1
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Yang H, Thompson B. Widespread changes to the translational landscape in a maize microRNA biogenesis mutant. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:1986-2000. [PMID: 38963711 DOI: 10.1111/tpj.16902] [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: 11/19/2023] [Revised: 06/08/2024] [Accepted: 06/17/2024] [Indexed: 07/06/2024]
Abstract
MicroRNAs are short, non-coding RNAs that repress gene expression in both plants and animals and have diverse functions related to growth, development, and stress responses. The ribonuclease, DICER-LIKE1 (DCL1) is required for two steps in plant miRNA biogenesis: cleavage of the primary miRNAs (pri-miRNAs) to release a hairpin structure, called the precursor miRNA (pre-miRNA) and cleavage of the pre-miRNA to generate the miRNA/miRNA* duplex. The mature miRNA guides the RNA-induced silencing complex to target RNAs with complementary sequences, resulting in translational repression and/or RNA cleavage of target mRNAs. However, the relative contribution of translational repression versus mRNA degradation by miRNAs remains unknown at the genome-level in crops, especially in maize. The maize fuzzy tassel (fzt) mutant contains a hypomorphic mutation in DCL1 resulting in broad developmental defects. While most miRNAs are reduced in fzt, the levels of miRNA-targeted mRNAs are not dramatically increased, suggesting that translational regulation by miRNAs may be common. To gain insight into the repression mechanism of plant miRNAs, we combined ribosome profiling and RNA-sequencing to globally survey miRNA activities in maize. Our data indicate that translational repression contributes significantly to regulation of most miRNA targets and that approximately one-third of miRNA targets are regulated primarily at the translational level. Surprisingly, ribosomes appear altered in fzt mutants suggesting that DCL1 may also have a role in ribosome biogenesis. Thus, DICER-LIKE1 shapes the translational landscape in plants through both miRNA-dependent and miRNA-independent mechanisms.
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Affiliation(s)
- Hailong Yang
- Biology Department, East Carolina University, Greenville, North Carolina, USA
| | - Beth Thompson
- Biology Department, East Carolina University, Greenville, North Carolina, USA
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2
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An L, Wang Z, Cui Y, Bai Y, Yao Y, Yao X, Wu K. Comparative Analysis of Hulless Barley Transcriptomes to Regulatory Effects of Phosphorous Deficiency. Life (Basel) 2024; 14:904. [PMID: 39063656 PMCID: PMC11278117 DOI: 10.3390/life14070904] [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: 06/22/2024] [Revised: 07/11/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
Hulless barley is a cold-resistant crop widely planted in the northwest plateau of China. It is also the main food crop in this region. Phosphorus (P), as one of the important essential nutrient elements, regulates plant growth and defense. This study aimed to analyze the development and related molecular mechanisms of hulless barley under P deficiency and explore the regulatory genes so as to provide a basis for subsequent molecular breeding research. Transcriptome analysis was performed on the root and leaf samples of hulless barley cultured with different concentrations of KH2PO4 (1 mM and 10 μM) Hoagland solution. A total of 46,439 genes were finally obtained by the combined analysis of leaf and root samples. Among them, 325 and 453 genes had more than twofold differences in expression. These differentially expressed genes (DEGs) mainly participated in the abiotic stress biosynthetic process through Gene Ontology prediction. Moreover, the Kyoto Encyclopedia of Genes and Genomes showed that DEGs were mainly involved in photosynthesis, plant hormone signal transduction, glycolysis, phenylpropanoid biosynthesis, and synthesis of metabolites. These pathways also appeared in other abiotic stresses. Plants initiated multiple hormone synergistic regulatory mechanisms to maintain growth under P-deficient conditions. Transcription factors (TFs) also proved these predictions. The enrichment of ARR-B TFs, which positively regulated the phosphorelay-mediated cytokinin signal transduction, and some other TFs (AP2, GRAS, and ARF) was related to plant hormone regulation. Some DEGs showed different values in their FPKM (fragment per kilobase of transcript per million mapped reads), but the expression trends of genes responding to stress and phosphorylation remained highly consistent. Therefore, in the case of P deficiency, the first response of plants was the expression of stress-related genes. The effects of this stress on plant metabolites need to be further studied to improve the relevant regulatory mechanisms so as to further understand the importance of P in the development and stress resistance of hulless barley.
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Affiliation(s)
- Likun An
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (L.A.); (Z.W.); (Y.C.); (Y.B.); (Y.Y.); (X.Y.)
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining 810016, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining 810016, China
- Qinghai Subcenter of National Hulless Barley Improvement, Xining 810016, China
| | - Ziao Wang
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (L.A.); (Z.W.); (Y.C.); (Y.B.); (Y.Y.); (X.Y.)
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining 810016, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining 810016, China
- Qinghai Subcenter of National Hulless Barley Improvement, Xining 810016, China
| | - Yongmei Cui
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (L.A.); (Z.W.); (Y.C.); (Y.B.); (Y.Y.); (X.Y.)
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining 810016, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining 810016, China
- Qinghai Subcenter of National Hulless Barley Improvement, Xining 810016, China
| | - Yixiong Bai
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (L.A.); (Z.W.); (Y.C.); (Y.B.); (Y.Y.); (X.Y.)
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining 810016, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining 810016, China
- Qinghai Subcenter of National Hulless Barley Improvement, Xining 810016, China
| | - Youhua Yao
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (L.A.); (Z.W.); (Y.C.); (Y.B.); (Y.Y.); (X.Y.)
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining 810016, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining 810016, China
- Qinghai Subcenter of National Hulless Barley Improvement, Xining 810016, China
| | - Xiaohua Yao
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (L.A.); (Z.W.); (Y.C.); (Y.B.); (Y.Y.); (X.Y.)
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining 810016, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining 810016, China
- Qinghai Subcenter of National Hulless Barley Improvement, Xining 810016, China
| | - Kunlun Wu
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (L.A.); (Z.W.); (Y.C.); (Y.B.); (Y.Y.); (X.Y.)
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining 810016, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining 810016, China
- Qinghai Subcenter of National Hulless Barley Improvement, Xining 810016, China
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3
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Ichinose T, Kondo S, Kanno M, Shichino Y, Mito M, Iwasaki S, Tanimoto H. Translational regulation enhances distinction of cell types in the nervous system. eLife 2024; 12:RP90713. [PMID: 39010741 PMCID: PMC11251722 DOI: 10.7554/elife.90713] [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: 07/17/2024] Open
Abstract
Multicellular organisms are composed of specialized cell types with distinct proteomes. While recent advances in single-cell transcriptome analyses have revealed differential expression of mRNAs, cellular diversity in translational profiles remains underinvestigated. By performing RNA-seq and Ribo-seq in genetically defined cells in the Drosophila brain, we here revealed substantial post-transcriptional regulations that augment the cell-type distinctions at the level of protein expression. Specifically, we found that translational efficiency of proteins fundamental to neuronal functions, such as ion channels and neurotransmitter receptors, was maintained low in glia, leading to their preferential translation in neurons. Notably, distribution of ribosome footprints on these mRNAs exhibited a remarkable bias toward the 5' leaders in glia. Using transgenic reporter strains, we provide evidence that the small upstream open-reading frames in the 5' leader confer selective translational suppression in glia. Overall, these findings underscore the profound impact of translational regulation in shaping the proteomics for cell-type distinction and provide new insights into the molecular mechanisms driving cell-type diversity.
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Grants
- 21K06369 Ministry of Education, Culture, Sports, Science and Technology
- 21H05713 Ministry of Education, Culture, Sports, Science and Technology
- JP20H05784 Ministry of Education, Culture, Sports, Science and Technology
- JP21K15023 Ministry of Education, Culture, Sports, Science and Technology
- 22H05481 Ministry of Education, Culture, Sports, Science and Technology
- 22KK0106 Ministry of Education, Culture, Sports, Science and Technology
- 20H00519 Ministry of Education, Culture, Sports, Science and Technology
- JP20gm1410001 Japan Agency for Medical Research and Development
- Biology of Intracellular Environments RIKEN
- Special Postdoctoral Researchers RIKEN
- Incentive Research Projects RIKEN
- Takeda Science Foundation
- Tohoku University Research Program "Frontier Research in Duo"
- The Uehara Memorial Foundation
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Affiliation(s)
- Toshiharu Ichinose
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku UniversitySendaiJapan
- Graduate School of Life Sciences, Tohoku UniversitySendaiJapan
| | - Shu Kondo
- Faculty of Advanced Engineering, Tokyo University of SciencesTokyoJapan
| | - Mai Kanno
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku UniversitySendaiJapan
- Graduate School of Life Sciences, Tohoku UniversitySendaiJapan
| | - Yuichi Shichino
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, WakoSaitamaJapan
| | - Mari Mito
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, WakoSaitamaJapan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, WakoSaitamaJapan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of TokyoKashiwaJapan
| | - Hiromu Tanimoto
- Graduate School of Life Sciences, Tohoku UniversitySendaiJapan
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4
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Yheskel M, Hatch HM, Pedrosa E, Terry BK, Siebels A, Zheng X, Blok LR, Fencková M, Sidoli S, Schenck A, Zheng D, Lachman H, Secombe J. KDM5-mediated transcriptional activation of ribosomal protein genes alters translation efficiency to regulate mitochondrial metabolism in neurons. Nucleic Acids Res 2024; 52:6201-6219. [PMID: 38597673 PMCID: PMC11194071 DOI: 10.1093/nar/gkae261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/20/2024] [Accepted: 03/31/2024] [Indexed: 04/11/2024] Open
Abstract
Genes encoding the KDM5 family of transcriptional regulators are disrupted in individuals with intellectual disability (ID). To understand the link between KDM5 and ID, we characterized five Drosophila strains harboring missense alleles analogous to those observed in patients. These alleles disrupted neuroanatomical development, cognition and other behaviors, and displayed a transcriptional signature characterized by the downregulation of many ribosomal protein genes. A similar transcriptional profile was observed in KDM5C knockout iPSC-induced human glutamatergic neurons, suggesting an evolutionarily conserved role for KDM5 proteins in regulating this class of gene. In Drosophila, reducing KDM5 changed neuronal ribosome composition, lowered the translation efficiency of mRNAs required for mitochondrial function, and altered mitochondrial metabolism. These data highlight the cellular consequences of altered KDM5-regulated transcriptional programs that could contribute to cognitive and behavioral phenotypes. Moreover, they suggest that KDM5 may be part of a broader network of proteins that influence cognition by regulating protein synthesis.
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Affiliation(s)
- Matanel Yheskel
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Hayden A M Hatch
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Erika Pedrosa
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Bethany K Terry
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Aubrey A Siebels
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Xiang Yu Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Laura E R Blok
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 Nijmegen, GA, The Netherlands
| | - Michaela Fencková
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 Nijmegen, GA, The Netherlands
- Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Ceske Budejovice 370 05, Czechia
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Annette Schenck
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 Nijmegen, GA, The Netherlands
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Neurology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
| | - Herbert M Lachman
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
| | - Julie Secombe
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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5
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Wu HYL, Jen J, Hsu PY. What, where, and how: Regulation of translation and the translational landscape in plants. THE PLANT CELL 2024; 36:1540-1564. [PMID: 37437121 PMCID: PMC11062462 DOI: 10.1093/plcell/koad197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 07/14/2023]
Abstract
Translation is a crucial step in gene expression and plays a vital role in regulating various aspects of plant development and environmental responses. It is a dynamic and complex program that involves interactions between mRNAs, transfer RNAs, and the ribosome machinery through both cis- and trans-regulation while integrating internal and external signals. Translational control can act in a global (transcriptome-wide) or mRNA-specific manner. Recent advances in genome-wide techniques, particularly ribosome profiling and proteomics, have led to numerous exciting discoveries in both global and mRNA-specific translation. In this review, we aim to provide a "primer" that introduces readers to this fascinating yet complex cellular process and provide a big picture of how essential components connect within the network. We begin with an overview of mRNA translation, followed by a discussion of the experimental approaches and recent findings in the field, focusing on unannotated translation events and translational control through cis-regulatory elements on mRNAs and trans-acting factors, as well as signaling networks through 3 conserved translational regulators TOR, SnRK1, and GCN2. Finally, we briefly touch on the spatial regulation of mRNAs in translational control. Here, we focus on cytosolic mRNAs; translation in organelles and viruses is not covered in this review.
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Affiliation(s)
- Hsin-Yen Larry Wu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Joey Jen
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Polly Yingshan Hsu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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6
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Perlegos AE, Byrns CN, Bonini NM. Cell type-specific regulation of m 6 A modified RNAs in the aging Drosophila brain. Aging Cell 2024; 23:e14076. [PMID: 38205931 PMCID: PMC10928574 DOI: 10.1111/acel.14076] [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: 08/15/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
The aging brain is highly vulnerable to cellular stress, and neurons employ numerous mechanisms to combat neurotoxic proteins and promote healthy brain aging. The RNA modification m6 A is highly enriched in the Drosophila brain and is critical for the acute heat stress response of the brain. Here we examine m6 A in the fly brain with the chronic stresses of aging and degenerative disease. m6 A levels dynamically increased with both age and disease in the brain, marking integral neuronal identity and signaling pathway transcripts that decline in level with age and disease. Unexpectedly, there is opposing impact of m6 A transcripts in neurons versus glia, which conferred different outcomes on animal health span upon Mettl3 knockdown to reduce m6 A: whereas Mettl3 function is normally beneficial to neurons, it is deleterious to glia. Moreover, knockdown of Mettl3 in glial tauopathy reduced tau pathology and increased animal survival. These findings provide mechanistic insight into regulation of m6 A modified transcripts with age and disease, highlighting an overall beneficial function of Mettl3 in neurons in response to chronic stresses, versus a deleterious impact in glia.
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Affiliation(s)
- Alexandra E. Perlegos
- Neuroscience Graduate Group, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - China N. Byrns
- Neuroscience Graduate Group, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Medical Scientist Training Program, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Nancy M. Bonini
- Neuroscience Graduate Group, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
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7
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Su D, Ding C, Qiu J, Yang G, Wang R, Liu Y, Tao J, Luo W, Weng G, Zhang T. Ribosome profiling: a powerful tool in oncological research. Biomark Res 2024; 12:11. [PMID: 38273337 PMCID: PMC10809610 DOI: 10.1186/s40364-024-00562-4] [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: 08/19/2023] [Accepted: 01/12/2024] [Indexed: 01/27/2024] Open
Abstract
Neoplastic cells need to adapt their gene expression pattern to survive in an ever-changing or unfavorable tumor microenvironment. Protein synthesis (or mRNA translation), an essential part of gene expression, is dysregulated in cancer. The emergence of distinct translatomic technologies has revolutionized oncological studies to elucidate translational regulatory mechanisms. Ribosome profiling can provide adequate information on diverse aspects of translation by aiding in quantitatively analyzing the intensity of translating ribosome-protected fragments. Here, we review the primary currently used translatomics techniques and highlight their advantages and disadvantages as tools for translatomics studies. Subsequently, we clarified the areas in which ribosome profiling could be applied to better understand translational control. Finally, we summarized the latest advances in cancer studies using ribosome profiling to highlight the extensive application of this powerful and promising translatomic tool.
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Affiliation(s)
- Dan Su
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Chen Ding
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Jiangdong Qiu
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Gang Yang
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Ruobing Wang
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Yueze Liu
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Jinxin Tao
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Wenhao Luo
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Guihu Weng
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
| | - Taiping Zhang
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China.
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China.
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8
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Wilinski D, Dus M. N 6-adenosine methylation controls the translation of insulin mRNA. Nat Struct Mol Biol 2023; 30:1260-1264. [PMID: 37488356 DOI: 10.1038/s41594-023-01048-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 06/26/2023] [Indexed: 07/26/2023]
Abstract
Control of insulin mRNA translation is crucial for energy homeostasis, but the mechanisms remain largely unknown. We discovered that insulin mRNAs across invertebrates, vertebrates and mammals feature the modified base N6-methyladenosine (m6A). In flies, this RNA modification enhances insulin mRNA translation by promoting the association of the transcript with polysomes. Depleting m6A in Drosophila melanogaster insulin 2 mRNA (dilp2) directly through specific 3' untranslated region (UTR) mutations, or indirectly by mutating the m6A writer Mettl3, decreases dilp2 protein production, leading to aberrant energy homeostasis and diabetic-like phenotypes. Together, our findings reveal adenosine mRNA methylation as a key regulator of insulin protein synthesis with notable implications for energy balance and metabolic disease.
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Affiliation(s)
- Daniel Wilinski
- Department of Molecular, Cellular, and Developmental Biology, The University of Michigan, Ann Arbor, MI, USA
| | - Monica Dus
- Department of Molecular, Cellular, and Developmental Biology, The University of Michigan, Ann Arbor, MI, USA.
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9
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Han Y, Goel P, Chen J, Perry S, Tran N, Nishimura S, Sanjani M, Chien C, Dickman D. Excess glutamate release triggers subunit-specific homeostatic receptor scaling. Cell Rep 2023; 42:112775. [PMID: 37436892 PMCID: PMC10529671 DOI: 10.1016/j.celrep.2023.112775] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 05/06/2023] [Accepted: 06/25/2023] [Indexed: 07/14/2023] Open
Abstract
Ionotropic glutamate receptors (GluRs) are targets for modulation in Hebbian and homeostatic synaptic plasticity and are remodeled by development, experience, and disease. We have probed the impact of synaptic glutamate levels on the two postsynaptic GluR subtypes at the Drosophila neuromuscular junction, GluRA and GluRB. We first demonstrate that GluRA and GluRB compete to establish postsynaptic receptive fields, and that proper GluR abundance and composition can be orchestrated in the absence of any synaptic glutamate release. However, excess glutamate adaptively tunes postsynaptic GluR abundance, echoing GluR scaling observed in mammalian systems. Furthermore, when GluRA vs. GluRB competition is eliminated, GluRB becomes insensitive to glutamate modulation. In contrast, GluRA is now homeostatically regulated by excess glutamate to maintain stable miniature activity, where Ca2+ permeability through GluRA receptors is required. Thus, excess glutamate, GluR competition, and Ca2+ signaling collaborate to selectively target GluR subtypes for homeostatic regulation at postsynaptic compartments.
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Affiliation(s)
- Yifu Han
- Department of Neurobiology, University of Southern California, Los Angeles, CA 90089, USA
| | - Pragya Goel
- Department of Neurobiology, University of Southern California, Los Angeles, CA 90089, USA
| | - Jiawen Chen
- Department of Neurobiology, University of Southern California, Los Angeles, CA 90089, USA
| | - Sarah Perry
- Department of Neurobiology, University of Southern California, Los Angeles, CA 90089, USA
| | - Nancy Tran
- Department of Neurobiology, University of Southern California, Los Angeles, CA 90089, USA
| | - Samantha Nishimura
- Department of Neurobiology, University of Southern California, Los Angeles, CA 90089, USA
| | - Manisha Sanjani
- Department of Neurobiology, University of Southern California, Los Angeles, CA 90089, USA
| | - Chun Chien
- Department of Neurobiology, University of Southern California, Los Angeles, CA 90089, USA
| | - Dion Dickman
- Department of Neurobiology, University of Southern California, Los Angeles, CA 90089, USA.
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10
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Rozich E, Randolph LK, Insolera R. An optimized temporally controlled Gal4 system in Drosophila reveals degeneration caused by adult-onset neuronal Vps13D knockdown. Front Neurosci 2023; 17:1204068. [PMID: 37457002 PMCID: PMC10339317 DOI: 10.3389/fnins.2023.1204068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/09/2023] [Indexed: 07/18/2023] Open
Abstract
Mutations in the human gene VPS13D cause the adult-onset neurodegenerative disease ataxia. Our previous work showed that disruptions in the Vps13D gene in Drosophila neurons causes mitochondrial defects. However, developmental lethality caused by Vps13D loss limited our understanding of the long-term physiological effects of Vps13D perturbation in neurons. Here, we optimized a previously generated system to temporally knock down Vps13D expression precisely in adult Drosophila neurons using a modification to the Gal4/UAS system. Adult-onset activation of Gal4 was enacted using the chemically-inducible tool which fuses a destabilization-domain to the Gal4 repressor Gal80 (Gal80-DD). Optimization of the Gal80-DD tool shows that feeding animals the DD-stabilizing drug trimethoprim (TMP) during development and rearing at a reduced temperature maximally represses Gal4 activity. Temperature shift and removal of TMP from the food after eclosion robustly activates Gal4 expression in adult neurons. Using the optimized Gal80-DD system, we find that adult-onset Vps13D RNAi expression in neurons causes the accumulation of mitophagy intermediates, progressive deficits in locomotor activity, early lethality, and brain vacuolization characteristic of neurodegeneration. The development of this optimized system allows us to more precisely examine the degenerative phenotypes caused by Vps13D disruption, and can likely be utilized in the future for other genes associated with neurological diseases whose manipulation causes developmental lethality in Drosophila.
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Affiliation(s)
- Emily Rozich
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University School of Medicine, Detroit, MI, United States
| | - Lynsey K. Randolph
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Ryan Insolera
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University School of Medicine, Detroit, MI, United States
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11
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Breznak SM, Peng Y, Deng L, Kotb NM, Flamholz Z, Rapisarda IT, Martin ET, LaBarge KA, Fabris D, Gavis ER, Rangan P. H/ACA snRNP-dependent ribosome biogenesis regulates translation of polyglutamine proteins. SCIENCE ADVANCES 2023; 9:eade5492. [PMID: 37343092 PMCID: PMC10284551 DOI: 10.1126/sciadv.ade5492] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 05/17/2023] [Indexed: 06/23/2023]
Abstract
Stem cells in many systems, including Drosophila germline stem cells (GSCs), increase ribosome biogenesis and translation during terminal differentiation. Here, we show that the H/ACA small nuclear ribonucleoprotein (snRNP) complex that promotes pseudouridylation of ribosomal RNA (rRNA) and ribosome biogenesis is required for oocyte specification. Reducing ribosome levels during differentiation decreased the translation of a subset of messenger RNAs that are enriched for CAG trinucleotide repeats and encode polyglutamine-containing proteins, including differentiation factors such as RNA-binding Fox protein 1. Moreover, ribosomes were enriched at CAG repeats within transcripts during oogenesis. Increasing target of rapamycin (TOR) activity to elevate ribosome levels in H/ACA snRNP complex-depleted germlines suppressed the GSC differentiation defects, whereas germlines treated with the TOR inhibitor rapamycin had reduced levels of polyglutamine-containing proteins. Thus, ribosome biogenesis and ribosome levels can control stem cell differentiation via selective translation of CAG repeat-containing transcripts.
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Affiliation(s)
- Shane M. Breznak
- Department of Biological Sciences, RNA Institute, University at Albany, 1400 Washington Avenue, LSRB 2033D, Albany, NY 12222, USA
| | - Yingshi Peng
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Limin Deng
- Department of Biological Sciences, RNA Institute, University at Albany, 1400 Washington Avenue, LSRB 2033D, Albany, NY 12222, USA
- Department of Chemistry, University of Connecticut, 55N Eagleville Rd, Storrs, CT 06269, USA
| | - Noor M. Kotb
- Department of Biological Sciences, RNA Institute, University at Albany, 1400 Washington Avenue, LSRB 2033D, Albany, NY 12222, USA
- Department of Biomedical Sciences, University at Albany School of Public Health, Albany, NY 12144, USA
| | - Zachary Flamholz
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Ian T. Rapisarda
- Department of Biological Sciences, RNA Institute, University at Albany, 1400 Washington Avenue, LSRB 2033D, Albany, NY 12222, USA
- Lake Erie College of Osteopathic Medicine, College of Medicine, 1858 W Grandview Blvd, Erie, PA 16509, USA
| | - Elliot T. Martin
- Department of Biological Sciences, RNA Institute, University at Albany, 1400 Washington Avenue, LSRB 2033D, Albany, NY 12222, USA
| | - Kara A. LaBarge
- Department of Biological Sciences, RNA Institute, University at Albany, 1400 Washington Avenue, LSRB 2033D, Albany, NY 12222, USA
| | - Dan Fabris
- Department of Biological Sciences, RNA Institute, University at Albany, 1400 Washington Avenue, LSRB 2033D, Albany, NY 12222, USA
- Department of Chemistry, University of Connecticut, 55N Eagleville Rd, Storrs, CT 06269, USA
| | - Elizabeth R. Gavis
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Prashanth Rangan
- Department of Biological Sciences, RNA Institute, University at Albany, 1400 Washington Avenue, LSRB 2033D, Albany, NY 12222, USA
- Black Family Stem Cell Institute, Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
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12
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He K, Han Y, Li X, Hernandez RX, Riboul DV, Feghhi T, Justs KA, Mahneva O, Perry S, Macleod GT, Dickman D. Physiologic and Nanoscale Distinctions Define Glutamatergic Synapses in Tonic vs Phasic Neurons. J Neurosci 2023; 43:4598-4611. [PMID: 37221096 PMCID: PMC10286941 DOI: 10.1523/jneurosci.0046-23.2023] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 05/05/2023] [Accepted: 05/11/2023] [Indexed: 05/25/2023] Open
Abstract
Neurons exhibit a striking degree of functional diversity, each one tuned to the needs of the circuitry in which it is embedded. A fundamental functional dichotomy occurs in activity patterns, with some neurons firing at a relatively constant "tonic" rate, while others fire in bursts, a "phasic" pattern. Synapses formed by tonic versus phasic neurons are also functionally differentiated, yet the bases of their distinctive properties remain enigmatic. A major challenge toward illuminating the synaptic differences between tonic and phasic neurons is the difficulty in isolating their physiological properties. At the Drosophila neuromuscular junction, most muscle fibers are coinnervated by two motor neurons: the tonic "MN-Ib" and phasic "MN-Is." Here, we used selective expression of a newly developed botulinum neurotoxin transgene to silence tonic or phasic motor neurons in Drosophila larvae of either sex. This approach highlighted major differences in their neurotransmitter release properties, including probability, short-term plasticity, and vesicle pools. Furthermore, Ca2+ imaging demonstrated ∼2-fold greater Ca2+ influx at phasic neuron release sites relative to tonic, along with an enhanced synaptic vesicle coupling. Finally, confocal and super-resolution imaging revealed that phasic neuron release sites are organized in a more compact arrangement, with enhanced stoichiometry of voltage-gated Ca2+ channels relative to other active zone scaffolds. These data suggest that distinctions in active zone nano-architecture and Ca2+ influx collaborate to differentially tune glutamate release at tonic versus phasic synaptic subtypes.SIGNIFICANCE STATEMENT "Tonic" and "phasic" neuronal subtypes, based on differential firing properties, are common across many nervous systems. Using a recently developed approach to selectively silence transmission from one of these two neurons, we reveal specialized synaptic functional and structural properties that distinguish these specialized neurons. This study provides important insights into how input-specific synaptic diversity is achieved, which could have implications for neurologic disorders that involve changes in synaptic function.
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Affiliation(s)
- Kaikai He
- Department of Neurobiology, University of Southern California, Los Angeles, California 90089
- USC Neuroscience Graduate Program, Los Angeles, California 90089
| | - Yifu Han
- Department of Neurobiology, University of Southern California, Los Angeles, California 90089
- USC Neuroscience Graduate Program, Los Angeles, California 90089
| | - Xiling Li
- Department of Neurobiology, University of Southern California, Los Angeles, California 90089
- USC Neuroscience Graduate Program, Los Angeles, California 90089
| | - Roberto X Hernandez
- Integrative Biology and Neuroscience Graduate Program, Department of Biological Sciences, Florida Atlantic University, Boca Raton, Florida 33431
- International Max Planck Research School for Brain and Behavior, Jupiter, Florida 33458
| | - Danielle V Riboul
- Integrative Biology Graduate Program, Department of Biological Sciences, Florida Atlantic University, Boca Raton, Florida 33431
| | - Touhid Feghhi
- Department of Physics, Florida Atlantic University, Boca Raton, Florida 33431
| | - Karlis A Justs
- Integrative Biology and Neuroscience Graduate Program, Department of Biological Sciences, Florida Atlantic University, Boca Raton, Florida 33431
| | - Olena Mahneva
- Wilkes Honors College, Florida Atlantic University, Jupiter, Florida 33458
| | - Sarah Perry
- Department of Neurobiology, University of Southern California, Los Angeles, California 90089
| | - Gregory T Macleod
- Wilkes Honors College, Florida Atlantic University, Jupiter, Florida 33458
- Institute for Human Health and Disease Intervention, Florida Atlantic University, Jupiter, Florida 33458
| | - Dion Dickman
- Department of Neurobiology, University of Southern California, Los Angeles, California 90089
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13
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Mallik B, Brusich DJ, Heyrman G, Frank CA. Precise mapping of one classic and three novel GluRIIA mutants in Drosophila melanogaster. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000784. [PMID: 37334199 PMCID: PMC10276266 DOI: 10.17912/micropub.biology.000784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/24/2023] [Accepted: 05/25/2023] [Indexed: 06/20/2023]
Abstract
Mutation of the Drosophila melanogaster GluRIIA gene or pharmacological agents targeting it are commonly used to assess homeostatic synaptic function at the larval neuromuscular junction (NMJ). The commonly used mutation, GluRIIA SP16 , is a null allele created by a large and imprecise excision of a P-element which affects GluRIIA and multiple upstream genes. Here we mapped the exact bounds of the GluRIIA SP16 allele, refined a multiplex PCR strategy for positive identification of GluRIIA SP16 in homozygous or heterozygous backgrounds, and sequenced and characterized three new CRISPR-generated GluRIIA mutants. We found the three new GluRIIA alleles are apparent nulls that lack GluRIIA immunofluorescence signal at the 3 rd instar larval NMJ and are predicted to cause premature truncations at the genetic level. Further, these new mutants have similar electrophysiological outcomes as GluRIIA SP16 , including reduced miniature excitatory postsynaptic potential (mEPSP) amplitude and frequency compared to controls, and they express robust homeostatic compensation as evidenced by normal excitatory postsynaptic potential (EPSP) amplitude and elevated quantal content. These findings and new tools extend the capacity of the D. melanogaster NMJ for assessment of synaptic function.
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Affiliation(s)
- Bhagaban Mallik
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, Iowa, United States
| | - Douglas J Brusich
- Human Biology Department, University of Wisconsin–Green Bay, Green Bay, Wisconsin, United States
| | - Georgette Heyrman
- Human Biology Department, University of Wisconsin–Green Bay, Green Bay, Wisconsin, United States
| | - C. Andrew Frank
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, Iowa, United States
- Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States
- Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa, United States
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14
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Wester LE, Lanjuin A, Bruckisch EH, Perez-Matos MC, Stine PG, Heintz C, Denzel MS, Mair WB. A single-copy knockin translating ribosome immunoprecipitation toolkit for tissue-specific profiling of actively translated mRNAs in C. elegans. CELL REPORTS METHODS 2023; 3:100433. [PMID: 37056370 PMCID: PMC10088236 DOI: 10.1016/j.crmeth.2023.100433] [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: 06/08/2022] [Revised: 01/11/2023] [Accepted: 02/28/2023] [Indexed: 03/29/2023]
Abstract
Here, we introduce a single-copy knockin translating ribosome immunoprecipitation (SKI TRIP) toolkit, a collection of Caenorhabditis elegans strains engineered by CRISPR in which tissue-specific expression of FLAG-tagged ribosomal subunit protein RPL-22 is driven by cassettes present in single copy from defined sites in the genome. Through in-depth characterization of the effects of the FLAG tag in animals in which endogenous RPL-22 has been tagged, we show that it incorporates into actively translating ribosomes and efficiently and cleanly pulls down cell-type-specific transcripts. Importantly, the presence of the tag does not impact overall mRNA translation, create bias in transcript use, or cause changes to fitness of the animal. We propose SKI TRIP use for the study of tissue-specific differences in translation and for investigating processes that are acutely sensitive to changes in translation like development or aging.
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Affiliation(s)
- Laura E. Wester
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Molecular Genetics of Ageing, Max Planck Institute for Biology of Ageing, 50668 Cologne, Germany
| | - Anne Lanjuin
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Emanuel H.W. Bruckisch
- Department of Molecular Genetics of Ageing, Max Planck Institute for Biology of Ageing, 50668 Cologne, Germany
| | - Maria C. Perez-Matos
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Peter G. Stine
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Caroline Heintz
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Martin S. Denzel
- Department of Molecular Genetics of Ageing, Max Planck Institute for Biology of Ageing, 50668 Cologne, Germany
- Altos Labs, Cambridge, UK
| | - William B. Mair
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
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15
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Sung H, Vaziri A, Wilinski D, Woerner RKR, Freddolino PL, Dus M. Nutrigenomic regulation of sensory plasticity. eLife 2023; 12:e83979. [PMID: 36951889 PMCID: PMC10036121 DOI: 10.7554/elife.83979] [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: 10/05/2022] [Accepted: 03/10/2023] [Indexed: 03/24/2023] Open
Abstract
Diet profoundly influences brain physiology, but how metabolic information is transmuted into neural activity and behavior changes remains elusive. Here, we show that the metabolic enzyme O-GlcNAc Transferase (OGT) moonlights on the chromatin of the D. melanogaster gustatory neurons to instruct changes in chromatin accessibility and transcription that underlie sensory adaptations to a high-sugar diet. OGT works synergistically with the Mitogen Activated Kinase/Extracellular signal Regulated Kinase (MAPK/ERK) rolled and its effector stripe (also known as EGR2 or Krox20) to integrate activity information. OGT also cooperates with the epigenetic silencer Polycomb Repressive Complex 2.1 (PRC2.1) to decrease chromatin accessibility and repress transcription in the high-sugar diet. This integration of nutritional and activity information changes the taste neurons' responses to sugar and the flies' ability to sense sweetness. Our findings reveal how nutrigenomic signaling generates neural activity and behavior in response to dietary changes in the sensory neurons.
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Affiliation(s)
- Hayeon Sung
- Department of Molecular, Cellular and Developmental Biology, College of Literature, Science, and the Arts, The University of MichiganAnn ArborUnited States
| | - Anoumid Vaziri
- Department of Molecular, Cellular and Developmental Biology, College of Literature, Science, and the Arts, The University of MichiganAnn ArborUnited States
- The Molecular, Cellular and Developmental Biology Graduate Program, The University of MichiganAnn ArborUnited States
| | - Daniel Wilinski
- Department of Molecular, Cellular and Developmental Biology, College of Literature, Science, and the Arts, The University of MichiganAnn ArborUnited States
| | - Riley KR Woerner
- Department of Molecular, Cellular and Developmental Biology, College of Literature, Science, and the Arts, The University of MichiganAnn ArborUnited States
| | - Peter L Freddolino
- Department of Biological Chemistry, The University of Michigan Medical SchoolAnn ArborUnited States
- Department of Computational Medicine and Bioinformatics, The University of Michigan Medical SchoolAnn ArborUnited States
| | - Monica Dus
- Department of Molecular, Cellular and Developmental Biology, College of Literature, Science, and the Arts, The University of MichiganAnn ArborUnited States
- The Molecular, Cellular and Developmental Biology Graduate Program, The University of MichiganAnn ArborUnited States
- The Michigan Neuroscience InstituteAnn ArborUnited States
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16
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Pueyo JI, Salazar J, Grincho C, Berni J, Towler BP, Newbury SF. Purriato is a conserved small open reading frame gene that interacts with the CASA pathway to regulate muscle homeostasis and epithelial tissue growth in Drosophila. Front Cell Dev Biol 2023; 11:1117454. [PMID: 36968202 PMCID: PMC10036370 DOI: 10.3389/fcell.2023.1117454] [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: 12/06/2022] [Accepted: 02/24/2023] [Indexed: 03/12/2023] Open
Abstract
Recent advances in proteogenomic techniques and bioinformatic pipelines have permitted the detection of thousands of translated small Open Reading Frames (smORFs), which contain less than 100 codons, in eukaryotic genomes. Hundreds of these actively translated smORFs display conserved sequence, structure and evolutionary signatures indicating that the translated peptides could fulfil important biological roles. Despite their abundance, only tens of smORF genes have been fully characterised; these act mainly as regulators of canonical proteins involved in essential cellular processes. Importantly, some of these smORFs display conserved functions with their mutations being associated with pathogenesis. Thus, investigating smORF roles in Drosophila will not only expand our understanding of their functions but it may have an impact in human health. Here we describe the function of a novel and essential Drosophila smORF gene named purriato (prto). prto belongs to an ancient gene family whose members have expanded throughout the Protostomia clade. prto encodes a transmembrane peptide which is localized in endo-lysosomes and perinuclear and plasma membranes. prto is dynamically expressed in mesodermal tissues and imaginal discs. Targeted prto knockdown (KD) in these organs results in changes in nuclear morphology and endo-lysosomal distributions correlating with the loss of sarcomeric homeostasis in muscles and reduction of mitosis in wing discs. Consequently, prto KD mutants display severe reduction of motility, and shorter wings. Finally, our genetic interaction experiments show that prto function is closely associated to the CASA pathway, a conserved mechanism involved in turnover of mis-folded proteins and linked to muscle dystrophies and neurodegenerative diseases. Thus, this study shows the relevance of smORFs in regulating important cellular functions and supports the systematic characterisation of this class of genes to understand their functions and evolution.
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Affiliation(s)
- Jose I. Pueyo
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
| | - Jorge Salazar
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
| | - Carolina Grincho
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
| | - Jimena Berni
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
| | - Benjamin P. Towler
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Sarah F. Newbury
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
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17
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Perry S, Han Y, Qiu C, Chien C, Goel P, Nishimura S, Sajnani M, Schmid A, Sigrist SJ, Dickman D. A glutamate receptor C-tail recruits CaMKII to suppress retrograde homeostatic signaling. Nat Commun 2022; 13:7656. [PMID: 36496500 PMCID: PMC9741633 DOI: 10.1038/s41467-022-35417-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 12/02/2022] [Indexed: 12/13/2022] Open
Abstract
Presynaptic homeostatic plasticity (PHP) adaptively enhances neurotransmitter release following diminished postsynaptic glutamate receptor (GluR) functionality to maintain synaptic strength. While much is known about PHP expression mechanisms, postsynaptic induction remains enigmatic. For over 20 years, diminished postsynaptic Ca2+ influx was hypothesized to reduce CaMKII activity and enable retrograde PHP signaling at the Drosophila neuromuscular junction. Here, we have interrogated inductive signaling and find that active CaMKII colocalizes with and requires the GluRIIA receptor subunit. Next, we generated Ca2+-impermeable GluRs to reveal that both CaMKII activity and PHP induction are Ca2+-insensitive. Rather, a GluRIIA C-tail domain is necessary and sufficient to recruit active CaMKII. Finally, chimeric receptors demonstrate that the GluRIIA tail constitutively occludes retrograde homeostatic signaling by stabilizing active CaMKII. Thus, the physical loss of the GluRIIA tail is sensed, rather than reduced Ca2+, to enable retrograde PHP signaling, highlighting a unique, Ca2+-independent control mechanism for CaMKII in gating homeostatic plasticity.
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Affiliation(s)
- Sarah Perry
- Department of Neurobiology, University of Southern California, Los Angeles, CA, USA
| | - Yifu Han
- Department of Neurobiology, University of Southern California, Los Angeles, CA, USA
| | - Chengjie Qiu
- Department of Neurobiology, University of Southern California, Los Angeles, CA, USA
| | - Chun Chien
- Department of Neurobiology, University of Southern California, Los Angeles, CA, USA
| | - Pragya Goel
- Department of Neurobiology, University of Southern California, Los Angeles, CA, USA
| | - Samantha Nishimura
- Department of Neurobiology, University of Southern California, Los Angeles, CA, USA
| | - Manisha Sajnani
- Department of Neurobiology, University of Southern California, Los Angeles, CA, USA
| | - Andreas Schmid
- Institute for Biology/Genetics, Freie Universität Berlin, Takustraße 6, 14195, Berlin, Germany
- Faculty of Life Sciences, Albstadt-Sigmaringen University, Sigmaringen, Germany
| | - Stephan J Sigrist
- Institute for Biology/Genetics, Freie Universität Berlin, Takustraße 6, 14195, Berlin, Germany
- NeuroCure Cluster of Excellence, Charité Universitätsmedizin, Charitéplatz 1, 10117, Berlin, Germany
| | - Dion Dickman
- Department of Neurobiology, University of Southern California, Los Angeles, CA, USA.
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18
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Mushtaq Z, Aavula K, Lasser DA, Kieweg ID, Lion LM, Kins S, Pielage J. Madm/NRBP1 mediates synaptic maintenance and neurodegeneration-induced presynaptic homeostatic potentiation. Cell Rep 2022; 41:111710. [PMID: 36450258 DOI: 10.1016/j.celrep.2022.111710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/05/2022] [Accepted: 11/02/2022] [Indexed: 12/03/2022] Open
Abstract
The precise regulation of synaptic connectivity and function is essential to maintain neuronal circuits. Here, we show that the Drosophila pseudo-kinase Madm/NRBP1 (Mlf-1-adapter-molecule/nuclear-receptor-binding protein 1) is required presynaptically to maintain synaptic stability and to coordinate synaptic growth and function. Presynaptic Madm mediates these functions by controlling cap-dependent translation via the target of rapamycin (TOR) effector 4E-BP/Thor (eukaryotic initiation factor 4E binding protein/Thor). Strikingly, at degenerating neuromuscular synapses, postsynaptic Madm induces a compensatory, transsynaptic signal that utilizes the presynaptic homeostatic potentiation (PHP) machinery to offset synaptic release deficits and to delay synaptic degeneration. Madm is not required for canonical PHP but induces a neurodegeneration-specific form of PHP and acts via the regulation of the cap-dependent translation regulators 4E-BP/Thor and S6-kinase. Consistently, postsynaptic induction of canonical PHP or TOR activation can compensate for postsynaptic Madm to alleviate functional and structural synaptic defects. Our results provide insights into the molecular mechanisms underlying neurodegeneration-induced PHP with potential neurotherapeutic applications.
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Affiliation(s)
- Zeeshan Mushtaq
- Department of Zoology and Neurobiology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Kumar Aavula
- Department of Zoology and Neurobiology, University of Kaiserslautern, 67663 Kaiserslautern, Germany; Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.
| | - Dario A Lasser
- Department of Zoology and Neurobiology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Ingrid D Kieweg
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Lena M Lion
- Department of Zoology and Neurobiology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Stefan Kins
- Department of Human Biology and Human Genetics, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Jan Pielage
- Department of Zoology and Neurobiology, University of Kaiserslautern, 67663 Kaiserslautern, Germany.
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19
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Bonini NM. A perspective on Drosophila genetics and its insight into human neurodegenerative disease. Front Mol Biosci 2022; 9:1060796. [PMID: 36518845 PMCID: PMC9743296 DOI: 10.3389/fmolb.2022.1060796] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 10/28/2022] [Indexed: 09/07/2023] Open
Abstract
Drosophila has been long appreciated as a classic genetic system for its ability to define gene function in vivo. Within the last several decades, the fly has also emerged as a premiere system for modeling and defining mechanisms of human disease by expressing dominant human disease genes and analyzing the effects. Here I discuss key aspects of this latter approach that first intrigued me to focus my laboratory research on this idea. Differences between the loss-of-function vs. the gain-of-function approach are raised-and the insight of these approaches for appreciating mechanisms that contribute to human neurodegenerative disease. The application of modifier genetics, which is a prominent goal of models of human disease, has implications for how specific genes or pathways intersect with the dominant disease-associated mechanisms. Models of human disease will continue to reveal unanticipated insight into fundamental cellular processes-insight that might be harder to glean from classical genetic methodologies vs modifier genetics of disease.
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Affiliation(s)
- Nancy M. Bonini
- Department of Biology, University of Pennsylvania, Philadelphia, PA, United States
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20
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Shirokikh NE. Translation complex stabilization on messenger RNA and footprint profiling to study the RNA responses and dynamics of protein biosynthesis in the cells. Crit Rev Biochem Mol Biol 2021; 57:261-304. [PMID: 34852690 DOI: 10.1080/10409238.2021.2006599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
During protein biosynthesis, ribosomes bind to messenger (m)RNA, locate its protein-coding information, and translate the nucleotide triplets sequentially as codons into the corresponding sequence of amino acids, forming proteins. Non-coding mRNA features, such as 5' and 3' untranslated regions (UTRs), start sites or stop codons of different efficiency, stretches of slower or faster code and nascent polypeptide interactions can alter the translation rates transcript-wise. Most of the homeostatic and signal response pathways of the cells converge on individual mRNA control, as well as alter the global translation output. Among the multitude of approaches to study translational control, one of the most powerful is to infer the locations of translational complexes on mRNA based on the mRNA fragments protected by these complexes from endonucleolytic hydrolysis, or footprints. Translation complex profiling by high-throughput sequencing of the footprints allows to quantify the transcript-wise, as well as global, alterations of translation, and uncover the underlying control mechanisms by attributing footprint locations and sizes to different configurations of the translational complexes. The accuracy of all footprint profiling approaches critically depends on the fidelity of footprint generation and many methods have emerged to preserve certain or multiple configurations of the translational complexes, often in challenging biological material. In this review, a systematic summary of approaches to stabilize translational complexes on mRNA for footprinting is presented and major findings are discussed. Future directions of translation footprint profiling are outlined, focusing on the fidelity and accuracy of inference of the native in vivo translation complex distribution on mRNA.
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Affiliation(s)
- Nikolay E Shirokikh
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
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21
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Juarez-Carreño S, Vallejo DM, Carranza-Valencia J, Palomino-Schätzlein M, Ramon-Cañellas P, Santoro R, de Hartog E, Ferres-Marco D, Romero A, Peterson HP, Ballesta-Illan E, Pineda-Lucena A, Dominguez M, Morante J. Body-fat sensor triggers ribosome maturation in the steroidogenic gland to initiate sexual maturation in Drosophila. Cell Rep 2021; 37:109830. [PMID: 34644570 DOI: 10.1016/j.celrep.2021.109830] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 06/25/2021] [Accepted: 09/23/2021] [Indexed: 12/18/2022] Open
Abstract
Fat stores are critical for reproductive success and may govern maturation initiation. Here, we report that signaling and sensing fat sufficiency for sexual maturation commitment requires the lipid carrier apolipophorin in fat cells and Sema1a in the neuroendocrine prothoracic gland (PG). Larvae lacking apolpp or Sema1a fail to initiate maturation despite accruing sufficient fat stores, and they continue gaining weight until death. Mechanistically, sensing peripheral body-fat levels via the apolipophorin/Sema1a axis regulates endocytosis, endoplasmic reticulum remodeling, and ribosomal maturation for the acquisition of the PG cells' high biosynthetic and secretory capacity. Downstream of apolipophorin/Sema1a, leptin-like upd2 triggers the cessation of feeding and initiates sexual maturation. Human Leptin in the insect PG substitutes for upd2, preventing obesity and triggering maturation downstream of Sema1a. These data show how peripheral fat levels regulate the control of the maturation decision-making process via remodeling of endomembranes and ribosomal biogenesis in gland cells.
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Affiliation(s)
- Sergio Juarez-Carreño
- Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas (CSIC), and Universidad Miguel Hernández (UMH), Campus de Sant Joan, Apartado 18, 03550 Sant Joan, Alicante, Spain
| | - Diana Marcela Vallejo
- Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas (CSIC), and Universidad Miguel Hernández (UMH), Campus de Sant Joan, Apartado 18, 03550 Sant Joan, Alicante, Spain
| | - Juan Carranza-Valencia
- Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas (CSIC), and Universidad Miguel Hernández (UMH), Campus de Sant Joan, Apartado 18, 03550 Sant Joan, Alicante, Spain
| | | | - Pol Ramon-Cañellas
- Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas (CSIC), and Universidad Miguel Hernández (UMH), Campus de Sant Joan, Apartado 18, 03550 Sant Joan, Alicante, Spain
| | - Roberto Santoro
- Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas (CSIC), and Universidad Miguel Hernández (UMH), Campus de Sant Joan, Apartado 18, 03550 Sant Joan, Alicante, Spain
| | - Emily de Hartog
- Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas (CSIC), and Universidad Miguel Hernández (UMH), Campus de Sant Joan, Apartado 18, 03550 Sant Joan, Alicante, Spain
| | - Dolors Ferres-Marco
- Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas (CSIC), and Universidad Miguel Hernández (UMH), Campus de Sant Joan, Apartado 18, 03550 Sant Joan, Alicante, Spain
| | - Aitana Romero
- Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas (CSIC), and Universidad Miguel Hernández (UMH), Campus de Sant Joan, Apartado 18, 03550 Sant Joan, Alicante, Spain
| | - Hannah Payette Peterson
- Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas (CSIC), and Universidad Miguel Hernández (UMH), Campus de Sant Joan, Apartado 18, 03550 Sant Joan, Alicante, Spain
| | - Esther Ballesta-Illan
- Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas (CSIC), and Universidad Miguel Hernández (UMH), Campus de Sant Joan, Apartado 18, 03550 Sant Joan, Alicante, Spain
| | - Antonio Pineda-Lucena
- Instituto de Investigación Sanitaria La Fe, Hospital Universitario y Politécnico La Fe, Avenida Fernando Abril Martorell, 106, 46026 Valencia, Spain; Programa de Terapias Moleculares, Centro de Investigación Médica Aplicada, Universidad de Navarra, Avenida Pío XII, 55, 31008 Pamplona, Spain
| | - Maria Dominguez
- Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas (CSIC), and Universidad Miguel Hernández (UMH), Campus de Sant Joan, Apartado 18, 03550 Sant Joan, Alicante, Spain.
| | - Javier Morante
- Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas (CSIC), and Universidad Miguel Hernández (UMH), Campus de Sant Joan, Apartado 18, 03550 Sant Joan, Alicante, Spain.
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22
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Xiang K, Bartel DP. The molecular basis of coupling between poly(A)-tail length and translational efficiency. eLife 2021; 10:66493. [PMID: 34213414 PMCID: PMC8253595 DOI: 10.7554/elife.66493] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/21/2021] [Indexed: 01/10/2023] Open
Abstract
In animal oocytes and early embryos, mRNA poly(A)-tail length strongly influences translational efficiency (TE), but later in development this coupling between tail length and TE disappears. Here, we elucidate how this coupling is first established and why it disappears. Overexpressing cytoplasmic poly(A)-binding protein (PABPC) in Xenopus oocytes specifically improved translation of short-tailed mRNAs, thereby diminishing coupling between tail length and TE. Thus, strong coupling requires limiting PABPC, implying that in coupled systems longer-tail mRNAs better compete for limiting PABPC. In addition to expressing excess PABPC, post-embryonic mammalian cell lines had two other properties that prevented strong coupling: terminal-uridylation-dependent destabilization of mRNAs lacking bound PABPC, and a regulatory regime wherein PABPC contributes minimally to TE. Thus, these results revealed three fundamental mechanistic requirements for coupling and defined the context-dependent functions for PABPC, which promotes TE but not mRNA stability in coupled systems and mRNA stability but not TE in uncoupled systems. Cells are microscopic biological factories that are constantly creating new proteins. To do so, a cell must first convert its master genetic blueprint, the DNA, into strands of messenger RNA or mRNA. These strands are subsequently translated to make proteins. Cells have two ways to adjust the number of proteins they generate so they do not produce too many or too few: by changing how many mRNA molecules are available for translation, and by regulating how efficiently they translate these mRNA molecules into proteins. In animals, both unfertilized eggs and early-stage embryos lack the ability to create or destroy mRNAs, and consequently cannot adjust the number of mRNA molecules available for translation. These cells can therefore only regulate how efficiently each mRNA is translated. They do this by changing the length of the so-called poly(A) tail at the end of each mRNA molecule, which is made up of a long stretch of repeating adenosine nucleotides. The mRNAs with longer poly(A) tails are translated more efficiently than those with shorter poly(A) tails. However, this difference disappears in older embryos, when both long and short poly(A) tails are translated with equal efficiency, and it is largely unknown why. To find out more, Xiang and Bartel studied frog eggs, and discovered that artificially raising levels of a protein that binds poly(A) tails, also known as PABPC, improved the translation of short-tailed mRNAs to create a situation in which both short- and long-tailed mRNAs were translated with near-equal efficiency. This suggested that short- and long-tailed mRNAs compete for limited amounts of the translation-enhancing PABPC, and that long-tailed mRNAs are better at it than short-tailed mRNAs. Further investigation revealed that eggs also had to establish the right conditions for PABPC to enhance translation and had to protect mRNAs not associated with PABPC from being destroyed before they could be translated. Overall, Xiang and Bartel found that in eggs and early embryos, PABPC and poly(A) tails enhanced the translation of mRNAs but did not influence their stability, whereas later in development, they enhanced mRNA stability but not translation. This research provides new insights into how protein production is controlled at different stages of animal development, from unfertilized eggs to older embryos. Understanding how this process is regulated during normal development is crucial for gaining insights into how it can become dysfunctional and cause disease. These findings may therefore have important implications for research into areas such as infertility, reproductive medicine and rare genetic diseases.
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Affiliation(s)
- Kehui Xiang
- Howard Hughes Medical Institute, Cambridge, United States.,Whitehead Institute for Biomedical Research, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - David P Bartel
- Howard Hughes Medical Institute, Cambridge, United States.,Whitehead Institute for Biomedical Research, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
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23
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Vaziri A, Dus M. Brain on food: The neuroepigenetics of nutrition. Neurochem Int 2021; 149:105099. [PMID: 34133954 DOI: 10.1016/j.neuint.2021.105099] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 04/29/2021] [Accepted: 06/10/2021] [Indexed: 12/17/2022]
Abstract
Humans have known for millennia that nutrition has a profound influence on health and disease, but it is only recently that we have begun mapping the mechanisms via which the dietary environment impacts brain physiology and behavior. Here we review recent evidence on the effects of energy-dense and methionine diets on neural epigenetic marks, gene expression, and behavior in invertebrate and vertebrate model organisms. We also discuss limitations, open questions, and future directions in the emerging field of the neuroepigenetics of nutrition.
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Affiliation(s)
- Anoumid Vaziri
- Molecular, Cellular and Developmental Biology Graduate Program, The University of Michigan, Ann Arbor, USA; Department of Molecular, Cellular and Developmental Biology, The University of Michigan, Ann Arbor, USA
| | - Monica Dus
- Molecular, Cellular and Developmental Biology Graduate Program, The University of Michigan, Ann Arbor, USA; Department of Molecular, Cellular and Developmental Biology, The University of Michigan, Ann Arbor, USA.
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24
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Goel P, Dickman D. Synaptic homeostats: latent plasticity revealed at the Drosophila neuromuscular junction. Cell Mol Life Sci 2021; 78:3159-3179. [PMID: 33449150 PMCID: PMC8044042 DOI: 10.1007/s00018-020-03732-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/19/2020] [Accepted: 12/04/2020] [Indexed: 12/11/2022]
Abstract
Homeostatic signaling systems are fundamental forms of biological regulation that maintain stable functionality in a changing environment. In the nervous system, synapses are crucial substrates for homeostatic modulation, serving to establish, maintain, and modify the balance of excitation and inhibition. Synapses must be sufficiently flexible to enable the plasticity required for learning and memory but also endowed with the stability to last a lifetime. In response to the processes of development, growth, remodeling, aging, and disease that challenge synapses, latent forms of adaptive plasticity become activated to maintain synaptic stability. In recent years, new insights into the homeostatic control of synaptic function have been achieved using the powerful Drosophila neuromuscular junction (NMJ). This review will focus on work over the past 10 years that has illuminated the cellular and molecular mechanisms of five homeostats that operate at the fly NMJ. These homeostats adapt to loss of postsynaptic neurotransmitter receptor functionality, glutamate imbalance, axonal injury, as well as aberrant synaptic growth and target innervation. These diverse homeostats work independently yet can be simultaneously expressed to balance neurotransmission. Growing evidence from this model glutamatergic synapse suggests these ancient homeostatic signaling systems emerged early in evolution and are fundamental forms of plasticity that also function to stabilize mammalian cholinergic NMJs and glutamatergic central synapses.
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Affiliation(s)
- Pragya Goel
- Department of Neurobiology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Dion Dickman
- Department of Neurobiology, University of Southern California, Los Angeles, CA, 90089, USA.
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25
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Buddika K, Xu J, Ariyapala IS, Sokol NS. I-KCKT allows dissection-free RNA profiling of adult Drosophila intestinal progenitor cells. Development 2021; 148:dev196568. [PMID: 33246929 PMCID: PMC7803463 DOI: 10.1242/dev.196568] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/19/2021] [Indexed: 12/13/2022]
Abstract
The adult Drosophila intestinal epithelium is a model system for stem cell biology, but its utility is limited by current biochemical methods that lack cell type resolution. Here, we describe a new proximity-based profiling method that relies upon a GAL4 driver, termed intestinal-kickout-GAL4 (I-KCKT-GAL4), that is exclusively expressed in intestinal progenitor cells. This method uses UV crosslinked whole animal frozen powder as its starting material to immunoprecipitate the RNA cargoes of transgenic epitope-tagged RNA binding proteins driven by I-KCKT-GAL4 When applied to the general mRNA-binder, poly(A)-binding protein, the RNA profile obtained by this method identifies 98.8% of transcripts found after progenitor cell sorting, and has low background noise despite being derived from whole animal lysate. We also mapped the targets of the more selective RNA binder, Fragile X mental retardation protein (FMRP), using enhanced crosslinking and immunoprecipitation (eCLIP), and report for the first time its binding motif in Drosophila cells. This method will therefore enable the RNA profiling of wild-type and mutant intestinal progenitor cells from intact flies exposed to normal and altered environments, as well as the identification of RNA-protein interactions crucial for stem cell function.
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Affiliation(s)
- Kasun Buddika
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Jingjing Xu
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | | | - Nicholas S Sokol
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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26
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Abstract
Robust mechanisms exist that serve to dynamically regulate the translation of mRNA into proteins across heterogeneous tissues. These processes ensure timely generation of proteins in quantities that scale with the demands of specific cell types. Importantly, this translational regulation occurs with spatiotemporal precision and is capable of recalibration as conditions change. Aberrant regulation of translation contributes to and exacerbates a wide range of diseases. Although dynamic control of translation is an essential and fundamental process shared by organisms, specific tissues and cell types can be differentially impacted by circumstances that challenge and impair basal translation, highlighting the heterogeneous nature of translational regulation. To understand how translation is differentially regulated during changing environments and across specific cells and tissues, methods capable of profiling translation in specific tissues and cells are crucial. Here, we describe a method for profiling genome-wide translation in specific tissues or cell types in Drosophila melanogaster, in which we combine ribosome affinity purification with ribosome profiling to enable a simplified protocol for robust analysis of translation in specific tissues.
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Affiliation(s)
- Xun Chen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Dion Dickman
- Department of Neurobiology, University of Southern California, Los Angeles, CA, USA.
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27
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Vaziri A, Khabiri M, Genaw BT, May CE, Freddolino PL, Dus M. Persistent epigenetic reprogramming of sweet taste by diet. SCIENCE ADVANCES 2020; 6:6/46/eabc8492. [PMID: 33177090 PMCID: PMC7673743 DOI: 10.1126/sciadv.abc8492] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 09/23/2020] [Indexed: 05/25/2023]
Abstract
Diets rich in sugar, salt, and fat alter taste perception and food preference, contributing to obesity and metabolic disorders, but the molecular mechanisms through which this occurs are unknown. Here, we show that in response to a high sugar diet, the epigenetic regulator Polycomb Repressive Complex 2.1 (PRC2.1) persistently reprograms the sensory neurons of Drosophila melanogaster flies to reduce sweet sensation and promote obesity. In animals fed high sugar, the binding of PRC2.1 to the chromatin of the sweet gustatory neurons is redistributed to repress a developmental transcriptional network that modulates the responsiveness of these cells to sweet stimuli, reducing sweet sensation. Half of these transcriptional changes persist despite returning the animals to a control diet, causing a permanent decrease in sweet taste. Our results uncover a new epigenetic mechanism that, in response to the dietary environment, regulates neural plasticity and feeding behavior to promote obesity.
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Affiliation(s)
- Anoumid Vaziri
- The Molecular, Cellular and Developmental Biology Graduate Program, The University of Michigan, Ann Arbor, MI 49109, USA
- Department of Molecular, Cellular and Developmental Biology, College of Literature, Science, and the Arts, The University of Michigan, Ann Arbor, MI 49109, USA
| | - Morteza Khabiri
- Department of Biological Chemistry, The University of Michigan, Ann Arbor, MI 48109, USA
| | - Brendan T Genaw
- Program in Biology, College of Literature, Science, and the Arts, The University of Michigan, Ann Arbor, MI, 48109, USA
| | - Christina E May
- Department of Molecular, Cellular and Developmental Biology, College of Literature, Science, and the Arts, The University of Michigan, Ann Arbor, MI 49109, USA
- The Neuroscience Graduate Program, The University of Michigan, Ann Arbor, MI 49109, USA
| | - Peter L Freddolino
- Department of Biological Chemistry, The University of Michigan, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, The University of Michigan, Ann Arbor, MI 48109, USA
| | - Monica Dus
- The Molecular, Cellular and Developmental Biology Graduate Program, The University of Michigan, Ann Arbor, MI 49109, USA.
- Department of Molecular, Cellular and Developmental Biology, College of Literature, Science, and the Arts, The University of Michigan, Ann Arbor, MI 49109, USA
- Program in Biology, College of Literature, Science, and the Arts, The University of Michigan, Ann Arbor, MI, 48109, USA
- The Neuroscience Graduate Program, The University of Michigan, Ann Arbor, MI 49109, USA
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28
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Patraquim P, Mumtaz MAS, Pueyo JI, Aspden JL, Couso JP. Developmental regulation of canonical and small ORF translation from mRNAs. Genome Biol 2020; 21:128. [PMID: 32471506 PMCID: PMC7260771 DOI: 10.1186/s13059-020-02011-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 04/08/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Ribosomal profiling has revealed the translation of thousands of sequences outside annotated protein-coding genes, including small open reading frames of less than 100 codons, and the translational regulation of many genes. Here we present an improved version of Poly-Ribo-Seq and apply it to Drosophila melanogaster embryos to extend the catalog of in vivo translated small ORFs, and to reveal the translational regulation of both small and canonical ORFs from mRNAs across embryogenesis. RESULTS We obtain highly correlated samples across five embryonic stages, with nearly 500 million putative ribosomal footprints mapped to mRNAs, and compare them to existing Ribo-Seq and proteomic data. Our analysis reveals, for the first time in Drosophila, footprints mapping to codons in a phased pattern, the hallmark of productive translation. We propose a simple binomial probability metric to ascertain translation probability. Our results also reveal reproducible ribosomal binding apparently not resulting in productive translation. This non-productive ribosomal binding seems to be especially prevalent amongst upstream short ORFs located in the 5' mRNA leaders, and amongst canonical ORFs during the activation of the zygotic translatome at the maternal-to zygotic transition. CONCLUSIONS We suggest that this non-productive ribosomal binding might be due to cis-regulatory ribosomal binding and to defective ribosomal scanning of ORFs outside periods of productive translation. Our results are compatible with the main function of upstream short ORFs being to buffer the translation of canonical canonical ORFs; and show that, in general, small ORFs in mRNAs display markers compatible with an evolutionary transitory state towards full coding function.
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Affiliation(s)
- Pedro Patraquim
- Centro Andaluz de Biologia del Desarrollo, CSIC-UPO, Seville, Spain
| | | | | | - Julie Louise Aspden
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Juan-Pablo Couso
- Centro Andaluz de Biologia del Desarrollo, CSIC-UPO, Seville, Spain. .,Previous address: Brighton and Sussex Medical School, Brighton, East Sussex, UK.
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29
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Premature termination codon readthrough in Drosophila varies in a developmental and tissue-specific manner. Sci Rep 2020; 10:8485. [PMID: 32444687 PMCID: PMC7244557 DOI: 10.1038/s41598-020-65348-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 03/31/2020] [Indexed: 12/29/2022] Open
Abstract
Despite their essential function in terminating translation, readthrough of stop codons occurs more frequently than previously supposed. However, little is known about the regulation of stop codon readthrough by anatomical site and over the life cycle of animals. Here, we developed a set of reporters to measure readthrough in Drosophila melanogaster. A focused RNAi screen in whole animals identified upf1 as a mediator of readthrough, suggesting that the stop codons in the reporters were recognized as premature termination codons (PTCs). We found readthrough rates of PTCs varied significantly throughout the life cycle of flies, being highest in older adult flies. Furthermore, readthrough rates varied dramatically by tissue and, intriguingly, were highest in fly brains, specifically neurons and not glia. This was not due to differences in reporter abundance or nonsense-mediated mRNA decay (NMD) surveillance between these tissues. Readthrough rates also varied within neurons, with cholinergic neurons having highest readthrough compared with lowest readthrough rates in dopaminergic neurons. Overall, our data reveal temporal and spatial variation of PTC-mediated readthrough in animals, and suggest that readthrough may be a potential rescue mechanism for PTC-harboring transcripts when the NMD surveillance pathway is inhibited.
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30
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Recent advances in ribosome profiling for deciphering translational regulation. Methods 2020; 176:46-54. [DOI: 10.1016/j.ymeth.2019.05.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 05/02/2019] [Accepted: 05/15/2019] [Indexed: 12/16/2022] Open
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31
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Traubenik S, Blanco F, Zanetti ME, Reynoso MA. TRAP-SEQ of Eukaryotic Translatomes Applied to the Detection of Polysome-Associated Long Noncoding RNAs. Methods Mol Biol 2020; 2166:451-472. [PMID: 32710425 DOI: 10.1007/978-1-0716-0712-1_26] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Translating ribosome affinity purification (TRAP) technology allows the isolation of polysomal complexes and the RNAs associated with at least one 80S ribosome. TRAP consists of the stabilization and affinity purification of polysomes containing a tagged version of a ribosomal protein. Quantitative assessment of the TRAP RNA is achieved by direct sequencing (TRAP-SEQ), which provides accurate quantitation of ribosome-associated RNAs, including long noncoding RNAs (lncRNAs). Here we present an updated procedure for TRAP-SEQ, as well as a primary analysis guide for identification of ribosome-associated lncRNAs. This methodology enables the study of dynamic association of lncRNAs by assessing rapid changes in their transcript levels in polysomes at organ or cell-type level, during development, or in response to endogenous or exogenous stimuli.
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Affiliation(s)
- Soledad Traubenik
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Argentina
| | - Flavio Blanco
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Argentina
| | - María Eugenia Zanetti
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Argentina
| | - Mauricio A Reynoso
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Argentina.
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32
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Yang X, Cui J, Song B, Yu Y, Mo B, Liu L. Construction of High-Quality Rice Ribosome Footprint Library. FRONTIERS IN PLANT SCIENCE 2020; 11:572237. [PMID: 33013996 PMCID: PMC7500414 DOI: 10.3389/fpls.2020.572237] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 08/20/2020] [Indexed: 05/20/2023]
Abstract
High-throughput sequencing of ribosome footprints precisely maps and quantifies in vivo mRNA translation. The ribosome footprint sequencing has undergone continuing development since its original report. Here we provide a detailed protocol for construction of high-quality ribosome footprint library of rice. Rice total polysomes are isolated with a modified low ionic polysome extraction buffer. After nuclease digestion, rice ribosome footprints are extracted using SDS method followed by column purification. High-quality rice ribosome footprint library with peak reads of approximately 28-nucleotide (nt) length and strong 3-nt periodicity is constructed via key steps including rRNA depletion, end repair, 3' adapter ligation, reverse transcription, circularization, PCR enrichment and several rounds of purification. Biological significance of rice ribosome footprint library is further revealed by the comparison of transcriptomic and translatomic responses to salt stress and the utilization for novel open reading frame (ORF) identification. This improved protocol for rice ribosome footprint library construction will facilitate the global comprehension and quantitative measurement of dynamic translation in rice.
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Affiliation(s)
- Xiaoyu Yang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Longhua Bioindustry and Innovation Research Institute, Shenzhen University, Shenzhen, China
| | - Jie Cui
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Longhua Bioindustry and Innovation Research Institute, Shenzhen University, Shenzhen, China
| | - Bo Song
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yu Yu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Longhua Bioindustry and Innovation Research Institute, Shenzhen University, Shenzhen, China
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Longhua Bioindustry and Innovation Research Institute, Shenzhen University, Shenzhen, China
| | - Lin Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Longhua Bioindustry and Innovation Research Institute, Shenzhen University, Shenzhen, China
- *Correspondence: Lin Liu,
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33
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Li X, Goel P, Wondolowski J, Paluch J, Dickman D. A Glutamate Homeostat Controls the Presynaptic Inhibition of Neurotransmitter Release. Cell Rep 2019; 23:1716-1727. [PMID: 29742428 PMCID: PMC5973541 DOI: 10.1016/j.celrep.2018.03.130] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 01/24/2018] [Accepted: 03/28/2018] [Indexed: 02/07/2023] Open
Abstract
We have interrogated the synaptic dialog that enables the bi-directional, homeostatic control of pre-synaptic efficacy at the glutamatergic Drosophila neuromuscular junction (NMJ). We find that homeo-static depression and potentiation use disparate genetic, induction, and expression mechanisms. Specifically, homeostatic potentiation is achieved through reduced CaMKII activity postsynaptically and increased abundance of active zone material presynaptically at one of the two neuronal subtypes innervating the NMJ, while homeostatic depression occurs without alterations in CaMKII activity and is expressed at both neuronal subtypes. Furthermore, homeostatic depression is only induced through excess presynaptic glutamate release and operates with disregard to the postsynaptic response. We propose that two independent homeostats modulate presynaptic efficacy at the Drosophila NMJ: one is an intercellular signaling system that potentiates synaptic strength following diminished postsynaptic excitability, while the other adaptively modulates presynaptic glutamate release through an autocrine mechanism without feedback from the postsynaptic compartment.
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Affiliation(s)
- Xiling Li
- Department of Neurobiology, University of Southern California, Los Angeles, CA; USC Neuroscience Graduate Program, University of Southern California, Los Angeles, CA
| | - Pragya Goel
- Department of Neurobiology, University of Southern California, Los Angeles, CA; USC Graduate Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA
| | - Joyce Wondolowski
- Department of Neurobiology, University of Southern California, Los Angeles, CA
| | - Jeremy Paluch
- Department of Neurobiology, University of Southern California, Los Angeles, CA
| | - Dion Dickman
- Department of Neurobiology, University of Southern California, Los Angeles, CA.
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34
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Reisacher C, Arbibe L. Not lost in host translation: The new roles of long noncoding RNAs in infectious diseases. Cell Microbiol 2019; 21:e13119. [PMID: 31634981 DOI: 10.1111/cmi.13119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 09/10/2019] [Accepted: 09/17/2019] [Indexed: 12/20/2022]
Abstract
Long non-coding RNAs (lncRNAs) play a central role in the regulation of gene expression. Although they were initially described as mRNA-like transcripts not encoding proteins, global approaches such as ribosome profiling have shown that they frequently associate with ribosomes, opening the possibility that lncRNAs are a source of cryptic translation events with functional roles. Recent studies have shed more light on small ORFs borne by lncRNAs and encoding short peptides potentially involved in infectious immunity. This review outlines the main strategies used to determine the coding potential of lncRNAs and discusses our emerging understanding of the implication of the encoded peptides in infectious diseases.
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Affiliation(s)
- Caroline Reisacher
- Department of Immunology, Infectiology and Hematology, Institut Necker-Enfants Malades (INEM), INSERM U1151, CNRS UMR 8253, Université Paris Descartes, Paris, France
| | - Laurence Arbibe
- Department of Immunology, Infectiology and Hematology, Institut Necker-Enfants Malades (INEM), INSERM U1151, CNRS UMR 8253, Université Paris Descartes, Paris, France
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35
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Kikuma K, Li X, Perry S, Li Q, Goel P, Chen C, Kim D, Stavropoulos N, Dickman D. Cul3 and insomniac are required for rapid ubiquitination of postsynaptic targets and retrograde homeostatic signaling. Nat Commun 2019; 10:2998. [PMID: 31278365 PMCID: PMC6611771 DOI: 10.1038/s41467-019-10992-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 06/14/2019] [Indexed: 01/05/2023] Open
Abstract
At the Drosophila neuromuscular junction, inhibition of postsynaptic glutamate receptors activates retrograde signaling that precisely increases presynaptic neurotransmitter release to restore baseline synaptic strength. However, the nature of the underlying postsynaptic induction process remains enigmatic. Here, we design a forward genetic screen to discover factors in the postsynaptic compartment necessary to generate retrograde homeostatic signaling. This approach identified insomniac (inc), a putative adaptor for the Cullin-3 (Cul3) ubiquitin ligase complex, which together with Cul3 is essential for normal sleep regulation. Interestingly, we find that Inc and Cul3 rapidly accumulate at postsynaptic compartments following acute receptor inhibition and are required for a local increase in mono-ubiquitination. Finally, we show that Peflin, a Ca2+-regulated Cul3 co-adaptor, is necessary for homeostatic communication, suggesting a relationship between Ca2+ signaling and control of Cul3/Inc activity in the postsynaptic compartment. Our study suggests that Cul3/Inc-dependent mono-ubiquitination, compartmentalized at postsynaptic densities, gates retrograde signaling and provides an intriguing molecular link between the control of sleep and homeostatic plasticity at synapses. The authors use a forward genetic screen to discover postsynaptic factors required for homeostatic synaptic plasticity at the Drosophila neuromuscular junction. They identify insomniac and the ubiquitin ligase Cul3, genes involved in sleep regulation, to be necessary for retrograde homeostatic signalling at this synapse.
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Affiliation(s)
- Koto Kikuma
- Department of Neurobiology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Xiling Li
- Department of Neurobiology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Sarah Perry
- Department of Neurobiology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Qiuling Li
- Neuroscience Institute, Department of Neuroscience and Physiology, NYU School of Medicine, New York, NY, 10016, USA
| | - Pragya Goel
- Department of Neurobiology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Catherine Chen
- Department of Neurobiology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Daniel Kim
- Department of Neurobiology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Nicholas Stavropoulos
- Neuroscience Institute, Department of Neuroscience and Physiology, NYU School of Medicine, New York, NY, 10016, USA
| | - Dion Dickman
- Department of Neurobiology, University of Southern California, Los Angeles, CA, 90089, USA.
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36
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James TD, Zwiefelhofer DJ, Frank CA. Maintenance of homeostatic plasticity at the Drosophila neuromuscular synapse requires continuous IP 3-directed signaling. eLife 2019; 8:39643. [PMID: 31180325 PMCID: PMC6557630 DOI: 10.7554/elife.39643] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 05/27/2019] [Indexed: 12/18/2022] Open
Abstract
Synapses and circuits rely on neuroplasticity to adjust output and meet physiological needs. Forms of homeostatic synaptic plasticity impart stability at synapses by countering destabilizing perturbations. The Drosophila melanogaster larval neuromuscular junction (NMJ) is a model synapse with robust expression of homeostatic plasticity. At the NMJ, a homeostatic system detects impaired postsynaptic sensitivity to neurotransmitter and activates a retrograde signal that restores synaptic function by adjusting neurotransmitter release. This process has been separated into temporally distinct phases, induction and maintenance. One prevailing hypothesis is that a shared mechanism governs both phases. Here, we show the two phases are separable. Combining genetics, pharmacology, and electrophysiology, we find that a signaling system consisting of PLCβ, inositol triphosphate (IP3), IP3 receptors, and Ryanodine receptors is required only for the maintenance of homeostatic plasticity. We also find that the NMJ is capable of inducing homeostatic signaling even when its sustained maintenance process is absent. Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).
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Affiliation(s)
- Thomas D James
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, Iowa City, United States.,Interdisciplinary Graduate Program in Neuroscience, University of Iowa, Iowa City, United States
| | - Danielle J Zwiefelhofer
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, Iowa City, United States
| | - C Andrew Frank
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, Iowa City, United States.,Interdisciplinary Programs in Neuroscience, Genetics and Molecular Medicine, University of Iowa, Iowa City, United States
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37
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Ingolia NT, Hussmann JA, Weissman JS. Ribosome Profiling: Global Views of Translation. Cold Spring Harb Perspect Biol 2019; 11:cshperspect.a032698. [PMID: 30037969 DOI: 10.1101/cshperspect.a032698] [Citation(s) in RCA: 159] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The translation of messenger RNA (mRNA) into protein and the folding of the resulting protein into an active form are prerequisites for virtually every cellular process and represent the single largest investment of energy by cells. Ribosome profiling-based approaches have revolutionized our ability to monitor every step of protein synthesis in vivo, allowing one to measure the rate of protein synthesis across the proteome, annotate the protein coding capacity of genomes, monitor localized protein synthesis, and explore cotranslational folding and targeting. The rich and quantitative nature of ribosome profiling data provides an unprecedented opportunity to explore and model complex cellular processes. New analytical techniques and improved experimental protocols will provide a deeper understanding of the factors controlling translation speed and its impact on protein function and cell physiology as well as the role of ribosomal RNA and mRNA modifications in regulating translation.
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Affiliation(s)
- Nicholas T Ingolia
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
| | - Jeffrey A Hussmann
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158.,Howard Hughes Medical Institute, San Francisco, California 94158
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158.,Howard Hughes Medical Institute, San Francisco, California 94158
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38
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Goel P, Dufour Bergeron D, Böhme MA, Nunnelly L, Lehmann M, Buser C, Walter AM, Sigrist SJ, Dickman D. Homeostatic scaling of active zone scaffolds maintains global synaptic strength. J Cell Biol 2019; 218:1706-1724. [PMID: 30914419 PMCID: PMC6504899 DOI: 10.1083/jcb.201807165] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 12/14/2018] [Accepted: 03/06/2019] [Indexed: 12/23/2022] Open
Abstract
Synaptic terminals grow and retract throughout life, yet synaptic strength is maintained within stable physiological ranges. To study this process, we investigated Drosophila endophilin (endo) mutants. Although active zone (AZ) number is doubled in endo mutants, a compensatory reduction in their size homeostatically adjusts global neurotransmitter output to maintain synaptic strength. We find an inverse adaptation in rab3 mutants. Additional analyses using confocal, STED, and electron microscopy reveal a stoichiometric tuning of AZ scaffolds and nanoarchitecture. Axonal transport of synaptic cargo via the lysosomal kinesin adapter Arl8 regulates AZ abundance to modulate global synaptic output and sustain the homeostatic potentiation of neurotransmission. Finally, we find that this AZ scaling can interface with two independent homeostats, depression and potentiation, to remodel AZ structure and function, demonstrating a robust balancing of separate homeostatic adaptations. Thus, AZs are pliable substrates with elastic and modular nanostructures that can be dynamically sculpted to stabilize and tune both local and global synaptic strength.
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Affiliation(s)
- Pragya Goel
- Department of Neurobiology, University of Southern California, Los Angeles, CA
| | | | - Mathias A Böhme
- Neurocure Cluster of Excellence, Charité Universitätsmedizin, Berlin, Germany
| | - Luke Nunnelly
- Department of Neurobiology, University of Southern California, Los Angeles, CA
| | - Martin Lehmann
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | | | - Alexander M Walter
- Neurocure Cluster of Excellence, Charité Universitätsmedizin, Berlin, Germany
| | | | - Dion Dickman
- Department of Neurobiology, University of Southern California, Los Angeles, CA
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39
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Zhang H, Dou S, He F, Luo J, Wei L, Lu J. Genome-wide maps of ribosomal occupancy provide insights into adaptive evolution and regulatory roles of uORFs during Drosophila development. PLoS Biol 2018; 16:e2003903. [PMID: 30028832 PMCID: PMC6070289 DOI: 10.1371/journal.pbio.2003903] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 08/01/2018] [Accepted: 07/03/2018] [Indexed: 11/19/2022] Open
Abstract
Upstream open reading frames (uORFs) play important roles in regulating the main coding DNA sequences (CDSs) via translational repression. Despite their prevalence in the genomes, uORFs are overall discriminated against by natural selection. However, it remains unclear why in the genomes there are so many uORFs more conserved than expected under the assumption of neutral evolution. Here, we generated genome-wide maps of translational efficiency (TE) at the codon level throughout the life cycle of Drosophila melanogaster. We identified 35,735 uORFs that were expressed, and 32,224 (90.2%) of them showed evidence of ribosome occupancy during Drosophila development. The ribosome occupancy of uORFs is determined by genomic features, such as optimized sequence contexts around their start codons, a shorter distance to CDSs, and higher coding potentials. Our population genomic analysis suggests the segregating mutations that create or disrupt uORFs are overall deleterious in D. melanogaster. However, we found for the first time that many (68.3% of) newly fixed uORFs that are associated with ribosomes in D. melanogaster are driven by positive Darwinian selection. Our findings also suggest that uORFs play a vital role in controlling the translational program in Drosophila. Moreover, we found that many uORFs are transcribed or translated in a developmental stage-, sex-, or tissue-specific manner, suggesting that selective transcription or translation of uORFs could potentially modulate the TE of the downstream CDSs during Drosophila development. Upstream open reading frames (uORFs) in the 5′ untranslated regions (UTRs) of messenger RNAs can potentially inhibit translation of the downstream regions that encode proteins by sequestering protein-making machinery the ribosome. Moreover, mutations that destroy existing uORFs or create new ones are known to cause human disease. Although mutations that create new uORFs are generally deleterious and are selected against, many uORFs are evolutionarily conserved across eukaryotic species. To resolve this dilemma, we used extensive mRNA-Seq and ribosome profiling to generate high-resolution genome-wide maps of ribosome occupancy and translational efficiency (TE) during the life cycle of the fruit fly D. melanogaster. This allowed us to identify the sequence features of uORFs that influence their ability to associate with ribosomes. We demonstrate for the first time that the majority of the newly fixed uORFs in D. melanogaster, especially the translated ones, are under positive Darwinian selection. We also show that uORFs exert widespread repressive effects on the translation of the downstream protein-coding region. We find that many uORFs are transcribed or translated in a developmental stage-, sex-, or tissue-specific manner. Our results suggest that during Drosophila development, changes in the TE of uORFs, as well as the inclusion/exclusion of uORFs, are frequently exploited to inversely influence the translation of the downstream protein-coding regions. Our study provides novel insights into the molecular mechanisms and functional consequences of uORF-mediated regulation.
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Affiliation(s)
- Hong Zhang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
| | - Shengqian Dou
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
| | - Feng He
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Junjie Luo
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
| | - Liping Wei
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
- * E-mail:
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40
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Distinct homeostatic modulations stabilize reduced postsynaptic receptivity in response to presynaptic DLK signaling. Nat Commun 2018; 9:1856. [PMID: 29748610 PMCID: PMC5945772 DOI: 10.1038/s41467-018-04270-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 04/16/2018] [Indexed: 11/08/2022] Open
Abstract
Synapses are constructed with the stability to last a lifetime, yet sufficiently flexible to adapt during injury. Although fundamental pathways that mediate intrinsic responses to neuronal injury have been defined, less is known about how synaptic partners adapt. We have investigated responses in the postsynaptic cell to presynaptic activation of the injury-related Dual Leucine Zipper Kinase pathway at the Drosophila neuromuscular junction. We find that the postsynaptic compartment reduces neurotransmitter receptor levels, thus depressing synaptic strength. Interestingly, this diminished state is stabilized through distinct modulations to two postsynaptic homeostatic signaling systems. First, a retrograde response normally triggered by reduced receptor levels is silenced, preventing a compensatory enhancement in presynaptic neurotransmitter release. However, when global presynaptic release is attenuated, a postsynaptic receptor scaling mechanism persists to adaptively stabilize this diminished neurotransmission state. Thus, the homeostatic set point of synaptic strength is recalibrated to a reduced state as synapses acclimate to injury.
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41
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Li X, Goel P, Chen C, Angajala V, Chen X, Dickman DK. Synapse-specific and compartmentalized expression of presynaptic homeostatic potentiation. eLife 2018; 7:34338. [PMID: 29620520 PMCID: PMC5927770 DOI: 10.7554/elife.34338] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 04/04/2018] [Indexed: 01/23/2023] Open
Abstract
Postsynaptic compartments can be specifically modulated during various forms of synaptic plasticity, but it is unclear whether this precision is shared at presynaptic terminals. Presynaptic homeostatic plasticity (PHP) stabilizes neurotransmission at the Drosophila neuromuscular junction, where a retrograde enhancement of presynaptic neurotransmitter release compensates for diminished postsynaptic receptor functionality. To test the specificity of PHP induction and expression, we have developed a genetic manipulation to reduce postsynaptic receptor expression at one of the two muscles innervated by a single motor neuron. We find that PHP can be induced and expressed at a subset of synapses, over both acute and chronic time scales, without influencing transmission at adjacent release sites. Further, homeostatic modulations to CaMKII, vesicle pools, and functional release sites are compartmentalized and do not spread to neighboring pre- or post-synaptic structures. Thus, both PHP induction and expression mechanisms are locally transmitted and restricted to specific synaptic compartments. Everything we think and do is the result of communication between neurons. This communication takes place at junctions called synapses. When two nerve cells or neurons communicate at a synapse, the output terminal of the first cell releases a chemical called a neurotransmitter. This binds to receiver proteins, or receptors, on the second cell. When this communication is interrupted, synapses can adapt to maintain a stable dialogue between them. This can occur in two ways. Either the first neuron starts to release more neurotransmitter from its output terminal, or the second neuron produces extra receptors with which to detect the neurotransmitter. But how specific are these changes? The brain contains far more synapses than neurons because each neuron can form synapses with many other cells. Can a neuron adjust how much of the neurotransmitter it releases at some of its synapses while leaving the others unchanged? Li et al. have now addressed this question by studying a special type of synapse that forms between neurons and muscles, known as a neuromuscular junction. At one particular neuromuscular junction in fruit flies, a single neuron splits into two output terminals, each of which forms a synapse with a different muscle. Li et al. show that when the number of neurotransmitter receptors in one of the muscles is artificially reduced, the associated output terminal compensates by increasing its neurotransmitter release. By contrast, the other output terminal remains unaffected. This suggests that a neuron can induce remarkably specific changes in a subset of its synapses. This discovery paves the way towards identifying the smallest possible unit of change that can occur in the neurons’ ability to communicate. This unit may in turn be the smallest change that can support learning. Such knowledge will help us understand how the nervous system processes and stabilizes information transfer, both in health and after injury or disease.
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Affiliation(s)
- Xiling Li
- Department of Neurobiology, University of Southern California, Los Angeles, United States.,Neuroscience Graduate Program, University of Southern California, California, United States
| | - Pragya Goel
- Department of Neurobiology, University of Southern California, Los Angeles, United States.,Graduate Program in Molecular and Computational Biology, University of Southern California, California, United States
| | - Catherine Chen
- Department of Neurobiology, University of Southern California, Los Angeles, United States
| | | | - Xun Chen
- Neuroscience Graduate Program, University of Southern California, California, United States
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