Molecular and structural evolution of Citrus satellite DNA

Highly repeated satellite DNA (stDNA) of citric plants was characterized by cloning and sequencing 10–14 repeats of each plant (Citrus limon, C. sinensis, C. ichangensis, Poncirus trifoliata). The monomers are mostly 181 bp in length with a GC-content between 60% and 68% (significantly higher than the average GC-content of the citrus group genomes). Similarity among the repeats indicates that they belong to a satellite family that underwent species-specific modifications, which are reflected in the phylogenetic relationships. Curvature provoked by dA-stretches of the repeats analyzed by gel shifts revealed structural conservation, even though the nucleotide sequences vary among species, thereby probably supporting the heterochromatic structure of stDNA. We show that the species-specific modification of the satellite consensus involves changes in the position and number of dA tracts. The molecule shapes of satellite oligomeres predicted by computer modelling indicate a superhelical structure of the tandem repeats which is in a good agreement with the satellite sequence dendrogram. The contribution of DNA bending elements to the evolution of plant satellite repeats is discussed. Received: 27 November 2000 / Accepted: 12 January 2001     

Difference in types of radiation-induced structural chromosome aberrations and their incidences between Chinese and Syrian hamster spermatozoa

The effects of ionizing radiations on sperm chromosomes were studied in the Chinese hamster (Crisetulus griseus) and the Syrian (golden) hamster (Mesocrisetus auratus). Testes of mature male Chinese hamsters (CH) were irradiated with X-rays (0.91, 1.82 and 3.63 Gy) and γ-rays (1.10, 2.15, 2.95 and 4.01 Gy) at a single acute dosage, whereas the irradiation was done with lower doses of X-rays (0.45, 0.91 and 1.82 Gy) and γ-rays (0.49, 0.99 and 1.98 Gy) in mature male Syrian hamsters (SH), taking the higher radiosensitivity of this species into consideration. They were mated with normal females within 6 days of exposure. Sperm-derived chromosomes were analyzed in 1125 and 1966 fertilized ova of the CH and the SH, respectively. In both species, there was no great difference in the induction of structural chromosome aberrations between X-irradiated and γ-irradiated spermatozoa. Chromosome-type aberrations were predominantly induced. The incidence of breakage-type aberrations increased linearly, and that of exchange-type aberrations linear-quadratically with increase of dosage. A species-specific difference in chromosomal radiosensitivity of spermatozoa was clear. In spite of the same radiation dosage, the incidence of chromosomally abnormal spermatozoa in the SH was about twice as high as that in the CH (e.g., 27.0% vs. 14.7% at 0.91 Gy of X-rays). The incidences of breakage-type aberrations (69–89%) were far higher than those of exchange-type aberrations (11–31%) in the SH, while the disparity of the two incidences was much smaller in the CH (46–65% vs. 35–54%). Exchange-type aberrations consisted of both chromosome-type and chromatid-type in the SH, while almost all of them were of the chromosome-type in the CH. These results suggest that the DNA-repairing capacity of oocytes is much higher in the CH than in the SH. Moreover, it seems likely that radiation-induced sperm DNA damage is repaired with both pre-replication repair (excision repair) and post-replication repair systems in SH oocytes, whereas the excision repair system operate most exclusively in CH oocytes.     

Global effects of DNA replication and DNA replication origin activity on eukaryotic gene expression

This report provides a global view of how gene expression is affected by DNA replication. We analyzed synchronized cultures of Saccharomyces cerevisiae under conditions that prevent DNA replication initiation without delaying cell cycle progression. We use a higher‐order singular value decomposition to integrate the global mRNA expression measured in the multiple time courses, detect and remove experimental artifacts and identify significant combinations of patterns of expression variation across the genes, time points and conditions. We find that, first, ～88% of the global mRNA expression is independent of DNA replication. Second, the requirement of DNA replication for efficient histone gene expression is independent of conditions that elicit DNA damage checkpoint responses. Third, origin licensing decreases the expression of genes with origins near their 3′ ends, revealing that downstream origins can regulate the expression of upstream genes. This confirms previous predictions from mathematical modeling of a global causal coordination between DNA replication origin activity and mRNA expression, and shows that mathematical modeling of DNA microarray data can be used to correctly predict previously unknown biological modes of regulation.     

Analysis of chromatin and DNA during chromosome endoreduplication in the endosperm ofTriticum durum Desf.

Summary Chromatin structure was studied in nuclei of the endosperm of durum wheat (Triticum durum Desf., cv. Creso), where a large number of cells undergo chromosome endoreduplication during caryopsis development. Optical density profiles of interphase nuclei at different ploidy levels after Feulgen staining were determined cytophotometrically. It was observed that, within each development stage, polyploid nuclei (6–12C and 12–24C) show more condensed chromatin than euploid nuclei (3–6C): this should indicate that endoreduplication is accompanied by some reduction of nuclear activity. Within the same ploidy level, 3–6C and 6–12C nuclei become increasingly condensed with development (except for the last stage), while 12-24C nuclei are identical at all stages. DNA methylation at different stages of caryopsis development was then analyzed in genomic DNA, highly repeated sequences and ribosomal DNA, by digestion with cytosine-methylation-sensitive restriction enzymes. We observed that (i), depending on the enzyme, DNA from caryopses may show higher mean length than DNA from shoot apices and variations occur during endosperm development; (ii) highly repeated DNA sequences also show some variation in base methylation between apices and endosperms and among endosperm development stages, even though to a lesser extent than genomic DNA; (iii) rDNA shows variations only between endosperm and apices while no variation was observed among endosperm development stages in relation to chromosome endoreduplication. Our data may be explained by assuming the occurrence, during endosperm development, of processes of chromatin condensation possibly involved in silencing the activity of extra copies of DNA resulting from chromosome endoreduplication. At least in part, DNA methylation is involved in the process of chromatin condensation. rDNA shows no variation during endosperm development: this suggests that rDNA copies are actively transcribed in both triploid and endoreduplicated nuclei.     

Mutagenesis by aflatoxin in M13 DNA: Base-substitution mechanisms and the origin of strand bias

Summary The two goals of the experiments described here are: (a) to examine whether there is a strand bias in mutagenic processing of bulky lesions in M13 replicative form (RF) DNA, and (b) to examine the mutational mechanisms of metabolically activated aflatoxin. For these experiments, two types of nicked heteroduplex M13 RF DNA molecules (+WT/-am1 and +am1/-WT) in which either the minus (-) or the plus (+) strand carried a gene 1 amber nonsense codon, were constructed. Heteroduplex DNAs were modified in vitro with aflatoxin B₁ activated by hamster liver S9 enzymes, and transfected into SOS(UV)-induced Escherichia coli (Sup^o/uvrA^-/mucAB⁺). Forward mutations in the lacZ -complementing gene segment were scored and sequenced. Results indicated that aflatoxin-induced mutation frequencies in the +WT/-am1 heteroduplex were significantly greater than those in the +am1/-WT heteroduplex, suggesting more efficient mutagenic processing of lesions in the plus strand. These results permit specific suggestions for improved mutation detection in the extensively used M13 forward mutagenesis system. Sequence analysis of point mutations from the +WT/-am1 experiments showed that most substitutions were targeted to plus-strand guanines. Both G-to-A transitions and G-to-T transversions were induced with equal effeciency. Since activated aflatoxin B₁ is known to react almost exclusively with DNA guanines at the N7 position, these results suggest that bulky lesions at guanine N7 position may have the properties of mis-instructional as well as non-instructional lesions.     

Molecular origin of the sequence-dependent kinetics of reactions between cisplatin derivatives and DNA

Experimental and theoretical studies related to the kinetics of interactions between cisplatin derivatives and DNA are critically reviewed. The reaction between DNA and cisplatin is a multistep reaction, consisting of aquation, electrostatic preassociation, nucleophilic substitution of one aqua ligand by a DNA guanine, and crosslink formation. If the reacting platinum complex is cis-[PtCl(NH₃)₂(H₂O)]⁺, the monoadduct bears one chlorido ligand, and the crosslink formation is preceded by a second aquation step. The kinetics of all these steps, including that of the monoadduct aquation, is significantly modulated by the flanking bases. In the case of the cisplatin derivatives carboplatin and oxaliplatin, recent work has clearly shown that the opening of the dicarboxylate chelate ring is faster than cisplatin hydrolysis; however, the even much faster ring closure keeps the concentration of the ring-opened species very low. Correlation of data from reactions with nucleotides on the one hand and from those with DNA on the other hand indicates that in vitro, the reactions with DNA proceed with the intact dicarboxylates as the reacting species. Thus, for carboplatin and oxaliplatin, the species reacting with DNA are electroneutral, while for cisplatin, the reactive species are cationic. The fact that nevertheless the in vitro sequence-selectivities appear similar for all three complexes suggests that hydrogen bonding between platinum leaving groups and DNA residues is not a factor determining the sequence-selective binding to GG and AG sequences.This review focuses at the studies designed to quantify and explain the physical origin of the influence of DNA sequence on the reaction kinetics.     

Molecular Dissection of Mycobacterium tuberculosis Integration Host Factor Reveals Novel Insights into the Mode of DNA Binding and Nucleoid Compaction

The annotated whole-genome sequence of Mycobacterium tuberculosis revealed that Rv1388 (Mtihf) is likely to encode for a putative 20-kDa integration host factor (mIHF). However, very little is known about the functional properties of mIHF or the organization of the mycobacterial nucleoid. Molecular modeling of the mIHF three-dimensional structure, based on the cocrystal structure of Streptomyces coelicolor IHF duplex DNA, a bona fide relative of mIHF, revealed the presence of Arg-170, Arg-171, and Arg-173, which might be involved in DNA binding, and a conserved proline (Pro-150) in the tight turn. The phenotypic sensitivity of Escherichia coli ΔihfA and ΔihfB strains to UV and methyl methanesulfonate could be complemented with the wild-type Mtihf but not its alleles bearing mutations in the DNA-binding residues. Protein-DNA interaction assays revealed that wild-type mIHF, but not its DNA-binding variants, binds with high affinity to fragments containing attB and attP sites and curved DNA. Strikingly, the functionally important amino acid residues of mIHF and the mechanism(s) underlying its binding to DNA, DNA bending, and site-specific recombination are fundamentally different from that of E. coli IHFαβ. Furthermore, we reveal novel insights into IHF-mediated DNA compaction depending on the placement of its preferred binding sites; mIHF promotes DNA compaction into nucleoid-like or higher order filamentous structures. We therefore propose that mIHF is a distinct member of a subfamily of proteins that serve as essential cofactors in site-specific recombination and nucleoid organization and that these findings represent a significant advance in our understanding of the role(s) of nucleoid-associated proteins.     

Characteristics of the interactions of cortisol-apolipoprotein A-I and tetrahydrocortisol-apolipoprotein A-I complexes with eukaryotic DNA

Primary hepatocyte culture has been used to demonstrate that the cortisol-apolipoprotein A-I complex does not affect the DNA and protein biosynthesis rates, whereas the tetrahydrocortisol-apolipoprotein A-I complex (THC-apoA-I) substantially increases the rates of ³H-thymidine and ¹⁴C-leucine incorporation into DNA and protein, respectively. Small-angle X-ray scattering data show that only THC-apoA-I effectively interacts with eukaryotic DNA, which is accompanied by local DNA melting. The (GCC)_n repeat, a component of many human and other eukaryotic genes, is the most probable region of the interaction of this complex with DNA. An oligonucleotide (duplex) of this type has been synthesized. Its interaction with THC-apoA-I yields a larger complex, which breaks up, giving rise to complementary oligonucleotide strands. They also interact with THC-apoA-I. The equilibrium kinetics of this multiphase process is described. The interaction of the cortisol-apolipoprotein A-I complex with the duplex is less specific and does not cause its breakup or the formation of complementary oligonucleotides.     

Molecular evidence for the hybrid origin of Paulownia Taiwaniana based on RAPD markers and RFLP of chloroplast DNA

Genomic DNA of Paulownia fortunei, P. kawakamii and P. taiwaniana were amplified with 10-base primers of arbitrary sequences using the polymerase chain reaction (PCR). A total of 351 DNA fragments were amplified from 23 primers and of these 265 fragments (75.5%) were polymorphic. Almost all of the PCR-amplified products of P. taiwaniana were shared by either P. fortunei or P. kawakamii, or both, and the number of polymorphic fragments shared by P. taiwaniana and P. fortunei was about equivalent to those shared by P. taiwaniana and P. kawakamii. Restriction fragments of chloroplast DNA (cpDNA) purified from Paulownia species and from reciprocal crosses between P. fortunei and P. kawakamii were analyzed. Restriction enzyme SalI-digested cpDNA showed an identical pattern in both P. kawakamii and P. taiwaniana. These results further support the hypothesis that P. taiwaniana is the natural hybrid between P. fortunei and P. kawakamii and that the maternal parent of P. taiwaniana is P. kawakamii.This work was supported in part by the National Science Council (NSC-80-0409-B-054-06), Republic of China     

Enabling association of the GINS protein tetramer with the mini chromosome maintenance (Mcm)2-7 protein complex by phosphorylated Sld2 protein and single-stranded origin DNA

The Cdc45-Mcm2-7-GINS (CMG) complex is the replication fork helicase in eukaryotes. Synthetic lethal with Dpb11-1 (Sld2) is required for the initiation of DNA replication, and the S phase cyclin-dependent kinase (S-CDK) phosphorylates Sld2 in vivo. We purified components of the replication initiation machinery and studied their interactions in vitro. We found that unphosphorylated or CDK-phosphorylated Sld2 binds to the mini chromosome maintenance (Mcm)2-7 complex with similar efficiency. Sld2 interaction with Mcm2-7 blocks the interaction between GINS and Mcm2-7. The interaction between CDK-phosphorylated Sld2 and Mcm2-7 is substantially inhibited by origin single-stranded DNA (ssDNA). Furthermore, origin ssDNA allows GINS to bind to Mcm2-7 in the presence of CDK-phosphorylated Sld2. However, unphosphorylated Sld2 blocks the interaction between GINS and Mcm2-7 even in the presence of origin ssDNA. We identified a mutant of Sld2 that does not bind to DNA. When this mutant is expressed in yeast cells, cell growth is severely inhibited with very slow progression into S phase. We propose a model wherein Sld2 blocks the interaction between GINS and Mcm2-7 in vivo. Once origin ssDNA is extruded from the Mcm2-7 ring and CDK phosphorylates Sld2, the origin ssDNA binds to CDK-phosphorylated Sld2. This event may allow the interaction between GINS and Mcm2-7 in vivo. Thus, CDK phosphorylation of Sld2 may be important to release Sld2 from Mcm2-7, thereby allowing GINS to bind Mcm2-7. Furthermore, origin ssDNA may stimulate the formation of the CMG complex by alleviating inhibitory interactions between Sld2 with Mcm2-7.     

An in vitro method generating base substitutions in preselected regions of plasmid DNA: application to structural analysis of the replication origin of the Escherichia coli K-12 chromosome

A method for introducing base substitutions in defined regions of plasmid DNA has been developed. In principle, a circular heteroduplex DNA containing a gap is constructed by annealing of two kinds of linear molecules derived from the same plasmid: One is the molecule shortened either by exonucleolytic digestion from the termini generated at a restriction site or by removal of a region flanked by two restriction sites, and the other the full-length molecule linearized at a different site. The deleted region in the shorter linear molecule becomes a single-stranded gap in the circular heteroduplex DNA. The heteroduplex is then treated with sodium bisulfite that converts specifically cytosine residues to uracil residues in single-stranded regions. After filling in the gap by repair synthesis, transformation is carried out to isolate mutant plasmids. Since two kinds of circular heteroduplexes are formed by annealing in which the sequences in the gaps are complementary to each other, mutagenesis of both strands can be accomplished in one experiment. This method was applied to construction of mutants with base substitutions in the replication origin region (oriC) of the Escherichia coli K-12 chromosome which had previously been cloned in colicin E1 plasmid vectors, and various mutants in defined regions of oriC were successfully isolated at high efficiencies. Analysis of these mutants provided evidence that oriC contains special regions, designated spacers, which separate neighboring important sequences specifying interactions with initiation factors for DNA replication at precise distances.     

Molecular DNA identity of the mouflon of Cyprus (Ovis orientalis ophion,Bovidae): Near Eastern origin and divergence from Western Mediterranean conspecific populations

The mouflon population of Cyprus (Ovis orientalis ophion) comprises historically preserved feral descendants of sheep domesticated during the Neolithic. We determined genetic identity of this taxon in order to elucidate its systematic placement and enforce its protection. We used 12 loci of microsatellite DNA to infer genetic relationships between the Cypriot mouflon and either long-time isolated (Corsica, Sardinia) or recently introduced (central Italy) European mouflons (O. o. musimon). We also sequenced the mitochondrial DNA (mtDNA) Cytochrome-b gene to infer the origin of the Cypriot mouflon including many National Centre for Biotechnology Information (NCBI) entries of European and Near Eastern conspecifics. Microsatellites disclosed net divergence between Western Mediterranean and Cypriot mouflon. The latter was included in the highly heterogeneous Near Eastern O. orientalis mtDNA group, Iran representing the most credited region as the source for its ancient introduction to Cyprus. Both international and national legislation protect the mouflon of Cyprus as a wild taxon (O. o. ophion). However, the IUCN Red List of Threatened Species and NCBI include the Cypriot mouflon as subspecies of its respective domestic species, the sheep (O. aries). Unfortunately, people charged with crime against protected mouflon may benefit from such taxonomic inconsistency between legislation and databases, as the latter can frustrate molecular DNA forensic outcomes. Until a definitive light can be shed on Near Eastern O. orientalis systematics, we suggest that the Cypriot mouflon should be unvaryingly referred to as O. o. ophion in order not to impair conservation in the country where it resides.     

Molecular and cytogenetic characterization of repetitive DNA sequences from Lolium and Festuca: applications in the analysis of Festulolium hybrids

Summary A set of species-specific repetitive DNA sequences was isolated from Lolium multiflorum and Festuca arundinacea. The degree of their species specificity as well as possible homologies among them were determined by dot-blot hybridization analysis. In order to understand the genomic organization of representative Lolium and Festuca-specific repetitive DNA sequences, we performed Southern blot hybridization and in situ hybridization to metaphase chromosomes.Southern blot hybridization analysis of eight different repetitive DNA sequences of L. multiflorum and one of F. arundinacea indicated either tandem and clustered arrangements of partially dispersed localization in their respective genomes. Some of these sequences, e.g. LMB3, showed a similar genomic organization in F. arundinacea and F. pratensis, but a slightly different organization and degree of redundancy in L. multiflorum. Clones sequences varied in size between 100 bp and 1.2 kb. Estimated copy number in the corresponding haploid genomes varied between 300 and 2×10⁴. Sequence analysis of the highly species-specific sequences from plasmids pLMH2 and pLMB4 (L. multiflorum specific) and from pFAH1 (F. arundinacea specific) revealed some internal repeats without higher order. No homologies between the sequences or to other repetitive sequences were observed. In situ hybridization with these latter sequences to metaphase chromosomes from L. multiflorum, F. arundinacea and from symmetric sexual Festulolium hybrid revealed their relatively even distribution in the corresponding genomes. The in situ hybridization thus also allowed a clearcut simple identification of parental chromosomes in the Festulolium hybrid.The potential use of these species-specific clones as hybridization probes in quantitative dot-blot analysis of the genomic make-up of Festulolium (sexual and somatic) hybrids is also demonstrated.Abbreviations bp Base pair (s) - CMA chromomycin A₃ - DAPI 4,6-diamidino-2-phenylindole - IPTG isopropyl -D-thio-galactopyranoside - kb kilobase pair(s) - NBT nitroblue tetrazolium chloride - X-gal 5-bromo-4-chloro-3-inonyl -D-galactopyranoside     

Molecular models of induced DNA premutational damage and mutational pathways for the carcinogen 4-nitroquinoline 1-oxide and its metabolites

The carcinogen 4-nitroquinoline 1-oxide (4NQO) and its metabolites undergo intercalative or covalent binding with DNA. Recent evidence indicates that the latter binding pattern is probably facilitated by an initial weaker intercalative interaction that can align potentially reactive sites on a 4NQO-metabolite and adjacent stacked bases. In the present study, we have proposed numerous possible covalent reaction products between 4NQO and its metabolites with DNA mini-helices based on chemical properties and key 'short-contacts' after energy-minimization in 21 different intercalative-like complexes. It is known from numerous experimental studies that 90% of the quinoline-bound DNAs in vivo involve guanine with the remaining 10% apparently involving adenine residues. The results of the present study suggest that this trend is not due to the greater affinity of the quinolines for guanine, but instead results from secondary processes involving the preferential formation of apurinic sites at aralkyl-adenine residues over that of aralkyl-guanine residues. In addition, observed mutational patterns can be rationalized in terms of the proposed reaction-products. The role of DNA repair mechanisms in the removal and correction of the different proposed reaction products are discussed. The binding pattern of several other aromatic carcinogens are similar to those depicted in the present work for the 4NQO-metabolites; hence the present study may be of some general significance.     

Evolutionary and demographic history among Maghrebian Medicago species (Fabaceae) based on the nucleotide sequences of the chloroplast DNA barcode trnH-psbA

Data from trnH-psbA intergenic spacer (cpDNA) were analyzed to elucidate molecular evolution within and among Maghrebian species of Medicago. The spacer highlighted a high interspecific variation and a low intraspecific diversity among species. Haplotype and nucleotide diversities revealed high level of variation. Parsimony and median-joining Network methods revealed (1) the segregation into 17 haplotypes; (2) the ancestral behaviour of the annual Medicago minima and (3) the clusters are independent of the geographic origin. The neutral evolution of Wright and Fisher is rejected since the Tajima's D values deviated from 0. Besides, the statistical analyses are in agreement with an evolution into stable populations' size.