1
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Aparicio B, Theunissen P, Hervas-Stubbs S, Fortes P, Sarobe P. Relevance of mutation-derived neoantigens and non-classical antigens for anticancer therapies. Hum Vaccin Immunother 2024; 20:2303799. [PMID: 38346926 PMCID: PMC10863374 DOI: 10.1080/21645515.2024.2303799] [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: 09/29/2023] [Accepted: 01/06/2024] [Indexed: 02/15/2024] Open
Abstract
Efficacy of cancer immunotherapies relies on correct recognition of tumor antigens by lymphocytes, eliciting thus functional responses capable of eliminating tumor cells. Therefore, important efforts have been carried out in antigen identification, with the aim of understanding mechanisms of response to immunotherapy and to design safer and more efficient strategies. In addition to classical tumor-associated antigens identified during the last decades, implementation of next-generation sequencing methodologies is enabling the identification of neoantigens (neoAgs) arising from mutations, leading to the development of new neoAg-directed therapies. Moreover, there are numerous non-classical tumor antigens originated from other sources and identified by new methodologies. Here, we review the relevance of neoAgs in different immunotherapies and the results obtained by applying neoAg-based strategies. In addition, the different types of non-classical tumor antigens and the best approaches for their identification are described. This will help to increase the spectrum of targetable molecules useful in cancer immunotherapies.
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Affiliation(s)
- Belen Aparicio
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA) University of Navarra, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
| | - Patrick Theunissen
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
- DNA and RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | - Sandra Hervas-Stubbs
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA) University of Navarra, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
| | - Puri Fortes
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
- DNA and RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
- Spanish Network for Advanced Therapies (TERAV ISCIII), Spain
| | - Pablo Sarobe
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA) University of Navarra, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
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2
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Diamantopoulos MA, Adamopoulos PG, Tsiakanikas P, Nisotakis T, Skourou PC, Scorilas A. Unraveling novel mRNA transcripts of the human DNA N-glycosylase 1 (NTHL1) gene with the implementation of an innovative targeted DNA-seq assay. Gene 2024; 930:148856. [PMID: 39147115 DOI: 10.1016/j.gene.2024.148856] [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: 02/15/2024] [Revised: 07/13/2024] [Accepted: 08/12/2024] [Indexed: 08/17/2024]
Abstract
The human NTHL1 gene encodes a DNA glycosylase that plays a key role in the base excision repair (BER) pathway, repairing oxidative DNA damage and maintaining genome integrity. The physiological activity of NTHL1 is crucial in preventing genetic alterations that can lead to cancer. In this study, we employed an innovative targeted DNA sequencing (DNA-seq) methodology to explore the transcriptional landscape of the NTHL1 gene, revealing previously uncharacterized alternative splicing events and novel exons. Our designed approach provided significantly improved sequencing depth and coverage, enabling the identification of novel NTHL1 mRNA transcripts. Bioinformatics analysis confirmed all annotated splice junctions of the main NTHL1 transcripts (v.1 - v.3) and revealed novel mRNA transcripts (NTHL1 v.4 - v.9) derived from splicing events between annotated exons as well as mRNAs containing previously uncharacterized exons (NTHL1 v.10 - v.14). Quantitative PCR analysis highlighted a diverse expression pattern of these novel transcripts across different human cell lines, suggesting cell-specific roles and regulatory mechanisms. Notably, NTHL1 v.5 was overexpressed in luminal A breast cancer cells (MCF-7), while v.13 was prominent in triple negative (BT-20), HER2 + breast cancer (SK-BR-3), prostate, colorectal cancer cells and HEK-293 cells. Our findings suggest that specific novel NTHL1 transcripts may encode protein isoforms with distinct structural features, as indicated by ribosome profiling datasets, while others containing premature termination codons could function as long non-coding RNAs. These insights enhance our understanding of NTHL1 regulatory role and its potential as a biomarker and therapeutic target in human malignancies. This study underscores the importance of exploring the transcriptional diversity of NTHL1 to fully elucidate its role in cancer pathobiology.
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Affiliation(s)
- Marios A Diamantopoulos
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Panagiotis G Adamopoulos
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Panagiotis Tsiakanikas
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Theodoros Nisotakis
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Paraskevi C Skourou
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece.
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3
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Tufail MA, Jordan B, Hadjeras L, Gelhausen R, Cassidy L, Habenicht T, Gutt M, Hellwig L, Backofen R, Tholey A, Sharma CM, Schmitz RA. Uncovering the small proteome of Methanosarcina mazei using Ribo-seq and peptidomics under different nitrogen conditions. Nat Commun 2024; 15:8659. [PMID: 39370430 PMCID: PMC11456600 DOI: 10.1038/s41467-024-53008-8] [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: 10/08/2023] [Accepted: 09/25/2024] [Indexed: 10/08/2024] Open
Abstract
The mesophilic methanogenic archaeal model organism Methanosarcina mazei strain Gö1 is crucial for climate and environmental research due to its ability to produce methane. Here, we establish a Ribo-seq protocol for M. mazei strain Gö1 under two growth conditions (nitrogen sufficiency and limitation). The translation of 93 previously annotated and 314 unannotated small ORFs, coding for proteins ≤ 70 amino acids, is predicted with high confidence based on Ribo-seq data. LC-MS analysis validates the translation for 62 annotated small ORFs and 26 unannotated small ORFs. Epitope tagging followed by immunoblotting analysis confirms the translation of 13 out of 16 selected unannotated small ORFs. A comprehensive differential transcription and translation analysis reveals that 29 of 314 unannotated small ORFs are differentially regulated in response to nitrogen availability at the transcriptional and 49 at the translational level. A high number of reported small RNAs are emerging as dual-function RNAs, including sRNA154, the central regulatory small RNA of nitrogen metabolism. Several unannotated small ORFs are conserved in Methanosarcina species and overproducing several (small ORF encoded) small proteins suggests key physiological functions. Overall, the comprehensive analysis opens an avenue to elucidate the function(s) of multitudinous small proteins and dual-function RNAs in M. mazei.
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Affiliation(s)
| | - Britta Jordan
- Institute for General Microbiology, Kiel University, 24118, Kiel, Germany
| | - Lydia Hadjeras
- Institute of Molecular Infection Biology, University of Würzburg, 97080, Würzburg, Germany
| | - Rick Gelhausen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110, Freiburg, Germany
| | - Liam Cassidy
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Kiel University, 24105, Kiel, Germany
| | - Tim Habenicht
- Institute for General Microbiology, Kiel University, 24118, Kiel, Germany
| | - Miriam Gutt
- Institute for General Microbiology, Kiel University, 24118, Kiel, Germany
| | - Lisa Hellwig
- Institute for General Microbiology, Kiel University, 24118, Kiel, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110, Freiburg, Germany
| | - Andreas Tholey
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Kiel University, 24105, Kiel, Germany
| | - Cynthia M Sharma
- Institute of Molecular Infection Biology, University of Würzburg, 97080, Würzburg, Germany
| | - Ruth A Schmitz
- Institute for General Microbiology, Kiel University, 24118, Kiel, Germany.
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4
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Dolcemascolo R, Ruiz R, Baldanta S, Goiriz L, Heras-Hernández M, Montagud-Martínez R, Rodrigo G. Probing the orthogonality and robustness of the mammalian RNA-binding protein Musashi-1 in Escherichia coli. J Biol Eng 2024; 18:52. [PMID: 39350178 PMCID: PMC11443895 DOI: 10.1186/s13036-024-00448-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Accepted: 09/15/2024] [Indexed: 10/04/2024] Open
Abstract
RNA recognition motifs (RRMs) are widespread RNA-binding protein domains in eukaryotes, which represent promising synthetic biology tools due to their compact structure and efficient activity. Yet, their use in prokaryotes is limited and their functionality poorly characterized. Recently, we repurposed a mammalian Musashi protein containing two RRMs as a translation regulator in Escherichia coli. Here, employing high-throughput RNA sequencing, we explored the impact of Musashi expression on the transcriptomic and translatomic profiles of E. coli, revealing certain metabolic interference, induction of post-transcriptional regulatory processes, and spurious protein-RNA interactions. Engineered Musashi protein mutants displayed compromised regulatory activity, emphasizing the importance of both RRMs for specific and sensitive RNA binding. We found that a mutation known to impede allosteric regulation led to similar translation control activity. Evolutionary experiments disclosed a loss of function of the synthetic circuit in about 40 generations, with the gene coding for the Musashi protein showing a stability comparable to other heterologous genes. Overall, this work expands our understanding of RRMs for post-transcriptional regulation in prokaryotes and highlight their potential for biotechnological and biomedical applications.
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Affiliation(s)
- Roswitha Dolcemascolo
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, Paterna, 46980, Spain
| | - Raúl Ruiz
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, Paterna, 46980, Spain
| | - Sara Baldanta
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, Paterna, 46980, Spain
| | - Lucas Goiriz
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, Paterna, 46980, Spain
- Pure and Applied Mathematics University Research Institute (IUMPA), Polytechnic University of Valencia, Valencia, 46022, Spain
| | - María Heras-Hernández
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, Paterna, 46980, Spain
| | - Roser Montagud-Martínez
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, Paterna, 46980, Spain
| | - Guillermo Rodrigo
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, Paterna, 46980, Spain.
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5
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Das D, Podder S. Microscale marvels: unveiling the macroscopic significance of micropeptides in human health. Brief Funct Genomics 2024; 23:624-638. [PMID: 38706311 DOI: 10.1093/bfgp/elae018] [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: 01/04/2024] [Revised: 04/07/2024] [Accepted: 04/15/2024] [Indexed: 05/07/2024] Open
Abstract
Non-coding RNA encodes micropeptides from small open reading frames located within the RNA. Interestingly, these micropeptides are involved in a variety of functions within the body. They are emerging as the resolving piece of the puzzle for complex biomolecular signaling pathways within the body. Recent studies highlight the pivotal role of small peptides in regulating important biological processes like DNA repair, gene expression, muscle regeneration, immune responses, etc. On the contrary, altered expression of micropeptides also plays a pivotal role in the progression of various diseases like cardiovascular diseases, neurological disorders and several types of cancer, including colorectal cancer, hepatocellular cancer, lung cancer, etc. This review delves into the dual impact of micropeptides on health and pathology, exploring their pivotal role in preserving normal physiological homeostasis and probing their involvement in the triggering and progression of diseases.
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Affiliation(s)
- Deepyaman Das
- Computational and Systems Biology Laboratory, Department of Microbiology, Raiganj University, Raiganj, Uttar Dinajpur, West Bengal-733134, India
| | - Soumita Podder
- Computational and Systems Biology Laboratory, Department of Microbiology, Raiganj University, Raiganj, Uttar Dinajpur, West Bengal-733134, India
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6
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Coscujuela Tarrero L, Famà V, D'Andrea G, Maestri S, de Polo A, Biffo S, Furlan M, Pelizzola M. Nanodynamo quantifies subcellular RNA dynamics revealing extensive coupling between steps of the RNA life cycle. Nat Commun 2024; 15:7725. [PMID: 39231948 PMCID: PMC11375098 DOI: 10.1038/s41467-024-51917-2] [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: 11/10/2023] [Accepted: 08/20/2024] [Indexed: 09/06/2024] Open
Abstract
The coordinated action of transcriptional and post-transcriptional machineries shapes gene expression programs at steady state and determines their concerted response to perturbations. We have developed Nanodynamo, an experimental and computational workflow for quantifying the kinetic rates of nuclear and cytoplasmic steps of the RNA life cycle. Nanodynamo is based on mathematical modelling following sequencing of native RNA from cellular fractions and polysomes. We have applied this workflow to triple-negative breast cancer cells, revealing widespread post-transcriptional RNA processing that is mutually exclusive with its co-transcriptional counterpart. We used Nanodynamo to unravel the coupling between transcription, processing, export, decay and translation machineries. We have identified a number of coupling interactions within and between the nucleus and cytoplasm that largely contribute to coordinating how cells respond to perturbations that affect gene expression programs. Nanodynamo will be instrumental in unravelling the determinants and regulatory processes involved in the coordination of gene expression responses.
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Affiliation(s)
| | - Valeria Famà
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milan, Italy
- Department of Oncology and Emato-Oncology, University of Milan, Milan, Italy
| | - Giacomo D'Andrea
- Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milano, Italy
- Department of Biosciences, University of Milan, Milan, Italy
| | - Simone Maestri
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - Anna de Polo
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - Stefano Biffo
- Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milano, Italy
- Department of Biosciences, University of Milan, Milan, Italy
| | - Mattia Furlan
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milan, Italy.
| | - Mattia Pelizzola
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milan, Italy.
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy.
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7
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Yasuda T, Morita R, Shigeta Y, Harada R. Ribosome Tunnel Environment Drives the Formation of α-Helix during Cotranslational Folding. J Chem Inf Model 2024; 64:6610-6622. [PMID: 39150098 PMCID: PMC11351022 DOI: 10.1021/acs.jcim.4c00901] [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: 05/24/2024] [Revised: 07/09/2024] [Accepted: 08/06/2024] [Indexed: 08/17/2024]
Abstract
Protein conformations in cells are not solely determined by amino acid sequences; they also depend on cellular environments. For instance, the ribosome tunnel induces its specific α-helix formation during cotranslational folding. Owing to the link between these temporally α-helix and biological functions, the mechanism of α-helix formation inside the ribosome tunnel has been previously explored. Consequently, the conformational restrictions of the tunnel were considered one of the driving forces of α-helix formation. Conversely, the ribosomal tunnel environment, including its chemical properties, appears to influence the α-helix formation. However, a comprehensive analysis of the ribosome tunnel environment's impact on the α-helix formation has not been conducted yet due to challenges in experimentally controlling it. Therefore, as a new computational approach, we proposed a ribosome environment-mimicking model (REMM) based on the radius and components of the experimentally determined ribosome tunnel structures. Using REMM, we assessed the impact of the ribosome tunnel environment on α-helix formation. Herein, we employed carbon nanotubes (CNT) as a reference model alongside REMM because CNT reproduce conformational restrictions rather than the ribosome tunnel environment. Quantitatively, the ability to reproduce the α-helix of nascent peptides in the experimental structure was compared between the CNT and REMM using enhanced all-atom molecular dynamics simulations. Consequently, the REMM more accurately reproduced the α-helix of the nascent peptides than the CNT, highlighting the significance of the ribosome tunnel environment in α-helix formation. Additionally, we analyzed the properties of the peptide inside each model to reveal the mechanism of ribosome tunnel-specific α-helix formation. Consequently, we revealed that the chemical diversities of the tunnel are essential for the formation of backbone-to-backbone hydrogen bonds in the peptides. In conclusion, the ribosome tunnel environment, with the diverse chemical properties, drives its specific α-helix formation. By proposing REMM, we newly provide the technical basis for investigating the protein conformations in various cellular environments.
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Affiliation(s)
- Takunori Yasuda
- Doctoral
Program in Biology, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Rikuri Morita
- Center
for Computational Sciences, University of
Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Yasuteru Shigeta
- Center
for Computational Sciences, University of
Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Ryuhei Harada
- Center
for Computational Sciences, University of
Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
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8
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Tomuro K, Mito M, Toh H, Kawamoto N, Miyake T, Chow SYA, Doi M, Ikeuchi Y, Shichino Y, Iwasaki S. Calibrated ribosome profiling assesses the dynamics of ribosomal flux on transcripts. Nat Commun 2024; 15:7061. [PMID: 39187487 PMCID: PMC11347596 DOI: 10.1038/s41467-024-51258-0] [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: 07/09/2023] [Accepted: 08/02/2024] [Indexed: 08/28/2024] Open
Abstract
Ribosome profiling, which is based on deep sequencing of ribosome footprints, has served as a powerful tool for elucidating the regulatory mechanism of protein synthesis. However, the current method has substantial issues: contamination by rRNAs and the lack of appropriate methods to measure ribosome numbers in transcripts. Here, we overcome these hurdles through the development of "Ribo-FilterOut", which is based on the separation of footprints from ribosome subunits by ultrafiltration, and "Ribo-Calibration", which relies on external spike-ins of stoichiometrically defined mRNA-ribosome complexes. A combination of these approaches estimates the number of ribosomes on a transcript, the translation initiation rate, and the overall number of translation events before its decay, all in a genome-wide manner. Moreover, our method reveals the allocation of ribosomes under heat shock stress, during aging, and across cell types. Our strategy of modified ribosome profiling measures kinetic and stoichiometric parameters of cellular translation across the transcriptome.
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Grants
- JP20H05784 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP24H02307 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP20H05782 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP24H02306 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP20H05786 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP24H02307 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP21H05734 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP23H04268 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP20gm1410001 Japan Agency for Medical Research and Development (AMED)
- JP20gm1410001 Japan Agency for Medical Research and Development (AMED)
- JP23gm6910005 Japan Agency for Medical Research and Development (AMED)
- JP22fk0108570 Japan Agency for Medical Research and Development (AMED)
- JP23H02415 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP23H00095 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP21K15023 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP23K05648 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP22K20765 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP23K14173 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP23KJ2178 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP23KJ2175 MEXT | Japan Society for the Promotion of Science (JSPS)
- Pioneering Project MEXT | RIKEN
- RIKEN TRIP initiative "TRIP-AGIS" MEXT | RIKEN
- Pioneering Project MEXT | RIKEN
- JPMJBS2418 MEXT | Japan Science and Technology Agency (JST)
- JPMJFR226F MEXT | Japan Science and Technology Agency (JST)
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Affiliation(s)
- Kotaro Tomuro
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan
| | - Mari Mito
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Hirotaka Toh
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Naohiro Kawamoto
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Takahito Miyake
- Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto, 606-8501, Japan
| | - Siu Yu A Chow
- Institute of Industrial Science, The University of Tokyo, Meguro-ku, Tokyo, 153-8505, Japan
| | - Masao Doi
- Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto, 606-8501, Japan
| | - Yoshiho Ikeuchi
- Institute of Industrial Science, The University of Tokyo, Meguro-ku, Tokyo, 153-8505, Japan
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Institute for AI and Beyond, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yuichi Shichino
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan.
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan.
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan.
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9
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Zhao G, Liu Z, Quan J, Lu J, Li L, Pan Y. Ribosome Profiling and RNA Sequencing Reveal Translation and Transcription Regulation under Acute Heat Stress in Rainbow Trout ( Oncorhynchus mykiss, Walbaum, 1792) Liver. Int J Mol Sci 2024; 25:8848. [PMID: 39201531 PMCID: PMC11354268 DOI: 10.3390/ijms25168848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 07/31/2024] [Accepted: 08/01/2024] [Indexed: 09/02/2024] Open
Abstract
Rainbow trout (Oncorhynchus mykiss, Walbaum, 1792) is an important economic cold-water fish that is susceptible to heat stress. To date, the heat stress response in rainbow trout is more widely understood at the transcriptional level, while little research has been conducted at the translational level. To reveal the translational regulation of heat stress in rainbow trout, in this study, we performed a ribosome profiling assay of rainbow trout liver under normal and heat stress conditions. Comparative analysis of the RNA-seq data with the ribosome profiling data showed that the folding changes in gene expression at the transcriptional level are moderately correlated with those at the translational level. In total, 1213 genes were significantly altered at the translational level. However, only 32.8% of the genes were common between both levels, demonstrating that heat stress is coordinated across both transcriptional and translational levels. Moreover, 809 genes exhibited significant differences in translational efficiency (TE), with the TE of these genes being considerably affected by factors such as the GC content, coding sequence length, and upstream open reading frame (uORF) presence. In addition, 3468 potential uORFs in 2676 genes were identified, which can potentially affect the TE of the main open reading frames. In this study, Ribo-seq and RNA-seq were used for the first time to elucidate the coordinated regulation of transcription and translation in rainbow trout under heat stress. These findings are expected to contribute novel data and theoretical insights to the international literature on the thermal stress response in fish.
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Affiliation(s)
| | - Zhe Liu
- Department of College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (G.Z.); (J.Q.); (J.L.); (L.L.); (Y.P.)
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10
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Horvath A, Janapala Y, Woodward K, Mahmud S, Cleynen A, Gardiner E, Hannan R, Eyras E, Preiss T, Shirokikh N. Comprehensive translational profiling and STE AI uncover rapid control of protein biosynthesis during cell stress. Nucleic Acids Res 2024; 52:7925-7946. [PMID: 38721779 PMCID: PMC11260467 DOI: 10.1093/nar/gkae365] [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: 01/09/2024] [Revised: 03/21/2024] [Accepted: 04/25/2024] [Indexed: 07/23/2024] Open
Abstract
Translational control is important in all life, but it remains a challenge to accurately quantify. When ribosomes translate messenger (m)RNA into proteins, they attach to the mRNA in series, forming poly(ribo)somes, and can co-localize. Here, we computationally model new types of co-localized ribosomal complexes on mRNA and identify them using enhanced translation complex profile sequencing (eTCP-seq) based on rapid in vivo crosslinking. We detect long disome footprints outside regions of non-random elongation stalls and show these are linked to translation initiation and protein biosynthesis rates. We subject footprints of disomes and other translation complexes to artificial intelligence (AI) analysis and construct a new, accurate and self-normalized measure of translation, termed stochastic translation efficiency (STE). We then apply STE to investigate rapid changes to mRNA translation in yeast undergoing glucose depletion. Importantly, we show that, well beyond tagging elongation stalls, footprints of co-localized ribosomes provide rich insight into translational mechanisms, polysome dynamics and topology. STE AI ranks cellular mRNAs by absolute translation rates under given conditions, can assist in identifying its control elements and will facilitate the development of next-generation synthetic biology designs and mRNA-based therapeutics.
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Affiliation(s)
- Attila Horvath
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
| | - Yoshika Janapala
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
| | - Katrina Woodward
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
| | - Shafi Mahmud
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
| | - Alice Cleynen
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
- Institut Montpelliérain Alexander Grothendieck, Université de Montpellier, CNRS, Montpellier, France
| | - Elizabeth E Gardiner
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The National Platelet Research and Referral Centre, The Australian National University, Canberra, ACT 2601, Australia
| | - Ross D Hannan
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville 3010, Australia
- Peter MacCallum Cancer Centre, Melbourne 3000, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton 3800, Australia
- School of Biomedical Sciences, University of Queensland, St Lucia 4067, Australia
| | - Eduardo Eyras
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Centre for Computational Biomedical Sciences, The Australian National University, Canberra, ACT 2601, Australia
- EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, ACT 2601, Australia
| | - Thomas Preiss
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Nikolay E Shirokikh
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
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11
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Rodrigues P, Bangali H, Ali E, Sharma MK, Abdullaev B, Alkhafaji AT, Deorari MM, Zabibah RS, Haslany A. Microproteins/micropeptides dysregulation contributes to cancer progression and development: A mechanistic review. Cell Biol Int 2024. [PMID: 39010637 DOI: 10.1002/cbin.12219] [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: 10/04/2023] [Revised: 05/06/2024] [Accepted: 07/02/2024] [Indexed: 07/17/2024]
Abstract
Microproteins, known as micropeptides, are small protein molecules encoded by short open reading frames. These recently identified molecules have been proven to be an essential part of the human proteome that participates in multiple processes, such as DNA repair, mitochondrial respiration, and regulating different signaling pathways. A growing body of studies has evidenced that microproteins exhibit dysregulated expression levels in various malignancies and contribute to tumor progression. It has been reported that microproteins interact with many proteins, such as enzymes (e.g., adenosine triphosphate synthase) and signal transducers (e.g., c-Jun), and regulate malignant cell metabolism, proliferation, and metastasis. Moreover, microproteins have been found to play a significant role in multidrug resistance in vitro and in vivo by their activity in DNA repair pathways. Considering that, this review intended to summarize the roles of microproteins in different aspects of tumorigenesis with diagnostic and therapeutic perspectives.
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Affiliation(s)
- Paul Rodrigues
- Department of Computer Engineering, College of Computer Science, King Khalid University, Al-Faraa, Asir-Abha, Kingdom of Saudi Arabia
| | - Harun Bangali
- Department of Computer Engineering, College of Computer Science, King Khalid University, Al-Faraa, Saudi Arabia
| | - Eyhab Ali
- College of Chemistry, Al-Zahraa University for Women, Karbala, Iraq
| | - M K Sharma
- Chaudhary Charan Singh University, Meerut, Uttar Pradesh, India
| | - Bekhzod Abdullaev
- Department of Biotechnology, New Uzbekistan University, Tashkent, Uzbekistan
| | | | - Maha Medha Deorari
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
| | - Rahman S Zabibah
- College of Technical Engineering, The Islamic University, Najaf, Iraq
- College of Technical Engineering, The Islamic University of Al Diwaniyah, Al Diwaniyah, Iraq
- College of Technical Engineering, The Islamic University of Babylon, Babylon, Iraq
| | - Ali Haslany
- College of Technical Engineering, Imam Ja'afar Al-Sadiq University, Al-Muthanna, Iraq
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12
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Roshan P, Biswas A, Anagnos S, Luebbers R, Harish K, Ahmed S, Li M, Nguyen N, Zhou G, Tedeschi F, Hathuc V, Lin Z, Hamilton Z, Origanti S. Modulation of ribosomal subunit associations by eIF6 is critical for mitotic exit and cancer progression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.24.600220. [PMID: 38979253 PMCID: PMC11230244 DOI: 10.1101/2024.06.24.600220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Moderating the pool of active ribosomal subunits is critical for maintaining global translation rates. A factor crucial for modulating the 60S ribosomal subunits is eukaryotic translation initiation factor 6. Release of eIF6 from 60S is essential to permit 60S interactions with 40S. Here, using the N106S mutant of eIF6, we show that disrupting eIF6 interaction with 60S leads to an increase in vacant 80S. It further highlights a dichotomy in the anti-association activity of eIF6 that is distinct from its role in 60S biogenesis and shows that the nucleolar localization of eIF6 is not dependent on uL14-BCCIP interactions. Limiting active ribosomal pools markedly deregulates translation especially in mitosis and leads to chromosome segregation defects, mitotic exit delays and mitotic catastrophe. Ribo-Seq analysis of the eIF6-N106S mutant shows a significant downregulation in the translation efficiencies of mitotic factors and specifically transcripts with long 3'UTRs. eIF6-N106S mutation also limits cancer invasion, and this role is correlated with the overexpression of eIF6 only in high-grade invasive cancers suggesting that deregulation of eIF6 is probably not an early event in cancers. Thus, this study highlights the segregation of eIF6 functions and its role in moderating 80S availability for mitotic translation and cancer progression.
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13
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Shen Z, Naveed M, Bao J. Untacking small RNA profiling and RNA fragment footprinting: Approaches and challenges in library construction. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1852. [PMID: 38715192 DOI: 10.1002/wrna.1852] [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: 02/21/2024] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 06/06/2024]
Abstract
Small RNAs (sRNAs) with sizes ranging from 15 to 50 nucleotides (nt) are critical regulators of gene expression control. Prior studies have shown that sRNAs are involved in a broad range of biological processes, such as organ development, tumorigenesis, and epigenomic regulation; however, emerging evidence unveils a hidden layer of diversity and complexity of endogenously encoded sRNAs profile in eukaryotic organisms, including novel types of sRNAs and the previously unknown post-transcriptional RNA modifications. This underscores the importance for accurate, unbiased detection of sRNAs in various cellular contexts. A multitude of high-throughput methods based on next-generation sequencing (NGS) are developed to decipher the sRNA expression and their modifications. Nonetheless, distinct from mRNA sequencing, the data from sRNA sequencing suffer frequent inconsistencies and high variations emanating from the adapter contaminations and RNA modifications, which overall skew the sRNA libraries. Here, we summarize the sRNA-sequencing approaches, and discuss the considerations and challenges for the strategies and methods of sRNA library construction. The pros and cons of sRNA sequencing have significant implications for implementing RNA fragment footprinting approaches, including CLIP-seq and Ribo-seq. We envision that this review can inspire novel improvements in small RNA sequencing and RNA fragment footprinting in future. This article is categorized under: RNA Evolution and Genomics > Computational Analyses of RNA RNA Processing > Processing of Small RNAs Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs.
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Affiliation(s)
- Zhaokang Shen
- Department of Obstetrics and Gynecology, Center for Reproduction and Genetics, The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Hefei, Anhui, China
| | - Muhammad Naveed
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Hefei, Anhui, China
- Department of Obstetrics and Gynecology, Center for Reproduction and Genetics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Jianqiang Bao
- Department of Obstetrics and Gynecology, Center for Reproduction and Genetics, The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Hefei, Anhui, China
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14
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Chandy M, Hill T, Jimenez-Tellez N, Wu JC, Sarles SE, Hensel E, Wang Q, Rahman I, Conklin DJ. Addressing Cardiovascular Toxicity Risk of Electronic Nicotine Delivery Systems in the Twenty-First Century: "What Are the Tools Needed for the Job?" and "Do We Have Them?". Cardiovasc Toxicol 2024; 24:435-471. [PMID: 38555547 DOI: 10.1007/s12012-024-09850-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/19/2024] [Indexed: 04/02/2024]
Abstract
Cigarette smoking is positively and robustly associated with cardiovascular disease (CVD), including hypertension, atherosclerosis, cardiac arrhythmias, stroke, thromboembolism, myocardial infarctions, and heart failure. However, after more than a decade of ENDS presence in the U.S. marketplace, uncertainty persists regarding the long-term health consequences of ENDS use for CVD. New approach methods (NAMs) in the field of toxicology are being developed to enhance rapid prediction of human health hazards. Recent technical advances can now consider impact of biological factors such as sex and race/ethnicity, permitting application of NAMs findings to health equity and environmental justice issues. This has been the case for hazard assessments of drugs and environmental chemicals in areas such as cardiovascular, respiratory, and developmental toxicity. Despite these advances, a shortage of widely accepted methodologies to predict the impact of ENDS use on human health slows the application of regulatory oversight and the protection of public health. Minimizing the time between the emergence of risk (e.g., ENDS use) and the administration of well-founded regulatory policy requires thoughtful consideration of the currently available sources of data, their applicability to the prediction of health outcomes, and whether these available data streams are enough to support an actionable decision. This challenge forms the basis of this white paper on how best to reveal potential toxicities of ENDS use in the human cardiovascular system-a primary target of conventional tobacco smoking. We identify current approaches used to evaluate the impacts of tobacco on cardiovascular health, in particular emerging techniques that replace, reduce, and refine slower and more costly animal models with NAMs platforms that can be applied to tobacco regulatory science. The limitations of these emerging platforms are addressed, and systems biology approaches to close the knowledge gap between traditional models and NAMs are proposed. It is hoped that these suggestions and their adoption within the greater scientific community will result in fresh data streams that will support and enhance the scientific evaluation and subsequent decision-making of tobacco regulatory agencies worldwide.
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Affiliation(s)
- Mark Chandy
- Robarts Research Institute, Western University, London, N6A 5K8, Canada
| | - Thomas Hill
- Division of Nonclinical Science, Center for Tobacco Products, US Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Nerea Jimenez-Tellez
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94304, USA
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94304, USA
| | - S Emma Sarles
- Biomedical and Chemical Engineering PhD Program, Rochester Institute of Technology, Rochester, NY, 14623, USA
| | - Edward Hensel
- Department of Mechanical Engineering, Rochester Institute of Technology, Rochester, NY, 14623, USA
| | - Qixin Wang
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Irfan Rahman
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Daniel J Conklin
- Division of Environmental Medicine, Department of Medicine, Center for Cardiometabolic Science, Christina Lee Brown Envirome Institute, University of Louisville, 580 S. Preston St., Delia Baxter, Rm. 404E, Louisville, KY, 40202, USA.
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15
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Tanaka M, Yokoyama T, Saito H, Nishimoto M, Tsuda K, Sotta N, Shigematsu H, Shirouzu M, Iwasaki S, Ito T, Fujiwara T. Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1. Nat Chem Biol 2024; 20:605-614. [PMID: 38267667 DOI: 10.1038/s41589-023-01513-0] [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: 02/11/2022] [Accepted: 11/24/2023] [Indexed: 01/26/2024]
Abstract
In response to environmental changes, cells flexibly and rapidly alter gene expression through translational controls. In plants, the translation of NIP5;1, a boric acid diffusion facilitator, is downregulated in response to an excess amount of boric acid in the environment through upstream open reading frames (uORFs) that consist of only AUG and stop codons. However, the molecular details of how this minimum uORF controls translation of the downstream main ORF in a boric acid-dependent manner have remained unclear. Here, by combining ribosome profiling, translation complex profile sequencing, structural analysis with cryo-electron microscopy and biochemical assays, we show that the 80S ribosome assembled at AUG-stop migrates into the subsequent RNA segment, followed by downstream translation initiation, and that boric acid impedes this process by the stable confinement of eukaryotic release factor 1 on the 80S ribosome on AUG-stop. Our results provide molecular insight into translation regulation by a minimum and environment-responsive uORF.
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Affiliation(s)
- Mayuki Tanaka
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Takeshi Yokoyama
- RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Hironori Saito
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
- RIKEN Cluster for Pioneering Research, Wako, Japan
| | - Madoka Nishimoto
- RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama, Japan
| | - Kengo Tsuda
- RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama, Japan
| | - Naoyuki Sotta
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Hideki Shigematsu
- RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama, Japan
- Life Science Research Infrastructure Group, RIKEN SPring-8 Center, Sayo, Japan
| | - Mikako Shirouzu
- RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama, Japan
| | - Shintaro Iwasaki
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.
- RIKEN Cluster for Pioneering Research, Wako, Japan.
| | - Takuhiro Ito
- RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama, Japan.
| | - Toru Fujiwara
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
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16
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Iosub IA, Wilkins OG, Ule J. Riboseq-flow: A streamlined, reliable pipeline for ribosome profiling data analysis and quality control. Wellcome Open Res 2024; 9:179. [PMID: 38846930 PMCID: PMC11153996 DOI: 10.12688/wellcomeopenres.21000.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2024] [Indexed: 06/09/2024] Open
Abstract
Ribosome profiling is a powerful technique to study translation at a transcriptome-wide level. However, ensuring good data quality is paramount for accurate interpretation, as is ensuring that the analyses are reproducible. We introduce a new Nextflow DSL2 pipeline, riboseq-flow, designed for processing and comprehensive quality control of ribosome profiling experiments. Riboseq-flow is user-friendly, versatile and upholds high standards in reproducibility, scalability, portability, version control and continuous integration. It enables users to efficiently analyse multiple samples in parallel and helps them evaluate the quality and utility of their data based on the detailed metrics and visualisations that are automatically generated. Riboseq-flow is available at https://github.com/iraiosub/riboseq-flow.
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Affiliation(s)
- Ira A. Iosub
- The Francis Crick Institute, London, England, UK
- UK Dementia Research Institute at King's College London, London, UK
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Oscar G. Wilkins
- The Francis Crick Institute, London, England, UK
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Jernej Ule
- The Francis Crick Institute, London, England, UK
- UK Dementia Research Institute at King's College London, London, UK
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
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17
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Zhang Q, Liu L. Novel insights into small open reading frame-encoded micropeptides in hepatocellular carcinoma: A potential breakthrough. Cancer Lett 2024; 587:216691. [PMID: 38360139 DOI: 10.1016/j.canlet.2024.216691] [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: 10/23/2023] [Revised: 01/13/2024] [Accepted: 01/27/2024] [Indexed: 02/17/2024]
Abstract
Traditionally, non-coding RNAs (ncRNAs) are regarded as a class of RNA transcripts that lack encoding capability; however, advancements in technology have revealed that some ncRNAs contain small open reading frames (sORFs) that are capable of encoding micropeptides of approximately 150 amino acids in length. sORF-encoded micropeptides (SEPs) have emerged as intriguing entities in hepatocellular carcinoma (HCC) research, shedding light on this previously unexplored realm. Recent studies have highlighted the regulatory functions of SEPs in the occurrence and progression of HCC. Some SEPs exhibit inhibitory effects on HCC, but others facilitate its development. This discovery has revolutionized the landscape of HCC research and clinical management. Here, we introduce the concept and characteristics of SEPs, summarize their associations with HCC, and elucidate their carcinogenic mechanisms in HCC metabolism, signaling pathways, cell proliferation, and metastasis. In addition, we propose a step-by-step workflow for the investigation of HCC-associated SEPs. Lastly, we discuss the challenges and prospects of applying SEPs in the diagnosis and treatment of HCC. This review aims to facilitate the discovery, optimization, and clinical application of HCC-related SEPs, inspiring the development of early diagnostic, individualized, and precision therapeutic strategies for HCC.
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Affiliation(s)
- Qiangnu Zhang
- Division of Hepatobiliary and Pancreas Surgery, Department of General Surgery, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), 518020, Shenzhen, China
| | - Liping Liu
- Division of Hepatobiliary and Pancreas Surgery, Department of General Surgery, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), 518020, Shenzhen, China.
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18
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O’Connor PBF, Mahony J, Casey E, Baranov PV, van Sinderen D, Yordanova MM. Ribosome profiling reveals downregulation of UMP biosynthesis as the major early response to phage infection. Microbiol Spectr 2024; 12:e0398923. [PMID: 38451091 PMCID: PMC10986495 DOI: 10.1128/spectrum.03989-23] [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: 11/23/2023] [Accepted: 02/14/2024] [Indexed: 03/08/2024] Open
Abstract
Bacteria have evolved diverse defense mechanisms to counter bacteriophage attacks. Genetic programs activated upon infection characterize phage-host molecular interactions and ultimately determine the outcome of the infection. In this study, we applied ribosome profiling to monitor protein synthesis during the early stages of sk1 bacteriophage infection in Lactococcus cremoris. Our analysis revealed major changes in gene expression within 5 minutes of sk1 infection. Notably, we observed a specific and severe downregulation of several pyr operons which encode enzymes required for uridine monophosphate biosynthesis. Consistent with previous findings, this is likely an attempt of the host to starve the phage of nucleotides it requires for propagation. We also observed a gene expression response that we expect to benefit the phage. This included the upregulation of 40 ribosome proteins that likely increased the host's translational capacity, concurrent with a downregulation of genes that promote translational fidelity (lepA and raiA). In addition to the characterization of host-phage gene expression responses, the obtained ribosome profiling data enabled us to identify two putative recoding events as well as dozens of loci currently annotated as pseudogenes that are actively translated. Furthermore, our study elucidated alterations in the dynamics of the translation process, as indicated by time-dependent changes in the metagene profile, suggesting global shifts in translation rates upon infection. Additionally, we observed consistent modifications in the ribosome profiles of individual genes, which were apparent as early as 2 minutes post-infection. The study emphasizes our ability to capture rapid alterations of gene expression during phage infection through ribosome profiling. IMPORTANCE The ribosome profiling technology has provided invaluable insights for understanding cellular translation and eukaryotic viral infections. However, its potential for investigating host-phage interactions remains largely untapped. Here, we applied ribosome profiling to Lactococcus cremoris cultures infected with sk1, a major infectious agent in dairy fermentation processes. This revealed a profound downregulation of genes involved in pyrimidine nucleotide synthesis at an early stage of phage infection, suggesting an anti-phage program aimed at restricting nucleotide availability and, consequently, phage propagation. This is consistent with recent findings and contributes to our growing appreciation for the role of nucleotide limitation as an anti-viral strategy. In addition to capturing rapid alterations in gene expression levels, we identified translation occurring outside annotated regions, as well as signatures of non-standard translation mechanisms. The gene profiles revealed specific changes in ribosomal densities upon infection, reflecting alterations in the dynamics of the translation process.
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Affiliation(s)
- Patrick B. F. O’Connor
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
- EIRNA Bio, Bioinnovation Hub, Cork, Ireland
| | - Jennifer Mahony
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Eoghan Casey
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Pavel V. Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Douwe van Sinderen
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
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19
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Fasciani I, Petragnano F, Wang Z, Edwards R, Telugu N, Pietrantoni I, Zabel U, Zauber H, Grieben M, Terzenidou ME, Di Gregorio J, Pellegrini C, Santini S, Taddei AR, Pohl B, Aringhieri S, Carli M, Aloisi G, Marampon F, Charlesworth E, Roman A, Diecke S, Flati V, Giorgi F, Amicarelli F, Tobin AB, Scarselli M, Tokatlidis K, Rossi M, Lohse MJ, Annibale P, Maggio R. The C-terminus of the prototypical M2 muscarinic receptor localizes to the mitochondria and regulates cell respiration under stress conditions. PLoS Biol 2024; 22:e3002582. [PMID: 38683874 PMCID: PMC11093360 DOI: 10.1371/journal.pbio.3002582] [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: 11/16/2022] [Revised: 05/14/2024] [Accepted: 03/11/2024] [Indexed: 05/02/2024] Open
Abstract
Muscarinic acetylcholine receptors are prototypical G protein-coupled receptors (GPCRs), members of a large family of 7 transmembrane receptors mediating a wide variety of extracellular signals. We show here, in cultured cells and in a murine model, that the carboxyl terminal fragment of the muscarinic M2 receptor, comprising the transmembrane regions 6 and 7 (M2tail), is expressed by virtue of an internal ribosome entry site localized in the third intracellular loop. Single-cell imaging and import in isolated yeast mitochondria reveals that M2tail, whose expression is up-regulated in cells undergoing integrated stress response, does not follow the normal route to the plasma membrane, but is almost exclusively sorted to the mitochondria inner membrane: here, it controls oxygen consumption, cell proliferation, and the formation of reactive oxygen species (ROS) by reducing oxidative phosphorylation. Crispr/Cas9 editing of the key methionine where cap-independent translation begins in human-induced pluripotent stem cells (hiPSCs), reveals the physiological role of this process in influencing cell proliferation and oxygen consumption at the endogenous level. The expression of the C-terminal domain of a GPCR, capable of regulating mitochondrial function, constitutes a hitherto unknown mechanism notably unrelated to its canonical signaling function as a GPCR at the plasma membrane. This work thus highlights a potential novel mechanism that cells may use for controlling their metabolism under variable environmental conditions, notably as a negative regulator of cell respiration.
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Affiliation(s)
- Irene Fasciani
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, Italy
| | - Francesco Petragnano
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, Italy
| | - Ziming Wang
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Ruairidh Edwards
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | - Ilaria Pietrantoni
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, Italy
| | - Ulrike Zabel
- Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany
| | - Henrik Zauber
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | | | - Maria E. Terzenidou
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Jacopo Di Gregorio
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, Italy
| | - Cristina Pellegrini
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, Italy
| | - Silvano Santini
- Department of Life, Health and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
| | - Anna R. Taddei
- Section of Electron Microscopy, Great Equipment Center, University of Tuscia, Viterbo, Italy
| | - Bärbel Pohl
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Stefano Aringhieri
- Department of Translational Research and New Technology in Medicine, University of Pisa, Pisa, Italy
| | - Marco Carli
- Department of Translational Research and New Technology in Medicine, University of Pisa, Pisa, Italy
| | - Gabriella Aloisi
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, Italy
| | | | - Eve Charlesworth
- School of Physics and Astronomy, University of St Andrews, St Andrews, United Kingdom
| | | | | | - Vincenzo Flati
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, Italy
| | - Franco Giorgi
- Department of Translational Research and New Technology in Medicine, University of Pisa, Pisa, Italy
| | - Fernanda Amicarelli
- Department of Life, Health and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
| | - Andrew B. Tobin
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Marco Scarselli
- Department of Translational Research and New Technology in Medicine, University of Pisa, Pisa, Italy
| | - Kostas Tokatlidis
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Mario Rossi
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, Italy
| | - Martin J. Lohse
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany
- ISAR Bioscience Institute, Munich, Germany
| | - Paolo Annibale
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
- School of Physics and Astronomy, University of St Andrews, St Andrews, United Kingdom
| | - Roberto Maggio
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, Italy
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20
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Xiao R, Chen Y, Hu Z, Tang Q, Wang P, Zhou M, Wu L, Liang D. Identification of the Efficient Enhancer Elements in FVIII-Padua for Gene Therapy Study of Hemophilia A. Int J Mol Sci 2024; 25:3635. [PMID: 38612447 PMCID: PMC11011560 DOI: 10.3390/ijms25073635] [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: 02/13/2024] [Revised: 03/13/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024] Open
Abstract
Hemophilia A (HA) is a common X-linked recessive hereditary bleeding disorder. Coagulation factor VIII (FVIII) is insufficient in patients with HA due to the mutations in the F8 gene. The restoration of plasma levels of FVIII via both recombinant B-domain-deleted FVIII (BDD-FVIII) and B-domain-deleted F8 (BDDF8) transgenes was proven to be helpful. FVIII-Padua is a 23.4 kb tandem repeat mutation in the F8 associated with a high F8 gene expression and thrombogenesis. Here we screened a core enhancer element in FVIII-Padua for improving the F8 expression. In detail, we identified a 400 bp efficient enhancer element, C400, in FVIII-Padua for the first time. The core enhancer C400 extensively improved the transcription of BDDF8 driven by human elongation factor-1 alpha in HepG2, HeLa, HEK-293T and induced pluripotent stem cells (iPSCs) with different genetic backgrounds, as well as iPSCs-derived endothelial progenitor cells (iEPCs) and iPSCs-derived mesenchymal stem cells (iMSCs). The expression of FVIII protein was increased by C400, especially in iEPCs. Our research provides a novel molecular target to enhance expression of FVIII protein, which has scientific value and application prospects in both viral and nonviral HA gene therapy strategies.
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Affiliation(s)
| | | | | | | | | | | | | | - Desheng Liang
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China; (R.X.); (Y.C.); (Z.H.); (M.Z.)
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21
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Teyssonniere EM, Shichino Y, Mito M, Friedrich A, Iwasaki S, Schacherer J. Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast. Nucleic Acids Res 2024; 52:2434-2445. [PMID: 38261993 PMCID: PMC10954453 DOI: 10.1093/nar/gkae030] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 12/21/2023] [Accepted: 01/11/2024] [Indexed: 01/25/2024] Open
Abstract
Gene expression is known to vary among individuals, and this variability can impact the phenotypic diversity observed in natural populations. While the transcriptome and proteome have been extensively studied, little is known about the translation process itself. Here, we therefore performed ribosome and transcriptomic profiling on a genetically and ecologically diverse set of natural isolates of the Saccharomyces cerevisiae yeast. Interestingly, we found that the Euclidean distances between each profile and the expression fold changes in each pairwise isolate comparison were higher at the transcriptomic level. This observation clearly indicates that the transcriptional variation observed in the different isolates is buffered through a phenomenon known as post-transcriptional buffering at the translation level. Furthermore, this phenomenon seemed to have a specific signature by preferentially affecting essential genes as well as genes involved in complex-forming proteins, and low transcribed genes. We also explored the translation of the S. cerevisiae pangenome and found that the accessory genes related to introgression events displayed similar transcription and translation levels as the core genome. By contrast, genes acquired through horizontal gene transfer events tended to be less efficiently translated. Together, our results highlight both the extent and signature of the post-transcriptional buffering.
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Affiliation(s)
| | - Yuichi Shichino
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Mari Mito
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Anne Friedrich
- Université de Strasbourg, CNRS, GMGM UMR, 7156 Strasbourg, France
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR, 7156 Strasbourg, France
- Institut Universitaire de France (IUF), Paris, France
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22
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Yang H, Li Q, Stroup EK, Wang S, Ji Z. Widespread stable noncanonical peptides identified by integrated analyses of ribosome profiling and ORF features. Nat Commun 2024; 15:1932. [PMID: 38431639 PMCID: PMC10908861 DOI: 10.1038/s41467-024-46240-9] [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: 07/18/2023] [Accepted: 02/18/2024] [Indexed: 03/05/2024] Open
Abstract
Studies have revealed dozens of functional peptides in putative 'noncoding' regions and raised the question of how many proteins are encoded by noncanonical open reading frames (ORFs). Here, we comprehensively annotate genome-wide translated ORFs across five eukaryotes (human, mouse, zebrafish, worm, and yeast) by analyzing ribosome profiling data. We develop a logistic regression model named PepScore based on ORF features (expected length, encoded domain, and conservation) to calculate the probability that the encoded peptide is stable in humans. Systematic ectopic expression validates PepScore and shows that stable complex-associating microproteins can be encoded in 5'/3' untranslated regions and overlapping coding regions of mRNAs besides annotated noncoding RNAs. Stable noncanonical proteins follow conventional rules and localize to different subcellular compartments. Inhibition of proteasomal/lysosomal degradation pathways can stabilize some peptides especially those with moderate PepScores, but cannot rescue the expression of short ones with low PepScores suggesting they are directly degraded by cellular proteases. The majority of human noncanonical peptides with high PepScores show longer lengths but low conservation across species/mammals, and hundreds contain trait-associated genetic variants. Our study presents a statistical framework to identify stable noncanonical peptides in the genome and provides a valuable resource for functional characterization of noncanonical translation during development and disease.
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Affiliation(s)
- Haiwang Yang
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Qianru Li
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Emily K Stroup
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Sheng Wang
- Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL, 60628, USA
| | - Zhe Ji
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
- Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL, 60628, USA.
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23
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Karousis ED. The art of hijacking: how Nsp1 impacts host gene expression during coronaviral infections. Biochem Soc Trans 2024; 52:481-490. [PMID: 38385526 PMCID: PMC10903449 DOI: 10.1042/bst20231119] [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: 01/18/2024] [Revised: 02/14/2024] [Accepted: 02/14/2024] [Indexed: 02/23/2024]
Abstract
Non-structural protein 1 (Nsp1) is one of the first proteins produced during coronaviral infections. It plays a pivotal role in hijacking and rendering the host gene expression under the service of the virus. With a focus on SARS-CoV-2, this review presents how Nsp1 selectively inhibits host protein synthesis and induces mRNA degradation of host but not viral mRNAs and blocks nuclear mRNA export. The clinical implications of this protein are highlighted by showcasing the pathogenic role of Nsp1 through the repression of interferon expression pathways and the features of viral variants with mutations in the Nsp1 coding sequence. The ability of SARS-CoV-2 Nsp1 to hinder host immune responses at an early step, the absence of homology to any human proteins, and the availability of structural information render this viral protein an ideal drug target with therapeutic potential.
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Affiliation(s)
- Evangelos D. Karousis
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
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24
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Zhao X, Perez JM, Faull PA, Chan C, Munting FW, Canadeo LA, Cenik C, Huibregtse JM. Cellular targets and lysine selectivity of the HERC5 ISG15 ligase. iScience 2024; 27:108820. [PMID: 38303729 PMCID: PMC10831901 DOI: 10.1016/j.isci.2024.108820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/21/2023] [Accepted: 01/02/2024] [Indexed: 02/03/2024] Open
Abstract
ISG15 is a type I interferon-induced ubiquitin-like modifier that functions in innate immune responses. The major human ISG15 ligase is hHERC5, a ribosome-associated HECT E3 that broadly ISGylates proteins cotranslationally. Here, we characterized the hHERC5-dependent ISGylome and identified over 2,000 modified lysines in over 1,100 proteins in IFN-β-stimulated cells. In parallel, we compared the substrate selectivity hHERC5 to the major mouse ISG15 ligase, mHERC6, and analysis of sequences surrounding ISGylation sites revealed that hHERC5 and mHERC6 have distinct preferences for amino acid sequence context. Several features of the datasets were consistent with ISGylation of ribosome-tethered nascent chains, and mHERC6, like hHERC5, cotranslationally modified nascent polypeptides. The ISGylome datasets presented here represent the largest numbers of protein targets and modification sites attributable to a single Ub/Ubl ligase and the lysine selectivities of the hHERC5 and mHERC6 enzymes may have implications for the activities of HECT domain ligases, generally.
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Affiliation(s)
- Xu Zhao
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Jessica M. Perez
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Peter A. Faull
- Biological Mass Spectrometry Facility, Center for Biomedical Research Support, University of Texas at Austin, Austin, TX 78712, USA
| | - Catherine Chan
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Femke W. Munting
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Larissa A. Canadeo
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Can Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Jon M. Huibregtse
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
- John Ring LaMontagne Center for Infectious Disease, University of Texas at Austin, Austin, TX 78712, USA
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25
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Huang S, Wylder AC, Pan T. Simultaneous nanopore profiling of mRNA m 6A and pseudouridine reveals translation coordination. Nat Biotechnol 2024:10.1038/s41587-024-02135-0. [PMID: 38321115 PMCID: PMC11300707 DOI: 10.1038/s41587-024-02135-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 01/10/2024] [Indexed: 02/08/2024]
Abstract
N6-methyladenosine (m6A) and pseudouridine (Ψ) are the two most abundant modifications in mammalian messenger RNA, but the coordination of their biological functions remains poorly understood. We develop a machine learning-based nanopore direct RNA sequencing method (NanoSPA) that simultaneously analyzes m6A and Ψ in the human transcriptome. Applying NanoSPA to polysome profiling, we reveal opposing transcriptomic co-occurrence of m6A and Ψ and synergistic, hierarchical effects of m6A and Ψ on the polysome.
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Affiliation(s)
- Sihao Huang
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Adam C Wylder
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, USA
| | - Tao Pan
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, IL, USA.
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26
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Zhang D, Gao Y, Zhu L, Wang Y, Li P. Advances and opportunities in methods to study protein translation - A review. Int J Biol Macromol 2024; 259:129150. [PMID: 38171441 DOI: 10.1016/j.ijbiomac.2023.129150] [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: 08/02/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 01/05/2024]
Abstract
It is generally believed that the regulation of gene expression involves protein translation occurring before RNA transcription. Therefore, it is crucial to investigate protein translation and its regulation. Recent advancements in biological sciences, particularly in the field of omics, have revolutionized protein translation research. These studies not only help characterize changes in protein translation during specific biological or pathological processes but also have significant implications in disease prevention and treatment. In this review, we summarize the latest methods in ribosome-based translation omics. We specifically focus on the application of fluorescence imaging technology and omics technology in studying overall protein translation. Additionally, we analyze the advantages, disadvantages, and application of these experimental methods, aiming to provide valuable insights and references to researchers studying translation.
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Affiliation(s)
- Dejiu Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Yanyan Gao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Lei Zhu
- College of Basic Medical, Qingdao Binhai University, Qingdao, China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.
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27
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Zhang T, Xue Y, Su S, Altouma V, Ho K, Martindale JL, Lee SK, Shen W, Park A, Zhang Y, De S, Gorospe M, Wang W. RNA-binding protein Nocte regulates Drosophila development by promoting translation reinitiation on mRNAs with long upstream open reading frames. Nucleic Acids Res 2024; 52:885-905. [PMID: 38000373 PMCID: PMC10810208 DOI: 10.1093/nar/gkad1122] [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: 06/20/2023] [Revised: 10/18/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
RNA-binding proteins (RBPs) with intrinsically disordered regions (IDRs) are linked to multiple human disorders, but their mechanisms of action remain unclear. Here, we report that one such protein, Nocte, is essential for Drosophila eye development by regulating a critical gene expression cascade at translational level. Knockout of nocte in flies leads to lethality, and its eye-specific depletion impairs eye size and morphology. Nocte preferentially enhances translation of mRNAs with long upstream open reading frames (uORFs). One of the key Nocte targets, glass mRNA, encodes a transcription factor critical for differentiation of photoreceptor neurons and accessory cells, and re-expression of Glass largely rescued the eye defects caused by Nocte depletion. Mechanistically, Nocte counteracts long uORF-mediated translational suppression by promoting translation reinitiation downstream of the uORF. Nocte interacts with translation factors eIF3 and Rack1 through its BAT2 domain, and a Nocte mutant lacking this domain fails to promote translation of glass mRNA. Notably, de novo mutations of human orthologs of Nocte have been detected in schizophrenia patients. Our data suggest that Nocte family of proteins can promote translation reinitiation to overcome long uORFs-mediated translational suppression, and disruption of this function can lead to developmental defects and neurological disorders.
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Affiliation(s)
- Tianyi Zhang
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Yutong Xue
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Shuaikun Su
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Valerie Altouma
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Katherine Ho
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Jennifer L Martindale
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Seung-Kyu Lee
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Weiping Shen
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Aaron Park
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Yongqing Zhang
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Supriyo De
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Weidong Wang
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
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28
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Sonia J, Kanodia P, Lozier Z, Miller WA. Ribosome Profiling of Plants. Methods Mol Biol 2024; 2724:139-163. [PMID: 37987904 PMCID: PMC11158114 DOI: 10.1007/978-1-0716-3485-1_11] [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: 11/22/2023]
Abstract
Translation is a key step in control of gene expression, yet most analyses of global responses to a stimulus focus on transcription and the transcriptome. For RNA viruses in particular, which have no DNA-templated transcriptional control, control of viral and host translation is crucial. Here, we describe the method of ribosome profiling (ribo-seq) in plants, applied to virus infection. Ribo-seq is a deep sequencing technique that reveals the translatome by presenting a snapshot of the positions and relative amounts of translating ribosomes on all mRNAs in the cell. In contrast to RNA-seq, a crude cell extract is first digested with ribonuclease to degrade all mRNA not protected by a translating 80S ribosome. The resulting ribosome-protected fragments (RPFs) are deep sequenced. The number of reads mapping to a specific mRNA compared to the standard RNA-seq reads reveals the translational efficiency of that mRNA. Moreover, the precise positions of ribosome pause sites, previously unknown translatable open reading frames, and noncanonical translation events can be characterized quantitatively using ribo-seq. As this technique requires meticulous technique, here we present detailed step-by-step instructions for cell lysate preparation by flash freezing of samples, nuclease digestion of cell lysate, monosome collection by sucrose cushion ultracentrifugation, size-selective RNA extraction and rRNA depletion, library preparation for sequencing and finally quality control of sequenced data. These experimental methods apply to many plant systems, with minor nuclease digestion modifications depending on the plant tissue and species. This protocol should be valuable for studies of plant virus gene expression, and the global translational response to virus infection, or any other biotic or abiotic stress, by the host plant.
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Affiliation(s)
- Jahanara Sonia
- Plant Pathology, Entomology & Microbiology Department, Iowa State University, Ames, IA, USA
- Molecular, Cellular & Developmental Biology, Iowa State University, Ames, IA, USA
| | - Pulkit Kanodia
- Plant Pathology, Entomology & Microbiology Department, Iowa State University, Ames, IA, USA
- Interdepartmental Genetics & Genomics, Iowa State University, Ames, IA, USA
- , Santa Clara, CA, USA
| | - Zachary Lozier
- Plant Pathology, Entomology & Microbiology Department, Iowa State University, Ames, IA, USA
- Bioinformatics & Computational Biology, Iowa State University, Ames, IA, USA
| | - W Allen Miller
- Plant Pathology, Entomology & Microbiology Department, Iowa State University, Ames, IA, USA.
- Molecular, Cellular & Developmental Biology, Iowa State University, Ames, IA, USA.
- Interdepartmental Genetics & Genomics, Iowa State University, Ames, IA, USA.
- Bioinformatics & Computational Biology, Iowa State University, Ames, IA, USA.
- Biochemistry, Biophysics & Molecular Biology Department, Iowa State University, Ames, IA, USA.
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29
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Zhao C, Ding Y, Zhang Y, Chu M, Ning X, Ji J, Wang T, Zhang G, Yin S, Zhang K. Integrated analysis of transcriptome, translatome and proteome reveals insights into yellow catfish (Pelteobagrus fulvidraco) brain in response to hypoxia. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2024; 266:106801. [PMID: 38096642 DOI: 10.1016/j.aquatox.2023.106801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 11/11/2023] [Accepted: 12/10/2023] [Indexed: 01/02/2024]
Abstract
Brain plays a central role in adapting to environmental changes and is highly sensitive to the oxygen level. Although previous studies investigated the molecular response of brain exposure to acute hypoxia in fish, the lack of studies at the translational level hinders further understanding of the regulatory mechanism response to hypoxia from multi-omics levels. Yellow catfish (Pelteobagrus fulvidraco) is an important freshwater aquaculture species; however, hypoxia severely restricts the sustainable development of its breeding industry. In the present study, the transcriptome, translatome, and proteome were integrated to study the global landscapes of yellow catfish brain response to hypoxia. The evidently increased amount of cerebral cortical cells with oedema and pyknotic nuclei has been observed in hypoxia group of yellow catfish. A total of 2750 genes were significantly changed at the translational level. Comparative transcriptional and translational analysis suggested the HIF-1 signaling pathway, autophagy and glycolysis/gluconeogenesis were up-regulated after hypoxia exposure. KEGG enrichment of translational efficiency (TE) differential genes suggested that the lysosome and autophagy were highly enriched. Our result showed that yellow catfish tends to inhibit the TE of genes by increasing the translation of uORFs to adapt to hypoxia. Correlation analysis showed that transcriptome and translatome exhibit higher correlation. In summary, this study demonstrated that hypoxia dysregulated the cerebral function of yellow catfish at the transcriptome, translatome, and proteome, which provides a better understanding of hypoxia adaptation in teleost.
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Affiliation(s)
- Cheng Zhao
- College of Marine Science and Engineering, Nanjing Normal University, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing 210023, China; Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang 222005, Jiangsu, China
| | - Yubing Ding
- College of Marine Science and Engineering, Nanjing Normal University, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing 210023, China
| | - Yufei Zhang
- College of Marine Science and Engineering, Nanjing Normal University, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing 210023, China
| | - Mingxu Chu
- College of Marine Science and Engineering, Nanjing Normal University, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing 210023, China
| | - Xianhui Ning
- College of Marine Science and Engineering, Nanjing Normal University, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing 210023, China; Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang 222005, Jiangsu, China
| | - Jie Ji
- College of Marine Science and Engineering, Nanjing Normal University, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing 210023, China; Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang 222005, Jiangsu, China
| | - Tao Wang
- College of Marine Science and Engineering, Nanjing Normal University, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing 210023, China; Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang 222005, Jiangsu, China
| | - Guosong Zhang
- Key Laboratory for Physiology Biochemistry and Application, Heze University, Heze 274015, China
| | - Shaowu Yin
- College of Marine Science and Engineering, Nanjing Normal University, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing 210023, China; Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang 222005, Jiangsu, China
| | - Kai Zhang
- College of Marine Science and Engineering, Nanjing Normal University, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing 210023, China; Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang 222005, Jiangsu, China.
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30
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Karousis ED, Schubert K, Ban N. Coronavirus takeover of host cell translation and intracellular antiviral response: a molecular perspective. EMBO J 2024; 43:151-167. [PMID: 38200146 PMCID: PMC10897431 DOI: 10.1038/s44318-023-00019-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 11/01/2023] [Accepted: 11/24/2023] [Indexed: 01/12/2024] Open
Abstract
Coronaviruses are a group of related RNA viruses that cause respiratory diseases in humans and animals. Understanding the mechanisms of translation regulation during coronaviral infections is critical for developing antiviral therapies and preventing viral spread. Translation of the viral single-stranded RNA genome in the host cell cytoplasm is an essential step in the life cycle of coronaviruses, which affects the cellular mRNA translation landscape in many ways. Here we discuss various viral strategies of translation control, including how members of the Betacoronavirus genus shut down host cell translation and suppress host innate immune functions, as well as the role of the viral non-structural protein 1 (Nsp1) in the process. We also outline the fate of viral RNA, considering stress response mechanisms triggered in infected cells, and describe how unique viral RNA features contribute to programmed ribosomal -1 frameshifting, RNA editing, and translation shutdown evasion.
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Affiliation(s)
- Evangelos D Karousis
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Katharina Schubert
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland.
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Schumacher K, Gelhausen R, Kion-Crosby W, Barquist L, Backofen R, Jung K. Ribosome profiling reveals the fine-tuned response of Escherichia coli to mild and severe acid stress. mSystems 2023; 8:e0103723. [PMID: 37909716 PMCID: PMC10746267 DOI: 10.1128/msystems.01037-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Bacteria react very differently to survive in acidic environments, such as the human gastrointestinal tract. Escherichia coli is one of the extremely acid-resistant bacteria and has a variety of acid-defense mechanisms. Here, we provide the first genome-wide overview of the adaptations of E. coli K-12 to mild and severe acid stress at both the transcriptional and translational levels. Using ribosome profiling and RNA sequencing, we uncover novel adaptations to different degrees of acidity, including previously hidden stress-induced small proteins and novel key transcription factors for acid defense, and report mRNAs with pH-dependent differential translation efficiency. In addition, we distinguish between acid-specific adaptations and general stress response mechanisms using denoising autoencoders. This workflow represents a powerful approach that takes advantage of next-generation sequencing techniques and machine learning to systematically analyze bacterial stress responses.
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Affiliation(s)
- Kilian Schumacher
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Rick Gelhausen
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Willow Kion-Crosby
- Helmholtz Institute for RNA-based Infection Research (HIRI)/Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
- University of Würzburg, Faculty of Medicine, Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI)/Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
- University of Würzburg, Faculty of Medicine, Würzburg, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Kirsten Jung
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
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Jariyasakulroj S, Zhang W, Bai J, Zhang M, Lu Z, Chen JF. Ribosome biogenesis controls cranial suture MSC fate via the complement pathway in mouse and human iPSC models. Stem Cell Reports 2023; 18:2370-2385. [PMID: 37977145 PMCID: PMC10724072 DOI: 10.1016/j.stemcr.2023.10.015] [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: 04/10/2023] [Revised: 10/22/2023] [Accepted: 10/23/2023] [Indexed: 11/19/2023] Open
Abstract
Disruption of global ribosome biogenesis selectively affects craniofacial tissues with unclear mechanisms. Craniosynostosis is a congenital craniofacial disorder characterized by premature fusion of cranial suture(s) with loss of suture mesenchymal stem cells (MSCs). Here we focused on ribosomopathy disease gene Snord118, which encodes a small nucleolar RNA (snoRNA), to genetically disturb ribosome biogenesis in suture MSCs using mouse and human induced pluripotent stem cell (iPSC) models. Snord118 depletion exhibited p53 activation, increased cell death, reduced proliferation, and premature osteogenic differentiation of MSCs, leading to suture growth and craniosynostosis defects. Mechanistically, Snord118 deficiency causes translational dysregulation of ribosomal proteins and downregulation of complement pathway genes. Further complement pathway disruption by knockout of complement C3a receptor 1 (C3ar1) exacerbated MSC and suture defects in mutant mice, whereas activating the complement pathway rescued MSC cell fate and suture growth defects. Thus, ribosome biogenesis controls MSC fate via the complement pathway to prevent craniosynostosis.
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Affiliation(s)
- Supawadee Jariyasakulroj
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA; Department of Masticatory Science, Faculty of Dentistry, Mahidol University, Bangkok 10400, Thailand
| | - Wei Zhang
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
| | - Jianhui Bai
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Minjie Zhang
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Zhipeng Lu
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Jian-Fu Chen
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA.
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Borteçen T, Müller T, Krijgsveld J. An integrated workflow for quantitative analysis of the newly synthesized proteome. Nat Commun 2023; 14:8237. [PMID: 38086798 PMCID: PMC10716174 DOI: 10.1038/s41467-023-43919-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
The analysis of proteins that are newly synthesized upon a cellular perturbation can provide detailed insight into the proteomic response that is elicited by specific cues. This can be investigated by pulse-labeling of cells with clickable and stable-isotope-coded amino acids for the enrichment and mass spectrometric characterization of newly synthesized proteins (NSPs), however convoluted protocols prohibit their routine application. Here we report the optimization of multiple steps in sample preparation, mass spectrometry and data analysis, and we integrate them into a semi-automated workflow for the quantitative analysis of the newly synthesized proteome (QuaNPA). Reduced input requirements and data-independent acquisition (DIA) enable the analysis of triple-SILAC-labeled NSP samples, with enhanced throughput while featuring high quantitative accuracy. We apply QuaNPA to investigate the time-resolved cellular response to interferon-gamma (IFNg), observing rapid induction of targets 2 h after IFNg treatment. QuaNPA provides a powerful approach for large-scale investigation of NSPs to gain insight into complex cellular processes.
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Affiliation(s)
- Toman Borteçen
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, Heidelberg, Germany
- Heidelberg University, Faculty of Biosciences, Im Neuenheimer Feld 581, Heidelberg, Germany
| | - Torsten Müller
- Heidelberg University, Medical Faculty, Im Neuenheimer Feld 581, Heidelberg, Germany
| | - Jeroen Krijgsveld
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, Heidelberg, Germany.
- Heidelberg University, Medical Faculty, Im Neuenheimer Feld 581, Heidelberg, Germany.
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Deng J, Xu W, Jie Y, Chong Y. Subcellular localization and relevant mechanisms of human cancer-related micropeptides. FASEB J 2023; 37:e23270. [PMID: 37994683 DOI: 10.1096/fj.202301019rr] [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: 05/21/2023] [Revised: 09/17/2023] [Accepted: 10/10/2023] [Indexed: 11/24/2023]
Abstract
Rapid advances in high-quality sequencing and bioinformatics have invalidated the argument that noncoding RNAs (ncRNAs) are junk transcripts that do not encode proteins. Increasing evidence suggests that small open reading frames (sORFs) in ncRNAs can encode micropeptides and polypeptides within 100 amino acids in length. Several micropeptides have been characterized and proven to have various functions in human physiology and pathology, particularly in cancer. The present review mainly highlights the latest studies on ncRNA-encoded micropeptides in different cancers and categorizes them based on their subcellular localization, thereby providing a theoretical basis for micropeptide applications in the early diagnosis and prognosis of cancer and as therapeutic targets. However, considering the inherent characteristics of micropeptides and the limitations of the assay technology methods, more detailed information is warranted.
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Affiliation(s)
- Jing Deng
- Department of Infectious Diseases, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wenli Xu
- Department of Infectious Diseases, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yusheng Jie
- Department of Infectious Diseases, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yutian Chong
- Department of Infectious Diseases, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
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Bravo‐Estupiñan DM, Aguilar‐Guerrero K, Quirós S, Acón M, Marín‐Müller C, Ibáñez‐Hernández M, Mora‐Rodríguez RA. Gene dosage compensation: Origins, criteria to identify compensated genes, and mechanisms including sensor loops as an emerging systems-level property in cancer. Cancer Med 2023; 12:22130-22155. [PMID: 37987212 PMCID: PMC10757140 DOI: 10.1002/cam4.6719] [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: 04/24/2023] [Revised: 10/31/2023] [Accepted: 11/07/2023] [Indexed: 11/22/2023] Open
Abstract
The gene dosage compensation hypothesis presents a mechanism through which the expression of certain genes is modulated to compensate for differences in the dose of genes when additional chromosomes are present. It is one of the means through which cancer cells actively cope with the potential damaging effects of aneuploidy, a hallmark of most cancers. Dosage compensation arises through several processes, including downregulation or overexpression of specific genes and the relocation of dosage-sensitive genes. In cancer, a majority of compensated genes are generally thought to be regulated at the translational or post-translational level, and include the basic components of a compensation loop, including sensors of gene dosage and modulators of gene expression. Post-translational regulation is mostly undertaken by a general degradation or aggregation of remaining protein subunits of macromolecular complexes. An increasingly important role has also been observed for transcriptional level regulation. This article reviews the process of targeted gene dosage compensation in cancer and other biological conditions, along with the mechanisms by which cells regulate specific genes to restore cellular homeostasis. These mechanisms represent potential targets for the inhibition of dosage compensation of specific genes in aneuploid cancers. This article critically examines the process of targeted gene dosage compensation in cancer and other biological contexts, alongside the criteria for identifying genes subject to dosage compensation and the intricate mechanisms by which cells orchestrate the regulation of specific genes to reinstate cellular homeostasis. Ultimately, our aim is to gain a comprehensive understanding of the intricate nature of a systems-level property. This property hinges upon the kinetic parameters of regulatory motifs, which we have termed "gene dosage sensor loops." These loops have the potential to operate at both the transcriptional and translational levels, thus emerging as promising candidates for the inhibition of dosage compensation in specific genes. Additionally, they represent novel and highly specific therapeutic targets in the context of aneuploid cancer.
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Affiliation(s)
- Diana M. Bravo‐Estupiñan
- CICICA, Centro de Investigación en Cirugía y Cáncer Research Center on Surgery and CancerUniversidad de Costa RicaSan JoséCosta Rica
- Programa de Doctorado en Ciencias, Sistema de Estudios de Posgrado (SEP)Universidad de Costa RicaSan JoséCosta Rica
- Laboratorio de Terapia Génica, Departamento de BioquímicaEscuela Nacional de Ciencias Biológicas del Instituto Politécnico NacionalCiudad de MéxicoMexico
- Speratum Biopharma, Inc.Centro Nacional de Innovación Biotecnológica Nacional (CENIBiot)San JoséCosta Rica
| | - Karol Aguilar‐Guerrero
- CICICA, Centro de Investigación en Cirugía y Cáncer Research Center on Surgery and CancerUniversidad de Costa RicaSan JoséCosta Rica
- Maestría académica en Microbiología, Programa de Posgrado en Microbiología, Parasitología, Química Clínica e InmunologíaUniversidad de Costa RicaSan JoséCosta Rica
| | - Steve Quirós
- CICICA, Centro de Investigación en Cirugía y Cáncer Research Center on Surgery and CancerUniversidad de Costa RicaSan JoséCosta Rica
- Laboratorio de Quimiosensibilidad tumoral (LQT), Centro de Investigación en enfermedades Tropicales (CIET), Facultad de MicrobiologíaUniversidad de Costa RicaSan JoséCosta Rica
| | - Man‐Sai Acón
- CICICA, Centro de Investigación en Cirugía y Cáncer Research Center on Surgery and CancerUniversidad de Costa RicaSan JoséCosta Rica
| | - Christian Marín‐Müller
- Speratum Biopharma, Inc.Centro Nacional de Innovación Biotecnológica Nacional (CENIBiot)San JoséCosta Rica
| | - Miguel Ibáñez‐Hernández
- Laboratorio de Terapia Génica, Departamento de BioquímicaEscuela Nacional de Ciencias Biológicas del Instituto Politécnico NacionalCiudad de MéxicoMexico
| | - Rodrigo A. Mora‐Rodríguez
- CICICA, Centro de Investigación en Cirugía y Cáncer Research Center on Surgery and CancerUniversidad de Costa RicaSan JoséCosta Rica
- Laboratorio de Quimiosensibilidad tumoral (LQT), Centro de Investigación en enfermedades Tropicales (CIET), Facultad de MicrobiologíaUniversidad de Costa RicaSan JoséCosta Rica
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Meydan S, Barros GC, Simões V, Harley L, Cizubu BK, Guydosh NR, Silva GM. The ubiquitin conjugase Rad6 mediates ribosome pausing during oxidative stress. Cell Rep 2023; 42:113359. [PMID: 37917585 PMCID: PMC10755677 DOI: 10.1016/j.celrep.2023.113359] [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: 03/16/2023] [Revised: 07/26/2023] [Accepted: 10/13/2023] [Indexed: 11/04/2023] Open
Abstract
Oxidative stress causes K63-linked ubiquitination of ribosomes by the E2 ubiquitin conjugase Rad6. How Rad6-mediated ubiquitination of ribosomes affects translation, however, is unclear. We therefore perform Ribo-seq and Disome-seq in Saccharomyces cerevisiae and show that oxidative stress causes ribosome pausing at specific amino acid motifs, which also leads to ribosome collisions. However, these redox-pausing signatures are lost in the absence of Rad6 and do not depend on the ribosome-associated quality control (RQC) pathway. We also show that Rad6 is needed to inhibit overall translation in response to oxidative stress and that its deletion leads to increased expression of antioxidant genes. Finally, we observe that the lack of Rad6 leads to changes during translation that affect activation of the integrated stress response (ISR) pathway. Our results provide a high-resolution picture of the gene expression changes during oxidative stress and unravel an additional stress response pathway affecting translation elongation.
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Affiliation(s)
- Sezen Meydan
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Postdoctoral Research Associate Training Fellowship, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, MD 20982, USA
| | | | - Vanessa Simões
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Lana Harley
- Department of Biology, Duke University, Durham, NC 27708, USA
| | | | - Nicholas R Guydosh
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Gustavo M Silva
- Department of Biology, Duke University, Durham, NC 27708, USA.
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37
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Bishop DJ, Hoffman NJ, Taylor DF, Saner NJ, Lee MJC, Hawley JA. Discordant skeletal muscle gene and protein responses to exercise. Trends Biochem Sci 2023; 48:927-936. [PMID: 37709636 DOI: 10.1016/j.tibs.2023.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 08/07/2023] [Accepted: 08/16/2023] [Indexed: 09/16/2023]
Abstract
The ability of skeletal muscle to adapt to repeated contractile stimuli is one of the most intriguing aspects of physiology. The molecular bases underpinning these adaptations involve increased protein activity and/or expression, mediated by an array of pre- and post-transcriptional processes, as well as translational and post-translational control. A longstanding dogma assumes a direct relationship between exercise-induced increases in mRNA levels and subsequent changes in the abundance of the proteins they encode. Drawing on the results of recent studies, we dissect and question the common assumption of a direct relationship between changes in the skeletal muscle transcriptome and proteome induced by repeated muscle contractions (e.g., exercise).
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Affiliation(s)
- David J Bishop
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, Australia.
| | - Nolan J Hoffman
- Exercise and Nutrition Research Program, Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, Australia
| | - Dale F Taylor
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, Australia
| | - Nicholas J Saner
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, Australia
| | - Matthew J-C Lee
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, Australia
| | - John A Hawley
- Exercise and Nutrition Research Program, Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, Australia
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38
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Brantl S, Ul Haq I. Small proteins in Gram-positive bacteria. FEMS Microbiol Rev 2023; 47:fuad064. [PMID: 38052429 PMCID: PMC10730256 DOI: 10.1093/femsre/fuad064] [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: 10/25/2023] [Revised: 11/27/2023] [Accepted: 12/04/2023] [Indexed: 12/07/2023] Open
Abstract
Small proteins comprising less than 100 amino acids have been often ignored in bacterial genome annotations. About 10 years ago, focused efforts started to investigate whole peptidomes, which resulted in the discovery of a multitude of small proteins, but only a number of them have been characterized in detail. Generally, small proteins can be either membrane or cytosolic proteins. The latter interact with larger proteins, RNA or even metal ions. Here, we summarize our current knowledge on small proteins from Gram-positive bacteria with a special emphasis on the model organism Bacillus subtilis. Our examples include membrane-bound toxins of type I toxin-antitoxin systems, proteins that block the assembly of higher order structures, regulate sporulation or modulate the RNA degradosome. We do not consider antimicrobial peptides. Furthermore, we present methods for the identification and investigation of small proteins.
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Affiliation(s)
- Sabine Brantl
- AG Bakteriengenetik, Matthias-Schleiden-Institut, Friedrich-Schiller-Universität Jena, Philosophenweg 12, Jena D-07743, Germany
| | - Inam Ul Haq
- AG Bakteriengenetik, Matthias-Schleiden-Institut, Friedrich-Schiller-Universität Jena, Philosophenweg 12, Jena D-07743, Germany
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39
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Wang L, Cui X, Jiang F, Hu Y, Wan W, Li G, Lin Y, Xiao J. Circular RNA Translation in Cardiovascular Diseases. Curr Genomics 2023; 24:66-71. [PMID: 37994328 PMCID: PMC10662380 DOI: 10.2174/1389202924666230911121358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 06/08/2023] [Accepted: 08/09/2023] [Indexed: 11/24/2023] Open
Abstract
Circular RNAs (circRNAs) are a class of endogenous functional RNA generated by back-splicing. Recently, circRNAs have been found to have certain coding potential. Proteins/peptides translated from circRNAs play essential roles in various diseases. Here, we briefly summarize the basic knowledge and technologies that are usually applied to study circRNA translation. Then, we focus on the research progress of circRNA translation in cardiovascular diseases and discuss the perspective and future direction of translatable circRNA study in cardiovascular diseases.
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Affiliation(s)
- Lijun Wang
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong, 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai, 200444, China
| | - Xinxin Cui
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong, 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai, 200444, China
| | - Fei Jiang
- Department of Nursing, Union Hospital, Fujian Medical University Union Hospital, Fuzhou, 350001, China
- Fujian Provincial Special Reserve Talents Laboratory, Fujian Medical University Union Hospital, Fuzhou, 350001, China
| | - Yuxue Hu
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong, 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai, 200444, China
| | - Wensi Wan
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong, 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai, 200444, China
| | - Guoping Li
- Cardiovascular Division of the Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Yanjuan Lin
- Department of Nursing, Union Hospital, Fujian Medical University Union Hospital, Fuzhou, 350001, China
- Fujian Provincial Special Reserve Talents Laboratory, Fujian Medical University Union Hospital, Fuzhou, 350001, China
| | - Junjie Xiao
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong, 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai, 200444, China
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Aksoylu IS, Martin P, Robert F, Szkop KJ, Redmond NE, Bhattacharyya S, Wang J, Chen S, Beauchamp RL, Nobeli I, Pelletier J, Larsson O, Ramesh V. Translatome analysis of tuberous sclerosis complex 1 patient-derived neural progenitor cells reveals rapamycin-dependent and independent alterations. Mol Autism 2023; 14:39. [PMID: 37880800 PMCID: PMC10601155 DOI: 10.1186/s13229-023-00572-3] [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: 05/16/2023] [Accepted: 10/13/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND Tuberous sclerosis complex (TSC) is an inherited neurocutaneous disorder caused by mutations in the TSC1 or TSC2 genes, with patients often exhibiting neurodevelopmental (ND) manifestations termed TSC-associated neuropsychiatric disorders (TAND) including autism spectrum disorder (ASD) and intellectual disability. Hamartin (TSC1) and tuberin (TSC2) proteins form a complex inhibiting mechanistic target of rapamycin complex 1 (mTORC1) signaling. Loss of TSC1 or TSC2 activates mTORC1 that, among several targets, controls protein synthesis by inhibiting translational repressor eIF4E-binding proteins. Using TSC1 patient-derived neural progenitor cells (NPCs), we recently reported early ND phenotypic changes, including increased cell proliferation and altered neurite outgrowth in TSC1-null NPCs, which were unaffected by the mTORC1 inhibitor rapamycin. METHODS Here, we used polysome profiling, which quantifies changes in mRNA abundance and translational efficiencies at a transcriptome-wide level, to compare CRISPR-edited TSC1-null with CRISPR-corrected TSC1-WT NPCs generated from one TSC donor (one clone/genotype). To assess the relevance of identified gene expression alterations, we performed polysome profiling in postmortem brains from ASD donors and age-matched controls. We further compared effects on translation of a subset of transcripts and rescue of early ND phenotypes in NPCs following inhibition of mTORC1 using the allosteric inhibitor rapamycin versus a third-generation bi-steric, mTORC1-selective inhibitor RMC-6272. RESULTS Polysome profiling of NPCs revealed numerous TSC1-associated alterations in mRNA translation that were largely recapitulated in human ASD brains. Moreover, although rapamycin treatment partially reversed the TSC1-associated alterations in mRNA translation, most genes related to neural activity/synaptic regulation or ASD were rapamycin-insensitive. In contrast, treatment with RMC-6272 inhibited rapamycin-insensitive translation and reversed TSC1-associated early ND phenotypes including proliferation and neurite outgrowth that were unaffected by rapamycin. CONCLUSIONS Our work reveals ample mRNA translation alterations in TSC1 patient-derived NPCs that recapitulate mRNA translation in ASD brain samples. Further, suppression of TSC1-associated but rapamycin-insensitive translation and ND phenotypes by RMC-6272 unveils potential implications for more efficient targeting of mTORC1 as a superior treatment strategy for TAND.
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Affiliation(s)
- Inci S Aksoylu
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, 171 77, Stockholm, Sweden
| | - Pauline Martin
- Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA
| | - Francis Robert
- Department of Biochemistry and Goodman Cancer Research Institute, McGill University, Montreal, PQ, H3G1Y6, Canada
| | - Krzysztof J Szkop
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, 171 77, Stockholm, Sweden
| | - Nicholas E Redmond
- Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA
| | - Srirupa Bhattacharyya
- Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA
| | - Jennifer Wang
- Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA
| | - Shan Chen
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, 171 77, Stockholm, Sweden
| | - Roberta L Beauchamp
- Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA
| | - Irene Nobeli
- Institute of Structural and Molecular Biology, Department of Biological Sciences,, Birkbeck, University of London, London, WC1E 7HX, UK
| | - Jerry Pelletier
- Department of Biochemistry and Goodman Cancer Research Institute, McGill University, Montreal, PQ, H3G1Y6, Canada
| | - Ola Larsson
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, 171 77, Stockholm, Sweden.
| | - Vijaya Ramesh
- Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA.
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Schumacher K, Brameyer S, Jung K. Bacterial acid stress response: from cellular changes to antibiotic tolerance and phenotypic heterogeneity. Curr Opin Microbiol 2023; 75:102367. [PMID: 37633223 DOI: 10.1016/j.mib.2023.102367] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/28/2023]
Abstract
Most bacteria are neutralophiles but can survive fluctuations in pH in their environment. Herein, we provide an overview of the adaptation of several human, soil, and food bacteria to acid stress, mainly based on next-generation sequencing studies, highlighting common and specific strategies. We also discuss the interplay between acid stress response and antibiotic tolerance, as well as the response of individual cells.
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Affiliation(s)
- Kilian Schumacher
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Sophie Brameyer
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Kirsten Jung
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany.
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42
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Rahaman S, Faravelli S, Voegeli S, Becskei A. Polysome propensity and tunable thresholds in coding sequence length enable differential mRNA stability. SCIENCE ADVANCES 2023; 9:eadh9545. [PMID: 37756413 PMCID: PMC10530222 DOI: 10.1126/sciadv.adh9545] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023]
Abstract
The half-life of mRNAs, as well as their translation, increases in proportion to the optimal codons, indicating a tight coupling of codon-dependent differential translation and degradation. Little is known about the regulation of this coupling. We found that the mRNA stability gain in yeast depends on the mRNA coding sequence length. Below a critical length, codon optimality fails to affect the stability of mRNAs although they can be efficiently translated into short peptides and proteins. Above this threshold length, codon optimality-dependent differential mRNA stability emerges in a switch-like fashion, which coincides with a similar increase in the polysome propensity of the mRNAs. This threshold length can be tuned by the untranslated regions (UTR). Some of these UTRs can destabilize mRNAs without reducing translation, which plays a role in controlling the amplitude of the oscillatory expression of cell cycle genes. Our findings help understand the translation of short peptides from noncoding RNAs and the translation by localized monosomes in neurons.
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Affiliation(s)
- Sayanur Rahaman
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
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43
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Weingarten-Gabbay S, Bauer MR, Stanton AC, Klaeger S, Verzani EK, López D, Clauser KR, Carr SA, Abelin JG, Rice CM, Sabeti PC. Pan-viral ORFs discovery using Massively Parallel Ribosome Profiling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.26.559641. [PMID: 37808651 PMCID: PMC10557741 DOI: 10.1101/2023.09.26.559641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Unveiling the complete proteome of viruses is crucial to our understanding of the viral life cycle and interaction with the host. We developed Massively Parallel Ribosome Profiling (MPRP) to experimentally determine open reading frames (ORFs) in 20,170 designed oligonucleotides across 679 human-associated viral genomes. We identified 5,381 ORFs, including 4,208 non-canonical ORFs, and show successful detection of both annotated coding sequences (CDSs) and reported non-canonical ORFs. By examining immunopeptidome datasets of infected cells, we found class I human leukocyte antigen (HLA-I) peptides originating from non-canonical ORFs identified through MPRP. By inspecting ribosome occupancies on the 5'UTR and CDS regions of annotated viral genes, we identified hundreds of upstream ORFs (uORFs) that negatively regulate the synthesis of canonical viral proteins. The unprecedented source of viral ORFs across a wide range of viral families, including highly pathogenic viruses, expands the repertoire of vaccine targets and exposes new cis-regulatory sequences in viral genomes.
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44
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Davyt M, Bharti N, Ignatova Z. Effect of mRNA/tRNA mutations on translation speed: Implications for human diseases. J Biol Chem 2023; 299:105089. [PMID: 37495112 PMCID: PMC10470029 DOI: 10.1016/j.jbc.2023.105089] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 07/18/2023] [Accepted: 07/20/2023] [Indexed: 07/28/2023] Open
Abstract
Recent discoveries establish tRNAs as central regulators of mRNA translation dynamics, and therefore cotranslational folding and function of the encoded protein. The tRNA pool, whose composition and abundance change in a cell- and tissue-dependent manner, is the main factor which determines mRNA translation velocity. In this review, we discuss a group of pathogenic mutations, in the coding sequences of either protein-coding genes or in tRNA genes, that alter mRNA translation dynamics. We also summarize advances in tRNA biology that have uncovered how variations in tRNA levels on account of genetic mutations affect protein folding and function, and thereby contribute to phenotypic diversity in clinical manifestations.
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Affiliation(s)
- Marcos Davyt
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Nikhil Bharti
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Zoya Ignatova
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.
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45
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Holly J, Yewdell JW. Game of Omes: ribosome profiling expands the MHC-I immunopeptidome. Curr Opin Immunol 2023; 83:102342. [PMID: 37247567 PMCID: PMC10524008 DOI: 10.1016/j.coi.2023.102342] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/31/2023]
Abstract
Peptide ligands presented by cell-surface MHC class-I molecules enable T cells to eradicate intracellular pathogens and cancers. The presented peptide repertoire, the class-I immunopeptidome, is generated from each cell's translatome in a highly biased manner to avoid overrepresenting highly abundant translation products. The immunopeptidome can only be defined by mass spectrometry (MS). Here, we review recent advances in immunopeptidomics, focusing on using ribosome profiling as the optimal MS database to optimize the false- and failed-discovery rates and relate these findings to the contribution of defective ribosomal products and cellular quality control mechanisms to MHC class-I antigen processing and presentation.
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Affiliation(s)
- Jaroslav Holly
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jonathan W Yewdell
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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46
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Arakawa K, Hirose T, Inada T, Ito T, Kai T, Oyama M, Tomari Y, Yoda T, Nakagawa S. Nondomain biopolymers: Flexible molecular strategies to acquire biological functions. Genes Cells 2023; 28:539-552. [PMID: 37249032 PMCID: PMC11448004 DOI: 10.1111/gtc.13050] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/31/2023]
Abstract
A long-standing assumption in molecular biology posits that the conservation of protein and nucleic acid sequences emphasizes the functional significance of biomolecules. These conserved sequences fold into distinct secondary and tertiary structures, enable highly specific molecular interactions, and regulate complex yet organized molecular processes within living cells. However, recent evidence suggests that biomolecules can also function through primary sequence regions that lack conservation across species or gene families. These regions typically do not form rigid structures, and their inherent flexibility is critical for their functional roles. This review examines the emerging roles and molecular mechanisms of "nondomain biomolecules," whose functions are not easily predicted due to the absence of conserved functional domains. We propose the hypothesis that both domain- and nondomain-type molecules work together to enable flexible and efficient molecular processes within the highly crowded intracellular environment.
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Grants
- 21H05273 Ministry of Education, Culture, Sports, Science and Technology
- 21H05274 Ministry of Education, Culture, Sports, Science and Technology
- 21H05275 Ministry of Education, Culture, Sports, Science and Technology
- 21H05276 Ministry of Education, Culture, Sports, Science and Technology
- 21H05277 Ministry of Education, Culture, Sports, Science and Technology
- 21H05278 Ministry of Education, Culture, Sports, Science and Technology
- 21H05279 Ministry of Education, Culture, Sports, Science and Technology
- 21H05280 Ministry of Education, Culture, Sports, Science and Technology
- 21H05281 Ministry of Education, Culture, Sports, Science and Technology
- 21H05282 Ministry of Education, Culture, Sports, Science and Technology
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Affiliation(s)
- Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Tokyo, Japan
| | - Tetsuro Hirose
- RNA Biofunction Laboratory, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Toshifumi Inada
- Division of RNA and Gene Regulation, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Takuhiro Ito
- Laboratory for Translation Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Toshie Kai
- Germline Biology Laboratory, Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Masaaki Oyama
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yukihide Tomari
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Takao Yoda
- Nagahama Institute of Bio-Science and Technology, Nagahama, Japan
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
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47
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Meindl A, Romberger M, Lehmann G, Eichner N, Kleemann L, Wu J, Danner J, Boesl M, Mesitov M, Meister G, König J, Leidel S, Medenbach J. A rapid protocol for ribosome profiling of low input samples. Nucleic Acids Res 2023; 51:e68. [PMID: 37246712 PMCID: PMC10359457 DOI: 10.1093/nar/gkad459] [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: 10/28/2022] [Revised: 05/04/2023] [Accepted: 05/13/2023] [Indexed: 05/30/2023] Open
Abstract
Ribosome profiling provides quantitative, comprehensive, and high-resolution snapshots of cellular translation by the high-throughput sequencing of short mRNA fragments that are protected by ribosomes from nucleolytic digestion. While the overall principle is simple, the workflow of ribosome profiling experiments is complex and challenging, and typically requires large amounts of sample, limiting its broad applicability. Here, we present a new protocol for ultra-rapid ribosome profiling from low-input samples. It features a robust strategy for sequencing library preparation within one day that employs solid phase purification of reaction intermediates, allowing to reduce the input to as little as 0.1 pmol of ∼30 nt RNA fragments. Hence, it is particularly suited for the analyses of small samples or targeted ribosome profiling. Its high sensitivity and its ease of implementation will foster the generation of higher quality data from small samples, which opens new opportunities in applying ribosome profiling.
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Affiliation(s)
- Andreas Meindl
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Markus Romberger
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Gerhard Lehmann
- Biochemistry I, University of Regensburg, Regensburg, Germany
| | - Norbert Eichner
- Biochemistry I, University of Regensburg, Regensburg, Germany
| | - Leon Kleemann
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Jie Wu
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Johannes Danner
- Biochemistry I, University of Regensburg, Regensburg, Germany
| | - Maria Boesl
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | | | - Gunter Meister
- Biochemistry I, University of Regensburg, Regensburg, Germany
| | - Julian König
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Sebastian Andreas Leidel
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Jan Medenbach
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
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48
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Livingston NM, Kwon J, Valera O, Saba JA, Sinha NK, Reddy P, Nelson B, Wolfe C, Ha T, Green R, Liu J, Wu B. Bursting translation on single mRNAs in live cells. Mol Cell 2023; 83:2276-2289.e11. [PMID: 37329884 PMCID: PMC10330622 DOI: 10.1016/j.molcel.2023.05.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 03/27/2023] [Accepted: 05/14/2023] [Indexed: 06/19/2023]
Abstract
Stochasticity has emerged as a mechanism of gene regulation. Much of this so-called "noise" has been attributed to bursting transcription. Although bursting transcription has been studied extensively, the role of stochasticity in translation has not been fully investigated due to the lack of enabling imaging technology. In this study, we developed techniques to track single mRNAs and their translation in live cells for hours, allowing the measurement of previously uncharacterized translation dynamics. We applied genetic and pharmacological perturbations to control translation kinetics and found that, like transcription, translation is not a constitutive process but instead cycles between inactive and active states, or "bursts." However, unlike transcription, which is largely frequency-modulated, complex structures in the 5'-untranslated region alter burst amplitudes. Bursting frequency can be controlled through cap-proximal sequences and trans-acting factors such as eIF4F. We coupled single-molecule imaging with stochastic modeling to quantitatively determine the kinetic parameters of translational bursting.
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Affiliation(s)
- Nathan M Livingston
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jiwoong Kwon
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Oliver Valera
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - James A Saba
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Niladri K Sinha
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Pranav Reddy
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Blake Nelson
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Clara Wolfe
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Rachel Green
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Jian Liu
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Bin Wu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Solomon H Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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49
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Wang W, Wang Y, Chen T, Qin G, Tian S. Current insights into posttranscriptional regulation of fleshy fruit ripening. PLANT PHYSIOLOGY 2023; 192:1785-1798. [PMID: 36250906 PMCID: PMC10315313 DOI: 10.1093/plphys/kiac483] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/27/2022] [Indexed: 05/26/2023]
Abstract
Fruit ripening is a complicated process that is accompanied by the formation of fruit quality. It is not only regulated at the transcriptional level via transcription factors or DNA methylation but also fine-tuned after transcription occurs. Here, we review recent advances in our understanding of key regulatory mechanisms of fleshy fruit ripening after transcription. We mainly highlight the typical mechanisms by which fruit ripening is controlled, namely, alternative splicing, mRNA N6-methyladenosine RNA modification methylation, and noncoding RNAs at the posttranscriptional level; regulation of translation efficiency and upstream open reading frame-mediated translational repression at the translational level; and histone modifications, protein phosphorylation, and protein ubiquitination at the posttranslational level. Taken together, these posttranscriptional regulatory mechanisms, along with transcriptional regulation, constitute the molecular framework of fruit ripening. We also critically discuss the potential usage of some mechanisms to improve fruit traits.
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Affiliation(s)
- Weihao Wang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yuying Wang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Tong Chen
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Guozheng Qin
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Shiping Tian
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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50
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Fangma Y, Liu M, Liao J, Chen Z, Zheng Y. Dissecting the brain with spatially resolved multi-omics. J Pharm Anal 2023; 13:694-710. [PMID: 37577383 PMCID: PMC10422112 DOI: 10.1016/j.jpha.2023.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 08/15/2023] Open
Abstract
Recent studies have highlighted spatially resolved multi-omics technologies, including spatial genomics, transcriptomics, proteomics, and metabolomics, as powerful tools to decipher the spatial heterogeneity of the brain. Here, we focus on two major approaches in spatial transcriptomics (next-generation sequencing-based technologies and image-based technologies), and mass spectrometry imaging technologies used in spatial proteomics and spatial metabolomics. Furthermore, we discuss their applications in neuroscience, including building the brain atlas, uncovering gene expression patterns of neurons for special behaviors, deciphering the molecular basis of neuronal communication, and providing a more comprehensive explanation of the molecular mechanisms underlying central nervous system disorders. However, further efforts are still needed toward the integrative application of multi-omics technologies, including the real-time spatial multi-omics analysis in living cells, the detailed gene profile in a whole-brain view, and the combination of functional verification.
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Affiliation(s)
- Yijia Fangma
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Mengting Liu
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Jie Liao
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhong Chen
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Yanrong Zheng
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
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