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Bortoletto E, Rosani U, Sakaguchi A, Yoon J, Nagasawa K, Venier P. Insights into ADAR gene complement, expression patterns, and RNA editing landscape in Chlamys farreri. FISH & SHELLFISH IMMUNOLOGY 2024; 151:109743. [PMID: 38964433 DOI: 10.1016/j.fsi.2024.109743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 06/26/2024] [Accepted: 07/01/2024] [Indexed: 07/06/2024]
Abstract
Adenosine Deaminases Acting on RNA (ADARs) are evolutionarily conserved enzymes known to convert adenosine to inosine in double-stranded RNAs and participate in host-virus interactions. Conducting a meta-analysis of available transcriptome data, we identified and characterised eight ADAR transcripts in Chlamys farreri, a farmed marine scallop susceptible to Acute viral necrosis virus (AVNV) infections and mortality outbreaks. Accordingly, we identified six ADAR genes in the Zhikong scallop genome, revised previous gene annotations, and traced alternative splicing variants. In detail, each ADAR gene encodes a unique combination of functional domains, always including the Adenosine deaminase domain, RNA binding domains and, in one case, two copies of a Z-DNA binding domain. After phylogenetic analysis, five C. farreri ADARs clustered in the ADAR1 clade along with sequences from diverse animal phyla. Gene expression analysis indicated CF051320 as the most expressed ADAR, especially in the eye and male gonad. The other four ADAR1 genes and one ADAR2 gene exhibited variable expression levels, with CF105370 and CF051320 significantly increasing during early scallop development. ADAR-mediated single-base editing, evaluated across adult C. farreri tissues and developmental stages, was mainly detectable in intergenic regions (83 % and 85 %, respectively). Overall, the expression patterns of the six ADAR genes together with the editing and hyper-editing values computed on scallops RNA-seq samples support the adaptive value of ADAR1-mediated editing, particularly in the pre-settling larval stages.
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Affiliation(s)
| | - Umberto Rosani
- Department of Biology, University of Padova, 35121, Padova, Italy
| | - Akari Sakaguchi
- Laboratory of Aquaculture Biology, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, 980-8572, Japan
| | - Jeongwoong Yoon
- Laboratory of Aquaculture Biology, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, 980-8572, Japan
| | - Kazue Nagasawa
- Laboratory of Aquaculture Biology, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, 980-8572, Japan
| | - Paola Venier
- Department of Biology, University of Padova, 35121, Padova, Italy.
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2
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Hamid R, Jacob F, Ghorbanzadeh Z, Khayam Nekouei M, Zeinalabedini M, Mardi M, Sadeghi A, Kumar S, Ghaffari MR. Genomic insights into CKX genes: key players in cotton fibre development and abiotic stress responses. PeerJ 2024; 12:e17462. [PMID: 38827302 PMCID: PMC11144395 DOI: 10.7717/peerj.17462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 05/05/2024] [Indexed: 06/04/2024] Open
Abstract
Cytokinin oxidase/dehydrogenase (CKX), responsible for irreversible cytokinin degradation, also controls plant growth and development and response to abiotic stress. While the CKX gene has been studied in other plants extensively, its function in cotton is still unknown. Therefore, a genome-wide study to identify the CKX gene family in the four cotton species was conducted using transcriptomics, quantitative real-time PCR (qRT-PCR) and bioinformatics. As a result, in G. hirsutum and G. barbadense (the tetraploid cotton species), 87 and 96 CKX genes respectively and 62 genes each in G. arboreum and G. raimondii, were identified. Based on the evolutionary studies, the cotton CKX gene family has been divided into five distinct subfamilies. It was observed that CKX genes in cotton have conserved sequence logos and gene family expansion was due to segmental duplication or whole genome duplication (WGD). Collinearity and multiple synteny studies showed an expansion of gene families during evolution and purifying selection pressure has been exerted. G. hirsutum CKX genes displayed multiple exons/introns, uneven chromosomal distribution, conserved protein motifs, and cis-elements related to growth and stress in their promoter regions. Cis-elements related to resistance, physiological metabolism and hormonal regulation were identified within the promoter regions of the CKX genes. Expression analysis under different stress conditions (cold, heat, drought and salt) revealed different expression patterns in the different tissues. Through virus-induced gene silencing (VIGS), the GhCKX34A gene was found to improve cold resistance by modulating antioxidant-related activity. Since GhCKX29A is highly expressed during fibre development, we hypothesize that the increased expression of GhCKX29A in fibres has significant effects on fibre elongation. Consequently, these results contribute to our understanding of the involvement of GhCKXs in both fibre development and response to abiotic stress.
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Affiliation(s)
- Rasmieh Hamid
- Department of Plant Breeding, Cotton Research Institute of Iran (CRII), Agricultural Research, Education and Extension Organization (AREEO), Gorgan, Golestan, Iran
| | - Feba Jacob
- Centre for Plant Biotechnology and Molecular Biology, Kerala Agricultural University, Thrissur, Kerala, India
| | - Zahra Ghorbanzadeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Alborz, Iran
| | | | - Mehrshad Zeinalabedini
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Alborz, Iran
| | - Mohsen Mardi
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Alborz, Iran
| | - Akram Sadeghi
- Department of Microbial Biotechnology and Biosafety, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Alborrz, Iran
| | - Sushil Kumar
- Agricultural Biotechnology, Anand agricultural University, Anand, Gujarat, India
| | - Mohammad Reza Ghaffari
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Alborz, Iran
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3
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Hao Z, Lu Q, Zhou Y, Liang Y, Gao Y, Ma H, Xu Y, Wang H. Molecular characterization of MyD88 as a potential biomarker for pesticide-induced stress in Bombyx mori. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2023; 196:105610. [PMID: 37945249 DOI: 10.1016/j.pestbp.2023.105610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/21/2023] [Accepted: 09/01/2023] [Indexed: 11/12/2023]
Abstract
The widespread use of pesticides hampers the immune system of non-target organisms, however, there is a lack of common biomarkers to detect such effects. Myeloid differentiation primary response factor 88 (MyD88) is a crucial junction protein in the Toll-like receptor signaling pathway, which plays an important role in the inflammatory response. In this study, we investigated MyD88 as a potential biomarker for pesticide-induced stress. Phylogenetic analysis revealed that MyD88 was a conserved protein in the evolution of vertebrates and invertebrates. MyD88s usually have death domain (DD) and Toll/interleukin-1 receptor (TIR) domain. Bombyx mori (B. mori) is an important economic insect that is sensitive to toxic substances. We found microbial pesticides enhanced the expression level of MyD88 in B. mori. Transcriptome analysis demonstrated that MyD88 expression level was increased in the fatbody after dinotefuran exposure, a third-generation neonicotinoid pesticide. Moreover, the expression of MyD88 was upregulated in fatbody and midgut by imidacloprid, a first-generation neonicotinoid pesticide. Additionally, insect growth regulator (IGR) pesticides, such as methoprene and fenoxycarb, could induce MyD88 expression in the fatbody of B. mori. These results indicated that MyD88 is a potential biomarker for pesticide-induced stress in B. mori. This study provides novel insights into screening common biomarkers for multiple pesticide stresses and important implications for the development of more sustainable pest management strategies.
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Affiliation(s)
- Zhihua Hao
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Qingyu Lu
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Yanyan Zhou
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Yanting Liang
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Yun Gao
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Huanyan Ma
- Agricultural Technology Extension Center of Zhejiang Province, Hangzhou, China
| | - Yusong Xu
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Huabing Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, China.
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4
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Grinchenko A, Buriak I, Kumeiko V. Invertebrate C1q Domain-Containing Proteins: Molecular Structure, Functional Properties and Biomedical Potential. Mar Drugs 2023; 21:570. [PMID: 37999394 PMCID: PMC10672478 DOI: 10.3390/md21110570] [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: 09/02/2023] [Revised: 10/23/2023] [Accepted: 10/28/2023] [Indexed: 11/25/2023] Open
Abstract
C1q domain-containing proteins (C1qDC proteins) unexpectedly turned out to be widespread molecules among a variety of invertebrates, despite their lack of an integral complement system. Despite the wide distribution in the genomes of various invertebrates, data on the structure and properties of the isolated and characterized C1qDC proteins, which belong to the C1q/TNF superfamily, are sporadic, although they hold great practical potential for the creation of new biotechnologies. This review not only summarizes the current data on the properties of already-isolated or bioengineered C1qDC proteins but also projects further strategies for their study and biomedical application. It has been shown that further broad study of the carbohydrate specificity of the proteins can provide great opportunities, since for many of them only interactions with pathogen-associated molecular patterns (PAMPs) was evaluated and their antimicrobial, antiviral, and fungicidal activities were studied. However, data on the properties of C1qDC proteins, which researchers originally discovered as lectins and therefore studied their fine carbohydrate specificity and antitumor activity, intriguingly show the great potential of this family of proteins for the creation of targeted drug delivery systems, vaccines, and clinical assays for the differential diagnosis of cancer. The ability of invertebrate C1qDC proteins to recognize patterns of aberrant glycosylation of human cell surfaces and interact with mammalian immunoglobulins indicates the great biomedical potential of these molecules.
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Affiliation(s)
- Andrei Grinchenko
- School of Medicine and Life Sciences, Far Eastern Federal University, 690922 Vladivostok, Russia; (A.G.); (I.B.)
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, 690041 Vladivostok, Russia
| | - Ivan Buriak
- School of Medicine and Life Sciences, Far Eastern Federal University, 690922 Vladivostok, Russia; (A.G.); (I.B.)
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, 690041 Vladivostok, Russia
| | - Vadim Kumeiko
- School of Medicine and Life Sciences, Far Eastern Federal University, 690922 Vladivostok, Russia; (A.G.); (I.B.)
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, 690041 Vladivostok, Russia
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5
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Saco A, Rey-Campos M, Novoa B, Figueras A. Mussel antiviral transcriptome response and elimination of viral haemorrhagic septicaemia virus (VHSV). FISH & SHELLFISH IMMUNOLOGY 2023; 136:108735. [PMID: 37044187 DOI: 10.1016/j.fsi.2023.108735] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/31/2023] [Accepted: 04/05/2023] [Indexed: 06/19/2023]
Abstract
As filter-feeding bivalves, mussels have been traditionally studied as possible vectors of different bacterial or viral pathogens. The absence of a known viral pathogen in these bivalves makes it particularly interesting to study the interaction of the mussel innate immune system with a virus of interest. In the present work, mussels were challenged with viral haemorrhagic septicaemia virus (VHSV), which is a pathogen in several fish species. The viral load was eliminated after 24 h and mussels evidenced antiviral activity towards VHSV, demonstrating that the virus was recognized and eliminated by the immune system of the host and confirming that mussels are not VHSV vectors in the marine environment. The transcriptome activating the antiviral response was studied, revealing the involvement of cytoplasmic viral sensors with the subsequent activation of the JAK-STAT pathway and several downstream antiviral effectors. The inflammatory response was inhibited with the profound downregulation of MyD88, shifting the immune balance towards antiviral functions. High modulation of retrotransposon activity was observed, revealing a mechanism that facilitates the antiviral response and that had not been previously observed in these species. The expression of several inhibitors of apoptosis and apoptosis-promoting genes was modulated, although clear inhibition of apoptosis in bivalves after severe viral infection and subsequent disease was not observed in this study. Finally, the modulated expression of several long noncoding RNAs that were correlated with genes involved in the immune response was detected.
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Affiliation(s)
- Amaro Saco
- Institute of Marine Research (IIM-CSIC), Vigo, Galicia, Spain
| | | | - Beatriz Novoa
- Institute of Marine Research (IIM-CSIC), Vigo, Galicia, Spain
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6
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Saco A, Suárez H, Novoa B, Figueras A. A Genomic and Transcriptomic Analysis of the C-Type Lectin Gene Family Reveals Highly Expanded and Diversified Repertoires in Bivalves. Mar Drugs 2023; 21:md21040254. [PMID: 37103393 PMCID: PMC10140915 DOI: 10.3390/md21040254] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 04/28/2023] Open
Abstract
C-type lectins belong to a widely conserved family of lectins characterized in Metazoa. They show important functional diversity and immune implications, mainly as pathogen recognition receptors. In this work, C-type lectin-like proteins (CTLs) of a set of metazoan species were analyzed, revealing an important expansion in bivalve mollusks, which contrasted with the reduced repertoires of other mollusks, such as cephalopods. Orthology relationships demonstrated that these expanded repertoires consisted of CTL subfamilies conserved within Mollusca or Bivalvia and of lineage-specific subfamilies with orthology only between closely related species. Transcriptomic analyses revealed the importance of the bivalve subfamilies in mucosal immunity, as they were mainly expressed in the digestive gland and gills and modulated with specific stimuli. CTL domain-containing proteins that had additional domains (CTLDcps) were also studied, revealing interesting gene families with different conservation degrees of the CTL domain across orthologs from different taxa. Unique bivalve CTLDcps with specific domain architectures were revealed, corresponding to uncharacterized bivalve proteins with putative immune function according to their transcriptomic modulation, which could constitute interesting targets for functional characterization.
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Affiliation(s)
- Amaro Saco
- Institute of Marine Research IIM-CSIC, 36208 Vigo, Spain
| | - Hugo Suárez
- Institute of Marine Research IIM-CSIC, 36208 Vigo, Spain
| | - Beatriz Novoa
- Institute of Marine Research IIM-CSIC, 36208 Vigo, Spain
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7
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Fujimoto K, Totani Y, Nakai J, Chikamoto N, Namiki K, Hatakeyama D, Ito E. Identification of Putative Molecules for Adiponectin and Adiponectin Receptor and Their Roles in Learning and Memory in Lymnaea stagnalis. BIOLOGY 2023; 12:biology12030375. [PMID: 36979067 PMCID: PMC10045044 DOI: 10.3390/biology12030375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/20/2023] [Accepted: 02/25/2023] [Indexed: 03/02/2023]
Abstract
Adiponectin enhances insulin sensitivity, which improves cognition in mammals. How adiponectin affects the mechanism’s underlying cognition, however, remains unknown. We hypothesized that experiments using the pond snail Lymnaea stagnalis, which has long been used in learning and memory studies and in which the function of insulin-like peptides affect learning and memory, could clarify the basic mechanisms by which adiponectin affects cognition. We first identified putative molecules of adiponectin and its receptor in Lymnaea. We then examined their distribution in the central nervous system and changes in their expression levels when hemolymph glucose concentrations were intentionally decreased by food deprivation. We also applied an operant conditioning protocol of escape behavior to Lymnaea and examined how the expression levels of adiponectin and its receptor changed after the conditioned behavior was established. The results demonstrate that adiponectin and adiponectin’s receptor expression levels were increased in association with a reduced concentration of hemolymph glucose and that expression levels of both adiponectin and insulin-like peptide receptors were increased after the conditioning behavior was established. Thus, the involvement of the adiponectin-signaling cascade in learning and memory in Lymnaea was suggested to occur via changes in the glucose concentrations and the activation of insulin.
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Affiliation(s)
- Kanta Fujimoto
- Department of Biology, Waseda University, Tokyo 162-8480, Japan
| | - Yuki Totani
- Department of Biology, Waseda University, Tokyo 162-8480, Japan
| | - Junko Nakai
- Department of Biology, Waseda University, Tokyo 162-8480, Japan
| | | | - Kengo Namiki
- Department of Biology, Waseda University, Tokyo 162-8480, Japan
| | - Dai Hatakeyama
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Tokushima 770-8514, Japan
| | - Etsuro Ito
- Department of Biology, Waseda University, Tokyo 162-8480, Japan
- Graduate Institute of Medicine, School of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Correspondence:
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8
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Li Y, Xue Y, Peng Z, Zhang L. Immune diversity in lophotrochozoans, with a focus on recognition and effector systems. Comput Struct Biotechnol J 2023; 21:2262-2275. [PMID: 37035545 PMCID: PMC10073891 DOI: 10.1016/j.csbj.2023.03.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 03/11/2023] [Accepted: 03/19/2023] [Indexed: 03/30/2023] Open
Abstract
Lophotrochozoa is one of the most species-rich but immunologically poorly explored phyla. Although lack of acquired response in a narrow sense, lophotrochozoans possess various genetic mechanisms that enhance the diversity and specificity of innate immune system. Here, we review the recent advances of comparative immunology studies in lophotrochozoans with focus on immune recognition and effector systems. Haemocytes and coelomocytes are general important yet understudied player. Comparative genomics studies suggest expansion and functional divergence of lophotrochozoan immune reorganization systems is not as "homogeneous and simple" as we thought including the large-scale expansion and molecular divergence of pattern recognition receptors (PRRs) (TLRs, RLRs, lectins, etc.) and signaling adapters (MyD88s etc.), significant domain recombination of immune receptors (RLR, NLRs, lectins, etc.), extensive somatic recombination of fibrinogenrelated proteins (FREPs) in snails. Furthermore, there are repeatedly identified molecular mechanisms that generate immune effector diversity, including high polymorphism of antimicrobial peptides and proteins (AMPs), reactive oxygen and nitrogen species (RONS) and cytokines. Finally, we argue that the next generation omics tools and the recently emerged genome editing technicism will revolutionize our understanding of innate immune system in a comparative immunology perspective.
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Affiliation(s)
- Yongnan Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yu Xue
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Qingdao Agricultural University, Qingdao, China
| | - Zhangjie Peng
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- College of Marine Science, University of Chinese Academy of Sciences, Beijing, China
| | - Linlin Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- College of Marine Science, University of Chinese Academy of Sciences, Beijing, China
- Corresponding author at: CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
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9
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Stanovova MV, Gazizova GR, Gorbushin AM. Transcriptomic profiling of immune-associated molecules in the coelomocytes of lugworm Arenicola marina (Linnaeus, 1758). JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2023; 340:34-55. [PMID: 35438249 DOI: 10.1002/jez.b.23135] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 02/04/2022] [Accepted: 03/11/2022] [Indexed: 12/16/2022]
Abstract
Organization and functioning of immune system remain unevenly studied in different taxa of lophotrochozoan animals. We analyzed transcriptomic data on coelomocytes of the lugworm Arenicola marina (Linnaeus, 1758; Annelida, Polychaeta) to gain insights into the molecular mechanisms involved in polychaete immunity. Coelomocytes are specialized motile cells populating coelomic fluid of annelids, responsible for cellular defense reactions and providing humoral immune factors. The transcriptome was enriched with immune-related transcripts by challenging the cells in vitro with lipopolysaccharides of Escherichia coli and Zymosan from Saccharomyces cerevisiae. Our analysis revealed a multifaceted and complex internal defense system of the lugworm. A. marina possesses orthologs of proto-complement-like factors: six thioester-containing proteins, a complement-like receptor, and a MASP-related serine protease (MReM2). A. marina coelomocytes employ pattern-recognition receptors to detect pathogens and regulate immune responses. Among them, there are 18 Toll-like receptors and various putative lectin-like proteins with evolutionary conserved and taxa-specific domains. C-type lectins and a novel family of Gal-binding and CUB domains containing receptors were the most abundant in the transcriptome. The array of pore-forming proteins in the coelomocytes was surprisingly reduced compared to that of other invertebrate species. We characterized a set of conserved proteins metabolizing reactive oxygen species and nitric oxide and expanded the arsenal of potential antimicrobial peptides. Phenoloxidase activity in immune cells of lugworm is mediated only by laccase enzyme. The described repertoire of immune-associated molecules provides valuable candidates for further functional and comparative research on the immunity of annelids.
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Affiliation(s)
- Maria V Stanovova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Guzel R Gazizova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Alexander M Gorbushin
- Sechenov Institute of Evolutionary Physiology and Biochemistry (IEPhB RAS), St. Petersburg, Russia
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10
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Evaluation of the Ruditapes decussatus immune response after differential injected doses of Perkinsus olseni. J Invertebr Pathol 2022; 195:107849. [DOI: 10.1016/j.jip.2022.107849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 08/05/2022] [Accepted: 10/30/2022] [Indexed: 11/06/2022]
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11
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Ahmmed MK, Bhowmik S, Giteru SG, Zilani MNH, Adadi P, Islam SS, Kanwugu ON, Haq M, Ahmmed F, Ng CCW, Chan YS, Asadujjaman M, Chan GHH, Naude R, Bekhit AEDA, Ng TB, Wong JH. An Update of Lectins from Marine Organisms: Characterization, Extraction Methodology, and Potential Biofunctional Applications. Mar Drugs 2022; 20:md20070430. [PMID: 35877723 PMCID: PMC9316650 DOI: 10.3390/md20070430] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 06/26/2022] [Accepted: 06/27/2022] [Indexed: 02/07/2023] Open
Abstract
Lectins are a unique group of nonimmune carbohydrate-binding proteins or glycoproteins that exhibit specific and reversible carbohydrate-binding activity in a non-catalytic manner. Lectins have diverse sources and are classified according to their origins, such as plant lectins, animal lectins, and fish lectins. Marine organisms including fish, crustaceans, and mollusks produce a myriad of lectins, including rhamnose binding lectins (RBL), fucose-binding lectins (FTL), mannose-binding lectin, galectins, galactose binding lectins, and C-type lectins. The widely used method of extracting lectins from marine samples is a simple two-step process employing a polar salt solution and purification by column chromatography. Lectins exert several immunomodulatory functions, including pathogen recognition, inflammatory reactions, participating in various hemocyte functions (e.g., agglutination), phagocytic reactions, among others. Lectins can also control cell proliferation, protein folding, RNA splicing, and trafficking of molecules. Due to their reported biological and pharmaceutical activities, lectins have attracted the attention of scientists and industries (i.e., food, biomedical, and pharmaceutical industries). Therefore, this review aims to update current information on lectins from marine organisms, their characterization, extraction, and biofunctionalities.
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Affiliation(s)
- Mirja Kaizer Ahmmed
- Department of Food Sciences, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand or (M.K.A.); (S.G.G.); (P.A.)
- Department of Fishing and Post-Harvest Technology, Faculty of Fisheries, Chittagong Veterinary and Animal Sciences University, Chittagong 4225, Bangladesh
| | - Shuva Bhowmik
- Centre for Bioengineering and Nanomedicine, Faculty of Dentistry, Division of Health Sciences, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand;
- Department of Fisheries and Marine Science, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| | - Stephen G. Giteru
- Department of Food Sciences, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand or (M.K.A.); (S.G.G.); (P.A.)
- Alliance Group Limited, Invercargill 9840, New Zealand
| | - Md. Nazmul Hasan Zilani
- Department of Pharmacy, Jashore University of Science and Technology, Jashore 7408, Bangladesh;
| | - Parise Adadi
- Department of Food Sciences, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand or (M.K.A.); (S.G.G.); (P.A.)
| | - Shikder Saiful Islam
- Institute for Marine and Antarctic Studies, University of Tasmania, Launceston 7250, Australia;
- Fisheries and Marine Resource Technology Discipline, Life Science School, Khulna University, Khulna 9208, Bangladesh
| | - Osman N. Kanwugu
- Institute of Chemical Engineering, Ural Federal University, Mira Street 28, 620002 Yekaterinburg, Russia;
| | - Monjurul Haq
- Department of Fisheries and Marine Bioscience, Jashore University of Science and Technology, Jashore 7408, Bangladesh;
| | - Fatema Ahmmed
- Department of Chemistry, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand;
| | | | - Yau Sang Chan
- Department of Obstetrics & Gynaecology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China;
| | - Md. Asadujjaman
- Department of Aquaculture, Faculty of Fisheries and Ocean Sciences, Khulna Agricultural University, Khulna 9100, Bangladesh;
| | - Gabriel Hoi Huen Chan
- Division of Science, Engineering and Health Studies, College of Professional and Continuing Education, The Hong Kong Polytechnic University, Hong Kong, China;
| | - Ryno Naude
- Department of Biochemistry and Microbiology, Nelson Mandela University, Port Elizabeth 6031, South Africa;
| | - Alaa El-Din Ahmed Bekhit
- Department of Food Sciences, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand or (M.K.A.); (S.G.G.); (P.A.)
- Correspondence: (A.E.-D.A.B.); (J.H.W.)
| | - Tzi Bun Ng
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China;
| | - Jack Ho Wong
- School of Health Sciences, Caritas Institute of Higher Education, Hong Kong, China
- Correspondence: (A.E.-D.A.B.); (J.H.W.)
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Liu S, Liu Y, Lu J, Mao J, Lin Z, Xue Q. Genome Wide Identification and Expression Profiling Indicate Expansion of Family I84 Protease Inhibitor via Gene Tandem Duplication and Divergence in Razor Clam Sinonovacula constricta. Front Immunol 2022; 13:907274. [PMID: 35720365 PMCID: PMC9198434 DOI: 10.3389/fimmu.2022.907274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/09/2022] [Indexed: 11/24/2022] Open
Abstract
Family I84 protease inhibitors represent a novel family in the MEROPS peptidase database and are likely unique for molluscan host defense. Two Family I84 members, scSI-1 and scSI-2, were reported from the razor clam Sinonovacula constricta in a previous research. In the present study, 12 additional genes, named scSI-3 to scSI-14, were identified via genome wide sequence analyses. Among them, 10 genes were predicted to have a signal sequence, but one (scSI-7) was not. Besides, one sequence (scSI-14) was likely to encode a prematurely terminated peptide. The predicted mature peptides shared characteristics including 12 conserved cysteine residues, isoelectric points of 4.98 to 6.11, and molecular weights of 7.1 to 9.3 kDa with previously reported family members. Four motifs were characterized in 13 predicted mature peptides (with exception of scSI-14), which shared two to four conserved cysteine residues, are possibly to form two functional domain comprised 6 cysteine residues, respectively. At genomic level, all the 14 razor clam Family I84 genes were organized into 3 exons and 2 introns; 13 of them clustered in 3 regions of 100 kb on 3 separate chromosomes, suggesting tandem duplications of related genes. The promoter region of all the 14 genes was predicted to share some transcription factor binding sites, in particular those responsive to pathological and physiological stimuli, but no shared motifs were identified. Analyses also revealed differences in expression patterns among the genes. One gene in a tandem duplicated gene pairs usually showed a higher expression level than the other whereas non-tandem duplicated genes exhibited a higher degree of correlation in expression level. In addition, 8 of the 14 genes demonstrated higher level of expression in Vibrio tolerant clams than in non-tolerant clams following challenges with Vibrio parahaemolyticus. These results generated important information about the evolution of Family I84 protease inhibitors in S. constricta.
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Affiliation(s)
- Sheng Liu
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ningbo, China.,Zhejiang Key Laboratory of Aquatic Germplasm Resource, Zhejiang Wanli University, Ningbo, China
| | - Youli Liu
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ningbo, China.,Zhejiang Key Laboratory of Aquatic Germplasm Resource, Zhejiang Wanli University, Ningbo, China
| | - Jiali Lu
- Zhejiang Key Laboratory of Aquatic Germplasm Resource, Zhejiang Wanli University, Ningbo, China
| | - Jinxia Mao
- Zhejiang Key Laboratory of Aquatic Germplasm Resource, Zhejiang Wanli University, Ningbo, China
| | - Zhihua Lin
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ningbo, China.,Zhejiang Key Laboratory of Aquatic Germplasm Resource, Zhejiang Wanli University, Ningbo, China
| | - Qinggang Xue
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ningbo, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
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13
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Liang X, Xiong X, Cao Y, Li Z, Chen J, Jiao Y, Deng Y, Du X. Globular C1q domain-containing protein from Pinctada fucata martensii participates in the immune defense process. FISH & SHELLFISH IMMUNOLOGY 2022; 123:521-527. [PMID: 35364260 DOI: 10.1016/j.fsi.2022.02.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/16/2022] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
The globular C1q domain-containing (C1qDC) protein can recognize a variety of ligands, such as pathogen-associated molecular patterns, and plays an important role in the innate immune response. Our previous studies showed that a novel globular C1q domain-containing protein (PmC1qDC-1) is involved in the damage repair process of pearl oyster shells. However, the function of PmC1qDC-1 in pearl oyster innate immunity remains unknown. In the present study, the high-level structural analysis showed that PmC1qDC-1 was a spherical structure composed of 10 strands and was similar to the AiC1qDC-2 of bay scallop (Argopecten irradians). In situ hybridization indicated that PmC1qDC-1 had strong fluorescence signal in gills. Furthermore, the mRNA expression of PmC1qDC-1 was highly induced at 6-48 h in gill after lipopolysaccharide, peptidoglycan and polyinosinic-polycytidylic acid stimulation. Additionally, we obtained the recombinant protein of PmC1qDC-1 (rPmC1qDC-1) and found that rPmC1qDC-1 had antibacterial activity against Gram-negative (i.e., Pseudomonas aeruginosa, Vibrio parahaemolyticus, Escherichia coli, and Aeromonas hydrophila) and Gram-positive (i.e., Staphylococcus aureus and Bacillus subtilis) bacteria. These results indicated that PmC1qDC-1 might play an important role in the immune response against bacteria and viruses. This study provides clues for further studying the immune defense of Pinctada fucata martensii against pathogens and exploring the evolution of the classic pathway of complement system.
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Affiliation(s)
- Xueru Liang
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Xinwei Xiong
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Yanfei Cao
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Zhixin Li
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Jiayi Chen
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Yu Jiao
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, 524088, China
| | - Yuewen Deng
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, 524088, China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, 524088, China
| | - Xiaodong Du
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, 524088, China.
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14
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Witkop EM, Proestou DA, Gomez-Chiarri M. The expanded inhibitor of apoptosis gene family in oysters possesses novel domain architectures and may play diverse roles in apoptosis following immune challenge. BMC Genomics 2022; 23:201. [PMID: 35279090 PMCID: PMC8917759 DOI: 10.1186/s12864-021-08233-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 12/06/2021] [Indexed: 11/23/2022] Open
Abstract
Background Apoptosis plays important roles in a variety of functions, including immunity and response to environmental stress. The Inhibitor of Apoptosis (IAP) gene family of apoptosis regulators is expanded in molluscs, including eastern, Crassostrea virginica, and Pacific, Crassostrea gigas, oysters. The functional importance of IAP expansion in apoptosis and immunity in oysters remains unknown. Results Phylogenetic analysis of IAP genes in 10 molluscs identified lineage specific gene expansion in bivalve species. Greater IAP gene family expansion was observed in C. virginica than C. gigas (69 vs. 40), resulting mainly from tandem duplications. Functional domain analysis of oyster IAP proteins revealed 3 novel Baculoviral IAP Repeat (BIR) domain types and 14 domain architecture types across gene clusters, 4 of which are not present in model organisms. Phylogenetic analysis of bivalve IAPs suggests a complex history of domain loss and gain. Most IAP genes in oysters (76% of C. virginica and 82% of C. gigas), representing all domain architecture types, were expressed in response to immune challenge (Ostreid Herpesvirus OsHV-1, bacterial probionts Phaeobacter inhibens and Bacillus pumilus, several Vibrio spp., pathogenic Aliiroseovarius crassostreae, and protozoan parasite Perkinsus marinus). Patterns of IAP and apoptosis-related differential gene expression differed between the two oyster species, where C. virginica, in general, differentially expressed a unique set of IAP genes in each challenge, while C. gigas differentially expressed an overlapping set of IAP genes across challenges. Apoptosis gene expression patterns clustered mainly by resistance/susceptibility of the oyster host to immune challenge. Weighted Gene Correlation Network Analysis (WGCNA) revealed unique combinations of transcripts for 1 to 12 IAP domain architecture types, including novel types, were significantly co-expressed in response to immune challenge with transcripts in apoptosis-related pathways. Conclusions Unprecedented diversity characterized by novel BIR domains and protein domain architectures was observed in oyster IAPs. Complex patterns of gene expression of novel and conserved IAPs in response to a variety of ecologically-relevant immune challenges, combined with evidence of direct co-expression of IAP genes with apoptosis-related transcripts, suggests IAP expansion facilitates complex and nuanced regulation of apoptosis and other immune responses in oysters. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08233-6.
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Farhat S, Bonnivard E, Pales Espinosa E, Tanguy A, Boutet I, Guiglielmoni N, Flot JF, Allam B. Comparative analysis of the Mercenaria mercenaria genome provides insights into the diversity of transposable elements and immune molecules in bivalve mollusks. BMC Genomics 2022; 23:192. [PMID: 35260071 PMCID: PMC8905726 DOI: 10.1186/s12864-021-08262-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/15/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The hard clam Mercenaria mercenaria is a major marine resource along the Atlantic coasts of North America and has been introduced to other continents for resource restoration or aquaculture activities. Significant mortality events have been reported in the species throughout its native range as a result of diseases (microbial infections, leukemia) and acute environmental stress. In this context, the characterization of the hard clam genome can provide highly needed resources to enable basic (e.g., oncogenesis and cancer transmission, adaptation biology) and applied (clam stock enhancement, genomic selection) sciences. RESULTS Using a combination of long and short-read sequencing technologies, a 1.86 Gb chromosome-level assembly of the clam genome was generated. The assembly was scaffolded into 19 chromosomes, with an N50 of 83 Mb. Genome annotation yielded 34,728 predicted protein-coding genes, markedly more than the few other members of the Venerida sequenced so far, with coding regions representing only 2% of the assembly. Indeed, more than half of the genome is composed of repeated elements, including transposable elements. Major chromosome rearrangements were detected between this assembly and another recent assembly derived from a genetically segregated clam stock. Comparative analysis of the clam genome allowed the identification of a marked diversification in immune-related proteins, particularly extensive tandem duplications and expansions in tumor necrosis factors (TNFs) and C1q domain-containing proteins, some of which were previously shown to play a role in clam interactions with infectious microbes. The study also generated a comparative repertoire highlighting the diversity and, in some instances, the specificity of LTR-retrotransposons elements, particularly Steamer elements in bivalves. CONCLUSIONS The diversity of immune molecules in M. mercenaria may allow this species to cope with varying and complex microbial and environmental landscapes. The repertoire of transposable elements identified in this study, particularly Steamer elements, should be a prime target for the investigation of cancer cell development and transmission among bivalve mollusks.
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Affiliation(s)
- Sarah Farhat
- Marine Animal Disease Laboratory, School of Marine and Atmospheric Sciences, 100 Nicolls Road, Stony Brook University, Stony Brook, NY, 11794-5000, USA
| | - Eric Bonnivard
- Sorbonne Université, CNRS, UMR 7144 AD2M, Station Biologique de Roscoff, Place Georges Teissier, 29688, Roscoff, France
| | - Emmanuelle Pales Espinosa
- Marine Animal Disease Laboratory, School of Marine and Atmospheric Sciences, 100 Nicolls Road, Stony Brook University, Stony Brook, NY, 11794-5000, USA
| | - Arnaud Tanguy
- Sorbonne Université, CNRS, UMR 7144 AD2M, Station Biologique de Roscoff, Place Georges Teissier, 29688, Roscoff, France
| | - Isabelle Boutet
- Sorbonne Université, CNRS, UMR 7144 AD2M, Station Biologique de Roscoff, Place Georges Teissier, 29688, Roscoff, France
| | - Nadège Guiglielmoni
- Université libre de Bruxelles (ULB), Evolutionary Biology & Ecology, Avenue F.D. Roosevelt 50, B-1050, Brussels, Belgium
| | - Jean-François Flot
- Université libre de Bruxelles (ULB), Evolutionary Biology & Ecology, Avenue F.D. Roosevelt 50, B-1050, Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels - (IB)2, B-1050, Brussels, Belgium
| | - Bassem Allam
- Marine Animal Disease Laboratory, School of Marine and Atmospheric Sciences, 100 Nicolls Road, Stony Brook University, Stony Brook, NY, 11794-5000, USA.
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First Insights into the Repertoire of Secretory Lectins in Rotifers. Mar Drugs 2022; 20:md20020130. [PMID: 35200659 PMCID: PMC8878817 DOI: 10.3390/md20020130] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/04/2022] [Accepted: 02/07/2022] [Indexed: 02/06/2023] Open
Abstract
Due to their high biodiversity and adaptation to a mutable and challenging environment, aquatic lophotrochozoan animals are regarded as a virtually unlimited source of bioactive molecules. Among these, lectins, i.e., proteins with remarkable carbohydrate-recognition properties involved in immunity, reproduction, self/nonself recognition and several other biological processes, are particularly attractive targets for biotechnological research. To date, lectin research in the Lophotrochozoa has been restricted to the most widespread phyla, which are the usual targets of comparative immunology studies, such as Mollusca and Annelida. Here we provide the first overview of the repertoire of the secretory lectin-like molecules encoded by the genomes of six target rotifer species: Brachionus calyciflorus, Brachionus plicatilis, Proales similis (class Monogononta), Adineta ricciae, Didymodactylos carnosus and Rotaria sordida (class Bdelloidea). Overall, while rotifer secretory lectins display a high molecular diversity and belong to nine different structural classes, their total number is significantly lower than for other groups of lophotrochozoans, with no evidence of lineage-specific expansion events. Considering the high evolutionary divergence between rotifers and the other major sister phyla, their widespread distribution in aquatic environments and the ease of their collection and rearing in laboratory conditions, these organisms may represent interesting targets for glycobiological studies, which may allow the identification of novel carbohydrate-binding proteins with peculiar biological properties.
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17
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Grinchenko AV, von Kriegsheim A, Shved NA, Egorova AE, Ilyaskina DV, Karp TD, Goncharov NV, Petrova IY, Kumeiko VV. A Novel C1q Domain-Containing Protein Isolated from the Mollusk Modiolus kurilensis Recognizing Glycans Enriched with Acidic Galactans and Mannans. Mar Drugs 2021; 19:668. [PMID: 34940667 PMCID: PMC8706970 DOI: 10.3390/md19120668] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/18/2021] [Accepted: 11/24/2021] [Indexed: 12/12/2022] Open
Abstract
C1q domain-containing (C1qDC) proteins are a group of biopolymers involved in immune response as pattern recognition receptors (PRRs) in a lectin-like manner. A new protein MkC1qDC from the hemolymph plasma of Modiolus kurilensis bivalve mollusk widespread in the Northwest Pacific was purified. The isolation procedure included ammonium sulfate precipitation followed by affinity chromatography on pectin-Sepharose. The full-length MkC1qDC sequence was assembled using de novo mass-spectrometry peptide sequencing complemented with N-terminal Edman's degradation, and included 176 amino acid residues with molecular mass of 19 kDa displaying high homology to bivalve C1qDC proteins. MkC1qDC demonstrated antibacterial properties against Gram-negative and Gram-positive strains. MkC1qDC binds to a number of saccharides in Ca2+-dependent manner which characterized by structural meta-similarity in acidic group enrichment of galactose and mannose derivatives incorporated in diversified molecular species of glycans. Alginate, κ-carrageenan, fucoidan, and pectin were found to be highly effective inhibitors of MkC1qDC activity. Yeast mannan, lipopolysaccharide (LPS), peptidoglycan (PGN) and mucin showed an inhibitory effect at concentrations three orders of magnitude greater than for the most effective saccharides. MkC1qDC localized to the mussel hemal system and interstitial compartment. Intriguingly, MkC1qDC was found to suppress proliferation of human adenocarcinoma HeLa cells in a dose-dependent manner, indicating to the biomedical potential of MkC1qDC protein.
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Affiliation(s)
- Andrei V. Grinchenko
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, 690041 Vladivostok, Russia; (A.V.G.); (N.A.S.); (N.V.G.); (I.Y.P.)
| | - Alex von Kriegsheim
- Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh EH4 2XU, UK;
| | - Nikita A. Shved
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, 690041 Vladivostok, Russia; (A.V.G.); (N.A.S.); (N.V.G.); (I.Y.P.)
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, 690922 Vladivostok, Russia; (A.E.E.); (D.V.I.); (T.D.K.)
| | - Anna E. Egorova
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, 690922 Vladivostok, Russia; (A.E.E.); (D.V.I.); (T.D.K.)
| | - Diana V. Ilyaskina
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, 690922 Vladivostok, Russia; (A.E.E.); (D.V.I.); (T.D.K.)
| | - Tatiana D. Karp
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, 690922 Vladivostok, Russia; (A.E.E.); (D.V.I.); (T.D.K.)
| | - Nikolay V. Goncharov
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, 690041 Vladivostok, Russia; (A.V.G.); (N.A.S.); (N.V.G.); (I.Y.P.)
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, 690922 Vladivostok, Russia; (A.E.E.); (D.V.I.); (T.D.K.)
| | - Irina Y. Petrova
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, 690041 Vladivostok, Russia; (A.V.G.); (N.A.S.); (N.V.G.); (I.Y.P.)
| | - Vadim V. Kumeiko
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, 690041 Vladivostok, Russia; (A.V.G.); (N.A.S.); (N.V.G.); (I.Y.P.)
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, 690922 Vladivostok, Russia; (A.E.E.); (D.V.I.); (T.D.K.)
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18
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Huang JH, Jiao YH, Li L, Li DW, Li HY, Yang WD. Small RNA analysis of Perna viridis after exposure to Prorocentrum lima, a DSP toxins-producing dinoflagellate. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2021; 239:105950. [PMID: 34474269 DOI: 10.1016/j.aquatox.2021.105950] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 06/13/2023]
Abstract
Diarrheic shellfish poisoning toxins (DSP toxins) are a set of the most important phycotoxins produced by some dinoflagellates. Studies have shown that DSP toxins have various toxicities such as genotoxicity, cytotoxicity, and immunotoxicity to bivalve mollusks. However, these toxicities appear decreasing with exposure time and concentration of DSP toxins. The underlying mechanism involved remains unclear. In this study, small RNA sequencing was performed in the digestive gland of the mussel Perna viridis after exposure to DSP toxins-producing dinoflagellate Prorocentrum lima for different time periods. The potential roles of miRNAs in response and detoxification to DSP toxins in the mussel were analyzed. Small RNA sequencing of 12 samples from 72 individuals was conducted by BGISEQ-500. A total of 123 mature miRNAs were identified, including 90 conserved miRNAs and 33 potential novel miRNAs. After exposure to P. lima, multiple important miRNAs displayed some alterations. Further miRNA target prediction revealed some important genes involved in cytoskeleton, apoptosis, complement system and immune stress. qPCR demonstrated that miR-71_5, miR-750_1 and novel_mir4 were significantly up-regulated at 6 h after exposure to P. lima, while miR-100_2 was significantly down-regulated after 96 h of exposure. Accordingly, putative target genes of these differentially expressed miRNAs experienced some changes. After 6 h of DSP toxins exposure, NHLRC2 and C1q-like were significantly down-regulated. After 96 h of DSP toxins exposure, NHLRC2 was significantly up-regulated. It is reasonable to speculate that the mussel P. viridis might respond to DSP toxins through miR-750_1, novel_mir4 and miR-71_5 regulating the expression of relevant target genes involved in apoptosis, cytoskeleton, and immune response, etc. This study might provide new clues to uncover the toxic response of bivalve to DSP toxins and lay a foundation for revealing the roles of miRNAs in the environmental adaptation in shellfish.
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Affiliation(s)
- Jia-Hui Huang
- College of Life Science and Technology, Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, Jinan University, Guangzhou 510632, China
| | - Yu-Hu Jiao
- College of Life Science and Technology, Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, Jinan University, Guangzhou 510632, China
| | - Li Li
- College of Life Science and Technology, Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, Jinan University, Guangzhou 510632, China
| | - Da-Wei Li
- College of Life Science and Technology, Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, Jinan University, Guangzhou 510632, China
| | - Hong-Ye Li
- College of Life Science and Technology, Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, Jinan University, Guangzhou 510632, China
| | - Wei-Dong Yang
- College of Life Science and Technology, Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, Jinan University, Guangzhou 510632, China.
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19
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A P, G M, M T, L B, N F. Characterisation and functional role of a novel C1qDC protein from a colonial ascidian. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 122:104077. [PMID: 33905781 DOI: 10.1016/j.dci.2021.104077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/18/2021] [Accepted: 03/18/2021] [Indexed: 06/12/2023]
Abstract
As an invertebrate, the compound ascidian Botryllus schlosseri faces nonself only with innate immunity. In this species, we already identified the key components of the lectin and alternative complement activation pathways. In the present work, by mining the transcriptome, we identified a single transcript codifying for a protein, member of the C1q-domain-containing protein family, with a signal peptide followed by two globular C1q (gC1q) domains. It shares a similar domain organisation with C1q/TNF-related proteins 4, the only vertebrate protein family with two gC1q domains. Our gC1q domain-containing protein, called BsC1qDC, is actively transcribed by immunocytes. The transcription is modulated during the Botryllus blastogenetic cycle and is upregulated following the injection of Bacillus clausii cells in the circulation. Furthermore, the injection of bsc1qdc iRNA in the vasculature results in decreased transcription of the gene and a significant impairment of phagocytosis and degranulation, suggesting the involvement of this molecule in immune responses.
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Affiliation(s)
- Peronato A
- Department of Biology, University of Padova, Italy
| | - Minervini G
- Department of Biomedical Sciences, University of Padova, Italy
| | - Tabarelli M
- PhD School in Agricultural Science and Biotechnology, University of Udine, Italy
| | - Ballarin L
- Department of Biology, University of Padova, Italy.
| | - Franchi N
- Department of Biology, University of Padova, Italy
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20
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Pan C, Lei Z, Wang S, Wang X, Wei D, Cai X, Luoreng Z, Wang L, Ma Y. Genome-wide identification of cyclin-dependent kinase (CDK) genes affecting adipocyte differentiation in cattle. BMC Genomics 2021; 22:532. [PMID: 34253191 PMCID: PMC8276410 DOI: 10.1186/s12864-021-07653-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 04/27/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Cyclin-dependent kinases (CDKs) are protein kinases regulating important cellular processes such as cell cycle and transcription. Many CDK genes also play a critical role during adipogenic differentiation, but the role of CDK gene family in regulating bovine adipocyte differentiation has not been studied. Therefore, the present study aims to characterize the CDK gene family in bovine and study their expression pattern during adipocyte differentiation. RESULTS We performed a genome-wide analysis and identified a number of CDK genes in several bovine species. The CDK genes were classified into 8 subfamilies through phylogenetic analysis. We found that 25 bovine CDK genes were distributed in 16 different chromosomes. Collinearity analysis revealed that the CDK gene family in Bos taurus is homologous with Bos indicus, Hybrid-Bos taurus, Hybrid Bos indicus, Bos grunniens and Bubalus bubalis. Several CDK genes had higher expression levels in preadipocytes than in differentiated adipocytes, as shown by RNA-seq analysis and qPCR, suggesting a role in the growth of emerging lipid droplets. CONCLUSION In this research, 185 CDK genes were identified and grouped into eight distinct clades in Bovidae, showing extensively homology. Global expression analysis of different bovine tissues and specific expression analysis during adipocytes differentiation revealed CDK4, CDK7, CDK8, CDK9 and CDK14 may be involved in bovine adipocyte differentiation. The results provide a basis for further study to determine the roles of CDK gene family in regulating adipocyte differentiation, which is beneficial for beef quality improvement.
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Affiliation(s)
- Cuili Pan
- School of Agriculture, Ningxia University, Yinchuan, 750021, China
- Key Laboratory of Ruminant Molecular and Cellular Breeding, Ningxia Hui Autonomous Region, Ningxia University, Yinchuan, 750021, China
| | - Zhaoxiong Lei
- School of Agriculture, Ningxia University, Yinchuan, 750021, China
- Key Laboratory of Ruminant Molecular and Cellular Breeding, Ningxia Hui Autonomous Region, Ningxia University, Yinchuan, 750021, China
| | - Shuzhe Wang
- School of Agriculture, Ningxia University, Yinchuan, 750021, China
- Key Laboratory of Ruminant Molecular and Cellular Breeding, Ningxia Hui Autonomous Region, Ningxia University, Yinchuan, 750021, China
| | - Xingping Wang
- School of Agriculture, Ningxia University, Yinchuan, 750021, China
- Key Laboratory of Ruminant Molecular and Cellular Breeding, Ningxia Hui Autonomous Region, Ningxia University, Yinchuan, 750021, China
| | - Dawei Wei
- School of Agriculture, Ningxia University, Yinchuan, 750021, China
- Key Laboratory of Ruminant Molecular and Cellular Breeding, Ningxia Hui Autonomous Region, Ningxia University, Yinchuan, 750021, China
| | - Xiaoyan Cai
- School of Agriculture, Ningxia University, Yinchuan, 750021, China
- Key Laboratory of Ruminant Molecular and Cellular Breeding, Ningxia Hui Autonomous Region, Ningxia University, Yinchuan, 750021, China
| | - Zhuoma Luoreng
- School of Agriculture, Ningxia University, Yinchuan, 750021, China
- Key Laboratory of Ruminant Molecular and Cellular Breeding, Ningxia Hui Autonomous Region, Ningxia University, Yinchuan, 750021, China
| | - Lei Wang
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, Henan, China
| | - Yun Ma
- School of Agriculture, Ningxia University, Yinchuan, 750021, China.
- Key Laboratory of Ruminant Molecular and Cellular Breeding, Ningxia Hui Autonomous Region, Ningxia University, Yinchuan, 750021, China.
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, Henan, China.
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21
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Modak TH, Literman R, Puritz JB, Johnson KM, Roberts EM, Proestou D, Guo X, Gomez-Chiarri M, Schwartz RS. Extensive genome-wide duplications in the eastern oyster ( Crassostrea virginica). Philos Trans R Soc Lond B Biol Sci 2021; 376:20200164. [PMID: 33813893 DOI: 10.1098/rstb.2020.0164] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Genomic structural variation is an important source of genetic and phenotypic diversity, playing a critical role in evolution. The recent availability of a high-quality reference genome for the eastern oyster, Crassostrea virginica, and whole-genome sequence data of samples from across the species range in the USA, provides an opportunity to explore structural variation across the genome of this species. Our analysis shows significantly greater individual-level duplications of regions across the genome than that of most model vertebrate species. Duplications are widespread across all ten chromosomes with variation in frequency per chromosome. The eastern oyster shows a large interindividual variation in duplications as well as particular chromosomal regions with a higher density of duplications. A high percentage of duplications seen in C. virginica lie completely within genes and exons, suggesting the potential for impacts on gene function. These results support the hypothesis that structural changes may play a significant role in standing genetic variation in C. virginica, and potentially have a role in their adaptive and evolutionary success. Altogether, these results suggest that copy number variation plays an important role in the genomic variation of C. virginica. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.
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Affiliation(s)
- Tejashree H Modak
- Department of Biological Sciences, University of Rhode Island, 120 Flagg Road, Kingston, RI 02881, USA
| | - Robert Literman
- Department of Biological Sciences, University of Rhode Island, 120 Flagg Road, Kingston, RI 02881, USA
| | - Jonathan B Puritz
- Department of Biological Sciences, University of Rhode Island, 120 Flagg Road, Kingston, RI 02881, USA
| | - Kevin M Johnson
- Center for Coastal Marine Sciences, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, CA 93407, USA.,Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.,California Sea Grant, University of California San Diego, La Jolla, CA 92093-0232, USA
| | - Erin M Roberts
- Department of Fisheries, Animal and Veterinary Sciences, University of Rhode Island, 120 Flagg Road, Kingston, RI 02881, USA
| | - Dina Proestou
- USDA Agricultural Research Service, National Cold Water Marine Aquaculture Center, 469 CBLS, 120 Flagg Road, Kingston, RI 02881, USA
| | - Ximing Guo
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, 6959 Miller Avenue, Port Norris, NJ 08349, USA
| | - Marta Gomez-Chiarri
- Department of Fisheries, Animal and Veterinary Sciences, University of Rhode Island, 120 Flagg Road, Kingston, RI 02881, USA
| | - Rachel S Schwartz
- Department of Biological Sciences, University of Rhode Island, 120 Flagg Road, Kingston, RI 02881, USA
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22
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Xiong X, Li C, Zheng Z, Du X. Novel globular C1q domain-containing protein (PmC1qDC-1) participates in shell formation and responses to pathogen-associated molecular patterns stimulation in Pinctada fucata martensii. Sci Rep 2021; 11:1105. [PMID: 33441832 PMCID: PMC7806589 DOI: 10.1038/s41598-020-80295-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/18/2020] [Indexed: 12/13/2022] Open
Abstract
The C1q protein, which contains the globular C1q (gC1q) domain, is involved in the innate immune response, and is found abundantly in the shell, and it participates in the shell formation. In this study, a novel gC1q domain-containing gene was identified from Pinctada fucata martensii (P. f. martensii) and designated as PmC1qDC-1. The full-length sequence of PmC1qDC-1 was 902 bp with a 534 bp open reading frame (ORF), encoding a polypeptide of 177 amino acids. Quantitative real-time PCR (qRT-PCR) result showed that PmC1qDC-1 was widely expressed in all tested tissues, including shell formation-associated tissue and immune-related tissue. PmC1qDC-1 expression was significantly high in the blastula and gastrula and especially among the juvenile stage, which is the most important stage of dissoconch shell formation. PmC1qDC-1 expression was located in the outer epithelial cells of mantle pallial and mantle edge and irregular crystal tablets were observed in the nacre upon knockdown of PmC1qDC-1 expression at mantle pallial. Moreover, the recombined protein PmC1qDC-1 increased the rate of calcium carbonate precipitation. Besides, PmC1qDC-1 expression was significantly up-regulated in the mantle pallial at 6 h and was significantly up-regulated in the mantle edge at 12 h and 24 h after shell notching. The expression level of PmC1qDC-1 in mantle edge was significantly up-regulated at 48 h after LPS stimulation and was significantly up-regulated at 12 h, 24 h and 48 h after poly I:C stimulation. Moreover, PmC1qDC-1 expression was significantly up-regulated in hemocytes at 6 h after lipopolysaccharide (LPS) and poly I:C challenge. These findings suggest that PmC1qDC-1 plays a crucial role both in the shell formation and the innate immune response in pearl oysters, providing new clues for understanding the shell formation and defense mechanism in mollusk.
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Affiliation(s)
- Xinwei Xiong
- Fishery College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Chuyi Li
- Fishery College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Zhe Zheng
- Fishery College, Guangdong Ocean University, Zhanjiang, 524088, China.
- Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, 524088, China.
- Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, 524088, China.
- Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Zhanjiang, 524088, China.
| | - Xiaodong Du
- Fishery College, Guangdong Ocean University, Zhanjiang, 524088, China.
- Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, 524088, China.
- Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, 524088, China.
- Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Zhanjiang, 524088, China.
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