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Shi X, Zhang R, Liu Z, Zhao G, Guo J, Mao X, Fan B. Alternative Splicing Reveals Acute Stress Response of Litopenaeus vannamei at High Alkalinity. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024; 26:103-115. [PMID: 38206418 DOI: 10.1007/s10126-023-10281-w] [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: 11/06/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024]
Abstract
Alkalinity is regarded as one of the primary stressors for aquatic animals in saline-alkaline water. Alternative splicing (AS) can significantly increase the diversity of transcripts and play key roles in stress response; however, the studies on AS under alkalinity stress of crustaceans are still limited. In the present study, we devoted ourselves to the study of AS under acute alkalinity stress at control (50 mg/L) and treatment groups (350 mg/L) by RNA-seq in pacific white shrimp (Litopenaeus vannamei). We identified a total of 10,556 AS events from 4865 genes and 619 differential AS (DAS) events from 519 DAS genes in pacific white shrimp. Functional annotation showed that the DAS genes primarily involved in spliceosome. Five splicing factors (SFs), U2AF1, PUF60, CHERP, SR140 and SRSF2 were significantly up-regulated and promoted AS. Furthermore, alkalinity activated the Leukocyte transendothelial migration, mTOR signaling pathway and AMPK signaling pathway, which regulated MAPK1, EIF3B and IGFP-RP1 associated with these pathways. We also studied three SFs (HSFP1, SRSF2 and NHE-RF1), which underwent AS to form different transcript isoforms. The above results demonstrated that AS was a regulatory mechanism in pacific white shrimp in response to acute alkalinity stress. SFs played vital roles in AS of pacific white shrimp, such as HSFP1, SRSF2 and NHE-RF1. DAS genes were significantly modified in immunity of pacific white shrimp to cope with alkalinity stress. This is the first study on the response of AS to acute alkalinity stress, which provided scientific basis for AS mechanism of crustaceans response to alkalinity stress.
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Affiliation(s)
- Xiang Shi
- College of Animal Science and Technology, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Gansu Province, Lanzhou, 730070, China
| | - Ruiqi Zhang
- College of Animal Science and Technology, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Gansu Province, Lanzhou, 730070, China.
| | - Zhe Liu
- College of Animal Science and Technology, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Gansu Province, Lanzhou, 730070, China
| | - Guiyan Zhao
- College of Animal Science and Technology, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Gansu Province, Lanzhou, 730070, China
| | - Jintao Guo
- College of Animal Science and Technology, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Gansu Province, Lanzhou, 730070, China
| | - Xue Mao
- College of Animal Science and Technology, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Gansu Province, Lanzhou, 730070, China
| | - Baoyi Fan
- College of Animal Science and Technology, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Gansu Province, Lanzhou, 730070, China
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Saha B, McNinch CM, Lu S, Ho MCW, De Carvalho SS, Barillas-Mury C. In-depth transcriptomic analysis of Anopheles gambiae hemocytes uncovers novel genes and the oenocytoid developmental lineage. BMC Genomics 2024; 25:80. [PMID: 38243165 PMCID: PMC10799387 DOI: 10.1186/s12864-024-09986-6] [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: 09/28/2023] [Accepted: 01/07/2024] [Indexed: 01/21/2024] Open
Abstract
BACKGROUND Hemocytes are immune cells that patrol the mosquito hemocoel and mediate critical cellular defense responses against pathogens. However, despite their importance, a comprehensive transcriptome of these cells was lacking because they constitute a very small fraction of the total cells in the insect, limiting the study of hemocyte differentiation and immune function. RESULTS In this study, an in-depth hemocyte transcriptome was built by extensive bulk RNA sequencing and assembly of hemocyte RNAs from adult A. gambiae female mosquitoes, based on approximately 2.4 billion short Illumina and about 9.4 million long PacBio high-quality reads that mapped to the A. gambiae PEST genome (P4.14 version). A total of 34,939 transcripts were annotated including 4,020 transcripts from novel genes and 20,008 novel isoforms that result from extensive differential splicing of transcripts from previously annotated genes. Most hemocyte transcripts identified (89.8%) are protein-coding while 10.2% are non-coding RNAs. The number of transcripts identified in the novel hemocyte transcriptome is twice the number in the current annotation of the A. gambiae genome (P4.14 version). Furthermore, we were able to refine the analysis of a previously published single-cell transcriptome (scRNAseq) data set by using the novel hemocyte transcriptome as a reference to re-define the hemocyte clusters and determine the path of hemocyte differentiation. Unsupervised pseudo-temporal ordering using the Tools for Single Cell Analysis software uncovered a novel putative prohemocyte precursor cell type that gives rise to prohemocytes. Pseudo-temporal ordering with the Monocle 3 software, which analyses changes in gene expression during dynamic biological processes, determined that oenocytoids derive from prohemocytes, a cell population that also gives rise to the granulocyte lineage. CONCLUSION A high number of mRNA splice variants are expressed in hemocytes, and they may account for the plasticity required to mount efficient responses to many different pathogens. This study highlights the importance of a comprehensive set of reference transcripts to perform robust single-cell transcriptomic data analysis of cells present in low abundance. The detailed annotation of the hemocyte transcriptome will uncover new facets of hemocyte development and function in adult dipterans and is a valuable community resource for future studies on mosquito cellular immunity.
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Affiliation(s)
- Banhisikha Saha
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, USA
| | - Colton M McNinch
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health, 20892, Bethesda, MD, USA
| | - Stephen Lu
- Vector Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Margaret C W Ho
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health, 20892, Bethesda, MD, USA
| | - Stephanie Serafim De Carvalho
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, USA
| | - Carolina Barillas-Mury
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, USA.
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Zhao S, Hu Q, Jiang H, Zhao Y, Wang Y, Feng C, Li X. Multi-omics analysis of oxidative stress and apoptosis in hepatopancreas cells induced by Polyascus gregaria parasitizing the Eriocheir sinensis. FISH & SHELLFISH IMMUNOLOGY 2023; 143:109180. [PMID: 37863124 DOI: 10.1016/j.fsi.2023.109180] [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: 08/11/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 10/22/2023]
Abstract
Polyascus gregaria, a parasitic barnacle, poses a significant threat to Eriocheir sinensis farms by inhibiting crab growth. However, the molecular and pathological mechanisms behind P. gregaria infection in the hepatopancreas of E. sinensis remain unclear. In this study, we investigated the impact and underlying mechanisms of P. gregaria infection on E. sinensis through analyzing the infected hepatopancreatic tissues by tandem mass tag technology and RNA-Seq high-throughput sequencing. Among the identified 10,693 differentially expressed genes, 294 genes were significantly altered following P. gregaria infection, including 92 upregulated and 202 downregulated genes. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses further revealed the involvement of these genes in oxidative decomposition, lipid metabolism, inflammation, and hepatopancreas metabolism. Meanwhile, the identified 253 differentially expressed proteins, including 143 upregulated and 110 downregulated proteins, are mainly related to cellular and metabolic processes, catalytic activity, and cell components. The pathway analysis indicated their enrichment in glycolysis/gluconeogenesis, oxidative phosphorylation, endoplasmic reticulum protein processing, and actin cytoskeleton regulation. The involvement of these differentially expressed genes and proteins in the peroxisome proliferator-activated receptors pathway during host immune responses against P. gregaria infection has been highlighted. Furthermore, pathological examinations and biochemical indicators jointly demonstrated the hepatopancreatic damage and increased oxidative stress and apoptosis in the infected E. sinensis. Collectively, our study provides crucial insights into the mechanisms underlying the E. sinensis-P. gregaria interactions, and may contribute to the development of novel strategies for parasite control and reducing economic losses in aquaculture.
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Affiliation(s)
- Shiwei Zhao
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Qingbiao Hu
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Hongbo Jiang
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yingying Zhao
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yanping Wang
- Linong Testing (Binzhou) Co., Ltd., Binzhou Bohai Advanced Technology Research Institute, Binzhou, 256600, China
| | - Chengcheng Feng
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China.
| | - Xiaodong Li
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China.
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Xu Y, Yang Y, Zheng J, Cui Z. Alternative splicing derived invertebrate variable lymphocyte receptor displays diversity and specificity in immune system of crab Eriocheir sinensis. Front Immunol 2023; 13:1105318. [PMID: 36999166 PMCID: PMC10045472 DOI: 10.3389/fimmu.2022.1105318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 12/22/2022] [Indexed: 03/16/2023] Open
Abstract
Variable lymphocyte receptors (VLRs) play vital roles in adaptive immune system of agnathan vertebrate. In the present study, we first discover a novel VLR gene, VLR2, from an invertebrate, the Chinese mitten crab, Eriocheir sinensis. VLR2 has ten different isoforms formed via alternative splicing, which is different from that in agnathan vertebrate with the assembly of LRR modules. The longest isoform, VLR2-L, responds to Gram-positive bacteria Staphylococcus aureus challenge specifically, while shows no response to Gram-negative bacteria Vibrio parahaemolyticus challenge, confirmed by recombinant expression and bacterial binding experiments. Interestingly, VLR2s with short LRRs regions (VLR2-S8 and VLR2-S9) tend to bind to Gram-negative bacteria rather than Gram-positive bacteria. Antibacterial activity assay proves six isoforms of VLR2 have pluralistic antibacterial effects on bacteria which were never reported in invertebrate. These results suggest that the diversity and specificity of VLR2 resulted from alternative splicing and the length of the LRRs region. This pathogen-binding receptor diversity will lay the foundation for the study of immune priming. Furthermore, studying the immune function of VLR2 will provide a new insight into the disease control strategy of crustacean culture.
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Affiliation(s)
- Yuanfeng Xu
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Yanan Yang
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Jinbin Zheng
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Zhaoxia Cui
- School of Marine Sciences, Ningbo University, Ningbo, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- *Correspondence: Zhaoxia Cui,
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Li W, Wang Q. Recent progress in the research of exosomes and Dscam regulated crab antiviral immunity. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 116:103925. [PMID: 33217412 DOI: 10.1016/j.dci.2020.103925] [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: 08/14/2020] [Revised: 11/01/2020] [Accepted: 11/09/2020] [Indexed: 06/11/2023]
Abstract
Crustaceans, including crab and shrimp, generally lack lymphocytes or adaptive immunity, and they rely solely on innate immunity for pathogen defense. The white spot syndrome virus (WSSV) causes the most prevalent viral disease in penaeid shrimps, which are widely cultured species in coastal waters worldwide. Numerous studies have elucidated the role of the immune system in protecting shrimps from WSSV infection for the development of safe and effective defensive strategies against WSSV. Although WSSV has a wide host range, it appears to exhibit high pathogenicity and virulence in only penaeid shrimps. Crabs are interesting models for studying immune responses after WSSV infection. Therefore, we reviewed recent information on the innate immune responses of crabs to WSSV and mainly focused on the antiviral functions of exosome-mediated apoptosis and alternatively spliced Down syndrome cell adhesion molecule. Our review may provide novel insights into antiviral management for crustaceans, especially penaeid shrimps.
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Affiliation(s)
- Weiwei Li
- Laboratory of Invertebrate Immunological Defense and Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Qun Wang
- Laboratory of Invertebrate Immunological Defense and Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China.
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Low CF, Chong CM. Peculiarities of innate immune memory in crustaceans. FISH & SHELLFISH IMMUNOLOGY 2020; 104:605-612. [PMID: 32619624 DOI: 10.1016/j.fsi.2020.06.047] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/31/2020] [Accepted: 06/23/2020] [Indexed: 06/11/2023]
Abstract
Classical characteristic of the innate immune system is the lack of ability to build up immunological memory, contrast to the adaptive immune system that is capable of "remembering" antigens, and rapidly mount a greater magnitude of immune response upon subsequent exposure to the same antigens. Peculiarly, immunological memory of innate immunity is evidenced in invertebrates. At least three different memory phenomena have been described, namely sustained unique response, recalled response, and immune shift. Studies attended to decipher the mechanistic biology of the innate immune memory reveals the role of epigenetics, which modulates the response of immune memory, and the heritability of immune memory to subsequent generations. A parthenogenetic Artemia model demonstrated successful transgenerational epigenetic inheritance of resistance trait against Vibrio campbellii. Following, the role of invertebrate hemocytes and Down syndrome cell adhesion molecule (Dscam) in innate immune memory is reviewed. While there is no vertebrate antibody homolog found in invertebrates, Dscam was found to resemble the functionality of vertebrate antibody. Insight of Dscam as immune factor was illustrated further in the current review.
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Affiliation(s)
- Chen Fei Low
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia.
| | - Chou Min Chong
- Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
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Ng TH, Kurtz J. Dscam in immunity: A question of diversity in insects and crustaceans. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 105:103539. [PMID: 31734281 DOI: 10.1016/j.dci.2019.103539] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 11/07/2019] [Accepted: 11/09/2019] [Indexed: 06/10/2023]
Abstract
In insects and crustaceans, thousands of Down syndrome cell adhesion molecules (Dscam) can be generated by alternative splicing of variable exons from a single-locus gene, Dscam-hv. This extraordinarily versatile gene (38,016 protein isoforms produced in Drosophila) was first proposed to be involved in exon guidance and subsequently implicated in immunity as a hypervariable immune molecule. Almost 20 y after discovery of Dscam-hv, there have been many studies in insects and crustaceans regarding roles of Dscam in immunity, with many similarities and concurrently, many differences. Here, we review the current status of Dscam-hv, presented as a comparison of similarities and differences in insects and crustaceans and discuss hypotheses of Dscam functions in immunity.
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Affiliation(s)
- Tze Hann Ng
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, 48149, Münster, Germany
| | - Joachim Kurtz
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, 48149, Münster, Germany.
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Xu B, Shi Y, Wu Y, Meng Y, Jin Y. Role of RNA secondary structures in regulating Dscam alternative splicing. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194381. [DOI: 10.1016/j.bbagrm.2019.04.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/21/2019] [Accepted: 04/22/2019] [Indexed: 12/19/2022]
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