1
|
Perez M, Aroh O, Sun Y, Lan Y, Juniper SK, Young CR, Angers B, Qian PY. Third-Generation Sequencing Reveals the Adaptive Role of the Epigenome in Three Deep-Sea Polychaetes. Mol Biol Evol 2023; 40:msad172. [PMID: 37494294 PMCID: PMC10414810 DOI: 10.1093/molbev/msad172] [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] [Received: 02/24/2023] [Revised: 06/16/2023] [Accepted: 07/17/2023] [Indexed: 07/28/2023] Open
Abstract
The roles of DNA methylation in invertebrates are poorly characterized, and critical data are missing for the phylum Annelida. We fill this knowledge gap by conducting the first genome-wide survey of DNA methylation in the deep-sea polychaetes dominant in deep-sea vents and seeps: Paraescarpia echinospica, Ridgeia piscesae, and Paralvinella palmiformis. DNA methylation calls were inferred from Oxford Nanopore sequencing after assembling high-quality genomes of these animals. The genomes of these worms encode all the key enzymes of the DNA methylation metabolism and possess a mosaic methylome similar to that of other invertebrates. Transcriptomic data of these polychaetes support the hypotheses that gene body methylation strengthens the expression of housekeeping genes and that promoter methylation acts as a silencing mechanism but not the hypothesis that DNA methylation suppresses the activity of transposable elements. The conserved epigenetic profiles of genes responsible for maintaining homeostasis under extreme hydrostatic pressure suggest DNA methylation plays an important adaptive role in these worms.
Collapse
Affiliation(s)
- Maeva Perez
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, China
- Department of Biological Sciences, Université de Montréal, Montréal, Canada
| | - Oluchi Aroh
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | - Yanan Sun
- Laboratory of Marine Organism Taxonomy and Phylogeny, Chinese Academy of Sciences, Institute of Oceanology, Qingdao, China
| | - Yi Lan
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, China
| | - Stanley Kim Juniper
- School of Earth and Ocean Sciences, University of Victoria, Victoria, Canada
| | | | - Bernard Angers
- Department of Biological Sciences, Université de Montréal, Montréal, Canada
| | - Pei-Yuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, China
| |
Collapse
|
2
|
Thomas-Bulle C, Bertrand D, Nagarajan N, Copley RR, Corre E, Hourdez S, Bonnivard É, Claridge-Chang A, Jollivet D. Genomic patterns of divergence in the early and late steps of speciation of the deep-sea vent thermophilic worms of the genus Alvinella. BMC Ecol Evol 2022; 22:106. [PMID: 36057769 PMCID: PMC9441076 DOI: 10.1186/s12862-022-02057-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 08/05/2022] [Indexed: 11/10/2022] Open
Abstract
Background The transient and fragmented nature of the deep-sea hydrothermal environment made of ridge subduction, plate collision and the emergence of new rifts is currently acting to separate of vent populations, promoting local adaptation and contributing to bursts of speciation and species specialization. The tube-dwelling worms Alvinella pompejana called the Pompeii worm and its sister species A. caudata live syntopically on the hottest part of deep-sea hydrothermal chimneys along the East Pacific Rise. They are exposed to extreme thermal and chemical gradients, which vary greatly in space and time, and thus represent ideal candidates for understanding the evolutionary mechanisms at play in the vent fauna evolution. Results We explored genomic patterns of divergence in the early and late stages of speciation of these emblematic worms using transcriptome assemblies and the first draft genome to better understand the relative role of geographic isolation and habitat preference in their genome evolution. Analyses were conducted on allopatric populations of Alvinella pompejana (early stage of separation) and between A. pompejana and its syntopic species Alvinella caudata (late stage of speciation). We first identified divergent genomic regions and targets of selection as well as their position in the genome over collections of orthologous genes and, then, described the speciation dynamics by documenting the annotation of the most divergent and/or positively selected genes involved in the isolation process. Gene mapping clearly indicated that divergent genes associated with the early stage of speciation, although accounting for nearly 30% of genes, are highly scattered in the genome without any island of divergence and not involved in gamete recognition or mito-nuclear incompatibilities. By contrast, genomes of A. pompejana and A. caudata are clearly separated with nearly all genes (96%) exhibiting high divergence. This congealing effect however seems to be linked to habitat specialization and still allows positive selection on genes involved in gamete recognition, as a possible long-duration process of species reinforcement.
Conclusion Our analyses highlight the non-negligible role of natural selection on both the early and late stages of speciation in the iconic thermophilic worms living on the walls of deep-sea hydrothermal chimneys. They shed light on the evolution of gene divergence during the process of speciation and species specialization over a very long period of time. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-02057-y.
Collapse
|
3
|
Zhang Q, Balourdas DI, Baron B, Senitzki A, Haran TE, Wiman KG, Soussi T, Joerger AC. Evolutionary history of the p53 family DNA-binding domain: insights from an Alvinella pompejana homolog. Cell Death Dis 2022; 13:214. [PMID: 35256607 PMCID: PMC8901663 DOI: 10.1038/s41419-022-04653-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/08/2022] [Accepted: 02/15/2022] [Indexed: 01/09/2023]
Abstract
The extremophile Alvinella pompejana, an annelid worm living on the edge of hydrothermal vents in the Pacific Ocean, is an excellent model system for studying factors that govern protein stability. Low intrinsic stability is a crucial factor for the susceptibility of the transcription factor p53 to inactivating mutations in human cancer. Understanding its molecular basis may facilitate the design of novel therapeutic strategies targeting mutant p53. By analyzing expressed sequence tag (EST) data, we discovered a p53 family gene in A. pompejana. Protein crystallography and biophysical studies showed that it has a p53/p63-like DNA-binding domain (DBD) that is more thermostable than all vertebrate p53 DBDs tested so far, but not as stable as that of human p63. We also identified features associated with its increased thermostability. In addition, the A. pompejana homolog shares DNA-binding properties with human p53 family DBDs, despite its evolutionary distance, consistent with a potential role in maintaining genome integrity. Through extensive structural and phylogenetic analyses, we could further trace key evolutionary events that shaped the structure, stability, and function of the p53 family DBD over time, leading to a potent but vulnerable tumor suppressor in humans.
Collapse
Affiliation(s)
- Qiang Zhang
- Department of Neuroscience, Biomedicum, Karolinska Institutet, Stockholm, Sweden
| | - Dimitrios-Ilias Balourdas
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Bruno Baron
- Plateforme de Biophysique Moléculaire, Centre de Ressources et de Recherches Technologique (C2RT), Institut Pasteur, 75015, Paris, France
| | - Alon Senitzki
- Department of Biology, Technion-Israel Institute of Technology, Technion City, Haifa, 32000, Israel
| | - Tali E Haran
- Department of Biology, Technion-Israel Institute of Technology, Technion City, Haifa, 32000, Israel.
| | - Klas G Wiman
- Department of Oncology-Pathology, Bioclinicum, Karolinska Institutet, Stockholm, Sweden.
| | - Thierry Soussi
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
- Sorbonne Université, UPMC Univ Paris 06, 75005, Paris, France.
| | - Andreas C Joerger
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany.
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany.
| |
Collapse
|
4
|
Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives. Mar Drugs 2019; 17:md17100576. [PMID: 31614509 PMCID: PMC6835618 DOI: 10.3390/md17100576] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/01/2019] [Accepted: 10/02/2019] [Indexed: 12/13/2022] Open
Abstract
The sea represents a major source of biodiversity. It exhibits many different ecosystems in a huge variety of environmental conditions where marine organisms have evolved with extensive diversification of structures and functions, making the marine environment a treasure trove of molecules with potential for biotechnological applications and innovation in many different areas. Rapid progress of the omics sciences has revealed novel opportunities to advance the knowledge of biological systems, paving the way for an unprecedented revolution in the field and expanding marine research from model organisms to an increasing number of marine species. Multi-level approaches based on molecular investigations at genomic, metagenomic, transcriptomic, metatranscriptomic, proteomic, and metabolomic levels are essential to discover marine resources and further explore key molecular processes involved in their production and action. As a consequence, omics approaches, accompanied by the associated bioinformatic resources and computational tools for molecular analyses and modeling, are boosting the rapid advancement of biotechnologies. In this review, we provide an overview of the most relevant bioinformatic resources and major approaches, highlighting perspectives and bottlenecks for an appropriate exploitation of these opportunities for biotechnology applications from marine resources.
Collapse
|
5
|
Fontanillas E, Galzitskaya OV, Lecompte O, Lobanov MY, Tanguy A, Mary J, Girguis PR, Hourdez S, Jollivet D. Proteome Evolution of Deep-Sea Hydrothermal Vent Alvinellid Polychaetes Supports the Ancestry of Thermophily and Subsequent Adaptation to Cold in Some Lineages. Genome Biol Evol 2017; 9:279-296. [PMID: 28082607 PMCID: PMC5381640 DOI: 10.1093/gbe/evw298] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2016] [Indexed: 12/22/2022] Open
Abstract
Temperature, perhaps more than any other environmental factor, is likely to influence the evolution of all organisms. It is also a very interesting factor to understand how genomes are shaped by selection over evolutionary timescales, as it potentially affects the whole genome. Among thermophilic prokaryotes, temperature affects both codon usage and protein composition to increase the stability of the transcriptional/translational machinery, and the resulting proteins need to be functional at high temperatures. Among eukaryotes less is known about genome evolution, and the tube-dwelling worms of the family Alvinellidae represent an excellent opportunity to test hypotheses about the emergence of thermophily in ectothermic metazoans. The Alvinellidae are a group of worms that experience varying thermal regimes, presumably having evolved into these niches over evolutionary times. Here we analyzed 423 putative orthologous loci derived from 6 alvinellid species including the thermophilic Alvinella pompejana and Paralvinella sulfincola. This comparative approach allowed us to assess amino acid composition, codon usage, divergence, direction of residue changes and the strength of selection along the alvinellid phylogeny, and to design a new eukaryotic thermophilic criterion based on significant differences in the residue composition of proteins. Contrary to expectations, the alvinellid ancestor of all present-day species seems to have been thermophilic, a trait subsequently maintained by purifying selection in lineages that still inhabit higher temperature environments. In contrast, lineages currently living in colder habitats likely evolved under selective relaxation, with some degree of positive selection for low-temperature adaptation at the protein level.
Collapse
Affiliation(s)
- Eric Fontanillas
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS UMR 7144, Adaptation et Diversité en Milieu Marin, Equipe ABICE, Station Biologique de Roscoff, 29688 Roscoff, France
| | - Oxana V Galzitskaya
- Laboratory of Protein Physics, Institute of Protein Research, RAS, Institutskaya street, 4, 142290 Pushchino, Moscow, Russia
| | - Odile Lecompte
- CSTB - ICUBE, UMR7357, Faculté de Médecine, 4 rue Kirschleger, 67085 Strasbourg, France
| | - Mikhail Y Lobanov
- Laboratory of Protein Physics, Institute of Protein Research, RAS, Institutskaya street, 4, 142290 Pushchino, Moscow, Russia
| | - Arnaud Tanguy
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS UMR 7144, Adaptation et Diversité en Milieu Marin, Equipe ABICE, Station Biologique de Roscoff, 29688 Roscoff, France
| | - Jean Mary
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS UMR 7144, Adaptation et Diversité en Milieu Marin, Equipe ABICE, Station Biologique de Roscoff, 29688 Roscoff, France
| | - Peter R Girguis
- Department of Organismic & Evolutionary Biology, Harvard University Biological Laboratories, Cambridge, MA
| | - Stéphane Hourdez
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS UMR 7144, Adaptation et Diversité en Milieu Marin, Equipe ABICE, Station Biologique de Roscoff, 29688 Roscoff, France
| | - Didier Jollivet
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS UMR 7144, Adaptation et Diversité en Milieu Marin, Equipe ABICE, Station Biologique de Roscoff, 29688 Roscoff, France
| |
Collapse
|
6
|
Tasiemski A, Salzet M. Neuro-immune lessons from an annelid: The medicinal leech. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 66:33-42. [PMID: 27381717 DOI: 10.1016/j.dci.2016.06.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 06/09/2016] [Accepted: 06/30/2016] [Indexed: 06/06/2023]
Abstract
An important question that remains unanswered is how the vertebrate neuroimmune system can be both friend and foe to the damaged nervous tissue. Some of the difficulty in obtaining responses in mammals probably lies in the conflation in the central nervous system (CNS), of the innate and adaptive immune responses, which makes the vertebrate neuroimmune response quite complex and difficult to dissect. An alternative strategy for understanding the relation between neural immunity and neural repair is to study an animal devoid of adaptive immunity and whose CNS is well described and regeneration competent. The medicinal leech offers such opportunity. If the nerve cord of this annelid is crushed or partially cut, axons grow across the lesion and conduction of signals through the damaged region is restored within a few days, even when the nerve cord is removed from the animal and maintained in culture. When the mammalian spinal cord is injured, regeneration of normal connections is more or less successful and implies multiple events that still remain difficult to resolve. Interestingly, the regenerative process of the leech lesioned nerve cord is even more successful under septic than under sterile conditions suggesting that a controlled initiation of an infectious response may be a critical event for the regeneration of normal CNS functions in the leech. Here are reviewed and discussed data explaining how the leech nerve cord sensu stricto (i.e. excluding microglia and infiltrated blood cells) recognizes and responds to microbes and mechanical damages.
Collapse
Affiliation(s)
- Aurélie Tasiemski
- Université de Lille, CNRS UMR8198, Unité d'Evolution, Ecologie et Paléontologie (EEP), Species Interactions and Comparative Immunology (SPICI) Team, 59655 Villeneuve d'Ascq, France.
| | - Michel Salzet
- Université de Lille, INSERM U-1192, Laboratoire de Protéomique, Réponse Inflammatoire, Spectrométrie de Masse (PRISM), 59655 Villeneuve d'Ascq, France
| |
Collapse
|
7
|
Li S, Hauser F, Skadborg SK, Nielsen SV, Kirketerp-Møller N, Grimmelikhuijzen CJP. Adipokinetic hormones and their G protein-coupled receptors emerged in Lophotrochozoa. Sci Rep 2016; 6:32789. [PMID: 27628442 PMCID: PMC5024129 DOI: 10.1038/srep32789] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 08/16/2016] [Indexed: 01/05/2023] Open
Abstract
Most multicellular animals belong to two evolutionary lineages, the Proto– and Deuterostomia, which diverged 640–760 million years (MYR) ago. Neuropeptide signaling is abundant in animals belonging to both lineages, but it is often unclear whether there exist evolutionary relationships between the neuropeptide systems used by proto- or deuterostomes. An exception, however, are members of the gonadotropin-releasing hormone (GnRH) receptor superfamily, which occur in both evolutionary lineages, where GnRHs are the ligands in Deuterostomia and GnRH-like peptides, adipokinetic hormone (AKH), corazonin, and AKH/corazonin-related peptide (ACP) are the ligands in Protostomia. AKH is a well-studied insect neuropeptide that mobilizes lipids and carbohydrates from the insect fat body during flight. In our present paper, we show that AKH is not only widespread in insects, but also in other Ecdysozoa and in Lophotrochozoa. Furthermore, we have cloned and deorphanized two G protein-coupled receptors (GPCRs) from the oyster Crassostrea gigas (Mollusca) that are activated by low nanomolar concentrations of oyster AKH (pQVSFSTNWGSamide). Our discovery of functional AKH receptors in molluscs is especially significant, because it traces the emergence of AKH signaling back to about 550 MYR ago and brings us closer to a more complete understanding of the evolutionary origins of the GnRH receptor superfamily.
Collapse
Affiliation(s)
- Shizhong Li
- Center for Functional and Comparative Insect Genomics, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Frank Hauser
- Center for Functional and Comparative Insect Genomics, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Signe K Skadborg
- Center for Functional and Comparative Insect Genomics, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Stine V Nielsen
- Center for Functional and Comparative Insect Genomics, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Nikolaj Kirketerp-Møller
- Center for Functional and Comparative Insect Genomics, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Cornelis J P Grimmelikhuijzen
- Center for Functional and Comparative Insect Genomics, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| |
Collapse
|
8
|
Wijckmans E, Nys M, Debaveye S, Brams M, Pardon E, Willegems K, Bertrand D, Steyaert J, Efremov R, Ulens C. Functional and Biochemical Characterization of Alvinella pompejana Cys-Loop Receptor Homologues. PLoS One 2016; 11:e0151183. [PMID: 26999666 PMCID: PMC4801368 DOI: 10.1371/journal.pone.0151183] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 02/24/2016] [Indexed: 11/22/2022] Open
Abstract
Cys-loop receptors are membrane spanning ligand-gated ion channels involved in fast excitatory and inhibitory neurotransmission. Three-dimensional structures of these ion channels, determined by X-ray crystallography or electron microscopy, have revealed valuable information regarding the molecular mechanisms underlying ligand recognition, channel gating and ion conductance. To extend and validate the current insights, we here present promising candidates for further structural studies. We report the biochemical and functional characterization of Cys-loop receptor homologues identified in the proteome of Alvinella pompejana, an extremophilic, polychaete annelid found in hydrothermal vents at the bottom of the Pacific Ocean. Seven homologues were selected, named Alpo1-7. Five of them, Alpo2-6, were unidentified prior to this study. Two-electrode voltage clamp experiments revealed that wild type Alpo5 and Alpo6, both sharing remarkably high sequence identity with human glycine receptor α subunits, are anion-selective channels that can be activated by glycine, GABA and taurine. Furthermore, upon expression in insect cells fluorescence size-exclusion chromatography experiments indicated that four homologues, Alpo1, Alpo4, Alpo6 and Alpo7, can be extracted out of the membrane by a wide variety of detergents while maintaining their oligomeric state. Finally, large-scale purification efforts of Alpo1, Alpo4 and Alpo6 resulted in milligram amounts of biochemically stable and monodisperse protein. Overall, our results establish the evolutionary conservation of glycine receptors in annelids and pave the way for future structural studies.
Collapse
Affiliation(s)
- Eveline Wijckmans
- Department of Cellular and Molecular Medicine, Laboratory of Structural Neurobiology, University of Leuven, Leuven, Belgium
| | - Mieke Nys
- Department of Cellular and Molecular Medicine, Laboratory of Structural Neurobiology, University of Leuven, Leuven, Belgium
- * E-mail:
| | - Sarah Debaveye
- Department of Cellular and Molecular Medicine, Laboratory of Structural Neurobiology, University of Leuven, Leuven, Belgium
| | - Marijke Brams
- Department of Cellular and Molecular Medicine, Laboratory of Structural Neurobiology, University of Leuven, Leuven, Belgium
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- Structural Biology Research Center, VIB, Brussels, Belgium
| | - Katrien Willegems
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- Structural Biology Research Center, VIB, Brussels, Belgium
| | | | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- Structural Biology Research Center, VIB, Brussels, Belgium
| | - Rouslan Efremov
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- Structural Biology Research Center, VIB, Brussels, Belgium
| | - Chris Ulens
- Department of Cellular and Molecular Medicine, Laboratory of Structural Neurobiology, University of Leuven, Leuven, Belgium
| |
Collapse
|
9
|
Mehr S, Verdes A, DeSalle R, Sparks J, Pieribone V, Gruber DF. Transcriptome sequencing and annotation of the polychaete Hermodice carunculata (Annelida, Amphinomidae). BMC Genomics 2015; 16:445. [PMID: 26059236 PMCID: PMC4462082 DOI: 10.1186/s12864-015-1565-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Background The amphinomid polychaete Hermodice carunculata is a cosmopolitan and ecologically important omnivore in coral reef ecosystems, preying on a diverse suite of reef organisms and potentially acting as a vector for coral disease. While amphinomids are a key group for determining the root of the Annelida, their phylogenetic position has been difficult to resolve, and their publically available genomic data was scarce. Results We performed deep transcriptome sequencing (Illumina HiSeq) and profiling on Hermodice carunculata collected in the Western Atlantic Ocean. We focused this study on 58,454 predicted Open Reading Frames (ORFs) of genes longer than 200 amino acids for our homology search, and Gene Ontology (GO) terms and InterPro IDs were assigned to 32,500 of these ORFs. We used this de novo assembled transcriptome to recover major signaling pathways and housekeeping genes. We also identify a suite of H. carunculata genes related to reproduction and immune response. Conclusions We provide a comprehensive catalogue of annotated genes for Hermodice carunculata and expand the knowledge of reproduction and immune response genes in annelids, in general. Overall, this study vastly expands the available genomic data for H. carunculata, of which previously consisted of only 279 nucleotide sequences in NCBI. This underscores the utility of Illumina sequencing for de novo transcriptome assembly in non-model organisms as a cost-effective and efficient tool for gene discovery and downstream applications, such as phylogenetic analysis and gene expression profiling. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1565-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Shaadi Mehr
- Biological Science Department, State University of New York, College at Old Westbury, Old Westbury, NY, 11568, USA. .,American Museum of Natural History, Sackler Institute for Comparative Genomics, Central Park W at 79th St, New York, NY, 10024, USA.
| | - Aida Verdes
- Baruch College and The Graduate Center, Department of Natural Sciences, City University of New York, New York, NY, 10010, USA.
| | - Rob DeSalle
- American Museum of Natural History, Sackler Institute for Comparative Genomics, Central Park W at 79th St, New York, NY, 10024, USA.
| | - John Sparks
- American Museum of Natural History, Sackler Institute for Comparative Genomics, Central Park W at 79th St, New York, NY, 10024, USA. .,American Museum of Natural History, Department of Ichthyology, American Museum of Natural History, Division of Vertebrate Zoology, New York, NY, 10024, USA.
| | - Vincent Pieribone
- John B. Pierce Laboratory, Cellular and Molecular Physiology, Yale University, New Haven, CT 06519, USA.
| | - David F Gruber
- American Museum of Natural History, Sackler Institute for Comparative Genomics, Central Park W at 79th St, New York, NY, 10024, USA. .,Baruch College and The Graduate Center, Department of Natural Sciences, City University of New York, New York, NY, 10010, USA.
| |
Collapse
|
10
|
Shigeno S, Ogura A, Mori T, Toyohara H, Yoshida T, Tsuchida S, Fujikura K. Sensing deep extreme environments: the receptor cell types, brain centers, and multi-layer neural packaging of hydrothermal vent endemic worms. Front Zool 2014; 11:82. [PMID: 25505488 PMCID: PMC4261566 DOI: 10.1186/s12983-014-0082-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 10/23/2014] [Indexed: 01/30/2023] Open
Abstract
INTRODUCTION Deep-sea alvinellid worm species endemic to hydrothermal vents, such as Alvinella and Paralvinella, are considered to be among the most thermotolerant animals known with their adaptability to toxic heavy metals, and tolerance of highly reductive and oxidative stressful environments. Despite the number of recent studies focused on their overall transcriptomic, proteomic, and metabolic stabilities, little is known regarding their sensory receptor cells and electrically active neuro-processing centers, and how these can tolerate and function in such harsh conditions. RESULTS We examined the extra- and intracellular organizations of the epidermal ciliated sensory cells and their higher centers in the central nervous system through immunocytochemical, ultrastructural, and neurotracing analyses. We observed that these cells were rich in mitochondria and possessed many electron-dense granules, and identified specialized glial cells and serial myelin-like repeats in the head sensory systems of Paralvinella hessleri. Additionally, we identified the major epidermal sensory pathways, in which a pair of distinct mushroom bodies-like or small interneuron clusters was observed. These sensory learning and memory systems are commonly found in insects and annelids, but the alvinellid inputs are unlikely derived from the sensory ciliary cells of the dorsal head regions. CONCLUSIONS Our evidence provides insight into the cellular and system-wide adaptive structure used to sense, process, and combat the deep-sea hydrothermal vent environment. The alvinellid sensory cells exhibit characteristics of annelid ciliary types, and among the most unique features were the head sensory inputs and structure of the neural cell bodies of the brain, which were surrounded by multiple membranes. We speculated that such enhanced protection is required for the production of normal electrical signals, and to avoid the breakdown of the membrane surrounding metabolically fragile neurons from oxidative stress. Such pivotal acquisition is not broadly found in the all body parts, suggesting the head sensory inputs are specific, and these heterogenetic protection mechanisms may be present in alvinellid worms.
Collapse
Affiliation(s)
- Shuichi Shigeno
- Department for Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, 237-0061, Kanagawa Japan
| | - Atsushi Ogura
- Nagahama Institute of Bio-Science and Technology, Institute of Bio-Science and Technology, 1266 Tamura-Cho, Nagahama, 526-0829, Shiga Japan
| | - Tsukasa Mori
- Nihon University, 1866 Kameino, Fujisawa, 252-0880, Kanagawa Japan
| | - Haruhiko Toyohara
- Division of Applied Biosciences, Kyoto University, Graduate School of Agriculture, Laboratory of Marine Biological Function, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8602 Japan
| | - Takao Yoshida
- Department for Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, 237-0061, Kanagawa Japan
| | - Shinji Tsuchida
- Department for Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, 237-0061, Kanagawa Japan
| | - Katsunori Fujikura
- Department for Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, 237-0061, Kanagawa Japan
| |
Collapse
|
11
|
Tasiemski A, Jung S, Boidin-Wichlacz C, Jollivet D, Cuvillier-Hot V, Pradillon F, Vetriani C, Hecht O, Sönnichsen FD, Gelhaus C, Hung CW, Tholey A, Leippe M, Grötzinger J, Gaill F. Characterization and function of the first antibiotic isolated from a vent organism: the extremophile metazoan Alvinella pompejana. PLoS One 2014; 9:e95737. [PMID: 24776651 PMCID: PMC4002450 DOI: 10.1371/journal.pone.0095737] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 03/30/2014] [Indexed: 01/06/2023] Open
Abstract
The emblematic hydrothermal worm Alvinella pompejana is one of the most thermo tolerant animal known on Earth. It relies on a symbiotic association offering a unique opportunity to discover biochemical adaptations that allow animals to thrive in such a hostile habitat. Here, by studying the Pompeii worm, we report on the discovery of the first antibiotic peptide from a deep-sea organism, namely alvinellacin. After purification and peptide sequencing, both the gene and the peptide tertiary structures were elucidated. As epibionts are not cultivated so far and because of lethal decompression effects upon Alvinella sampling, we developed shipboard biological assays to demonstrate that in addition to act in the first line of defense against microbial invasion, alvinellacin shapes and controls the worm's epibiotic microflora. Our results provide insights into the nature of an abyssal antimicrobial peptide (AMP) and into the manner in which an extremophile eukaryote uses it to interact with the particular microbial community of the hydrothermal vent ecosystem. Unlike earlier studies done on hydrothermal vents that all focused on the microbial side of the symbiosis, our work gives a view of this interaction from the host side.
Collapse
Affiliation(s)
- Aurélie Tasiemski
- Université de Lille1-CNRS UMR8198, Laboratoire GEPV, Ecoimmunology of Marine Annelids (EMA), Villeneuve d'Ascq, France
| | - Sascha Jung
- Institute of Biochemistry, Christian-Albrechts-Universität, Kiel, Germany
| | - Céline Boidin-Wichlacz
- Université de Lille1-CNRS UMR8198, Laboratoire GEPV, Ecoimmunology of Marine Annelids (EMA), Villeneuve d'Ascq, France
| | - Didier Jollivet
- Université Pierre et Marie Curie-CNRS UMR7144, Laboratoire AD2M, Adaptation et Biologie des Invertébrés en Conditions Extrêmes (ABICE), Station Biologique, Roscoff, France
| | - Virginie Cuvillier-Hot
- Université de Lille1-CNRS UMR8198, Laboratoire GEPV, Ecoimmunology of Marine Annelids (EMA), Villeneuve d'Ascq, France
| | | | - Costantino Vetriani
- Department of Biochemistry and Microbiology and Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Oliver Hecht
- Institute of Biochemistry, Christian-Albrechts-Universität, Kiel, Germany
| | - Frank D. Sönnichsen
- Otto Diels Institute for Organic Chemistry, Christian-Albrechts-Universität, Kiel, Germany
| | - Christoph Gelhaus
- Institute of Zoology, Zoophysiology, Christian-Albrechts-Universität, Kiel, Germany
| | - Chien-Wen Hung
- Division of Systematic Proteome Research, Institute for Experimental Medicine, Christian-Albrechts-Universität, Kiel, Germany
| | - Andreas Tholey
- Division of Systematic Proteome Research, Institute for Experimental Medicine, Christian-Albrechts-Universität, Kiel, Germany
| | - Matthias Leippe
- Institute of Zoology, Zoophysiology, Christian-Albrechts-Universität, Kiel, Germany
| | - Joachim Grötzinger
- Institute of Biochemistry, Christian-Albrechts-Universität, Kiel, Germany
| | - Françoise Gaill
- Université Pierre et Marie Curie-Muséum National d'Histoires Naturelles CNRS BOREA IRD, Paris, France
| |
Collapse
|
12
|
Juneja P, Horlacher R, Bertrand D, Krause R, Marger F, Welte W. An internally modulated, thermostable, pH-sensitive Cys loop receptor from the hydrothermal vent worm Alvinella pompejana. J Biol Chem 2014; 289:15130-40. [PMID: 24719323 DOI: 10.1074/jbc.m113.525576] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Cys loop receptors (CLRs) are commonly known as ligand-gated channels that transiently open upon binding of neurotransmitters to modify the membrane potential. However, a class of cation-selective bacterial homologues of CLRs have been found to open upon a sudden pH drop, suggesting further ligands and more functions of the homologues in prokaryotes. Here we report an anion-selective CLR from the hydrothermal vent annelid worm Alvinella pompejana that opens at low pH. A. pompejana expressed sequence tag databases were explored by us, and two full-length CLR sequences were identified, synthesized, cloned, expressed in Xenopus oocytes, and studied by two-electrode voltage clamp. One channel, named Alv-a1-pHCl, yielded functional receptors and opened upon a sudden pH drop but not by other known agonists. Sequence comparison showed that both CLR proteins share conserved characteristics with eukaryotic CLRs, such as an N-terminal helix, a cysteine loop motif, and an intracellular loop intermediate in length between the long loops of other eukaryotic CLRs and those of prokaryotic CLRs. Both full-length Alv-a1-pHCl and a truncated form, termed tAlv-a1-pHCl, lacking 37 amino-terminal residues that precede the N-terminal helix, formed functional channels in oocytes. After pH activation, tAlv-a1-pHCl showed desensitization and was not modulated by ivermectin. In contrast, pH-activated, full-length Alv-a1-pHCl showed a marked rebound current and was modulated significantly by ivermectin. A thermostability assay indicated that purified tAlv-a1-pHCl expressed in Sf9 cells denatured at a higher temperature than the nicotinic acetylcholine receptor from Torpedo californica.
Collapse
Affiliation(s)
- Puneet Juneja
- From the Fachbereich Biologie, Universität Konstanz, Universitätsstraβe 10, 78457 Konstanz, Germany
| | | | - Daniel Bertrand
- HiQScreen Sàrl, 6, rte. de Compois, 1222 Vésenaz, Geneva, Switzerland
| | - Ryoko Krause
- HiQScreen Sàrl, 6, rte. de Compois, 1222 Vésenaz, Geneva, Switzerland
| | - Fabrice Marger
- HiQScreen Sàrl, 6, rte. de Compois, 1222 Vésenaz, Geneva, Switzerland
| | - Wolfram Welte
- From the Fachbereich Biologie, Universität Konstanz, Universitätsstraβe 10, 78457 Konstanz, Germany,
| |
Collapse
|
13
|
Borda E, Kudenov JD, Chevaldonné P, Blake JA, Desbruyères D, Fabri MC, Hourdez S, Pleijel F, Shank TM, Wilson NG, Schulze A, Rouse GW. Cryptic species of Archinome (Annelida: Amphinomida) from vents and seeps. Proc Biol Sci 2013; 280:20131876. [PMID: 24026823 DOI: 10.1098/rspb.2013.1876] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Since its description from the Galapagos Rift in the mid-1980s, Archinome rosacea has been recorded at hydrothermal vents in the Pacific, Atlantic and Indian Oceans. Only recently was a second species described from the Pacific Antarctic Ridge. We inferred the identities and evolutionary relationships of Archinome representatives sampled from across the hydrothermal vent range of the genus, which is now extended to cold methane seeps. Species delimitation using mitochondrial cytochrome c oxidase subunit I (COI) recovered up to six lineages, whereas concatenated datasets (COI, 16S, 28S and ITS1) supported only four or five of these as clades. Morphological approaches alone were inconclusive to verify the identities of species owing to the lack of discrete diagnostic characters. We recognize five Archinome species, with three that are new to science. The new species, designated based on molecular evidence alone, include: Archinome levinae n. sp., which occurs at both vents and seeps in the east Pacific, Archinome tethyana n. sp., which inhabits Atlantic vents and Archinome jasoni n. sp., also present in the Atlantic, and whose distribution extends to the Indian and southwest Pacific Oceans. Biogeographic connections between vents and seeps are highlighted, as are potential evolutionary links among populations from vent fields located in the east Pacific and Atlantic Oceans, and Atlantic and Indian Oceans; the latter presented for the first time.
Collapse
Affiliation(s)
- Elizabeth Borda
- Scripps Institution of Oceanography, , UC San Diego, La Jolla, CA 93093, USA, Department of Biological Sciences, University of Alaska Anchorage, , Anchorage, AK 99508, USA, CNRS, UMR 7263 IMBE, Institut Méditerranéen de la Biodiversité et d'Ecologie Marine et Continentale, Aix-Marseille Université, , Station Marine d'Endoume, Rue de la Batterie des Lions, 13007 Marseille, France, AECOM Marine and Coastal Center, , Woods Hole, MA 02543, USA, Woods Hole Oceanographic Institution, , Woods Hole, MA 02543, USA, Département Etude des Ecosystèmes Profonds, Centre de Brest de l'IFREMER, , 29280 Plouzané Cedex, France, CNRS, UPMC UMR 7127, , Station Biologique de Roscoff, 29682 Roscoff, France, Department of Marine Ecology, University of Gothenburg, , Tjärnö, Strömstad, Sweden, Marine Biology Department, Texas A&M University at Galveston, , Galveston, TX 77553, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Ravaux J, Hamel G, Zbinden M, Tasiemski AA, Boutet I, Léger N, Tanguy A, Jollivet D, Shillito B. Thermal limit for metazoan life in question: in vivo heat tolerance of the Pompeii worm. PLoS One 2013; 8:e64074. [PMID: 23734185 PMCID: PMC3667023 DOI: 10.1371/journal.pone.0064074] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 04/08/2013] [Indexed: 01/23/2023] Open
Abstract
The thermal limit for metazoan life, expected to be around 50°C, has been debated since the discovery of the Pompeii worm Alvinella pompejana, which colonizes black smoker chimney walls at deep-sea vents. While indirect evidence predicts body temperatures lower than 50°C, repeated in situ temperature measurements depict an animal thriving at temperatures of 60°C and more. This controversy was to remain as long as this species escaped in vivo investigations, due to irremediable mortalities upon non-isobaric sampling. Here we report from the first heat-exposure experiments with live A. pompejana, following isobaric sampling and subsequent transfer in a laboratory pressurized aquarium. A prolonged (2 hours) exposure in the 50-55°C range was lethal, inducing severe tissue damages, cell mortalities and triggering a heat stress response, therefore showing that Alvinella's upper thermal limit clearly is below 55°C. A comparison with hsp70 stress gene expressions of individuals analysed directly after sampling in situ confirms that Alvinella pompejana does not experience long-term exposures to temperature above 50°C in its natural environment. The thermal optimum is nevertheless beyond 42°C, which confirms that the Pompeii worm ranks among the most thermotolerant metazoans.
Collapse
Affiliation(s)
- Juliette Ravaux
- Adaptations aux Milieux Extrêmes, UMR CNRS 7138, Université Pierre et Marie Curie - Paris 06, Paris, France
- * E-mail: (JR); (BS)
| | - Gérard Hamel
- Institut de Minéralogie et de Physique des Milieux Condensés, UMR CNRS 7590, Paris, France
| | - Magali Zbinden
- Adaptations aux Milieux Extrêmes, UMR CNRS 7138, Université Pierre et Marie Curie - Paris 06, Paris, France
| | - Aurélie A. Tasiemski
- Ecoimmunology of Marine Annelids, UMR CNRS 8198, Université de Lille 1, Villeneuve d’Ascq, France
| | - Isabelle Boutet
- Génétique de l’Adaptation en Milieux Extrêmes, UMR CNRS 7144, Station Biologique de Roscoff, Université Pierre et Marie Curie - Paris 06, Roscoff, France
| | - Nelly Léger
- Adaptations aux Milieux Extrêmes, UMR CNRS 7138, Université Pierre et Marie Curie - Paris 06, Paris, France
| | - Arnaud Tanguy
- Génétique de l’Adaptation en Milieux Extrêmes, UMR CNRS 7144, Station Biologique de Roscoff, Université Pierre et Marie Curie - Paris 06, Roscoff, France
| | - Didier Jollivet
- Génétique de l’Adaptation en Milieux Extrêmes, UMR CNRS 7144, Station Biologique de Roscoff, Université Pierre et Marie Curie - Paris 06, Roscoff, France
| | - Bruce Shillito
- Adaptations aux Milieux Extrêmes, UMR CNRS 7138, Université Pierre et Marie Curie - Paris 06, Paris, France
- * E-mail: (JR); (BS)
| |
Collapse
|
15
|
Detection and Characterisation of Mutations Responsible for Allele-Specific Protein Thermostabilities at the Mn-Superoxide Dismutase Gene in the Deep-Sea Hydrothermal Vent Polychaete Alvinella pompejana. J Mol Evol 2013; 76:295-310. [DOI: 10.1007/s00239-013-9559-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2012] [Accepted: 03/27/2013] [Indexed: 12/19/2022]
|
16
|
Holder T, Basquin C, Ebert J, Randel N, Jollivet D, Conti E, Jékely G, Bono F. Deep transcriptome-sequencing and proteome analysis of the hydrothermal vent annelid Alvinella pompejana identifies the CvP-bias as a robust measure of eukaryotic thermostability. Biol Direct 2013; 8:2. [PMID: 23324115 PMCID: PMC3564776 DOI: 10.1186/1745-6150-8-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 01/11/2013] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Alvinella pompejana is an annelid worm that inhabits deep-sea hydrothermal vent sites in the Pacific Ocean. Living at a depth of approximately 2500 meters, these worms experience extreme environmental conditions, including high temperature and pressure as well as high levels of sulfide and heavy metals. A. pompejana is one of the most thermotolerant metazoans, making this animal a subject of great interest for studies of eukaryotic thermoadaptation. RESULTS In order to complement existing EST resources we performed deep sequencing of the A. pompejana transcriptome. We identified several thousand novel protein-coding transcripts, nearly doubling the sequence data for this annelid. We then performed an extensive survey of previously established prokaryotic thermoadaptation measures to search for global signals of thermoadaptation in A. pompejana in comparison with mesophilic eukaryotes. In an orthologous set of 457 proteins, we found that the best indicator of thermoadaptation was the difference in frequency of charged versus polar residues (CvP-bias), which was highest in A. pompejana. CvP-bias robustly distinguished prokaryotic thermophiles from prokaryotic mesophiles, as well as the thermophilic fungus Chaetomium thermophilum from mesophilic eukaryotes. Experimental values for thermophilic proteins supported higher CvP-bias as a measure of thermal stability when compared to their mesophilic orthologs. Proteome-wide mean CvP-bias also correlated with the body temperatures of homeothermic birds and mammals. CONCLUSIONS Our work extends the transcriptome resources for A. pompejana and identifies the CvP-bias as a robust and widely applicable measure of eukaryotic thermoadaptation.
Collapse
Affiliation(s)
- Thomas Holder
- Max-Planck-Institute for Developmental Biology, Spemannstr, 35, Tübingen, D-72076, Germany
| | | | | | | | | | | | | | | |
Collapse
|
17
|
Nyholm SV, Song P, Dang J, Bunce C, Girguis PR. Expression and putative function of innate immunity genes under in situ conditions in the symbiotic hydrothermal vent tubeworm Ridgeia piscesae. PLoS One 2012; 7:e38267. [PMID: 22701617 PMCID: PMC3372519 DOI: 10.1371/journal.pone.0038267] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Accepted: 05/05/2012] [Indexed: 11/19/2022] Open
Abstract
The relationships between hydrothermal vent tubeworms and sulfide-oxidizing bacteria have served as model associations for understanding chemoautotrophy and endosymbiosis. Numerous studies have focused on the physiological and biochemical adaptations that enable these symbioses to sustain some of the highest recorded carbon fixation rates ever measured. However, far fewer studies have explored the molecular mechanisms underlying the regulation of host and symbiont interactions, specifically those mediated by the innate immune system of the host. To that end, we conducted a series of studies where we maintained the tubeworm, Ridgeia piscesae, in high-pressure aquaria and examined global and quantitative changes in gene expression via high-throughput transcriptomics and quantitative real-time PCR (qPCR). We analyzed over 32,000 full-length expressed sequence tags as well as 26 Mb of transcript sequences from the trophosome (the organ that houses the endosymbiotic bacteria) and the plume (the gas exchange organ in contact with the free-living microbial community). R. piscesae maintained under conditions that promote chemoautotrophy expressed a number of putative cell signaling and innate immunity genes, including pattern recognition receptors (PRRs), often associated with recognizing microbe-associated molecular patterns (MAMPs). Eighteen genes involved with innate immunity, cell signaling, cell stress and metabolite exchange were further analyzed using qPCR. PRRs, including five peptidoglycan recognition proteins and a Toll-like receptor, were expressed significantly higher in the trophosome compared to the plume. Although PRRs are often associated with mediating host responses to infection by pathogens, the differences in expression between the plume and trophosome also implicate similar mechanisms of microbial recognition in interactions between the host and symbiont. We posit that regulation of this association involves a molecular "dialogue" between the partners that includes interactions between the host's innate immune system and the symbiont.
Collapse
Affiliation(s)
- Spencer V. Nyholm
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
- * E-mail: (SVN); (PRG)
| | - Pengfei Song
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Jeanne Dang
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Corey Bunce
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
| | - Peter R. Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- * E-mail: (SVN); (PRG)
| |
Collapse
|
18
|
Jollivet D, Mary J, Gagnière N, Tanguy A, Fontanillas E, Boutet I, Hourdez S, Segurens B, Weissenbach J, Poch O, Lecompte O. Proteome adaptation to high temperatures in the ectothermic hydrothermal vent Pompeii worm. PLoS One 2012; 7:e31150. [PMID: 22348046 PMCID: PMC3277501 DOI: 10.1371/journal.pone.0031150] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Accepted: 01/03/2012] [Indexed: 12/19/2022] Open
Abstract
Taking advantage of the massive genome sequencing effort made on thermophilic prokaryotes, thermal adaptation has been extensively studied by analysing amino acid replacements and codon usage in these unicellular organisms. In most cases, adaptation to thermophily is associated with greater residue hydrophobicity and more charged residues. Both of these characteristics are positively correlated with the optimal growth temperature of prokaryotes. In contrast, little information has been collected on the molecular 'adaptive' strategy of thermophilic eukaryotes. The Pompeii worm A. pompejana, whose transcriptome has recently been sequenced, is currently considered as the most thermotolerant eukaryote on Earth, withstanding the greatest thermal and chemical ranges known. We investigated the amino-acid composition bias of ribosomal proteins in the Pompeii worm when compared to other lophotrochozoans and checked for putative adaptive changes during the course of evolution using codon-based Maximum likelihood analyses. We then provided a comparative analysis of codon usage and amino-acid replacements from a greater set of orthologous genes between the Pompeii worm and Paralvinella grasslei, one of its closest relatives living in a much cooler habitat. Analyses reveal that both species display the same high GC-biased codon usage and amino-acid patterns favoring both positively-charged residues and protein hydrophobicity. These patterns may be indicative of an ancestral adaptation to the deep sea and/or thermophily. In addition, the Pompeii worm displays a set of amino-acid change patterns that may explain its greater thermotolerance, with a significant increase in Tyr, Lys and Ala against Val, Met and Gly. Present results indicate that, together with a high content in charged residues, greater proportion of smaller aliphatic residues, and especially alanine, may be a different path for metazoans to face relatively 'high' temperatures and thus a novelty in thermophilic metazoans.
Collapse
Affiliation(s)
- Didier Jollivet
- Adaptation & Diversité en Milieu Marin, CNRS UMR 7144, Roscoff, France.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Boutet I, Ripp R, Lecompte O, Dossat C, Corre E, Tanguy A, Lallier FH. Conjugating effects of symbionts and environmental factors on gene expression in deep-sea hydrothermal vent mussels. BMC Genomics 2011; 12:530. [PMID: 22034982 PMCID: PMC3218092 DOI: 10.1186/1471-2164-12-530] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Accepted: 10/28/2011] [Indexed: 11/17/2022] Open
Abstract
Background The deep-sea hydrothermal vent mussel Bathymodiolus azoricus harbors thiotrophic and methanotrophic symbiotic bacteria in its gills. While the symbiotic relationship between this hydrothermal mussel and these chemoautotrophic bacteria has been described, the molecular processes involved in the cross-talking between symbionts and host, in the maintenance of the symbiois, in the influence of environmental parameters on gene expression, and in transcriptome variation across individuals remain poorly understood. In an attempt to understand how, and to what extent, this double symbiosis affects host gene expression, we used a transcriptomic approach to identify genes potentially regulated by symbiont characteristics, environmental conditions or both. This study was done on mussels from two contrasting populations. Results Subtractive libraries allowed the identification of about 1000 genes putatively regulated by symbiosis and/or environmental factors. Microarray analysis showed that 120 genes (3.5% of all genes) were differentially expressed between the Menez Gwen (MG) and Rainbow (Rb) vent fields. The total number of regulated genes in mussels harboring a high versus a low symbiont content did not differ significantly. With regard to the impact of symbiont content, only 1% of all genes were regulated by thiotrophic (SOX) and methanotrophic (MOX) bacteria content in MG mussels whereas 5.6% were regulated in mussels collected at Rb. MOX symbionts also impacted a higher proportion of genes than SOX in both vent fields. When host transcriptome expression was analyzed with respect to symbiont gene expression, it was related to symbiont quantity in each field. Conclusions Our study has produced a preliminary description of a transcriptomic response in a hydrothermal vent mussel host of both thiotrophic and methanotrophic symbiotic bacteria. This model can help to identify genes involved in the maintenance of symbiosis or regulated by environmental parameters. Our results provide evidence of symbiont effect on transcriptome regulation, with differences related to type of symbiont, even though the relative percentage of genes involved remains limited. Differences observed between the vent site indicate that environment strongly influences transcriptome regulation and impacts both activity and relative abundance of each symbiont. Among all these genes, those participating in recognition, the immune system, oxidative stress, and energy metabolism constitute new promising targets for extended studies on symbiosis and the effect of environmental parameters on the symbiotic relationships in B. azoricus.
Collapse
Affiliation(s)
- Isabelle Boutet
- CNRS, UMR 7144, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, 29682 Roscoff, France.
| | | | | | | | | | | | | |
Collapse
|