Nucleosomal Positioning and Genetic Divergence Study Based on DNA Flexibility Map

Abstract

Based on worm like chain model, DNA structural parameters—tilt, roll and rise, derived from crystallographic database have been used to determine the flexibility of DNA that regulates the nucleosomal translational positioning. Theoretically derived data has been compared to the experimental values available in Ioshikhes and Trifonov's database. The methodology has been extended to determine the flexibility of 18S rRNA genome in eukarya, where yeast shows a distinct difference when compared with mammals like human, mouse and rabbit.     

The Impact of Message Mutation on the Fitness of a Genetic Code

The Standard Genetic Code is organized such that similar codons encode similar amino acids. One explanation suggested that the Standard Code is the result of natural selection to reduce the fitness ``load' that derives from the mutation and mistranslation of protein-coding genes. We review the arguments against the mutational load-minimizing hypothesis and argue that they need to be reassessed. We review recent analyses of the organization of the Standard Code and conclude that under cautious interpretation they support the mutational load-minimizing hypothesis. We then present a deterministic asexual model with which we study the mode of selection for load minimization. In this model, individual fitness is determined by a protein phenotype resulting from the translation of a mutable set of protein-coding genes. We show that an equilibrium fitness may be associated with a population with the same genetic code and that genetic codes that assign similar codons to similar amino acids have a higher fitness. We also show that the number of mutant codons in each individual at equilibrium, which determines the strength of selection for load minimization, reflects a long-term evolutionary balance between mutations in messages and selection on proteins, rather than the number of mutations that occur in a single generation, as has been assumed by previous authors. We thereby establish that selection for mutational load minimization acts at the level of an individual in a single generation. We conclude with comments on the shortcomings and advantages of load minimization over other hypotheses for the origin of the Standard Code. Received: 4 April 2001 / Accepted: 22 October 2001     

Impact of translational selection on codon usage bias in the archaeon Methanococcus maripaludis

Patterns of codon usage have been extensively studied among Bacteria and Eukaryotes, but there has been little investigation of species from the third domain of life, the Archaea. Here, we examine the nature of codon usage bias in a methanogenic archaeon, Methanococcus maripaludis. Genome-wide patterns of codon usage are dominated by a strong A + T bias, presumably largely reflecting mutation patterns. Nevertheless, there is variation among genes in the use of a subset of putatively translationally optimal codons, which is strongly correlated with gene expression level. In comparison with Bacteria such as Escherichia coli, the strength of selected codon usage bias in highly expressed genes in M. maripaludis seems surprisingly high given its moderate growth rate. However, the pattern of selected codon usage differs between M. maripaludis and E. coli: in the archaeon, strongly selected codon usage bias is largely restricted to twofold degenerate amino acids (AAs). Weaker bias among the codons for fourfold degenerate AAs is consistent with the small number of tRNA genes in the M. maripaludis genome.     

Mechanistic Studies on Metal-pyrophosphate Hydrolysis. Structure of Tetraammine(chloroaquo)cobait(III) dichloride ([CO(NH3)4ClH20]2+•-2Cl−), an Acid Hydrolysis Product of Co(NH3)4HP2O7 and Co(NH3)4PO4

Abstract

The octahedral complex tetraammine(chloroaquo)cobalt(III) dichloride is shown to be the HCl hydrolysis product of both P¹,^2-bidentate tetraammine(pyrophosphato)cobalt(III) [CO(NH₃)₄HP₂0₇ or CoPP] and bidentate tetraammine(phosphato)cobalt(III) [Co(NH₃)₄P0₄or CoP]. The complex crystallizes in the orthorhombic space group Pna2¹ with cell dimensions α=13.033(2)Å, b=6.710(1) Å, and c=10.318(2)Å; the crystal structure was refined to a final disagreement index of 0.033. The average of the four Co-N distances is 1.944±6Å. The Co-Cl distance is 2.257(2)Å and the Co-O(W) distance is 1.971(4)Å. Both protons of the coordinated water molecule are engaged in strong hydrogen bonds to the two nonbonded chloride counterions with 0(W)-C1 distances of 3.087(6)Å and 3.123(6)Å. Each nonbonded chloride is engaged in seven hydrogen bonding interactions resulting from the high ratio of hydrogen bond donors to acceptors in the CoP structure. Cobalt bisphosphate (CoP₂) is the final enzyme hydrolysis product when CoPP is used as substrate in the yeast inorganic pyrophosphatase reaction. The bridge oxygen atom is the site of initial CoPP cleavage both, for HCl catalyzed hydrolysis as well as for enzyme catalyzed hydrolysis.     

斑翅草螽线粒体基因组序列测定与分析

已经测定的昆虫线粒体基因组中, 直翅目草螽亚科的疑钩额螽Ruspolia dubia线粒体控制区长度最短, 仅70 bp。为此, 本研究采用L-PCR结合二次PCR扩增策略对另一种草螽亚科昆虫斑翅草螽Conocephalus maculates线粒体基因组序列进行了测定。序列注释发现: 斑翅草螽线粒体基因组序列全长15 898 bp, A+T含量为72.05%, 基因排列与典型的节肢动物线粒体基因组一致。全部蛋白质编码基因以典型的ATN作为起始密码子, 9个蛋白质编码基因具有完整的终止密码子, 其余4个以不完整的T作为终止信号。除trnS^AGN外, 其余21个tRNAs均可折叠形成典型的三叶草结构, 依照Steinberg等(1997)线粒体特殊tRNA结构类型-9, trnS^AGN的DHU臂形成一个7 nt环, 反密码子臂则长达9 bp, 含1个突起碱基, 而不是正常的5 bp。斑翅草螽与其他直翅目昆虫线粒体基因组的主要区别在于, 在trnS^UCN和nad1, nad1和trnL^CUN基因间各存在一段罕见的、大段的基因间隔序列, 长度分别为78 bp和360 bp。其中, 位于nad1和trnL^CUN之间的基因间隔序列N链可形成一个包含完整起始、终止密码子(ATT/TAA)、编码103个氨基酸的未知开放阅读框。同义密码子使用偏好与线粒体基因组编码的tRNA反密码子匹配情况无关, 但与密码子第3位点的碱基组成紧密相关; 相对密码子使用频率(relative synonymous codon usage, RSCU)大于1的密码子, 其第3位点全部是A或T。在已经测定的直翅目昆虫线粒体基因组tRNAs中, 均存在一定数量的碱基错配, 且以G-U弱配对为主, 表明G-U配对在线粒体基因组中可能是一种正常的碱基配对形式。本研究测定的斑翅草螽线粒体基因组序列, 和先前已经测定的直翅目线粒体基因组序列一起, 可以为重建直翅目的进化历史提供数据资源。     

Selected codon usage bias in members of the class Mollicutes

Mollicutes are parasitic microorganisms mainly characterized by small cell sizes, reduced genomes and great A and T mutational bias. We analyzed the codon usage patterns of the completely sequenced genomes of bacteria that belong to this class. We found that for many organisms not only mutational bias but also selection has a major effect on codon usage. Through a comparative perspective and based on three widely used criteria we were able to classify Mollicutes according to the effect of selection on codon usage. We found conserved optimal codons in many species and study the tRNA gene pool in each genome. Previous results are reinforced by the fact that, when selection is operative, the putative optimal codons found match the respective cognate tRNA. Finally, we trace selection effect backwards to the common ancestor of the class and estimate the phylogenetic inertia associated with this character. We discuss the possible scenarios that explain the observed evolutionary patterns.     

Comparing expression level-dependent features in codon usage with protein abundance: an analysis of 'predictive proteomics'

Synonymous codon usage is a commonly used means for estimating gene expression levels of Escherichia coli genes and has also been used for predicting highly expressed genes for a number of prokaryotic genomes. By comparison of expression level-dependent features in codon usage with protein abundance data from two proteome studies of exponentially growing E. coli and Bacillus subtilis cells, we try to evaluate whether the implicit assumption of this approach can be confirmed with experimental data. Log-odds ratio scores are used to model differences in codon usage between highly expressed genes and genomic average. Using these, the strength and significance of expression level-dependent features in codon usage were determined for the genes of the Escherichia coli, Bacillus subtilis and Haemophilus influenzae genomes. The comparison of codon usage features with protein abundance data confirmed a relationship between these to be present, although exceptions to this, possibly related to functional context, were found. For species with expression level-dependent features in their codon usage, the applied methodology could be used to improve in silico simulations of the outcome of two-dimensional gel electrophoretic experiments.