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Santini S, Schenkelaars Q, Jourda C, Duchesne M, Belahbib H, Rocher C, Selva M, Riesgo A, Vervoort M, Leys SP, Kodjabachian L, Le Bivic A, Borchiellini C, Claverie JM, Renard E. The compact genome of the sponge Oopsacas minuta (Hexactinellida) is lacking key metazoan core genes. BMC Biol 2023; 21:139. [PMID: 37337252 DOI: 10.1186/s12915-023-01619-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 05/09/2023] [Indexed: 06/21/2023] Open
Abstract
BACKGROUND Explaining the emergence of the hallmarks of bilaterians is a central focus of evolutionary developmental biology-evodevo-and evolutionary genomics. For this purpose, we must both expand and also refine our knowledge of non-bilaterian genomes, especially by studying early branching animals, in particular those in the metazoan phylum Porifera. RESULTS We present a comprehensive analysis of the first whole genome of a glass sponge, Oopsacas minuta, a member of the Hexactinellida. Studying this class of sponge is evolutionary relevant because it differs from the three other Porifera classes in terms of development, tissue organization, ecology, and physiology. Although O. minuta does not exhibit drastic body simplifications, its genome is among the smallest of animal genomes sequenced so far, and surprisingly lacks several metazoan core genes (including Wnt and several key transcription factors). Our study also provides the complete genome of a symbiotic Archaea dominating the associated microbial community: a new Thaumarchaeota species. CONCLUSIONS The genome of the glass sponge O. minuta differs from all other available sponge genomes by its compactness and smaller number of encoded proteins. The unexpected loss of numerous genes previously considered ancestral and pivotal for metazoan morphogenetic processes most likely reflects the peculiar syncytial tissue organization in this group. Our work further documents the importance of convergence during animal evolution, with multiple convergent evolution of septate-like junctions, electrical-signaling and multiciliated cells in metazoans.
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Affiliation(s)
- Sébastien Santini
- Aix Marseille Univ, CNRS, IGS, UMR 7256, IMM, IM2B, IOM, Marseille, France
| | - Quentin Schenkelaars
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Marseille, France
- Institut Jacques Monod, CNRS, UMR 7592, Univ Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Cyril Jourda
- Aix Marseille Univ, CNRS, IGS, UMR 7256, IMM, IM2B, IOM, Marseille, France
- CIRAD, UMR PVBMT, La Réunion, France
| | - Marc Duchesne
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Hassiba Belahbib
- Aix Marseille Univ, CNRS, IGS, UMR 7256, IMM, IM2B, IOM, Marseille, France
| | - Caroline Rocher
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Marseille, France
| | - Marjorie Selva
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Marseille, France
| | - Ana Riesgo
- Department of Biodiversity and Evolutionary Biology, Madrid, Spain
- Department of Life Sciences, Natural History Museum of London, London, SW7 5BD, UK
| | - Michel Vervoort
- Institut Jacques Monod, CNRS, UMR 7592, Univ Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Sally P Leys
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Laurent Kodjabachian
- Aix Marseille Univ, CNRS, IBDM, UMR 7288, Turing Center for Living Systems, Marseille, France
| | - André Le Bivic
- Aix Marseille Univ, CNRS, IBDM, UMR 7288, Marseille, France
| | | | | | - Emmanuelle Renard
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Marseille, France.
- Aix Marseille Univ, CNRS, IBDM, UMR 7288, Marseille, France.
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Li H, Chenglin G, Yae Z, Wanyu Z, Rong C. Identification and genetic characterisatin of cathepsin L in Demodex. EXPERIMENTAL & APPLIED ACAROLOGY 2023; 89:329-344. [PMID: 37058174 DOI: 10.1007/s10493-023-00789-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 03/23/2023] [Indexed: 05/09/2023]
Abstract
Owing to difficulties in obtaining functional gene sequences, molecular pathogenic mechanisms in Demodex have been understudied. In this study, overlap extension PCR was used to obtain the sequences of cathepsin L (CatL), a pathogenicity-related gene, to provide a foundation for subsequent functional research. Demodex folliculorum and Demodex brevis mites were obtained from the face skin of Chinese individuals, and Demodex canis mites were isolated from the skin lesions of a dog. RNA was extracted and used to synthesise double-stranded cDNA. PCR amplification, cloning, sequencing, and bioinformatics analysis of CatL were performed. CatL gene sequences of 1005, 1008, and 1008 bp were successfully amplified for D. brevis, D. folliculorum, and D. canis, respectively. These sequences showed 99.9 or 100% identity with templates previously obtained by RNA-seq. The Maximum Likelihood (ML) phylogenetic tree showed that D. folliculorum clustered with D. canis first, then with D. brevis, and finally with other Acariformes mite species. The three Demodex species had nine similar motifs to those of Sarcoptes scabies, Dermatophagoides pteronyssinus, and Dermatophagoides farinae, and motifs 10-13 were valuable for identification. CatL proteins of Demodex species were predicted to be approximately 38 kDa, be located in lysosomes, have a signal peptide but no transmembrane region, and have two functional domains, I29 and Pept_C1. However, interspecific differences were observed in secondary and tertiary protein structures. In conclusion, we successfully obtained CatL sequences of three Demodex species by overlap extension PCR, which creates conditions for further pathogenic mechanism studies.
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Affiliation(s)
- Hu Li
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, No.76 Yanta West Road, Xi'an, 710061, Shaanxi Province, China
| | - Guan Chenglin
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, No.76 Yanta West Road, Xi'an, 710061, Shaanxi Province, China
| | - Zhao Yae
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, No.76 Yanta West Road, Xi'an, 710061, Shaanxi Province, China.
| | - Zhang Wanyu
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, No.76 Yanta West Road, Xi'an, 710061, Shaanxi Province, China
| | - Chai Rong
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, No.76 Yanta West Road, Xi'an, 710061, Shaanxi Province, China
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Ricardo-Gonzalez RR, Kotas ME, O'Leary CE, Singh K, Damsky W, Liao C, Arouge E, Tenvooren I, Marquez DM, Schroeder AW, Cohen JN, Fassett MS, Lee J, Daniel SG, Bittinger K, Díaz RE, Fraser JS, Ali N, Ansel KM, Spitzer MH, Liang HE, Locksley RM. Innate type 2 immunity controls hair follicle commensalism by Demodex mites. Immunity 2022; 55:1891-1908.e12. [PMID: 36044899 PMCID: PMC9561030 DOI: 10.1016/j.immuni.2022.08.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 06/27/2022] [Accepted: 08/02/2022] [Indexed: 01/05/2023]
Abstract
Demodex mites are commensal parasites of hair follicles (HFs). Normally asymptomatic, inflammatory outgrowth of mites can accompany malnutrition, immune dysfunction, and aging, but mechanisms restricting Demodex outgrowth are not defined. Here, we show that control of mite HF colonization in mice required group 2 innate lymphoid cells (ILC2s), interleukin-13 (IL-13), and its receptor, IL-4Ra-IL-13Ra1. HF-associated ILC2s elaborated IL-13 that attenuated HFs and epithelial proliferation at anagen onset; in their absence, Demodex colonization led to increased epithelial proliferation and replacement of gene programs for repair by aberrant inflammation, leading to the loss of barrier function and HF exhaustion. Humans with rhinophymatous acne rosacea, an inflammatory condition associated with Demodex, had increased HF inflammation with decreased type 2 cytokines, consistent with the inverse relationship seen in mice. Our studies uncover a key role for skin ILC2s and IL-13, which comprise an immune checkpoint that sustains cutaneous integrity and restricts pathologic infestation by colonizing HF mites.
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Affiliation(s)
- Roberto R Ricardo-Gonzalez
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Maya E Kotas
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Claire E O'Leary
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Katelyn Singh
- Department of Dermatology, Yale School of Medicine, New Haven, CT, USA
| | - William Damsky
- Department of Dermatology, Yale School of Medicine, New Haven, CT, USA; Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Chang Liao
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Elizabeth Arouge
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
| | - Iliana Tenvooren
- Department of Otolaryngology and Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Diana M Marquez
- Department of Otolaryngology and Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Andrew W Schroeder
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Jarish N Cohen
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Marlys S Fassett
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Jinwoo Lee
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Scott G Daniel
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Roberto Efraín Díaz
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA; Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Niwa Ali
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
| | - K Mark Ansel
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Matthew H Spitzer
- Department of Otolaryngology and Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Hong-Erh Liang
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Richard M Locksley
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA.
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