A High Polymorphism Level in <Emphasis Type="Italic">Rhinopithecus roxellana</Emphasis>

The Sichuan golden monkey (Rhinopithecus roxellana) is a famous and beautiful endangered primate. Owing to the dearth of samples and technical limitations, previous studies could not adequately assess the levels of genetic polymorphisms in the species. To evaluate the polymorphisms further, we sequenced the entire mitochondrial control regions (D-loop) of 35 individuals from the 3 major habitats: Minshan, Qinglin, and Shennongjia. We observed many polymorphisms and estimated that the effective population size of the current total population is less than ca. 480–2300, and the time to the most recent common ancestor is ca. 4000–62,700 years. Through comparisons, we showed that the population of Rhinopithecus roxellana has a relatively higher polymorphism level than that of other endangered primates.     

小口白甲鱼都柳江种群mtDNA D环的序列变异及遗传多样性

采用PCR结合DNA测序技术,测定分析了易危鱼类小口白甲鱼(Onychostoma lini)都柳江种群36个个体mtDNA D环约470bp序列的变异及遗传多样性。结果表明,在36个个体中,该序列的长度为469～475bp,其碱基组成为A+T的平均含量(68.4%)高于G+C(31.6%)。共检测到25个多态位点,其中转换19个、颠换6个。核苷酸多样性(π)为0.00575,平均核苷酸差异数(K)为2.695。36个个体分属5个单倍型,单倍型多样度(Hd)为0.260,单倍型间的平均遗传距离(P)为0.026。5个单倍型构建的UPGMA系统树聚为2个分支。目前小口白甲鱼都柳江种群mtDNA D环序列存在着较丰富的变异和遗传多样性。     

Structure of a Longitudinal Actin Dimer Assembled by Tandem W Domains: Implications for Actin Filament Nucleation

Actin filament nucleators initiate polymerization in cells in a regulated manner. A common architecture among these molecules consists of tandem WASP homology 2 domains (W domains) that recruit three to four actin subunits to form a polymerization nucleus. We describe a low-resolution crystal structure of an actin dimer assembled by tandem W domains, where the first W domain is cross-linked to Cys374 of the actin subunit bound to it, whereas the last W domain is followed by the C-terminal pointed end-capping helix of thymosin β4. While the arrangement of actin subunits in the dimer resembles that of a long-pitch helix of the actin filament, important differences are observed. These differences result from steric hindrance of the W domain with intersubunit contacts in the actin filament. We also determined the structure of the first W domain of Vibrio parahaemolyticus VopL cross-linked to actin Cys374 and show it to be nearly identical with non-cross-linked W-Actin structures. This result validates the use of cross-linking as a tool for the study of actin nucleation complexes, whose natural tendency to polymerize interferes with most structural methods. Combined with a biochemical analysis of nucleation, the structures may explain why nucleators based on tandem W domains with short inter-W linkers have relatively weak activity, cannot stay bound to filaments after nucleation, and are unlikely to influence filament elongation. The findings may also explain why nucleation-promoting factors of the Arp2/3 complex, which are related to tandem-W-domain nucleators, are ejected from branch junctions after nucleation. We finally show that the simple addition of the C-terminal pointed end-capping helix of thymosin β4 to tandem W domains can change their activity from actin filament nucleation to monomer sequestration.     

F-Actin Structure Destabilization and DNase I Binding Loop Fluctuations: Mutational Cross-Linking and Electron Microscopy Analysis of Loop States and Effects on F-Actin

The conformational dynamics of filamentous actin (F-actin) is essential for the regulation and functions of cellular actin networks. The main contribution to F-actin dynamics and its multiple conformational states arises from the mobility and flexibility of the DNase I binding loop (D-loop; residues 40-50) on subdomain 2. Therefore, we explored the structural constraints on D-loop plasticity at the F-actin interprotomer space by probing its dynamic interactions with the hydrophobic loop (H-loop), the C-terminus, and the W-loop via mutational disulfide cross-linking. To this end, residues of the D-loop were mutated to cysteines on yeast actin with a C374A background. These mutants showed no major changes in their polymerization and nucleotide exchange properties compared to wild-type actin. Copper-catalyzed disulfide cross-linking was investigated in equimolar copolymers of cysteine mutants from the D-loop with either wild-type (C374) actin or mutant S265C/C374A (on the H-loop) or mutant F169C/C374A (on the W-loop). Remarkably, all tested residues of the D-loop could be cross-linked to residues 374, 265, and 169 by disulfide bonds, demonstrating the plasticity of the interprotomer region. However, each cross-link resulted in different effects on the filament structure, as detected by electron microscopy and light-scattering measurements. Disulfide cross-linking in the longitudinal orientation produced mostly no visible changes in filament morphology, whereas the cross-linking of D-loop residues > 45 to the H-loop, in the lateral direction, resulted in filament disruption and the presence of amorphous aggregates on electron microscopy images. A similar aggregation was also observed upon cross-linking the residues of the D-loop (> 41) to residue 169. The effects of disulfide cross-links on F-actin stability were only partially accounted for by the simulations of current F-actin models. Thus, our results present evidence for the high level of conformational plasticity in the interprotomer space and document the link between D-loop interactions and F-actin stability.     

Escherichia coli RecA promotes strand invasion with cisplatin-damaged DNA

The antitumor drug cisplatin causes intrastrand cross-linking of adjacent guanine residues that severely distorts the DNA backbone. These DNA adducts impede the progress of the replisome and may result in replication fork arrest. In Escherichia coli, the response to cisplatin involves the action of the prototypic recombinase RecA. Here we show that RecA can utilize, albeit at reduced levels, oligonucleotides that bear site-specific cisplatin-induced 1,2 d(GpG) intrastrand cross-links in strand invasion reactions. Binding of RecA to cisplatin-damaged oligonucleotides was not affected, indicating that the impediment was in the pairing step. The cognate E. coli single-strand DNA-binding protein specifically stimulated strand invasion particularly with cisplatin-damaged DNA. These results indicate that RecA is capable of processing the major cisplatin-induced lesion via a recombination mechanism.     

牦牛的分类学地位及起源研究:mtDNA D-loop序列的分析

牦牛的起源与属级分类学地位至今仍然存在一定的争议。我们测定了家养牦牛和野生牦牛线粒体控制区(D-loop)序列,并以此构建牦牛和牛属、野牛属、水牛属以及非洲水牛属相关种的系统发育树。研究结果表明线粒体D-loop区与Cytb基因序列在构建牛族的系统发育具有同样重要的价值。系统发育关系显示野牛属的灭绝种草原野牛与现存种美洲野牛先聚合为一单系群,然后再和牦牛形成一单系分支,表明牦牛与野牛属的草原野牛、美洲野牛亲缘关系最近,具有最近的共同祖先,而与牛属的其它亚洲物种亲缘关系较远。因此,本研究不支持将牦牛独立为牦牛属———Poephagus,牛属与野牛属在分类上也应合并为一个属。基于上述研究结果和化石证据,我们进一步对牦牛起源的历史背景进行了讨论,认为牦牛与野牛属的分化是由于第四纪气候变化在欧亚大陆发生的,野牛通过白令陆桥进入北美;冰期结束后,由于欧亚大陆其它地区温度升高,牦牛只能局限分布在较为寒冷的青藏高原;而野牛属在北美先后分化为草原野牛和美洲野牛,前者可能是后者的直接祖先。     

Complete mtDNA of Meretrix lusoria (Bivalvia: Veneridae) reveals the presence of an atp8 gene, length variation and heteroplasmy in the control region

The complete nucleotide sequence of the mitochondrial genome of the clam Meretrix lusoria (Bivalvia: Veneridae) was determined. It comprises 20,268 base pairs (bp) and contains 13 protein-coding genes, including ATPase subunit 8 (atp8), two ribosomal RNAs, 22 transfer RNAs, and a non-coding control region. The atp8 encodes a protein of 39 amino acids. All genes are encoded on the same strand. A putative control region (CR or D-loop) was identified in the major non-coding region (NCR) between the tRNA^Gly and tRNA^Gln. A 1087 bp tandem repeat fragment was identified that comprises nearly 11 copies of a 101 bp motif and accounts for approximately 41% of the NCR. The 101 bp tandem repeat motif of the NCR can be folded into a stem–loop secondary structure. Samples of eight individuals from Hainan and Fujian provinces were collected and their NCR regions were successfully amplified and sequenced. The data revealed a highly polymorphic VNTR (variable number of tandem repeats) associated with high levels of heteroplasmy in the D-loop region. The size of the CR ranged from 1942 to 3354 bp depending upon the copy number of the repeat sequence.     

马鹿阿拉善亚种遗传多样性和群体结构

马鹿阿拉善亚种（Cervus elaphus alashanicus）又称阿拉善马鹿,目前仅分布于贺兰山地区,是我国马鹿亚种分布范围最狭窄的一个隔离种群。为了解阿拉善马鹿的种群遗传多样性及遗传变异情况,以对该种群的保护提供科学参考,对在贺兰山采集的93个野生个体新鲜粪便样本的线粒体控制区部分序列（991 bp）进行扩增和分析,共检测到68个变异位点,定义16种单倍型,平均单倍型多样性为0.405,平均核苷酸多样性为0.00232,说明种群遗传多样性水平较低。中性检验和错配分布分析表明阿拉善马鹿曾出现过种群扩张,贝叶斯天际线分析（BSP）显示扩张时间约在末次冰盛期（0.028—0.010 Ma）。FST检验表明阿拉善马鹿种群内存在显著遗传分化,系统发育树和单倍型网络图分析表明群体间没有明显的系统地理格局。本研究表明阿拉善马鹿目前种群遗传多样性较低,建议加大对该亚种的关注和保护力度。       

黑琴鸡北方亚种mtDNA D-loop遗传多样性初步研究

黑琴鸡(Tetrao tetrix)为国家Ⅱ级保护动物,但近年来种群数量不断减少。因此,了解不同种群的遗传变异情况,可为制定保护管理策略提供依据,以便恢复野外种群的数量。本文测定加格达奇(42个个体)和呼伦贝尔市扎兰屯(76个个体)两个黑琴鸡种群的共118个个体的mtDNA D-loop 序列,共发现25个变异位点,定义了33个单倍型,整体的平均核苷酸差异数(K)为2.608,核苷酸多样性(π)为0.228%,种群的遗传多样性偏低,两个种群有一定的基因交流,N_m为14.63,群体间无显著的遗传分化。Tajima's D和Fu&Li's D的估算结果表明,这两个黑琴鸡种群相对于中性的歧异度并没有明显的偏离(P>0.1),两个种群可能未经过大规模的种群扩张过程。     

The complete mitochondrial genome sequence analysis of Tibetan argali (Ovis ammon hodgsoni): Implications of Tibetan argali and Gansu argali as the same subspecies

The genus Ovis (Bovidae, Artiodactyla) includes six species, i.e. Ovis ammon, Ovis aries, Ovis canadensis, Ovis dalli, Ovis nivicola and Ovis vignei. Based on morphology, geographical location, habitat, etc., the species O. ammon is divided into nine subspecies. The near threatened Tibetan argali is distributed across the Tibetan Plateau and its peripheral mountains, and believed to be one of the O. ammon subspecies (O. a. hodgsoni). However, considering its morphological features and distributions, a question has been proposed by some researchers about the subspecies status of Tibetan argali. In this study, we employed complete mitochondrial DNA (mtDNA) to explore the phylogenetic relationship and population genetic structure of Tibetan argali. The results revealed that the nucleotide composition, gene arrangement and codon usage pattern of the mitochondrial genome of Tibetan argali are similar to those of other caprines. Phylogenetic analyses showed that Tibetan argali was clustered with O. ammon. Interestingly, five Tibetan argali individuals and one of the three Gansu argali (O. a. dalailamae) individuals were clustered in the same branch, which is a sister group to other two Gansu argali individuals. Together with morphological characteristics, our results suggested that Tibetan argali and Gansu argali may belong to the same subspecies (O. a. hodgsoni) of O. ammon, rather than two different subspecies.