1
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Vrbnjak K, Sewduth RN. Multi-Omic Approaches in Cancer-Related Micropeptide Identification. Proteomes 2024; 12:26. [PMID: 39311199 PMCID: PMC11417835 DOI: 10.3390/proteomes12030026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Revised: 09/02/2024] [Accepted: 09/11/2024] [Indexed: 09/26/2024] Open
Abstract
Despite the advances in modern cancer therapy, malignant diseases are still a leading cause of morbidity and mortality worldwide. Conventional treatment methods frequently lead to side effects and drug resistance in patients, highlighting the need for novel therapeutic approaches. Recent findings have identified the existence of non-canonical micropeptides, an additional layer of the proteome complexity, also called the microproteome. These small peptides are a promising class of therapeutic agents with the potential to address the limitations of current cancer treatments. The microproteome is encoded by regions of the genome historically annotated as non-coding, and its existence has been revealed thanks to recent advances in proteomic and bioinformatic technology, which dramatically improved the understanding of proteome complexity. Micropeptides have been shown to be biologically active in several cancer types, indicating their therapeutic role. Furthermore, they are characterized by low toxicity and high target specificity, demonstrating their potential for the development of better tolerated drugs. In this review, we survey the current landscape of known micropeptides with a role in cancer progression or treatment, discuss their potential as anticancer agents, and describe the methodological challenges facing the proteome field of research.
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Affiliation(s)
- Katarina Vrbnjak
- VIB-KU Leuven Center for Cancer Biology (VIB), 3000 Leuven, Belgium
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2
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Chakraborty N. Metabolites: a converging node of host and microbe to explain meta-organism. Front Microbiol 2024; 15:1337368. [PMID: 38505556 PMCID: PMC10949987 DOI: 10.3389/fmicb.2024.1337368] [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: 11/15/2023] [Accepted: 02/13/2024] [Indexed: 03/21/2024] Open
Abstract
Meta-organisms encompassing the host and resident microbiota play a significant role in combatting diseases and responding to stress. Hence, there is growing traction to build a knowledge base about this ecosystem, particularly to characterize the bidirectional relationship between the host and microbiota. In this context, metabolomics has emerged as the major converging node of this entire ecosystem. Systematic comprehension of this resourceful omics component can elucidate the organism-specific response trajectory and the communication grid across the ecosystem embodying meta-organisms. Translating this knowledge into designing nutraceuticals and next-generation therapy are ongoing. Its major hindrance is a significant knowledge gap about the underlying mechanisms maintaining a delicate balance within this ecosystem. To bridge this knowledge gap, a holistic picture of the available information has been presented with a primary focus on the microbiota-metabolite relationship dynamics. The central theme of this article is the gut-brain axis and the participating microbial metabolites that impact cerebral functions.
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Affiliation(s)
- Nabarun Chakraborty
- Medical Readiness Systems Biology, CMPN, WRAIR, Silver Spring, MD, United States
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3
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Provencher N, Leblanc S, Jacques JF, Roucou X. Exploring the Alternative Proteome with OpenProt and Mass Spectrometry. Methods Mol Biol 2024; 2836:3-17. [PMID: 38995532 DOI: 10.1007/978-1-0716-4007-4_1] [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] [Indexed: 07/13/2024]
Abstract
Proteogenomics has revealed the translation of unannotated open reading frames (ORFs) present in mRNAs and in noncoding RNAs (ncRNAs). OpenProt annotates all ORFs with a minimum of 30 codons in the transcriptome of several species and displays many functional features associated with the corresponding proteins. Two types of proteins are annotated: reference or canonical proteins which are proteins already annotated in UniProt, RefSeq, or Ensembl and noncanonical proteins. Noncanonical proteins form two groups: predicted novel isoforms that display a significant level of homology with a reference protein and alternative proteins that are new proteins with no significant homology to known proteins. This chapter describes how to check whether a gene and/or transcript contains multiple open reading frames and how to use OpenProt databases for the detection of alternative proteins and novel isoforms by mass spectrometry-based proteomics.
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Affiliation(s)
- Nicolas Provencher
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Sébastien Leblanc
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Jean-François Jacques
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Xavier Roucou
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, QC, Canada.
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CRCHUS), Sherbrooke, QC, Canada.
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4
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Chen Y, Su H, Zhao J, Na Z, Jiang K, Bacchiocchi A, Loh KH, Halaban R, Wang Z, Cao X, Slavoff SA. Unannotated microprotein EMBOW regulates the interactome and chromatin and mitotic functions of WDR5. Cell Rep 2023; 42:113145. [PMID: 37725512 PMCID: PMC10629662 DOI: 10.1016/j.celrep.2023.113145] [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: 11/15/2022] [Revised: 07/20/2023] [Accepted: 08/31/2023] [Indexed: 09/21/2023] Open
Abstract
The conserved WD40-repeat protein WDR5 interacts with multiple proteins both inside and outside the nucleus. However, it is currently unclear whether and how the distribution of WDR5 between complexes is regulated. Here, we show that an unannotated microprotein EMBOW (endogenous microprotein binder of WDR5) dually encoded in the human SCRIB gene interacts with WDR5 and regulates its binding to multiple interaction partners, including KMT2A and KIF2A. EMBOW is cell cycle regulated, with two expression maxima at late G1 phase and G2/M phase. Loss of EMBOW decreases WDR5 interaction with KIF2A, aberrantly shortens mitotic spindle length, prolongs G2/M phase, and delays cell proliferation. In contrast, loss of EMBOW increases WDR5 interaction with KMT2A, leading to WDR5 binding to off-target genes, erroneously increasing H3K4me3 levels, and activating transcription of these genes. Together, these results implicate EMBOW as a regulator of WDR5 that regulates its interactions and prevents its off-target binding in multiple contexts.
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Affiliation(s)
- Yanran Chen
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA; Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Brain Functional Genomics, Ministry of Education and Shanghai, School of Life Sciences, East China Normal University, Shanghai 200062, China
| | - Haomiao Su
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
| | - Jianing Zhao
- Frontier Innovation Center, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200433, China; Shanghai Fifth People's Hospital, Fudan University, Shanghai 200433, China
| | - Zhenkun Na
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
| | - Kevin Jiang
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
| | - Antonella Bacchiocchi
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Ken H Loh
- Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA; Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Ruth Halaban
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Zhentian Wang
- Frontier Innovation Center, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200433, China; Shanghai Fifth People's Hospital, Fudan University, Shanghai 200433, China
| | - Xiongwen Cao
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA; Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Brain Functional Genomics, Ministry of Education and Shanghai, School of Life Sciences, East China Normal University, Shanghai 200062, China.
| | - Sarah A Slavoff
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06529, USA.
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5
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Parmar BS, Kieswetter A, Geens E, Vandewyer E, Ludwig C, Temmerman L. azyx-1 is a new gene that overlaps with zyxin and affects its translation in C. elegans, impacting muscular integrity and locomotion. PLoS Biol 2023; 21:e3002300. [PMID: 37713439 PMCID: PMC10575671 DOI: 10.1371/journal.pbio.3002300] [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: 09/12/2022] [Revised: 10/13/2023] [Accepted: 08/16/2023] [Indexed: 09/17/2023] Open
Abstract
Overlapping genes are widely prevalent; however, their expression and consequences are poorly understood. Here, we describe and functionally characterize a novel zyx-1 overlapping gene, azyx-1, with distinct regulatory functions in Caenorhabditis elegans. We observed conservation of alternative open reading frames (ORFs) overlapping the 5' region of zyxin family members in several animal species, and find shared sites of azyx-1 and zyxin proteoform expression in C. elegans. In line with a standard ribosome scanning model, our results support cis regulation of zyx-1 long isoform(s) by upstream initiating azyx-1a. Moreover, we report on a rare observation of trans regulation of zyx-1 by azyx-1, with evidence of increased ZYX-1 upon azyx-1 overexpression. Our results suggest a dual role for azyx-1 in influencing zyx-1 proteoform heterogeneity and highlight its impact on C. elegans muscular integrity and locomotion.
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Affiliation(s)
- Bhavesh S. Parmar
- Animal Physiology and Neurobiology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Amanda Kieswetter
- Animal Physiology and Neurobiology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Ellen Geens
- Animal Physiology and Neurobiology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Elke Vandewyer
- Animal Physiology and Neurobiology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technische Universität München, München, Germany
| | - Liesbet Temmerman
- Animal Physiology and Neurobiology, University of Leuven (KU Leuven), Leuven, Belgium
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6
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Capuz A, Osien S, Cardon T, Karnoub MA, Aboulouard S, Raffo-Romero A, Duhamel M, Cizkova D, Trerotola M, Devos D, Kobeissy F, Vanden Abeele F, Bonnefond A, Fournier I, Rodet F, Salzet M. Heimdall, an alternative protein issued from a ncRNA related to kappa light chain variable region of immunoglobulins from astrocytes: a new player in neural proteome. Cell Death Dis 2023; 14:526. [PMID: 37587118 PMCID: PMC10432539 DOI: 10.1038/s41419-023-06037-y] [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: 01/04/2023] [Revised: 07/27/2023] [Accepted: 08/02/2023] [Indexed: 08/18/2023]
Abstract
The dogma "One gene, one protein" is clearly obsolete since cells use alternative splicing and generate multiple transcripts which are translated into protein isoforms, but also use alternative translation initiation sites (TISs) and termination sites on a given transcript. Alternative open reading frames for individual transcripts give proteins originate from the 5'- and 3'-UTR mRNA regions, frameshifts of mRNA ORFs or from non-coding RNAs. Longtime considered as non-coding, recent in-silico translation prediction methods enriched the protein databases allowing the identification of new target structures that have not been identified previously. To gain insight into the role of these newly identified alternative proteins in the regulation of cellular functions, it is crucial to assess their dynamic modulation within a framework of altered physiological modifications such as experimental spinal cord injury (SCI). Here, we carried out a longitudinal proteomic study on rat SCI from 12 h to 10 days. Based on the alternative protein predictions, it was possible to identify a plethora of newly predicted protein hits. Among these proteins, some presented a special interest due to high homology with variable chain regions of immunoglobulins. We focus our interest on the one related to Kappa variable light chains which is similarly highly produced by B cells in the Bence jones disease, but here expressed in astrocytes. This protein, name Heimdall is an Intrinsically disordered protein which is secreted under inflammatory conditions. Immunoprecipitation experiments showed that the Heimdall interactome contained proteins related to astrocyte fate keepers such as "NOTCH1, EPHA3, IPO13" as well as membrane receptor protein including "CHRNA9; TGFBR, EPHB6, and TRAM". However, when Heimdall protein was neutralized utilizing a specific antibody or its gene knocked out by CRISPR-Cas9, sprouting elongations were observed in the corresponding astrocytes. Interestingly, depolarization assays and intracellular calcium measurements in Heimdall KO, established a depolarization effect on astrocyte membranes KO cells were more likely that the one found in neuroprogenitors. Proteomic analyses performed under injury conditions or under lipopolysaccharides (LPS) stimulation, revealed the expression of neuronal factors, stem cell proteins, proliferation, and neurogenesis of astrocyte convertor factors such as EPHA4, NOTCH2, SLIT3, SEMA3F, suggesting a role of Heimdall could regulate astrocytic fate. Taken together, Heimdall could be a novel member of the gatekeeping astrocyte-to-neuroprogenitor conversion factors.
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Affiliation(s)
- Alice Capuz
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France
| | - Sylvain Osien
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France
| | - Tristan Cardon
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France
| | - Mélodie Anne Karnoub
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France
| | - Soulaimane Aboulouard
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France
| | - Antonella Raffo-Romero
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France
| | - Marie Duhamel
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France
| | - Dasa Cizkova
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dúbravská cesta 9, 845 10, Bratislava, Slovakia
- Centre for Experimental and Clinical Regenerative Medicine, University of Veterinary Medicine and Pharmacy in Kosice, Kosice, Slovakia
| | - Marco Trerotola
- Laboratory of Cancer Pathology, Center for Advanced Studies and Technology (CAST), University 'G. d'Annunzio', Chieti, Italy
- Department of Medical, Oral and Biotechnological Sciences, University 'G. d'Annunzio', Chieti, Italy
| | - David Devos
- Université de Lille, INSERM, U1172, CHU-Lille, Lille Neuroscience Cognition Research Centre, 1 place de Verdun, 59000, Lille, France
| | - Firas Kobeissy
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Fabien Vanden Abeele
- Université de Lille, INSERM U1003, Laboratory of Cell Physiology, 59650, Villeneuve d'Ascq, France
| | - Amélie Bonnefond
- Univ. Lille, Inserm UMR1283, CNRS UMR8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, CHU de Lille, 1 place de Verdun, 59000, Lille, France
| | - Isabelle Fournier
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France
- Institut Universitaire de France, 75005, Paris, France
| | - Franck Rodet
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France.
| | - Michel Salzet
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France.
- Institut Universitaire de France, 75005, Paris, France.
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7
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Jeffery CJ. Current successes and remaining challenges in protein function prediction. FRONTIERS IN BIOINFORMATICS 2023; 3:1222182. [PMID: 37576715 PMCID: PMC10415035 DOI: 10.3389/fbinf.2023.1222182] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 07/03/2023] [Indexed: 08/15/2023] Open
Abstract
In recent years, improvements in protein function prediction methods have led to increased success in annotating protein sequences. However, the functions of over 30% of protein-coding genes remain unknown for many sequenced genomes. Protein functions vary widely, from catalyzing chemical reactions to binding DNA or RNA or forming structures in the cell, and some types of functions are challenging to predict due to the physical features associated with those functions. Other complications in understanding protein functions arise due to the fact that many proteins have more than one function or very small differences in sequence or structure that correspond to different functions. We will discuss some of the recent developments in predicting protein functions and some of the remaining challenges.
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Affiliation(s)
- Constance J. Jeffery
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States
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8
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Leblanc S, Brunet MA, Jacques JF, Lekehal AM, Duclos A, Tremblay A, Bruggeman-Gascon A, Samandi S, Brunelle M, Cohen AA, Scott MS, Roucou X. Newfound Coding Potential of Transcripts Unveils Missing Members of Human Protein Communities. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:515-534. [PMID: 36183975 PMCID: PMC10787177 DOI: 10.1016/j.gpb.2022.09.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/10/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Recent proteogenomic approaches have led to the discovery that regions of the transcriptome previously annotated as non-coding regions [i.e., untranslated regions (UTRs), open reading frames overlapping annotated coding sequences in a different reading frame, and non-coding RNAs] frequently encode proteins, termed alternative proteins (altProts). This suggests that previously identified protein-protein interaction (PPI) networks are partially incomplete because altProts are not present in conventional protein databases. Here, we used the proteogenomic resource OpenProt and a combined spectrum- and peptide-centric analysis for the re-analysis of a high-throughput human network proteomics dataset, thereby revealing the presence of 261 altProts in the network. We found 19 genes encoding both an annotated (reference) and an alternative protein interacting with each other. Of the 117 altProts encoded by pseudogenes, 38 are direct interactors of reference proteins encoded by their respective parental genes. Finally, we experimentally validate several interactions involving altProts. These data improve the blueprints of the human PPI network and suggest functional roles for hundreds of altProts.
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Affiliation(s)
- Sébastien Leblanc
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada; PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Quebec City, QC G1V 0A6, Canada
| | - Marie A Brunet
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada; PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Quebec City, QC G1V 0A6, Canada
| | - Jean-François Jacques
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada; PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Quebec City, QC G1V 0A6, Canada
| | - Amina M Lekehal
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada; PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Quebec City, QC G1V 0A6, Canada
| | - Andréa Duclos
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Alexia Tremblay
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Alexis Bruggeman-Gascon
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Sondos Samandi
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada; PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Quebec City, QC G1V 0A6, Canada
| | - Mylène Brunelle
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada; PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Quebec City, QC G1V 0A6, Canada
| | - Alan A Cohen
- Department of Family Medicine, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Michelle S Scott
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Xavier Roucou
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada; PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Quebec City, QC G1V 0A6, Canada.
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9
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Liu H, Liu H, Wang L, Song L, Jiang G, Lu Q, Yang T, Peng H, Cai R, Zhao X, Zhao T, Wu H. Cochlear transcript diversity and its role in auditory functions implied by an otoferlin short isoform. Nat Commun 2023; 14:3085. [PMID: 37248244 DOI: 10.1038/s41467-023-38621-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 05/10/2023] [Indexed: 05/31/2023] Open
Abstract
Isoforms of a gene may contribute to diverse biological functions. In the cochlea, the repertoire of alternative isoforms remains unexplored. We integrated single-cell short-read and long-read RNA sequencing techniques and identified 236,012 transcripts, 126,612 of which were unannotated in the GENCODE database. Then we analyzed and verified the unannotated transcripts using RNA-seq, RT-PCR, Sanger sequencing, and MS-based proteomics approaches. To illustrate the importance of identifying spliced isoforms, we investigated otoferlin, a key protein involved in synaptic transmission in inner hair cells (IHCs). Upon deletion of the canonical otoferlin isoform, the identified short isoform is able to support normal hearing thresholds but with reduced sustained exocytosis of IHCs, and further revealed otoferlin functions in endocytic membrane retrieval that was not well-addressed previously. Furthermore, we found that otoferlin isoforms are associated with IHC functions and auditory phenotypes. This work expands our mechanistic understanding of auditory functions at the level of isoform resolution.
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Affiliation(s)
- Huihui Liu
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, 200011, China
| | - Hongchao Liu
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, 200011, China
| | - Longhao Wang
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, 200011, China
| | - Lei Song
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, 200011, China
| | - Guixian Jiang
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, 200011, China
| | - Qing Lu
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, 200011, China
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Tao Yang
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, 200011, China
| | - Hu Peng
- Department of Otolaryngology-Head and Neck Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, 200003, China
| | - Ruijie Cai
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, 200011, China
| | - Xingle Zhao
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, 200011, China
| | - Ting Zhao
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, 200011, China
| | - Hao Wu
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China.
- Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China.
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, 200011, China.
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10
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Kienzle L, Bettinazzi S, Choquette T, Brunet M, Khorami HH, Jacques JF, Moreau M, Roucou X, Landry CR, Angers A, Breton S. A small protein coded within the mitochondrial canonical gene nd4 regulates mitochondrial bioenergetics. BMC Biol 2023; 21:111. [PMID: 37198654 DOI: 10.1186/s12915-023-01609-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 05/03/2023] [Indexed: 05/19/2023] Open
Abstract
BACKGROUND Mitochondria have a central role in cellular functions, aging, and in certain diseases. They possess their own genome, a vestige of their bacterial ancestor. Over the course of evolution, most of the genes of the ancestor have been lost or transferred to the nucleus. In humans, the mtDNA is a very small circular molecule with a functional repertoire limited to only 37 genes. Its extremely compact nature with genes arranged one after the other and separated by short non-coding regions suggests that there is little room for evolutionary novelties. This is radically different from bacterial genomes, which are also circular but much larger, and in which we can find genes inside other genes. These sequences, different from the reference coding sequences, are called alternatives open reading frames or altORFs, and they are involved in key biological functions. However, whether altORFs exist in mitochondrial protein-coding genes or elsewhere in the human mitogenome has not been fully addressed. RESULTS We found a downstream alternative ATG initiation codon in the + 3 reading frame of the human mitochondrial nd4 gene. This newly characterized altORF encodes a 99-amino-acid-long polypeptide, MTALTND4, which is conserved in primates. Our custom antibody, but not the pre-immune serum, was able to immunoprecipitate MTALTND4 from HeLa cell lysates, confirming the existence of an endogenous MTALTND4 peptide. The protein is localized in mitochondria and cytoplasm and is also found in the plasma, and it impacts cell and mitochondrial physiology. CONCLUSIONS Many human mitochondrial translated ORFs might have so far gone unnoticed. By ignoring mtaltORFs, we have underestimated the coding potential of the mitogenome. Alternative mitochondrial peptides such as MTALTND4 may offer a new framework for the investigation of mitochondrial functions and diseases.
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Affiliation(s)
- Laura Kienzle
- Département de sciences biologiques, Université de Montréal, Montréal, Canada
| | - Stefano Bettinazzi
- Département de sciences biologiques, Université de Montréal, Montréal, Canada
| | - Thierry Choquette
- Département de sciences biologiques, Université de Montréal, Montréal, Canada
| | - Marie Brunet
- Service de génétique médicale, Département de pédiatrie, Université de Sherbrooke, Sherbrooke, Canada
- Centre de recherche du Centre hospitalier universitaire de Sherbrooke (CRCHUS), Sherbrooke, Canada
| | | | - Jean-François Jacques
- Département de biochimie et génomique fonctionnelle, Université de Sherbrooke, Sherbrooke, Canada
| | - Mathilde Moreau
- Département de biochimie et génomique fonctionnelle, Université de Sherbrooke, Sherbrooke, Canada
| | - Xavier Roucou
- Centre de recherche du Centre hospitalier universitaire de Sherbrooke (CRCHUS), Sherbrooke, Canada
- Département de biochimie et génomique fonctionnelle, Université de Sherbrooke, Sherbrooke, Canada
| | - Christian R Landry
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, Canada
- Institut de biologie intégrative et des systèmes, Université Laval, Québec, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec, Canada
- Centre de recherche sur les données massives, Université Laval, Québec, Canada
- Département de biologie, Faculté des sciences et de génie, Université Laval, Québec, Canada
| | - Annie Angers
- Département de sciences biologiques, Université de Montréal, Montréal, Canada
| | - Sophie Breton
- Département de sciences biologiques, Université de Montréal, Montréal, Canada.
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11
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Muraleedharan A, Vanderperre B. The endo-lysosomal system in Parkinson's disease: expanding the horizon. J Mol Biol 2023:168140. [PMID: 37148997 DOI: 10.1016/j.jmb.2023.168140] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 04/22/2023] [Accepted: 04/27/2023] [Indexed: 05/08/2023]
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disorder after Alzheimer's disease, and its prevalence is increasing with age. A wealth of genetic evidence indicates that the endo-lysosomal system is a major pathway driving PD pathogenesis with a growing number of genes encoding endo-lysosomal proteins identified as risk factors for PD, making it a promising target for therapeutic intervention. However, detailed knowledge and understanding of the molecular mechanisms linking these genes to the disease are available for only a handful of them (e.g. LRRK2, GBA1, VPS35). Taking on the challenge of studying poorly characterized genes and proteins can be daunting, due to the limited availability of tools and knowledge from previous literature. This review aims at providing a valuable source of molecular and cellular insights into the biology of lesser-studied PD-linked endo-lysosomal genes, to help and encourage researchers in filling the knowledge gap around these less popular genetic players. Specific endo-lysosomal pathways discussed range from endocytosis, sorting, and vesicular trafficking to the regulation of membrane lipids of these membrane-bound organelles and the specific enzymatic activities they contain. We also provide perspectives on future challenges that the community needs to tackle and propose approaches to move forward in our understanding of these poorly studied endo-lysosomal genes. This will help harness their potential in designing innovative and efficient treatments to ultimately re-establish neuronal homeostasis in PD but also other diseases involving endo-lysosomal dysfunction.
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Affiliation(s)
- Amitha Muraleedharan
- Centre d'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois and Biological Sciences Department, Université du Québec à Montréal
| | - Benoît Vanderperre
- Centre d'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois and Biological Sciences Department, Université du Québec à Montréal
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12
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Manuel JM, Guilloy N, Khatir I, Roucou X, Laurent B. Re-evaluating the impact of alternative RNA splicing on proteomic diversity. Front Genet 2023; 14:1089053. [PMID: 36845399 PMCID: PMC9947481 DOI: 10.3389/fgene.2023.1089053] [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: 11/03/2022] [Accepted: 01/23/2023] [Indexed: 02/11/2023] Open
Abstract
Alternative splicing (AS) constitutes a mechanism by which protein-coding genes and long non-coding RNA (lncRNA) genes produce more than a single mature transcript. From plants to humans, AS is a powerful process that increases transcriptome complexity. Importantly, splice variants produced from AS can potentially encode for distinct protein isoforms which can lose or gain specific domains and, hence, differ in their functional properties. Advances in proteomics have shown that the proteome is indeed diverse due to the presence of numerous protein isoforms. For the past decades, with the help of advanced high-throughput technologies, numerous alternatively spliced transcripts have been identified. However, the low detection rate of protein isoforms in proteomic studies raised debatable questions on whether AS contributes to proteomic diversity and on how many AS events are really functional. We propose here to assess and discuss the impact of AS on proteomic complexity in the light of the technological progress, updated genome annotation, and current scientific knowledge.
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Affiliation(s)
- Jeru Manoj Manuel
- Research Center on Aging, Centre Intégré Universitaire de Santé et Services Sociaux de l’Estrie-Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada,Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Noé Guilloy
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Inès Khatir
- Research Center on Aging, Centre Intégré Universitaire de Santé et Services Sociaux de l’Estrie-Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada,Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Xavier Roucou
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada,Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CRCHUS), Sherbrooke, QC, Canada,Quebec Network for Research on Protein Function Structure and Engineering, PROTEO, Québec, QC, Canada
| | - Benoit Laurent
- Research Center on Aging, Centre Intégré Universitaire de Santé et Services Sociaux de l’Estrie-Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada,Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada,*Correspondence: Benoit Laurent,
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13
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Álvarez-Urdiola R, Borràs E, Valverde F, Matus JT, Sabidó E, Riechmann JL. Peptidomics Methods Applied to the Study of Flower Development. Methods Mol Biol 2023; 2686:509-536. [PMID: 37540375 DOI: 10.1007/978-1-0716-3299-4_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Understanding the global and dynamic nature of plant developmental processes requires not only the study of the transcriptome, but also of the proteome, including its largely uncharacterized peptidome fraction. Recent advances in proteomics and high-throughput analyses of translating RNAs (ribosome profiling) have begun to address this issue, evidencing the existence of novel, uncharacterized, and possibly functional peptides. To validate the accumulation in tissues of sORF-encoded polypeptides (SEPs), the basic setup of proteomic analyses (i.e., LC-MS/MS) can be followed. However, the detection of peptides that are small (up to ~100 aa, 6-7 kDa) and novel (i.e., not annotated in reference databases) presents specific challenges that need to be addressed both experimentally and with computational biology resources. Several methods have been developed in recent years to isolate and identify peptides from plant tissues. In this chapter, we outline two different peptide extraction protocols and the subsequent peptide identification by mass spectrometry using the database search or the de novo identification methods.
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Affiliation(s)
- Raquel Álvarez-Urdiola
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Cerdanyola del Vallès, Barcelona, Spain
| | - Eva Borràs
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Federico Valverde
- Institute for Plant Biochemistry and Photosynthesis CSIC - University of Seville, Seville, Spain
| | - José Tomás Matus
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Cerdanyola del Vallès, Barcelona, Spain
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, Valencia, Spain
| | - Eduard Sabidó
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - José Luis Riechmann
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Cerdanyola del Vallès, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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14
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Bogaert A, Fijalkowska D, Staes A, Van de Steene T, Demol H, Gevaert K. Limited evidence for protein products of non-coding transcripts in the HEK293T cellular cytosol. Mol Cell Proteomics 2022; 21:100264. [PMID: 35788065 PMCID: PMC9396073 DOI: 10.1016/j.mcpro.2022.100264] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 06/22/2022] [Accepted: 06/30/2022] [Indexed: 10/25/2022] Open
Abstract
Ribosome profiling has revealed translation outside of canonical coding sequences (CDSs) including translation of short upstream ORFs, long non-coding RNAs, overlapping ORFs, ORFs in UTRs or ORFs in alternative reading frames. Studies combining mass spectrometry, ribosome profiling and CRISPR-based screens showed that hundreds of ORFs derived from non-coding transcripts produce (micro)proteins, while other studies failed to find evidence for such types of non-canonical translation products. Here, we attempted to discover translation products from non-coding regions by strongly reducing the complexity of the sample prior to mass spectrometric analysis. We used an extended database as the search space and applied stringent filtering of the identified peptides to find evidence for novel translation events. We show that, theoretically our strategy facilitates the detection of translation events of transcripts from non-coding regions, but experimentally only find 19 peptides that might originate from such translation events. Finally, Virotrap based interactome analysis of two N-terminal proteoforms originating from non-coding regions finally showed the functional potential of these novel proteins.
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Affiliation(s)
- Annelies Bogaert
- VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, 9052, Belgium
| | - Daria Fijalkowska
- VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, 9052, Belgium
| | - An Staes
- VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, 9052, Belgium
| | - Tessa Van de Steene
- VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, 9052, Belgium
| | - Hans Demol
- VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, 9052, Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, 9052, Belgium.
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15
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Fabre B, Choteau SA, Duboé C, Pichereaux C, Montigny A, Korona D, Deery MJ, Camus M, Brun C, Burlet-Schiltz O, Russell S, Combier JP, Lilley KS, Plaza S. In Depth Exploration of the Alternative Proteome of Drosophila melanogaster. Front Cell Dev Biol 2022; 10:901351. [PMID: 35721519 PMCID: PMC9204603 DOI: 10.3389/fcell.2022.901351] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 04/25/2022] [Indexed: 12/13/2022] Open
Abstract
Recent studies have shown that hundreds of small proteins were occulted when protein-coding genes were annotated. These proteins, called alternative proteins, have failed to be annotated notably due to the short length of their open reading frame (less than 100 codons) or the enforced rule establishing that messenger RNAs (mRNAs) are monocistronic. Several alternative proteins were shown to be biologically active molecules and seem to be involved in a wide range of biological functions. However, genome-wide exploration of the alternative proteome is still limited to a few species. In the present article, we describe a deep peptidomics workflow which enabled the identification of 401 alternative proteins in Drosophila melanogaster. Subcellular localization, protein domains, and short linear motifs were predicted for 235 of the alternative proteins identified and point toward specific functions of these small proteins. Several alternative proteins had approximated abundances higher than their canonical counterparts, suggesting that these alternative proteins are actually the main products of their corresponding genes. Finally, we observed 14 alternative proteins with developmentally regulated expression patterns and 10 induced upon the heat-shock treatment of embryos, demonstrating stage or stress-specific production of alternative proteins.
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Affiliation(s)
- Bertrand Fabre
- Laboratoire de Recherche en Sciences Végétales, UMR5546, Université de Toulouse, UPS, INP, CNRS, Auzeville-Tolosane, France,Cambridge Centre for Proteomics, Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom,*Correspondence: Bertrand Fabre, ; Serge Plaza,
| | - Sebastien A. Choteau
- Aix-Marseille Université, INSERM, TAGC, Turing Centre for Living Systems, Marseille, France
| | - Carine Duboé
- Laboratoire de Recherche en Sciences Végétales, UMR5546, Université de Toulouse, UPS, INP, CNRS, Auzeville-Tolosane, France
| | - Carole Pichereaux
- Fédération de Recherche (FR3450), Agrobiosciences, Interactions et Biodiversité (AIB), CNRS, Toulouse, France,Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France,Infrastructure Nationale de Protéomique, ProFI, FR 2048, Toulouse, France
| | - Audrey Montigny
- Laboratoire de Recherche en Sciences Végétales, UMR5546, Université de Toulouse, UPS, INP, CNRS, Auzeville-Tolosane, France
| | - Dagmara Korona
- Cambridge Systems Biology Centre and Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Michael J. Deery
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Mylène Camus
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France,Infrastructure Nationale de Protéomique, ProFI, FR 2048, Toulouse, France
| | - Christine Brun
- Aix-Marseille Université, INSERM, TAGC, Turing Centre for Living Systems, Marseille, France,CNRS, Marseille, France
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France,Infrastructure Nationale de Protéomique, ProFI, FR 2048, Toulouse, France
| | - Steven Russell
- Cambridge Systems Biology Centre and Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Jean-Philippe Combier
- Laboratoire de Recherche en Sciences Végétales, UMR5546, Université de Toulouse, UPS, INP, CNRS, Auzeville-Tolosane, France
| | - Kathryn S. Lilley
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Serge Plaza
- Laboratoire de Recherche en Sciences Végétales, UMR5546, Université de Toulouse, UPS, INP, CNRS, Auzeville-Tolosane, France,*Correspondence: Bertrand Fabre, ; Serge Plaza,
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16
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Leong AZX, Lee PY, Mohtar MA, Syafruddin SE, Pung YF, Low TY. Short open reading frames (sORFs) and microproteins: an update on their identification and validation measures. J Biomed Sci 2022; 29:19. [PMID: 35300685 PMCID: PMC8928697 DOI: 10.1186/s12929-022-00802-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 03/09/2022] [Indexed: 12/17/2022] Open
Abstract
A short open reading frame (sORFs) constitutes ≤ 300 bases, encoding a microprotein or sORF-encoded protein (SEP) which comprises ≤ 100 amino acids. Traditionally dismissed by genome annotation pipelines as meaningless noise, sORFs were found to possess coding potential with ribosome profiling (RIBO-Seq), which unveiled sORF-based transcripts at various genome locations. Nonetheless, the existence of corresponding microproteins that are stable and functional was little substantiated by experimental evidence initially. With recent advancements in multi-omics, the identification, validation, and functional characterisation of sORFs and microproteins have become feasible. In this review, we discuss the history and development of an emerging research field of sORFs and microproteins. In particular, we focus on an array of bioinformatics and OMICS approaches used for predicting, sequencing, validating, and characterizing these recently discovered entities. These strategies include RIBO-Seq which detects sORF transcripts via ribosome footprints, and mass spectrometry (MS)-based proteomics for sequencing the resultant microproteins. Subsequently, our discussion extends to the functional characterisation of microproteins by incorporating CRISPR/Cas9 screen and protein–protein interaction (PPI) studies. Our review discusses not only detection methodologies, but we also highlight on the challenges and potential solutions in identifying and validating sORFs and their microproteins. The novelty of this review lies within its validation for the functional role of microproteins, which could contribute towards the future landscape of microproteomics.
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Affiliation(s)
- Alyssa Zi-Xin Leong
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - Pey Yee Lee
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - M Aiman Mohtar
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - Saiful Effendi Syafruddin
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - Yuh-Fen Pung
- Division of Biomedical Science, School of Pharmacy, University of Nottingham Malaysia, Semenyih, 43500, Selangor, Malaysia
| | - Teck Yew Low
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia.
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17
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Miller RM, Jordan BT, Mehlferber MM, Jeffery ED, Chatzipantsiou C, Kaur S, Millikin RJ, Dai Y, Tiberi S, Castaldi PJ, Shortreed MR, Luckey CJ, Conesa A, Smith LM, Deslattes Mays A, Sheynkman GM. Enhanced protein isoform characterization through long-read proteogenomics. Genome Biol 2022; 23:69. [PMID: 35241129 PMCID: PMC8892804 DOI: 10.1186/s13059-022-02624-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 02/02/2022] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND The detection of physiologically relevant protein isoforms encoded by the human genome is critical to biomedicine. Mass spectrometry (MS)-based proteomics is the preeminent method for protein detection, but isoform-resolved proteomic analysis relies on accurate reference databases that match the sample; neither a subset nor a superset database is ideal. Long-read RNA sequencing (e.g., PacBio or Oxford Nanopore) provides full-length transcripts which can be used to predict full-length protein isoforms. RESULTS We describe here a long-read proteogenomics approach for integrating sample-matched long-read RNA-seq and MS-based proteomics data to enhance isoform characterization. We introduce a classification scheme for protein isoforms, discover novel protein isoforms, and present the first protein inference algorithm for the direct incorporation of long-read transcriptome data to enable detection of protein isoforms previously intractable to MS-based detection. We have released an open-source Nextflow pipeline that integrates long-read sequencing in a proteomic workflow for isoform-resolved analysis. CONCLUSIONS Our work suggests that the incorporation of long-read sequencing and proteomic data can facilitate improved characterization of human protein isoform diversity. Our first-generation pipeline provides a strong foundation for future development of long-read proteogenomics and its adoption for both basic and translational research.
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Affiliation(s)
- Rachel M Miller
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Ben T Jordan
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Madison M Mehlferber
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Erin D Jeffery
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | | | - Simi Kaur
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Robert J Millikin
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Yunxiang Dai
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Simone Tiberi
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Peter J Castaldi
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of General Medicine and Primary Care, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Chance John Luckey
- Department of Pathology, University of Virginia, Charlottesville, VA, USA
| | - Ana Conesa
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain
- Microbiology and Cell Science Department, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Anne Deslattes Mays
- Office of Data Science and Sharing, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Rockville, MD, USA
| | - Gloria M Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA.
- UVA Cancer Center, University of Virginia, Charlottesville, VA, USA.
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18
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Cardon T, Fournier I, Salzet M. Unveiling a Ghost Proteome in the Glioblastoma Non-Coding RNAs. Front Cell Dev Biol 2022; 9:703583. [PMID: 35004666 PMCID: PMC8733697 DOI: 10.3389/fcell.2021.703583] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 12/03/2021] [Indexed: 12/13/2022] Open
Abstract
Glioblastoma is the most common brain cancer in adults. Nevertheless, the median survival time is 15 months, if treated with at least a near total resection and followed by radiotherapy in association with temozolomide. In glioblastoma (GBM), variations of non-coding ribonucleic acid (ncRNA) expression have been demonstrated in tumor processes, especially in the regulation of major signaling pathways. Moreover, many ncRNAs present in their sequences an Open Reading Frame (ORF) allowing their translations into proteins, so-called alternative proteins (AltProt) and constituting the “ghost proteome.” This neglected world in GBM has been shown to be implicated in protein–protein interaction (PPI) with reference proteins (RefProt) reflecting involvement in signaling pathways linked to cellular mobility and transfer RNA regulation. More recently, clinical studies have revealed that AltProt is also involved in the patient’s survival and bad prognosis. We thus propose to review the ncRNAs involved in GBM and highlight their function in the disease.
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Affiliation(s)
- Tristan Cardon
- University of Lille, Inserm, CHU Lille, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Lille, France
| | - Isabelle Fournier
- University of Lille, Inserm, CHU Lille, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Lille, France.,Institut Universitaire de France, Paris, France
| | - Michel Salzet
- University of Lille, Inserm, CHU Lille, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Lille, France.,Institut Universitaire de France, Paris, France
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19
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In-Depth Annotation of the Drosophila Bithorax-Complex Reveals the Presence of Several Alternative ORFs That Could Encode for Motif-Rich Peptides. Cells 2021; 10:cells10112983. [PMID: 34831206 PMCID: PMC8616405 DOI: 10.3390/cells10112983] [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: 09/13/2021] [Revised: 10/17/2021] [Accepted: 10/26/2021] [Indexed: 11/19/2022] Open
Abstract
It is recognized that a large proportion of eukaryotic RNAs and proteins is not produced from conventional genes but from short and alternative (alt) open reading frames (ORFs) that are not captured by gene prediction programs. Here we present an in silico prediction of altORFs by applying several selecting filters based on evolutionary conservation and annotations of previously characterized altORF peptides. Our work was performed in the Bithorax-complex (BX-C), which was one of the first genomic regions described to contain long non-coding RNAs in Drosophila. We showed that several altORFs could be predicted from coding and non-coding sequences of BX-C. In addition, the selected altORFs encode for proteins that contain several interesting molecular features, such as the presence of transmembrane helices or a general propensity to be rich in short interaction motifs. Of particular interest, one altORF encodes for a protein that contains a peptide sequence found in specific isoforms of two Drosophila Hox proteins. Our work thus suggests that several altORF proteins could be produced from a particular genomic region known for its critical role during Drosophila embryonic development. The molecular signatures of these altORF proteins further suggests that several of them could make numerous protein–protein interactions and be of functional importance in vivo.
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20
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Fesenko I, Shabalina SA, Mamaeva A, Knyazev A, Glushkevich A, Lyapina I, Ziganshin R, Kovalchuk S, Kharlampieva D, Lazarev V, Taliansky M, Koonin EV. A vast pool of lineage-specific microproteins encoded by long non-coding RNAs in plants. Nucleic Acids Res 2021; 49:10328-10346. [PMID: 34570232 DOI: 10.1093/nar/gkab816] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 08/17/2021] [Accepted: 09/17/2021] [Indexed: 12/17/2022] Open
Abstract
Pervasive transcription of eukaryotic genomes results in expression of long non-coding RNAs (lncRNAs) most of which are poorly conserved in evolution and appear to be non-functional. However, some lncRNAs have been shown to perform specific functions, in particular, transcription regulation. Thousands of small open reading frames (smORFs, <100 codons) located on lncRNAs potentially might be translated into peptides or microproteins. We report a comprehensive analysis of the conservation and evolutionary trajectories of lncRNAs-smORFs from the moss Physcomitrium patens across transcriptomes of 479 plant species. Although thousands of smORFs are subject to substantial purifying selection, the majority of the smORFs appear to be evolutionary young and could represent a major pool for functional innovation. Using nanopore RNA sequencing, we show that, on average, the transcriptional level of conserved smORFs is higher than that of non-conserved smORFs. Proteomic analysis confirmed translation of 82 novel species-specific smORFs. Numerous conserved smORFs containing low complexity regions (LCRs) or transmembrane domains were identified, the biological functions of a selected LCR-smORF were demonstrated experimentally. Thus, microproteins encoded by smORFs are a major, functionally diverse component of the plant proteome.
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Affiliation(s)
- Igor Fesenko
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Svetlana A Shabalina
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Anna Mamaeva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Andrey Knyazev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Anna Glushkevich
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Irina Lyapina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Rustam Ziganshin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Sergey Kovalchuk
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Daria Kharlampieva
- Department of Cell Biology, Federal Research and Clinical Center of Physical -Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russian Federation
| | - Vassili Lazarev
- Department of Cell Biology, Federal Research and Clinical Center of Physical -Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russian Federation.,Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Moscow region, 141701, Russian Federation
| | - Michael Taliansky
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation.,The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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21
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Na Z, Luo Y, Cui DS, Khitun A, Smelyansky S, Loria JP, Slavoff SA. Phosphorylation of a Human Microprotein Promotes Dissociation of Biomolecular Condensates. J Am Chem Soc 2021; 143:12675-12687. [PMID: 34346674 DOI: 10.1021/jacs.1c05386] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Proteogenomic identification of translated small open reading frames in humans has revealed thousands of microproteins, or polypeptides of fewer than 100 amino acids, that were previously invisible to geneticists. Hundreds of microproteins have been shown to be essential for cell growth and proliferation, and many regulate macromolecular complexes. However, the vast majority of microproteins remain functionally uncharacterized, and many lack secondary structure and exhibit limited evolutionary conservation. One such intrinsically disordered microprotein is NBDY, a 68-amino acid component of membraneless organelles known as P-bodies. In this work, we show that NBDY can undergo liquid-liquid phase separation, a biophysical process thought to underlie the formation of membraneless organelles, in the presence of RNA in vitro. Phosphorylation of NBDY drives liquid phase remixing in vitro and macroscopic P-body dissociation in cells undergoing growth factor signaling and cell division. These results suggest that NBDY phosphorylation enables regulation of P-body dynamics during cell proliferation and, more broadly, that intrinsically disordered microproteins may contribute to liquid-liquid phase separation and remixing behavior to affect cellular processes.
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Affiliation(s)
- Zhenkun Na
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States.,Institute of Biomolecular Design and Discovery, Yale University, New Haven, Connecticut 06529, United States
| | - Yang Luo
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States.,Institute of Biomolecular Design and Discovery, Yale University, New Haven, Connecticut 06529, United States
| | - Danica S Cui
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Alexandra Khitun
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States.,Institute of Biomolecular Design and Discovery, Yale University, New Haven, Connecticut 06529, United States
| | - Stephanie Smelyansky
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States.,Institute of Biomolecular Design and Discovery, Yale University, New Haven, Connecticut 06529, United States.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06529, United States
| | - J Patrick Loria
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06529, United States
| | - Sarah A Slavoff
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States.,Institute of Biomolecular Design and Discovery, Yale University, New Haven, Connecticut 06529, United States.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06529, United States
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22
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Cohen AA, Leblanc S, Roucou X. Robust Physiological Metrics From Sparsely Sampled Networks. Front Physiol 2021; 12:624097. [PMID: 33643068 PMCID: PMC7902772 DOI: 10.3389/fphys.2021.624097] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/12/2021] [Indexed: 12/14/2022] Open
Abstract
Physiological and biochemical networks are highly complex, involving thousands of nodes as well as a hierarchical structure. True network structure is also rarely known. This presents major challenges for applying classical network theory to these networks. However, complex systems generally share the property of having a diffuse or distributed signal. Accordingly, we should predict that system state can be robustly estimated with sparse sampling, and with limited knowledge of true network structure. In this review, we summarize recent findings from several methodologies to estimate system state via a limited sample of biomarkers, notably Mahalanobis distance, principal components analysis, and cluster analysis. While statistically simple, these methods allow novel characterizations of system state when applied judiciously. Broadly, system state can often be estimated even from random samples of biomarkers. Furthermore, appropriate methods can detect emergent underlying physiological structure from this sparse data. We propose that approaches such as these are a powerful tool to understand physiology, and could lead to a new understanding and mapping of the functional implications of biological variation.
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Affiliation(s)
- Alan A. Cohen
- Groupe de Recherche PRIMUS, Département de Médecine de Famille et de Médecine d’Urgence, Université de Sherbrooke, Sherbrooke, QC, Canada
- Centre de Recherche, Centre Hospitalier Universitaire de Sherbrooke (CRCHUS), Sherbrooke, QC, Canada
- Research Center on Aging, CIUSSS-de-l’Estrie-CHUS, Sherbrooke, QC, Canada
| | - Sebastien Leblanc
- Département de Biochimie et de Génomique Fonctionnelle, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Xavier Roucou
- Département de Biochimie et de Génomique Fonctionnelle, Université de Sherbrooke, Sherbrooke, QC, Canada
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23
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Brunet MA, Lucier JF, Levesque M, Leblanc S, Jacques JF, Al-Saedi HRH, Guilloy N, Grenier F, Avino M, Fournier I, Salzet M, Ouangraoua A, Scott M, Boisvert FM, Roucou X. OpenProt 2021: deeper functional annotation of the coding potential of eukaryotic genomes. Nucleic Acids Res 2021; 49:D380-D388. [PMID: 33179748 PMCID: PMC7779043 DOI: 10.1093/nar/gkaa1036] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 12/12/2022] Open
Abstract
OpenProt (www.openprot.org) is the first proteogenomic resource supporting a polycistronic annotation model for eukaryotic genomes. It provides a deeper annotation of open reading frames (ORFs) while mining experimental data for supporting evidence using cutting-edge algorithms. This update presents the major improvements since the initial release of OpenProt. All species support recent NCBI RefSeq and Ensembl annotations, with changes in annotations being reported in OpenProt. Using the 131 ribosome profiling datasets re-analysed by OpenProt to date, non-AUG initiation starts are reported alongside a confidence score of the initiating codon. From the 177 mass spectrometry datasets re-analysed by OpenProt to date, the unicity of the detected peptides is controlled at each implementation. Furthermore, to guide the users, detectability statistics and protein relationships (isoforms) are now reported for each protein. Finally, to foster access to deeper ORF annotation independently of one's bioinformatics skills or computational resources, OpenProt now offers a data analysis platform. Users can submit their dataset for analysis and receive the results from the analysis by OpenProt. All data on OpenProt are freely available and downloadable for each species, the release-based format ensuring a continuous access to the data. Thus, OpenProt enables a more comprehensive annotation of eukaryotic genomes and fosters functional proteomic discoveries.
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Affiliation(s)
- Marie A Brunet
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, 3201 Jean Mignault, Sherbrooke, QC J1E 4K8, Canada
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Université Laval, Quebec City, QC G1V0A6, Canada
| | - Jean-François Lucier
- Center for Computational Science, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
- Biology Department, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Maxime Levesque
- Center for Computational Science, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
- Biology Department, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Sébastien Leblanc
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, 3201 Jean Mignault, Sherbrooke, QC J1E 4K8, Canada
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Université Laval, Quebec City, QC G1V0A6, Canada
| | - Jean-Francois Jacques
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, 3201 Jean Mignault, Sherbrooke, QC J1E 4K8, Canada
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Université Laval, Quebec City, QC G1V0A6, Canada
| | - Hassan R H Al-Saedi
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, 3201 Jean Mignault, Sherbrooke, QC J1E 4K8, Canada
| | - Noé Guilloy
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, 3201 Jean Mignault, Sherbrooke, QC J1E 4K8, Canada
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Université Laval, Quebec City, QC G1V0A6, Canada
| | - Frederic Grenier
- Center for Computational Science, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
- Biology Department, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Mariano Avino
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, 3201 Jean Mignault, Sherbrooke, QC J1E 4K8, Canada
| | - Isabelle Fournier
- INSERM U1192, Laboratoire Protéomique, Réponse Inflammatoire & Spectrométrie de Masse (PRISM), Université de Lille, F-59000 Lille, France
| | - Michel Salzet
- INSERM U1192, Laboratoire Protéomique, Réponse Inflammatoire & Spectrométrie de Masse (PRISM), Université de Lille, F-59000 Lille, France
| | - Aïda Ouangraoua
- Informatics Department, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Michelle S Scott
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, 3201 Jean Mignault, Sherbrooke, QC J1E 4K8, Canada
| | - François-Michel Boisvert
- Department of Immunology and Cellular Biology, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Xavier Roucou
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, 3201 Jean Mignault, Sherbrooke, QC J1E 4K8, Canada
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Université Laval, Quebec City, QC G1V0A6, Canada
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24
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Witkowski JM, Bryl E, Fulop T. Proteodynamics and aging of eukaryotic cells. Mech Ageing Dev 2021; 194:111430. [PMID: 33421431 DOI: 10.1016/j.mad.2021.111430] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 12/28/2020] [Accepted: 12/30/2020] [Indexed: 12/11/2022]
Abstract
All aspects of each protein existence in the eukaryotic cells, starting from the pre-translation events, through translation, multiple different post-translational modifications, functional life and eventual proteostatic removal after loss of functionality and changes in physico-chemical properties, can be collectively called the proteodynamics. With aging, passing of time as well as accumulating effects of exposures, interactions and wearing-off lead to problems at each of the above mentioned stages, eventually leading to general malfunction of the proteome. This work briefly reviews and summarizes current knowledge concerning this important topic.
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Affiliation(s)
- Jacek M Witkowski
- Department of Pathophysiology, Medical University of Gdańsk, Gdańsk, Poland.
| | - Ewa Bryl
- Department of Pathology and Experimental Rheumatology, Medical University of Gdańsk, Gdańsk, Poland
| | - Tamas Fulop
- Research Center on Aging, Graduate Program in Immunology, Faculty of Medicine and Health Sciences, University of Sherbrooke, Sherbrooke, Quebec, Canada
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25
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Fabre B, Combier JP, Plaza S. Recent advances in mass spectrometry-based peptidomics workflows to identify short-open-reading-frame-encoded peptides and explore their functions. Curr Opin Chem Biol 2021; 60:122-130. [PMID: 33401134 DOI: 10.1016/j.cbpa.2020.12.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/26/2020] [Accepted: 12/03/2020] [Indexed: 12/12/2022]
Abstract
Short open reading frame (sORF)-encoded polypeptides (SEPs) have recently emerged as key regulators of major cellular processes. Computational methods for the annotation of sORFs combined with transcriptomics and ribosome profiling approaches predicted the existence of tens of thousands of SEPs across the kingdom of life. Although, we still lack unambiguous evidence for most of them. The method of choice to validate the expression of SEPs is mass spectrometry (MS)-based peptidomics. Peptides are less abundant than proteins, which tends to hinder their detection. Therefore, optimization and enrichment methods are necessary to validate the existence of SEPs. In this article, we discuss the challenges for the detection of SEPs by MS and recent developments of biochemical approaches applied to the study of these peptides. We detail the advances made in the different key steps of a typical peptidomics workflow and highlight possible alternatives that have not been explored yet.
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Affiliation(s)
- Bertrand Fabre
- Laboratoire de Recherche en Sciences Végétales, UMR5546, Université de Toulouse, UPS, CNRS, 31320, Auzeville-Tolosane, France.
| | - Jean-Philippe Combier
- Laboratoire de Recherche en Sciences Végétales, UMR5546, Université de Toulouse, UPS, CNRS, 31320, Auzeville-Tolosane, France
| | - Serge Plaza
- Laboratoire de Recherche en Sciences Végétales, UMR5546, Université de Toulouse, UPS, CNRS, 31320, Auzeville-Tolosane, France
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26
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Cardon T, Fournier I, Salzet M. Shedding Light on the Ghost Proteome. Trends Biochem Sci 2020; 46:239-250. [PMID: 33246829 DOI: 10.1016/j.tibs.2020.10.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 01/19/2023]
Abstract
Conventionally, eukaryotic mRNAs were thought to be monocistronic, leading to the translation of a single protein. However, large-scale proteomics has led to the identification of proteins translated from alternative open reading frames (AltORFs) in mRNAs. AltORFs are found in addition to predicted reference ORFs and noncoding RNA. Alternative proteins are not represented in the conventional protein databases, and this 'Ghost proteome' was not considered until recently. Some of these proteins are functional, and there is growing evidence that they are involved in central functions in physiological and physiopathological contexts. Here, we review how this Ghost proteome fills the gap in our understanding of signaling pathways, establishes new markers of pathologies, and highlights therapeutic targets.
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Affiliation(s)
- Tristan Cardon
- Laboratoire Protéomique, Réponse Inflammatoire Spectrométrie de Masse (PRISM), Inserm U1192, University of Lille, CHU Lille, F-59000 Lille, France.
| | - Isabelle Fournier
- Laboratoire Protéomique, Réponse Inflammatoire Spectrométrie de Masse (PRISM), Inserm U1192, University of Lille, CHU Lille, F-59000 Lille, France; Institut Universitaire de France, Paris, France.
| | - Michel Salzet
- Laboratoire Protéomique, Réponse Inflammatoire Spectrométrie de Masse (PRISM), Inserm U1192, University of Lille, CHU Lille, F-59000 Lille, France; Institut Universitaire de France, Paris, France.
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27
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The hidden world of non-canonical ORFs. Exp Cell Res 2020; 396:112267. [PMID: 32926940 DOI: 10.1016/j.yexcr.2020.112267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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