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Gomis-Rüth FX, Stöcker W. Structural and evolutionary insights into astacin metallopeptidases. Front Mol Biosci 2023; 9:1080836. [PMID: 36685277 PMCID: PMC9848320 DOI: 10.3389/fmolb.2022.1080836] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 11/30/2022] [Indexed: 01/05/2023] Open
Abstract
The astacins are a family of metallopeptidases (MPs) that has been extensively described from animals. They are multidomain extracellular proteins, which have a conserved core architecture encompassing a signal peptide for secretion, a prodomain or prosegment and a zinc-dependent catalytic domain (CD). This constellation is found in the archetypal name-giving digestive enzyme astacin from the European crayfish Astacus astacus. Astacin catalytic domains span ∼200 residues and consist of two subdomains that flank an extended active-site cleft. They share several structural elements including a long zinc-binding consensus sequence (HEXXHXXGXXH) immediately followed by an EXXRXDRD motif, which features a family-specific glutamate. In addition, a downstream SIMHY-motif encompasses a "Met-turn" methionine and a zinc-binding tyrosine. The overall architecture and some structural features of astacin catalytic domains match those of other more distantly related MPs, which together constitute the metzincin clan of metallopeptidases. We further analysed the structures of PRO-, MAM, TRAF, CUB and EGF-like domains, and described their essential molecular determinants. In addition, we investigated the distribution of astacins across kingdoms and their phylogenetic origin. Through extensive sequence searches we found astacin CDs in > 25,000 sequences down the tree of life from humans beyond Metazoa, including Choanoflagellata, Filasterea and Ichtyosporea. We also found < 400 sequences scattered across non-holozoan eukaryotes including some fungi and one virus, as well as in selected taxa of archaea and bacteria that are pathogens or colonizers of animal hosts, but not in plants. Overall, we propose that astacins originate in the root of Holozoa consistent with Darwinian descent and that the latter genes might be the result of horizontal gene transfer from holozoan donors.
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Affiliation(s)
- F. Xavier Gomis-Rüth
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (IBMB), Higher Scientific Research Council (CSIC), Barcelona, Catalonia, Spain,*Correspondence: F. Xavier Gomis-Rüth, ; Walter Stöcker,
| | - Walter Stöcker
- Institute of Molecular Physiology (IMP), Johannes Gutenberg-University Mainz (JGU), Mainz, Germany,*Correspondence: F. Xavier Gomis-Rüth, ; Walter Stöcker,
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Zhong S, Ma X, Jiang Y, Qiao Y, Zhao L, Huang L, Huang G, Zhao Y, Liu Y, Chen X. The Draft Genome of Chinese Endemic Species Phascolosoma esculenta (Sipuncula, Phascolosomatidae) Reveals the Phylogenetic Position of Sipuncula. Front Genet 2022; 13:910344. [PMID: 35937983 PMCID: PMC9354978 DOI: 10.3389/fgene.2022.910344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/26/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Shengping Zhong
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China
- Guangxi Engineering Technology Research Center for Marine Aquaculture, Guangxi Institute of Oceanology Co., Ltd., Beihai, China
- *Correspondence: Shengping Zhong, ; Yonghong Liu, ; Xiuli Chen,
| | - Xiaowan Ma
- Key Laboratory of Tropical Marine Ecosystem and Bioresource, Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, China
| | - Yan Jiang
- Guangxi Engineering Technology Research Center for Marine Aquaculture, Guangxi Institute of Oceanology Co., Ltd., Beihai, China
| | - Ying Qiao
- Key Laboratory of Tropical Marine Ecosystem and Bioresource, Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, China
| | - Longyan Zhao
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China
| | - Lianghua Huang
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China
| | - Guoqiang Huang
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China
| | - Yongzhen Zhao
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Yonghong Liu
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China
- *Correspondence: Shengping Zhong, ; Yonghong Liu, ; Xiuli Chen,
| | - Xiuli Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
- *Correspondence: Shengping Zhong, ; Yonghong Liu, ; Xiuli Chen,
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Appah JKM, Lynch SA, Lim A, O' Riordan R, O'Reilly L, de Oliveira L, Wheeler AJ. A health survey of the reef forming scleractinian cold-water corals Lophelia pertusa and Madrepora oculata in a remote submarine canyon on the European continental margin, NE Atlantic. J Invertebr Pathol 2022; 192:107782. [PMID: 35667398 DOI: 10.1016/j.jip.2022.107782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 05/26/2022] [Accepted: 05/30/2022] [Indexed: 11/30/2022]
Abstract
Monitoring of cold-water corals (CWCs) for pathogens and diseases is limited due to the environment, protected nature of the corals and their habitat and as well as the challenging and sampling effort required. It is recognised that environmental factors such as temperature and pH can expedite the ability of pathogens to cause diseases in cold-water corals therefore the characterisation of pathogen diversity, prevalence and associated pathologies is essential. The present study combined histology and polymerase chain reaction (PCR) diagnostic techniques to screen for two significant pathogen groups (bacteria of the genus Vibrio and the protozoan Haplosporidia) in the dominant NE Atlantic deep-water framework corals Lophelia pertusa (13 colonies) and Madrepora oculata (2 colonies) at three sampling locations (canyon head, south branch and the flank) in the Porcupine Bank Canyon (PBC), NE Atlantic. One M. oculata colony and four L. pertusa colonies were collected from both the canyon flank and the south branch whilst five L. pertusa colonies were collected from the canyon head. No pathogens were detected in the M. oculata samples. Neither histology nor PCR detected Vibrio spp. in L. pertusa, although Illumina technology used in this study to profile the CWCs microbiome, detected V. shilonii (0.03%) in a single L. pertusa individual, from the canyon head, that had also been screened in this study. A macroborer was observed at a prevalence of 0.07% at the canyon head only. Rickettsiales-like organisms (RLOs) were visualised with an overall prevalence of 40% and with a low intensity of 1 to 4 (RLO) colonies per individual polyp by histology. L. pertusa from the PBC canyon head had an RLO prevalence of 13.3% with the highest detection of 26.7% recorded in the south branch corals. Similarly, unidentified cells observed in L. pertusa from the south branch (20%) were more common than those observed in L. pertusa from the canyon head (6.7%). No RLOs or unidentified cells were observed in corals from the flank. Mean particulate organic matter concentration is highest in the south branch (2,612 μg l-1) followed by the canyon head (1,065 μg l-1) and lowest at the canyon flank (494 μg l-1). Although the route of pathogen entry and the impact of RLO infection on L. pertusa is unclear, particulate availability and the feeding strategies employed by the scleractinian corals may be influencing their exposure to pathogens. The absence of a pathogen in M. oculata may be attributed to the smaller number of colonies screened or the narrower diet in M. oculata compared to the unrestricted diet exhibited in L. pertusa, if ingestion is a route of entry for pathogen groups. The findings of this study also shed some light on how environmental conditions experienced by deep sea organisms and their life strategies may be limiting pathogen diversity and prevalence.
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Affiliation(s)
- J K M Appah
- School of Biological, Earth and Environmental Sciences / Environmental Research Institute, University College Cork, Distillery Fields, North Mall, Cork, Ireland.
| | - S A Lynch
- School of Biological, Earth and Environmental Sciences / Environmental Research Institute, University College Cork, Distillery Fields, North Mall, Cork, Ireland
| | - A Lim
- School of Biological, Earth and Environmental Sciences / Environmental Research Institute, University College Cork, Distillery Fields, North Mall, Cork, Ireland; Green Rebel Marine, Crosshaven Boatyard, Crosshaven, Co Cork, Ireland
| | - R O' Riordan
- School of Biological, Earth and Environmental Sciences / Environmental Research Institute, University College Cork, Distillery Fields, North Mall, Cork, Ireland
| | - L O'Reilly
- School of Biological, Earth and Environmental Sciences / Environmental Research Institute, University College Cork, Distillery Fields, North Mall, Cork, Ireland
| | - L de Oliveira
- School of Biological, Earth and Environmental Sciences / Environmental Research Institute, University College Cork, Distillery Fields, North Mall, Cork, Ireland
| | - A J Wheeler
- School of Biological, Earth and Environmental Sciences / Environmental Research Institute, University College Cork, Distillery Fields, North Mall, Cork, Ireland; Irish Centre for Research in Applied Geosciences / Marine & Renewable Energy Institute (MaREI), University College, Cork
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Simon CA, du Toit AN, Lamberth SJ, Branch GM. Standardising English and Afrikaans common names for polychaetes harvested as bait in South Africa. AFRICAN ZOOLOGY 2022. [DOI: 10.1080/15627020.2022.2085063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Carol A Simon
- Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa
| | - Alheit N du Toit
- Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa
| | - Stephen J Lamberth
- Department of Forestry, Fisheries and Environment, Cape Town, South Africa
- Institute for Coastal and Marine Research, Nelson Mandela University, Port Elizabeth, South Africa
| | - George M Branch
- Department of Biological Science, University of Cape Town, Cape Town, South Africa
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Abstract
Annelida is a ubiquitous, common and diverse group of organisms, found in terrestrial, fresh waters and marine environments. Despite the large efforts put into resolving the evolutionary relationships of these and other Lophotrochozoa, and the delineation of the basal nodes within the group, these are still unanswered. Annelida holds an enormous diversity of forms and biological strategies alongside a large number of species, following Arthropoda, Mollusca, Vertebrata and perhaps Platyhelminthes, among the species most rich in phyla within Metazoa. The number of currently accepted annelid species changes rapidly when taxonomic groups are revised due to synonymies and descriptions of a new species. The group is also experiencing a recent increase in species numbers as a consequence of the use of molecular taxonomy methods, which allows the delineation of the entities within species complexes. This review aims at succinctly reviewing the state-of-the-art of annelid diversity and summarizing the main systematic revisions carried out in the group. Moreover, it should be considered as the introduction to the papers that form this Special Issue on Systematics and Biodiversity of Annelids.
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