1
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Mayeur H, Leyhr J, Mulley J, Leurs N, Michel L, Sharma K, Lagadec R, Aury JM, Osborne OG, Mulhair P, Poulain J, Mangenot S, Mead D, Smith M, Corton C, Oliver K, Skelton J, Betteridge E, Dolucan J, Dudchenko O, Omer AD, Weisz D, Aiden EL, McCarthy SA, Sims Y, Torrance J, Tracey A, Howe K, Baril T, Hayward A, Martinand-Mari C, Sanchez S, Haitina T, Martin K, Korsching SI, Mazan S, Debiais-Thibaud M. The Sensory Shark: High-quality Morphological, Genomic and Transcriptomic Data for the Small-spotted Catshark Scyliorhinus Canicula Reveal the Molecular Bases of Sensory Organ Evolution in Jawed Vertebrates. Mol Biol Evol 2024; 41:msae246. [PMID: 39657112 PMCID: PMC11979771 DOI: 10.1093/molbev/msae246] [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: 07/07/2024] [Revised: 11/21/2024] [Accepted: 11/21/2024] [Indexed: 12/16/2024] Open
Abstract
Cartilaginous fishes (chondrichthyans: chimeras and elasmobranchs -sharks, skates, and rays) hold a key phylogenetic position to explore the origin and diversifications of jawed vertebrates. Here, we report and integrate reference genomic, transcriptomic, and morphological data in the small-spotted catshark Scyliorhinus canicula to shed light on the evolution of sensory organs. We first characterize general aspects of the catshark genome, confirming the high conservation of genome organization across cartilaginous fishes, and investigate population genomic signatures. Taking advantage of a dense sampling of transcriptomic data, we also identify gene signatures for all major organs, including chondrichthyan specializations, and evaluate expression diversifications between paralogs within major gene families involved in sensory functions. Finally, we combine these data with 3D synchrotron imaging and in situ gene expression analyses to explore chondrichthyan-specific traits and more general evolutionary trends of sensory systems. This approach brings to light, among others, novel markers of the ampullae of Lorenzini electrosensory cells, a duplication hotspot for crystallin genes conserved in jawed vertebrates, and a new metazoan clade of the transient-receptor potential (TRP) family. These resources and results, obtained in an experimentally tractable chondrichthyan model, open new avenues to integrate multiomics analyses for the study of elasmobranchs and jawed vertebrates.
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Affiliation(s)
- Hélène Mayeur
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, Banyuls-sur-mer, France
| | - Jake Leyhr
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - John Mulley
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Nicolas Leurs
- Institut des Sciences de l'Evolution de Montpellier, ISEM, University of Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Léo Michel
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, Banyuls-sur-mer, France
| | - Kanika Sharma
- Institute of Genetics, Faculty of Mathematics and Natural Sciences of the University at Cologne, Cologne 50674, Germany
| | - Ronan Lagadec
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, Banyuls-sur-mer, France
| | - Jean-Marc Aury
- Génomique Métabolique, Génoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry 91057, France
| | - Owen G Osborne
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Peter Mulhair
- Department of Biology, University of Oxford, Oxford OX1 3SZ, UK
| | - Julie Poulain
- Génomique Métabolique, Génoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry 91057, France
| | - Sophie Mangenot
- Génomique Métabolique, Génoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry 91057, France
| | - Daniel Mead
- Sequencing Department, Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Michelle Smith
- Sequencing Department, Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Craig Corton
- Sequencing Department, Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Karen Oliver
- Sequencing Department, Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Jason Skelton
- Sequencing Department, Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Emma Betteridge
- Sequencing Department, Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Jale Dolucan
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- The Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - Olga Dudchenko
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- The Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - Arina D Omer
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- The Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - David Weisz
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- The Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - Erez L Aiden
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- The Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shane A McCarthy
- Sequencing Department, Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Ying Sims
- Sequencing Department, Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - James Torrance
- Sequencing Department, Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Alan Tracey
- Sequencing Department, Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Kerstin Howe
- Sequencing Department, Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Tobias Baril
- Centre for Ecology and Conservation, University of Exeter, Cornwall TR10 9FE, UK
| | - Alexander Hayward
- Centre for Ecology and Conservation, University of Exeter, Cornwall TR10 9FE, UK
| | - Camille Martinand-Mari
- Institut des Sciences de l'Evolution de Montpellier, ISEM, University of Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Sophie Sanchez
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
- European Synchrotron Radiation Facility, Grenoble, France
| | - Tatjana Haitina
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Kyle Martin
- Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
| | - Sigrun I Korsching
- Institute of Genetics, Faculty of Mathematics and Natural Sciences of the University at Cologne, Cologne 50674, Germany
| | - Sylvie Mazan
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, Banyuls-sur-mer, France
| | - Mélanie Debiais-Thibaud
- Institut des Sciences de l'Evolution de Montpellier, ISEM, University of Montpellier, CNRS, IRD, EPHE, Montpellier, France
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2
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Li J, Buonfiglio F, Zeng Y, Pfeiffer N, Gericke A. Oxidative Stress in Cataract Formation: Is There a Treatment Approach on the Horizon? Antioxidants (Basel) 2024; 13:1249. [PMID: 39456502 PMCID: PMC11505147 DOI: 10.3390/antiox13101249] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2024] [Revised: 10/04/2024] [Accepted: 10/15/2024] [Indexed: 10/28/2024] Open
Abstract
Cataracts, a leading cause of blindness worldwide, are closely linked to oxidative stress-induced damage to lens epithelial cells (LECs). Key factors contributing to cataract formation include aging, arterial hypertension, and diabetes mellitus. Given the high global prevalence of cataracts, the burden of cataract-related visual impairment is substantial, highlighting the need for pharmacological strategies to supplement surgical interventions. Understanding the molecular pathways involved in oxidative stress during cataract development may offer valuable insights for designing novel therapeutic approaches. This review explores the role of oxidative stress in cataract formation, focusing on critical mechanisms, such as mitochondrial dysfunction, endoplasmic reticulum stress, loss of gap junctions, and various cell death pathways in LECs. Additionally, we discuss emerging therapeutic strategies and potential targeting options, including antioxidant-based treatments.
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Affiliation(s)
- Jingyan Li
- Department of Ophthalmology, University Medical Center, Johannes Gutenberg University Mainz, Langenbeckstrasse 1, 55131 Mainz, Germany; (F.B.); (Y.Z.); (N.P.)
| | | | | | | | - Adrian Gericke
- Department of Ophthalmology, University Medical Center, Johannes Gutenberg University Mainz, Langenbeckstrasse 1, 55131 Mainz, Germany; (F.B.); (Y.Z.); (N.P.)
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3
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Mayeur H, Leyhr J, Mulley J, Leurs N, Michel L, Sharma K, Lagadec R, Aury JM, Osborne OG, Mulhair P, Poulain J, Mangenot S, Mead D, Smith M, Corton C, Oliver K, Skelton J, Betteridge E, Dolucan J, Dudchenko O, Omer AD, Weisz D, Aiden EL, McCarthy S, Sims Y, Torrance J, Tracey A, Howe K, Baril T, Hayward A, Martinand-Mari C, Sanchez S, Haitina T, Martin K, Korsching SI, Mazan S, Debiais-Thibaud M. The sensory shark: high-quality morphological, genomic and transcriptomic data for the small-spotted catshark Scyliorhinus canicula reveal the molecular bases of sensory organ evolution in jawed vertebrates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.23.595469. [PMID: 39005470 PMCID: PMC11244906 DOI: 10.1101/2024.05.23.595469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Cartilaginous fishes (chimaeras and elasmobranchs -sharks, skates and rays) hold a key phylogenetic position to explore the origin and diversifications of jawed vertebrates. Here, we report and integrate reference genomic, transcriptomic and morphological data in the small-spotted catshark Scyliorhinus canicula to shed light on the evolution of sensory organs. We first characterise general aspects of the catshark genome, confirming the high conservation of genome organisation across cartilaginous fishes, and investigate population genomic signatures. Taking advantage of a dense sampling of transcriptomic data, we also identify gene signatures for all major organs, including chondrichthyan specializations, and evaluate expression diversifications between paralogs within major gene families involved in sensory functions. Finally, we combine these data with 3D synchrotron imaging and in situ gene expression analyses to explore chondrichthyan-specific traits and more general evolutionary trends of sensory systems. This approach brings to light, among others, novel markers of the ampullae of Lorenzini electro-sensory cells, a duplication hotspot for crystallin genes conserved in jawed vertebrates, and a new metazoan clade of the Transient-receptor potential (TRP) family. These resources and results, obtained in an experimentally tractable chondrichthyan model, open new avenues to integrate multiomics analyses for the study of elasmobranchs and jawed vertebrates.
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Kwok CSN, Lai KKY, Lam W, Xu SJL, Lam SW, Lee FWF. Proteome Analysis of Whole-Body Responses in Medaka Experimentally Exposed to Fish-Killing Dinoflagellate Karenia mikimotoi. Int J Mol Sci 2021; 22:11625. [PMID: 34769058 PMCID: PMC8583777 DOI: 10.3390/ijms222111625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/13/2021] [Accepted: 10/24/2021] [Indexed: 11/17/2022] Open
Abstract
Karenia mikimotoi is a well-known harmful algal bloom species. Blooms of this dinoflagellate have become a serious threat to marine life, including fish, shellfish, and zooplanktons and are usually associated with massive fish death. Despite the discovery of several toxins such as gymnocins and gymnodimines in K. mikimotoi, the mechanisms underlying the ichthyotoxicity of this species remain unclear, and molecular studies on this topic have never been reported. The present study investigates the fish-killing mechanisms of K. mikimotoi through comparative proteomic analysis. Marine medaka, a model fish organism, was exposed to K. mikimotoi for a three-part time period (LT25, LT50 and LT90). Proteins extracted from the whole fish were separated by using two-dimensional gel electrophoresis, and differentially expressed proteins were identified with reference to an untreated control. The change in fish proteomes over the time-course of exposure were analyzed. A total of 35 differential protein spots covering 19 different proteins were identified, of which most began to show significant change in expression levels at the earliest stage of intoxication. Among the 19 identified proteins, some are closely related to the oxidative stress responses, energy metabolism, and muscle contraction. We propose that oxidative stress-mediated muscle damage might explain the symptoms developed during the ichthyotoxicity test, such as gasping for breath, loss of balance, and body twitching. Our findings lay the foundations for more in-depth studies of the mechanisms of K. mikimotoi's ichthyotoxicity.
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Affiliation(s)
| | | | | | | | | | - Fred Wang-Fat Lee
- Department of Science, School of Science and Technology, Hong Kong Metropolitan University, Hong Kong, China; (C.S.-N.K.); (K.K.-Y.L.); (W.L.); (S.J.-L.X.); (S.-W.L.)
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Khago D, Bierma JC, Roskamp KW, Kozlyuk N, Martin RW. Protein refractive index increment is determined by conformation as well as composition. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:435101. [PMID: 30280702 PMCID: PMC6387658 DOI: 10.1088/1361-648x/aae000] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The refractive index gradient of the eye lens is controlled by the concentration and distribution of its component crystallin proteins, which are highly enriched in polarizable amino acids. The current understanding of the refractive index increment ([Formula: see text]) of proteins is described using an additive model wherein the refractivity and specific volume of each amino acid type contributes according to abundance in the primary sequence. Here we present experimental measurements of [Formula: see text] for crystallins from the human lens and those of aquatic animals under uniform solvent conditions. In all cases, the measured values are much higher than those predicted from primary sequence alone, suggesting that structural factors also contribute to protein refractive index.
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Affiliation(s)
- Domarin Khago
- Department of Chemistry, University of California, Irvine, CA 92697, United States of America
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6
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Fan Z, Wu Z, Wang L, Zou Y, Zhang P, You F. Characterization of Embryo Transcriptome of Gynogenetic Olive Flounder Paralichthys olivaceus. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2016; 18:545-553. [PMID: 27638397 DOI: 10.1007/s10126-016-9716-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 07/06/2016] [Indexed: 06/06/2023]
Abstract
Olive flounder Paralichthys olivaceus is an important commercially cultured marine flatfish in China, Korea, and Japan. Gynogenesis, via meiogynogenesis and mitogynogenesis, shows advantages in breeding and sex control, but the low survival rate, especially for mitogynogenesis, limits its application. In this study, we sequenced the embryo transcriptomes of gynogenetic haploid, meiogynogenetic diploid, mitogynogenetic diploid, and common diploid flounder and investigated their respective genetic characteristics by analyzing differentiated expressed genes. Compared with common diploid, the gynogenetic haploid showed significant downregulation in notch signaling and wingless-related integration site (Wnt) signaling pathways, which may be the source of haploid syndrome. In both meiogynogenesis and mitogynogenesis, several upregulated genes including complement C3, formin-2, and intelectin may be related to increased survival compared to the haploid. The downregulation of immune system and energy metabolism-related genes caused retarded development of gynogenetic diploids compared with the common diploid. These data provided new and important information for application of artificially induced gynogenesis to aquaculture.
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Affiliation(s)
- Zhaofei Fan
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, People's Republic of China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 10049, People's Republic of China
| | - Zhihao Wu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, People's Republic of China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, People's Republic of China
| | - Lijuan Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, People's Republic of China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 10049, People's Republic of China
| | - Yuxia Zou
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, People's Republic of China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, People's Republic of China
| | - Peijun Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, People's Republic of China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, People's Republic of China
| | - Feng You
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, People's Republic of China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, People's Republic of China.
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Lin YG, Weadick CJ, Santini F, Chang BSW. Molecular evolutionary analysis of vertebrate transducins: a role for amino acid variation in photoreceptor deactivation. J Mol Evol 2013; 77:231-45. [PMID: 24145862 DOI: 10.1007/s00239-013-9589-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 09/25/2013] [Indexed: 01/05/2023]
Abstract
Transducin is a heterotrimeric G protein that plays a critical role in phototransduction in the rod and cone photoreceptor cells of the vertebrate retina. Rods, highly sensitive cells that recover from photoactivation slowly, underlie dim-light vision, whereas cones are less sensitive, recover more quickly, and underlie bright-light vision. Transducin deactivation is a critical step in photoreceptor recovery and may underlie the functional distinction between rods and cones. Rods and cones possess distinct transducin α subunits, yet they share a common deactivation mechanism, the GTPase activating protein (GAP) complex. Here, we used codon models to examine patterns of sequence evolution in rod (GNAT1) and cone (GNAT2) α subunits. Our results indicate that purifying selection is the dominant force shaping GNAT1 and GNAT2 evolution, but that GNAT2 has additionally been subject to positive selection operating at multiple phylogenetic scales; phylogeny-wide analysis identified several sites in the GNAT2 helical domain as having substantially elevated dN/dS estimates, and branch-site analysis identified several nearby sites as targets of strong positive selection during early vertebrate history. Examination of aligned GNAT and GAP complex crystal structures revealed steric clashes between several positively selected sites and the deactivating GAP complex. This suggests that GNAT2 sequence variation could play an important role in adaptive evolution of the vertebrate visual system via effects on photoreceptor deactivation kinetics and provides an alternative perspective to previous work that focused instead on the effect of GAP complex concentration. Our findings thus further the understanding of the molecular biology, physiology, and evolution of vertebrate visual systems.
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Affiliation(s)
- Yi G Lin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
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Zhao H, Brown PH, Magone MT, Schuck P. The molecular refractive function of lens γ-Crystallins. J Mol Biol 2011; 411:680-99. [PMID: 21684289 PMCID: PMC3146585 DOI: 10.1016/j.jmb.2011.06.007] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Revised: 06/01/2011] [Accepted: 06/02/2011] [Indexed: 10/18/2022]
Abstract
γ-Crystallins constitute the major protein component in the nucleus of the vertebrate eye lens. Present at very high concentrations, they exhibit extreme solubility and thermodynamic stability to prevent scattering of light and formation of cataracts. However, functions beyond this structural role have remained mostly unclear. Here, we calculate molecular refractive index increments of crystallins. We show that all lens γ-crystallins have evolved a significantly elevated molecular refractive index increment, which is far above those of most proteins, including nonlens members of the βγ-crystallin family from different species. The same trait has evolved in parallel in crystallins of different phyla, including S-crystallins of cephalopods. A high refractive index increment can lower the crystallin concentration required to achieve a suitable refractive power of the lens and thereby reduce their propensity to aggregate and form cataracts. To produce a significant increase in the refractive index increment, a substantial global shift in amino acid composition is required, which can naturally explain the highly unusual amino acid composition of γ-crystallins and their functional homologues. This function provides a new perspective for interpreting their molecular structure.
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Affiliation(s)
- Huaying Zhao
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, U.S.A
| | - Patrick H. Brown
- Biomedical Engineering and Physical Sciences Shared Resource, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, U.S.A
| | - M. Teresa Magone
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, U.S.A
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, U.S.A
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9
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Dynamic programming procedure for searching optimal models to estimate substitution rates based on the maximum-likelihood method. Proc Natl Acad Sci U S A 2011; 108:7860-5. [PMID: 21521791 DOI: 10.1073/pnas.1018621108] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The substitution rate in a gene can provide valuable information for understanding its functionality and evolution. A widely used method to estimate substitution rates is the maximum-likelihood method implemented in the CODEML program in the PAML package. A limited number of branch models, chosen based on a priori information or an interest in a particular lineage(s), are tested, whereas a large number of potential models are neglected. A complementary approach is also needed to test all or a large number of possible models to search for the globally optional model(s) of maximum likelihood. However, the computational time for this search even in a small number of sequences becomes impractically long. Thus, it is desirable to explore the most probable spaces to search for the optimal models. Using dynamic programming techniques, we developed a simple computational method for searching the most probable optimal branch-specific models in a practically feasible computational time. We propose three search methods to find the optimal models, which explored O(n) (method 1) to O(n(2)) (method 2 and method 3) models when the given phylogeny has n branches. In addition, we derived a formula to calculate the number of all possible models, revealing the complexity of finding the optimal branch-specific model. We show that in a reanalysis of over 50 previously published studies, the vast majority obtained better models with significantly higher likelihoods than the conventional hypothesis model methods.
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10
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Kappé G, Purkiss AG, van Genesen ST, Slingsby C, Lubsen NH. Explosive expansion of betagamma-crystallin genes in the ancestral vertebrate. J Mol Evol 2010; 71:219-30. [PMID: 20725717 PMCID: PMC2929430 DOI: 10.1007/s00239-010-9379-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2010] [Accepted: 07/29/2010] [Indexed: 11/23/2022]
Abstract
In jawed vertebrates, betagamma-crystallins are restricted to the eye lens and thus excellent markers of lens evolution. These betagamma-crystallins are four Greek key motifs/two domain proteins, whereas the urochordate betagamma-crystallin has a single domain. To trace the origin of the vertebrate betagamma-crystallin genes, we searched for homologues in the genomes of a jawless vertebrate (lamprey) and of a cephalochordate (lancelet). The lamprey genome contains orthologs of the gnathostome betaB1-, betaA2- and gammaN-crystallin genes and a single domain gammaN-crystallin-like gene. It contains at least two gamma-crystallin genes, but lacks the gnathostome gammaS-crystallin gene. The genome also encodes a non-lenticular protein containing betagamma-crystallin motifs, AIM1, also found in gnathostomes but not detectable in the uro- or cephalochordate genome. The four cephalochordate betagamma-crystallin genes found encode two-domain proteins. Unlike the vertebrate betagamma-crystallins but like the urochordate betagamma-crystallin, three of the predicted proteins contain calcium-binding sites. In the cephalochordate betagamma-crystallin genes, the introns are located within motif-encoding region, while in the urochordate and in the vertebrate betagamma-crystallin genes the introns are between motif- and/or domain encoding regions. Coincident with the evolution of the vertebrate lens an ancestral urochordate type betagamma-crystallin gene rapidly expanded and diverged in the ancestral vertebrate before the cyclostomes/gnathostomes split. The beta- and gammaN-crystallin genes were maintained in subsequent evolution, and, given the selection pressure imposed by accurate vision, must be essential for lens function. The gamma-crystallin genes show lineage specific expansion and contraction, presumably in adaptation to the demands on vision resulting from (changes in) lifestyle.
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Affiliation(s)
- Guido Kappé
- Biomolecular Chemistry 271, NCMLS, Radboud University Nijmegen, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Andrew G. Purkiss
- Department of Biological Sciences, Crystallography, Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London, WC1E 7HX UK
| | - Siebe T. van Genesen
- Biomolecular Chemistry 271, NCMLS, Radboud University Nijmegen, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Christine Slingsby
- Department of Biological Sciences, Crystallography, Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London, WC1E 7HX UK
| | - Nicolette H. Lubsen
- Biomolecular Chemistry 271, NCMLS, Radboud University Nijmegen, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
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