Evolution of major histocompatibility complex by “en bloc” duplication before mammalian radiation

Duplications are an important mechanism for the emergence of genetic novelties. Reports on duplicated genes are numerous, and mechanisms for polyploidization or local gene duplication are beginning to be understood. When a local duplication is studied, searches are usually done gene-by-gene, and the size of duplicated segments is not often investigated. Therefore, we do not know if the gene in question has duplicated alone or with other genes, implying that "en bloc" duplications are poorly studied. We propose a method for identification of "en bloc" duplication using mapping, phylogenetic and statistical analyses. We show that two segments present in the major histocompatibility complex (MHC) region of human chromosome 6 have resulted from an "en bloc" duplication that took place between divergence of amniotes and methaterian/eutherian separation. These segments contain members of the same multigenic families, namely olfactory receptors genes, genes encoding proteins containing B30.2 domain, genes encoding proteins containing immunoglobulin V domain and MHC class I genes. We will discuss the fact that olfactory receptors and MHC genes have undergone positive selection, which could have helped in fixation of the surrounding genes.     

Multiple Gene Duplication and Rapid Evolution in the groEL Gene: Functional Implications

The chaperonins, GroEL and GroES, are present ubiquitously and provide a paradigm in the understanding of assisted protein folding. Due to its essentiality of function, GroEL exhibits high sequence conservation across species. Complete genome sequencing has shown the occurrence of duplicate or multiple copies of groEL genes in bacteria such as Mycobacterium tuberculosis and Corynebacterium glutamicum. Monophyly of each bacterial clade in the phylogenetic tree generated for the GroEL protein suggests a lineage-specific duplication. The duplicated groEL gene in Actinobacteria is not accompanied by the operonic groES despite the presence of upstream regulatory elements. Our analysis suggests that in these bacteria the duplicated groEL genes have undergone rapid evolution and divergence to function in a GroES-independent manner. Evaluation of multiple sequence alignment demonstrates that the duplicated genes have acquired mutations at functionally significant positions including those involved in substrate binding, ATP binding, and GroES binding and those involved in inter-ring and intra-ring interactions. We propose that the duplicate groEL genes in different bacterial clades have evolved independently to meet specific requirements of each clade. We also propose that the groEL gene, although essential and conserved, accumulates nonconservative substitutions to exhibit structural and functional variations. Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users. [Reviewing Editor: Dr. Debashish Bhattacharya]     

A molecule bearing an immunoglobulin-like V region of the CTX subfamily in amphioxus

An expressed sequence tag with significant similarity to a vertebrate T-cell receptor (Tcr) sequence was found in a cDNA library prepared from the posterior part of the adult amphioxus, Branchiostoma lanceolatum (Brla). Characterization of the corresponding cDNA clone revealed the presence of an open reading frame encoding a 351 amino acid residue-long polypeptide. The putative protein, tentatively designated Brla-VDB for V-domain bearing, appears to consist of two domains. The N-terminal domain begins with a putative leader peptide followed by a sequence resembling the V domain of the CTX protein originally found to be expressed in the cortical thymocytes of the clawed frog Xenopus. The C-terminal domain of the VDB protein does not show significant sequence similarity to any entry in the databases and contains five hydrophobic segments separated by short intervening hydrophilic stretches. It may therefore belong to a protein that crosses the plasma membrane five times. These findings support the notion that V domains resembling those found in Tcrs evolved in nonvertebrates before the emergence of the adaptive immune system and may have participated in functions not involved directly in immunity.The sequence reported in this paper has been deposited in the GenBank database (Accession No. AY293854)     

Evolution of vertebrate central nervous system is accompanied by novel expression changes of duplicate genes

The evolution of the central nervous system (CNS) is one of the most striking changes during the transition from invertebrates to vertebrates. As a major source of genetic novelties, gene duplication might play an important role in the functional innovation of vertebrate CNS. In this study, we focused on a group of CNS-biased genes that duplicated during early vertebrate evolution. We investigated the tempo-spatial expression patterns of 33 duplicate gene families and their orthologs during the embryonic development of the vertebrate Xenopus laevis and the cephalochordate Brachiostoma belcheri. Almost all the identified duplicate genes are differentially expressed in the CNS in Xenopus embryos, and more than 50% and 30% duplicate genes are expressed in the telencephalon and mid-hindbrain boundary, respectively, which are mostly considered as two innovations in the vertebrate CNS. Interestingly, more than 50% of the amphioxus orthologs do not show apparent expression in the CNS in amphioxus embryos as detected by in situ hybridization, indicating that some of the vertebrate CNS-biased duplicate genes might arise from non-CNS genes in invertebrates. Our data accentuate the functional contribution of gene duplication in the CNS evolution of vertebrate and uncover an invertebrate non-CNS history for some vertebrate CNS-biased duplicate genes.     

MHC class I genes in a New World primate, the cotton-top tamarin (Saguinus oedipus), have evolved by an active process of loci turnover

 Lymphocytes of a New World primate, the cotton-top tamarin (Saguinus oedipus), express classical G–related major histocompatibility complex (MHC) class I molecules with unusually limited polymorphism and variability. Three G-related loci, an F locus, an E locus, and two pseudogenes (So-N1 and So-N3) have been identified by cDNA library screening and extensive PCR analysis of both cDNA and genomic DNA from the cotton-top tamarin. Furthermore, each genus of the subfamily Callitrichinae (tamarins and marmosets) appears to express its own unique set of MHC class I genes, likely due to a rapid turnover of loci. The rapid emergence of unique MHC class I genes in the Callitrichinae genera, resulting from an active process of duplication and inactivation of loci, may account for the limited diversity of the MHC class I genes in the cotton-top tamarin. To determine the nature of the entire complement of MHC class I genes in the cotton-top tamarin, we synthesized a genomic DNA library and screened it with MHC class I-specific probes. We isolated nine new MHC class I pseudogenes from this library. These newly isolated tamarin G–related MHC class I pseudogenes are not closely related to any of their functional counterparts in the tamarin, suggesting that they do not share a recent common ancestral gene with the tamarin's currently expressed MHC class I loci. In addition, these tamarin sequences display a high rate of nonsynonymous substitutions in their putative peptide binding region. This indicates that the genes from which they have derived were likely subject to positive selection and, therefore, were once functional. Our data support the notion that an extremely high rate of loci turnover is largely responsible for the limited diversity of the MHC class I genes in the cotton-top tamarin. Received: 15 September 1997 / Revised: 2 July 1998     

锚头鳋科（寄生桡足类）的系统发育

错头鳋科Ｌｅｒｎａｅｉｄａｅ是剑水蚤目Ｃｙｃｌｏｐｏｉｄａ中以第１触短和第１小颚单枝型或退化消失为共同离征的一个自然类群,因此以剑水蚤科Ｃｙｃｌｏｐｉｄａｅ作为外群,把锚头鳋科各属筛选出的性状与剑水蚤科的相应性状比较,以确定其性质,即该性状为祖征,还是离征。经比较,发现２１个性状在锚头鳋科１１个属中呈镶嵌分布。根据性状的镶嵌分布和简约性原则,推导出锚头鳋科的属间系统发育分支图。     

白鱀豚MHC基因类DQB1座位第二外元的序列变异分析

测定了 4 5个克隆的白豚 (Lipotesvexillifer)MHCⅡ类基因DQB座位第二外元 172bp的核苷酸序列 ,共获得 15种序列 ,发现了 2 2个变异位点。核苷酸的非同义替换明显多于同义替换 ,并造成了 15个氨基酸的改变。氨基酸的替换趋于集中在假定的与抗原的选择性识别相关的位点附近。白豚DQB基因的核苷酸和氨基酸序列与文献报道的白鲸 (Delphinapterusleucas)和一角鲸 (Monodonmonoceros)DQB1序列具有较高的同源性。氨基酸序列不具备人及其它一些灵长类动物DQB2基因所共有的基序 (Motif) ,而与牛DQB1基因的基序相近 ,说明本研究得到的白豚MHC序列应属于类DQB1基因。同一个体出现了多种序列的情况 ,提示白豚的DQB基因可能存在着座位重复。白豚的类DQB1座位的序列中存在多种基序的不同组合 ,推测是由于基因转换造成的.     

钙调素在文昌鱼性腺和表皮分布的研究

用免疫组织化学技术首次发现雌、雄文昌鱼成熟性腺内分布有丰富的钙调素免疫反应物质。钙调素免疫阳性反应分别定位于精细胞和卵细胞的胞核内。文昌鱼表皮细胞尤其细胞顶端胞浆对钙调素抗体显示强阳性反应。作者讨论了文昌鱼性腺和表皮内钙调素的可能作用。     

与麦芽糖结合蛋白构象有关的单克隆抗体的制备

利用麦芽糖结合蛋白（ＭＢＰ）在大肠杆菌中的高效表达,分别采用亲和层析和变性复性,疑胶过滤的方法纯化了可溶性和包涵体部分的ＭＢＰ。将得到的这两种构象不同的ＭＢＰ分别免疫小鼠并进一步筛选和克隆,各得到５株单克隆抗体株。经制备腹水获得抗体后,地其和构象不同的麦芽糖结合蛋白的结合能力的测定,发现由包涵体部分的ＭＢＰ轩和筛选得到的单克隆抗体中有两对变性蛋白具有更高的结合能力。     

The Evolution of the Calpain Family as Reflected in Paralogous Chromosome Regions

Calpains, the Ca²⁺-dependent intracellular proteinases, are involved in the regulation of distinct cellular pathways including signal transduction and processing, cytoskeleton dynamics, and muscle homeostasis. To investigate the evolutionary origin of diverse calpain subfamilies, a phylogenetic study was carried out. The topology of the calpain phylogenetic tree has shown that some of the gene duplications occurred before the divergence of the protostome and deuterostome lineages. Other gene doublings, leading to vertebrate-specific calpain forms, took place during early chordate evolution and coincided with genome duplications as disclosed by the localization of calpain genes to paralogous chromosome regions in the human genome. On the basis of the phylogenetic tree, the time of gene duplications, and the localization of calpain genes, we propose a model of tandem and chromosome duplications for the evolution of vertebrate-specific calpain forms. The data presented here are consistent with scenarios proposed for the evolution of other multigene families. Received: 17 November 1998 / Accepted: 30 April 1999     

Amino acids defining the acyl pocket of an invertebrate cholinesterase

Amphioxus (Branchiostoma floridae) cholinesterase 2 (ChE2) hydrolyzes acetylthiocholine (AsCh) almost exclusively. We constructed a homology model of ChE2 on the basis of Torpedo californica acetylcholinesterase (AChE) and found that the acyl pocket of the enzyme resembles that of Drosophila melanogaster AChE, which is proposed to be comprised of Phe330 (Phe290 in T. californica AChE) and Phe440 (Val400), rather than Leu328 (Phe288) and Phe330 (Phe290), as in vertebrate AChE. In ChE2, the homologous amino acids are Phe312 (Phe290) and Phe422 (Val400). To determine if these amino acids define the acyl pocket of ChE2 and its substrate specificity, and to obtain information about the hydrophobic subsite, partially comprised of Tyr352 (Phe330) and Phe353 (Phe331), we performed site-directed mutagenesis and in vitro expression. The aliphatic substitution mutant F312I ChE2 hydrolyzes AsCh preferentially but also butyrylthiocholine (BsCh), and the change in substrate specificity is due primarily to an increase in k_cat for BsCh; K_m and K_ss are also altered. F422L and F422V produce enzymes that hydrolyze BsCh and AsCh equally due to an increase in k_cat for BsCh and a decrease in k_cat for AsCh. Our data suggest that Phe312 and Phe422 define the acyl pocket. We also screened mutants for changes in sensitivity to various inhibitors. Y352A increases the sensitivity of ChE2 to the bulky inhibitor ethopropazine. Y352A decreases inhibition by BW284c51, consistent with its role as part of the choline-binding site. Aliphatic replacement mutations produce enzymes that are more sensitive to inhibition by iso-OMPA, presumably by increasing access to the active site serine. Y352A, F353A and F353V make ChE2 considerably more resistant to inhibition by eserine and neostigmine, suggesting that binding of these aromatic inhibitors is mediated by π–π or cation–π interactions at the hydrophobic site. Our results also provide information about the aromatic trapping of the active site histidine and the inactivation of ChE2 by sulfhydryl reagents.     

昌黎海区文昌鱼初步调查

描述了秦皇岛昌黎海区文昌鱼栖息的自然生态环境,测定了文昌鱼的种群结构、生物学特征等,并进一步对秦皇岛文昌鱼的分类地位进行了研究。结果认为,秦皇岛文昌鱼与厦门文昌鱼及青岛文昌鱼同属于一个种,从亲缘关系上,秦皇岛文昌鱼与青岛文昌鱼要更近些。     

Polymorphism, natural selection, and structural modeling of class Ia MHC in the African clawed frog (Xenopus laevis)

In the African clawed frog (Xenopus laevis), two deeply divergent allelic lineages of multiple genes of the class I MHC region have been discovered. For the MHC class I UAA locus, functional differences and the molecular basis for lineages maintenance are unknown. Alleles of linked class I region genes also exhibit strong disequilibrium with specific MHC alleles, but the underlying cause is not clear. We use MHC class Ia sequence data to estimate substitution rates and investigate structural differences between allelic lineages from protein models. Results indicate the operation of natural selection, and differences in the steric properties in the F pocket of the peptide-binding region among lineages. Variability in this pocket likely enables allelic lineages to bind very different sets of peptides and to interact differently with MHC chaperones in the endoplasmic reticulum. These results constitute evidence of the molecular evolutionary basis for 1) the maintenance of allelic lineages, 2) functional differences among lineages, and 3) strong linkage disequilibrium of allelic variants of class I region genes in X. laevis.Electronic Supplementary Material Supplementary material is available for this article at