORFs based on their different characteristics. First, smORFs were divided into nonexpressed (intergenic) and expressed (genic) smORFs. Second, genic smORFs were classified as smORFs located in noncoding RNAs (ncRNAs) or canonical mRNAs. Finally, smORFs in ncRNAs were further subdivided into sequences located in small or long RNAs, whereas smORFs located in canonical mRNAs were subdivided into several specific classes depending on their localization along the gene. We hope that this review provides new insights into large-scale annotations and reinforces the role of smORFs as essential components of a hidden coding DNA world.
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Affiliation(s)
- Diego Guerra-Almeida
- Institute of Biodiversity and Sustainability, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Diogo Antonio Tschoeke
- Alberto Luiz Coimbra Institute of Graduate Studies and Engineering Research (COPPE), Biomedical Engineering Program, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rodrigo Nunes- da-Fonseca
- Institute of Biodiversity and Sustainability, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,National Institute of Science and Technology in Molecular Entomology, Rio de Janeiro, Brazil
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20
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Cassidy L, Kaulich PT, Maaß S, Bartel J, Becher D, Tholey A. Bottom-up and top-down proteomic approaches for the identification, characterization, and quantification of the low molecular weight proteome with focus on short open reading frame-encoded peptides. Proteomics 2021; 21:e2100008. [PMID: 34145981 DOI: 10.1002/pmic.202100008] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/09/2021] [Accepted: 06/09/2021] [Indexed: 01/14/2023]
Abstract
The recent discovery of alternative open reading frames creates a need for suitable analytical approaches to verify their translation and to characterize the corresponding gene products at the molecular level. As the analysis of small proteins within a background proteome by means of classical bottom-up proteomics is challenging, method development for the analysis of small open reading frame encoded peptides (SEPs) have become a focal point for research. Here, we highlight bottom-up and top-down proteomics approaches established for the analysis of SEPs in both pro- and eukaryotes. Major steps of analysis, including sample preparation and (small) proteome isolation, separation and mass spectrometry, data interpretation and quality control, quantification, the analysis of post-translational modifications, and exploration of functional aspects of the SEPs by means of proteomics technologies are described. These methods do not exclusively cover the analytics of SEPs but simultaneously include the low molecular weight proteome, and moreover, can also be used for the proteome-wide analysis of proteolytic processing events.
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Affiliation(s)
- Liam Cassidy
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Philipp T Kaulich
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Sandra Maaß
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Jürgen Bartel
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Dörte Becher
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Andreas Tholey
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
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21
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Tokarz J, Schmitt SM, Möller G, Brändli AW, Adamski J. Functional characterization of two 20β-hydroxysteroid dehydrogenase type 2 homeologs from Xenopus laevis reveals multispecificity. J Steroid Biochem Mol Biol 2021; 210:105874. [PMID: 33722706 DOI: 10.1016/j.jsbmb.2021.105874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/25/2021] [Accepted: 03/09/2021] [Indexed: 11/23/2022]
Abstract
The African clawed frog, Xenopus laevis, is a versatile model for biomedical research and is largely similar to mammals in terms of organ development, anatomy, physiology, and hormonal signaling mechanisms. Steroid hormones control a variety of processes and their levels are regulated by hydroxysteroid dehydrogenases (HSDs). The subfamily of 20β-HSD type 2 enzymes currently comprises eight members from teleost fish and mammals. Here, we report the identification of three 20β-HSD type 2 genes in X. tropicalis and X. laevis and the functional characterization of the two homeologs from X. laevis. X. laevis Hsd20b2.L and Hsd20b2.S showed high sequence identity with known 20β-HSD type 2 enzymes and mapped to the two subgenomes of the allotetraploid frog genome. Both homeologs are expressed during embryonic development and in adult tissues, with strongest signals in liver, kidney, intestine, and skin. After recombinant expression in human cell lines, both enzymes co-localized with the endoplasmic reticulum and catalyzed the conversion of cortisone to 20β-dihydrocortisone. Both Hsd20b2.L and Hsd20b2.S catalyzed the 20β-reduction of further C21 steroids (17α-hydroxyprogesterone, progesterone, 11-deoxycortisol, 11-deoxycorticosterone), while only Hsd20b2.S was able to convert corticosterone and cortisol to their 20β-reduced metabolites. Estrone was only a poor and androstenedione no substrate for both enzymes. Our results demonstrate multispecificity of 20β-HSD type 2 enzymes from X. laevis similar to other teleost 20β-HSD type 2 enzymes. X. laevis 20β-HSD type 2 enzymes are probably involved in steroid catabolism and in the generation of pheromones for intraspecies communication. A role in oocyte maturation is unlikely.
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Affiliation(s)
- Janina Tokarz
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Molecular Endocrinology and Metabolism, Neuherberg, Germany.
| | - Stefan M Schmitt
- Walter Brendel Centre of Experimental Medicine, University Hospital and Ludwig-Maximilians-University Munich, Munich, Germany
| | - Gabriele Möller
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Molecular Endocrinology and Metabolism, Neuherberg, Germany
| | - André W Brändli
- Walter Brendel Centre of Experimental Medicine, University Hospital and Ludwig-Maximilians-University Munich, Munich, Germany
| | - Jerzy Adamski
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Molecular Endocrinology and Metabolism, Neuherberg, Germany; German Center for Diabetes Research, Neuherberg, Germany; Lehrstuhl für Experimentelle Genetik, Technische Universität München, Freising-Weihenstephan, Germany; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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22
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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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23
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Ghosh S, Liu H, Yazdankhah M, Stepicheva N, Shang P, Vaidya T, Hose S, Gupta U, Calderon MJ, Hu MW, Nair AP, Weiss J, Fitting CS, Bhutto IA, Gadde SGK, Naik NK, Jaydev C, Lutty GA, Handa JT, Jayagopal A, Qian J, Sahel JA, Rajasundaram D, Sergeev Y, Zigler JS, Sethu S, Watkins S, Ghosh A, Sinha D. βA1-crystallin regulates glucose metabolism and mitochondrial function in mouse retinal astrocytes by modulating PTP1B activity. Commun Biol 2021; 4:248. [PMID: 33627831 PMCID: PMC7904954 DOI: 10.1038/s42003-021-01763-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 01/28/2021] [Indexed: 02/08/2023] Open
Abstract
βA3/A1-crystallin, a lens protein that is also expressed in astrocytes, is produced as βA3 and βA1-crystallin isoforms by leaky ribosomal scanning. In a previous human proteome high-throughput array, we found that βA3/A1-crystallin interacts with protein tyrosine phosphatase 1B (PTP1B), a key regulator of glucose metabolism. This prompted us to explore possible roles of βA3/A1-crystallin in metabolism of retinal astrocytes. We found that βA1-crystallin acts as an uncompetitive inhibitor of PTP1B, but βA3-crystallin does not. Loss of βA1-crystallin in astrocytes triggers metabolic abnormalities and inflammation. In CRISPR/cas9 gene-edited βA1-knockdown (KD) mice, but not in βA3-knockout (KO) mice, the streptozotocin (STZ)-induced diabetic retinopathy (DR)-like phenotype is exacerbated. Here, we have identified βA1-crystallin as a regulator of PTP1B; loss of this regulation may be a new mechanism by which astrocytes contribute to DR. Interestingly, proliferative diabetic retinopathy (PDR) patients showed reduced βA1-crystallin and higher levels of PTP1B in the vitreous humor.
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Affiliation(s)
- Sayan Ghosh
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Haitao Liu
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Meysam Yazdankhah
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Nadezda Stepicheva
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Peng Shang
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Tanuja Vaidya
- GROW Research Laboratory, Narayana Nethralaya Foundation, Bengaluru, India
| | - Stacey Hose
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Urvi Gupta
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Michael Joseph Calderon
- Department of Cell Biology and Center for Biologic Imaging, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Ming-Wen Hu
- Wilmer Eye Institute, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Joseph Weiss
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Christopher S Fitting
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Imran A Bhutto
- Wilmer Eye Institute, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Naveen Kumar Naik
- GROW Research Laboratory, Narayana Nethralaya Foundation, Bengaluru, India
| | - Chaitra Jaydev
- GROW Research Laboratory, Narayana Nethralaya Foundation, Bengaluru, India
| | - Gerard A Lutty
- Wilmer Eye Institute, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - James T Handa
- Wilmer Eye Institute, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Jiang Qian
- Wilmer Eye Institute, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - José-Alain Sahel
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Institut de la Vision, INSERM, CNRS, Sorbonne Université, Paris, France
| | - Dhivyaa Rajasundaram
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Yuri Sergeev
- National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - J Samuel Zigler
- Wilmer Eye Institute, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Swaminathan Sethu
- GROW Research Laboratory, Narayana Nethralaya Foundation, Bengaluru, India
| | - Simon Watkins
- Department of Cell Biology and Center for Biologic Imaging, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Arkasubhra Ghosh
- GROW Research Laboratory, Narayana Nethralaya Foundation, Bengaluru, India
| | - Debasish Sinha
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Department of Cell Biology and Center for Biologic Imaging, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Wilmer Eye Institute, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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24
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Degraeve-Guilbault C, Pankasem N, Gueirrero M, Lemoigne C, Domergue F, Kotajima T, Suzuki I, Joubès J, Corellou F. Temperature Acclimation of the Picoalga Ostreococcus tauri Triggers Early Fatty-Acid Variations and Involves a Plastidial ω3-Desaturase. FRONTIERS IN PLANT SCIENCE 2021; 12:639330. [PMID: 33815446 PMCID: PMC8018280 DOI: 10.3389/fpls.2021.639330] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/19/2021] [Indexed: 05/07/2023]
Abstract
Alteration of fatty-acid unsaturation is a universal response to temperature changes. Marine microalgae display the largest diversity of polyunsaturated fatty-acid (PUFA) whose content notably varies according to temperature. The physiological relevance and the molecular mechanisms underlying these changes are however, still poorly understood. The ancestral green picoalga Ostreococcus tauri displays original lipidic features that combines PUFAs from two distinctive microalgal lineages (Chlorophyceae, Chromista kingdom). In this study, optimized conditions were implemented to unveil early fatty-acid and desaturase transcriptional variations upon chilling and warming. We further functionally characterized the O. tauri ω3-desaturase which is closely related to ω3-desaturases from Chromista species. Our results show that the overall omega-3 to omega-6 ratio is swiftly and reversibly regulated by temperature variations. The proportion of the peculiar 18:5 fatty-acid and temperature are highly and inversely correlated pinpointing the importance of 18:5 temperature-dependent variations across kingdoms. Chilling rapidly and sustainably up-regulated most desaturase genes. Desaturases involved in the regulation of the C18-PUFA pool as well as the Δ5-desaturase appear to be major transcriptional targets. The only ω3-desaturase candidate, related to ω3-desaturases from Chromista species, is localized at chloroplasts in Nicotiana benthamiana and efficiently performs ω3-desaturation of C18-PUFAs in Synechocystis sp. PCC6803. Overexpression in the native host further unveils a broad impact on plastidial and non-plastidial glycerolipids illustrated by the alteration of omega-3/omega-6 ratio in C16-PUFA and VLC-PUFA pools. Global glycerolipid features of the overexpressor recall those of chilling acclimated cells.
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Affiliation(s)
| | - Nattiwong Pankasem
- School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Maurean Gueirrero
- Univ. Bordeaux, CNRS, Laboratoire de Biogenèse membranaire, UMR 5200, Villenave d’Ornon, France
| | - Cécile Lemoigne
- Univ. Bordeaux, CNRS, Laboratoire de Biogenèse membranaire, UMR 5200, Villenave d’Ornon, France
| | - Frédéric Domergue
- Univ. Bordeaux, CNRS, Laboratoire de Biogenèse membranaire, UMR 5200, Villenave d’Ornon, France
| | - Tomonori Kotajima
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Iwane Suzuki
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Jérôme Joubès
- Univ. Bordeaux, CNRS, Laboratoire de Biogenèse membranaire, UMR 5200, Villenave d’Ornon, France
| | - Florence Corellou
- Univ. Bordeaux, CNRS, Laboratoire de Biogenèse membranaire, UMR 5200, Villenave d’Ornon, France
- *Correspondence: Florence Corellou,
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25
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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: 1] [Impact Index Per Article: 0.3] [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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26
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Flegel WA, Srivastava K. Frameshift variations in the RHD coding sequence: Molecular mechanisms permitting protein expression. Transfusion 2020; 60:2737-2744. [PMID: 33037655 DOI: 10.1111/trf.16123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 07/08/2020] [Accepted: 07/17/2020] [Indexed: 12/31/2022]
Affiliation(s)
- Willy A Flegel
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Kshitij Srivastava
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
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27
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Wu LY, Lv YQ, Ye Y, Liang YR, Ye JH. Transcriptomic and Translatomic Analyses Reveal Insights into the Developmental Regulation of Secondary Metabolism in the Young Shoots of Tea Plants ( Camellia sinensis L.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:10750-10762. [PMID: 32818378 DOI: 10.1021/acs.jafc.0c03341] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Accumulation of secondary metabolites in the young shoots of tea plants is developmentally modulated, especially flavonoids. Here, we investigate the developmental regulation mechanism of secondary metabolism in the developing leaves of tea plants using an integrated multiomic approach. For the pair of Leaf2/Bud, the correlation coefficient of the fold change of mRNA and RPFs abundances involved in flavonoid biosynthesis was 0.9359, being higher than that of RPFs and protein (R2 = 0.6941). These correlations were higher than the corresponding correlation coefficients for secondary metabolisms and genome-wide scale. Metabolomic analysis demonstrates that the developmental modulations of the structural genes for flavonoid biosynthesis-related pathways align with the concentration changes of catechin and flavonol glycoside groups. Relatively high translational efficiency (TE > 2) was observed in the four flavonoid structural genes (chalcone isomerase, dihydroflavonol 4-reductase, anthocyanidin synthase, and flavonol synthase). In addition, we originally provided the information on identified small open reading frames (small ORFs) and main ORFs in tea leaves and elaborated that the presence of upstream ORFs may have a repressive effect on the translation of downstream ORFs. Our data suggest that transcriptional regulation coordinates with translational regulation and may contribute to the elevation of translational efficiencies for the structural genes involved in the flavonoid biosynthesis pathways during tea leaf development.
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Affiliation(s)
- Liang-Yu Wu
- College of Horticulture, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, Fuzhou, China
| | - Yi-Qing Lv
- Tea Research Institute, Zhejiang University, Hangzhou 310013, China
| | - Ying Ye
- Tea Research Institute, Zhejiang University, Hangzhou 310013, China
| | - Yue-Rong Liang
- Tea Research Institute, Zhejiang University, Hangzhou 310013, China
| | - Jian-Hui Ye
- Tea Research Institute, Zhejiang University, Hangzhou 310013, China
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28
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Two Doublesex1 mutants revealed a tunable gene network underlying intersexuality in Daphnia magna. PLoS One 2020; 15:e0238256. [PMID: 32866176 PMCID: PMC7458346 DOI: 10.1371/journal.pone.0238256] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 08/12/2020] [Indexed: 11/19/2022] Open
Abstract
In recent years, the binary definition of sex is being challenged by repetitive reports about individuals with ambiguous sexual identity from various animal groups. This has created an urge to decode the molecular mechanism underlying sexual development. However, sexual ambiguities are extremely uncommon in nature, limiting their experimental value. Here, we report the establishment of a genetically modified clone of Daphnia magna from which intersex daphniids can be readily generated. By mutating the conserved central sex determining factor Doublesex1, body-wide feminization of male daphniid could be achieved. Comparative transcriptomic analysis also revealed a genetic network correlated with Doublesex1 activity which may account for the establishment of sexual identity in D. magna. We found that Dsx1 repressed genes related to growth and promoted genes related to signaling. We infer that different intersex phenotypes are the results of fluctuation in activity of these Dsx1 downstream factors. Our results demonstrated that the D. magna genome is capable of expressing sex in a continuous array, supporting the idea that sex is actually a spectrum.
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29
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Verkest C, Häfner S, Ávalos Prado P, Baron A, Sandoz G. Migraine and Two-Pore-Domain Potassium Channels. Neuroscientist 2020; 27:268-284. [PMID: 32715910 DOI: 10.1177/1073858420940949] [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] [Indexed: 12/14/2022]
Abstract
Migraine is a common, disabling neurological disorder with a genetic, environmental, and hormonal component with an annual prevalence estimated at ~15%. It is characterized by attacks of severe, usually unilateral and throbbing headache, and can be accompanied by nausea, vomiting, and photophobia. Migraine is clinically divided into two main subtypes: migraine with aura, when it is preceded by transient neurological disturbances due to cortical spreading depression (CSD), and migraine without aura. Activation and sensitization of trigeminal sensory neurons, leading to the release of pro-inflammatory peptides, is likely a key component in headache pain initiation and transmission in migraine. In the present review, we will focus on the function of two-pore-domain potassium (K2P) channels, which control trigeminal sensory neuron excitability and their potential interest for developing new drugs to treat migraine.
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Affiliation(s)
- Clément Verkest
- CNRS, INSERM, iBV, Université Cote d'Azur, Nice, France.,Laboratories of Excellence, Ion Channel Science and Therapeutics Nice, France.,Université Cote d'Azur, CNRS, INSERM, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Stephanie Häfner
- CNRS, INSERM, iBV, Université Cote d'Azur, Nice, France.,Laboratories of Excellence, Ion Channel Science and Therapeutics Nice, France
| | - Pablo Ávalos Prado
- CNRS, INSERM, iBV, Université Cote d'Azur, Nice, France.,Laboratories of Excellence, Ion Channel Science and Therapeutics Nice, France
| | - Anne Baron
- Laboratories of Excellence, Ion Channel Science and Therapeutics Nice, France.,Université Cote d'Azur, CNRS, INSERM, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Guillaume Sandoz
- CNRS, INSERM, iBV, Université Cote d'Azur, Nice, France.,Laboratories of Excellence, Ion Channel Science and Therapeutics Nice, France
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30
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Hosur V, Low BE, Li D, Stafford GA, Kohar V, Shultz LD, Wiles MV. Genes adapt to outsmart gene-targeting strategies in mutant mouse strains by skipping exons to reinitiate transcription and translation. Genome Biol 2020; 21:168. [PMID: 32646486 PMCID: PMC7350591 DOI: 10.1186/s13059-020-02086-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 06/29/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Gene disruption in mouse embryonic stem cells or zygotes is a conventional genetics approach to identify gene function in vivo. However, because different gene disruption strategies use different mechanisms to disrupt genes, the strategies can result in diverse phenotypes in the resulting mouse model. To determine whether different gene disruption strategies affect the phenotype of resulting mutant mice, we characterized Rhbdf1 mouse mutant strains generated by three commonly used strategies-definitive-null, targeted knockout (KO)-first, and CRISPR/Cas9. RESULTS We find that Rhbdf1 responds differently to distinct KO strategies, for example, by skipping exons and reinitiating translation to potentially yield gain-of-function alleles rather than the expected null or severe hypomorphic alleles. Our analysis also revealed that at least 4% of mice generated using the KO-first strategy show conflicting phenotypes. CONCLUSIONS Exon skipping is a widespread phenomenon occurring across the genome. These findings have significant implications for the application of genome editing in both basic research and clinical practice.
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Affiliation(s)
- Vishnu Hosur
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME USA
| | - Benjamin E. Low
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME USA
| | - Daniel Li
- Arthritis and Tissue Degeneration Program, Hospital for Special Surgery at Weill Cornell Medicine, New York, NY 10021 USA
| | | | - Vivek Kohar
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME USA
| | | | - Michael V. Wiles
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME USA
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31
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Azuma N, Uchida T, Kikuchi S, Sadahiro M, Shintani T, Yanagi K, Higashita R, Yamashita A, Makita Y, Kaname T. NT5E Genetic Mutation Is a Rare But Important Cause of Intermittent Claudication and Chronic Limb-Threatening Ischemia. Circ J 2020; 84:1183-1188. [DOI: 10.1253/circj.cj-20-0153] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Nobuyoshi Azuma
- Department of Vascular Surgery, Asahikawa Medical University
| | - Tetsuro Uchida
- Division of Cardiovascular Surgery, Department of Surgery II, Yamagata University
| | | | - Mitsuaki Sadahiro
- Division of Cardiovascular Surgery, Department of Surgery II, Yamagata University
| | | | - Kumiko Yanagi
- Department of Genome Medicine, National Center for Child Health and Development
| | - Ryuji Higashita
- Department of Cardiovascular Surgery, Yokohama General Hospital
| | - Atsushi Yamashita
- Division of Cardiovascular Surgery, Department of Surgery II, Yamagata University
| | | | - Tadashi Kaname
- Department of Genome Medicine, National Center for Child Health and Development
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32
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33
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Integrative transcriptome analysis discloses the molecular basis of a heterogeneous fungal phytopathogen complex, Rhizoctonia solani AG-1 subgroups. Sci Rep 2019; 9:19626. [PMID: 31873088 PMCID: PMC6928066 DOI: 10.1038/s41598-019-55734-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 11/26/2019] [Indexed: 02/06/2023] Open
Abstract
Rhizoctonia solani is a fungal species complex that causes necrotrophic crop diseases. It comprises several anastomosis groups, some of which include intra-subgroups, such as AG-1 IA and AG-1 IB, exhibiting varying pathogenicity. Owing to its heterozygous and multinucleate features, genomic analyses of R. solani are still challenging, and understanding of its genetic diversity and genic components is limited. In this study, in order to elucidate the molecular basis of this phytopathogen complex, an integrated transcriptome analysis was undertaken for three subgroups of AG-1, i.e. AG-1 IA, AG-1 IB, and AG-1 IC. Sequence variations suggested substantial evolutionary distances within AG-1. Transcript simple sequence repeats showed comparable characteristics among AG-1, but contained polymorphic sites. Intra-subgroup polymorphisms suggested varying genic heterozygosity within AG-1, suggesting their independent evolutionary trajectory. Sequences of pathogenic factors, phytotoxin biosynthesis pathway enzymes, secreted lignocellulosic enzymes, secreted reactive oxygen species detoxification enzymes, apoplastic/cytoplasmic effector candidates, were conserved among those subgroups. dN/dS ratios of a secretome subset suggested core secreted proteins in AG-1 and distinct evolution of Cys-rich small secreted proteins after differentiation of AG-1 subgroups. Identification of likely pathogenic factors including allergen protein homologues, oxidative phosphorylation and ethylene biosynthesis pathways, and diversification of polysaccharide monooxygenases provides molecular insight into key genomic components that play a role in R. solani pathogenesis.
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34
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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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35
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Manek R, Nelson T, Tseng E, Rodriguez-Lebron E. 5'UTR-mediated regulation of Ataxin-1 expression. Neurobiol Dis 2019; 134:104564. [PMID: 31381977 DOI: 10.1016/j.nbd.2019.104564] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 07/05/2019] [Accepted: 08/01/2019] [Indexed: 12/27/2022] Open
Abstract
Expression of mutant Ataxin-1 with an abnormally expanded polyglutamine domain is necessary for the onset and progression of spinocerebellar ataxia type 1 (SCA1). Understanding how Ataxin-1 expression is regulated in the human brain could inspire novel molecular therapies for this fatal, dominantly inherited neurodegenerative disease. Previous studies have shown that the ATXN1 3'UTR plays a key role in regulating the Ataxin-1 cellular pool via diverse post-transcriptional mechanisms. Here we show that elements within the ATXN1 5'UTR also participate in the regulation of Ataxin-1 expression. PCR and PacBio sequencing analysis of cDNA obtained from control and SCA1 human brain samples revealed the presence of three major, alternatively spliced ATXN1 5'UTR variants. In cell-based assays, fusion of these variants upstream of an EGFP reporter construct revealed significant and differential impacts on total EGFP protein output, uncovering a type of genetic rheostat-like function of the ATXN1 5'UTR. We identified ribosomal scanning of upstream AUG codons and increased transcript instability as potential mechanisms of regulation. Importantly, transcript-based analyses revealed significant differences in the expression pattern of ATXN1 5'UTR variants between control and SCA1 cerebellum. Together, the data presented here shed light into a previously unknown role for the ATXN1 5'UTR in the regulation of Ataxin-1 and provide new opportunities for the development of SCA1 therapeutics.
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Affiliation(s)
- Rachna Manek
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL 32610, USA; Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL 32610, USA
| | - Tiffany Nelson
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL 32610, USA; Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL 32610, USA
| | | | - Edgardo Rodriguez-Lebron
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL 32610, USA; Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL 32610, USA.
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36
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Mortz M, Dégletagne C, Romestaing C, Duchamp C. Comparative genomic analysis identifies small open reading frames (sORFs) with peptide-encoding features in avian 16S rDNA. Genomics 2019; 112:1120-1127. [PMID: 31247329 DOI: 10.1016/j.ygeno.2019.06.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 06/01/2019] [Accepted: 06/21/2019] [Indexed: 12/14/2022]
Abstract
The mitochondrial genome (mt-DNA) functional repertoire has recently been enriched in mammals by the identification of functional small open reading frames (sORFs) embedded in ribosomal DNAs. Through comparative genomic analyses the presence of putatively functional sORFs was investigated in birds. Alignment of available avian mt-DNA sequences revealed highly conserved regions containing four putative sORFs that presented low insertion/deletion polymorphism rate (<0.1%) and preserved in frame start/stop codons in >80% of species. Detected sORFs included avian homologs of human Humanin and Short-Humanin-Like-Peptide 6 and two new sORFs not yet described in mammals. The amino-acid sequences of the four putative encoded peptides were strongly conserved among birds, with amino-acid p-distances (5.6 to 25.4%) similar to those calculated for typical avian mt-DNA-encoded proteins (14.8%). Conservation resulted from either drastic conservation of the nucleotide sequence or negative selection pressure. These data extend to birds the possibility that mitochondrial rDNA may encode small bioactive peptides.
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Affiliation(s)
- Mathieu Mortz
- Université de Lyon, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, UMR 5023 CNRS, Université Claude Bernard Lyon 1, ENTPE, Villeurbanne Cedex, France
| | - Cyril Dégletagne
- Université de Lyon, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, UMR 5023 CNRS, Université Claude Bernard Lyon 1, ENTPE, Villeurbanne Cedex, France
| | - Caroline Romestaing
- Université de Lyon, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, UMR 5023 CNRS, Université Claude Bernard Lyon 1, ENTPE, Villeurbanne Cedex, France
| | - Claude Duchamp
- Université de Lyon, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, UMR 5023 CNRS, Université Claude Bernard Lyon 1, ENTPE, Villeurbanne Cedex, France.
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37
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Dvorak P, Leupen S, Soucek P. Functionally Significant Features in the 5' Untranslated Region of the ABCA1 Gene and Their Comparison in Vertebrates. Cells 2019; 8:cells8060623. [PMID: 31234415 PMCID: PMC6627321 DOI: 10.3390/cells8060623] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/17/2019] [Accepted: 06/19/2019] [Indexed: 02/07/2023] Open
Abstract
Single nucleotide polymorphisms located in 5′ untranslated regions (5′UTRs) can regulate gene expression and have clinical impact. Recognition of functionally significant sequences within 5′UTRs is crucial in next-generation sequencing applications. Furthermore, information about the behavior of 5′UTRs during gene evolution is scarce. Using the example of the ATP-binding cassette transporter A1 (ABCA1) gene (Tangier disease), we describe our algorithm for functionally significant sequence finding. 5′UTR features (upstream start and stop codons, open reading frames (ORFs), GC content, motifs, and secondary structures) were studied using freely available bioinformatics tools in 55 vertebrate orthologous genes obtained from Ensembl and UCSC. The most conserved sequences were suggested as hot spots. Exon and intron enhancers and silencers (sc35, ighg2 cgamma2, ctnt, gh-1, and fibronectin eda exon), transcription factors (TFIIA, TATA, NFAT1, NFAT4, and HOXA13), some of them cancer related, and microRNA (hsa-miR-4474-3p) were localized to these regions. An upstream ORF, overlapping with the main ORF in primates and possibly coding for a small bioactive peptide, was also detected. Moreover, we showed several features of 5′UTRs, such as GC content variation, hairpin structure conservation or 5′UTR segmentation, which are interesting from a phylogenetic point of view and can stimulate further evolutionary oriented research.
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Affiliation(s)
- Pavel Dvorak
- Department of Biology, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 32300 Pilsen, Czech Republic.
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 32300 Pilsen, Czech Republic.
| | - Sarah Leupen
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250, USA.
| | - Pavel Soucek
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 32300 Pilsen, Czech Republic.
- Toxicogenomics Unit, National Institute of Public Health, Srobarova 48, 100 42 Prague 10, Czech Republic.
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38
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Sharma AK, Sormanni P, Ahmed N, Ciryam P, Friedrich UA, Kramer G, O’Brien EP. A chemical kinetic basis for measuring translation initiation and elongation rates from ribosome profiling data. PLoS Comput Biol 2019; 15:e1007070. [PMID: 31120880 PMCID: PMC6559674 DOI: 10.1371/journal.pcbi.1007070] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 06/11/2019] [Accepted: 05/06/2019] [Indexed: 01/23/2023] Open
Abstract
Analysis methods based on simulations and optimization have been previously developed to estimate relative translation rates from next-generation sequencing data. Translation involves molecules and chemical reactions, hence bioinformatics methods consistent with the laws of chemistry and physics are more likely to produce accurate results. Here, we derive simple equations based on chemical kinetic principles to measure the translation-initiation rate, transcriptome-wide elongation rate, and individual codon translation rates from ribosome profiling experiments. Our methods reproduce the known rates from ribosome profiles generated from detailed simulations of translation. By applying our methods to data from S. cerevisiae and mouse embryonic stem cells, we find that the extracted rates reproduce expected correlations with various molecular properties, and we also find that mouse embryonic stem cells have a global translation speed of 5.2 AA/s, in agreement with previous reports that used other approaches. Our analysis further reveals that a codon can exhibit up to 26-fold variability in its translation rate depending upon its context within a transcript. This broad distribution means that the average translation rate of a codon is not representative of the rate at which most instances of that codon are translated, and it suggests that translational regulation might be used by cells to a greater degree than previously thought.
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Affiliation(s)
- Ajeet K. Sharma
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Nabeel Ahmed
- Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Prajwal Ciryam
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Ulrike A. Friedrich
- Center for Molecular Biology of the Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Günter Kramer
- Center for Molecular Biology of the Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Edward P. O’Brien
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Institute for CyberScience, Pennsylvania State University, University Park, Pennsylvania, United States of America
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39
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Illig D, Navratil M, Kelečić J, Conca R, Hojsak I, Jadrešin O, Ćorić M, Vuković J, Rohlfs M, Hollizeck S, Bohne J, Klein C, Kotlarz D. Alternative Splicing Rescues Loss of Common Gamma Chain Function and Results in IL-21R-like Deficiency. J Clin Immunol 2019; 39:207-215. [PMID: 30903457 DOI: 10.1007/s10875-019-00606-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 02/25/2019] [Indexed: 11/27/2022]
Abstract
Inborn errors in interleukin 2 receptor, gamma (IL2RG) perturb signaling of the common gamma chain family cytokines and cause severe combined immunodeficiency (SCID). Here, we report two brothers suffering from chronic cryptosporidiosis, severe diarrhea, and cholangitis. Pan T, B, and NK cell numbers were normal, but immunophenotyping revealed defective B cell differentiation. Using whole exome sequencing, we identified a base pair deletion in the first exon of IL2RG predicted to cause a frameshift and premature stop. However, flow cytometry revealed normal surface expression of the IL-2Rγ chain. While IL-2, IL-7, and IL-15 signaling showed only mild defects of STAT5 phosphorylation in response to the respective cytokines, IL-4- and IL-21-induced phosphorylation of STAT3 and STAT6 was markedly reduced. Examination of RNA isoforms detected alternative splicing downstream of IL2RG exon 1 in both patients resulting in resolution of the predicted frameshift and 16 mutated amino acids. In silico modeling suggested that the IL-2Rγ mutation reduces the stabilization of IL-4 and IL-21 cytokine binding by affecting the N-terminal domain of the IL-2Rγ. Thus, our study shows that IL2RG deficiency can be associated with differential signaling defects. Confounding effects of alternative splicing may partially rescue genetic defects and should be considered in patients with inborn errors of immunity.
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Affiliation(s)
- David Illig
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital, LMU Munich, Lindwurmstrasse 4, 80337, Munich, Germany
| | - Marta Navratil
- Department of Pulmonology, Allergology, Rheumatology and Clinical Immunology, Children's Hospital Zagreb, Zagreb, Croatia
- School of Medicine, University J.J. Strossmayer, Osijek, Croatia
| | - Jadranka Kelečić
- Department of Pediatrics, Division of Clinical Immunology, Allergology, Respiratory Diseases and Rheumatology, University Hospital Centre Zagreb, Kišpatićeva 12, Zagreb, 10000, Croatia
| | - Raffaele Conca
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital, LMU Munich, Lindwurmstrasse 4, 80337, Munich, Germany
| | - Iva Hojsak
- School of Medicine, University J.J. Strossmayer, Osijek, Croatia
- Referral Center for Pediatric Gastroenterology and Nutrition, Children's Hospital Zagreb, Zagreb, Croatia
- School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Oleg Jadrešin
- Referral Center for Pediatric Gastroenterology and Nutrition, Children's Hospital Zagreb, Zagreb, Croatia
| | - Marijana Ćorić
- Department of Pathology and Cytology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Jurica Vuković
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Meino Rohlfs
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital, LMU Munich, Lindwurmstrasse 4, 80337, Munich, Germany
| | - Sebastian Hollizeck
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital, LMU Munich, Lindwurmstrasse 4, 80337, Munich, Germany
| | - Jens Bohne
- Institute for Virology, Hannover Medical School, Hannover, Germany
| | - Christoph Klein
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital, LMU Munich, Lindwurmstrasse 4, 80337, Munich, Germany
| | - Daniel Kotlarz
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital, LMU Munich, Lindwurmstrasse 4, 80337, Munich, Germany.
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40
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Retapamulin-Assisted Ribosome Profiling Reveals the Alternative Bacterial Proteome. Mol Cell 2019; 74:481-493.e6. [PMID: 30904393 DOI: 10.1016/j.molcel.2019.02.017] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/25/2019] [Accepted: 02/12/2019] [Indexed: 12/21/2022]
Abstract
The use of alternative translation initiation sites enables production of more than one protein from a single gene, thereby expanding the cellular proteome. Although several such examples have been serendipitously found in bacteria, genome-wide mapping of alternative translation start sites has been unattainable. We found that the antibiotic retapamulin specifically arrests initiating ribosomes at start codons of the genes. Retapamulin-enhanced Ribo-seq analysis (Ribo-RET) not only allowed mapping of conventional initiation sites at the beginning of the genes, but strikingly, it also revealed putative internal start sites in a number of Escherichia coli genes. Experiments demonstrated that the internal start codons can be recognized by the ribosomes and direct translation initiation in vitro and in vivo. Proteins, whose synthesis is initiated at internal in-frame and out-of-frame start sites, can be functionally important and contribute to the "alternative" bacterial proteome. The internal start sites may also play regulatory roles in gene expression.
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41
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van der Horst S, Snel B, Hanson J, Smeekens S. Novel pipeline identifies new upstream ORFs and non-AUG initiating main ORFs with conserved amino acid sequences in the 5' leader of mRNAs in Arabidopsis thaliana. RNA (NEW YORK, N.Y.) 2019; 25:292-304. [PMID: 30567971 PMCID: PMC6380273 DOI: 10.1261/rna.067983.118] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 12/10/2018] [Indexed: 05/10/2023]
Abstract
Eukaryotic mRNAs contain a 5' leader sequence preceding the main open reading frame (mORF) and, depending on the species, 20%-50% of eukaryotic mRNAs harbor an upstream ORF (uORF) in the 5' leader. An unknown fraction of these uORFs encode sequence conserved peptides (conserved peptide uORFs, CPuORFs). Experimentally validated CPuORFs demonstrated to regulate the translation of downstream mORFs often do so in a metabolite concentration-dependent manner. Previous research has shown that most CPuORFs possess a start codon context suboptimal for translation initiation, which turns out to be favorable for translational regulation. The suboptimal initiation context may even include non-AUG start codons, which makes CPuORFs hard to predict. For this reason, we developed a novel pipeline to identify CPuORFs unbiased of start codon using well-annotated sequence data from 31 eudicot plant species and rice. Our new pipeline was able to identify 29 novel Arabidopsis thaliana (Arabidopsis) CPuORFs, conserved across a wide variety of eudicot species of which 15 do not initiate with an AUG start codon. In addition to CPuORFs, the pipeline was able to find 14 conserved coding regions directly upstream and in frame with the mORF, which likely initiate translation on a non-AUG start codon. Altogether, our pipeline identified highly conserved coding regions in the 5' leaders of Arabidopsis transcripts, including in genes with proven functional importance such as LHY, a key regulator of the circadian clock, and the RAPTOR1 subunit of the target of rapamycin (TOR) kinase.
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Affiliation(s)
- Sjors van der Horst
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Berend Snel
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Johannes Hanson
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, 3584 CH, Utrecht, The Netherlands
- Umeå Plant Science Center, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden
| | - Sjef Smeekens
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, 3584 CH, Utrecht, The Netherlands
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42
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Klein JR. Novel Splicing of Immune System Thyroid Stimulating Hormone β-Subunit-Genetic Regulation and Biological Importance. Front Endocrinol (Lausanne) 2019; 10:44. [PMID: 30804891 PMCID: PMC6371030 DOI: 10.3389/fendo.2019.00044] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 01/18/2019] [Indexed: 12/29/2022] Open
Abstract
Thyroid stimulating hormone (TSH), a glycoprotein hormone produced by the anterior pituitary, controls the production of thyroxine (T4) and triiodothyronine (T3) in the thyroid. TSH is also known to be produced by the cells of the immune system; however, the physiological importance of that to the organism is unclear. We identified an alternatively-spliced form of TSHβ that is present in both humans and mice. The TSHβ splice variant (TSHβv), although produced at low levels by the pituitary, is the primary form made by hematopoietic cells in the bone marrow, and by peripheral leukocytes. Recent studies have linked TSHβv functionally to a number of health-related conditions, including enhanced host responses to infection and protection against osteoporosis. However, TSHβv also has been associated with autoimmune thyroiditis in humans. Yet to be identified is the process by which the TSHβv isoform is produced. Here, a set of genetic steps is laid out through which human TSHβv is generated using splicing events that result in a novel transcript in which exon 2 is deleted, exon 3 is retained, and the 3' end of intron 2 codes for a signal peptide of the TSHβv polypeptide.
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43
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Migraine-Associated TRESK Mutations Increase Neuronal Excitability through Alternative Translation Initiation and Inhibition of TREK. Neuron 2018; 101:232-245.e6. [PMID: 30573346 DOI: 10.1016/j.neuron.2018.11.039] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 10/03/2018] [Accepted: 11/20/2018] [Indexed: 12/12/2022]
Abstract
It is often unclear why some genetic mutations to a given gene contribute to neurological disorders and others do not. For instance, two mutations have previously been found to produce a dominant negative for TRESK, a two-pore-domain K+ channel implicated in migraine: TRESK-MT, a 2-bp frameshift mutation, and TRESK-C110R. Both mutants inhibit TRESK, but only TRESK-MT increases sensory neuron excitability and is linked to migraine. Here, we identify a new mechanism, termed frameshift mutation-induced alternative translation initiation (fsATI), that may explain why only TRESK-MT is associated with migraine. fsATI leads to the production of a second protein fragment, TRESK-MT2, which co-assembles with and inhibits TREK1 and TREK2, two other two-pore-domain K+ channels, to increase trigeminal sensory neuron excitability, leading to a migraine-like phenotype in rodents. These findings identify TREK1 and TREK2 as potential molecular targets in migraine and suggest that fsATI should be considered as a distinct class of mutations.
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44
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Wang T, Liu Y, Liu Q, Cummins S, Zhao M. Integrative proteomic analysis reveals potential high-frequency alternative open reading frame-encoded peptides in human colorectal cancer. Life Sci 2018; 215:182-189. [PMID: 30419281 DOI: 10.1016/j.lfs.2018.11.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 10/31/2018] [Accepted: 11/08/2018] [Indexed: 11/30/2022]
Abstract
Identification of alternative open reading frame-encoded peptides (AEPs) for the diagnosis of colorectal cancer at the proteome level is largely unexplored because of a lack of comprehensive proteomics data. Here, we performed a comprehensive integrative analysis of mass spectral data published by Clinical Proteomic Tumor Analysis Consortium and characterized 93 high-confident AEPs encoded within 75 genes. There are four cancer-related genes appeared to have AEPs identified frequently in >20 out of 95 colorectal cancer samples, including ABCF2, AR, RBM10 and NRG1. Further network analysis of the identified AEPs found the enrichment of novel AEPs within hormone androgen receptor and a highly-modularised network with 42 genes associated with patient survival. Our results not only suggested a mechanistic view of how AEPs work in cancer progression, but also shed light on somatic amino acid mutations in AEPs, which might be overlooked previously because of their low frequencies. In particular, potential high-frequency mutations in 77 samples associated with EDARADD may contribute to the discovery of new biomarkers and the development of innovative therapeutic approaches.
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Affiliation(s)
- Tianfang Wang
- School of Science and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland, 4558, Australia.
| | - Yining Liu
- The School of Public Health, Institute for Chemical Carcinogenesis, Guangzhou Medical University, 195 Dongfengxi Road, Guangzhou 510182, China
| | - Qi Liu
- Department of Biomedical Informatics, School of Medicine, Vanderbilt University, Nashville, TN 37232, United States; Center for Quantitative Sciences, School of Medicine, Vanderbilt University, Nashville, TN 37232, United States
| | - Scott Cummins
- School of Science and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland, 4558, Australia
| | - Min Zhao
- School of Science and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland, 4558, Australia.
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45
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Fei JF, Lou WPK, Knapp D, Murawala P, Gerber T, Taniguchi Y, Nowoshilow S, Khattak S, Tanaka EM. Application and optimization of CRISPR-Cas9-mediated genome engineering in axolotl (Ambystoma mexicanum). Nat Protoc 2018; 13:2908-2943. [PMID: 30429597 DOI: 10.1038/s41596-018-0071-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Genomic manipulation is essential to the use of model organisms to understand development, regeneration and adult physiology. The axolotl (Ambystoma mexicanum), a type of salamander, exhibits an unparalleled regenerative capability in a spectrum of complex tissues and organs, and therefore serves as a powerful animal model for dissecting mechanisms of regeneration. We describe here an optimized stepwise protocol to create genetically modified axolotls using the CRISPR-Cas9 system. The protocol, which takes 7-8 weeks to complete, describes generation of targeted gene knockouts and knock-ins and includes site-specific integration of large targeting constructs. The direct use of purified CAS9-NLS (CAS9 containing a C-terminal nuclear localization signal) protein allows the prompt formation of guide RNA (gRNA)-CAS9-NLS ribonucleoprotein (RNP) complexes, which accelerates the creation of double-strand breaks (DSBs) at targeted genomic loci in single-cell-stage axolotl eggs. With this protocol, a substantial number of F0 individuals harboring a homozygous-type frameshift mutation can be obtained, allowing phenotype analysis in this generation. In the presence of targeting constructs, insertions of exogenous genes into targeted axolotl genomic loci can be achieved at efficiencies of up to 15% in a non-homologous end joining (NHEJ) manner. Our protocol bypasses the long generation time of axolotls and allows direct functional analysis in F0 genetically manipulated axolotls. This protocol can be potentially applied to other animal models, especially to organisms with a well-characterized transcriptome but lacking a well-characterized genome.
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Affiliation(s)
- Ji-Feng Fei
- Institute for Brain Research and Rehabilitation (IBRR), Guangdong Key Laboratory of Mental Health and Cognitive Science, South China Normal University, Guangzhou, China.
| | - Wilson Pak-Kin Lou
- School of Life Sciences, South China Normal University, Guangzhou, China
- The Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Dunja Knapp
- DFG Center for Regenerative Therapies, Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Prayag Murawala
- The Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Tobias Gerber
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Yuka Taniguchi
- The Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Sergej Nowoshilow
- The Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Shahryar Khattak
- DFG Center for Regenerative Therapies, Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Elly M Tanaka
- The Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
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Pei J, Kinch LN, Grishin NV. FlyXCDB—A Resource for Drosophila Cell Surface and Secreted Proteins and Their Extracellular Domains. J Mol Biol 2018; 430:3353-3411. [DOI: 10.1016/j.jmb.2018.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 05/31/2018] [Accepted: 06/02/2018] [Indexed: 02/06/2023]
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Wang J, Yuan Z, Zhang Y. Alternative translation initiation from two in-frame start codons in DHX33 gene. Biochem Biophys Res Commun 2018; 502:501-507. [PMID: 29864424 DOI: 10.1016/j.bbrc.2018.05.201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 05/29/2018] [Indexed: 11/20/2022]
Abstract
DHX33 has been shown to play key roles in promoting cell proliferation. We have previously found that DHX33 protein is a doublet. In this report, we discovered that DHX33 doublet is due to alternative translation initiation by two in-frame initiation codons. This is supported by studies from both cell lines and mouse models. DHX33 translation initiation from either AUG codon happens at equal efficiency. Short DHX33 protein has similar cellular location and functions with full-length DHX33. Our results suggest that leaky scanning normally occur in DHX33 mRNA translation, which may serve as a safeguard mechanism to ensure optimal DHX33 translation efficiency. This is the first report of DEAD/DEAH box proteins that can be regulated by alternative translation initiation.
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Affiliation(s)
- Jiuling Wang
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China; Bioimaging Core, Faculty of Health Sciences, University of Macau, Macau, China
| | - Zhen Yuan
- Bioimaging Core, Faculty of Health Sciences, University of Macau, Macau, China
| | - Yandong Zhang
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China.
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Abstract
ABSTRACT
Previously, leaderless mRNAs (lmRNAs) were perceived to make up only a minor fraction of the transcriptome in bacteria. However, advancements in RNA sequencing technology are uncovering vast numbers of lmRNAs, particularly in archaea,
Actinobacteria
, and extremophiles and thus underline their significance in cellular physiology and regulation. Due to the absence of conventional ribosome binding signals, lmRNA translation initiation is distinct from canonical mRNAs and can therefore be differentially regulated. The ribosome’s inherent ability to bind a 5′-terminal AUG can stabilize and protect the lmRNA from degradation or allow ribosomal loading for downstream initiation events. As a result, lmRNAs remain translationally competent during a variety of physiological conditions, allowing them to contribute to multiple regulatory mechanisms. Furthermore, the abundance of lmRNAs can increase during adverse conditions through the upregulation of lmRNA transcription from alternative promoters or by the generation of lmRNAs from canonical mRNAs cleaved by an endonucleolytic toxin. In these ways, lmRNA translation can continue during stress and contribute to regulation, illustrating their importance in the cell. Due to their presence in all domains of life and their ability to be translated by heterologous hosts, lmRNAs appear further to represent ancestral transcripts that might allow us to study the evolution of the ribosome and the translational process.
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Zhu Y, Vaughn JC. Experimental Verification and Evolutionary Origin of 5'-UTR Polyadenylation Sites in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2018; 9:969. [PMID: 30026753 PMCID: PMC6041940 DOI: 10.3389/fpls.2018.00969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 06/15/2018] [Indexed: 06/08/2023]
Abstract
Messenger RNA (mRNA) polyadenylation is an indispensable step during post-transcriptional pre-mRNA processing for most genes in eukaryotes. The usage of one poly(A) site over another is known as alternative polyadenylation (APA). APA has been implicated in gene expression regulation through its role of selecting the ends of a transcript. Recent studies of polyadenylation profiles in the Arabidopsis database unexpectedly predicted that a portion of the poly(A) sites are located in the 5'-UTR, which remains to be experimentally verified. We selected 16 genes from a dataset of 744, based on criteria designed to minimize problems in interpretation. Here, we experimentally verify 5'-UTR-APA in Arabidopsis for 10 of the 16 selected genes, and show for the first time existence of independent polyadenylated 5'-UTR transcripts, arising due to alternative polyadenylation. We used 3'-RACE and sequencing to validate poly(A) sites and northern blot to show that the observed short upstream transcripts do not arise from the 3'-end of a previously unrecognized convergent gene. Evidence is reported showing that two of the independent upstream open reading frame (uORF) transcripts studied, one containing a complex dual uORF, very likely arose by exon shuffling following duplication of the 5'-end from the downstream major open reading frame (mORF). Finally, results are presented to show that the uORF in this gene may encode two short functional proteins, based on observation of amino acid sequence conservation encoded by the dual uORFs.
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Ruan J, Guo F, Wang Y, Li X, Wan S, Shan L, Peng Z. Transcriptome analysis of alternative splicing in peanut (Arachis hypogaea L.). BMC PLANT BIOLOGY 2018; 18:139. [PMID: 29973157 PMCID: PMC6032549 DOI: 10.1186/s12870-018-1339-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 06/04/2018] [Indexed: 05/02/2023]
Abstract
BACKGROUND Alternative splicing (AS) represents a mechanism widely used by eukaryotes for the post-transcriptional regulation of genes. The detailed exploration of AS in peanut has not been documented. RESULTS The strand-specific RNA-Seq technique was exploited to characterize the distribution of AS in the four samples of peanut (FH1-seed1, FH1-seed2, FH1-root and FH1-leaf). AS was detected as affecting around 37.2% of the full set of multi-exon genes. Some of these genes experienced AS throughout the plant, while in the case of others, the effect was organ-specific. Overall, AS was more frequent in the seed than in either the root or leaf. The predominant form of AS was intron retention, and AS in transcription start site and transcription terminal site were commonly identified in all the four samples. It is interesting that in genes affected by AS, the majority experienced only a single type of event. Not all of the in silico predicted transcripts appeared to be translated, implying that these are either degraded or sequestered away from the translation machinery. With respect to genes involved in fatty acid metabolism, about 61.6% were shown to experience AS. CONCLUSION Our report contributes significantly in AS analysis of peanut genes in general, and these results have not been mentioned before. The specific functions of different AS forms need further investigation.
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Affiliation(s)
- Jian Ruan
- College of Life Science, Shandong University, Jinan, China
| | - Feng Guo
- Bio-Tech Research Center, Shandong Academy of Agricultural Science/Shandong Provincial Key Laboratory of Genetic Improvement, Ecology and Physiology of Crops, Jinan, China
| | - Yingying Wang
- Bio-Tech Research Center, Shandong Academy of Agricultural Science/Shandong Provincial Key Laboratory of Genetic Improvement, Ecology and Physiology of Crops, Jinan, China
| | - Xinguo Li
- Bio-Tech Research Center, Shandong Academy of Agricultural Science/Shandong Provincial Key Laboratory of Genetic Improvement, Ecology and Physiology of Crops, Jinan, China
| | - Shubo Wan
- College of Life Science, Shandong University, Jinan, China
- Bio-Tech Research Center, Shandong Academy of Agricultural Science/Shandong Provincial Key Laboratory of Genetic Improvement, Ecology and Physiology of Crops, Jinan, China
| | - Lei Shan
- College of Life Science, Shandong University, Jinan, China
- Bio-Tech Research Center, Shandong Academy of Agricultural Science/Shandong Provincial Key Laboratory of Genetic Improvement, Ecology and Physiology of Crops, Jinan, China
| | - Zhenying Peng
- College of Life Science, Shandong University, Jinan, China
- Bio-Tech Research Center, Shandong Academy of Agricultural Science/Shandong Provincial Key Laboratory of Genetic Improvement, Ecology and Physiology of Crops, Jinan, China
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