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Castel J, Pradillon F, Cueff V, Leger G, Daguin-Thiébaut C, Ruault S, Mary J, Hourdez S, Jollivet D, Broquet T. Genetic sex determination in three closely related hydrothermal vent gastropods, including one species with intersex individuals. J Evol Biol 2024; 37:779-794. [PMID: 38699972 DOI: 10.1093/jeb/voae051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/27/2024] [Accepted: 05/02/2024] [Indexed: 05/05/2024]
Abstract
Molluscs have undergone many transitions between separate sexes and hermaphroditism, which is of interest in studying the evolution of sex determination and differentiation. Here, we combined multi-locus genotypes obtained from restriction site-associated DNA (RAD) sequencing with anatomical observations of the gonads of three deep-sea hydrothermal vent gastropods of the genus Alviniconcha living in the southwest Pacific. We found that all three species (Alviniconcha boucheti, Alviniconcha strummeri, and Alviniconcha kojimai) share the same male-heterogametic XY sex-determination system but that the gonads of XX A. kojimai individuals are invaded by a variable proportion of male reproductive tissue. The identification of Y-specific RAD loci (found only in A. boucheti) and the phylogenetic analysis of three sex-linked loci shared by all species suggested that X-Y recombination has evolved differently within each species. This situation of three species showing variation in gonadal development around a common sex-determination system provides new insights into the reproductive mode of poorly known deep-sea species and opens up an opportunity to study the evolution of recombination suppression on sex chromosomes and its association with mixed or transitory sexual systems.
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Affiliation(s)
- Jade Castel
- UMR 7144 AD2M CNRS-Sorbonne Université, Station Biologique de Roscoff, Roscoff, France
| | - Florence Pradillon
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, Plouzané, France
| | - Valérie Cueff
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, Plouzané, France
| | - Guillaume Leger
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, Plouzané, France
| | | | - Stéphanie Ruault
- UMR 7144 AD2M CNRS-Sorbonne Université, Station Biologique de Roscoff, Roscoff, France
| | - Jean Mary
- UMR 7144 AD2M CNRS-Sorbonne Université, Station Biologique de Roscoff, Roscoff, France
| | - Stéphane Hourdez
- UMR 8222 LECOB CNRS-Sorbonne Université, Observatoire Océanologique de Banyuls, Banyuls-sur-Mer, France
| | - Didier Jollivet
- UMR 7144 AD2M CNRS-Sorbonne Université, Station Biologique de Roscoff, Roscoff, France
| | - Thomas Broquet
- UMR 7144 AD2M CNRS-Sorbonne Université, Station Biologique de Roscoff, Roscoff, France
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Panteleev PV, Safronova VN, Duan S, Komlev AS, Bolosov IA, Kruglikov RN, Kombarova TI, Korobova OV, Pereskokova ES, Borzilov AI, Dyachenko IA, Shamova OV, Huang Y, Shi Q, Ovchinnikova TV. Novel BRICHOS-Related Antimicrobial Peptides from the Marine Worm Heteromastus filiformis: Transcriptome Mining, Synthesis, Biological Activities, and Therapeutic Potential. Mar Drugs 2023; 21:639. [PMID: 38132960 PMCID: PMC10745061 DOI: 10.3390/md21120639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023] Open
Abstract
Marine polychaetes represent an extremely rich and underexplored source of novel families of antimicrobial peptides (AMPs). The rapid development of next generation sequencing technologies and modern bioinformatics approaches allows us to apply them for characterization of AMP-derived genes and the identification of encoded immune-related peptides with the aid of genome and transcriptome mining. Here, we describe a universal bioinformatic approach based on the conserved BRICHOS domain as a search query for the identification of novel structurally unique AMP families in annelids. In this paper, we report the discovery of 13 novel BRICHOS-related peptides, ranging from 18 to 91 amino acid residues in length, in the cosmopolitan marine worm Heteromastus filiformis with the assistance of transcriptome mining. Two characteristic peptides with a low homology in relation to known AMPs-the α-helical amphiphilic linear peptide, consisting of 28 amino acid residues and designated as HfBRI-28, and the 25-mer β-hairpin peptide, specified as HfBRI-25 and having a unique structure stabilized by two disulfide bonds-were obtained and analyzed as potential antimicrobials. Interestingly, both peptides showed the ability to kill bacteria via membrane damage, but mechanisms of their action and spectra of their activity differed significantly. Being non-cytotoxic towards mammalian cells and stable to proteolysis in the blood serum, HfBRI-25 was selected for further in vivo studies in a lethal murine model of the Escherichia coli infection, where the peptide contributed to the 100% survival rate in animals. A high activity against uropathogenic strains of E. coli (UPEC) as well as a strong ability to kill bacteria within biofilms allow us to consider the novel peptide HfBRI-25 as a promising candidate for the clinical therapy of urinary tract infections (UTI) associated with UPEC.
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Affiliation(s)
- Pavel V. Panteleev
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.P.); (V.N.S.); (S.D.); (I.A.B.); (R.N.K.)
| | - Victoria N. Safronova
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.P.); (V.N.S.); (S.D.); (I.A.B.); (R.N.K.)
| | - Shuting Duan
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.P.); (V.N.S.); (S.D.); (I.A.B.); (R.N.K.)
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen 518081, China; (Y.H.); (Q.S.)
| | - Alexey S. Komlev
- Institute of Experimental Medicine, WCRC “Center for Personalized Medicine”, 197022 St. Petersburg, Russia; (A.S.K.); (O.V.S.)
| | - Ilia A. Bolosov
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.P.); (V.N.S.); (S.D.); (I.A.B.); (R.N.K.)
| | - Roman N. Kruglikov
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.P.); (V.N.S.); (S.D.); (I.A.B.); (R.N.K.)
| | - Tatiana I. Kombarova
- State Research Center for Applied Microbiology & Biotechnology (SRCAMB), 142279 Obolensk, Russia; (T.I.K.); (O.V.K.); (E.S.P.); (A.I.B.)
| | - Olga V. Korobova
- State Research Center for Applied Microbiology & Biotechnology (SRCAMB), 142279 Obolensk, Russia; (T.I.K.); (O.V.K.); (E.S.P.); (A.I.B.)
| | - Eugenia S. Pereskokova
- State Research Center for Applied Microbiology & Biotechnology (SRCAMB), 142279 Obolensk, Russia; (T.I.K.); (O.V.K.); (E.S.P.); (A.I.B.)
| | - Alexander I. Borzilov
- State Research Center for Applied Microbiology & Biotechnology (SRCAMB), 142279 Obolensk, Russia; (T.I.K.); (O.V.K.); (E.S.P.); (A.I.B.)
| | - Igor A. Dyachenko
- The Branch of M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Russia;
| | - Olga V. Shamova
- Institute of Experimental Medicine, WCRC “Center for Personalized Medicine”, 197022 St. Petersburg, Russia; (A.S.K.); (O.V.S.)
| | - Yu Huang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen 518081, China; (Y.H.); (Q.S.)
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen 518081, China; (Y.H.); (Q.S.)
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518057, China
| | - Tatiana V. Ovchinnikova
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.P.); (V.N.S.); (S.D.); (I.A.B.); (R.N.K.)
- Department of Biotechnology, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
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Chen G, Andrade-Talavera Y, Zhong X, Hassan S, Biverstål H, Poska H, Abelein A, Leppert A, Kronqvist N, Rising A, Hebert H, Koeck PJB, Fisahn A, Johansson J. Abilities of the BRICHOS domain to prevent neurotoxicity and fibril formation are dependent on a highly conserved Asp residue. RSC Chem Biol 2022; 3:1342-1358. [PMID: 36349220 PMCID: PMC9627735 DOI: 10.1039/d2cb00187j] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/15/2022] [Indexed: 09/23/2023] Open
Abstract
Proteins can self-assemble into amyloid fibrils or amorphous aggregates and thereby cause disease. Molecular chaperones can prevent both these types of protein aggregation, but to what extent the respective mechanisms are overlapping is not fully understood. The BRICHOS domain constitutes a disease-associated chaperone family, with activities against amyloid neurotoxicity, fibril formation, and amorphous protein aggregation. Here, we show that the activities of BRICHOS against amyloid-induced neurotoxicity and fibril formation, respectively, are oppositely dependent on a conserved aspartate residue, while the ability to suppress amorphous protein aggregation is unchanged by Asp to Asn mutations. The Asp is evolutionarily highly conserved in >3000 analysed BRICHOS domains but is replaced by Asn in some BRICHOS families. The conserved Asp in its ionized state promotes structural flexibility and has a pK a value between pH 6.0 and 7.0, suggesting that chaperone effects can be differently affected by physiological pH variations.
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Affiliation(s)
- Gefei Chen
- Department of Biosciences and Nutrition, Karolinska Institutet 141 52 Huddinge Sweden
| | - Yuniesky Andrade-Talavera
- Neuronal Oscillations Laboratory, Center for Alzheimer Research, Departments of NVS and KBH, Karolinska Institutet 171 77 Stockholm Sweden
| | - Xueying Zhong
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Biomedical Engineering and Health Systems, KTH Royal Institute of Technology 141 52 Huddinge Sweden
| | - Sameer Hassan
- Department of Biosciences and Nutrition, Karolinska Institutet 141 52 Huddinge Sweden
| | - Henrik Biverstål
- Department of Biosciences and Nutrition, Karolinska Institutet 141 52 Huddinge Sweden
- Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis Riga LV-1006 Latvia
| | - Helen Poska
- Department of Biosciences and Nutrition, Karolinska Institutet 141 52 Huddinge Sweden
- School of Natural Sciences and Health, Tallinn University Tallinn Estonia
| | - Axel Abelein
- Department of Biosciences and Nutrition, Karolinska Institutet 141 52 Huddinge Sweden
| | - Axel Leppert
- Department of Biosciences and Nutrition, Karolinska Institutet 141 52 Huddinge Sweden
| | - Nina Kronqvist
- Department of Biosciences and Nutrition, Karolinska Institutet 141 52 Huddinge Sweden
| | - Anna Rising
- Department of Biosciences and Nutrition, Karolinska Institutet 141 52 Huddinge Sweden
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences 750 07 Uppsala Sweden
| | - Hans Hebert
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Biomedical Engineering and Health Systems, KTH Royal Institute of Technology 141 52 Huddinge Sweden
| | - Philip J B Koeck
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Biomedical Engineering and Health Systems, KTH Royal Institute of Technology 141 52 Huddinge Sweden
| | - André Fisahn
- Neuronal Oscillations Laboratory, Center for Alzheimer Research, Departments of NVS and KBH, Karolinska Institutet 171 77 Stockholm Sweden
| | - Jan Johansson
- Department of Biosciences and Nutrition, Karolinska Institutet 141 52 Huddinge Sweden
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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.
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Bruno R, Maresca M, Canaan S, Cavalier JF, Mabrouk K, Boidin-Wichlacz C, Olleik H, Zeppilli D, Brodin P, Massol F, Jollivet D, Jung S, Tasiemski A. Worms' Antimicrobial Peptides. Mar Drugs 2019; 17:md17090512. [PMID: 31470685 PMCID: PMC6780910 DOI: 10.3390/md17090512] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/22/2019] [Accepted: 08/27/2019] [Indexed: 12/20/2022] Open
Abstract
Antimicrobial peptides (AMPs) are natural antibiotics produced by all living organisms. In metazoans, they act as host defense factors by eliminating microbial pathogens. But they also help to select the colonizing bacterial symbionts while coping with specific environmental challenges. Although many AMPs share common structural characteristics, for example having an overall size between 10-100 amino acids, a net positive charge, a γ-core motif, or a high content of cysteines, they greatly differ in coding sequences as a consequence of multiple parallel evolution in the face of pathogens. The majority of AMPs is specific of certain taxa or even typifying species. This is especially the case of annelids (ringed worms). Even in regions with extreme environmental conditions (polar, hydrothermal, abyssal, polluted, etc.), worms have colonized all habitats on Earth and dominated in biomass most of them while co-occurring with a large number and variety of bacteria. This review surveys the different structures and functions of AMPs that have been so far encountered in annelids and nematodes. It highlights the wide diversity of AMP primary structures and their originality that presumably mimics the highly diverse life styles and ecology of worms. From the unique system that represents marine annelids, we have studied the effect of abiotic pressures on the selection of AMPs and demonstrated the promising sources of antibiotics that they could constitute.
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Affiliation(s)
- Renato Bruno
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France.
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France.
| | - Marc Maresca
- Aix-Marseille Univ, CNRS, Centrale Marseille, iSm2, F-13013 Marseille, France
| | - Stéphane Canaan
- Aix-Marseille Univ, CNRS, LISM, IMM FR3479, F-13009 Marseille, France
| | | | - Kamel Mabrouk
- Aix-Marseille Univ, CNRS, UMR7273, ICR, F-13013Marseille, France
| | - Céline Boidin-Wichlacz
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
| | - Hamza Olleik
- Aix-Marseille Univ, CNRS, Centrale Marseille, iSm2, F-13013 Marseille, France
| | - Daniela Zeppilli
- IFREMER Centre Brest REM/EEP/LEP, ZI de la Pointe du Diable, CS10070, F-29280Plouzané, France
| | - Priscille Brodin
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - François Massol
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
| | - Didier Jollivet
- Sorbonne Université, CNRS, UMR 7144 AD2M, Station Biologique de Roscoff, Place Georges Teissier CS90074, F-29688 Roscoff, France
| | - Sascha Jung
- Department of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Aurélie Tasiemski
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France.
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France.
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Novel Antimicrobial Peptides from the Arctic Polychaeta Nicomache minor Provide New Molecular Insight into Biological Role of the BRICHOS Domain. Mar Drugs 2018; 16:md16110401. [PMID: 30360541 PMCID: PMC6265681 DOI: 10.3390/md16110401] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 10/16/2018] [Accepted: 10/20/2018] [Indexed: 12/12/2022] Open
Abstract
Endogenous antimicrobial peptides (AMPs) are among the earliest molecular factors in the evolution of animal innate immunity. In this study, novel AMPs named nicomicins were identified in the small marine polychaeta Nicomache minor in the Maldanidae family. Full-length mRNA sequences encoded 239-residue prepropeptides consisting of a putative signal sequence region, the BRICHOS domain within an acidic proregion, and 33-residue mature cationic peptides. Nicomicin-1 was expressed in the bacterial system, and its spatial structure was analyzed by circular dichroism and nuclear magnetic resonance spectroscopy. Nicomicins are unique among polychaeta AMPs scaffolds, combining an amphipathic N-terminal α-helix and C-terminal extended part with a six-residue loop stabilized by a disulfide bridge. This structural arrangement resembles the Rana-box motif observed in the α-helical host-defense peptides isolated from frog skin. Nicomicin-1 exhibited strong in vitro antimicrobial activity against Gram-positive bacteria at submicromolar concentrations. The main mechanism of nicomicin-1 action is based on membrane damage but not on the inhibition of bacterial translation. The peptide possessed cytotoxicity against cancer and normal adherent cells as well as toward human erythrocytes.
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