Scottish Fish Immunology Research Centre, University of Aberdeen, UK.
BMC Genomics. 2010 Dec 9;11:697. doi: 10.1186/1471-2164-11-697.
Several novel immunoglobulin-like transcripts (NILTs) which have previously been identified in the salmonid species rainbow trout (Oncorhynchus mykiss) contain either one or two extracellular Ig domains of the V-type. NILTs also possess either an immunoreceptor tyrosine-based activating motif (ITAM) or immunoreceptor tyrosine-based inhibitory motifs (ITIMs) in the cytoplasmic region resulting in different signalling abilities. Here we report for the first time the genomic organisation and structure of the multigene family of NILTs in Atlantic salmon (Salmo salar) using a BAC sequencing approach.
We have identified six novel Atlantic salmon NILT genes (Ssa-NILT1-6), two pseudogenes (Ssa-NILTp1 and Ssa-NILTp2) and seven genes encoding putative transposable elements in one BAC covering more than 200 kbp. Ssa-NILT1, 2, 4, 5 and 6 contain one Ig domain, all having a CX₃C motif, whereas Ssa-NILT3 contains two Ig domains, having a CX₆C motif in Ig1 and a CX₇C motif in Ig2. Atlantic salmon NILTs possess several ITIMs in the cytoplasmic region and the ITIM-bearing exons are in phase 0. A comparison of identity between the amino acid sequences of the CX₃C Ig domains from NILTs varies from 77% to 96%. Ssa-NILT1, 2, 3 and 4 were all confirmed to be expressed either by their presence in EST databases (Ssa-NILT1) or RT-PCR (Ssa-NILT2, 3, and 4) using cDNA as template. A survey of the repertoire of putative NILT genes in a single individual revealed three novel genes (Ssa-NILT7-9) represented by the Ig domain, which together with Ig domains from Ssa-NILT1-6 could be divided into different groups based on specific motifs.
This report reveals a tightly clustered, multigene NILT family in Atlantic salmon. By screening a highly redundant Atlantic salmon BAC library we have identified and characterised the genomic organisation of six genes encoding NILT receptors. The genes show similar characteristics to NILTs previously identified in rainbow trout, having highly conserved cysteines in the Ig domain and several inhibitory signalling motifs in the cytoplasmic region. In a single individual three unique NILT Ig domain sequences were discovered at the genomic DNA level, which were divided into two different groups based on a four residue motif after the third cysteine. Our results from the BAC screening and analysis on the repertoire of NILT genes in a single individual indicates that many genes of this expanding Ig containing NILT family are still to be discovered in fish.
先前在鲑鱼物种虹鳟鱼（Oncorhynchus mykiss）中鉴定的几种新型免疫球蛋白样转录物（NILTs）含有一个或两个 V 型细胞外 Ig 结构域。NILTs 在细胞质区域中还具有免疫受体酪氨酸基激活基序（ITAM）或免疫受体酪氨酸基抑制基序（ITIM），从而具有不同的信号转导能力。在这里，我们首次使用 BAC 测序方法报告了大西洋鲑鱼（Salmo salar）中 NILT 多基因家族的基因组组织和结构。
我们使用一个 BAC 覆盖超过 200 kbp 的方法，鉴定了 6 种新型大西洋鲑鱼 NILT 基因（Ssa-NILT1-6），2 个假基因（Ssa-NILTp1 和 Ssa-NILTp2）和 7 种编码推定转座元件的基因。Ssa-NILT1、2、4、5 和 6 均含有一个 Ig 结构域，均具有 CX₃C 基序，而 Ssa-NILT3 含有两个 Ig 结构域，Ig1 中具有 CX₆C 基序，Ig2 中具有 CX₇C 基序。大西洋鲑鱼 NILTs 在细胞质区域中具有几个 ITIM，并且携带 ITIM 的外显子处于相位 0。NILTs 的 CX₃C Ig 结构域的氨基酸序列之间的同一性比较在 77%到 96%之间变化。通过存在于 EST 数据库中（Ssa-NILT1）或通过使用 cDNA 作为模板进行 RT-PCR（Ssa-NILT2、3 和 4），证实了 Ssa-NILT1、2、3 和 4 的表达。对单个个体中假定的 NILT 基因库的调查揭示了三个新基因（Ssa-NILT7-9），它们以 Ig 结构域为代表，可根据特定基序将它们与 Ssa-NILT1-6 的 Ig 结构域一起分为不同的组。
本报告揭示了大西洋鲑鱼中紧密聚集的多基因 NILT 家族。通过筛选高度冗余的大西洋鲑鱼 BAC 文库，我们鉴定并表征了编码 NILT 受体的六个基因的基因组组织。这些基因与先前在虹鳟鱼中鉴定的 NILTs 具有相似的特征，在 Ig 结构域中具有高度保守的半胱氨酸，并且在细胞质区域中具有几个抑制信号基序。在单个个体中，在基因组 DNA 水平上发现了三个独特的 NILT Ig 结构域序列，根据第三个半胱氨酸之后的四个残基基序，将它们分为两个不同的组。我们从 BAC 筛选和单个个体中 NILT 基因库分析的结果表明，该不断扩展的含 Ig 的 NILT 家族的许多基因仍有待在鱼类中发现。
