Nomiyama Hisayuki, Hieshima Kunio, Osada Naoki, Kato-Unoki Yoko, Otsuka-Ono Kaori, Takegawa Sumio, Izawa Toshiaki, Yoshizawa Akio, Kikuchi Yutaka, Tanase Sumio, Miura Retsu, Kusuda Jun, Nakao Miki, Yoshie Osamu
Department of Molecular Enzymology, Kumamoto University Graduate School of Medical Sciences, Kumamoto 860-8556, Japan.
BMC Genomics. 2008 May 15;9:222. doi: 10.1186/1471-2164-9-222.
The chemokine family plays important roles in cell migration and activation. In humans, at least 44 members are known. Based on the arrangement of the four conserved cysteine residues, chemokines are now classified into four subfamilies, CXC, CC, XC and CX3C. Given that zebrafish is an important experimental model and teleost fishes constitute an evolutionarily diverse group that forms half the vertebrate species, it would be useful to compare the zebrafish chemokine system with those of mammals. Prior to this study, however, only incomplete lists of the zebrafish chemokine genes were reported.
We systematically searched chemokine genes in the zebrafish genome and EST databases, and identified more than 100 chemokine genes. These genes were CXC, CC and XC subfamily members, while no CX3C gene was identified. We also searched chemokine genes in pufferfish fugu and Tetraodon, and found only 18 chemokine genes in each species. The majority of the identified chemokine genes are unique to zebrafish or teleost fishes. However, several groups of chemokines are moderately similar to human chemokines, and some chemokines are orthologous to human homeostatic chemokines CXCL12 and CXCL14. Zebrafish also possesses a novel species-specific subfamily consisting of five members, which we term the CX subfamily. The CX chemokines lack one of the two N-terminus conserved cysteine residues but retain the third and the fourth ones. (Note that the XC subfamily only retains the second and fourth of the signature cysteines residues.) Phylogenetic analysis and genome organization of the chemokine genes showed that successive tandem duplication events generated the CX genes from the CC subfamily. Recombinant CXL-chr24a, one of the CX subfamily members on chromosome 24, showed marked chemotactic activity for carp leukocytes. The mRNA was expressed mainly during a certain period of the embryogenesis, suggesting its role in the zebrafish development.
The phylogenic and genomic organization analyses suggest that a substantial number of chemokine genes in zebrafish were generated by zebrafish-specific tandem duplication events. During such duplications, a novel chemokine subfamily termed CX was generated in zebrafish. Only two human chemokines CXCL12 and CXCL14 have the orthologous chemokines in zebrafish. The diversification observed in the numbers and sequences of chemokines in the fish may reflect the adaptation of the individual species to their respective biological environment.
趋化因子家族在细胞迁移和激活过程中发挥着重要作用。在人类中，已知至少有44个成员。根据四个保守半胱氨酸残基的排列方式，趋化因子现在被分为四个亚家族，即CXC、CC、XC和CX3C。鉴于斑马鱼是一种重要的实验模型，硬骨鱼构成了一个进化上多样化的群体，占脊椎动物物种的一半，将斑马鱼趋化因子系统与哺乳动物的趋化因子系统进行比较将会很有意义。然而，在本研究之前，仅报道了斑马鱼趋化因子基因的不完整列表。
我们系统地在斑马鱼基因组和EST数据库中搜索趋化因子基因，鉴定出100多个趋化因子基因。这些基因是CXC、CC和XC亚家族成员，未鉴定出CX3C基因。我们还在河豚和四齿鲀中搜索趋化因子基因，在每个物种中仅发现18个趋化因子基因。大多数已鉴定的趋化因子基因是斑马鱼或硬骨鱼所特有的。然而，几组趋化因子与人类趋化因子有一定程度的相似性，一些趋化因子与人类稳态趋化因子CXCL12和CXCL14是直系同源的。斑马鱼还拥有一个由五个成员组成的新的物种特异性亚家族，我们将其称为CX亚家族。CX趋化因子缺少两个N端保守半胱氨酸残基中的一个，但保留了第三个和第四个。（注意，XC亚家族仅保留了标志性半胱氨酸残基中的第二个和第四个。）趋化因子基因的系统发育分析和基因组组织显示，连续的串联重复事件从CC亚家族产生了CX基因。重组CXL-chr24a是24号染色体上的CX亚家族成员之一，对鲤鱼白细胞显示出明显的趋化活性。该mRNA主要在胚胎发育的特定时期表达，表明其在斑马鱼发育中的作用。
系统发育和基因组组织分析表明，斑马鱼中大量的趋化因子基因是由斑马鱼特异性串联重复事件产生的。在这些重复过程中，斑马鱼产生了一个新的趋化因子亚家族，称为CX。在斑马鱼中，只有两个人类趋化因子CXCL12和CXCL14有直系同源趋化因子。鱼类趋化因子在数量和序列上观察到的多样化可能反映了各个物种对其各自生物环境的适应。
