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Perez M, Breusing C, Angers B, Beinart RA, Won YJ, Young CR. Divergent paths in the evolutionary history of maternally transmitted clam symbionts. Proc Biol Sci 2022; 289:20212137. [PMID: 35259985 PMCID: PMC8905170 DOI: 10.1098/rspb.2021.2137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Vertical transmission of bacterial endosymbionts is accompanied by virtually irreversible gene loss that results in a progressive reduction in genome size. While the evolutionary processes of genome reduction have been well described in some terrestrial symbioses, they are less understood in marine systems where vertical transmission is rarely observed. The association between deep-sea vesicomyid clams and chemosynthetic Gammaproteobacteria is one example of maternally inherited symbioses in the ocean. Here, we assessed the contributions of drift, recombination and selection to genome evolution in two extant vesicomyid symbiont clades by comparing 15 representative symbiont genomes (1.017-1.586 Mb) to those of closely related bacteria and the hosts' mitochondria. Our analyses suggest that drift is a significant force driving genome evolution in vesicomyid symbionts, though selection and interspecific recombination appear to be critical for maintaining symbiont functional integrity and creating divergent patterns of gene conservation. Notably, the two symbiont clades possess putative functional differences in sulfide physiology, anaerobic respiration and dependency on environmental vitamin B12, which probably reflect adaptations to different ecological habitats available to each symbiont group. Overall, these results contribute to our understanding of the eco-evolutionary processes shaping reductive genome evolution in vertically transmitted symbioses.
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Affiliation(s)
- Maëva Perez
- Department of Biological Sciences, Université de Montréal, Montreal, Canada
| | - Corinna Breusing
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, USA
| | - Bernard Angers
- Department of Biological Sciences, Université de Montréal, Montreal, Canada
| | - Roxanne A Beinart
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, USA
| | - Yong-Jin Won
- Division of EcoScience, Ewha Womans University, Seoul, South Korea
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Russell SL, Pepper-Tunick E, Svedberg J, Byrne A, Ruelas Castillo J, Vollmers C, Beinart RA, Corbett-Detig R. Horizontal transmission and recombination maintain forever young bacterial symbiont genomes. PLoS Genet 2020; 16:e1008935. [PMID: 32841233 PMCID: PMC7473567 DOI: 10.1371/journal.pgen.1008935] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 09/04/2020] [Accepted: 06/16/2020] [Indexed: 12/30/2022] Open
Abstract
Bacterial symbionts bring a wealth of functions to the associations they participate in, but by doing so, they endanger the genes and genomes underlying these abilities. When bacterial symbionts become obligately associated with their hosts, their genomes are thought to decay towards an organelle-like fate due to decreased homologous recombination and inefficient selection. However, numerous associations exist that counter these expectations, especially in marine environments, possibly due to ongoing horizontal gene flow. Despite extensive theoretical treatment, no empirical study thus far has connected these underlying population genetic processes with long-term evolutionary outcomes. By sampling marine chemosynthetic bacterial-bivalve endosymbioses that range from primarily vertical to strictly horizontal transmission, we tested this canonical theory. We found that transmission mode strongly predicts homologous recombination rates, and that exceedingly low recombination rates are associated with moderate genome degradation in the marine symbionts with nearly strict vertical transmission. Nonetheless, even the most degraded marine endosymbiont genomes are occasionally horizontally transmitted and are much larger than their terrestrial insect symbiont counterparts. Therefore, horizontal transmission and recombination enable efficient natural selection to maintain intermediate symbiont genome sizes and substantial functional genetic variation.
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Affiliation(s)
- Shelbi L. Russell
- Department of Molecular Cellular and Developmental Biology. University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Biomolecular Engineering. University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Evan Pepper-Tunick
- Department of Biomolecular Engineering. University of California Santa Cruz, Santa Cruz, California, United States of America
- Genomics Institute, University of California, Santa Cruz, California, United States of America
| | - Jesper Svedberg
- Department of Biomolecular Engineering. University of California Santa Cruz, Santa Cruz, California, United States of America
- Genomics Institute, University of California, Santa Cruz, California, United States of America
| | - Ashley Byrne
- Department of Molecular Cellular and Developmental Biology. University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Jennie Ruelas Castillo
- Department of Molecular Cellular and Developmental Biology. University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Christopher Vollmers
- Department of Biomolecular Engineering. University of California Santa Cruz, Santa Cruz, California, United States of America
- Genomics Institute, University of California, Santa Cruz, California, United States of America
| | - Roxanne A. Beinart
- Graduate School of Oceanography. University of Rhode Island, Narragansett, Rhode Island, United States of America
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering. University of California Santa Cruz, Santa Cruz, California, United States of America
- Genomics Institute, University of California, Santa Cruz, California, United States of America
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3
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Sapriel G, Brosch R. Shared Pathogenomic Patterns Characterize a New Phylotype, Revealing Transition toward Host-Adaptation Long before Speciation of Mycobacterium tuberculosis. Genome Biol Evol 2020; 11:2420-2438. [PMID: 31368488 PMCID: PMC6736058 DOI: 10.1093/gbe/evz162] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/09/2019] [Indexed: 02/06/2023] Open
Abstract
Tuberculosis remains one of the deadliest infectious diseases of humanity. To better understand the evolutionary history of host-adaptation of tubercle bacilli (MTB), we sought for mycobacterial species that were more closely related to MTB than the previously used comparator species Mycobacterium marinum and Mycobacterium kansasii. Our phylogenomic approach revealed some recently sequenced opportunistic mycobacterial pathogens, Mycobacterium decipiens, Mycobacterium lacus, Mycobacterium riyadhense, and Mycobacterium shinjukuense, to constitute a common clade with MTB, hereafter called MTB-associated phylotype (MTBAP), from which MTB have emerged. Multivariate and clustering analyses of genomic functional content revealed that the MTBAP lineage forms a clearly distinct cluster of species that share common genomic characteristics, such as loss of core genes, shift in dN/dS ratios, and massive expansion of toxin–antitoxin systems. Consistently, analysis of predicted horizontal gene transfer regions suggests that putative functions acquired by MTBAP members were markedly associated with changes in microbial ecology, for example adaption to intracellular stress resistance. Our study thus considerably deepens our view on MTB evolutionary history, unveiling a decisive shift that promoted conversion to host-adaptation among ancestral founders of the MTBAP lineage long before Mycobacterium tuberculosis has adapted to the human host.
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Affiliation(s)
- Guillaume Sapriel
- UFR des Sciences de La Santé, Université de Versailles St. Quentin, Montigny le Bretonneux, France.,Atelier de Bioinformatique, ISYEB, UMR 7205, Paris, France
| | - Roland Brosch
- Unit for Integrated Mycobacterial Pathogenomics, Institut Pasteur, CNRS UMR 3525, Paris, France
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Chemosynthetic symbiont with a drastically reduced genome serves as primary energy storage in the marine flatworm Paracatenula. Proc Natl Acad Sci U S A 2019; 116:8505-8514. [PMID: 30962361 PMCID: PMC6486704 DOI: 10.1073/pnas.1818995116] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Animals typically store their primary energy reserves in specialized cells. Here, we show that in the small marine flatworm Paracatenula, this function is performed by its bacterial chemosynthetic symbiont. The intracellular symbiont occupies half of the biomass in the symbiosis and has a highly reduced genome but efficiently stocks up and maintains carbon and energy, particularly sugars. The host rarely digests the symbiont cells to access these stocks. Instead, the symbionts appear to provide the bulk nutrition by secreting outer-membrane vesicles. This is in contrast to all other described chemosynthetic symbioses, where the hosts continuously digest full cells of a small and ideally growing symbiont population that cannot provide a long-term buffering capacity during nutrient limitation. Hosts of chemoautotrophic bacteria typically have much higher biomass than their symbionts and consume symbiont cells for nutrition. In contrast to this, chemoautotrophic Candidatus Riegeria symbionts in mouthless Paracatenula flatworms comprise up to half of the biomass of the consortium. Each species of Paracatenula harbors a specific Ca. Riegeria, and the endosymbionts have been vertically transmitted for at least 500 million years. Such prolonged strict vertical transmission leads to streamlining of symbiont genomes, and the retained physiological capacities reveal the functions the symbionts provide to their hosts. Here, we studied a species of Paracatenula from Sant’Andrea, Elba, Italy, using genomics, gene expression, imaging analyses, as well as targeted and untargeted MS. We show that its symbiont, Ca. R. santandreae has a drastically smaller genome (1.34 Mb) than the symbiont´s free-living relatives (4.29–4.97 Mb) but retains a versatile and energy-efficient metabolism. It encodes and expresses a complete intermediary carbon metabolism and enhanced carbon fixation through anaplerosis and accumulates massive intracellular inclusions such as sulfur, polyhydroxyalkanoates, and carbohydrates. Compared with symbiotic and free-living chemoautotrophs, Ca. R. santandreae’s versatility in energy storage is unparalleled in chemoautotrophs with such compact genomes. Transmission EM as well as host and symbiont expression data suggest that Ca. R. santandreae largely provisions its host via outer-membrane vesicle secretion. With its high share of biomass in the symbiosis and large standing stocks of carbon and energy reserves, it has a unique role for bacterial symbionts—serving as the primary energy storage for its animal host.
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Evolutionary dynamics of the chromatophore genome in three photosynthetic Paulinella species. Sci Rep 2019; 9:2560. [PMID: 30796245 PMCID: PMC6384880 DOI: 10.1038/s41598-019-38621-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 01/04/2019] [Indexed: 11/21/2022] Open
Abstract
The thecate amoeba Paulinella is a valuable model for understanding plastid organellogenesis because this lineage has independently gained plastids (termed chromatophores) of alpha-cyanobacterial provenance. Plastid primary endosymbiosis in Paulinella occurred relatively recently (90–140 million years ago, Mya), whereas the origin of the canonical Archaeplastida plastid occurred >1,500 Mya. Therefore, these two events provide independent perspectives on plastid formation on vastly different timescales. Here we generated the complete chromatophore genome sequence from P. longichromatophora (979,356 bp, GC-content = 38.8%, 915 predicted genes) and P. micropora NZ27 (977,190 bp, GC-content = 39.9%, 911 predicted genes) and compared these data to that from existing chromatophore genomes. Our analysis suggests that when a basal split occurred among photosynthetic Paulinella species ca. 60 Mya, only 35% of the ancestral orthologous gene families from the cyanobacterial endosymbiont remained in chromatophore DNA. Following major gene losses during the early stages of endosymbiosis, this process slowed down significantly, resulting in a conserved gene content across extant taxa. Chromatophore genes faced relaxed selection when compared to homologs in free-living alpha-cyanobacteria, likely reflecting the homogeneous intracellular environment of the Paulinella host. Comparison of nucleotide substitution and insertion/deletion events among different P. micropora strains demonstrates that increases in AT-content and genome reduction are ongoing and dynamic processes in chromatophore evolution.
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Shimamura S, Kaneko T, Ozawa G, Matsumoto MN, Koshiishi T, Takaki Y, Kato C, Takai K, Yoshida T, Fujikura K, Barry JP, Maruyama T. Loss of genes related to Nucleotide Excision Repair (NER) and implications for reductive genome evolution in symbionts of deep-sea vesicomyid clams. PLoS One 2017; 12:e0171274. [PMID: 28199404 PMCID: PMC5310779 DOI: 10.1371/journal.pone.0171274] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 01/17/2017] [Indexed: 01/08/2023] Open
Abstract
Intracellular thioautotrophic symbionts of deep-sea vesicomyid clams lack some DNA repair genes and are thought to be undergoing reductive genome evolution (RGE). In this study, we addressed two questions, 1) how these symbionts lost their DNA repair genes and 2) how such losses affect RGE. For the first question, we examined genes associated with nucleotide excision repair (NER; uvrA, uvrB, uvrC, uvrD, uvrD paralog [uvrDp] and mfd) in 12 symbionts of vesicomyid clams belonging to two clades (5 clade I and 7 clade II symbionts). While uvrA, uvrDp and mfd were conserved in all symbionts, uvrB and uvrC were degraded in all clade I symbionts but were apparently intact in clade II symbionts. UvrD was disrupted in two clade II symbionts. Among the intact genes in Ca. Vesicomyosocius okutanii (clade I), expressions of uvrD and mfd were detected by reverse transcription-polymerase chain reaction (RT-PCR), but those of uvrA and uvrDp were not. In contrast, all intact genes were expressed in the symbiont of Calyptogena pacifica (clade II). To assess how gene losses affect RGE (question 2), genetic distances of the examined genes in symbionts from Bathymodiolus septemdierum were shown to be larger in clade I than clade II symbionts. In addition, these genes had lower guanine+cytosine (GC) content and higher repeat sequence densities in clade I than measured in clade II. Our results suggest that NER genes are currently being lost from the extant lineages of vesicomyid clam symbionts. The loss of NER genes and mutY in these symbionts is likely to promote increases in genetic distance and repeat sequence density as well as reduced GC content in genomic genes, and may have facilitated reductive evolution of the genome.
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Affiliation(s)
- Shigeru Shimamura
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, 2–15, Natsushima-cho, Yokosuka-shi, Kanagawa, Japan
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology, Natsushima-cho, Yokosuka-shi, Kanagawa, Japan
| | - Takashi Kaneko
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, 2–15, Natsushima-cho, Yokosuka-shi, Kanagawa, Japan
- Tokyo College of Biotechnology, Kitakoujiya, Ota-ku,Tokyo, Japan
| | - Genki Ozawa
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, 2–15, Natsushima-cho, Yokosuka-shi, Kanagawa, Japan
- Kitasato University, School of Marine Biosciences, Kitasato Minami-ku Sagamihara-shi Kanagawa, Japan
| | - Mamiko Nishino Matsumoto
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, 2–15, Natsushima-cho, Yokosuka-shi, Kanagawa, Japan
| | - Takeru Koshiishi
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, 2–15, Natsushima-cho, Yokosuka-shi, Kanagawa, Japan
| | - Yoshihiro Takaki
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology, Natsushima-cho, Yokosuka-shi, Kanagawa, Japan
| | - Chiaki Kato
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, 2–15, Natsushima-cho, Yokosuka-shi, Kanagawa, Japan
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology, Natsushima-cho, Yokosuka-shi, Kanagawa, Japan
| | - Takao Yoshida
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, 2–15, Natsushima-cho, Yokosuka-shi, Kanagawa, Japan
- Kitasato University, School of Marine Biosciences, Kitasato Minami-ku Sagamihara-shi Kanagawa, Japan
| | - Katsunori Fujikura
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, 2–15, Natsushima-cho, Yokosuka-shi, Kanagawa, Japan
| | - James P. Barry
- Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America
| | - Tadashi Maruyama
- Kitasato University, School of Marine Biosciences, Kitasato Minami-ku Sagamihara-shi Kanagawa, Japan
- Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science and Technology, Natsushima-cho, Yokosuka-shi, Kanagawa, Japan
- * E-mail:
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7
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Ikuta T, Igawa K, Tame A, Kuroiwa T, Kuroiwa H, Aoki Y, Takaki Y, Nagai Y, Ozawa G, Yamamoto M, Deguchi R, Fujikura K, Maruyama T, Yoshida T. Surfing the vegetal pole in a small population: extracellular vertical transmission of an 'intracellular' deep-sea clam symbiont. ROYAL SOCIETY OPEN SCIENCE 2016; 3:160130. [PMID: 27293794 PMCID: PMC4892456 DOI: 10.1098/rsos.160130] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 04/21/2016] [Indexed: 06/06/2023]
Abstract
Symbiont transmission is a key event for understanding the processes underlying symbiotic associations and their evolution. However, our understanding of the mechanisms of symbiont transmission remains still fragmentary. The deep-sea clam Calyptogena okutanii harbours obligate sulfur-oxidizing intracellular symbiotic bacteria in the gill epithelial cells. In this study, we determined the localization of their symbiont associating with the spawned eggs, and the population size of the symbiont transmitted via the eggs. We show that the symbionts are located on the outer surface of the egg plasma membrane at the vegetal pole, and that each egg carries approximately 400 symbiont cells, each of which contains close to 10 genomic copies. The very small population size of the symbiont transmitted via the eggs might narrow the bottleneck and increase genetic drift, while polyploidy and its transient extracellular lifestyle might slow the rate of genome reduction. Additionally, the extracellular localization of the symbiont on the egg surface may increase the chance of symbiont exchange. This new type of extracellular transovarial transmission provides insights into complex interactions between the host and symbiont, development of both host and symbiont, as well as the population dynamics underlying genetic drift and genome evolution in microorganisms.
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Affiliation(s)
- Tetsuro Ikuta
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan
| | - Kanae Igawa
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
| | - Akihiro Tame
- Marine Works Japan, Ltd, 3-54-1 Oppamahigashi, Yokosuka, Kanagawa 237-0063, Japan
| | - Tsuneyoshi Kuroiwa
- Department of Chemical and Biological Sciences, Japan Women's University, 2-8-1 Mejirodai, Bunkyo-ku, Tokyo 112-8681, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Haruko Kuroiwa
- Department of Chemical and Biological Sciences, Japan Women's University, 2-8-1 Mejirodai, Bunkyo-ku, Tokyo 112-8681, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Yui Aoki
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan
| | - Yoshihiro Takaki
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan
| | - Yukiko Nagai
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan
| | - Genki Ozawa
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan
- Department of Marine Biosciences, School of Marine Biosciences, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Masahiro Yamamoto
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan
| | - Ryusaku Deguchi
- Department of Biology, Miyagi University of Education, Aoba-ku, Sendai, Miyagi 980-0845, Japan
| | - Katsunori Fujikura
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan
| | - Tadashi Maruyama
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan
| | - Takao Yoshida
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
- Department of Marine Biosciences, School of Marine Biosciences, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
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Wentrup C, Wendeberg A, Schimak M, Borowski C, Dubilier N. Forever competent: deep‐sea bivalves are colonized by their chemosynthetic symbionts throughout their lifetime. Environ Microbiol 2014; 16:3699-713. [DOI: 10.1111/1462-2920.12597] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 08/08/2014] [Indexed: 01/17/2023]
Affiliation(s)
- Cecilia Wentrup
- Department of Symbiosis Max Planck Institute for Marine Microbiology Celsiusstrasse 1 Bremen 28359 Germany
| | - Annelie Wendeberg
- Department of Environmental Microbiology UFZ, Helmholtz Centre for Environmental Research Permoserstrasse 15 Leipzig 04318 Germany
| | - Mario Schimak
- Department of Symbiosis Max Planck Institute for Marine Microbiology Celsiusstrasse 1 Bremen 28359 Germany
| | - Christian Borowski
- Department of Symbiosis Max Planck Institute for Marine Microbiology Celsiusstrasse 1 Bremen 28359 Germany
| | - Nicole Dubilier
- Department of Symbiosis Max Planck Institute for Marine Microbiology Celsiusstrasse 1 Bremen 28359 Germany
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Dmytrenko O, Russell SL, Loo WT, Fontanez KM, Liao L, Roeselers G, Sharma R, Stewart FJ, Newton ILG, Woyke T, Wu D, Lang JM, Eisen JA, Cavanaugh CM. The genome of the intracellular bacterium of the coastal bivalve, Solemya velum: a blueprint for thriving in and out of symbiosis. BMC Genomics 2014; 15:924. [PMID: 25342549 PMCID: PMC4287430 DOI: 10.1186/1471-2164-15-924] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 09/23/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Symbioses between chemoautotrophic bacteria and marine invertebrates are rare examples of living systems that are virtually independent of photosynthetic primary production. These associations have evolved multiple times in marine habitats, such as deep-sea hydrothermal vents and reducing sediments, characterized by steep gradients of oxygen and reduced chemicals. Due to difficulties associated with maintaining these symbioses in the laboratory and culturing the symbiotic bacteria, studies of chemosynthetic symbioses rely heavily on culture independent methods. The symbiosis between the coastal bivalve, Solemya velum, and its intracellular symbiont is a model for chemosynthetic symbioses given its accessibility in intertidal environments and the ability to maintain it under laboratory conditions. To better understand this symbiosis, the genome of the S. velum endosymbiont was sequenced. RESULTS Relative to the genomes of obligate symbiotic bacteria, which commonly undergo erosion and reduction, the S. velum symbiont genome was large (2.7 Mb), GC-rich (51%), and contained a large number (78) of mobile genetic elements. Comparative genomics identified sets of genes specific to the chemosynthetic lifestyle and necessary to sustain the symbiosis. In addition, a number of inferred metabolic pathways and cellular processes, including heterotrophy, branched electron transport, and motility, suggested that besides the ability to function as an endosymbiont, the bacterium may have the capacity to live outside the host. CONCLUSIONS The physiological dexterity indicated by the genome substantially improves our understanding of the genetic and metabolic capabilities of the S. velum symbiont and the breadth of niches the partners may inhabit during their lifecycle.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Jonathan A Eisen
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, 4081 Biological Laboratories, Cambridge, MA 02138, USA.
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10
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Kucho KI, Yamanaka T, Sasakawa H, Mansour SR, Uchiumi T. Different dynamics of genome content shuffling among host-specificity groups of the symbiotic actinobacterium Frankia. BMC Genomics 2014; 15:609. [PMID: 25038796 PMCID: PMC4117964 DOI: 10.1186/1471-2164-15-609] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 07/09/2014] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Frankia is a genus of soil actinobacteria forming nitrogen-fixing root-nodule symbiotic relationships with non-leguminous woody plant species, collectively called actinorhizals, from eight dicotyledonous families. Frankia strains are classified into four host-specificity groups (HSGs), each of which exhibits a distinct host range. Genome sizes of representative strains of Alnus, Casuarina, and Elaeagnus HSGs are highly diverged and are positively correlated with the size of their host ranges. RESULTS The content and size of 12 Frankia genomes were investigated by in silico comparative genome hybridization and pulsed-field gel electrophoresis, respectively. Data were collected from four query strains of each HSG and compared with those of reference strains possessing completely sequenced genomes. The degree of difference in genome content between query and reference strains varied depending on HSG. Elaeagnus query strains were missing the greatest number (22-32%) of genes compared with the corresponding reference genome; Casuarina query strains lacked the fewest (0-4%), with Alnus query strains intermediate (14-18%). In spite of the remarkable gene loss, genome sizes of Alnus and Elaeagnus query strains were larger than would be expected based on total length of the absent genes. In contrast, Casuarina query strains had smaller genomes than expected. CONCLUSIONS The positive correlation between genome size and host range held true across all investigated strains, supporting the hypothesis that size and genome content differences are responsible for observed diversity in host plants and host plant biogeography among Frankia strains. In addition, our results suggest that different dynamics of shuffling of genome content have contributed to these symbiotic and biogeographic adaptations. Elaeagnus strains, and to a lesser extent Alnus strains, have gained and lost many genes to adapt to a wide range of environments and host plants. Conversely, rather than acquiring new genes, Casuarina strains have discarded genes to reduce genome size, suggesting an evolutionary orientation towards existence as specialist symbionts.
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MESH Headings
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Cluster Analysis
- Comparative Genomic Hybridization
- DNA/chemistry
- DNA/metabolism
- DNA Gyrase/genetics
- DNA Gyrase/metabolism
- Electrophoresis, Gel, Pulsed-Field
- Frankia/genetics
- Genome, Bacterial
- High-Throughput Nucleotide Sequencing
- Nitrogen Fixation/genetics
- Phylogeny
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/classification
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Symbiosis/genetics
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Affiliation(s)
- Ken-ichi Kucho
- />Graduate School of Science and Engineering, Kagoshima University, 1-21-35 Korimoto, Kagoshima, 890-0065 Japan
| | - Takashi Yamanaka
- />Department of Forest Microbiology, Forestry and Forest Products Research Institute (FFPRI), 1 Matsunosato, Tsukuba, Ibaraki, 305-8687 Japan
| | - Hideo Sasakawa
- />Graduate School of Natural Science and Technology, Okayama University, Tsushimanaka, Okayama, 700-8530 Japan
| | - Samira R Mansour
- />Botany Department, Faculty of Science, Suez Canal University, Ismailia, 41522 Egypt
| | - Toshiki Uchiumi
- />Graduate School of Science and Engineering, Kagoshima University, 1-21-35 Korimoto, Kagoshima, 890-0065 Japan
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11
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Decker C, Olu K, Arnaud-Haond S, Duperron S. Physical proximity may promote lateral acquisition of bacterial symbionts in vesicomyid clams. PLoS One 2013; 8:e64830. [PMID: 23861734 PMCID: PMC3704533 DOI: 10.1371/journal.pone.0064830] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 04/18/2013] [Indexed: 11/19/2022] Open
Abstract
Vesicomyid clams harbor intracellular sulfur-oxidizing bacteria that are predominantly maternally inherited and co-speciate with their hosts. Genome recombination and the occurrence of non-parental strains were recently demonstrated in symbionts. However, mechanisms favoring such events remain to be identified. In this study, we investigated symbionts in two phylogenetically distant vesicomyid species, Christineconcha regab and Laubiericoncha chuni, which sometimes co-occur at a cold-seep site in the Gulf of Guinea. We showed that each of the two species harbored a single dominant bacterial symbiont strain. However, for both vesicomyid species, the symbiont from the other species was occasionally detected in the gills using fluorescence in situ hybridization and gene sequences analyses based on six symbiont marker genes. Symbiont strains co-occurred within a single host only at sites where both host species were found; whereas one single symbiont strain was detected in C. regab specimens from a site where no L. chuni individuals had been observed. These results suggest that physical proximity favored the acquisition of non-parental symbiont strains in Vesicomyidae. Over evolutionary time, this could potentially lead to genetic exchanges among symbiont species and eventually symbiont displacement. Symbiont densities estimated using 3D fluorescence in situ hybridization varied among host species and sites, suggesting flexibility in the association despite the fact that a similar type of metabolism is expected in all symbionts.
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Affiliation(s)
- Carole Decker
- IFREMER Centre de Brest, Laboratoire Environnement Profond, REM-EEP, Plouzané, France.
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12
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ROUNDS MEGANA, CROWDER CHRISTOPHERD, MATTHEWS HEATHERE, PHILIPSON CURTISA, SCOLES GLENA, ECKER DAVIDJ, SCHUTZER STEVENE, ESHOO MARKW. Identification of endosymbionts in ticks by broad-range polymerase chain reaction and electrospray ionization mass spectrometry. JOURNAL OF MEDICAL ENTOMOLOGY 2012; 49:843-850. [PMID: 22897044 PMCID: PMC3535486 DOI: 10.1603/me12038] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Many organisms, such as insects, filarial nematodes, and ticks, contain heritable bacterial endosymbionts that are often closely related to transmissible tickborne pathogens. These intracellular bacteria are sometimes unique to the host species, presumably due to isolation and genetic drift. We used a polymerase chain reaction/electrospray ionization-mass spectrometry assay designed to detect a wide range of vectorborne microorganisms to characterize endosymbiont genetic signatures from Amblyomma americanum (L.), Amblyomma maculatum Koch, Dermacentor andersoni Stiles, Dermacentor occidentalis Marx, Dermacentor variabilis (Say), Ixodes scapularis Say, Ixodes pacificus Cooley & Kohls, Ixodes ricinus (L.), and Rhipicephalus sanguineus (Latreille) ticks collected at various sites and of different stages and both sexes. The assay combines the abilities to simultaneously detect pathogens and closely related endosymbionts and to identify tick species via characterization of their respective unique endosymbionts in a single test.
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Affiliation(s)
- MEGAN A. ROUNDS
- Ibis Biosciences, Inc., an Abbott Company, Carlsbad, CA 92008
| | | | | | | | - GLEN A. SCOLES
- USDA–ARS, Animal Disease Research Unit, 3003 ADBF, Washington State University, P.O. Box 646630 Pullman, WA 99164
| | - DAVID J. ECKER
- Ibis Biosciences, Inc., an Abbott Company, Carlsbad, CA 92008
| | - STEVEN E. SCHUTZER
- Department of Medicine, University of Medicine and Dentistry of New Jersey, New Jersey Medical School, Newark, NJ 07103
| | - MARK W. ESHOO
- Ibis Biosciences, Inc., an Abbott Company, Carlsbad, CA 92008
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13
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The smaller vesicomyid bivalves in the genus Isorropodon (Bivalvia, Vesicomyidae, Pliocardiinae) also harbour chemoautotrophic symbionts. Symbiosis 2012. [DOI: 10.1007/s13199-012-0168-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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14
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Dewall MT, Cheng DW. The minimal genome: a metabolic and environmental comparison. Brief Funct Genomics 2012; 10:312-5. [PMID: 21987714 DOI: 10.1093/bfgp/elr030] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The field of Synthetic Biology seeks to apply engineering principles to biology in order to produce novel biological systems. One approach to accomplish this goal is the genome-driven cell engineering approach, which searches for functioning minimal genomes in naturally occurring microorganisms, which can then be used as a template for future systems. Currently a prototypical minimal genome has not been discovered. This review analyzes the organisms Mycoplasma pneumoniae, Pelagibacter ubique, Vesicomyosocius okutanii and Prochlorococcus marinus as models of heterotrophic symbiont, heterotrophic free-living, autotrophic symbiont and autotrophic free-living organisms respectively and compares them to the current minimal cell model in order to determine which most closely resembles a true minimal genome. M. pneumoniae possesses a genome of 816 394 base pairs (bp) with 688 open reading frames (ORF) and a severely limited metabolism. Pelagibacter ubique possesses a 1 308 000 bp genome with 1354 ORF and has a fully functional metabolism but requires a reduced form of sulphur. Vesicomyosocius okutanii possesses a 1 020 000 bp genome with 975 ORF and is deficient in the production of threonine, isoleucine and ubiquinone. Prochlorococcus marinus possesses a 1 751 080 bp genome with 1884 ORF and has a complete metabolism with no deficiencies. The current minimal cell model requires a genome to be of limited size, culturalble and having minimal media requirements as such it is the conclusion of this review that P. marinus best fits this model. Further, future research should concentrate on genome reduction experiments using P. marinus and the search for additional minimal genomes should concentrate on autotrophic free-living organisms.
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Affiliation(s)
- Michael Thomas Dewall
- Department of Biology, Research Infrastructure for Minority Institutions, California State University, Fresno, CA 93740, USA
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15
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Kjeldsen KU, Bataillon T, Pinel N, De Mita S, Lund MB, Panitz F, Bendixen C, Stahl DA, Schramm A. Purifying selection and molecular adaptation in the genome of Verminephrobacter, the heritable symbiotic bacteria of earthworms. Genome Biol Evol 2012; 4:307-15. [PMID: 22333491 PMCID: PMC3318438 DOI: 10.1093/gbe/evs014] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
While genomic erosion is common among intracellular symbionts, patterns of genome evolution in heritable extracellular endosymbionts remain elusive. We study vertically transmitted extracellular endosymbionts (Verminephrobacter, Betaproteobacteria) that form a beneficial, species-specific, and evolutionarily old (60–130 Myr) association with earthworms. We assembled a draft genome of Verminephrobacter aporrectodeae and compared it with the genomes of Verminephrobacter eiseniae and two nonsymbiotic close relatives (Acidovorax). Similar to V. eiseniae, the V. aporrectodeae genome was not markedly reduced in size and showed no A–T bias. We characterized the strength of purifying selection (ω = dN/dS) and codon usage bias in 876 orthologous genes. Symbiont genomes exhibited strong purifying selection (ω = 0.09 ± 0.07), although transition to symbiosis entailed relaxation of purifying selection as evidenced by 50% higher ω values and less codon usage bias in symbiont compared with reference genomes. Relaxation was not evenly distributed among functional gene categories but was overrepresented in genes involved in signal transduction and cell envelope biogenesis. The same gene categories also harbored instances of positive selection in the Verminephrobacter clade. In total, positive selection was detected in 89 genes, including also genes involved in DNA metabolism, tRNA modification, and TonB-dependent iron uptake, potentially highlighting functions important in symbiosis. Our results suggest that the transition to symbiosis was accompanied by molecular adaptation, while purifying selection was only moderately relaxed, despite the evolutionary age and stability of the host association. We hypothesize that biparental transmission of symbionts and rare genetic mixing during transmission can prevent genome erosion in heritable symbionts.
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16
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Kuwahara H, Takaki Y, Shimamura S, Yoshida T, Maeda T, Kunieda T, Maruyama T. Loss of genes for DNA recombination and repair in the reductive genome evolution of thioautotrophic symbionts of Calyptogena clams. BMC Evol Biol 2011; 11:285. [PMID: 21966992 PMCID: PMC3202245 DOI: 10.1186/1471-2148-11-285] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Accepted: 10/03/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Two Calyptogena clam intracellular obligate symbionts, Ca. Vesicomyosocius okutanii (Vok; C. okutanii symbiont) and Ca. Ruthia magnifica (Rma; C. magnifica symbiont), have small genomes (1.02 and 1.16 Mb, respectively) with low G+C contents (31.6% and 34.0%, respectively) and are thought to be in an ongoing stage of reductive genome evolution (RGE). They lack recA and some genes for DNA repair, including mutY. The loss of recA and mutY is thought to contribute to the stabilization of their genome architectures and GC bias, respectively. To understand how these genes were lost from the symbiont genomes, we surveyed these genes in the genomes from 10 other Calyptogena clam symbionts using the polymerase chain reaction (PCR). RESULTS Phylogenetic trees reconstructed using concatenated 16S and 23S rRNA gene sequences showed that the symbionts formed two clades, clade I (symbionts of C. kawamurai, C. laubieri, C. kilmeri, C. okutanii and C. soyoae) and clade II (those of C. pacifica, C. fausta, C. nautilei, C. stearnsii, C. magnifica, C. fossajaponica and C. phaseoliformis). recA was detected by PCR with consensus primers for recA in the symbiont of C. phaseoliformis. A detailed homology search revealed a remnant recA in the Rma genome. Using PCR with a newly designed primer set, intact recA or its remnant was detected in clade II symbionts. In clade I symbionts, the recA coding region was found to be mostly deleted.In the Rma genome, a pseudogene of mutY was found. Using PCR with newly designed primer sets, mutY was not found in clade I symbionts but was found in clade II symbionts. The G+C content of 16S and 23S rRNA genes in symbionts lacking mutY was significantly lower than in those with mutY. CONCLUSIONS The extant Calyptogena clam symbionts in clade II were shown to have recA and mutY or their remnants, while those in clade I did not. The present results indicate that the extant symbionts are losing these genes in RGE, and that the loss of mutY contributed to the GC bias of the genomes during their evolution.
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Affiliation(s)
- Hirokazu Kuwahara
- Marine Biodiversity Research Program, Japan Agency for Marine-Earth Science and Technology, Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
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17
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Paracatenula, an ancient symbiosis between thiotrophic Alphaproteobacteria and catenulid flatworms. Proc Natl Acad Sci U S A 2011; 108:12078-83. [PMID: 21709249 DOI: 10.1073/pnas.1105347108] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Harnessing chemosynthetic symbionts is a recurring evolutionary strategy. Eukaryotes from six phyla as well as one archaeon have acquired chemoautotrophic sulfur-oxidizing bacteria. In contrast to this broad host diversity, known bacterial partners apparently belong to two classes of bacteria--the Gamma- and Epsilonproteobacteria. Here, we characterize the intracellular endosymbionts of the mouthless catenulid flatworm genus Paracatenula as chemoautotrophic sulfur-oxidizing Alphaproteobacteria. The symbionts of Paracatenula galateia are provisionally classified as "Candidatus Riegeria galateiae" based on 16S ribosomal RNA sequencing confirmed by fluorescence in situ hybridization together with functional gene and sulfur metabolite evidence. 16S rRNA gene phylogenetic analysis shows that all 16 Paracatenula species examined harbor host species-specific intracellular Candidatus Riegeria bacteria that form a monophyletic group within the order Rhodospirillales. Comparing host and symbiont phylogenies reveals strict cocladogenesis and points to vertical transmission of the symbionts. Between 33% and 50% of the body volume of the various worm species is composed of bacterial symbionts, by far the highest proportion among all known endosymbiotic associations between bacteria and metazoans. This symbiosis, which likely originated more than 500 Mya during the early evolution of flatworms, is the oldest known animal-chemoautotrophic bacteria association. The distant phylogenetic position of the symbionts compared with other mutualistic or parasitic Alphaproteobacteria promises to illuminate the common genetic predispositions that have allowed several members of this class to successfully colonize eukaryote cells.
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18
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Wanarska M, Krawczyk B, Hildebrandt P, Kur J. RecA proteins from Deinococcus geothermalis and Deinococcus murrayi--cloning, purification and biochemical characterisation. BMC Mol Biol 2011; 12:17. [PMID: 21513512 PMCID: PMC3103430 DOI: 10.1186/1471-2199-12-17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Accepted: 04/22/2011] [Indexed: 11/12/2022] Open
Abstract
Background Escherichia coli RecA plays a crucial role in recombinational processes, the induction of SOS responses and mutagenic lesion bypasses. It has also been demonstrated that RecA protein is indispensable when it comes to the reassembly of shattered chromosomes in γ-irradiated Deinococcus radiodurans, one of the most radiation-resistant organisms known. Moreover, some functional differences between E. coli and D. radiodurans RecA proteins have also been shown. Results In this study, recA genes from Deinococcus geothermalis and Deinococcus murrayi, bacteria that are slightly thermophilic and extremely γ-radiation resistant, were isolated, cloned and expressed in E. coli. After production and purification, the biochemical properties of DgeRecA and DmuRecA proteins were determined. Both proteins continued to exist in the solutions as heterogenous populations of oligomeric forms. The DNA binding by DgeRecA and DmuRecA proteins is stimulated by Mg2+ ions. Furthermore, both proteins bind more readily to ssDNA when ssDNA and dsDNA are in the same reaction mixture. Both proteins are slightly thermostable and were completely inactivated in 10 s at 80°C. Both proteins hydrolyze ATP and dATP in the presence of ssDNA or complementary ssDNA and dsDNA, but not in the absence of DNA or in the presence of dsDNA only, and dATP was hydrolyzed more rapidly than ATP. They were also able to promote DNA strand exchange reactions by a pathway common for other RecA proteins. However, we did not obtain DNA strand exchange products when reactions were performed on an inverse pathway, characteristic for RecA of D. radiodurans. Conclusions The characterization of DgeRecA and DmuRecA proteins made in this study indicates that the unique properties of D. radiodurans RecA are probably not common among RecA proteins from Deinococcus sp.
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Affiliation(s)
- Marta Wanarska
- Department of Microbiology, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
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19
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Harada M, Yoshida T, Kuwahara H, Shimamura S, Takaki Y, Kato C, Miwa T, Miyake H, Maruyama T. Expression of genes for sulfur oxidation in the intracellular chemoautotrophic symbiont of the deep-sea bivalve Calyptogena okutanii. Extremophiles 2010; 13:895-903. [PMID: 19730970 DOI: 10.1007/s00792-009-0277-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2009] [Accepted: 08/19/2009] [Indexed: 11/30/2022]
Abstract
To understand sulfur oxidation in thioauto-trophic deep-sea clam symbionts, we analyzed the recently reported genomes of two chemoautotrophic symbionts of Calyptogena okutanii (Candidatus Vesicomyosocius okutanii strain HA: Vok) and C. magnifica (Candidatus Ruthia magnifica strain Cm: Rma), and examined the sulfur oxidation gene expressions in the Vok by RT-PCR. Both symbionts have genes for sulfide-quinone oxidoreductase (sqr), dissimilatory sulfite reductase (dsr), reversible dissimilatory sulfite reductase (rdsr), sulfur-oxidizing multienzyme system (sox)(soxXYZA and soxB but lacking soxCD), adenosine phosphosulfate reductase (apr), and ATP sulfurylase (sat). While these genomes share 29 orthologous genes for sulfur oxidation implying that both symbionts possess the same sulfur oxidation pathway, Rma has a rhodanese-related sulfurtransferase putative gene (Rmag0316) that has no corresponding ortholog in Vok, and Vok has one unique dsrR (COSY0782). We propose that Calyptogena symbionts oxidize sulfide and thiosulfate, and that sulfur oxidation proceeds as follows. Sulfide is oxidized to sulfite by rdsr. Sulfite is oxidized to sulfate by apr and sat. Thiosulfate is oxidized to zero-valence sulfur by sox, which is then reduced to sulfide by dsr. In addition, thiosulfate may also be oxidized into sulfate by another component of sox. The result of the RT-PCR showed that genes (dsrA, dsrB, dsrC, aprA, aprB, sat, soxB, and sqr) encoding key enzymes catalyzing sulfur oxidation were all equally expressed in the Vok under three different environmental conditions (aerobic, semioxic, and aerobic under high pressure at 9 MPa), indicating that all sulfur oxidation pathways function simultaneously to support intracellular symbiotic life.
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Affiliation(s)
- Maiko Harada
- Marine Biodiversity Research Program, Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology(JAMSTEC), Yokosuka 237-0061, Japan
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20
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Abstract
Insect heritable symbionts have proven to be ubiquitous, based on molecular screening of various insect lineages. Recently, molecular and experimental approaches have yielded an immensely richer understanding of their diverse biological roles, resulting in a burgeoning research literature. Increasingly, commonalities and intermediates are being discovered between categories of symbionts once considered distinct: obligate mutualists that provision nutrients, facultative mutualists that provide protection against enemies or stress, and symbionts such as Wolbachia that manipulate reproductive systems. Among the most far-reaching impacts of widespread heritable symbiosis is that it may promote speciation by increasing reproductive and ecological isolation of host populations, and it effectively provides a means for transfer of genetic information among host lineages. In addition, insect symbionts provide some of the extremes of cellular genomes, including the smallest and the fastest evolving, raising new questions about the limits of evolution of life.
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Affiliation(s)
- Nancy A Moran
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA.
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Newton ILG, Girguis PR, Cavanaugh CM. Comparative genomics of vesicomyid clam (Bivalvia: Mollusca) chemosynthetic symbionts. BMC Genomics 2008; 9:585. [PMID: 19055818 PMCID: PMC2642828 DOI: 10.1186/1471-2164-9-585] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2008] [Accepted: 12/04/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Vesicomyidae (Bivalvia: Mollusca) are a family of clams that form symbioses with chemosynthetic gamma-proteobacteria. They exist in environments such as hydrothermal vents and cold seeps and have a reduced gut and feeding groove, indicating a large dependence on their endosymbionts for nutrition. Recently, two vesicomyid symbiont genomes were sequenced, illuminating the possible nutritional contributions of the symbiont to the host and making genome-wide evolutionary analyses possible. RESULTS To examine the genomic evolution of the vesicomyid symbionts, a comparative genomics framework, including the existing genomic data combined with heterologous microarray hybridization results, was used to analyze conserved gene content in four vesicomyid symbiont genomes. These four symbionts were chosen to include a broad phylogenetic sampling of the vesicomyid symbionts and represent distinct chemosynthetic environments: cold seeps and hydrothermal vents. CONCLUSION The results of this comparative genomics analysis emphasize the importance of the symbionts' chemoautotrophic metabolism within their hosts. The fact that these symbionts appear to be metabolically capable autotrophs underscores the extent to which the host depends on them for nutrition and reveals the key to invertebrate colonization of these challenging environments.
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Affiliation(s)
- Irene L G Newton
- Harvard University, Organismic and Evolutionary Biology, Cambridge, MA 02138, USA.
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22
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Dubilier N, Bergin C, Lott C. Symbiotic diversity in marine animals: the art of harnessing chemosynthesis. Nat Rev Microbiol 2008; 6:725-40. [DOI: 10.1038/nrmicro1992] [Citation(s) in RCA: 687] [Impact Index Per Article: 42.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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