Fractal landscapes and molecular evolution: modeling the myosin heavy chain gene family.

Mapping nucleotide sequences onto a "DNA walk" produces a novel representation of DNA that can then be studied quantitatively using techniques derived from fractal landscape analysis. We used this method to analyze 11 complete genomic and cDNA myosin heavy chain (MHC) sequences belonging to 8 different species. Our analysis suggests an increase in fractal complexity for MHC genes with evolution with vertebrate > invertebrate > yeast. The increase in complexity is measured by the presence of long-range power-law correlations, which are quantified by the scaling exponent alpha. We develop a simple iterative model, based on known properties of polymeric sequences, that generates long-range nucleotide correlations from an initially noncorrelated coding region. This new model-as well as the DNA walk analysis-both support the intron-late theory of gene evolution.     

Escherichia coli sbcC mutants permit stable propagation of DNA replicons containing a long palindrome

Recombinant DNA libraries generated in vitro should in theory contain all of the sequences of the genomes from which they are derived. However, the literature is dotted with reports of sequences that cannot be recovered, are under-represented, or are highly unstable. In particular, long palindromic nucleotide sequences of perfect or near-perfect symmetry are either lethal to the vector or suffer deletions or other rearrangements that remove symmetry [Collins, Cold Spring Harbor Symp. Quant. Biol. 45 (1981) 409-416; Collins et al., Gene 19 (1982) 139-146; Hagan and Warren, Gene 24 (1983) 317-326]. We report here that mutation of a single gene, namely sbcC, can overcome this inviability and allow for the stable propagation of a 571-bp nearly perfect palindrome in Escherichia coli. This has implications for the choice of strains used for the recovery and analysis of cloned nucleotide sequences.     

Cloning and characterization of the genes for ribosomal proteins L10 and L12 from Synechocystis Sp. PCC 6803: comparison of gene clustering pattern and protein sequence homology between cyanobacteria and chloroplasts

The endosymbiont theory proposes that chloroplasts have originated from ancestral cyanobacteria through a process of engulfment and subsequent symbiotic adaptation. The molecular data for testing this theory have mainly been the nucleotide sequence of rRNAs and of photosystem component genes. In order to provide additional data in this area, we have isolated genomic clones of Synechocystis DNA containing the ribosomal protein gene cluster rplJL. The nucleotide sequence of this cluster and flanking regions was determined and the derived amino acid sequences were compared to the available homologous sequences from other eubacteria and chloroplasts. In Escherichia coli these two genes are part of a larger cluster, i.e., rplKAJL-rpoBC. In Synechocystis, the genes for the RNA polymerase subunit (rpoBC) are shown to be widely separated from the r-protein genes. The Synechocystis gene arrangement is similar to that in the chloroplast system, where the rpoBC1C2 and rplKAJL clusters are separated and located in two cell compartments, the chloroplast and the nucleus, respectively.     

Rate of divergence of cellular sequences homologous to segments of Moloney sarcoma virus.

The RNA genome of the Moloney isolate of murine sarcoma virus (M-MSV) consists of two parts--a sarcoma-specific region with no homology to known leukemia viral RNAs, and a shared region present also in Moloney murine leukemia virus RNA. Complementary DNA was isolated which was specific for each part of the M-MSV genome. The DNA of a number of mammalian species was examined for the presence of nucleotide sequences homologous with the two M-MSV regions. Both sets of viral sequences had homologous nucleotide sequences present in normal mouse cellular DNA. MSV-specific sequences found in mouse cellular DNA closely matched those nucleotide sequences found in M-MSV as seen by comparisons of thermal denaturation profiles. In all normal mouse cells tested, the cellular set of M-MSV-specific nucleotide sequences was present in DNA as one to a few copies per cell. The rate of base substitution of M-MSV nucleotide sequences was compared with the rate of evolution of both unique sequences and the hemoglobin gene of various species. Conservation of MSV-specific nucleotide sequences among species was similar to that of mouse globin gene(s) and greater than that of average unique cellular sequences. In contrast, cellular nucleotide sequences that are homologous to the M-MSV-murine leukemia virus "common" nucleotide region were present in multiple copies in mouse cells and were less well matched, as seen by reduced melting profiles of the hybrids. The cellular common nucleotide sequences diverged very rapidly during evolution, with a base substitution rate similar to that reported for some primate and avian endogenous virogenes. The observation that two sets of covalently linked viral sequences evolved at very different rates suggests that the origin of M-MSV may be different from endogenous helper viruses and that cellular sequences homologous to MSV-specific nucleotide sequences may be important to survival.     

Mean free energy topology for nucleotide sequences of varying composition based on secondary structure calculations.

The mean free energy generated from the secondary structure of RNA sequences of varying length and composition has been studied by way of probability theory. The expected boundaries or maximal and minimal values of a given distribution are explored and a method for estimating error as a function of the number of shuffled sequences is also examined. For typical nucleotide sequences found in biologically active organisms, the mean free energy, free energy distributions and errors appear to be scalable in terms of a fixed set of algorithm-dependent parameters and the nucleotide composition of the particular sequence under evaluation. In addition, a general semi-analytical formula for predicting the mean free energy is proposed which, at least to first-order approximation, can be used to rapidly predict the mean free energy of any sequence length and composition of RNA. The general methodology appears to be algorithm independent. The results are expected to provide a reference point for certain types of analysis related to structure of RNA or DNA sequences and to assist in measuring the somewhat related matter of complexity in algorithm development. Some related applications are discussed.     

The old REH theory remains unsatisfactory and the new REH theory is problematical - a reply to holmquist and jukes

Summary In response to criticism of REH theory (Fitch 1980), Holmquist and Jukes (1981) have mostly avoided the criticism or misunderstood it. Since they themselves state in their response that Amino acid sequence data alone cannot be used to estimate total nucleotide substitutions, they agree with the criticism. Most of their paper treats the newer theory (here designated as the REHN theory) which attempts to use the nucleotide sequences encoding proteins to better estimate total nucleotide substitutions (Holmquist and Pearl 1980). Since I made no criticism of REHN theory, their comments are frequently beside the point of my original criticism of REH theory. Nevertheless, it is shown here that REHN theory is also unsatisfactory in that: One, the varions are now more clearly defined but in such a way as to preclude the same codon from suffering a nucleotide substitution in more than one evolutionary interval. Two, the set of codons that accepts silent substitutions is identical to the set that accepts amino acid changing nucleotide substitutions. Three, the uncertainty in the REH estimate is considerable in that alternative excellent fits to the same observatuonal data may give alternative REH values that differ significantly even before stochastic variation and selective bias are considered. Four, the fit of their model to data is an irrelevancy where there are zero degrees of freedom.     

An index of substitution saturation and its application

We introduce a new index to measure substitution saturation in a set of aligned nucleotide sequences. The index is based on the notion of entropy in information theory. We derive the critical values of the index based on computer simulation with different sequence lengths, different number of OTUs and different topologies. The critical value enables researchers to quickly judge whether a set of aligned sequences is useful in phylogenetics. We illustrate the index by applying it to an analysis of the aligned sequences of the elongation factor-1alpha gene originally used to resolve the deep phylogeny of major arthropod groups. The method has been implemented in DAMBE.     

Nucleotide sequences of immunoglobulin-epsilon pseudogenes in man and apes and their phylogenetic relationships

To understand the phylogenetic relationships between hominoids, the nucleotide sequences of immunoglobulin-epsilon processed pseudogenes from chimpanzee, gorilla and orangutan were determined. The basic structures of these processed pseudogenes agreed with their human counterpart. Although the degrees of nucleotide differences between man and the African apes had no statistical significance, all the analytical data examined supported the theory that chimpanzee is the closest relative of man. This result was consistent with that deduced by our recent qualitative study. Studies on the nucleotide sequences of globin genes have suggested that the molecular clock runs more slowly in hominoids than in non-hominoid primates. According to the present data, however, further retardation of the evolutionary rate was not observed in the human lineage. Assuming that orangutan diverged 14 million years ago and that the evolutionary rate between the orangutan lineage and the lineage leading to the other three species is constant, the divergence dates of chimpanzee and gorilla were estimated to be 4.9(+/- 0.9) and 5.9(+/- 0.9) million years ago, respectively.     

Nucleotide sequences at the ends of the mercury resistance transposon, Tn501.

The nucleotide sequences at the ends of the mercury-resistance transposon, Tn501, have been determined. The terminal sequences are inverted repeated sequences 38 nucleotide pairs in length, which differ in 3 nucleotide pairs. The transposon is flanked by directly repeated sequences of 5 nucleotide pairs, originating from a single pentanucleotide sequence in the recipient replicon. There is no obvious homology between recipient replicons at the site of insertion of the transposon. The structures of the ends of Tn501 are compared with those of other transposons and insertion sequences. The use of Tn501 to locate an EcoRI site within a genetically defined sequence of interest is discussed.     

Significance of nucleotide sequence alignments: a method for random sequence permutation that preserves dinucleotide and codon usage

The similarity of two nucleotide sequences is often expressed in terms of evolutionary distance, a measure of the amount of change needed to transform one sequence into the other. Given two sequences with a small distance between them, can their similarity be explained by their base composition alone? The nucleotide order of these sequences contributes to their similarity if the distance is much smaller than their average permutation distance, which is obtained by calculating the distances for many random permutations of these sequences. To determine whether their similarity can be explained by their dinucleotide and codon usage, random sequences must be chosen from the set of permuted sequences that preserve dinucleotide and codon usage. The problem of choosing random dinucleotide and codon-preserving permutations can be expressed in the language of graph theory as the problem of generating random Eulerian walks on a directed multigraph. An efficient algorithm for generating such walks is described. This algorithm can be used to choose random sequence permutations that preserve (1) dinucleotide usage, (2) dinucleotide and trinucleotide usage, or (3) dinucleotide and codon usage. For example, the similarity of two 60-nucleotide DNA segments from the human beta-1 interferon gene (nucleotides 196-255 and 499-558) is not just the result of their nonrandom dinucleotide and codon usage.      

Plant chitinase consensus sequences

Eighty-six plant chitinase sequences from 29 different species and one hybrid were obtained from the on-line GenBank nucleotide database. These sequences were grouped into five gene families based on previously published guidelines (Meins et al., 1994), and the amino-acid and nucleotide sequences of each gene family were aligned. Consensus amino-acid and nucleotide sequences were derived for each gene family based on the alignments. The consensus sequences were analyzed to determine, their amino-acid composition, hydropathy profiles, and codon usage.     

Equilibrium binding of four anthracyclines to nucleic acids: thermodynamic properties and sequence selectivity.

The thermodynamic parameters of the interaction of the two anthracyclines 13-dihydrodaunomycin and marcellomycin with calf thymus DNA were examined by equilibrium binding studies. Enthalpy and entropy changes of the binding of both drugs show salt dependence profiles that cannot be rationalized by the polyelectrolyte theory. This feature is common to other anthracycline compounds. The nucleotide sequence binding preferences of daunomycin, adriamycin, 13-dihydrodaunomycin and marcellomycin have been studied by monitoring the degree of protection from cleavage by restriction endonucleases of linearized pBR322. Differential protection of pBR322 DNA against the cleavage of Bgl I and Ava II suggests that these drugs recognize changes in the sequences near the enzyme recognition site. Alterations of the electrophoretic restriction pattern of pBR322 in the presence of anthracyclines are dependent on time and on concentration. These results are discussed in relation to the existence of nucleotide sequences with different affinity for these drugs.     

Absence of short period interspersion of repetitive and non-repetitive sequences in the DNA of Drosophila melanogaster

A sensitive search has been made in Drosophila melanogaster DNA for short repetitive sequences interspersed with single copy sequences. Five kinds of measurements all yield the conclusion that there are few short repetitive sequences in this genome: 1) Comparison of the kinetics of reassociation of short (360 nucleotide) and long (1,830 nucleotide) fragments of DNA; 2) reassociation kinetics of long fragments (2,200 nucleotide) with an excess of short (390 short nucleotide) fragments; 3) measurement of the size of S1 nuclease resistant reassociated repeated sequences; 4) measurement of the hyperchromicity of reassociated repetitive fragments as a function of length; 5) direct assay by kinetics of reassociation of the amount of single copy sequence present on 1,200 nucleotide long fragments which also contain repetitive sequences.     

The sequence organization of bovine DNA

The organization of repetitive DNA sequences has been investigated in bovine DNA. Repetitive sequences of all kinds constitute 25% to 30% of the total. Five density satellites constitute about 20% of the genome, and most of the remainder consists of alternating repeating and nonrepeating sequences. The nonrepeating sequences have a very broad size distribution averaging 4,000 nucleotide pairs in length, with the longest exceeding 10,000 nucleotide pairs. The interspersed repetitive sequences are much more nearly homogeneous in size, averaging 350 nucleotide pairs in length, and are divided into 8 to 14 sequence families.     

Study of T-DNA integration loci in tobacco transgenic plants

From the total DNA of 17 transgenic tobacco plants the DNA fragments containing T-DNA/plant DNA junctions were amplified using inverse polymerase chain reaction. Comparison of the nucleotide sequences of 34 fragments with the GENEBANK sequences revealed homology with vector sequences outside T-DNA in 10 cases and no homology with the known nucleotide sequences in most clones. The AT-content varied from 51 up to 72% that is close to the total percentage of AT pairs in tobacco genome. Alignment of the sequences truncated during embedding of the left and the right borders has shown that for the left border significant clusterization (10 bp region) of truncation sites was observed, and five sequences had identical sites of truncation (+23 T) that showed the preferable use of this nucleotide. Nine created nucleotide sequences were homologous to the repeating sequences in tobacco genome. The percentage of homology varied from 70 up to 90%. The identified repeats belong to different types.     

Nucleotide Sequences Derived from Pheasant DNA in the Genome of Recombinant Avian Leukosis Viruses with Subgroup F Specificity

Recombination between viral and cellular genes can give rise to new strains of retroviruses. For example, Rous-associated virus 61 (RAV-61) is a recombinant between the Bryan high-titer strain of Rous sarcoma virus (RSV) and normal pheasant DNA. Nucleic acid hybridization techniques were used to study the genome of RAV-61 and another RAV with subgroup F specificity (RAV-F) obtained by passage of RSV-RAV-0 in cells from a ring-necked pheasant embryo. The nucleotide sequences acquired by these two independent isolates of RAV-F that were not shared with the parental virus comprised 20 to 25% of the RAV-F genomes and were indistinguishable by nucleic acid hybridization. (In addition, RAV-F genomes had another set of nucleotide sequences that were homologous to some pheasant nucleotide sequences and also were present in the parental viruses.) A specific complementary DNA, containing only nucleotide sequences complementary to those acquired by RAV-61 through recombination, was prepared. These nucleotide sequences were pheasant derived and were not present in the genomes of reticuloendotheliosis viruses, pheasant viruses, and avian leukosis-sarcoma viruses of subgroups A, B, C, D, and E. They were partially endogenous, however, to avian DNA other than pheasant. The fraction of these nucleotide sequences present in other avian DNAs generally paralleled the genetic relatedness of these avian species to pheasants. However, there was a high degree of homology between these pheasant nucleotide sequences and related nucleotide sequences in the DNA of normal chickens as indicated by the identical melting profiles of the respective hybrids.     

Evolutionary Relationship of DNA Sequences in Finite Populations

With the aim of analyzing and interpreting data on DNA polymorphism obtained by DNA sequencing or restriction enzyme technique, a mathematical theory on the expected evolutionary relationship among DNA sequences (nucleons) sampled is developed under the assumption that the evolutionary change of nucleons is determined solely by mutation and random genetic drift. The statistical property of the number of nucleotide differences between randomly chosen nucleons and that of heterozygosity or nucleon diversity is investigated using this theory. These studies indicate that the estimates of the average number of nucleotide differences and nucleon diversity have a large variance, and a large part of this variance is due to stochastic factors. Therefore, increasing sample size does not help reduce the variance significantly. The distribution of sample allele (nucleomorph) frequencies is also studied, and it is shown that a small number of samples are sufficient in order to know the distribution pattern.     

利用序列比较寻找胰岛素基因表达启动区与DNA结合蛋白的结合位点

NDFl、IPFl和HNF4是与胰岛素基因表达有关的DNA结合蛋白,通过比较SWISSPROT蛋白质数据库中人类、小鼠、大鼠这三种核蛋白氨基酸一级序列、模体和结构域,发现其结构十分相似,根据蛋白质结构和功能的关系,推测这些DNA结合蛋白与胰岛素基因结合的核苷酸序列相似;从GenBanl(核酸数据库中获得人类、小鼠、大鼠胰岛素DNA序列,用ClustalW比较三者Promoter区的核苷酸序列,显示有一段核苷酸序列较为相似,同时搜索TRANSFAC基因转录数据库中NDFl、IPFl和NHF4蛋白核苷酸结合位点,发现核酸比对保守的部分序列与TRANSFAC数据库中这三个转录因子的DNA结合位点一致,另外一些核酸保守序列可能为其他未知DNA结合蛋白的结合位点。这种核酸序列比对设计为分子生物学实验寻找和验证胰岛素DNA结合蛋白与核苷酸的结合位点提供了简单而实用的方法。     

An organismic critique of molecular darwinism

The molecular darwinian approach to the emergence of life treats the competition between RNA sequences for nucleotide resources as the primordial selective process in prebiotic evolution, which prescribes possible pathways for the subsequent elaboration of organizational relationships. Since success in this competition is determined by the "phenotypic" properties of RNA strands in the absence of organizational context, the genesis of biotic organization is dependent upon the establishment of co-operative, hypercyclic interactions between competing RNA sequences. The thesis of this paper is that hypercycle theory is based on unwarranted assumptions about the conditions of prebiotic evolution, and that the implications of these assumptions run counter to both empirical evidence and to the rational by which natural selection operates in evolution generally. An organismic alternative to hypercycle theory is suggested, based on the catalytic microsphere and the thermodynamics of selection.     

Base sequence studies of 300 nucleotide renatured repeated human DNA clones

A band of 300 nucleotide long duplex DNA is released by treating renatured repeated human DNA with the single strand-specific endonuclease S₁. Since many of the interspersed repeated sequences in human DNA are 300 nucleotides long, this band should be enriched in such repeats. We have determined the nucleotide sequences of 15 clones constructed from these 300 nucleotide S₁-resistant repeats. Ten of these cloned sequences are members of the Alu family of interspersed repeats. These ten sequences share a recognizable consensus sequence from which individual clones have an average divergence of 12.8%. The 300 nucleotide Alu family consensus sequence has a dimeric structure and was evidently formed from a head to tail duplication of an ancestral monomeric sequence. Three of the remaining clones are variations on a simple pentanucleotide sequence previously reported for human satellite III DNA. Two of the 15 clones have distinct and complex sequences and may represent other families of interspersed repeated sequences.