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Zheng C, Ma L, Song F, Tian L, Cai W, Li H, Duan Y. Comparative genomic analyses reveal evidence for adaptive A-to-I RNA editing in insect Adar gene. Epigenetics 2024; 19:2333665. [PMID: 38525798 DOI: 10.1080/15592294.2024.2333665] [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: 11/07/2023] [Accepted: 03/17/2024] [Indexed: 03/26/2024] Open
Abstract
Although A-to-I RNA editing leads to similar effects to A-to-G DNA mutation, nonsynonymous RNA editing (recoding) is believed to confer its adaptiveness by 'epigenetically' regulating proteomic diversity in a temporospatial manner, avoiding the pleiotropic effect of genomic mutations. Recent discoveries on the evolutionary trajectory of Ser>Gly auto-editing site in insect Adar gene demonstrated a selective advantage to having an editable codon compared to uneditable ones. However, apart from pure observations, quantitative approaches for justifying the adaptiveness of individual RNA editing sites are still lacking. We performed a comparative genomic analysis on 113 Diptera species, focusing on the Adar Ser>Gly auto-recoding site in Drosophila. We only found one species having a derived Gly at the corresponding site, and this occurrence was significantly lower than genome-wide random expectation. This suggests that the Adar Ser>Gly site is unlikely to be genomically replaced with G during evolution, and thus indicating the advantage of editable status over hardwired genomic alleles. Similar trends were observed for the conserved Ile>Met recoding in gene Syt1. In the light of evolution, we established a comparative genomic approach for quantitatively justifying the adaptiveness of individual editing sites. Priority should be given to such adaptive editing sites in future functional studies.
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Affiliation(s)
- Caiqing Zheng
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Ling Ma
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Fan Song
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Li Tian
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Wanzhi Cai
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Hu Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Yuange Duan
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
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Zhao T, Ma L, Xu S, Cai W, Li H, Duan Y. Narrowing down the candidates of beneficial A-to-I RNA editing by comparing the recoding sites with uneditable counterparts. Nucleus 2024; 15:2304503. [PMID: 38286757 PMCID: PMC10826634 DOI: 10.1080/19491034.2024.2304503] [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: 10/20/2023] [Accepted: 01/08/2024] [Indexed: 01/31/2024] Open
Abstract
Adar-mediated adenosine-to-inosine (A-to-I) RNA editing mainly occurs in nucleus and diversifies the transcriptome in a flexible manner. It has been a challenging task to identify beneficial editing sites from the sea of total editing events. The functional Ser>Gly auto-recoding site in insect Adar gene has uneditable Ser codons in ancestral nodes, indicating the selective advantage to having an editable status. Here, we extended this case study to more metazoan species, and also looked for all Drosophila recoding events with potential uneditable synonymous codons. Interestingly, in D. melanogaster, the abundant nonsynonymous editing is enriched in the codons that have uneditable counterparts, but the Adar Ser>Gly case suggests that the editable orthologous codons in other species are not necessarily edited. The use of editable versus ancestral uneditable codon is a smart way to infer the selective advantage of RNA editing, and priority might be given to these editing sites for functional studies due to the feasibility to construct an uneditable allele. Our study proposes an idea to narrow down the candidates of beneficial recoding sites. Meanwhile, we stress that the matched transcriptomes are needed to verify the conservation of editing events during evolution.
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Affiliation(s)
- Tianyou Zhao
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Ling Ma
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Shiwen Xu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Wanzhi Cai
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Hu Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Yuange Duan
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
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Duan Y, Ma L, Zhao T, Liu J, Zheng C, Song F, Tian L, Cai W, Li H. Conserved A-to-I RNA editing with non-conserved recoding expands the candidates of functional editing sites. Fly (Austin) 2024; 18:2367359. [PMID: 38889318 PMCID: PMC11188811 DOI: 10.1080/19336934.2024.2367359] [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: 03/06/2024] [Accepted: 06/07/2024] [Indexed: 06/20/2024] Open
Abstract
Adenosine-to-inosine (A-to-I) RNA editing recodes the genome and confers flexibility for the organisms to adapt to the environment. It is believed that RNA recoding sites are well suited for facilitating adaptive evolution by increasing the proteomic diversity in a temporal-spatial manner. The function and essentiality of a few conserved recoding sites are recognized. However, the experimentally discovered functional sites only make up a small corner of the total sites, and there is still the need to expand the repertoire of such functional sites with bioinformatic approaches. In this study, we define a new category of RNA editing sites termed 'conserved editing with non-conserved recoding' and systematically identify such sites in Drosophila editomes, figuring out their selection pressure and signals of adaptation at inter-species and intra-species levels. Surprisingly, conserved editing sites with non-conserved recoding are not suppressed and are even slightly overrepresented in Drosophila. DNA mutations leading to such cases are also favoured during evolution, suggesting that the function of those recoding events in different species might be diverged, specialized, and maintained. Finally, structural prediction suggests that such recoding in potassium channel Shab might increase ion permeability and compensate the effect of low temperature. In conclusion, conserved editing with non-conserved recoding might be functional as well. Our study provides novel aspects in considering the adaptive evolution of RNA editing sites and meanwhile expands the candidates of functional recoding sites for future validation.
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Affiliation(s)
| | | | | | - Jiyao Liu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Caiqing Zheng
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Fan Song
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Li Tian
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Wanzhi Cai
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Hu Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
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Sampaio E, Sridhar VH, Francisco FA, Nagy M, Sacchi A, Strandburg-Peshkin A, Nührenberg P, Rosa R, Couzin ID, Gingins S. Multidimensional social influence drives leadership and composition-dependent success in octopus-fish hunting groups. Nat Ecol Evol 2024:10.1038/s41559-024-02525-2. [PMID: 39313585 DOI: 10.1038/s41559-024-02525-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 07/25/2024] [Indexed: 09/25/2024]
Abstract
Collective behaviour, social interactions and leadership in animal groups are often driven by individual differences. However, most studies focus on same-species groups, in which individual variation is relatively low. Multispecies groups, however, entail interactions among highly divergent phenotypes, ranging from simple exploitative actions to complex coordinated networks. Here we studied hunting groups of otherwise-solitary Octopus cyanea and multiple fish species, to unravel hidden mechanisms of leadership and associated dynamics in functional nature and complexity, when divergence is maximized. Using three-dimensional field-based tracking and field experiments, we found that these groups exhibit complex functional dynamics and composition-dependent properties. Social influence is hierarchically distributed over multiscale dimensions representing role specializations: fish (particularly goatfish) drive environmental exploration, deciding where, while the octopus decides if, and when, the group moves. Thus, 'classical leadership' can be insufficient to describe complex heterogeneous systems, in which leadership instead can be driven by both stimulating and inhibiting movement. Furthermore, group composition altered individual investment and collective action, triggering partner control mechanisms (that is, punching) and benefits for the de facto leader, the octopus. This seemingly non-social invertebrate flexibly adapts to heterospecific actions, showing hallmarks of social competence and cognition. These findings expand our current understanding of what leadership is and what sociality is.
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Affiliation(s)
- Eduardo Sampaio
- MARE-Marine and Environmental Sciences Centre, Laboratório Marítimo da Guia, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal.
- Department of Collective Behaviour, Max Planck Institute of Animal Behavior, Konstanz, Germany.
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz, Germany.
- Department of Biology, University of Konstanz, Konstanz, Germany.
| | - Vivek H Sridhar
- Department of Collective Behaviour, Max Planck Institute of Animal Behavior, Konstanz, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz, Germany
- Department of Biology, University of Konstanz, Konstanz, Germany
- Department for the Ecology of Animal Societies, Max Planck Institute of Animal Behavior, Konstanz, Germany
| | - Fritz A Francisco
- Science of Intelligence (SCIoI), Technische University, Berlin, Germany
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA
| | - Máté Nagy
- Department of Collective Behaviour, Max Planck Institute of Animal Behavior, Konstanz, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz, Germany
- Department of Biology, University of Konstanz, Konstanz, Germany
- MTA-ELTE 'Lendület' Collective Behaviour Research Group, Hungarian Academy of Sciences, Budapest, Hungary
- Department of Biological Physics, Eötvös Loránd University, Budapest, Hungary
| | - Ada Sacchi
- Department of Collective Behaviour, Max Planck Institute of Animal Behavior, Konstanz, Germany
| | - Ariana Strandburg-Peshkin
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz, Germany
- Department of Biology, University of Konstanz, Konstanz, Germany
- Department for the Ecology of Animal Societies, Max Planck Institute of Animal Behavior, Konstanz, Germany
| | - Paul Nührenberg
- Department of Collective Behaviour, Max Planck Institute of Animal Behavior, Konstanz, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz, Germany
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Rui Rosa
- MARE-Marine and Environmental Sciences Centre, Laboratório Marítimo da Guia, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Cascais, Portugal
| | - Iain D Couzin
- Department of Collective Behaviour, Max Planck Institute of Animal Behavior, Konstanz, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz, Germany
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Simon Gingins
- Department of Collective Behaviour, Max Planck Institute of Animal Behavior, Konstanz, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz, Germany
- Department of Biology, University of Konstanz, Konstanz, Germany
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Zheng C, Liu J, Duan Y. Adaptive evolution of A-to-I auto-editing site in Adar of eusocial insects. BMC Genomics 2024; 25:803. [PMID: 39187830 PMCID: PMC11346018 DOI: 10.1186/s12864-024-10709-0] [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: 04/22/2024] [Accepted: 08/14/2024] [Indexed: 08/28/2024] Open
Abstract
BACKGROUND Adenosine-to-inosine (A-to-I) RNA editing is a co-/post-transcriptional modification introducing A-to-G variations in RNAs. There is extensive discussion on whether the flexibility of RNA editing exerts a proteomic diversification role, or it just acts like hardwired mutations to correct the genomic allele. Eusocial insects evolved the ability to generate phenotypically differentiated individuals with the same genome, indicating the involvement of epigenetic/transcriptomic regulation. METHODS We obtained the genomes of 104 Hymenoptera insects and the transcriptomes of representative species. Comparative genomic analysis was performed to parse the evolutionary trajectory of a regulatory Ile > Met auto-recoding site in Adar gene. RESULTS At genome level, the pre-editing Ile codon is conserved across a node containing all eusocial hymenopterans. At RNA level, the editing events are confirmed in representative species and shows considerable condition-specificity. Compared to random expectation, the editable Ile codon avoids genomic substitutions to Met or to uneditable Ile codons, but does not avoid mutations to other unrelated amino acids. CONCLUSIONS The flexibility of Adar auto-recoding site in Hymenoptera is selectively maintained, supporting the flexible RNA editing hypothesis. We proposed a new angle to view the adaptation of RNA editing, providing another layer to explain the great phenotypical plasticity of eusocial insects.
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Affiliation(s)
- Caiqing Zheng
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Jiyao Liu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Yuange Duan
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.
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Bortoletto E, Rosani U, Sakaguchi A, Yoon J, Nagasawa K, Venier P. Insights into ADAR gene complement, expression patterns, and RNA editing landscape in Chlamys farreri. FISH & SHELLFISH IMMUNOLOGY 2024; 151:109743. [PMID: 38964433 DOI: 10.1016/j.fsi.2024.109743] [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: 04/17/2024] [Revised: 06/26/2024] [Accepted: 07/01/2024] [Indexed: 07/06/2024]
Abstract
Adenosine Deaminases Acting on RNA (ADARs) are evolutionarily conserved enzymes known to convert adenosine to inosine in double-stranded RNAs and participate in host-virus interactions. Conducting a meta-analysis of available transcriptome data, we identified and characterised eight ADAR transcripts in Chlamys farreri, a farmed marine scallop susceptible to Acute viral necrosis virus (AVNV) infections and mortality outbreaks. Accordingly, we identified six ADAR genes in the Zhikong scallop genome, revised previous gene annotations, and traced alternative splicing variants. In detail, each ADAR gene encodes a unique combination of functional domains, always including the Adenosine deaminase domain, RNA binding domains and, in one case, two copies of a Z-DNA binding domain. After phylogenetic analysis, five C. farreri ADARs clustered in the ADAR1 clade along with sequences from diverse animal phyla. Gene expression analysis indicated CF051320 as the most expressed ADAR, especially in the eye and male gonad. The other four ADAR1 genes and one ADAR2 gene exhibited variable expression levels, with CF105370 and CF051320 significantly increasing during early scallop development. ADAR-mediated single-base editing, evaluated across adult C. farreri tissues and developmental stages, was mainly detectable in intergenic regions (83 % and 85 %, respectively). Overall, the expression patterns of the six ADAR genes together with the editing and hyper-editing values computed on scallops RNA-seq samples support the adaptive value of ADAR1-mediated editing, particularly in the pre-settling larval stages.
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Affiliation(s)
| | - Umberto Rosani
- Department of Biology, University of Padova, 35121, Padova, Italy
| | - Akari Sakaguchi
- Laboratory of Aquaculture Biology, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, 980-8572, Japan
| | - Jeongwoong Yoon
- Laboratory of Aquaculture Biology, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, 980-8572, Japan
| | - Kazue Nagasawa
- Laboratory of Aquaculture Biology, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, 980-8572, Japan
| | - Paola Venier
- Department of Biology, University of Padova, 35121, Padova, Italy.
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Jiang D, Kejiou N, Qiu Y, Palazzo AF, Pennell M. Genetic and selective constraints on the optimization of gene product diversity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.17.603951. [PMID: 39091777 PMCID: PMC11291005 DOI: 10.1101/2024.07.17.603951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
RNA and protein expressed from the same gene can have diverse isoforms due to various post-transcriptional and post-translational modifications. For the vast majority of alternative isoforms, It is unknown whether they are adaptive or simply biological noise. As we cannot experimentally probe the function of each isoform, we can ask whether the distribution of isoforms across genes and across species is consistent with expectations from different evolutionary processes. However, there is currently no theoretical framework that can generate such predictions. To address this, we developed a mathematical model where isoform abundances are determined collectively by cis-acting loci, trans-acting factors, gene expression levels, and isoform decay rates to predict isoform abundance distributions across species and genes in the face of mutation, genetic drift, and selection. We found that factors beyond selection, such as effective population size and the number of cis-acting loci, significantly influence evolutionary outcomes. Notably, suboptimal phenotypes are more likely to evolve when the population is small and/or when the number of cis-loci is large. We also explored scenarios where modification processes have both beneficial and detrimental effects, revealing a non-monotonic relationship between effective population size and optimization, demonstrating how opposing selection pressures on cis- and trans-acting loci can constrain the optimization of gene product diversity. As a demonstration of the power of our theory, we compared the expected distribution of A-to-I RNA editing levels in coleoids and found this to be largely consistent with non-adaptive explanations.
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Affiliation(s)
- Daohan Jiang
- Department of Quantitative and Computational Biology, University of Southern California, USA
| | - Nevraj Kejiou
- Department of Biochemistry, University of Toronto, Canada
| | - Yi Qiu
- Department of Biochemistry, University of Toronto, Canada
| | | | - Matt Pennell
- Department of Quantitative and Computational Biology, University of Southern California, USA
- Department of Biological Sciences, University of Southern California, USA
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Zhang N, Chen P, Cui Z, Zhou X, Hao C, Xie B, Hao P, Ye BC, Li X, Jing X. Revealing Differential RNA Editing Specificity of Human ADAR1 and ADAR2 in Schizosaccharomyces pombe. Genes (Basel) 2024; 15:898. [PMID: 39062677 PMCID: PMC11276115 DOI: 10.3390/genes15070898] [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: 04/17/2024] [Revised: 06/21/2024] [Accepted: 06/28/2024] [Indexed: 07/28/2024] Open
Abstract
Adenosine-to-inosine (A-to-I) RNA editing is an important post-transcriptional modification mediated by the adenosine deaminases acting on RNA (ADAR) family of enzymes, expanding the transcriptome by altering selected nucleotides A to I in RNA molecules. Recently, A-to-I editing has been explored for correcting disease-causing mutations in RNA using therapeutic guide oligonucleotides to direct ADAR editing at specific sites. Humans have two active ADARs whose preferences and specificities are not well understood. To investigate their substrate specificity, we introduced hADAR1 and hADAR2, respectively, into Schizosaccharomyces pombe (S. pombe), which lacks endogenous ADARs, and evaluated their editing activities in vivo. Using transcriptome sequencing of S. pombe cultured at optimal growth temperature (30 °C), we identified 483 A-to-I high-confident editing sites for hADAR1 and 404 for hADAR2, compared with the non-editing wild-type control strain. However, these sites were mostly divergent between hADAR1 and hADAR2-expressing strains, sharing 33 common sites that are less than 9% for each strain. Their differential specificity for substrates was attributed to their differential preference for neighboring sequences of editing sites. We found that at the -3-position relative to the editing site, hADAR1 exhibits a tendency toward T, whereas hADAR2 leans toward A. Additionally, when varying the growth temperature for hADAR1- and hADAR2-expressing strains, we observed increased editing sites for them at both 20 and 35 °C, compared with them growing at 30 °C. However, we did not observe a significant shift in hADAR1 and hADAR2's preference for neighboring sequences across three temperatures. The vast changes in RNA editing sites at lower and higher temperatures were also observed for hADAR2 previously in budding yeast, which was likely due to the influence of RNA folding at these different temperatures, among many other factors. We noticed examples of longer lengths of dsRNA around the editing sites that induced editing at 20 or 35 °C but were absent at the other two temperature conditions. We found genes' functions can be greatly affected by editing of their transcripts, for which over 50% of RNA editing sites for both hADAR1 and hADAR2 in S. pombe were in coding sequences (CDS), with more than 60% of them resulting in amino acid changes in protein products. This study revealed the extensive differences in substrate selectivity between the two active human ADARS, i.e., ADAR1 and ADAR2, and provided novel insight when utilizing the two different enzymes for in vivo treatment of human genetic diseases using the RNA editing approach.
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Affiliation(s)
- Niubing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Ping Chen
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zilin Cui
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Xiaojuan Zhou
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Chenhui Hao
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Bingran Xie
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Pei Hao
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Bang-Ce Ye
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Xuan Li
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Xinyun Jing
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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Chattopadhyay P, Mehta P, Kanika, Mishra P, Chen Liu CS, Tarai B, Budhiraja S, Pandey R. RNA editing in host lncRNAs as potential modulator in SARS-CoV-2 variants-host immune response dynamics. iScience 2024; 27:109846. [PMID: 38770134 PMCID: PMC11103575 DOI: 10.1016/j.isci.2024.109846] [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: 02/06/2024] [Revised: 03/18/2024] [Accepted: 04/25/2024] [Indexed: 05/22/2024] Open
Abstract
Both host and viral RNA editing plays a crucial role in host's response to infection, yet our understanding of host RNA editing remains limited. In this study of in-house generated RNA sequencing (RNA-seq) data of 211 hospitalized COVID-19 patients with PreVOC, Delta, and Omicron variants, we observed a significant differential editing frequency and patterns in long non-coding RNAs (lncRNAs), with Delta group displaying lower RNA editing compared to PreVOC/Omicron patients. Notably, multiple transcripts of UGDH-AS1 and NEAT1 exhibited high editing frequencies. Expression of ADAR1/APOBEC3A/APOBEC3G and differential abundance of repeats were possible modulators of differential editing across patient groups. We observed a shift in crucial infection-related pathways wherein the pathways were downregulated in Delta compared to PreVOC and Omicron. Our genomics-based evidence suggests that lncRNA editing influences stability, miRNA binding, and expression of both lncRNA and target genes. Overall, the study highlights the role of lncRNAs and how editing within host lncRNAs modulates the disease severity.
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Affiliation(s)
- Partha Chattopadhyay
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Priyanka Mehta
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Kanika
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
| | - Pallavi Mishra
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
| | - Chinky Shiu Chen Liu
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
| | - Bansidhar Tarai
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi 110017, India
| | - Sandeep Budhiraja
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi 110017, India
| | - Rajesh Pandey
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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Zawisza-Álvarez M, Peñuela-Melero J, Vegas E, Reverter F, Garcia-Fernàndez J, Herrera-Úbeda C. Exploring functional conservation in silico: a new machine learning approach to RNA-editing. Brief Bioinform 2024; 25:bbae332. [PMID: 38980372 PMCID: PMC11232462 DOI: 10.1093/bib/bbae332] [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: 04/19/2024] [Revised: 06/09/2024] [Accepted: 06/25/2024] [Indexed: 07/10/2024] Open
Abstract
Around 50 years ago, molecular biology opened the path to understand changes in forms, adaptations, complexity, or the basis of human diseases through myriads of reports on gene birth, gene duplication, gene expression regulation, and splicing regulation, among other relevant mechanisms behind gene function. Here, with the advent of big data and artificial intelligence (AI), we focus on an elusive and intriguing mechanism of gene function regulation, RNA editing, in which a single nucleotide from an RNA molecule is changed, with a remarkable impact in the increase of the complexity of the transcriptome and proteome. We present a new generation approach to assess the functional conservation of the RNA-editing targeting mechanism using two AI learning algorithms, random forest (RF) and bidirectional long short-term memory (biLSTM) neural networks with an attention layer. These algorithms, combined with RNA-editing data coming from databases and variant calling from same-individual RNA and DNA-seq experiments from different species, allowed us to predict RNA-editing events using both primary sequence and secondary structure. Then, we devised a method for assessing conservation or divergence in the molecular mechanisms of editing completely in silico: the cross-testing analysis. This novel method not only helps to understand the conservation of the editing mechanism through evolution but could set the basis for achieving a better understanding of the adenosine-targeting mechanism in other fields.
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Affiliation(s)
- Michał Zawisza-Álvarez
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Av. Digonal 643, 08028 Barcelona, Spain
- Institut de Biomedicina (IBUB), Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain
| | - Jesús Peñuela-Melero
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Av. Digonal 643, 08028 Barcelona, Spain
| | - Esteban Vegas
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Av. Digonal 643, 08028 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Fragilidad y Envejecimiento Saludable (CIBERFES), Instituto de Salud Carlos III, Calle Sinesio Delgado 4, 28029 Madrid, Spain
| | - Ferran Reverter
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Av. Digonal 643, 08028 Barcelona, Spain
| | - Jordi Garcia-Fernàndez
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Av. Digonal 643, 08028 Barcelona, Spain
- Institut de Biomedicina (IBUB), Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain
| | - Carlos Herrera-Úbeda
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Av. Digonal 643, 08028 Barcelona, Spain
- Institut de Biomedicina (IBUB), Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain
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11
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Liu J, Zheng C, Duan Y. New comparative genomic evidence supporting the proteomic diversification role of A-to-I RNA editing in insects. Mol Genet Genomics 2024; 299:46. [PMID: 38642133 DOI: 10.1007/s00438-024-02141-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 12/29/2023] [Indexed: 04/22/2024]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing, resembling A-to-G mutation, confers adaptiveness by increasing proteomic diversity in a temporal-spatial manner. This evolutionary theory named "proteomic diversifying hypothesis" has only partially been tested in very few organisms like Drosophila melanogaster, mainly by observing the positive selection on nonsynonymous editing events. To find additional genome-wide evidences supporting this interesting assumption, we retrieved the genomes of four Drosophila species and collected 20 deep-sequenced transcriptomes of different developmental stages and neuron populations of D. melanogaster. We systematically profiled the RNA editomes in these samples and performed meticulous comparative genomic analyses. Further evidences were found to support the diversifying hypothesis. (1) None of the nonsynonymous editing sites in D. melanogaster had ancestral G-alleles, while the silent editing sites had an unignorable fraction of ancestral G-alleles; (2) Only very few nonsynonymous editing sites in D. melanogaster had corresponding G-alleles derived in the genomes of sibling species, and the fraction of such situation was significantly lower than that of silent editing sites; (3) The few nonsynonymous editing with corresponding G-alleles had significantly more variable editing levels (across samples) than other nonsynonymous editing sites in D. melanogaster. The proteomic diversifying nature of RNA editing in Drosophila excludes the restorative role which favors an ancestral G-allele. The few fixed G-alleles in sibling species might facilitate the adaptation to particular environment and the corresponding nonsynonymous editing in D. melanogaster would introduce stronger advantage of flexible proteomic diversification. With multi-Omics data, our study consolidates the nature of evolutionary significance of A-to-I RNA editing sites in model insects.
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Affiliation(s)
- Jiyao Liu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Caiqing Zheng
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Yuange Duan
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.
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12
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Sykes AV, Galligioni V, Estefanell J, Hetherington S, Brocca M, Correia J, Ferreira A, Pieroni EM, Fiorito G. FELASA Working Group report: Capture and transport of live cephalopods - recommendations for scientific purposes. Lab Anim 2024; 58:170-182. [PMID: 39003772 PMCID: PMC11102646 DOI: 10.1177/00236772231176347] [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: 10/17/2022] [Accepted: 04/29/2023] [Indexed: 07/16/2024]
Abstract
On 1 January 2013, research using cephalopod molluscs, from hatchlings to adults, became regulated within Directive 2010/63/EU. There are significant difficulties in captive breeding in the great majority of currently utilised species. Thus, scientific research relies upon the use of wild-caught animals. Furthermore, live cephalopods are shared and transported between different stakeholders and laboratories across Europe and other continents. Despite existing European and national legislation, codes, guidelines and reports from independent organisations, a set of recommendations specifically addressing the requirements for the capture and transport of animals belonging to this taxon are missing. In addition, although training and development of competence for all people involved in the supply chain are essential and aim to ensure that animals do not suffer from pain, distress or lasting harm, the requirements for those capturing and transporting wild cephalopods have not been considered. This Working Group reviewed the current literature to recognise scientific evidence and the best practice, and compiled a set of recommendations to provide guidance on the 'techniques' to be used for the capture and transport of live cephalopods for their use in scientific procedures. In addition, we propose to (a) develop standardised approaches able to assess recommended methods and objectively quantify the impact of these processes on animals' health, welfare and stress response, and (b) design a training programme for people attaining the necessary competence for capture and transportation of live cephalopods, as required by Directive 2010/63/EU.
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Affiliation(s)
- Antonio V Sykes
- CCMAR – Centro de Ciências do Mar do Algarve, Universidade do Algarve, Portugal
| | - Viola Galligioni
- Comparative Medicine Unit, institution-id-type="Ringgold" />Trinity College Dublin, Ireland
| | - Juan Estefanell
- Ciclo Superior Cultivos Acuicolas, Instituto de Educacion Secundaria les Profesor Cabrera Pérez, Spain
| | | | | | | | | | | | - Graziano Fiorito
- Association for Cephalopod Research ‘CephRes’, Italy
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Italy
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13
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Duan Y, Ma L, Liu J, Liu X, Song F, Tian L, Cai W, Li H. The first A-to-I RNA editome of hemipteran species Coridius chinensis reveals overrepresented recoding and prevalent intron editing in early-diverging insects. Cell Mol Life Sci 2024; 81:136. [PMID: 38478033 PMCID: PMC10937787 DOI: 10.1007/s00018-024-05175-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 03/17/2024]
Abstract
BACKGROUND Metazoan adenosine-to-inosine (A-to-I) RNA editing resembles A-to-G mutation and increases proteomic diversity in a temporal-spatial manner, allowing organisms adapting to changeable environment. The RNA editomes in many major animal clades remain unexplored, hampering the understanding on the evolution and adaptation of this essential post-transcriptional modification. METHODS We assembled the chromosome-level genome of Coridius chinensis belonging to Hemiptera, the fifth largest insect order where RNA editing has not been studied yet. We generated ten head RNA-Seq libraries with DNA-Seq from the matched individuals. RESULTS We identified thousands of high-confidence RNA editing sites in C. chinensis. Overrepresentation of nonsynonymous editing was observed, but conserved recoding across different orders was very rare. Under cold stress, the global editing efficiency was down-regulated and the general transcriptional processes were shut down. Nevertheless, we found an interesting site with "conserved editing but non-conserved recoding" in potassium channel Shab which was significantly up-regulated in cold, serving as a candidate functional site in response to temperature stress. CONCLUSIONS RNA editing in C. chinensis largely recodes the proteome. The first RNA editome in Hemiptera indicates independent origin of beneficial recoding during insect evolution, which advances our understanding on the evolution, conservation, and adaptation of RNA editing.
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Affiliation(s)
- Yuange Duan
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.
| | - Ling Ma
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Jiyao Liu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Xinzhi Liu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Fan Song
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Li Tian
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Wanzhi Cai
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Hu Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.
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14
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Azad MTA, Sugi T, Qulsum U, Kato K. Detection of Developmental Asexual Stage-Specific RNA Editing Events in Plasmodium falciparum 3D7 Malaria Parasite. Microorganisms 2024; 12:137. [PMID: 38257964 PMCID: PMC10819399 DOI: 10.3390/microorganisms12010137] [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: 10/27/2023] [Revised: 12/24/2023] [Accepted: 12/30/2023] [Indexed: 01/24/2024] Open
Abstract
Transcriptional variation has been studied but post-transcriptional modification due to RNA editing has not been investigated in Plasmodium. We investigated developmental stage-specific RNA editing in selected genes in Plasmodium falciparum 3D7. We detected extensive amination- and deamination-type RNA editing at 8, 16, 24, 32, 40, and 46 h in tightly synchronized Plasmodium. Most of the editing events were observed in 8 and 16 h ring-stage parasites. Extensive A-to-G deamination-type editing was detected more during the 16 h ring stage (25%) than the 8 h ring stage (20%). Extensive U-to-C amination-type editing was detected more during the 16 h ring stage (31%) than the 8 h ring stage (22%). In 28S, rRNA editing converted the loop structure to the stem structure. The hemoglobin binding activity of PF3D7_0216900 was also altered due to RNA editing. Among the expressed 28S rRNA genes, PF3D7_0532000 and PF3D7_0726000 expression was higher. Increased amounts of the transcripts of these two genes were found, particularly PF3D7_0726000 in the ring stage and PF3D7_0532000 in the trophozoite and schizont stages. Adenosine deaminase (ADA) expression did not correlate with the editing level. This first experimental report of RNA editing will help to identify the editing machinery that might be useful for antimalarial drug discovery and malaria control.
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Affiliation(s)
- Md Thoufic Anam Azad
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
- Department of Veterinary and Animal Sciences, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Tatsuki Sugi
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Nishi10-Kita 20, Sapporo 001-0020, Japan
| | - Umme Qulsum
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
- Department of Botany, Faculty of Biological Sciences, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Kentaro Kato
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
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15
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Liu J, Zhao T, Zheng C, Ma L, Song F, Tian L, Cai W, Li H, Duan Y. An orthology-based methodology as a complementary approach to retrieve evolutionarily conserved A-to-I RNA editing sites. RNA Biol 2024; 21:29-45. [PMID: 39256954 PMCID: PMC11404581 DOI: 10.1080/15476286.2024.2397757] [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] [Revised: 08/14/2024] [Accepted: 08/19/2024] [Indexed: 09/12/2024] Open
Abstract
Adar-mediated adenosine-to-inosine (A-to-I) mRNA editing is a conserved mechanism that exerts diverse regulatory functions during the development, evolution, and adaptation of metazoans. The accurate detection of RNA editing sites helps us understand their biological significance. In this work, with an improved genome assembly of honeybee (Apis mellifera), we used a new orthology-based methodology to complement the traditional pipeline of (de novo) RNA editing detection. Compared to the outcome of traditional pipeline, we retrieved many novel editing sites in CDS that are deeply conserved between honeybee and other distantly related insects. The newly retrieved sites were missed by the traditional de novo identification due to the stringent criteria for controlling false-positive rate. Caste-specific editing sites are identified, including an Ile>Met auto-recoding site in Adar. This recoding was even conserved between honeybee and bumblebee, suggesting its putative regulatory role in shaping the phenotypic plasticity of eusocial Hymenoptera. In summary, we proposed a complementary approach to the traditional pipeline and retrieved several previously unnoticed CDS editing sites. From both technical and biological aspects, our works facilitate future researches on finding the functional editing sites and advance our understanding on the connection between RNA editing and the great phenotypic diversity of organisms.
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Affiliation(s)
- Jiyao Liu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Tianyou Zhao
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Caiqing Zheng
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Ling Ma
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Fan Song
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Li Tian
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Wanzhi Cai
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Hu Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
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16
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Borges FO, Sampaio E, Santos CP, Rosa R. Climate-Change Impacts on Cephalopods: A Meta-Analysis. Integr Comp Biol 2023; 63:1240-1265. [PMID: 37468442 DOI: 10.1093/icb/icad102] [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: 06/07/2023] [Revised: 07/13/2023] [Accepted: 07/16/2023] [Indexed: 07/21/2023] Open
Abstract
Aside from being one of the most fascinating groups of marine organisms, cephalopods play a major role in marine food webs, both as predators and as prey, while representing key living economic assets, namely for artisanal and subsistence fisheries worldwide. Recent research suggests that cephalopods are benefitting from ongoing environmental changes and the overfishing of certain fish stocks (i.e., of their predators and/or competitors), putting forward the hypothesis that this group may be one of the few "winners" of climate change. While many meta-analyses have demonstrated negative and overwhelming consequences of ocean warming (OW), acidification (OA), and their combination for a variety of marine taxa, such a comprehensive analysis is lacking for cephalopod molluscs. In this context, the existing literature was surveyed for peer-reviewed articles featuring the sustained (≥24 h) and controlled exposure of cephalopod species (Cephalopoda class) to these factors, applying a comparative framework of mixed-model meta-analyses (784 control-treatment comparisons, from 47 suitable articles). Impacts on a wide set of biological categories at the individual level (e.g., survival, metabolism, behavior, cell stress, growth) were evaluated and contrasted across different ecological attributes (i.e., taxonomic lineages, climates, and ontogenetic stages). Contrary to what is commonly assumed, OW arises as a clear threat to cephalopods, while OA exhibited more restricted impacts. In fact, OW impacts were ubiquitous across different stages of ontogeny, taxonomical lineages (i.e., octopuses, squids, and cuttlefish). These results challenge the assumption that cephalopods benefit from novel ocean conditions, revealing an overarching negative impact of OW in this group. Importantly, we also identify lingering literature gaps, showing that most studies to date focus on OW and early life stages of mainly temperate species. Our results raise the need to consolidate experimental efforts in a wider variety of taxa, climate regions, life stages, and other key environmental stressors, such as deoxygenation and hypoxia, to better understand how cephalopods will cope with future climate change.
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Affiliation(s)
- Francisco O Borges
- MARE-Marine and Environmental Sciences Centre/ARNET-Aquatic Research Network, Laboratório Marítimo da Guia, Faculdade de Ciências, Universidade de Lisboa, Cascais, Lisboa 1749-016, Portugal
| | - Eduardo Sampaio
- Department of Collective Behaviour, Max Planck Institute of Animal Behavior, Universitatsstrasse 10, Konstanz 78464, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz 78464, Germany
- Department of Biology, University of Konstanz, Universitatsstrasse 10, Konstanz 78464, Germany
| | - Catarina P Santos
- MARE-Marine and Environmental Sciences Centre/ARNET-Aquatic Research Network, Laboratório Marítimo da Guia, Faculdade de Ciências, Universidade de Lisboa, Cascais, Lisboa 1749-016, Portugal
- Environmental Economics Knowledge Center, Nova School of Business and Economics, New University of Lisbon, Carcavelos 2775-405, Portugal
- Sphyrna Association, Boa Vista Island, Sal Rei, Cape Verde
| | - Rui Rosa
- MARE-Marine and Environmental Sciences Centre/ARNET-Aquatic Research Network, Laboratório Marítimo da Guia, Faculdade de Ciências, Universidade de Lisboa, Cascais, Lisboa 1749-016, Portugal
- Department of Animal Biology, Faculdade de Ciências da Universidade de Lisboa, Lisboa1 749-016, Portugal
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17
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Baden T, Briseño J, Coffing G, Cohen-Bodénès S, Courtney A, Dickerson D, Dölen G, Fiorito G, Gestal C, Gustafson T, Heath-Heckman E, Hua Q, Imperadore P, Kimbara R, Król M, Lajbner Z, Lichilín N, Macchi F, McCoy MJ, Nishiguchi MK, Nyholm SV, Otjacques E, Pérez-Ferrer PA, Ponte G, Pungor JR, Rogers TF, Rosenthal JJC, Rouressol L, Rubas N, Sanchez G, Santos CP, Schultz DT, Seuntjens E, Songco-Casey JO, Stewart IE, Styfhals R, Tuanapaya S, Vijayan N, Weissenbacher A, Zifcakova L, Schulz G, Weertman W, Simakov O, Albertin CB. Cephalopod-omics: Emerging Fields and Technologies in Cephalopod Biology. Integr Comp Biol 2023; 63:1226-1239. [PMID: 37370232 PMCID: PMC10755191 DOI: 10.1093/icb/icad087] [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: 12/05/2022] [Revised: 06/09/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Few animal groups can claim the level of wonder that cephalopods instill in the minds of researchers and the general public. Much of cephalopod biology, however, remains unexplored: the largest invertebrate brain, difficult husbandry conditions, and complex (meta-)genomes, among many other things, have hindered progress in addressing key questions. However, recent technological advancements in sequencing, imaging, and genetic manipulation have opened new avenues for exploring the biology of these extraordinary animals. The cephalopod molecular biology community is thus experiencing a large influx of researchers, emerging from different fields, accelerating the pace of research in this clade. In the first post-pandemic event at the Cephalopod International Advisory Council (CIAC) conference in April 2022, over 40 participants from all over the world met and discussed key challenges and perspectives for current cephalopod molecular biology and evolution. Our particular focus was on the fields of comparative and regulatory genomics, gene manipulation, single-cell transcriptomics, metagenomics, and microbial interactions. This article is a result of this joint effort, summarizing the latest insights from these emerging fields, their bottlenecks, and potential solutions. The article highlights the interdisciplinary nature of the cephalopod-omics community and provides an emphasis on continuous consolidation of efforts and collaboration in this rapidly evolving field.
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Affiliation(s)
- Tom Baden
- School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK
| | - John Briseño
- Molecular and Cell Biology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Gabrielle Coffing
- Biology Department: Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA
| | - Sophie Cohen-Bodénès
- Laboratoire des Systèmes Perceptifs, Département d'Etudes Cognitives, Ecole Normale Supérieure, PSL University, CNRS, 75005 Paris, France
| | - Amy Courtney
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Dominick Dickerson
- Friday Harbor Laboratory, University of Washington, Seattle, WA 98250, USA
| | - Gül Dölen
- Department of Neuroscience, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Graziano Fiorito
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy
| | - Camino Gestal
- Laboratory of Marine Molecular Pathobiology, Institute of Marine Research (IIM), Spanish National Research Council (CSIC), Vigo 36208, Spain
| | | | - Elizabeth Heath-Heckman
- Departments of Integrative Biology and Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Qiaz Hua
- Department of Ecology and Evolution, University of Adelaide, Adelaide, South Australia 5000, Australia
| | - Pamela Imperadore
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy
| | - Ryosuke Kimbara
- Misaki Marine Biological Station, School of Science, The University of Tokyo, Miura, Kanagawa 238-0225, Japan
| | - Mirela Król
- Adam Mickiewicz University in Poznań, Poznań 61-712, Poland
| | - Zdeněk Lajbner
- Physics and Biology Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Kunigami District, Okinawa 904-0495, Japan
| | - Nicolás Lichilín
- Department of Neurosciences and Developmental Biology, University of Vienna, Vienna 1010, Austria
| | - Filippo Macchi
- Program in Biology, New York University Abu Dhabi, P.O. Box 129188 Abu Dhabi, United Arab Emirates
| | - Matthew J McCoy
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Michele K Nishiguchi
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, 5200 N. Lake Blvd., Merced, CA 95343, USA
| | - Spencer V Nyholm
- Molecular and Cell Biology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Eve Otjacques
- MARE—Marine and Environmental Sciences Centre & ARNET—Aquatic Research Network, Laboratório Marítimo da Guia, Faculdade de Ciências, Universidade de Lisboa, Av. Nossa Senhora do Cabo, 939, 2750-374 Cascais, Portugal
- Division of Biosphere Sciences and Engineering, Carnegie Institution for Science, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Pedro Antonio Pérez-Ferrer
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, 5200 N. Lake Blvd., Merced, CA 95343, USA
| | - Giovanna Ponte
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy
| | - Judit R Pungor
- Biology Department: Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA
| | - Thea F Rogers
- Department of Neurosciences and Developmental Biology, University of Vienna, Vienna 1010, Austria
| | - Joshua J C Rosenthal
- Marine Biological Laboratory, The Eugene Bell Center for Regenerative Biology and Tissue Engineering, Woods Hole, MA 02543-1015, USA
| | - Lisa Rouressol
- Department of Neurosciences and Developmental Biology, University of Vienna, Vienna 1010, Austria
| | - Noelle Rubas
- Department of Molecular Biosciences and Bioengineering, University of Hawaii Manoa, Honolulu, HI 96822, USA
| | - Gustavo Sanchez
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Catarina Pereira Santos
- MARE—Marine and Environmental Sciences Centre & ARNET—Aquatic Research Network, Laboratório Marítimo da Guia, Faculdade de Ciências, Universidade de Lisboa, Av. Nossa Senhora do Cabo, 939, 2750-374 Cascais, Portugal
| | - Darrin T Schultz
- Department of Neurosciences and Developmental Biology, University of Vienna, Vienna 1010, Austria
| | - Eve Seuntjens
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven 3000, Belgium
| | - Jeremea O Songco-Casey
- Biology Department: Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA
| | - Ian Erik Stewart
- Neural Circuits and Behaviour Lab, Max‐Delbrück‐Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin 13125, Germany
| | - Ruth Styfhals
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven 3000, Belgium
| | - Surangkana Tuanapaya
- Laboratory of genetics and applied breeding of molluscs, Fisheries College, Ocean University of China, Qingdao 266100, China
| | - Nidhi Vijayan
- Molecular and Cell Biology Department, University of Connecticut, Storrs, CT 06269, USA
| | | | - Lucia Zifcakova
- Physics and Biology Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Kunigami District, Okinawa 904-0495, Japan
| | | | - Willem Weertman
- Friday Harbor Laboratory, University of Washington, Seattle, WA 98250, USA
| | - Oleg Simakov
- Department of Neurosciences and Developmental Biology, University of Vienna, Vienna 1010, Austria
| | - Caroline B Albertin
- Marine Biological Laboratory, The Eugene Bell Center for Regenerative Biology and Tissue Engineering, Woods Hole, MA 02543-1015, USA
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18
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Chaung K, Baharav TZ, Henderson G, Zheludev IN, Wang PL, Salzman J. SPLASH: A statistical, reference-free genomic algorithm unifies biological discovery. Cell 2023; 186:5440-5456.e26. [PMID: 38065078 PMCID: PMC10861363 DOI: 10.1016/j.cell.2023.10.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 08/31/2023] [Accepted: 10/26/2023] [Indexed: 12/18/2023]
Abstract
Today's genomics workflows typically require alignment to a reference sequence, which limits discovery. We introduce a unifying paradigm, SPLASH (Statistically Primary aLignment Agnostic Sequence Homing), which directly analyzes raw sequencing data, using a statistical test to detect a signature of regulation: sample-specific sequence variation. SPLASH detects many types of variation and can be efficiently run at scale. We show that SPLASH identifies complex mutation patterns in SARS-CoV-2, discovers regulated RNA isoforms at the single-cell level, detects the vast sequence diversity of adaptive immune receptors, and uncovers biology in non-model organisms undocumented in their reference genomes: geographic and seasonal variation and diatom association in eelgrass, an oceanic plant impacted by climate change, and tissue-specific transcripts in octopus. SPLASH is a unifying approach to genomic analysis that enables expansive discovery without metadata or references.
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Affiliation(s)
- Kaitlin Chaung
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Tavor Z Baharav
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
| | - George Henderson
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Ivan N Zheludev
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Peter L Wang
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Julia Salzman
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University, Stanford, CA 94305, USA; Department of Statistics (by courtesy), Stanford University, Stanford, CA 94305, USA; Department of Biology (by courtesy), Stanford University, Stanford, CA 94305, USA.
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19
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Xu Y, Liu J, Zhao T, Song F, Tian L, Cai W, Li H, Duan Y. Identification and Interpretation of A-to-I RNA Editing Events in Insect Transcriptomes. Int J Mol Sci 2023; 24:17126. [PMID: 38138955 PMCID: PMC10742984 DOI: 10.3390/ijms242417126] [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: 09/30/2023] [Revised: 12/01/2023] [Accepted: 12/03/2023] [Indexed: 12/24/2023] Open
Abstract
Adenosine-to-inosine (A-to-I) RNA editing is the most prevalent RNA modification in the nervous systems of metazoans. To study the biological significance of RNA editing, we first have to accurately identify these editing events from the transcriptome. The genome-wide identification of RNA editing sites remains a challenging task. In this review, we will first introduce the occurrence, regulation, and importance of A-to-I RNA editing and then describe the established bioinformatic procedures and difficulties in the accurate identification of these sit esespecially in small sized non-model insects. In brief, (1) to obtain an accurate profile of RNA editing sites, a transcriptome coupled with the DNA resequencing of a matched sample is favorable; (2) the single-cell sequencing technique is ready to be applied to RNA editing studies, but there are a few limitations to overcome; (3) during mapping and variant calling steps, various issues, like mapping and base quality, soft-clipping, and the positions of mismatches on reads, should be carefully considered; (4) Sanger sequencing of both RNA and the matched DNA is the best verification of RNA editing sites, but other auxiliary evidence, like the nonsynonymous-to-synonymous ratio or the linkage information, is also helpful for judging the reliability of editing sites. We have systematically reviewed the understanding of the biological significance of RNA editing and summarized the methodology for identifying such editing events. We also raised several promising aspects and challenges in this field. With insightful perspectives on both scientific and technical issues, our review will benefit the researchers in the broader RNA editing community.
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Affiliation(s)
| | | | | | | | | | | | | | - Yuange Duan
- MOA Key Lab of Pest Monitoring and Green Management, Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (Y.X.); (J.L.); (T.Z.); (F.S.); (L.T.); (W.C.); (H.L.)
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20
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Dissegna A, Borrelli L, Ponte G, Chiandetti C, Fiorito G. Octopus vulgaris Exhibits Interindividual Differences in Behavioural and Problem-Solving Performance. BIOLOGY 2023; 12:1487. [PMID: 38132313 PMCID: PMC10740590 DOI: 10.3390/biology12121487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 11/26/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023]
Abstract
By presenting individual Octopus vulgaris with an extractive foraging problem with a puzzle box, we examined the possible correlation between behavioural performances (e.g., ease of adaptation to captive conditions, prevalence of neophobic and neophilic behaviours, and propensity to learn individually or by observing conspecifics), biotic (body and brain size, age, sex) and abiotic (seasonality and place of origin) factors. We found more neophilic animals showing shorter latencies to approach the puzzle box and higher probability of solving the task; also, shorter times to solve the task were correlated with better performance on the individual learning task. However, the most neophilic octopuses that approached the puzzle box more quickly did not reach the solution earlier than other individuals, suggesting that strong neophilic tendency may lead to suboptimal performance at some stages of the problem-solving process. In addition, seasonal and environmental characteristics of location of origin appear to influence the rate of expression of individual traits central to problem solving. Overall, our analysis provides new insights into the traits associated with problem solving in invertebrates and highlights the presence of adaptive mechanisms that promote population-level changes in octopuses' behavioural traits.
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Affiliation(s)
- Andrea Dissegna
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (A.D.); (C.C.)
| | - Luciana Borrelli
- Animal Physiology and Evolution Lab, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy;
| | - Giovanna Ponte
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy;
| | - Cinzia Chiandetti
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (A.D.); (C.C.)
| | - Graziano Fiorito
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy;
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21
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Xie Y, Chan LY, Cheung MY, Li MW, Lam HM. Current technical advancements in plant epitranscriptomic studies. THE PLANT GENOME 2023; 16:e20316. [PMID: 36890704 DOI: 10.1002/tpg2.20316] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/05/2023] [Indexed: 06/18/2023]
Abstract
The growth and development of plants are the result of the interplay between the internal developmental programming and plant-environment interactions. Gene expression regulations in plants are made up of multi-level networks. In the past few years, many studies were carried out on co- and post-transcriptional RNA modifications, which, together with the RNA community, are collectively known as the "epitranscriptome." The epitranscriptomic machineries were identified and their functional impacts characterized in a broad range of physiological processes in diverse plant species. There is mounting evidence to suggest that the epitranscriptome provides an additional layer in the gene regulatory network for plant development and stress responses. In the present review, we summarized the epitranscriptomic modifications found so far in plants, including chemical modifications, RNA editing, and transcript isoforms. The various approaches to RNA modification detection were described, with special emphasis on the recent development and application potential of third-generation sequencing. The roles of epitranscriptomic changes in gene regulation during plant-environment interactions were discussed in case studies. This review aims to highlight the importance of epitranscriptomics in the study of gene regulatory networks in plants and to encourage multi-omics investigations using the recent technical advancements.
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Affiliation(s)
- Yichun Xie
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Long-Yiu Chan
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Ming-Yan Cheung
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Man-Wah Li
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Hon-Ming Lam
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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22
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Voss G, Rosenthal JJC. High-level RNA editing diversifies the coleoid cephalopod brain proteome. Brief Funct Genomics 2023; 22:525-532. [PMID: 37981860 DOI: 10.1093/bfgp/elad034] [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: 06/11/2023] [Revised: 07/20/2023] [Accepted: 07/25/2023] [Indexed: 11/21/2023] Open
Abstract
Coleoid cephalopods (octopus, squid and cuttlefish) have unusually complex nervous systems. The coleoid nervous system is also the only one currently known to recode the majority of expressed proteins through A-to-I RNA editing. The deamination of adenosine by adenosine deaminase acting on RNA (ADAR) enzymes produces inosine, which is interpreted as guanosine during translation. If this occurs in an open reading frame, which is the case for tens of thousands of editing sites in coleoids, it can recode the encoded protein. Here, we describe recent findings aimed at deciphering the mechanisms underlying high-level recoding and its adaptive potential. We describe the complement of ADAR enzymes in cephalopods, including a recently discovered novel domain in sqADAR1. We further summarize current evidence supporting an adaptive role of high-level RNA recoding in coleoids, and review recent studies showing that a large proportion of recoding sites is temperature-sensitive. Despite these new findings, the mechanisms governing the high level of RNA recoding in coleoid cephalopods remain poorly understood. Recent advances using genome editing in squid may provide useful tools to further study A-to-I RNA editing in these animals.
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Affiliation(s)
- Gjendine Voss
- The Eugene Bell Center, The Marine Biological Laboratory, 7 MBL Street, Woods Hole MA 02543, United States
| | - Joshua J C Rosenthal
- The Eugene Bell Center, The Marine Biological Laboratory, 7 MBL Street, Woods Hole MA 02543, United States
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23
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Nguyen TA, Heng JWJ, Ng YT, Sun R, Fisher S, Oguz G, Kaewsapsak P, Xue S, Reversade B, Ramasamy A, Eisenberg E, Tan MH. Deep transcriptome profiling reveals limited conservation of A-to-I RNA editing in Xenopus. BMC Biol 2023; 21:251. [PMID: 37946231 PMCID: PMC10636886 DOI: 10.1186/s12915-023-01756-2] [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: 07/25/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Xenopus has served as a valuable model system for biomedical research over the past decades. Notably, ADAR was first detected in frog oocytes and embryos as an activity that unwinds RNA duplexes. However, the scope of A-to-I RNA editing by the ADAR enzymes in Xenopus remains underexplored. RESULTS Here, we identify millions of editing events in Xenopus with high accuracy and systematically map the editome across developmental stages, adult organs, and species. We report diverse spatiotemporal patterns of editing with deamination activity highest in early embryogenesis before zygotic genome activation and in the ovary. Strikingly, editing events are poorly conserved across different Xenopus species. Even sites that are detected in both X. laevis and X. tropicalis show largely divergent editing levels or developmental profiles. In protein-coding regions, only a small subset of sites that are found mostly in the brain are well conserved between frogs and mammals. CONCLUSIONS Collectively, our work provides fresh insights into ADAR activity in vertebrates and suggest that species-specific editing may play a role in each animal's unique physiology or environmental adaptation.
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Affiliation(s)
- Tram Anh Nguyen
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
| | - Jia Wei Joel Heng
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
| | - Yan Ting Ng
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Rui Sun
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
| | - Shira Fisher
- Faculty of Life Sciences, The Mina and Everard Goodman, Bar-Ilan University, Ramat Gan, Israel
| | - Gokce Oguz
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
| | - Pornchai Kaewsapsak
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Shifeng Xue
- Institute of Molecular and Cell Biology, Agency for Science Technology and Research, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Bruno Reversade
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
- Institute of Molecular and Cell Biology, Agency for Science Technology and Research, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Medical Genetics, School of Medicine (KUSoM), Koç University, Istanbul, Turkey
| | - Adaikalavan Ramasamy
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv, Israel
| | - Meng How Tan
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore.
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore.
- HP-NTU Digital Manufacturing Corporate Lab, Nanyang Technological University, Singapore, Singapore.
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24
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Tan MH. Identification of Bona Fide RNA Editing Sites: History, Challenges, and Opportunities. Acc Chem Res 2023; 56:3033-3044. [PMID: 37827987 DOI: 10.1021/acs.accounts.3c00462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing, catalyzed by the adenosine deaminase acting on the RNA (ADAR) family of enzymes of which there are three members (ADAR1, ADAR2, and ADAR3), is a major gene regulatory mechanism that diversifies the transcriptome. It is widespread in many metazoans, including humans. As inosine is interpreted by cellular machineries mainly as guanosine, A-to-I editing effectively gives A-to-G nucleotide changes. Depending on its location, an editing event can generate new protein isoforms or influence other RNA processing pathways. Researchers have found that ADAR-mediated editing performs diverse functions. For example, it enables living organisms such as cephalopods to adapt rapidly to fluctuating environmental conditions such as water temperature. In development, the loss of ADAR1 is embryonically lethal partly because endogenous double-stranded RNAs (dsRNAs) are no longer marked by inosines, which signal "self", and thus cause the melanoma differentiation-associated protein 5 (MDA5) sensor to trigger a deleterious interferon response. Hence, ADAR1 plays a key role in preventing aberrant activation of the innate immune system. Furthermore, ADAR enzymes have been implicated in myriad human diseases. Intriguingly, some cancer cells are known to exploit ADAR1 activity to dodge immune responses. However, the exact identities of immunogenic RNAs in different biological contexts have remained elusive. Consequently, there is tremendous interest in identifying inosine-containing RNAs in the cell.The identification of A-to-I RNA editing sites is dependent on the sequencing of nucleic acids. Technological and algorithmic advancements over the past decades have revolutionized the way editing events are detected. At the beginning, the discovery of editing sites relies on Sanger sequencing, a first-generation technology. Both RNA, which is reverse transcribed into complementary DNA (cDNA), and genomic DNA (gDNA) from the same source are analyzed. After sequence alignment, one would require an adenosine to be present in the genome but a guanosine to be detected in the RNA sample for a position to be declared as an editing site. However, an issue with Sanger sequencing is its low throughput. Subsequently, Illumina sequencing, a second-generation technology, was invented. By permitting the simultaneous interrogation of millions of molecules, it enables many editing sites to be identified rapidly. However, a key challenge is that the Illumina platform produces short sequencing reads that can be difficult to map accurately. To tackle the challenge, we and others developed computational workflows with a series of filters to discard sites that are likely to be false positives. When Illumina sequencing data sets are properly analyzed, A-to-G variants should emerge as the most dominant mismatch type. Moreover, the quantitative nature of the data allows us to build a comprehensive atlas of editing-level measurements across different biological contexts, providing deep insights into the spatiotemporal dynamics of RNA editing. However, difficulties remain in identifying true A-to-I editing sites in short protein-coding exons or in organisms and diseases where DNA mutations and genomic polymorphisms are prevalent and mostly unknown. Nanopore sequencing, a third-generation technology, promises to address the difficulties, as it allows native RNAs to be sequenced without conversion to cDNA, preserving base modifications that can be directly detected through machine learning. We recently demonstrated that nanopore sequencing could be used to identify A-to-I editing sites in native RNA directly. Although further work is needed to enhance the detection accuracy in single molecules from fewer cells, the nanopore technology holds the potential to revolutionize epitranscriptomic studies.
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Affiliation(s)
- Meng How Tan
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore 637459, Singapore
- HP-NTU Digital Manufacturing Corporate Laboratory, Nanyang Technological University, Singapore 637460, Singapore
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25
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Dyakonova VE. DNA Instability in Neurons: Lifespan Clock and Driver of Evolution. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1719-1731. [PMID: 38105193 DOI: 10.1134/s0006297923110044] [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: 07/17/2023] [Revised: 07/19/2023] [Accepted: 09/20/2023] [Indexed: 12/19/2023]
Abstract
In the last ten years, the discovery of neuronal DNA postmitotic instability has changed the theoretical landscape in neuroscience and, more broadly, biology. In 2003, A. M. Olovnikov suggested that neuronal DNA is the "initial substrate of aging". Recent experimental data have significantly increased the likelihood of this hypothesis. How does neuronal DNA accumulate damage and in what genome regions? What factors contribute to this process and how are they associated with aging and lifespan? These questions will be discussed in the review. In the course of Metazoan evolution, the instability of neuronal DNA has been accompanied by searching for the pathways to reduce the biological cost of brain activity. Various processes and activities, such as sleep, evolutionary increase in the number of neurons in the vertebrate brain, adult neurogenesis, distribution of neuronal activity, somatic polyploidy, and RNA editing in cephalopods, can be reconsidered in the light of the trade-off between neuronal plasticity and DNA instability in neurons. This topic is of considerable importance for both fundamental neuroscience and translational medicine.
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Affiliation(s)
- Varvara E Dyakonova
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
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26
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Zhang Y, Duan Y. Genome-Wide Analysis on Driver and Passenger RNA Editing Sites Suggests an Underestimation of Adaptive Signals in Insects. Genes (Basel) 2023; 14:1951. [PMID: 37895300 PMCID: PMC10606203 DOI: 10.3390/genes14101951] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
Adenosine-to-inosine (A-to-I) RNA editing leads to a similar effect to A-to-G mutations. RNA editing provides a temporo-spatial flexibility for organisms. Nonsynonymous (Nonsyn) RNA editing in insects is over-represented compared with synonymous (Syn) editing, suggesting adaptive signals of positive selection on Nonsyn editing during evolution. We utilized the brain RNA editome of Drosophila melanogaster to systematically study the LD (r2) between editing sites and infer its impact on the adaptive signals of RNA editing. Pairs of editing sites (PESs) were identified from the transcriptome. For CDS PESs of two consecutive editing sites, their occurrence was significantly biased to type-3 PES (Syn-Nonsyn). The haplotype frequency of type-3 PES exhibited a significantly higher abundance of AG than GA, indicating that the rear Nonsyn site is the driver that promotes the editing of the front Syn site (passenger). The exclusion of passenger Syn sites dramatically amplifies the adaptive signal of Nonsyn RNA editing. Our study for the first time quantitatively demonstrates that the linkage between RNA editing events comes from hitchhiking effects and leads to the underestimation of adaptive signals for Nonsyn editing. Our work provides novel insights for studying the evolutionary significance of RNA editing events.
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Affiliation(s)
| | - Yuange Duan
- MOA Key Lab of Pest Monitoring and Green Management, Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China;
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27
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Wang J, Li G, Wu M. Cephalopod RNA recoding: linking protein plasticity to thermal adaptation and catalyzing beyond-species protein characterization. Signal Transduct Target Ther 2023; 8:387. [PMID: 37840034 PMCID: PMC10577124 DOI: 10.1038/s41392-023-01632-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 08/10/2023] [Accepted: 08/28/2023] [Indexed: 10/17/2023] Open
Affiliation(s)
- Junyi Wang
- Laboratory of Allergy and Precision Medicine, Department of Pulmonary and Critical Care Medicine, Chengdu Institute of Respiratory Health, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China.
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau SAR, China.
| | - Guoping Li
- Laboratory of Allergy and Precision Medicine, Department of Pulmonary and Critical Care Medicine, Chengdu Institute of Respiratory Health, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China.
| | - Min Wu
- Wenzhou Institute, University of Chinese Academy of Sciences, 325000, Wenzhou, Zhejiang, China.
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28
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Duan Y, Ma L, Song F, Tian L, Cai W, Li H. Autorecoding A-to-I RNA editing sites in the Adar gene underwent compensatory gains and losses in major insect clades. RNA (NEW YORK, N.Y.) 2023; 29:1509-1519. [PMID: 37451866 PMCID: PMC10578469 DOI: 10.1261/rna.079682.123] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 06/13/2023] [Indexed: 07/18/2023]
Abstract
As one of the most prevalent RNA modifications in animals, adenosine-to-inosine (A-to-I) RNA editing facilitates the environmental adaptation of organisms by diversifying the proteome in a temporal-spatial manner. In flies and bees, the editing enzyme Adar has independently gained two different autorecoding sites that form an autofeedback loop, stabilizing the overall editing efficiency. This ensures cellular homeostasis by keeping the normal function of target genes. However, in a broader range of insects, the evolutionary dynamics and significance of this Adar autoregulatory mechanism are unclear. We retrieved the genomes of 377 arthropod species covering the five major insect orders (Hemiptera, Hymenoptera, Coleoptera, Diptera, and Lepidoptera) and aligned the Adar autorecoding sites across all genomes. We found that the two autorecoding sites underwent compensatory gains and losses during the evolution of two orders with the most sequenced species (Diptera and Hymenoptera), and that the two editing sites were mutually exclusive among them: One editable site is significantly linked to another uneditable site. This autorecoding mechanism of Adar could flexibly diversify the proteome and stabilize global editing activity. Many insects independently selected different autorecoding sites to achieve a feedback loop and regulate the global RNA editome, revealing an interesting phenomenon during evolution. Our study reveals the evolutionary force acting on accurate regulation of RNA editing activity in insects and thus deepens our understanding of the functional importance of RNA editing in environmental adaptation and evolution.
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Affiliation(s)
- Yuange Duan
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Ling Ma
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Fan Song
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Li Tian
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Wanzhi Cai
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Hu Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
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29
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Barrera Grijalba CC, Rodríguez Monje SV, Gestal C, Wollesen T. Octopod Hox genes and cephalopod plesiomorphies. Sci Rep 2023; 13:15492. [PMID: 37726311 PMCID: PMC10509229 DOI: 10.1038/s41598-023-42435-0] [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: 06/30/2023] [Accepted: 09/10/2023] [Indexed: 09/21/2023] Open
Abstract
Few other invertebrates captivate our attention as cephalopods do. Octopods, cuttlefish, and squids amaze with their behavior and sophisticated body plans that belong to the most intriguing among mollusks. Little is, however, known about their body plan formation and the role of Hox genes. The latter homeobox genes pattern the anterior-posterior body axis and have only been studied in a single decapod species so far. Here, we study developmental Hox and ParaHox gene expression in Octopus vulgaris. Hox genes are expressed in a near-to-staggered fashion, among others in homologous organs of cephalopods such as the stellate ganglia, the arms, or funnel. As in other mollusks Hox1 is expressed in the nascent octopod shell rudiment. While ParaHox genes are expressed in an evolutionarily conserved fashion, Hox genes are also expressed in some body regions that are considered homologous among mollusks such as the cephalopod arms and funnel with the molluscan foot. We argue that cephalopod Hox genes are recruited to a lesser extent into the formation of non-related organ systems than previously thought and emphasize that despite all morphological innovations molecular data still reveal the ancestral molluscan heritage of cephalopods.
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Affiliation(s)
| | - Sonia Victoria Rodríguez Monje
- Department of Evolutionary Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Camino Gestal
- Institute of Marine Research (IIM-CSIC), Eduardo Cabello 6, 36208, Vigo, Spain
| | - Tim Wollesen
- Department of Evolutionary Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
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Xie Y, Chan PL, Kwan HS, Chang J. The Genome-Wide Characterization of Alternative Splicing and RNA Editing in the Development of Coprinopsis cinerea. J Fungi (Basel) 2023; 9:915. [PMID: 37755023 PMCID: PMC10532568 DOI: 10.3390/jof9090915] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/17/2023] [Accepted: 09/07/2023] [Indexed: 09/28/2023] Open
Abstract
Coprinopsis cinerea is one of the model species used in fungal developmental studies. This mushroom-forming Basidiomycetes fungus has several developmental destinies in response to changing environments, with dynamic developmental regulations of the organism. Although the gene expression in C. cinerea development has already been profiled broadly, previous studies have only focused on a specific stage or process of fungal development. A comprehensive perspective across different developmental paths is lacking, and a global view on the dynamic transcriptional regulations in the life cycle and the developmental paths is far from complete. In addition, knowledge on co- and post-transcriptional modifications in this fungus remains rare. In this study, we investigated the transcriptional changes and modifications in C. cinerea during the processes of spore germination, vegetative growth, oidiation, sclerotia formation, and fruiting body formation by inducing different developmental paths of the organism and profiling the transcriptomes using the high-throughput sequencing method. Transition in the identity and abundance of expressed genes drive the physiological and morphological alterations of the organism, including metabolism and multicellularity construction. Moreover, stage- and tissue-specific alternative splicing and RNA editing took place and functioned in C. cinerea. These modifications were negatively correlated to the conservation features of genes and could provide extra plasticity to the transcriptome during fungal development. We suggest that C. cinerea applies different molecular strategies in its developmental regulation, including shifts in expressed gene sets, diversifications of genetic information, and reversible diversifications of RNA molecules. Such features would increase the fungal adaptability in the rapidly changing environment, especially in the transition of developmental programs and the maintenance and balance of genetic and transcriptomic divergence. The multi-layer regulatory network of gene expression serves as the molecular basis of the functioning of developmental regulation.
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Affiliation(s)
- Yichun Xie
- State Key Laboratory of Agrobiotechnology, Food Research Center, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China;
| | - Po-Lam Chan
- Food Research Center, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Hoi-Shan Kwan
- Food Research Center, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Jinhui Chang
- Department of Food Science and Nutrition, and Research Institute for Future Food, The Hong Kong Polytechnic University, Hong Kong SAR, China
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31
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Chaung K, Baharav TZ, Henderson G, Zheludev IN, Wang PL, Salzman J. [WITHDRAWN] SPLASH: a statistical, reference-free genomic algorithm unifies biological discovery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.17.549408. [PMID: 37503014 PMCID: PMC10370119 DOI: 10.1101/2023.07.17.549408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The authors have withdrawn this manuscript due to a duplicate posting of manuscript number BIORXIV/2022/497555. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author. The correct preprint can be found at doi: https://doi.org/10.1101/2022.06.24.497555.
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Ahuja N, Hwaun E, Pungor JR, Rafiq R, Nemes S, Sakmar T, Vogt MA, Grasse B, Diaz Quiroz J, Montague TG, Null RW, Dallis DN, Gavriouchkina D, Marletaz F, Abbo L, Rokhsar DS, Niell CM, Soltesz I, Albertin CB, Rosenthal JJC. Creation of an albino squid line by CRISPR-Cas9 and its application for in vivo functional imaging of neural activity. Curr Biol 2023:S0960-9822(23)00739-X. [PMID: 37343558 DOI: 10.1016/j.cub.2023.05.066] [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: 02/23/2023] [Revised: 05/17/2023] [Accepted: 05/26/2023] [Indexed: 06/23/2023]
Abstract
Cephalopods are remarkable among invertebrates for their cognitive abilities, adaptive camouflage, novel structures, and propensity for recoding proteins through RNA editing. Due to the lack of genetically tractable cephalopod models, however, the mechanisms underlying these innovations are poorly understood. Genome editing tools such as CRISPR-Cas9 allow targeted mutations in diverse species to better link genes and function. One emerging cephalopod model, Euprymna berryi, produces large numbers of embryos that can be easily cultured throughout their life cycle and has a sequenced genome. As proof of principle, we used CRISPR-Cas9 in E. berryi to target the gene for tryptophan 2,3 dioxygenase (TDO), an enzyme required for the formation of ommochromes, the pigments present in the eyes and chromatophores of cephalopods. CRISPR-Cas9 ribonucleoproteins targeting tdo were injected into early embryos and then cultured to adulthood. Unexpectedly, the injected specimens were pigmented, despite verification of indels at the targeted sites by sequencing in injected animals (G0s). A homozygote knockout line for TDO, bred through multiple generations, was also pigmented. Surprisingly, a gene encoding indoleamine 2,3, dioxygenase (IDO), an enzyme that catalyzes the same reaction as TDO in vertebrates, was also present in E. berryi. Double knockouts of both tdo and ido with CRISPR-Cas9 produced an albino phenotype. We demonstrate the utility of these albinos for in vivo imaging of Ca2+ signaling in the brain using two-photon microscopy. These data show the feasibility of making gene knockout cephalopod lines that can be used for live imaging of neural activity in these behaviorally sophisticated organisms.
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Affiliation(s)
- Namrata Ahuja
- Eugene Bell Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Ernie Hwaun
- Department of Neurosurgery and Stanford Neurosciences Institute, Stanford University, Stanford, CA 94305, USA
| | - Judit R Pungor
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Ruhina Rafiq
- Eugene Bell Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Sal Nemes
- Eugene Bell Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Taylor Sakmar
- Marine Resources Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Miranda A Vogt
- Marine Resources Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Bret Grasse
- Marine Resources Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Juan Diaz Quiroz
- Eugene Bell Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Tessa G Montague
- Department of Neuroscience, Columbia University, New York, NY 10027, USA
| | - Ryan W Null
- Eugene Bell Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Danielle N Dallis
- Marine Resources Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Daria Gavriouchkina
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0412, Japan
| | - Ferdinand Marletaz
- Centre for Life's Origin & Evolution, Department of Ecology, Evolution & Environment, University College London, WC1E 6BT London, UK
| | - Lisa Abbo
- Marine Resources Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Daniel S Rokhsar
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0412, Japan; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | | | - Ivan Soltesz
- Department of Neurosurgery and Stanford Neurosciences Institute, Stanford University, Stanford, CA 94305, USA
| | - Caroline B Albertin
- Eugene Bell Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA.
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Rangan KJ, Reck-Peterson SL. RNA recoding in cephalopods tailors microtubule motor protein function. Cell 2023; 186:2531-2543.e11. [PMID: 37295401 PMCID: PMC10467349 DOI: 10.1016/j.cell.2023.04.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 03/05/2023] [Accepted: 04/24/2023] [Indexed: 06/12/2023]
Abstract
RNA editing is a widespread epigenetic process that can alter the amino acid sequence of proteins, termed "recoding." In cephalopods, most transcripts are recoded, and recoding is hypothesized to be an adaptive strategy to generate phenotypic plasticity. However, how animals use RNA recoding dynamically is largely unexplored. We investigated the function of cephalopod RNA recoding in the microtubule motor proteins kinesin and dynein. We found that squid rapidly employ RNA recoding in response to changes in ocean temperature, and kinesin variants generated in cold seawater displayed enhanced motile properties in single-molecule experiments conducted in the cold. We also identified tissue-specific recoded squid kinesin variants that displayed distinct motile properties. Finally, we showed that cephalopod recoding sites can guide the discovery of functional substitutions in non-cephalopod kinesin and dynein. Thus, RNA recoding is a dynamic mechanism that generates phenotypic plasticity in cephalopods and can inform the characterization of conserved non-cephalopod proteins.
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Affiliation(s)
- Kavita J Rangan
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA.
| | - Samara L Reck-Peterson
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA.
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Koenig KM. Chilling with cephalopods: Temperature-responsive RNA editing in octopus and squid. Cell 2023; 186:2518-2520. [PMID: 37295397 DOI: 10.1016/j.cell.2023.05.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 05/15/2023] [Accepted: 05/15/2023] [Indexed: 06/12/2023]
Abstract
The molecular mechanisms that generate the developmental and physiological complexity found within cephalopods are not well understood. In this issue of Cell, Birk et al. and Rangan and Reck-Peterson show that cephalopods differentially edit their RNA in response to temperature changes and that this editing has consequences on protein function.
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Affiliation(s)
- Kristen M Koenig
- John Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA 02138, USA; Department of Organismic and Evolutionary Biology, Harvard University, Harvard University, Cambridge, MA 02138, USA; Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
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Birk MA, Liscovitch-Brauer N, Dominguez MJ, McNeme S, Yue Y, Hoff JD, Twersky I, Verhey KJ, Sutton RB, Eisenberg E, Rosenthal JJC. Temperature-dependent RNA editing in octopus extensively recodes the neural proteome. Cell 2023; 186:2544-2555.e13. [PMID: 37295402 PMCID: PMC10445230 DOI: 10.1016/j.cell.2023.05.004] [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: 01/31/2023] [Revised: 04/24/2023] [Accepted: 05/04/2023] [Indexed: 06/12/2023]
Abstract
In poikilotherms, temperature changes challenge the integration of physiological function. Within the complex nervous systems of the behaviorally sophisticated coleoid cephalopods, these problems are substantial. RNA editing by adenosine deamination is a well-positioned mechanism for environmental acclimation. We report that the neural proteome of Octopus bimaculoides undergoes massive reconfigurations via RNA editing following a temperature challenge. Over 13,000 codons are affected, and many alter proteins that are vital for neural processes. For two highly temperature-sensitive examples, recoding tunes protein function. For synaptotagmin, a key component of Ca2+-dependent neurotransmitter release, crystal structures and supporting experiments show that editing alters Ca2+ binding. For kinesin-1, a motor protein driving axonal transport, editing regulates transport velocity down microtubules. Seasonal sampling of wild-caught specimens indicates that temperature-dependent editing occurs in the field as well. These data show that A-to-I editing tunes neurophysiological function in response to temperature in octopus and most likely other coleoids.
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Affiliation(s)
- Matthew A Birk
- Bell Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA; Department of Biology, Saint Francis University, Loretto, PA 15940, USA
| | | | - Matthew J Dominguez
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79410, USA
| | - Sean McNeme
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX 77550, USA
| | - Yang Yue
- Department of Cell & Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - J Damon Hoff
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Itamar Twersky
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Kristen J Verhey
- Department of Cell & Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - R Bryan Sutton
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79410, USA
| | - Eli Eisenberg
- School of Physics and Astronomy, Tel Aviv University, Tel Aviv 69978, Israel.
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Vallecillo-Viejo IC, Voss G, Albertin CB, Liscovitch-Brauer N, Eisenberg E, Rosenthal JJC. Squid express conserved ADAR orthologs that possess novel features. Front Genome Ed 2023; 5:1181713. [PMID: 37342458 PMCID: PMC10278661 DOI: 10.3389/fgeed.2023.1181713] [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: 03/07/2023] [Accepted: 05/15/2023] [Indexed: 06/23/2023] Open
Abstract
The coleoid cephalopods display unusually extensive mRNA recoding by adenosine deamination, yet the underlying mechanisms are not well understood. Because the adenosine deaminases that act on RNA (ADAR) enzymes catalyze this form of RNA editing, the structure and function of the cephalopod orthologs may provide clues. Recent genome sequencing projects have provided blueprints for the full complement of coleoid cephalopod ADARs. Previous results from our laboratory have shown that squid express an ADAR2 homolog, with two splice variants named sqADAR2a and sqADAR2b and that these messages are extensively edited. Based on octopus and squid genomes, transcriptomes, and cDNA cloning, we discovered that two additional ADAR homologs are expressed in coleoids. The first is orthologous to vertebrate ADAR1. Unlike other ADAR1s, however, it contains a novel N-terminal domain of 641 aa that is predicted to be disordered, contains 67 phosphorylation motifs, and has an amino acid composition that is unusually high in serines and basic amino acids. mRNAs encoding sqADAR1 are themselves extensively edited. A third ADAR-like enzyme, sqADAR/D-like, which is not orthologous to any of the vertebrate isoforms, is also present. Messages encoding sqADAR/D-like are not edited. Studies using recombinant sqADARs suggest that only sqADAR1 and sqADAR2 are active adenosine deaminases, both on perfect duplex dsRNA and on a squid potassium channel mRNA substrate known to be edited in vivo. sqADAR/D-like shows no activity on these substrates. Overall, these results reveal some unique features in sqADARs that may contribute to the high-level RNA recoding observed in cephalopods.
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Affiliation(s)
| | - Gjendine Voss
- The Eugene Bell Center, Marine Biological Laboratory, Woods Hole, MA, United States
| | - Caroline B. Albertin
- The Eugene Bell Center, Marine Biological Laboratory, Woods Hole, MA, United States
| | - Noa Liscovitch-Brauer
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv, Israel
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv, Israel
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37
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Duan Y, Li H, Cai W. Adaptation of A-to-I RNA editing in bacteria, fungi, and animals. Front Microbiol 2023; 14:1204080. [PMID: 37293227 PMCID: PMC10244538 DOI: 10.3389/fmicb.2023.1204080] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 05/09/2023] [Indexed: 06/10/2023] Open
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38
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Imperadore P, Cagnin S, Allegretti V, Millino C, Raffini F, Fiorito G, Ponte G. Transcriptome-wide selection and validation of a solid set of reference genes for gene expression studies in the cephalopod mollusk Octopus vulgaris. Front Mol Neurosci 2023; 16:1091305. [PMID: 37266373 PMCID: PMC10230085 DOI: 10.3389/fnmol.2023.1091305] [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: 11/06/2022] [Accepted: 02/20/2023] [Indexed: 06/03/2023] Open
Abstract
Octopus vulgaris is a cephalopod mollusk and an active marine predator that has been at the center of a number of studies focused on the understanding of neural and biological plasticity. Studies on the machinery involved in e.g., learning and memory, regeneration, and neuromodulation are required to shed light on the conserved and/or unique mechanisms that these animals have evolved. Analysis of gene expression is one of the most essential means to expand our understanding of biological machinery, and the selection of an appropriate set of reference genes is the prerequisite for the quantitative real-time polymerase chain reaction (qRT-PCR). Here we selected 77 candidate reference genes (RGs) from a pool of stable and relatively high-expressed transcripts identified from the full-length transcriptome of O. vulgaris, and we evaluated their expression stabilities in different tissues through geNorm, NormFinder, Bestkeeper, Delta-CT method, and RefFinder. Although various algorithms provided different assemblages of the most stable reference genes for the different kinds of tissues tested here, a comprehensive ranking revealed RGs specific to the nervous system (Ov-RNF7 and Ov-RIOK2) and Ov-EIF2A and Ov-CUL1 across all considered tissues. Furthermore, we validated RGs by assessing the expression profiles of nine target genes (Ov-Naa15, Ov-Ltv1, Ov-CG9286, Ov-EIF3M, Ov-NOB1, Ov-CSDE1, Ov-Abi2, Ov-Homer2, and Ov-Snx20) in different areas of the octopus nervous system (gastric ganglion, as control). Our study allowed us to identify the most extensive set of stable reference genes currently available for the nervous system and appendages of adult O. vulgaris.
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Affiliation(s)
- Pamela Imperadore
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Stefano Cagnin
- Department of Biology, University of Padova, Padova, Italy
- CIR-Myo Myology Center, University of Padova, Padova, Italy
| | - Vittoria Allegretti
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | | | - Francesca Raffini
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Graziano Fiorito
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Giovanna Ponte
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
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39
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Avram-Shperling A, Kopel E, Twersky I, Gabay O, Ben-David A, Karako-Lampert S, Rosenthal JJC, Levanon EY, Eisenberg E, Ben-Aroya S. Identification of exceptionally potent adenosine deaminases RNA editors from high body temperature organisms. PLoS Genet 2023; 19:e1010661. [PMID: 36877730 PMCID: PMC10019624 DOI: 10.1371/journal.pgen.1010661] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 03/16/2023] [Accepted: 02/08/2023] [Indexed: 03/07/2023] Open
Abstract
The most abundant form of RNA editing in metazoa is the deamination of adenosines into inosines (A-to-I), catalyzed by ADAR enzymes. Inosines are read as guanosines by the translation machinery, and thus A-to-I may lead to protein recoding. The ability of ADARs to recode at the mRNA level makes them attractive therapeutic tools. Several approaches for Site-Directed RNA Editing (SDRE) are currently under development. A major challenge in this field is achieving high on-target editing efficiency, and thus it is of much interest to identify highly potent ADARs. To address this, we used the baker yeast Saccharomyces cerevisiae as an editing-naïve system. We exogenously expressed a range of heterologous ADARs and identified the hummingbird and primarily mallard-duck ADARs, which evolved at 40-42°C, as two exceptionally potent editors. ADARs bind to double-stranded RNA structures (dsRNAs), which in turn are temperature sensitive. Our results indicate that species evolved to live with higher core body temperatures have developed ADAR enzymes that target weaker dsRNA structures and would therefore be more effective than other ADARs. Further studies may use this approach to isolate additional ADARs with an editing profile of choice to meet specific requirements, thus broadening the applicability of SDRE.
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Affiliation(s)
- Adi Avram-Shperling
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
- The Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Eli Kopel
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Itamar Twersky
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Orshay Gabay
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Amit Ben-David
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | | | - Joshua J. C. Rosenthal
- The Eugene Bell Center, The Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America
| | - Erez Y. Levanon
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
- The Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv, Israel
- * E-mail: (EE); (SB-A)
| | - Shay Ben-Aroya
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
- * E-mail: (EE); (SB-A)
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40
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Zhang P, Zhu Y, Guo Q, Li J, Zhan X, Yu H, Xie N, Tan H, Lundholm N, Garcia-Cuetos L, Martin MD, Subirats MA, Su YH, Ruiz-Trillo I, Martindale MQ, Yu JK, Gilbert MTP, Zhang G, Li Q. On the origin and evolution of RNA editing in metazoans. Cell Rep 2023; 42:112112. [PMID: 36795564 PMCID: PMC9989829 DOI: 10.1016/j.celrep.2023.112112] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 11/28/2022] [Accepted: 01/30/2023] [Indexed: 02/16/2023] Open
Abstract
Extensive adenosine-to-inosine (A-to-I) editing of nuclear-transcribed mRNAs is the hallmark of metazoan transcriptional regulation. Here, by profiling the RNA editomes of 22 species that cover major groups of Holozoa, we provide substantial evidence supporting A-to-I mRNA editing as a regulatory innovation originating in the last common ancestor of extant metazoans. This ancient biochemistry process is preserved in most extant metazoan phyla and primarily targets endogenous double-stranded RNA (dsRNA) formed by evolutionarily young repeats. We also find intermolecular pairing of sense-antisense transcripts as an important mechanism for forming dsRNA substrates for A-to-I editing in some but not all lineages. Likewise, recoding editing is rarely shared across lineages but preferentially targets genes involved in neural and cytoskeleton systems in bilaterians. We conclude that metazoan A-to-I editing might first emerge as a safeguard mechanism against repeat-derived dsRNA and was later co-opted into diverse biological processes due to its mutagenic nature.
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Affiliation(s)
- Pei Zhang
- BGI-Shenzhen, Shenzhen 518083, China; Section for Ecology and Evolution, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | | | - Qunfei Guo
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ji Li
- BGI Research-Wuhan, BGI, Wuhan 430074, China
| | | | - Hao Yu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Nianxia Xie
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Nina Lundholm
- Natural History Museum of Denmark, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Lydia Garcia-Cuetos
- Natural History Museum of Denmark, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway; Center for Theoretical Evolutionary Genomics, Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | | | - Yi-Hsien Su
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Iñaki Ruiz-Trillo
- Institute of Evolutionary Biology, UPF-CSIC Barcelona, 08003 Barcelona, Spain; ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Catalonia, Spain; Departament de Genètica, Microbiologia i Estadística, Facultat de Bilogia, Universitat de Barcelona (UB), 08028 Barcelona, Spain
| | - Mark Q Martindale
- The Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan; Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan 26242, Taiwan
| | - M Thomas P Gilbert
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway; Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Guojie Zhang
- Center of Evolutionary and Organismal Biology, & Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark.
| | - Qiye Li
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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Evidence Supporting That C-to-U RNA Editing Is the Major Force That Drives SARS-CoV-2 Evolution. J Mol Evol 2023; 91:214-224. [PMID: 36799984 PMCID: PMC9936484 DOI: 10.1007/s00239-023-10097-1] [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] [Received: 11/16/2022] [Accepted: 02/03/2023] [Indexed: 02/18/2023]
Abstract
Mutations of DNA organisms are introduced by replication errors. However, SARS-CoV-2, as an RNA virus, is additionally subjected to rampant RNA editing by hosts. Both resources contributed to SARS-CoV-2 mutation and evolution, but the relative prevalence of the two origins is unknown. We performed comparative genomic analyses at intra-species (world-wide SARS-CoV-2 strains) and inter-species (SARS-CoV-2 and RaTG13 divergence) levels. We made prior predictions of the proportion of each mutation type (nucleotide substitution) under different scenarios and compared the observed versus the expected. C-to-T alteration, representing C-to-U editing, is far more abundant that all other mutation types. Derived allele frequency (DAF) as well as novel mutation rate of C-to-T are the highest in SARS-CoV-2 population, and C-T substitution dominates the divergence sites between SARS-CoV-2 and RaTG13. This is compelling evidence suggesting that C-to-U RNA editing is the major source of SARS-CoV-2 mutation. While replication errors serve as a baseline of novel mutation rate, the C-to-U editing has elevated the mutation rate for orders of magnitudes and accelerates the evolution of the virus.
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42
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Rosenthal JJC, Eisenberg E. Extensive Recoding of the Neural Proteome in Cephalopods by RNA Editing. Annu Rev Anim Biosci 2023; 11:57-75. [PMID: 36790891 DOI: 10.1146/annurev-animal-060322-114534] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
The coleoid cephalopods have the largest brains, and display the most complex behaviors, of all invertebrates. The molecular and cellular mechanisms that underlie these remarkable advancements remain largely unexplored. Early molecular cloning studies of squid ion channel transcripts uncovered an unusually large number of A→I RNA editing sites that recoded codons. Further cloning of other neural transcripts showed a similar pattern. The advent of deep-sequencing technologies and the associated bioinformatics allowed the mapping of RNA editing events across the entire neural transcriptomes of various cephalopods. The results were remarkable: They contained orders of magnitude more recoding editing sites than any other taxon. Although RNA editing sites are abundant in most multicellular metazoans, they rarely recode. In cephalopods, the majority of neural transcripts are recoded. Recent studies have focused on whether these events are adaptive, as well as other noncanonical aspects of cephalopod RNA editing.
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Affiliation(s)
- Joshua J C Rosenthal
- The Eugene Bell Center, The Marine Biological Laboratory, Woods Hole, Massachusetts, USA;
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv, Israel
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43
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Lactobacillus for ribosome peptide editing cancer. Clin Transl Oncol 2023; 25:1522-1544. [PMID: 36694080 PMCID: PMC9873400 DOI: 10.1007/s12094-022-03066-5] [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: 09/28/2022] [Accepted: 12/24/2022] [Indexed: 01/25/2023]
Abstract
This study reviews newly discovered insect peptide point mutations as new possible cancer research targets. To interpret newly discovered peptide point mutations in insects as new possible cancer research targets, we focused on the numerous peptide changes found in the 'CSP' family on the sex pheromone gland of the female silkworm moth Bombyx mori. We predict that the Bombyx peptide modifications will have a significant effect on cancer CUP (cancers of unknown primary) therapy and that bacterial peptide editing techniques, specifically Lactobacillus combined to CRISPR, will be used to regulate ribosomes and treat cancer in humans.
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44
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De Sio F, Imperadore P. Deciphering regeneration through non-model animals: A century of experiments on cephalopod mollusks and an outlook at the future. Front Cell Dev Biol 2023; 10:1072382. [PMID: 36699008 PMCID: PMC9868252 DOI: 10.3389/fcell.2022.1072382] [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: 10/17/2022] [Accepted: 12/12/2022] [Indexed: 01/11/2023] Open
Abstract
The advent of marine stations in the last quarter of the 19th Century has given biologists the possibility of observing and experimenting upon myriad marine organisms. Among them, cephalopod mollusks have attracted great attention from the onset, thanks to their remarkable adaptability to captivity and a great number of biologically unique features including a sophisticate behavioral repertoire, remarkable body patterning capacities under direct neural control and the complexity of nervous system rivalling vertebrates. Surprisingly, the capacity to regenerate tissues and complex structures, such as appendages, albeit been known for centuries, has been understudied over the decades. Here, we will first review the limited in number, but fundamental studies on the subject published between 1920 and 1970 and discuss what they added to our knowledge of regeneration as a biological phenomenon. We will also speculate on how these relate to their epistemic and disciplinary context, setting the base for the study of regeneration in the taxon. We will then frame the peripherality of cephalopods in regeneration studies in relation with their experimental accessibility, and in comparison, with established models, either simpler (such as planarians), or more promising in terms of translation (urodeles). Last, we will explore the potential and growing relevance of cephalopods as prospective models of regeneration today, in the light of the novel opportunities provided by technological and methodological advances, to reconsider old problems and explore new ones. The recent development of cutting-edge technologies made available for cephalopods, like genome editing, is allowing for a number of important findings and opening the way toward new promising avenues. The contribution offered by cephalopods will increase our knowledge on regenerative mechanisms through cross-species comparison and will lead to a better understanding of the complex cellular and molecular machinery involved, shedding a light on the common pathways but also on the novel strategies different taxa evolved to promote regeneration of tissues and organs. Through the dialogue between biological/experimental and historical/contextual perspectives, this article will stimulate a discussion around the changing relations between availability of animal models and their specificity, technical and methodological developments and scientific trends in contemporary biology and medicine.
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Affiliation(s)
- Fabio De Sio
- Heinrich Heine Universität, Institut für Geschichte, Theorie und Ethik der Medizin, Centre for Health and Society, Medizinische Fakultät, Düsseldorf, Germany,*Correspondence: Fabio De Sio, ; Pamela Imperadore, ,
| | - Pamela Imperadore
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy,Association for Cephalopod Research—CephRes, Napoli, Italy,*Correspondence: Fabio De Sio, ; Pamela Imperadore, ,
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45
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Sadler KC. Epigenetics across the evolutionary tree: New paradigms from non-model animals. Bioessays 2023; 45:e2200036. [PMID: 36403219 DOI: 10.1002/bies.202200036] [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: 02/13/2022] [Revised: 10/28/2022] [Accepted: 11/03/2022] [Indexed: 11/21/2022]
Abstract
All animals have evolved solutions to manage their genomes, enabling the efficient organization of meters of DNA strands in the nucleus and allowing for nuanced regulation of gene expression while keeping transposable elements suppressed. Epigenetic modifications are central to accomplishing all these. Recent advances in sequencing technologies and the development of techniques that profile epigenetic marks and chromatin accessibility using reagents that can be used in any species has catapulted epigenomic studies in diverse animal species, shedding light on the multitude of epigenomic mechanisms utilized across the evolutionary tree. Now, comparative epigenomics is a rapidly growing field that is uncovering mechanistic aspects of epigenetic modifications and chromatin organization in non-model invertebrates, ranging from octopus to sponges. This review puts recent discoveries in the epigenetics of non-model invertebrates in historical context, and describes new insight into the patterning and functions of DNA methylation and other highly conserved epigenetic modifications.
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Affiliation(s)
- Kirsten C Sadler
- Program in Biology, New York University, Abu Dhabi, United Arab Emirates
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46
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Welden JR, Margvelani G, Arizaca Maquera KA, Gudlavalleti B, Miranda Sardón S, Campos A, Robil N, Lee D, Hernandez A, Wang WX, Di J, de la Grange P, Nelson P, Stamm S. RNA editing of microtubule-associated protein tau circular RNAs promotes their translation and tau tangle formation. Nucleic Acids Res 2022; 50:12979-12996. [PMID: 36533443 PMCID: PMC9825173 DOI: 10.1093/nar/gkac1129] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 10/06/2022] [Accepted: 11/09/2022] [Indexed: 12/23/2022] Open
Abstract
Aggregation of the microtubule-associated protein tau characterizes tauopathies, including Alzheimer's disease and frontotemporal lobar degeneration (FTLD-Tau). Gene expression regulation of tau is complex and incompletely understood. Here we report that the human tau gene (MAPT) generates two circular RNAs (circRNAs) through backsplicing of exon 12 to either exon 7 (12→7 circRNA) or exon 10 (12→10 circRNA). Both circRNAs lack stop codons. The 12→7 circRNA contains one start codon and is translated in a rolling circle, generating a protein consisting of multimers of the microtubule-binding repeats R1-R4. For the 12→10 circRNA, a start codon can be introduced by two FTLD-Tau mutations, generating a protein consisting of multimers of the microtubule-binding repeats R2-R4, suggesting that mutations causing FTLD may act in part through tau circRNAs. Adenosine to inosine RNA editing dramatically increases translation of circRNAs and, in the 12→10 circRNA, RNA editing generates a translational start codon by changing AUA to AUI. Circular tau proteins self-aggregate and promote aggregation of linear tau proteins. Our data indicate that adenosine to inosine RNA editing initiates translation of human circular tau RNAs, which may contribute to tauopathies.
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Affiliation(s)
| | - Giorgi Margvelani
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | | | - Bhavani Gudlavalleti
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Sandra C Miranda Sardón
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Alexandre Rosa Campos
- Sanford Burnham Prebys Medical Discovery Institute Proteomics Core, La Jolla, CA, USA
| | | | - Daniel C Lee
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA,Alzheimer's Disease Research Center Neuroscience, University of Kentucky, Lexington, KY, USA
| | | | - Wang-Xia Wang
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA,Alzheimer's Disease Research Center and Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, KY, USA
| | - Jing Di
- Alzheimer's Disease Research Center and Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, KY, USA
| | | | - Peter T Nelson
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA,Alzheimer's Disease Research Center and Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, KY, USA
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47
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The role of post-transcriptional modifications during development. Biol Futur 2022:10.1007/s42977-022-00142-3. [PMID: 36481986 DOI: 10.1007/s42977-022-00142-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022]
Abstract
AbstractWhile the existence of post-transcriptional modifications of RNA nucleotides has been known for decades, in most RNA species the exact positions of these modifications and their physiological function have been elusive until recently. Technological advances, such as high-throughput next-generation sequencing (NGS) methods and nanopore-based mapping technologies, have made it possible to map the position of these modifications with single nucleotide accuracy, and genetic screens have uncovered the “writer”, “reader” and “eraser” proteins that help to install, interpret and remove such modifications, respectively. These discoveries led to intensive research programmes with the aim of uncovering the roles of these modifications during diverse biological processes. In this review, we assess novel discoveries related to the role of post-transcriptional modifications during animal development, highlighting how these discoveries can affect multiple aspects of development from fertilization to differentiation in many species.
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48
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Zolotarov G, Fromm B, Legnini I, Ayoub S, Polese G, Maselli V, Chabot PJ, Vinther J, Styfhals R, Seuntjens E, Di Cosmo A, Peterson KJ, Rajewsky N. MicroRNAs are deeply linked to the emergence of the complex octopus brain. SCIENCE ADVANCES 2022; 8:eadd9938. [PMID: 36427315 PMCID: PMC9699675 DOI: 10.1126/sciadv.add9938] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/27/2022] [Indexed: 05/25/2023]
Abstract
Soft-bodied cephalopods such as octopuses are exceptionally intelligent invertebrates with a highly complex nervous system that evolved independently from vertebrates. Because of elevated RNA editing in their nervous tissues, we hypothesized that RNA regulation may play a major role in the cognitive success of this group. We thus profiled messenger RNAs and small RNAs in three cephalopod species including 18 tissues of the Octopus vulgaris. We show that the major RNA innovation of soft-bodied cephalopods is an expansion of the microRNA (miRNA) gene repertoire. These evolutionarily novel miRNAs were primarily expressed in adult neuronal tissues and during the development and had conserved and thus likely functional target sites. The only comparable miRNA expansions happened, notably, in vertebrates. Thus, we propose that miRNAs are intimately linked to the evolution of complex animal brains.
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Affiliation(s)
- Grygoriy Zolotarov
- Laboratory of Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str 28, 10115 Berlin, Germany
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Bastian Fromm
- UiT The Arctic University of Norway, Tromsø, Norway
- SciLifeLab, Stockholm University, Stockholm, Sweden
| | - Ivano Legnini
- Laboratory of Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str 28, 10115 Berlin, Germany
| | - Salah Ayoub
- Laboratory of Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str 28, 10115 Berlin, Germany
| | - Gianluca Polese
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Valeria Maselli
- Department of Biology, University of Naples Federico II, Naples, Italy
| | | | - Jakob Vinther
- School of Earth Sciences, University of Bristol, Bristol, UK
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Ruth Styfhals
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Eve Seuntjens
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
| | - Anna Di Cosmo
- Department of Biology, University of Naples Federico II, Naples, Italy
| | | | - Nikolaus Rajewsky
- Laboratory of Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str 28, 10115 Berlin, Germany
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49
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Wang YM, Ye LQ, Wang MS, Zhang JJ, Khederzadeh S, Irwin DM, Ren XD, Zhang YP, Wu DD. Unveiling the functional and evolutionary landscape of RNA editing in chicken using genomics and transcriptomics. Zool Res 2022; 43:1011-1022. [PMID: 36266925 PMCID: PMC9700494 DOI: 10.24272/j.issn.2095-8137.2022.331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/17/2022] [Indexed: 09/10/2024] Open
Abstract
The evolutionary and functional features of RNA editing are well studied in mammals, cephalopods, and insects, but not in birds. Here, we integrated transcriptomic and whole-genomic analyses to exhaustively characterize the expansive repertoire of adenosine-to-inosine (A-to-I) RNA editing sites (RESs) in the chicken. In addition, we investigated the evolutionary status of the chicken editome as a potential mechanism of domestication. We detected the lowest editing level in the liver of chickens, compared to muscles in humans, and found higher editing activity and specificity in the brain than in non-neural tissues, consistent with the brain's functional complexity. To a certain extent, specific editing activity may account for the specific functions of tissues. Our results also revealed that sequences critical to RES secondary structures remained conserved within avian evolution. Furthermore, the RNA editome was shaped by purifying selection during chicken domestication and most RESs may have served as a selection pool for a few functional RESs involved in chicken domestication, including evolution of nervous and immune systems. Regulation of RNA editing in chickens by adenosine deaminase acting on RNA (ADAR) enzymes may be affected by non-ADAR factors whose expression levels changed widely after ADAR knockdown. Collectively, we provide comprehensive lists of candidate RESs and non-ADAR-editing regulators in the chicken, thus contributing to our current understanding of the functions and evolution of RNA editing in animals.
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Affiliation(s)
- Yun-Mei Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Ling-Qun Ye
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Ming-Shan Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Department of Ecology and Evolutionary Biology, Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jin-Jin Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Saber Khederzadeh
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Xiao-Die Ren
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China. E-mail:
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China. E-mail:
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50
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Yoshida MA, Hirota K, Imoto J, Okuno M, Tanaka H, Kajitani R, Toyoda A, Itoh T, Ikeo K, Sasaki T, Setiamarga DHE. Gene Recruitments and Dismissals in the Argonaut Genome Provide Insights into Pelagic Lifestyle Adaptation and Shell-like Eggcase Reacquisition. Genome Biol Evol 2022; 14:evac140. [PMID: 36283693 PMCID: PMC9635652 DOI: 10.1093/gbe/evac140] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2022] [Indexed: 10/01/2023] Open
Abstract
The paper nautilus or greater argonaut, Argonauta argo, is a species of octopods which is characterized by its pelagic lifestyle and by the presence of a protective spiral-shaped shell-like eggcase in females. To reveal the genomic background of how the species adapted to the pelagic lifestyle and acquired its shell-like eggcase, we sequenced the draft genome of the species. The genome size was 1.1 Gb, which is the smallest among the cephalopods known to date, with the top 215 scaffolds (average length 5,064,479 bp) covering 81% (1.09 Gb) of the total assembly. A total of 26,433 protein-coding genes were predicted from 16,802 assembled scaffolds. From these, we identified nearly intact HOX, Parahox, Wnt clusters, and some gene clusters that could probably be related to the pelagic lifestyle, such as reflectin, tyrosinase, and opsin. The gene models also revealed several homologous genes related to calcified shell formation in Conchiferan mollusks, such as Pif-like, SOD, and TRX. Interestingly, comparative genomics analysis revealed that the homologous genes for such genes were also found in the genome of the shell-less octopus, as well as Nautilus, which has a true outer shell. Therefore, the draft genome sequence of Arg. argo presented here has helped us to gain further insights into the genetic background of the dynamic recruitment and dismissal of genes to form an important, converging extended phenotypic structure such as the shell and the shell-like eggcase. Additionally, it allows us to explore the evolution of from benthic to pelagic lifestyles in cephalopods and octopods.
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Affiliation(s)
- Masa-aki Yoshida
- Marine Biological Science Section, Education and Research Center for Biological Resources, Faculty of Life and Environmental Science, Shimane University, Okinoshima, Shimane 685-0024, Japan
| | - Kazuki Hirota
- Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-8654, Japan
- Department of Applied Chemistry and Biochemistry, National Institute of Technology (KOSEN), Wakayama College, Gobo, Wakayama 644-0012, Japan
| | - Junichi Imoto
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Miki Okuno
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Fukuoka 830-0011, Japan
| | - Hiroyuki Tanaka
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Rei Kajitani
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Kazuho Ikeo
- Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Takenori Sasaki
- Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-8654, Japan
- The University Museum, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Davin H E Setiamarga
- Department of Applied Chemistry and Biochemistry, National Institute of Technology (KOSEN), Wakayama College, Gobo, Wakayama 644-0012, Japan
- The University Museum, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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