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Pattern recognition receptors in grass carp Ctenopharyngodon idella: II. Organization and expression analysis of NOD-like receptors.
Developmental & Comparative Immunology ( IF 2.9 ) Pub Date : 2020-05-11 , DOI: 10.1016/j.dci.2020.103734 Tianbing Xu 1 , Zhiwei Liao 2 , Jianguo Su 1
Developmental & Comparative Immunology ( IF 2.9 ) Pub Date : 2020-05-11 , DOI: 10.1016/j.dci.2020.103734 Tianbing Xu 1 , Zhiwei Liao 2 , Jianguo Su 1
Affiliation
Nucleotide-binding domain and leucine-rich repeat containing receptors (NLRs) are a pivotal intracellular pattern recognition receptor family. However, studies on NLR genes in important economic fish grass carp (Ctenopharyngodon idella) are sporadic. The accumulations of genomic resource and transcriptomic sequences make it feasible to conduct a systematic analysis of these genes. In this study, we systematically conducted the genome-wide study of C. idella NLR genes and characterized their phylogeny, gene structure, conserved domain, evolutionary mechanism, and expression profiles post viral or bacterial challenge. A total of 65 NLR genes were identified and clustered into five subfamilies based on structural and phylogenetic features, including eight NODs (NLR-A), five NLRP-like receptors (NLR-B), forty-seven teleost-specific NLRs (NLR-C), two members with a B30.2 domain at the C-terminal (NLR-B30.2), and three additional NLRs (other NLRs). Gene structure analysis showed that NLRs were significantly different, with exon numbers from 3 to 31. Conserved domain analysis showed that most members of C. idella NLRs had additional domains besides the typical NLR domains. Gene duplication analysis indicated that the evolution of the NLR gene family was mainly related to segment duplication. mRNA expression analysis indicated that many members were differently expressed in multiple tissues post grass carp reovirus (GCRV) or Aeromonas hydrophila infection. The expression was particularly enhanced in liver post GCRV infection, and obviously lower post A. hydrophila infection than that post GCRV infection in spleen. These results provide systematic basic data for further functional studies of NLR, and insight into the immune responses of piscine fish NLRs to pathogen infections.
中文翻译:
草鱼 Ctenopharyngodon idella 的模式识别受体:II. NOD样受体的组织和表达分析。
核苷酸结合域和富含亮氨酸重复序列的受体 (NLR) 是关键的细胞内模式识别受体家族。然而,对重要经济鱼类草鱼 (Ctenopharyngodon idella) NLR 基因的研究是零星的。基因组资源和转录组序列的积累使得对这些基因进行系统分析成为可能。在这项研究中,我们系统地对 C. idella NLR 基因进行了全基因组研究,并表征了它们的系统发育、基因结构、保守域、进化机制和病毒或细菌攻击后的表达谱。共鉴定出 65 个 NLR 基因,并根据结构和系统发育特征分为 5 个亚家族,包括 8 个 NOD(NLR-A)、5 个 NLRP 样受体(NLR-B)、47 个硬骨鱼特异性 NLR(NLR- C),两个成员在 C 端具有 B30.2 域 (NLR-B30.2),以及三个额外的 NLR(其他 NLR)。基因结构分析表明,NLRs 存在显着差异,外显子数从 3 到 31。保守域分析表明,C. idella NLRs 的大多数成员除了典型的 NLR 域外,还有其他域。基因重复分析表明,NLR基因家族的进化主要与片段重复有关。mRNA 表达分析表明,许多成员在草鱼呼肠孤病毒 (GCRV) 或嗜水气单胞菌感染后的多个组织中表达不同。GCRV感染后肝脏中的表达尤为增强,而嗜水嗜水菌感染后脾脏中的表达明显低于GCRV感染后的表达。
更新日期:2020-05-11
中文翻译:
草鱼 Ctenopharyngodon idella 的模式识别受体:II. NOD样受体的组织和表达分析。
核苷酸结合域和富含亮氨酸重复序列的受体 (NLR) 是关键的细胞内模式识别受体家族。然而,对重要经济鱼类草鱼 (Ctenopharyngodon idella) NLR 基因的研究是零星的。基因组资源和转录组序列的积累使得对这些基因进行系统分析成为可能。在这项研究中,我们系统地对 C. idella NLR 基因进行了全基因组研究,并表征了它们的系统发育、基因结构、保守域、进化机制和病毒或细菌攻击后的表达谱。共鉴定出 65 个 NLR 基因,并根据结构和系统发育特征分为 5 个亚家族,包括 8 个 NOD(NLR-A)、5 个 NLRP 样受体(NLR-B)、47 个硬骨鱼特异性 NLR(NLR- C),两个成员在 C 端具有 B30.2 域 (NLR-B30.2),以及三个额外的 NLR(其他 NLR)。基因结构分析表明,NLRs 存在显着差异,外显子数从 3 到 31。保守域分析表明,C. idella NLRs 的大多数成员除了典型的 NLR 域外,还有其他域。基因重复分析表明,NLR基因家族的进化主要与片段重复有关。mRNA 表达分析表明,许多成员在草鱼呼肠孤病毒 (GCRV) 或嗜水气单胞菌感染后的多个组织中表达不同。GCRV感染后肝脏中的表达尤为增强,而嗜水嗜水菌感染后脾脏中的表达明显低于GCRV感染后的表达。