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Ariza-Mateos A, Briones C, Perales C, Bayo-Jiménez MT, Domingo E, Gómez J. Viruses as archaeological tools for uncovering ancient molecular relationships. Ann N Y Acad Sci 2023; 1529:3-13. [PMID: 37801367 DOI: 10.1111/nyas.15071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/08/2023]
Abstract
The entry of a virus into the host cell always implies the alteration of certain intracellular molecular relationships, some of which may involve the recovery of ancient cellular activities. In this sense, viruses are archaeological tools for identifying unexpressed activities in noninfected cells. Among these, activities that hinder virus propagation may represent cellular defense mechanisms, for example, activities that mutagenize the viral genome such as ADAR-1 or APOBEC activities. Instead, those that facilitate virus propagation can be interpreted as the result of viral adaptation to-or mimicking-cellular structures, enabling the virus to perform anthropomorphic activities, including hijacking, manipulating, and reorganizing cellular factors for their own benefit. The alternative we consider here is that some of these second set of cellular activities were already in the uninfected cell but silenced, under the negative control of the cell or lineage, and that they represent a necessary precondition for viral infection. For example, specifically loading an amino acid at the 3'-end of the mRNA of some plant viruses by aminoacyl-tRNA synthetases has proved essential for virus infection despite this reaction not occurring with cellular mRNAs. Other activities of this type are discussed here, together with the biological context in which they acquire a coherent meaning, that is, genetic latency and molecular conflict.
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Affiliation(s)
- Ascensión Ariza-Mateos
- Laboratory of RNA Archaeology, Instituto de Parasitología y Biomedicina "López-Neyra" (CSIC), Granada, Spain
| | - Carlos Briones
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | - Celia Perales
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CSIC), Madrid, Spain
| | - María Teresa Bayo-Jiménez
- Laboratory of RNA Archaeology, Instituto de Parasitología y Biomedicina "López-Neyra" (CSIC), Granada, Spain
| | - Esteban Domingo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Madrid, Spain
| | - Jordi Gómez
- Laboratory of RNA Archaeology, Instituto de Parasitología y Biomedicina "López-Neyra" (CSIC), Granada, Spain
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Christa G, Pütz L, Sickinger C, Melo Clavijo J, Laetz EMJ, Greve C, Serôdio J. Photoprotective Non-photochemical Quenching Does Not Prevent Kleptoplasts From Net Photoinactivation. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00121] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Laetz EMJ, Wägele H. Chloroplast digestion and the development of functional kleptoplasty in juvenile Elysia timida (Risso, 1818) as compared to short-term and non-chloroplast-retaining sacoglossan slugs. PLoS One 2017; 12:e0182910. [PMID: 29020043 PMCID: PMC5636068 DOI: 10.1371/journal.pone.0182910] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 07/26/2017] [Indexed: 01/13/2023] Open
Abstract
Sacoglossan sea slugs are the only metazoans known to perform functional kleptoplasty, the sequestration and retention of functional chloroplasts within their digestive gland cells. Remarkably, a few species with this ability can survive starvation periods of 3–12 months likely due to their stolen chloroplasts. There are no reports of kleptoplast transfer from mother slug to either eggs or juveniles, demonstrating that each animal must independently acquire its kleptoplasts and develop the ability to maintain them within its digestive gland. We present here an investigation into the development of functional kleptoplasty in a long-term kleptoplast retaining species, Elysia timida. Laboratory-reared juvenile slugs of different post-metamorphic ages were placed in starvation and compared to 5 known short-term retaining slug species and 5 non-retaining slug species. The subsequent results indicate that functional kleptoplasty is not performed by E. timida until after 15 days post-metamorphosis and that by 25 days, these animals outlive many of the short-term retention species. Digestive activity was also monitored using lysosomal abundance as an indicator, revealing different patterns in starving juveniles versus adults. Starved juveniles were reintroduced to food to determine any differences in digestive activity when starvation ends, resulting in an increase in the number of kleptoplasts, but no overall change in lysosomal activity. By revealing some of the changes that occur during early development in these animals, which begin as non-kleptoplast-retaining and grow into long-term retaining slugs, this investigation provides a basis for future inquiries into the origin and development of this remarkable ability.
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Affiliation(s)
- Elise Marie Jerschabek Laetz
- Center for Molecular Biodiversity Research (ZMB), Zoological Research Museum Alexander Koenig Adenauerallee 160 Bonn, Germany
- Institute for Evolutionary Biology and Ecology, University of Bonn, An der Immenburg 1 Bonn, Germany
- * E-mail:
| | - Heike Wägele
- Center for Molecular Biodiversity Research (ZMB), Zoological Research Museum Alexander Koenig Adenauerallee 160 Bonn, Germany
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Rauch C, Christa G, de Vries J, Woehle C, Gould SB. Mitochondrial Genome Assemblies of Elysia timida and Elysia cornigera and the Response of Mitochondrion-Associated Metabolism during Starvation. Genome Biol Evol 2017; 9:1873-1879. [PMID: 28854599 PMCID: PMC5534330 DOI: 10.1093/gbe/evx129] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2017] [Indexed: 12/11/2022] Open
Abstract
Some sacoglossan sea slugs sequester functional plastids (kleptoplasts) from their food, which continue to fix CO2 in a light dependent manner inside the animals. In plants and algae, plastid and mitochondrial metabolism are linked in ways that reach beyond the provision of energy-rich carbon compounds through photosynthesis, but how slug mitochondria respond to starvation or alterations in plastid biochemistry has not been explored. We assembled the mitochondrial genomes of the plastid-sequestering sea slugs Elysia timida and Elysia cornigera from RNA-Seq data that was complemented with standard sequencing of mitochondrial DNA through primer walking. Our data confirm the sister species relationship of the two Sacoglossa and from the analysis of changes in mitochondrial-associated metabolism during starvation we speculate that kleptoplasts might aid in the rerouting or recycling of reducing power independent of, yet maybe improved by, photosynthesis.
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Affiliation(s)
- Cessa Rauch
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Germany
| | - Gregor Christa
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Germany
- Department of Biology and CESAM, University of Aveiro, Portugal
| | - Jan de Vries
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Germany
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Christian Woehle
- Institute for Genomic Microbiology, Christian-Albrechts-University Kiel, Germany
| | - Sven B. Gould
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Germany
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Wade RM, Sherwood AR. Molecular determination of kleptoplast origins from the sea slug Plakobranchus ocellatus (Sacoglossa, Gastropoda) reveals cryptic bryopsidalean (Chlorophyta) diversity in the Hawaiian Islands. JOURNAL OF PHYCOLOGY 2017; 53:467-475. [PMID: 27992652 DOI: 10.1111/jpy.12503] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 09/30/2016] [Indexed: 06/06/2023]
Abstract
The sacoglossan sea slug species complex Plakobranchus ocellatus is a common algivore throughout the tropical Pacific, including the Hawaiian Islands. Plakobranchus ocellatus is kleptoplastic-it sequesters and retains algal chloroplasts-a characteristic that can be exploited to molecularly characterize diminutive bryopsidalean algae that are typically difficult to locate, collect, and identify. Previous DNA barcode analyses of both P. ocellatus and its kleptoplasts have been conducted primarily in the western Pacific and have only minimally sampled the most eastern populations in the Hawaiian Islands. Using two chloroplast markers, rbcL and tufA, kleptoplast samples from an Oahu population of P. ocellatus were amplified and cloned to identify their algal sources. Plakobranchus ocellatus sequester chloroplasts from up to 11 bryopsidalean algal species, all but one being diminutive in thallus size. Notably, eight of the detected algal species were new records to the Hawaiian Islands. A sequestration preference study demonstrated that the O'ahu population of P. ocellatus preferentially sequesters chloroplasts from diminutive, epilithic taxa. Using coxI barcoding of P. ocellatus, we showed the O'ahu population to be part of a clade that includes sequences from the neighboring island Maui, Australia, and the Philippines. The use of P. ocellatus as a novel sampling tool allows the exploration of the green algal community diversity and composition at a fine scale.
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Affiliation(s)
- Rachael M Wade
- Department of Botany, University of Hawaii at Mānoa, 3190 Maile Way, Honolulu, Hawaii, 96822, USA
| | - Alison R Sherwood
- Department of Botany, University of Hawaii at Mānoa, 3190 Maile Way, Honolulu, Hawaii, 96822, USA
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Gómez J, Ariza-Mateos A, Cacho I. Virus is a Signal for the Host Cell. BIOSEMIOTICS 2015; 8:483-491. [PMID: 26640606 PMCID: PMC4661187 DOI: 10.1007/s12304-015-9245-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 06/25/2015] [Indexed: 06/05/2023]
Abstract
Currently, the concept of the cell as a society or an ecosystem of molecular elements is gaining increasing acceptance. The basic idea arose in the 19th century, from the surmise that there is not just a single unit underlying an individual's appearance, but a plurality of entities with both collaborative and conflicting relationships. The following hypothesis is based around this model. The incompatible activities taking place between different original elements, which were subsumed into the first cell and could not be eliminated, had to be controlled very closely. Similarly, a strong level of control had to be developed over many cellular elements after the cell changed its genome to DNA. We assume that at least some of those original RNA agents and other biomolecules which carry incompatibilities and risks, are retained within current cells, although they are now under strict control. A virus functions as a signal informing these repressed cellular RNAs and other elements of ancient origin how to restore suppressed degrees of molecular freedom, favoring pre-existing molecular affinities and activities, re-establishing ancient molecular webs of interactions, and giving fragments of ancient coded information (mostly in the form of RNA structural motifs) the opportunity to be re-expressed. Collectively, these newly activated mechanisms lead to different possibilities for pathological cell states. All these processes are opposed by cell-control mechanisms. Thus, in this new scenario, the battle is considered intracellular rather than between the virus and the cell. And so the virus is treated as the signal that precipitates the cell's change from a latent to an active pathological state.
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Affiliation(s)
- Jordi Gómez
- Laboratory of RNA Archeology, Instituto de Parasitología y Biomedicina 'López-Neyra', Consejo Superior de Ivestigaciones Científicas, Armilla 18100 Granada, Spain
- Centro de Investigación Biomedicina En Red de enfermedades hepáticas y digestivas, Barcelona, Spain
| | - Ascensión Ariza-Mateos
- Laboratory of RNA Archeology, Instituto de Parasitología y Biomedicina 'López-Neyra', Consejo Superior de Ivestigaciones Científicas, Armilla 18100 Granada, Spain
- Centro de Investigación Biomedicina En Red de enfermedades hepáticas y digestivas, Barcelona, Spain
| | - Isabel Cacho
- Laboratory of RNA Archeology, Instituto de Parasitología y Biomedicina 'López-Neyra', Consejo Superior de Ivestigaciones Científicas, Armilla 18100 Granada, Spain
- Centro de Investigación Biomedicina En Red de enfermedades hepáticas y digestivas, Barcelona, Spain
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Baumgartner FA, Pavia H, Toth GB. Acquired phototrophy through retention of functional chloroplasts increases growth efficiency of the sea slug Elysia viridis. PLoS One 2015; 10:e0120874. [PMID: 25830355 PMCID: PMC4382131 DOI: 10.1371/journal.pone.0120874] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 01/27/2015] [Indexed: 11/29/2022] Open
Abstract
Photosynthesis is a fundamental process sustaining heterotrophic organisms at all trophic levels. Some mixotrophs can retain functional chloroplasts from food (kleptoplasty), and it is hypothesized that carbon acquired through kleptoplasty may enhance trophic energy transfer through increased host growth efficiency. Sacoglossan sea slugs are the only known metazoans capable of kleptoplasty, but the relative fitness contributions of heterotrophy through grazing, and phototrophy via kleptoplasts, are not well understood. Fitness benefits (i.e. increased survival or growth) of kleptoplasty in sacoglossans are commonly studied in ecologically unrealistic conditions under extended periods of complete darkness and/or starvation. We compared the growth efficiency of the sacoglossan Elysia viridis with access to algal diets providing kleptoplasts of differing functionality under ecologically relevant light conditions. Individuals fed Codium fragile, which provide highly functional kleptoplasts, nearly doubled their growth efficiency under high compared to low light. In contrast, individuals fed Cladophora rupestris, which provided kleptoplasts of limited functionality, showed no difference in growth efficiency between light treatments. Slugs feeding on Codium, but not on Cladophora, showed higher relative electron transport rates (rETR) in high compared to low light. Furthermore, there were no differences in the consumption rates of the slugs between different light treatments, and only small differences in nutritional traits of algal diets, indicating that the increased growth efficiency of E. viridis feeding on Codium was due to retention of functional kleptoplasts. Our results show that functional kleptoplasts from Codium can provide sacoglossan sea slugs with fitness advantages through photosynthesis.
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Affiliation(s)
- Finn A. Baumgartner
- University of Gothenburg, Department of Biological and Environmental Sciences-Tjärnö, Strömstad, Sweden
| | - Henrik Pavia
- University of Gothenburg, Department of Biological and Environmental Sciences-Tjärnö, Strömstad, Sweden
| | - Gunilla B. Toth
- University of Gothenburg, Department of Biological and Environmental Sciences-Tjärnö, Strömstad, Sweden
- * E-mail:
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de Vries J, Woehle C, Christa G, Wägele H, Tielens AGM, Jahns P, Gould SB. Comparison of sister species identifies factors underpinning plastid compatibility in green sea slugs. Proc Biol Sci 2015; 282:rspb.2014.2519. [PMID: 25652835 PMCID: PMC4344150 DOI: 10.1098/rspb.2014.2519] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The only animal cells known that can maintain functional plastids (kleptoplasts) in their cytosol occur in the digestive gland epithelia of sacoglossan slugs. Only a few species of the many hundred known can profit from kleptoplasty during starvation long-term, but why is not understood. The two sister taxa Elysia cornigera and Elysia timida sequester plastids from the same algal species, but with a very different outcome: while E. cornigera usually dies within the first two weeks when deprived of food, E. timida can survive for many months to come. Here we compare the responses of the two slugs to starvation, blocked photosynthesis and light stress. The two species respond differently, but in both starvation is the main denominator that alters global gene expression profiles. The kleptoplasts' ability to fix CO2 decreases at a similar rate in both slugs during starvation, but only E. cornigera individuals die in the presence of functional kleptoplasts, concomitant with the accumulation of reactive oxygen species (ROS) in the digestive tract. We show that profiting from the acquisition of robust plastids, and key to E. timida's longer survival, is determined by an increased starvation tolerance that keeps ROS levels at bay.
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Affiliation(s)
- Jan de Vries
- Institute of Molecular Evolution, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Christian Woehle
- Institute of Molecular Evolution, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Gregor Christa
- Institute of Molecular Evolution, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Heike Wägele
- Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany
| | - Aloysius G M Tielens
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Peter Jahns
- Plant Biochemistry and Stress Physiology, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Sven B Gould
- Institute of Molecular Evolution, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
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de Vries J, Christa G, Gould SB. Plastid survival in the cytosol of animal cells. TRENDS IN PLANT SCIENCE 2014; 19:347-50. [PMID: 24767983 DOI: 10.1016/j.tplants.2014.03.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 03/19/2014] [Accepted: 03/26/2014] [Indexed: 05/28/2023]
Abstract
Some marine slugs sequester plastids from their algae food, which can remain photosynthetically functional in the animal's digestive gland cells in the absence of algal nuclei. The sequestered plastids (kleptoplasts) appear to maintain functional photosystems through a greater autonomy than land plant plastids. If so, kleptoplast robustness is a plastid-intrinsic property, and it depends on the animal to manage an alien organelle on the loose in order to maintain it long term.
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Affiliation(s)
- Jan de Vries
- Institute of Molecular Evolution, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Gregor Christa
- Institute of Molecular Evolution, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany; Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany
| | - Sven B Gould
- Institute of Molecular Evolution, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany.
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