Phylogenetic analyses of Fringillidae (Aves : Passeriformes) using mitochondrial tRNA gene sequences and secondary structure

Fringillidae is a large and diverse family of Passeriformes. So far, however, Fringillidae relationships deduced from morphological features and by a number of molecular approaches have remained unproven. Recently, much attention has been attracted to mitochondrial tRNA genes, whose sequence and secondary structural characteristics have shown to be useful for Acrodont Lizards and deep-branch phylogenetic studies. In order to identify useful phylogenetic markers and test Fringillidae relationships, we have sequenced three major clusters of mitochondrial tRNA genes from 15 Fringillidae, taxa. A coincident tree, with coturnix as outgroup, was obtained through Maximum-likelihood method using combined dataset of 11 mitochondrial tRNA gene sequences. The result was similar to that through Neighbor-joining but different from Maximum-parsimony methods. Phylogenetic trees constructed with stem-region sequences of 11 genes had many different topologies and lower confidence than with total sequences. On the other hand, some secondary structural characteristics may provide phylogenetic information on relatively short internal branches at under-genus level. In summary, our data indicate that mitochondrial tRNA genes can achieve high confidence on Fringillidae phylogeny at subfamily level, and stem-region sequences may be suitable only at above-family level. Secondary structural characteristics may also be useful to resolve phylogenetic relationship between different genera of Fringillidae with good performance.

氨酰-tRNA合成酶的进化差异

下载PDF阅读器大量研究显示,细菌与真核生物中的许多氨酰-tRNA合成酶(aaRS)在一些细菌与真核生物中的基因进化机制与模式、氨酰化途径和结构与功能的进化模式等方面往往有着明显的差异.通过对这些差异的深入研究,对于理解蛋白质的结构与功能的进化将是非常有帮助的.虽然造成这些差异的机制目前仍不清楚,但是,所有的这些差异似乎提示,在细菌与真核生物的一些基本生命活动过程中的某些方面,可能还存在着目前尚未被人们所认识到的较大差异.

氨酰-tRNA合成酶专一性识别的进化

氨酰-tRNA合成酶(AARS)是一类在蛋白质合成过程中起着重要作用的酶,它通过与tRNA及其相应氨基酸的专一性识别作用,使得基因序列能够被精确地翻译成蛋白质序列。然而,氨酰-tRNA合成酶的这种识别作用既有专一性,也具有“兼容性”。氨酰-tRNA合成酶的这种双重性质不仅与其结构的进化有关,而且还与其所处的各类生物的不同进化阶段有关。AARS似乎经历了一个由“模糊专一性”(多重专一性)到“精确专一性”(单一专一性)的演变历程。

苯丙氨酰tRNA合成酶的进化与结构域丢失

基因的复制、融合以及基因的水平转移是许多蛋白质包括氨酚t RNA合成酶(aminoacyl-tRNA synthetase , AARS)进化过程中的常见事件。然而作者研究的结果显示，苯丙氨酚 t RNA合成酶( phenylalanyl-tRNA synthetase , PheRS)的进化主要表现为 一些结构域的丢失;并且这种结构域的丢失不影响Phe RS的功能或活性。通常在生物从细菌到真核生物的进化过程中，其基因组的大小和基因的数目都有所增加，然而有趣的是，真核生物中Phe RS的结构域类型和数目都明显少于细菌的Phe RS oPhe RS通过结构域的丢失而进化的现象，似乎与某些AARS功能由多重专一性向单一专一性的演化有着“异曲同工”之妙。

Evolution of structures and specific recognitions in aminoacyl-tRNA synthetases

The aminoacyl-tRNA synthetases (AARS) are very important during the protein biosynthesis, which can make the gene sequence be accurately translated into the protein sequence by the specific recognition between AARS and tRNA/amino acids. However, the recog

Evolution of phenylalanyl-tRNA synthetase by domain losing

The gene duplication, fusion and horizontal transfer are the frequent events during evolution of many proteins, including the aminoacyl-tRNA synthetases (AARSs). However, in this work, it was shown that the main event during evolution of phenylalanyl-tRNA synthetase (PheRS) is a domain loss, and the function/activity of PheRS is not affected by domain losing. Generally, the size of genome and number of genes are increased during evolution from bacteria to eukaryote, but the interesting thing is that the type and number of PheRS domains in eukaryotae are obviously less than those in bacteria. The evolution of PheRS by domain losing seems to be related to the functional evolution of some AARSs from the multiple specificities to the single specificity.

Evolution of different oligorneric glycyl-tRNA synthetases

There are two oligomeric types of glycyl-tRNA synthetases (GlyRSs) in genome, the alpha(2)beta(2) tetramer and alpha(2) dimer. Here, we showed that the anticodon-binding domains (ABDs) of dimeric and tetrameric GlyRSs are non-homologous, although their catalytic central domains (CCDs) are homologous. The dimeric GlyRS_ABD is fused to the C-terminal of CCD in alpha-subunit, but the tetrameric GlyRS_ABD is to the C-terminal in beta-subunit during evolution. Generally, one species only contains one oligomeric type of GlyRS, but the both oligomeric GlyRSs with the multiple homologous domains can be observed in Magnetospirillum magnetotacticum genome, nevertheless, these homologous domains are probably from different genomes. (C) 2005 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Molecular Mechanics Simulation of Recognition Identity of tRNA~(His/GUG)

本文选用经过实验验证的碱基序列 ,用简化的方式 ,构建了被水分子和镁离子修饰的核酸序列的分子模型 ,应用分子力学模拟方法对序列进行能量优化 ,对优化后序列的构象参数、成键状况和能量数据等进行了分析。对tRNAHHis GUG的识别特性作了初步的探索 ,得到了和实验结果相近的结论。此外 ,还从能力学的角度讨论了溶剂 -溶质 -溶剂相互作用形成的网状氢键网络对核酸结构稳定性的影响 ,探讨了非Crick_WatsonGU、UU配对的能力学特征并存在于被水分子和镁离子修饰的核酸序列中的GU、UU配对情况。

细胞分化中的tRNA修饰现象

<正> Kersten和Katze等人的实验表明,真菌、粘菌和脊椎动物癌组织的细胞分化过程中存在着tRNA的核苷酸被修饰的现象。修饰发生在某些tRNA特定的位置上。tRNA~(Asn)、tRNA~(Asp)、tRNA~(His)和tRNA~(Tyr)的反密码子第一位(第34号位)的鸟苷(G)被queosine(Q)代替。Q是鸟嘌呤的嘌呤骨架修饰成一个7-去氮结构,它的化学名称应叫7-(4,5-顺式-二羟-2-环戊烯

氨酰-tRNA合成酶结构域的进化研究

氨酰-tRNA合成酶(Aminoacyl-tRNA synthetases, aaRS)是一类在蛋白质生物合成中具有重要作用的酶，它可以活化氨基酸，并与相应的tRNA相识别，使得基因序列能够被精确的翻译成蛋白质序列，保证了生命体的严谨性和多样性。通常，每一类aaRS都包含有一个催化核心结构域(Catalytic central domain, CCD)和一个结合反密码子的结构域(Anticodon-binding domain, ABD)。大量研究显示，细菌与真核生物中的许多aaRS在一些细菌与真核生物中的基因进化机制与模式、氨酰化途径、结构与功能的进化模式等方面往往有着明显的差异。通过对这些差异的深入研究，对于理解蛋白质的结构、功能的进化将是非常有帮助的。虽然，造成这些差异的本质，目前仍不清楚，但是，所有的这些差异似乎提示，在细菌与真核生物的一些基本生命活动过程中的某些方面，可能还存在着目前尚未被人们所认识到的较大差异。 甘氨酰-tRNA合成酶(Glycyl-tRNA synthetase，GlyRS)在基因组中存在着两种寡聚体形式，即α2β2四聚体和α2二聚体。本研究的结果显示，四聚体和二聚体GlyRS的ABD并不同源，而它们的CCD却具有共同的起源。在进化过程中，由于基因的融合，二聚体GlyRS的ABD融合到α亚基上CCD后的C-末端，而四聚体GlyRS的ABD则加在了β亚基的C-末端。通常，同一物种中只存在一种寡聚体形式的GlyRS，但是在Magnetospirillum magnetotacticum基因组中同时存在GlyRS的两种寡聚体形式，并有多个同源的结构域，而这些同源的结构域很可能来源于不同的基因组。二聚体GlyRS存在于细菌、古细菌和真核生物中，而四聚体GlyRS仅在大多数细菌中发现。在从细菌到真核生物的进化过程中，GlyRS可能经历了一个复杂的进化历程。频繁的基因丢失和获得事件导致了GlyRS分布的差异。水平基因转移是四聚体GlyRS进化的一个主要因素。大量的细菌基因水平转移导致四聚体GlyRS基因可在植物中表达，而在动物中形成假基因。 通常，由于aaRS-I和aaRS-II具有不同的结构和催化机制，它们被认为在进化上没有联系。虽然，苯丙氨酰-tRNA合成酶(phenylalanyl-tRNA synthetase, PheRS)属于aaRS-II，但它的催化机制却类似于aaRS-I。结构域的进化分析表明，细菌、古细菌和真核生物的PheRS具有明显不同的结构，因而导致从细菌到真核生物的进化过程中，PheRS和 tRNAPhe间的识别机制发生了变化。序列分析表明，PheRS的结构域(包括CCD、ABD及其它结构域)与aaRS-I的某些结构域同源，因此，在进化上，PheRS是aaRS-II与aaRS-I之间联系的纽带。这些结果表明，在进化的过程中，aaRS-I和aaRS-II可能是由同一个共同的祖先CCD经过可变剪接和插入演化而来的，结构域间的不同组合导致aaRS-I和aaRS-II在结构和催化机制上的显著差异。

Probing lanthanide ions binding on tRNA(Phe) by H-1 NMR

The structure of phenylalanine transfer ribonucleic acid (tRNA(Phe)) in solution was explored by H-1 NMR spectroscopy to evaluate the effect of lanthanide ion on the structural and conformational change. It was found that La3+ ions possess specific effects on the imino proton region of the H-1 NMR spectra for yeast tRNA(Phe). The dependence of the imino proton spectra of yeast tRNA(Phe) as a function of La3+ concentration was examined, and the results suggest that the tertiary base pair G(15). C-48, which is located in the terminal in the augmented dihydrouridine helix (D-helix), was markedly affected by La3+ (shifted to downfield by as much as 0.35). Base pair U-8. A(14) in yeast tRNA(Phe), which are stacked on G(15). C-48, was also affected by added La3+ when 1 similar to 2 Mg2+ were also present. Another imino proton that may be affected by La3+ in yeast tRNA(Phe) is that of the tertiary base pair G(19). C-56. The assignment of this resonance in yeast tRNA(Phe) is tentative since it is located in the region of highly overlapping resonances beween 12.6 and 12.2. This base pair helps to anchor the D-loop to the T Psi C loop. The binding of La3+ caused conformational change of tRNA, which is responsible for shifts to upfield or downfield in H-1 NMR spectra.

Effect of lanthanum ions on tRNA(Phe) structure: Imino proton NMR spectroscopy

The effect of lanthanum ions on the structural and conformational change of yeast tRNA(Phe) was studied by H-1 NMR. The results suggest that the tertiary base pair (G-15)(C-48), which was located in the terminal in the augmented dihydrouridine helix (D-helix), was markedly affected by adding La3+ and shifted 0.33 downfield. Based pair (U-8)(A-14), which is associated with a tertiary interaction, links the base of the acceptor stem to the D-stem and anchors the elbow of the L structure, shifted 0.20 upfield. Another imino proton that may be affected by La3+ in tRNA(Phe) is the tertiary base pair (G-19)(C-56). The assignment of this resonance is tentative since it is located in the region of highly overlapping resonances between 12.6 and 12.2. This base pair helps to anchor the D-loop to the T psi C loop.

镧离子对tRNA~(Phe)结构的影响:亚胺质子NMR谱

采用1HNMR方法研究了镧离子对酵母tRNAPhe分子结构和构象变化的影响 .结果表明位于扩大二氢尿嘧啶螺旋 (D 螺旋 )的端梢三级碱基对 (G_15) (C_4 8)明显受加入La3+ 的影响 ,向低场位移 0 33;与三级相互作用相关 ,连接D 茎和接受茎起固定L结构转折的 (U_8) (A_14)碱基对向高场位移 0 2 0 ;另一可能受La3+影响的亚胺质子碱基对为 (G_19) (C_56 ) ,由于该碱基对位于高度叠加的 12 6和 12 2之间 ,其归属仅供参考 ,该碱基对有助于D 环对TΨC环的连接.

铕离子对tRNA~(Phe)结构影响的NMR研究

采用ＮＭＲ波谱方法研究了溶液中铕离子对酵母苯丙氨酸转移核糖核酸（ｐｈｅｎｙｌａｌａ－ｎｉｎｅｔｒａｎｓｆｅｒｒｉｂｏｎｕｃｌｅｉｃａｃｉｄ，简称ｔＲＮＡＰｈｅ）结构和构象变化的影响．Ｅｕ３＋离子对ｔＲＮＡＰｈｅ亚胺质子范围的１ＨＮＭＲ谱具有特殊的影响，酵母ｔＲＮＡＰｈｅ亚胺质子谱作为Ｅｕ３＋浓度函数的研究表明位于扩大二氢尿嘧啶螺旋（Ｄ－螺旋）的端梢三级碱基对Ｇ１５·Ｃ４８明显地受加入Ｅｕ３＋的影响（向低场位移０．８５）；堆积在Ｇ１５·Ｃ４８上的Ｕ８·Ａ１４碱基对在存有１～２个Ｍｇ２＋离子下亦受加入Ｅｕ３＋的影响．酵母ｔＲＮＡＰｈｅ中可能受到Ｅｕ３＋影响的另一亚胺质子为Ｇ１９·Ｃ５６三级碱基对，由于Ｇ１９·Ｃ５６的亚胺质子共振位于高度叠加的１２．６与１２．２之间，其归属仅供参考．该碱基对有助于Ｄ－环对ＴΨＣ环的联接．配位Ｅｕ３＋引起ｔＲＮＡ分子构象的变化并且导致一些谱峰向高场或低场位移.

The complete mitochondrial genome of the ridgetail white prawn Exopalaemon carinicauda Holthuis, 1950 (Crustacean: Decapoda: Palaemonidae) revealed a novel rearrangement of tRNA genes

The complete mitochondrial (mt) DNA sequence was determined for a ridgetail white prawn, Exopalaemon carinicauda Holthuis, 1950 (Crustacea: Decopoda: Palaemonidae). The mt genome is 15,730 bp in length, encoding a standard set of 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes, which is typical for metazoans. The majority-strand consists of 33.6% A, 23.0% C, 13.4% G, and 30.0% T bases (AT skew = 0.057: GC skew = -0.264). A total of 1045 bp of non-coding nucleotides were observed in 16 intergenic regions,,including a major A+ T rich (79.7%) noncoding region (886 bp). A novel translocation of tRNA(Pro) and tRNA(Thr) was found when comparing this genome with the pancrustacean ground pattern indicating that gene order is not conserved among caridean mitochondria. Furthermore, the rate of Ka/Ks in 13 protein-coding genes between three caridean species is Much less than 1, which indicates a strong Purifying selection within this group. To investigate the phylogenetic relationship within Malacostraca, phylogenetic trees based oil Currently available malacostracan complete mitochondrial sequences were built with the maximum likelihood and Bayesian models. All analyses based oil nucleotide and amino acid data strongly support the monophyly of Decapoda. The Penaeidae, Reptantia, Caridea, and Meiura clades were also recovered as monophyletic groups with Strong Statistical Support. However, the phylogenetic relationships within Pleocyemata are unstable, as represented by the inclusion or exclusion of Caridea. (C) 2009 Elsevier B.V. All rights reserved.