Genome-Wide Identification and Expression Analysis of Potential Antiviral Tripartite Motif Proteins (TRIMs) in Grass Carp (Ctenopharyngodon idella)

Qin, Beibei; Xiao, Tiaoyi; Ding, Chunhua; Deng, Yadong; Lv, Zhao; Su, Jianming

doi:10.3390/biology10121252

Cited by 9 publications

(7 citation statements)

References 76 publications

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“…Teleost fish had three separate expansions of B30.2/PRY-SPRY TRIM genes, with some specific to teleost fish as they are not found in amphibians, birds, or mammals. Zebrafish have 208 TRIM genes ( Danio rerio ), pufferfish have 67 ( Tetraodon nigroviridis ) ( 39 ), and grass carp ( Ctenopharyngodon idella ) have 42 TRIM genes ( 115 ). The differences in TRIM gene repertoire numbers in fish are partly due to the whole genome duplication events ( 116 ).…”

Section: Discussionmentioning

confidence: 99%

Evolution and expression of the duck TRIM gene repertoire

2023

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Tripartite motif (TRIM) proteins are involved in development, innate immunity, and viral restriction. TRIM gene repertoires vary between species, likely due to diversification caused by selective pressures from pathogens; however, this has not been explored in birds. We mined a de novo assembled transcriptome for the TRIM gene repertoire of the domestic mallard duck (Anas platyrhynchos), a reservoir host of influenza A viruses. We found 57 TRIM genes in the duck, which represent all 12 subfamilies based on their C-terminal domains. Members of the C-IV subfamily with C-terminal PRY-SPRY domains are known to augment immune responses in mammals. We compared C-IV TRIM proteins between reptiles, birds, and mammals and show that many C-IV subfamily members have arisen independently in these lineages. A comparison of the MHC-linked C-IV TRIM genes reveals expansions in birds and reptiles. The TRIM25 locus with related innate receptor modifiers is adjacent to the MHC in reptile and marsupial genomes, suggesting the ancestral organization. Within the avian lineage, both the MHC and TRIM25 loci have undergone significant TRIM gene reorganizations and divergence, both hallmarks of pathogen-driven selection. To assess the expression of TRIM genes, we aligned RNA-seq reads from duck tissues. C-IV TRIMs had high relative expression in immune relevant sites such as the lung, spleen, kidney, and intestine, and low expression in immune privileged sites such as in the brain or gonads. Gene loss and gain in the evolution of the TRIM repertoire in birds suggests candidate immune genes and potential targets of viral subversion.

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Section: Discussionmentioning

confidence: 99%

Evolution and expression of the duck TRIM gene repertoire

2023

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“…The MADS-box family HMM model file SRF-TF (PF00319) was downloaded from the Pfam database [ 57 ]. The candidate MADS-box Type II genes were aligned to HMM file by hmmsearch with default parameters to filter out the candidates without the MADS-box domain [ 58 ]. The retained candidate genes were analyzed in NCBI-CDD online databases to verify the existence of MADS domain [ 59 ].…”

Section: Materials and Methodsmentioning

confidence: 99%

Genomic and Transcriptomic Insights into the Evolution and Divergence of MIKC-Type MADS-Box Genes in Carica papaya

Dai,

Wang,

Zeng

et al. 2023

IJMS

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MIKC-type MADS-box genes, also known as type II genes, play a crucial role in regulating the formation of floral organs and reproductive development in plants. However, the genome-wide identification and characterization of type II genes as well as a transcriptomic survey of their potential roles in Carica papaya remain unresolved. Here, we identified and characterized 24 type II genes in the C. papaya genome, and investigated their evolutional scenario and potential roles with a widespread expression profile. The type II genes were divided into thirteen subclades, and gene loss events likely occurred in papaya, as evidenced by the contracted member size of most subclades. Gene duplication mainly contributed to MIKC-type gene formation in papaya, and the duplicated gene pairs displayed prevalent expression divergence, implying the evolutionary significance of gene duplication in shaping the diversity of type II genes in papaya. A large-scale transcriptome analysis of 152 samples indicated that different subclasses of these genes showed distinct expression patterns in various tissues, biotic stress response, and abiotic stress response, reflecting their divergent functions. The hub-network of male and female flowers and qRT-PCR suggested that TT16-3 and AGL8 participated in male flower development and seed germination. Overall, this study provides valuable insights into the evolution and functions of MIKC-type genes in C. papaya.

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“…Recently, among teleost fish, TRIM21 and TRIM39 orthologs have been identified from Orange‐spotted Grouper Epinephelus coioides , and overexpression of TRIM21 and TRIM39 has been demonstrated to inhibit Singapore grouper iridovirus (SGIV) and red‐spotted grouper nervous necrosis virus (RGNNV) in vitro, suggesting that they play a role in fish antiviral immunity (Wang et al 2016; Zheng et al 2022). In silico analysis of the genome and transcriptome of Grass Carp Ctenopharyngodon idella has predicted TRIM genes, including TRIM39 ‐like genes (Qin et al 2021).…”

Section: Introductionmentioning

confidence: 99%

Characterization of two tripartite motif‐containing genes from Asian Seabass Lates calcarifer and their expression in response to virus infection and microbial molecular motifs

Sathyan

Premraj²,

Puthiyedathu

2023

J Aqua Anim Hlth

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The tripartite motif‐containing gene (TRIM) is an E3 ubiquitin ligase exhibiting antiviral activity by targeting the viral proteins via proteasome mediated ubiquitination. In the present study, we identified and cloned two TRIM gene homologues from Asian seabass (Lates calcarifer), LcTRIM21 and LcTRIM39, each encoding 547 amino acid proteins. The deduced LcTRIM21 protein has a theoretical pI of 6.32 and a predicted molecular mass of 62.11 kDa. LcTRIM39 is predicted to have a pI of 5.57 and a molecular mass of 62.11 kDa. In silico protein localisation results predict that LcTRIM21 and LcTRIM39 homologues were localised in the cytoplasm. Structurally, both the proteins contain an N‐terminal RING zinc‐finger domain, B‐box domain, coiled‐coil domain and C‐terminal PRY/SPRY domain. LcTRIM21 and LcTRIM39 were constitutively expressed in all the tissues and organs examined. LcTRIM21 and LcTRIM39 mRNA expression was significantly upregulated upon challenge with immunostimulants like poly(I:C) challenge, glucan Zymosan A and red‐spotted grouper nervous necrosis virus (RGNNV), which suggests the role of LcTRIM21 and LcTRIM39 in antiviral response against fish viruses. The antiviral role of TRIM homologues can be explored in developing antivirals and strategies to control diseases like Viral nervous necrosis (VNN) caused by fish viruses like RGNNV that cause economic loss to the aquaculture sector.

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Genome-Wide Identification and Expression Analysis of Potential Antiviral Tripartite Motif Proteins (TRIMs) in Grass Carp (Ctenopharyngodon idella)

Cited by 9 publications

References 76 publications

Evolution and expression of the duck TRIM gene repertoire

Evolution and expression of the duck TRIM gene repertoire

Genomic and Transcriptomic Insights into the Evolution and Divergence of MIKC-Type MADS-Box Genes in Carica papaya

Characterization of two tripartite motif‐containing genes from Asian Seabass Lates calcarifer and their expression in response to virus infection and microbial molecular motifs

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