Using Triplet Periodicity of Nucleotide Sequences for Finding Potential Reading Frame Shifts in Genes

We introduce a novel approach for the detection of possible mutations leading to a reading frame (RF) shift in a gene. Deletions and insertions of DNA coding regions are considerable events for genes because an RF shift results in modifications of the extensive region of amino acid sequence coded by a gene. The suggested method is based on the phenomenon of triplet periodicity (TP) in coding regions of genes and its relative resistance to substitutions in DNA sequence. We attempted to extend 326 933 regions of continuous TP found in genes from the KEGG databank by considering possible insertions and deletions. We revealed totally 824 genes where such extension was possible and statistically significant. Then we generated amino acid sequences according to active (KEGG''s) and hypothetically ancient RFs in order to find confirmation of a shift at a protein level. Consequently, 64 sequences have protein similarities only for ancient RF, 176 only for active RF, 3 for both and 581 have no protein similarity at all. We aimed to have revealed lower bound for the number of genes in which a shift between RF and TP is possible. Further ways to increase the number of revealed RF shifts are discussed.     

生物序列的聚类分析

通过不同的聚类方式,对公共数据库中生物序列数据进行生物信息的挖掘,以达到在更广泛和更深入的框架中了解它们之间的相互关系的目的。以帕金森病相关基因所对应的mRNA序列为例,使用双序列比对的得分值作为序列之间的距离定义。同时为解决不同聚类分析之间的差异,分别采用模糊聚类和层次聚类两种不同的方法进行聚类分析。并由不同聚类方法得到的一致分类聚类的结果为基因功能分类提供支持,为进一步揭示生物序列所蕴涵的生物学知识和生物学规律提供可参考的依据。     

An Approach for Searching Insertions in Bacterial Genes Leading to the Phase Shift of Triplet Periodicity

The concept of the phase shift of triplet periodicity (TP) was used for searching potential DNA insertions in genes from 17 bacterial genomes. A mathematical algorithm for detection of these insertions has been developed. This approach can detect potential insertions and deletions with lengths that are not multiples of three bases, especially insertions of relatively large DNA fragments (>100 bases). New similarity measure between triplet matrixes was employed to improve the sensitivity for detecting the TP phase shift. Sequences of 17,220 bacterial genes with each consisting of more than 1,200 bases were analyzed, and the presence of a TP phase shift has been shown in ~16% of analysed genes (2,809 genes), which is about 4 times more than that detected in our previous work. We propose that shifts of the TP phase may indicate the shifts of reading frame in genes after insertions of the DNA fragments with lengths that are not multiples of three bases. A relationship between the phase shifts of TP and the frame shifts in genes is discussed.     

Hydrolases: The Correlation Between Informational Structure and the Catalytic Sites Organization

Abstract

The novel method allowing identification of protein structure elements responsible for catalytic activity manifestation is proposed. Structural organization of various hydrolases was studied using the ANIS (ANalysis of Informational Structure) method. ANIS allows to reveal a hierarchy of the ELements of Information Structure (ELIS) using protein amino acid sequence. The ELIS corresponds to the variable length sites with an increased density of structural information. The amino acid residues forming the enzyme catalytic site were shown to belong to the different top-ranking ELIS located in the contact area of the corresponding spatial structure clusters. In the protein spatial structure catalytic sites are located in the area of contact between fragments of polypeptide chain (structural blocs) allocation to the different top-ranking ELIS. According to our results we concluded that structural blocks corresponding to top-ranking ELIS are crucial for protein functioning. Such regions are structurally independent, and their determinate mobility relative to each other is vital for an efficient enzymatic reaction to occur.     

Study of the periodic arrangement of amino acid residues in fiber proteins of bacteriophage T4

The amino acid sequences of some fiber proteins possibly have a periodic structure. This periodicity can be analyzed using the Fourier transform of the mathematical image of the symbol sequence of amino acid residues in proteins. One of several possible methods of Fourier transform has been chosen as optimal for the given study. This optimal Fourier transform has been used to analyze the periodic structures in several fiber proteins of bacteriophage T4. Amino acids from some groups form sequences of alternating elements with a relatively small period (T=15); those from other groups form sequences with other small periods (T=10 and T=8). Relatively large periods of amino acid arrangement, with the entire amino acid sequence of the protein being divided between them into four or six equal parts, is a new finding. The data on protein structural periodicity make it possible to align the amino acid sequences according to the periodic structures of both type. The results obtained agree with the results of previous crystallographic and electron microscopic studies.__________Translated from Molekulyarnaya Biologiya, Vol. 39, No. 2, 2005, pp. 321–329.Original Russian Text Copyright © 2005 by Simakova, Simakov.     

蛋白质序列的特征周期研究

利用Fourier乘积谱(Fourier product spectrum,FPS)系统计算了76个蛋白质亚家族的疏水自由能(HΦ)序列、电子离子相互作用势(electron-ion interaction potential,EIIP)序列和结构拓扑指数(Balaban指数)序列的特征周期;讨论了特征周期的规律;并以时间周期谱(time periodicity spectrum,TPS)演示了如何定位特征周期在蛋白质序列上的热区.结果表明EIIP特征周期热区与蛋白质结合位点有较好的对应关系.     

Quantitation of Repetitive Sequences in Human Genomic DNA and Detection of an Elevated Ribosomal Repeat Copy Number in Schizophrenia: The Results of Molecular and Cytogenetic Analyses

A modified version of quantitating repetitive sequences in genomic DNA was developed to allow comparisons for numerous individual genomes and simultaneous analysis of several sequences in each DNA specimen. The relative genomic content of ribosomal repeats (rDNA) was estimated for 75 individuals, including 33 healthy donors (HD) and 42 schizophrenic patients (SP). The rDNA copy number in HD was 427 ± 18 (mean ± SE) per diploid nucleus, ranging 250–600. In SP, the rDNA copy number was 494 ± 15 and ranged 280–670, being significantly higher than in HD. The two samples did not differ in contents of sequences hybridizing with probes directed to a subfraction of human satellite III or to the histone genes. Cytogenetic analysis (silver staining of metaphase chromosomes) showed that the content of active rRNA genes in nucleolus organizer regions is higher in SP compared with HD. The possible causes of the elevated rRNA gene dosage in SP were considered. The method employed was proposed for studying the polymorphism for genomic content of various repeats in higher organisms, including humans.     

Conserved Sequences of Prokaryotic Proteomes and Their Compositional Age

A full repertoire of octapeptides which are present in at least 30 bacterial proteomes of total 131 currently available is computationally derived and filtered. An original search technique is used that, in terms of computational time and memory, is similar to the Suffix tree method. The presence of a given sequence in a large number of proteomes qualifies it as a conserved sequence. The larger the number of proteomes where it is found, the higher is the conservation. The concept of compositional age of the amino acid sequences (“compositional clock”) is introduced for the first time. The compositional age is calculated on the basis of the consensus temporal order of appearance of amino acids in early evolution. The correlation between the compositional age and the sequence conservation is established. [Reviewing Editor: Martin Kreitman]     

A new member of the Balbiani ring multigene family in the dipteran Chironomus tentans consists of a single-copy version of a unit repeated in other gene family members

The known Balbiani ring (BR) multigene family members in the dipteran Chironomus tentans encode salivary gland secretory proteins in the size range between 38 and 1,000 kDa. The proteins interact to form protein fibers used by the aquatic larvae to spin feeding and protective larval tubes or pupation tubes. Here, we describe a new BR multigene family member, the spl7 gene, which codes for an 89-amino-acid-long protein with a relative mobility of 17k. The gene has a high content of charged amino acid residues and consists of two structurally different halves. Five regularly spaced cysteine codons are present in the 5 half while the 3 half contains five proline codons. These two different halves exhibit similarities to the C and SR regions, respectively, which form the tandemly repeated units in the about 40-kb-long BR genes and which also, in different versions, are the building blocks of all genes in the BR multigene family.In this multigene family, encoding interacting structural proteins, the long BR genes with their 125–150 tandemly arranged repeat units as well as the short sp17 gene with its single-copy version of such a repeat unit, have therefore evolved from a common ancestor.Correspondence to: L. Wieslander     

四川省珍稀濒危植物优先保护序列的研究

以四川省已公布的78种珍稀濒危植物为对象,系统地研究和制定了该地区重点保护植物的综合评价指标体系.通过对一系列评价指标的定量化和权重分配,获得植物种的“濒危系数”和“综合评价系数”,进而获得该地区各重点保护植物的受威胁程度和它们的优先保护序列,该序列比较真实地反映了此地区受威胁植物保护的先后顺序.     

A new member of a secretory protein gene family in the dipteranChironomus tentans has a variant repeat structure

Summary We describe the structure of a gene expressed in the salivary gland cells of the dipteranChironomus tentans and show that it encodes 1 of the approximately 15 secretory proteins exported by the gland cells. This sp115,140 gene consists of approximately 65 copies of a 42-bp sequence in a central uninterrupted core block, surrounded by short nonrepetitive regions. The repeats within the gene are highly similar to each other, but divergent repeats are present in a pattern which suggests that the repeat structure has been remodeled during evolution. The 42-bp repeat in the gene is a simple variant of the more complex repeat unit present in the Balbiani ring genes, encoding four of the other secretory proteins. The structure of the sp115,140 gene suggests that related repeat structures have evolved from a common origin and resulted in the set of genes whose secretory proteins interact in the assembly of the secreted protein fibers.     

植物碱性亮氨酸拉链(bZIP)蛋白的研究进展(二)———DNA结合特性、基因表达、功能及应用

植物碱性亮氨酸拉链(bZIP)蛋白在高等植物基因表达与调控中起重要作用。本文介绍了植物bZIP蛋白与DNA结合特性,探讨了它们的基因表达和功能,综述了它们在分子生物学和基因工程研究中的应用。 Abstract:Plant basic leucine zipper (bZIP) proteins play an important role in the expression and regulation of higher plant genes.The DNA-binding properties of plant bZIP protein are introduced first in this article.Then their expression and function are discussed.Finally,their application to the studies of molecular biology and genetic engineering is reviewed.     

貉源阿留申病毒全基因组测序及末端序列分子特征分析

貉源阿留申病毒(Raccoon dog and arctic fox amdoparvovirus,RFAV)是自然感染貉和蓝狐的新种阿留申病毒(Amdoparvovirus),为测序RFAV全基因组序列,预测分析RFAV末端发夹结构序列分子特征。本研究采用分段克隆成功获得3株长4832nt、4827nt、4830nt的RFAV全基因组序列,分别命名为RFAV-Y9J、RFAV-RD15、RFAV-HS-R,利用在线软件预测RFAV末端序列二级结构,并与水貂阿留申病毒(AMDV)末端序列进行同源性比对。结果显示阿留申病毒种间、种内3’末端基因组序列保守性强,均存在116nt的Y型发夹结构;RFAV-Y9J与RFAV-RD15毒株5′末端分别存在310nt、305nt的U型发夹结构,RFAV和AMDV种内5′末端基因组序列保守性强,而种间5′末端基因组序列有较大变异。本研究首次完整测序了RFAV的3′和5′末端序列,为其他种阿留申病毒的末端序列扩增提供一种有效方法,为构建RFAV的全基因组序列感染性克隆奠定了基础。     

Structural basis for diversity of the EF-hand calcium-binding proteins

The calcium binding proteins of the EF-hand super-family are involved in the regulation of all aspects of cell function. These proteins exhibit a great diversity of composition, structure, Ca2+-binding and target interaction properties. Here, our current understanding of the Ca2+-binding mechanism is assessed. The structures of the EF-hand motifs containing 11-14 amino acid residues in the Ca2+-binding loop are analyzed within the framework of the recently proposed two-step Ca2+-binding mechanism. A hypothesis is put forward that in all EF-hand proteins the Ca2+-binding and the resultant conformational responses are governed by the central structure connecting the Ca2+-binding loops in the two-EF-hand domain. This structure, named EFbeta-scaffold, defines the position of the bound Ca2+, and coordinates the function of the N-terminal (variable and flexible) with the C-terminal (invariable and rigid) parts of the Ca2+-binding loop. It is proposed that the nature of the first ligand of the Ca2+-binding loop is an important determinant of the conformational change. Additional factors, including the interhelical contacts, the length, structure and flexibility of the linker connecting the EF-hand motifs, and the overall energy balance provide the fine-tuning of the Ca2+-induced conformational change in the EF-hand proteins.     

Periodicity in the fine structure of histograms during nuclear decay

A theoretical explanation is offered for the appearance of periodicity in the fine structure of histograms describing the processes of nuclear decay. This effect is observed in a sample containing nonpolarized radioactive nuclei, with largely isotropic spin distribution over directions. However, because of fluctuations occurring in any real sample, the number of nuclei having spin directed along some isolated axis would differ somewhat from the number of nuclei with spin directed along another axis. The same is immobile relating to the Earth but rotates in space together with it. At the same time, the nuclear spins, owing to quite weak interaction with the environment, keep their directions in space. Therefore, the spin ensemble rotates both relative to the sample itself and relative to the detector of α-particles directed onto the sample. Since fluctuations in the number of nuclei with spins directed at a certain angle relative to the detector direction affect the fine structure of histograms, the latter proves to depend, among other things, of the rotation of the Earth. Consequently, when the Earth makes a full revolution and the distribution of fluctuations in the number of nuclei with given spin direction returns to the initial one, the shape of the fine structure of histograms will be repeated, and repeated over the same definite time intervals.     

Periodicity of Cambium Activity and Seasonal Changes of the Secondary Phloem in Two Species of Dalbergia

Periodicity of cambium activity, seasonal changes of the secondary phloem and longevity of sieve tube in main trunk of Dalbergia balansae Prain and in the twig of D. szemaoensis Prain were observed. The results are as follows: 1. All cambia fall under the category of storied type. 2. In D. balansae cambial activity begins in late April and ends in early November. Phloem differentiation is completed by early November. Xylem differentiation ceases in December. In D. szemaoensis cambial activity continues from mid-April to late October. Phloem and xylem differentiation ceases by late November. 3. The width of functional phloem zone is maximal (400—600 μm) in autumn and minimal (200—370 μm) in February to April. In overwintering, functional sieve tube elements contain P-protein, and the pores of sieve plate are open. It could be one of the reasons that these two species are promising host trees of Kerria yunnanensis during winter. 4. The longevity of sieve tubes in D. balansae and D. szemaoensis last 8—12 months and 9—11 months respectively. 5. During dormancy of cambium, the parenchyma cells of the secondary phloem contain large quantities of starch grains and calcium oxalate crystals, which decrease as cambium becomes active and remain little or even non visualized in summer.     

植物Rab蛋白的研究进展

Rab蛋白是小G蛋白超级家族中的成员之一。通过Rab蛋白氨基酸序列的系统进化分析表明,植物Rab家族又可分为8个亚家族,分别为RabA、RabB、RabC、RabD、RabE、RabF、RabG和RabH。Rab蛋白一般位于胞内特异膜系统的胞质面,它们是小泡运输的关键调节因子。Rab蛋白有非常保守的结构域,同时又具有功能多样性,它们在细胞分化、顶端优势、花粉管发育、根瘤形成以及生物和非生物胁迫反应中均起着非常重要的作用。该文对近年来国内外有关植物Rab蛋白的结构特点及其多样性功能的研究进展进行综述。