Independent origin of the growth hormone gene family in New World monkeys and Old World monkeys/hominoids

The growth hormone (GH) gene family represents an erratic and complex evolutionary pattern, involving many evolutionary events, such as multiple gene duplications, positive selection, the birth-and-death process and gene conversions. In the present study, we cloned and sequenced GH-like genes from three species of New World monkeys (NWM). Phylogenetic analysis strongly suggest monophyly for NWM GH-like genes with respect to those of Old World monkeys (OWM) and hominoids, indicating that independent gene duplications have occurred in NWM GH-like genes. There are three main clusters of genes in putatively functional NWM GH-like genes, according to our gene tree. Comparison of the ratios of nonsynonymous and synonymous substitutions revealed that these three clusters of genes evolved under different kinds of selective pressures. Detailed analysis of the evolution of pseudogenes showed that the evolutionary pattern of this gene family in platyrrhines is in agreement with the so-called birth-and-death process.

Molecular evolution of growth hormone gene family in old world monkeys and hominoids

Growth hormone is a classic molecule in the study of the molecular clock hypothesis as it exhibits a relatively constant rate of evolution in most mammalian orders except primates and artiodactyls, where dramatically enhanced rate of evolution (25-50-fold) has been reported. The rapid evolution of primate growth hormone occurred after the divergence of tarsiers and simians, but before the separation of old world monkeys (OWM) from new world monkeys (NWM). Interestingly, this event of rapid sequence evolution coincided with multiple duplications of the growth hormone gene, suggesting gene duplication as a possible cause of the accelerated sequence evolution. Here we determined 21 different GH-like sequences from four species of OWM and hominoids. Combining with published sequences from OWM and hominoids, our analysis demonstrates that multiple gene duplications and several gene conversion events both occurred in the evolutionary history of this gene family in OWM/hominoids. The episode of recent duplications of CSH-like genes in gibbon is accompanied with rapid sequence evolution likely resulting from relaxation of purifying selection. GHN genes in both hominoids and OWM are under strong purifying selection. In contrast, CSH genes in both lineages are probably not. GHV genes in OWM and hominoids evolved at different evolutionary rates and underwent different selective constraints. Our results disclosed the complex history of the primate growth hormone gene family and raised intriguing questions on the consequences of these evolutionary events. © 2005 Elsevier B.V. All rights reserved.

Evolution of genome organizations of squirrels (Sciuridae) revealed by cross-species chromosome painting

With complete sets of chromosome-specific painting probes derived from flow-sorted chromosomes of human and grey squirrel (Sciurus carolinensis), the whole genome homologies between human and representatives of tree squirrels (Sciurus carolinensis, Callosciurus erythraeus), flying squirrels (Petaurista albiventer) and chipmunks (Tamias sibiricus) have been defined by cross-species chromosome painting. The results show that, unlike the highly rearranged karyotypes of mouse and rat, the karyotypes of squirrels are highly conserved. Two methods have been used to reconstruct the genome phylogeny of squirrels with the laboratory rabbit (Oryctolagus cuniculus) as the out-group: ( 1) phylogenetic analysis by parsimony using chromosomal characters identified by comparative cytogenetic approaches; ( 2) mapping the genome rearrangements onto recently published sequence-based molecular trees. Our chromosome painting results, in combination with molecular data, show that flying squirrels are phylogenetically close to New World tree squirrels. Chromosome painting and G-banding comparisons place chipmunks ( Tamias sibiricus), with a derived karyotype, outside the clade comprising tree and flying squirrels. The superorder Glires (order Rodentia + order Lagomorpha) is firmly supported by two conserved syntenic associations between human chromosomes 1 and 10p homologues, and between 9 and 11 homologues.

Construction and characterization of bacterial artificial chromosome library of black-handed spider monkey (Ateles geoffroyi)

The large-insert genomic DNA library is a critical resource for genome-wide genetic dissection of target species. We constructed a high-redundancy bacterial artificial chromosome (BAC) library of a New World monkey species, the black-handed spider monkey

Genetic evidence of a strong functional constraint of neurotrypsin during primate evolution

Neurotrypsin is one of the extra-cellular serine proteases that are predominantly expressed in the brain and involved in neuronal development and function. Mutations in humans are associated with autosomal recessive non-syndromic mental retardation (MR). We studied the molecular evolution of neurotrypsin by sequencing the coding region of neurotrypsin in 11 representative non-human primate species covering great apes, lesser apes, Old World monkeys and New World monkeys. Our results demonstrated a strong functional constraint of neurotrypsin that was caused by strong purifying selection during primate evolution, an implication of an essential functional role of neurotrypsin in primate cognition. Further analysis indicated that the purifying selection was in fact acting on the SRCR domains of neurotrypsin, which mediate the binding activity of neurotrypsin to cell surface or extracellular proteins. In addition, by comparing primates with three other mammalian orders, we demonstrated that the absence of the first copy of the SRCR domain (exon 2 and 3) in mouse and rat was due to the deletion of this segment in the murine lineage. Copyright (C) 2005 S. Karger AG, Basel.

Distinctive Paleo-Indian Migration Routes from Beringia Marked by Two Rare mtDNA Haplogroups

Background: It is widely accepted that the ancestors of Native Americans arrived in the New World via Beringia approximately 10 to 30 thousand years ago (kya). However, the arrival time(s), number of expansion events, and migration routes into the Western

TRIM5-CypA融合基因与北平顶猴易感HIV-1的机制研究

天然免疫分子TRIM5α（tripartite motif protein 5α）是近年来发现的一种重要的宿主细胞内逆转录病毒限制因子。在灵长类动物细胞中，TRIM5α蛋白可以在病毒进入细胞后、逆转录前的阶段抑制HIV-1、N-MLV和EIAV等逆转录病毒的复制。由于TRIM5α分子的作用，绝大部分旧大陆猴（Old World monkey）都不能感染HIV-1。而在新大陆猴（New World monkey）中，鹰猴是唯一不感染HIV-1的灵长类动物。研究证明，鹰猴细胞中存在的TRIM5-CypA融合蛋白（owl monkey TRIM5-CypA，omTRIMCyp）介导了抗HIV-1的作用，从而使鹰猴不能感染HIV-1。研究证明，平顶猴是旧大陆猴中唯一报道可以感染HIV-1的灵长类动物，但是其感染HIV-1的机制并不清楚。根据现行的灵长类动物分类学，原属平顶猴群体（M. nemestrina group）的三个亚种分为猕猴属的三个不同种：巽他平顶猴（Sunda pig-tailed macaque，M. nemestrina），北平顶猴（Northern pig-tailed macaque，M. leonina）和明打威猴（Mentawai macaque，M. pagensis）。本论文对中国云南境内北平顶猴TRIM5基因座和感染HIV-1的相关性进行了研究。通过PCR和测序对北平顶猴基因组TRIM5基因座进行分析，发现一个CypA假基因的cDNA通过逆转座机制插入至TRIM5基因座的3’-UTR区域，形成了一个不同于鹰猴TRIM5-CypA的新型融合基因npmTRIMCyp（northern pig-tailed macaque TRIM5-CypA）。通过RT-PCR对npmTRIMCyp融合基因的转录本进行分析，我们鉴定出npmTRIMCyp共有3种不同的选择性剪接产物，分别为npmTRIMCypV1-V3。进一步克隆和测序这3种不同选择性剪接体，通过丰度和序列分析证实：npmTRIMCypV2是优势剪接体，可能在该融合基因产物的功能中发挥作用。研究发现北平顶猴npmTRIMCyp融合基因主要转录本中外显子7和8均被剪切掉。外显子7剪接丢失机制源于TRIM5第6内含子内 3’剪接位点的G/T突变。我们克隆了npmTRIMCyp融合基因cDNA的蛋白编码区ORF，并构建了重组表达npmTRIMCyp的载体，转染HeLa和HeLa-T4细胞并获得稳定表达的细胞株。通过感染HIV-1证实，npmTRIMCyp融合蛋白不能够限制HIV-1的感染和复制，这可能是北平顶猴作为旧大陆猴中唯一对HIV-1易感的灵长类动物的重要分子机制之一。通过HIV-1感染灵长类动物PBMCs实验证实，北平顶猴可以感染HIV-1。npmTRIMCyp可以有效地限制HIV-2ROD的复制，但对SIVmac239只有十分微弱的限制活性。通过构建鹰猴omTRIMCyp和北平顶猴npmTRIMCyp的置换剪接体（SWAP-1和SWAP-2），转染融合基因及其置换剪接体的CRFK细胞激光共聚焦实验证明，npmTRIMCyp、SWAP1和SWAP2在细胞内主要存在于胞浆中。稳定表达融合蛋白和置换剪接体的CRFK细胞感染HIV-1-GFP-VSVG分析表明，含omTRIMCyp外显子7的SWAP-1和SWAP-2均具有限制HIV-1活性，但SWAP-1的活性更强一些，这表明TRIM5结构域的外显子7可能在介导对HIV-1的限制活性中发挥了协同辅助作用。免疫共沉淀研究表明，npmTRIMCyp不能识别和结合HIV-1的衣壳蛋白。对北平顶猴中介导识别逆转录病毒区域的基因组部分进行了测序，共鉴定出46个多态性位点，表明在北平顶猴识别逆转录病毒衣壳区域存在较高的多态性。