Molecular-evolutionary mechanisms for genomic disorders

Molecular studies of unstable regions in the human genome have identified region-specific low-copy repeats (LCRs). Unlike highly repetitive sequences (e.g. Alus and LINEs), LCRs are usually of 10-400 kb in size and exhibit > or = 95-97% similarity. According to computer analyses of available sequencing data, LCRs may constitute >5% of the human genome. Through the process of non-allelic homologous recombination using paralogous genomic segments as substrates, LCRs have been shown to facilitate meiotic DNA rearrangements associated with disease traits, referred to as genomic disorders. In addition, this LCR-based complex genome architecture appears to play a major role in both primate karyotype evolution and human tumorigenesis.     

Complete sequence and genetic organization of pDTG1, the 83 kilobase naphthalene degradation plasmid from Pseudomonas putida strain NCIB 9816-4

The complete 83,042 bp sequence of the circular naphthalene degradation plasmid pDTG1 from Pseudomonas putida strain NCIB 9816-4 was determined in order to examine the process by which the nah and sal operons may have been compiled and distributed in nature. Eighty-nine open reading frames were predicted using computer analyses, comprising 80.0% of the pDTG1 DNA sequence. The most distinctive feature of the plasmid is the upper and lower naphthalene degradation operons, which occupy 9.5 kb and 13.4 kb regions, respectively, bordered by numerous defective mobile genetic element fragments. Identified on this plasmid were homologues of genes required for large plasmid replication, maintenance, and conjugation, as well as transposases, resolvases, and integrases, suggesting an evolution that involved the lateral transfer of DNA between bacterial species. Also found were genes that contain a high degree of sequence similarity to other known degradation genes, as well as genes involved in chemotaxis. Although the incompatibility group designation of pDTG1 remains unresolved, striking sequence organization and homology exists between the plasmid backbones of pDTG1 and the IncP-9 toluene-degradation plasmid pWW0, which suggests a divergent evolution from a progenitor plasmid prior to degradative gene incorporation.     

The Jackprot Simulation Couples Mutation Rate with Natural Selection to Illustrate How Protein Evolution Is Not Random

Protein evolution is not a random process. Views which attribute randomness to molecular change, deleterious nature to single-gene mutations, insufficient geological time, or population size for molecular improvements to occur, or invoke “design creationism” to account for complexity in molecular structures and biological processes, are unfounded. Scientific evidence suggests that natural selection tinkers with molecular improvements by retaining adaptive peptide sequence. We used slot-machine probabilities and ion channels to show biological directionality on molecular change. Because ion channels reside in the lipid bilayer of cell membranes, their residue location must be in balance with the membrane’s hydrophobic/philic nature; a selective “pore” for ion passage is located within the hydrophobic region. We contrasted the random generation of DNA sequence for KcsA, a bacterial two-transmembrane-domain (2TM) potassium channel, from Streptomyces lividans, with an under-selection scenario, the “jackprot,” which predicted much faster evolution than by chance. We wrote a computer program in JAVA APPLET version 1.0 and designed an online interface, The Jackprot Simulation , to model a numerical interaction between mutation rate and natural selection during a scenario of polypeptide evolution. Winning the “jackprot,” or highest-fitness complete-peptide sequence, required cumulative smaller “wins” (rewarded by selection) at the first, second, and third positions in each of the 161 KcsA codons (“jackdons” that led to “jackacids” that led to the “jackprot”). The “jackprot” is a didactic tool to demonstrate how mutation rate coupled with natural selection suffices to explain the evolution of specialized proteins, such as the complex six-transmembrane (6TM) domain potassium, sodium, or calcium channels. Ancestral DNA sequences coding for 2TM-like proteins underwent nucleotide “edition” and gene duplications to generate the 6TMs. Ion channels are essential to the physiology of neurons, ganglia, and brains, and were crucial to the evolutionary advent of consciousness. The Jackprot Simulation illustrates in a computer model that evolution is not and cannot be a random process as conceived by design creationists.     

EXPERIMENTAL MOLECULAR EVOLUTION OF BACTERIOPHAGE T7

We present an analysis of molecular evolution in a laboratory-generated phylogeny of the bacteriophage T7, a virus of 40 kilo-base pairs of double-stranded DNA. The known biology of T7 is used in concert with observed changes in restriction sites and in DNA sequences to produce a model of restriction-site convergence and divergence in the experimental lineages. During laboratory propagation in the presence of a mutagen, the phage lineages changed an estimated 0.5%-1.5% in base pairs; most change appears to have been G → A or C → T, presumably because of the mutagen employed. Some classes of restriction-site losses can be explained adequately as simple outcomes of random processes, given the mutation rate and the bias in mutation spectrum. However, some other classes of sites appear to have undergone accelerated rates of loss, as though the losses were selectively favored. Overall, the wealth of knowledge available for T7 biology contributes only modestly to these explanations of restriction-site evolution, but rates of restriction-site gains remain poorly explained, perhaps requiring an even deeper understanding of T7 genetics than was employed here. Having measured these properties of molecular evolution, we programmed computer simulations with the parameter estimates and pseudo-replicated the empirical study, thereby providing a data base for statistical evaluation of phylogeny reconstruction methods. By these criteria, replicates of the experimental phylogeny would be correctly reconstructed over 97% of the time for the three methods tested, but the methods differed significantly both in their ability to recover the correct topology and in their ability to predict branch lengths. More generally, the study illustrates how analyses of experimental evolution in bacteriophage can be exploited to reveal relationships between the basics of molecular evolution and abstract models of evolutionary processes.     

DNA芯片在0-1规划问题中的应用

生物芯片技术和DNA计算分别是近年来生命科学与信息科学的新兴研究领域,对信息高度并行的获取与处理是二者的本质特性.而0-1规划问题作为运筹学中一个重要的问题,到目前为止还没有好的算法.在DNA计算和DNA芯片基础上,提出了基于DNA芯片解决0-1规划问题的DNA计算新模型,与以往DNA计算模型相比,该模型具有高信息量和操作易自动化的优点.同时指出DNA芯片技术有望作为新型生物计算的芯片.     

Microcomputer programs for DNA sequence analysis.

Computer programs are described which allow (a) analysis of DNA sequences to be performed on a laboratory microcomputer or (b) transfer of DNA sequences between a laboratory microcomputer and another computer system, such as a DNA library. The sequence analysis programs are interactive, do not require prior experience with computers and in many other respects resemble programs which have been written for larger computer systems (1-7). The user enters sequence data into a text file, accesses this file with the programs, and is then able to (a) search for restriction enzyme sites or other specified sequences, (b) translate in one or more reading frames in one or both directions in order to find open reading frames, or (c) determine codon usage in the sequence in one or more given reading frames. The results are given in table format and a restriction map is generated. The modem program permits collection of large amounts of data from a sequence library into a permanent file on the microcomputer disc system, or transfer of laboratory data in the reverse direction to a remote computer system.     

DNA bend sites in the human beta-globin locus: evidence for a basic and universal structural component of genomic DNA.

Here we summarize the DNA bend sites in a 66-kb region of the human beta-globin locus. A total of 98 sites were mapped by circular permutation assay along the locus with an average interval of 679.2 +/- 229.6 bp between them. The distribution of the bend sites indicated that although the most frequent distance was about 650-700 bp, there appeared to be preferences at 300-400, 500-550, 800-850, 1,000-1,050, and 1,150-1,200 bp, indicating that these distances are multimers of a 170-bp basic unit. DNA bend sites in the globin-encoding regions indicated that most of their locations relative to the cap sites were conserved during evolution. Insertion of Alu and L1 sequences that occurred at various times and changed the distances of the sites was corrected for the epsilon-, psi beta-, and delta-globin genes. The only exception of the conservation was observed at the duplication junctions of the two gamma-globin genes, which occurred 25-35 MYA. Among the 75 A/A/A (A2N8A2N8A2) sequences found in the 51 bend sites, 59 sequences from 47 sites showed bending profiles by oligonucleotide-based assay. All of these sites were included in the sites predicted by computer analysis based on the distribution of AA and TT dinucleotides. These lines of evidence suggest that these DNA bend sites are one of the basic structural components universally present in genomic DNA.     

How to load a replicative helicase onto chromatin: A more and more complex matter during evolution

In all eukaryotes, the heterohexameric MCM2-7 complex functions as the main replicative helicase during S phase. During early G1 phase, it is recruited onto chromatin in a sequence of reactions called pre-replication complex (pre-RC) formation or DNA licensing. This process is ATP-dependent and at least two different chromatin-bound ATPase activities are required besides several others essential, but not enzymatically active, proteins. Although functionally conserved during evolution, pre-RC formation and the way the MCM2-7 helicase is loaded onto DNA are more complex in metazoans than in single-cell eukaryotes. Recently, we characterized a new essential factor for pre-RC assembly and DNA licensing, the vertebrate-specific MCM9 protein that contains not only an ATPase but also a helicase domain. MCM9 adds another layer of complexity to how vertebrates achieve and regulate the loading of the MCM2-7 helicase and DNA replication.     

Empirical codon substitution matrix

Background  

Codon substitution probabilities are used in many types of molecular evolution studies such as determining Ka/Ks ratios, creating ancestral DNA sequences or aligning coding DNA. Until the recent dramatic increase in genomic data enabled construction of empirical matrices, researchers relied on parameterized models of codon evolution. Here we present the first empirical codon substitution matrix entirely built from alignments of coding sequences from vertebrate DNA and thus provide an alternative to parameterized models of codon evolution.     

Statistical characteristics in primary structures of functional regions of Escherichia coli genome. I. Frequency characteristics

Analysis of the frequencies of occurrence of mono- and dinucleotides in sequenced E. coli DNA fragments was performed. The DNA sequences of total length 135 000 nucleotides were considered. It was demonstrated that the fragments of DNA which have different functional properties also have different parameters of neighbour nucleotides correlation. Moreover, periodical positional dependence of correlation parameters in coding regions was found. The evolution significance of stated observation is discussed, so as the opportunity of using them in the special model of nucleotide's sequences, which is needed for development of the computer recognition algorithms for genomic functional units.     

The impact of the nucleosome code on protein-coding sequence evolution in yeast

Coding sequence evolution was once thought to be the result of selection on optimal protein function alone. Selection can, however, also act at the RNA level, for example, to facilitate rapid translation or ensure correct splicing. Here, we ask whether the way DNA works also imposes constraints on coding sequence evolution. We identify nucleosome positioning as a likely candidate to set up such a DNA-level selective regime and use high-resolution microarray data in yeast to compare the evolution of coding sequence bound to or free from nucleosomes. Controlling for gene expression and intra-gene location, we find a nucleosome-free "linker" sequence to evolve on average 5-6% slower at synonymous sites. A reduced rate of evolution in linker is especially evident at the 5' end of genes, where the effect extends to non-synonymous substitution rates. This is consistent with regular nucleosome architecture in this region being important in the context of gene expression control. As predicted, codons likely to generate a sequence unfavourable to nucleosome formation are enriched in linker sequence. Amino acid content is likewise skewed as a function of nucleosome occupancy. We conclude that selection operating on DNA to maintain correct positioning of nucleosomes impacts codon choice, amino acid choice, and synonymous and non-synonymous rates of evolution in coding sequence. The results support the exclusion model for nucleosome positioning and provide an alternative interpretation for runs of rare codons. As the intimate association of histones and DNA is a universal characteristic of genic sequence in eukaryotes, selection on coding sequence composition imposed by nucleosome positioning should be phylogenetically widespread.     

Frequent false detection of positive selection by the likelihood method with branch-site models

Positive Darwinian selection promotes fixations of advantageous mutations during gene evolution and is probably responsible for most adaptations. Detecting positive selection at the DNA sequence level is of substantial interest because such information provides significant insights into possible functional alterations during gene evolution as well as important nucleotide substitutions involved in adaptation. Efficient detection of positive selection, however, has been difficult because selection often operates on only a few sites in a short period of evolutionary time. A likelihood-based method with branch-site models was recently introduced to overcome such difficulties. Here I examine the accuracy of the method using computer simulation. I find that the method detects positive selection in 20%-70% of cases when the DNA sequences are generated by computer simulation under no positive selection. Although the frequency of such false detection varies depending on, among other things, the tree topology, branch length, and selection scheme, the branch-site likelihood method generally gives misleading results. Thus, detection of positive selection by this method alone is unreliable. This unreliability may have resulted from its over-sensitivity to violations of assumptions made in the method, such as certain distributions of selective strength among sites and equal transition/transversion ratios for synonymous and nonsynonymous substitutions.     

Sequence-selective targeting of long stretches of the DNA minor groove by a novel dimeric bis-benzimidazole

A dimeric bis-benzimidazole molecule has been designed by computer modeling to bind to a DNA sequence via the DNA minor groove that covers a complete turn of B-DNA. A series of bis-benzimidazole dimers incorporating a -O-(CH(2))(n)()-X-CH(2))(n)()-O- linker, with n = 2 or 3 and X = O or N(+)H(Me), were screened for their capacity to fit the DNA minor groove. The modeling studies enabled an optimal linker to be devised (n = 3, X = N(+)H(Me)), and the synthesis of the predicted "best" molecule, N-methyl-N,N-bis-3,3-[4'-[5' '-(2' "-p-methoxyphenyl)-5' "-1H-benzimidazolyl]-2' '-1H-benzimidazolyl]phenoxypropylamine (5), is reported. The optimized linker permits the two symmetric bis-benzimidazole motifs to maintain hydrogen-bonded contacts with the floor of the DNA minor groove. DNase I footprinting studies have shown that this ligand binds with high affinity to sequences representing approximately a complete turn of B-DNA, represented by the [A.T](4)-[G.C]-[A.T](4) motif, and only poorly to sequences of half this site size, in accord with the computer modeling studies. Compound 5 does not show acute cellular cytotoxicity, in contrast with its monomeric bis-benzimidazole precursors, yet is rapidly taken up into cells.     

Divergent evolution of fucosyltransferase genes from vertebrates, invertebrates, and bacteria

On the basis of function and sequence similarities, the vertebrate fucosyltransferases can be classified into three groups: alpha-2-, alpha-3-, and alpha-6-fucosyltransferases. Thirty new putative fucosyltransferase genes from invertebrates and bacteria and six conserved peptide motifs have been identified in DNA and protein databanks. Two of these motifs are specific of alpha-3-fucosyltransferases, one is specific of alpha-2-fucosyltransferases, another is specific of alpha-6-fucosyltransferases, and two are shared by both alpha-2- and alpha-6-fucosyltranserases. Based on these data, literature data, and the phylogenetic analysis of the conserved peptide motifs, a model for the evolution offucosyltransferase genes by successive duplications, followed by divergent evolution is proposed, with either two different ancestors, one for the alpha-2/6-fucosyltransferases and one for the alpha-3-fucosyltransferases or a single common ancestor for the two families. The expected properties of such an hypothetical ancestor suggest that the plant or insect alpha-3-fucosyltransferases using chitobiose as acceptor might be the present forms of this ancestor, since fucosyltransferases using chitobiose as acceptor are expected to be of earlier appearance in evolution than enzymes using N -acetyllactosamine. However, an example of convergent evolution of fucosyltransferase genes is suggested for the appearance of the Leaepitopes found in plants and primates.     

Mutagenesis and the three R's in yeast

Mutagenesis is a prerequisite for evolution and also is an important contributor to human diseases. Most mutations in actively dividing cells originate during DNA replication as errors introduced when copying an undamaged DNA template or during the bypass of DNA lesions. In addition, mutations can be introduced during the repair of DNA double-strand breaks by either homologous recombination or non-homologous end-joining pathways. Finally, although generally considered to be a very high-fidelity process, the excision repair of DNA damage may be an important contributor to mutagenesis in non-dividing cells. In this review, we will discuss the well-known contributions of DNA replication to mutagenesis in Saccharomyces cerevisiae, as well as the less-appreciated contributions of recombination and repair to mutagenesis in this organism.     

DNA计算机的分子生物学研究进展

DNA(脱氧核糖核酸)计算机研究是一个新领域。从字面上看,它既包含DNA研究也包含计算机的研究,因而也包含DNA技术与计算机技术如何交融的研究。1994年,Adleman在Science上报道了首例DNA计算的研究结果;2001年,Benenson等在Nature报道了一种由DNA分子和相应的酶分子构成的、有图灵机功能的可程序试管型DNA计算机,标志着DNA计算机研究的重大进展。DNA计算机最大的特点是超大规模的并行运算能力和潜在的巨大的数据储存能力。目前DNA计算机研究已涉及许多领域,包括生物学、数学、物理、化学、计算机科学和自动化工程等具体应用,是计算概念上的一次革命。DNA计算机的研究大大促进了DNA分子操作技术尤其是在纳米尺度下操作DNA分子的研究速度。从DNA计算机的基本原理、应用形式、与基因组学研究的重要关系等方面总结和评述了相关研究进展。     

A computer program that simulates cloning of DNA

Easy Cloner is a computer program that manipulates DNA sequences as in cloning experiments and produces maps of the resulting plasmids. The program runs in the graphics mode of an IBM PC or compatible computer and is operated by using a mouse to point to the required actions. The program is available in the public domain.     

A multi-neighbor-joining approach for phylogenetic tree reconstruction and visualization

The computationally challenging problem of reconstructing the phylogeny of a set of contemporary data, such as DNA sequences or morphological attributes, was treated by an extended version of the neighbor-joining (NJ) algorithm. The original NJ algorithm provides a single-tree topology, after a cascade of greedy pairing decisions that tries to simultaneously optimize the minimum evolution and the least squares criteria. Given that some sub-trees are more stable than others, and that the minimum evolution tree may not be achieved by the original NJ algorithm, we propose a multi-neighbor-joining (MNJ) algorithm capable of performing multiple pairing decisions at each level of the tree reconstruction, keeping various partial solutions along the recursive execution of the NJ algorithm. The main advantages of the new reconstruction procedure are: 1) as is the case for the original NJ algorithm, the MNJ algorithm is still a low-cost reconstruction method; 2) a further investigation of the alternative topologies may reveal stable and unstable sub-trees; 3) the chance of achieving the minimum evolution tree is greater; 4) tree topologies with very similar performances will be simultaneously presented at the output. When there are multiple unrooted tree topologies to be compared, a visualization tool is also proposed, using a radial layout to uniformly distribute the branches with the help of well-known metaheuristics used in computer science.