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Gornik SG, Bergheim BG, Morel B, Stamatakis A, Foulkes NS, Guse A. Photoreceptor Diversification Accompanies the Evolution of Anthozoa. Mol Biol Evol 2021; 38:1744-1760. [PMID: 33226083 PMCID: PMC8097283 DOI: 10.1093/molbev/msaa304] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Anthozoan corals are an ecologically important group of cnidarians, which power the productivity of reef ecosystems. They are sessile, inhabit shallow, tropical oceans and are highly dependent on sun- and moonlight to regulate sexual reproduction, phototaxis, and photosymbiosis. However, their exposure to high levels of sunlight also imposes an increased risk of UV-induced DNA damage. How have these challenging photic environments influenced photoreceptor evolution and function in these animals? To address this question, we initially screened the cnidarian photoreceptor repertoire for Anthozoa-specific signatures by a broad-scale evolutionary analysis. We compared transcriptomic data of more than 36 cnidarian species and revealed a more diverse photoreceptor repertoire in the anthozoan subphylum than in the subphylum Medusozoa. We classified the three principle opsin classes into distinct subtypes and showed that Anthozoa retained all three classes, which diversified into at least six subtypes. In contrast, in Medusozoa, only one class with a single subtype persists. Similarly, in Anthozoa, we documented three photolyase classes and two cryptochrome (CRY) classes, whereas CRYs are entirely absent in Medusozoa. Interestingly, we also identified one anthozoan CRY class, which exhibited unique tandem duplications of the core functional domains. We next explored the functionality of anthozoan photoreceptors in the model species Exaiptasia diaphana (Aiptasia), which recapitulates key photo-behaviors of corals. We show that the diverse opsin genes are differentially expressed in important life stages common to reef-building corals and Aiptasia and that CRY expression is light regulated. We thereby provide important clues linking coral evolution with photoreceptor diversification.
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Affiliation(s)
- Sebastian G Gornik
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | | | - Benoit Morel
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Alexandros Stamatakis
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.,Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Nicholas S Foulkes
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany.,Institute of Biological and Chemical Systems, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Annika Guse
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
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Hayashi T, Murakami Y, Mizobuchi K, Koyanagi Y, Sonoda KH, Nakano T. Complete congenital stationary night blindness associated with a novel NYX variant (p.Asn216Lys) in middle-aged and older adult patients. Ophthalmic Genet 2021; 42:412-419. [PMID: 33769208 DOI: 10.1080/13816810.2021.1904422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND Complete congenital stationary night blindness (CSNB) is a retinal disorder thought to be non-progressive. The purpose of this study was to characterize the clinical and genetic findings of middle-aged and older adult patients with X-linked complete CSNB. METHODS Three male CSNB patients (aged 62, 72, and 51 years) and one unaffected female carrier in a Japanese family were included in this study. Whole-exome sequencing (WES) was performed to determine the disease-causing variants. Co-segregation was confirmed in the family members. We performed a comprehensive ophthalmic examination on each patient. RESULTS In the 62-year-old patient, a novel hemizygous variant (c.648 C > A; p.Asn216Lys) of the NYX gene was identified by WES analysis. The other two patients carried the variant hemizygously, and the unaffected carrier harbored the variant heterozygously. The clinical and electroretinography (ERG) findings were very similar among all three patients. Fundus images exhibited high myopic chorioretinal atrophy with long axial length. Ultra-wide field fundus autofluorescence images showed no retinal degenerative changes except for changes resulting from high myopia and previous retinal diseases. The ERG findings showed no response in rod ERG, electronegative configuration with preserved a-waves in standard/bright-flash ERG, and preserved responses in cone and 30-Hz flicker ERG, which were compared with age-matched controls with high myopia. CONCLUSIONS We identified a novel missense NYX variant in a Japanese family with complete CSNB. Our clinical findings indicated that photoreceptor mediated ERG responses are well preserved even in middle-aged and older adult patients.
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Affiliation(s)
- Takaaki Hayashi
- Department of Ophthalmology, The Jikei University School of Medicine, Tokyo, Japan.,Department of Ophthalmology, Katsushika Medical Center, The Jikei University School of Medicine, Tokyo, Japan
| | - Yusuke Murakami
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kei Mizobuchi
- Department of Ophthalmology, The Jikei University School of Medicine, Tokyo, Japan
| | - Yoshito Koyanagi
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Koh-Hei Sonoda
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tadashi Nakano
- Department of Ophthalmology, The Jikei University School of Medicine, Tokyo, Japan
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Darris C, Revert F, Revert-Ros F, Gozalbo-Rovira R, Feigley A, Fidler A, Lopez-Pascual E, Saus J, Hudson BG. Unicellular ancestry and mechanisms of diversification of Goodpasture antigen-binding protein. J Biol Chem 2018; 294:759-769. [PMID: 30377252 DOI: 10.1074/jbc.ra118.006225] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Indexed: 01/21/2023] Open
Abstract
The emergence of the basement membrane (BM), a specialized form of extracellular matrix, was essential in the unicellular transition to multicellularity. However, the mechanism is unknown. Goodpasture antigen-binding protein (GPBP), a BM protein, was uniquely poised to play diverse roles in this transition owing to its multiple isoforms (GPBP-1, -2, and -3) with varied intracellular and extracellular functions (ceramide trafficker and protein kinase). We sought to determine the evolutionary origin of GPBP isoforms. Our findings reveal the presence of GPBP in unicellular protists, with GPBP-2 as the most ancient isoform. In vertebrates, GPBP-1 assumed extracellular function that is further enhanced by membrane-bound GPBP-3 in mammalians, whereas GPBP-2 retained intracellular function. Moreover, GPBP-2 possesses a dual intracellular/extracellular function in cnidarians, an early nonbilaterian group. We conclude that GPBP functioning both inside and outside the cell was of fundamental importance for the evolutionary transition to animal multicellularity and tissue evolution.
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Affiliation(s)
- Carl Darris
- From the Department of Medicine/Division of Nephrology and Hypertension and Vanderbilt University Medical Center, Vanderbilt University, Nashville, Tennessee 37232,
| | - Fernando Revert
- Fibrostatin, SL, Scientific Park of the University of Valencia, 46980 Paterna, Valencia, Spain
| | - Francisco Revert-Ros
- Fibrostatin, SL, Scientific Park of the University of Valencia, 46980 Paterna, Valencia, Spain
| | - Roberto Gozalbo-Rovira
- Fibrostatin, SL, Scientific Park of the University of Valencia, 46980 Paterna, Valencia, Spain
| | - Andrew Feigley
- From the Department of Medicine/Division of Nephrology and Hypertension and Vanderbilt University Medical Center, Vanderbilt University, Nashville, Tennessee 37232.,the Aspirnaut Program
| | - Aaron Fidler
- From the Department of Medicine/Division of Nephrology and Hypertension and Vanderbilt University Medical Center, Vanderbilt University, Nashville, Tennessee 37232.,the Aspirnaut Program
| | - Ernesto Lopez-Pascual
- Fibrostatin, SL, Scientific Park of the University of Valencia, 46980 Paterna, Valencia, Spain
| | - Juan Saus
- Fibrostatin, SL, Scientific Park of the University of Valencia, 46980 Paterna, Valencia, Spain.,the Department of Biochemistry and Molecular Biology, Faculty of Medicine and Dentistry, University of València, 46010 Valencia, Spain, and
| | - Billy G Hudson
- From the Department of Medicine/Division of Nephrology and Hypertension and Vanderbilt University Medical Center, Vanderbilt University, Nashville, Tennessee 37232, .,the Aspirnaut Program.,Center for Matrix Biology.,Department of Pathology, Microbiology, and Immunology.,Department of Cell and Developmental Biology.,Department of Biochemistry.,Vanderbilt-Ingram Cancer Center, and.,Vanderbilt Institute of Chemical Biology, Vanderbilt University Medical Center, Nashville, Tennessee 37232
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Troczka BJ, Richardson E, Homem RA, Davies TGE. An analysis of variability in genome organisation of intracellular calcium release channels across insect orders. Gene 2018; 670:70-86. [PMID: 29792951 PMCID: PMC6026295 DOI: 10.1016/j.gene.2018.05.075] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 05/15/2018] [Accepted: 05/18/2018] [Indexed: 10/25/2022]
Abstract
Using publicly available genomic data, combined with RT-PCR validation, we explore structural genomic variation for two major ion channels across insect classes. We have manually curated ryanodine receptor (RyR) and inositol 1,4,5-trisphosphate receptor (IP3R) ORFs and their corresponding genomic structures from 26 different insects covering major insect orders. We found that, despite high protein identity for both RyRs (>75%) and IP3Rs (~67%), the overall complexity of the gene structure varies greatly between different insect orders with the simplest genes (fewest introns) found in Diptera and the most complex in Lepidoptera. Analysis of intron conservation patterns indicated that the majority of conserved introns are found close to the 5' end of the channels and in RyR around the highly conserved mutually exclusive splice site. Of the two channels the IP3Rs appear to have a less well conserved organisation with a greater overall number of unique introns seen between insect orders. We experimentally validated two of the manually curated ORFs for IP3Rs and confirmed an atypical (3799aa) IP3R receptor in Myzus persicae, which is approximately 1000 amino acids larger than previously reported for IP3Rs.
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Affiliation(s)
- Bartlomiej J Troczka
- Biointeractions and Crop Protection Department, Rothamsted Research, Harpenden AL5 2JQ, UK.
| | - Ewan Richardson
- Biointeractions and Crop Protection Department, Rothamsted Research, Harpenden AL5 2JQ, UK.
| | - Rafael A Homem
- Biointeractions and Crop Protection Department, Rothamsted Research, Harpenden AL5 2JQ, UK.
| | - T G Emyr Davies
- Biointeractions and Crop Protection Department, Rothamsted Research, Harpenden AL5 2JQ, UK.
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Kollmar M, Mühlhausen S. Myosin repertoire expansion coincides with eukaryotic diversification in the Mesoproterozoic era. BMC Evol Biol 2017; 17:211. [PMID: 28870165 PMCID: PMC5583752 DOI: 10.1186/s12862-017-1056-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 08/25/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The last eukaryotic common ancestor already had an amazingly complex cell possessing genomic and cellular features such as spliceosomal introns, mitochondria, cilia-dependent motility, and a cytoskeleton together with several intracellular transport systems. In contrast to the microtubule-based dyneins and kinesins, the actin-filament associated myosins are considerably divergent in extant eukaryotes and a unifying picture of their evolution has not yet emerged. RESULTS Here, we manually assembled and annotated 7852 myosins from 929 eukaryotes providing an unprecedented dense sequence and taxonomic sampling. For classification we complemented phylogenetic analyses with gene structure comparisons resulting in 79 distinct myosin classes. The intron pattern analysis and the taxonomic distribution of the classes suggest two myosins in the last eukaryotic common ancestor, a class-1 prototype and another myosin, which is most likely the ancestor of all other myosin classes. The sparse distribution of class-2 and class-4 myosins outside their major lineages contradicts their presence in the last eukaryotic common ancestor but instead strongly suggests early eukaryote-eukaryote horizontal gene transfer. CONCLUSIONS By correlating the evolution of myosin diversity with the history of Earth we found that myosin innovation occurred in independent major "burst" events in the major eukaryotic lineages. Most myosin inventions happened in the Mesoproterozoic era. In the late Neoproterozoic era, a process of extensive independent myosin loss began simultaneously with further eukaryotic diversification. Since the Cambrian explosion, myosin repertoire expansion is driven by lineage- and species-specific gene and genome duplications leading to subfunctionalization and fine-tuning of myosin functions.
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Affiliation(s)
- Martin Kollmar
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany.
| | - Stefanie Mühlhausen
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany.,Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, Bath, UK
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Slos D, Sudhaus W, Stevens L, Bert W, Blaxter M. Caenorhabditis monodelphis sp. n.: defining the stem morphology and genomics of the genus Caenorhabditis. BMC ZOOL 2017. [DOI: 10.1186/s40850-017-0013-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Wang Y, Xu L, Thilmony R, You FM, Gu YQ, Coleman-Derr D. PIECE 2.0: an update for the plant gene structure comparison and evolution database. Nucleic Acids Res 2016; 45:1015-1020. [PMID: 27742820 PMCID: PMC5210635 DOI: 10.1093/nar/gkw935] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 10/04/2016] [Accepted: 10/12/2016] [Indexed: 11/30/2022] Open
Abstract
PIECE (Plant Intron Exon Comparison and Evolution) is a web-accessible database that houses intron and exon information of plant genes. PIECE serves as a resource for biologists interested in comparing intron–exon organization and provides valuable insights into the evolution of gene structure in plant genomes. Recently, we updated PIECE to a new version, PIECE 2.0 (http://probes.pw.usda.gov/piece or http://aegilops.wheat.ucdavis.edu/piece). PIECE 2.0 contains annotated genes from 49 sequenced plant species as compared to 25 species in the previous version. In the current version, we also added several new features: (i) a new viewer was developed to show phylogenetic trees displayed along with the structure of individual genes; (ii) genes in the phylogenetic tree can now be also grouped according to KOG (The annotation of Eukaryotic Orthologous Groups) and KO (KEGG Orthology) in addition to Pfam domains; (iii) information on intronless genes are now included in the database; (iv) a statistical summary of global gene structure information for each species and its comparison with other species was added; and (v) an improved GSDraw tool was implemented in the web server to enhance the analysis and display of gene structure. The updated PIECE 2.0 database will be a valuable resource for the plant research community for the study of gene structure and evolution.
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Affiliation(s)
- Yi Wang
- USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA.,USDA-ARS, Plant Gene Expression Center, Albany, CA 94710, USA
| | - Ling Xu
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA.,USDA-ARS, Plant Gene Expression Center, Albany, CA 94710, USA
| | - Roger Thilmony
- USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA
| | - Frank M You
- Cereal Research Centre, Agriculture and Agri-Food Canada, Morden R6M 1Y5 MB, Canada
| | - Yong Q Gu
- USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA
| | - Devin Coleman-Derr
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA .,USDA-ARS, Plant Gene Expression Center, Albany, CA 94710, USA
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Chorev M, Guy L, Carmel L. JuncDB: an exon-exon junction database. Nucleic Acids Res 2016; 44:D101-9. [PMID: 26519469 PMCID: PMC4702826 DOI: 10.1093/nar/gkv1142] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 10/14/2015] [Accepted: 10/15/2015] [Indexed: 11/13/2022] Open
Abstract
Intron positions upon the mRNA transcript are sometimes remarkably conserved even across distantly related eukaryotic species. This has made the comparison of intron-exon architectures across orthologous transcripts a very useful tool for studying various evolutionary processes. Moreover, the wide range of functions associated with introns may confer biological meaning to evolutionary changes in gene architectures. Yet, there is currently no database that offers such comparative information. Here, we present JuncDB (http://juncdb.carmelab.huji.ac.il/), an exon-exon junction database dedicated to the comparison of architectures between orthologous transcripts. It covers nearly 40,000 sets of orthologous transcripts spanning 88 eukaryotic species. JuncDB offers a user-friendly interface, access to detailed information, instructive graphical displays of the comparative data and easy ways to download data to a local computer. In addition, JuncDB allows the analysis to be carried out either on specific genes, or at a genome-wide level for any selected group of species.
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Affiliation(s)
- Michal Chorev
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 91904, Israel
| | - Lotem Guy
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 91904, Israel
| | - Liran Carmel
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel
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