1
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Ewart KV. Further diversity in the origins of fish antifreeze proteins. FEBS J 2024. [PMID: 39206672 DOI: 10.1111/febs.17260] [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: 07/08/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024]
Abstract
Shifts in environmental conditions can impose strong selection for adaptive traits. During the Cenozoic era, as the oceans cooled, many marine teleost fish species were at risk of freezing. This led to the independent emergence of distinct ice-binding antifreeze proteins (AFPs). The report in this issue by Graham and Davies reveals the development of AFP genes in shorthorn and longhorn sculpin from a copy of the lunapark gene. The predicted sculpin AFP sequences are unrelated to that of lunapark; the coding sequences for the AFPs appear to have arisen from small portions of the lunapark gene by codon frameshifting along with a series of mutations.
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Affiliation(s)
- Kathryn Vanya Ewart
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Canada
- Department of Biology, Dalhousie University, Halifax, Canada
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2
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Aubin E, Llauro C, Garrigue J, Mirouze M, Panaud O, El Baidouri M. Genome-wide analysis of horizontal transfer in non-model wild species from a natural ecosystem reveals new insights into genetic exchange in plants. PLoS Genet 2023; 19:e1010964. [PMID: 37856455 PMCID: PMC10586619 DOI: 10.1371/journal.pgen.1010964] [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: 04/18/2023] [Accepted: 09/11/2023] [Indexed: 10/21/2023] Open
Abstract
Horizontal transfer (HT) refers to the exchange of genetic material between divergent species by mechanisms other than reproduction. In recent years, several studies have demonstrated HTs in eukaryotes, particularly in the context of parasitic relationships and in model species. However, very little is known about HT in natural ecosystems, especially those involving non-parasitic wild species, and the nature of the ecological relationships that promote these HTs. In this work, we conducted a pilot study investigating HTs by sequencing the genomes of 17 wild non-model species from a natural ecosystem, the Massane forest, located in southern France. To this end, we developed a new computational pipeline called INTERCHANGE that is able to characterize HTs at the whole genome level without prior annotation and directly in the raw sequencing reads. Using this pipeline, we identified 12 HT events, half of which occurred between lianas and trees. We found that mainly low copy number LTR-retrotransposons from the Copia superfamily were transferred between these wild plant species, especially those of the Ivana and Ale lineages. This study revealed a possible new route for HTs between non-parasitic plants and provides new insights into the genomic characteristics of horizontally transferred DNA in plant genomes.
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Affiliation(s)
- Emilie Aubin
- Laboratoire Génome et Développement des Plantes, Perpignan, Université de Perpignan Via Domitia, Perpignan, France
| | - Christel Llauro
- Laboratoire Génome et Développement des Plantes, Perpignan, Université de Perpignan Via Domitia, Perpignan, France
- Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, Perpignan, France
| | - Joseph Garrigue
- Réserve Naturelle Nationale de la forêt de la Massane, France
| | - Marie Mirouze
- Laboratoire Génome et Développement des Plantes, Perpignan, Université de Perpignan Via Domitia, Perpignan, France
- Diversité, Adaptation, Développement des Plantes, Institut de Recherche pour le Développement, Université de Montpellier, Montpellier, France
| | - Olivier Panaud
- Laboratoire Génome et Développement des Plantes, Perpignan, Université de Perpignan Via Domitia, Perpignan, France
- Institut Universitaire de France, Paris, France
| | - Moaine El Baidouri
- Laboratoire Génome et Développement des Plantes, Perpignan, Université de Perpignan Via Domitia, Perpignan, France
- Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, Perpignan, France
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3
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Davies PL. Reflections on antifreeze proteins and their evolution. Biochem Cell Biol 2022; 100:282-291. [PMID: 35580352 DOI: 10.1139/bcb-2022-0029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The discovery of radically different antifreeze proteins (AFPs) in fishes during the 1970s and 1980s suggested that these proteins had recently and independently evolved to protect teleosts from freezing in icy seawater. Early forays into the isolation and characterization of AFP genes in these fish showed they were massively amplified, often in long tandem repeats. The work of many labs in the 1980s onward led to the discovery and characterization of AFPs in other kingdoms, such as insects, plants, and many different microorganisms. The distinct ice-binding property that these ice-binding proteins (IBPs) share has facilitated their purification through adsorption to ice, and the ability to produce recombinant versions of IBPs has enabled their structural characterization and the mapping of their ice-binding sites (IBSs) using site-directed mutagenesis. One hypothesis for their ice affinity is that the IBS organizes surface waters into an ice-like pattern that freezes the protein onto ice. With access now to a rapidly expanding database of genomic sequences, it has been possible to trace the origins of some fish AFPs through the process of gene duplication and divergence, and to even show the horizontal transfer of an AFP gene from one species to another.
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Affiliation(s)
- Peter L Davies
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
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Ahmad A, Su X, Harris AJ, Ren Z. Closing the Gap: Horizontal Transfer of Mariner Transposons between Rhus Gall Aphids and Other Insects. BIOLOGY 2022; 11:731. [PMID: 35625459 PMCID: PMC9139091 DOI: 10.3390/biology11050731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 11/17/2022]
Abstract
Horizontal transfer of transposons (HTT) is an essential source of genomic evolution in eukaryotes. The HTT dynamics are well characterized in eukaryotes, including insects; however, there is a considerable gap in knowledge about HTT regarding many eukaryotes' species. In this study, we analyzed the events of the HTT between Rhus gall aphids (Hemiptera) and other insects. We analyzed the Mariner-like transposable elements (MLEs) belonging to Rhus gall aphids for the possible HT events. The MLEs have a patchy distribution and high similarity over the entire element length with insect MLEs from different orders. We selected representative sequences from the Rhus gall MLEs and identified five events of HT between MLEs of Rhus gall aphids and other insects from five different orders. We also found multiple HTT events among the MLEs of insects from the five orders, demonstrating that these Mariner elements have been involved in recurrent HT between Rhus gall aphids and other insects. Our current study closed the knowledge gap surrounding HTT and reported the events between Rhus gall aphids and other insects for the first time. We believe that this study about HTT events will help us understand the evolution and spread of transposable elements in the genomes of Rhus gall aphids.
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Affiliation(s)
- Aftab Ahmad
- School of Life Science, Shanxi University, Taiyuan 030006, China;
| | - Xu Su
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining 810016, China;
- School of Life Sciences, Qinghai Normal University, Xining 810008, China
| | - AJ Harris
- South China Botanical Garden, Chinese Academy of Sciences, Tianhe District, Guangzhou 510650, China;
| | - Zhumei Ren
- School of Life Science, Shanxi University, Taiyuan 030006, China;
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5
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Box ICH, Matthews BJ, Marshall KE. Molecular evidence of intertidal habitats selecting for repeated ice-binding protein evolution in invertebrates. J Exp Biol 2022; 225:274373. [PMID: 35258616 DOI: 10.1242/jeb.243409] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 12/20/2021] [Indexed: 12/21/2022]
Abstract
Ice-binding proteins (IBPs) have evolved independently in multiple taxonomic groups to improve their survival at sub-zero temperatures. Intertidal invertebrates in temperate and polar regions frequently encounter sub-zero temperatures, yet there is little information on IBPs in these organisms. We hypothesized that there are far more IBPs than are currently known and that the occurrence of freezing in the intertidal zone selects for these proteins. We compiled a list of genome-sequenced invertebrates across multiple habitats and a list of known IBP sequences and used BLAST to identify a wide array of putative IBPs in those invertebrates. We found that the probability of an invertebrate species having an IBP was significantly greater in intertidal species than in those primarily found in open ocean or freshwater habitats. These intertidal IBPs had high sequence similarity to fish and tick antifreeze glycoproteins and fish type II antifreeze proteins. Previously established classifiers based on machine learning techniques further predicted ice-binding activity in the majority of our newly identified putative IBPs. We investigated the potential evolutionary origin of one putative IBP from the hard-shelled mussel Mytilus coruscus and suggest that it arose through gene duplication and neofunctionalization. We show that IBPs likely readily evolve in response to freezing risk and that there is an array of uncharacterized IBPs, and highlight the need for broader laboratory-based surveys of the diversity of ice-binding activity across diverse taxonomic and ecological groups.
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Affiliation(s)
- Isaiah C H Box
- Department of Zoology, University of British Columbia, 6270 University Blvd, Vancouver, BC, CanadaV6T 1Z4
| | - Benjamin J Matthews
- Department of Zoology, University of British Columbia, 6270 University Blvd, Vancouver, BC, CanadaV6T 1Z4
| | - Katie E Marshall
- Department of Zoology, University of British Columbia, 6270 University Blvd, Vancouver, BC, CanadaV6T 1Z4
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Wanner NM, Faulk C. Suggested Absence of Horizontal Transfer of Retrotransposons between Humans and Domestic Mammal Species. Genes (Basel) 2021; 12:1223. [PMID: 34440397 PMCID: PMC8391136 DOI: 10.3390/genes12081223] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/02/2021] [Accepted: 08/05/2021] [Indexed: 02/01/2023] Open
Abstract
Transposable element sequences are usually vertically inherited but have also spread across taxa via horizontal transfer. Previous investigations of ancient horizontal transfer of transposons have compared consensus sequences, but this method resists detection of recent single or low copy number transfer events. The relationship between humans and domesticated animals represents an opportunity for potential horizontal transfer due to the consistent shared proximity and exposure to parasitic insects, which have been identified as plausible transfer vectors. The relatively short period of extended human-animal contact (tens of thousands of years or less) makes horizontal transfer of transposons between them unlikely. However, the availability of high-quality reference genomes allows individual element comparisons to detect low copy number events. Using pairwise all-versus-all megablast searches of the complete suite of retrotransposons of thirteen domestic animals against human, we searched a total of 27,949,823 individual TEs. Based on manual comparisons of stringently filtered BLAST search results for evidence of vertical inheritance, no plausible instances of HTT were identified. These results indicate that significant recent HTT between humans and domesticated animals has not occurred despite the close proximity, either due to the short timescale, inhospitable recipient genomes, a failure of vector activity, or other factors.
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Affiliation(s)
- Nicole M. Wanner
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, 301 Veterinary Science Building, 1971 Commonwealth Avenue, St. Paul, MN 55108, USA;
| | - Christopher Faulk
- Department of Animal Science, College of Food, Agriculture, and Natural Resource Sciences, University of Minnesota, 277 Coffey Hall, 1420 Eckles Avenue, St. Paul, MN 55108, USA
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7
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Hedenäs L, Larsson P, Cronholm B, Bisang I. Evidence of horizontal gene transfer between land plant plastids has surprising conservation implications. ANNALS OF BOTANY 2021; 127:903-908. [PMID: 33608721 PMCID: PMC8225274 DOI: 10.1093/aob/mcab021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 02/13/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND AND AIMS Horizontal gene transfer (HGT) is an important evolutionary mechanism because it transfers genetic material that may code for traits or functions between species or genomes. It is frequent in mitochondrial and nuclear genomes but has not been demonstrated between plastid genomes of different green land plant species. METHODS We Sanger-sequenced the nuclear internal transcribed spacers (ITS1 and 2) and the plastid rpl16 G2 intron (rpl16). In five individuals with foreign rpl16 we also sequenced atpB-rbcL and trnLUAA-trnFGAA. KEY RESULTS We discovered 14 individuals of a moss species with typical nuclear ITSs but foreign plastid rpl16 from a species of a distant lineage. None of the individuals with three plastid markers sequenced contained all foreign markers, demonstrating the transfer of plastid fragments rather than the entire plastid genome, i.e. entire plastids were not transferred. The two lineages diverged 165-185 Myr BP. The extended time interval since lineage divergence suggests that the foreign rpl16 is more likely explained by HGT than by hybridization or incomplete lineage sorting. CONCLUSIONS We provide the first conclusive evidence of interspecific plastid-to-plastid HGT among land plants. Two aspects are critical: it occurred at several localities during the massive colonization of recently disturbed open habitats that were created by large-scale liming as a freshwater biodiversity conservation measure; and it involved mosses whose unique life cycle includes spores that first develop a filamentous protonema phase. We hypothesize that gene transfer is facilitated when protonema filaments of different species intermix intimately when colonizing disturbed early succession habitats.
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Affiliation(s)
- Lars Hedenäs
- Department of Botany, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
- For correspondence. E-mail
| | - Petter Larsson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Bodil Cronholm
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
| | - Irene Bisang
- Department of Botany, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
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Analysis of the Sequence Characteristics of Antifreeze Protein. Life (Basel) 2021; 11:life11060520. [PMID: 34204983 PMCID: PMC8226703 DOI: 10.3390/life11060520] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/27/2021] [Accepted: 05/31/2021] [Indexed: 12/31/2022] Open
Abstract
Antifreeze protein (AFP) is a proteinaceous compound with improved antifreeze ability and binding ability to ice to prevent its growth. As a surface-active material, a small number of AFPs have a tremendous influence on the growth of ice. Therefore, identifying novel AFPs is important to understand protein–ice interactions and create novel ice-binding domains. To date, predicting AFPs is difficult due to their low sequence similarity for the ice-binding domain and the lack of common features among different AFPs. Here, a computational engine was developed to predict the features of AFPs and reveal the most important 39 features for AFP identification, such as antifreeze-like/N-acetylneuraminic acid synthase C-terminal, insect AFP motif, C-type lectin-like, and EGF-like domain. With this newly presented computational method, a group of previously confirmed functional AFP motifs was screened out. This study has identified some potential new AFP motifs and contributes to understanding biological antifreeze mechanisms.
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9
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Graham LA, Davies PL. Horizontal Gene Transfer in Vertebrates: A Fishy Tale. Trends Genet 2021; 37:501-503. [PMID: 33714557 DOI: 10.1016/j.tig.2021.02.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 02/21/2021] [Accepted: 02/23/2021] [Indexed: 11/25/2022]
Abstract
The recent assembly of the herring genome suggests this fish acquired its antifreeze protein gene by horizontal transfer and then passed a copy on to the smelt. The direction of gene transfer is confirmed by some accompanying transposable elements and by the breakage of gene synteny.
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Affiliation(s)
- Laurie A Graham
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Peter L Davies
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada.
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10
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Hobbs RS, Hall JR, Graham LA, Davies PL, Fletcher GL. Antifreeze protein dispersion in eelpouts and related fishes reveals migration and climate alteration within the last 20 Ma. PLoS One 2020; 15:e0243273. [PMID: 33320906 PMCID: PMC7737890 DOI: 10.1371/journal.pone.0243273] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 11/18/2020] [Indexed: 12/31/2022] Open
Abstract
Antifreeze proteins inhibit ice growth and are crucial for the survival of supercooled fish living in icy seawater. Of the four antifreeze protein types found in fishes, the globular type III from eelpouts is the one restricted to a single infraorder (Zoarcales), which is the only clade know to have antifreeze protein-producing species at both poles. Our analysis of over 60 unique antifreeze protein gene sequences from several Zoarcales species indicates this gene family arose around 18 Ma ago, in the Northern Hemisphere, supporting recent data suggesting that the Arctic Seas were ice-laden earlier than originally thought. The Antarctic was subject to widespread glaciation over 30 Ma and the Notothenioid fishes that produce an unrelated antifreeze glycoprotein extensively exploited the adjoining seas. We show that species from one Zoarcales family only encroached on this niche in the last few Ma, entering an environment already dominated by ice-resistant fishes, long after the onset of glaciation. As eelpouts are one of the dominant benthic fish groups of the deep ocean, they likely migrated from the north to Antarctica via the cold depths, losing all but the fully active isoform gene along the way. In contrast, northern species have retained both the fully active (QAE) and partially active (SP) isoforms for at least 15 Ma, which suggests that the combination of isoforms is functionally advantageous.
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Affiliation(s)
- Rod S. Hobbs
- Department of Ocean Sciences, Memorial University of Newfoundland, St John’s, Newfoundland, Canada
| | - Jennifer R. Hall
- Aquatic Research Cluster, CREAIT Network, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Laurie A. Graham
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
- * E-mail:
| | - Peter L. Davies
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
| | - Garth L. Fletcher
- Department of Ocean Sciences, Memorial University of Newfoundland, St John’s, Newfoundland, Canada
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11
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Zhang HH, Peccoud J, Xu MRX, Zhang XG, Gilbert C. Horizontal transfer and evolution of transposable elements in vertebrates. Nat Commun 2020; 11:1362. [PMID: 32170101 PMCID: PMC7070016 DOI: 10.1038/s41467-020-15149-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 02/20/2020] [Indexed: 11/13/2022] Open
Abstract
Horizontal transfer of transposable elements (HTT) is an important process shaping eukaryote genomes, yet very few studies have quantified this phenomenon on a large scale or have evaluated the selective constraints acting on transposable elements (TEs) during vertical and horizontal transmission. Here we screen 307 vertebrate genomes and infer a minimum of 975 independent HTT events between lineages that diverged more than 120 million years ago. HTT distribution greatly differs from null expectations, with 93.7% of these transfers involving ray-finned fishes and less than 3% involving mammals and birds. HTT incurs purifying selection (conserved protein evolution) on all TEs, confirming that producing functional transposition proteins is required for a TE to invade new genomes. In the absence of HTT, DNA transposons appear to evolve neutrally within genomes, unlike most retrotransposons, which evolve under purifying selection. This selection regime indicates that proteins of most retrotransposon families tend to process their own encoding RNA (cis-preference), which helps retrotransposons to persist within host lineages over long time periods. Horizontal transfer (HT) and evolution of transposable elements (TEs) has rarely been quantified on a large scale. Here, the authors screen 307 vertebrate genomes and infer 975 HT events (93% in ray-finned fishes); all TEs involved in HT evolve within genomes under purifying selection, as do most retrotransposons.
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Affiliation(s)
- Hua-Hao Zhang
- College of Pharmacy and Life Science, Jiujiang University, 332000, Jiujiang, China
| | - Jean Peccoud
- UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Université de Poitiers, 86073, Poitiers, France
| | - Min-Rui-Xuan Xu
- College of Pharmacy and Life Science, Jiujiang University, 332000, Jiujiang, China
| | - Xiao-Gu Zhang
- College of Pharmacy and Life Science, Jiujiang University, 332000, Jiujiang, China.
| | - Clément Gilbert
- Laboratoire Evolution, Génomes, Comportement, Écologie, UMR 9191 CNRS, UMR 247 IRD, Université Paris-Saclay, 91198, Gif-sur-Yvette, France.
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12
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Horizontal Transfer and Gene Loss Shaped the Evolution of Alpha-Amylases in Bilaterians. G3-GENES GENOMES GENETICS 2020; 10:709-719. [PMID: 31810981 PMCID: PMC7003070 DOI: 10.1534/g3.119.400826] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The subfamily GH13_1 of alpha-amylases is typical of Fungi, but it is also found in some unicellular eukaryotes (e.g., Amoebozoa, choanoflagellates) and non-bilaterian Metazoa. Since a previous study in 2007, GH13_1 amylases were considered ancestral to the Unikonts, including animals, except Bilateria, such that it was thought to have been lost in the ancestor of this clade. The only alpha-amylases known to be present in Bilateria so far belong to the GH13_15 and 24 subfamilies (commonly called bilaterian alpha-amylases) and were likely acquired by horizontal transfer from a proteobacterium. The taxonomic scope of Eukaryota genomes in databases has been greatly increased ever since 2007. We have surveyed GH13_1 sequences in recent data from ca. 1600 bilaterian species, 60 non-bilaterian animals and also in unicellular eukaryotes. As expected, we found a number of those sequences in non-bilaterians: Anthozoa (Cnidaria) and in sponges, confirming the previous observations, but none in jellyfishes and in Ctenophora. Our main and unexpected finding is that such fungal (also called Dictyo-type) amylases were also consistently retrieved in several bilaterian phyla: hemichordates (deuterostomes), brachiopods and related phyla, some molluscs and some annelids (protostomes). We discuss evolutionary hypotheses possibly explaining the scattered distribution of GH13_1 across bilaterians, namely, the retention of the ancestral gene in those phyla only and/or horizontal transfers from non-bilaterian donors.
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Abstract
Antifreeze proteins (AFPs) protect marine fishes from freezing in icy seawater. They evolved relatively recently, most likely in response to the formation of sea ice and Cenozoic glaciations that occurred less than 50 million years ago, following a greenhouse Earth event. Based on their diversity, AFPs have independently evolved on many occasions to serve the same function, with some remarkable examples of convergent evolution at the structural level, and even instances of lateral gene transfer. For some AFPs, the progenitor gene is recognizable. The intense selection pressure exerted by icy seawater, which can rapidly kill unprotected fish, has led to massive AFP gene amplification, as well as some partial gene duplications that have increased the size and activity of the antifreeze. The many protein evolutionary processes described in Gordon H. Dixon's Essays in Biochemistry article will be illustrated here by examples from studies on AFPs. Abbreviations: AFGP: antifreeze glycoproteins; AFP: antifreeze proteins; GHD: Gordon H. Dixon; SAS: sialic acid synthase; TH: thermal hysteresis.
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Affiliation(s)
- Peter L Davies
- a Department of Biomedical and Molecular Sciences , Queen's University , Kingston , Canada
| | - Laurie A Graham
- a Department of Biomedical and Molecular Sciences , Queen's University , Kingston , Canada
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14
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Hall JPJ, Brockhurst MA, Harrison E. Sampling the mobile gene pool: innovation via horizontal gene transfer in bacteria. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0424. [PMID: 29061896 DOI: 10.1098/rstb.2016.0424] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/05/2017] [Indexed: 12/26/2022] Open
Abstract
In biological systems, evolutionary innovations can spread not only from parent to offspring (i.e. vertical transmission), but also 'horizontally' between individuals, who may or may not be related. Nowhere is this more apparent than in bacteria, where novel ecological traits can spread rapidly within and between species through horizontal gene transfer (HGT). This important evolutionary process is predominantly a by-product of the infectious spread of mobile genetic elements (MGEs). We will discuss the ecological conditions that favour the spread of traits by HGT, the evolutionary and social consequences of sharing traits, and how HGT is shaped by inherent conflicts between bacteria and MGEs.This article is part of the themed issue 'Process and pattern in innovations from cells to societies'.
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Affiliation(s)
- James P J Hall
- Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Michael A Brockhurst
- Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Ellie Harrison
- P3 Institute, Department of Animal and Plant Sciences, Arthur Willis Environment Centre, University of Sheffield, 1 Maxfield Avenue, Sheffield S10 1AE, UK
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15
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Soyano K, Mushirobira Y. The Mechanism of Low-Temperature Tolerance in Fish. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1081:149-164. [DOI: 10.1007/978-981-13-1244-1_9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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16
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Peccoud J, Loiseau V, Cordaux R, Gilbert C. Massive horizontal transfer of transposable elements in insects. Proc Natl Acad Sci U S A 2017; 114:4721-4726. [PMID: 28416702 PMCID: PMC5422770 DOI: 10.1073/pnas.1621178114] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Horizontal transfer (HT) of genetic material is central to the architecture and evolution of prokaryote genomes. Within eukaryotes, the majority of HTs reported so far are transfers of transposable elements (TEs). These reports essentially come from studies focusing on specific lineages or types of TEs. Because of the lack of large-scale survey, the amount and impact of HT of TEs (HTT) in eukaryote evolution, as well as the trends and factors shaping these transfers, are poorly known. Here, we report a comprehensive analysis of HTT in 195 insect genomes, representing 123 genera and 13 of the 28 insect orders. We found that these insects were involved in at least 2,248 HTT events that essentially occurred during the last 10 My. We show that DNA transposons transfer horizontally more often than retrotransposons, and unveil phylogenetic relatedness and geographical proximity as major factors facilitating HTT in insects. Even though our study is restricted to a small fraction of insect biodiversity and to a recent evolutionary timeframe, the TEs we found to be horizontally transferred generated up to 24% (2.08% on average) of all nucleotides of insect genomes. Together, our results establish HTT as a major force shaping insect genome evolution.
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Affiliation(s)
- Jean Peccoud
- UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Université de Poitiers, Poitiers F-86073, France
| | - Vincent Loiseau
- UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Université de Poitiers, Poitiers F-86073, France
| | - Richard Cordaux
- UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Université de Poitiers, Poitiers F-86073, France
| | - Clément Gilbert
- UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Université de Poitiers, Poitiers F-86073, France
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Majhi RK, Saha S, Kumar A, Ghosh A, Swain N, Goswami L, Mohapatra P, Maity A, Kumar Sahoo V, Kumar A, Goswami C. Expression of temperature-sensitive ion channel TRPM8 in sperm cells correlates with vertebrate evolution. PeerJ 2015; 3:e1310. [PMID: 26500819 PMCID: PMC4614861 DOI: 10.7717/peerj.1310] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 09/19/2015] [Indexed: 12/13/2022] Open
Abstract
Transient Receptor Potential cation channel, subfamily Melastatin, member 8 (TRPM8) is involved in detection of cold temperature, different noxious compounds and in execution of thermo- as well as chemo-sensitive responses at cellular levels. Here we explored the molecular evolution of TRPM8 by analyzing sequences from various species. We elucidate that several regions of TRPM8 had different levels of selection pressure but the 4th-5th transmembrane regions remain highly conserved. Analysis of synteny suggests that since vertebrate origin, TRPM8 gene is linked with SPP2, a bone morphogen. TRPM8, especially the N-terminal region of it, seems to be highly variable in human population. We found 16,656 TRPM8 variants in 1092 human genomes with top variations being SNPs, insertions and deletions. A total of 692 missense mutations are also mapped to human TRPM8 protein of which 509 seem to be delateroiours in nature as supported by Polyphen V2, SIFT and Grantham deviation score. Using a highly specific antibody, we demonstrate that TRPM8 is expressed endogenously in the testis of rat and sperm cells of different vertebrates ranging from fish to higher mammals. We hypothesize that TRPM8 had emerged during vertebrate evolution (ca 450 MYA). We propose that expression of TRPM8 in sperm cell and its role in regulating sperm function are important factors that have guided its molecular evolution, and that these understandings may have medical importance.
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Affiliation(s)
- Rakesh Kumar Majhi
- School of Biological Sciences, National Institute of Science Education and Research, Institute of Physics Campus, Bhubaneswar, Orissa, India
| | - Somdatta Saha
- School of Biological Sciences, National Institute of Science Education and Research, Institute of Physics Campus, Bhubaneswar, Orissa, India
- School of Biotechnology, KIIT University, Bhubaneswar, Orissa, India
| | - Ashutosh Kumar
- School of Biological Sciences, National Institute of Science Education and Research, Institute of Physics Campus, Bhubaneswar, Orissa, India
| | - Arijit Ghosh
- School of Biological Sciences, National Institute of Science Education and Research, Institute of Physics Campus, Bhubaneswar, Orissa, India
| | - Nirlipta Swain
- School of Biological Sciences, National Institute of Science Education and Research, Institute of Physics Campus, Bhubaneswar, Orissa, India
| | - Luna Goswami
- School of Biotechnology, KIIT University, Bhubaneswar, Orissa, India
| | - Pratyush Mohapatra
- Department of Zoology, Government Science College, Chatrapur, Ganjam, Odisha, India
| | - Apratim Maity
- Department of Veterinary Biochemistry, CVSc & AH, Orissa University of Agriculture & Technology, Bhubaneswar, Orissa, India
| | - Vivek Kumar Sahoo
- School of Biological Sciences, National Institute of Science Education and Research, Institute of Physics Campus, Bhubaneswar, Orissa, India
| | - Abhishek Kumar
- Department of Genetics & Molecular Biology in Botany, Institute of Botany, Christian-Albrechts-University at Kiel, Kiel, SH, Germany
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, BW, Germany
| | - Chandan Goswami
- School of Biological Sciences, National Institute of Science Education and Research, Institute of Physics Campus, Bhubaneswar, Orissa, India
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18
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Abstract
Horizontal gene transfer (HGT) is the sharing of genetic material between organisms that are not in a parent-offspring relationship. HGT is a widely recognized mechanism for adaptation in bacteria and archaea. Microbial antibiotic resistance and pathogenicity are often associated with HGT, but the scope of HGT extends far beyond disease-causing organisms. In this Review, we describe how HGT has shaped the web of life using examples of HGT among prokaryotes, between prokaryotes and eukaryotes, and even between multicellular eukaryotes. We discuss replacement and additive HGT, the proposed mechanisms of HGT, selective forces that influence HGT, and the evolutionary impact of HGT on ancestral populations and existing populations such as the human microbiome.
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19
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Driedzic WR. Rainbow smelt: the unusual case of cryoprotection by sustained glycerol production in an aquatic animal. J Comp Physiol B 2015; 185:487-99. [DOI: 10.1007/s00360-015-0903-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 03/12/2015] [Accepted: 04/19/2015] [Indexed: 12/18/2022]
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20
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Graham LA, Hobbs RS, Fletcher GL, Davies PL. Helical antifreeze proteins have independently evolved in fishes on four occasions. PLoS One 2013; 8:e81285. [PMID: 24324684 PMCID: PMC3855684 DOI: 10.1371/journal.pone.0081285] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 10/21/2013] [Indexed: 12/25/2022] Open
Abstract
Alanine-rich α-helical (type I) antifreeze proteins (AFPs) are produced by a variety of fish species from three different orders to protect against freezing in icy seawater. Interspersed amongst and within these orders are fishes making AFPs that are completely different in both sequence and structure. The origin of this variety of types I, II, III and antifreeze glycoproteins (AFGPs) has been attributed to adaptation following sea-level glaciations that occurred after the divergence of most of the extant families of fish. The presence of similar types of AFPs in distantly related fishes has been ascribed to lateral gene transfer in the case of the structurally complex globular type II lectin-like AFPs and to convergent evolution for the AFGPs, which consist of a well-conserved tripeptide repeat. In this paper, we examine the genesis of the type I AFPs, which are intermediate in complexity. These predominantly α-helical peptides share many features, such as putative capping structures, Ala-richness and amphipathic character. We have added to the type I repertoire by cloning additional sequences from sculpin and have found that the similarities between the type I AFPs of the four distinct groups of fishes are not borne out at the nucleotide level. Both the non-coding sequences and the codon usage patterns are strikingly different. We propose that these AFPs arose via convergence from different progenitor helices with a weak affinity for ice and that their similarity is dictated by the propensity of specific amino acids to form helices and to align water on one side of the helix into an ice-like pattern.
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Affiliation(s)
- Laurie A. Graham
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
| | - Rod S. Hobbs
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Garth L. Fletcher
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Peter L. Davies
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
- * E-mail:
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Epithelial dominant expression of antifreeze proteins in cunner suggests recent entry into a high freeze-risk ecozone. Comp Biochem Physiol A Mol Integr Physiol 2012; 164:111-8. [PMID: 23085291 DOI: 10.1016/j.cbpa.2012.10.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 10/12/2012] [Accepted: 10/15/2012] [Indexed: 11/23/2022]
Abstract
Most marine teleost fishes residing in a high freeze-risk ecozone, such as the coastal waters of Newfoundland during winter, avoid freezing by secreting high concentrations of antifreeze proteins (AFP) into their blood plasma where they can bind to and prevent the growth of ice that enter the fish. Cunner (Tautogolabrus adspersus), which overwinter in such shallow waters are the only known exception. Although this species does produce type I AFP, the plasma levels are too low to be of value as a freeze protectant. Southern and Northern blot analyses carried out in this study establish that the cunner AFP genes belong to a multigene family that is predominantly expressed in external epithelia (skin and gill filaments). These results support the hypothesis that the survival of cunner in icy waters is attributable in part to epithelial AFP that help block ice propagation into their interior milieu. In contrast to the cunner, heterospecifics occupying the same habitat have greater freeze protection because they produce AFP in the liver for export to the plasma as well as in external epithelia. Since the external epithelia would be the first tissue to come into contact with ice it is possible that one of the earliest steps involved in the evolution of freeze resistant fish could have been the expression of AFP in tissues such as the skin. We suggest that this epithelial-dominant AFP expression represents a primitive stage in AFP evolution and propose that cunner began to inhabit "freeze-risk ecozones" more recently than heterospecifics.
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