Simple sequences in a "minimal' genome.
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Algorithms↗
Biomedical subjects
J M Hancock
Publications and source records attributed to J M Hancock.
Do light-induced pH changes within the chloroplast drive turnip yellow mosaic virus assembly?
Turnip yellow mosaic virus (TYMV) induces gross morphological and biochemical changes in the chloroplasts of infected cells. Viral RNA is synthesized in vesicles formed by invagination of the outer chloroplast bilayer. Virion assembly occurs at the neck of these vesicles and requires illumination. Data collected over the last three decades are consistent with the hypothesis that light-induced generation of a low pH drives TYMV assembly within the intermembrane space of chloroplasts. In a low-pH environment, poly(C) regions within the genomic RNA of TYMV may interact to form tertiary structures, and the recognition of these structures by TYMV coat protein initiates virion assembly.
Chloroplasts↗
The contribution of DNA slippage to eukaryotic nuclear 18S rRNA evolution.
Six of 204 eukaryotic nuclear small-subunit ribosomal RNA sequences analyzed show a highly significant degree of clustering of short sequence motifs that indicates the fixation of products of replication slippage within them in their recent evolutionary history. A further 72 sequences show weaker indications of sequence repetition. Repetitive sequences in SSU rRNAs are preferentially located in variable regions and in particular in V4 and V7. The conserved region immediately 5' to V7 (C7) is also consistently repetitive. Whereas variable regions vary in length and appear to have evolved by the fixation of slippage products, C7 shows no indication of length variation. Repetition within C7 is therefore either not a consequence of slippage or reflects very ancient slippage events. The phylogenetic distribution of sequence simplicity in small-subunit rRNAs is patchy, being largely confined to the Mammalia, Apicomplexa, Tetrahymenidae, and Trypanosomatidae. The regions of the molecule associated with sequence simplicity vary with taxonomic grouping as do the sequence motifs undergoing slippage. Comparison of rates of insertion and substitution in a lineage within the genus Plasmodium confirms that both rates are higher in variable regions than in conserved regions. The insertion rate in variable regions is substantially lower than the substitution rate, suggesting that selection acts more strongly on slippage products than on point mutations in these regions. Patterns of coevolution between variable regions may reflect the consequences of selection acting on the incorporation of slippage-derived sequences across the gene.
Animals↗
The contribution of slippage-like processes to genome evolution.
Simple sequences present in long (> 30 kb) sequences representative of the single-copy genome of five species (Homo sapiens, Caenorhabditis elegans, Saccharomyces cerevisiae, E. coli, and Mycobacterium leprae) have been analyzed. A close relationship was observed between genome size and the overall level of sequence repetition. This suggested that the incorporation of simple sequences had accompanied increases of genome size during evolution. Densities of simple sequence motifs were higher in noncoding regions than in coding regions in eukaryotes but not in eubacteria. All five genomes showed very biased frequency distributions of simple sequence motifs in all species, particularly in eukaryotes where AAA and TTT predominated. Interspecific comparisons showed that noncoding sequences in eukaryotes showed highly significantly similar frequency distributions of simple sequence motifs but this was not true of coding sequences. ANOVA of the frequency distributions of simple sequence motifs indicated strong contributions from motif base composition and repeat unit length, but much of the variation remained unexplained by these parameters. The sequence composition of simple sequences therefore appears to reflect both underlying sequence biases in slippage-like processes and the action of selection. Frequency distributions of simple sequence motifs in coding sequences correlated weakly or not at all with those in noncoding sequences. Selection on coding sequences to eliminate undesirable sequences may therefore have been strong, particularly in the human lineage.
Animals↗
Replication slippage in the evolution of potyviruses.
Recently published evidence for sequence repetition in potyvirus genomes prompted us to analyse the published complete genome sequences and coat protein gene sequences of viruses of this family for evidence of replication slippage. Five of nine complete genomic sequences and 17 of 32 coat protein genes had significant sequence repetitions. Most of these were in coat protein genes, although the 5' region of the turnip mosaic virus genome also showed evidence of slippage. The results suggest that replication slippage may be involved in the evolution of viruses, as well as prokaryotes and eukaryotes, and that slippage can occur in both RNA and DNA when it is being replicated.
Biological Evolution↗
Polycytosine regions contained in DNA hairpin loops interact via a four-stranded, parallel structure similar to the i-motif.
Thermal denaturation profiles of an oligodeoxynucleotide that forms a hairpin structure with a cytidine-rich loop show an unexpected transition at 60 degrees C at pH 5.0 but not at pH 8.0. Analytical ultracentrifugation shows that this transition reflects dimer formation via the interaction of loops from two molecules to form a novel structure termed the h-dimer. The dependence of this structure on low pH implies the formation of cytosine-protonated cytosine base pairs. NMR spectroscopy, thermal denaturation and ultraviolet absorption spectral analysis suggest a similarity to the i-motif structure recently proposed for the interaction of deoxycytidine oligomers. The use of hairpin loops to form i-motif-like structures may prove useful in searches for cognate proteins and possibly in the production of antibodies.
Base Sequence↗
SIMPLE34: an improved and enhanced implementation for VAX and Sun computers of the SIMPLE algorithm for analysis of clustered repetitive motifs in nucleotide sequences.
SIMPLE34 is an improved and enhanced version of SIMPLE for Vax and SunOS systems. It now provides a length-independent measure of the overall level of tri- and tetranucleotide motif clustering within nucleotide sequences and its significant deviation from random expectation. It now also provides information on tri- and tetranucleotide motifs showing higher levels of clustering than would be expected in random sequences. Sequence simplicity of test sequences can be judged with respect to random sequences generated on the basis of base composition, positional base composition or doublet frequency. These options can be used to investigate factors resulting in sequence simplicity.
Algorithms↗
Evolution of sequence repetition and gene duplications in the TATA-binding protein TBP (TFIID).
Analysis of TBP gene sequences from a variety of species for clustering of short sequence motifs and for over- and underrepresentation of short sequence motifs suggests involvement of slippage in the recent evolution of the TBP N-terminal domains in metazoans, Acanthamoeba and wheat. AGC, GCA and CAG are overrepresented in TBP genes of other species, suggesting that opa arrays were amplified from motifs overrepresented in ancestral species. The phylogenetic distribution of recently slippage-derived sequences in TBP is similar to that observed in the large subunit ribosomal RNAs, suggesting a propensity for certain evolutionary lineages to incorporate slippage-generated motifs into protein-coding as well as ribosomal RNA genes. Because length increase appears to have taken place independently in lineages leading to vertebrates, insects and nematodes, TBP N-terminal domains in these lineages are not homologous. All gene duplications in the TBP gene family appear to have been recent events despite strong protein sequence similarity between TRF and P. falciparum TBP. The enlargement of the TBP N-terminal domain may have coincided with acquisition of new functions and may have accompanied molecular coevolution with domains of other proteins, resulting in the acquisition of new or more complex mechanisms of transcription regulation.
Acanthamoeba↗
Generation of VNTRs and heteroplasmy by sequence turnover in the mitochondrial control region of two elephant seal species.
We describe an unusual repetitive DNA region located in the 3' end of the light (L)-strand in the mitochondrial control region of two elephant seal species. The array of tandem repeats shows both VNTR (variable-number tandem repeat) and sequence variation and is absent from 12 compared mammalian species, except for the occurrence in the same location of a distinct repetitive region in rabbit mtDNA and a similar repeat in the harbor seal. The sequence composition and arrangement of the repeats differ considerably between the northern elephant seal (Mirounga angustirostris) and the southern species (M. leonina) despite an estimated divergence time of 1 MY (based on an mtDNA-RNA gene and the nonrepetitive control region). Analysis of repeat sequence relationships within and between species indicate that divergence in sequence and structure of repeats has involved both slippage-like and unequal crossingover processes of turnover, generating very high levels of divergence and heteroplasmy.
Animals↗
Detection and quantification of concerted evolution and molecular drive.
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Animals↗
Secondary structure constraints on the evolution of Drosophila 28 S ribosomal RNA expansion segments.
Eukaryotic ribosomal RNA genes contain rapidly evolving regions of unknown function termed expansion segments. We present the comparative analysis of the primary and secondary structure of two expansion segments from the large subunit rRNA gene of ten species of Drosophila and the tsetse fly species Glossina morsitans morsitans. At the primary sequence level, most of the differences observed in the sequences obtained are single base substitutions. This is in marked contrast with observations in vertebrate species in which the insertion or deletion of repetitive motifs, probably generated by a DNA-slippage mechanism, is a major factor in the evolution of these regions. The secondary structure of the two regions, supported by multiple compensatory base changes, is highly conserved between the species examined and supports the existence of a general folding pattern for all eukaryotes. Intriguingly, the evolutionary rate of expansion segments is very slow relative to other genic and non-genic regions of the Drosophila genome. These results suggest that the evolution of expansion segments in the rDNA multigene family is a balance between the homogenization of new mutations by unequal crossing over and a combination of selection against some such mutations per se and selection for subsequent compensatory mutations, in order to maintain a particular RNA secondary structure.
Animals↗
Evolution of the cetacean mitochondrial D-loop region.
We sequenced the mitochondrial DNA D-loop regions from two cetacean species and compared these with the published D-loop sequences of several other mammalian species, including one other cetacean. Nucleotide substitution rates, DNA sequence simplicity, possible open reading frames (ORFs), and potential RNA secondary structure were investigated. The substitution rate is an order of magnitude lower than would be expected on the basis of reports on human sequence variation in this region but are consistent with interspecific primate and rodent D-loop sequence variation and with estimates of substitution rates from whole mitochondrial genomes. Deletions/insertions are less common in the cetacean D-loop than in other vertebrate species. Areas of high sequence simplicity (clusters of short repetitive motifs) across the region correspond to areas of high sequence divergence. Three regions predicted to form secondary structures are homologous to such putative structures in other species; however, the presumptive structures most conserved in cetaceans are different from those reported for other taxa. While all three species have possible long ORFs, only a short sequence of seven amino acids is shared with other mammalian species, and those changes that had occurred within it are all nonsynonymous. We conclude that DNA slippage, in addition to point mutation, contributes to the evolution of the D-loop and that regions of conserved secondary structure in cetaceans and an ORF are unlikely to contribute significantly to the conservation of the central region.
Amino Acid Sequence↗
'Compensatory slippage' in the evolution of ribosomal RNA genes.
The distribution patterns of shared short repetitive motifs in the expansion segments of the large subunit rRNA genes of different species show that these segments are coevolving as a set and that in two examined vertebrate species the RNA secondary structures are conserved as a consequence of runs of motifs in one region being compensated by complementary motifs in another. These unusual processes, involving replication-slippage, have implications for the evolution of ribosomal RNA and for the use of the rDNA multigene family as a 'molecular clock' for assessing relationships between species.
Animals↗
Complete sequences of the rRNA genes of Drosophila melanogaster.
In this, the first of three papers, we present the sequence of the ribosomal RNA (rRNA) genes of Drosophila melanogaster. The gene regions of D. melanogaster rDNA encode four individual rRNAs: 18S (1,995 nt), 5.8S (123 nt), 2S (30 nt), and 28S (3,945 nt). The ribosomal DNA (rDNA) repeat of D. melanogaster is AT rich (65.9% overall), with the spacers being particularly AT rich. Analysis of DNA simplicity reveals that, in contrast to the intergenic spacer (IGS) and the external transcribed spacer (ETS), most of the rRNA gene regions have been refractory to the action of slippage-like events, with the exception of the 28S rRNA gene expansion segments. It would seem that the 28S rRNA can accommodate the products of slippage-like events without loss of activity. In the following two papers we analyze the effects of sequence divergence on the evolution of (1) the 28S gene "expansion segments" and (2) the 28S and 18S rRNA secondary structures among eukaryotic species, respectively. Our detailed analyses reveal, in addition to unequal crossing-over, (1) the involvement of slippage and biased mutation in the evolution of the rDNA multigene family and (2) the molecular coevolution of both expansion segments and the nucleotides involved with compensatory changes required to maintain secondary structures of RNA.
Animals↗
Evolution of the secondary structures and compensatory mutations of the ribosomal RNAs of Drosophila melanogaster.
This paper examines the effects of DNA sequence evolution on RNA secondary structures and compensatory mutations. Models of the secondary structures of Drosophila melanogaster 18S ribosomal RNA (rRNA) and of the complex between 2S, 5.8S, and 28S rRNAs have been drawn on the basis of comparative and energetic criteria. The overall AU richness of the D. melanogaster rRNAs allows the resolution of some ambiguities in the structures of both large rRNAs. Comparison of the sequence of expansion segment V2 in D. melanogaster 18S rRNA with the same region in three other Drosophila species and the tsetse fly (Glossina morsitans morsitans) allows us to distinguish between two models for the secondary structure of this region. The secondary structures of the expansion segments of D. melanogaster 28S rRNA conform to a general pattern for all eukaryotes, despite having highly divergent sequences between D. melanogaster and vertebrates. The 70 novel compensatory mutations identified in the 28S rRNA show a strong (70%) bias toward A-U base pairs, suggesting that a process of biased mutation and/or biased fixation of A and T point mutations or AT-rich slippage-generated motifs has occurred during the evolution of D. melanogaster rDNA. This process has not occurred throughout the D. melanogaster genome. The processes by which compensatory pairs of mutations are generated and spread are discussed, and a model is suggested by which a second mutation is more likely to occur in a unit with a first mutation as such a unit begins to spread through the family and concomitantly through the population. Alternatively, mechanisms of proofreading in stem-loop structures at the DNA level, or between RNA and DNA, might be involved. The apparent tolerance of noncompensatory mutations in some stems which are otherwise strongly supported by comparative criteria within D. melanogaster 28S rRNA must be borne in mind when compensatory mutations are used as a criterion in secondary-structure modeling. Noncompensatory mutation may extend to the production of unstable structures where a stem is stabilized by RNA-protein or additional RNA-RNA interactions in the mature ribosome. Of motifs suggested to be involved in rRNA processing, one (CGAAAG) is strongly overrepresented in the 28S rRNA sequence. The data are discussed both in the context of the forces involved with the evolution of multigene families and in the context of molecular coevolution in the rDNA family in particular.
Animals↗
Molecular coevolution among cryptically simple expansion segments of eukaryotic 26S/28S rRNAs.
The set of "expansion segments" of any eukaryotic 26S/28S ribosomal RNA (rRNA) gene is responsible for the bulk of the difference in length between the prokaryotic 23S rRNA gene and the eukaryotic 26S/28S rRNA gene. The expansion segments are also responsible for interspecific fluctuations in length during eukaryotic evolution. They show a consistent bias in base composition in any species; for example, they are AT rich in Drosophila melanogaster and GC rich in vertebrate species. Dot-matrix comparisons of sets of expansion segments reveal high similarities between members of a set within any 28S rRNA gene of a species, in contrast to the little or spurious similarity that exists between sets of expansion segments from distantly related species. Similarities among members of a set of expansion segments within any 28S rRNA gene cannot be accounted for by their base-compositional bias alone. In contrast, no significant similarity exists within a set of "core" segments (regions between expansion segments) of any 28S rRNA gene, although core segments are conserved between species. The set of expansion segments of a 26S/28S gene is coevolving as a unit in each species, at the same time as the family of 28S rRNA genes, as a whole, is undergoing continual homogenization, making all sets of expansion segments from all ribosomal DNA (rDNA) arrays in a species similar in sequence. Analysis of DNA simplicity of 26S/28S rRNA genes shows a direct correlation between significantly high relative simplicity factors (RSFs) and sequence similarity among a set of expansion segments. A similar correlation exists between RSF values, overall rDNA lengths, and the lengths of individual expansion segments. Such correlations suggest that most length fluctuations reflect the gain and loss of simple sequence motifs by slippage-like mechanisms. We discuss the molecular coevolution of expansion segments, which takes place against a background of slippage-like and unequal crossing-over mechanisms of turnover that are responsible for the accumulation of interspecific differences in rDNA sequences.
Animals↗
Specificity and biological significance of microtubule-associated protein-DNA interactions in chick.
The interactions between chick brain microtubule associated proteins (MAPs) and chick DNA have been examined using DNA-cellulose chromatography, cross-blotting, and nitrocellulose filter-binding. Comparison of nitrocellulose filter-binding and cross-blotting results show that while MAPs and a minor, Mr 48,000, protein show significant binding at 50 mM NaCl, only the latter continues to bind a significant amount of DNA at 150 mM NaCl, suggesting an ionic basis for the MAP-DNA interactions. MAP-DNA interactions also show weak preference for AT-rich fractions, and are sensitive to S1 nuclease digestion. We suggest that the MAPs bind preferentially to single-stranded DNA. The binding may involve an interaction between the DNA phosphates and the highly cationic tubulin-binding domain of the MAPs. Repetitive fractions of the chick genome prepared both by hydroxyapatite chromatography and by S1 nuclease digestion show binding to a number of minor proteins present in preparations of microtubule proteins, as well as to the MAPs. We conclude that the MAPs probably do not bind specifically to repetitive DNA, in contrast to earlier reports using mouse DNA. MAP-DNA interactions are therefore unlikely to be involved in the attachment of microtubules to mitotic chromosomes.
Animals↗
The role of proteins in the production of different types of chromosome bands.
Experiments have been carried out to try and answer two questions on the role of proteins in chromosome banding: firstly, what degree of protein extraction is required before banding can be produced; and secondly, to what extent are redistribution and reorganization of chromosomal components required for the production of banding. Partial extraction of all histones, and of a group of non-histones with molecular weights mainly between 50,000 and 70,000 appears to be necessary before G-, C- or R-banding can be produced. More extensive 'dehistonization' to produce chromosome scaffolds inhibits the production of all types of bands. Protein-protein and protein-DNA cross-linking inhibits all types of banding tested, the degree of inhibition being roughly related to the degree of cross-linking, but not apparently to the type of cross-linking. The results of both sets of experiments indicate that chromosome banding of all types is dependent on the prior loss from chromosomes of a specific set of proteins, and on some alteration of the arrangement of remaining chromosomal components during the banding procedure.
Chromosomal Proteins, Non-Histone↗