Biswas Gouranga, Kinoshita Shunsuke, Kono Tomoya, Hikima Jun-ichi, Sakai Masahiro
Interdisciplinary Graduate School of Agriculture and Engineering, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki 889-2192, Japan.
Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki 889-2192, Japan.
Mar Genomics. 2015 Aug;22:25-36. doi: 10.1016/j.margen.2015.03.003. Epub 2015 Mar 17.
Tumor necrosis factor (TNF) and its superfamily (TNFSF) members are important inflammatory cytokines. Although fish have fourteen TNFSF genes, their genomic location and existence are yet to be described and confirmed in the Japanese pufferfish (Fugu) (Takifugu rubripes). Therefore, we conducted in silico identification, synteny analysis of TNFSF genes from Fugu with that of zebrafish and human TNFSF loci and their expression analysis in various tissues. We identified ten novel TNFSF genes, viz. TNFSF5 (CD40L), TNFSF6 (FasL), three TNFSF10 (TRAIL) (-1, 2 and 3), TNFSF11 (RANKlg), TNFSF12 (TWEAK), two TNFSF13B (BAFF) (1 and 2) and TNFSF14 (LIGHT) belonging to seven TNFSFs in Fugu. Several features such as existence of TNF family signature, conservation of genes in TNF loci with human and zebrafish chromosomes and phylogenetic clustering with other teleost TNFSF orthologs confirmed their identity. Fugu TNFSF genes were constitutively expressed in all eight different tissues with most of them expressed highly in liver. Fugu TNFSF10 gene has three homologs present on chromosomes 10 (TNFSF10-1), 8 (TNFSF10-2) and 2 (TNFSF10-3). Moreover, a phylogenetic analysis containing all available vertebrate (mammals, birds, reptiles, amphibians and fish) TNFSF10 orthologs showed that Fugu TNFSF10-1 and 10-3 are present in all vertebrates, whereas TNFSF10-2 was not related to any mammalian and avian orthologs. Viral double-stranded RNA mimic poly (I:C) caused an elevated expression of three Fugu TNFSF10 genes in head kidney cells at 4h indicating probable role of these genes to induce apoptosis in virus-infected cells. In conclusion, Fugu possesses genes belonging to nine TNFSFs including the newly identified seven and previously reported two, TNFSF New (TNF-N) and TNFSF2 (TNF-α). Our findings would add up information to TNFSF evolution among vertebrates.
肿瘤坏死因子（TNF）及其超家族（TNFSF）成员是重要的炎性细胞因子。尽管鱼类有14个TNFSF基因，但在日本河豚（Fugu）（红鳍东方鲀）中，它们的基因组定位和存在情况尚未得到描述和证实。因此，我们进行了电子鉴定，将河豚的TNFSF基因与斑马鱼和人类TNFSF基因座进行共线性分析，并分析了它们在各种组织中的表达情况。我们鉴定出10个新的TNFSF基因，即TNFSF5（CD40L）、TNFSF6（FasL）、3个TNFSF10（TRAIL）（-1、2和3）、TNFSF11（RANKlg）、TNFSF12（TWEAK）、2个TNFSF13B（BAFF）（1和2）以及TNFSF14（LIGHT），它们属于河豚中的7个TNFSF家族。TNF家族特征的存在、与人类和斑马鱼染色体上TNF基因座的基因保守性以及与其他硬骨鱼TNFSF直系同源基因的系统发育聚类等几个特征证实了它们的身份。河豚TNFSF基因在所有8种不同组织中组成性表达，其中大多数在肝脏中高表达。河豚TNFSF10基因有3个同源基因，分别位于第10号染色体（TNFSF10-1）、第8号染色体（TNFSF10-2）和第2号染色体（TNFSF10-3）上。此外，一项包含所有可用脊椎动物（哺乳动物、鸟类、爬行动物、两栖动物和鱼类）TNFSF10直系同源基因的系统发育分析表明，河豚TNFSF10-1和10-3存在于所有脊椎动物中，而TNFSF10-2与任何哺乳动物和鸟类的直系同源基因均无关联。病毒双链RNA模拟物聚肌苷酸:聚胞苷酸（poly (I:C)）在4小时时导致河豚头部肾细胞中3个TNFSF10基因的表达升高，表明这些基因可能在病毒感染细胞中诱导凋亡。总之，河豚拥有属于9个TNFSF家族的基因，包括新鉴定出的7个以及先前报道的2个，即TNFSF New（TNF-N）和TNFSF2（TNF-α）。我们的研究结果将为脊椎动物TNFSF的进化增添信息。
