裸子植物中光敏色素PHY-PAS1结构域的适应性进化

光敏色素是一类红光／远红光受体,在植物种子萌发到成熟的整个生长发育过程中均起重要的调节作用。光敏色素PHY-PAS1结构域存在于光敏色素基因家族的所有成员中,对调节发色团的光谱特性和光信号转导非常关键。光敏色素基因家族通过基因重复产生,而基因重复可能与物种形成有关。PHYP基因是裸子植物光敏色素基因家族发生第1次重复后产生的,并且以单拷贝形式存在。为了研究不同裸子植物PHYP基因编码蛋白的PHY-PAS1结构域在进化过程中是否受到相同的选择压力以及是否发生了适应性进化,该研究利用分支模型、位点模型以及分支．位点模型对裸子植物31条PHYP基因序列编码蛋白的PHY-PAS1结构域所受到的选择压力进行了分析。结果表明,在由PHY-PAS1结构域序列构建的系统树中,多数分支处于强烈的负选择压力下（ω〈1）：有14个分支处于正选择压力下（ω〉1）,其中13个分支发生在属内种间;与之相比,在较为古老的谱系中相对缺少这种正选择压力。     

蕨类植物和裸子植物的起源与进化

最近笔者拜读了由中山大学生物系与南京大学生物系合编的《植物学》(系统、分类部分),高等教育出版社,1984年3月第四次印刷本,发现在该书的157—188页,即于论述“蕨类植物的起源与进化”和“裸子植物的起源与进化”两节中,存在一些值得与作者商榷的问题,现评论如下,谨希同行专家广为讨论。     

裸子植物psbA基因分子进化式样的研究

为阐明裸子植物对陆生生境生态响应的分子机制,以新近的裸子植物分类系统为指导,基于psb A基因编码全序列对4亚纲53种代表植物进行分子进化分析。首先,依据"放松分子钟"模型重建裸子植物在时间尺度下系统发育关系;其次,采用6个模型(MEC/JTT、MEC/cp REV、M5、M7、M8、M8a)估测氨基酸位点ω值,并对各模型结果进行统计检测;随后,利用Bootstrap方法检PSBA蛋白内部氨基酸位点的共进化动态。结果表明,系统树提示的物种分化历程支持前期分类结果;光合系统反应中心核心PSBA蛋白有3个氨基酸位点(13、19和243)曾经受正选择压力;PSBA蛋白内部有多对氨基酸位点间构成了共进化网络。因此,psb A基因编码序列具有作为描绘裸子植物系统发育关系标记的潜力,PSBA蛋白部分位点经历了适应性进化,通过位点间共进化网络协同作用方式辅助裸子植物响应陆生生境。     

裸子植物的幼苗类型及其进化关系

裸子植物的幼苗可分为3个类型、8个亚型。即：1．苏铁型,包括苏铁亚型、银杏亚型、南洋杉亚型;2．松型,包括杉亚型,松亚型,麻黄亚型;3．买麻膝型,包括买麻滕亚型,百岁兰亚型。类型和亚型都有特征描述,并有一个检索表。文中首先讨论了种子的起源是多元的,因而裸子植物的起源也应是多元的,是前裸子植物不同类型平行进化的结果。 又根据裸子植物幼苗类型的形态特征,提出裸子植物有4条进化路线,即：苏铁路线,银杏路线,松柏路线和买麻滕路线。还讨论幼苗类型之间的进化关系,认为除买麻滕型幼苗因其形态特殊有自己独特的发展路线外,总的趋势是由留土萌发向出土萌发发展。     

适应性实验室进化在工业生产菌株选育中应用的进展

适应性实验室进化是一种在实验室里将微生物置于一定选择压力下,通过长期驯化,筛选获得具有特定表型突变菌株的方法.近年来,该方法通过改进特定进化条件和筛选策略,已广泛应用于筛选具有优良特性的工业生产菌株,如特定表型筛选、底物高效利用、目标产物合成及生长特性优化等工业微生物菌株选育.本文综述了适应性实验室进化技术在工业生产菌...     

寄生原生动物线粒体与适应性进化

真核生物的线粒体一般具有一定的典型的结构和功能。然而,在单细胞的寄生原生动物中却不断发现从数量、结构到功能均与典型线粒体明显不同的线粒体,表现出线粒体的巨大可塑性和丰富的多样性。该文对寄生原生动物中这些多样的线粒体进行了概述,并对形成这种多样性的根本原因,即这些生物对寄生生活微氧或无氧环境线粒体所发生的种种适应性进化进行了分析探讨。     

昆虫与寄主植物的适应性及协调进化

昆虫与寄主植物的适应性及协调进化钦俊德（中国科学院动物研究所北京１０００８０）昆虫和植物都是地球上起源很早的生物类群。从化石的证据来推断，它们至少在３亿多年前已生活在一起，在不同地域建立起密切关系的生物群落。它们中不同的种类为了自身的生存和发展，并根...     

中国台湾地区H6N1禽流感病毒血凝素基因的适应性进化

2013年在中国台湾地区发现了第一例人感染H6N1禽流感,研究该地区H6N1病毒血凝素基因(HA)的适应性进化特征和种群动力学,将为人感染H6N1病毒的来源、进化及致病机制的理解提供更多信息,为进一步的研究和防治提供一定帮助。本研究从Flu和GISAID两大数据库中获得中国台湾地区所有已释放的H6N1病毒的HA序列,构建系统发育树和进化动力曲线,并推测其进化速率,分析其适应性进化特征。结果表明中国台湾地区H6N1病毒的HA有五种类型,其中人感染H6N1病毒的HA所属类型为目前当地优势类型;该病毒种群于1971年底第一次扩张,2008年迅速减少,而后又略有增加。同时在长期的进化过程中,3个位点受到正选择作用的影响,增加了病毒的适应能力;89个位点受负选择作用的影响,它们在病毒的复制、流行中可能具有重要的功能;其中剪切位点附近的329位所受负选择作用强烈(PSLAC0.001、PFEL0.000、BFREL137),此位点可能与病毒毒力有关。中国台湾地区H6N1病毒的HA已发生了明显的适应性进化,具有发生疫情的可能性,人们应高度重视,并能及时给与监测和防治。     

CVNH结构域的进化分析和选择压力检测

蓝藻抗病毒蛋白-N(Cyanovirin-N,CV-N)具有广谱抗病毒活性,其同源物构成CVNH(Cyanovirin-N homology)蛋白家族,并且家族成员的抗人类免疫缺陷病毒结构域在进化上非常保守。文章通过重建基因树对CVNH结构域的"零散分布"特点作了更为细致的了解,发现在黑曲霉、费氏曲菌、产黄青霉、粗糙脉孢霉、蓝杆藻和水蕨等物种中存在多份该结构域拷贝。在此基础上,分别采用机理式模型(Mechanistic model)和MEC模型(Mechanistic-empirical combination model)对CVNH结构域序列位点进行适应性进化分析,结果显示:1)两类模型均未检测到统计上显著的正选择位点;2)净化选择对CVNH起主导作用;3)MEC模型更适合所研究的数据。进一步使用"支-特异"模型和"支-位点"模型对蓝杆菌菌株7822和7424的祖先分支进行检测,发现该分支经历过适应性进化,并且鉴定出6个正选择位点(34L、63L、13H、76C、78K和80I)。     

Adaptive Evolution in the GAF Domain of Phytochromes in Gymnosperms

The GAF domain of phytochrome is essential for photoconversion and signal transduction. In gymnosperms, it exists in all members of the phytochrome family that experience gene duplication. Maximum-likelihood models of codon substitution can provide a framework for constructing likelihood ratio tests of changes in selective pressure and make clear predictions about patterns of genetic change following gene duplication. In this study, 68 gymnosperm GAF sequences were analyzed to identify lineages and sites under positive selection. Our results indicate that (1) positive selection at a few sites (3.6%), rather than relaxation of selective constraints, has played a major role in the evolution of the gymnosperm GAF domain; (2) strong positive selective pressure tends to occur in the recent PHYP lineages of cogeneric species, but is absent in old lineages consisting of distantly related species; and (3) the selective pressure indicated by the ω ratio varies greatly among lineages and sites in the GAF domain.     

Adaptive Evolution in LINE-1 Retrotransposons

We traced the sequence evolution of the active lineage of LINE-1(L1) retrotransposons over the last     

Widespread Adaptive Evolution in the Human Immunodeficiency Virus Type 1 Genome

We investigated variable selective pressures among amino acid sites in HIV-1 genes. Selective pressure at the amino acid level was measured by using the nonsynonymous/synonymous substitution rate ratio ( = d_N/d_S). To identify amino acid sites under positive selection with > 1, we applied maximum likelihood models that allow variable ratios among sites to analyze genomic sequences of 26 HIV-1 lineages including subtypes A, B, and C. Likelihood ratio tests detected sites under positive selection in each of the major genes in the genome: env, gag, pol, vif, and vpr. Positive selection was also detected in nef, tat, and vpu, although those genes are very small. The majority of positive selection sites is located in gp160. Positive selection was not detected if was estimated as an average across all sites, indicating the lack of power of the averaging approach. Candidate positive selection sites were mapped onto the available protein tertiary structures and immunogenic epitopes. We measured the physiochemical properties of amino acids and found that those at positive selection sites were more diverse than those at variable sites. Furthermore, amino acid residues at exposed positive selection sites were more physiochemically diverse than at buried positive selection sites. Our results demonstrate genomewide diversifying selection acting on the HIV-1.     

Cytosolic ascorbate peroxidase in Gymnosperms

ABSTRACT

Sixteen species of Gymnosperms have been screened for cytosolic ascorbate peroxidase by means of native polyacrylamide gel electrophoresis. This analysis shows that a single form of the enzyme is the most common situation. The enzyme reveals a similar electrophoretic mobility in species belonging to the same genus and sometimes to different genera. In some Pinaceae, two bands of activity were observed. The presence in the archaic spermatophyte Ginkgo biloba, as well as in the more advanced monocotyledons, of three isoforms of ascorbate peroxidase, might suggest that three different cytosolic ascorbate peroxidase genes were already present in this archaic species.     

Gymnosperms of Laos

The present review includes keys for identification and summary data on the nomenclature, morphology, ecology and distribution for all 33 species of gymnosperms hitherto recorded in the flora of Laos. They belong to 8 families and 15 genera. Important additions to these data were obtained during fieldwork in 2009–2013, when 58 localities containing 25 species from 14 genera and 8 families were explored and initially studied. Two species, Cycas laotica and Pinus cernua, are described as new species for science. Seven species, Cycas dolichophylla, C. inermis, C. macrocarpa, C. micholitzii, C. nongnoochiae, C. petraea and Taxus wallichiana, are found in Laos and represent new records for the flora of the country. Maps of the distribution and illustrations for the newly discovered gymnosperm species are provided. All observations, records and discoveries are based on reliable scientific literature and collected voucher herbarium specimens housed in main regional herbaria.     

Evolution of Xylan Substitution Patterns in Gymnosperms and Angiosperms: Implications for Xylan Interaction with Cellulose

The interaction between cellulose and xylan is important for the load-bearing secondary cell wall of flowering plants. Based on the precise, evenly spaced pattern of acetyl and glucuronosyl (MeGlcA) xylan substitutions in eudicots, we recently proposed that an unsubstituted face of xylan in a 2-fold helical screw can hydrogen bond to the hydrophilic surfaces of cellulose microfibrils. In gymnosperm cell walls, any role for xylan is unclear, and glucomannan is thought to be the important cellulose-binding polysaccharide. Here, we analyzed xylan from the secondary cell walls of the four gymnosperm lineages (Conifer, Gingko, Cycad, and Gnetophyta). Conifer, Gingko, and Cycad xylan lacks acetylation but is modified by arabinose and MeGlcA. Interestingly, the arabinosyl substitutions are located two xylosyl residues from MeGlcA, which is itself placed precisely on every sixth xylosyl residue. Notably, the Gnetophyta xylan is more akin to early-branching angiosperms and eudicot xylan, lacking arabinose but possessing acetylation on alternate xylosyl residues. All these precise substitution patterns are compatible with gymnosperm xylan binding to hydrophilic surfaces of cellulose. Molecular dynamics simulations support the stable binding of 2-fold screw conifer xylan to the hydrophilic face of cellulose microfibrils. Moreover, the binding of multiple xylan chains to adjacent planes of the cellulose fibril stabilizes the interaction further. Our results show that the type of xylan substitution varies, but an even pattern of xylan substitution is maintained among vascular plants. This suggests that 2-fold screw xylan binds hydrophilic faces of cellulose in eudicots, early-branching angiosperm, and gymnosperm cell walls.The plant secondary cell wall is a complex network of various polysaccharides and phenolic compounds that act in concert to provide strength to the cell wall (Kumar et al., 2016). Cellulose, formed of strong crystalline fibrils of linear β1,4 glucan, comprises about 40% of dry plant biomass. The other secondary cell wall polysaccharides, largely xylan and glucomannan, comprise about 30% of dry plant biomass. The abundance and structure of these hemicelluloses vary with plant species and tissues, but they have in common that they are tightly associated with cellulose. It is believed that the most important biological role of hemicelluloses is their contribution to strengthening the cell wall by interaction with cellulose and, in some walls, with lignin (Scheller and Ulvskov, 2010). However, it is unclear how hemicelluloses interact with cellulose in the cell wall (Cosgrove and Jarvis, 2012). In this work, we were interested in the interaction of cellulose with xylan, one of the most abundant polysaccharides in nature.To understand polysaccharide interactions in the cell wall, we need to know not only the hemicellulose primary structure, but also the conformation of the polysaccharide chains. The glucan chains in cellulose are similar to a flat ribbon known as a 2-fold helical screw and associate through lateral hydrogen bonding into sheets. The sheets of glucan chains stack on top of each other, resulting in highly ordered crystalline cellulose. It is still unclear how many glucan chains form a microfibril and whether the microfibril has a hexagonal or rectangular cross section. However, recent studies shed some light onto these questions (Fernandes et al., 2011; Newman et al., 2013; Thomas et al., 2013; Cosgrove, 2014; Oehme et al., 2015; Thomas et al., 2015; Wang and Hong, 2016; Vandavasi et al., 2016). Whichever model is favored, hydrophobic (e.g. 100 or 200) and hydrophilic (e.g. 110 or 010) crystal faces are exposed for interaction with other molecules such as hemicelluloses (Zhao et al., 2014; Cosgrove, 2014; Li et al., 2015).The β1,4 xylan backbone is always further modified, often by acetyl (Ac), arabinosyl (Ara), and glucuronosyl (MeGlcA) side-chain substitutions. These substitutions are supposed to be necessary to maintain xylan solubility (Mikkelsen et al., 2015). Unsubstituted xylan forms crystalline fibers of chains adopting a 3-fold screw helix (Nieduszynski and Marchessault, 1971). Consequently, xylan substitutions are essential for xylan function and vascular plant viability (Mortimer et al., 2010; Xiong et al., 2013, 2015). In vitro experiments and in silico modeling suggest xylan interacts with cellulose, and it is widely accepted that this is partly through interactions on the hydrophobic faces of the cellulose fibrils (Bosmans et al., 2014; Köhnke et al., 2011; Kabel et al., 2007; Busse-Wicher et al., 2014). In contrast to the binding to the hydrophobic faces, the backbones of highly substituted hemicelluloses are thought to be unable to hydrogen bond effectively with the hydrophilic surfaces of cellulose fibrils because of steric hindrance. For example, hydrogen bonding of the xyloglucan backbone to cellulose would be blocked by steric restrictions of the side chains (Finkenstadt et al., 1995; Zhang et al., 2011). How then does the naturally occurring, highly substituted, xylan interact with cellulose? Our recent findings in the eudicot Arabidopsis (Arabidopsis thaliana) revealed that the majority of xylan bears substitutions solely on alternate xylosyl residues. Every second Xyl is acetylated (Busse-Wicher et al., 2014; Chong et al., 2014), and MeGlcA side chains reside on evenly spaced xylosyl residues, largely at 6-, 8-, 10-, or 12-residue intervals (Bromley et al., 2013). In this scenario, on a xylan backbone in the ribbon-like 2-fold helical screw conformation, all the decorations will face one side, creating an unsubstituted xylan surface. Therefore, in addition to forming stacking interactions on the hydrophobic surface, this xylan structure is compatible with hydrogen bonding to the hydrophilic surface of cellulose (Busse-Wicher et al., 2014; Busse-Wicher et al., 2016).Both xylan and glucomannan are substantial components of vascular plant secondary cell walls (Timell, 1967; Willfor et al., 2005; McKee et al., 2016). In conifers (gymnosperms, Pinales), the main hemicellulose is glucomannan, but eudicots possess relatively little glucomannan (Scheller and Ulvskov, 2010; Huang et al., 2015), and the secondary cell walls are dominated by xylan, suggesting xylan might have adopted additional functions in these flowering plants that produce hardwoods (Dammström et al., 2009). Conifers, providing softwood for the paper, pulp, and construction industries, are of major ecological and economical value. Consequently, understanding the function and architecture of the cell wall components of softwoods and hardwoods is of great importance.To investigate whether the precise arrangement of xylan decorations on evenly spaced xylosyl residues, as seen in eudicots, is a novel feature of hardwood xylan, we analyzed the pattern of xylan substitution in various gymnosperms and angiosperms. In addition to conifers, there are three further gymnosperm lineages: Cycad, Gingko and Gnetophyta (Fig. 1). There has been a debate whether Gnetophyta are the gymnosperm lineage most closely related to the angiosperms (Davis and Schaefer, 2011; Uddenberg et al., 2015). There are few studies across gymnosperm lineages to determine any divergence in the structure of xylans.Open in a separate windowFigure 1.Schematic representation of the phylogenetic relationship between gymnosperm and angiosperm species studied in this work. The distances do not correspond to phylogenetic distances.Our work shows that some gymnosperm xylans have decorations and decoration patterns that are different to those of eudicot xylans. Nevertheless, these modifications largely reside on even xylosyl residues on the backbone. Molecular dynamics simulations support the hypothesis that this highly conserved organization of substitutions allows an unsubstituted surface of xylan to bind stably to hydrophilic faces of cellulose fibrils.