植物进化中的正选择作用

正选择是指将因含有有利突变而提高个体适合度的等位基因固定下来的选择作用,研究正选择对理解生物进化过程具有重要意义。本文回顾了近年来在植物基因中发现的正选择作用,分别对陆生植物和藻类中经历正选择作用的基因进行了总结,其中在陆生植物中发现的正选择位点主要集中在与生殖相关及与抗逆相关的基因上,这为以后对植物中正选择作用的研究提供了线索。     

水稻抗逆相关基因的分子进化分析

植物在进化过程中为了适应外界环境,已经具有一套完整的抵抗外界特殊环境的调控系统。但是,关于水稻抗逆相关基因的分子进化方面的研究还未见报道。文章通过Plant Tolerance Gene Database数据库,获得22个水稻抗逆相关基因。利用比较基因组学和生物信息学方法对水稻抗逆相关基因的进化动态进行研究,结果表明水稻抗逆相关基因在低等植物中比较保守;随着植物的不断进化和生存环境的改变,其基因数量也随之增加。具有相似抗性功能的基因往往具有相似的基因结构和基序(motif)结构。文章还发现4个保守motif 的存在：HRDXK、DXXSXG、LLPR和GXGXXG(X代表任意氨基酸)。在GSK1、RAN2抗逆基因中发现了3个特有的motif结构：GSK1特有的P-rich motif,RAN2特有的G-rich motif和E-rich motif。推测这些保守的motif结构与基因的抗逆功能密切相关。进化速率分析结果表明,尽管植物抗逆性相关基因在进化过程中受到较强的纯化选择作用,但是仍然有50%的抗逆性相关基因存在正选择位点。这些正选择位点的存在有可能为基因适应外界环境变化提供了重要的物质基础。     

MIR166基因家族在陆生植物中的进化模式分析

MicroRNA（miRNA）是一类广泛存在于真核生物中的具有转录后水平调控功能的内源非编码小分子RNA。在植物中．miRNA通过对靶基因的剪切或沉默来实现对植物生命活动的调控,它是基因表达调控网络的重要组成部分。miR165／166（miR166）是陆生植物中最为古老的MIRNA家族之一,它通过对3型同源异域型-亮氨酸拉链（1id—ZIPⅢ）等靶标的调控,在植物的众多发育时期起着关键的调控作用。本文分析了MIR166基因在陆生植物中的进化关系,并对MIR166在基部陆生植物小立碗藓（Physcomitrella patens）中的复制及进化进行了研究。此外,HD—ZIPⅢ蛋白是植物中重要的一类转录因子,miR166对HD-ZIP Ⅲ基因的调控作用在陆地植物保守的存在,本文对HD—ZIP Ⅲ基因和miR166在进化中的相互作用进行了初步的探讨。     

百合属5种植物的比较转录组分析

百合属植物是多年生的宿根草本植物,具有重要的观赏价值,有的种可食用也可药用。本研究对百合属4种植物(细叶百合、川百合、卷丹和百合)花的转录组进行测序,并结合前期的野百合的转录组数据进行比较转录组分析,鉴别花发育相关基因。并筛选出5种植物的直系同源基因,进而检测正选择基因,分析它们对环境的适应性。通过组装分别在细叶百合、川百合、卷丹以及百合花中获得了44565、51413、41638和44716个unigene。为了了解unigene功能信息,将其在公共数据库中进行比对和注释,发现了13个花发育相关基因。另外,在5个物种间共获得8247对直系同源基因,并计算其Ka、Ks及Ka/Ks值。在5个物种中有33对直系同源基因受到了强烈的正选择作用,随后对其进行GO、KEGG功能富集分析及基因功能注释,发现这些基因主要是与抗性以及生物合成相关的基因。     

miR156靶基因SPL在植物中的系统分布和进化模式分析

Squamosa promoterbinding proteinlike genes （SPLs）在植物发育过程中具有重要作用。很多SPLs被miR156调节,然而,对于它们在植物中的系统分布和进化模式还知之甚少。本文对9个测序物种（藻类,苔藓,石松,单子叶和双子叶植物）的183个SPLs进行了生物信息学分析。结果表明miR156应答元件（MREs）仅在陆生植物SPLs中发现,藻类中不存在。系统进化分析显示陆生植物SPLs分为两大分支：group I和group II。 MiR156靶基因仅分布于group II,表明它们有着共同的祖先。Group II进一步分为7个亚支（IIaIIg）,miR156靶基因分布在除IId外的其余6个亚支的特定SPLs。系统分类与基因结构的相关性反映了SPL靶基因结构上的变化。在进化过程中,它们可能发生外显子的丢失且伴随MRE的丢失。另外,基因重复对SPL靶基因的丰度变化影响很大,尤其是被子植物与低等植物分歧后它们数量明显增加。以拟南芥为模式植物分析发现串联重复和片段重复是SPL靶基因扩张的主要机制。     

miR156靶基因SPL在植物中的系统分布和进化模式分析

Squamosa promoter binding protein like genes (SPLs)在植物发育过程中具有重要作用。很多SPLs被miR156调节,然而,对于它们在植物中的系统分布和进化模式还知之甚少。本文对9个测序物种（藻类,苔藓,石松,单子叶和双子叶植物）的183个SPLs进行了生物信息学分析。结果表明miR156应答元件（MREs）仅在陆生植物SPLs中发现,藻类中不存在。系统进化分析显示陆生植物SPLs分为两大分支：group I和group II。 MiR156靶基因仅分布于group II,表明它们有着共同的祖先。Group II进一步分为7个亚支(IIa IIg),miR156靶基因分布在除IId外的其余6个亚支的特定SPLs。系统分类与基因结构的相关性反映了SPL靶基因结构上的变化。在进化过程中,它们可能发生外显子的丢失且伴随MRE的丢失。另外,基因重复对SPL靶基因的丰度变化影响很大,尤其是被子植物与低等植物分歧后它们数量明显增加。以拟南芥为模式植物分析发现串联重复和片段重复是SPL靶基因扩张的主要机制。     

精子发生相关基因的研究进展

哺乳类动物的精子发生历经有丝分裂、减数分裂和精子形成三个阶段,这一特殊的细胞分化过程受多种因素的调控,而生精细胞内基因水平的调节,在精子发生过程中起着决定性的作用.许多生精细胞特异性的基因或转录具有发育阶段特异性表达特征,参与精子发生过程中特异的细胞分化活动,如减数分裂、遗传物质重组、染色质的浓缩和发育后期的一系列形态变化.近年来随着基因克隆、表达及功能研究技术的发展与应用,发现了许多精子发生的相关基因,有的已被证明在精子发生中起重要作用.然而对这一过程中许多现象的关键基因还所知甚少,需要进行更加广泛深入的研究.本文旨在较全面地综述这一领域研究的最新进展,着重讨论了与精子发生有关的转录因子基因、细胞周期相关基因、原癌基因、细胞凋亡相关基因、核蛋白转型相关基因方面的研究,为从事该领域研究的工作者提供参考信息.     

欧李DAM5基因的克隆及表达分析

休眠相关MADS-box(DAM)基因在植物芽休眠诱导过程中发挥重要作用。该研究以欧李‘农大4号’不同阶段的芽为材料,利用PCR技术,克隆获得ChDAM基因。ChDAM基因全长705 bp,编码234个氨基酸。多序列比对与结构域分析发现,ChDAM基因编码的蛋白具有典型的MADS-box结构域和K-box结构域,其氨基酸序列与桃的DAM5蛋白相似性较高。启动子分析发现,ChDAM5基因的表达可能会受到低温和脱落酸的调控。实时荧光定量PCR分析发现,ChDAM5基因的表达随着休眠诱导进程逐渐升高。研究推测,ChDAM基因在诱导欧李芽休眠中发挥关键作用,为后续深入的代谢途径研究奠定了基础。     

植物果实成熟相关基因的转录调控

本文综述了番茄和苹果的一些果实成熟相关基因启动子的结构和作用特点,以及植物果实相关基因转录调控机制的研究现状。     

植物Mg2+转运蛋白与相关基因及其功能的研究进展

镁离子是植物细胞中最丰富的二价阳离子.在植物的生长发育中起着重要的作用.对Mg2+独特的几何和化学性质,Mg2对植物细胞体内中动态平衡的影响,植物中Mg2+转运相关蛋白与相关基因及其功能的研究进展进行了综述.     

Evolutionary History of Cathepsin L (L-like) Family Genes in Vertebrates

Cathepsin L family, an important cysteine protease found in lysosomes, is categorized into cathepsins B, F, H, K, L, S, and W in vertebrates. This categorization is based on their sequence alignment and traditional functional classification, but the evolutionary relationship of family members is unclear. This study determined the evolutionary relationship of cathepsin L family genes in vertebrates through phylogenetic construction. Results showed that cathepsins F, H, S and K, and L and V were chronologically diverged. Tandem-repeat duplication was found to occur in the evolutionary history of cathepsin L family. Cathepsin L in zebrafish, cathepsins S and K in xenopus, and cathepsin L in mice and rats underwent evident tandem-repeat events. Positive selection was detected in cathepsin L-like members in mice and rats, and amino acid sites under positive selection pressure were calculated. Most of these sites appeared at the connection of secondary structures, suggesting that the sites may slightly change spatial structure. Severe positive selection was also observed in cathepsin V (L2) of primates, indicating that this enzyme had some special functions. Our work provided a brief evolutionary history of cathepsin L family and differentiated cathepsins S and K from cathepsin L based on vertebrate appearance. Positive selection was the specific cause of differentiation of cathepsin L family genes, confirming that gene function variation after expansion events was related to interactions with the environment and adaptability.     

Positive selection vectors

This review describes information concerning positive selection vectors on their mechanism, classification, property, and limitation. A total of 72 positive selection vectors collected were discussed. Positive selection vectors can reduce background and directly screen transformants containing cloned DNA fragments. The mechanisms to perform positive selection include insertional inactivation and the replacement of functional genes of the vectors. In general, the former is much more convenient than the latter. The functional genes are controlled either by their promoters or by heterologous promoters introduced. On the basis of the structures, positive selection vectors could be classified into five groups. The positive selection vectors are commonly based on the mechanisms of lethal genes and the sensitivity of compounds. The vectors, with molecular weights ranging from 2.6 to 17.0 kb, have diverse genetic markers and wide host ranges, including Escherichia coli, Bacillus, Streptomyces, lactic acid bacteria, yeasts, and mammalian cells. Although some limitations exist for using some positive selection vectors, they are useful in recombinant DNA experiments.     

Selectable marker genes in transgenic plants: applications, alternatives and biosafety

Approximately fifty marker genes used for transgenic and transplastomic plant research or crop development have been assessed for efficiency, biosafety, scientific applications and commercialization. Selectable marker genes can be divided into several categories depending on whether they confer positive or negative selection and whether selection is conditional or non-conditional on the presence of external substrates. Positive selectable marker genes are defined as those that promote the growth of transformed tissue whereas negative selectable marker genes result in the death of the transformed tissue. The positive selectable marker genes that are conditional on the use of toxic agents, such as antibiotics, herbicides or drugs were the first to be developed and exploited. More recent developments include positive selectable marker genes that are conditional on non-toxic agents that may be substrates for growth or that induce growth and differentiation of the transformed tissues. Newer strategies include positive selectable marker genes which are not conditional on external substrates but which alter the physiological processes that govern plant development. A valuable companion to the selectable marker genes are the reporter genes, which do not provide a cell with a selective advantage, but which can be used to monitor transgenic events and manually separate transgenic material from non-transformed material. They fall into two categories depending on whether they are conditional or non-conditional on the presence of external substrates. Some reporter genes can be adapted to function as selectable marker genes through the development of novel substrates. Despite the large number of marker genes that exist for plants, only a few marker genes are used for most plant research and crop development. As the production of transgenic plants is labor intensive, expensive and difficult for most species, practical issues govern the choice of selectable marker genes that are used. Many of the genes have specific limitations or have not been sufficiently tested to merit their widespread use. For research, a variety of selection systems are essential as no single selectable marker gene was found to be sufficient for all circumstances. Although, no adverse biosafety effects have been reported for the marker genes that have been adopted for widespread use, biosafety concerns should help direct which markers will be chosen for future crop development. Common sense dictates that marker genes conferring resistance to significant therapeutic antibiotics should not be used. An area of research that is growing rapidly but is still in its infancy is the development of strategies for eliminating selectable marker genes to generate marker-free plants. Among the several technologies described, two have emerged with significant potential. The simplest is the co-transformation of genes of interest with selectable marker genes followed by the segregation of the separate genes through conventional genetics. The more complicated strategy is the use of site-specific recombinases, under the control of inducible promoters, to excise the marker genes and excision machinery from the transgenic plant after selection has been achieved. In this review each of the genes and processes will be examined to assess the alternatives that exist for producing transgenic plants.     

Positive Selection Vectors

ABSTRACT:?

This review describes information concerning positive selection vectors on their mechanism, classification, property, and limitation. A total of 72 positive selection vectors collected were discussed. Positive selection vectors can reduce background and directly screen transformants containing cloned DNA fragments. The mechanisms to perform positive selection include insertional inacti-vation and the replacement of functional genes of the vectors. In general, the former is much more convenient than the latter. The functional genes are controlled either by their promoters or by heter-ologous promoters introduced. On the basis of the structures, positive selection vectors could be classified into five groups. The positive selection vectors are commonly based on the mechanisms of lethal genes and the sensitivity of compounds. The vectors, with molecular weights ranging from 2.6 to 17.0?kb, have diverse genetic markers and wide host ranges, including Escherichia coli, Bacillus, Streptomyces, lactic acid bacteria, yeasts, and mammalian cells. Although some limitations exist for using some positive selection vectors, they are useful in recombinant DNA experiments.     

The 35S promoter used in a selectable marker gene of a plant transformation vector affects the expression of the transgene

Positive selection of transgenic plants is essential during plant transformation. Thus, strong promoters are often used in selectable marker genes to ensure successful selection. Many plant transformation vectors, including pPZP family vectors, use the 35S promoter as a regulatory sequence for their selectable marker genes. We found that the 35S promoter used in a selectable marker gene affected the expression pattern of a transgene, possibly leading to a misinterpretation of the result obtained from transgenic plants. It is likely that the 35S enhancer sequence in the 35S promoter is responsible for the interference, as in the activation tagging screen. This affected expression mostly disappeared in transgenic plants generated using vectors without the 35S sequences within their T-DNA region. Therefore, we suggest that caution should be used in selecting a plant transformation vector and in the interpretation of the results obtained from transgenic approaches using vectors carrying the 35S promoter sequences within their T-DNA regions.     

正向选择的生物安全标记基因

标记基因的产生方便了植物的转化,随着转基因植物的迅速发展及商品化,人类更关注抗性标记基因的安全性。目前解决的有效途径是发展正向选择系统,使用非抗性的生物安全标记基因,主要包括糖类代谢酶基因（pmi和xylA）、干扰氨基酸代谢酶基因（ak和dapA）、绿色荧光蛋白基因（gfp）、β-葡萄糖苷酸酶基因（gus）、核糖醇操纵子（rtl）和叶绿素生物合成基因（hemL）等。     

The divergence and positive selection of the plant‐specific BURP‐containing protein family

BURP domain‐containing proteins belong to a plant‐specific protein family and have diverse roles in plant development and stress responses. However, our understanding about the genetic divergence patterns and evolutionary rates of these proteins remain inadequate. In this study, 15 plant genomes were explored to elucidate the genetic origins, divergence, and functions of these proteins. One hundred and twenty‐five BURP protein‐encoding genes were identified from four main plant lineages, including 13 higher plant species. The absence of BURP family genes in unicellular and multicellular algae suggests that this family (1) appeared when plants shifted from relatively stable aquatic environments to land, where conditions are more variable and stressful, and (2) is critical in the adaptation of plants to adverse environments. Promoter analysis revealed that several responsive elements to plant hormones and external environment stresses are concentrated in the promoter region of BURP protein‐encoding genes. This finding confirms that these genes influence plant stress responses. Several segmentally and tandem‐duplicated gene pairs were identified from eight plant species. Thus, in general, BURP domain‐containing genes have been subject to strong positive selection, even though these genes have conformed to different expansion models in different species. Our study also detected certain critical amino acid sites that may have contributed to functional divergence among groups or subgroups. Unexpectedly, all of the critical amino acid residues of functional divergence and positive selection were exclusively located in the C‐terminal region of the BURP domain. In conclusion, our results contribute novel insights into the genetic divergence patterns and evolutionary rates of BURP proteins.